WorldWideScience

Sample records for blm ortholog sgs1

  1. Disruption of SUMO-targeted ubiquitin ligases Slx5-Slx8/RNF4 alters RecQ-like helicase Sgs1/BLM localization in yeast and human cells.

    Science.gov (United States)

    Böhm, Stefanie; Mihalevic, Michael Joseph; Casal, Morgan Alexandra; Bernstein, Kara Anne

    2015-02-01

    RecQ-like helicases are a highly conserved protein family that functions during DNA repair and, when mutated in humans, is associated with cancer and/or premature aging syndromes. The budding yeast RecQ-like helicase Sgs1 has important functions in double-strand break (DSB) repair of exogenously induced breaks, as well as those that arise endogenously, for example during DNA replication. To further investigate Sgs1's regulation, we analyzed the subcellular localization of a fluorescent fusion of Sgs1 upon DNA damage. Consistent with a role in DSB repair, Sgs1 recruitment into nuclear foci in asynchronous cultures increases after ionizing radiation (IR) and after exposure to the alkylating agent methyl methanesulfonate (MMS). Yet, despite the importance of Sgs1 in replicative damage repair and in contrast to its elevated protein levels during S-phase, we find that the number of Sgs1 foci decreases upon nucleotide pool depletion by hydroxyurea (HU) treatment and that this negative regulation depends on the intra S-phase checkpoint kinase Mec1. Importantly, we identify the SUMO-targeted ubiquitin ligase (STUbL) complex Slx5-Slx8 as a negative regulator of Sgs1 foci, both spontaneously and upon replicative damage. Slx5-Slx8 regulation of Sgs1 foci is likely conserved in eukaryotes, since expression of the mammalian Slx5-Slx8 functional homologue, RNF4, restores Sgs1 focus number in slx8 cells and furthermore, knockdown of RNF4 leads to more BLM foci in U-2 OS cells. Our results point to a model where RecQ-like helicase subcellular localization is regulated by STUbLs in response to DNA damage, presumably to prevent illegitimate recombination events. PMID:25588990

  2. Esc2 and Sgs1 act in functionally distinct branches of the homologous recombination repair pathway in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Mankouri, Hocine W; Ngo, Hien-Ping; Hickson, Ian D

    2009-01-01

    homologous recombination repair (HRR) intermediates. These roles are qualitatively similar to those of Sgs1, the yeast ortholog of the human Bloom's syndrome protein, BLM. However, whereas mutation of either ESC2 or SGS1 leads to the accumulation of unprocessed HRR intermediates in the presence of MMS, the...... accumulation of these structures in esc2 (but not sgs1) mutants is entirely dependent on Mph1, a protein that shows structural similarity to the Fanconi anemia group M protein (FANCM). In the absence of both Esc2 and Sgs1, the intra-S-phase DNA damage checkpoint response is compromised after exposure to MMS......, and sgs1esc2 cells attempt to undergo mitosis with unprocessed HRR intermediates. We propose a model whereby Esc2 acts in an Mph1-dependent process, separately from Sgs1, to influence the repair/tolerance of MMS-induced lesions during S-phase....

  3. Processing of homologous recombination repair intermediates by the Sgs1-Top3-Rmi1 and Mus81-Mms4 complexes

    DEFF Research Database (Denmark)

    Hickson, Ian D; Mankouri, Hocine W

    2011-01-01

    Homologous recombination repair (HRR) is an evolutionarily conserved cellular process that is important for the maintenance of genome stability during S phase. Inactivation of the Saccharomyces cerevisiae Sgs1-Top3-Rmi1 complex leads to the accumulation of unprocessed, X-shaped HRR intermediates (X...... structures) following replicative stress. Further characterization of these X structures may reveal why loss of BLM (the human Sgs1 ortholog) leads to the human cancer predisposition disorder, Bloom syndrome. In two recent complementary studies, we examined the nature of the X structures arising in yeast strains...... lacking Sgs1, Top3 or Rmi1 by identifying which proteins could process these structures in vivo. We revealed that the unprocessed X structures that accumulate in these strains could be resolved by the ectopic overexpression of two different Holliday junction (HJ) resolvases, and that the endogenous Mus81...

  4. Differential genetic interactions between Sgs1, DNA-damage checkpoint components and DNA repair factors in the maintenance of chromosome stability

    Directory of Open Access Journals (Sweden)

    Doerfler Lillian

    2011-10-01

    Full Text Available Abstract Background Genome instability is associated with human cancers and chromosome breakage syndromes, including Bloom's syndrome, caused by inactivation of BLM helicase. Numerous mutations that lead to genome instability are known, yet how they interact genetically is poorly understood. Results We show that spontaneous translocations that arise by nonallelic homologous recombination in DNA-damage-checkpoint-defective yeast lacking the BLM-related Sgs1 helicase (sgs1Δ mec3Δ are inhibited if cells lack Mec1/ATR kinase. Tel1/ATM, in contrast, acts as a suppressor independently of Mec3 and Sgs1. Translocations are also inhibited in cells lacking Dun1 kinase, but not in cells defective in a parallel checkpoint branch defined by Chk1 kinase. While we had previously shown that RAD51 deletion did not inhibit translocation formation, RAD59 deletion led to inhibition comparable to the rad52Δ mutation. A candidate screen of other DNA metabolic factors identified Exo1 as a strong suppressor of chromosomal rearrangements in the sgs1Δ mutant, becoming even more important for chromosomal stability upon MEC3 deletion. We determined that the C-terminal third of Exo1, harboring mismatch repair protein binding sites and phosphorylation sites, is dispensable for Exo1's roles in chromosomal rearrangement suppression, mutation avoidance and resistance to DNA-damaging agents. Conclusions Our findings suggest that translocations between related genes can form by Rad59-dependent, Rad51-independent homologous recombination, which is independently suppressed by Sgs1, Tel1, Mec3 and Exo1 but promoted by Dun1 and the telomerase-inhibitor Mec1. We propose a model for the functional interaction between mitotic recombination and the DNA-damage checkpoint in the suppression of chromosomal rearrangements in sgs1Δ cells.

  5. Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1-Top3

    DEFF Research Database (Denmark)

    Cejka, Petr; Plank, Jody L; Bachrati, Csanad Z;

    2010-01-01

    A double Holliday junction (dHJ) is a central intermediate of homologous recombination that can be processed to yield crossover or non-crossover recombination products. To preserve genomic integrity, cells possess mechanisms to avoid crossing over. We show that Saccharomyces cerevisiae Sgs1 and Top......3 proteins are sufficient to migrate and disentangle a dHJ to produce exclusively non-crossover recombination products, in a reaction termed "dissolution." We show that Rmi1 stimulates dHJ dissolution at low Sgs1-Top3 protein concentrations, although it has no effect on the initial rate of Holliday...

  6. Recombination-mediated lengthening of terminal telomeric repeats requires the Sgs1 DNA helicase

    OpenAIRE

    Cohen, Haim; Sinclair, David A.

    2001-01-01

    The Saccharomyces cerevisiae SGS1 gene encodes a RecQ-like DNA helicase, human homologues of which are implicated in the genetic instability disorders, Bloom syndrome (BS), Rothmund-Thomson syndrome (RTS), and Werner syndrome (WS). Telomerase-negative yeast cells can recover from senescence via two recombinational telomere elongation pathways. The “type I” pathway generates telomeres with large blocks of telomeric and subtelomeric sequences and short terminal repea...

  7. Holliday junction-containing DNA structures persist in cells lacking Sgs1 or Top3 following exposure to DNA damage

    DEFF Research Database (Denmark)

    Mankouri, Hocine W; Ashton, Thomas M; Hickson, Ian D

    2011-01-01

    The Sgs1-Rmi1-Top3 "dissolvasome" is required for the maintenance of genome stability and has been implicated in the processing of various types of DNA structures arising during DNA replication. Previous investigations have revealed that unprocessed (X-shaped) homologous recombination repair (HRR......) intermediates persist when S-phase is perturbed by using methyl methanesulfonate (MMS) in Saccharomyces cerevisiae cells with impaired Sgs1 or Top3. However, the precise nature of these persistent DNA structures remains poorly characterized. Here, we report that ectopic expression of either of two heterologous...... to RusA or GEN1(1-527), demonstrating specificity of these HJ resolvases for MMS-induced X-structures in vivo. These data suggest that the X-structures persisting in cells with impaired Sgs1 or Top3 contain HJs. Furthermore, we demonstrate that Sgs1 directly promotes X-structure removal, because the...

  8. Shu proteins promote the formation of homologous recombination intermediates that are processed by Sgs1-Rmi1-Top3

    DEFF Research Database (Denmark)

    Mankouri, Hocine W; Ngo, Hien-Ping; Hickson, Ian D

    2007-01-01

    CSM2, PSY3, SHU1, and SHU2 (collectively referred to as the SHU genes) were identified in Saccharomyces cerevisiae as four genes in the same epistasis group that suppress various sgs1 and top3 mutant phenotypes when mutated. Although the SHU genes have been implicated in homologous recombination...... formation of MMS-induced HRR intermediates (X-molecules) arising during replication in sgs1 cells, mutation of SHU genes attenuated the level of these structures. Similar findings were also observed in shu1 cells in which Rmi1 or Top3 function was impaired. We propose a model in which the Shu proteins act...... in HRR to promote the formation of HRR intermediates that are processed by the Sgs1-Rmi1-Top3 complex....

  9. Sgs1 and Exo1 suppress targeted chromosome duplication during ends-in and ends-out gene targeting.

    Science.gov (United States)

    Štafa, Anamarija; Miklenić, Marina; Zunar, Bojan; Lisnić, Berislav; Symington, Lorraine S; Svetec, Ivan-Krešimir

    2014-10-01

    Gene targeting is extremely efficient in the yeast Saccharomyces cerevisiae. It is performed by transformation with a linear, non-replicative DNA fragment carrying a selectable marker and containing ends homologous to the particular locus in a genome. However, even in S. cerevisiae, transformation can result in unwanted (aberrant) integration events, the frequency and spectra of which are quite different for ends-out and ends-in transformation assays. It has been observed that gene replacement (ends-out gene targeting) can result in illegitimate integration, integration of the transforming DNA fragment next to the target sequence and duplication of a targeted chromosome. By contrast, plasmid integration (ends-in gene targeting) is often associated with multiple targeted integration events but illegitimate integration is extremely rare and a targeted chromosome duplication has not been reported. Here we systematically investigated the influence of design of the ends-out assay on the success of targeted genetic modification. We have determined transformation efficiency, fidelity of gene targeting and spectra of all aberrant events in several ends-out gene targeting assays designed to insert, delete or replace a particular sequence in the targeted region of the yeast genome. Furthermore, we have demonstrated for the first time that targeted chromosome duplications occur even during ends-in gene targeting. Most importantly, the whole chromosome duplication is POL32 dependent pointing to break-induced replication (BIR) as the underlying mechanism. Moreover, the occurrence of duplication of the targeted chromosome was strikingly increased in the exo1Δ sgs1Δ double mutant but not in the respective single mutants demonstrating that the Exo1 and Sgs1 proteins independently suppress whole chromosome duplication during gene targeting. PMID:25089886

  10. A Rad53 Independent Function of Rad9 Becomes Crucial for Genome Maintenance in the Absence of the RecQ Helicase Sgs1

    DEFF Research Database (Denmark)

    Nielsen, Ida; Bentsen, Iben Bach; Andersen, Anni Hangaard;

    2013-01-01

    The conserved family of RecQ DNA helicases consists of caretaker tumour suppressors, that defend genome integrity by acting on several pathways of DNA repair that maintain genome stability. In budding yeast, Sgs1 is the sole RecQ helicase and it has been implicated in checkpoint responses......, replisome stability and dissolution of double Holliday junctions during homologous recombination. In this study we investigate a possible genetic interaction between SGS1 and RAD9 in the cellular response to methyl methane sulphonate (MMS) induced damage and compare this with the genetic interaction between...... SGS1 and RAD24. The Rad9 protein, an adaptor for effector kinase activation, plays well-characterized roles in the DNA damage checkpoint response, whereas Rad24 is characterized as a sensor protein also in the DNA damage checkpoint response. Here we unveil novel insights into the cellular response to...

  11. Survival and growth of yeast without telomere capping by Cdc13 in the absence of Sgs1, Exo1, and Rad9.

    Directory of Open Access Journals (Sweden)

    Hien-Ping Ngo

    2010-08-01

    Full Text Available Maintenance of telomere capping is absolutely essential to the survival of eukaryotic cells. Telomere capping proteins, such as Cdc13 and POT1, are essential for the viability of budding yeast and mammalian cells, respectively. Here we identify, for the first time, three genetic modifications that allow budding yeast cells to survive without telomere capping by Cdc13. We found that simultaneous inactivation of Sgs1, Exo1, and Rad9, three DNA damage response (DDR proteins, is sufficient to allow cell division in the absence of Cdc13. Quantitative amplification of ssDNA (QAOS was used to show that the RecQ helicase Sgs1 plays an important role in the resection of uncapped telomeres, especially in the absence of checkpoint protein Rad9. Strikingly, simultaneous deletion of SGS1 and the nuclease EXO1, further reduces resection at uncapped telomeres and together with deletion of RAD9 permits cell survival without CDC13. Pulsed-field gel electrophoresis studies show that cdc13-1 rad9Delta sgs1Delta exo1Delta strains can maintain linear chromosomes despite the absence of telomere capping by Cdc13. However, with continued passage, the telomeres of such strains eventually become short and are maintained by recombination-based mechanisms. Remarkably, cdc13Delta rad9Delta sgs1Delta exo1Delta strains, lacking any Cdc13 gene product, are viable and can grow indefinitely. Our work has uncovered a critical role for RecQ helicases in limiting the division of cells with uncapped telomeres, and this may provide one explanation for increased tumorigenesis in human diseases associated with mutations of RecQ helicases. Our results reveal the plasticity of the telomere cap and indicate that the essential role of telomere capping is to counteract specific aspects of the DDR.

  12. Rmi1, a member of the Sgs1–Top3 complex in budding yeast, contributes to sister chromatid cohesion

    OpenAIRE

    Lai, Mong Sing; Seki, Masayuki; Ui, Ayako; Enomoto, Takemi

    2007-01-01

    The Saccharomyces cerevisiae RecQ-mediated genome instability (Rmi1) protein was recently identified as the third member of the slow growth suppressor 1–DNA topoisomerase III (Sgs1–Top3) complex, which is required for maintaining genomic stability. Here, we show that cells lacking RMI1 have a mitotic delay, which is partly dependent on the spindle checkpoint, and are sensitive to the microtubule depolymerizing agent benomyl. We show that rmi1 and top3 single mutants are defective in sister ch...

  13. A transient α-helical molecular recognition element in the disordered N-terminus of the Sgs1 helicase is critical for chromosome stability and binding of Top3/Rmi1.

    Science.gov (United States)

    Kennedy, Jessica A; Daughdrill, Gary W; Schmidt, Kristina H

    2013-12-01

    The RecQ-like DNA helicase family is essential for the maintenance of genome stability in all organisms. Sgs1, a member of this family in Saccharomyces cerevisiae, regulates early and late steps of double-strand break repair by homologous recombination. Using nuclear magnetic resonance spectroscopy, we show that the N-terminal 125 residues of Sgs1 are disordered and contain a transient α-helix that extends from residue 25 to 38. Based on the residue-specific knowledge of transient secondary structure, we designed proline mutations to disrupt this α-helix and observed hypersensitivity to DNA damaging agents and increased frequency of genome rearrangements. In vitro binding assays show that the defects of the proline mutants are the result of impaired binding of Top3 and Rmi1 to Sgs1. Extending mutagenesis N-terminally revealed a second functionally critical region that spans residues 9-17. Depending on the position of the proline substitution in the helix functional impairment of Sgs1 function varied, gradually increasing from the C- to the N-terminus. The multiscale approach we used to interrogate structure/function relationships in the long disordered N-terminal segment of Sgs1 allowed us to precisely define a functionally critical region and should be generally applicable to other disordered proteins. PMID:24038467

  14. Embryonic stem cells deficient for Brca2 or Blm exhibit divergent genotoxic profiles that support opposing activities during homologous recombination

    International Nuclear Information System (INIS)

    The breast cancer susceptibility protein, Brca2 and the RecQ helicase, Blm (Bloom syndrome mutated) are tumor suppressors that maintain genome integrity, at least in part, through homologous recombination (HR). Brca2 facilitates HR by interacting with Rad51 in multiple regions, the BRC motifs encoded by exon 11 and a single domain encoded by exon 27; however, the exact importance of these regions is not fully understood. Blm also interacts with Rad51 and appears to suppress HR in most circumstances; however, its yeast homologue Sgs1 facilitates HR in response to some genotoxins. To better understand the biological importance of these two proteins, we performed a genotoxic screen on mouse embryonic stem (ES) cells impaired for either Brca2 or Blm to establish their genotoxic profiles (a cellular dose-response to a wide range of agents). This is the first side-by-side comparison of these two proteins in an identical genetic background. We compared cells deleted for Brca2 exon 27 to cells reduced for Blm expression and find that the Brca2- and Blm-impaired cells exhibit genotoxic profiles that reflect opposing activities during HR. Cells deleted for Brca2 exon 27 are hypersensitive to γ-radiation, streptonigrin, mitomycin C and camptothecin and mildly resistant to ICRF-193 which is similar to HR defective cells null for Rad54. By contrast, Blm-impaired cells are hypersensitive to ICRF-193, mildly resistant to camptothecin and mitomycin C and more strongly resistant to hydroxyurea. These divergent profiles support the notion that Brca2 and Blm perform opposing functions during HR in mouse ES cells

  15. BLM Scale Fixing in Event Shape Distributions

    CERN Document Server

    Gehrmann, Thomas; Monni, Pier Francesco

    2014-01-01

    We study the application of the Brodsky-Lepage-Mackenzie (BLM) scale setting prescription to event shape distributions in electron-positron collisions. The renormalization scale is set dynamically according to the BLM method. We study NLO predictions and we discuss extensions of the prescription to NNLO.

  16. DNA double strand break repair in mammalian cells: role of MRE11 and BLM proteins at the initiation of Non Homologous End Joining (NHEJ)

    International Nuclear Information System (INIS)

    DNA double strand breaks (DSBs) are highly cytotoxic lesions, which can lead to genetic rearrangements. Two pathways are responsible for repairing these lesions: homologous recombination (HR) and non homologous end joining (NHEJ). In our laboratory, an intrachromosomal substrate has been established in order to measure the efficiency and the fidelity of NHEJ in living cells (Guirouilh-Barbat 2004). This approach led us to identify a KU-independent alternative pathway, which uses micro homologies in the proximity of the junction to accomplish repair - the alternative NHEJ (Guirouilh-Barbat 2004, Guirouilh-Barbat et Rass 2007). The goal of my thesis consisted in identifying and characterising major actors of this pathway. In the absence of KU, alternative NHEJ would be initiated by ssDNA resection of damaged ends. We showed that the nuclease activity of MRE11 is necessary for this mechanism. MRE11 overexpression leads to a two fold stimulation of NHEJ efficiency, while the extinction of MRE11 by siRNA results in a two fold decrease. Our results demonstrate that the proteins RAD50 and CtIP act in the same pathway as MRE11. Moreover, in cells deficient for XRCC4, MIRIN - an inhibitor of the MRN complex - leads to a decrease in repair efficiency, implicating MRE11 in alternative NHEJ. We also showed that MRE11 can act in an ATM-dependent and independent manner (Rass et Grabarz Nat Struct Mol Biol 2009). The initiation of break resection needs to be pursued by a more extensive degradation of DNA, which is accomplished in yeast by the proteins Exo1 and Sgs1/Dna2. In human cells, in vitro studies have recently proposed a similar model of a two-step break resection. We chose to elucidate the role of one of the human homologs of Sgs1 - the RecQ helicase BLM - in the resection process. Our experiments show, that he absence of BLM decreases the efficiency of end joining by NHEJ, accompanied by an increase in error-prone events, especially long-range deletions (≥200 nt). This

  17. A Small Molecule Inhibitor of the BLM Helicase Modulates Chromosome Stability in Human Cells

    DEFF Research Database (Denmark)

    Nguyen, Giang Huong; Dexheimer, Thomas S; Rosenthal, Andrew S; Chu, Wai Kit; Singh, Dharmendra Kumar; Mosedale, Georgina; Bachrati, Csanád Z; Schultz, Lena; Sakurai, Masaaki; Savitsky, Pavel; Abu, Mika; McHugh, Peter J; Bohr, Vilhelm A; Harris, Curtis C; Jadhav, Ajit; Gileadi, Opher; Maloney, David J; Simeonov, Anton; Hickson, Ian D

    2013-01-01

    The Bloom's syndrome protein, BLM, is a member of the conserved RecQ helicase family. Although cell lines lacking BLM exist, these exhibit progressive genomic instability that makes distinguishing primary from secondary effects of BLM loss problematic. In order to be able to acutely disable BLM...

  18. Semihard processes with BLM renormalization scale setting

    Energy Technology Data Exchange (ETDEWEB)

    Caporale, Francesco [Instituto de Física Teórica UAM/CSIC, Nicolás Cabrera 15 and U. Autónoma de Madrid, E-28049 Madrid (Spain); Ivanov, Dmitry Yu. [Sobolev Institute of Mathematics and Novosibirsk State University, 630090 Novosibirsk (Russian Federation); Murdaca, Beatrice; Papa, Alessandro [Dipartimento di Fisica, Università della Calabria, and Istituto Nazionale di Fisica Nucleare, Gruppo collegato di Cosenza, Arcavacata di Rende, I-87036 Cosenza (Italy)

    2015-04-10

    We apply the BLM scale setting procedure directly to amplitudes (cross sections) of several semihard processes. It is shown that, due to the presence of β{sub 0}-terms in the NLA results for the impact factors, the obtained optimal renormalization scale is not universal, but depends both on the energy and on the process in question. We illustrate this general conclusion considering the following semihard processes: (i) inclusive production of two forward high-p{sub T} jets separated by large interval in rapidity (Mueller-Navelet jets); (ii) high-energy behavior of the total cross section for highly virtual photons; (iii) forward amplitude of the production of two light vector mesons in the collision of two virtual photons.

  19. Commissioning and optimization of the LHC BLM System

    CERN Document Server

    Holzer, E B; Effinger, E; Emery, J; Hajdu, C F; Jackson, S; Kurfurst, C; Marsili, A; Misiowiec, M; Nebot Del Busto, E; Nordt, A; Roderick, C; Sapinski, M; Zamantzas, C; Grishin, V

    2011-01-01

    Due to rapid progress with the LHC commissioning in 2010, set-up beam intensities were soon surpassed and damage potential was reached. One of the key systems for machine protection is the beam loss monitoring (BLM) system. Around 4000 monitors are installed at likely or critical loss locations. Each monitor has 384 associated beam abort thresholds (12 integrated loss durations from 40 μs to 84 s for 32 energy intervals). A single integrated loss over threshold on a single monitor aborts the beam. Simulations of deposited energy, critical energy deposition for damage or quench and BLM signal response backedup by control measurements determined the initial threshold settings. The commissioning and optimization of the BLM system is presented. Test procedures were used to verify the machine protection functionalities. Accidental magnet quenches were used to fine-tune threshold settings. The most significant changes to the BLM system during the 2010 run concern the injection, the collimation and the beam dump re...

  20. Number of New Leases Issued During Fiscal Year by BLM

    Data.gov (United States)

    Bureau of Land Management, Department of the Interior — This table contains the total number of new leases, by state, issued by the BLM during each fiscal year. Leases issued over the course of a fiscal year may or may...

  1. Hyperbolas, orthology, and antipedal triangles

    OpenAIRE

    Čerin, Zvonko

    1998-01-01

    We obtain several characterizations of the Kiepert, Jarabek, and Feuerbach hyperbolas of a tringle ABC using the antipedal tringles of a variable point P in the plane and the notion of orthologic tringles. Our arguments are algebraic and use complex numbers.

  2. Blm10 facilitates nuclear import of proteasome core particles

    OpenAIRE

    Weberruss, Marion H; Savulescu, Anca F; Jando, Julia; Bissinger, Thomas; Harel, Amnon; Glickman, Michael H.; Enenkel, Cordula

    2013-01-01

    Short-lived proteins are degraded by proteasome complexes, which contain a proteolytic core particle (CP) but differ in the number of regulatory particles (RPs) and activators. A recently described member of conserved proteasome activators is Blm10. Blm10 contains 32 HEAT-like modules and is structurally related to the nuclear import receptor importin/karyopherin β. In proliferating yeast, RP-CP assemblies are primarily nuclear and promote cell division. During quiescence, RP-CP assemblies di...

  3. Standardized benchmarking in the quest for orthologs

    OpenAIRE

    Altenhoff, A.M.; Boeckmann, B; Capella-Gutierrez, S.; Dalquen, D. A.; DeLuca, T.; Forslund, K.; Huerta-Cepas, J.; Linard, B.; Pereira, C; Pryszcz, L.P.; Schreiber, F.; DA SILVA, A S; Szklarczyk, D.; Train, C.M.; Bork, P.

    2016-01-01

    Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to fac...

  4. Standardized benchmarking in the quest for orthologs.

    Science.gov (United States)

    Altenhoff, Adrian M; Boeckmann, Brigitte; Capella-Gutierrez, Salvador; Dalquen, Daniel A; DeLuca, Todd; Forslund, Kristoffer; Huerta-Cepas, Jaime; Linard, Benjamin; Pereira, Cécile; Pryszcz, Leszek P; Schreiber, Fabian; da Silva, Alan Sousa; Szklarczyk, Damian; Train, Clément-Marie; Bork, Peer; Lecompte, Odile; von Mering, Christian; Xenarios, Ioannis; Sjölander, Kimmen; Jensen, Lars Juhl; Martin, Maria J; Muffato, Matthieu; Gabaldón, Toni; Lewis, Suzanna E; Thomas, Paul D; Sonnhammer, Erik; Dessimoz, Christophe

    2016-05-01

    Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods. PMID:27043882

  5. Standardized benchmarking in the quest for orthologs

    DEFF Research Database (Denmark)

    Altenhoff, Adrian M; Boeckmann, Brigitte; Capella-Gutierrez, Salvador;

    2016-01-01

    Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision......-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods...... and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods....

  6. Handling of BLM abort thresholds in the LHC

    CERN Document Server

    Nebot Del Busto, E; Holzer, EB; Zamantzas, C; Kruk, G; Nordt, A; Sapinski, M; Nemcic, M; Orecka, A; Jackson, S; Roderick, C; Skaugen, A

    2011-01-01

    The Beam Loss Monitoring system (BLM) for the LHC consists of about 3600 Ionization Chambers (IC) located around the ring. Its main purpose is to request a beam abort when the measured losses exceed a certain threshold. The BLM detectors integrate the measured signals in 12 different time intervals (running from 40us to 83.8s) enabling for a different set of abort thresholds depending on the duration of the beam loss. Furthermore, 32 energy levels running from 450GeV to 7TeV account for the fact that the energy density of a particle shower increases with the energy of the primary particle, i.e. the beam energy. Thus, a set of ! 3600 × 12 × 32 = 1.3 · 106 thresholds must be handled. These thresholds are highly critical for the safety of the machine and depend to a large part on human judgment, which cannot be replaced by automatic test procedures. The BLM team has defined well established procedures to compute, set and check new BLM thresholds, in order to avoid and/or find non-conformities due to manipulat...

  7. Assessment of orthologous splicing isoforms in human and mouse orthologous genes

    Directory of Open Access Journals (Sweden)

    Horner David S

    2010-10-01

    Full Text Available Abstract Background Recent discoveries have highlighted the fact that alternative splicing and alternative transcripts are the rule, rather than the exception, in metazoan genes. Since multiple transcript and protein variants expressed by the same gene are, by definition, structurally distinct and need not to be functionally equivalent, the concept of gene orthology should be extended to the transcript level in order to describe evolutionary relationships between structurally similar transcript variants. In other words, the identification of true orthology relationships between gene products now should progress beyond primary sequence and "splicing orthology", consisting in ancestrally shared exon-intron structures, is required to define orthologous isoforms at transcript level. Results As a starting step in this direction, in this work we performed a large scale human- mouse gene comparison with a twofold goal: first, to assess if and to which extent traditional gene annotations such as RefSeq capture genuine splicing orthology; second, to provide a more detailed annotation and quantification of true human-mouse orthologous transcripts defined as transcripts of orthologous genes exhibiting the same splicing patterns. Conclusions We observed an identical exon/intron structure for 32% of human and mouse orthologous genes. This figure increases to 87% using less stringent criteria for gene structure similarity, thus implying that for about 13% of the human RefSeq annotated genes (and about 25% of the corresponding transcripts we could not identify any mouse transcript showing sufficient similarity to be confidently assigned as a splicing ortholog. Our data suggest that current gene and transcript data may still be rather incomplete - with several splicing variants still unknown. The observation that alternative splicing produces large numbers of alternative transcripts and proteins, some of them conserved across species and others truly species

  8. On the BLM optimal renormalization scale setting for semihard processes

    CERN Document Server

    Caporale, Francesco; Murdaca, Beatrice; Papa, Alessandro

    2015-01-01

    The BFKL approach for the investigation of semihard processes is plagued by large next-to-leading corrections, both in the kernel of the universal BFKL Green's function and in the process-dependent impact factors, as well as by large uncertainties in the renormalization scale setting. All that calls for some optimization procedure of the perturbative series. In this respect, one of the most common methods is the Brodsky-Lepage-Mackenzie (BLM) one, that eliminates the renormalization scale ambiguity by absorbing the non-conformal $\\beta_0$-terms into the running coupling. In this paper, we apply BLM scale setting procedure directly to the amplitudes (cross sections) of several semihard processes. We show that, due to the presence of $\\beta_0$-terms in the next-to-leading expressions for the impact factors, the optimal renormalization scale is not universal, but depends both on the energy and on the type of process in question.

  9. Is the BLM system ready to go to higher intensities?

    CERN Document Server

    Sapinski, M; Dehning, B; Effinger, E; Emery, J; Goddard, B; Guerrero, A; Grishin, S; Holzer, E; Jackson, S; Kurfuerst, C; Lechner, A; Marsili, A; Misiowiec, M; Nebot, E; Nordt, A; Priebe, A; Roderick, C; Schmidt, R; Verweij, A; Wenninger, J; Zamantzas, C; Zimmermann, F

    2011-01-01

    The higher beam intensities will enhance the effects of the beam losses observed during 2010 run. In particular beam losses due to so called UFO events are discussed, but also other beam loss phenomena like luminosity losses, injection losses and the leakage from the collimation system are considered. The current understanding of the quench limits reflected in the BLM thresholds on the cold magnets is presented. The thresholds for possible increased beam energy are reviewed.

  10. Identifying single copy orthologs in Metazoa.

    Directory of Open Access Journals (Sweden)

    Christopher J Creevey

    2011-12-01

    Full Text Available The identification of single copy (1-to-1 orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene.Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence.To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis to 99.8% (human with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.

  11. Transcriptomic and Protein Expression Analysis Reveals Clinicopathological Significance of Bloom Syndrome Helicase (BLM) in Breast Cancer.

    Science.gov (United States)

    Arora, Arvind; Abdel-Fatah, Tarek M A; Agarwal, Devika; Doherty, Rachel; Moseley, Paul M; Aleskandarany, Mohammed A; Green, Andrew R; Ball, Graham; Alshareeda, Alaa T; Rakha, Emad A; Chan, Stephen Y T; Ellis, Ian O; Madhusudan, Srinivasan

    2015-04-01

    Bloom syndrome helicase (BLM) has key roles in homologous recombination repair, telomere maintenance, and DNA replication. Germ-line mutations in the BLM gene causes Bloom syndrome, a rare disorder characterized by premature aging and predisposition to multiple cancers, including breast cancer. The clinicopathologic significance of BLM in sporadic breast cancers is unknown. We investigated BLM mRNA expression in the Molecular Taxonomy of Breast Cancer International Consortium cohort (n = 1,950) and validated in an external dataset of 2,413 tumors. BLM protein level was evaluated in the Nottingham Tenovus series comprising 1,650 breast tumors. BLM mRNA overexpression was significantly associated with high histologic grade, larger tumor size, estrogen receptor-negative (ER(-)), progesterone receptor-negative (PR(-)), and triple-negative phenotypes (ps < 0.0001). BLM mRNA overexpression was also linked to aggressive molecular phenotypes, including PAM50.Her2 (P < 0.0001), PAM50.Basal (P < 0.0001), and PAM50.LumB (P < 0.0001) and Genufu subtype (ER(+)/Her2(-)/high proliferation; P < 0.0001). PAM50.LumA tumors and Genufu subtype (ER(+)/Her2(-)/low proliferation) were more likely to express low levels of BLM mRNA (ps < 0.0001). Integrative molecular clusters (intClust) intClust.1 (P < 0.0001), intClust.5 (P < 0.0001), intClust.9 (P < 0.0001), and intClust.10 (P < 0.0001) were also more likely in tumors with high BLM mRNA expression. BLM mRNA overexpression was associated with poor breast cancer-specific survival (BCSS; ps < 0.000001). At the protein level, altered subcellular localization with high cytoplasmic BLM and low nuclear BLM was linked to aggressive phenotypes. In multivariate analysis, BLM mRNA and BLM protein levels independently influenced BCSS. This is the first and the largest study to provide evidence that BLM is a promising biomarker in breast cancer. PMID:25673821

  12. A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology.

    Science.gov (United States)

    Ballesteros, Jesús A; Hormiga, Gustavo

    2016-08-01

    Current sequencing technologies are making available unprecedented amounts of genetic data for a large variety of species including nonmodel organisms. Although many phylogenomic surveys spend considerable time finding orthologs from the wealth of sequence data, these results do not transcend the original study and after being processed for specific phylogenetic purposes these orthologs do not become stable orthology hypotheses. We describe a procedure to detect and document the phylogenetic distribution of orthologs allowing researchers to use this information to guide selection of loci best suited to test specific evolutionary questions. At the core of this pipeline is a new phylogenetic orthology method that is neither affected by the position of the root nor requires explicit assignment of outgroups. We discuss the properties of this new orthology assessment method and exemplify its utility for phylogenomics using a small insects dataset. In addition, we exemplify the pipeline to identify and document stable orthologs for the group of orb-weaving spiders (Araneoidea) using RNAseq data. The scripts used in this study, along with sample files and additional documentation, are available at https://github.com/ballesterus/UPhO. PMID:27189539

  13. Completing the Calculation of BLM corrections to B -> Xs gamma

    OpenAIRE

    Misiak, Mikolaj; Poradzinski, Michal

    2010-01-01

    Perturbative O(alpha_s^2) corrections to BR(B -> Xs gamma) in the BLM approximation receive contributions from two-, three- and four-body final states. While all the two-body results are well established by now, the other ones have remained incomplete for several years. Here, we calculate the last contribution that has been missing to date, namely the one originating from interference of the current-current and gluonic dipole operators (K_18^{(2)beta_0} and K_{28}^{(2)beta_0}). Moreover, we c...

  14. Collaborating functions of BLM and DNA topoisomerase I in regulating human rDNA transcription

    Energy Technology Data Exchange (ETDEWEB)

    Grierson, Patrick M. [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States); Acharya, Samir, E-mail: samir.acharya@osumc.edu [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States); Groden, Joanna [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States)

    2013-03-15

    Bloom's syndrome (BS) is an inherited disorder caused by loss of function of the recQ-like BLM helicase. It is characterized clinically by severe growth retardation and cancer predisposition. BLM localizes to PML nuclear bodies and to the nucleolus; its deficiency results in increased intra- and inter-chromosomal recombination, including hyper-recombination of rDNA repeats. Our previous work has shown that BLM facilitates RNA polymerase I-mediated rRNA transcription in the nucleolus (Grierson et al., 2012 [18]). This study uses protein co-immunoprecipitation and in vitro transcription/translation (IVTT) to identify a direct interaction of DNA topoisomerase I with the C-terminus of BLM in the nucleolus. In vitro helicase assays demonstrate that DNA topoisomerase I stimulates BLM helicase activity on a nucleolar-relevant RNA:DNA hybrid, but has an insignificant effect on BLM helicase activity on a control DNA:DNA duplex substrate. Reciprocally, BLM enhances the DNA relaxation activity of DNA topoisomerase I on supercoiled DNA substrates. Our study suggests that BLM and DNA topoisomerase I function coordinately to modulate RNA:DNA hybrid formation as well as relaxation of DNA supercoils in the context of nucleolar transcription.

  15. Collaborating functions of BLM and DNA topoisomerase I in regulating human rDNA transcription

    International Nuclear Information System (INIS)

    Bloom's syndrome (BS) is an inherited disorder caused by loss of function of the recQ-like BLM helicase. It is characterized clinically by severe growth retardation and cancer predisposition. BLM localizes to PML nuclear bodies and to the nucleolus; its deficiency results in increased intra- and inter-chromosomal recombination, including hyper-recombination of rDNA repeats. Our previous work has shown that BLM facilitates RNA polymerase I-mediated rRNA transcription in the nucleolus (Grierson et al., 2012 [18]). This study uses protein co-immunoprecipitation and in vitro transcription/translation (IVTT) to identify a direct interaction of DNA topoisomerase I with the C-terminus of BLM in the nucleolus. In vitro helicase assays demonstrate that DNA topoisomerase I stimulates BLM helicase activity on a nucleolar-relevant RNA:DNA hybrid, but has an insignificant effect on BLM helicase activity on a control DNA:DNA duplex substrate. Reciprocally, BLM enhances the DNA relaxation activity of DNA topoisomerase I on supercoiled DNA substrates. Our study suggests that BLM and DNA topoisomerase I function coordinately to modulate RNA:DNA hybrid formation as well as relaxation of DNA supercoils in the context of nucleolar transcription

  16. BLM has early and late functions in homologous recombination repair in mouse embryonic stem cells

    DEFF Research Database (Denmark)

    Chu, W K; Hanada, K; Kanaar, R;

    2010-01-01

    ' roles, such as dissolution of double Holliday junctions. However, most of the evidence for these putative roles comes from in vitro biochemical data. In this study, we report the characterization of mouse embryonic stem cells with disruption of Blm and/or Rad54 genes. We show that Blm has roles both...

  17. Association of BLM and BRCA1 during Telomere Maintenance in ALT Cells.

    Directory of Open Access Journals (Sweden)

    Samir Acharya

    Full Text Available Fifteen percent of tumors utilize recombination-based alternative lengthening of telomeres (ALT to maintain telomeres. The mechanisms underlying ALT are unclear but involve several proteins involved in homologous recombination including the BLM helicase, mutated in Bloom's syndrome, and the BRCA1 tumor suppressor. Cells deficient in either BLM or BRCA1 have phenotypes consistent with telomere dysfunction. Although BLM associates with numerous DNA damage repair proteins including BRCA1 during DNA repair, the functional consequences of BLM-BRCA1 association in telomere maintenance are not completely understood. Our earlier work showed the involvement of BRCA1 in different mechanisms of ALT, and telomere shortening upon loss of BLM in ALT cells. In order to delineate their roles in telomere maintenance, we studied their association in telomere metabolism in cells using ALT. This work shows that BLM and BRCA1 co-localize with RAD50 at telomeres during S- and G2-phases of the cell cycle in immortalized human cells using ALT but not in cells using telomerase to maintain telomeres. Co-immunoprecipitation of BRCA1 and BLM is enhanced in ALT cells at G2. Furthermore, BRCA1 and BLM interact with RAD50 predominantly in S- and G2-phases, respectively. Biochemical assays demonstrate that full-length BRCA1 increases the unwinding rate of BLM three-fold in assays using a DNA substrate that models a forked structure composed of telomeric repeats. Our results suggest that BRCA1 participates in ALT through its interactions with RAD50 and BLM.

  18. A Blm-Recql5 partnership in replication stress response

    Institute of Scientific and Technical Information of China (English)

    Xincheng Lu; Hua Lou; Guangbin Luo

    2011-01-01

    Deficiencies in DNA damage response and repair not only can result in genome instability and cancer predisposition, but also can render the cancer cells intrinsically more vulnerable to certain types of DNA damage insults. Particularly, replication stress is both a hallmark of human cancers and a common instigator for genome instability and cell death. Here, we review our work based on the genetic knockout studies on Blm and Recql5, two members of the mammalian RecQ helicase family. These studies have uncovered a unique partnership between these two helicases in the implementation of proper mitigation strategies under different circumstances to promote DNA replication and cell survival and suppress genome instability and cancer. In particular, current studies have revealed the presence of a novel Recql5/RECQL5-dependent mechanism for suppressing replication fork collapse in response to global replication fork stalling following exposure to camptothecin (CPT), a topoisomerase I inhibitor, and a potent inhibitor of DNA replication. The unique partnership between Blm and Recql5 in coping with the challenge imposed by replication stress is discussed. In addition, given that irinotecan and topotecan, two CPT derivatives, are currently used in clinic for treating human cancer patients with very promising results, the potential implication of the new findings from these studies in anticancer treatments is also discussed.

  19. Zebrafish orthologs of human muscular dystrophy genes

    OpenAIRE

    Zon Leonard I; Zhou Yi; Pusack Timothy J; Beltre Rosanna; Vogel Emily D; Guyon Jeffrey R; Steffen Leta S; Kunkel Louis M

    2007-01-01

    Abstract Background Human muscular dystrophies are a heterogeneous group of genetic disorders which cause decreased muscle strength and often result in premature death. There is no known cure for muscular dystrophy, nor have all causative genes been identified. Recent work in the small vertebrate zebrafish Danio rerio suggests that mutation or misregulation of zebrafish dystrophy orthologs can also cause muscular degeneration phenotypes in fish. To aid in the identification of new causative g...

  20. Benchmarking ortholog identification methods using functional genomics data

    OpenAIRE

    Hulsen, T.; Huynen, M.A.; de Vlieg, J; Groenen, P.M.A.

    2006-01-01

    BACKGROUND: The transfer of functional annotations from model organism proteins to human proteins is one of the main applications of comparative genomics. Various methods are used to analyze cross-species orthologous relationships according to an operational definition of orthology. Often the definition of orthology is incorrectly interpreted as a prediction of proteins that are functionally equivalent across species, while in fact it only defines the existence of a common ancestor for a gene...

  1. Number of Drilling Permits Approved by Fiscal Year on Federal Lands by BLM

    Data.gov (United States)

    Bureau of Land Management, Department of the Interior — This table contains the total number of Applications for Permit to Drill (APDs) by state approved by the BLM each fiscal year. Oil and gas operators may not begin...

  2. 2012 Oregon Department of Interior, Bureau of Land Management (BLM) Lidar: Panther Creek Study Area

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Oregon Department of Interior, Bureau of Land Management (BLM) contracted with Watershed Sciences, Inc. to collect high resolution topographic LiDAR data for...

  3. BLM/OCS South Texas Outer Continental Shelf (STOCS) Project Sediment Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The South Texas Outer Continental Shelf Project (STOCS) conducted by the University of Texas and the USGS with funding from BLM/NOAA. The USGS produced geochemical...

  4. Meiotic and Mitotic Phenotypes Conferred by the blm1-1 Mutation in Saccharomyces cerevisiae and MSH4 Suppression of the Bleomycin Hypersusceptibility

    Directory of Open Access Journals (Sweden)

    Carol Wood Moore

    2003-01-01

    Full Text Available Abstract: Oxidative damage can lead to a number of diseases, and can be fatal. The blm1-1 mutation of Saccharomyces cerevisiae confers hypersusceptibility to lethal effects of the oxidative, anticancer and antifungal agent, bleomycin. For the current report, additional defects conferred by the mutation in meiosis and mitosis were investigated. The viability of spores produced during meiosis by homozygous normal BLM1/BLM1, heterozygous BLM1/blm1-1, and homozygous mutant blm1-1/blm1-1 diploid strains was studied and compared. Approximately 88% of the tetrads derived from homozygous blm1-1/blm1-1 mutant diploid cells only produced one or two viable spores. In contrast, just one tetrad among all BLM1/BLM1 and BLM1/blm1-1 tetrads only produced one or two viable spores. Rather, 94% of BLM1/BLM1 tetrads and 100% of BLM1/blm1-1 tetrads produced asci with four or three viable spores. Thus, at least one copy of the BLM1 gene is essential for the production of four viable spores after meiosis. During mitotic growth, mutant blm1-1 strains grew at reduced rates and produced cells with high frequencies of unusual morphologies compared to wild-type strains. These results indicated BLM1 is also essential for normal mitotic growth. We also investigated the suppression by the MSH4 gene, a meiosis-specific MutS homolog, of the bleomycin hypersusceptibility of blm1-1 mutant cells, and the relationship of MSH4 to BLM1. We screened a genomic library, and isolated the MSH4 gene on the basis of its ability to suppress lethal effects of bleomycin in blm1-1 cells. However, genetic mapping studies indicated that BLM1 and MSH4 are not the same gene. The possibility that chromosomal nondisjunction could be the basis for the inability of blm1-1/blm1-1 mutant cells to produce four viable spores after meiosis is discussed.

  5. The SMC-5/6 Complex and the HIM-6 (BLM Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis.

    Directory of Open Access Journals (Sweden)

    Ye Hong

    2016-03-01

    Full Text Available Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs to generate crossovers (COs during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis.

  6. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus

    Science.gov (United States)

    Next generation sequencing is helping to solve the data insufficiency problem hindering well-resolved dominant gene phylogenies. We used Roche 454 technology to obtain DNA sequences from 93 nuclear orthologs, dispersed throughout all linkage groups of Daucus. Of these 93 orthologs, ten were designed...

  7. Structural mechanisms of human RecQ helicases WRN and BLM

    Directory of Open Access Journals (Sweden)

    Ken eKitano

    2014-10-01

    Full Text Available The RecQ family DNA helicases WRN (Werner syndrome protein and BLM (Bloom syndrome protein play a key role in protecting the genome against deleterious changes. In humans, mutations in these proteins lead to rare genetic diseases associated with cancer predisposition and accelerated aging. WRN and BLM are distinguished from other helicases by possessing signature tandem domains toward the C terminus, referred to as the RecQ C-terminal (RQC and helicase-and-ribonuclease D-C-terminal (HRDC domains. Although the precise function of the HRDC domain remains unclear, the previous crystal structure of a WRN RQC-DNA complex visualized a central role for the RQC domain in recognizing, binding and unwinding DNA at branch points. In particular, a prominent hairpin structure (the β-wing within the RQC winged-helix motif acts as a scalpel to induce the unpairing of a Watson-Crick base pair at the DNA duplex terminus. A similar RQC-DNA interaction was also observed in the recent crystal structure of a BLM-DNA complex. I review the latest structures of WRN and BLM, and then provide a docking simulation of BLM with a Holliday junction. The model offers an explanation for the efficient branch migration activity of the RecQ family toward recombination and repair intermediates.

  8. BLM realization for ${\\mathcal U}_{\\mathbb Z}(\\hat{\\frak{gl}}_n)$

    OpenAIRE

    Fu, Qiang

    2012-01-01

    In 1990, Beilinson-Lusztig-MacPherson (BLM) discovered a realization \\cite[5.7]{BLM} for quantum $\\frak{gl}_n$ via a geometric setting of quantum Schur algebras. We will generailze their result to the classical affine case. More precisely, we first use Ringel-Hall algebras to construct an integral form ${\\mathcal U}_{\\mathbb Z}(\\hat{\\frak{gl}}_n)$ of ${\\mathcal U}(\\hat{\\frak{gl}}_n)$, where ${\\mathcal U}(\\hat{\\frak{gl}}_n)$ is the universal enveloping algebra of the loop algebra $\\hat{\\frak{g...

  9. Self Testing Functionality of the LHC BLM System

    CERN Document Server

    Dehning, B; Emery, J; Nordt, A; Zamantzas, C

    2011-01-01

    Re­li­a­bil­i­ty con­cerns have driv­en the de­sign of the LHC BLM sys­tem through­out its development, from the early con­cep­tu­al stage right through the com­mis­sion­ing phase and up to the lat­est de­vel­op­ment of di­ag­nos­tic tools. To pro­tect the sys­tem against non-conformities, new ways of au­to­mat­ic check­ing have been de­vel­oped and im­ple­ment­ed. These checks are reg­u­lar­ly and sys­tem­at­i­cal­ly ex­e­cut­ed by the LHC op­er­a­tion team to in­sure that the sys­tem sta­tus after each test is "as good as new". This checks the elec­tri­cal part of the de­tec­tors (ion­i­sa­tion cham­ber or sec­ondary emis­sion mon­i­tor), their cable con­nec­tions to the front-end elec­tron­ics, the con­nec­tions to the back-end electronics and their ability to re­quest a beam abort. Dur­ing the instal­la­tion and in the early com­mis­sion­ing phase, these checks proved in­valu­able in find­ing non-con­for­mi­ties caused by un...

  10. Combinatorial Approaches to Accurate Identification of Orthologous Genes

    OpenAIRE

    Shi, Guanqun

    2011-01-01

    The accurate identification of orthologous genes across different species is a critical and challenging problem in comparative genomics and has a wide spectrum of biological applications including gene function inference, evolutionary studies and systems biology. During the past several years, many methods have been proposed for ortholog assignment based on sequence similarity, phylogenetic approaches, synteny information, and genome rearrangement. Although these methods share many commonly a...

  11. Assessing performance of orthology detection strategies applied to eukaryotic genomes.

    Directory of Open Access Journals (Sweden)

    Feng Chen

    Full Text Available Orthology detection is critically important for accurate functional annotation, and has been widely used to facilitate studies on comparative and evolutionary genomics. Although various methods are now available, there has been no comprehensive analysis of performance, due to the lack of a genomic-scale 'gold standard' orthology dataset. Even in the absence of such datasets, the comparison of results from alternative methodologies contains useful information, as agreement enhances confidence and disagreement indicates possible errors. Latent Class Analysis (LCA is a statistical technique that can exploit this information to reasonably infer sensitivities and specificities, and is applied here to evaluate the performance of various orthology detection methods on a eukaryotic dataset. Overall, we observe a trade-off between sensitivity and specificity in orthology detection, with BLAST-based methods characterized by high sensitivity, and tree-based methods by high specificity. Two algorithms exhibit the best overall balance, with both sensitivity and specificity>80%: INPARANOID identifies orthologs across two species while OrthoMCL clusters orthologs from multiple species. Among methods that permit clustering of ortholog groups spanning multiple genomes, the (automated OrthoMCL algorithm exhibits better within-group consistency with respect to protein function and domain architecture than the (manually curated KOG database, and the homolog clustering algorithm TribeMCL as well. By way of using LCA, we are also able to comprehensively assess similarities and statistical dependence between various strategies, and evaluate the effects of parameter settings on performance. In summary, we present a comprehensive evaluation of orthology detection on a divergent set of eukaryotic genomes, thus providing insights and guides for method selection, tuning and development for different applications. Many biological questions have been addressed by multiple

  12. ncRNA orthologies in the vertebrate lineage

    OpenAIRE

    Pignatelli, M.; Vilella, A. J.; Muffato, M.; Gordon, L; White, S.; Flicek, P.; Herrero, J.

    2016-01-01

    Annotation of orthologous and paralogous genes is necessary for many aspects of evolutionary analysis. Methods to infer these homology relationships have traditionally focused on protein-coding genes and evolutionary models used by these methods normally assume the positions in the protein evolve independently. However, as our appreciation for the roles of non-coding RNA genes has increased, consistently annotated sets of orthologous and paralogous ncRNA genes are increasingly needed. At the ...

  13. Differences in evolutionary pressure acting within highly conserved ortholog groups

    Directory of Open Access Journals (Sweden)

    Aravind L

    2008-07-01

    Full Text Available Abstract Background In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence occurring by accumulation of neutral substitutions. Using a set of ortholog groups from prokaryotes, with a single representative in each studied organism, we asked the question if this evolutionary pressure is acting similarly on different subgroups of orthologs defined as major lineages (e.g. Proteobacteria or Firmicutes. Results Using correlations in entropy measures as a proxy for evolutionary pressure, we observed two distinct behaviors within our ortholog collection. The first subset of ortholog groups, called here informational, consisted mostly of proteins associated with information processing (i.e. translation, transcription, DNA replication and the second, the non-informational ortholog groups, mostly comprised of proteins involved in metabolic pathways. The evolutionary pressure acting on non-informational proteins is more uniform relative to their informational counterparts. The non-informational proteins show higher level of correlation between entropy profiles and more uniformity across subgroups. Conclusion The low correlation of entropy profiles in the informational ortholog groups suggest that the evolutionary pressure acting on the informational ortholog groups is not uniform across different clades considered this study. This might suggest "fine-tuning" of informational proteins in each lineage leading to lineage-specific differences in selection. This, in turn, could make these proteins less exchangeable between lineages. In contrast, the uniformity of the selective pressure acting on the non-informational groups might allow the exchange of the genetic material via lateral gene transfer.

  14. Evolution of orthologous tandemly arrayed gene clusters

    Directory of Open Access Journals (Sweden)

    Bertrand Denis

    2011-10-01

    Full Text Available Abstract Background Tandemly Arrayed Gene (TAG clusters are groups of paralogous genes that are found adjacent on a chromosome. TAGs represent an important repertoire of genes in eukaryotes. In addition to tandem duplication events, TAG clusters are affected during their evolution by other mechanisms, such as inversion and deletion events, that affect the order and orientation of genes. The DILTAG algorithm developed in 1 makes it possible to infer a set of optimal evolutionary histories explaining the evolution of a single TAG cluster, from an ancestral single gene, through tandem duplications (simple or multiple, direct or inverted, deletions and inversion events. Results We present a general methodology, which is an extension of DILTAG, for the study of the evolutionary history of a set of orthologous TAG clusters in multiple species. In addition to the speciation events reflected by the phylogenetic tree of the considered species, the evolutionary events that are taken into account are simple or multiple tandem duplications, direct or inverted, simple or multiple deletions, and inversions. We analysed the performance of our algorithm on simulated data sets and we applied it to the protocadherin gene clusters of human, chimpanzee, mouse and rat. Conclusions Our results obtained on simulated data sets showed a good performance in inferring the total number and size distribution of duplication events. A limitation of the algorithm is however in dealing with multiple gene deletions, as the algorithm is highly exponential in this case, and becomes quickly intractable.

  15. Phylogenetic and functional assessment of orthologs inference projects and methods.

    Directory of Open Access Journals (Sweden)

    Adrian M Altenhoff

    2009-01-01

    Full Text Available Accurate genome-wide identification of orthologs is a central problem in comparative genomics, a fact reflected by the numerous orthology identification projects developed in recent years. However, only a few reports have compared their accuracy, and indeed, several recent efforts have not yet been systematically evaluated. Furthermore, orthology is typically only assessed in terms of function conservation, despite the phylogeny-based original definition of Fitch. We collected and mapped the results of nine leading orthology projects and methods (COG, KOG, Inparanoid, OrthoMCL, Ensembl Compara, Homologene, RoundUp, EggNOG, and OMA and two standard methods (bidirectional best-hit and reciprocal smallest distance. We systematically compared their predictions with respect to both phylogeny and function, using six different tests. This required the mapping of millions of sequences, the handling of hundreds of millions of predicted pairs of orthologs, and the computation of tens of thousands of trees. In phylogenetic analysis or in functional analysis where high specificity is required, we find that OMA and Homologene perform best. At lower functional specificity but higher coverage level, OrthoMCL outperforms Ensembl Compara, and to a lesser extent Inparanoid. Lastly, the large coverage of the recent EggNOG can be of interest to build broad functional grouping, but the method is not specific enough for phylogenetic or detailed function analyses. In terms of general methodology, we observe that the more sophisticated tree reconstruction/reconciliation approach of Ensembl Compara was at times outperformed by pairwise comparison approaches, even in phylogenetic tests. Furthermore, we show that standard bidirectional best-hit often outperforms projects with more complex algorithms. First, the present study provides guidance for the broad community of orthology data users as to which database best suits their needs. Second, it introduces new methodology

  16. 2012 U.S. Department of Interior, Bureau of Land Management (BLM) Lidar: Panther Creek Study Area

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The U.S. Department of Interior, Bureau of Land Management (BLM) contracted with Watershed Sciences, Inc. to collect high resolution topographic LiDAR data for...

  17. Road and Street Centerlines, BLM Horse Valley, Published in 2007, 1:24000 (1in=2000ft) scale, Iron County.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — , published at 1:24000 (1in=2000ft) scale, was produced all or in part from Other information as of 2007. It is described as 'BLM Horse Valley'. The extent of these...

  18. The roles of WRN and BLM RecQ helicases in the Alternative Lengthening of Telomeres

    OpenAIRE

    Mendez-Bermudez, Aaron; Hidalgo-Bravo, Alberto; Cotton, Victoria E.; Gravani, Athanasia; Jeyapalan, Jennie N.; Royle, Nicola J.

    2012-01-01

    Approximately 10% of all cancers, but a higher proportion of sarcomas, use the recombination-based alternative lengthening of telomeres (ALT) to maintain telomeres. Two RecQ helicase genes, BLM and WRN, play important roles in homologous recombination repair and they have been implicated in telomeric recombination activity, but their precise roles in ALT are unclear. Using analysis of sequence variation present in human telomeres, we found that a WRN– ALT+ cell line lacks the class of complex...

  19. The human RecQ helicases BLM and RECQL4 cooperate to preserve genome stability

    Czech Academy of Sciences Publication Activity Database

    Singh, D.K.; Popuri, V.; Kulikowicz, T.; Shevelev, Igor; Ghosh, A.K.; Ramamoorthy, M.; Rossi, M.L.; Janščák, Pavel; Croteau, D.L.; Bohr, V.A.

    2012-01-01

    Roč. 40, č. 14 (2012), s. 6632-6648. ISSN 0305-1048 R&D Projects: GA ČR GAP305/10/0281 Grant ostatní: NIH(US) Z01-AG000726-17 Institutional research plan: CEZ:AV0Z50520514 Institutional support: RVO:68378050 Keywords : RecQ helicase * genome stability * BLM * RECQL4 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.278, year: 2012

  20. Measurements and simulations of the BLM response to a radiation field inside the CERF target area

    CERN Document Server

    Lebbos, E; Dehning, B; Effinger, E; Ferrari, A; Kramer, D; Nordt, A; Roeed, K; Roesler, S; Sapinski, M; Vlachoudis, V

    2010-01-01

    The CERN-EU high-energy reference field (CERF) facility is installed in one of the secondary beam lines (H6) of the Super Proton Synchrotron (SPS), in the North Experimental Area at CERN. This facility is used as a reference for testing, inter-comparing and calibrating passive and active instruments. In May 2009, the SPS provided a mixed hadron beam (protons, pions and kaons) during a few days, in order to perform several measurements with different devices such as the Radiation Protection Monitor used for residual dose rates due to Induced Radioactivity in the LHC (PMI), the Secondary Emission Monitor used for high beam losses (SEM), the Radiation Monitor for electronics (RadMon), and the Beam Loss Monitor for the LHC (BLM). This report focuses on the measurements of the BLM response during this year’s operation at CERF. The measurements evaluate the sensitivity of the BLM signal to the particle energy spectrum, with special attention to the contribution coming from thermal neutrons. For this purpose, meas...

  1. The generalized BLM approach to fix scale-dependence in QCD: the current status of investigations

    CERN Document Server

    Kataev, A L

    2014-01-01

    I present a brief review of the generalized Brodsky-Lepage-McKenzie (BLM) approaches to fix the scale-dependence of the renormalization group (RG) invariant quantities in QCD. At first, these approaches are based on the expansions of the coefficients of the perturbative series for the RG-invariant quantities in the products of the coefficients $\\beta_i$ of the QCD $\\beta$-function, which are evaluated in the MS-like schemes. As a next step all $\\beta_i$-dependent terms are absorbed into the BLM-type scale(s) of the powers of the QCD couplings. The difference between two existing formulations of the above mentioned generalizations based on the seBLM approach and the Principle of Maximal Conformality (PMC) are clarified in the case of the Bjorken polarized deep-inelastic scattering sum rule. Using the conformal symmetry-based relations for the non-singlet coefficient functions of the Adler D-function and of Bjorken polarized deep-inelastic scattering sum rules $C^{\\rm Bjp}_{\\rm NS}(a_s)$ the $\\beta_i$-dependent...

  2. Factors affecting the concordance between orthologous gene trees and species tree in bacteria

    Directory of Open Access Journals (Sweden)

    González Víctor

    2008-10-01

    Full Text Available Abstract Background As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. Here, using a method that allows the detection and exclusion of false positives during identification of orthologous genes, we address the question of whether putative orthologous genes within bacteria really reflect the history of the species. Results We identified a set of 370 orthologous genes from the bacterial order Rhizobiales. Although manifesting strong vertical signal, almost every orthologous gene had a distinct phylogeny, and the most common topology among the orthologous gene trees did not correspond with the best estimate of the species tree. However, each orthologous gene tree shared an average of 70% of its bipartitions with the best estimate of the species tree. Stochastic error related to gene size affected the concordance between the best estimated of the species tree and the orthologous gene trees, although this effect was weak and distributed unevenly among the functional categories. The nodes showing the greatest discordance were those defined by the shortest internal branches in the best estimated of the species tree. Moreover, a clear bias was evident with respect to the function of the orthologous genes, and the degree of divergence among the orthologous genes appeared to be related to their functional classification. Conclusion Orthologous genes do not reflect the history of the species when taken as individual markers, but they do when taken as a whole. Stochastic error affected the concordance of orthologous genes with the species tree, albeit weakly. We conclude that two important biological causes of discordance among

  3. Orthology between genomes of Brachypodium, wheat and rice

    Directory of Open Access Journals (Sweden)

    Balyan Harindra S

    2009-05-01

    Full Text Available Abstract Background In the past, rice genome served as a good model for studies involving comparative genomics of grass species. More recently, however, Brachypodium distachyon genome has emerged as a better model system for genomes of temperate cereals including wheat. During the present study, Brachypodium EST contigs were utilized to resolve orthologous relationships among the genomes of Brachypodium, wheat and rice. Findings Comparative sequence analysis of 3,818 Brachypodium EST (bEST contigs and 3,792 physically mapped wheat EST (wEST contigs revealed that as many as 449 bEST contigs were orthologous to 1,154 wEST loci that were bin-mapped on all the 21 wheat chromosomes. Similarly 743 bEST contigs were orthologous to specific rice genome sequences distributed on all the 12 rice chromosomes. As many as 183 bEST contigs were orthologous to both wheat and rice genome sequences, which harbored as many as 17 SSRs conserved across the three species. Primers developed for 12 of these 17 conserved SSRs were used for a wet-lab experiment, which resolved relatively high level of conservation among the genomes of Brachypodium, wheat and rice. Conclusion The present study confirmed that Brachypodium is a better model than rice for analysis of the genomes of temperate cereals like wheat and barley. The whole genome sequence of Brachypodium, which should become available in the near future, will further facilitate greatly the studies involving comparative genomics of cereals.

  4. The generalized BLM approach to fix scale- dependence in QCD: the current status of investigations

    Science.gov (United States)

    Kataev, A. L.

    2015-05-01

    I present a brief review of the generalized Brodsky-Lepage-McKenzie (BLM) approaches to fix the scale-dependence of the renormalization group (RG) invariant quantities in QCD. At first, these approaches are based on the expansions of the coefficients of the perturbative series for the RG-invariant quantities in the products of the coefficients βi of the QCD β-function, which are evaluated in the MS-like schemes. As a next step all βi-dependent terms are absorbed into the BLM-type scale(s) of the powers of the QCD couplings. The difference between two existing formulations of the above mentioned generalizations based on the seBLM approach and the Principle of Maximal Conformality (PMC) are clarified in the case of the Bjorken polarized deep-inelastic scattering sum rule. Using the conformal symmetry-based relations for the non-singlet coefficient functions of the Adler D-function and of Bjorken polarized deep-inelastic scattering sum rules CBjpNS (as) the βi-dependent structure of the NNLO approximation for CBjpNS (as) is predicted in QCD with ngl-multiplet of gluino degrees of freedom, which appear in SUSY extension of QCD. The importance of performing the analytical calculation of the N3LO additional contributions of ngl gluino multiplet to CBjpNS (as) for checking the presented in the report NNLO prediction and for the studies of the possibility to determine the discussed β-expansion pattern of this sum rule at the O(a4s)-level is emphasised.

  5. 78 FR 65356 - Notice of Mailing/Street Address Change for the BLM-Utah West Desert District and Salt Lake Field...

    Science.gov (United States)

    2013-10-31

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF THE INTERIOR Bureau of Land Management Notice of Mailing/Street Address Change for the BLM-Utah West Desert District... mailing/street address for the Bureau of Land Management (BLM), West Desert District and Salt Lake...

  6. Retrotranspositions in orthologous regions of closely related grass species

    Directory of Open Access Journals (Sweden)

    Swigoňová Zuzana

    2006-08-01

    Full Text Available Abstract Background Retrotransposons are commonly occurring eukaryotic transposable elements (TEs. Among these, long terminal repeat (LTR retrotransposons are the most abundant TEs and can comprise 50–90% of the genome in higher plants. By comparing the orthologous chromosomal regions of closely related species, the effects of TEs on the evolution of plant genomes can be studied in detail. Results Here, we compared the composition and organization of TEs within five orthologous chromosomal regions among three grass species: maize, sorghum, and rice. We identified a total of 132 full or fragmented LTR retrotransposons in these regions. As a percentage of the total cumulative sequence in each species, LTR retrotransposons occupy 45.1% of the maize, 21.1% of the rice, and 3.7% of the sorghum regions. The most common elements in the maize retrotransposon-rich regions are the copia-like retrotransposons with 39% and the gypsy-like retrotransposons with 37%. Using the contiguous sequence of the orthologous regions, we detected 108 retrotransposons with intact target duplication sites and both LTR termini. Here, we show that 74% of these elements inserted into their host genome less than 1 million years ago and that many retroelements expanded in size by the insertion of other sequences. These inserts were predominantly other retroelements, however, several of them were also fragmented genes. Unforeseen was the finding of intact genes embedded within LTR retrotransposons. Conclusion Although the abundance of retroelements between maize and rice is consistent with their different genome sizes of 2,364 and 389 Mb respectively, the content of retrotransposons in sorghum (790 Mb is surprisingly low. In all three species, retrotransposition is a very recent activity relative to their speciation. While it was known that genes re-insert into non-orthologous positions of plant genomes, they appear to re-insert also within retrotransposons, potentially

  7. Drill baby drill: An analysis of how energy development displaced ranching's dominance over the BLM's subgovernment policymaking environment

    Science.gov (United States)

    Forbis, Robert Earl, Jr.

    Academic literature analyzing the Bureau of Land Management (BLM) land-use subgovernment stops at the Taylor Grazing Act and concludes that the historical development of administering grazing on public lands led to the capture of the BLM by ranching interests. Using a two-pronged methodological approach of process tracing and elite interviews this dissertation seeks to advance our collective knowledge of subgovernment theory by (a) clarifying the impact executive decision-making has on subgovernments and (b) identifying the conditions under which strategically competitive behavior between two competing subgovernment actors occurs. The dissertation seeks to update the literature by explaining what has caused the BLM to shift from a rancher-dominated agency to an energy dominated agency by identifying conditions under which subgovernment actors strategically respond to a political conflict. The research poses two questions: (1) how have executive actions disrupted an existing balance of power in a so-called "strong corner" of an entrenched subgovernment system and (2) what happens when conflict and competition break out between allied members of the system? Analysis indicates that as the BLM responded to Executive actions emphasizing domestic energy production, a conflict emerged between traditional allies: ranching and energy. Triggered by the unintended consequence of awakening long-dormant legislation, split-estate energy development---where property rights are severed between private surface and federal mineral estates---expanded across the West. In turn, this expansion helped establish the conditions for conflict and in doing so disrupted the balance of power between large public resource use interests in the relatively stable land-use subgovernment of the BLM. Indicative of energy's emerging dominance of the BLM's subgovernment, split-estate energy development led ranching interests to seek the protection of their Western state legislatures. This shift in

  8. An economic analysis of alternative fertility control and associated management techniques for three BLM wild horse herds

    Science.gov (United States)

    Bartholow, John M.

    2004-01-01

    Contemporary cost projections were computed for several alternative strategies that could be used by BLM to manage three wild horse populations. The alternatives included existing gather and selective removal methods, combined with potential contraceptive applications of varying duration and other potentially useful management techniques. Costs were projected for a 20-year economic life using the Jenkins wild horse population model and cost estimates from BLM that reflect state-by-state per horse removal, adoption, long-term holding, and contraceptive application expenses. Important findings include: Application of currently available 2-year contraceptives appears capable of reducing variable operating costs for wild horse populations by about 21% on average.

  9. Characterization of the ovine ortholog of secretory leukoprotease inhibitor.

    Science.gov (United States)

    Brown, Thomas I; Mistry, Rohit; Gray, Robert; Imrie, Margaret; Collie, David D; Sallenave, Jean-Michel

    2005-08-01

    There is great interest in the use of the sheep as a model for the investigation of inflammation in the lung. The serine antiproteases secretory leukoprotease inhibitor (SLPI) and elafin are important "alarm antiproteases" in the lung and have potentially important roles in the innate immune response. SLPI was first characterized in man and subsequently in murine, porcine, and rat tissues. Here we present the first data concerning the gene and cDNA sequence encoding for the ovine ortholog of SLPI, a protein of 132 amino acids with 66% sequence identity at the amino acid level with human SLPI. A 24-amino-acid signal sequence signifies that, like the other mammalian orthologs, ovine SLPI is a secreted protein. Tissue distribution of expression is demonstrated by reverse transcription polymerase chain reaction (RT-PCR) and shows features similar to SLPI expression in other mammals, specifically at mucosal surfaces such as the upper respiratory and intestinal tracts, and also the skin, liver, and kidney. This distribution lends credence to SLPI having important roles in innate immunity. We have also cloned the ovine SLPI cDNA into an expression vector and expressed the ovine SLPI protein in vitro. This has enabled us to demonstrate that ovine SLPI is correctly processed (Western blot analysis and SELDI-TOF mass spectrometry analysis) and has biological antihuman neutrophil elastase activity. In summary, the ovine ortholog of SLPI shows similarities to other members of the SLPI family and has all the features of a modulator of innate immunity. PMID:16180144

  10. Excavation of Pid3 Orthologs with Differential Resistance Spectra to Magnaporthe oryzae in Rice Resource

    OpenAIRE

    Xu, Xiao; Lv, Qiming; Shang, Junjun; Pang, Zhiqian; Zhou, Zhuangzhi; Wang, Jing; Jiang, Guanghuai; Tao, Yong; Xu, Qian; Li, Xiaobing; Zhao, Xianfeng; Li, Shigui; Xu, Jichen; Zhu, Lihuang

    2014-01-01

    Twenty-six orthologs of the rice blast resistance gene Pid3 from cultivated varieties and wild rice accessions distributed in different areas were cloned by allele mining. Sequence analysis showed that while each of the orthologous genes from indica varieties and most wild accessions encodes a complete NBS-LRR protein, each of the proteins encoded by those from japonica varieties and few wild rice accessions presents a premature termination. Eleven of the 26 orthologs were selected for blast ...

  11. Factors affecting the concordance between orthologous gene trees and species tree in bacteria

    OpenAIRE

    González Víctor; Castillo-Ramírez Santiago

    2008-01-01

    Abstract Background As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. Here, using a method that allows the detection and exclusion of false positives during identificat...

  12. Update History of This Database - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...PGDBj - Ortholog DB Update History of This Database Date Update contents 2014/05/12 PGDBj Ortholog DB Englis...a SEF URLs by Artio About This Database Database Description Download License Update History... of This Database Site Policy | Contact Us Update History of This Database - PGDBj - Ortholog DB | LSDB Archive ...

  13. Analysis of fast losses in the LHC with the BLM system

    CERN Document Server

    Nebot, E; Holzer, E; Dehning, B; Nordt, A; Sapinski, M; Emery, J; Zamantzas, C; Effinger, E; Marsili, A; Wenninger, J; Baer, T; Schmidt, R; Yang, Z; Zimmerman, F; Fuster, N

    2011-01-01

    About 3600 Ionization Chambers are located around the LHC ring to detect beam losses that could damage the equipment or quench superconducting magnets. The Beam Loss Monitors (BLMs) integrate the losses in 12 different time intervals (from 40 us to 83.8 s) allowing for different abort thresholds depending on the duration of the loss and the beam energy. The signals are also recorded in a database at 1 Hz for offline analysis. During the 2010 run, a limiting factor in the machine availability were sudden losses appearing around the ring on the ms time scale and detected exclusively by the BLM system. It is believed that such losses originate from dust particles falling into the beam, or being attracted by its strong electromagnetic field. This document describes some of the properties of these ”Unidentified Falling Objects” (UFOs) putting special emphasis on their dependence on beam parameters (energy, intensity, etc). The subsequent modification of the BLM beam abort thresholds for the 2011 run that were ...

  14. A Low-Noise Transimpedance Amplifier for BLM-Based Ion Channel Recording.

    Science.gov (United States)

    Crescentini, Marco; Bennati, Marco; Saha, Shimul Chandra; Ivica, Josip; de Planque, Maurits; Morgan, Hywel; Tartagni, Marco

    2016-01-01

    High-throughput screening (HTS) using ion channel recording is a powerful drug discovery technique in pharmacology. Ion channel recording with planar bilayer lipid membranes (BLM) is scalable and has very high sensitivity. A HTS system based on BLM ion channel recording faces three main challenges: (i) design of scalable microfluidic devices; (ii) design of compact ultra-low-noise transimpedance amplifiers able to detect currents in the pA range with bandwidth >10 kHz; (iii) design of compact, robust and scalable systems that integrate these two elements. This paper presents a low-noise transimpedance amplifier with integrated A/D conversion realized in CMOS 0.35 μm technology. The CMOS amplifier acquires currents in the range ±200 pA and ±20 nA, with 100 kHz bandwidth while dissipating 41 mW. An integrated digital offset compensation loop balances any voltage offsets from Ag/AgCl electrodes. The measured open-input input-referred noise current is as low as 4 fA/√Hz at ±200 pA range. The current amplifier is embedded in an integrated platform, together with a microfluidic device, for current recording from ion channels. Gramicidin-A, α-haemolysin and KcsA potassium channels have been used to prove both the platform and the current-to-digital converter. PMID:27213382

  15. Very High Radiation Detector for the LHC BLM System Based on Secondary Electron Emission

    CERN Document Server

    Dehning, B; Holzer, EB; Kramer, D

    2007-01-01

    Beam Loss Monitoring (BLM) system plays a vital role in the active protection of the LHC accelerators elements. It should provide the number of particles lost from the primary hadron beam by measuring the radiation field induced by their interaction with matter surrounding the beam pipe. The LHC BLM system will use ionization chambers as standard detectors but in the areas where very high dose rates are expected, the Secondary Emission Monitor (SEM) chambers will be employed because of their high linearity, low sensitivity and fast response. The SEM needs a high vacuum for proper operation and has to be functional for up to 20 years, therefore all the components were designed according to the UHV requirements and a getter pump was included. The SEM electrodes are made of Ti because of its Secondary Emission Yield (SEY) stability. The sensitivity of the SEM was modeled in Geant4 via the Photo-Absorption Ionization module together with custom parameterization of the very low energy secondary electron production...

  16. A Low-Noise Transimpedance Amplifier for BLM-Based Ion Channel Recording

    Directory of Open Access Journals (Sweden)

    Marco Crescentini

    2016-05-01

    Full Text Available High-throughput screening (HTS using ion channel recording is a powerful drug discovery technique in pharmacology. Ion channel recording with planar bilayer lipid membranes (BLM is scalable and has very high sensitivity. A HTS system based on BLM ion channel recording faces three main challenges: (i design of scalable microfluidic devices; (ii design of compact ultra-low-noise transimpedance amplifiers able to detect currents in the pA range with bandwidth >10 kHz; (iii design of compact, robust and scalable systems that integrate these two elements. This paper presents a low-noise transimpedance amplifier with integrated A/D conversion realized in CMOS 0.35 μm technology. The CMOS amplifier acquires currents in the range ±200 pA and ±20 nA, with 100 kHz bandwidth while dissipating 41 mW. An integrated digital offset compensation loop balances any voltage offsets from Ag/AgCl electrodes. The measured open-input input-referred noise current is as low as 4 fA/√Hz at ±200 pA range. The current amplifier is embedded in an integrated platform, together with a microfluidic device, for current recording from ion channels. Gramicidin-A, α-haemolysin and KcsA potassium channels have been used to prove both the platform and the current-to-digital converter.

  17. A Low-Noise Transimpedance Amplifier for BLM-Based Ion Channel Recording

    Science.gov (United States)

    Crescentini, Marco; Bennati, Marco; Saha, Shimul Chandra; Ivica, Josip; de Planque, Maurits; Morgan, Hywel; Tartagni, Marco

    2016-01-01

    High-throughput screening (HTS) using ion channel recording is a powerful drug discovery technique in pharmacology. Ion channel recording with planar bilayer lipid membranes (BLM) is scalable and has very high sensitivity. A HTS system based on BLM ion channel recording faces three main challenges: (i) design of scalable microfluidic devices; (ii) design of compact ultra-low-noise transimpedance amplifiers able to detect currents in the pA range with bandwidth >10 kHz; (iii) design of compact, robust and scalable systems that integrate these two elements. This paper presents a low-noise transimpedance amplifier with integrated A/D conversion realized in CMOS 0.35 μm technology. The CMOS amplifier acquires currents in the range ±200 pA and ±20 nA, with 100 kHz bandwidth while dissipating 41 mW. An integrated digital offset compensation loop balances any voltage offsets from Ag/AgCl electrodes. The measured open-input input-referred noise current is as low as 4 fA/√Hz at ±200 pA range. The current amplifier is embedded in an integrated platform, together with a microfluidic device, for current recording from ion channels. Gramicidin-A, α-haemolysin and KcsA potassium channels have been used to prove both the platform and the current-to-digital converter. PMID:27213382

  18. Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive ...

  19. Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ...

  20. DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants

    OpenAIRE

    Barta, Endre; Sebestyén, Endre; Pálfy, Tamás B.; Tóth, Gábor; Ortutay, Csaba P.; Patthy, László

    2004-01-01

    DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and pl...

  1. Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs

    DEFF Research Database (Denmark)

    Nguyen, Giang Huong; Tang, Weiliang; Robles, Ana I;

    2014-01-01

    Bloom syndrome is a rare autosomal recessive disorder characterized by genetic instability and cancer predisposition, and caused by mutations in the gene encoding the Bloom syndrome, RecQ helicase-like (BLM) protein. To determine whether altered gene expression might be responsible for pathologic...

  2. Tables of co-located geothermal-resource sites and BLM Wilderness Study Areas

    Energy Technology Data Exchange (ETDEWEB)

    Foley, D.; Dorscher, M.

    1982-11-01

    Matched pairs of known geothermal wells and springs with BLM proposed Wilderness Study Areas (WSAs) were identified by inspection of WSA and Geothermal resource maps for the states of Arizona, California, Colorado, Idaho, Montana, Nevada, New Mexico, Oregon, Utah, Washington and Wyoming. A total of 3952 matches, for geothermal sites within 25 miles of a WSA, were identified. Of these, only 71 (1.8%) of the geothermal sites are within one mile of a WSA, and only an additional 100 (2.5%) are within one to three miles. Approximately three-fourths of the matches are at distances greater than ten miles. Only 12 of the geothermal sites within one mile of a WSA have surface temperatures reported above 50/sup 0/C. It thus appears that the geothermal potential of WSAs overall is minimal, but that evaluation of geothermal resources should be considered in more detail for some areas prior to their designation as Wilderness.

  3. On calculating the probability of a set of orthologous sequences

    Directory of Open Access Journals (Sweden)

    Junfeng Liu

    2009-02-01

    Full Text Available Junfeng Liu1,2, Liang Chen3, Hongyu Zhao4, Dirk F Moore1,2, Yong Lin1,2, Weichung Joe Shih1,21Biometrics Division, The Cancer, Institute of New Jersey, New Brunswick, NJ, USA; 2Department of Biostatistics, School of Public Health, University of Medicine and Dentistry of New Jersey, Piscataway, NJ, USA; 3Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; 4Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USAAbstract: Probabilistic DNA sequence models have been intensively applied to genome research. Within the evolutionary biology framework, this article investigates the feasibility for rigorously estimating the probability of a set of orthologous DNA sequences which evolve from a common progenitor. We propose Monte Carlo integration algorithms to sample the unknown ancestral and/or root sequences a posteriori conditional on a reference sequence and apply pairwise Needleman–Wunsch alignment between the sampled and nonreference species sequences to estimate the probability. We test our algorithms on both simulated and real sequences and compare calculated probabilities from Monte Carlo integration to those induced by single multiple alignment.Keywords: evolution, Jukes–Cantor model, Monte Carlo integration, Needleman–Wunsch alignment, orthologous

  4. A Role for BLM in Double-Strand Break Repair Pathway Choice: Prevention of CtIP/Mre11-Mediated Alternative Nonhomologous End-Joining

    DEFF Research Database (Denmark)

    Grabarz, Anastazja; Guirouilh-Barbat, Josée; Barascu, Aurelia; Pennarun, Gaëlle; Genet, Diane; Rass, Emilie; Germann, Susanne Manuela; Bertrand, Pascale; Hickson, Ian David; Lopez, Bernard S.

    2013-01-01

    represses A-EJ in an epistatic manner with 53BP1 and RIF1 and is required for ionizing-radiation-induced 53BP1 focus assembly. Conversely, in the absence of 53BP1 or RIF1, BLM promotes formation of A-EJ long deletions, consistent with a role for BLM in DSB end resection. These data highlight a dual role for...

  5. Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs

    Directory of Open Access Journals (Sweden)

    Baillie David L

    2004-11-01

    Full Text Available Abstract Background The complete genome sequences for human and the nematode Caenorhabditis elegans offer an opportunity to learn more about human gene function through functional characterization of orthologs in the worm. Based on a previous genome-wide analysis of worm-human orthologous transmembrane proteins, we selected seventeen genes to explore experimentally in C. elegans. These genes were selected on the basis that they all have high confidence candidate human orthologs and that their function is unknown. We first analyzed their phylogeny, membrane topology and domain organization. Then gene functions were studied experimentally in the worm by using RNA interference and transcriptional gfp reporter gene fusions. Results The experiments gave functional insights for twelve of the genes studied. For example, C36B1.12, the worm ortholog of three presenilin-like genes, was almost exclusively expressed in head neurons, suggesting an ancient conserved role important to neuronal function. We propose a new transmembrane topology for the presenilin-like protein family. sft-4, the worm ortholog of surfeit locus gene Surf-4, proved to be an essential gene required for development during the larval stages of the worm. R155.1, whose human ortholog is entirely uncharacterized, was implicated in body size control and other developmental processes. Conclusions By combining bioinformatics and C. elegans experiments on orthologs, we provide functional insights on twelve previously uncharacterized human genes.

  6. Blm-s, a BH3-Only Protein Enriched in Postmitotic Immature Neurons, Is Transcriptionally Upregulated by p53 during DNA Damage

    Directory of Open Access Journals (Sweden)

    Wei-Wen Liu

    2014-10-01

    Full Text Available Programmed cell death is a pivotal process that regulates neuronal number during development. Key regulators of this process are members of the BCL-2 family. Using mRNA differential display, we identified a Bcl-2 family gene, Blm-s (Bcl-2-like molecule, short form, enriched in postmitotic neurons of the developing cerebral cortex. BLM-s functions as a BH3-only apoptosis sensitizer/derepressor and causes BAX-dependent mitochondria-mediated apoptosis by selectively binding to prosurvival BCL-2 or MCL-1. When challenged with γ-irradiation that produces DNA double-strand breaks (DSBs, Blm-s is transcriptionally upregulated in postmitotic immature neurons with concurrently increased apoptosis. RNAi-mediated depletion of Blm-s protects immature neurons from irradiation-induced apoptosis. Furthermore, Blm-s is a direct target gene of p53 and AP1 via the ataxia telangiectasia mutated (ATM- and c-Jun N-terminal kinase (JNK-signaling pathways activated by DSBs. Thus, BLM-s is likely an apoptosis sensor activated by DSBs accumulating in postmitotic immature neurons.

  7. Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

    Science.gov (United States)

    Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo

    2015-01-01

    Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO). While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis. PMID:25875762

  8. An in vitro biotic ligand model (BLM) for silver binding to cultured gill epithelia of freshwater rainbow trout (Oncorhynchus mykiss)

    International Nuclear Information System (INIS)

    'Reconstructed' gill epithelia on filter supports were grown in primary culture from dispersed gill cells of freshwater rainbow trout (Oncorhynchus mykiss). This preparation contains both pavement cells and chloride cells, and after 7-9 days in culture, permits exposure of the apical surface to true freshwater while maintaining blood-like culture media on the basolateral surface, and exhibits a stable transepithelial resistance (TER) and transepithelial potential (TEP) under these conditions. These epithelia were used to develop a possible in vitro version of the biotic ligand model (BLM) for silver; the in vivo BLM uses short-term gill binding of the metal to predict acute silver toxicity as a function of freshwater chemistry. Radio-labeled silver (110mAg as AgNO3) was placed on the apical side (freshwater), and the appearance of 110mAg in the epithelia (binding) and in the basolateral media (flux) over 3 h were monitored. Silver binding (greater than the approximate range 0-100 μg l-1) and silver flux were concentration-dependent with a 50% saturation point (apparent Kd) value of about 10 μg l-1 or 10-7 M, very close to the 96-h LC50 in vivo in the same water chemistry. There were no adverse effects of silver on TER, TEP, or Na+, K+-ATPase activity, though the latter declined over longer exposures, as in vivo. Silver flux over 3 h was small (+ and dissolved organic carbon (humic acid) concentrations, increased by elevations in freshwater Cl- and reductions in pH, and insensitive to elevations in Ca2+. With the exception of the pH response, these effects were qualitatively and quantitatively similar to in vivo BLM responses. The results suggest that an in vitro BLM approach may provide a simple and cost-effective way for evaluating the protective effects of site-specific waters

  9. Genetic variation in the NBS1, MRE11, RAD50 and BLM genes and susceptibility to non-Hodgkin lymphoma

    OpenAIRE

    Gascoyne Randy D; Connors Joseph M; Gallagher Richard P; Lai Agnes S; Leach Stephen; MacArthur Amy C; Schuetz Johanna M; Spinelli John J; Brooks-Wilson Angela R

    2009-01-01

    Abstract Background Translocations are hallmarks of non-Hodgkin lymphoma (NHL) genomes. Because lymphoid cell development processes require the creation and repair of double stranded breaks, it is not surprising that disruption of this type of DNA repair can cause cancer. The members of the MRE11-RAD50-NBS1 (MRN) complex and BLM have central roles in maintenance of DNA integrity. Severe mutations in any of these genes cause genetic disorders, some of which are characterized by increased risk ...

  10. Virtual Screening and Molecular Docking Study of Bloom’s Syndrome Protein (BLM for Finding Potential Lead Drug Candidate

    Directory of Open Access Journals (Sweden)

    Manoj Kumar Verma

    2014-06-01

    Full Text Available Increased levels of locus-specific mutations within the BLM result in development of Bloom Syndrome and patients are found to be immune deficient. HRDC domain amino acid Lys1270 is presumably to play role in mediating interactions with DNA. Single point mutation of Lys1270 (K1270V reduces the potency of Double Holliday junction (DHJ DNA unwinding so BLM lead to its functional loss. Quadruplex formation have role in immunoglobulin heavy chain switching and inhibiting RecQ helicases activity in-vitro in BLM. Variety of G-Quadruplex ligands are employed by molecular docking for arriving at lead compound identification. The scoring function of docking results describes protein-ligand interaction and it conjointly instructed that docking of ligand at mutational binding site shows some repressing function to make potential lead drug molecule. So as to know the elaborated purposeful functional mechanism of protein and to relate impact of mutation with function and activity; dock screening, hit identification and lead optimization facilitate in design of lead drug compound.

  11. R2E-related MD: slow controlled losses for RadMon/BLM cross-checks

    CERN Document Server

    Calviani, M; Spiezia, G; Sapinski, M; Priebe, A; Nordt, A; Pojer, M; CERN. Geneva. ATS Department

    2011-01-01

    The purpose of the dedicated R2E MD has been to evaluate the R factor (i.e. the ratio between the thermal neutron fluence and the high energy hadron fluence (>20MeV) for various tunnel locations, to measure the HEH radiation level gradient along the MBC dipole and on the MQ, to check the ratio the BLM measured dose and RadMon SEU counts and to study the dose gradient between the standard BLM beam axis location and at the level of the equipment location. Within the R2E Mitigation Project, these accurate measurement and cross-check of the mentioned parameters are of great importance for the evaluation and interpretation of the R2E-related radiation levels, as well as for the evaluation of the failure cross-section of specific equipment (i.e. QPS ISO150). In addition, a short part of the MD has been devoted to the comparison of BLM signals generated by loss directed inwards and outwards with respect to the LHC ring.

  12. ncRNA orthologies in the vertebrate lineage.

    Science.gov (United States)

    Pignatelli, Miguel; Vilella, Albert J; Muffato, Matthieu; Gordon, Leo; White, Simon; Flicek, Paul; Herrero, Javier

    2016-01-01

    Annotation of orthologous and paralogous genes is necessary for many aspects of evolutionary analysis. Methods to infer these homology relationships have traditionally focused on protein-coding genes and evolutionary models used by these methods normally assume the positions in the protein evolve independently. However, as our appreciation for the roles of non-coding RNA genes has increased, consistently annotated sets of orthologous and paralogous ncRNA genes are increasingly needed. At the same time, methods such as PHASE or RAxML have implemented substitution models that consider pairs of sites to enable proper modelling of the loops and other features of RNA secondary structure. Here, we present a comprehensive analysis pipeline for the automatic detection of orthologues and paralogues for ncRNA genes. We focus on gene families represented in Rfam and for which a specific covariance model is provided. For each family ncRNA genes found in all Ensembl species are aligned using Infernal, and several trees are built using different substitution models. In parallel, a genomic alignment that includes the ncRNA genes and their flanking sequence regions is built with PRANK. This alignment is used to create two additional phylogenetic trees using the neighbour-joining (NJ) and maximum-likelihood (ML) methods. The trees arising from both the ncRNA and genomic alignments are merged using TreeBeST, which reconciles them with the species tree in order to identify speciation and duplication events. The final tree is used to infer the orthologues and paralogues following Fitch's definition. We also determine gene gain and loss events for each family using CAFE. All data are accessible through the Ensembl Comparative Genomics ('Compara') API, on our FTP site and are fully integrated in the Ensembl genome browser, where they can be accessed in a user-friendly manner.Database URL: http://www.ensembl.org. PMID:26980512

  13. Cluster (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available tions of each amino acid sequence in the ortholog cluster. Frequency of the words.... Then, a most suitable annotation, which contains high-frequency words most, was selected as the explanator

  14. Cluster (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ations of each amino acid sequence in the ortholog cluster. Frequency of the word...d. Then, a most suitable annotation, which contains high-frequency words most, was selected as the explanato

  15. The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists

    OpenAIRE

    Sven Heinicke; Livstone, Michael S.; Charles Lu; Rose Oughtred; Fan Kang; Angiuoli, Samuel V; Owen White; David Botstein; Kara Dolinski

    2007-01-01

    Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic r...

  16. Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species

    OpenAIRE

    Thomas, James W; Prasad, Arjun B.; Summers, Tyrone J.; Lee-Lin, Shih-Queen; Maduro, Valerie V.B.; Idol, Jacquelyn R.; Ryan, Joseph F.; Pamela J Thomas; McDowell, Jennifer C.; Green, Eric D.

    2002-01-01

    Comparison is a fundamental tool for analyzing DNA sequence. Interspecies sequence comparison is particularly powerful for inferring genome function and is based on the simple premise that conserved sequences are likely to be important. Thus, the comparison of a genomic sequence with its orthologous counterpart from another species is increasingly becoming an integral component of genome analysis. In ideal situations, such comparisons are performed with orthologous sequences from multiple spe...

  17. Orthologous transcription factors in bacteria have different functions and regulate different genes.

    Directory of Open Access Journals (Sweden)

    Morgan N Price

    2007-09-01

    Full Text Available Transcription factors (TFs form large paralogous gene families and have complex evolutionary histories. Here, we ask whether putative orthologs of TFs, from bidirectional best BLAST hits (BBHs, are evolutionary orthologs with conserved functions. We show that BBHs of TFs from distantly related bacteria are usually not evolutionary orthologs. Furthermore, the false orthologs usually respond to different signals and regulate distinct pathways, while the few BBHs that are evolutionary orthologs do have conserved functions. To test the conservation of regulatory interactions, we analyze expression patterns. We find that regulatory relationships between TFs and their regulated genes are usually not conserved for BBHs in Escherichia coli K12 and Bacillus subtilis. Even in the much more closely related bacteria Vibrio cholerae and Shewanella oneidensis MR-1, predicting regulation from E. coli BBHs has high error rates. Using gene-regulon correlations, we identify genes whose expression pattern differs between E. coli and S. oneidensis. Using literature searches and sequence analysis, we show that these changes in expression patterns reflect changes in gene regulation, even for evolutionary orthologs. We conclude that the evolution of bacterial regulation should be analyzed with phylogenetic trees, rather than BBHs, and that bacterial regulatory networks evolve more rapidly than previously thought.

  18. Amphioxus (Branchiostoma floridae has orthologs of vertebrate odorant receptors

    Directory of Open Access Journals (Sweden)

    Taylor John S

    2009-10-01

    Full Text Available Abstract Background A common feature of chemosensory systems is the involvement of G protein-coupled receptors (GPCRs in the detection of environmental stimuli. Several lineages of GPCRs are involved in vertebrate olfaction, including trace amine-associated receptors, type 1 and 2 vomeronasal receptors and odorant receptors (ORs. Gene duplication and gene loss in different vertebrate lineages have lead to an enormous amount of variation in OR gene repertoire among species; some fish have fewer than 100 OR genes, while some mammals possess more than 1000. Fascinating features of the vertebrate olfactory system include allelic exclusion, where each olfactory neuron expresses only a single OR gene, and axonal guidance where neurons expressing the same receptor project axons to common glomerulae. By identifying homologous ORs in vertebrate and in non-vertebrate chordates, we hope to expose ancestral features of the chordate olfactory system that will help us to better understand the evolution of the receptors themselves and of the cellular components of the olfactory system. Results We have identified 50 full-length and 11 partial ORs in Branchiostoma floridae. No ORs were identified in Ciona intestinalis. Phylogenetic analysis places the B. floridae OR genes in a monophyletic clade with the vertebrate ORs. The majority of OR genes in amphioxus are intronless and many are also tandemly arrayed in the genome. By exposing conserved amino acid motifs and testing the ability of those motifs to discriminate between ORs and non-OR GPCRs, we identified three OR-specific amino acid motifs common in cephalochordate, fish and mammalian and ORs. Conclusion Here, we show that amphioxus has orthologs of vertebrate ORs. This conclusion demonstrates that the receptors, and perhaps other components of vertebrate olfaction, evolved at least 550 million years ago. We have also identified highly conserved amino acid motifs that may be important for maintaining

  19. Human and mouse mitochondrial orthologs of bacterial ClpX

    DEFF Research Database (Denmark)

    Corydon, T J; Wilsbech, M; Jespersgaard, C;

    2000-01-01

    mapping placing the CLPX gene 4.6 cR distal to D15S159. Murine ClpX cDNA was sequenced, and the mouse Clpx locus was mapped to a position between 31 and 42 cM offset from the centromere on mouse Chr 9. Experimental observations indicate the presence of a pseudogene in the mouse genome and sequence...... variability between mouse ClpX cDNAs from different strains. Alignment of the human and mouse ClpX amino acid sequences with ClpX sequences from other organisms shows that they display the typical modular organization of domains with one AAA(+) domain common to a large group of ATPases and several other...... domains conserved in ClpX orthologs linked by non-conserved sequences. Notably, a C-4 zinc finger type motif is recognized in human and mouse ClpX. This motif of so far unknown function is present only in a subset of the known ClpX sequences....

  20. An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species

    Directory of Open Access Journals (Sweden)

    Deborah Galpert

    2015-01-01

    Full Text Available Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiae-Schizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification.

  1. The radiation hardness of silica optical fiber used in the LED-fiber monitor of BLM and BESIII EMC

    International Nuclear Information System (INIS)

    LED-fiber system has been used to monitor BLM and BESIII EMC. A radiation hard silica optical fiber is essential for its stability and reliability. Three types of silica optical fibers, silicone-clad silica optical fiber with high OH- content (SeCS), silica-clad silica optical fiber with low OH- content (SCSL) and silica-clad silica opical fiber with high OH- content (SCSH) were studied. In the experiment, 12 groups of fiber samples were irradiated by 60Co and 3 groups of fiber samples were irradiated by BEPCII background radiation. Radiation hardness: the radiation hardness of SCSH is best and meets the radiation hardness requirement for LED-fiber monitor of BLM and BESIII EMC. The transmission of SeCS and SCSH decreased to around 80% under the 60Co-irradiation of 5 Gy and 10 Gy, respectively. The radiation hardness of SeCS is worst because of its silicone cladding. Recovery characteristics: 60Co-irradiated by the same doses, there were both more annealable and more permanent color centers formed in SeCS than SCSL, and for the same kind of fibers, as long as the irradiated doses are under a certain amount (for example, less than 5 Gy for SeCS), the higher the doses, both the more annealable and the more permanent color centers are formed.

  2. Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events1[OPEN

    Science.gov (United States)

    Haberer, Georg; Panda, Arup; Das Laha, Shayani; Ghosh, Tapas Chandra; Schäffner, Anton R.

    2016-01-01

    The identification of functionally equivalent, orthologous genes (functional orthologs) across genomes is necessary for accurate transfer of experimental knowledge from well-characterized organisms to others. This frequently relies on automated, coding sequence-based approaches such as OrthoMCL, Inparanoid, and KOG, which usually work well for one-to-one homologous states. However, this strategy does not reliably work for plants due to the occurrence of extensive gene/genome duplication. Frequently, for one query gene, multiple orthologous genes are predicted in the other genome, and it is not clear a priori from sequence comparison and similarity which one preserves the ancestral function. We have studied 11 organ-dependent and stress-induced gene expression patterns of 286 Arabidopsis lyrata duplicated gene groups and compared them with the respective Arabidopsis (Arabidopsis thaliana) genes to predict putative expressologs and nonexpressologs based on gene expression similarity. Promoter sequence divergence as an additional tool to substantiate functional orthology only partially overlapped with expressolog classification. By cloning eight A. lyrata homologs and complementing them in the respective four Arabidopsis loss-of-function mutants, we experimentally proved that predicted expressologs are indeed functional orthologs, while nonexpressologs or nonfunctionalized orthologs are not. Our study demonstrates that even a small set of gene expression data in addition to sequence homologies are instrumental in the assignment of functional orthologs in the presence of multiple orthologs. PMID:27303025

  3. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

    Science.gov (United States)

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

  4. Functional identification of an Arabidopsis snf4 ortholog by screening for heterologous multicopy suppressors of snf4 deficiency in yeast

    DEFF Research Database (Denmark)

    Kleinow, T.; Bhalerao, R.; Breuer, F.; Umeda, M.; Salchert, Klaus-Dieter; Koncz, C.

    2000-01-01

    , zinc-finger factors AZF2 and ZAT10, as well as orthologs of hexose/UDP-hexose transporters, calmodulin, SMC1-cohesin and Snf4. Here we describe the characterization of AtSNF4, a functional Arabidopsis Snf4 ortholog, that interacts with yeast Snf1 and specifically binds to the C-terminal regulatory...

  5. RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs

    Directory of Open Access Journals (Sweden)

    Eddy Sean R

    2002-05-01

    Full Text Available Abstract Background When analyzing protein sequences using sequence similarity searches, orthologous sequences (that diverged by speciation are more reliable predictors of a new protein's function than paralogous sequences (that diverged by gene duplication. The utility of phylogenetic information in high-throughput genome annotation ("phylogenomics" is widely recognized, but existing approaches are either manual or not explicitly based on phylogenetic trees. Results Here we present RIO (Resampled Inference of Orthologs, a procedure for automated phylogenomics using explicit phylogenetic inference. RIO analyses are performed over bootstrap resampled phylogenetic trees to estimate the reliability of orthology assignments. We also introduce supplementary concepts that are helpful for functional inference. RIO has been implemented as Perl pipeline connecting several C and Java programs. It is available at http://www.genetics.wustl.edu/eddy/forester/. A web server is at http://www.rio.wustl.edu/. RIO was tested on the Arabidopsis thaliana and Caenorhabditis elegans proteomes. Conclusion The RIO procedure is particularly useful for the automated detection of first representatives of novel protein subfamilies. We also describe how some orthologies can be misleading for functional inference.

  6. Translational research combining orthologous genes and human diseases with the OGOLOD dataset

    OpenAIRE

    Miñarro-Giménez, José Antonio; Egaña Aranguren, Mikel; Villazón-Terrazas, Boris; Fernández-Breis, Jesualdo Tomás

    2012-01-01

    OGOLOD is a Linked Open Data dataset derived from different biomedical resources by an automated pipeline, using a tailored ontology as a scaffold. The key contribution of OGOLOD is that it links, in new RDF triples, genetic human diseases and orthologous genes, paving the way for a more efficient translational biomedical research exploiting the Linked Open Data cloud.

  7. License - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available in using this database. The license for this database is specified in the Creative Commons Attribution-Share...DBj - Ortholog DB © Akihiro Nakaya (Osaka University) licensed under CC Attribution...-Share Alike 2.1 Japan . The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found he

  8. Proteinortho: Detection of (Co-orthologs in large-scale analysis

    Directory of Open Access Journals (Sweden)

    Steiner Lydia

    2011-04-01

    Full Text Available Abstract Background Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. Results The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Conclusions Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.

  9. MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.

    Science.gov (United States)

    Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

    2015-01-01

    The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase in microbial genome data owing to the next-generation sequencing technology, it becomes increasingly challenging to maintain high-quality orthology relationships while allowing the users to incorporate the latest genomic data available into an analysis. Because many of the recently accumulating genomic data are draft genome sequences for which some complete genome sequences of the same or closely related species are available, MBGD now stores draft genome data and allows the users to incorporate them into a user-specific ortholog database using the MyMBGD functionality. In this function, draft genome data are incorporated into an existing ortholog table created only from the complete genome data in an incremental manner to prevent low-quality draft data from affecting clustering results. In addition, to provide high-quality orthology relationships, the standard ortholog table containing all the representative genomes, which is first created by the rapid classification program DomClust, is now refined using DomRefine, a recently developed program for improving domain-level clustering using multiple sequence alignment information. PMID:25398900

  10. Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.

    Science.gov (United States)

    Yang, Ya; Smith, Stephen A

    2014-11-01

    Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly include transcriptomes and low-coverage genomes that are incomplete and contain errors and isoforms. These properties can severely violate the underlying assumptions of orthology inference with existing heuristics. We present a procedure that uses phylogenies for both homology and orthology assignment. The procedure first uses similarity scores to infer putative homologs that are then aligned, constructed into phylogenies, and pruned of spurious branches caused by deep paralogs, misassembly, frameshifts, or recombination. These final homologs are then used to identify orthologs. We explore four alternative tree-based orthology inference approaches, of which two are new. These accommodate gene and genome duplications as well as gene tree discordance. We demonstrate these methods in three published data sets including the grape family, Hymenoptera, and millipedes with divergence times ranging from approximately 100 to over 400 Ma. The procedure significantly increased the completeness and accuracy of the inferred homologs and orthologs. We also found that data sets that are more recently diverged and/or include more high-coverage genomes had more complete sets of orthologs. To explicitly evaluate sources of conflicting phylogenetic signals, we applied serial jackknife analyses of gene regions keeping each locus intact. The methods described here can scale to over 100 taxa. They have been implemented in python with independent scripts for each step, making it easy to modify or incorporate them into existing pipelines. All scripts are available from https://bitbucket.org/yangya/phylogenomic_dataset_construction. PMID:25158799

  11. Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

    Directory of Open Access Journals (Sweden)

    Lespinet Olivier

    2007-11-01

    Full Text Available Abstract Background Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. Results We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing bona fide orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs, and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms. Conclusion The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene

  12. Conserved repertoire of orthologous vomeronasal type 1 receptor genes in ruminant species

    Directory of Open Access Journals (Sweden)

    Okamura Hiroaki

    2009-09-01

    Full Text Available Abstract Background In mammals, pheromones play an important role in social and innate reproductive behavior within species. In rodents, vomeronasal receptor type 1 (V1R, which is specifically expressed in the vomeronasal organ, is thought to detect pheromones. The V1R gene repertoire differs dramatically between mammalian species, and the presence of species-specific V1R subfamilies in mouse and rat suggests that V1R plays a profound role in species-specific recognition of pheromones. In ruminants, however, the molecular mechanism(s for pheromone perception is not well understood. Interestingly, goat male pheromone, which can induce out-of-season ovulation in anestrous females, causes the same pheromone response in sheep, and vice versa, suggesting that there may be mechanisms for detecting "inter-species" pheromones among ruminant species. Results We isolated 23 goat and 21 sheep intact V1R genes based on sequence similarity with 32 cow V1R genes in the cow genome database. We found that all of the goat and sheep V1R genes have orthologs in their cross-species counterparts among these three ruminant species and that the sequence identity of V1R orthologous pairs among these ruminants is much higher than that of mouse-rat V1R orthologous pairs. Furthermore, all goat V1Rs examined thus far are expressed not only in the vomeronasal organ but also in the main olfactory epithelium. Conclusion Our results suggest that, compared with rodents, the repertoire of orthologous V1R genes is remarkably conserved among the ruminants cow, sheep and goat. We predict that these orthologous V1Rs can detect the same or closely related chemical compound(s within each orthologous set/pair. Furthermore, all identified goat V1Rs are expressed in the vomeronasal organ and the main olfactory epithelium, suggesting that V1R-mediated ligand information can be detected and processed by both the main and accessory olfactory systems. The fact that ruminant and rodent V1Rs

  13. Differential Effects of a Mutation on the Normal and Promiscuous Activities of Orthologs: Implications for Natural and Directed Evolution

    OpenAIRE

    Khanal, Akhil; Yu McLoughlin, Sean; Kershner, Jamie P.; Copley, Shelley D.

    2014-01-01

    Neutral drift occurring over millions or billions of years results in substantial sequence divergence among enzymes that catalyze the same reaction. Although natural selection maintains the primary activity of orthologous enzymes, there is, by definition, no selective pressure to maintain physiologically irrelevant promiscuous activities. Thus, the levels and the evolvabilities of promiscuous activities may vary among orthologous enzymes. Consistent with this expectation, we have found that t...

  14. In-vitro rescue and recovery studies of human melanoma (BLM) cell growth, adhesion and migration functions after treatment with progesterone

    OpenAIRE

    Leder, Douglas C; Brown, Jason R; Ramaraj, Pandurangan

    2015-01-01

    Treatment of human melanoma (BLM) cells for 48 hrs with progesterone resulted in a significant inhibition of cell growth. The mechanism of growth inhibition was due to autophagy and this action of progesterone was not mediated through progesterone receptor. As cells were floating during treatment, adhesion assay was performed, which showed complete loss of adhesion. When cells were allowed to recover after treatment by culturing in growth medium without progesterone, there was recovery in cel...

  15. Analyses of hydrocarbons in BLM sediment intercalibration sample from Santa Barbara basin and spiked with API South Louisiana crude oil. A preliminary report

    Energy Technology Data Exchange (ETDEWEB)

    Farrington, J W; Tripp, B W; Sass, J

    1977-01-01

    A preliminary report is made of a BLM intercalibration sediment sample from the Santa Barbara basin spiked with South Louisiana crude oil. The two subsamples reported were analyzed by a procedure described in the appendix for which a separate abstract was written. Because of the high oil content of the sediment the usual thin layer chromatography procedure resulted in an overloaded plate. An appendix was indexed separately. (JSR)

  16. Assessment Fargas and BLM Models for Identification of Erosion Degree and Critical Sediment Sources (Case Study: Aghbolagh Drainage Basin, Hashtrood City

    Directory of Open Access Journals (Sweden)

    Naser Abdi

    2014-08-01

    Full Text Available The identification of the different areas in drainage basin (as a natural planning unit for occurring the sedimentation and its severity in different phases of basic studies has been always one of the most important purposes of the natural resources experts. For achieving to this purpose some experimental models has been presented that Some of them have high efficiency and others have weaknesses. Fargas and BLM models are used in this research and they are run in Aghbolagh drainage basin in Hashtrood town, East Azarbayjan province with 7.8 km2 area. Fargas model includes only two factors, the rock type erosivity and drainage density in the every rock unit, whereas BLM model includes seven factors; the surface erosion, the litter cover, the rock cover on the surface, the affection of destruction on the surface, the surface rill erosion, the affection of the sedimentation due to the water flow and the amplification of gully erosion. The objective of this research is the handling of these two models for different phases of basic studies in the study area. The results of two models showed, in Fargas model 3.67% area of the basin has high erosion, 14.26% area of the basin has severe erosion and 81.04% has very severe erosion and in BLM model 42.97% area of the basin has moderate erosion and 24.93% has high erosion, therefore 52.85% of the study area in Fargas and BLM models has concurrence in the erosion severity.

  17. Assessment Fargas and BLM Models for Identification of Erosion Degree and Critical Sediment Sources (Case Study: Aghbolagh Drainage Basin, Hashtrood City)

    OpenAIRE

    Naser Abdi; Aliasghar Mohammadi

    2014-01-01

    The identification of the different areas in drainage basin (as a natural planning unit) for occurring the sedimentation and its severity in different phases of basic studies has been always one of the most important purposes of the natural resources experts. For achieving to this purpose some experimental models has been presented that Some of them have high efficiency and others have weaknesses. Fargas and BLM models are used in this research and they are run in Aghbolagh drainage basin in ...

  18. Impact of a CXCL12/CXCR4 Antagonist in Bleomycin (BLM) Induced Pulmonary Fibrosis and Carbon Tetrachloride (CCl4) Induced Hepatic Fibrosis in Mice

    Science.gov (United States)

    Chow, Leola N.; Schreiner, Petra; Ng, Betina Y. Y.; Lo, Bernard; Hughes, Michael R.; Scott, R. Wilder; Gusti, Vionarica; Lecour, Samantha; Simonson, Eric; Manisali, Irina; Barta, Ingrid; McNagny, Kelly M.; Crawford, Jason; Webb, Murray; Underhill, T. Michael

    2016-01-01

    Modulation of chemokine CXCL12 and its receptor CXCR4 has been implicated in attenuation of bleomycin (BLM)-induced pulmonary fibrosis and carbon tetrachloride (CCl4)-induced hepatic injury. In pulmonary fibrosis, published reports suggest that collagen production in the injured lung is derived from fibrocytes recruited from the circulation in response to release of pulmonary CXCL12. Conversely, in hepatic fibrosis, resident hepatic stellate cells (HSC), the key cell type in progression of fibrosis, upregulate CXCR4 expression in response to activation. Further, CXCL12 induces HSC proliferation and subsequent production of collagen I. In the current study, we evaluated AMD070, an orally bioavailable inhibitor of CXCL12/CXCR4 in alleviating BLM-induced pulmonary and CCl4-induced hepatic fibrosis in mice. Similar to other CXCR4 antagonists, treatment with AMD070 significantly increased leukocyte mobilization. However, in these two models of fibrosis, AMD070 had a negligible impact on extracellular matrix deposition. Interestingly, our results indicated that CXCL12/CXCR4 signaling has a role in improving mortality associated with BLM induced pulmonary injury, likely through dampening an early inflammatory response and/or vascular leakage. Together, these findings indicate that the CXCL12-CXCR4 signaling axis is not an effective target for reducing fibrosis. PMID:26998906

  19. Membrane Thickness Sensitivity of Prestin Orthologs: The Evolution of a Piezoelectric Protein

    OpenAIRE

    Izumi, Chisako; Bird, Jonathan E.; Iwasa, Kuni H.

    2011-01-01

    How proteins evolve new functionality is an important question in biology; prestin (SLC26A5) is a case in point. Prestin drives outer hair cell somatic motility and amplifies mechanical vibrations in the mammalian cochlea. The motility of mammalian prestin is analogous to piezoelectricity, in which charge transfer is coupled to changes in membrane area occupied by the protein. Intriguingly, nonmammalian prestin orthologs function as anion exchangers but are apparently nonmotile. We previously...

  20. cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes

    OpenAIRE

    Castillo-Davis, Cristian I.; Hartl, Daniel L.; Achaz, Guillaume

    2004-01-01

    The relationship between protein and regulatory sequence evolution is a central question in molecular evolution. It is currently not known to what extent changes in gene expression are coupled with the evolution of protein coding sequences, or whether these changes differ among orthologs (species homologs) and paralogs (duplicate genes). Here, we develop a method to measure the extent of functionally relevant cis-regulatory sequence change in homologous genes, and validate it using microarray...

  1. Conserved Quantitative Stability/Flexibility Relationships (QSFR) in an Orthologous RNase H Pair

    OpenAIRE

    Livesay, Dennis R.; Jacobs, Donald J.

    2006-01-01

    Many reports qualitatively describe conserved stability and flexibility profiles across protein families, but biophysical modeling schemes have not been available to robustly quantify both. Here we investigate an orthologous RNase H pair by using a minimal distance constraint model (DCM). The DCM is an all atom microscopic model that accurately reproduces heat capacity measurements, and is unique in its ability to harmoniously calculate thermodynamic stability and flexibility in practical com...

  2. Characterization of the Drosophila ortholog of the human Usher Syndrome type 1G protein sans.

    Directory of Open Access Journals (Sweden)

    Fabio Demontis

    Full Text Available BACKGROUND: The Usher syndrome (USH is the most frequent deaf-blindness hereditary disease in humans. Deafness is attributed to the disorganization of stereocilia in the inner ear. USH1, the most severe subtype, is associated with mutations in genes encoding myosin VIIa, harmonin, cadherin 23, protocadherin 15, and sans. Myosin VIIa, harmonin, cadherin 23, and protocadherin 15 physically interact in vitro and localize to stereocilia tips in vivo, indicating that they form functional complexes. Sans, in contrast, localizes to vesicle-like structures beneath the apical membrane of stereocilia-displaying hair cells. How mutations in sans result in deafness and blindness is not well understood. Orthologs of myosin VIIa and protocadherin 15 have been identified in Drosophila melanogaster and their genetic analysis has identified essential roles in auditory perception and microvilli morphogenesis, respectively. PRINCIPAL FINDINGS: Here, we have identified and characterized the Drosophila ortholog of human sans. Drosophila Sans is expressed in tubular organs of the embryo, in lens-secreting cone cells of the adult eye, and in microvilli-displaying follicle cells during oogenesis. Sans mutants are viable, fertile, and mutant follicle cells appear to form microvilli, indicating that Sans is dispensable for fly development and microvilli morphogenesis in the follicle epithelium. In follicle cells, Sans protein localizes, similar to its vertebrate ortholog, to intracellular punctate structures, which we have identified as early endosomes associated with the syntaxin Avalanche. CONCLUSIONS: Our work is consistent with an evolutionary conserved function of Sans in vesicle trafficking. Furthermore it provides a significant basis for further understanding of the role of this Usher syndrome ortholog in development and disease.

  3. Sugar and abscisic acid signaling orthologs are activated at the onset of ripening in grape

    OpenAIRE

    Gambetta, Gregory A.; Matthews, Mark A.; Shaghasi, Tarana H.; McElrone, Andrew J.; Castellarin, Simone D.

    2010-01-01

    The onset of ripening involves changes in sugar metabolism, softening, and color development. Most understanding of this process arises from work in climacteric fruits where the control of ripening is predominately by ethylene. However, many fruits such as grape are nonclimacteric, where the onset of ripening results from the integration of multiple hormone signals including sugars and abscisic acid (ABA). In this study, we identified ten orthologous gene families in Vitis vinifera containing...

  4. Identification and Functional Analysis of Three MAX2 Orthologs in Chrysanthemum

    Institute of Scientific and Technical Information of China (English)

    Lili Dong; Abdurazak Ishak; Jing Yu; Ruiyan Zhao; Liangjun Zhao

    2013-01-01

    MORE AXILLARY BRANCHING 2 (MAX2),initially identified in Arabidopsis thaliana,is a key regulatory gene in strigolactone signal transduction.Three orthologs of MAX2 were cloned from Dendranthema grandiflorum (DgMAX2a,b,and c).Each of the genes has an open reading frame of 2,049 bp and encodes 682 amino acid proteins.The predicted amino acid sequences of the three DgMAX2s are most closely related to the MAX2 orthologs identified in petunia (PhMAX2A and PhMAX2B),and display the highest amino acid sequence similarity with PhMAX2A compared to other MAX2s.Expression analysis revealed that DgMAX2s are predominantly expressed in the stem and axillary buds.On a cellular level,we localized the DgMAX2a::GFP fusion protein to the nucleus in onion epidermal cells,which is consistent with the nuclear localization of MAX2 in Arabidopsis.The chrysanthemum DgMAX2a is able to restore the max2-1 mutant branching to wild-type (WT) Arabidopsis,suggesting that it is a functional MAX2 ortholog.These results suggest that DgMAX2s may be candidate genes for reducing the shoot branching of chrysanthemum.

  5. Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae.

    Science.gov (United States)

    Yamamoto, Naoki; Kudo, Toru; Fujiwara, Shoko; Takatsuka, Yukiko; Hirokawa, Yasutaka; Tsuzuki, Mikio; Takano, Tomoyuki; Kobayashi, Masaaki; Suda, Kunihiro; Asamizu, Erika; Yokoyama, Koji; Shibata, Daisuke; Tabata, Satoshi; Yano, Kentaro

    2016-01-01

    Pleurochrysis is a coccolithophorid genus, which belongs to the Coccolithales in the Haptophyta. The genus has been used extensively for biological research, together with Emiliania in the Isochrysidales, to understand distinctive features between the two coccolithophorid-including orders. However, molecular biological research on Pleurochrysis such as elucidation of the molecular mechanism behind coccolith formation has not made great progress at least in part because of lack of comprehensive gene information. To provide such information to the research community, we built an open web database, the Pleurochrysome (http://bioinf.mind.meiji.ac.jp/phapt/), which currently stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences sharing significant homology, conserved domains, Gene Ontology, KEGG Orthology, predicted subcellular localization, open reading frames and orthologous relationship with genes of 10 other algal species, a cyanobacterium and the yeast Saccharomyces cerevisiae. This sequence and annotation information can be easily accessed via several search functions. Besides fundamental functions such as BLAST and keyword searches, this database also offers search functions to explore orthologous genes in the 12 organisms and to seek novel genes. The Pleurochrysome will promote molecular biological and phylogenetic research on coccolithophorids and other haptophytes by helping scientists mine data from the primary transcriptome of P. haptonemofera. PMID:26746174

  6. Total Glucosides of Danggui Buxue Tang Attenuate BLM-Induced Pulmonary Fibrosis via Regulating Oxidative Stress by Inhibiting NOX4

    Directory of Open Access Journals (Sweden)

    Ping Zhao

    2015-01-01

    Full Text Available Pulmonary fibrosis (PF is a serious chronic lung disease with unknown pathogenesis. Researches have confirmed that oxidative stress which is regulated by NADPH oxidase-4 (NOX4, a main source of reactive oxygen species (ROS, is an important molecular mechanism underlying PF. Previous studies showed that total glucosides of Danggui Buxue Tang (DBTG, an extract from a classical traditional Chinese herbal formula, Danggui Buxue Tang (DBT, attenuated bleomycin-induced PF in rats. However, the mechanisms of DBTG are still not clear. We hypothesize that DBTG attenuates PF through regulating the level of oxidative stress by inhibiting NOX4. And we found that fibrosis indexes hydroxyproline (HYP and type I collagen (Col-I were lower in DBTG groups compared with the model group. In addition, the expression of transforming growth factor-β1 (TGF-β1 and expression of alpha smooth muscle actin (α-SMA were also much more decreased than the model group. For oxidative stress indicators, DBTG blunted the decrease of superoxide dismutase (SOD activity, total antioxidant capacity (T-AOC, and the increase in malondialdehyde (MDA, 8-iso-prostaglandin in lung homogenates. Treatment with DBTG restrained the expression of NOX4 compared to the model group. Present study confirms that DBTG inhibits BLM-induced PF by modulating the level of oxidative stress via suppressing NOX4.

  7. Genetic variation in the NBS1, MRE11, RAD50 and BLM genes and susceptibility to non-Hodgkin lymphoma

    Directory of Open Access Journals (Sweden)

    Gascoyne Randy D

    2009-11-01

    Full Text Available Abstract Background Translocations are hallmarks of non-Hodgkin lymphoma (NHL genomes. Because lymphoid cell development processes require the creation and repair of double stranded breaks, it is not surprising that disruption of this type of DNA repair can cause cancer. The members of the MRE11-RAD50-NBS1 (MRN complex and BLM have central roles in maintenance of DNA integrity. Severe mutations in any of these genes cause genetic disorders, some of which are characterized by increased risk of lymphoma. Methods We surveyed the genetic variation in these genes in constitutional DNA of NHL patients by means of gene re-sequencing, then conducted genetic association tests for susceptibility to NHL in a population-based collection of 797 NHL cases and 793 controls. Results 114 SNPs were discovered in our sequenced samples, 61% of which were novel and not previously reported in dbSNP. Although four variants, two in RAD50 and two in NBS1, showed association results suggestive of an effect on NHL, they were not significant after correction for multiple tests. Conclusion These results suggest an influence of RAD50 and NBS1 on susceptibility to diffuse large B-cell lymphoma and marginal zone lymphoma. Larger association and functional studies could confirm such a role.

  8. The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification.

    Science.gov (United States)

    Afrasiabi, Cyrus; Samad, Bushra; Dineen, David; Meacham, Christopher; Sjölander, Kimmen

    2013-07-01

    The PhyloFacts 'Fast Approximate Tree Classification' (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT's high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts' broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases. The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/. PMID:23685612

  9. Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments

    LENUS (Irish Health Repository)

    OhEigeartaigh, Sean S

    2011-07-26

    Abstract Background In standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline similarity in a BLAST search, the discovery that the genes are located within a region of conserved gene order (synteny) can provide additional evidence that they are orthologs. Thus, for interpreting borderline search results, it would be useful to know whether the syntenic context of a database hit is similar to that of the query. This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically. Results We made use of the synteny information contained in the Yeast Gene Order Browser database for 11 yeast species to carry out a systematic search for protein-coding genes that were overlooked in the original annotations of one or more yeast genomes but which are syntenic with their orthologs. Such genes tend to have been overlooked because they are short, highly divergent, or contain introns. The key features of our software - called SearchDOGS - are that the database entries are classified into sets of genomic segments that are already known to be orthologous, and that very weak BLAST hits are retained for further analysis if their genomic location is similar to that of the query. Using SearchDOGS we identified 595 additional protein-coding genes among the 11 yeast species, including two new genes in Saccharomyces cerevisiae. We found additional genes for the mating pheromone a-factor in six species including Kluyveromyces lactis. Conclusions SearchDOGS has proven highly successful for identifying overlooked genes in the yeast genomes. We anticipate that our approach can be adapted for study of further groups of species, such as bacterial genomes. More generally, the concept of doing sequence similarity searches against databases to which external

  10. Structural implications of mutations in the pea SYM8 symbiosis gene, the DMI1 ortholog, encoding a predicted ion channel

    DEFF Research Database (Denmark)

    Edwards, Anne; Heckmann, Anne Birgitte Lau; Yousafzai, Faridoon;

    2007-01-01

    ortholog can complement a M. truncatula dmil mutant for nodulation. Each of the five pea sym8 mutants carries a mutation in the DMI1 ortholog, confirming that the pea SYM8 is the DMI1 ortholog. Based on predicted structural similarities with an archaebacterial ion channel, we propose that SYM8 forms a...... tetrameric calcium-gated channel of a predicted structure similar to the archaebacterial potassium channel but containing a filter region that is different. The predicted structure identifies four aspartate residues (one from each subunit) forming the channel opening. We made a mutation changing the...... link the predicted channel and the gating ring domains, indicating that this mutation may block function by preventing a protein conformational change being transmitted from the gating-ring domain to the pore domain....

  11. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL.

    Science.gov (United States)

    Rinaldi, Riccardo; Van Deynze, Allen; Portis, Ezio; Rotino, Giuseppe L; Toppino, Laura; Hill, Theresa; Ashrafi, Hamid; Barchi, Lorenzo; Lanteri, Sergio

    2016-01-01

    Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous

  12. Molecular cloning and characterization of the human RNase κ, an ortholog of Cc RNase

    OpenAIRE

    Economopoulou, Marie-angela I.; Fragoulis, Emmanouel G.; Sideris, Diamantis C.

    2007-01-01

    A novel protein family, designated hereafter as RNase κ (kappa) family, has been recently introduced with the characterization of the specific Cc RNase, isolated from the insect Ceratitis capitata. The human ortholog of this family consists of 98 amino acids and shares > 98% identity with its mammalian counterparts. This RNase is encoded by a single-copy gene found to be expressed in a wide spectrum of normal and cancer tissues. The cDNA of the human ribonuclease has been isolated and subclon...

  13. Extracellular ionic locks determine variation in constitutive activity and ligand potency between species orthologs of the free fatty acid receptors FFA2 and FFA3

    DEFF Research Database (Denmark)

    Hudson, Brian D; Tikhonova, Irina G; Pandey, Sunil K;

    2012-01-01

    ) is non-selective. Although C2 was confirmed to be selective for human FFA2 over FFA3, this ligand was not selective between the mouse orthologs. Moreover, although C3 was indeed not selective between the human orthologs, it displayed clear selectivity for mouse FFA3 over mouse FFA2. This altered...... selectivity to C2 and C3 resulted from broad differences in SCFAs potency at the mouse orthologs. In studies to define the molecular basis for these observations, marked variation in ligand-independent constitutive activity was identified using a [(35)S]GTPγS assay. The orthologs with higher potency for the...... SCFAs, human FFA2 and mouse FFA3, displayed high constitutive activity in this assay, whereas the orthologs with lower potency for the agonist ligands, mouse FFA2 and human FFA3, did not. Sequence alignments of the second extracellular loop identified single negatively charged residues in FFA2 and FFA3...

  14. Membrane thickness sensitivity of prestin orthologs: the evolution of a piezoelectric protein.

    Science.gov (United States)

    Izumi, Chisako; Bird, Jonathan E; Iwasa, Kuni H

    2011-06-01

    How proteins evolve new functionality is an important question in biology; prestin (SLC26A5) is a case in point. Prestin drives outer hair cell somatic motility and amplifies mechanical vibrations in the mammalian cochlea. The motility of mammalian prestin is analogous to piezoelectricity, in which charge transfer is coupled to changes in membrane area occupied by the protein. Intriguingly, nonmammalian prestin orthologs function as anion exchangers but are apparently nonmotile. We previously found that mammalian prestin is sensitive to membrane thickness, suggesting that prestin's extended conformation has a thinner hydrophobic height in the lipid bilayer. Because prestin-based motility is a mammalian specialization, we initially hypothesized that nonmotile prestin orthologs, while functioning as anion transporters, should be much less sensitive to membrane thickness. We found the exact opposite to be true. Chicken prestin was the most sensitive to thickness changes, displaying the largest shift in voltage dependence. Platypus prestin displayed an intermediate response to membrane thickness and gerbil prestin was the least sensitive. To explain these observations, we present a theory where force production, rather than displacement, was selected for the evolution of prestin as a piezoelectric membrane motor. PMID:21641306

  15. Mining from transcriptomes: 315 single-copy orthologous genes concatenated for the phylogenetic analyses of Orchidaceae.

    Science.gov (United States)

    Deng, Hua; Zhang, Guo-Qiang; Lin, Min; Wang, Yan; Liu, Zhong-Jian

    2015-09-01

    Phylogenetic relationships are hotspots for orchid studies with controversial standpoints. Traditionally, the phylogenies of orchids are based on morphology and subjective factors. Although more reliable than classic phylogenic analyses, the current methods are based on a few gene markers and PCR amplification, which are labor intensive and cannot identify the placement of some species with degenerated plastid genomes. Therefore, a more efficient, labor-saving and reliable method is needed for phylogenic analysis. Here, we present a method of orchid phylogeny construction using transcriptomes. Ten representative species covering five subfamilies of Orchidaceae were selected, and 315 single-copy orthologous genes extracted from the transcriptomes of these organisms were applied to reconstruct a more robust phylogeny of orchids. This approach provided a rapid and reliable method of phylogeny construction for Orchidaceae, one of the most diversified family of angiosperms. We also showed the rigorous systematic position of holomycotrophic species, which has previously been difficult to determine because of the degenerated plastid genome. We concluded that the method presented in this study is more efficient and reliable than methods based on a few gene markers for phylogenic analyses, especially for the holomycotrophic species or those whose DNA sequences have been difficult to amplify. Meanwhile, a total of 315 single-copy orthologous genes of orchids are offered and more informative loci could be used in the future orchid phylogenetic studies. PMID:26380706

  16. Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases.

    Science.gov (United States)

    Qian, Xinlei; Hamid, Fursham M; El Sahili, Abbas; Darwis, Dina Amallia; Wong, Yee Hwa; Bhushan, Shashi; Makeyev, Eugene V; Lescar, Julien

    2016-04-22

    Many eukaryotic organisms encode more than one RNA-dependent RNA polymerase (RdRP) that probably emerged as a result of gene duplication. Such RdRP paralogs often participate in distinct RNA silencing pathways and show characteristic repertoires of enzymatic activities in vitro However, to what extent members of individual paralogous groups can undergo functional changes during speciation remains an open question. We show that orthologs of QDE-1, an RdRP component of the quelling pathway in Neurospora crassa, have rapidly diverged in evolution at the amino acid sequence level. Analyses of purified QDE-1 polymerases from N. crassa (QDE-1(Ncr)) and related fungi, Thielavia terrestris (QDE-1(Tte)) and Myceliophthora thermophila (QDE-1(Mth)), show that all three enzymes can synthesize RNA, but the precise modes of their action differ considerably. Unlike their QDE-1(Ncr) counterpart favoring processive RNA synthesis, QDE-1(Tte) and QDE-1(Mth) produce predominantly short RNA copies via primer-independent initiation. Surprisingly, a 3.19 Å resolution crystal structure of QDE-1(Tte) reveals a quasisymmetric dimer similar to QDE-1(Ncr) Further electron microscopy analyses confirm that QDE-1(Tte) occurs as a dimer in solution and retains this status upon interaction with a template. We conclude that divergence of orthologous RdRPs can result in functional innovation while retaining overall protein fold and quaternary structure. PMID:26907693

  17. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

    DEFF Research Database (Denmark)

    Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer;

    2016-01-01

    eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making ...

  18. Mycoplasma hyopneumoniae and Mycoplasma flocculare differential domains from orthologous surface proteins induce distinct cellular immune responses in mice.

    Science.gov (United States)

    Leal, Fernanda Munhoz Dos Anjos; Virginio, Veridiana Gomes; Martello, Carolina Lumertz; Paes, Jéssica Andrade; Borges, Thiago J; Jaeger, Natália; Bonorino, Cristina; Ferreira, Henrique Bunselmeyer

    2016-07-15

    Mycoplasma hyopneumoniae and Mycoplasma flocculare are two genetically close species found in the swine respiratory tract. Despite their similarities, while M. hyopneumoniae is the causative agent of porcine enzootic pneumonia, M. flocculare is a commensal bacterium. Genomic and transcriptional comparative analyses so far failed to explain the difference in pathogenicity between these two species. We then hypothesized that such difference might be, at least in part, explained by amino acid sequence and immunological or functional differences between ortholog surface proteins. In line with that, it was verified that approximately 85% of the ortholog surface proteins from M. hyopneumoniae 7448 and M. flocculare present one or more differential domains. To experimentally assess possible immunological implications of this kind of difference, the extracellular differential domains from one pair of orthologous surface proteins (MHP7448_0612, from M. hyopneumoniae, and MF_00357, from M. flocculare) were expressed in E. coli and used to immunize mice. The recombinant polypeptides (rMHP61267-169 and rMF35767-196, respectively) induced distinct cellular immune responses. While, rMHP61267-169 induced both Th1 and Th2 responses, rMF35767-196 induced just an early pro-inflammatory response. These results indicate that immunological properties determined by differential domains in orthologous surface protein might play a role in pathogenicity, contributing to elicit specific and differential immune responses against each species. PMID:27283856

  19. BLM Solar Energy Zones

    Data.gov (United States)

    Bureau of Land Management, Department of the Interior — Priority development areas for utility-scale solar energy facilities as identified in the Solar PEIS Record of Decision. An additional Solar Energy Zone identified...

  20. The Drosophila ortholog of TMEM18 regulates insulin and glucagon-like signaling.

    Science.gov (United States)

    Wiemerslage, Lyle; Gohel, Priya A; Maestri, Giulia; Hilmarsson, Torfi G; Mickael, Michel; Fredriksson, Robert; Williams, Michael J; Schiöth, Helgi B

    2016-06-01

    Transmembrane protein 18 (TMEM18) is an ill-described, obesity-related gene, but few studies have explored its molecular function. We found single-nucleotide polymorphism data, suggesting that TMEM18 may be involved in the regulation/physiology of metabolic syndrome based on associations with insulin, homeostatic model assessment-β (HOMAβ), triglycerides, and blood sugar. We then found an ortholog in the Drosophila genome, knocked down Drosophila Tmem18 specifically in insulin-producing cells, and tested for its effects on metabolic function. Our results suggest that TMEM18 affects substrate levels through insulin and glucagon signaling, and its downregulation induces a metabolic state resembling type 2 diabetes. This work is the first to experimentally describe the metabolic consequences of TMEM18 knockdown, and further supports its association with obesity. PMID:27029472

  1. Expression and in vitro properties of guinea pig IL-5: Comparison to human and murine orthologs

    Directory of Open Access Journals (Sweden)

    Clay W Scott

    2000-01-01

    Full Text Available Interleukin-5 (IL-5 is a key mediator of eosinophilic inflammation. The biological role of this cytokine in an allergic airway inflammatory response has been widely demonstrated in guinea pigs, yet the interaction of guinea pig IL-5 (gpIL-5 with its receptor has not been studied. Experiments were performed to quantitate the interaction of gpIL-5 with gpIL-5r and to compare this affinity with that of hIL-5 and mIL-5 and their cognate receptors. The cross-species affinity and agonist efficacy were evaluated to see if gpIL-5r had a restricted species reactivity (as is the case with mIL-5r or did not distinguish between IL-5 orthologs (similar to hIL-5r. gpIL-5 was cloned using mRNA isolated from cells obtained by bronchoalveolar lavage. Recombinant gpIL-5 was expressed in T.ni insect cells and purified from spent media. Binding assays were performed using insect cells expressing hIL-5rαβ or gpIL-5rαβ1 as previously described (Cytokine, 12:858–866, 2000 or using B13 cells which express mIL-5r. The agonist potency and efficacy properties of each IL-5 ortholog were evaluated by quantitating the proliferative response of hum an TF-1 cells and murine B13 cells. gpIL-5 bound with high affinity to recombinant gpIL-5r as demonstrated by displacing [125I]hIL-5 (Ki = 160 pM. gpIL-5 also bound to hIL-5r with high affinity (Ki = 750 pM. hIL-5 and mIL-5 showed similar, high-affinity binding profiles to both gpIL-5r and hIL-5r. In contrast, gpIL-5 and hIL5 did not bind to the mIL-5r as demonstrated by an inability to displace [125I]mIL-5, even at 1000-fold molar excess. These differences in affinity for IL-5r orthologs correlated with bioassay results: human TF1 cells showed roughly com parable proliferative responses to guinea pig, hum an and murine IL-5 whereas murine B13 cells showed a strong preference for murine over guinea pig and human IL-5(EC50 = 1.9, 2200 and 720 pM, respectively. Recombinant gpIL-5 binds to the gpIL-5r with high affinity, similar

  2. Alternative splicing of the AGAMOUS orthologous gene in double flower of Magnolia stellata (Magnoliaceae).

    Science.gov (United States)

    Zhang, Bo; Liu, Zhi-Xiong; Ma, Jiang; Song, Yi; Chen, Fa-Ju

    2015-12-01

    Magnolia stellata is a woody ornamental shrub with more petaloid tepals than related plants from family Magnoliaceae. Recent studies revealed that expression changes in an AGAMOUS (AG) orthologous gene could resulted in double flowers with increased numbers of petals. We isolated three transcripts encoding different isoforms of a single AG orthologous gene, MastAG, mastag_2 and mastag_3, from M. stellata. Sequence alignments and Southern blot analyses suggested that MastAG was a single-copy gene in M. stellata genomes, and that mastag_2 and mastag_3 were abnormally spliced isoforms of MastAG. An 144bp exon skipping in MastAG results in the truncated mastag_2 protein lacking the completely I domain and 18 aa of the K1 subdomain, whereas an 165bp exon skipping of MastAG produces a truncated mastag_3 protein lacking 6 aa of the K3 subdomain and the completely C terminal region. Expression analyses showed that three alternative splicing (AS) isoforms expressed only in developing stamens and carpels. Functional analyses revealed that MastAG could mimic the endogenous AG to specify carpel identity, but failed to regulate stamen development in an Arabidopsis ag-1 mutant. Moreover, the key domain or subdomain deletions represented by mastag_2 and mastag_3 resulted in loss of C-function. However, ectopic expression of mastag_2 in Arabidopsis produced flowers with sepals converted into carpeloid organs, but without petals and stamens, whereas ectopic expression of mastag_3 in Arabidopsis could mimic the flower phenotype of the ag mutant and produced double flowers with homeotic transformation of stamens into petals and carpels into another ag flower. Our results also suggest that mastag_3 holds some potential for biotechnical engineering to create multi-petal phenotypes in commercial ornamental cultivars. PMID:26706078

  3. The fission yeast MTREC and EJC orthologs ensure the maturation of meiotic transcripts during meiosis

    Science.gov (United States)

    Marayati, Bahjat Fadi; Hoskins, Victoria; Boger, Robert W.; Tucker, James F.; Fishman, Emily S.; Bray, Andrew S.; Zhang, Ke

    2016-01-01

    Meiosis is a highly regulated process by which genetic information is transmitted through sexual reproduction. It encompasses unique mechanisms that do not occur in vegetative cells, producing a distinct, well-regulated meiotic transcriptome. During vegetative growth, many meiotic genes are constitutively transcribed, but most of the resulting mRNAs are rapidly eliminated by the Mmi1-MTREC (Mtl1-Red1 core) complex. While Mmi1-MTREC targets premature meiotic RNAs for degradation by the nuclear 3′–5′ exoribonuclease exosome during mitotic growth, its role in meiotic gene expression during meiosis is not known. Here, we report that Red5, an essential MTREC component, interacts with pFal1, an ortholog of eukaryotic translation initiation factor eIF4aIII in the fission yeast Schizosaccharomyces pombe. In mammals, together with MAGO (Mnh1), Rnps1, and Y14, elF4AIII (pFal1) forms the core of the exon junction complex (EJC), which is essential for transcriptional surveillance and localization of mature mRNAs. In fission yeast, two EJC orthologs, pFal1 and Mnh1, are functionally connected with MTREC, specifically in the process of meiotic gene expression during meiosis. Although pFal1 interacts with Mnh1, Y14, and Rnps1, its association with Mnh1 is not disrupted upon loss of Y14 or Rnps1. Mutations of Red1, Red5, pFal1, or Mnh1 produce severe meiotic defects; the abundance of meiotic transcripts during meiosis decreases; and mRNA maturation processes such as splicing are impaired. Since studying meiosis in mammalian germline cells is difficult, our findings in fission yeast may help to define the general mechanisms involved in accurate meiotic gene expression in higher eukaryotes. PMID:27365210

  4. The fission yeast MTREC and EJC orthologs ensure the maturation of meiotic transcripts during meiosis.

    Science.gov (United States)

    Marayati, Bahjat Fadi; Hoskins, Victoria; Boger, Robert W; Tucker, James F; Fishman, Emily S; Bray, Andrew S; Zhang, Ke

    2016-09-01

    Meiosis is a highly regulated process by which genetic information is transmitted through sexual reproduction. It encompasses unique mechanisms that do not occur in vegetative cells, producing a distinct, well-regulated meiotic transcriptome. During vegetative growth, many meiotic genes are constitutively transcribed, but most of the resulting mRNAs are rapidly eliminated by the Mmi1-MTREC (Mtl1-Red1 core) complex. While Mmi1-MTREC targets premature meiotic RNAs for degradation by the nuclear 3'-5' exoribonuclease exosome during mitotic growth, its role in meiotic gene expression during meiosis is not known. Here, we report that Red5, an essential MTREC component, interacts with pFal1, an ortholog of eukaryotic translation initiation factor eIF4aIII in the fission yeast Schizosaccharomyces pombe In mammals, together with MAGO (Mnh1), Rnps1, and Y14, elF4AIII (pFal1) forms the core of the exon junction complex (EJC), which is essential for transcriptional surveillance and localization of mature mRNAs. In fission yeast, two EJC orthologs, pFal1 and Mnh1, are functionally connected with MTREC, specifically in the process of meiotic gene expression during meiosis. Although pFal1 interacts with Mnh1, Y14, and Rnps1, its association with Mnh1 is not disrupted upon loss of Y14 or Rnps1. Mutations of Red1, Red5, pFal1, or Mnh1 produce severe meiotic defects; the abundance of meiotic transcripts during meiosis decreases; and mRNA maturation processes such as splicing are impaired. Since studying meiosis in mammalian germline cells is difficult, our findings in fission yeast may help to define the general mechanisms involved in accurate meiotic gene expression in higher eukaryotes. PMID:27365210

  5. Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes

    Directory of Open Access Journals (Sweden)

    Hall Ross S

    2010-04-01

    Full Text Available Abstract Background New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Saccharomyces cerevisiae, to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset. Results Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from Ancylostoma caninum and Haemonchus contortus - two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools. Conclusions The present study demonstrates the utility of using orthology information from multiple, diverse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.

  6. Landscape Measures of Rangeland Condition in the BLM Owyhee Pilot Project: Shrub Canopy Mapping, Vegetation Classification, and Detection of Anomalous Land Areas

    Energy Technology Data Exchange (ETDEWEB)

    Tagestad, Jerry D.; Downs, Janelle L.

    2007-12-28

    In 2006, the BLM tasked PNNL to collaborate in research being conducted under the Owyhee Uplands Pilot Project to assess rangeland condition. The objective of this effort was to provide Owyhee Uplands Pilot Project with a sophisticated suite of data and tools to assist in evaluating the health and condition of the Owyhee Uplands study area. We focused on three technical areas. The first involved enhancing existing algorithms to estimate shrub canopy cover in the Lower Reynolds Creek Watershed. The second task involved developing and applying a strategy to assess and compare three vegetation map products for the Idaho portion of the Owyhee study area. The third task developed techniques and data that can be used to identify areas exhibiting anomalous rangeland conditions (for example exotic plants or excessive bare soil exposure). This report documents the methods used, results obtained, and conclusions drawn.

  7. pH modulates transport rates of manganese and cadmium in the green alga Chlamydomonas reinhardtii through non-competitive interactions: Implications for an algal BLM

    International Nuclear Information System (INIS)

    The influence of pH on short-term uptake of manganese and cadmium by the green alga Chlamydomonas reinhardtii was studied to better understand the nature of proton interactions with metal membrane transporters. Manganese and cadmium internalization fluxes (Jint) were measured over a wide range of free metal ion concentrations from 1 x 10-10 to 4 x 10-4 M at several pH values (Mn: 5.0, 6.5 and 8.0; Cd: 5.0 and 6.5). For both metals, first-order biological internalization kinetics were observed but the maximum transport flux (Jmax) decreased when pH decreased, in contradiction with the Biotic Ligand Model (BLM). This result suggested a non-competitive inhibition of metal uptake by the H+-ion. A Michaelis-Menten type inhibition model considering proton and calcium competition was tested. The metal biotic ligand stability constants and the stability constants for competitive binding of Ca2+ and H+ with the metal transporters were calculated: for manganese, KMn = 104.20 and KCa = 103.71; for cadmium, KCd = 104.19 and KCa = 104.76; for both metal transport systems, KH was not a significant parameter. Furthermore, metal uptake was not significantly influenced by the pH of the antecedent growth medium, suggesting that increases in metal fluxes as the pH is raised are caused by conformational changes of the surface transport proteins rather than by the synthesis of additional transport sites. Our results demonstrate that the BLM in its present state does not properly describe the true influence of pH on manganese and cadmium uptake by algae and that a non-competitive inhibition component must be integrated

  8. High rate of mutations in the BRCA1, BRCA2, CHEK2, NBN, and BLM genes in Russian ovarian cancer patients

    Directory of Open Access Journals (Sweden)

    Ye. I. Bateneva

    2015-01-01

    Full Text Available Background. The early diagnosis of ovarian cancer (OC is an important problem in modern gynecological oncology due to significant detection rates for late-stage tumors. Intensive screening of patients from high-risk groups that include OC predisposition gene mutation carriers is indicated.Subjects and methods. An unselected group of 202 patients with OC and two control groups of blood donors: 591 healthy females; 1197 persons (including 591 females, 606 males were examined. Patients and healthy individuals who identified themselves as ethnic Russians and residents of the Russian Federation participated in the study. Whole peripheral blood samples were collected at the Clinical Subdivisions of the N.N. Blokhin Russian Cancer Research Center and at the Department of Transfusiology of the Acad. B.V. Petrovsky Russian Research Center of Surgery in 2012–2013. Informed consent was obtained from all the participants. DNA was extracted using a Prep-GS-Genetics reagent kit. Real-time polymerase chain reaction genotyping assay was carried out by melting-curve analysis employing an BRCA SNP genotyping kit(BRCA1 and BRCA2 gene mutations and original oligonucleotides (CHEK2, NBN, and BLM gene mutations. Thirteen population-specific mutations, including 7 (185delAG, 4153delA, 5382insC, 3819delGTAAA, 3875delGTCT, 300T>G, and 2080delA in the BRCA1 gene, 1 (6174delT in the BRCA2 gene, 3 (1100delC, IVS2+1G>A, and 470T>C in the CHEK2 gene, 1 (657delACAAA in the NBN gene, and 1 (1642C>T in the BLM gene, were genotyped. Polymerase chain reaction was performed using a DTprime real-time detection thermal cycler.Results and discussion. BRCA1 and BRCA2 gene mutations were detected in 46 (22.8 % patients with OC; the prevailing mutation in the BRCA1 gene was 5382insC (58.7 %. OC was diagnosed in 32.6 % of the patients aged 51 years or older. The rate of moderate-penetrance mutations (1100delC and IVS2+1G>A in the CHEK2 gene, 657del5 in the NBN gene, and 1642

  9. Structural implications of mutations in the pea SYM8 symbiosis gene, the DMI1 ortholog, encoding a predicted ion channel.

    Science.gov (United States)

    Edwards, Anne; Heckmann, Anne B; Yousafzai, Faridoon; Duc, Gerard; Downie, J Allan

    2007-10-01

    The Pisum sativum SYM8 gene plays an essential part in both rhizobial and mycorrhizal symbioses. Mutation of sym8 in the original type line R25 blocks nodulation, mycorrhization, and Nod-factor-induced calcium spiking, an early component of the nodulation signaling pathway. We describe four new sym8 alleles of pea, which fall into the same complementation group as R25. The sym8 mutants are phenotypically similar to Medicago truncatula dmi1 mutants and map to a syntenic location. We used sequence homology to isolate the pea ortholog of M. truncatula DMI1 and have shown that the cloned pea ortholog can complement a M. truncatula dmi1 mutant for nodulation. Each of the five pea sym8 mutants carries a mutation in the DMI1 ortholog, confirming that the pea SYM8 is the DMI1 ortholog. Based on predicted structural similarities with an archaebacterial ion channel, we propose that SYM8 forms a tetrameric calcium-gated channel of a predicted structure similar to the archaebacterial potassium channel but containing a filter region that is different. The predicted structure identifies four aspartate residues (one from each subunit) forming the channel opening. We made a mutation changing the aspartate to valine and identified a missense mutation (changing alanine to valine adjacent to the aspartate residues) in this predicted filter region; both mutations caused a loss of function. We also identified a loss-of-function missense mutation (changing arginine to isoleucine) in a domain proposed to link the predicted channel and the gating ring domains, indicating that this mutation may block function by preventing a protein conformational change being transmitted from the gating-ring domain to the pore domain. PMID:17918620

  10. Trappin ovine molecule (TOM), the ovine ortholog of elafin, is an acute phase reactant in the lung

    OpenAIRE

    Brown, Thomas I; Mistry, Rohit; Collie, D David; Tate, Steven; Sallenave, Jean-Michel

    2004-01-01

    As large animal models continue to play an important role in translating lung-directed therapeutic strategies from laboratory animals to humans, there is an increasing interest in the analysis of endogenous regulators of inflammation at both a genomic and a therapeutic level. To this end, we have sought to characterize the ovine ortholog of elafin, an important regulator of inflammation in humans. We have isolated both the elafin cDNA and gene, which have a similar structure to other species'...

  11. Hot spots in cold adaptation: Localized increases in conformational flexibility in lactate dehydrogenase A4 orthologs of Antarctic notothenioid fishes

    OpenAIRE

    Fields, Peter A.; Somero, George N.

    1998-01-01

    To elucidate mechanisms of enzymatic adaptation to extreme cold, we determined kinetic properties, thermal stabilities, and deduced amino acid sequences of lactate dehydrogenase A4 (A4-LDH) from nine Antarctic (−1.86 to 1°C) and three South American (4 to 10°C) notothenioid teleosts. Higher Michaelis–Menten constants (Km) and catalytic rate constants (kcat) distinguish orthologs of Antarctic from those of South American species, but no relationship exists between adaptation temperature and th...

  12. Bacterial and fungal chitinase chiJ orthologs evolve under different selective constraints following horizontal gene transfer

    Directory of Open Access Journals (Sweden)

    Ubhayasekera Wimal

    2012-10-01

    Full Text Available Abstract Background Certain bacteria from the genus Streptomyces are currently used as biological control agents against plant pathogenic fungi. Hydrolytic enzymes that degrade fungal cell wall components, such as chitinases, are suggested as one possible mechanism in biocontrol interactions. Adaptive evolution of chitinases are previously reported for plant chitinases involved in defence against fungal pathogens, and in fungal chitinases involved in fungal-fungal interactions. In this study we investigated the molecular evolution of chitinase chiJ in the bacterial genus Streptomyces. In addition, as chiJ orthologs are previously reported in certain fungal species as a result from horizontal gene transfer, we conducted a comparative study of differences in evolutionary patterns between bacterial and fungal taxa. Findings ChiJ contained three sites evolving under strong positive selection and four groups of co-evolving sites. Regions of high amino acid diversity were predicted to be surface-exposed and associated with coil regions that connect certain α-helices and β-strands in the family 18 chitinase TIM barrel structure, but not associated with the catalytic cleft. The comparative study with fungal ChiJ orthologs identified three regions that display signs of type 1 functional divergence, where unique adaptations in the bacterial and fungal taxa are driven by positive selection. Conclusions The identified surface-exposed regions of chitinase ChiJ where sequence diversification is driven by positive selection may putatively be related to functional divergence between bacterial and fungal orthologs. These results show that ChiJ orthologs have evolved under different selective constraints following the horizontal gene transfer event.

  13. Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes

    OpenAIRE

    Li, Guojun; Ma, Qin; Mao, Xizeng; Yin, Yanbin; Zhu, Xiaoran; Xu, Ying

    2011-01-01

    Existing methods for orthologous gene mapping suffer from two general problems: (i) they are computationally too slow and their results are difficult to interpret for automated large-scale applications when based on phylogenetic analyses; or (ii) they are too prone to making mistakes in dealing with complex situations involving horizontal gene transfers and gene fusion due to the lack of a sound basis when based on sequence similarity information. We present a novel algorithm, Global Optimiza...

  14. Vaccination with recombinant Boophilus annulatus Bm86 ortholog protein, Ba86, protects cattle against B. annulatus and B. microplus infestations

    OpenAIRE

    Jongejan Frans; Naranjo Victoria; Almazán Consuelo; Canales Mario; de la Fuente José

    2009-01-01

    Abstract Background The cattle ticks, Boophilus spp., affect cattle production in tropical and subtropical regions of the world. Tick vaccines constitute a cost-effective and environmentally friendly alternative to tick control. The recombinant B. microplus Bm86 protective antigen has been shown to protect cattle against tick infestations. Recently, the gene coding for B. annulatus Bm86 ortholog, Ba86, was cloned and the recombinant protein was secreted and purified from the yeast Pichia past...

  15. Identification and characterization of orthologs of AtNHX5 and AtNHX6 in Brassica napus

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    Brett Andrew Ford

    2012-09-01

    Full Text Available Improving crop species by breeding for salt tolerance or introducing salt tolerant traits is one method of increasing crop yields in saline affected areas. The model plant species Arabidopsis thaliana has been extensively studied and there is substantial information available about the function and importance of many genes and proteins involved in salt tolerance. The identification and characterization of A. thaliana orthologs in species such as Brassica napus (oilseed rape can prove difficult due to the significant genomic changes that have occurred since their divergence approximately 20 million years ago. The recently released B. rapa genome provides an excellent resource for comparative studies of Arabidopsis and the cultivated Brassica species, and facilitates the identification of Brassica species orthologs which may be of agronomic importance. Sodium hydrogen antiporter (NHX proteins transport a sodium or potassium ion in exchange for a hydrogen ion in the other direction across a membrane. In A. thaliana there are eight members of the NHX family designated AtNHX1-8 that can be sub-divided into three clades (plasma membrane (PM, intracellular class I (IC-I and intracellular class II (IC-II based on their subcellular localization. In plants, many NHX proteins are primary determinants of salt tolerance and act by transporting Na+ out of the cytosol where it would otherwise accumulate to toxic levels. Significant work has been done analyzing both PM and IC-I clade members role in salt tolerance in a variety of plant species but relatively little analysis has been described for the IC-II clade. Here we describe the identification of B. napus orthologs of AtNHX5 and AtNHX6, using the Brassica rapa genome sequence, macro- and micro-synteny analysis, comparative expression and promoter motif analysis, and highlight the value of these multiple approaches for identifying true orthologs in closely related species with multiple paralogs.

  16. Tissue expression and enzymologic characterization of human prostate specific membrane antigen and its rat and pig orthologs

    Czech Academy of Sciences Publication Activity Database

    Rovenská, Miroslava; Hlouchová, Klára; Šácha, Pavel; Mlčochová, Petra; Horák, Vratislav; Zámečník, J.; Bařinka, C.; Konvalinka, Jan

    2008-01-01

    Roč. 68, č. 2 (2008), s. 171-182. ISSN 0270-4137 R&D Projects: GA MŠk 1M0508; GA ČR GA524/04/0102 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50450515 Keywords : prostate specific membrane antigen * glutamate carboxypeptidase II * animal orthologs * prostate cancer * animal model Subject RIV: CE - Biochemistry Impact factor: 3.069, year: 2008

  17. Trappin ovine molecule (TOM), the ovine ortholog of elafin, is an acute phase reactant in the lung.

    Science.gov (United States)

    Brown, Thomas I; Mistry, Rohit; Collie, D David; Tate, Steven; Sallenave, Jean-Michel

    2004-09-16

    As large animal models continue to play an important role in translating lung-directed therapeutic strategies from laboratory animals to humans, there is an increasing interest in the analysis of endogenous regulators of inflammation at both a genomic and a therapeutic level. To this end, we have sought to characterize the ovine ortholog of elafin, an important regulator of inflammation in humans. We have isolated both the elafin cDNA and gene, which have a similar structure to other species' orthologs. Interestingly, we have isolated two alleles for ovine elafin, which contain a very high number of transglutamination repeats, thought to be important in binding elafin to the interstitium. The mainly mucosal mRNA distribution for ovine elafin suggests that ovine elafin may, like its human ortholog, have functions in innate immunity. This is supported by analysis of elafin and the related protein secretory leukocyte protease inhibitor (SLPI) in ovine bronchoalveolar fluid in response to locally administered lipopolysaccharide and confirmation of them acting as "alarm" antiproteases. We have also cloned the ovine elafin cDNA into an adenoviral vector and have demonstrated correct processing of the secreted protein as well as biological activity. Overexpression of ovine elafin in a lung-derived epithelial cell line has a protective effect against the enzymes human neutrophil and porcine pancreatic elastase. The identification of the ovine elafin gene and its translated protein are important in developing practical strategies aimed at regulating inflammation in the large mammalian lung. PMID:15292488

  18. Orthologous genes identified by transcriptome sequencing in the spider genus Stegodyphus

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    Mattila Tiina M

    2012-02-01

    Full Text Available Abstract Background The evolution of sociality in spiders involves a transition from an outcrossing to a highly inbreeding mating system, a shift to a female biased sex ratio, and an increase in the reproductive skew among individuals. Taken together, these features are expected to result in a strong reduction in the effective population size. Such a decline in effective population size is expected to affect population genetic and molecular evolutionary processes, resulting in reduced genetic diversity and relaxed selective constraint across the genome. In the genus Stegodyphus, permanent sociality and regular inbreeding has evolved independently three times from periodic-social (outcrossing ancestors. This genus is therefore an ideal model for comparative studies of the molecular evolutionary and population genetic consequences of the transition to a regularly inbreeding mating system. However, no genetic resources are available for this genus. Results We present the analysis of high throughput transcriptome sequencing of three Stegodyphus species. Two of these are periodic-social (Stegodyphus lineatus and S.tentoriicola and one is permanently social (S. mimosarum. From non-normalized cDNA libraries, we obtained on average 7,000 putative uni-genes for each species. Three-way orthology, as predicted from reciprocal BLAST, identified 1,792 genes that could be used for cross-species comparison. Open reading frames (ORFs could be deduced from 1,345 of the three-way alignments. Preliminary molecular analyses suggest a five- to ten-fold reduction in heterozygosity in the social S. mimosarum compared with the periodic-social species. Furthermore, an increased ratio of non-synonymous to synonymous polymorphisms in the social species indicated relaxed efficiency of selection. However, there was no sign of relaxed selection on the phylogenetic branch leading to S. mimosarum. Conclusions The 1,792 three-way ortholog genes identified in this study provide

  19. Computational Identification of the Paralogs and Orthologs of Human Cytochrome P450 Superfamily and the Implication in Drug Discovery

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    Shu-Ting Pan

    2016-06-01

    Full Text Available The human cytochrome P450 (CYP superfamily consisting of 57 functional genes is the most important group of Phase I drug metabolizing enzymes that oxidize a large number of xenobiotics and endogenous compounds, including therapeutic drugs and environmental toxicants. The CYP superfamily has been shown to expand itself through gene duplication, and some of them become pseudogenes due to gene mutations. Orthologs and paralogs are homologous genes resulting from speciation or duplication, respectively. To explore the evolutionary and functional relationships of human CYPs, we conducted this bioinformatic study to identify their corresponding paralogs, homologs, and orthologs. The functional implications and implications in drug discovery and evolutionary biology were then discussed. GeneCards and Ensembl were used to identify the paralogs of human CYPs. We have used a panel of online databases to identify the orthologs of human CYP genes: NCBI, Ensembl Compara, GeneCards, OMA (“Orthologous MAtrix” Browser, PATHER, TreeFam, EggNOG, and Roundup. The results show that each human CYP has various numbers of paralogs and orthologs using GeneCards and Ensembl. For example, the paralogs of CYP2A6 include CYP2A7, 2A13, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 2F1, 2J2, 2R1, 2S1, 2U1, and 2W1; CYP11A1 has 6 paralogs including CYP11B1, 11B2, 24A1, 27A1, 27B1, and 27C1; CYP51A1 has only three paralogs: CYP26A1, 26B1, and 26C1; while CYP20A1 has no paralog. The majority of human CYPs are well conserved from plants, amphibians, fishes, or mammals to humans due to their important functions in physiology and xenobiotic disposition. The data from different approaches are also cross-validated and validated when experimental data are available. These findings facilitate our understanding of the evolutionary relationships and functional implications of the human CYP superfamily in drug discovery.

  20. BRCA1/BARD1 orthologs required for DNA repair in Caenorhabditis elegans.

    Science.gov (United States)

    Boulton, Simon J; Martin, Julie S; Polanowska, Jolanta; Hill, David E; Gartner, Anton; Vidal, Marc

    2004-01-01

    Inherited germline mutations in the tumor suppressor gene BRCA1 predispose individuals to early onset breast and ovarian cancer. BRCA1 together with its structurally related partner BARD1 is required for homologous recombination and DNA double-strand break repair, but how they perform these functions remains elusive. As part of a comprehensive search for DNA repair genes in C. elegans, we identified a BARD1 ortholog. In protein interaction screens, Ce-BRD-1 was found to interact with components of the sumoylation pathway, the TACC domain protein TAC-1, and most importantly, a homolog of mammalian BRCA1. We show that animals depleted for either Ce-brc-1 or Ce-brd-1 display similar abnormalities, including a high incidence of males, elevated levels of p53-dependent germ cell death before and after irradiation, and impaired progeny survival and chromosome fragmentation after irradiation. Furthermore, depletion of ubc-9 and tac-1 leads to radiation sensitivity and a high incidence of males, respectively, potentially linking these genes to the C. elegans BRCA1 pathway. Our findings support a shared role for Ce-BRC-1 and Ce-BRD-1 in C. elegans DNA repair processes, and this role will permit studies of the BRCA1 pathway in an organism amenable to rapid genetic and biochemical analysis. PMID:14711411

  1. No Distinction of Orthology/Paralogy between Human and Chimpanzee Rh Blood Group Genes.

    Science.gov (United States)

    Kitano, Takashi; Kim, Choong-Gon; Blancher, Antoine; Saitou, Naruya

    2016-03-01

    On human (Homo sapiens) chromosome 1, there is a tandem duplication encompassing Rh blood group genes (Hosa_RHD and Hosa_RHCE). This duplication occurred in the common ancestor of humans, chimpanzees (Pan troglodytes), and gorillas, after splitting from their common ancestor with orangutans. Although several studies have been conducted on ape Rh blood group genes, the clear genome structures of the gene clusters remain unknown. Here, we determined the genome structure of the gene cluster of chimpanzee Rh genes by sequencing five BAC (Bacterial Artificial Chromosome) clones derived from chimpanzees. We characterized three complete loci (Patr_RHα, Patr_RHβ, and Patr_RHγ). In the Patr_RHβ locus, a short version of the gene, which lacked the middle part containing exons 4-8, was observed. The Patr_RHα and Patr_RHβ genes were located on the locations corresponding to Hosa_RHD and Hosa_RHCE, respectively, and Patr_RHγ was in the immediate vicinity of Patr_RHβ. Sequence comparisons revealed high sequence similarity between Patr_RHβ and Hosa_RHCE, while the chimpanzee Rh gene closest to Hosa_RHD was not Patr_RHα but rather Patr_RHγ. The results suggest that rearrangements and gene conversions frequently occurred between these genes and that the classic orthology/paralogy dichotomy no longer holds between human and chimpanzee Rh blood group genes. PMID:26872772

  2. Inference of gene-phenotype associations via protein-protein interaction and orthology.

    Directory of Open Access Journals (Sweden)

    Panwen Wang

    Full Text Available One of the fundamental goals of genetics is to understand gene functions and their associated phenotypes. To achieve this goal, in this study we developed a computational algorithm that uses orthology and protein-protein interaction information to infer gene-phenotype associations for multiple species. Furthermore, we developed a web server that provides genome-wide phenotype inference for six species: fly, human, mouse, worm, yeast, and zebrafish. We evaluated our inference method by comparing the inferred results with known gene-phenotype associations. The high Area Under the Curve values suggest a significant performance of our method. By applying our method to two human representative diseases, Type 2 Diabetes and Breast Cancer, we demonstrated that our method is able to identify related Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. The web server can be used to infer functions and putative phenotypes of a gene along with the candidate genes of a phenotype, and thus aids in disease candidate gene discovery. Our web server is available at http://jjwanglab.org/PhenoPPIOrth.

  3. Deletion of Serpina1a, a murine α1-antitrypsin ortholog, results in embryonic lethality.

    Science.gov (United States)

    Wang, Dongmei; Wang, Weimin; Dawkins, Paul; Paterson, Trevor; Kalsheker, Noor; Sallenave, Jean-Michel; Houghton, A McGarry

    2011-06-01

    Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States Approximately 1% to 2% of COPD patients suffer from α(1)-antitrypsin (A1AT) deficiency, the major inheritable predisposition to COPD/emphysema. To further study the role of A1AT deficiency in the pathogenesis of COPD/emphysema, the authors attempted to generate null-mutant mice for Serpina1a, 1 of 2 A1AT orthologs in mice. Here the authors show that targeted deletion of Serpina1a results in embryonic lethality prior to 8.5 days post conception (dpc). The results are surprising given that A1AT-null humans exist and therefore do not require this gene product for normal development. The Serpina1 gene cluster is substantially different between mouse and man. Through gene duplication, mice have 3 to 5 (depending on the strain) highly homologous proteinase inhibiting (Pi) genes, 2 of which inhibit neutrophil elastase. Despite the abundance of Pi genes in mice, Serpina1a serves a critical, nonredundant function during early mouse development. A1AT-deficient mice have been highly sought after to study emphysema, cancer, and liver disease, and as a model to perfect gene replacement therapy. These results highlight important differences between human and murine serpins and point to the difficulty inherent to using gene-targeted mice to study this common human genetic disease. PMID:21574874

  4. Identification and functional characterization of the AGO1 ortholog in maize.

    Science.gov (United States)

    Xu, Dongdong; Yang, Hailong; Zou, Cheng; Li, Wen-Xue; Xu, Yunbi; Xie, Chuanxiao

    2016-08-01

    Eukaryotic Argonaute proteins play primary roles in miRNA and siRNA pathways that are essential for numerous developmental and biological processes. However, the functional roles of the four ZmAGO1 genes have not yet been characterized in maize (Zea mays L.). In the present study, ZmAGO1a was identified from four putative ZmAGO1 genes for further characterization. Complementation of the Arabidopsis ago1-27 mutant with ZmAGO1a indicated that constitutive overexpression of ZmAGO1a could restore the smaller rosette, serrated leaves, later flowering and maturation, lower seed set, and darker green leaves at late stages of the mutant to the wild-type phenotype. The expression profiles of ZmAGO1a under five different abiotic stresses indicated that ZmAGO1a shares expression patterns similar to those of Argonaute genes in rice, Arabidopsis, and wheat. Further, variation in ZmAGO1a alleles among diverse maize germplasm that resulted in several amino acid changes revealed genetic diversity at this locus. The present data suggest that ZmAGO1a might be an important AGO1 ortholog in maize. The results presented provide further insight into the function of ZmAGO1a. PMID:26848539

  5. A Leishmania Ortholog of Macrophage Migration Inhibitory Factor Modulates Host Macrophage Responses

    Energy Technology Data Exchange (ETDEWEB)

    Kamir,D.; Zierow, S.; Leng, L.; Cho, Y.; Diaz, Y.; Griffith, J.; McDonald, C.; Merk, M.; Mitchell, R.; et al

    2008-01-01

    Parasitic organisms have evolved specialized strategies to evade immune defense mechanisms. We describe herein an ortholog of the cytokine, macrophage migration inhibitory factor (MIF), which is produced by the obligate intracellular parasite, Leishmania major. The Leishmania MIF protein, Lm1740MIF, shows significant structural homology with human MIF as revealed by a high-resolution x-ray crystal structure (1.03 A). Differences between the two proteins in the N-terminal tautomerization site are evident, and we provide evidence for the selective, species-specific inhibition of MIF by small-molecule antagonists that target this site. Lm1740MIF shows significant binding interaction with the MIF receptor, CD74 (K(d) = 2.9 x 10(-8) M). Like its mammalian counterpart, Lm1740MIF induces ERK1/2 MAP kinase activation in a CD74-dependent manner and inhibits the activation-induced apoptosis of macrophages. The ability of Lm1740MIF to inhibit apoptosis may facilitate the persistence of Leishmania within the macrophage and contribute to its evasion from immune destruction.

  6. Identifying the activation motif in the N-terminal of rainbow trout and zebrafish melanocortin-2 receptor accessory protein 1 (MRAP1) orthologs.

    Science.gov (United States)

    Dores, Robert M; Liang, Liang; Hollmann, Rebecca E; Sandhu, Navdeep; Vijayan, Mathilakath M

    2016-08-01

    The activation of mammalian melanocortin-2 receptor (MC2R) orthologs is dependent on a four-amino acid activation motif (LDYL/I) located in the N-terminal of mammalian MRAP1 (melanocortin-2 receptor accessory protein). Previous alanine substitution analysis had shown that the Y residue in this motif appears to be the most important for mediating the activation of mammalian MC2R orthologs. Similar, but not identical amino acid motifs were detected in rainbow trout MRAP1 (YDYL) and zebrafish MRAP1 (YDYV). To determine the importance of these residues in the putative activation motifs, rainbow trout and zebrafish MRAP1 orthologs were individually co-expressed in CHO cells with rainbow trout MC2R, and the activation of this receptor with either the wild-type MRAP1 ortholog or alanine-substituted analogs of the two teleost MRAP1s was analyzed. Alanine substitutions at all four amino acid positions in rainbow trout MRAP1 blocked activation of the rainbow trout MC2R. Single alanine substitutions of the D and Y residues in rainbow trout and zebrafish MRAP1 indicate that these two residues play a significant role in the activation of rainbow trout MC2R. These observations indicate that there are subtle differences in the way that teleost and mammalian MRAPs are involved in the activation of their corresponding MC2R orthologs. PMID:26752246

  7. Comparative integromics on FZD7 orthologs: conserved binding sites for PU.1, SP1, CCAAT-box and TCF/LEF/SOX transcription factors within 5'-promoter region of mammalian FZD7 orthologs.

    Science.gov (United States)

    Katoh, Masuko; Katoh, Masaru

    2007-03-01

    Canonical WNT signals are transduced through Frizzled (FZD) family receptor and LRP5/LRP6 co-receptor to upregulate MYC, CCND1, FGF20, JAG1, WISP1 and DKK1 genes, while non-canonical WNT signals are transduced through FZD family receptor and PTK7/ROR2/RYK co-receptor to activate RHOA/RHOU/RAC/CDC42, JNK, PKC, NFAT and NLK signaling cascades. FZD7, expressed in the normal gastrointestinal tract, is upregulated in esophageal cancer, gastric cancer, colorectal cancer, and hepatocellular carcinoma. Here, chimpanzee FZD7 and cow Fzd7 genes were identified and characterized by using bioinformatics (Techint) and human intelligence (Humint). Chimpanzee FZD7 and cow Fzd7 genes were identified within NW_001232110.1 and AC173037.2 genome sequences, respectively. Chimpanzee FZD7 and cow Fzd7 showed 100% and 97.2% total-amino-acid identity with human FZD7. All of the nine amino-acid residues substituted between human FZD7 and human FzE3 were identical to those of human FZD7 in chimpanzee, cow, mouse and rat FZD7 orthologs. Functional analyses using FzE3 with multiple cloning artifacts and/or sequencing errors are invalid. FZD7 orthologs were seven-transmembrane proteins with extracellular Frizzled domain, leucine zipper motif around the 5th transmembrane domain, and cytoplasmic DVL- and PDZ-binding motifs. Ser550 and Ser556 of FZD7 orthologs were putative aPKC phosphorylation sites. Dimerization and Ser550/556 phosphorylation were predicted as regulatory mechanisms for the signaling through FZD7. Transcriptional start site of human FZD7 gene was 735-bp upstream of NM_003507.1 RefSeq 5'-end. In addition to gastrointestinal cancer, hepatocellular cancer and pancreatic cancer, human FZD7 mRNAs were expressed in blastocysts, undifferentiated embryonic stem (ES) cells, ES-derived endodermal progenitors, ES-derived neural progenitors, fetal cochlea, retinal pigment epithelium, olfactory epithelium, regenerating liver, and multiple sclerosis. Comparative genomics analyses revealed

  8. Gene cloning, expression and characterization of avian cathelicidin orthologs, Cc-CATHs, from Coturnix coturnix.

    Science.gov (United States)

    Feng, Feifei; Chen, Chen; Zhu, Wenjuan; He, Weiyu; Guang, Huijuan; Li, Zheng; Wang, Duo; Liu, Jingze; Chen, Ming; Wang, Yipeng; Yu, Haining

    2011-05-01

    Cathelicidins comprise a family of antimicrobial peptides sharing a highly conserved cathelin domain, which play a central role in the early innate host defense against infection. In the present study, we report three novel avian cathelicidin orthologs cloned from a constructed spleen cDNA library of Coturnix coturnix, using a nested-PCR-based cloning strategy. Three coding sequences containing ORFs of 447, 465 and 456 bp encode three mature antimicrobial peptides (named Cc-CATH1, 2 and 3) of 26, 32 and 29 amino acid residues, respectively. Phylogenetic analysis indicated that precursors of Cc-CATHs are significantly conserved with known avian cathelicidins. Synthetic Cc-CATH2 and 3 displayed broad and potent antimicrobial activity against most of the 41 strains of bacteria and fungi tested, especially the clinically isolated drug-resistant strains, with minimum inhibitory concentration values in the range 0.3-2.5 μm for most strains with or without the presence of 100 mm NaCl. Cc-CATH2 and 3 showed considerable reduction of cytotoxic activity compared to other avian cathelicidins, with average IC(50) values of 20.18 and 17.16 μm, respectively. They also exerted a negligible hemolytic activity against human erythrocytes, lysing only 3.6% of erythrocytes at a dose up to 100 μg·mL(-1) . As expected, the recombinant Cc-CATH2 (rCc-CATH2) also showed potent bactericidal activity. All these features of Cc-CATHs encourage further studies aiming to estimate their therapeutic potential as drug leads, as well as coping with current widespread antibiotic resistance, especially the new prevalent and dangerous 'superbug' that is resistant to almost all antibiotics. PMID:21375690

  9. Subolesin/akirin orthologs from Ornithodoros spp. soft ticks: cloning, RNAi gene silencing and protective effect of the recombinant proteins.

    Science.gov (United States)

    Manzano-Román, Raúl; Díaz-Martín, Verónica; Oleaga, Ana; Siles-Lucas, Mar; Pérez-Sánchez, Ricardo

    2012-04-30

    Subolesin/akirin is a well characterized protective antigen highly conserved across vector species and thus potentially useful for the development of a broad-spectrum vaccine for the control of arthropod infestations including hard ticks, mosquitoes, sand flies and the poultry red mite Dermanyssus gallinae. Soft ticks could be also targeted by this vaccine if proved that the soft tick subolesin orthologs are conserved and induce protective immune responses too. However, to date no soft tick subolesin orthologs have been fully characterized nor tested as recombinant antigens in vaccination trials. The objectives of the present work were to clone and characterize the subolesin orthologs from two important vector species of soft ticks as Ornithodoros erraticus and O. moubata, to evaluate the effect of subolesin gene silencing by RNAi, and to test the protective value of the recombinant antigens in vaccination trials. The obtained results demonstrate that both soft tick subolesins are highly conserved showing more than 69% and 74% identity with those of hard ticks in their nucleotide and amino acid sequences, respectively. Additionally, we demonstrate that both soft ticks possess fully operative RNAi machinery, and that subolesin gene silencing by dsRNA injection inhibits oviposition indicating the involvement of subolesin in tick reproduction. Finally, vaccination with the recombinant soft tick subolesins induced a partial protective effect resulting in the reduction of the oviposition rate. These preliminary results encourage further studies on the use of recombinant subolesins as vaccines for the control of soft tick infestations, either alone or in combination with other specific molecules. PMID:22105082

  10. From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development.

    Science.gov (United States)

    Khodiyar, Varsha K; Howe, Doug; Talmud, Philippa J; Breckenridge, Ross; Lovering, Ruth C

    2013-01-01

    For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer's vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer's vesicle determine asymmetry in the developing heart, the direction of 'heart jogging' and the direction of 'heart looping'.  'Heart jogging' is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward 'jog'. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish 'heart jogging orthologs' are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach. PMID:24627794

  11. A murine ortholog of the human serpin SCCA2 maps to chromosome 1 and inhibits chymotrypsin-like serine proteinases.

    Science.gov (United States)

    Bartuski, A J; Kamachi, Y; Schick, C; Massa, H; Trask, B J; Silverman, G A

    1998-12-01

    Squamous cell carcinoma antigens (SCCA) 1 and 2 are inhibitory members of the high-molecular-weight serine proteinase inhibitor (serpin) family. The biological functions of SCCA1 and 2 are unknown. One approach to determining the function of human proteins is to study orthologs in other species, such as the mouse. The purpose of this study was to determine whether orthologs to human SCCA1 or 2 exist in the mouse. We report the identification and characterization of a novel serpin, sqn5 (now designated Scca2). Comparative amino acid sequence analysis suggests that Scca2 is a member of the ov-serpin subfamily of serpins with highest homology to SCCA1 and SCCA2. Fluorescence in situ hybridization revealed that the Scca2 mapped near Bcl2 on mouse chromosome 1. This region is syntenic with the human locus for SCCA1 and SCCA2 on 18q21.3. The tissue expression patterns as determined by RT-PCR showed a restricted distribution. Scca2 was detected in the lung, thymus, skin, and uterus, as are SCCA1 and SCCA2. Unlike the SCCAs, however, Scca2 was detected also in the gastrointestinal tract. Enzyme-inhibition assays using a GST-SCCA2 fusion protein revealed that SCCA2 inhibited chymotrypsin-like serine proteinases, but not papain-like cysteine proteinases. SCCA2 inhibited CTSG at 1:1 stoichiometry and with a second-order rate constant of kass = 1.7 x 10(5) M-1 s-1. SCCA2 also inhibited human mast cell chymase but the stoichiometry was 2:1, and the second-order rate constant was kass = 0.9 x 10(4) M-1 s-1. This inhibitory profile is identical to that observed for human SCCA2. Based on these findings, Scca2 appears to be the murine ortholog of human SCCA2. PMID:9828132

  12. High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans.

    Science.gov (United States)

    Lipovich, Leonard; Hou, Zhuo-Cheng; Jia, Hui; Sinkler, Christopher; McGowen, Michael; Sterner, Kirstin N; Weckle, Amy; Sugalski, Amara B; Pipes, Lenore; Gatti, Domenico L; Mason, Christopher E; Sherwood, Chet C; Hof, Patrick R; Kuzawa, Christopher W; Grossman, Lawrence I; Goodman, Morris; Wildman, Derek E

    2016-02-01

    The human brain and human cognitive abilities are strikingly different from those of other great apes despite relatively modest genome sequence divergence. However, little is presently known about the interspecies divergence in gene structure and transcription that might contribute to these phenotypic differences. To date, most comparative studies of gene structure in the brain have examined humans, chimpanzees, and macaque monkeys. To add to this body of knowledge, we analyze here the brain transcriptome of the western lowland gorilla (Gorilla gorilla gorilla), an African great ape species that is phylogenetically closely related to humans, but with a brain that is approximately one-third the size. Manual transcriptome curation from a sample of the planum temporale region of the neocortex revealed 12 protein-coding genes and one noncoding-RNA gene with exons in the gorilla unmatched by public transcriptome data from the orthologous human loci. These interspecies gene structure differences accounted for a total of 134 amino acids in proteins found in the gorilla that were absent from protein products of the orthologous human genes. Proteins varying in structure between human and gorilla were involved in immunity and energy metabolism, suggesting their relevance to phenotypic differences. This gorilla neocortical transcriptome comprises an empirical, not homology- or prediction-driven, resource for orthologous gene comparisons between human and gorilla. These findings provide a unique repository of the sequences and structures of thousands of genes transcribed in the gorilla brain, pointing to candidate genes that may contribute to the traits distinguishing humans from other closely related great apes. PMID:26132897

  13. A search of Brassica SI-involved orthologs in buckwheat leads to novel buckwheat sequence identification: MLPK possibly involved in SI response

    Directory of Open Access Journals (Sweden)

    Banović Bojana

    2010-01-01

    Full Text Available Self-incompatibility (SI systems, gamethophytic (GSI and sporophytic (SSI, prevent self-pollination in angiosperms. Buckwheat displays heteromorphic SSI, with pollination allowed only between different flower morphs - thrum and pin. The physiology of thrum and pin morph SI responses are entirely different, resembling homomorphic Brassica SSI and Prunus GSI responses, respectively. Considering angiosperm species may share ancestral SI genes, we examined the presence of Brassica and Prunus SI-involved gene orthologs in the buckwheat genome. We did not find evidence of SRK, SLG and SP11 Brassica or S-RNase and SFB Prunus orthologs in the buckwheat genome, but we found a Brassica MLPK ortholog. We report the partial nucleotide sequence of the buckwheat MLPK and discuss the possible implications of this finding.

  14. Vaccine Efficacy of Bm86 Ortholog of H. a. anatolicum, rHaa86 Expressed in Prokaryotic Expression System

    OpenAIRE

    Azhahianambi, P.; D. D. Ray; Pallab Chaudhuri; Rohita Gupta; Srikanta Ghosh

    2010-01-01

    The use of tick vaccine in controlling ticks and tick borne diseases has been proved effective in integrated tick management format. For the control of H. a. anatolicum, Bm86 ortholog of H. a. anatolicum was cloned and expressed as fusion protein in E. coli as E. coli-pETHaa86. The molecular weight of the rHaa86 was 97 kDa with a 19 kDa fusion tag of thioredoxin protein. The expressed protein was characterized immunologically and vaccine efficacy was evaluated. After 120 hours of challenge, o...

  15. Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

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    Singh Rama S

    2008-08-01

    Full Text Available Abstract Background Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern of gene expression. Using the fully sequenced genomes of three Caenorhabditid nematode species as well as genome information from additional more distantly related organisms (fruit fly, mouse, and human we sought to identify orthologous TFs and characterized their patterns of evolution. Results We identified 988 TF genes in C. elegans, and inferred corresponding sets in C. briggsae and C. remanei, containing 995 and 1093 TF genes, respectively. Analysis of the three gene sets revealed 652 3-way reciprocal 'best hit' orthologs (nematode TF set, approximately half of which are zinc finger (ZF-C2H2 and ZF-C4/NHR types and HOX family members. Examination of the TF genes in C. elegans and C. briggsae identified the presence of significant tandem clustering on chromosome V, the majority of which belong to ZF-C4/NHR family. We also found evidence for lineage-specific duplications and rapid evolution of many of the TF genes in the two species. A search of the TFs conserved among nematodes in Drosophila melanogaster, Mus musculus and Homo sapiens revealed 150 reciprocal orthologs, many of which are associated with important biological processes and human diseases. Finally, a comparison of the sequence, gene interactions and function indicates that nematode TFs conserved across phyla exhibit significantly more interactions and are enriched in genes with annotated mutant phenotypes compared to those that lack orthologs in other species. Conclusion Our study represents the first comprehensive genome-wide analysis of TFs across three nematode species and other organisms. The findings indicate substantial conservation of transcription

  16. Roles of Werner syndrome protein in protection of genome integrity

    DEFF Research Database (Denmark)

    Rossi, Marie L; Ghosh, Avik K; Bohr, Vilhelm A

    2010-01-01

    Werner syndrome protein (WRN) is one of a family of five human RecQ helicases implicated in the maintenance of genome stability. The conserved RecQ family also includes RecQ1, Bloom syndrome protein (BLM), RecQ4, and RecQ5 in humans, as well as Sgs1 in Saccharomyces cerevisiae, Rqh1 in Schizosacc......Werner syndrome protein (WRN) is one of a family of five human RecQ helicases implicated in the maintenance of genome stability. The conserved RecQ family also includes RecQ1, Bloom syndrome protein (BLM), RecQ4, and RecQ5 in humans, as well as Sgs1 in Saccharomyces cerevisiae, Rqh1 in...

  17. 'Ca. Liberibacter asiaticus' proteins orthologous with pSymA-encoded proteins of Sinorhizobium meliloti: hypothetical roles in plant host interaction.

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    L David Kuykendall

    Full Text Available Sinorhizobium meliloti strain 1021, a nitrogen-fixing, root-nodulating bacterial microsymbiont of alfalfa, has a 3.5 Mbp circular chromosome and two megaplasmids including 1.3 Mbp pSymA carrying nonessential 'accessory' genes for nitrogen fixation (nif, nodulation and host specificity (nod. A related bacterium, psyllid-vectored 'Ca. Liberibacter asiaticus,' is an obligate phytopathogen with a reduced genome that was previously analyzed for genes orthologous to genes on the S. meliloti circular chromosome. In general, proteins encoded by pSymA genes are more similar in sequence alignment to those encoded by S. meliloti chromosomal orthologs than to orthologous proteins encoded by genes carried on the 'Ca. Liberibacter asiaticus' genome. Only two 'Ca. Liberibacter asiaticus' proteins were identified as having orthologous proteins encoded on pSymA but not also encoded on the chromosome of S. meliloti. These two orthologous gene pairs encode a Na(+/K+ antiporter (shared with intracellular pathogens of the family Bartonellacea and a Co++, Zn++ and Cd++ cation efflux protein that is shared with the phytopathogen Agrobacterium. Another shared protein, a redox-regulated K+ efflux pump may regulate cytoplasmic pH and homeostasis. The pSymA and 'Ca. Liberibacter asiaticus' orthologs of the latter protein are more highly similar in amino acid alignment compared with the alignment of the pSymA-encoded protein with its S. meliloti chromosomal homolog. About 182 pSymA encoded proteins have sequence similarity (≤ E-10 with 'Ca. Liberibacter asiaticus' proteins, often present as multiple orthologs of single 'Ca. Liberibacter asiaticus' proteins. These proteins are involved with amino acid uptake, cell surface structure, chaperonins, electron transport, export of bioactive molecules, cellular homeostasis, regulation of gene expression, signal transduction and synthesis of amino acids and metabolic cofactors. The presence of multiple orthologs defies mutational

  18. TaWRKY68 responses to biotic stresses are revealed by the orthologous genes from major cereals

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    Bo Ding

    2014-01-01

    Full Text Available WRKY transcription factors have been extensively characterized in the past 20 years, but in wheat, studies onWRKY genes and their function are lagging behind many other species. To explore the function of wheat WRKY genes, we identified a TaWRKY68 gene from a common wheat cultivar. It encodes a protein comprising 313 amino acids which harbors 19 conserved motifs or active sites. Gene expression patterns were determined by analyzing microarray data of TaWRKY68 in wheat and of orthologous genes from maize, rice and barley using Genevestigator. TaWRKY68 orthologs were identified and clustered using DELTA-BLAST and COBALT programs available at NCBI. The results showed that these genes, which are expressed in all tissues tested, had relatively higher levels in the roots and were up-regulated in response to biotic stresses. Bioinformatics results were confirmed by RT-PCR experiments using wheat plants infected by Agrobacterium tumefaciens and Blumeria graminis, or treated with Deoxynivalenol, a Fusarium graminearum-induced mycotoxin in wheat or barley. In summary,TaWRKY68 functions differ during plant developmental stages and might be representing a hub gene function in wheat responses to various biotic stresses. It was also found that including data from major cereal genes in the bioinformatics analysis gave more accurate and comprehensive predictions of wheat gene functions.

  19. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V.; Dubchak, Inna

    2009-07-23

    The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.

  20. Orthologs of Human Disease Associated Genes and RNAi Analysis of Silencing Insulin Receptor Gene in Bombyx mori

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    Zan Zhang

    2014-10-01

    Full Text Available The silkworm, Bombyx mori L., is an important economic insect that has been domesticated for thousands of years to produce silk. It is our great interest to investigate the possibility of developing the B. mori as human disease model. We searched the orthologs of human disease associated genes in the B. mori by bi-directional best hits of BLAST and confirmed by searching the OrthoDB. In total, 5006 genes corresponding to 1612 kinds of human diseases had orthologs in the B. mori, among which, there are 25 genes associated with diabetes mellitus. Of these, we selected the insulin receptor gene of the B. mori (Bm-INSR to study its expression in different tissues and at different developmental stages and tissues. Quantitative PCR showed that Bm-INSR was highly expressed in the Malpighian tubules but expressed at low levels in the testis. It was highly expressed in the 3rd and 4th instar larvae, and adult. We knocked down Bm-INSR expression using RNA interference. The abundance of Bm-INSR transcripts were dramatically reduced to ~4% of the control level at 6 days after dsRNA injection and the RNAi-treated B. mori individuals showed apparent growth inhibition and malformation such as abnormal body color in black, which is the typical symptom of diabetic patients. Our results demonstrate that B. mori has potential use as an animal model for diabetic mellitus research.

  1. Expression of recombinant Rhipicephalus (Boophilus microplus, R. annulatus and R. decoloratus Bm86 orthologs as secreted proteins in Pichia pastoris

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    Jongejan Frans

    2008-02-01

    Full Text Available Abstract Background Rhipicephalus (Boophilus spp. ticks economically impact on cattle production in Africa and other tropical and subtropical regions of the world. Tick vaccines constitute a cost-effective and environmentally friendly alternative to tick control. The R. microplus Bm86 protective antigen has been produced by recombinant DNA technology and shown to protect cattle against tick infestations. Results In this study, the genes for Bm86 (R. microplus, Ba86 (R. annulatus and Bd86 (R. decoloratus were cloned and characterized from African or Asian tick strains and the recombinant proteins were secreted and purified from P. pastoris. The secretion of recombinant Bm86 ortholog proteins in P. pastoris allowed for a simple purification process rendering a final product with high recovery (35–42% and purity (80–85% and likely to result in a more reproducible conformation closely resembling the native protein. Rabbit immunization experiments with recombinant proteins showed immune cross-reactivity between Bm86 ortholog proteins. Conclusion These experiments support the development and testing of vaccines containing recombinant Bm86, Ba86 and Bd86 secreted in P. pastoris for the control of tick infestations in Africa.

  2. Frequent and recent retrotransposition of orthologous genes plays a role in the evolution of sperm glycolytic enzymes

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    de Villena Fernando

    2010-05-01

    Full Text Available Abstract Background The central metabolic pathway of glycolysis converts glucose to pyruvate, with the net production of 2 ATP and 2 NADH per glucose molecule. Each of the ten reactions in this pathway is typically catalyzed by multiple isozymes encoded by a multigene family. Several isozymes in this pathway are expressed only during spermatogenesis, and gene targeting studies indicate that they are essential for sperm function and male fertility in mouse. At least three of the novel glycolytic isozymes are encoded by retrogenes (Pgk2, Aldoart1, and Aldoart2. Their restricted expression profile suggests that retrotransposition may play a significant role in the evolution of sperm glycolytic enzymes. Results We conducted a comprehensive genomic analysis of glycolytic enzymes in the human and mouse genomes and identified several intronless copies for all enzymes in the pathway, except Pfk. Within each gene family, a single orthologous gene was typically retrotransposed frequently and independently in both species. Several retroposed sequences maintained open reading frames (ORFs and/or provided evidence of alternatively spliced exons. We analyzed expression of sequences with ORFs and Gpi1 transcript in mouse spermatogenic cells. Conclusions Our analysis detected frequent, recent, and lineage-specific retrotransposition of orthologous glycolytic enzymes in the human and mouse genomes. Retrotransposition events are associated with LINE/LTR and genomic integration is random. We found evidence for the alternative splicing of parent genes. Many retroposed sequences have maintained ORFs, suggesting a functional role for these genes.

  3. ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

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    Meiler Arno

    2012-09-01

    Full Text Available Abstract Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

  4. Systemic acquired resistance in soybean is regulated by two proteins, Orthologous to Arabidopsis NPR1

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    Sandhu Devinder

    2009-08-01

    Full Text Available Abstract Background Systemic acquired resistance (SAR is induced in non-inoculated leaves following infection with certain pathogenic strains. SAR is effective against many pathogens. Salicylic acid (SA is a signaling molecule of the SAR pathway. The development of SAR is associated with the induction of pathogenesis related (PR genes. Arabidopsis non-expressor of PR1 (NPR1 is a regulatory gene of the SA signal pathway 123. SAR in soybean was first reported following infection with Colletotrichum trancatum that causes anthracnose disease. We investigated if SAR in soybean is regulated by a pathway, similar to the one characterized in Arabidopsis. Results Pathogenesis-related gene GmPR1 is induced following treatment of soybean plants with the SAR inducer, 2,6-dichloroisonicotinic acid (INA or infection with the oomycete pathogen, Phytophthora sojae. In P. sojae-infected plants, SAR was induced against the bacterial pathogen, Pseudomonas syringae pv. glycinea. Soybean GmNPR1-1 and GmNPR1-2 genes showed high identities to Arabidopsis NPR1. They showed similar expression patterns among the organs, studied in this investigation. GmNPR1-1 and GmNPR1-2 are the only soybean homologues of NPR1and are located in homoeologous regions. In GmNPR1-1 and GmNPR1-2 transformed Arabidopsis npr1-1 mutant plants, SAR markers: (i PR-1 was induced following INA treatment and (ii BGL2 following infection with Pseudomonas syringae pv. tomato (Pst, and SAR was induced following Pst infection. Of the five cysteine residues, Cys82, Cys150, Cys155, Cys160, and Cys216 involved in oligomer-monomer transition in NPR1, Cys216 in GmNPR1-1 and GmNPR1-2 proteins was substituted to Ser and Leu, respectively. Conclusion Complementation analyses in Arabidopsis npr1-1 mutants revealed that homoeologous GmNPR1-1 and GmNPR1-2 genes are orthologous to Arabidopsis NPR1. Therefore, SAR pathway in soybean is most likely regulated by GmNPR1 genes. Substitution of Cys216 residue, essential

  5. Conserved POU/OCT- and GATA-binding sites in 5'-flanking promoter region of mammalian WNT8B orthologs.

    Science.gov (United States)

    Katoh, Masuko; Katoh, Masaru

    2007-05-01

    WNT family members are secreted-type glycoproteins regulating cell fate, planar cell polarity, cell adhesion, and cell movement. WNT signals are context-dependently transduced to the canonical pathway for the transcriptional up-regulation of MYC, CCND1, FGF20, JAG1, WISP1 and DKK1 genes, and also to the non-canonical pathway for the activation of RHOA, JNK, PKC, NFAT and NLK signaling cascades. We cloned and characterized the wild-type human WNT8B, while another group the aberrant human WNT8B with Gly230Ala and Arg284Leu amino-acid substitutions. Although WNT8B is undetectable in normal adult tissues by using Northern blot analyses, WNT8B is expressed in gastric cancer, pancreatic cancer, colorectal cancer, breast cancer, and embryonal tumors. Here, comparative integromics on WNT8B orthologs were investigated by using bioinformatics (Techint) and human intelligence (Humint). Cow Wnt8b gene was identified within NW_001494361.1 genome sequence. Predicted sequence XM_582222.3 was an artificial cow Wnt8b with aberrant prediction for the first exon. Cow Wnt8b complete coding sequence was found to encode a 350-amino-acid protein, which showed 96.9% total-amino-acid identity with human WNT8B. Comparative proteomics revealed that N-terminal signal peptide, 22 Cys residues, two Asn-linked glycosylation sites, Gly230, and Arg284 of human WNT8B were conserved among mammalian WNT8B orthologs. Comparative genomics revealed that POU/OCT- and GATA-binding sites in the 5'-flanking promoter region were conserved among human, chimpanzee, cow, mouse, and rat WNT8B orthologs. In silico expression analyses revealed that human WNT8B was expressed in embryoid body derived from embryonic stem (ES) cells, hepatocyte progenitors derived from ES cells, fetal brain, diffuse-type gastric cancer, colorectal cancer, prostate cancer, and ovarian fibrotheoma. Based on the expression profiles of POU and GATA family transcription factors, it was revealed that WNT8B expression in hepatocyte

  6. Loss-of-function mutations in the C9ORF72 mouse ortholog cause fatal autoimmune disease.

    Science.gov (United States)

    Burberry, Aaron; Suzuki, Naoki; Wang, Jin-Yuan; Moccia, Rob; Mordes, Daniel A; Stewart, Morag H; Suzuki-Uematsu, Satomi; Ghosh, Sulagna; Singh, Ajay; Merkle, Florian T; Koszka, Kathryn; Li, Quan-Zhen; Zon, Leonard; Rossi, Derrick J; Trowbridge, Jennifer J; Notarangelo, Luigi D; Eggan, Kevin

    2016-07-13

    C9ORF72 mutations are found in a significant fraction of patients suffering from amyotrophic lateral sclerosis and frontotemporal dementia, yet the function of the C9ORF72 gene product remains poorly understood. We show that mice harboring loss-of-function mutations in the ortholog of C9ORF72 develop splenomegaly, neutrophilia, thrombocytopenia, increased expression of inflammatory cytokines, and severe autoimmunity, ultimately leading to a high mortality rate. Transplantation of mutant mouse bone marrow into wild-type recipients was sufficient to recapitulate the phenotypes observed in the mutant animals, including autoimmunity and premature mortality. Reciprocally, transplantation of wild-type mouse bone marrow into mutant mice improved their phenotype. We conclude that C9ORF72 serves an important function within the hematopoietic system to restrict inflammation and the development of autoimmunity. PMID:27412785

  7. The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99.

    Science.gov (United States)

    Periyannan, Sambasivam; Moore, John; Ayliffe, Michael; Bansal, Urmil; Wang, Xiaojing; Huang, Li; Deal, Karin; Luo, Mingcheng; Kong, Xiuying; Bariana, Harbans; Mago, Rohit; McIntosh, Robert; Dodds, Peter; Dvorak, Jan; Lagudah, Evans

    2013-08-16

    Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici, afflicts bread wheat (Triticum aestivum). New virulent races collectively referred to as "Ug99" have emerged, which threaten global wheat production. The wheat gene Sr33, introgressed from the wild relative Aegilops tauschii into bread wheat, confers resistance to diverse stem rust races, including the Ug99 race group. We cloned Sr33, which encodes a coiled-coil, nucleotide-binding, leucine-rich repeat protein. Sr33 is orthologous to the barley (Hordeum vulgare) Mla mildew resistance genes that confer resistance to Blumeria graminis f. sp. hordei. The wheat Sr33 gene functions independently of RAR1, SGT1, and HSP90 chaperones. Haplotype analysis from diverse collections of Ae. tauschii placed the origin of Sr33 resistance near the southern coast of the Caspian Sea. PMID:23811228

  8. Critical role of the virus-encoded microRNA-155 ortholog in the induction of Marek's disease lymphomas.

    Directory of Open Access Journals (Sweden)

    Yuguang Zhao

    2011-02-01

    Full Text Available Notwithstanding the well-characterised roles of a number of oncogenes in neoplastic transformation, microRNAs (miRNAs are increasingly implicated in several human cancers. Discovery of miRNAs in several oncogenic herpesviruses such as KSHV has further highlighted the potential of virus-encoded miRNAs to contribute to their oncogenic capabilities. Nevertheless, despite the identification of several possible cancer-related genes as their targets, the direct in vivo role of virus-encoded miRNAs in neoplastic diseases such as those induced by KSHV is difficult to demonstrate in the absence of suitable models. However, excellent natural disease models of rapid-onset Marek's disease (MD lymphomas in chickens allow examination of the oncogenic potential of virus-encoded miRNAs. Using viruses modified by reverse genetics of the infectious BAC clone of the oncogenic RB-1B strain of MDV, we show that the deletion of the six-miRNA cluster 1 from the viral genome abolished the oncogenicity of the virus. This loss of oncogenicity appeared to be primarily due to the single miRNA within the cluster, miR-M4, the ortholog of cellular miR-155, since its deletion or a 2-nucleotide mutation within its seed region was sufficient to inhibit the induction of lymphomas. The definitive role of this miR-155 ortholog in oncogenicity was further confirmed by the rescue of oncogenic phenotype by revertant viruses that expressed either the miR-M4 or the cellular homolog gga-miR-155. This is the first demonstration of the direct in vivo role of a virus-encoded miRNA in inducing tumors in a natural infection model. Furthermore, the use of viruses deleted in miRNAs as effective vaccines against virulent MDV challenge, enables the prospects of generating genetically defined attenuated vaccines.

  9. From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development.

    Science.gov (United States)

    Lovering, Ruth C

    2014-01-01

    For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer’s vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer’s vesicle determine asymmetry in the developing heart, the direction of ‘heart jogging’ and the direction of ‘heart looping’.  ‘Heart jogging’ is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward ‘jog’. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish ‘heart jogging orthologs’ are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach. PMID:24627794

  10. Vaccination with recombinant Boophilus annulatus Bm86 ortholog protein, Ba86, protects cattle against B. annulatus and B. microplus infestations

    Directory of Open Access Journals (Sweden)

    Jongejan Frans

    2009-03-01

    Full Text Available Abstract Background The cattle ticks, Boophilus spp., affect cattle production in tropical and subtropical regions of the world. Tick vaccines constitute a cost-effective and environmentally friendly alternative to tick control. The recombinant B. microplus Bm86 protective antigen has been shown to protect cattle against tick infestations. Recently, the gene coding for B. annulatus Bm86 ortholog, Ba86, was cloned and the recombinant protein was secreted and purified from the yeast Pichia pastoris. Results Recombinant Ba86 (Israel strain was used to immunize cattle to test its efficacy for the control of B. annulatus (Mercedes, Texas, USA strain and B. microplus (Susceptible, Mexico strain infestations. Bm86 (Gavac and Mozambique strain and adjuvant/saline were used as positive and negative controls, respectively. Vaccination with Ba86 reduced tick infestations (71% and 40%, weight (8% and 15%, oviposition (22% and 5% and egg fertility (25% and 50% for B. annulatus and B. microplus, respectively. The efficacy of both Ba86 and Bm86 was higher for B. annulatus than for B. microplus. The efficacy of Ba86 was higher for B. annulatus (83.0% than for B. microplus (71.5%. The efficacy of Bm86 (Gavac; 85.2% but not Bm86 (Mozambique strain; 70.4% was higher than that of Ba86 (71.5% on B. microplus. However, the efficacy of Bm86 (both Gavac and Mozambique strain; 99.6% was higher than that of Ba86 (83.0% on B. annulatus. Conclusion These experiments showed the efficacy of recombinant Ba86 for the control of B. annulatus and B. microplus infestations in cattle and suggested that physiological differences between B. microplus and B. annulatus and those encoded in the sequence of Bm86 orthologs may be responsible for the differences in susceptibility of these tick species to Bm86 vaccines.

  11. Identification of the minus-dominance gene ortholog in the mating-type locus of Gonium pectorale.

    Science.gov (United States)

    Hamaji, Takashi; Ferris, Patrick J; Coleman, Annette W; Waffenschmidt, Sabine; Takahashi, Fumio; Nishii, Ichiro; Nozaki, Hisayoshi

    2008-01-01

    The evolution of anisogamy/oogamy in the colonial Volvocales might have occurred in an ancestral isogamous colonial organism like Gonium pectorale. The unicellular, close relative Chlamydomonas reinhardtii has a mating-type (MT) locus harboring several mating-type-specific genes, including one involved in mating-type determination and another involved in the function of the tubular mating structure in only one of the two isogametes. In this study, as the first step in identifying the G. pectorale MT locus, we isolated from G. pectorale the ortholog of the C. reinhardtii mating-type-determining minus-dominance (CrMID) gene, which is localized only in the MT- locus. 3'- and 5'-RACE RT-PCR using degenerate primers identified a CrMID-orthologous 164-amino-acid coding gene (GpMID) containing a leucine-zipper RWP-RK domain near the C-terminal, as is the case with CrMID. Genomic Southern blot analysis showed that GpMID was coded only in the minus strain of G. pectorale. RT-PCR revealed that GpMID expression increased during nitrogen starvation. Analysis of F1 progeny suggested that GpMID and isopropylmalate dehydratase LEU1S are tightly linked, suggesting that they are harbored in a chromosomal region under recombinational suppression that is comparable to the C. reinhardtii MT locus. However, two other genes present in the C. reinhardtii MT locus are not linked to the G. pectorale LEU1S/MID, suggesting that the gene content of the volvocalean MT loci is not static over time. Inheritance of chloroplast and mitochondria genomes in G. pectorale is uniparental from the plus and minus parents, respectively, as is also the case in C. reinhardtii. PMID:18202374

  12. A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement

    Directory of Open Access Journals (Sweden)

    Finan Christopher L

    2005-03-01

    Full Text Available Abstract Background In Micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. This autocrine resuscitation-promoting factor (Rpf is the founder member of a family of proteins found throughout and confined to the actinobacteria (high G + C Gram-positive bacteria. The aim of this work was to search for and characterise a cognate gene family in the firmicutes (low G + C Gram-positive bacteria and obtain information about how they may control bacterial growth and resuscitation. Results In silico analysis of the accessory domains of the Rpf proteins permitted their classification into several subfamilies. The RpfB subfamily is related to a group of firmicute proteins of unknown function, represented by YabE of Bacillus subtilis. The actinobacterial RpfB and firmicute YabE proteins have very similar domain structures and genomic contexts, except that in YabE, the actinobacterial Rpf domain is replaced by another domain, which we have called Sps. Although totally unrelated in both sequence and secondary structure, the Rpf and Sps domains fulfil the same function. We propose that these proteins have undergone "non-orthologous domain displacement", a phenomenon akin to "non-orthologous gene displacement" that has been described previously. Proteins containing the Sps domain are widely distributed throughout the firmicutes and they too fall into a number of distinct subfamilies. Comparative analysis of the accessory domains in the Rpf and Sps proteins, together with their weak similarity to lytic transglycosylases, provide clear evidence that they are muralytic enzymes. Conclusions The results indicate that the firmicute Sps proteins and the actinobacterial Rpf proteins are cognate and that they control bacterial culturability via enzymatic modification of the bacterial cell envelope.

  13. Combinatorial regulation of meiotic holliday junction resolution in C. elegans by HIM-6 (BLM helicase, SLX-4, and the SLX-1, MUS-81 and XPF-1 nucleases.

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    Ana Agostinho

    Full Text Available Holliday junctions (HJs are cruciform DNA structures that are created during recombination events. It is a matter of considerable importance to determine the resolvase(s that promote resolution of these structures. We previously reported that C. elegans GEN-1 is a symmetrically cleaving HJ resolving enzyme required for recombinational repair, but we could not find an overt role in meiotic recombination. Here we identify C. elegans proteins involved in resolving meiotic HJs. We found no evidence for a redundant meiotic function of GEN-1. In contrast, we discovered two redundant HJ resolution pathways likely coordinated by the SLX-4 scaffold protein and also involving the HIM-6/BLM helicase. SLX-4 associates with the SLX-1, MUS-81 and XPF-1 nucleases and has been implicated in meiotic recombination in C. elegans. We found that C. elegans [mus-81; xpf-1], [slx-1; xpf-1], [mus-81; him-6] and [slx-1; him-6] double mutants showed a similar reduction in survival rates as slx-4. Analysis of meiotic diakinesis chromosomes revealed a distinct phenotype in these double mutants. Instead of wild-type bivalent chromosomes, pairs of "univalents" linked by chromatin bridges occur. These linkages depend on the conserved meiosis-specific transesterase SPO-11 and can be restored by ionizing radiation, suggesting that they represent unresolved meiotic HJs. This suggests the existence of two major resolvase activities, one provided by XPF-1 and HIM-6, the other by SLX-1 and MUS-81. In all double mutants crossover (CO recombination is reduced but not abolished, indicative of further redundancy in meiotic HJ resolution. Real time imaging revealed extensive chromatin bridges during the first meiotic division that appear to be eventually resolved in meiosis II, suggesting back-up resolution activities acting at or after anaphase I. We also show that in HJ resolution mutants, the restructuring of chromosome arms distal and proximal to the CO still occurs, suggesting that

  14. BLM's ecosystem approach to management

    OpenAIRE

    Dombeck, Mike

    1995-01-01

    Ecosystem management is about maintaining the health, diversity, and productivity of the land, i.e., clean water, abundant native perennial grasses, sustainable fish populations, healthy watersheds. We will use the ecosystem approach to streamline administrative processes and improve fiscal and environmental accountability. It involves coordinated planning at the local level, forming partnerships, and using good information to manage the land Education is key. The principles of ecosystem mana...

  15. Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs

    Indian Academy of Sciences (India)

    Aditya Kumar; Manju Bansal

    2012-07-01

    Promoter regions in the genomes of all domains of life show similar trends in several structural properties such as stability, bendability, curvature, etc. In current study we analysed the stability and bendability of various classes of promoter regions (based on the recent identification of different classes of transcription start sites) of Helicobacter pylori 26695 strain. It is found that primary TSS and operon-associated TSS promoters show significantly strong features in their promoter regions. DNA free-energy-based promoter prediction tool PromPredict was used to annotate promoters of different classes, and very high recall values (∼80%) are obtained for primary TSS. Orthologous genes from other strains of H. pylori show conservation of structural properties in promoter regions as well as coding regions. PromPredict annotates promoters of orthologous genes with very high recall and precision.

  16. Set Domain-Dependent Regulation of Transcriptional Silencing and Growth Control by SUV39H1, a Mammalian Ortholog of Drosophila Su(var)3-9

    OpenAIRE

    Firestein, Ron; Cui, Xiangmin; Huie, Phil; Cleary, Michael L.

    2000-01-01

    Mammalian SET domain-containing proteins define a distinctive class of chromatin-associated factors that are targets for growth control signals and oncogenic activation. SUV39H1, a mammalian ortholog of Drosophila Su(var)3-9, contains both SET and chromo domains, signature motifs for proteins that contribute to epigenetic control of gene expression through effects on the regional organization of chromatin structure. In this report we demonstrate that SUV39H1 represses transcription in a trans...

  17. Lack of Benefit of Early Intervention with Dietary Flax and Fish Oil and Soy Protein in Orthologous Rodent Models of Human Hereditary Polycystic Kidney Disease

    Science.gov (United States)

    Monirujjaman, Md; Gabbs, Melissa

    2016-01-01

    Rationale for dietary advice in polycystic kidney disease (PKD) is based in part on animal studies that have examined non-orthologous models with progressive development of cystic disease. Since no model completely mimics human PKD, the purpose of the current studies was to examine the effects of dietary soy protein (compared to casein) or oils enriched in omega-3 fatty acids (fish or flax oil compared to soy oil) on early disease progression in two orthologous models of PKD. The models studied were Pkd2WS25/- mice as a model of autosomal dominant PKD, and PCK rats as a model of autosomal recessive PKD. After 13 weeks of feeding, dietary fish (but not flax) oil resulted in larger kidneys and greater kidney water content in female Pkd2WS25/- compared to control mice. After 12 weeks of feeding male PCK compared to control rats, both fish and flax compared to soy oil resulted in enlarged kidneys and livers, greater kidney water content and higher kidney cyst area in diseased rats. Dietary soy protein compared to casein had no effects in Pkd2WS25/- compared to control mice. In PCK rats, kidney and liver histology were not improved, but lower proteinuria and higher urine pH suggest that soy protein could be beneficial in the long term. Therefore, in contrast to studies in non-orthologous models during the progressive development phase, these studies in orthologous PKD models do not support dietary advice to increase soy protein or oils enriched in omega-3 oils in early PKD. PMID:27213553

  18. A comparative gene analysis with rice identified orthologous group II HKT genes and their association with Na+ concentration in bread wheat

    OpenAIRE

    Ariyarathna, H. A. Chandima K.; Oldach, Klaus H; Francki, Michael G

    2016-01-01

    Background Although the HKT transporter genes ascertain some of the key determinants of crop salt tolerance mechanisms, the diversity and functional role of group II HKT genes are not clearly understood in bread wheat. The advanced knowledge on rice HKT and whole genome sequence was, therefore, used in comparative gene analysis to identify orthologous wheat group II HKT genes and their role in trait variation under different saline environments. Results The four group II HKTs in rice identifi...

  19. Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint

    OpenAIRE

    Silverman, Joshua; Takai, Hiroyuki; Buonomo, Sara B C; Eisenhaber, Frank; de Lange, Titia

    2004-01-01

    We report on the function of the human ortholog of Saccharomyces cerevisiae Rif1 (Rap1-interacting factor 1). Yeast Rif1 associates with telomeres and regulates their length. In contrast, human Rif1 did not accumulate at functional telomeres, but localized to dysfunctional telomeres and to telomeric DNA clusters in ALT cells, a pattern of telomere association typical of DNA-damage-response factors. After induction of double-strand breaks (DSBs), Rif1 formed foci that colocalized with other DN...

  20. Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species.

    Science.gov (United States)

    Guyot, Romain; Garavito, Andrea; Gavory, Frédérick; Samain, Sylvie; Tohme, Joe; Ghesquière, Alain; Lorieux, Mathias

    2011-01-01

    A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S(1)A, S(1) and S(1)B (called together the S(1) regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S(1) locus (including a putative F-box gene) were proposed, but candidates for S(1)A and S(1)B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S(1) regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S(1)A, S(1) and the majority of the S(1)B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S(1), (2) the multiple duplication and subsequent divergence of the same F-box gene within S(1)A, (3) an interspecific chromosomal inversion in S(1)B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S(1) regions. Hence, the S(1) regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the

  1. Patterns of Sequence Divergence and Evolution of the S1 Orthologous Regions between Asian and African Cultivated Rice Species

    Science.gov (United States)

    Gavory, Frédérick; Samain, Sylvie; Tohme, Joe; Ghesquière, Alain; Lorieux, Mathias

    2011-01-01

    A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S1A, S1 and S1B (called together the S1 regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S1 locus (including a putative F-box gene) were proposed, but candidates for S1A and S1B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S1 regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S1A, S1 and the majority of the S1B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S1, (2) the multiple duplication and subsequent divergence of the same F-box gene within S1A, (3) an interspecific chromosomal inversion in S1B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S1 regions. Hence, the S1 regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal inversion might participate to

  2. Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species.

    Directory of Open Access Journals (Sweden)

    Romain Guyot

    Full Text Available A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S(1A, S(1 and S(1B (called together the S(1 regions interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S(1 locus (including a putative F-box gene were proposed, but candidates for S(1A and S(1B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S(1 regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S(1A, S(1 and the majority of the S(1B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1 a local invasion of transposable elements around a putative F-box gene within S(1, (2 the multiple duplication and subsequent divergence of the same F-box gene within S(1A, (3 an interspecific chromosomal inversion in S(1B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S(1 regions. Hence, the S(1 regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal

  3. Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa.

    Science.gov (United States)

    Franks, Steven J; Perez-Sweeney, Beatriz; Strahl, Maya; Nowogrodzki, Anna; Weber, Jennifer J; Lalchan, Rebecca; Jordan, Kevin P; Litt, Amy

    2015-01-01

    Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of

  4. DNA microarray data integration by ortholog gene analysis reveals potential molecular mechanisms of estrogen-dependent growth of human uterine fibroids

    Directory of Open Access Journals (Sweden)

    Shou Jianyong

    2007-04-01

    Full Text Available Abstract Background Uterine fibroids or leiomyoma are a common benign smooth muscle tumor. The tumor growth is well known to be estrogen-dependent. However, the molecular mechanisms of its estrogen-dependency is not well understood. Methods Differentially expressed genes in human uterine fibroids were either retrieved from published papers or from our own statistical analysis of downloaded array data. Probes for the same genes on different Affymetrix chips were mapped based on probe comparison information provided by Affymetrix. Genes identified by two or three array studies were submitted for ortholog analysis. Human and rat ortholog genes were identified by using ortholog gene databases, HomoloGene and TOGA and were confirmed by synteny analysis with MultiContigView tool in the Ensembl genome browser. Results By integrated analysis of three recently published DNA microarray studies with human tissue, thirty-eight genes were found to be differentially expressed in the same direction in fibroid compared to adjacent uterine myometrium by at least two research groups. Among these genes, twelve with rat orthologs were identified as estrogen-regulated from our array study investigating uterine expression in ovariectomized rats treated with estrogen. Functional and pathway analyses of the twelve genes suggested multiple molecular mechanisms for estrogen-dependent cell survival and tumor growth. Firstly, estrogen increased expression of the anti-apoptotic PCP4 gene and suppressed the expression of growth inhibitory receptors PTGER3 and TGFBR2. Secondly, estrogen may antagonize PPARγ signaling, thought to inhibit fibroid growth and survival, at two points in the PPAR pathway: 1 through increased ANXA1 gene expression which can inhibit phospholipase A2 activity and in turn decrease arachidonic acid synthesis, and 2 by decreasing L-PGDS expression which would reduce synthesis of PGJ2, an endogenous ligand for PPARγ. Lastly, estrogen affects retinoic

  5. A role in immunity for Arabidopsis cysteine protease RD21, the ortholog of the tomato immune protease C14.

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    Takayuki Shindo

    Full Text Available Secreted papain-like Cys proteases are important players in plant immunity. We previously reported that the C14 protease of tomato is targeted by cystatin-like EPIC proteins that are secreted by the oomycete pathogen Phytophthora infestans (Pinf during infection. C14 has been under diversifying selection in wild potato species coevolving with Pinf and reduced C14 levels result in enhanced susceptibility for Pinf. Here, we investigated the role C14-EPIC-like interactions in the natural pathosystem of Arabidopsis with the oomycete pathogen Hyaloperonospora arabidopsidis (Hpa. In contrast to the Pinf-solanaceae pathosystem, the C14 orthologous protease of Arabidopsis, RD21, does not evolve under diversifying selection in Arabidopsis, and rd21 null mutants do not show phenotypes upon compatible and incompatible Hpa interactions, despite the evident lack of a major leaf protease. Hpa isolates express highly conserved EPIC-like proteins during infections, but it is unknown if these HpaEPICs can inhibit RD21 and one of these HpaEPICs even lacks the canonical cystatin motifs. The rd21 mutants are unaffected in compatible and incompatible interactions with Pseudomonas syringae pv. tomato, but are significantly more susceptible for the necrotrophic fungal pathogen Botrytis cinerea, demonstrating that RD21 provides immunity to a necrotrophic pathogen.

  6. Expression of an ortholog of replication protein A1 (RPA1) is induced by gibberellin in deepwater rice

    Science.gov (United States)

    van der Knaap, Esther; Jagoueix, Sandrine; Kende, Hans

    1997-01-01

    Internodes of deepwater rice are induced to grow rapidly when plants become submerged. This adaptation enables deepwater rice to keep part of its foliage above the rising flood waters during the monsoon season and to avoid drowning. This growth response is, ultimately, elicited by the plant hormone gibberellin (GA). The primary target tissue for GA action is the intercalary meristem of the internode. Using differential display of mRNA, we have isolated a number of genes whose expression in the intercalary meristem is regulated by GA. The product of one of these genes was identified as an ortholog of replication protein A1 (RPA1). RPA is a heterotrimeric protein involved in DNA replication, recombination, and repair and also in regulation of transcription. A chimeric construct, in which the single-stranded DNA-binding domain of rice RPA1 was spliced into the corresponding region of yeast RPA1, was able to complement a yeast rpa1 mutant. The transcript level of rice RPA1 is high in tissues containing dividing cells. RPA1 mRNA levels increase rapidly in the intercalary meristem during submergence and treatment with GA before the increase in the level of histone H3 mRNA, a marker for DNA replication. PMID:9275237

  7. Serine- and threonine/valine-dependent activation of PDK and Tor orthologs converge on Sch9 to promote aging.

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    Mario G Mirisola

    2014-02-01

    Full Text Available Dietary restriction extends longevity in organisms ranging from bacteria to mice and protects primates from a variety of diseases, but the contribution of each dietary component to aging is poorly understood. Here we demonstrate that glucose and specific amino acids promote stress sensitization and aging through the differential activation of the Ras/cAMP/PKA, PKH1/2 and Tor/S6K pathways. Whereas glucose sensitized cells through a Ras-dependent mechanism, threonine and valine promoted cellular sensitization and aging primarily by activating the Tor/S6K pathway and serine promoted sensitization via PDK1 orthologs Pkh1/2. Serine, threonine and valine activated a signaling network in which Sch9 integrates TORC1 and Pkh signaling via phosphorylation of threonines 570 and 737 and promoted intracellular relocalization and transcriptional inhibition of the stress resistance protein kinase Rim15. Because of the conserved pro-aging role of nutrient and growth signaling pathways in higher eukaryotes, these results raise the possibility that similar mechanisms contribute to aging in mammals.

  8. Serine- and threonine/valine-dependent activation of PDK and Tor orthologs converge on Sch9 to promote aging.

    Science.gov (United States)

    Mirisola, Mario G; Taormina, Giusi; Fabrizio, Paola; Wei, Min; Hu, Jia; Longo, Valter D

    2014-02-01

    Dietary restriction extends longevity in organisms ranging from bacteria to mice and protects primates from a variety of diseases, but the contribution of each dietary component to aging is poorly understood. Here we demonstrate that glucose and specific amino acids promote stress sensitization and aging through the differential activation of the Ras/cAMP/PKA, PKH1/2 and Tor/S6K pathways. Whereas glucose sensitized cells through a Ras-dependent mechanism, threonine and valine promoted cellular sensitization and aging primarily by activating the Tor/S6K pathway and serine promoted sensitization via PDK1 orthologs Pkh1/2. Serine, threonine and valine activated a signaling network in which Sch9 integrates TORC1 and Pkh signaling via phosphorylation of threonines 570 and 737 and promoted intracellular relocalization and transcriptional inhibition of the stress resistance protein kinase Rim15. Because of the conserved pro-aging role of nutrient and growth signaling pathways in higher eukaryotes, these results raise the possibility that similar mechanisms contribute to aging in mammals. PMID:24516402

  9. Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII markers

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    Felix Enciso-Rodríguez

    2010-01-01

    Full Text Available The Lulo or naranjilla (Solanum quitoense Lam. and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt. are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32 and tree tomatoes (n = 30 through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII in other Solanaceae (Asterid species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested and tree tomatoes (26 out of 41 for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with F ST > 0.90, which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.

  10. TP0326, a Treponema pallidum β-Barrel Assembly Machinery A (BamA) Ortholog and Rare Outer Membrane Protein

    Science.gov (United States)

    Desrosiers, Daniel C.; Anand, Arvind; Luthra, Amit; Dunham-Ems, Star M; LeDoyt, Morgan; Cummings, Michael A. D.; Eshghi, Azad; Cameron, Caroline E.; Cruz, Adriana R.; Salazar, Juan C.; Caimano, Melissa J.; Radolf, Justin D.

    2011-01-01

    SUMMARY Definitive identification of Treponema pallidum (Tp) rare outer membrane proteins (OMPs) has long eluded researchers. TP0326, the sole protein in Tp with sequence homology to a Gram-negative OMP, belongs to the BamA family of proteins essential for OM biogenesis. Structural modeling predicted that five polypeptide transport-associated (POTRA) domains comprise the N-terminus of TP0326, while the C-terminus forms an 18-stranded amphipathic β-barrel. Circular dichroism, heat-modifiability by SDS-PAGE, Triton X-114 phase partitioning and liposome incorporation supported these topological predictions and confirmed that the β-barrel is responsible for the native protein's amphiphilicity. Expression analyses revealed that native TP0326 is expressed at low abundance, while a protease-surface accessibility assay confirmed surface exposure. Size-exclusion chromatography and blue native polyacrylamide gel electrophoresis revealed a modular Bam complex in Tp considerably larger than that of E. coli. Non-orthologous ancillary factors and self-association of TP0326 via its β-barrel may both contribute to the Bam complex. Tp-infected rabbits mount a vigorous antibody response to both POTRA and β-barrel portions of TP0326, whereas humans with secondary syphilis respond predominantly to POTRA. The syphilis spirochete appears to have devised a stratagem for harnessing the Bam pathway while satisfying its need to limit surface antigenicity. PMID:21488980

  11. N15 Cro And Gamma Cro Orthologous DNA-Binding Domains With Completely Different But Equally Effective Homodimer Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Dubrava, M.S.; Ingram, W.M.; Roberts, S.A.; Weichsel, A.; Montfort, W.R.; Cordes, M.H.J.

    2009-05-18

    Bacteriophage Cro proteins bind to target DNA as dimers but do not all dimerize with equal strength, and differ in fold in the region of the dimer interface. We report the structure of the Cro protein from Enterobacteria phage N15 at 1.05 {angstrom} resolution. The subunit fold contains five alpha-helices and is closely similar to the structure of P22 Cro (1.3 {angstrom} backbone room mean square difference over 52 residues), but quite different from that of lambda Cro, a structurally diverged member of this family with a mixed alpha-helix/beta-sheet fold. N15 Cro crystallizes as a biological dimer with an extensive interface (1303 {angstrom}{sub 2} change in accessible surface area per dimer) and also dimerizes in solution with a K(d) of 5.1 {+-} 1.5 {micro}M. Its dimerization is much stronger than that of its structural homolog P22 Cro, which does not self-associate detectably in solution. Instead, the level of self-association and interfacial area for N15 Cro is similar to that of lambda Cro, even though these two orthologs do not share the same fold and have dimer interfaces that are qualitatively different in structure. The common Cro ancestor is thought to be an all-helical monomer similar to P22 Cro. We propose that two Cro descendants independently developed stronger dimerization by entirely different mechanisms.

  12. Vaccine Efficacy of Bm86 Ortholog of H. a. anatolicum, rHaa86 Expressed in Prokaryotic Expression System

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    P. Azhahianambi

    2009-01-01

    Full Text Available The use of tick vaccine in controlling ticks and tick borne diseases has been proved effective in integrated tick management format. For the control of H. a. anatolicum, Bm86 ortholog of H. a. anatolicum was cloned and expressed as fusion protein in E. coli as E. coli-pETHaa86. The molecular weight of the rHaa86 was 97 kDa with a 19 kDa fusion tag of thioredoxin protein. The expressed protein was characterized immunologically and vaccine efficacy was evaluated. After 120 hours of challenge, only 26% tick could successfully fed on immunized animals. Besides significant reduction in feeding percentages, a significant reduction of 49.6 mg; P<.01 in the weight of fed females in comparison to the females fed on control animals was recorded. Following oviposition, a significant reduction of 68.1 mg; P<.05 in the egg masses of ticks fed on immunized animals in comparison to the ticks fed on control animals was noted. The reduction of number of females, mean weight of eggs, adult females and efficacy of immunogen were 73.8%, 31.3%, 15.8%, and 82.3%, respectively. The results indicated the possibility of development of rHaa86 based vaccine as a component of integrated control of tick species.

  13. Vaccine Efficacy of Bm86 Ortholog of H. a. anatolicum, rHaa86 Expressed in Prokaryotic Expression System.

    Science.gov (United States)

    Azhahianambi, P; Ray, D D; Chaudhuri, Pallab; Gupta, Rohita; Ghosh, Srikanta

    2009-01-01

    The use of tick vaccine in controlling ticks and tick borne diseases has been proved effective in integrated tick management format. For the control of H. a. anatolicum, Bm86 ortholog of H. a. anatolicum was cloned and expressed as fusion protein in E. coli as E. coli-pETHaa86. The molecular weight of the rHaa86 was 97 kDa with a 19 kDa fusion tag of thioredoxin protein. The expressed protein was characterized immunologically and vaccine efficacy was evaluated. After 120 hours of challenge, only 26% tick could successfully fed on immunized animals. Besides significant reduction in feeding percentages, a significant reduction of 49.6 mg; P < .01 in the weight of fed females in comparison to the females fed on control animals was recorded. Following oviposition, a significant reduction of 68.1 mg; P < .05 in the egg masses of ticks fed on immunized animals in comparison to the ticks fed on control animals was noted. The reduction of number of females, mean weight of eggs, adult females and efficacy of immunogen were 73.8%, 31.3%, 15.8%, and 82.3%, respectively. The results indicated the possibility of development of rHaa86 based vaccine as a component of integrated control of tick species. PMID:20721331

  14. Telmisartan Ameliorates Fibrocystic Liver Disease in an Orthologous Rat Model of Human Autosomal Recessive Polycystic Kidney Disease

    Science.gov (United States)

    Yoshihara, Daisuke; Kugita, Masanori; Sasaki, Mai; Horie, Shigeo; Nakanishi, Koichi; Abe, Takaaki; Aukema, Harold M.; Yamaguchi, Tamio; Nagao, Shizuko

    2013-01-01

    Human autosomal recessive polycystic kidney disease (ARPKD) produces kidneys which are massively enlarged due to multiple cysts, hypertension, and congenital hepatic fibrosis characterized by dilated bile ducts and portal hypertension. The PCK rat is an orthologous model of human ARPKD with numerous fluid-filled cysts caused by stimulated cellular proliferation in the renal tubules and hepatic bile duct epithelia, with interstitial fibrosis developed in the liver. We previously reported that a peroxisome proliferator activated receptor (PPAR)-γ full agonist ameliorated kidney and liver disease in PCK rats. Telmisartan is an angiotensin receptor blocker (ARB) used widely as an antihypertensive drug and shows partial PPAR-γ agonist activity. It also has nephroprotective activity in diabetes and renal injury and prevents the effects of drug-induced hepatotoxicity and hepatic fibrosis. In the present study, we determined whether telmisartan ameliorates progression of polycystic kidney and fibrocystic liver disease in PCK rats. Five male and 5 female PCK and normal control (+/+) rats were orally administered 3 mg/kg telmisartan or vehicle every day from 4 to 20 weeks of age. Treatment with telmisartan decreased blood pressure in both PCK and +/+ rats. Blood levels of aspartate amino transferase, alanine amino transferase and urea nitrogen were unaffected by telmisartan treatment. There was no effect on kidney disease progression, but liver weight relative to body weight, liver cystic area, hepatic fibrosis index, expression levels of Ki67 and TGF-β, and the number of Ki67- and TGF-β-positive interstitial cells in the liver were significantly decreased in telmisartan-treated PCK rats. Therefore, telmisartan ameliorates congenital hepatic fibrosis in ARPKD, possibly through the inhibition of signaling cascades responsible for cellular proliferation and interstitial fibrosis in PCK rats. The present results support the potential therapeutic use of ARBs for the

  15. Saccharomyces cerevisiae Bat1 and Bat2 aminotransferases have functionally diverged from the ancestral-like Kluyveromyces lactis orthologous enzyme.

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    Maritrini Colón

    Full Text Available BACKGROUND: Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. PRINCIPAL FINDINGS: Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs. This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1, while catabolic substrates are accumulated in the cytosol (Bat2. Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. CONCLUSIONS: Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the

  16. Fermitins, the orthologs of mammalian Kindlins, regulate the development of a functional cardiac syncytium in Drosophila melanogaster.

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    James H Catterson

    Full Text Available The vertebrate Kindlins are an evolutionarily conserved family of proteins critical for integrin signalling and cell adhesion. Kindlin-2 (KIND2 is associated with intercalated discs in mice, suggesting a role in cardiac syncytium development; however, deficiency of Kind2 leads to embryonic lethality. Morpholino knock-down of Kind2 in zebrafish has a pleiotropic effect on development that includes the heart. It therefore remains unclear whether cardiomyocyte Kind2 expression is required for cardiomyocyte junction formation and the development of normal cardiac function. To address this question, the expression of Fermitin 1 and Fermitin 2 (Fit1, Fit2, the two Drosophila orthologs of Kind2, was silenced in Drosophila cardiomyocytes. Heart development was assessed in adult flies by immunological methods and videomicroscopy. Silencing both Fit1 and Fit2 led to a severe cardiomyopathy characterised by the failure of cardiomyocytes to develop as a functional syncytium and loss of synchrony between cardiomyocytes. A null allele of Fit1 was generated but this had no impact on the heart. Similarly, the silencing of Fit2 failed to affect heart function. In contrast, the silencing of Fit2 in the cardiomyocytes of Fit1 null flies disrupted syncytium development, leading to severe cardiomyopathy. The data definitively demonstrate a role for Fermitins in the development of a functional cardiac syncytium in Drosophila. The findings also show that the Fermitins can functionally compensate for each other in order to control syncytium development. These findings support the concept that abnormalities in cardiomyocyte KIND2 expression or function may contribute to cardiomyopathies in humans.

  17. Expansion and diversification of BTL ring-H2 ubiquitin ligases in angiosperms: putative Rabring7/BCA2 orthologs.

    Science.gov (United States)

    Aguilar-Hernández, Victor; Medina, Juliana; Aguilar-Henonin, Laura; Guzmán, Plinio

    2013-01-01

    RING finger E3 ligases are components of the ubiquitin proteasome system (UPS) that mediate the transfer of ubiquitin to substrates. Single-subunit RING finger E3s binds the E2 ubiquitin-conjugating enzyme and contains recognition sequences for the substrate within the same polypeptide. Here we describe the characterization of a class of RING finger E3 ligases that is conserved among eukaryotes. This class encodes a RING-H2 domain related in sequence to the ATL RING-H2 domain, another class of E3 ligases, and a C2/C2 zing finger at the amino-terminus, formerly described as BZF. In viridiplantae (green algae and land plants), we designed this family as BTL for BZF ATLs. BTLs are putative orthologs of the mammalian Rabring7/BCA2 RING-H2 E3s that have expanded in angiosperms. They are found in numbers ranging from three to thirty-one, which is in contrast to the one to three members normally found in animals, fungi, and protists. Furthermore, the number of sequence LOGOs generated in angiosperms is four times greater than that in other eukaryotes. In contrast to ATLs, which show expansion by tandem duplication, tandemly duplicated BTLs are scarce. The mode of action of Rabring7/BCA2 and BTLs may be similar since both the Rabring7/BCA2 BZF and the ath|BTL4 BZF are likely to mediate the binding of ubiquitin. This study introduces valuable information on the evolution and domain structure of the Rabring7/BCA2/BTL class of E3 ligases which may be important for core eukaryotic genes. PMID:23951330

  18. New species of Ehrlichia isolated from Rhipicephalus (Boophilus microplus shows an ortholog of the E. canis major immunogenic glycoprotein gp36 with a new sequence of tandem repeats

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    Cruz Alejandro Cabezas

    2012-12-01

    Full Text Available Abstract Background Ehrlichia species are the etiological agents of emerging and life-threatening tick-borne human zoonoses that inflict serious and fatal infections in companion animals and livestock. The aim of this paper was to phylogeneticaly characterise a new species of Ehrlichia isolated from Rhipicephalus (Boophilus microplus from Minas Gerais, Brazil. Methods The agent was isolated from the hemolymph of Rhipicephalus (B. microplus engorged females that had been collected from naturally infested cattle in a farm in the state of Minas Gerais, Brazil. This agent was then established and cultured in IDE8 tick cells. The molecular and phylogenetic analysis was based on 16S rRNA, groEL, dsb, gltA and gp36 genes. We used the maximum likelihood method to construct the phylogenetic trees. Results The phylogenetic trees based on 16S rRNA, groEL, dsb and gltA showed that the Ehrlichia spp isolated in this study falls in a clade separated from any previously reported Ehrlichia spp. The molecular analysis of the ortholog of gp36, the major immunoreactive glycoproteins in E. canis and ortholog of the E. chaffeensis gp47, showed a unique tandem repeat of 9 amino acids (VPAASGDAQ when compared with those reported for E. canis, E. chaffeensis and the related mucin-like protein in E. ruminantium. Conclusions Based on the molecular and phylogenetic analysis of the 16S rRNA, groEL, dsb and gltA genes we concluded that this tick-derived microorganism isolated in Brazil is a new species, named E. mineirensis (UFMG-EV, with predicted novel antigenic properties in the gp36 ortholog glycoprotein. Further studies on this new Ehrlichia spp should address questions about its transmissibility by ticks and its pathogenicity for mammalian hosts.

  19. Cloning and Function Characteristic of GhDWF 4,an Ortholog of Arabidopsis DWF 4 from Upland Cotton (Gossypium hirsutum L.)

    Institute of Scientific and Technical Information of China (English)

    HU Ming-yu; LUO Ming; TAN Kun-ling; XIAO Zhong-yi; PEI Yan

    2008-01-01

    @@ As one of the longest cells characterized in plant kingdom,cotton fibers were regarded as an ideal material for studying plant cell growth and development.In recent years,several reports revealed that brassinosteroids (BRs) play an important role in the growth and development of cotton fiber.To further investigate the effect of BRs on fiber cell development and illuminate the mechanism of BRs action,we cloned GhDWF4,an ortholog of Arabidopsis DWF4 from upland cotton (Gossypium hirsuturn L.).

  20. The Structure of YqeH: AN AtNOS1/AtNOA1 ORTHOLOG THAT COUPLES GTP HYDROLYSIS TO MOLECULAR RECOGNITION*S⃞

    OpenAIRE

    Sudhamsu, Jawahar; Lee, Gyu In; Klessig, Daniel F; Crane, Brian R.

    2008-01-01

    AtNOS1/AtNOA1 was identified as a nitric oxide-generating enzyme in plants, but that function has recently been questioned. To resolve issues surrounding AtNOA1 activity, we report the biochemical properties and a 2.36 Å resolution crystal structure of a bacterial AtNOA1 ortholog (YqeH). Geobacillus YqeH fused to a putative AtNOA1 leader peptide complements growth and morphological defects of Atnoa1 mutant plants. YqeH does not synthesize nitric oxide from l-arginine b...

  1. The Maize PI/GLO Ortholog Zmm16/sterile tassel silky ear1 Interacts with the Zygomorphy and Sex Determination Pathways in Flower Development.

    Science.gov (United States)

    Bartlett, Madelaine E; Williams, Steven K; Taylor, Zac; DeBlasio, Stacy; Goldshmidt, Alexander; Hall, Darren H; Schmidt, Robert J; Jackson, David P; Whipple, Clinton J

    2015-11-01

    In monocots and eudicots, B class function specifies second and third whorl floral organ identity as described in the classic ABCE model. Grass B class APETALA3/DEFICIENS orthologs have been functionally characterized; here, we describe the positional cloning and characterization of a maize (Zea mays) PISTILLATA/GLOBOSA ortholog Zea mays mads16 (Zmm16)/sterile tassel silky ear1 (sts1). We show that, similar to many eudicots, all the maize B class proteins bind DNA as obligate heterodimers and positively regulate their own expression. However, sts1 mutants have novel phenotypes that provide insight into two derived aspects of maize flower development: carpel abortion and floral asymmetry. Specifically, we show that carpel abortion acts downstream of organ identity and requires the growth-promoting factor grassy tillers1 and that the maize B class genes are expressed asymmetrically, likely in response to zygomorphy of grass floral primordia. Further investigation reveals that floral phyllotactic patterning is also zygomorphic, suggesting significant mechanistic differences with the well-characterized models of floral polarity. These unexpected results show that despite extensive study of B class gene functions in diverse flowering plants, novel insights can be gained from careful investigation of homeotic mutants outside the core eudicot model species. PMID:26518212

  2. Molecular cloning, genomic structure, and genetic mapping of two Rdl-orthologous genes of GABA receptors in the diamondback moth, Plutella xylostella.

    Science.gov (United States)

    Yuan, Guorui; Gao, Weiyue; Yang, Yihua; Wu, Yidong

    2010-06-01

    The Resistance to dieldrin (Rdl) gene encodes a subunit of the insect gamma-aminobutyric acid (GABA) receptor. Cyclodiene resistance in many insects is associated with replacement of a single amino acid (alanine at position 302) with either a serine or a glycine in the Rdl gene. Two Rdl-orthologous genes of GABA receptors (PxGABARalpha1 and PxGABARalpha2) were cloned and sequenced from a susceptible strain (Roth) of Plutella xylostella. PxGABARalpha1 and PxGABARalpha2 showed 84% and 77% identity with the Rdl gene of Drosophila melanogaster at an amino acid level, respectively. The coding regions of PxGABARalpha1 and PxGABARalpha2 both comprise ten exons, with two alternative RNA-splicing forms in exon 3 of both genes. At the orthologous position of alanine-302 in D. melanogaster Rdl, PxGABARalpha1 has a conserved alanine at position 282. PxGABARalpha2 has a serine instead of an alanine at the equivalent position. With two informative DNA markers, both PxGABARalpha1 and PxGABARalpha2 were mapped onto the Z chromosome of P. xylostella. PMID:20513056

  3. acon-3, the Neurospora crassa ortholog of the developmental modifier, medA, complements the conidiation defect of the Aspergillus nidulans mutant.

    Science.gov (United States)

    Chung, Da-Woon; Greenwald, Charles; Upadhyay, Srijana; Ding, Shengli; Wilkinson, Heather H; Ebbole, Daniel J; Shaw, Brian D

    2011-04-01

    Aspergillus nidulans and Neurospora crassa are ascomycetes that produce asexual spores through morphologically distinct processes. MedA, a protein with unknown function, is required for normal asexual and sexual development in A. nidulans. We determined that the N. crassa ortholog of medA is acon-3, a gene required for early conidiophore development and female fertility. To test hypotheses about the evolutionary origins of asexual development in distinct fungal lineages it is important to understand the degree of conservation of developmental regulators. The amino acid sequences of A. nidulans MedA and N. crassa ACON-3 shared 37% identity and 51% similarity. acon-3 is induced at late time points of conidiation. In contrast, medA is constitutively expressed and MedA protein localizes to nuclei in all tissue types. Nonetheless, expression of acon-3 using its native promoter complemented the conidiation defects of the A. nidulans ΔmedA and medA15 mutants. We conclude that the biochemical activity of the medA orthologs is conserved for conidiation. PMID:21220038

  4. An ortholog of farA of Aspergillus nidulans is implicated in the transcriptional activation of genes involved in fatty acid utilization in the yeast Yarrowia lipolytica

    International Nuclear Information System (INIS)

    Research highlights: → POR1 is a Yarrowia lipolytica ortholog of farA involved in fatty acid response in A. nidulans. → Deletion of POR1 caused growth defects on fatty acids. → Δpor1 strain exhibited defects in the induction of genes involved in fatty acid utilization. -- Abstract: The yeast Yarrowia lipolytica effectively utilizes hydrophobic substrates such as fatty acids and n-alkanes. To identify a gene(s) regulating fatty acid utilization in Y. lipolytica, we first studied homologous genes to OAF1 and PIP2 of Saccharomyces cerevisiae, but their disruption did not change growth on oleic acid at all. We next characterized a Y. lipolytica gene, POR1 (primary oleate regulator 1), an ortholog of farA encoding a transcriptional activator that regulates fatty acid utilization in Aspergillus nidulans. The deletion mutant of POR1 was defective in the growth on various fatty acids, but not on glucose, glycerol, or n-hexadecane. It exhibited slight defect on n-decane. The transcriptional induction of genes involved in β-oxidation and peroxisome proliferation by oleate was distinctly diminished in the Δpor1 strains. These data suggest that POR1 encodes a transcriptional activator widely regulating fatty acid metabolism in Y. lipolytica.

  5. An ortholog of farA of Aspergillus nidulans is implicated in the transcriptional activation of genes involved in fatty acid utilization in the yeast Yarrowia lipolytica

    Energy Technology Data Exchange (ETDEWEB)

    Poopanitpan, Napapol; Kobayashi, Satoshi; Fukuda, Ryouichi; Horiuchi, Hiroyuki [Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 (Japan); Ohta, Akinori, E-mail: aaohta@mail.ecc.u-tokyo.ac.jp [Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 (Japan)

    2010-11-26

    Research highlights: {yields} POR1 is a Yarrowia lipolytica ortholog of farA involved in fatty acid response in A. nidulans. {yields} Deletion of POR1 caused growth defects on fatty acids. {yields} {Delta}por1 strain exhibited defects in the induction of genes involved in fatty acid utilization. -- Abstract: The yeast Yarrowia lipolytica effectively utilizes hydrophobic substrates such as fatty acids and n-alkanes. To identify a gene(s) regulating fatty acid utilization in Y. lipolytica, we first studied homologous genes to OAF1 and PIP2 of Saccharomyces cerevisiae, but their disruption did not change growth on oleic acid at all. We next characterized a Y. lipolytica gene, POR1 (primary oleate regulator 1), an ortholog of farA encoding a transcriptional activator that regulates fatty acid utilization in Aspergillus nidulans. The deletion mutant of POR1 was defective in the growth on various fatty acids, but not on glucose, glycerol, or n-hexadecane. It exhibited slight defect on n-decane. The transcriptional induction of genes involved in {beta}-oxidation and peroxisome proliferation by oleate was distinctly diminished in the {Delta}por1 strains. These data suggest that POR1 encodes a transcriptional activator widely regulating fatty acid metabolism in Y. lipolytica.

  6. Molecular characterization of Bm86 gene orthologs from Hyalomma excavatum, Hyalomma dromedarii and Hyalomma marginatum marginatum and comparison with a vaccine candidate from Hyalomma scupense.

    Science.gov (United States)

    Ben Said, Mourad; Galai, Yousr; Mhadhbi, Moez; Jedidi, Mohamed; de la Fuente, José; Darghouth, Mohamed Aziz

    2012-11-23

    The ixodid ticks from the Hyalomma genus are important pests of livestock, having major medical and veterinary significance in Northern Africa. Beside their direct pathogenic effects, these species are vectors of important diseases of livestock and in some instances of zoonoses. Anti-tick vaccines developed in Australia and Cuba based on the concealed antigen Bm86 have variable efficacy against H. anatolicum and H. dromedarii. This variation in vaccine efficacy could be explained by the variability in protein sequence between the recombinant Bm86 vaccine and Bm86 orthologs expressed in different Hyalomma species. Bm86 orthologs from three Hyalomma tick species were amplified in two overlapping fragments and sequenced. The rate of identity of the amino acid sequence of Hm86, He86 and Hdr86, the orthologs of Bm86, respectively, in H. marginatum marginatum, H. excavatum and H. dromedarii, with the Bm86 proteins from Rhipicephalus microplus (Australia, Argentina and Mozambique) ranged between 60 and 66%. The obtained amino-acid sequences of Hmm86, He86 and Hdr86 were compared with the Hd86-A1 sequence from H. scupense used as an experimental vaccine. The results showed an identity of 91, 88 and 87% for Hmm86, He86 and Hdr86, respectively. A specific program has been used to predict B cells epitopes sites. The comparison of antigenic sites between Hd86-A1 and Hm86/Hdr86/He86 revealed a diversity affecting 4, 8 and 12 antigenic peptides out of a total of 28 antigenic peptides, respectively. When the Bm86 orthologs amplification protocol adopted in this study was applied to H. excavatum, two alleles named He86p2a1 and He86p2a2 were detected in this species. This is the first time that two different alleles of Bm86 gene are recorded in the same tick specimen. He86p2a1 and He86p2a2 showed an amino acid identity of 92%. When He86p2a1 and He86p2a2 were compared to the corresponding sequence of Hd86-A1 protein, an identity of 86.4 and 91.0% was recorded, respectively. When

  7. Expression conservation within the circadian clock of a monocot: natural variation at barley Ppd-H1 affects circadian expression of flowering time genes, but not clock orthologs

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    Campoli Chiara

    2012-06-01

    Full Text Available Abstract Background The circadian clock is an endogenous mechanism that coordinates biological processes with daily changes in the environment. In plants, circadian rhythms contribute to both agricultural productivity and evolutionary fitness. In barley, the photoperiod response regulator and flowering-time gene Ppd-H1 is orthologous to the Arabidopsis core-clock gene PRR7. However, relatively little is known about the role of Ppd-H1 and other components of the circadian clock in temperate crop species. In this study, we identified barley clock orthologs and tested the effects of natural genetic variation at Ppd-H1 on diurnal and circadian expression of clock and output genes from the photoperiod-response pathway. Results Barley clock orthologs HvCCA1, HvGI, HvPRR1, HvPRR37 (Ppd-H1, HvPRR73, HvPRR59 and HvPRR95 showed a high level of sequence similarity and conservation of diurnal and circadian expression patterns, when compared to Arabidopsis. The natural mutation at Ppd-H1 did not affect diurnal or circadian cycling of barley clock genes. However, the Ppd-H1 mutant was found to be arrhythmic under free-running conditions for the photoperiod-response genes HvCO1, HvCO2, and the MADS-box transcription factor and vernalization responsive gene Vrn-H1. Conclusion We suggest that the described eudicot clock is largely conserved in the monocot barley. However, genetic differentiation within gene families and differences in the function of Ppd-H1 suggest evolutionary modification in the angiosperm clock. Our data indicates that natural variation at Ppd-H1 does not affect the expression level of clock genes, but controls photoperiodic output genes. Circadian control of Vrn-H1 in barley suggests that this vernalization responsive gene is also controlled by the photoperiod-response pathway. Structural and functional characterization of the barley circadian clock will set the basis for future studies of the adaptive significance of the circadian clock in

  8. Characterization of gana-1, a Caenorhabditis elegans gene encoding a single ortholog of vertebrate α-galactosidase and α-N-acetylgalactosaminidase

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    Kostrouchová Marta

    2005-01-01

    Full Text Available Abstract Background Human α-galactosidase A (α-GAL and α-N-acetylgalactosaminidase (α-NAGA are presumed to share a common ancestor. Deficiencies of these enzymes cause two well-characterized human lysosomal storage disorders (LSD – Fabry (α-GAL deficiency and Schindler (α-NAGA deficiency diseases. Caenorhabditis elegans was previously shown to be a relevant model organism for several late endosomal/lysosomal membrane proteins associated with LSDs. The aim of this study was to identify and characterize C. elegans orthologs to both human lysosomal luminal proteins α-GAL and α-NAGA. Results BlastP searches for orthologs of human α-GAL and α-NAGA revealed a single C. elegans gene (R07B7.11 with homology to both human genes (α-galactosidase and α-N-acetylgalactosaminidase – gana-1. We cloned and sequenced the complete gana-1 cDNA and elucidated the gene organization. Phylogenetic analyses and homology modeling of GANA-1 based on the 3D structure of chicken α-NAGA, rice α-GAL and human α-GAL suggest a close evolutionary relationship of GANA-1 to both human α-GAL and α-NAGA. Both α-GAL and α-NAGA enzymatic activities were detected in C. elegans mixed culture homogenates. However, α-GAL activity on an artificial substrate was completely inhibited by the α-NAGA inhibitor, N-acetyl-D-galactosamine. A GANA-1::GFP fusion protein expressed from a transgene, containing the complete gana-1 coding region and 3 kb of its hypothetical promoter, was not detectable under the standard laboratory conditions. The GFP signal was observed solely in a vesicular compartment of coelomocytes of the animals treated with Concanamycin A (CON A or NH4Cl, agents that increase the pH of the cellular acidic compartment. Immunofluorescence detection of the fusion protein using polyclonal anti-GFP antibody showed a broader and coarsely granular cytoplasmic expression pattern in body wall muscle cells, intestinal cells, and a vesicular compartment of

  9. Two Poplar Glycosyltransferase Genes, PdGATL1.1 and PdGATL1.2, Are Functional Orthologs to PARVUS/AtGATL 1 in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Yingzhen Kong; Gongke Zhou; Utku Avci; Xiaogang Gu; Chelsea Jones; Yanbin Yin; Ying Xu; Michael G. Hahn

    2009-01-01

    Several genes in Arabidopsis, including PARVUS/AtGATL1, have been implicated in xylan synthesis. However, the biosynthesis of xylan in woody plants, where this polysaccharide is a major component of wood, is poorly understood. Here, we characterize two Populus genes, PdGATL1.1 and PdGATL1.2, the closest orthologs to the Arabidopsis PARVUS/GATL 1 gene, with respect to their gene expression in poplar, their sub-cellular localization, and their ability to complement the parvus mutation in Arabidopsis. Overexpression of the two poplar genes in the parvus mutant rescued most of the defects caused by the parvus mutation, including morphological changes, collapsed xylem, and altered cell wall mono-saccharide composition. Quantitative RT-PCR showed that PdGATL1.1 is expressed most strongly in developing xylem of poplar. In contrast, PdGATL1.2 is expressed much more uniformly in leaf, shoot tip, cortex, phloem, and xylem, and the transcript level of PdGATL1.2 is much lower than that of PdGATL1.1 in all tissues examined. Sub-cellular localization experi-ments showed that these two proteins are localized to both ER and Golgi in comparison with marker proteins resident to these sub-cellular compartments. Our data indicate that PdGATLI.1 and PdGATL1.2 are functional orthologs of PARVUS/ GATL1 and can play a role in xylan synthesis, but may also have role(s) in the synthesis of other wall polymers.

  10. An ortholog of the Leptospira interrogans lipoprotein LipL32 aids in the colonization of Pseudoalteromonas tunicata to host surfaces

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    SuhelenEgan

    2014-07-01

    Full Text Available The bacterium P. tunicata is a common surface colonizer of marine eukaryotes, including the macroalga Ulva australis. Genomic analysis of P. tunicata identified genes potentially involved in surface colonization, including genes with homology to bacterial virulence factors that mediate attachment. Of particular interest is the presence of a gene, designated ptlL32, encoding an ortholog to the Leptospira lipoprotein LipL32, which has been shown to facilitate the interaction of Leptospira sp. with host extracellular matrix (ECM structures and is thought to be an important virulence trait for pathogenic Leptospira. To investigate the role of PtlL32 in the colonization by P. tunicata we constructed and characterized a ΔptlL32 mutant strain. Whilst P. tunicata ΔptlL32 bound to an abiotic surface with the same capacity as the wild type strain, it had a marked effect on the ability of P. tunicata to bind to ECM, suggesting a specific role in attachment to biological surfaces. Loss of PtlL32 also significantly reduced the capacity for P. tunciata to colonize the host algal surface demonstrating a clear role for this protein as a host-colonization factor. PtlL32 appears to have a patchy distribution across specific groups of environmental bacteria and phylogenetic analysis of PtlL32 orthologous proteins from non-Leptospira species suggests it may have been acquired via horizontal gene transfer between distantly related lineages. This study provides the first evidence for an attachment function for a LipL32- like protein outside the Leptospira and thereby contributes to the understanding of host colonization in ecologically distinct bacterial species.

  11. Virus-encoded miR-155 ortholog is an important potential regulator but not essential for the development of lymphomas induced by very virulent Marek's disease virus.

    Science.gov (United States)

    Yu, Zu-Hua; Teng, Man; Sun, Ai-Jun; Yu, Le-Le; Hu, Bo; Qu, Liang-Hu; Ding, Ke; Cheng, Xiang-Chao; Liu, Ju-Xiong; Cui, Zhi-Zhong; Zhang, Gai-Ping; Luo, Jun

    2014-01-01

    The microRNA (miRNA) mdv1-miR-M4, a functional miR-155 ortholog encoded by oncogenic Marek's disease virus (MDV), has previously been suggested to be involved in MDV pathogenesis. Using the technique of bacterial artificial chromosome mutagenesis, we have presently evaluated the potential role of mdv1-miR-M4 in the oncogenesis of the very virulent (vv) MDV strain GX0101. Unexpectedly, deletions of the Meq-cluster or mdv1-miR-M4 alone from the viral genome strongly decreased rather than abolished its oncogenicity. Compared to GX0101, mortalities of mutants GXΔmiR-M4 and GXΔMeq-miRs were reduced from 100% to 18% and 4%, coupled with the gross tumor incidence reduction from 28% to 22% and 8%, respectively. Our data suggests that the mdv1-miR-M4 is possibly an important regulator in the development of Marek's disease (MD) lymphomas but is not essential for the oncogenicity of vvMDV. In addition, some of the other Meq-clustered miRNAs may also play potentially critical roles in vvMDV induction of lymphomas. PMID:24314636

  12. The Caenorhabditis elegans iodotyrosine deiodinase ortholog SUP-18 functions through a conserved channel SC-box to regulate the muscle two-pore domain potassium channel SUP-9.

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    Ignacio Perez de la Cruz

    2014-02-01

    Full Text Available Loss-of-function mutations in the Caenorhabditis elegans gene sup-18 suppress the defects in muscle contraction conferred by a gain-of-function mutation in SUP-10, a presumptive regulatory subunit of the SUP-9 two-pore domain K(+ channel associated with muscle membranes. We cloned sup-18 and found that it encodes the C. elegans ortholog of mammalian iodotyrosine deiodinase (IYD, an NADH oxidase/flavin reductase that functions in iodine recycling and is important for the biosynthesis of thyroid hormones that regulate metabolism. The FMN-binding site of mammalian IYD is conserved in SUP-18, which appears to require catalytic activity to function. Genetic analyses suggest that SUP-10 can function with SUP-18 to activate SUP-9 through a pathway that is independent of the presumptive SUP-9 regulatory subunit UNC-93. We identified a novel evolutionarily conserved serine-cysteine-rich region in the C-terminal cytoplasmic domain of SUP-9 required for its specific activation by SUP-10 and SUP-18 but not by UNC-93. Since two-pore domain K(+ channels regulate the resting membrane potentials of numerous cell types, we suggest that the SUP-18 IYD regulates the activity of the SUP-9 channel using NADH as a coenzyme and thus couples the metabolic state of muscle cells to muscle membrane excitability.

  13. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.

    Science.gov (United States)

    Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai

    2012-01-01

    The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis. PMID:23166835

  14. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.

    Directory of Open Access Journals (Sweden)

    Jingli Wei

    Full Text Available The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG Release2.3 Predicted CDS (SL2.40 discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2% of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis.

  15. Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley.

    Science.gov (United States)

    Barboza, Luis; Effgen, Sigi; Alonso-Blanco, Carlos; Kooke, Rik; Keurentjes, Joost J B; Koornneef, Maarten; Alcázar, Rubén

    2013-09-24

    Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5), which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis, are found in different populations from southern, western, and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection, whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore, because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes, this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants. PMID:24023067

  16. The orthologous Tbx transcription factors Omb and TBX2 induce epithelial cell migration and extrusion in vivo without involvement of matrix metalloproteinases

    Science.gov (United States)

    Shen, Jie; Lu, Juan; Sui, Liyuan; Wang, Dan; Yin, Meizhen; Hoffmann, Inka; Legler, Anne; Pflugfelder, Gert O.

    2014-01-01

    The transcription factors TBX2 and TBX3 are overexpressed in various human cancers. Here, we investigated the effect of overexpressing the orthologous Tbx genes Drosophila optomotor-blind (omb) and human TBX2 in the epithelium of the Drosophila wing imaginal disc and observed two types of cell motility. Omb/TBX2 overexpressing cells could move within the plane of the epithelium. Invasive cells migrated long-distance as single cells retaining or regaining normal cell shape and apico-basal polarity in spite of attenuated apical DE-cadherin concentration. Inappropriate levels of DE-cadherin were sufficient to drive cell migration in the wing disc epithelium. Omb/TBX2 overexpression and reduced DE-cadherin-dependent adhesion caused the formation of actin-rich lateral cell protrusions. Omb/TBX2 overexpressing cells could also delaminate basally, penetratingthe basal lamina, however, without degradation of extracellular matrix. Expression of Timp, an inhibitor of matrix metalloproteases, blocked neither intraepithelial motility nor basal extrusion. Our results reveal an MMP-independent mechanism of cell invasion and suggest a conserved role of Tbx2-related proteins in cell invasion and metastasis-related processes. PMID:25344916

  17. Characterization of a highly conserved binding site of Mlh1 required for exonuclease I-dependent mismatch repair

    DEFF Research Database (Denmark)

    Dherin, Claudine; Gueneau, Emeric; Francin, Mathilde;

    2009-01-01

    Mlh1 is an essential factor of mismatch repair (MMR) and meiotic recombination. It interacts through its C-terminal region with MutL homologs and proteins involved in DNA repair and replication. In this study, we identified the site of yeast Mlh1 critical for the interaction with Exo1, Ntg2, and...... Sgs1 proteins, designated as site S2 by reference to the Mlh1/Pms1 heterodimerization site S1. We show that site S2 is also involved in the interaction between human MLH1 and EXO1 or BLM. Binding at this site involves a common motif on Mlh1 partners that we called the MIP-box for the Mlh1 interacting...... protein box. Direct and specific interactions between yeast Mlh1 and peptides derived from Exo1, Ntg2, and Sgs1 and between human MLH1 and peptide derived from EXO1 and BLM were measured with K(d) values ranging from 8.1 to 17.4 microM. In Saccharomyces cerevisiae, a mutant of Mlh1 targeted at site S2...

  18. Endo-(1,4-β-Glucanase gene families in the grasses: temporal and spatial Co-transcription of orthologous genes1

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    Buchanan Margaret

    2012-12-01

    Full Text Available Abstract Background Endo-(1,4-β-glucanase (cellulase glycosyl hydrolase GH9 enzymes have been implicated in several aspects of cell wall metabolism in higher plants, including cellulose biosynthesis and degradation, modification of other wall polysaccharides that contain contiguous (1,4-β-glucosyl residues, and wall loosening during cell elongation. Results The endo-(1,4-β-glucanase gene families from barley (Hordeum vulgare, maize (Zea mays, sorghum (Sorghum bicolor, rice (Oryza sativa and Brachypodium (Brachypodium distachyon range in size from 23 to 29 members. Phylogenetic analyses show variations in clade structure between the grasses and Arabidopsis, and indicate differential gene loss and gain during evolution. Map positions and comparative studies of gene structures allow orthologous genes in the five species to be identified and synteny between the grasses is found to be high. It is also possible to differentiate between homoeologues resulting from ancient polyploidizations of the maize genome. Transcript analyses using microarray, massively parallel signature sequencing and quantitative PCR data for barley, rice and maize indicate that certain members of the endo-(1,4-β-glucanase gene family are transcribed across a wide range of tissues, while others are specifically transcribed in particular tissues. There are strong correlations between transcript levels of several members of the endo-(1,4-β-glucanase family and the data suggest that evolutionary conservation of transcription exists between orthologues across the grass family. There are also strong correlations between certain members of the endo-(1,4-β-glucanase family and other genes known to be involved in cell wall loosening and cell expansion, such as expansins and xyloglucan endotransglycosylases. Conclusions The identification of these groups of genes will now allow us to test hypotheses regarding their functions and joint participation in wall synthesis, re

  19. Insights into the origin of nematode chemosensory GPCRs: putative orthologs of the Srw family are found across several phyla of protostomes.

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    Arunkumar Krishnan

    Full Text Available Nematode chemosensory GPCRs in Caenorhabditis elegans (NemChRs are classified into 19 gene families, and are initially thought to have split from the ancestral Rhodopsin family of GPCRs. However, earlier studies have shown that among all 19 NemChR gene families, only the srw family has a clear sequence relationship to the ancestral Rhodopsin GPCR family. Yet, the phylogenetic relationships between the srw family of NemChRs and the Rhodopsin subfamilies are not fully understood. Also, a widespread search was not previously performed to check for the presence of putative srw family-like sequences or the other 18 NemChR families in several new protostome species outside the nematode lineage. In this study, we have investigated for the presence of 19 NemChR families across 26 eukaryotic species, covering basal eukaryotic branches and provide the first evidence that the srw family of NemChRs is indeed present across several phyla of protostomes. We could identify 29 putative orthologs of the srw family in insects (15 genes, molluscs (11 genes and Schistosoma mansoni (3 genes. Furthermore, using HMM-HMM profile based comparisons and phylogenetic analysis we show that among all Rhodopsin subfamilies, the peptide and SOG (somatostatin/opioid/galanin subfamilies are phylogenetically the closest relatives to the srw family of NemChRs. Taken together, we demonstrate that the srw family split from the large Rhodopsin family, possibly from the peptide and/or SOG subfamilies, well before the split of the nematode lineage, somewhere close to the divergence of the common ancestor of protostomes. Our analysis also suggests that the srsx family of NemChRs shares a clear sequence homology with the Rhodopsin subfamilies, as well as with few of the vertebrate olfactory receptors. Overall, this study provides further insights into the evolutionary events that shaped the GPCR chemosensory system in protostome species.

  20. Luciferase reporter gene assay on human, murine and rat histamine H4 receptor orthologs: correlations and discrepancies between distal and proximal readouts.

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    Uwe Nordemann

    Full Text Available The investigation of the (pathophysiological role of the histamine H4 receptor (H4R and its validation as a possible drug target in translational animal models are compromised by distinct species-dependent discrepancies regarding potencies and receptor subtype selectivities of the pharmacological tools. Such differences were extremely pronounced in case of proximal readouts, e. g. [(32P]GTPase or [(35S]GTPγS binding assays. To improve the predictability of in vitro investigations, the aim of this study was to establish a reporter gene assay for human, murine and rat H4Rs, using bioluminescence as a more distal readout. For this purpose a cAMP responsive element (CRE controlled luciferase reporter gene assay was established in HEK293T cells, stably expressing the human (h, the mouse (m or the rat (r H4R. The potencies and efficacies of 23 selected ligands (agonists, inverse agonists and antagonists were determined and compared with the results obtained from proximal readouts. The potencies of the examined ligands at the human H4R were consistent with reported data from [(32P]GTPase or [(35S]GTPγS binding assays, despite a tendency toward increased intrinsic efficacies of partial agonists. The differences in potencies of individual agonists at the three H4R orthologs were generally less pronounced compared to more proximal readouts. In conclusion, the established reporter gene assay is highly sensitive and reliable. Regarding discrepancies compared to data from functional assays such as [(32P]GTPase and [(35S]GTPγS binding, the readout may reflect multifactorial causes downstream from G-protein activation, e.g. activation/amplification of or cross-talk between different signaling pathways.

  1. Identification of functionally important residues of the silkmoth pheromone biosynthesis-activating neuropeptide receptor, an insect ortholog of the vertebrate neuromedin U receptor.

    Science.gov (United States)

    Kawai, Takeshi; Katayama, Yukie; Guo, Linjun; Liu, Desheng; Suzuki, Tatsuya; Hayakawa, Kou; Lee, Jae Min; Nagamine, Toshihiro; Hull, J Joe; Matsumoto, Shogo; Nagasawa, Hiromichi; Tanokura, Masaru; Nagata, Koji

    2014-07-01

    The biosynthesis of sex pheromone components in many lepidopteran insects is regulated by the interaction between pheromone biosynthesis-activating neuropeptide (PBAN) and the PBAN receptor (PBANR), a class A G-protein-coupled receptor. To identify functionally important amino acid residues in the silkmoth PBANR, a series of 27 alanine substitutions was generated using a PBANR chimera C-terminally fused with enhanced GFP. The PBANR mutants were expressed in Sf9 insect cells, and their ability to bind and be activated by a core PBAN fragment (C10PBAN(R2K)) was monitored. Among the 27 mutants, 23 localized to the cell surface of transfected Sf9 cells, whereas the other four remained intracellular. Reduced binding relative to wild type was observed with 17 mutants, and decreased Ca(2+) mobilization responses were observed with 12 mutants. Ala substitution of Glu-95, Glu-120, Asn-124, Val-195, Phe-276, Trp-280, Phe-283, Arg-287, Tyr-307, Thr-311, and Phe-319 affected both binding and Ca(2+) mobilization. The most pronounced effects were observed with the E120A mutation. A molecular model of PBANR indicated that the functionally important PBANR residues map to the 2nd, 3rd, 6th, and 7th transmembrane helices, implying that the same general region of class A G-protein-coupled receptors recognizes both peptidic and nonpeptidic ligands. Docking simulations suggest similar ligand-receptor recognition interactions for PBAN-PBANR and the orthologous vertebrate pair, neuromedin U (NMU) and NMU receptor (NMUR). The simulations highlight the importance of two glutamate residues, Glu-95 and Glu-120, in silkmoth PBANR and Glu-117 and Glu-142 in human NMUR1, in the recognition of the most functionally critical region of the ligands, the C-terminal residue and amide. PMID:24847080

  2. A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria

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    Axmann Ilka M

    2007-10-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNA are regulators of gene expression in all domains of life. They control growth and differentiation, virulence, motility and various stress responses. The identification of ncRNAs can be a tedious process due to the heterogeneous nature of this molecule class and the missing sequence similarity of orthologs, even among closely related species. The small ncRNA Yfr1 has previously been found in the Prochlorococcus/Synechococcus group of marine cyanobacteria. Results Here we show that screening available genome sequences based on an RNA motif and followed by experimental analysis works successfully in detecting this RNA in all lineages of cyanobacteria. Yfr1 is an abundant ncRNA between 54 and 69 nt in size that is ubiquitous for cyanobacteria except for two low light-adapted strains of Prochlorococcus, MIT 9211 and SS120, in which it must have been lost secondarily. Yfr1 consists of two predicted stem-loop elements separated by an unpaired sequence of 16–20 nucleotides containing the ultraconserved undecanucleotide 5'-ACUCCUCACAC-3'. Conclusion Starting with an ncRNA previously found in a narrow group of cyanobacteria only, we show here the highly specific and sensitive identification of its homologs within all lineages of cyanobacteria, whereas it was not detected within the genome sequences of E. coli and of 7 other eubacteria belonging to the alpha-proteobacteria, chlorobiaceae and spirochaete. The integration of RNA motif prediction into computational pipelines for the detection of ncRNAs in bacteria appears as a promising step to improve the quality of such predictions.

  3. The role of the RACK1 ortholog Cpc2p in modulating pheromone-induced cell cycle arrest in fission yeast.

    Directory of Open Access Journals (Sweden)

    Magdalena Mos

    Full Text Available The detection and amplification of extracellular signals requires the involvement of multiple protein components. In mammalian cells the receptor of activated C kinase (RACK1 is an important scaffolding protein for signal transduction networks. Further, it also performs a critical function in regulating the cell cycle by modulating the G1/S transition. Many eukaryotic cells express RACK1 orthologs, with one example being Cpc2p in the fission yeast Schizosaccharomyces pombe. In contrast to RACK1, Cpc2p has been described to positively regulate, at the ribosomal level, cells entry into M phase. In addition, Cpc2p controls the stress response pathways through an interaction with Msa2p, and sexual development by modulating Ran1p/Pat1p. Here we describe investigations into the role, which Cpc2p performs in controlling the G protein-mediated mating response pathway. Despite structural similarity to Gβ-like subunits, Cpc2p appears not to function at the G protein level. However, upon pheromone stimulation, cells overexpressing Cpc2p display substantial cell morphology defects, disorientation of septum formation and a significantly protracted G1 arrest. Cpc2p has the potential to function at multiple positions within the pheromone response pathway. We provide a mechanistic interpretation of this novel data by linking Cpc2p function, during the mating response, with its previous described interactions with Ran1p/Pat1p. We suggest that overexpressing Cpc2p prolongs the stimulated state of pheromone-induced cells by increasing ste11 gene expression. These data indicate that Cpc2p regulates the pheromone-induced cell cycle arrest in fission yeast by delaying cells entry into S phase.

  4. Rapid isolation of gene homologs across taxa: Efficient identification and isolation of gene orthologs from non-model organism genomes, a technical report

    Directory of Open Access Journals (Sweden)

    Heffer Alison

    2011-03-01

    Full Text Available Abstract Background Tremendous progress has been made in the field of evo-devo through comparisons of related genes from diverse taxa. While the vast number of species in nature precludes a complete analysis of the molecular evolution of even one single gene family, this would not be necessary to understand fundamental mechanisms underlying gene evolution if experiments could be designed to systematically sample representative points along the path of established phylogenies to trace changes in regulatory and coding gene sequence. This isolation of homologous genes from phylogenetically diverse, representative species can be challenging, especially if the gene is under weak selective pressure and evolving rapidly. Results Here we present an approach - Rapid Isolation of Gene Homologs across Taxa (RIGHT - to efficiently isolate specific members of gene families. RIGHT is based upon modification and a combination of degenerate polymerase chain reaction (PCR and gene-specific amplified fragment length polymorphism (AFLP. It allows targeted isolation of specific gene family members from any organism, only requiring genomic DNA. We describe this approach and how we used it to isolate members of several different gene families from diverse arthropods spanning millions of years of evolution. Conclusions RIGHT facilitates systematic isolation of one gene from large gene families. It allows for efficient gene isolation without whole genome sequencing, RNA extraction, or culturing of non-model organisms. RIGHT will be a generally useful method for isolation of orthologs from both distant and closely related species, increasing sample size and facilitating the tracking of molecular evolution of gene families and regulatory networks across the tree of life.

  5. miR-1279, miR-548j, miR-548m, and miR-548d-5p Binding Sites in CDSs of Paralogous and Orthologous PTPN12, MSH6, and ZEB1 Genes

    Directory of Open Access Journals (Sweden)

    Anatoliy T. Ivashchenko

    2013-01-01

    Full Text Available Only PTPN12, MSH6, and ZEB1 have significant miR-1279 binding sites among paralogous genes of human tyrosine phosphatase family, DNA mismatch repair family, and zinc finger family, respectively. All miRNA binding sites are located within CDSs of studied mRNAs. Nucleotide sequences of hsa-miR-1279 binding sites with mRNAs of human PTPN12, MSH6, and ZEB1 genes encode TKEQYE, EGSSDE, and GEKPYE oligopeptides, respectively. The conservation of miRNA binding sites encoding oligopeptides has been revealed. MRNAs of many paralogs of zinc finger gene family have from 1 to 12 binding sites coding the same GEKPYE hexapeptide. MRNAs of PTPN12, MSH6, and ZEB1 orthologous genes from different animal species have binding sites for hsa-miR-1279 which consist of homologous oligonucleotides encoding similar human oligopeptides TKEQYE, EGSSDE, and GEKPYE. MiR-548j, miR-548m, and miR-548d-5p have homologous binding sites in the mRNA of PTPN12 orthologous genes which encode PRTRSC, TEATDI, and STASAT oligopeptides, respectively. All regions of miRNA are important for binding with the mRNA.

  6. Candida albicans AGE3, the ortholog of the S. cerevisiae ARF-GAP-encoding gene GCS1, is required for hyphal growth and drug resistance.

    Directory of Open Access Journals (Sweden)

    Thomas Lettner

    Full Text Available BACKGROUND: Hyphal growth and multidrug resistance of C. albicans are important features for virulence and antifungal therapy of this pathogenic fungus. METHODOLOGY/PRINCIPAL FINDINGS: Here we show by phenotypic complementation analysis that the C. albicans gene AGE3 is the functional ortholog of the yeast ARF-GAP-encoding gene GCS1. The finding that the gene is required for efficient endocytosis points to an important functional role of Age3p in endosomal compartments. Most C. albicans age3Delta mutant cells which grew as cell clusters under yeast growth conditions showed defects in filamentation under different hyphal growth conditions and were almost completely disabled for invasive filamentous growth. Under hyphal growth conditions only a fraction of age3Delta cells shows a wild-type-like polarization pattern of the actin cytoskeleton and lipid rafts. Moreover, age3Delta cells were highly susceptible to several unrelated toxic compounds including antifungal azole drugs. Irrespective of the AGE3 genotype, C-terminal fusions of GFP to the drug efflux pumps Cdr1p and Mdr1p were predominantly localized in the plasma membrane. Moreover, the plasma membranes of wild-type and age3Delta mutant cells contained similar amounts of Cdr1p, Cdr2p and Mdr1p. CONCLUSIONS/SIGNIFICANCE: The results indicate that the defect in sustaining filament elongation is probably caused by the failure of age3Delta cells to polarize the actin cytoskeleton and possibly of inefficient endocytosis. The high susceptibility of age3Delta cells to azoles is not caused by inefficient transport of efflux pumps to the cell membrane. A possible role of a vacuolar defect of age3Delta cells in drug susceptibility is proposed and discussed. In conclusion, our study shows that the ARF-GAP Age3p is required for hyphal growth which is an important virulence factor of C. albicans and essential for detoxification of azole drugs which are routinely used for antifungal therapy. Thus, it

  7. GCPII Variants, Paralogs and Orthologs

    Czech Academy of Sciences Publication Activity Database

    Hlouchová, Klára; Navrátil, Václav; Tykvart, Jan; Šácha, Pavel; Konvalinka, Jan

    2012-01-01

    Roč. 19, č. 9 (2012), s. 1316-1322. ISSN 0929-8673 R&D Projects: GA ČR GAP304/12/0847 Institutional research plan: CEZ:AV0Z40550506 Keywords : PSMA * GCPIII * NAALADase L * splice variants * homologs * PSMAL Subject RIV: CE - Biochemistry Impact factor: 4.070, year: 2012

  8. AP1- and NF-kappaB-binding sites conserved among mammalian WNT10B orthologs elucidate the TNFalpha-WNT10B signaling loop implicated in carcinogenesis and adipogenesis.

    Science.gov (United States)

    Katoh, Masuko; Katoh, Masaru

    2007-04-01

    WNT signals are context-dependently transduced to canonical and non-canonical signaling cascades. We cloned and characterized wild-type human WNT10B, while another group cloned aberrant human WNT10B with Gly60Asp amino-acid substitution. Proto-oncogene WNT10B is expressed in gastric cancer, pancreatic cancer, breast cancer, esophageal cancer, and cervical cancer. Because WNT10B blocks adipocyte differentiation, coding SNP of WNT10B gene is associated with familial obesity. In 2001, we reported WNT10B upregulation by TNFalpha. Here, comparative integromics analyses on WNT10B orthologs were performed to elucidate the transcriptional mechanism of WNT10B. Chimpanzee WNT10B and cow Wnt10b genes were identified within NW_001223159.1 and AC150975.2 genome sequences, respectively, by using bioinformatics (Techint) and human intelligence (Humint). Chimpanzee WNT10B and cow Wnt10b showed 98.7% and 95.1% total-amino-acid identity with human WNT10B, respectively. N-terminal signal peptide, 24 Cys residues, two Asn-linked glycosylation sites, and Gly60 of human WNT10B were conserved among mammalian WNT10B orthologs. Transcription start site of human WNT10B gene was 106-bp upstream of NM_003394.2 RefSeq 5'-end. Number of GC di-nucleotide repeats just down-stream of WNT10B transcription start site varied among primates and human population. Comparative genomics analyses revealed that double AP1-binding sites in the 5'-flanking promoter region and NF-kappaB-binding site in intron 3 were conserved among human, chimpanzee, cow, mouse, and rat WNT10B orthologs. Because TNFalpha signaling through TNFR1 and TRADD/RIP/TRAF2 complex activates JUN kinase (JNK) and IkappaB kinase (IKK) signaling cascades, conserved AP1- and NF-kappaB-binding sites explain the mechanism of TNFalpha-induced WNT10B upregulation. TNFalpha-WNT10B signaling loop is the negative feedback mechanism of adipogenesis to prevent obesity and metabolic syndrome. On the other hand, TNFalpha-WNT10B signaling loop is

  9. From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. [v2; ref status: indexed, http://f1000r.es/2ys

    Directory of Open Access Journals (Sweden)

    Varsha K Khodiyar

    2014-02-01

    Full Text Available For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer’s vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer’s vesicle determine asymmetry in the developing heart, the direction of ‘heart jogging’ and the direction of ‘heart looping’.  ‘Heart jogging’ is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward ‘jog’. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish ‘heart jogging orthologs’ are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach.

  10. From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. [v1; ref status: indexed, http://f1000r.es/28b

    Directory of Open Access Journals (Sweden)

    Varsha K Khodiyar

    2013-11-01

    Full Text Available For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer’s vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer’s vesicle determine asymmetry in the developing heart, the direction of ‘heart jogging’ and the direction of ‘heart looping’.  ‘Heart jogging’ is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward ‘jog’. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish ‘heart jogging orthologs’ are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach.

  11. DNA End Resection:Facts and Mechanisms

    Institute of Scientific and Technical Information of China (English)

    Ting Liu; a Jun Huang; b

    2016-01-01

    DNA double-strand breaks (DSBs), which arise following exposure to a number of endogenous and exogenous agents, can be repaired by either the homologous recombination (HR) or non-homologous end-joining (NHEJ) pathways in eukaryotic cells. A vital step in HR repair is DNA end resection, which generates a long 30 single-stranded DNA (ssDNA) tail that can invade the homologous DNA strand. The generation of 30 ssDNA is not only essential for HR repair, but also promotes activation of the ataxia telangiectasia and Rad3-related protein (ATR). Multiple fac-tors, including the MRN/X complex, C-terminal-binding protein interacting protein (CtIP)/Sae2, exonuclease 1 (EXO1), Bloom syndrome protein (BLM)/Sgs1, DNA2 nuclease/helicase, and several chromatin remodelers, cooperate to complete the process of end resection. Here we review the basic machinery involved in DNA end resection in eukaryotic cells.

  12. Hd86, the Bm86 tick protein ortholog in Hyalomma scupense (syn. H. detritum): expression in Pichia pastoris and analysis of nucleotides and amino acids sequences variations prior to vaccination trials.

    Science.gov (United States)

    Ben Said, Mourad; Galai, Yousr; Canales, Mario; Nijhof, Ard Menzo; Mhadhbi, Moez; Jedidi, Mohamed; de la Fuente, José; Darghouth, Mohamed Aziz

    2012-02-10

    The genus Hyalomma includes the most frequent tick species infesting livestock in North Africa, one of these species, Hyalomma scupense (syn. H. detritum) is particularly important due to its role in the transmission of tropical theileriosis to cattle (Theileria annulata infection). We have cloned and characterized the orthologs of the Bm86 gene from H. scupense strains collected over Tunisia in 2006 and 2009. The recombinant protein rHd86 was expressed in Pichia pastoris for vaccination purpose using a transcript from the 2006 strain. The rHd86 was then purified from the yeast culture supernatant by a filtration and a size exclusion process. It was recognized by specific anti-Bm86 antisera. An important extent of inter-specific diversity ranging from 35 to 40% was recorded between Hd86 and Bm86/Bm95 proteins whilst a very limited level of intra-specific diversity (1.7%) occurred between the Hd86 vaccine candidate protein and its homologues from H. scupense strains collected in 2009. These results emphasise the need for assessing the efficacy against H. scupense and others important cattle Hyalomma species in Tunisia of our Hd86 vaccine candidate alongside with a Bm86 vaccine. PMID:21871736

  13. ASYMMETRIC-LEAVES2 and an ortholog of eukaryotic NudC domain proteins repress expression of AUXIN-RESPONSE-FACTOR and class 1 KNOX homeobox genes for development of flat symmetric leaves in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Nanako Ishibashi

    2012-01-01

    Leaf primordia form around the shoot apical meristem, which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial-abaxial patterning is crucial for appropriate lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many genes that specify such patterning have been identified, but regulation by upstream factors of the expression of relevant effector genes remains poorly understood. In Arabidopsis thaliana, ASYMMETRIC LEAVES2 (AS2 and AS1 play important roles in repressing transcription of class 1 KNOTTED1-like homeobox (KNOX genes and leaf abaxial-determinant effector genes. We report here a mutation, designated enhancer of asymmetric leaves2 and asymmetric leaves1 (eal, that is associated with efficient generation of abaxialized filamentous leaves on the as2 or as1 background. Levels of transcripts of many abaxial-determinant genes, including ETTIN (ETT/AUXIN RESPONSE FACTOR3 (ARF3, and all four class 1 KNOX genes were markedly elevated in as2 eal shoot apices. Rudimentary patterning in as2 eal leaves was suppressed by the ett mutation. EAL encodes BOBBER1 (BOB1, an Arabidopsis ortholog of eukaryotic NudC domain proteins. BOB1 was expressed in plant tissues with division potential and bob1 mutations resulted in lowered levels of transcripts of some cell-cycle genes and decreased rates of cell division in shoot and root apices. Coordinated cellular proliferation, supported by BOB1, and repression of all class 1 KNOX genes, ETT/ARF3 by AS2 (AS1 and BOB1 might be critical for repression of the indeterminate state and of aberrant abaxialization in the presumptive adaxial domain of leaf primordia, which might ensure the formation of flat symmetric leaves.

  14. BLM protein mitigates formaldehyde-induced genomic instability

    OpenAIRE

    Kumari, Anuradha; Owen, Nichole; Juarez, Eleonora; McCullough, Amanda K.

    2015-01-01

    Formaldehyde is a reactive aldehyde that has been classified as a class I human carcinogen by the International Agency for Cancer Research. There are growing concerns over the possible adverse health effects related to the occupational and environmental human exposures to formaldehyde. Although formaldehyde-induced DNA and protein adducts have been identified, the genomic instability mechanisms and the cellular tolerance pathways associated with formaldehyde exposure are not fully characteriz...

  15. The Mammalian Orthologs of Drosophila Lgd, CC2D1A and CC2D1B, Function in the Endocytic Pathway, but Their Individual Loss of Function Does Not Affect Notch Signalling.

    Directory of Open Access Journals (Sweden)

    Nadja Drusenheimer

    2015-12-01

    Full Text Available CC2D1A and CC2D1B belong to the evolutionary conserved Lgd protein family with members in all multi-cellular animals. Several functions such as centrosomal cleavage, involvement in signalling pathways, immune response and synapse maturation have been described for CC2D1A. Moreover, the Drosophila melanogaster ortholog Lgd was shown to be involved in the endosomal trafficking of the Notch receptor and other transmembrane receptors and physically interacts with the ESCRT-III component Shrub/CHMP4. To determine if this function is conserved in mammals we generated and characterized Cc2d1a and Cc2d1b conditional knockout mice. While Cc2d1b deficient mice displayed no obvious phenotype, we found that Cc2d1a deficient mice as well as conditional mutants that lack CC2D1A only in the nervous system die shortly after birth due to respiratory distress. This finding confirms the suspicion that the breathing defect is caused by the central nervous system. However, an involvement in centrosomal function could not be confirmed in Cc2d1a deficient MEF cells. To analyse an influence on Notch signalling, we generated intestine specific Cc2d1a mutant mice. These mice did not display any alterations in goblet cell number, proliferating cell number or expression of the Notch reporter Hes1-emGFP, suggesting that CC2D1A is not required for Notch signalling. However, our EM analysis revealed that the average size of endosomes of Cc2d1a mutant cells, but not Cc2d1b mutant cells, is increased, indicating a defect in endosomal morphogenesis. We could show that CC2D1A and its interaction partner CHMP4B are localised on endosomes in MEF cells, when the activity of the endosomal protein VPS4 is reduced. This indicates that CC2D1A cycles between the cytosol and the endosomal membrane. Additionally, in rescue experiments in D. melanogaster, CC2D1A and CC2D1B were able to functionally replace Lgd. Altogether our data suggest a functional conservation of the Lgd protein family

  16. Protein (Viridiplantae): 356556652 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET2-like Glycine max MSLFGAYSICEVGKDAAGVAGNIFAFGLFVS...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  17. Protein (Viridiplantae): 356554726 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET2-like Glycine max MSLFSAYSICEVGKDAAGVTGNIFAFGLFVP...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  18. Protein (Viridiplantae): 357130727 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ectional sugar transporter SWEET6a-like Brachypodium distachyon MTEQRFPQNGNTSVPAGNS...24:4295 3398:4295 4447:4380 4734:4380 38820:4380 4479:4380 359160:3487 147368:3422 147385:3422 15367:3422 15368:3422 PREDICTED: bidir

  19. Protein (Viridiplantae): 356573875 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET17-like Glycine max MMQTYVLENIKIKKHGSTEDFLSLPYICTL...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  20. Protein (Viridiplantae): 356509295 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET3-like Glycine max MAETIRLGVAVLGNAASVALYAAPMVTFRRV...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  1. Protein (Viridiplantae): 356544144 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET2-like Glycine max MSLFAAFSICKVAKDAAGVAGNVFAFGLFVS...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  2. Protein (Viridiplantae): 356554435 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter NEC1-like Glycine max MVSFSDHELVLIFGLLGNIVSFMVFLAPLSNFY...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  3. Protein (Viridiplantae): 357135133 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ectional sugar transporter SWEET2a-like Brachypodium distachyon MASLGLPGVSSYHDLCCYG...24:4295 3398:4295 4447:4380 4734:4380 38820:4380 4479:4380 359160:3487 147368:3422 147385:3422 15367:3422 15368:3422 PREDICTED: bidir

  4. Protein (Viridiplantae): 356524569 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter N3-like Glycine max MVITHHTLAFTFGMLGNVISFLVFLAPVPTFYRIY...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  5. Protein (Viridiplantae): 356513594 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET5-like Glycine max MVDTGAIRTVIGVIGNVISFCLFMSPVPTFI...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  6. Protein (Cyanobacteria): 319556 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available cal protein Cha6605_6427 Chamaesiphon minutus PCC 6605 MGGDGFPPDRNHFSRAFSTSFNNMTFKRTQAEPLSCQCNIRLTPSEMEELKDAASVAGITVSTYIRQRALGRRVAANTDMTTIRELRRIGGLLKHIHNESGGAYSQLTADTLIEIQKAIVSIGNGL ...

  7. Protein (Cyanobacteria): 243777 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available occus sp. JA-3-3Ab MATPFSWPYRTPGIPDSAFERIPGIPMSPREVRVLVLSQLRLGEDHCLWDIGAGTGTIAIEAAILCPRARVIAIERDAEVVSLIESNCE...KFGLNNVQVIQGTAPDCLHQLSPPPDRICIEGGHPLREILEASWNHLKPNGRIVATTNSLEGLYGLSAGLAAVRAHHVEVIQSAVNRLEHRGRSQLLLPLDPTFVLSGEKSS ...

  8. Protein (Cyanobacteria): 170237 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8802_4468 Cyanothece sp. PCC 8802 MNFDFPSPISPDSSKQQELSPKKLNPSRIRDHLANERTYLAWMRTAVGLMGFGVVILRIRAFQPPSIPGPGFGWKLGLIFAGVGLLTVLLSTVQYFIVRRDIEEDTYEPPDRWVILFSLTIALLGSGIIYFVSTSSFDLVDIIM ...

  9. Protein (Cyanobacteria): 320772 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available MC7420_6233 Coleofasciculus chthonoplastes PCC 7420 MIRHTSNNTTKPALPHHQTTKSILIFHAIARQSSTPSCRGGFRNSIITHTANKTTKPALSPPPDR...EIYPNFQAIARQSSTPSCRGGFRNSIITHTANKTTKPALSPPPDREIYPNFQAIAHQSSTPSCRGGFRDSIITHTANKTTKPALSPPPDREIYPNFQAI

  10. Protein (Cyanobacteria): 69702 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available osphatase Oscillatoria sp. PCC 6506 MNHLIKQADLADRIICDSAGTGGYHVGNPPDRRMAIAASKRELELRGSARKFQRSDFENFDLILAMDKDNYQDILSLDPHGKYRDKVRLMCEFCQKYDLREVPDPYYGGPEGFDRVIDLLWDACEGLLEYVTKEKLIFNS ...

  11. Protein (Cyanobacteria): 438681 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8 Synechococcus sp. JA-2-3B'a(2-13) MNDLLFEPTSERPSLAEIRRLSPAALAYLGDAIYELHVRRQRLFPPDRLERYHQQVVRRVRGSAQAKLLLALLPHLNPEEQEIVRWGRNGCGRPPRHLPLADYQNASGLETVLGYLYLANPERLRHILALTDVLAETLGEWEG ...

  12. Protein (Cyanobacteria): 69717 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available osine phosphatase Moorea producens 3L MNHLIAQANLSDQIVCDSAGTSSYHIGSPPDRRMTAAAKRRGIILQGKARQFNRSDLEEFDLILAMDQQNYEDIISLDPAGKYKDKVRLMCDFASHHTERSVPDPYYGGPEGFNKVIDLLLDACEGLLEHVVDNYTKTRQN ...

  13. Protein (Cyanobacteria): 197706 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available porter Synechococcus sp. WH 5701 MWLRLDSASRLKPPFTPAPLPPDRQLPEGYDTLEGERGYQLSGGQRQRISLARAILRKPELLILDEATSALDSQSEHLVQQAIERFARKHTVLVIAHRPSTVVHPDLICVMDQGRIVERGHHGELLARDGLYADLWKKQVRHDHGL ...

  14. Protein (Cyanobacteria): 170238 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 01_4405 Cyanothece sp. PCC 8801 MNFDFPSPISPDSSKQQELSRKKLNPSRIRDHLANERTYLAWMRTAVGLMGFGVVILRIRAFQPPSIPGPGFGWKLGLIFAGVGLLTVLLSTVQYFIVRRDIEEDTYEPPDRWVILFSLAIALLGSGIIYFVSTSSFDLVDIIM ...

  15. Protein (Cyanobacteria): 313833 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ELVGSPLPDTVPSTISEAAIETKIDEILEKKLSNHLPDNVPSIVESIILDKLPSMILEYLPSDLMARIENMERLLRLQQSASIADHSPIPTGEPYPLPPSPPDRPAIE...AVTPEVSPSPLVTDAIASIDGTVEGGNGDIFPDSPPDRPAIASSAKKGLTDSELARELGIDKSNITRWKQKGRPTQKYENWELRGRFWYEKD ...

  16. Protein (Cyanobacteria): 316111 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rotein MC7420_6734 Coleofasciculus chthonoplastes PCC 7420 MSELLYERHGKTESNSIGEKGDFVERESATVGEILALQCFCHLAQVTLTPYQRTVTPYPGTVTSYPGTMTP...YQRTVTSYPGTMTPYPGTMTPYPGTMTPYPGTMTPYPGTMTPYPGTMTPYPETIH ...

  17. Protein (Viridiplantae): 308802215 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available teins containing BTB/POZ and Kelch domains, involved in regulatory/signal transduction processes (ISS) Ostreococ...XP_003078421.1 33090:7785 3041:2315 1035538:252 13792:252 70447:1563 70448:2092 Pro

  18. Protein (Viridiplantae): 308810419 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available teins containing BTB/POZ and Kelch domains, involved in regulatory/signal transduction processes (ISS) Ostreococ...XP_003082518.1 33090:7785 3041:2315 1035538:252 13792:252 70447:1563 70448:2092 Pro

  19. Protein (Cyanobacteria): 449752 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein MAE_27120 Microcystis aeruginosa NIES-843 MLAKPIMGLGFVNVWLTGIGVIGGVPIRVIAFKTLTAAKPRPANSPVGVPTNPVVVPGVRVGLVVPHEPAVAFPPTAIILAAWAAPAKLRAATLAAIATVPVASCLEMLVIILSRLLREHLTYAISNYT ...

  20. Protein (Cyanobacteria): 276821 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available eceiver protein Chroococcidiopsis thermalis PCC 7203 MTAKRILVVDNEPYIQEVAQICLEMVAGWQVSTASSGSECLTKAAAEQPDAILLDVMMPEMDGLTTYKELQANKATKHIPVIFLTAKVQPADRRRYALLGMKDAIAKPFDPLQLASQVATTLGWN ...

  1. Protein (Cyanobacteria): 380452 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein PMT1441 Prochlorococcus marinus str. MIT 9313 MIQQEGPGWRLARDPARKAFPVLIGGEGWAIELTQDEWQCLQSLVVELTDQHQQLVDQLLAEESVCLEMERQPWWACLDGDRHSWSLQVILQGDGEKARGAEGCWSVPAAQAMATAMRTTWDFDQ ...

  2. Protein (Viridiplantae): 225431324 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RPPDSRIPFEFCYDMSPGENTSLIPSMSLTMKGGSQFPVYDPIIIISSQSELIYCMAVVRSAELNIIGQNFMTGYRIIFDR...GLEKISVPSILSKEGFTADSFSMCFGPDGIGRISFGDKGSPDQEETPFNLNALHPTYNITVTQVRVGTTLIDLDFTALFDSGTSFTYLVDPIYTNVLKSFHSQAQDSR

  3. Protein (Cyanobacteria): 22493 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FIRWMAALTITVGVFIVSISENPPTSKPITSALEHRTKSWFKRSMFFLLPLSFSLPKIWLFAVIIAFADGFGDIFNAKGMKQIGAVKLGSLPEMLQIGQKIITNHWIIQGITCQTLSFLSFVSALSWADISFVRPATALTYVISLLGAYFILKERIELGRLIGIVVVGIGILIITLDPSMSL ...

  4. Protein (Viridiplantae): 303290558 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NTMGWIDKAGYGLLLHALEALAIDVVLVVDHEKLHAELSRDLRGKKIKVWKLQKSGGVVERTPEFRRRSRDARVREYFYGPLGDLSPHSQTLEFGKVSIFKIGAGPSAPRSALPIGQESSADPLRVSTVAPSM...SLLNAVLGVSHGKTQAELLSSNVAGFIFVTDVDVANGRFTYLTPCPGELPSRNLIAGTLKWIETR ...

  5. Protein (Viridiplantae): 359473770 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HHSRSASATGISNIKRTQNFAAKAAAQRLAQVMASQTADDDEDDEDDDLGFRYSAPPPPAFSRTVNSGKPAVPASRVTRSPSPGLGRNFVEETPSVRSTSAGRPSM...SLNAIPLVSPSRAPLRTPVPIPPIEPPNRQKEKRFSSNVGHFNPKDTGDQREASALRDEVDMLQEENENILDKLRLEEERCKD

  6. Protein (Cyanobacteria): 123908 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RQWQSEHREIEMGDRYQAVLQEKVPSMSLAELGKITTEMVARFQACYQQSLRLPDGVKDMLEFWHGRVRLGVVSNFYIQGWPTELLESFGLRSYFDFVVDSAACGWRK...genase-like hydrolase Acaryochloris marina MBIC11017 MTLDWIFFDCFNTLIDDFDQTGEELALLPVYSLPAEVGLYTSAAEFRQHYHAWRN

  7. Protein (Viridiplantae): 302848830 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EAASGPADAVADASPEAAAAAVAIPVALPKMPDLAAAAVPATDVRGLSQEALERAGTSEAVAAKAMVTDVAEVTELTVLTE...ATELAEVAMAAESTVPSVVTEPAEVTVPAQVAEVMETVETTEPAEAMEPADATETAEVTEPAEVTEPAEVTEPAEVTEPAEVAEVTEPAEVAEVTEPAEPAEATEPAEVTEAAEPAEATEQVEVTEPAVEVT...EATEPAATEATEPAVTEATEATEQVQVTEATEPTEVTEMLETTKPAVATEPAQAMEPAEVVEPAQAAEVAEVKELAEVTEPEETAVATAAAEVMESAAATEPAEVT...ETAEVTEPAEVTEPAEVTEPAEVTEPAEVTEPAEVTETAEVTEPAEVTEPAEVTEPAEVTEPAEVAEVTEPAEVAEVTEPAEVAEVTEPAEATEPAEVVEVTEPAEVT...EATEVTEPAAATEPAAATEPAATTESAEVTEPAATTESAEVTEPAATTESAEVTEATEPAEATEPAETAEATEPAEVT

  8. Protein (Cyanobacteria): 470883 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available etical protein P9211_14491 Prochlorococcus marinus str. MIT 9211 MAAAAFLSAAAFLSAAAFLSAAAFLAAAACLSAAAFLSAAAFLSAAAFLAAAACL...SAAAFLSAAAFLAAAAFLSAAACLSAAAFLSAAAFLAAAACLSAAAFLAAAACLSAAAFLSAAAFLAAAACLSAAAFLSAAAFLAAAACLSAAAFLSAAAFLAAAACLSAAAFLAAAACL...SAAAFLAAAAFLAAAACLSAAAFLSAAAFLAAAAFLSAAACLSAAAFLSAAAFLAAAACLSAAAFLAAAACL...SAAAFLSAAAFLAAAACLSAAAFLSAAAFLAAAACLSAAAFLAAAACLSAAAFLAAAACLSTPCLLAATCKSILYVLIYSSTLIVSKRPSLLKVNQLH ...

  9. Protein (Cyanobacteria): 196033 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ate transport system, ATPase component Chamaesiphon minutus PCC 6605 MSTISSELSSIDIDKQRAKLPNLGS...YP_007099625.1 1117:3837 1118:1190 217161:169 1173032:169 1173020:169 ABC-type phosphate/phosphon

  10. Protein (Cyanobacteria): 383571 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available in Chamaesiphon minutus PCC 6605 MSTVTQMKCACESCLCIVSLSDAIVKDGKHYCGDACANGHPAGQGCGHTGCGCDK ... ...YP_007095769.1 1117:24391 1118:5806 217161:1032 1173032:1032 1173020:1032 Prokaryotic metallothione

  11. Protein (Cyanobacteria): 148864 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nt Chamaesiphon minutus PCC 6605 MEVWLTPGKISMISLDRLTAEILSLPSASRAILADKLIESLEFDIDTDIQSAWSSEAKKRRDEVRDGSVRAIPGDDALAQVRNSIDL ... ...YP_007098443.1 1117:2988 1118:7866 217161:2517 1173032:2517 1173020:2517 Putative addiction module compone

  12. Protein (Cyanobacteria): 308586 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available /menaquinone biosynthesis Chamaesiphon minutus PCC 6605 MSSSSTTKDLYSGVEFSTWLELENLDAQEEYLI...YP_007097312.1 1117:6279 1118:2789 217161:237 1173032:237 1173020:237 methylase involved in ubiquinone

  13. Protein (Cyanobacteria): 394660 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available centre component Chamaesiphon minutus PCC 6605 MDAALIIAKLPEAYAIFDPLVDVLPIIPVLFLALAFVWQAAVGFR ... ...YP_007099370.1 1117:24543 1118:6143 217161:3013 1173032:3013 1173020:3013 Photosystem II 4 kDa reaction

  14. Protein (Viridiplantae): 302855606 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 68:667 hypothetical protein VOLCADRAFT_100718 Volvox carteri f. nagariensis MRIALYEACTAFIPTRKRVLKRASNCATKRALNPAADCTLNCMSNCAIRAMRI...ALYEARTAFIPTRKRVLKRASNCATKRALNPAADCTLNCMSNCAIRAMRIALYEACTAFIRGSAF ...

  15. Protein (Cyanobacteria): 321324 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available Synechococcus sp. JA-3-3Ab MNGQDRLDRVEQLLAQAAEQTAANSREIQELRQAIRESHAELSEQNAARSREIEQLRQAIRESHAELSEQNAARSREIEQLRQAIR...ESHAELSEQNAARSREIEQLRQAIRESHAELSEQNAARSREIEQLRQAIRESHAELSEQNAARSREIEQLRQAIRESHAELSEQNAARSREIEQLRQAIRESHAELSEQNAARSREIEQLRQAIR...ESHAELSEQNAARSREIEQLRQAIRESYEQNVAQAQGLRDLQEVVRETRSDLAHLAEWAEEVTQALITLTALQQEHERAIQAINQRQIENDQRFNVLLEEVRYLIRRQGLDGSSSPPSG ...

  16. Protein (Cyanobacteria): 325701 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ohol dehydrogenase family Arthrospira platensis C1 MVGVQPGNMSAPVAEMDRFFQADVPDVSAWEEMAQKWRGEVARVDALVNNAAVMVGQPGSGNDTPAVGGGVVGELPRSILPCVSWPRGGAVVNVSPVHAIATSANIPAYGGSNGGCGLGVGGWRSL ...

  17. Protein (Viridiplantae): 168040746 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GGTMFPEGAEGYVQKLEKHIPFGTSAIRTALDLGCGVASFGAYLLDKEVLTMSVAPRDSYKAQIQFALERGLPAFVGMLGTQRLPFPASSFDLIHCSRCRISFSSFNGSYFIEMDR...PVPGPNTLGTIYDRGLLGVFHDWQVLTSLFCFLIPFSTYPRTYDLLHVSSVEALTTSQNRYLSVPSLCSLAEIMVEMDRILRPKGTVIIRDTPAMLARVSKVANGIQWNYEIFDGEPGATDRILIATKQFWKAEIAEPQ ...

  18. Protein (Viridiplantae): 302755490 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EQYIPLSDGQIRTALDAGCGVASFGAYMLRKDVLTMSFAPRDSHKAQIQFALERGIPAFVAMLGTQKLPFPAFSYDLVHCSRCLIHFSAYNGSYMIEMDRLLRPGGFF...IGVLHDWCEAFSTYPRTYDFIHVSNMQSFTTQASTSCSLVDVMLEMDRILRPQGTILVRDTTKMVEKISKIAYALQWTTEVLTTEGGVLGKERLFVATKPFHT ...

  19. Protein (Cyanobacteria): 20524 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 375DRAFT_4878 Leptolyngbya sp. PCC 7375 MELYERIEQIIVTFRPAFSRNATFGWFVLLLWGALLTTQPPAVTSYLNALGLGAEYYHQALHWFHSSGYEMDRVCRRWGRWLSHQTDGYRLKGHRVYVGDGIKVSKEGRKMPGLKACIKSPITSVNQNGYGGIILVRWAF ...

  20. Protein (Viridiplantae): 302821216 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ENQIQFALERGIPALVAALGTKRLPYPSRSFDAVHCSRCRVDWHEDGGILLREMDRILRPGGFFIYSAPPAYRKDKDFPEVWNILTNITESLCWKLIARHVQTAVWRK...ALLLQNNPVWIMNVVPSESSNTLNVVYGRGLVGTLHSWCESFSSYPRSYDLLHAYRVMSLYPGRKGCQIEDIMLEMDRLLRPNALAIFQDSSPAVQRILELAPRFLWVARVHRILEKDEQLLICSKKFWIVDV ...

  1. Protein (Viridiplantae): 225433261 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8 PREDICTED: mitochondrial import receptor subunit TOM22 homolog 2 Vitis vinifera MAGGSSDSKSNSGLVSRISNSISGSGIMFHGKRAASDAAYVTKKLLRSTGKAAWIAGTTFVILVVPLIIEMDREQQLNDLDLQQATLLGTTPLPARN ...

  2. Protein (Cyanobacteria): 316244 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available _3027 Synechocystis sp. PCC 6803 MLKLAGKKASALTCKKTKAKIGILEMDRQWYQSVKRFLCPSFEISAINFQDILFNNVDVGEYHSILVGCGIKYESIDISATLDLVTIIKKLSAKPPALLLITDCADSQITVQARSYLPQIDGVFAKDHDLALLLKVMKIIAKQKYFK ...

  3. Protein (Cyanobacteria): 42724 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available anothece sp. PCC 7425 MAITRWEPFRRIERWEPLREMETLRREMDRLFDRMIPFGDGEEGLLAFTPSVEMEETDEAINLRLEIPGMDPKDLDIQVSEESVSIRGERKSESRTEEQGTIRSEFRYGKFQRIIPLPAHIQTDQVKAENRQGVLHLILPKAEEERRKVVKVQID ...

  4. Protein (Viridiplantae): 302766834 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LEQYIPLSDGQIRTALDAGCGVASFGAYMLRKDVLTMSFAPRDSHKAQIQFALERGIPAFVAMLGTQKLPFPAFSYDLVHCSRCLIHFSAYNGSYMIEMDRLLRPGGF...LIGVLHDWCEAFSTYPRTYDFIHVSNMQSFTTQASTSCSLVDVMLEMDRILRPQGTILVRDTTKMVEKISKIAYALQWTTEVLTTEGGVLGKERLFVATKPFHT ...

  5. Protein (Viridiplantae): 302830432 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2914 3068:2914 hypothetical protein VOLCADRAFT_56324, partial Volvox carteri f. nagariensis CMIASCTMIAPCTVSPCTIASCTIASCTIAPCTIAPCT...IALCMIAPCTIAPCTIAPCTVALVRLPLYDCPFYGCTLYGCPCTIAPCTIAPFTIAPCTMVAPCTIALCMIALLYDCPFHDCPLYDCTLHDCPCTIAPCTVAPCTIALV ...

  6. Protein (Cyanobacteria): 418448 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available g data, contig C327 Microcystis aeruginosa PCC 9717 MLIEDYFQQIQTIIATCSVVKFFTLDCEKRDSYEGFIRAEIKFIDNSVLHIREFVNIETIINRNMYAYQYMNTMNTLIFRYDNTPHHKKLNLPTYPHHKHDSSEENVISSAAPTLLEVLQEITARIRSFL ...

  7. Protein (Cyanobacteria): 418439 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available g data, contig C327 Microcystis aeruginosa PCC 9808 MLIEDYFQQIQTIIATCSVVKFFTLDCEKRDTYEGFIRAEIKFIDNSVLHIREFVNIETIINRNMYAYQYMNTMNTLIFRYDNTPHHKKLNLPTYPHHKHDSSEENVISSAAPTLLEVLQEITARIRSFL ...

  8. Protein (Cyanobacteria): 330129 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RSEKVTNIAFQIYDQTKNIFHSDTDSKAKKLLWAACHLYSCGKYVNINSYHKHSWYLIKHCELLGYSQLETNIIASIARYHRKTLPKKRHESWQSLISKEEKTIVLEMSLILRLAASLDQRPENVISSIKIKLQKNALSMEIIPFNSNQDLLLEKWSLESCRNAIKELKNLELKVV ...

  9. Protein (Cyanobacteria): 88192 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein Cyan10605_1136 Cyanobacterium aponinum PCC 10605 MKDSNNLEQIRNKANKNRWIAGVLTFFVAPVGYFYTLRYKAALISFIVYIILVGASEENETMETLLGFFAISVTVENV...ISINKAKNKFKELEGNTNQLTNYPSSFSGNSPDIIILKAINNRGEMTVSEIVIATELSPQIVKKTLLDLENEHLIYGYNRESDGAVVYKNI ...

  10. Protein (Viridiplantae): 297851234 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SSPEIFRGSKLFRMYVISGTTIGLFLPLAYVLGGFARGDDQAVRSATPHLFLLSCQILTENVISGLSLFSPPVRALVPLLYTVWRIFVIIGWSKDVWLNKSLPINATPNVVAWFWFGRYLAIANLGYFGVNLLCFLIPRFLPRAFEIYFRERDEIMSKCQEDKPVQVPRSKPSDHKSD ...

  11. Protein (Cyanobacteria): 235609 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RVQQRITEGSELLIRAPFSGVITARYAEPGAFVTPTTAASATAGASSSSLVELSEGMEVNAKVPESDIGRIRIGQNASVRVDAFPEQRFMARVSEIAPRAAKTENV...ISFAVKLNLIKPSPQLLIGMSADVDFQTGKTAPTTLVPTVAIVTEKGKPGVLLVGQKNQPRFQAVELGTSSGSKTAILSGLKPGTRIFIDLPPWAKTKRD ...

  12. Protein (Cyanobacteria): 418441 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available g data, contig C327 Microcystis aeruginosa PCC 9701 MLIEDYFQQIQTIIATCSVIKFFTLDCEKRDTYEGFIRAEIKFIDNSVLHIREFVNIETIINRNMYAYQYMNTMNTLIFRYDNTPHHKKLNLPTYPHHKHDSSEENVISSAAPTLLEVLQEITARIRIFL ...

  13. Protein (Viridiplantae): 356515098 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PQSEDPNMVHPQSEDQNMAQPLMEDENTALPQLEDENTAQPQLEDENTAQLQGSSKLEDENTAQPQVTSRSEEGNTAQPQMSSRSEEGNTAQPQMSSRSEEGNTAQPQ...DQNMVQTEVGSGLEDGNKAQPRGEDQNMAQTQEGSRLEDENTAQPPGEDHNLAQTQVNSRLEDGDMAQPQLDDQNMVQPQSEDQNMAQSQSEDHIMAQPQSEDQNMAQ

  14. Protein (Cyanobacteria): 340993 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FT_3714 Oscillatoriales cyanobacterium JSC-12 MTQLLEHGQIISSPGCHFNYRVIGPCCRLFDREQLPYPCCRLQWRGKEPSWRRIGKRFVLDMATRAHPTYSVEMLDQGRNRSSPQSNLSLPMLLTLYWIKLPQPLNEWWYSDRSRRSEIFSTQPPTIRELTTR ... ...ZP_11392149.1 1117:11925 1150:9766 44887:805 864702:805 hypothetical protein OsccyDRA

  15. Protein (Viridiplantae): 308082002 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 575:8071 4577:8071 uncharacterized protein LOC100501617 Zea mays MNQNSNPSVVASRTYFCSGRCLFSLGRTALTFRSGMATLYGTRAVPPRGVGTGTGTASARSLRKATRA...VDTNSTPAMGPAVVDRWHCEARSSFSFLSAENHRRNTFSTPPARTIFATRENFPFTVSERFGPRVTACVRTYTSEQAT...SVQFSNSVQSASFFFSYICRTRGEEESLGFLPHGKFVPFRSIMEKQSNITVLFDALSDTASLPAGGALLIARRPIGGRR ...

  16. Protein (Viridiplantae): 226506732 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :5525 4577:5525 uncharacterized protein LOC100280132 Zea mays MSMATPLNSSTTRSTSLTERRRAPSSAARARSTAFSCSTRAFCDATSAARAATRA...FSACRSAASWASSSRCCCFRSRDRRADSRFDSRRFSRRRVSAAESPSDPDVLPAGDSDDDDIKTRSFFPRSVWLLYLQQNSSIASASVLLFGGCSGRQERREKQEGTERERERERERERERGHGEWRIRGRASYEIT ...

  17. Protein (Viridiplantae): 145350763 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 36017:3474 predicted protein Ostreococcus lucimarinus CCE9901 MFAVEYEAVPRLSGEGMRAGAKIALTDPYVGEDGTIWLERATTELLGGVVERLERARTRAMA...VFEAPNRPGVGEGDRVKAATRAAWEEEANEARALDGARDVEGAAPRVVVTPNAARGVVPDSQVVDILEIGGEDDALAGDARAMGAVASPRRSTR...SSLQASGEPIFSSRERSSVPSSSAPALDDRTMALVQRVNESAVKGLWTYLGCLRAARASLDDKSAMATVHAWITRTGRL...EVQEDARPPLWRVKIQISDPTGAASAYLRNAPLDAFAGTTATAYVAADARERESIEASIRKRLEEFCGRIRLASLKEKIMVVQKLDAQPTGFKPSVVGALRARKAYL ...

  18. Protein (Viridiplantae): 255076441 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available REEGERRAQDWWDRVSGHQPGGAGGTDGGRDPPTPPSRQPHYASSSPVHAPPTREPSMATPPHLDPSFLRGPGGGSAGDEAPGPVDRRGAPAAGSIAPEELEETR...icted protein Micromonas sp. RCC299 MKSEARRAREHAIRAAQAAEAAELRARHLEERFQFEARTTPTKDWRPGEDVEVDFGVAMNARAGAWDEEDEDAFTLAEALRISEEEFERATRSRA...QLLEALARSKEEADLVEALRRSEAESTTRTTTRAKTTDGVDVNDVRLSPRSPGRVRYGGEDLDLAGMA...FRRTVFGAGERPDPSAPPAAFRDGGSSGKFFFGGDGNGFSDGGGEGEDDVVERRAAERAAETEARLRRMEERLNAEKAAAEERRVERERVREERERRELEEREKEATRRANEAARAARA...AEAARREAAMKAAARRAAEEREELERARERAEELREDAAKRAEDDIGGEDLPGALRALGLGDVDEGDPAAVKRAYRKAALRYHPDRTRGYTLEQRLKGEEVWKLLAQKMEAFNRRIS ...

  19. Protein (Cyanobacteria): 270223 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FKDLPADYWAEDAIKEVAQTGLLKGYPAQDFRPDQPVTRAEVLVALATALKLKTPSVPVKTLQAFQDSDQVLNYARAKVAAAKEAGLVAGYPKDKILVPNKPATRAEMATMVYQALAMSKNGEKLANR ... ...SADLSRSRLSQQLPKPESTEEETSKASALDIALSKPKPAAPTPTSVVEFSDVPDNSWASRSIKFLNQRQIIAGLPDGSFRPNKFATRGEFATLLQKIFNQENGQSAIN

  20. Protein (Viridiplantae): 145354891 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:4521 predicted protein Ostreococcus lucimarinus CCE9901 MATTWTTARDGAGRGRGAARASTRRALDDARATRGIATRAVRSGGTGEVGEASRA...AVEGSAVETVETVEADLDLGSAAANATTATRAEASADLARGAVSGAWRSDVVPEVAYVVTWCCGNSVAHLTKRFDGLAATTLGLVFAAKTPESACDALTDDLRA...MTWMCAEMPNSQAREVDAMAWFLRETYVGDAPKIFIFAHDDRPFWPSLRAFVEELRTGERDGTVTRVVDARARK...MEKEFSVARDGKAPTDFDGDTFIAYSVAREPLVGTYMYTNAFALLLRTFFDVVKDVEDPASELADAPDRNASERPGWRVSSRYLGERLDWPISAIFAVTRDMAKHRSQ...KFYEALSLLVACDGKLTSAVDFEYFAALEWAHTLERAWLPIVFNPALRERAEGVPECLLDAEARCYEVLDWNAGVRDVVRYDPARHADVPWSFPQGADSRGLSVATEPRDVVDKCGARTWHDHPIAMGGGKNLEI ...

  1. Protein (Viridiplantae): 242076498 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :9001 4558:9001 hypothetical protein SORBIDRAFT_06g022585, partial Sorghum bicolor DSNPDLQQPKRWNLAAAMATMASALLRAARARDASRSAAVAATRAAEMA...SRSARAGAAAAAATRAAAMASRSARAAGVAAAAARAAAARCRGDSGVILRIKSCPSCPGLENGSTKPRDDALSYTSPCADYYAKLSDAGIIPMDKDLESDEAVWALSERWSRSTFVCL ...

  2. Protein (Viridiplantae): 303276298 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 608:3238 predicted protein Micromonas pusilla CCMP1545 MATRAREDDVDHADENHDGNDARDARGARASTSGGSDSLRSGATAAGLGFKCA...NSSVSWPIDELSVFDTANIAECRVCGDVDATDRGDVRETCDCGDFTAHVHQGCMARWVETQGTRCACGKSFQSVARGLNGGDEGSVHSAHVREVIFDATSKRRRTSAFAPPTAEDEDARRA...HLLLTAAYLRLTMDVPKPEDMRTLRKLAPFCDGPWNEFLRRRDEGRHRGGGLWNKIKKKFGFANTSHGGLDDDARVGDGRWSALNGDGEEGQPCEVFVPLFTRAPSRESSGGGGMSVHGGTHFAAGELVTGGG ...

  3. Protein (Viridiplantae): 303283188 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SVEKGDDDDANAAVVETFDALVVCNGHYSVPRTWPGTQTHSHNYRTPEGFEGKTVVVLGAMASGEDLAREIATRAKT...1 predicted protein Micromonas pusilla CCMP1545 MATSSSSSSTAAHASRRVAKVAVVGAGAAGLAAAKELREFGHDVRVFEKGRDVGGVWVYDAAVEDDALGVDPNRA...IVHSSVYASLRTNLPREVMGYASFPFASSKSFSGSDDRRFCGHEEVRAYLRAYATRHDLLDAISLGEEVTDATPVVAKASDDDDATRWGPKWRVTTR...EKKAFSVAAVDNCVSPLYKHVFPPRSAPSLSFIGLPWKVVPFPQFELQARWIAKTLAEGGLPSREAMAEEAAAFEESLARDGVARRHAHRMGETQFAYNDELSTLCGEEPLAGWRAEMYRATGRRKRSKPTEYRDAAPWDDEAAREAAREEFARFID ... ...VHLAARGWTPPREGPEDGDPGDFPASSYPRNCVLRPGIAELRSEGVAVVFEDGAIVEGVDAVVYATGYHYVFPFLEGETDREKSLRIGVHHASAVVWEPVYLEGGGET

  4. Protein (Cyanobacteria): 326741 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tein Cyagr_0021 Cyanobium gracile PCC 6307 MATRRTASAPADAPATSPSAGGSSAPGVASETQPLRHPLDQDTVSEWITRALDEGVRPEQALAFI...GLGLMRRMGGGIGDGFADWKDAAEADHPVDLAALRQRLEITELAIRTGAPLSTAEVTQLMGARPGAALVERGGLMARRLGRNVWKLSRSADGEREERSIGFSEGFRRRL ...

  5. Protein (Viridiplantae): 303281608 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PVNGMKRCYNPEKGYEFTYPETYLGDATMATRAANQREARLALDPGPATRAAPPKIFGQTVQEPQSAFGPMGGTGEENVSVIVARSPPGGFRLDRFGDARNQAEWLLGNVLAPPNSGKTSELYDAFTR...08:4710 predicted protein Micromonas pusilla CCMP1545 MALDSQAIAPPSPRRVFLGVLATTALALGGNFLGVTGKLLNEDLAASLRLDILY

  6. Protein (Viridiplantae): 308801465 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available unnamed protein product Ostreococcus tauri MATRIRGRRSTRNATVASRSDCFPSPLGFFSATASNPATTKSSETSSALSALFVRARFFGRASTG...GASTGGGGGDGFFSAIFMYLSISSVVPHPLGTRINNRSAPFFRSICHGLVDVSACKISNSGSRIVPHRSSPRSLSVSPLNPLTRAQNSFTVSPSYTGTLVG ...

  7. Protein (Viridiplantae): 145346810 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available STSAPTLGGRRSAIVGGGAVALEQRAMATRAERRRVVTRAGGVAKAAPGEPKKVFGLTLPEGEGISFAILAAGSLGSALGFAALQEGVFRIPGF...KFSAWMTVLTTFTYFLCGALEMKLTKDSRKGSWKNYGILSVYTYGGMALTNYALSYLNYATRIVFKSAKIIPVMAFSVLIV...6017:996 DMT family transporter: UDP-galactose/UDP-glucose Ostreococcus lucimarinus CCE9901 MISRATTVAIAPNARAQTHARQRRAPSVRA...GKKYNWKEWLSAAILVAGIVLFTLGDVASSPAFAPIGVALIAAALCVDAICANFEEKNFFRCETPSTTQEVLCYASLIGTAYGLVPLIASGGLAPALAFSQANPQVVPMIMA

  8. Protein (Viridiplantae): 255083392 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LEVLGYYSPLLAWHLTHGYAAHAVAASVSGLTKSRSSGLAKSGERAETHWHVAGANATVEDVRAVLERHGARMEDPAVVMSSDGSMRRVSTRGDEERPWGQSGWGGVHSERRSGSMATRTTSREPMATRTTSREPMRRKTMTTGTLRDG ... ...DHLGFVAFGGMDGPGYKPIADVFTGLGWQERDTFELENGLVTARWYQPPSVDFPMVVVRELRVDRFGEECVEVCEKYVDDANDAGEETTRAAALTGGTPWRIEPGEDD... hypothetical protein MICPUN_61490 Micromonas sp. RCC299 MAFMLGMAAQVRARETVDGYVETYMRRNPAARKALEAVVMQLTERSDHLRF

  9. Protein (Viridiplantae): 145356447 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:4912 predicted protein Ostreococcus lucimarinus CCE9901 MATTTVARASIAPTVSRAIARRSSRSRPRVARVGARATTTTRETRARTRRPTTTTTRAATTTATATAT...ATRRTTRGTTTTTRATREEDALATAIGATAAALARTRARTGRALTLALVAGAWAQSVNLGGTFALALFRAHEVPIVAAAFALGV...IPYLGLIKLLDFAVAGPVLVNEGKTPREAMARSRELMYGYRVLLMKTTFLCSTVCAALVCGTVGAFVACVPSLPNLMLGAEATTVGEAAAGFINGAAFDRVWVLGTPLERAATFALLVCGLVLSFLFTLGFRELLSLFYEETTARYSPPPPLDASAIDAPNKPSLWRRAQFWRKE ... ...AAWKFACAQYARTCVLRREGEKEGEARSDRRGALAAVNSMGWSVRAAHGELKDARGVLASLCVLDLRRLASVAWNSLITVP

  10. Protein (Viridiplantae): 308804385 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nnamed protein product Ostreococcus tauri MATSSAVEAADGSDDDDGRWWARLVPASEDAMAATHVDRAEMGATRARAVDGQRRAMKLRLKSTVIGRVVMNREGTARA...RGQPADLALEVPSGASMGDFDSDAGALNDAVSAKHVVVTCEVKDASKWPPEFDVKIVDVSRNGASLNGERMEKDKYYALADGDMLTLPFQLDYRFELNPEGTVPRATRAPIEETAT...PLQKKRASPAGRAIRTSSVPVGPVTELEQKLREMNEANEKLRTLVQELQGNIEQKEKRETELVAELERTKASSDEQRPQVDLVENEALVKELEETRAQRDEAKSKIEVEARARADAEEH ...

  11. Protein (Viridiplantae): 357155122 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RRRMLQCQGVSLLPRVLRLLVSAGAGNVSTGSPTEKKNFFFFSAACLALVDALGVSADEIRPLLEAEPDVLSVGLVDALTGVLLVTLEEEEKVTSARQRAARLMESVTAAATRA...AVAGHAAGIAAVARHVRARGCSPAAVRVLASVCGSGAAPETVREMARVGAVGKLCCVLQSPECHPWTKEMATR...VTYERGAIERWLAAGHTTCPVSGHGPLSLADLVPNLTLQRLILSWKPSHAAPPPNPLAKLVQKVMATEDADVLREAAAMAAADARA...LLELLRLHLRPDLFRALKTVLRDRDQGTTRAALQTVLNLRAARCDFRLAAESGFVHELIELIKIKLSAGNNGDGIGSGHGDATMTRDLAMEVLSMVCGRSAEARA...VLRLHAEEWARSPCVRSDMLYRSAEAQAAVARYVRGRSPAVAVHIRASVVRNSGSRAAPETVRVMTRMGAVGKLCCVGRKLGGRRALQSPECHPWVKEMARRALRLHAGEWARSPCVSSYMLYRYL ...

  12. Protein (Viridiplantae): 303284703 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8:201 predicted protein Micromonas pusilla CCMP1545 MATRARIQPSRVMTPRAPARVSRVSGRSATVLVRAAEKGIAGDGRVKMCNSKDAFE...AACNAAGDNLVAVQISTKTCGPCKVVYPHFAKLSEELADVTFCKIMGDHDADTRALMKEWGVRVVPLFMTFRNGEKVEEWSGAKPDVLREKVLAACTDAEKASVVNA ...

  13. Protein (Viridiplantae): 308805901 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available med protein product Ostreococcus tauri MATRAVAVRANARAGGIARERRRRSVGAGVVGRGRSIETRAWVGAPEGATKRQTRLRAVLKDDDGVGCA...IAFLISRYVARDKVRKIADGYPKFKAIDKAIGEDSLRVVCIMRLSPLMPFAISNYLYGLTSVKFRSYVIGSFFGMMPGTFAYVSAGMATR...DVNDGGMTEREDESSAVVLGSEGSGEKGVNVSLIVSITALVALAVSGITFKDDIIGSLGVFVDYVDSLGPTGYALFLVGYVALEVLAVPAFPLTMSAGALFGTYSGTLLVTVSATIAAT...QAVEGTAGLGALLSTAFGIGLAAFSAGYVGKLATKAVEEDTGECLTDECDASRSFEEST ...

  14. Protein (Viridiplantae): 308801020 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TVAGVADARVGFDRDRWCEGDRYAKFVGHARCAAHEAIEDAGLMATARTGEGRDDVGVSVGSGMGGVSDLTRAGALMARGELRKISPYFVPRILANAAAGRVSMDHGFRGPNLAATTACAT...hain A, Arabidopsis Thaliana Mitochondrial Kas (ISS) Ostreococcus tauri MLENMRALERGRAGARALEVVDVPEIERGWFDATRR...SAHCIGDAVMIAGGTEGCIDLVSLAGFAKARALSASGIARPFDSRRDGFVMGEGAGILVLETLEHARARGATKIYAEVRGYAASGDAYHVTRA...SPDGEGAARAMRAAMRDAGIVDPLDIGYVNAHATGTPLGDAAETMALKSVFGARAIESGDVLVTSTKGATGHLLGAAGAVEAAYAIMA...LHTGEAPPTVGYDVIDESLNIPIVGGASGVSSRLRPSTRAVVTNSFGFGGTNASLIFAKPPPLDAQSAAGVVRY ...

  15. Protein (Viridiplantae): 159490044 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 08 glutaredoxin, CPYC type Chlamydomonas reinhardtii MLATRSAAFASVAGRRTLVTRAMATKLDSIRETVAKNKVVVYSKTHCPYCMKAKSSINQFLQPSQYTVIELDGRADMDEMQDALRELTGARSVPRVFVGGKFLGGGDDTAAAAANGTLKKLLQEAGAL ...

  16. Protein (Cyanobacteria): 459484 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FT_0816 Oscillatoriales cyanobacterium JSC-12 MMEKPSSVEPMTSHELTQSLNLARALNLVVSSRIINGVLYVYNTTGHAKPWESFAAEFPLERLQAMATRAQLNQKLAN ... ...ZP_11389407.1 1117:34015 1150:18502 44887:884 864702:884 hypothetical protein OsccyDRA

  17. Protein (Viridiplantae): 145351138 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:3572 predicted protein Ostreococcus lucimarinus CCE9901 MATRATRATATATPTLRQSMTALVRLVHPDVLAATHPEHARANG...DALAHLQGTLDDARGRGALPGARVRRLRFYVRDDARAEGVRDVGFTLRTTGGDCRNVMRRDLGALFAQVGIEREFEWGEGDWGATRTETEAEDEGARGRGEGETSRSSETPEVAQAYREQTTTNAGGGGTR

  18. Protein (Viridiplantae): 145350462 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DETRGFGARARARVAVAKTRAREGATRGGTRGDGTRREATRDDDDARTRDAGGADSVKGARGEDARDGRLPTIPRGTYASLATALV...E) family transporter: multidrug efflux Ostreococcus lucimarinus CCE9901 MLARVGVGVGARPRGGGSGTGRATRRAATATRGRANGRTR...XP_001419624.1 33090:1988 3041:64 1035538:2580 13792:2580 70447:1423 242159:3392 436017:3392 MOP(MAT...ALGFPALLNSVNEPVVSLLETVLVARVGTVFLAALAPASALFGLVEEVCFAFSVVVTTAVSSARAEFEDVDAAVPERVKQTVSMSVMA...LTVGQTFIFFYLWKIAHGRGLFSMRSVFKGAESVGAAIARLYRRLEEEHIASEFRWLVLSATARMTTYVIITSCATNLGVISAAVNKTLLDLYILLGLCAEPVFTVGNVLLPRKRRSLVEVLTYRRA

  19. Protein (Cyanobacteria): 434328 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RYAFGGGSYSSAEMVDQLAALAGRFPIVSIEDGLAEDDWEGWRLLTERLGGTVQLVGDDLFVTNTTRLQQGIEQGIANSILIKVNQIGSLTETLQAIDMATRAGYTSVISHRSGETEDVTIADLAVATRAGQIKTGSLSRSDRVAKYNQLLRIEDELGSQAVYAGVEDRGPRGKG ... ...VSKAVENIEERIAPALCGLSALDQGAVDEAMNELDGSDNKSALGANAILAVSLATAHAAAKALGLPLYRYLGGPMATLLPVPLMNVINGGAHASNNLDFQEFMLVPHG...ate hydratase Cyanobium gracile PCC 6307 MYDSLDLVIDSIVAREVLDSRGTPTVEAEVYLEGGASGRAIVPSGASTGAHEAHELRDGEKAYFGKG

  20. Protein (Viridiplantae): 303276404 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AASDVVDLISPEDARRRQSAVAVAATRAPSPSPSSSSSPPPPPLRARLGRATTTTTMATTPVEVSVVSSSEDEDEDDDDDEVPARLTPPRGGG...564608:3271 predicted protein Micromonas pusilla CCMP1545 MAPVPPSALWSQVATRAGGTEDEVQRAVLRAAGFEWDDATGLLTAWPSDGAIALTPPRPRPHPRA...GGKRPRPRDAAAAAASALLTFEDKIGLWIKSKPELYDRVLLMESVDVDDVLRAINAEVAPSTGGGGGGGGEKKTKTFGVGARVPRARLLAYLDDEGVAFTQTKSRQAKAARYGNARF ...

  1. Protein (Viridiplantae): 303272942 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 564608:2204 predicted protein Micromonas pusilla CCMP1545 MATAAWTASPTRALAPSRRASSSSSSSSSAASSSSSSSSSSSRSSFRRWRGGCRTRLASRMARAT...SKRDDDDAADAVATSENVGDKAKSALTELVVRPFTSFIVERVLSPLYETRDAKRDECGPGMYTDPRTETCVFICRERRLYAHDGEGIVDRFVRFFVNKLTGAGGDCDVGFFYDPATRACVPICKPGYVYDPTVKKCVAMEDELRT ...

  2. Protein (Viridiplantae): 145355084 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 17:1506 AAAP family transporter: amino acid Ostreococcus lucimarinus CCE9901 MATTTATRATRGCVAGRATARPTRRGVAIERRARARRGFARVPLDAGRARRDDAT...TIAGRGTREARATRTFASAGDASGENAAIVNTVKAIFGAGGFALPWAFAQGGIALVGTCMAASLVFALEALRMLIKAQDALVGAGASTASEVATYAGLTNAAMGRA...GDAACRVMNVLTCFGITVSYLIFIAETMKVVVPALGVSAFGASPTTASMLALVGPLMIA...LSWLREMSGVAVISAVGTASVAVGMAVTTATALSNPLQLGALPVANFAAFPGFFGTVAFLFFIHFTLFGIKEAMPQPDKFFGAAVKAFTGAAVIAGLFGVAGAAGFGT...GVSSVVVTMLTGPSGIAVQLLLCLNLLSTYPIMAQSALRICENVLEGDKPGSIGAPQALAVRTAFTAGALWTAANVPNFGVVLGYVGGVCCSILSLVLPAMILYLTQKKVKAEIVPLELARIGGVFVTGVTCIVLSIVL ...

  3. Protein (Viridiplantae): 159468059 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PEVLLKRPYLCPPADVWALGCTLAEMATGRTLLPGTSSLDQLWRCLGALPAEPWPATEQLRPVRLPGRPLAARLAHLDTQFVEVVTACLRLDPATRASADQLLRLPYFDDV ... ...hypothetical protein CHLREDRAFT_136163, partial Chlamydomonas reinhardtii MQVLHRDIKPPNVLLDPDGSIRLCDFGGGGGRRVYELQYEDLTKYVVTRAYRA

  4. Protein (Viridiplantae): 303288297 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 564608:6414 predicted protein Micromonas pusilla CCMP1545 MATTATTATRLASSERASPPPPPRRATVRSHHRRRIARDRRHRLPAATRASSSSSSSSSSDEEEINVPGRA...RVRVVLSTAPRTSAPRRSELGWATRTVFESKPFALFQTLFATFLIAYAASHVDAETLEGFATLWREQSALACVSSCDLLVLSLAMYDALSEDMKRRGVFERGKALGFCALPVLGPCLWLLTRPALEE ... ...ALALGWLALGGVATTVAPSGTAAFDAELVTSLVTSPFSGAANPIFEALFNSLGVVPAVYAALLLPGARDQPRVPTLPPVVASFALGFFALGPYLITR

  5. Protein (Viridiplantae): 303278414 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 564608:3836 predicted protein Micromonas pusilla CCMP1545 MATRGATPTAGFRAYAKPRGGRPVARRPGVRVALLAGLAAVLTLALAWAA...EHAGGTKEYDAAAPEEEENAAETTTTTTTTTTRAAEDEATTTTTTTATTTDAPPPPPPPPPSPQSPSRPPPRSRHRPRDASSNSVGFLLQMAREPKASLEIVKATR...FGRGGDDGSRVVRISSRDAAGEGGGASTRAARIADAASAATASFVPFKRAKKRAGGAAPGAGRAGRAGAIDASGAATNATDAVARHFSRDTPHRFTAEDAAAARKRKE...PRDGVDAGGVDDRGWGTPMTPALSRELAKRAGGKRPREHYGLCGGSVLRVDALLRAVGATTREDLKTFQARSPHTGPHTTASAW ...

  6. Protein (Viridiplantae): 145343508 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LAMPAYDASRGLARASTTRRDATRRGGLADVACEGVRAATSWDGEHHVGIAVRGYEFEHQHAFYPGLAMATRATTAAVGRAARLAGARTTRDDARE...17:1275 predicted protein Ostreococcus lucimarinus CCE9901 MPRDGDGATDGRATRAAFGTFLRDASRRRDGGATTTTTRAMMFRRGARTRAVALCVVLATR...RNLGNVLLGAPAIALGFYLTKRFAWSRDARVFVKEEQRFFVGAYFVKLGVMTVIAATYMHVQVATRFLSTSPAMYWGLAHLGRHSKAWRRFIATYHVSYALVGAALFANFYPWT ... ...MFRSNGVLCVVLLLGHAGREMFRLLRDANDETRHRRAARHLKRAMIAIALTVAPHYAFAQFGDMRYCNGAVFDGAERPYCRPKSWRNLYGYVPSGMYSFIQRHYWNLGFMSSYRA...ECAAGAAAVAINAYAFARSVEAMYALSTQLLRDEALAEAAATLYAMNPANVFYGSAYAEAGFAYAQFAAGSLLQENKVLHSGVLFGVAT

  7. Protein (Viridiplantae): 303280011 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LARVASAAATRVSRRRLARSARDYYAPDDVRVGHAIAYVKRDRHVLAVVTAPTRRRQVAVVTHDGASDKVELKHVEKVFALTTEDGRRLKTKQMMATRAFATAEVDANARA...64608:4285 predicted protein Micromonas pusilla CCMP1545 MAPLVVDRRAHHGCASSIFASGRGRSPARVRASSSWTTPTTLFSTRLLSARRALSPSLDAVRRVADATR...SDDDASASASASARLAAVAAKSGAPPSLLRAYATHRVLSEDATMFKAMSKGFYAPRTRVGIEARSDAQTGPRTTASAW ... ...GGGVARDAWARVVAARAGDGDGDGDGDGDGDGASHQLAPISTAELAAFFYPEEGSGSGSG

  8. Protein (Viridiplantae): 303286593 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 564608:5973 predicted protein Micromonas pusilla CCMP1545 MATGGNNVDAARRKAATRAYNALPMKLVIVSKGGGASVDAACGEWADKIRRYAPFDEIVVRPNPKNAKDPRA...QLEAEGERVMRHVDARDFVVLMDERGKDLSSEALAAVVADVGDGGHSGIVFCVGGPFGHGDAVTRRADARVRLSSMVMNHQVARIVLLEQAYRAHTILRGEPYHH ...

  9. Protein (Viridiplantae): 302837448 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KHGETAFLDLYQKLYEAPDPAPALAMAFEHATRATDLEAQCKKMATELAEYKAESAQIKNQDLTVRKLEEKVRALE ... ...78 3068:4778 hypothetical protein VOLCADRAFT_47269, partial Volvox carteri f. nagariensis KTVGPLLKQYQEEIDRLTKRA

  10. Protein (Viridiplantae): 303288534 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LRNGVHHANAVVWEPVTMTGREGRRPNPIHRDRPFATRRDPPSVEARRRAEARVAFESTTSKKRTERERLPSSSSPPPARREREPPLFTSSERRAAETTASSAVKAATLAARLARAERELRAAMATR...4 predicted protein Micromonas pusilla CCMP1545 MEAAAATHAVNYGVATRAASEAAAAEAAARDDADAARSAAEAARALADDLREELRNVRGDVASAAAAALEMERHVAATQRA...VTEAVRKLAADSGGLGVRVKVSDNLRTLLGADFAALLPPPPSDATTTLETTGFVTDVPVPVGRAGGGRLVILYRAMTSPATRENDLAGSDSVEVGVGGLHTHAPFVLESLWIDASTPSADRQVLTVAARA...RDAEATAADARARVFALESELRAVRAELKCATAATADLERARADLTAGVAVMRDEWRAASDAATLNETRAAEKARVVEETKLAARAKLRDARAEADRRVAT...ASKASPIDARYKAIKRVDAVMRREEEAWRAAKVLRDQRGGGGGGGGGGWEAPATSSRIARPVPARRGDVVVAARTPPAFGASATRTPKRTTTTTRTPARATRSAAAKS

  11. Protein (Viridiplantae): 145350768 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 17:3476 predicted protein Ostreococcus lucimarinus CCE9901 MATRANVDDGAREANALRTFLRDAKEAFARDPGACDVSVGNEACDLDSVACAVATARAASAKRGRDDGERETRA...DRVIELIGSCSSLVYRDVVAKAADEGVARDVARLLLGAIVLDTRMLDATTTRAAPVDFAAAESLRDILGWDEDATRAEYESLSRA...VPIVSCAREELKLRPDVVLALANAGVKLGDLTCAEDVAAAATKATPRSVTLVDHNALSARLFPDAWQARVVRVIDHHEDSGMYAERA...RHDQSSFSCAQLLAKDYKQWTMGSLEVGIASFGVRFQDLLARQDASSVNDEIVAFVDARRIDVLFMMSSFEDADADGAFARQIDVTKSSACSIELEAVMRDLGERTPLAPLRLPENDFGVFKSARAQLDVKASRKKVQPILLEILARF ...

  12. Protein (Viridiplantae): 145341964 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 17:1029 predicted protein Ostreococcus lucimarinus CCE9901 MATRDGDGDAATTFTPATLRALVERSNGALCAFACDGVVFDATLGKDFYGVGGPYAALNGRDATRALATMKINVSDADEALGARGLTEEELKTLGEWRAKFESKYPRLGTFERRGEGN ...

  13. Protein (Viridiplantae): 308800738 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available dual specificity phosphatase Cdc25 (IC) Ostreococcus tauri MDDDRRRLSTRATIARVRPRPPSRRVSRSVFVVRKIRALGIRRTATRATAARERIRGDRGGLFFIPAARA...VAQAERVEERGEGSGASTATPLLKRKARTARAEGVDEVSFLTPFARALSDASNGRCVDGGQGGAAAMAAAAASAMPCRPLASPPPMAT...LASPPAPPRKLALGQNMSYGYTPSRGDTRYDASQRVDYDEPETPALAGSCALIPSALDAALGLPTIDGATLRGLMSSHDAELVVIDCRFPYEYSGGRA...RGALNFHLPHDVQRFLASRASISANTVYVFYCEFSSERAPRMWRHVRNLDRRDHIANYPSLSFPHTYVLAGGFSKFYEQHPDCCEGQMISMSDSRFTNLCREYVTRSREVWHVAQRATSLRHIPSDQDLIATARASNREVQRRGAINFDEVADMDNE ... ...WRSTSVARGGSDGVARENLKTRDSNRRAPRVDASIGRGRRARVTWWCARRLISYDAWSSARGKHGGGMCFASPPARKSLAFDDTEDASERSKIVTTIAFDTPRA

  14. Protein (Cyanobacteria): 349129 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FT_2986 Synechococcus sp. WH 8016 MATRALNSGLWVRRLLIGGSPDQGRCPASEVNDEACPEKPVHLTYEALEHINKIRISRKNNSSQQI ... ...ZP_08957639.1 1117:13116 1118:13267 1129:5245 166318:2387 hypothetical protein Syn8016DRA

  15. Protein (Viridiplantae): 303282965 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RGPRDSAAAAAPDDDDAFVVEAVGSCLASGGDESSVAPRVAALAAARFDDAELVVSAPCHVPFLEVRDGVDDPRVRVAAAALLEKEESQGDDARARAVAAFAELGLAASRRRCVASEDLARLTRAATR...RMAAAERAMATRHGSVRFGEDAFAFREMGSRGGQRFDLLFPREGEEEEEGGGEGAGEGGGESPQGTAFTTR...:873 predicted protein Micromonas pusilla CCMP1545 MASSAPTPTPTLDDLWASDRARVSVVVAATPKPGVDFATARDALLAVRWDERSLEWHSTR...NHAGVGASPPYAICVFVPLVDLNGEVGFTQFWAGSHKADALIGFGSAAEVLRGGVDGKGASYFHTVDAGGFAAYDYRLMHRGMGNFSESTTRPVLQFLYAKSTYKETKNYGSASLFEGGTEGPATR ... ...TGSYGNQSGLERDERDGGDGGEGDAAFVRAFARRAPWVRALVDPILSPPPLSSSSSSSANSASPRRTWWCDVSIVYSKPGARAQDWHCDGRHLAGAARA

  16. Protein (Viridiplantae): 145348646 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available MLAREETERVEKWLRDSAAATRRGEGARGEGSRGRRSDDDGGVKMAMASEEDVEVEEYDYGVEEERAMRSSMATTLVARESMSSLFVPQRSPARSVIHRPIPRRPLSASVEGTEWTTLRAKATR... 436017:2871 predicted protein Ostreococcus lucimarinus CCE9901 MGAVRTMRDGTTRGEGERDAREGTRARGTTTTTTTTTSLDAFDARLARARERA...SGDTRTNVSIVSDEDGRSAFQSLARDNRAGLDGLGDMVARTTISSGVLDDGGLDGG...MSTPPRPHRSPLRPPVARPRNRTLSEDFSSPVRLSSSMELRHSTSSRMTLLESVAHEAEYERARMSEKSYDDSEPR ...

  17. Protein (Viridiplantae): 145348312 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PGAIGDAARVVSSAAMCARGRGRGGAAERLRDAALATCSHESDFAVACFAGSMFAKMAETERRVREAVGTRASAPATVAFALALGMATNAAAAASARALGYGDACWRGAGGLVFALKTYRA... 436017:2775 predicted protein Ostreococcus lucimarinus CCE9901 MFYYLAWRSLEAIARCWRATRDAFGFEPVGAAATLGVVFVERVARRA...RVDYARGYRGRVSFFGFIDVPAETASVAEIVILALMDSSPTALNLYGAGAAVGFMVASFERETMRGLACATRGVKKLLGVALGPSVRVGSRVVLARMRNASLNGNWGIVVETRGDQVTVSLDVDGRNITALRDNLIVV ...

  18. Protein (Viridiplantae): 303287218 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AAEAQRRRADAAERELSRLEVASCAAAKKCRATEDELARLRATRAQTETRASEASRAAAAAVAAAEARDAETAAKIAKATADARDAADAARRDASAAEASRA...RLAAARGDGGDVIETAVNEALLEQAGAHEKAMDALRTTHAFDLEEATRAYEETVARLEREKEDAAAAAVEAAEAADAMARRMEEDAAAAAAAAVAVTARKKKARADEEAAEARRA...:103 predicted protein Micromonas pusilla CCMP1545 MAHVDASPPVSPAPDVVAVAPPPHPGKLAHARVERARWKERVVAARAESDRPLQTLRENAARHRPAPSSPRPDWVGGATR...KARLNAVGIEFVQGAVASRDARDAVDGGAHVFVAGGRRRGGRVGVDGLGGEDRDDDGGDDDDDDDATVHPAFVDVDAALRAMTDRAYVIEGADATAAASTRVVKAWSDNFADAVSRYRVEAKEATR...KALESAKEERESAVGALKLEIERLRATTRATRVDAGEKEEEEDDDEEEEDSTDSKGRKKGGASARRKATRKSPIVSADAAGWATATEQCKTLTTRLYKERA

  19. Protein (Viridiplantae): 145349555 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:344 predicted protein Ostreococcus lucimarinus CCE9901 MSRASSRVAPALARRARAATRDARGATTTTRDDDATRRRRRATTEARDDGQRRALDALERFYDGARLGTRA...GRGVYLHGGVGRGKTALADATSEDAREKGGLEVERTHFHAFMARIHRALHESAMKARGEGGGGADDPLWTLGKNMATKTRQHV...LCLDEMEISDVADAMVIERLMRSYFAHGGALVTTSNCAPERLYYGGINRAAFAGFADGLRARCEVVDLDARESVDYRRRARDEDVEDGVIFVGDDDATRERLSRA...DVLYEHRVVLLANLWTSPDDLFDVVDGAVDDSDAFRELAPRERTRIENAFQSTLSVTRDGGSSGRSTTMLAPELEWSATGRVGASLAHVSGVNFTLAASPRAASRLHHMRSSAYFNTSP ... ...WDRFTRDAEGEREVDADVGRLRAKARVGAHARFTFDDICGRRSRAAPSDYVALAERFKVICVEDVPRLPVDASENEARRFINLI

  20. Protein (Viridiplantae): 145353482 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:4191 predicted protein Ostreococcus lucimarinus CCE9901 MATRRRARGARAAKRALACALALVACVTVGARWRSGGEASSTASTSSATTSVDDDAREGAEAAT...AARDDATRSTLKATLLAGAKDEGACTNERDVRGRFATRDFALVREVERRTRARVGFGWARWGDAEMISSARDGSPMRLAVRALMSVSAT...VEGLPFIGHSAFVDASGKGMGGDGAADSVVQRIFEIGDAFDEPPVVIMAAGMAAKTAILSAQDRINSKGWGLIDAGTTLDGYAGVKSRDYNDPRVYCRKSRERARDEHDGVDFWFAKGVCEKFGA ...

  1. Protein (Viridiplantae): 255078172 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AQKTSEELALEKSRAAAAEEKERMRVAARRAAARSGGLGGVARAKPSTRPTTPSFARTHRMATRAVVAHGARDENSPFRSVAQTFRKETFKPKEESKSFHNRAPTKPKSPALSKSNAAGRA...VPHVPPAVATRTTRAMAARAAAIAGAKREREPPAPPRTHATRSSAGQRMRAKLTVPISPNLSRPPKRARA...TDKRGAYARKVLERREAEEEEAAAAKRRVVAKPVPATTRRRSSQCFVPNEIKVTQFQPFNLKGEALHEYERKREAQRREEEEAAARARAEFKARPLPFSTFNPMFEVNPSDAAPTVPMDLKLPGDTRAESRA...RFEEANARRIAEQERARAEEERERVASDERERRRLRRSTVFKARAVPDYAELATVGVAPVPEAELTVPESPFATRRSRRVYRYN ... ...LKTPVALLDKAQTNAAAKQAAAEVTAEQAKENPPSAVKSAAKAARTPGATSSTRVLTPRSHNGAMPGSSSRVAKTPATGRSAMGAASRAGGTPFPTEPPSVDDGATDEDSAEYAT

  2. Protein (Viridiplantae): 145353460 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TTTDDGGAGGWFGGGGGWLGGGGGGGFGGDGDDATRGARRAAFALAAATATGAGGAREANATTTTTRRRGDGGRRATKLGDMATSALYGFA... 436017:4186 predicted protein Ostreococcus lucimarinus CCE9901 MRRLATPRVAVAGVGRREDARGNRRDVARARRSETASTTRSETRTTTRDGIEKSSATTRAT...AFYGIKIALKRLFAPFALFWGTTQLLFRMHAVKISPAMLHERLVRPYLPIEYQKSLNDFGVAAMKTKAAKNAMRDGWWDKQERRFWTCAHRLLPACDSAMGERAFVFGVILAGLA ...

  3. Protein (Viridiplantae): 145349678 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:3185 predicted protein Ostreococcus lucimarinus CCE9901 MATRAGDARARATTTTRVRQGVRFGARRAATGRRRAVNEAPLETATR...NQTEHALACREIAAYAPSDADGASAFARTRAKRREMIEAAEGSDAVVPVFGFDESNVVIFVGVKANAGGVDANDWATTFGI...TSAQAIVGAGAFQDASLFEVVKSSKANEVDHRFTHVARVSLGPVGQDEALVSAAEDVIRRACAAIDPSALIAPYACVYNIGKKGTPPGALPAMREIAKKKKENDEMSTQSTRTTADV ...

  4. Protein (Viridiplantae): 303286998 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8:429 predicted protein Micromonas pusilla CCMP1545 MMMTTTTRAPAAARASTAPRVDRAARASSASAPRHHRAIGAAHRASSRRRPGGPSVVALAALPRGAAAAMAMAMATRA...DADAASARPRDGVVARGRKGMLGRVIDGEDDETTSKKKKEKRAAAAADKAATFDGAGRAPKGSASMAASLEGGLGKASSKGKNWIV

  5. Protein (Cyanobacteria): 146853 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SMNWGYLHYGVVVWLDVPVDQLYDRLRSDTARPLLQEGEIKSKLQSLLNERERLYTQADVRVCAGVGERAEAMATRAIEEIQKVIKPETGPDLN ... ...se Oscillatoria nigro-viridis PCC 7112 MDGLRGVNIYLVGMMGAGKTTVGRILAKKLKYRFFDTDELIVRVTNQSIAEIFDREGEEAFRELETKVLGELSAYKNSVVATGGGIVTR

  6. Protein (Viridiplantae): 115482898 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LRTNQQHQQLNTHQKPQGDKETTTQILLAGETLSETRAGIHPQAMRAAEAAILATTMTGTIRAANHGVVAQIIPGDQIIVKNMATVARRDHRRRGGNLKGGSVDTTRMATAGRALPASSSTVENALTFLYSPK ... ...4527:8158 4530:8158 39947:8158 Os10g0511900 Oryza sativa Japonica Group MWAEKLQHGNHQVLRLLQGAQKHQVGSHHLARARNLSLIPHGVPAKAATR

  7. Protein (Viridiplantae): 145347182 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 17:748 predicted protein, partial Ostreococcus lucimarinus CCE9901 MATASGRVVAPRARVDGGRATTRVGRRTRGAATRARADADK...EDDSDSAGAVVTSARKASFGPSRKDADAVRRDLLEKSLASAGWDDARMFLAKRASTALGKAACETLEASTTSREARKALDETEAAMAMESKHGVSLEFGGMLTAEVRRGFYKTRQGSPLGGDELAAT...VIPFFDKVLVDIGDDQSLLTSLSTFSGRLTRAQAILEQSTPESLVLMDEVGTGTSPAEGAAIGYALLKALAGIIPGQLGACLTFATTHHGQL...IKLDVIAAKCRYSQALNGVRPEFSVFADDDDGFYEAYEDEDEDEDEDIEEQDDEGFDEAREQTKKPPIEKSSLLLELVGLRQPVLASQAIEAAAERRQAAAEAVESQNSRGSSSTGYKVATR...KALKYEHEEFENAAVEFDEADLRPTYKLLWGVPGRSSALQIATRYKLDADVVHEARELLGEGLVSLDDTISKLETARRDADADIATAIGM ...

  8. Protein (Viridiplantae): 159473078 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YSQDFFYTVTRQKGYRFAMEGKRRLHSPSEMLLQQATRAIEAQEAPPAAPANKPAGKRGSRKREQARQLPSRPTVQLPAPSRGTAAATETQPTTAPVRLRRASATTQSQK ... ...3 predicted protein, partial Chlamydomonas reinhardtii MTPVALAMLSPPPHETYPMPCLYPGENDLAGVDFMLSLHKGQHAKDTRVVSGFKPGDRVRLLEATGLFDKEMAT

  9. Protein (Viridiplantae): 255083951 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QVRRLERSVTLARDDARMATRREHTAVANLALATSNLERERGRLERACEARIDEAAKRAKDEGAAARLELKRRVENRERANTNLRERIDEARAALRDARA...HGEAAETDARDVARERDDLAARINALEADLAATSRRLDDTERALRSTVASAEARTRALDAELARERARGQDARAKLGEAT...ERISSLDAEVAARRAAAEAYTRRITQAEERTRGMERKVTHVRSRLADRERDLANAAKVRAREMEKEAERRREFESARGWFDAQMSAMRGEHARLMALVKRFESAALPDWMS ... ... predicted protein Micromonas sp. RCC299 MVPADEQTRTHAPLMLAPYLNDAKDLARRDDVFIARQPPAAAPPVTARSPVTSRGEPIVAQPVSSVKSADIPPMDGSETREQRECRVLRA

  10. Protein (Viridiplantae): 303277717 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VLLNNSGVKDTEEWTALQNLPSLPRDMSAVDICGDALTDRPSDAWAAWDDASLRAAREAASAARARATRARDDATRATAAATALTIHAKEILDVAT...DALARGDASDVPTRAHLAGFSSRGEKTFDGSTTAHASTETRGGKDEKASTSYANATTFPPANFGDLDAEQQADAFYEKGPLRTLSARTFD...FVAADGETTDVRPMATDSIITASGKKMRRGCLNCQAQKTPQWRMGPEGPKTLCNACGVRYRKGLPMDGV ... ...4608:113 predicted protein Micromonas pusilla CCMP1545 MTDVARPLPLDTHSRQTSLSAADFLFDFSAAAPGGPLLTSNCATAAAQMASLGAFVNVDDARETMDVGHAT...SVKLDKAGEAGSTREDSGSGVVTPNVLSERGGGGGGGGGGGGFGVGGFYADVSSPFLGGGRRSGRKRWRPAGSDDETDMEDDENGVGVGVGVGIGVGNGIGNGGARKPPARRA

  11. Protein (Viridiplantae): 145351503 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:2527 predicted protein Ostreococcus lucimarinus CCE9901 MATATIGRATLEATRARARATATRARGRWDAGRAARARATGRARAT...GVDMLPPLDETTMLKGIDLNRLTDGVHSKEALDMVREHLMAVLGGAGENAYSSQLVRMSKLQAAQVYAASIMFGYFVTRADKRFQLDRMVGTLPMDPMESAMA...GRGDGFGDAETNPAAGLKAPSTPESPRGQQLAYILRTAPEMFDAAVDSQLDGLGEEVEREAKSASEEAKTEQLVLFKRIADVRALERRNGLEDIMYTTIIQKFLSV

  12. Protein (Viridiplantae): 308800982 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available dehydrogenase 12, like (ISS), partial Ostreococcus tauri AMTRVVTRAGATTGRPTHCVVTGANTGIGLETARALARTYDVVTLACRDETRARAAMAT...IGADDLCDAELRFASLDLSSLASIEDFGRAMRAADEAIDAFVANAGVMALPTATRTRDGFETQVGVNHLGHYAAIGWVFPLIERAGRETGDARVVVVSSEAHRIASRGLRRDDLFGETR...YGAWTQYGQSKLANVLFANELARRCEGRGVTVASLHPGAVDTELGRYLQPPDAEVKWWQKKLYNFIRKFLKTPEQGAATSVFLARDVERGVANGKYFSDCREKTPAKTCLDEDDALWLWNRSAELTGVAFDLERV ...

  13. Protein (Viridiplantae): 224121822 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QNQGKSGRLKSSLREADDEFVKVLAVKTRKEAKQMATRESISATRARIHELQKSVLVQRARRDEFATIMSQLSLALATSEE...9:9477 3694:9477 predicted protein Populus trichocarpa MQRKATETVRTQMECMRLICDRDAKIQLHKVDSFMASFCNSLDSIKAIVEETM

  14. Protein (Viridiplantae): 145355665 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 6017:2814 HAAAP family transporter: tyrosine, partial Ostreococcus lucimarinus CCE9901 MTTVPTRATTRATTVSTRARATRAMATTTTTASTARHAATGGRRA...RDGRARLEMTRGGGGVNVNDASTAGRARRRARGGRRTTTTTTNAISDATEPELAATRATIPISSFDEEERAVDEERDEETHTGSLAGVVALIVGSTVGAGVLALPAAT...PSTIPIIFLTLVYHDLIPVMCAFLQGDMKQIRRAILIGSSIPLAMFLLWNTVALAMAGGDITADPLSIISEDLGGSASVLLSLFGVSAIGTSFIGVSLGMSEYLMPFM...ENAVSRVLTFAAFLSVPLFVAEQCPNIFLPVTNFVGAYGMTTLYGVMPPIMAYTMRQERRESRRADPFAPLALRFKTNTLLPGGRLTLSALSLSAVAIALSKVYEDIS ... ...AEAGILPASGALIGVWILLVCDALLLAEVNVGIMRERDEDRLTHGRGHSPVVISLSDMA

  15. Protein (Viridiplantae): 303284062 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 564608:5354 predicted protein Micromonas pusilla CCMP1545 MPRAAAALASSFAFEDTPEARLRAALLRAKTAEAEVAALRDENESLRHELAVMMATTTTTAQTRCQPCARRA...ANAAPVASPSPPPSRPSAAEMFEHVALEATAEKEAAAASLLFSSTSRATRLFDAESEEEEEDDDDATDAVLVVTSPSREIFATPVKTRAASATTRTKAPAPDAAT...TSASAARARAKVDATVEAAATRAYRAAMRTRANRALLGAGETPRERYSPPTPTPRGRGRRRG...AEKENAEGDGGGGGGGGSVKKAAAAAWARRRRGEGGREDQSSTVAPPGRGRSIAERAARAALAAMASPRPATARPKTPPRTP ...

  16. Protein (Viridiplantae): 308807431 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KEFCDVPVRWRRPGADDMATRAHARCMSERSRVRRRDARKSRSALRELSRYK ... ...unnamed protein product Ostreococcus tauri MSHPRRGILRRVHPHAADGGGLCRNSNRERSGESVTFGLAGRSVNCVRSSGGRRYPPASDASSASFECARVARAALTDAPPTKRRTRAT

  17. Protein (Viridiplantae): 145345647 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:1985 predicted protein Ostreococcus lucimarinus CCE9901 MATARATAGAPARATTARWIATRSRATRATRGTRGRARATPNDGEAHAAYLRDVAATRA...PAELEALARVLDALGCETIAPNARRGIHPLVMPLARTREGGVIGLMVTEDDGEATPVVEVRDGAHATMLAKSARDYVHRAIVEEEAMSDEQTT...TVAAAAGAVGVSLHAHGAFKTSGKEFDVYVTTQIGKFPSSMEGLVRRHLKRNDEQSALITCDLYKATFGDWGAPHVFISDL...YSKLGRDEEARDAARQALQTPWSTIGGRDAITRMIDVAGWSGKTVAEIKEVLESRRGPSAAAFDGPKSEKQLAREEGELLLDQIAAGEIESSTVNQRLAECYMNAGKPALAKFIMCGAGMPAL ...

  18. Protein (Viridiplantae): 303290272 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 4608:6886 predicted protein Micromonas pusilla CCMP1545 MVGDDDATRAFTRTWTNGSSSSALRGAGVPAGSALVYSTGRSLESFASLIEEKAAVMAT...PDALICAVGTKVYRRVVVPNAPASVARAAAAARGFRAGAYAWIEDDAWTSRLDDGWDFEKVAAAAAAAVAAAGTEDAHFRPEEEARSIHWSPYDRVGVFTTHKITLGVRDEKVELVTASIAAATR...KEGLDVKTIASGVGGWQYLDSLEYVRETFGADVDRTVACGDSGNDLMMLEGACKAIVVGNAQPALMDWATDAVRRERDGGRVFIAKETTARGILEGLESFGFLTR ...

  19. Protein (Viridiplantae): 145351089 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:3561 FNT family transporter: formate/nitrite Ostreococcus lucimarinus CCE9901 MMTTTTTTTTLTTLTTATRGTARRATRTVARVARPTFARAT...AVGGASRTRTTRARRGGAVVTRADALAPPAVFDAACAASEKKSAQAPTTTLTLGFAAGALIGLGALLMTCVGGASPALAANNPGLSAFV...AKASLPFVAAFTKGVLCNWLVCLAVWGTMATTSVAGKILAIFWPITMFVALGFEHSVANMFLIPHGMLLGANVSWAQMMTGNIIPVTLGNIVGAAVFVAGVHWLAYGKK ... ...KGAIGLPAGLTMVILTGAELFTGNVFVMLSGALNGVANERQVARSWALSYAGNFAGSVFMAYMAYTAMTAASPAASAAAVGIAT

  20. Protein (Viridiplantae): 303290779 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RRDAAAADAAYVKTLMRRALVSGWQKATWDARIRRIKTMRAEAHHVNRVLRATSHAWRMAAMATTKRRRVAAALHAARIKTRSGEALRAWKVTSVSRRAHRTLLLARAVDARERATRRA...564608:7000 predicted protein Micromonas pusilla CCMP1545 MHAEWRALRVATRAWSALATVNRVPNREAMMKLETAADEAFRYNASLRFLLRWEDAAKTMKRA...AFNGWRVYAESEVDARASAAEMANVAAASEHWKRVASSNCARAWRVQTVAAKRAREEAEARRASVLRCETRRAFKLWRLNAAEAATRRAASDAAV...LDAWRLFIRGKRENRTRVARRVAVVASALATLKRDRAWCAWAEWTRSAAVKTIRKARAAEHFRMATTLRALAAWWDRVLRRRDKDDAMVVANDARDRRYAYGALEGWVRYVVTR...AHHAARLVSTWLSTWRDNVREVREVREREETAEAHHAVAVAARAFRGFEDAARRGRRRRIAARWWQDTHARRALRRWRARTVAKLRAEVEARIATRHAYGKRSRGAWGTWKAFLWDRREKRLRA

  1. Protein (Viridiplantae): 145356904 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 7:304 predicted protein Ostreococcus lucimarinus CCE9901 MATRSRGFPRAARPDVVRAAQKDETHAAATAERLHDACARALGPRLSVRWNRALRACGRAAYPALTYLSGRAT...LGEEYCDLASGDARGRKSSARALWTRFVIDAFGEEIARELRGCVVRNHERGVGLGGGETSAATRAMDASARTALALVGRRVERGMG...DETTSHGQAMIDARGGFANAAHLALFYANGEYYDWSCRASGTRRAFTGAYAGEERPSYALLGVFVAFQLAVVTCENVASFA...RGGGSSETSGAPSVGARVLESDGSPAIEAAIVASPRLDVFGNPVDEGASASRKSKSTSPLIAAKCALCLSPRESPTATPCGHVFCWRCIAGWASKKPECPLCRAPTTPQSLVPLSNLA ...

  2. Protein (Viridiplantae): 145354124 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:4321 predicted protein Ostreococcus lucimarinus CCE9901 MSSGEDDEVDLSALATISETCREFRRLHEASDRAMAVIPRWYALCVNDAAVELGEAATAATRA...APSARLDAFLERGFAHESEKARAPEKLTSAIEDVGRCVAFMGDAVTRANEALGEFVEATSGRRPSDDGDARWIADVPVPVMRTAFKWGSEEEYTIEQWLWMAT...SVVEQLERELETRRKILDYVRGGVASARAEELDGCVALWSAQPFVDDRLFAIVCGDSADADAAAAS ...

  3. Protein (Viridiplantae): 159473719 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available predicted protein Chlamydomonas reinhardtii MPRMGWKLSGSETLKVPLAKLSVRMATSMQLDDVATRRADLHEDYERAAQGLPPRAVVRQAQLWLVQAPPGFQQRVWDVVVMAALAAT...EHGRVRLRGMTRATAALGIQTAAAAAPEAAVAGVNPVELACARAVADFWSRLMQFAQLGVPQKGWDGVDATHPSWWW ...

  4. Protein (Cyanobacteria): 124547 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LAEQWVLFANATLATALFVESAREREFPRLMAALDQLLAKGSPLIGEAWGVADCAVNAHLAYLPIFFPQLDLSPYPAVQATIEATRARPAYQAAMATD ... ...erase Synechococcus sp. WH 5701 MTLTLYGGARSRASMPRWYLAEKEIPYTWRLLDMQAGEHRQEAFLALNPFGKVPALEDTSAEAPLGGPLRLFESGAILLYLADRYGQEYTSPEQRA

  5. Protein (Viridiplantae): 308810681 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available unnamed protein product Ostreococcus tauri MATTTARWAPRTSTAARARASSSRRTSPTEKGARVTSTRATTTRERRRRVRARASEGDAKGDVPFGYTRA...DVMLIGGGVTGAGFAAYYGLQSALGWEATRAGNAVQLTFVFGLTVAWVGSYVLRVFNKDMTYVKQLKDYEEAVMQKRLEEMPAQELEKMMSDLEEK ...

  6. Protein (Viridiplantae): 145356534 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:4933 predicted protein Ostreococcus lucimarinus CCE9901 MATARIARVAPARADARARRARGARASSTAPSTPARATRRRAEA...PRRDERLEVITFDLDDTLWPTTPVVNAANEALIEWCSARLGGRFPRTARVHATMKRIREQRECEAAARGTTAEPMSYAAIRIAGATRAAIECGIPESDAVATVARGYHLAWIPMRNAMA...RELVYPGAAEALRAIRERHPGVAVGSITNGFGSAAGAGLGEFFDFEISAEALIDEHMVHGEMARKPNAYP

  7. Protein (Viridiplantae): 303287222 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :523 predicted protein Micromonas pusilla CCMP1545 MAMAMATTTRASATRVGRVVAPLATRTTRSVVAASSVVASAASPRLATVRRRASVVVASASASAT...KRDAAAPLAVVDAAPARLVDDDRPRESSSSSFWRAIAPKTTNDDDTSASILRALATGGLASLALASLAHPELARAGEDALALAAEEDPVGLFDGFLSAFL...LIFFSEIGDKARSDSHRSPYDPIGVVNATFFIAVLLALQQDKATVFAGTFGALAVMTVISVGIGQVFHLADEALAGFGASSWDDYLAVALLLVFGIQARSISHWSPYDRVGVVNADSQGLSLPAHLSAQGPSLSTPALDAFHLRF ...

  8. Protein (Viridiplantae): 308798627 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RPHRRPVRRRRAHRTLRVPARASVRAVVSARMLLRAIVERLAGKPRGRGPALVAIVVVAVANIAYVATTRRATTTMATRDDGASEDEATRAX ... ...unnamed protein product, partial Ostreococcus tauri MPSLNAINPSAFNPLVDGSDVSESSTTSRGNLLSSSSYTLSRCARPGDVLDTPSESTNHAQSSFSNRFSNESNVRERA...QSSPRVPHLRRDRHAHAQRPPSPRIAHPSTSSPFPSIAPVVRVVRLIRVRFERQSRASVGVAARIISRPRPHRTDADAEREDDDDRTDDRPRPSSSSFRARA

  9. Protein (Viridiplantae): 308806313 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ed protein product Ostreococcus tauri MATRAWTTDICSHPSTSARSRARTLTRAKRAAKDPSEFDNDYDLIRAELMGEREGNVGAPTIGATLNWFS...ELSFGWRKAGERVRGPVDKLAELYGDLLDFLPYRRQDGTPLSGRSKTIEDGVRRLRRRAASARNIETERSVEAFWSERDRRRGFAKMAMEHTVALAIDFERGAIATETVEDERA...LRSMTDEPTLASLCERLDSVRNICLCSNAADACKMAYSYPEILLTSNGAIVSRLSALRSMIPGADVGKILRADAR

  10. Protein (Viridiplantae): 145349039 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:2992 predicted protein Ostreococcus lucimarinus CCE9901 MATSRRRRARLGALVLACVAALAARARASDVDTECAEARRACARDARRAIDSDARLQKFLATATRDATR...ADGDAALGASRYGGFVADDAPRLAFAELVALGCCLFDGECARDAATRAARRGDDEAAATRDALEIGGALLFRASEHEHWTKMPGIGTLGADARTCAEATGTTR...LFKRLLTSNRFDKVAAERLREVTRAEELWVDPTRGGTPDKAYLMADALIRLASRGATAIAVCVVFYVFRNFTFIGGAWRFARSVFLAVTGISLVTRVFKRVRAFVKWLRWKPPVVDTRQARREEARKSKKRV ... ...CDDALVATYVKAGDAGDELGVLRAGDAMLRRYVAGLATRVQGEGAREECDATRGGDVGDAAGARA

  11. Protein (Viridiplantae): 145355788 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:1518 predicted protein Ostreococcus lucimarinus CCE9901 MRRARRACQRALGAARGARAATTLTSTSVDARASTRARGATRRRRPPTERA...LPRLPPTTLTPRPGDRERYARSLREQFARCAVVREREHGVPRATRLTRDAPGGTTRALERLRRRAGADAYVVGGAVRDWIALGERAKPRDVDLVTSATYEEIEAAMDGRAKVVGRRFRVALVRA...NAGRWIEVASFESEGEGEGEGESEEDATRADAEGAPVTASGETDYDAMLRRRRAERAKREATSTSTTSSRRA...LASASPRRVASEIETLMQNGYSEASFKLLWHSTLMKYAFPVQHEFFKPRLPNKSSLTYDLESLVSPNRDFDGGARVLFDALKAYDGHVSDDISKSSVAQWLAIIVAPVAMHRMATR...SECASALLLLLAHGPVFADAPSGDLKWRHASFESLVDRGERVFALVKTKRRNEWSDANKASPTAEAEVVRASLEVATTTTTR ...

  12. Protein (Cyanobacteria): 426840 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WH 7803 MIDTIKASIRRLIQRIPLLDRWLIGELLSPLLFAIAAFTVVSLSVGVMFELVRQIVESGLPVAIAVQVLLLRLPSFLVISFAMATLMATLLAYSRLSANSELTALRSVGVTATR...MIVPALIVALLMSGLTFVFNDVVVPRANRSAEITLRRALGKAIATEKGSNIVYSRFGRIQDPDGSSSKGLAQLFYARQFKDGVMSGVTVLDFTRAGFTQMLVADRA...VWNERQAKWQFFDGQILTLTPSGSTTSADFDQYLYPLSAAPIRIAQLPKDANNMTVAEALRARELLEQAGDIKEARRLQVRIQEKFTLPMA

  13. Protein (Viridiplantae): 308813325 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DSLRASVDESHSRVECTRAAHERTIKHMEEERLMATASIARLRQRDEDLRRENGRLRQEMAYRSRSTADRTRILAEAKMAVRNLVRRCATNDPAPAHDRRELDFVEERARVLRQIAGSNVCASVKS ... ...named protein product Ostreococcus tauri MTRFASEDAEDAEDAEDADWFLTAIASSSSARAAPTVDDARAIARAARGATRASKALEARAQGVVAA...ALVAKRRERDARFELCERRERDLRSMQERIRADVGRFEAFVRENEVKRVSALRREREEARANELRDERLREMRSESKSRAEASRALDKDVERARVFETFLARVATAATNGDAFEDIADVLGRHDTLRRTR

  14. Protein (Cyanobacteria): 22424 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YQPAGSGTTPDGDPIGNDVTADLAIRQAVNYAVDRQALVEGILEGYGSPAYGPVSGLAWEEPEANIEDAQPERAKEILAEAGWADSDGDGIVEKDGLDAEFTVLYKADDSIRQALALATAEMLEP...IGIRVNVEGKSWDDIEPLMHSNVVVFGWGSHDQTEMYNLYHSQSAQGDYYNTGYYANAAIDSRLDLAMGAPSEAEAITYWKAAQWDGDEGVTTKGDAAWAWLVNLDHTYFVDECLDVGESQVEPHGHGWPITANIADWQWTCD ... ...VNDLATDYSVSEDGLTWTVTIREDAVFSDGEPLTATDVAYTFNKAAESGGLTDVTQLEQATAVDETTVELKLKQPQSTFVNRLITLGIVPEHAHDDDYARNPIGSGPYKMVQWDEGQQLIVEANPE...YYGQAPGIERLVFLFVEEDGAFAAAKAGQAQVAAVPQSLAVQDVEGMTLRDVVSVDNRGLMFP

  15. Protein (Cyanobacteria): 173668 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ADACPINMGEVIGMEIASKLQQQALAIVDNRAIRQSRFQGNIEGLIPTHPIELYFDIEAEPERNLDYLLGVLVVERSTQTEIFYPFLAETPEEEGSIWQQFLHLVNRY...01_2870 Cyanothece sp. PCC 8801 MLLTDVLLLDYKRCERRAFLNVYGDPLERKTERDFLLKLRQEIQSHIASTLENFYPHYQQPDNSLTTWEDKAKATESLMAKGVSCIYQGTLYQPHLPIEP...SVDLDQWLPKLQETVEDCSEMLIQSQEPEVFISRQRCNLCHWYDHCYAIAQSQQHLSLVPGVTPSRYQSLVEMGVETVESL...HHSQSSLLLKDYPFHCLGKPHLLIKQAGQSKFGDWLYYPVSIHLGRRPKPEYKIVAAFYAQLLGNLQETPPPTPLLILRQQNHY...QNAPIFHFSEYEVETIKRLGKLYKTPEKQLKALLPRFVDLHYHVINSVILPVESYSLKSLANWIGFHWRDPGVGGDQCVWWYDQWLRTGDRNLLTSILRYNEDDCWATFHLKNWLLEFLS ...

  16. Protein (Viridiplantae): 18394111 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GKVSENVLEGGDNIEFAEKEKDTTDSVQIESEGKVSGNVLEGGEGENIVFTEKEKDTADPVQIEPERKVLEEGDNIESSGKEKDTGDSVQIE...VVEAEKKRPKRSIKKPSGTTSGTGPSRFTAERNKPKRNVRKASTLSKDPLRNESDKANHNSRKSRSGSKEGSPLEIKDEKPSPSLKRSSLSNGSKKATLRSAEKKKKDIPDSSVQIQPE...ALVRGQKARSSDIAIQFQKKHMEASDSEVLQSSTCSWMDNPTKFVFVDKLLASSPTALPLKIQYGPEEPNSAKVWLERWTQLQVWSSGSRVPRIEIPKSQSKKRNYQA...SEGKVLEGGDNIEFGEKEKDKADAVPIEFDIVKDEKSPVLDRTEEDELKTAETSDKAEALKCADVKVSSENGNVGSDNTKQSEKRALLPANI

  17. Protein (Cyanobacteria): 176761 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GAVVGALSTVGEEAQVSPGVRVWPSKHIEPGAALNINLIWGSTAPRNLFGQRGVAGLANVDITPEFAVKLGAAYASTLKPGSQVTISRDQRSISRMVSRSLISGIMSV...GIDVQNLEATALPIARCVPRNALVVGGVHVRIHPERSDFILIEFFDEQGINISKAKEKKIEGAYFKEDFRRAPIGEIGGIT...QSHQICRFLEKPSTSEVFSDTVNTGIYILEPEVLDYLPSDQQTDFSKDLFPLLLEKGEPMFGYVAEGYWCDVGSLDSYREAQYDALQGNVRIE...FAYQEMNPGLWMGQNVHVDPEAKLHPPILIGDNCRIGPRANIEAGTVIGDNVTIGNDADLKRPIIWNGVLIGEEAHLRACGIARGARVDRRAHVLE...LLKHHQIYEIIATLYYLPDVMRDYFRDGSDFGVQMTYGIEEEQALGTAGCVKNISALLTDTFLVISGDCITDFDLTAAIKFHRQKGSKATLVLARVPDPMEFGVVITD

  18. Protein (Viridiplantae): 297850328 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SIRVKSRITSVGCSEDGKESGSVLNLTDSPFFFGFRNSLVAIGCNSKASLTNIEPNKVGCELNCTTSKEKFPSKSIPFFDKTGCTSNALPYTYTPVCTKNKGEEERSCDGNGCCRSSLPGDEAQQVIGVKIE...SFDHGNTTSRECRVAFLTDEVYTLSNATEPERFFAKGYAIVRIGWVLQTKNLSFLNSLSCKNTEEYDKLTYNMQLRTSCRCNNI...LIIMSIFDSKVFTLSTSCQTECGNIKIPYPFGIGKGCYLNKWYKIECKNASFPFLFKMGMEVVNISLPGDEYGYYNSGSFG...SQINHRHVVKLLGCCLETEVPILVYEFIVNGNLFQHIHEESDDYTVSWGVRLRIAVDIAGALSYLHSAACSPIYHRDIKSTNILLDEKYRAKVSDFGTSRSVTVDHTHWTTIISGTVGYVDPE...QVMAVANLANRCLNSKGKKRPNMRRVFTELEKICSSPEDSLVHLENDNDVDEEEEGINTADIADMWTIGATAPASSIVASSFSLEVEPLLPRPTW ...

  19. Protein (Cyanobacteria): 156167 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YSHVMHIVSNAIGELSPDKTAWDLLKACFPAGTVSGAPKIRAMEIIHELEPERRGPYSGVYGYYDFEGQLNTAIAIRTMVVRPLGGNQHRVSVQAGAGLVADSDPEKEYEETLNKARGLLEAIRCLS ... ...QAYQQACDRVTKLVIKLQLPLPVEAKTLELNPKSAESDPLNYNSNIERSRFCENVLKAKEYIRAGDIFQVVLSQRLTAHYS...ETTTQTYRDGSIKIFQGNPLDILPQCLATIHPVMLPQLPSGIGGLFGFWGYELIHWIEPRVPIYPYTQEDLPDGIWMQVDNLIIFDQVKRKIWAIAYADLRGEKVDLK...DDPFNLYRSLRLINPSPYMAYYNFGDWQIIGSSPEVMVKAERIEEKKIKATLRPIAGTRKRGKTVAEDQALAQDLLQDPKEIAEHVMLVDLGRNDLGRVCVEGTVTIDELMVIER

  20. Protein (Viridiplantae): 357471497 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PTFLRLRGSFEYEIQSWKYSIPLFFATQGFDTFRNREISSGAGAIREQLVDLDLRIIMDSSLVEWKELGEEGSADNENENEWEDRKVGRRKNFLVRRMELVKHFIRTNIEPEWMVLSLLPVLPPE...MPYLQDGRPVDMVFNPLGVPSRMNVGQILECSLGLAGSMLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTSNPWIFEPEYPGKSGIFDGRTGNLFEQPVIIGKPY...ALGKNVLVAYMPWEGYNSEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSHGPERITNKIPHLEAHLLRNLDKNGIVILGS...GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFLIRGLIRKHFASNIGVAKSKIREKEPIVWEILQEVMRG...77:2394 3880:2394 DNA-directed RNA polymerase Medicago truncatula MGKLKMLGVGNEGMSTLPGLNQIQFEGFCRFIDRGLTEELFKFPKIEDTDQEIE

  1. Protein (Viridiplantae): 168020027 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TPQQIHLLPTPPTEILSPQRGRKRESYPGRLTQDNDLKEGHKKLVTAEGAIDVEPEEEVDDLPETGPTLEEIRAQKVLEWEVEEAEREKERERER...EETALHGASGLVFLVRKGHSIIDERARLHSLVETFPVGVRLPLLLLYSPKERNIEAETEKLKSSLGLFDFEGLRIGWQNVSPVSSRNDGGFYSDGFISGGLVWLANSA...SGQPNLRPIHVRELVSNNLDGHGKILLASSSTNVTPERCISIFNRSLKSAAMEIRKAVGAAPPHWPPPEAESEVRDVLPGVLPQQGWNEP...DLLDPIFKALHLAQLPRFPLIEQLKPSSPTSAWENVRYQKAAVERALQKYLASVDKLKEDDPVLVRQVQVMVQRNSSLEWTDSGRVLVPRWANIFQAIYQTRLLLLNSEP...RESRQLNQSPKPVGDSSQNDTMETDALGEDFNNTEAIVGTCEDMCSGESLSRVQSSVMCHLWLNVRRIQGCREAEHYAMQEIERHERERKGDLDKFERVDGDRNLTSADLAVKKYTRTPSREP

  2. Protein (Cyanobacteria): 244420 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ENPYRLARDIRGIGFRTADAIAARLGIEPEAMIRLRAGINYALLEASGDGHCGLPSAELLKLAGELLAVERPSGPLDETGA...KYLGSGMIRGIGPIYASKLVAVFGDQVFEVIEQAPERLREVPGIGPVRGQRISQAWADQKVVREIMVFLHSHGVGTARAVRIFKTYGNDAVQVMA...RFGLDPIAQVQVLCPMARGGCGSRSLNIELQHLLNPDPTEQVERFGWRFAPADKVMQVANDYEKEVFNGDVGTVETIDADASELTVRFDGREVTYGWGELDNLVPAYACTIHKSQGSEYPAVVIPLLTQHYAMLQRNLVYTGITRGKQLVVLVGQKKALAMAVKNHLGRRRFTKLAEWLS ... ...TKRVPLESGLIQSALDLELSEGSLVADTLGAEPAIFLSNLHRDERRIAAALQELAQGRPPWGTIEAGKAMGWVEQRLGLELAASQKAAVEQALSSKVLVITGGPGVGK...us sp. WH 5701 MSEQATLALARPSPTDPAQASPQPTEVLAGSIERVTFHNAENGFCVLRIKARGHRELVTVVGHAAEISAGEWVTVSGTWVNSREHGQQFKASFLRASAPTTAEGIE

  3. Protein (Cyanobacteria): 156164 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YSHVMHIVSNAIGELSPDKTAWDLLKACFPAGTVSGAPKIRAMEIIHELEPERRGPYSGVYGYYDFEGQLNTAIAIRTMVVRPLGGNQHRVSVQAGAGLVADSDPEKEYEETLNKARGLLEAIRCLS ... ...AYQQACDRVTKLVIKLQLPLPVEAKTLELNPKSAESDPLNYNSNIERSRFCENVLKAKEYIRAGDIFQVVLSQRLTAHYSD...TTTQTYRDGSIKIFQGNPLDILPQCLATIHPVMLPQLPSGIGGLFGFWGYELIHWIEPRVPIYPCTQEDLPDGIWMQVDNLIIFDQVKRKIWAIAYADLRGEKVDLKQ...DPFNLYRSLRLINPSPYMAYYNFGDWQIIGSSPEVMVKAERIEEKKIKATLRPIAGTRKRGKTVAEDQALAQDLLQDPKEIAEHVMLVDLGRNDLGRVCVEGTVTIDELMVIER

  4. Protein (Viridiplantae): 303283252 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QLARQLLWAQYVAATSAVDVSLLDSPPPTSLVDATSRRGARKSPTDRSAAARAKTSPIEGKGRGDSADAPGTGRVSLTVQWRARTRVRSDLQPPSVKSVTVNIEP...PVGTELVNTHWGNSKLPFTIYRRIVRWVLKANEVARVSDEATVNALNAAQLDPRALMAEKGLAVDTLKSPSLPSMEPERGGGAKASGGAKAKTTTTKKNEGEKTEKIRISIKVVRV ... ...GRTASASSKPPKASGAAGAKRNRAAVVGDESEMVSAKKPTKPGKKTSSPGRRVGPKGTPIRKERKLKDVGGKGGGRAQAERTDRSSSESKNELTPE...GEMCARFLSRVVQMPPGAAYNQTQLAWGSMVLPPTQVLETYKNGGWSIDVHGKKPPELTLVVPVGTLLLHPGLCKAAGWKSSVPHATAVAGTQPATKVSVDGFLDMER...REHGVMNDRDPCTFVDVGCGDGTFVKGSPETYKNGGWSIDVHGKKPPELTLVVPVGTLLLHPGLCKAAGWKSSVPHATAVAGTQPATKVSVDGFLDMERSSPPKGDKT

  5. Protein (Viridiplantae): 79317970 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GKVSENVLEGGDNIEFAEKEKDTTDSVQIESEGKVSGNVLEGGEGENIVFTEKEKDTADPVQIEPERKVLEEGDNIE...KFQALVRGQKARSSDIAIQFQKKHMEASDSEVLQSSTCSWMDNPTKFVFVDKLLASSPTALPLKIQYGPEEPNSAKVWLERWTQLQVWSSGSRVPRIEIPKSQSKKRN...SSGKEKDTGDSVQIESEGKVLEGGDNIEFGEKEKDKADAVPIEFDIVKDEKSPVLDRTEEDELKTAETSDKAEALKCADVKVSSENGNVGSDNTKQSEKRALLPANI...YQAVVEAEKKRPKRSIKKPSGTTSGTGPSRFTAERNKPKRNVRKASTLSKDPLRNESDKANHNSRKSRSGSKEGSPLEIKDEKPSPSLKRSSLSNGSKKATLRSAEKKKKDIPDSSVQIQPE

  6. Protein (Cyanobacteria): 229127 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GGPNYEFIDTPGLVPAFENEDGEIVRPTGGQPGGNIRNAFLYNPERVDLVEDSVEPLTDPQDQAQNEDNPFFGGRIPLSATFEFNGEQITLVNNHFSSKGGSSPIFGVEQPFEERQEEVEVNGSLDER...FDESGNLIFDSGDDFEKIIADQIQQGILPEIAFNNDNDENEFDARSDAKGPEPEAIATGVIEGTPYAFIGLERIGGIMVYNLSDPTSPE...VEGEVEEFFGLTQIANGTVNVLSSGNDLPEAEVLPTGNVGQEQWESVFVRTEDVAVTDANPDGPDDDFGEFAIDDGSGSVRVDDLGDITFDPEGGENLEFLQGPLNFSFSNFKIEP...RFGEIFTVVDGGENATGISDRGTLNISPDDFNPEKVQIDFNEALLANFEFPQVNVGSQLGDVTGVISYDFGNFQIHPTQEFNATDSDLEPETTEIEAGGEQFTIATYN...TALENSITIGDTNSAFNSVAVNNGIVAVAVENTNVADDSIQERGAVLFYDVDGNFLSIVQVGFLPDMVTFTPDGSKVLVANEGEPNDDYTVDPEGSISIIEISSGVEN

  7. Protein (Cyanobacteria): 375924 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RRPLLRFARSKDNKIRLTGMPVLGLLYPSMVLAIEGDPLSFAIKTDAPGIPALEEVQSRIANRIEALLQALNIEPFEAGAEDESWYWVAPILLDRHFEP...KLRHKIQYEEQQGQPDLFTRFTELCEPFSHHTNNISWEDNQKRNQLIGDLRLLLAKACVSALEPDLIILDEFQRFKHLLEPE...TGKKDFSLASRITLLPLELNNLNQNRINFVSFTPGTSFDLKSGTGIEKERALLYWLLYEEWFFRGKASPLNILQGRSRADRFREYINRFRDIFPIDATLAQVFIE...NELNKIAQELFNFSNTHSSTKVVLLSATPYKMYTLAHEAAEENHYEDFLRTIQFLQSNQNQTDYLRKLLEQYRRELFRLGQNNYDNLLELKSGLESELRRVMVRTERLAASPER...NGMLVEIPCSNIKLEPQDLETYLSLQTIARILGHSDTLEYWKSAPYLLNFMDDYELKRSFIQALDDRDQETSLAHAIATSSALLLSRQDIETY

  8. Protein (Viridiplantae): 357130506 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RARFTLKAPPSKTVQNVDFSQLLNIEDPEEYFSTLEQLERADKEIKRLRGEVPTKAADYHRAIEPPKKRPGMARRKSVFSYKFSVDADTPDVIEEPASQIETITEPQFTQDDMAPSVPER...CLLFQTLSPAAFAQSSSMAREALLGGSLVQKGSKELMEQASLTLKQRGDIEKLYQEDHVEVAATGNDKKNQQGRRPGLDRK...ISVQGSHHARISQWEKDILGGDILNNESYLSEDDDSDDSPETVMGKRSPVHSSYNEVVLTGGEASTARVVKSPDHVLEPALNLSNDVSDKSEPE...SSSRGAHIDNEVHKEKDASSRHNISLEEGVVPINHPITEKPNHGTEVSSPRPLEGDSAEVPGSSTPGRNASALHEEDDNCEHQGVVGGDGLLQDQSIHPTPEKTAEDNDSHNQSNI...QDGNIKNQAADINNELSLSKDGKQNAVRKGKNRKQPSKRGKRVAEEARHSSDPETQPMEDQILEEVIGANGNIQGAGIHTSEIPLGD

  9. Protein (Cyanobacteria): 197808 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IIDHLLRLPLRYFENRPVGEISTRVNELENIRQFLTGTALTVVLDSVFSVVYIVVMIIYSPLLTAVALGIVPIFVILTLVFSPLIRRQLRLKAERNAQTQSYLVEVMSGIQTVKAQNIE...IAGEVKFENVSFRFKKQGPLQLNNINLSFPPGTFVALVGQSGAGKSTLTKLLSRLYEPEGGR...rter ATP-binding protein Synechocystis sp. PCC 6803 substr. PCC-N MSLTIADYQSFLREIEPFAQLPAPAIAEIAAKLRPLRFRMGQ...AQGNVDLRQLTLEMLPQSQVYELQPGSHSLPSDLPDPERLWLVSSGELEQCPRGSALPDPDSALVLKAQTLVRLIGLPPLP...LRSRWQWQDKYSRYVGAGFNTVITSTLASSSSHFLNQLSGLLVLWVGASLVLDGDLTLGQLIAFRIIAGYVTSPILRLTQLWQNFQETALSLERLADIVDTPQESERDRQNIPMPE

  10. Protein (Cyanobacteria): 173669 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ESLADACPINMGEVIGMEIASKLQQQALAIVDNRAIRQSRFQGNIEGLIPTHPIELYFDIEAEPERNLDYLLGVLVVERSTQTEIFYPFLAETPEEEGSIWQQFLHLV...ke protein Cyanothece sp. PCC 8802 MLLTDVLLLDYKRCERRAFLNVYGDPLERKTERDFLLKLRQEIQSHIASTLENFYPHYQQPDNSLTTWEDKAK...NHYSVDLDQWLPKLQETVEDCSEMLIQSQEPEVFISRQRCNLCHWYDHCYAIAQSQQHLSLVPGVTPSRYQSLVEMGVETV...ATESLMAKGVSCIYQGTLYQPHLPIEPHHSQSSLLLKDYPFHCLGKPHLLIKQAGQSKFGDWLYYPVSIHLGRRPKPEYKIVAAFYAQLLGNLQETPPPTPLLILRQQ...NRYQNAPIFHFSEYEVETIKRLGKLYKTPEKQLKALLPRFVDLHYHVINSVILPVESYSLKSLANWIGFHWRDPGVGGDQCVWWYDQWLRTGDRNLLTSILRYNEDDCWATFHLKNWLLEFLS ...

  11. Protein (Cyanobacteria): 323306 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RDVVSRAIFHYLQSQKADPPQTNVYLDLRPIEPERIRHRFPNIIRVCQKWGIDVFHEPIPVAPAAHYWMGGVKVNLNNATSIEGLYAIGETASTGVHGANRLASNSLL...HAPSAIQSLVDMGVAFDRKGQQLAMTLEAAHSHPRVLHAADTTGRAIISTLTEKVIQRPNIEIIAQAIALQLWIEPEPKRCQGLSVLYQGQIYWLQASAVILATGGGG...ece sp. ATCC 51472 METKGLTTQFDIIVVGSGAAGLYAALCLPTHYHVGLITKDTLKTGASDWAQGGIAAAIAPEDSPIFHQEDTLKAGAGLCDESAVQFLVN...ECLVFAGQLSKLKVTAPVPITKTTEFMINNESQWEQEIPEVREIRQALPQLMWQSAGISRRQTVLEAALSQVSLWQKQMKAFSLSQPILNLLPGQSVKFEGANGQTYLRTCSETLNLLDIAYLILNSALFRTESRGGHYRQDYPQPSQQWEKHTLVCDRRWWKDEIH ...

  12. Protein (Viridiplantae): 225434871 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IGVEKDVYVRSALVDMYAKCGYISEAKILFYMMPERNTVTWNSLIFGYANHGYCNEAIELFNQMEESDTKLDHLTFTAVLN...ACSHAGMVELGESLFRKMQEKYRIEPRLEHYACMVDLLGRAGKLSEAYDLIKAMPVEPDKFVWGALLGACRNHGNIELAEVAAEHLFELEPESPGSSLLLSNLYADAGRWGNAAKMKKMMKQRKFGKFPGCSWIEAV ... ...ED: pentatricopeptide repeat-containing protein At5g59600-like Vitis vinifera MQSLINRANVYRVYRNISTHRTFQSSSDTY...AKAIDMYARDRALYRGRALHAHLVIIGLARLTYFAAKLMSFYTECGQLSNARKLFDKIPNTNIRRWIVLTGACARRGFYEE...MQQAGVKPNVVSWNTLIAGFSQVGDKSMVSEVFRLMTANGVEPDVVSWTSVISGFVQNFHNHEGFDAFKEMLDQGFCPSSVTISSLLPACTNVANLRHGKEIHGYAMV

  13. Protein (Cyanobacteria): 141116 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YTLQANDVDLSPKSTQAVVADTAANSIKTDQDSNIYSGFSILTPYANSLLQTRIETYLQKHNVLASYYQDQNIEPDQQNIEFLAQQIDDIEVWYANKSFSDPVYTAIK...TDDLTEVKVPIRIGEYQQLNDGVIGYWKEQPVADGDYGYENDIFYAQQSDLNESDKIETQRDEPEINPEVDEGPINIIQSISSPPQMLTMLVDPRGSIHATAGILPSKVITIPPEQYAEALANI...AYQRLQSLNCLSQSIGGFNEALLMHKQTLQLDIEDPIGFADYQAFTAEVAAAVDGETESAPQPLDDFSPIRSGELRIIDLQ...KVTFLTTPILTERTQQGRLNLPLPTAPDYDWVWLEQKGRETWSEILTTPVIEKATFIESYAEAKLDTNPDPEP...7375DRAFT_0518 Leptolyngbya sp. PCC 7375 MSYLLLVPVHVDALHLKFGTGVAESMTALNRLPYFSGNRDVNPDIVNLSEPIVSQPFQNKNLHLKAGIHLHWSLPDALTQEIE

  14. Protein (Cyanobacteria): 284953 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LITKTIQHFNTALAQLRQIQFWQQRCQQLANFNQELERTNQLKNQFLANTSHEIRTPLSSIIGFTHLLLAQGYEPERQRHQ...SSRIFINTSRVILLVEDDLANSELIRVYLGRLGYQVTCVKNAQEMWTMLPQIEPAVILMDVSLPNANGLNLVKQLRDNIEYQQIPIIAQTAMTMKGDRETCLAAGVDDYISKPIDLQLLGSIVAKYS ... ...nase 'Nostoc azollae' 0708 MQQPSSLPEQNSQIDGTPTLLQTIQQLRDDLWLESSLNQLQSRLYECLLSAANTMSQVITPEAEIFQTVVNELHQALNGSW...IGCTHCAVGIAQCQPQEKNGRICYVSRFSTVETRTTEISYKQRTKLEFKLDAAIRLEDLQQMERQKPRIAWPLVDDSRDVMAWLIIATAKPRDHREQIHPLQIQLRSQ...EYLHIIQSSGKHLLDLINDILDLSKIEANQLEVQWEIVEVSTLCRNVLALVKEKAANKGLKLRLEIENDVTNLVVDPLRLKQMLLNLLFNAVKFTNLGSVGLRVSIKD

  15. Protein (Viridiplantae): 356539676 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LATGCYEHACSKFPSNLELMMGLFNCYVREYSFVKQQQTAIKMYKQYQQVGEEKERFLLWAVCSIQLQVLCGSGEDKLLFLAEGLLKKHVASHSLHEPEALMIYISILERQAKFGDALEILSGKLGSLLQIE...LDSMLEKYILENVKSIEPQLCSPWSVMELLMQLVTEPLAWHGLVIQSCLRSCFPSGKKKKKSGSAYQSSANLAHAITDSVMHLFHVLEVVLKWITEWNKRPEDEHLENI... 3846:7015 3847:7015 PREDICTED: phagocyte signaling-impaired protein-like Glycine max MASKFGLAGGIPERKVRPIWDA...RYVSQYKILLLHLYSHCGALSVAHEWYKSLDVKNILMESILHHILPQMLVSPLWTELNHLLKDYLKFMDDHFRESADLTFLAYRHRNYSKVIEFVQFKDRLQHSSQYLVARVETPILQLKQNADNIE...IASACVQKLQADTINNLIRCPYLATIEIERRKHLRGKGNDDNLMDGIVQYFCRFGHLACFTSDVEMFVEVLTTDKKIELLE

  16. Protein (Cyanobacteria): 26104 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GQQRLTSLSLLLIFLNNLQKKTSSKTINIESLILSENIFGKSFNLDVPERNACMEALFIDEPFDATQQPDSIVNLVERYNDIEELFPEEIRHEALPFFIFWLQTKVLLVEIE...WFIDSWLNRRLWHFKSNSYSNMSYGIFQITKKIRGLDVETLRTTLIQRFEEVISAEKLDFSNHLYLHKQNSKTLHRQLARMMDWLERECGMNGNYQQYIVRSGKNAYEIEPEVLNDSYKEKKSPLK ... ...echocystis sp. PCC 6803 MQEIQGKTRTVQELLGNAKYGIDYYQREYQWQTKNISELIDDLTNRFLEDYQPGDGETEFAKYGYYFLGSILISVNDTKKFIVD...DIRDRKKDAKPKDFDLIGTEYHRWIRNNAESVGLKTSNSFFKWINNDLNFYARIYKQLLDASKGLTEGWERVRYNADHGFTLQFQLLMAPLQSSDTEEIIKQKVALVA

  17. Protein (Viridiplantae): 357438933 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VRRSNRIRAEIGLRKTQCVDTTVHEIHDSEDETNHREVVPTEPSVDVSHEDPSPPKSPEKSQTVASKVREESKKIPIPKATPKPPPPKKDKGKGKAVSAPTKAPQEAPKPKRNKTNNLSINTSKFFPLIEPE...IIYHMFFEKQLCLPYVIIHHMMAAAAKDNKKYCLPYGMMLTRIFKEKGVVLENEDSVFENSKFTPKNISHMKADPSDFSSMKMNEETVCEETPPFVPTQEATPERSPLIPER...PPSPNSPPLSPPPSDSSLSPLLTQHQPNTPEDEPPLNIMPLDMISKPLFQASPPIITQTAPHLKNFSQSKPKKTKSSQSIG...FEEDFHDKWITRPIANGRFVDFEAFDNEEIFLKAITDLLGWTSFLQMRERYYPELVQAFYFMSETFPEKSLIRSTVKGVEISLTPEDIGTLFNI...SQQASPVANEHLDLLANFKNQSSSFSTAQATEVLHGFQNTASQPFPNVSQSNYLHVSSPHDSYSALFNDSYVSKFFNSAPNTSVPLHSFSTLQSTTPTLPSMPTNACGNTSQPGPTNDPRDQRRPKRSKLEKDVSKLRKDLPRLFEGQQAILSYLVYNNIENQILRD ...

  18. Protein (Cyanobacteria): 57679 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GIYIQDQIKLAENLKLLIGGRYDFANQSFLSIVDGVKFFDISDQAFSPRIGIVYQPIAPLSLYASYSRSFAQNFGIQRDNSRIEPERGTQYE...VGVRGEFLDGKLITSLAGYEITKTNVSTPDPADLNFSIPVGEVRSRGIEFDIAGELVKGWNIIASYAYTDAKITEDNTDVKGNRLNRVPENSASIWTTYELQSGALQGLGMGVGLFFVGER...LVVTGQQDSYRVQNAATATRTDTPLRDIPQSIQVIPRQVIEDQRATQLNEALRNVSGVQPSNSAGRTRDRFVIR...GFDDFNSVIRDGFKENTSVYRETANIERIEVLKGPASVLFGQLEPGGVINVITKQPQREPFLTMGLEAGSYGFFRPTVDFNSPLNDSKTLRLRVNAAVEVSESFRDFD...GSLDEATGLLSRDFGVDRPTPDETYAFQTDLIGKFKTGGIEHELVIGFDFNRQTNFVDDRRSAPAPAIDIFNPIYLTARPNIESDPFRGLFAADNI

  19. Protein (Cyanobacteria): 104350 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LRACPDFSEFHPNANIEIAARLKPDLLPNLTPYLDNIPDYFKNLNSSQPDNPLLSTSSWLVLQVNQETTGYRTFWDYLPSDAITIDRIEPEK...PPLPSEESEDVQDSDRAETIQEKKQQLDFSPSLPQPDIETTYLSLDVETPEDIEGEQTLENYPDKDEQLQDTQTLSQPERQNSWPPSPLER...LQTIANFFTAENWPFVTVQDEQILQMAVEGQNEKLTCYAQVIEEQSLFIFYSICPIEAPESKRKALAEFLTLVNYDLIIGNFQLNLTSGQIRYKTSLDVSDSTLSTTQIKNLVYTNITMMDSHLPE...ELKPYFGTLKQIYRYWDISSQLKPLLERIENIGSDRLKRSSQTTKDTLRASQRLPPCIQARLLQLAAEKLASQLEVDILIELGEVQELLAKTKRILNTEFL ... ...wn function DUF1790 Oscillatoria nigro-viridis PCC 7112 MNTHKETYQLDNSLTLLSPSSSGVTVRAIALTLTQQHNTLIEVILTFEITPIIYQRADNEGLFNLLPE

  20. Protein (Viridiplantae): 302830242 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DAPYGGADKVWLRDWNGIKVGIVGLVEEEWLETLGAVNVEEMEYRDFFKVGRQLASELKAQGAELLIAVTHMREVNDRRLAAELPEFHIVLGGHDHHYVSAFIEPHNN...REIPLVQDQNGIGGGRGGSGTQGRGDWHRRGRGGTVVPMSAPAGITEAEDVPPRVKSRGATGEFKTNWSELGGIDPYACCISGGIRGWFIGAKTGNIENIINHVKTRQ...LLVKSGTDFRDLSVVEVEFDEGSKDPRLSVERIPIDSSIPEDPAMKAIVDENLKVMGERMAEEVGETLEPLDGRFQTVRSR...ESNLGNFVTDVWRKEAKADMVITNSGSLRSDMIHPEGKLAIKDFVAVLPYIAPTVVLECTGAQVVAALENGVSQWPSLEGRFPQVSGLKFKFDPSKPPGQRIVPGSVFATEVGSEPEP...IRDDHNYRVAVGKYLASGRDGFDVFASCKVLVDDEAGVVVPTTIRNHFLKLQVLNKMSRSHLALKPLASKWLERVDTSEKASFKSAVSFGNGSPNEERESWLGARKKDHGLAVRHPERGTFCIAPVVEGRIINVLEELQEGCTQ ...

  1. Protein (Cyanobacteria): 323327 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DYHPRGELAPRDVVSRAIFQHLANTEKDPTQATVFLDLSPIEPERIQRRFPNIIRRCLHWGVDIFREPIPVAPAAHYWMGGITTDINCQTTIPGLYALGETASTGVHG...DGEAVDFLVNHAPQAIAELVQFGVSFDRHGQHLALTLEAAHSQPRVLHAADTTGRAIVSTLMGQVQARPNVEIFSQAIALSLNIEPTTGHCRGIQVFVNQTIETFHSR...ANRLASNSLLECIVFASQLRNLSLPPLASSDSNVNQSIKEIRLDTTNDLALLNHWRSELPRLMWQTAGICRQAETLQMAIAKLEQWQEQWQQLSSSKLLAHLPEDQKISLSGPGLNEFMQLWAETHNLLDIAQLILTSALFREESRGGHYRLDCPDTKREWQSHTVIEGTRVFLQPSQSQD ...

  2. Protein (Viridiplantae): 255088868 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GSSMRGNFSVDYEDVGMGSTPPTSAAGGDAAFDVERGGVSLDDEDFEAGSRRVRRAAKSRTSVRASAARKDEDVQVNEVAAGVAGVAAAAVVFGAPDAAMADAYTDYLEAMKAQNIEP...YHATRDGQVVAGLVADILGVLGCESTLRVLNTESGVNEPMSRDALERTLRLEGSEGPLLAGLLTRSDEADEGRESSRTRDRTPEVTKREPPEPIVLAVGVLEEKDTNRPER...KAAAAEAEKAEKAAAAEAAKAEKAAAAEAAAAEKEAAKAALAEARAEKAAAAKAAAAKSKASKPASSSSSGDAGSFAPVAGIAVVGAAAALVGGGKKKEPEPEPEPEPVNTPFSFFGRKPEPEPEPEP...PKKKGFSFGAKKTPPPPPPAPEPVKKALFSFGAKKPEPEPEPEPVKKKPAFSFGGTQKMKKAPEPEPEPEPVKKKPMFSFGGTQKMKKAPEPEPEPEPEP...VKKKPMFSFGGTRKMKKAPEPEPEFEPEPEPVKKTPPKPLFARKAPVKKAPEPEPEPEPEPEPEPVKKAPE

  3. Protein (Viridiplantae): 168059203 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LNVHLNSLQPPSPGAAGRSDSDSELSSPAALTLRSAKGFTLGSSLRGSGRVRSAASRLNNACGGVFIEEPESPARLPERPSFGRRGVDRDSCLPRIISDNTSGGTAQSDVER...VGENIETLLREQREGSRPRRETLERVAEKLHLRSKENIAQELQALTKEREEAGAQEDKSEEELIRRLLQLVKQMEGLLEGAATEGL...WVLDLQSPDTETQRQAACELRMLAKHNMENRVTIANAGAIEPLVALLSSVDAKTQENAVTALLNLSINDNNKSEIARAGAIGPLVNVLRVGNAEAMENAAATLF...:616 114656:616 3215:616 3216:616 3217:616 3218:616 145481:616 predicted protein, partial Physcomitrella patens subsp. patens AEER...EIPADFRCPLSGELMSDPVILASGQTYERIYIQHWLNEGHSRCPKTHQKLSRRNLIPNYTVKALIANWCETHGVPVPRPVQ

  4. Protein (Cyanobacteria): 205986 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LYTQPALFTVCVALAQRARKQGELGEPALVAGHSLGEYAALWAAAVFDFETGLELVAERARLMDAQQAGAMSAIVGFDRDKLEKLCAERPGVVIANDNNPMQVVISGEPER...VAEVSAAIRAKRVIPLAVSGAFHSPLMAPAAAEFAAVLARAELHPAHIPVLFNADPTRPVADVASMRELLRRQIDHPVRWRETILRMADSGITELVEIGPGAVLTGLAKRTVPALALRNIEPAAALAV ... ...CoA-ACP transacylase Gloeobacter violaceus PCC 7421 MATAWIFPGQGSQVVGMADALSGHPDTAALFERASGILGWSVAAVCAGPQERLDRT

  5. Protein (Cyanobacteria): 273618 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QLGDEEMKAGILLSMGNLLIHEGDFAEGVKRASQAIEIAKQHNLPEREKIENIALAVQYEKLRHLFDSAQEKCESQEFEEVLNLAHQCLELSEILKDVRWCSEVLSMLGQIKAHQGDYQGGVQDLER...QGCRAVLGWGRPIADVVATQAAAYLYSKLAAGYELSEALASTYQYLREAKVEDWHLLRLYIRGQCPKALIEPLGDQVWLPEEPIYE...EKAAILHDLADLYVKQGNYQQALTICQQVMKIDEKDNNKLGKAKSLSQIADIKRELGEPEEALKLYMEVLELTQETGDKNFLYTVQNNIATLQVDLGQTDAWDNLLPS...GYQLFCWLDGTGRWLSRAINNCTEEGLILALDVRERLGHLPWETLHNGEQFLIERVNPVVVPIRWVDRSIQDLEDTQQRPLRILFMATSPDDVEPPLDFEQEEAQILT...ETRDIPLNLRVEESGCIAELSKLWGRYREPFDVFHLTGHASIKDERPFFLTETETGELHPAYASEIASALRFRIPQLVFLSGCRTGEAASDGAVSSLAESLIE

  6. Protein (Cyanobacteria): 83958 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EEESYYPPTVKAENQLPTGVPVGPPIATPIETRTPVMEETWDEDEWQEARVVPPVQKAQAVPYVEYEEDLEEDNWGGIEPEPERVYDTPVYEARTVEEYEYQEQPEDMWDDDENPKPYNPPPLNIPERQKEKAPEYEEEAG ... ...AYTKLISCEVITEAGEPLGKVRDFQFNIEDGKIYSIIIASLGIPQIPEQIISTYELSIEEVVSSGPNRLIVFEGAEEKITQITVGLLERLGIGRPPWER...ain protein Stanieria cyanosphaera PCC 7437 MTTENIRLRSEFLNTQVIARNSGKRLGVVKEILVDIDRREIVALGLRDNFLSVSGIPKYMYLESIRQTGDVILVEDENVIEDIEIE

  7. Protein (Cyanobacteria): 285966 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YFLRKDNCLQVVRKLREKLLFAPHDLTKDAGFTRMDLISCRNVLIYLQSDLQQQVLRNLHFSLASKGFLFLGEAENLGYIEPEFQHIDTKNKIYQKRRDVRLNIPVKTIE...TDFILSSFLDNLEAMIRIRCQQKGIEFEHLILSDLPLIVRGDETRLRQLLLNLLSNAVKFTPSGKVTFSIGYVRDFIQTKEEGWNCNKEQDNIEPDNADKIRFHVADT...AILRQDLLISVTQFFRDPAAWDVLEMSVIPQLVDKANPHEELRCWVTACATGEEAYSLAILFDEAVTKSDKPIRFKIFATDIDKAALEKATQGIYPLTINKNINPERLER...NSVYLIPPGKNLVLENRKLHLLEQEERSRHGLNFPIDIFLESLAKNYVERAIGVILSGTGSDGTNGLRAINEAGGFAMVQEPTTAEFDGMPRTAIATGVVDRILSPQE...KTAHQIFPFTPSRSQSESHLEPMLDKAFSAFLAKYKATCFLADREYKLFHSFNDDINILKVPFGRTTTDITKM

  8. Protein (Cyanobacteria): 270128 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available family 2 Calothrix sp. PCC 7507 MQSIGIVVIGRNEGNRLHQCLLSVVGEGITVVYVDSGSTDGSVTLARSLGAYIVELDLSIPFTAARARNSGFAYLLQIEPNIE...FVQFVDGDCRVVEGWLELAQRELLTQHDVVVVCGRRREEFPNNSIYNLLCDIEWDTPIGEALACGGDSMMRVTALKNVGGFNPTLIAGEEPELCVRLRQAG...GRILRIDAEMTLHDAQITRLSQWWKRSLRGGHAYAEGSWLHGAAPERHWVRESQRIWFWGLLLPFLAIAAVWSTKGLSILLLLLAYTFLAYRVYQNTRQRGLNTREAISYSLFCVLDKFPQLQGQIQFHLSRLFRQQRTLVEYKN ...

  9. Protein (Cyanobacteria): 206257 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EYLKSGEEMKLLFRDHLTDDVIAEAIATTEEVADKIEPYHIMGEPRIPNYPIPSGHTPDTYVEEVAWQGLLDKLNRKSRNEVEPVYRERLEYELKMLQQMGFSSYFLVVWDYIKFARDNNI...PVGPGRGSAAGSLVAYTMGITNIDPVHHGLLFERFLNPERKSMPDIDTDFCIEQRDKVIEYVTDKYGKERVAQIITFNRLTSKAVLKDVARVLNI...erase III subunit alpha Anabaena variabilis ATCC 29413 MSFVPLHIHSDYSLLDGASQLPELIDQAIALGMKAIAVTDHGVMYGAIELLKICRSKNI...PYGEADKMAKLIPVVRGKPTKLKVMVSDTTPEPEFKEKYDNDPRVRHWLDMAMRIEGTNKTFGVHAAGVVISADPLDEIVP...LQKNNDGSVITQYFMEDLESMGLLKMDFLGLKNLTMIQKTIDLIEEKHGFRIDPYEITSQERKAQKILAKGEYKTLPKDVQKTYELLESGELEGIFQLESSGMKQIVRDLKPSNIE

  10. Protein (Cyanobacteria): 205794 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available THIPNARVIAAVKTAEWLFSTEEFKTVSQIREALQKFDNLGIEPEEFWGLGEQLGYKVEISWSDFSNNEHYDVAFVNQNLPDHINIPSQPTYSSSWRDYTNNPLQAKT...NQLLFGWNNTQRDYHKNLCVHELFEKQVKQNPDATALVCDKQKITYQELNIRSNQLARYLQKLGVNSEVLVGICVERSIDMVVGILAILKAGGAYLPLDPNYPPERLSFMLDDAQVSILLTQER...LYRYTQQEDITIGSPIANRNRSETEGLIGFFVNSLVLRTDLSGNPTFREVLQQVREVALGAYAHQDLPFEKLVEELHPERHLNQNPLFQVVFAVQNAPVEALELPNLTLRPQHIDIRTTRFDLEFHLWER...SHPFKVVNNYGPTENTVVTTSGYLPVDQNSDFPPAIGRPIANTQVYILDSYLQPVPIGVAGELYIAGNGLARGYFNRPDLTAEKFIPHPFTEDLSPSSLLPPPSKARLYKTGDLVRYRADGNIE...ARQLIPHLQHHLTQKLPDYMIPSAFVVLESLPLTPNGKIDRRALPLPDLIKPEIAGNYVAPRNQIEERLVKIWCEVLGVKRLGIE

  11. Protein (Cyanobacteria): 3179 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QISNFIPRFENLKLTLARNIQIQQSNLLNVVAQGDLRVTGPLRPFRAIEPEGTIRLRSGRINLLTTTFRLAGRDNVARFVPER...QALPSYCGAPDVADSIYRFNGNVQLDTLAYNANVSVENGDIKDVFTALAITDLDDLIQTFQAPTWVENQPSPEEIPQVLATQATGNIEAALLDQVRRLAEIQDIQDQE...LSWNGLRVGPSKLNATETDPTYATAETVEVGFNPLQVLFQRELEIDLRLIGAEGYVEQHPDDGWLGIDVPTFEPVEDPLIKVRMDDIDLVDSQITVVPLPADGAEPTPLTLVDLNGTVAIEP...TLGQQNLPLAATAGRVSGNWTVSFLPDQPVTVDGAGSLDNGQLQLTSLPNTGPWGNTIEDIDAEARFKGTTITVDSARGNYEDLVATATGTVDWNGDYDLTAQVADVDLEQLLERSEVELPIALRGVFDSNI...GQYGNGRLQAAGSFPLSFPFIIDSAELALLGADDPSDVAAEDNDATPAVINPPADAAIPMHPSGALTFTLDDIDLDLRGIYEGGVNGQVVVGGSLLLGGPQLGGVVELANGRLFLPEGGDAASTSEPE

  12. Protein (Cyanobacteria): 186274 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KFRGSPAVLTTSMKSVGEAMAIGRCFEESFQKAMRSLETGFSGWGGDREEPELTDGELDRQLRTPSPERILSVRTAMVRGRSDEEIHRISRIDPWFLAKLRRIIEAEA...large subunit Synechococcus sp. WH 8109 MPRRSDLRRILLLGSGPIVIGQACEFDYSGTQAIKALRAEGFEVILINSNPASIMTDPEMADRTYIEPLTPDVVTRVIEKER...TDREYQRLRDQSIAIIREIGVATGGSNIQFAINPDNGDVVVIEMNPRVSRSSALASKATGFPIAKIAARLAVGYTLDEILNDITGKTPACFEPTIDYVVTKIPRFAFE...QADGSLKPLPASSEVSRRDDGRKMMILGGGPNRIGQGIEFDYCCCHASFAGQDQGITTVMVNSNPETVSTDYDTSDSLYFEPLTLEDVLNVIEAEVPDGVVVQFGGQT...PLKLAIPLLRWLDSDEGRATGTSIWGTSPESIDQAEDREQFEAILRNLNIRQPRNGLARSEEEARAVATRVGYPVVVRPSYVLGGRAMEVVFDEEELNRYMREAVQVEP

  13. Protein (Viridiplantae): 168039389 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QIIVQVAKEYGEQLGVDACVKLFESFKSFEGLYFFLGAYLSTSEEPEIHYKYIEAAAKTGQIKEVERVTRESNFYPPERTK...QVVFWKWISPRLLGLVTQTSVYHWTIEGESEPVKMFERTANLSGNQIINYRCDPAEKWLVLIGIAPGAPER.... patens MAAASAPITMKEALTLTSLGINQQFVTFTHVTMESDKYICVRETSPQNSVVIIDMSMPNQPLRRPITADSALMNPNSRVLALKALIPGSTQDHLQIFNIELKAKMKSYQMPE...HALLQTKVLEINLVTFPNVADAILANGMFSHYDRPRVAQLCEKAGLYMRALQHYTELNDIKRVVINTHAIEPQGLVEFFGTLSKEWALDCMKELLQVNMRGNL...NFLMESKLPDARPLINVCDRHGFVPDLTHYLYVNNMLRYIEGYVQKVNPQNAPLVVGQLLDDDCPEDFIKGLILSVRSLLPVEPLVDECEKRNRLRLLTQFLEHLVSEGSQDVHVHNALGKIIIDTNNNPE

  14. Protein (Viridiplantae): 255573685 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VNFSARCDIRNLVRDLTKCAEMKGIPIEPPFDVFEENPQFRRAPPTVRVEKMFDSIQSKLPGAPKFLLCLLPERKNSDLYGPWKKKNLSDFGIVTQCIAPQRVNDQYL...MIDSLYKPVSDTEDEGMMRELLLDFYSSSGKRKPEQIIIFRDGVSESQFNQVLNIELNQIIEACKHLDEKWNPKFVVIIAQKNHHTKFFQPGLPDNVPPGTVIDNKVC...5610 3988:5610 eukaryotic translation initiation factor 2c, putative Ricinus communis MDSFEPDGNGLREGNGIHEGNGSQEGLPPPPPVVPPDVVPMRAEPE...CSLVSLQRYTKALNTLQRASLVEKSRQKPQERMSTLSNALKSSNYDAEPMLRSCGVSISTSFVQVDGRQLQAPKLKVGNGEDFFPRNGRWNFNNKKLVDPSKIERWAV...QESENSQEAIRVLDIILRQHAAKQGCLLVRQNFFHNDPKNFADVGGGVLGCRGFHSSFRTTQGGLSLNIDVSTTMIIQPGPVVDFLIANQNVRDPFQLDWAKAKRTLK

  15. Protein (Cyanobacteria): 57582 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FSPQFKALAGLRYDFVEQLRSTQDLGGPRNEFFQSDEALSPRLGVVYQPIEPISLYASYSKSFEPTFGTSRDPDGMNFEPERGRQWEVGV...TTIITDVAIATEGDQVELQFTATAPLENATVIQRAATTEITIPNANVTQAEVLQEFAPESGLEQIEIRNQADNSVQILIRNGDRQIQTQLITTATGLTLNIEPVLVSTDEDNIE...TFSLAALDTNDIERVEVLKGPASVLFGQGDPGGVINLVSKEPLAEPFFGIDAAIGSFANYRGNLDLSDALTENGAARYRLNFSYSNFGSFRDLVDGER...VVVSPRLSFDLSEATSLDVYGQYAYTRETIDEGIPFTASGPVDVPRSRFVGEDFGEFSEKRFNLGYDLNHEVNENFSLKHQLQFLQYRPRRYAPLYTFFDETTGNVDRLEYFAGGSYQRFFTNIE...AIAKFETGGIKHQVLGGVEYRNTLEQPEFQFSNDYTPINVFDPVYTGVPYAIAPEFFRDDTIKTVGVYIQDQIE

  16. Protein (Cyanobacteria): 197865 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IIDHLLRLPLRYFENRPVGEISTRVNELENIRQFLTGTALTVVLDSVFSVVYIVVMIIYSPLLTAVALGIVPIFVILTLVFSPLIRRQLRLKAERNAQTQSYLVEVMSGIQTVKAQNIE...IAGEVKFENVSFRFKKQGPLQLNNINLSFPPGTFVALVGQSGAGKSTLTKLLSRLYEPEGGR...rter ATP-binding protein Synechocystis sp. PCC 6803 substr. PCC-P MSLTIADYQSFLREIEPFAQLPAPAIAEIAAKLRPLRFRMGQ...AQGNVDLRQLTLEMLPQSQVYELQPGSHSLPSDLPDPERLWLVSSGELEQCPRGSALPDPDSALVLKAQTLVRLIGLPPLP...LRSRWQWQDKYSRYVGAGFNTVITSTLASSSSHFLNQLSGLLVLWVGASLVLDGDLTLGQLIAFRIIAGYVTSPILRLTQLWQNFQETALSLERLADIVDTPQESERDRQNIPMPE

  17. Protein (Viridiplantae): 255552089 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GSKSVKLENLSCGISLASSVASFHSLPTCEELNESLLPLAPERDTDPTEDGVPLVEDVSQASACLVTEERKLEGEGEACKRCNCKKSKCLKLYCECFAAGVYCIEP...SINCRCEGCKNAFGRKDGSAPSETEAEPEEETEGDENNGADKVAQNIEIENNEEQIPNSALPMTPLPLCRPLLQLPFSSKSKPPRSFLGIGSSSGLYTSQKYGKPNILRPEQKFEKQLQTVPDDDMPE...NDATPCCGPQVDCVSKLTGMSALEVSQKCLPEHEAHLQGMYHTEQKKESMECDWEMISDAADLLIFSSPIDTESFKVLMQKSMGPSKQHDLENPSTQPGETIEP...LPSQNGNKVGSNEGATLDVAQLYDDNSSELQETFDPVVSIGEVSVEPSSEQVKFAIELPRRLKYDCGSPE...CSCQECFNKPIHEDTVLATRKQIESRNPLAFAPKVIRSSEPVTEIGDEFSKTPASARHKRGCNCKKSNCLKKYCECYQGGVGC

  18. Protein (Cyanobacteria): 197941 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LVLWVGASLVLDGDLTLGQLIAFRIIAGYVTSPILRLTQLWQNFQETALSLERLADIVDTPQESERDRQNIPMPEIAGEVKFENVSFRFKKQGPLQLNNINLSFPPGT...IVVMIIYSPLLTAVALGIVPIFVILTLVFSPLIRRQLRLKAERNAQTQSYLVEVMSGIQTVKAQNIELRSRWQWQDKYSRYVGAGFNTVITSTLASSSSHFLNQLSGL... sp. PCC 6803 MSLTIADYQSFLREIEPFAQLPAPAIAEIAAKLRPLRFRMGQIILARGKLANNVYFLVSGQARLLGYDPGTGYPATMALLQNGAVIGDNNAIRN...VPCETAIASTETICASLTRDEFLALVDKYPELARVYRHQCGRVELFDLLGEQLQRTAQGNVDLRQLTLEMLPQSQVYELQPGSHSLPSDLPDPERLWLVSSGELEQCP...RGSALPDPDSALVLKAQTLVRLIGLPPLPRFFPGSSGSKTNGNGNGHGEVPLATVTRLAPEDSPWDDIPYADPNQLGEPLPEP

  19. Protein (Cyanobacteria): 206270 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PVGPGRGSAAGSLVAYCMGITNIDPVHHGLLFERFLNPERKSMPDIDTDFCIENRDEVIDYVTRQYGKDKVAQIITFNRMTSKAVLKDVARVLDIPYGEADKMAKMIPVARGKPAKLSKMISDDTPEPE...EAVSNTLEVADKIEPYKILSPPRTPHFPIPAGHTTETFLEEVAWDGLLEKLNRKSRSEVDKSYTDRLKYELKLIQEMGFPGYFLIVWDYIKFARDSNI...TQYYMEDVEAMGLLKMDFLGLRNLTMIDKTIDLVEKKIGRRIDPYDITSHERKAQKVLARGGDAAKLPNDVRKTYELLEAGELEGVFQLESSGMRQIVRDLKPSNIED...NA polymerase III PolC Rivularia sp. PCC 7116 MSFVPLHIHSDYSLLDGASQLPALIDRAIELGMEAIALTDHGVMYGAVELIKICKKKSFKPIIGNEMYIINGDITKQER...YYLEIQDHGSQEDRVVNVEIVKIAKELGIKIIATNDSHYISCNDVEAHDALLCIQTGKKIFEDKRMRYSGTEYLKSAEEMKQLFRDHLPEDVIE

  20. Protein (Cyanobacteria): 205663 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GNTQIYILDRNLQPVPIGVPGEIYIGSVGLARGYLNQPQLTQEKFISYPLRNLTEEKLYKTGDLARYLPDGNIEFLGRIDNQVKIRGFRIEPGEIESVLRRNPQVQQAVVIDKEDTPGNKRLVAYFVPEPE...IIHGDAMTVNLPELADVCVSEIVGAIGGSEGAAVIINNARRFLKPDGAMIPERSVTKIAAVTLPEPLLNQPRFTKVSGYYTQKIFEQVG...AVCSRKLCENNLNPDYAIQGRIIRQQGEYIDFEHISYHWKQQFKQTPFYQRLFAETETVSTSNLQLLDTHINSWQNLFNQQIDEHKSEVTDPLFNISGWRSSYDNQSLPER...ITHVQIRLQRGTEHNELNKYRYSVLLHIEAQPGTVITPTVESGADLSVQQIETYLRSKGPESICFSGLVNGRVANDVELVELLSQPESKQNVQQLRQSLQENLVNGIDPER...MTELIQNKNVSQEPISQSINNEVQETLNKEVVQTKNSEYVQFESRSLLSLFTVGKIPPVDAAALCYWGEYDPEMFDWSRDYMIENI

  1. Protein (Cyanobacteria): 312097 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PTFKQVSAVQEEINKRQDVRFRLVVQRTAVDIVGPKEQPNIESPTPKQPINSHTNTQPFNNIKPVDSIRPFKEVPLIDQLPFLDNMQSQKKENNNNLNSTIEPEAIKAPGLPLDSRTADQTQD ... ...FRQELRRSQLGAASFALTGLLLIPLGGSFINLLVQAKNENTRESVEKTIAKFLTQETLTFGDKKKIDVEKVDIDWDQNPPVIRVIVRVADPER

  2. Protein (Cyanobacteria): 323283 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QGRRFAFDYHPAGELAPRDVVSRAIFSHLQKTSDDPAHAKVYLDLRPIEPERLRYRFPNIIRICQKWGINVFEDVIPVAPAAHYWMGGVATDLNARTSLPGLYAIGEA...ASTGVHGANRLASNSLLECIVFAANLVEIGLEPENLVGERPEKPLEIAENWQEEQEYWQKVRRELPILMWENAGICRFQNELETAILRVHQWKQQLQSLKMGQFLQNLLPDKGQLFLCPSVQLEIRIAIE...se Microcystis aeruginosa NIES-843 MVVSSQLPSYQDVLVVGSGAAGLYAALCLPPNLKVGLITKEDLKTGASDWAQGGIAAATSPADSPVFHLEDTL...KAGAGLCDRYAVQFLVEKAPQAIADLLRLGVSFDRSGDDLARTLEAAHSQARVLHAADRTGRAIVSTLMEKVTERPNITIIPQAIALKLWLDPEGQRCQGICLLHQDH...LCWLRAQAVILATGGGGQVYAQTTNPAVSTGDGVALAWRAGAVIRDPEFFQFHPTALTVPGAPRFLISEAVRGEGAHLIDA

  3. Protein (Viridiplantae): 308810431 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TALDGVWLDVKRGTLFMLLGPNGCGKSTLLRTLAGLGTLDSGEADAPERKAFVFQNPDHQVIMPTVGADVGFGLGRNPDMSEREIRERVVRALKTVNLSDEDAYERQTSTLSGGQKQRVAIAGALVEEPE...VRKVGTGREIRAFIRQMQDAYVPAFENIEKPIATHRRDSIPIECPPPTRHRRRAIDEDIKRNYRKLALKHHPDKCDGDDAQFKRIALAHKILSDPKSRAAYDKGGVDA...GAMSGLEVSLQEVSSRFDLVKPKRSHAGFYFTGSQSFNYEPMHAVKLAKLESRDLAVFHSLDNWSPRECVTIEPGEHVFGVYGDNFFDKCKFEIE...ed Response to Gravity (ISS) Ostreococcus tauri MTRALPPESTRAVDVRLARVSRPRASATTVCATTNDLEDVAVRVREARKRFTPDGAAAPV...LLLLDELTTFLDEADQRQVIESVRRAVDESNGRTTAIWVTHRLEELEFCDGAAYMENGR

  4. Protein (Cyanobacteria): 197750 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IDHLLRLPLRYFENRPVGEISTRVNELENIRQFLTGTALTVVLDSVFSVVYIVVMIIYSPLLTAVALGIVPIFVILTLVFSPLIRRQLRLKAERNAQTQSYLVEVMSGIQTVKAQNIE...IAGEVKFENVSFRFKKQGPLQLNNINLSFPPGTFVALVGQSGAGKSTLTKLLSRLYEPEGGRI...rter ATP-binding protein Synechocystis sp. PCC 6803 substr. GT-I MSLTIADYQSFLREIEPFAQLPAPAIAEIAAKLRPLRFRMGQI...QGNVDLRQLTLEMLPQSQVYELQPGSHSLPSDLPDPERLWLVSSGELEQCPRGSALPDPDSALVLKAQTLVRLIGLPPLPR...LRSRWQWQDKYSRYVGAGFNTVITSTLASSSSHFLNQLSGLLVLWVGASLVLDGDLTLGQLIAFRIIAGYVTSPILRLTQLWQNFQETALSLERLADIVDTPQESERDRQNIPMPE

  5. Protein (Cyanobacteria): 63829 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SSTDAVVKDGAGRVLGELTAMNALNANPRGKAVGLADWQASQLLIEPENDGYVWINDRWYRGRTRIIRQGSGVTALNLVDLEEYLYSVVGAEAIPSWPQEALKAQSVA...tein MAE_58180 Microcystis aeruginosa NIES-843 MRSPIPMTNKHTARLLSSYLQRLPAHSWLILVFWALIIAPVQAAVELRIAISKGVSAVSVG...YLRGVIDYDQVAPVFQWSKNFSAWELGRLIGGVGRVRSLSPERTTPHGRVIRMRVVGDQGSKLISDTQLRRILELRSTLFTISADNGTFAINGRGFGHGIGLSQWGAFSLADQGVTYDRILGHYYQNARLTEMPN ...

  6. Protein (Cyanobacteria): 186354 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TIDYVVTKIPRFAFEKFKGSPAVLSTAMKSVGEAMAIGRCFEESFQKAMRSLEIGRAGWGCDRQEPELTPTEIERLLRTPSPERIMAVRTAMLA...MADRTYIEPLTPEVVARVIELERPDALLPTMGGQTALNLAVALAENHTLERFGVELIGADLAAIRKAEDRQLFKQAMERIGVDVCPSG...PLYRLDSDDQLYKLEPESEVVADERSKVMILGGGPNRIGQGIEFDYCCCHASFAAQDKGFVTVMVNSNPETVSTDYDTSDRLYFEPLTLEDVLNVIEAER...GRSDQDIYALSKIDIWFLAKLRHLINIETTHMHGRKLDELDQECLLSLKQLGYSDRQIAWATGSEELAVRARRELLNIKPVFKTVDTCAAEFSSTTPYHYSTYER...MRSTGEVMGSASSFGMAFAKSEIAAGDPLPIRGTVFLSTHDRDKPALLLVAERLIELGFDLTATSGTAQALNQAGLNVQPVLKVHEGRPNIEDLIRSGQIQLVINTPIGRQAAHDDKYLRRAALDYSVPTLTTIAGARAAVEGITALQQQSLSVAALQDIHV ...

  7. Protein (Cyanobacteria): 104388 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SPDPSIAPNDISATSEIIQPKHQSHIGSELKTDPDLSTGQIQANSTLLAESSNTDTPTPDLQKHPTDNLGESPPENVERIQSQPDQNESSHRRIIEIPAQRPDGNIE...KANLSDQDIASSSSLELNENQSLQRSSEANSSLPERNFDPANPKPSSNIAEQSEISALPQADSSPQKVEHIQPQLDQIDSPHRRIIEIPAQRPDENLANDNLHPK...PNAPLQRKDDDETGRSGEGYEINTEDAIAPTIQPSNNPTLPSNWSSIEDLFTTQPSVIQPKAEKPTATPEDTSDFVLTPTGIYPEKQVPRKTVFAQRTAQPLQKSPTTAPPVSSTPQTTEVVMRQFQTEKLTEPEVDEQSFEILAREIYHVLRQRLEVERERHGGYQSGRLPW ... ...QVSPQESVREEALLEKTEIANHEQNSLTVQAAPESKDSPQKHPHATPATSEPTIEPTIDQDI...NLESQGHQAPQAPSKSSDASGKTTTTDGIIQRKIEAHIDSDQPFFTPKEDSSTASKPLNDQSISSETSIPGKTSAQIEPHTEPSNLELKQASTVPIQSVEISVIQPATEPQLQKDNLGQSFDNCDRTPE

  8. Protein (Viridiplantae): 15220741 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QMEHYSSLVNVTSGQGQFEEAMYIITSMPFEPDKTVWGALLDACRIYNNVGLAHVAAEAMSRLEPESSTPYVLLYNMYADMGLWDEASQVRMNMESKRIKKERGSSWVDSST ... ...DSFSWNTMISGYAKNRRIGEALLLFEKMPERNAVSWSAMITGFCQNGEVDSAVVLFRKMPVKDSSPLCALVAGLIKNERLSEAAWVLGQYGSLVSGREDLVYAYNTLI...KHTVSWNSIIAAYEKNKDYKEAVDLFIRMNIEGEKPDPHTLTSLLSASTGLVNLRLGMQM...HQIVVKTVIPDVPVHNALITMYSRCGEIMESRRIFDEMKLKREVITWNAMIGGYAFHGNASEALNLFGSMKSNGIYPSHITFVSVLNACAHAGLVDEAKAQFVSMMSVYKIEP...VGYGQRGQVEAARCLFDQIPDLCGDDHGGEFRERFCKNVVSWNSMIKAYLKVGDVVSARLLFDQMKDRDTISWNTMIDGYVHVSRMEDAFALFSEMPNRDAHSWNMMVSGYASVGNVELARHYFEKTPE

  9. Protein (Cyanobacteria): 57516 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ISLYASYARSFTPVLFGTAFDGSPFEPERGTQYEVGVKADLSNQLSATLAFYNLTRTNVPTDDPDNIGFSIQTGEQRSRGIELNIGGEILPGWNIIAGYAYTDAQITQDNIFPVGNRLNNVPE...QVIRDQQATRVEDALRNVPSVTQEGGYYSSTSNFRIRGFRTDAENVLRDGLFEGVGNVTGQTVETDLFNIERVEVLLGPASVLYGSAAPGGTINLVTKQPLSDPFYQV...QLLVGVDWNRDNATYTRSNRGISPIDVFNPVYNQPRTEPFEISFSDDYEINSLGIYIQDLVSLTENLKLLLGLRYDTQDYNLRSRVDDFTLSRFDSAFSPRVGIVYQPIEP...AEQPMGETPQEEPAAQGDELIEILVTGEQDEGYNPSEASTATRTDTPLRDIPQSIQVVPQ...e receptor Gloeocapsa sp. PCC 7428 MKLKNLLQLLLLTSSVWPWGAVSVTAQEVAKLDHDKTITSVLRKSRLIREIPQIGERERPSTSAIMLVQSPAP

  10. Protein (Cyanobacteria): 282607 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RKRDGKLVLVDFGAAKDTEAADLSVTGTIIGSAAYIAPEQAVGKPKFASDLYSLGATCLHLLTNIEPTELFDVAEGEWIWR...RGKAKYITLKLSQDITMDLVGIPGGQFLMGSPENEPERGNDESPQHSVNIRPFLLGKYLVTQAQWQAVMKKNPARFIHPNRPVEKVSWYDCLEFCQKLSNLIGREFRL...EAMRLDELGKHEQIPELFAYFSQEERQYLIQEFIDGDDLAKELAQKGVFSEQQIQELLKDLLTVLKFVHVNNVIHRDIKPENIIR...PTESEWEYACRGKTNTPFHFGTTITTDLANYNGEYSYEIEIQGKYRHETTEVGSFSSNSFGLYDMHGNLAEWCFDSWHPSYDNASIDGSAWTSNQEKDNRILRGGSWLHLPGCCRSSHRLSAAPNIKSDAFGFRIAASV ... ...rotein kinase Stanieria cyanosphaera PCC 7437 MSQCLNPNCLHLNPQSTQICEQCGAKLLLVDRYRAIKILGKGGFGRTFLAIDEFKPSKPRCVIKQFLPDVKGEKSLKKAAELFER

  11. Protein (Cyanobacteria): 206256 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FLNPERKSMPDIDTDFCIAQRDKVIEYVTQKYGTERVAQIITFNRLTSKAVLKDVARVLNIPYAEADKMAKLIPVSRGKPAKLKVMISDDTPEPE...NNHGFKIDPYVITAQERKAQKILAKGGEGAKLPPDVKKTYELLEAGELEGVFQLESSGMRQIVRDLKPSNIEDISSILALYRPGPLDAGLIPKFINRKHGRENIDYEHTILEP...NVEIVKIARELDIKIVATNDSHYISCYDVEAHDALLCIQTGKLITEDNRMRYSGTEYLKSAEEMKQLFRDHLPDDVIEEAIANTVEVADKIEPYNILGEP...RIPNYPIPSGHTADTYVEEIAWQGLLQKLNRKSRNEIDQVYKERLEYELKMIQQMGFSSYFLVVWDYIKFARDNDIPVGPGRGSAAGSLVAYTMGITNIDPVHHGLLFER...ubunit Fischerella sp. JSC-11 MSFVPLHIHSDYSLLDGASQLPDLVDRAIELGIKAIALTDHGVMYGAIELIKICRNKNIKPIIGNEMYIINGDITKQER

  12. Protein (Cyanobacteria): 323331 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FDYHPRGELAPRDVVSRAIFQHLANTEKDPTQATVFLDLSPIEPERIQRRFPNIIRRCLHWGVDIFREPIPVAPAAHYWMGGITTDINCQTTIPGLYALGETASTGVH...CDGEAVDFLVNHAPQAIAELVQFGVSFDRHGQHLALTLEAAHSQPRVLHAADTTGRAIVSTLMGQVQARPNVEIFSQAIALSLNIEPTTGHCRGIQVFVNQTIETFHS...GANRLASNSLLECIVFASQLRNLSLPPLASSDSNVNQSIKEIRLDTTNDLALLNHWRSELPRLMWQTAGICRQAETLQMAIAKLEQWQEQWQQLSSSKLLAHLPEDQKISLSGPGLNEFMQLWAETHNLLDIAQLILTSALFREESRGGHYRLDCPDTKREWQSHTVIEGTRVFLQPSQSQD ...

  13. Protein (Cyanobacteria): 56032 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WDGPASIAFTDGTMMGAVLDRNGLRPSRYYVTKDDLVIMASEAGVLPIEPERVAFKGRLQPGRMFLVDMKEGRIVADEEIKEGIAKAHPYRQWLNENLVNLDDLLAVETAPPE...AHPYRYIAHNGEINTLRGNINWMHARQSMFASPLFGEDIKKIQPVINIEGSDSLIFDNALELMVLSGRSLPHAVMMMIPEPWAAHESMSDEKKAFYEYHSCLMEP...utamate synthase large subunit Microcystis aeruginosa NIES-843 MNNNQTPRKQGLYDPRFEHDACGVGFIVHKTGKKSHDIVEQALTI...LLNLDHRGACGAEKNTGDGAGILCQIPDLFFRKVTSNLGFTLPAAGQYGVGMLYTAPDAEIRGKSRQEFEKIAAEEGLKVLGWRDVPTDNSSLGNSAKSTEPFIEQVFIERDANLSDDLAFER...DLFKKYSQLVNQQNQKFFTLRGLLTFKNRESIPIEEVEPIEAIMKRFKTGAMSYGSISKEAHESLAIAMNRIGGKSNTGEGGEDSERYTWTNEQGDSKNSAIKQVASG

  14. Protein (Cyanobacteria): 289136 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YSVPNHPGFYRVRYQISEQKLVSIIIPTRNLGNILDRCLESIFTQTTYPNYEVIVIDNGSDEPETLSIIEKWKNQQPERFKCYEKNIPFNFSKLNNYAVEKAEGDYLL...SLINQIYPNWELCYISDKLPQNIEANNKIKLVIKSENRDIATDLNAALALATGDFVTLLNPEDILTPDALYEMVLFLNRYPDSDMIYSDEDKLTSEGKLIEP...IYANLGSLYAMQQKWEEAISYYQKAVDIKPDFAGAYRNMRKVWLSLGNQKLATYCQYKVLSIEPEKATFEEFMNVGKTLEKEGSLNDAIS...SNKVNGHNTLVRATIPTTSPTVNAEDIETYMVEAETYVNQKKWEQAIAVSKQVIQTKTEPKAYKIIGNSLQAMGKLQEALDWYNKALKIKPDFGEVYANIGTIFAQQKQWGQAIQNYLRAIEIKPE...IVGCSIDVPSPGVKQNISSICIGGWVVGKKSSPVTVKLISLTKSGKVLREVPANLHRPDVGKIHPEYPYAQHSGFWGEIEVIEIAPESKISLEAIFKDGSHVRLGMVSFKCPNLI ...

  15. Protein (Cyanobacteria): 323329 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FDYHPRGELAPRDVVSRAIFQHLANTEKDPTQATVFLDLSPIEPERIQRRFPNIIRRCLHWGVDIFREPIPVAPAAHYWMGGITTDINCQTTIPGLYALGETASTGVH...CDGEAVDFLVNHAPQAIAELVQFGVSFDRHGQHLALTLEAAHSQPRVLHAADTTGRAIVSTLMGQVQARPNVEIFSQAIALSLNIEPTTGHCRGIQVFVNQTIETFHS...GANRLASNSLLECIVFASQLRNLSLPPLASSDSNVNQSIKEIRLDTTNDLALLNHWRSELPRLMWQTAGICRQAETLQMAIAKLEQWQEQWQQLSSSKLLAHLPEDQKISLSGPGLNEFMQLWAETHNLLDIAQLILTSALFREESRGGHYRLDCPDTKREWQSHTVIEGTRVFLQPSQSQD ...

  16. Protein (Cyanobacteria): 186351 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TIDYVVTKIPRFAFEKFKGSPAVLSTAMKSVGEAMAIGRCFEESFQKAMRSLEIGRAGWGCDRQEPEFTPTEIERLLRTPSPERIMAVRTAMLAGRSDHDIYALSKIDIWFLAKLRHMINIE...PLYRLDSDDQLYKLEPESEVVTDNRAKVMILGGGPNRIGQGIEFDYCCCHASFASQDKGFVTVMVNSNPETVSTDYDTSDRLYFEPLTLEDVLNVIEAER...hate synthase large subunit Prochlorococcus marinus str. MIT 9313 MPRRSDLRRILLLGSGPIVIGQACEFDYSGTQACKALRDEGFEVVLVNSNPASIMTDPE...MRSTGEVMGSASSFGMAFAKSEIAAGDSLPIRGTVFLSTHDRDKPALILVAERLIELGFDLTATSGTAQALNRAGLNVQPVLKVHEGRPNIEDLIRSGQIQLVINTPIGRQAAHDDKYLRRAALDYSVPTLTTIAGARAAVEGITALQQQSLSVAALQDIHV ... ...MADRTYIEPLTPEVVTRVIELERPDALLPTMGGQTALNLAVELAENHTLERFGVELIGADLAAIRKAEDRQLFKQAMERIGVNVCPSGIAS

  17. Protein (Cyanobacteria): 197940 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RQFLTGTALTVVLDSVFSVVYIVVMIIYSPLLTAVALGIVPIFVILTLVFSPLIRRQLRLKAERNAQTQSYLVEVMSGIQTVKAQNIELRSRWQ...IAGEVKFENVSFRFKKQGPLQLNNINLSFPPGTFVALVGQSGAGKSTLTKLLSRLYEPEGGRILVDGLDIGKVELYSLRRQVGVVPQETLLFEGTVQENI...r ATP-binding protein Synechocystis sp. PCC 6803 MSLTIADYQSFLREIEPFAQLPAPAIAEIAAKLRPLRFRMGQIILARGKLANNVYFLVS...GQARLLGYDPGTGYPATMALLQNGAVIGDNNAIRNVPCETAIASTETICASLTRDEFLALVDKYPELARVYRHQCGRVELFDLLGEQLQRTAQGNVDLRQLTLEMLPQSQVYELQPGSHSLPSDLPDPER...WQDKYSRYVGAGFNTVITSTLASSSSHFLNQLSGLLVLWVGASLVLDGDLTLGQLIAFRIIAGYVTSPILRLTQLWQNFQETALSLERLADIVDTPQESERDRQNIPMPE

  18. Protein (Cyanobacteria): 57640 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GIYIQDQIKLAENLKLLIGGRYDFTNQSFLSIVDGVKFFDISDQAFSPRIGIVYQPITPLSLYASYSRSFAQNFGIQRDNSRIEPERGTQYEVGVRGEFLDGKLIASL...LQLVNRSQGNAYIADIPNAQLRLPNGDTFTFTSPKPVEGISEIIVSNLDANTIRVTVTGEAGLPVVELFDSDEGLILGVLSAAPSQTQATPTPEPEQPAATTDQPIEL...VVTGQQDSYRVTNAATATKTDTPLRDIPQSIQVIPRQVIEDQRATQLNEALRNVSGVQPSNSAGRTRDRFVIRGFDDFNSVIRDGFKENTSVYRETANIERIE...AGYQITKTNVATPDPADLNFSIPVGEVRSRGIEFDIAGELAKGWNIIASYAYTDAKITEDNTDNEGNRLNRVPENSASIWTTYELQSGALQGLGMGVGLFFVGERQGDLSNSFTVPGYTRTDAALFYRRDNWNIGLNFKNIFDVNYIESTTSRTSIDAGIPFTVIGSLSVKF ... ...VDRPTPDETYAFQTDLIGKFKTGAIEHELVIGFDFNRQTNFVDDRRSAPAPAIDIFNPVYLTARPNIESDPFRGLFAADNI

  19. Protein (Cyanobacteria): 323335 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KVSTGDGIALAWRSGAQVRDLEFFQFHPTALTKPGVPHFLISEAVRGEGAHLLDRQGKRFAFDYHPRGELAPRDVVSRAIFQHLANTEKDPTQATVFLDLSPIEPE...VQFGVSFDRHGQHLALTLEAAHSQPRVLHAADTTGRAIVSTLMGQVQARPNVEIFSQAIALSLNIEPTTGHCRGIQVFVNQTIETFHSRAVLLATGGGGQVFAQTTNP...RIQRRFPNIIRRCLHWGVDIFREPIPVAPAAHYWMGGITTDINCQTTIPGLYALGETASTGVHGANRLASNSLLECIVFASQL...RNLSLPPLASSDSNVNQSIKEIRLDTTNDLALLNHWRSELPRLMWQTAGICRQAETLQMAIAKLEQWQEQWQQLSSSKLLAHLPEDQKISLSGPGLNEFMQLWAETHNLLDIAQLILTSALFREESRGGHYRLDCPDTKREWQSHTVIEGTRVFLQPSQSQD ...

  20. Protein (Viridiplantae): 255549966 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NNEIQFVETSDLMVAKILFPDIISTNFIGIVKSEPERYTAYEGTFDMEKISQFLVHNKFPLVTRLNELNSVRVYSSPIKLQVIVFAKADDFKNLIEPLQEVARKFKSK...IMFIYIDIADENQAKPLLTLFGLEDSQNTLVIAFDNNMNSKYLLELDPAPSNIEDFCSRLLHGSLSTYYKSQPVPDNKEAS...IQVIVGKTFDDLVLSSPKNVLLEVFTPWCINCETTSKQIEKLAKHFKGLDSLVFAKIDASANEHPKMQVEEYPTLLFYPASDKANPIKLSTKSSSKELAAAINKHLKGKEQAAKDEL ...

  1. Protein (Viridiplantae): 308801707 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PMELAARAHVGSMEQYRSMYNRSIKEPEMFWSEIAGELRWETAFDGVDKPEEVLEWNFDPSKGEVYVKWFAGGRTNMSFNCLDLQIERGLGDSPALIFEANDAVNSR...YENSYFKVFEGGYYASGDGARRDADGYLYVTGRLDDVMNVSGHRIGTAEVESALVQHPLCIEAAVVSIGHEIKGETIVAFVILDPLRKKEATQYPEQELVFKVRAEIGPFAAPER...CoA synthetase (ISS) Ostreococcus tauri MRATTTTTRAVTTTRRRGKTSGNVVTRATGGDDGGAKSRSSSIDVPRNHAVSPGRRGRARGTNGDAIEP...VIVVKNLPKTRSGKIMRRILKKIAAGNIEDLGDVSALADPGSIEHCIQAEQRARGTR ... ...GGYLVYAYATSKFVFDLHPGEDIVFCTADLGWITGHSYTLYGPLLNGCATVLFEGTPTYPNAEIWWNIVDKHRVTIFYTSPTALRTLQGFGDAPVHKSSRATLRILGTVGEP

  2. Protein (Cyanobacteria): 272438 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VDNSQQGSKIYRPKEPERIYSQQQFFSEFLDKRKAKRIAIIGEPGAGKTTLLQKISDYVLKENLGLPIWISLSELTTTENLDNIE...DPTNQEAIAGLIALLFECEDECIRIRTAQSLKIDLGNQETISGLITLFNSSQEESTLMKVTYSFKKIEPGNKYLTLVVSRLKPNLTNTVYQNNFDLYENSFNILWQCAANLPYPDFYHAWHS ... ...ith Nacht domain-containing protein Cyanothece sp. PCC 7424 METWIEWDNFIKIKATEKKFTPEQSKCFQKFFKKDNIDFEQNKFNSPR...EEIDKKLQITEDDRKKRLTAIYEKFKKDCEFPKNNKYKYLIEHLKKKYQEWISQINQQPSSSTTPTETPETKINWHEICEKILQQQKRLTTNPLLHDNEKAKKEYPDVYIELGLVHRKKRENPEP...TYRLLDYEYPQQVYEFIDKFFKVKSDLTPPIPLPYEERGKLATRLKTALNQPEKASVRDLIRNPLRLTLLCYFGLDREILPDTQAQLYDFYRDYFYKWKPDRFLLTHS

  3. Protein (Cyanobacteria): 176770 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EEQALGTAGCVKNISALLTDTFLVISGDCITDFDLTAAIEFHRQNGSKATLVLARVPDPMEFGVVITDKSHRIRRFLEKPSTSEVFSDTVNTGIYILEPE...AKLHPPILIGDNCRIGPRANIEAGTVIGDNVTIGNDADLKRPIIWNGVLIGEEAHLRACGIARGARVDRRAHVLEGAVVGALSTVGEEAQVSPGVRVWPSKHIEPGAALNI...NLIWGSTAPRNLFGQRGVAGLANVDITPEFAVKLGAAYASTLKPGSQVTISRDQRSISRMVSRSLISGIMSVGIDVQNLEATALPIARCVPRNALVVGGVHVRIHPER...VLDYLPSDQQTDFSKDLFPLLLEKGEPMFGYVAEGYWCDVGSLDSYREAQYDALQGNVRIEFAYQEMNPGLWMGQNVHIDPE...SDFILIEFFDEQGINISKAKEKKIEGAYFKEDFRRAPIGEIGGITYPGVLLDDYAQIFEKWLN

  4. Protein (Viridiplantae): 242040035 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VAADYFDAQADYQQLENYEDCELRAQEFHRIALNLCMQQEPTLEGHNAGIDALLLAAECYVNPFFLLEFQPNLEPLDNIER...MPRIVHILVSLCRASYTDVAFLKSVLCLMKPLISYFLRKGTNDTKRRIEMLGSLLVWIDCISFDPPSLLCSYLQGFQTLLDGCEAVLIQNIELLGVSILSATSQSIEP...hypothetical protein SORBIDRAFT_01g027630 Sorghum bicolor MEAAAAAPPERDTSADWGDGVVALGFRVKASSRESPSQKAGNLLEADLRSHWSTATNTKEWILLELQEP...DSDALRTSLASTPTVSSNFEASKVLQKLLEPEPFLDKSMNTSVMLPSQVSDEIPKSDAFSLVLSTDYSSMFGEEFSLSENQFDGSFVNILDIAAVEEGILHVLYAAAS...AVKHFCSHAPRISWRLQTDKWLSLLVSGGIEGFKNSEICLIDLFCTMLNHSEPEQRSVAVQQLGRIINKTSSTEADLKYPNYDQNFLISGSTVTSLLVTHTWDRVAAL

  5. Protein (Cyanobacteria): 228852 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SFVIDGNGDIWVGEEFGPYLLHFNSDGELIEAPTATPNPLELNTLNGQDPIVIGHRGASGILPEHTLEAYATAIAQGADFIEPDLVITKDGVLIARHEPLLDDTTNIADVFGPER...DIGDWESSGILDVSELFGEDPGNLFVFDVQAHSLRDGVIEDANLVQGGQLSFLEAPEEPEPEPINFDTMEPAQMVGLEEYT...YNQIDGLNYVWVNHELGDSVTTDISSTQIGQINGARVSLYIFDENWDVIGGRNLINDVVIDGETYSLNIETGNYETADGTVLNLRDHDNLSRFCSAYLASMGFVDDSG...TKHPTFFDLQDLSLEEPLIATLQETGFTDPSRLFIQSFEFQNLIELQGMLDAEGLGDIPLVQLYGNTTASASPDSGFSVPYDIRYNVEQGNDLAAI...EEIKQLIDIGVDGFFTDFPGTGDAVRDQIVADVVRSPDNPDVLAGDEVSNLLRSRGFEGMAISPDRMTLYPMLEGTVEGDPEGSLRIYEFDVASGQYEGLVGRYQLEDPSHAIGDFTVINQNEYLVIE

  6. Protein (Cyanobacteria): 239585 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LAVEAPTASPCGECEVCRAIARGSALDVIEIDAASNTGVDNIREIIERSQFAPVQCRYKVYVIDECHMLSVAAFNALLKTLEEPPERVIFVLATTDPQRVLPTIISRC...QRFDYRRIPLEAMVSHLTVIAQKENIEIEPEALTLVAQIANGGLRDAESLLDQLSLLSGSITSEKVWDLVGAVPERDLLSLLKAINSNNPEIVIE...SCRKLMDRGREPLVVLQNLAGFYLNLLIAKTAPERSDLVAVTSTTWDDLCTEANQWQTETILRGQQKLKESEVQLKNTTQPRLWLEVTLLGLLPQACTPEVIIQSSTIPTQTKNNIE...SKTTTLQPQQPRSKVVENSGKEQPKTLSKPPKTVINTPETSINNDDLDLDQIWQLVLGKLVPFISALIKQYGHLISYKGTVATVGMKNKELLKLAQDKVPQIE...SAFQEVVGHKVKVNLQVRTASKIANKSHNPPSTTPTVPSPNNHNNPVKDKKKIDDDNKVNLDKKPTINLENNNNGQKQVIESANI

  7. Protein (Cyanobacteria): 449410 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LVDQDNWRHELLQDLAQQWESLANLSIICEKEARIASKNKRQYRFWRILVGLTITLFSALWCARNPRNENSNSPLSRRSFLIGALTGLVGIFTAGGPLVDAVNDLIEPER...HRNRAIGFRSLKIDTDSQMLNIEMMIFYDLSKKELNFSAFYQKFKAIKEETNRIYKKSYELGINI ... ...tein MICAB_810002 Microcystis aeruginosa PCC 9717 MTFYECMTTNITQQNNQNNFSFAKFKEQITARRIDLNKAIDKVKQDHYVKEDKQKKELSPIIFEKSLFPE

  8. Protein (Cyanobacteria): 249071 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LLLGAKQTFGVDTDILAVTASNSNRALNNIEPERMVVAQGSIDTLPKMYPEPFDGIVCNILAEIIIELIPKMSAIAKPDTWGILSGILIEQIQPIADTLEQNGWAIAALWKKDEWCCFNIRRN ... ...QDAVLAHLPKPVVKWHLIDEEDWSSSWKSHWQPEEIGDRLLIYPAWLEVPTHSERLLLRLDPGSAFGTGAHQTTQLCLEALEMRLGQQPETQVIADIGCGSGILSIGS

  9. Protein (Viridiplantae): 356577041 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 1602 3847:1602 PREDICTED: LOW QUALITY PROTEIN: protein SRG1-like Glycine max MEPETAKLGSSLLVDSVKELAKEALIKVPERYVHPNIEP...LGLNAHTDGSALTILLQGNEVEGLQVKKDGTWIPVKPLPNAFIVSLGDVLEVMTNGIYRSTMHRAVVNSQKERLSIATFYGPGWSGNIGPAPILVTPERPALFKTIGVEDFYKGYLSPQHLGKPKSYINDVLRIQNGHVKG ... ...LWQKPXRTEGFGQMFGYKEGPSDWVDLFYIFTLPSHLRNPHLFPNIPLPFRENLEDYCIKMRDLAINIFVLIGKALGIELKDIKESLGEGGQSIRFNYYPPCPQPENV...PILFHKDTLPQLPIIDLNKLLSEDVTELEKLDFACKEWGFFQLVNHGVGIKLVEDIKKGAQELLNLSIEEKKK

  10. Protein (Cyanobacteria): 28175 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EAQVKITINREKNTLTISDNGIGMNDEEIKKYINQVAFSSAEEFLTKYKKDNDEFIGHFGLGFYSSFMVADKVDILTKSAIGESKAFKWSCDGSPNFTLEESERETIGTDVILHLLEEEKEFIEPER...DEKFAELVNNSIIFETIINSEKNVTKNIENKSLIKSNDKYFTTLANYKERNKLTDSKKIIYCSDLIAQSSALKICLSDNKEVIKSDPLIDAQFLPWLESKNEDFQFQRVDSEINEIE...NTDYPYDIQGILYFPKLSGRADWEKGEIKLFCNQVFVSDSIKEIVPKYLLPLRGVIDSTDIPLNVSRSALQTDRKVRSISSFISKKIANKLKDLIKNSPEFYAEIWDSISAFIKIGAIE...ck protein 90 Prochlorococcus marinus str. MIT 9301 MEKGEIRINTENIFPIIKKAVYSDHEIFLRELVSNGVDAISKRRMASMAGDCENTE...IKSLIKKYCDFMPIDVLLEGETINKKNPPWRKQPSELKDEDYIELYKYLYPFQGDPLLWIHL

  11. Protein (Cyanobacteria): 156191 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available onent I Cyanothece sp. PCC 7424 MISPTFAEFESLAKQGNFIPVYREWIADLETPVSAWYKVCAGEEYSFLLESVEGGETIGRYSFLGCEPMWVLEARGNTTTQTYRNGNIER...YSHVMHIVSNVVGELAPHKTAWDLLKACFPAGTVSGAPKIRAMEIIQELEPERRGPYSGVYGYYDFEGQLNSAITIRTMIVRPVSANQYIVSVQAGAGLVADSIPEKEYEETLNKARGLLEAIRSLK ... ...FEGNPFEILSSCIDPIKPVKLPQLPPGIGGLFGYWGYELIRWIEPRVPIGEATEKDLPDGIWMQVDNLIIFDQVKRKIWAIAYGDLRDETVSLE...KGHPFDLYRSLRLINPSPYMGFYQFKDWQIIGSSPEVMVKAELNENKTLKATLRPIAGTRPRGKTLAEDLAFEKDLLQDPKEIAEHIMLVDLGRNDLGRVCMKGTVKVDQLMVIER

  12. Protein (Cyanobacteria): 323304 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HPAGELAPRDVVSRAIFHYLQSQKADPPQTNVYLDLRPIEPERIRHRFPNIIRVCQKWGIDVFHEPIPVAPAAHYWMGGVKVNLNNATSIEGLYAIGETASTGVHGAN...SAVQFLVNHAPSAIQSLVDMGVAFDRKGQQLAMTLEAAHSHPRVLHAADTTGRAIISTLTEKVIQRPNIEIIAQAIALQLWIEPEPKRCQGLSVLYQGQIYWLQASAV...ce sp. ATCC 51142 MTLISSANSVETKGLTTQFDIIVVGSGAAGLYAALCLPTHYHVGLITKDTLKTGASDWAQGGIAAAIAPEDSPIFHQEDTLKAGAGLCDE...RLASNSLLECLVFAGQLSKLKVTAPVPITKTTEFMINNESQWEQEIPEVREIRQALPQLMWQSAGISRRQTVLEAALSQVSLWQKQMKAFSLSQPILNLLPGQSVKFEGANGQTYLRTCSETLNLLDIAYLILNSALFRTESRGGHYRQDYPQPSQQWEKHTLVCDRRWWKDEIH ...

  13. Protein (Viridiplantae): 357131165 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DFLGHGIFNSDGDQWLWQRKASSYEFSKRSLRNFVVSTVRFEVVERLLPLLSQAEQDGRTLDVQDVLERFAFDNICCVAFDEDPACLTEEGLGVNGRAEFMHALTDAQNIVMARFMSPIKSAWRIKKLLNIEP...EEKIVREICTVRASSRSTDAAFSFSELRKMNYLQAAITESMRLYPPVAMDSRCCQHDDVLPDGTFVGKGWQVSYSAYAMARLEEIWGNDCQEYRPER...WLDAEGMFQPESTSKYPIFHGGPRMCLGKEMAYIQMKSIVACVFERFSFQFVGGESRPGLVFSVTLRMEGGLPMQVKKREQ ... ...DGLKAYPVVGTLPHFVKNQHRLVEWSAGIIARCPTHTMSFNFKGLGLMAGAITANPANVEYVMKTNFQNYPKGDFVVSVIE...ERRMHEALATIHGYVDRIVRERSERGAAGLARKDDFLSRFASSGEHSNESLRDVVTNFILAGRDTTSSALTWFFWLLSSRPDV

  14. Protein (Cyanobacteria): 323334 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AIFQHLANTEKDPTQATVFLDLSPIEPERIQRRFPNIIRRCLHWGVDIFREPIPVAPAAHYWMGGITTDINCQTTIPGLYALGETASTGVHGANRLASNSLLECIVFA...AELVQFGVSFDRHGQHLALTLEAAHSQPRVLHAADTTGRAIVSTLMGQVQARPNVEIFSQAIALSLNIEPTTGHCRGIQVFVNQTIETFHSRAVLLATGGGGQVFAQT...TNPKVSTGDGIALAWRSGAQVRDLEFFQFHPTALTKPGVPHFLISEAVRGEGAHLLDRQGKRFAFDYHPRGELAPRDVVSR...SQLRNLSLPPLASSDSNVNQSIKEIRLDTTNDLALLNHWRSELPRLMWQTAGICRQAETLQMAIAKLEQWQEQWQQLSSSKLLAHLPEDQKISLSGPGLNEFMQLWAETHNLLDIAQLILTSALFREESRGGHYRLDCPDTKREWQSHTVIEGTRVFLQPSQSQD ...

  15. Protein (Cyanobacteria): 323309 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LAPRDVVSRAIFSHLQKTATDPAHDPVYLDLRPIEPERIRRRFPNIIRVCQEWGIDLFCEPIPVAPAAHYWMGGVKVDLTNQTSIKGLYAIGETASTGVHGANRLASN...QFLVDQASSAINSLVQMGVAFDRQGTHLAMTLEAAHSHPRVLHAADTTGRAIVDTLTEKVLERPNIEIVSQAVALQLWIEHEECLGISVLYQEQIYWIRSGAVILATG...SLLECLVFASQLSQLRVISPQNSDLPGIYPIEHQGHWTAEMDVIGSIRHDLPSLVWKSAGICREAAVLTSALEQVKLWRSQLEKLKISHYVLGLSPGQAVIFDSPLAPIQLKSCAETLNLLDIAYLILKSALFRQESRGGHYRIDYPQSSPEWIVHTLICGEQWWTGQVD ... ...GGGQVYAQTTNPSVSTGDGVALGWRGGAILRDIEFFQFHPTALTKPGAPRFLISEAVRGEGAHLIDRQGRRFAFDYHPNGE

  16. Protein (Viridiplantae): 22327500 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LTNDKSLFLHIACFFNYAKVDNVTALLADSNLDVGNGFNTLADRSLVRISTYDDGISVLSDSNLDIVLEQSKEPGKREFIIEPEEIRDVLTNETGTGSVIGISFDTSNI...GEVSVSKDAFEGMRNLRFLRIYRLLGGEVTLQIPEDMDYIPRLRLLYWDRYPRKSLPRRFKPERLVELHMPRSNLELLWGGIEPLPNLKIINLNRSYRLKEIPNLSKATNLER...69 TIR-NBS-LRR class disease resistance protein Arabidopsis thaliana MASSSSSSSSSHIRRHHVFSRFHGPDVRKGFLSHLHSLFASKGITTFNDQNIERGQTIGPE...LTLESCLSLVELPSSISNLHKLEILDVKFCSMLQVIPTNINLASLERLDVSGCSRLRTFPDISSNIKTLIFGNIKIE...KCFMGNLKGSIKGVADHDSKLRLQKQLLSKIFKEENMKIHHLGAIRERLHDQRVLIILDDVDDLKQLEVLAKEISWFGSGSRIIGTTEDKKILKAHGIHNIYRVDFPS

  17. Protein (Viridiplantae): 238481459 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DRLLTNDKSLFLHIACFFNYAKVDNVTALLADSNLDVGNGFNTLADRSLVRISTYDDGISVLSDSNLDIVLEQSKEPGKREFIIEPEEIRDVLTNETGTGSVIGISFDTSNI...GEVSVSKDAFEGMRNLRFLRIYRLLGGEVTLQIPEDMDYIPRLRLLYWDRYPRKSLPRRFKPERLVELHMPRSNLELLWGGIEPLPNLKIINLNRSYRLKEIPNLSKATNLER...2:769 TIR-NBS-LRR class disease resistance protein Arabidopsis thaliana MASSSSSSSSSHIRRHHVFSRFHGPDVRKGFLSHLHSLFASKGITTFNDQNIER...GDLFPQGNKYHEVDVTMSEITFEFSHTKIGDKIIECGVQIMTEGAEGDSSRELEVLKLRVAAAQLGDLLGNLNLEATTITTQMEMEMETMKQKVPSSLKMKTSKPANVGFMSWLRKLDGDGEYEPE...LTLESCLSLVELPSSISNLHKLEILDVKFCSMLQVIPTNINLASLERLDVSGCSRLRTFPDISSNIKTLIFGNIKIE

  18. Protein (Viridiplantae): 297837963 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available MKLRIVGGRSYSGPYPNFSFARPITKKPTFLRLRGSFEYEIQSWKYSIPLFFTTQGFDIFRNREISTGAGAIREQLADLDLRIIIENSLVEWKQLGEEGPTGNEWEDRKIVRRKDFLVRRMELAKHFIRTNIE...DIDHEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVSAGLIWKTSRNMQEQIIFIGNI...NKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPER...IRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPE...QDMLIGLYVLTSGTRRGICANRYNPCNRKNYKNERIYETNYKYTKEPFFCNSYDAIGAYRQKRINLDSPLWLRWQLDQRVIASREVPIEVHYESFGNYHEIYAHYLIVRSVKKETFCIYIRTTVGHISFYREIEEAIQGFSQACSYDT ...

  19. Protein (Cyanobacteria): 239583 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DPQRVLPTIISRCQRFDYRRIPLEAMVSHLTVIAQKENIEIEPEALTLVAQIANGGLRDAESLLDQLSLLSGSITSEKVWDLVGAVPERDLLSLLKAINSNNPE...TSSARILAKSLNCLAVEAPTASPCGECEVCRAIARGSALDVIEIDAASNTGVDNIREIIERSQFAPVQCRYKVYVIDECHMLSVAAFNALLKTLEEPPERVIFVLATT...IVIESCRKLMDRGREPLVVLQNLAGFYLNLLIAKTAPERSDLVAVTSTTWDDLCTEANQWQTETILRGQQKLKESEVQLKNTTQPRLWLEVTLLGLLPQACTPE...VIIQSSTIPTQTKNNIESKTTTLQPQQPRSKVVENSGKEQPKTLSKQPKTVINTPEISINNDDLDLDQIWQLVLGKLVPFVSALIKQYG...KKIDDDNKVNLDKKPTINLENNNNGQKQVIESANITEAQSNENSFDDVDFSDNKIQEVAEQFAKVFKGEIIADHEDLIHEEENFKNHKSAAKDDIELSNQTLEELTIEEEIDNNVNSDNPQDKTEETSINAQKIIGRPKITKKEEELEF ...

  20. Protein (Cyanobacteria): 261251 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VPCFTLDSLIDTYQLERVDLLKIDAEGHEVPVLEGSQLLIERFAPIILYENIAANQGSNLAVARWLEGKGYRLYRYRPYLQELLEIESEADLQGILNVIALPERELRD ... ...Microcystis aeruginosa NIES-843 MSDYLALYRQYLQSINPALDGEFLIAENLSTNWDEPETALDFHNCAVMALIEAENSPMRSMYVEMAFQSLQRVLEM...YP_001656533.1 1117:4755 1118:3263 1125:506 1126:938 449447:1381 methyltransferase ...DITLAVEASFRSFVTGVLLAQGDWFEAEMEFWRHSIREGMTVIDVGANAGVYTFSAAHRVGKTGKVIAIEPFSQCIQLLEETCRVNQFSWVYPCRGAASNQGGNVYLSLYQASELNEVVTDAAQLKSDNYEP...LNRQLGIAKLINQQLEGLFNLHRAVNLDPEDADNLQALYLAYRGLGQQQLANFWLETAKVTGKSWTNLDINQPFTYLDFDR

  1. Protein (Viridiplantae): 297802258 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TSLIGGYAQNGKPDEALKYFDLLLKSGTKPDHVTFVNVLSACTHAGLVEKGLEFFYSITEKHDLTHTSDHYTCLVDLLARSGRFEQLKSVLSEMPMKPSKFLWASVLGGCSTYGNIDLAEEAAQELFKIEPE...IQVCSQTRALEEGKKVHEHIRTSGFVPGIVIWNRILGMYAKCGSLVDARKVFDEMPERDVCSWNVMVNGYAEVGLLEEARNLFDEMPERDSYSWTAMVTGYVKKDQPEEALVLYSLMQRVPNSKPNI...PNEYTFSGVLNACADLTTEELGRQVHGYMTRVGFDPYSFASSSLIDMYTKCGNIESARHVVDGCPKPDLVSL...FTVSSAVAAAAAIKCIRRGKEIHGHIVRAGLDSDEVLWSSLMDMYGKCGCIDEARNIFDKIIDKDVVSWTSMIDRYFKSSRWREGFSLFSELIGSCER...NPVTYVTMANIYAAAGKWEEEGKMRKRMQEIGITKKPGSSWTEIKRKRHVFIAADTSHPMYNQIIEFLGELRKKMKEEGYVPAT

  2. Protein (Viridiplantae): 242059275 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TREFRAQRCSAGEPETVCTVDDGTHEVQPSKSICLNDSKEKGLPTSGCMLDTGSVPFVNVQNVQESEVSAPVKDTIVCLSSQDEKIEPLESNSQLNMRSYAPE...DDEMLKKSNCMVTDKESEKSLFLSLDSDQKVHSQAEAEVQDIMVSTSCSISEILAQKITSKEQSFKKSIEVGDECFRPQDMDYVMMFDSSKDDNGPNPER...MTAEGDCGDPHEGLDSVTLGVIGKNVVYNAIIEDVKSINPNANNVNHGELYVSLQLPEGNADSGMTGVSTASPDSKEGNIE...QDNSYDCGLFLLHYVEQFLTDAPSNFNPLKIDVFSGFLSDDWFPPPEASLKRSVVRKLILELVTGSFQNHPKLACGGEQLDERDQRSSNAELEP...hypothetical protein SORBIDRAFT_03g040230 Sorghum bicolor MDSLKGSHTGLKDIIQSYLWEEWKERHPEAASDNSDKFLNLRFVSLELPQ

  3. Protein (Cyanobacteria): 186261 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e subunit Synechococcus sp. WH 8102 MPRRTDLRRILLLGSGPIVIGQACEFDYSGTQACKALRSEGYEVILVNSNPASIMTDPEMADRTYIEPLTPDVVTRVIERER...SPAVLTTSMKSVGEAMAIGRSFEESFQKAMRSLETGYSGWGGDRPEPELSEADIDRLLRTPSPERILCVRSAMLRGRSDAEIHRISSIDPWFLAKLRSIVDAEQQLLR...LGAGEALPTTGTVFLSTHNRDKPALVPVAERLAKLGFDLIATSGTADVLTKAGLTVNAVLKVHEGRPNIEDMIRSNQVQLVINTPIGRQAAHDDKYLRRAALDYAVPTVTTLAGARAAVEAIATLQSQPTLSINALQDVHGTRR ... ...SLTTLSPASEVSNSSSGRKVMILGGGPNRIGQGIEFDYCCCHASFAAQDAGITSVMVNSNPETVSTDYDTSDSLYFEPLTLEDVLNVIEVEQPDGVVVQFGGQTPLKL...VLIDQYLENAVEVDVDALCDHEGNVVIGGLMEHIEPAGIHSGDSACCLPAVSLGEGALGTIREWSRGLALALKVQGLINLQFAVQRNAEGEEVVYIIE

  4. Protein (Cyanobacteria): 323307 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PRDVVSRAIFSHLQKTATDPAHDPVYLDLRPIEPERIRRRFPNIIRVCQEWGIDLFCEPIPVAPAAHYWMGGVKVDLTNQTSIKGLYAIGETASTGVHGANRLASNSL...LVDQASSAINSLVQMGVAFDRQGTHLAMTLEAAHSHPRVLHAADTTGRAIVDTLTEKVLERPNIEIVSQAVALQLWIEHEECLGISVLYQEQIYWIRSGAVILATGGG...LECLVFASQLSQLRVISPQNSDLPGIYPIEHQGHWTAEMDVIGSIRHDLPSLVWKSAGICREAAVLTSALEQVKLWRSQLEKLKISHYVLGLSPGQAVIFDSPLAPIQLKSCAETLNLLDIAYLILKSALFRQESRGGHYRIDYPQSSPEWIVHTLICGEQWWTGQVD ... ...GQVYAQTTNPSVSTGDGVALGWRGGAILRDIEFFQFHPTALTKPGAPRFLISEAVRGEGAHLIDRQGRRFAFDYHPNGELA

  5. Protein (Cyanobacteria): 229589 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NDTLIGSNGGNGLAASSAVEENDTIHGHRNDDLLQGGPGDDLMYSGQEDDFSYGGKGNDIVWGDLGNDTLHGDEGNDTLVGDTVDESEIEPERGLSGMIDLVWGGAGD...GTISRSENGEALVYTPAPGFSGTDTFTYEATDGTNTDIATVTVTVNPATNTEPSAIDDERRTEVNTAVTVNVLTNDTDPENDPLTIENFDETSANGGIIEPSEEGQAL...VISISTFKLRRVNNNQVTGKQQIIWYETTPDSTNTEIKLAPNLATGTGDQEAMEVALSSDLINRGTDNIFANTGNNQGMVNNIER...VSPSANGQLIYTPAENFTGTDTFTYTLNDGNGGTDTATVTVTVEEPVNTNPDAVDDERSIRSNTAIIINVVGNDSDPENDPLNI...FGTVPLPEPLGLTPSAFNAFDNVIDGSDNADDIVAGSLGSDVVFAFGGDDSIEAFEGNDTVFGGIGNDLTFGDQGNDSLLGGDG

  6. Protein (Viridiplantae): 115462607 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KNTNENEEHNRTSEDIVESVMMLGGSKSDTELDAEPERTAGEAEVRNCDHSKDIDYIALGDINKDAAKQSLNRNIVEAEDIKCEGTLVDHTVVEDATPYNVNETSASA...RLTFSADGFKIEYWDSCENDEMAAQYWKISDITCIDCKWAQSVGSVLITLHVGSGTETGNSSHDRIQFCLIDSQWPRKQQNIWHLASRYQEIWNNIPSGDFASENWNIEP...SLFFPKQYFSDTEEFEDVIYPKGDHDAVSISKRDVELLLPETFVNDTIIDFYVKHLSTRIEPAEKHRYHFFNSFFFRKLADLDKDQGRAPE...GRAAFLRVRKWTRKINIFTKEFLFIPVNFNLHWSLIVICYPGEVETFKDGDTNISAKIPCILHMDSLKGSHSGLKDIIQSYLWEEWKERHPE...NANACVDDYQHTKMMAGIQPMEEVGFGCTQPFELQSQGIVPDSEEESLPSSPETSSTSNYDMPDLAEQNLEHIYNVLGEMVDKEGPVVLSPEYVMCGTTSHVEP

  7. Protein (Cyanobacteria): 385906 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available oxin reductase subunit beta Trichodesmium erythraeum IMS101 MTLATEKKNLSSDKSLNAIKNFAERYAKKTNTYFCIDPSVTAVVIEGLAKHKEDLGAPLCPCRHYEDKQAEVKATYWNCPCVPMRERKECHCMLFLTPDNDFAGEQQEITQEDLESTRKNM ...

  8. Protein (Viridiplantae): 15227263 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 93 putative protein kinase Arabidopsis thaliana MKLVLEGVDSFETLRVVGTFNCIDPDYVGSKRVTKKADVYAFEVILMELITGRKANYETLSVDEQNLVMWLRPKIKISTFLNLVDGTIATDKETIKRIKKIAKLAEYCTSQEVESRPLRASRTKSGNEVTSED ...

  9. Protein (Cyanobacteria): 209938 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available _00595 Cyanothece sp. CCY0110 MRLCYAFKWNLLNSLIQLRCPYVNHISTEELAIWLEDKNRPDPLLLDARSPLEYTISHLQGAYLIPHDLPKIEPLIHCSNASPIITYCSVGYRSAILAQRLQKMGYEKVFNLKGSIFLWFSEHRPVFCGEKIVSFIHPLNLFWSFWL ...

  10. Protein (Cyanobacteria): 210008 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e Crocosphaera watsonii WH 8501 MKNFDSLKWNLLNWLIQFLFPHINHISTEELALLLSDKEERQPLILDARNKIEYAISHLKEASLIPYDSPDIKSLVQCSLNTPIITYCSVGYRSAILAQRLQKMGYKKVFNLQGSLFLWFSENRPIVCGEEIVSYIHPFNLFWSLWL ...

  11. Protein (Cyanobacteria): 99327 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FNIEEEQTQQLFSEEEVIDNKLDVDEFSSDTEDTIGELSQFEDDTDNFLNELNEDNNDDSTEELSQFEDDTDNFLNELNEDNNDDSAEELSQFEDDTDNFLNELNEDS...NDDSAEELSQFEDDTDNFLNELNEDNNDDSTEELSQFEDDTDNFLNELNEDNNDDSTEELSQFEDDTDNFLNELNEDNNDDSTEELSQFEDDTDNFLNELNEDNNDDSTEEL...SQFENDTDNFLNELNEDNTDDSTEELSPFKETVANDTNHHANVELSSTFLEENTANSIFDDNNDEETEVLNNLFVEE

  12. Protein (Cyanobacteria): 341533 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein P9215_03981 Prochlorococcus marinus str. MIT 9215 MWSKIRLTIYGTTAIAGILWPFYFIIQFINLVRNGNIQGTFIDIGNAFFDDAWITPTSGFISADTAILLIAIFVFYAAEGKRLKLRFWGIYFPLTFIISLAFSFGAFMFIRELEINKELNETD ...

  13. Protein (Cyanobacteria): 99176 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ILTPLPGIGINFDIVESRGPMIDPPIRSVEQIEKLHPLEPAESLPFIREILQTLRQEVGDRSTVLGFVGAPWTLAAYAIEGKSSKDYTVIKGMAFSEPAMLHQFLSKL...VDWTVDMAEARARLGSKVGVQGNIDPCVLFGSKDFIRERILETIRKAGNKGHILNLGHGVLQNTPEENVAFFFKTAKQADKLLS ...

  14. Protein (Cyanobacteria): 462892 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available I7407_2252 Geitlerinema sp. PCC 7407 MRFKLLVSGLVTAAAIALSGTGAEAQTLMRTGLMRNVLVDALANRSTVFSSGVLADLETDENFGGDYQQIFDYASGILNDYTVVDRGGVFPENAGIPRDRQLPRTDVVYTVFTLDNGNELFLYRSPLEDTARYFIRESVPFGG ...

  15. Protein (Viridiplantae): 15230093 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VCRRDLFVGKFEVCGENNSSSNLSFIRENNSSANLKIYSSAKKRFVREIYSSAKKRFVEEIYSSANLRFVGENNSSANLSFIGQNNLSANLSFIRE...NNSSANLSSFLAIVSQTCEGNIRRKVCDGIASWSCSFGEIYSSKKRFVREIYSSAKKRFVGEIYSSANLRFVGENNLSANLSFIRENNLSANL...02:4271 uncharacterized protein Arabidopsis thaliana MTYTQFPRNCLANVRGKYSSQNLRRNSELVMFPRRDLFVGEEEVCRRDLFVGEEE

  16. Protein (Cyanobacteria): 440743 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ocystis aeruginosa PCC 9809 MTTSPESQFLQALEMCQSLSNLTAQFSSIPCRIIEILSDISQEPRVLYSLLIKYSREVDSALVALDIYAKSADNWRVKDRDKTCSLGFGVKDHCTILSCLLNFGKRPFSFISYTGNFASEAIIFELLKDWKNLDIAPFFEEKMQEFIREAKIA ...

  17. Protein (Viridiplantae): 168051496 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :614 114656:614 3215:614 3216:614 3217:614 3218:614 145481:614 predicted protein, partial Physcomitrella patens subsp. patens TSLTSLN...LSGCLSLITLPNELGNFTSLTSLNLSGCWKLISLPNELGNLTSLSSLNLVECWKLTSLPNELGNLTSLTSLNLSGCWNGFLNL...TSLPNELGNLTSLTSLSISEYWELTSLPNEFGNLTSLTSLNLSWCSRLTSLSNNLGNLTSLASLSLSRCSNLTSLPNELGNLTSLTSLN...LSGCLSLITLPNELGNFTSLTSLNLSGCWKLISLPNELGNLTSLTSLNLSGCLSLTSLPNELGNLTSLTSLNLSGCLSLITLPNELGNFTSLTSLNLSGCWKLISLPNELDNLTSLSSLNLVECWKLTSLPNELGNLTSLTSLNLSGCWKLTSLPNELDNLTSFTSLNLSGC ...

  18. Protein (Viridiplantae): 168042943 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ens subsp. patens LNLRDCSRLTSLPNELGNLSSLTTLNMSKCRSLASLPNELGNLTSLTSLNLSGCWELTSLPNELGNLTSLTSLNLCDCSRLTSLPNELGN...LTSLTSLDMSKCPYLTSLPNELGNLASLTSLNLSGCWKLTSLPNELGNLTSLAFLNLCDCSRLTSLPNELGNLTTLTSLNISGCLKLTSLPNELGNLTSLTSLN...LSRCWKLISLPNELGNLISLTSLNLSGCWELTSLPNDLNNLTSLVSLNLFECPSLIILPNELGNLTTLTSLNISECLKLTSLPNELGNLTSLTSLN...LSGCWDLTSLPNELGNMTTLTSLNISGCQKLTSLPNELGNLTTLTSLNISRCQKLTSLPNELGNLTSLTSINLCDCSRLKSLPNELSNLTTLTSSNISGCLKLTSLPNELGNLISLISLN...LSGCWELTSLRNELGNLTSLTSLNISGCQKLTSLPNELGNLTSLTSINLRHCSRLKSLPNELGNLTSLTSLNISGCWELTSLPNELGNLTSLISLNLSRCWELTSLPNKLSNLTSLTS ...

  19. Protein (Cyanobacteria): 321356 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein MC7420_5364 Coleofasciculus chthonoplastes PCC 7420 MPQRLSARFTIQSLNPPLQFTLLTHQPLHSHQLFLKKGRVLPQTLSARFTIKSLN...PPLQFTLLSHHPLHSHQLFLKKGRVLPQRLSARFTIQSLNPPLQFALLSHHPLHSHQLFLKKGRVLPQRLSARFTIQSLNPPLQITLFSHQPLHSHQLFLKKGRVLPQRLSARFTIQSLN...PPLQITLFSHQPLHSHQLFLKKGRVLPQTLSARFTIKSLNPPRQITLFSHQPLHSHQLFLKKGRVLPQTLSARFTIKSLN...PPLQFALLSHHPLHSHQLFLKKGRVLPQTLSARFTIQSLNPPLQFTLLTHQPLHSHQLFLKKGRVLPQTLSARFTIQSLNPPLQITLLSHQPLH

  20. Protein (Viridiplantae): 168043922 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ens subsp. patens TSLTSLHISQCHELRSLPNELGNLVSLTSLNLVNCWKLTSLPKELVNLTSLTSLNLSGFWEVTLLPNELGNLTSLTSLEISGCSKLTSLPNKLGNLTSLTSLN...LSGNSSLTSLPNEMGNLTSLTSLNLKRCSNLTSLPNELGNLASLTSLKLSRCSSLKSLPIELSNLTSL...PSLSLSGCWKLTSLPNELGNLTSLTSLNLSGCSNLTSLPNELGNLTSLTSLKLRRCSNLTSLPNEFGNLASLTSLNLDGWKNLTSLPKVLVNLTSLTSLNLSRCSSLTSLPNELGNLASLTSLN...LSGCWRLRSLPNELGNLTSLTSLHISKCWELTSLPNELGNLTSLILLNLSECSNLTSLPNELCNLTSLISLDLSGCSNLTSMPNELHNITSLTSLNINE ...