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Sample records for annulatus bm86 ortholog

  1. Vaccination against Bm86 Homologues in Rabbits Does Not Impair Ixodes ricinus Feeding or Oviposition.

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    Jeroen Coumou

    Full Text Available Human tick-borne diseases that are transmitted by Ixodes ricinus, such as Lyme borreliosis and tick borne encephalitis, are on the rise in Europe. Diminishing I. ricinus populations in nature can reduce tick exposure to humans, and one way to do so is by developing an anti-vector vaccine against tick antigens. Currently, there is only one anti-vector vaccine available against ticks, which is a veterinary vaccine based on the tick antigen Bm86 in the gut of Rhipicephalus microplus. Bm86 vaccine formulations cause a reduction in the number of Rhipicephalus microplus ticks that successfully feed, i.e. lower engorgement weights and a decrease in the number of oviposited eggs. Furthermore, Bm86 vaccines reduce transmission of bovine Babesia spp. Previously two conserved Bm86 homologues in I. ricinus ticks, designated as Ir86-1 and Ir86-2, were described. Here we investigated the effect of a vaccine against recombinant Ir86-1, Ir86-2 or a combination of both on Ixodes ricinus feeding. Recombinant Ixodes ricinus Bm86 homologues were expressed in a Drosophila expression system and rabbits were immunized with rIr86-1, rIr86-2, a combination of both or ovalbumin as a control. Each animal was infested with 50 female adults and 50 male adults Ixodes ricinus and tick mortality, engorgement weights and egg mass were analyzed. Although serum IgG titers against rIr86 proteins were elicited, no effect was found on tick feeding between the rIr86 vaccinated animals and ovalbumin vaccinated animals. We conclude that vaccination against Bm86 homologues in Ixodes ricinus is not an effective approach to control Ixodes ricinus populations, despite the clear effects of Bm86 vaccination against Rhipicephalus microplus.

  2. Rhipicephalus (Boophilus microplus: expression and characterization of Bm86-CG in Pichia pastoris Rhipicephalus (Boophilus microplus: expressão e caracterização da Bm86-CG em Pichia pastoris

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    Rodrigo Casquero Cunha

    2011-06-01

    Full Text Available The cattle tick Rhipicephalus (Boophilus microplus is responsible for great economic losses. It is mainly controlled chemically, with limitations regarding development of resistance to the chemicals. Vaccines may help control this parasite, thereby reducing tick pesticide use. In this light, we performed subcloning of the gene of the protein Bm86-GC, the homologue protein that currently forms the basis of vaccines (GavacTM and TickGardPLUS that have been developed against cattle ticks. The subcloning was done in the pPIC9 expression vector, for transformation in the yeast Pichia pastoris. This protein was characterized by expression of the recombinant Mut+ strain, which expressed greater quantities of protein. The expressed protein (rBm86-CG was recognized in the Western-blot assay using anti-Gavac, anti-TickGard, anti-larval extract and anti-rBm86-CG polyclonal sera. The serum produced in cattle vaccinated with the antigen CG rBm86 presented high antibody titers and recognized the native protein. The rBm86-GC has potential relevance as an immunogen for vaccine formulation against cattle ticks.O carrapato-do-boi Rhipicephalus (Boophilus microplus é responsável por grandes perdas econômicas. Seu controle é principalmente químico e apresenta limitações quanto ao desenvolvimento de resistência aos princípios ativos. As vacinas podem auxiliar no controle deste parasita diminuindo as aplicações de carrapaticidas. Considerando isso, foi realizada a subclonagem do gene da proteína Bm86-CG, proteína homologa a que atualmente é a base das vacinas desenvolvidas (GavacTM e TickGardPLUS contra o carrapato-do-boi, no vetor de expressão pPIC9, para ser transformado em levedura, Pichia pastoris. Esta proteína foi caracterizada pela expressão da cepa recombinante Mut+ que expressou maior quantidade de proteína. A proteína expressa, rBm86-CG, foi reconhecida no ensaio de Western-blot pelos soros policlonais anti-Gavac, anti-TickGard, anti

  3. Bovine immunoprotection against Rhipicephalus (Boophilus microplus with recombinant Bm86-Campo Grande antigen Imunoproteção de bovinos contra Rhipicephalus (Boophilus microplus com antígeno recombinante Bm86-Campo Grande

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    Rodrigo Casquero Cunha

    2012-09-01

    Full Text Available The southern cattle fever tick, Rhipicephalus (Boophilus microplus, is no doubt the most economically important ectoparasite of cattle globally. The inappropriate use of chemical acaricides has driven the evolution of resistance in populations of R. (B. microplus. Anti-tick vaccines represent a technology that can be combined with acaricides in integrated control programs to mitigate the impact of R. (B. microplus. The recombinant form of Bm86 antigen from the Campo Grande (rBm86-CG strain of R. (B. microplus was produced using the Pichiapastoris expression system to test its ability to immunoprotect cattle against tick infestation. Secretion of rBm86-CG by P. pastoris through the bioprocess reported here simplified purification of the antigen. A specific humoral immune response was detected by ELISA in vaccinated cattle. Immunoblot results revealed that polyclonal antibodies from vaccinated cattle recognized a protein in larval extracts with a molecular weight corresponding to Bm86. The rBm86-CG antigen showed 31% efficacy against the Campo Grande strain of R. (B. microplus infesting vaccinated cattle. The rBm86-CG is an antigen that could be used in a polyvalent vaccine as part of an integrated program for the control of R. (B. microplus in the region that includes Mato Grosso do Sul.O carrapato Rhipicephalus (Boophilus microplus é, sem dúvidas, o ectoparasito economicamente mais importante para o gado a nível mundial. A utilização inadequada de acaricidas tem impulsionado a evolução da resistência em populações de R. (B. microplus. Vacinas contra o carrapato representam uma tecnologia que pode ser combinada com acaricidas em programas de controle integrado para diminuir o impacto de R. (B. microplus. A forma recombinante da Bm86 da cepa Campo Grande (rBm86-CG de R. (B. microplus foi produzido utilizando o sistema de expressão em Pichia pastoris para testar sua capacidade de imunoproteção ao gado contra a infestação de

  4. Vaccination with BM86, subolesin and akirin protective antigens for the control of tick infestations in white tailed deer and red deer.

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    Carreón, Diana; de la Lastra, José M Pérez; Almazán, Consuelo; Canales, Mario; Ruiz-Fons, Francisco; Boadella, Mariana; Moreno-Cid, Juan A; Villar, Margarita; Gortázar, Christian; Reglero, Manuel; Villarreal, Ricardo; de la Fuente, José

    2012-01-05

    Red deer (Cervus elaphus) and white-tailed deer (Odocoileus virginianus) are hosts for different tick species and tick-borne pathogens and play a role in tick dispersal and maintenance in some regions. These factors stress the importance of controlling tick infestations in deer and several methods such as culling and acaricide treatment have been used. Tick vaccines are a cost-effective alternative for tick control that reduced cattle tick infestations and tick-borne pathogens prevalence while reducing the use of acaricides. Our hypothesis is that vaccination with vector protective antigens can be used for the control of tick infestations in deer. Herein, three experiments were conducted to characterize (1) the antibody response in red deer immunized with recombinant BM86, the antigen included in commercial tick vaccines, (2) the antibody response and control of cattle tick infestations in white-tailed deer immunized with recombinant BM86 or tick subolesin (SUB) and experimentally infested with Rhipicephalus (Boophilus) microplus, and (3) the antibody response and control of Hyalomma spp. and Rhipicephalus spp. field tick infestations in red deer immunized with mosquito akirin (AKR), the SUB ortholog and candidate protective antigen against different tick species and other ectoparasites. The results showed that deer produced an antibody response that correlated with the reduction in tick infestations and was similar to other hosts vaccinated previously with these antigens. The overall vaccine efficacy was similar between BM86 (E=76%) and SUB (E=83%) for the control of R. microplus infestations in white-tailed deer. The field trial in red deer showed a 25-33% (18-40% when only infested deer were considered) reduction in tick infestations, 14-20 weeks after the first immunization. These results demonstrated that vaccination with vector protective antigens could be used as an alternative method for the control of tick infestations in deer to reduce tick populations

  5. The Rhipicephalus (Boophilus microplus Bm86 gene plays a critical role in the fitness of ticks fed on cattle during acute Babesia bovis infection

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    Knowles Donald P

    2010-11-01

    Full Text Available Abstract Background Rhipicephalus (Boophilus microplus is an economically important tick of cattle involved in the transmission of Babesia bovis, the etiological agent of bovine babesiosis. Commercial anti-tick vaccines based on the R. microplus Bm86 glycoprotein have shown some effect in controlling tick infestation; however their efficacy as a stand-alone solution for tick control has been questioned. Understanding the role of the Bm86 gene product in tick biology is critical to identifying additional methods to utilize Bm86 to reduce R. microplus infestation and babesia transmission. Additionally, the role played by Bm86 in R. microplus fitness during B. bovis infection is unknown. Results Here we describe in two independent experiments that RNA interference-mediated silencing of Bm86 decreased the fitness of R. microplus females fed on cattle during acute B. bovis infection. Notably, Bm86 silencing decreased the number and survival of engorged females, and decreased the weight of egg masses. However, gene silencing had no significant effect on the efficiency of transovarial transmission of B. bovis from surviving female ticks to their larval offspring. The results also show that Bm86 is expressed, in addition to gut cells, in larvae, nymphs, adult males and ovaries of partially engorged adult R. microplus females, and its expression was significantly down-regulated in ovaries of ticks fed on B. bovis-infected cattle. Conclusion The R. microplus Bm86 gene plays a critical role during tick feeding and after repletion during blood digestion in ticks fed on cattle during acute B. bovis infection. Therefore, the data indirectly support the rationale for using Bm86-based vaccines, perhaps in combination with acaricides, to control tick infestation particularly in B. bovis endemic areas.

  6. Selection of reference genes for quantitative RT-PCR studies in Rhipicephalus (Boophilus) microplus and Rhipicephalus appendiculatus ticks and determination of the expression profile of Bm86.

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    Nijhof, Ard M; Balk, Jesper A; Postigo, Milagros; Jongejan, Frans

    2009-12-29

    For accurate and reliable gene expression analysis, normalization of gene expression data against reference genes is essential. In most studies on ticks where (semi-)quantitative RT-PCR is employed, normalization occurs with a single reference gene, usually beta-actin, without validation of its presumed expression stability. The first goal of this study was to evaluate the expression stability of commonly used reference genes in Rhipicephalus appendiculatus and Rhipicephalus (Boophilus) microplus ticks. To demonstrate the usefulness of these results, an unresolved issue in tick vaccine development was examined. Commercial vaccines against R. microplus were developed based on the recombinant antigen Bm86, but despite a high degree of sequence homology, these vaccines are not effective against R. appendiculatus. In fact, Bm86-based vaccines give better protection against some tick species with lower Bm86 sequence homology. One possible explanation is the variation in Bm86 expression levels between R. microplus and R. appendiculatus. The most stable reference genes were therefore used for normalization of the Bm86 expression profile in all life stages of both species to examine whether antigen abundance plays a role in Bm86 vaccine susceptibility. The transcription levels of nine potential reference genes: beta-actin (ACTB), beta-tubulin (BTUB), elongation factor 1alpha (ELF1A), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), glutathione S-transferase (GST), H3 histone family 3A (H3F3A), cyclophilin (PPIA), ribosomal protein L4 (RPL4) and TATA box binding protein (TBP) were measured in all life stages of R. microplus and R. appendiculatus. ELF1A was found to be the most stable expressed gene in both species following analysis by both geNorm and Normfinder software applications, GST showed the least stability. The expression profile of Bm86 in R. appendiculatus and R. microplus revealed a more continuous Bm86 antigen abundance in R. microplus throughout its one

  7. Selection of reference genes for quantitative RT-PCR studies in Rhipicephalus (Boophilus microplus and Rhipicephalus appendiculatus ticks and determination of the expression profile of Bm86

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    Jongejan Frans

    2009-12-01

    Full Text Available Abstract Background For accurate and reliable gene expression analysis, normalization of gene expression data against reference genes is essential. In most studies on ticks where (semi-quantitative RT-PCR is employed, normalization occurs with a single reference gene, usually β-actin, without validation of its presumed expression stability. The first goal of this study was to evaluate the expression stability of commonly used reference genes in Rhipicephalus appendiculatus and Rhipicephalus (Boophilus microplus ticks. To demonstrate the usefulness of these results, an unresolved issue in tick vaccine development was examined. Commercial vaccines against R. microplus were developed based on the recombinant antigen Bm86, but despite a high degree of sequence homology, these vaccines are not effective against R. appendiculatus. In fact, Bm86-based vaccines give better protection against some tick species with lower Bm86 sequence homology. One possible explanation is the variation in Bm86 expression levels between R. microplus and R. appendiculatus. The most stable reference genes were therefore used for normalization of the Bm86 expression profile in all life stages of both species to examine whether antigen abundance plays a role in Bm86 vaccine susceptibility. Results The transcription levels of nine potential reference genes: β-actin (ACTB, β-tubulin (BTUB, elongation factor 1α (ELF1A, glyceraldehyde 3-phosphate dehydrogenase (GAPDH, glutathione S-transferase (GST, H3 histone family 3A (H3F3A, cyclophilin (PPIA, ribosomal protein L4 (RPL4 and TATA box binding protein (TBP were measured in all life stages of R. microplus and R. appendiculatus. ELF1A was found to be the most stable expressed gene in both species following analysis by both geNorm and Normfinder software applications, GST showed the least stability. The expression profile of Bm86 in R. appendiculatus and R. microplus revealed a more continuous Bm86 antigen abundance in R

  8. Toxicity of Cultured Bullseye Puffer Fish Sphoeroides annulatus

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    Nuñez-Vazquez, Erick J.; Garcia-Ortega, Armando; Campa-Cordova, Angel I.; de la Parra, Isabel Abdo; Ibarra-Martinez, Lilia; Heredia-Tapia, Alejandra; Ochoa, Jose L.

    2012-01-01

    The toxin content in various life cycle stages of tank-cultivated bullseye puffer (Sphoeroides annulatus) were analyzed by mouse bioassay and ESI-MS spectrometry analysis. The presence of toxin content was determined in extracts of sperm, eggs, embryo, larvae, post-larvae, juvenile, pre-adult, and adult fish, as well as in food items used during the cultivation of the species. Our findings show that only the muscle of juveniles, the viscera of pre-adults, and muscle, liver, and gonad of adult specimens were slightly toxic (<1 mouse unit). Thus, cultivated S. annulatus, as occurs with other cultivated puffer fish species, does not represent a food safety risk to consumers. This is the first report of toxin analysis covering the complete life stages of a puffer fish under controlled conditions. PMID:22412804

  9. Toxicity of Cultured Bullseye Puffer Fish Sphoeroides annulatus

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    Jose L. Ochoa

    2012-02-01

    Full Text Available The toxin content in various life cycle stages of tank-cultivated bullseye puffer (Sphoeroides annulatus were analyzed by mouse bioassay and ESI-MS spectrometry analysis. The presence of toxin content was determined in extracts of sperm, eggs, embryo, larvae, post-larvae, juvenile, pre-adult, and adult fish, as well as in food items used during the cultivation of the species. Our findings show that only the muscle of juveniles, the viscera of pre-adults, and muscle, liver, and gonad of adult specimens were slightly toxic ( < 1 mouse unit. Thus, cultivated S. annulatus, as occurs with other cultivated puffer fish species, does not represent a food safety risk to consumers. This is the first report of toxin analysis covering the complete life stages of a puffer fish under controlled conditions.

  10. Predation by Corallus annulatus (Boidae on Rhynchonycteris naso (Emballonuridae in a lowland tropical wet forest, Costa Rica

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    Lewis, Todd R.

    2009-11-01

    Full Text Available Corallus annulatus (Northern Annulated Tree-boa is a little-studied tropical Boid occurring disjunctively throughout Central America and tropical South America in mostly lowland tropical moist and wet forests (Holdridge, 1967; Stafford & Henderson, 1996; Smith & Acevedo, 1997; Henderson et al., 2001. Prior to this report and to the best of our knowledge, small rodents were the only documented prey for wild specimens of C. annulatus (Henderson et al., 1995. Caño Palma Biological Station is situated on the northeast coast of Costa Rica approximately 8 km north of Tortuguero. C. annulatus has previously been recorded from Manicaria forest at Caño Palma (Myers, 1990; Burger, 2001. On 12th January 2002 and 15th July 2003 we found two separate C. annulatus specimens with Rhynchonycteris naso (Proboscis bat in their stomachs.

  11. Histoarchitecture of the Ovary of Rhipicephalus (Boophilus annulatus during Pre- and Postengorgement Period

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    Sreelekha Kanapadinchareveetil

    2015-01-01

    Full Text Available The present communication describes the detailed day wise study of histological changes of the ovary of Rhipicephalus (Boophilus annulatus in the postengorgement period together with the systematic classification of their oocytes. The ovary of R. (B. annulatus is panoistic type with an asynchronous development of oocytes. All the stages (II, III, IV, and V of oocytes except stage I were similar to R. (B. microplus. The stage I oocytes showed basophilia, which was not reported earlier in other species of ticks. Day wise changes were in the form of presence of oogonia in partially fed and day one engorged adults, considerable degeneration of oocytes on day two, emergence of new wave of oocytes on day three, presence of mature oocytes up to day eight, and complete degeneration of ovarian tissue from day eight onwards. The degenerative changes in the ovary appeared initially in the oocytes followed by germinal epithelium.

  12. Histoarchitecture of the Ovary of Rhipicephalus (Boophilus) annulatus during Pre- and Postengorgement Period

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    Kanapadinchareveetil, Sreelekha; Chandrasekhar, Leena; Gopi, Jyothimol; Ranjan Lenka, Dibya; Vasu, Aswathi; KGopalan, Ajith Kumar; Nair, Suresh N.; Juliet, Sanis; Ghosh, Srikanta

    2015-01-01

    The present communication describes the detailed day wise study of histological changes of the ovary of Rhipicephalus (Boophilus) annulatus in the postengorgement period together with the systematic classification of their oocytes. The ovary of R. (B.) annulatus is panoistic type with an asynchronous development of oocytes. All the stages (II, III, IV, and V) of oocytes except stage I were similar to R. (B.) microplus. The stage I oocytes showed basophilia, which was not reported earlier in other species of ticks. Day wise changes were in the form of presence of oogonia in partially fed and day one engorged adults, considerable degeneration of oocytes on day two, emergence of new wave of oocytes on day three, presence of mature oocytes up to day eight, and complete degeneration of ovarian tissue from day eight onwards. The degenerative changes in the ovary appeared initially in the oocytes followed by germinal epithelium. PMID:25664337

  13. Field observations of mating behavior in the neck-banded snake Scaphiodontophis annulatus (Serpentes: Colubridae

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    Mahmood Sasa

    2006-06-01

    Full Text Available We observed the mating behavior of the neck-banded snake Scaphiodontophis annulatus (a common species of colubrid in the South Pacific of Costa Rica in the pre-montane wet forest of Las Cruces Biological Station (San Vito de Java, Costa Rica. Three S. annulatus were observed during courtship between 10-12 AM in a patch of primary forest. The two males were observed to interact with the female, but not signs of male-male agonistic interactions were observed. Their behavior includes grabbing and holding the female, copula, and biting during the copula. Rev. Biol. Trop. 54(2: 647-650. Epub 2006 Jun 01.El comportamiento de apareamiento es descrito para la serpiente Scaphiodontophis annulatus, una especie de colúbrido común en el Pacífico sur de Costa Rica. El comportamiento incluye capturar y sujetar a la hembra, mordiscos durante la cópula y coito. Dos machos fueron observados al interactuar con una sola hembra, pero no se detectó señales de interacciones antagónicas macho-macho.

  14. Laboratory evaluation of Mesocyclops annulatus (Wierzejski, 1892 (Copepoda: Cyclopidea as a predator of container-breeding mosquitoes in Argentina

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    María V Micieli

    2002-09-01

    Full Text Available In laboratory bioassays we tested the predatory capacity of the copepod Mesocyclops annulatus on Aedes aegypti and Culex pipiens larvae. A single adult female of M. annulatus caused 51.6% and 52.3% mortality of 50 first instar larvae of Ae. aegypti and Cx. pipiens respectively, in a 72 h test period. When alternative food was added to the containers, mortality rates declined to 16% and 10.3% for Ae. aegypti and Cx. pipiens respectively. When 50 first instar larvae of each of the two mosquito species tested were placed together with a single adult female of M. annulatus, mortality rates were 75.5% for Ae. aegypti larvae and 23.5% for Cx. pipiens larvae in a three day test period. Different density of adult females of M. annulatus ranged from 5 to 25 females produced mortality rates of Ae. aegypti first instar larvae from 50% to 100% respectively. When a single adult female of M. annulatus was exposed to an increasing number of first-instar Ae. aegypti larvae ranging from 10 to 100, 100% mortality was recorded from 1 to 25 larvae, then mortality declined to 30% with 100 larvae. The average larvae killed per 24 h period by a single copepod were 29.

  15. Pyrosequencing based assessment of bacterial diversity in Turkish Rhipicephalus annulatus and Dermacentor marginatus ticks (Acari: Ixodidae).

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    Tekin, Saban; Dowd, Scot E; Davinic, Marko; Bursali, Ahmet; Keskin, Adem

    2017-03-01

    Ticks continue to be a threat to human and animal health in Turkey, as they are considered important vectors of human and animal diseases. The objectives of this investigation are to characterize the microbial communities of two tick species, Rhipicephalus annulatus and Dermacenter marginatus, analyze patterns of co-occurrence among microbial taxa, identify and compare pathogens contributing human diseases, and determine whether avirulent symbionts could exclude human pathogens from tick communities. Furthermore, this study explores a microbiome of the R. annulatus and D. marginatus via the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) technique to describe their bacterial diversity. Pyrosequencing was performed on adult males and females isolated from humans from two high-risk Turkish provinces, Sivas and Amasya, during tick outbreaks in 2009. A total of 36,253 sequences were utilized for analyses of the 8 tick samples. Several pathogenic genera such as Francisella, Coxiella, Rickettsia, and Shigella were detected in the ticks tested. The most distinguishable difference between the two species of ticks was the lack of known human pathogen Rickettsia in R. annulatus and in samples 9 and 10 of D. marginatus. These samples had higher relative abundance of Flavobacterium sp., Curvibacter sp., Acidovorax sp., and Bacteroidaceae genera mostly representing symbionts which form a large component of normal tick microbiota. The outcome of this study is consistent with the predictions of the community ecological theory that diversity-rich bacteriomes are more resistant to bacterial invasion (and consequent pathogen dissemination) than diversity-deprived ones.

  16. Cattle fever tick, Rhipicephalus annulatus (Acari: Ixodidae), and the quest for discovery of its natural enemies in the Balkan Region

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    Cattle fever tick, Rhipicephalus annulatus (CFT), is a hard tick native to the Mediterranean region that is invasive in the southwestern USA. The tick is known to develop on cattle and white tailed deer, and it transmits two lethal diseases, piroplasmosis and babesiosis. Extensive use of acaricides...

  17. Domain architecture conservation in orthologs

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    2011-01-01

    Background As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence. To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. Results The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation. The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. Conclusions On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the

  18. Lepeophtheirus simplex sp. n., a caligid copepod (Siphonostomatoida) parasitic on "botete" (bullseye puffer, Sphoeroides annulatus) in Sinaloa, Mexico.

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    Ho, J S; Gómez, S; Fajer-Avila, E

    2001-01-01

    A new species of caligid copepod, Lepeophtheirus simplex sp. n., parasitic on bullseye puffer, Sphoeroides annulatus (Jenyns) in Sinaloa, Mexico is described. The new species is distinguished from its congeners by the possession of (1) a maxillule with simple dentiform process; (2) a sternal furca with sharply pointed, curved tines; (3) a 2-segmented exopod of leg 3 with simple, slender spine on proximal segment; (4) a 3-segmented exopod of leg 4 with a long proximal, outer spine; and (5) the terminal claw of male antenna with a large, tridentate, medial protuberance.

  19. Patterns of occurrence of the platyhelminth parasites of the wild bullseye puffer (Sphoeroides annulatus) off Sinaloa, Mexico.

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    Fajer-Avila, Emma Josefina; Roque, Ana; Aguilar, Gabriela; Duncan, Neil

    2004-04-01

    This study provides basic information on the occurrence of platyhelminths in the wild bullseye puffer (Sphoeroides annulatus) from Sinaloa, Mexico. Specimens of pufferfish were collected from 2 localities: Teacapan (n = 161) and Mazatlan (n = 66). Six species of platyhelminths were recorded: 2 monogeneans (Diclidophoridae: Heterobothrium ecuadori and Capsalidae: Neobenedenia melleni) and 4 digeneans (Apocreadiidae: Homalometron longisinosum, Lepocreadiidae: Bianium plicitum, Gorgoridae: Phyllodristomum mirandai, and Fellodistomidae: Lintonium vibex). This is the first record of the platyhelminth L. vibex in S. annulatus in the Mexican Pacific. Bianium plicitum was the most abundant species, and H. ecuadori was the most prevalent species. The fish from Teacapan had the higher prevalence of platyhelminths. Teacapan had higher specific richness index, whereas Mazatlan had a higher dominance, 3.098 (Teacapan = 2.38). A relative risk analysis showed that B. plicitum was more likely to be present on fish in water within the temperature range of 21-25 C and from Teacapan compared with fish from the warmer water (26-30 C) or from Mazatlan. Heterobothrium ecuadori was more likely to be present at water temperatures of 23-24.5 C on fish from Teacapan and when other ectoparasites were present. Neobenedenia melleni also was more likely to be present when other parasites were present.

  20. Standardized benchmarking in the quest for orthologs

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    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...

  1. Identifying single copy orthologs in Metazoa.

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    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.

  2. Orthology Guided Assembly in highly heterozygous crops

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    Ruttink, Tom; Sterck, Lieven; Rohde, Antje

    2013-01-01

    of polymorphism and avoid transcript fragmentation. Here, we propose an Orthology Guided Assembly procedure that first uses sequence similarity (tBLASTn) to proteins of a model species to select allelic and fragmented contigs from all genotypes and then performs CAP3 clustering on a gene-by-gene basis. Thus, we...

  3. Effect of UV radiation on the genetic inactivation of sperm of the bullseye puffer Sphoeroides annulatus (Jenyns, 1842); Efecto de la radiacion UV en la inactivacion genetica del esperma de botete diana Sphoeroides annulatus (Jenyns, 1842)

    Energy Technology Data Exchange (ETDEWEB)

    Arias-Rodriguez, Lenin; Rodriguez-Ibarra, Luz Estela; Del Valle-Pignataro, Gabriela [Laboratorio de Genetica, Centro de Investigacion en Alimentacion y Desarrollo, A. C., Sinaloa (Mexico)

    2004-09-15

    Genetic (DNA) inactivation of fish sperm with ultraviolet irradiation is generally accompanied by a paradoxical effect on survival rates (Hertwig effect). In the present study, sperm samples from ten males bullseye puffer fish (Sphoeroides annulatus) were diluted 1:50 using Cortland's extender solution and used to test the effect of nine ultraviolet doses (0.2-1.0 J cm{sup -}2 ) on motility time in seconds, motility index, and embryo survival rate after fertilizing eggs from five bullseye puffer females. Motility time of sperm irradiated with 0.2-0.9 J cm{sup -}2 were not statistically different from the controls, but sperm irradiated with a dosage of 1.0 J cm{sup -}2 dosage had significant lower motility time. Motility indices (MI) allowed for the statistical differentiation of four groups in relation to their response to different radiation doses: the first had high MI, and included the controls and 0.2-0.3 J cm{sup -}2 treatments; the second had lower MI and included the 0.4-0.7 J cm{sup -}2 treatments; the third showed recovery of MI and included the 0.8-0.9 J cm{sup -}2 treatments; and the fourth showed the lowest MI with the 1.0 J cm{sup -}2 treatment. Embryo survival was highest for the controls and 0.2 J cm{sup -}2 treatment, decreasing in the 0.3-0.4 J cm{sup -}2 treatments, increasing again in the 0.5-0.8 J cm{sup -}2 treatments, until reaching lowest survival in the 0.9-1.0 J cm{sup -}2 treatments. These results indicate that the best ultraviolet dosage to achieve genetic inactivation of sperm of this species is close to 0.7 J cm{sup -}2, a dosage in which fish fry showed typical haploid syndrome characteristics. [Spanish] La inactivacion genetica (ADN) del esperma de peces se realiza mediante luz ultravioleta que, en irradiaciones crecientes, genera efectos paradojicos (efecto Hertwig) en los porcentajes de supervivencia. En este trabajo se diluyeron muestras de semen provenientes de diez machos de botete diana (Sphoeroides annulatus) en solucion

  4. Orthology prediction at scalable resolution by phylogenetic tree analysis

    Directory of Open Access Journals (Sweden)

    Huynen Martijn A

    2007-03-01

    Full Text Available Abstract Background Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups. Results We introduce "levels of orthology" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable. Conclusion The "levels of orthology" concept offers high resolution, reliable orthology, while preserving the relations between orthologous groups. A Windows as well as a preliminary Java version of LOFT is available from the LOFT website http://www.cmbi.ru.nl/LOFT.

  5. Vaccination against Bm86 Homologues in Rabbits Does Not Impair Ixodes ricinus Feeding or Oviposition

    NARCIS (Netherlands)

    Coumou, Jeroen; Wagemakers, Alex; Trentelman, Jos J.; Nijhof, Ard M.; Hovius, Joppe W.

    2014-01-01

    Human tick-borne diseases that are transmitted by Ixodes ricinus, such as Lyme borreliosis and tick borne encephalitis, are on the rise in Europe. Diminishing I. ricinus populations in nature can reduce tick exposure to humans, and one way to do so is by developing an anti-vector vaccine against

  6. Ultrastructural analysis of oocytes of Rhipicephalus (Boophilus) annulatus during postengorgement period as a tool to evaluate the cytotoxic effects of amitraz and deltamethrin on the germinative cells.

    Science.gov (United States)

    Sreelekha, Kanapadinchareveetil; Chandrasekhar, Leena; Kartha, Harikumar S; Ravindran, Reghu; Juliet, Sanis; Ajithkumar, Karapparambu G; Nair, Suresh N; Ghosh, Srikanta

    2017-11-30

    The present study utilizes the ultrastructural analysis of the fully engorged female Rhipicephalus (Boophilus) annulatus ticks, as a tool to evaluate the cytotoxic potential of deltamethrin and amitraz on the germinative cells. The ultrastructural analysis of the ovary of the normal (untreated) R (B.) annulatus revealed, oocytes in different stages of development, attached to the ovary wall by pedicel cells. The attachment site of oocyte to the pedicel cell was characterized by indentations of the plasma membrane. The oocyte was bound by three cell membranes viz., plasma membrane, chorion and basal lamina. The stages of oocytes were differentiated ultrastructurally based on the features of their outer membrane and the number and size of lipid and yolk droplets. Detailed day wise analysis of ultrastructural changes in the ovary during the post-engorgement period revealed the occurrence of the degenerative changes from day five onwards. These appeared first in the oocytes followed by the germinal epithelium. The ovary of ticks treated with methanol (control), revealed similar topographies as that of a normal ovary except for the presence of very few oocytes with ring shaped nucleoli. Ultrastructurally, treatment with deltamethrin produced more prominent and extensive morphological alterations when compared to amitraz. In the case of ticks treated with amitraz, the oocytes of stage IV and V showed wavy and disrupted outer boundaries along with the loss of integrity of the yolk droplets. Uneven nuclear membranes of stage II oocytes and cristolysis of mitochondria of mature oocytes were the other changes noticed. Ticks treated with deltamethrin revealed prominent modifications such as, detachment of the basal lamina, wrinkled boundary, inconsistent nuclear membrane, ring shaped nucleoli and chromatin clumping in the case of the early stage oocytes (I and II), whereas swelling and cristolysis of mitochondria were seen in mature oocytes. The study further indicated that

  7. Population structure and reproductive aspects of puffer fish Sphoeroides annulatus (Jenyns, 1842 (Osteichthyes: Tetraodontidae, landed in Teacapán, Sinaloa, Mexico

    Directory of Open Access Journals (Sweden)

    María Candelaria Valdez-Pineda

    2014-03-01

    Full Text Available The puffer fish Sphoeroides annulatus is an important target species for the artisanal fishing fleets of NW Mexico. To obtain information on population structure of the local stock, we determined the total length and total weight (TL and TW ranges, sex ratio and reproductive stages of 745 specimens of this species, landed from May 2010 to April 2011 in Teacapán, Sinaloa, NW Mexico. TL ranged from 15 to 40 cm and TW from 100 to 1600 g. There were no differences between mean TL (27.41 ± 4.14 cm and TW (534.5 ± 226.0 g of males and females respectively. Sex ratio was not significantly different (χ2 = 0.03, P > 0.05 from 1F:1M. The length-weight relationship for both sexes was TW = 0.044TL2.815, R² = 0.895. The value of the slope b was significantly lower than 3 (P < 0.05, and indicated negative allometric growth. The distribution of maturity stages indicated one main reproductive period from June to September and one less intense, from November to December for females, and in December for males. Size at first maturity (L50% of females was 26.52 cm and that of males was 27.41 cm.

  8. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

    Science.gov (United States)

    Sutphin, George L; Mahoney, J Matthew; Sheppard, Keith; Walton, David O; Korstanje, Ron

    2016-11-01

    The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.

  9. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

    Directory of Open Access Journals (Sweden)

    George L Sutphin

    2016-11-01

    Full Text Available The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.

  10. 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.

  11. Effects of season, sex and body size on the feeding ecology of turtle-headed sea snakes ( Emydocephalus annulatus) on IndoPacific inshore coral reefs

    Science.gov (United States)

    Goiran, C.; Dubey, S.; Shine, R.

    2013-06-01

    In terrestrial snakes, many cases of intraspecific shifts in dietary habits as a function of predator sex and body size are driven by gape limitation and hence are most common in species that feed on relatively large prey and exhibit a wide body-size range. Our data on sea snakes reveal an alternative mechanism for intraspecific niche partitioning, based on sex-specific seasonal anorexia induced by reproductive activities. Turtle-headed sea snakes ( Emydocephalus annulatus) on coral reefs in the New Caledonian Lagoon feed entirely on the eggs of demersal-spawning fishes. DNA sequence data (cytochrome b gene) on eggs that we palpated from stomachs of 37 snakes showed that despite this ontogenetic stage specialization, the prey comes from a taxonomically diverse array of species including damselfish (41 % of samples, at least 5 species), blennies (41 %, 4 species) and gobies (19 %, 5 species). The composition of snake diets shifted seasonally (with damselfish dominating in winter but not summer), presumably reflecting seasonality of fish reproduction. That seasonal shift affects male and female snakes differently, because reproduction is incompatible with foraging. Adult female sea snakes ceased feeding when they became heavily distended with developing embryos in late summer, and males ceased feeding while they were mate searching in winter. The sex divergence in foraging habits may be amplified by sexual size dimorphism; females grow larger than males, and larger snakes (of both sexes) feed more on damselfish (which often lay their eggs in exposed sites) than on blennies and gobies (whose eggs are hidden within narrow crevices). Specific features of reproductive biology of coral reef fish (seasonality and nest type) have generated intraspecific niche partitioning in these sea snakes, by mechanisms different from those that apply to terrestrial snakes.

  12. Ortholog identification in genera of high genetic diversity and evolution

    DEFF Research Database (Denmark)

    Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Frisvad, Jens Christian

    In the era of high-throughput sequencing, comparative genomics is vastly used in the discovery of genetic diversity between species, but also in defining the core and pan genome of single species to whole genera. Current comparative approaches are implementing ortholog identification to establish...... genome annotations, gene or protein evolutions or defining functional features in individual species and groups.......In the era of high-throughput sequencing, comparative genomics is vastly used in the discovery of genetic diversity between species, but also in defining the core and pan genome of single species to whole genera. Current comparative approaches are implementing ortholog identification to establish...

  13. Database Description - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj - Ortholog DB Database Description General information of database Database name PGDBj - Orth...olog DB Alternative name Plant Genome Database Japan - Ortholog Database DOI 10.18908/lsdba.nbdc01194...teria Taxonomy ID: 1117 Database description Orthology is a homologous relationship among genes derived from...o predict the divergence of gene function based on syntenic relationships among species. PGDBj Ortholog DB i...f utilization of database PGDBj Ortholog DB is hierarchically organized to reflect evolutionary relationship

  14. Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

    DEFF Research Database (Denmark)

    Huerta-Cepas, Jaime; Forslund, Kristoffer; Coelho, Luis Pedro

    2017-01-01

    Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines are relatively inaccessible (e.g., new assignments only available through database updates), less precise homology-based functiona...

  15. Ortholog - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us MicrobeDB.jp Ortholog Data detail Data name Ortholog DOI 10.18908/lsdba.nbdc01181-010.V002 V...814 triples - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Ortholog - MicrobeDB.jp | LSDB Archive ...

  16. Large-Scale Orthology Predictions for Inferring Gene Functions Across Multiple Species

    Science.gov (United States)

    2010-06-01

    mutations associated with cancer by studying their corresponding orthologous genes in mice (Denny, 2000). Moreover, the identification of orthologous...taxonomic profiling of eukaryotic model organisms: a comparison of orthologous proteins encoded by the human, fly, nematode , and yeast genomes.” Genome

  17. 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

  18. A meta-approach for improving the prediction and the functional annotation of ortholog groups.

    Science.gov (United States)

    Pereira, Cécile; Denise, Alain; Lespinet, Olivier

    2014-01-01

    In comparative genomics, orthologs are used to transfer annotation from genes already characterized to newly sequenced genomes. Many methods have been developed for finding orthologs in sets of genomes. However, the application of different methods on the same proteome set can lead to distinct orthology predictions. We developed a method based on a meta-approach that is able to combine the results of several methods for orthologous group prediction. The purpose of this method is to produce better quality results by using the overlapping results obtained from several individual orthologous gene prediction procedures. Our method proceeds in two steps. The first aims to construct seeds for groups of orthologous genes; these seeds correspond to the exact overlaps between the results of all or several methods. In the second step, these seed groups are expanded by using HMM profiles. We evaluated our method on two standard reference benchmarks, OrthoBench and Orthology Benchmark Service. Our method presents a higher level of accurately predicted groups than the individual input methods of orthologous group prediction. Moreover, our method increases the number of annotated orthologous pairs without decreasing the annotation quality compared to twelve state-of-the-art methods. The meta-approach based method appears to be a reliable procedure for predicting orthologous groups. Since a large number of methods for predicting groups of orthologous genes exist, it is quite conceivable to apply this meta-approach to several combinations of different methods.

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

    Lifescience Database Archive (English)

    Full Text Available database as follows: PGDBj - Ortholog DB © Akihiro Nakaya (Osaka University) licensed under CC Attribution-...ice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB License License to Use This Database Last updated : 2017/03/07 You may u...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

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

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    Full Text Available 0”. This cluster ID is uniquely-assigned by the PGDBj Ortholog Database. Cluster size Number of proteins aff...r About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Cluster (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Cluster (Viridiplantae) Data detail Data name Cluster (Viridiplantae) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

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

    Lifescience Database Archive (English)

    Full Text Available 3090”. This cluster ID is uniquely-assigned by the PGDBj Ortholog Database. Cluster size Number of proteins ...ster About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Cluster (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Cluster (Cyanobacteria) Data detail Data name Cluster (Cyanobacteria) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

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

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    Full Text Available List Contact us PGDBj - Ortholog DB Update History of This Database Date Update contents 2017/03/07 PGDBj Orth...L of the Whole data download The URL of The original website information 2014/05/12 PGDBj Ortholog DB (Relea...se57 ver.) English archive site is opened. (Archive V1) 2012/08/01 PGDBj Ortholog DB ( http://pgdbj.jp/ortho...e Update History of This Database Site Policy | Contact Us Update History of This Database - PGDBj - Ortholog DB | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  3. Human and mouse mitochondrial orthologs of bacterial ClpX

    DEFF Research Database (Denmark)

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

    2000-01-01

    We have determined the cDNA sequence and exon/intron structure of the human CLPX gene encoding a human ortholog of the E. coli ClpX chaperone and protease subunit. The CLPX gene comprises 14 exons and encodes a 633-amino acid-long precursor polypeptide. The polypeptide contains an N-terminal puta......We have determined the cDNA sequence and exon/intron structure of the human CLPX gene encoding a human ortholog of the E. coli ClpX chaperone and protease subunit. The CLPX gene comprises 14 exons and encodes a 633-amino acid-long precursor polypeptide. The polypeptide contains an N......-terminal putative mitochondrial transit peptide, and expression of a full-length ClpX cDNA tagged at its C-terminus (Myc-His) shows that the polypeptide is transported into mitochondria. FISH analysis localized the CLPX gene to human Chromosome (Chr) 15q22.1-22.32. This localization was refined by radiation hybrid...... 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...

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

    Lifescience Database Archive (English)

    Full Text Available of This Database Site Policy | Contact Us Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Taxon (Viridiplantae) Data detail Data name Taxon (Viridiplantae) DOI 10...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  5. Download - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

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    Full Text Available e Description Download License Update History of This Database Site Policy | Contact Us Download - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Download First of all, please read the license of this database. Data na...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

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

    Lifescience Database Archive (English)

    Full Text Available ut This Database Database Description Download License Update History of This Database Site Policy | Contact Us Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Protein (Cyanobacteria) Data detail Data name Protein (Cyanobacteria) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

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

    Lifescience Database Archive (English)

    Full Text Available of This Database Site Policy | Contact Us Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Taxon (Cyanobacteria) Data detail Data name Taxon (Cyanobacteria) DOI 10...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

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

    Lifescience Database Archive (English)

    Full Text Available ase Description Download License Update History of This Database Site Policy | Contact Us Protein (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Protein (Viridiplantae) Data detail Data name Protein (Viridiplantae) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  9. 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.

  10. Calculating orthologs in bacteria and Archaea: a divide and conquer approach.

    Directory of Open Access Journals (Sweden)

    Mihail R Halachev

    Full Text Available Among proteins, orthologs are defined as those that are derived by vertical descent from a single progenitor in the last common ancestor of their host organisms. Our goal is to compute a complete set of protein orthologs derived from all currently available complete bacterial and archaeal genomes. Traditional approaches typically rely on all-against-all BLAST searching which is prohibitively expensive in terms of hardware requirements or computational time (requiring an estimated 18 months or more on a typical server. Here, we present xBASE-Orth, a system for ongoing ortholog annotation, which applies a "divide and conquer" approach and adopts a pragmatic scheme that trades accuracy for speed. Starting at species level, xBASE-Orth carefully constructs and uses pan-genomes as proxies for the full collections of coding sequences at each level as it progressively climbs the taxonomic tree using the previously computed data. This leads to a significant decrease in the number of alignments that need to be performed, which translates into faster computation, making ortholog computation possible on a global scale. Using xBASE-Orth, we analyzed an NCBI collection of 1,288 bacterial and 94 archaeal complete genomes with more than 4 million coding sequences in 5 weeks and predicted more than 700 million ortholog pairs, clustered in 175,531 orthologous groups. We have also identified sets of highly conserved bacterial and archaeal orthologs and in so doing have highlighted anomalies in genome annotation and in the proposed composition of the minimal bacterial genome. In summary, our approach allows for scalable and efficient computation of the bacterial and archaeal ortholog annotations. In addition, due to its hierarchical nature, it is suitable for incorporating novel complete genomes and alternative genome annotations. The computed ortholog data and a continuously evolving set of applications based on it are integrated in the xBASE database, available

  11. The plant Apolipoprotein D ortholog protects Arabidopsis against oxidative stress

    Directory of Open Access Journals (Sweden)

    Houde Mario

    2008-07-01

    Full Text Available Abstract Background Lipocalins are a large and diverse family of small, mostly extracellular proteins implicated in many important functions. This family has been studied in bacteria, invertebrate and vertebrate animals but little is known about these proteins in plants. We recently reported the identification and molecular characterization of the first true lipocalins from plants, including the Apolipoprotein D ortholog AtTIL identified in the plant model Arabidopsis thaliana. This study aimed to determine its physiological role in planta. Results Our results demonstrate that the AtTIL lipocalin is involved in modulating tolerance to oxidative stress. AtTIL knock-out plants are very sensitive to sudden drops in temperature and paraquat treatment, and dark-grown plants die shortly after transfer to light. These plants accumulate a high level of hydrogen peroxide and other ROS, which causes an oxidative stress that is associated with a reduction in hypocotyl growth and sensitivity to light. Complementation of the knock-out plants with the AtTIL cDNA restores the normal phenotype. On the other hand, overexpression enhances tolerance to stress caused by freezing, paraquat and light. Moreover, this overexpression delays flowering and maintains leaf greenness. Microarray analyses identified several differentially-regulated genes encoding components of oxidative stress and energy balance. Conclusion This study provides the first functional evidence that a plant lipocalin is involved in modulating tolerance to oxidative stress. These findings are in agreement with recently published data showing that overexpression of ApoD enhances tolerance to oxidative stress and increases life span in mice and Drosophila. Together, the three papers strongly support a similar function of lipocalins in these evolutionary-distant species.

  12. 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.

  13. MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

    Directory of Open Access Journals (Sweden)

    Zhang Liqing

    2010-01-01

    Full Text Available Abstract Background Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related species on a genome scale. It attempts to reconstruct the evolutionary history of input genomes in terms of genome rearrangement and gene duplication events. It assumes that a gene duplication event inserts a duplicated gene into the genome of interest at a random location (i.e., the random duplication model. However, in practice, biologists believe that genes are often duplicated by tandem duplications, where a duplicated gene is located next to the original copy (i.e., the tandem duplication model. Results In this paper, we develop MSOAR 2.0, an improved system for one-to-one ortholog assignment. For a pair of input genomes, the system first focuses on the tandemly duplicated genes of each genome and tries to identify among them those that were duplicated after the speciation (i.e., the so-called inparalogs, using a simple phylogenetic tree reconciliation method. For each such set of tandemly duplicated inparalogs, all but one gene will be deleted from the concerned genome (because they cannot possibly appear in any one-to-one ortholog pairs, and MSOAR is invoked. Using both simulated and real data experiments, we show that MSOAR 2.0 is able to achieve a better sensitivity and specificity than MSOAR. In comparison with the well-known genome-scale ortholog assignment tool InParanoid, Ensembl ortholog database, and the orthology information extracted from the well-known whole-genome multiple alignment program MultiZ, MSOAR 2.0 shows the highest sensitivity. Although the specificity of MSOAR 2.0 is slightly worse than that of InParanoid in the real data experiments

  14. Testing the ortholog conjecture with comparative functional genomic data from mammals.

    Directory of Open Access Journals (Sweden)

    Nathan L Nehrt

    2011-06-01

    Full Text Available A common assumption in comparative genomics is that orthologous genes share greater functional similarity than do paralogous genes (the "ortholog conjecture". Many methods used to computationally predict protein function are based on this assumption, even though it is largely untested. Here we present the first large-scale test of the ortholog conjecture using comparative functional genomic data from human and mouse. We use the experimentally derived functions of more than 8,900 genes, as well as an independent microarray dataset, to directly assess our ability to predict function using both orthologs and paralogs. Both datasets show that paralogs are often a much better predictor of function than are orthologs, even at lower sequence identities. Among paralogs, those found within the same species are consistently more functionally similar than those found in a different species. We also find that paralogous pairs residing on the same chromosome are more functionally similar than those on different chromosomes, perhaps due to higher levels of interlocus gene conversion between these pairs. In addition to offering implications for the computational prediction of protein function, our results shed light on the relationship between sequence divergence and functional divergence. We conclude that the most important factor in the evolution of function is not amino acid sequence, but rather the cellular context in which proteins act.

  15. IONS: Identification of Orthologs by Neighborhood and Similarity-an Automated Method to Identify Orthologs in Chromosomal Regions of Common Evolutionary Ancestry and its Application to Hemiascomycetous Yeasts.

    Science.gov (United States)

    Seret, Marie-Line; Baret, Philippe V

    2011-01-01

    Comparative sequence analysis is widely used to infer gene function and study genome evolution and requires proper ortholog identification across different genomes. We have developed a program for the Identification of Orthologs in one-to-one relationship by Neighborhood and Similarity (IONS) between closely related species. The algorithm combines two levels of evidence to determine co-ancestrality at the genome scale: sequence similarity and shared neighborhood. The method was initially designed to provide anchor points for syntenic blocks within the Génolevures project concerning nine hemiascomycetous yeasts (about 50,000 genes) and is applicable to different input databases. Comparison based on use of a Rand index shows that the results are highly consistent with the pillars of the Yeast Gene Order Browser, a manually curated database. Compared with SYNERGY, another algorithm reporting homology relationships, our method's main advantages are its automation and the absence of dataset-dependent parameters, facilitating consistent integration of newly released genomes.

  16. Vaccination with BM86, subolesin and akirin protective antigens for the control of tick infestations in white tailed deer and red deer

    OpenAIRE

    Carreón, Diana; Pérez de Lastra, José Manuel; Pérez de Lastra, José Manuel; Canales, Mario; Ruiz Fons, Francisco; Boadella, Mariana; Moreno-Cid, Juan A.; Villar, Margarita; Gortázar, Christian; Reglero, Manuel; Fuente, José de la

    2012-01-01

    Red deer (Cervus elaphus) and white-tailed deer (Odocoileus virginianus) are hosts for different tick species and tick-borne pathogens and play a role in tick dispersal and maintenance in some regions. These factors stress the importance of controlling tick infestations in deer and several methods such as culling and acaricide treatment have been used. Tick vaccines are a cost-effective alternative for tick control that reduced cattle tick infestations and tick-borne pathogens prevalence whil...

  17. 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.

    2000-01-01

    -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 domain...

  18. 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

  19. Cloning and transcription analysis of an AGAMOUS- and SEEDSTICK ortholog in the orchid Dendrobium thyrsiflorum (Reichb. f.)

    DEFF Research Database (Denmark)

    Skipper, Martin; Johansen, Louise Buchholt; Pedersen, Kim B.

    2006-01-01

    Studies have shown that several plant species posses AGAMOUS (AG) and SEEDSTICK (STK) orthologs. These genes are part of the so-called C- and D MADS-box gene lineages and play key roles in ovule development in Arabidopsis thaliana. We have cloned an AG- and STK ortholog in the orchid Dendrobium...

  20. Evolutionary aspects of variability in bHLH orthologous families: insights from the pearl oyster, Pinctada fucata.

    Science.gov (United States)

    Gyoja, Fuki; Satoh, Nori

    2013-10-01

    Basic helix-loop-helix (bHLH) transcription factors play significant roles in multiple biological processes in metazoan cells. In recent work, we showed that three orthologous HLH families, pearl, amber, and peridot, have apparently been lost in the Drosophila melanogaster, Caenorhabditis elegans, and Homo sapiens lineages. To further address the gain and loss of bHLH proteins during bilaterian evolution, we examined the genome of the pearl oyster, Pinctada fucata, which has recently been sequenced. We characterized the putative full set 65 bHLH genes and showed that genes previously categorized into the orthologous family PTFb, actually fall into two distinct orthologous families, 48-related-1 and 48-related-2. We also identified a novel orthologous family, clockwork orange. Based on these newly identified orthologous family members and on orphan bHLH factors, we propose that genes encoding bHLH factors in bilaterians are not as evolutionarily stable as previously thought.

  1. Synteny of orthologous genes conserved in human, mouse, snake, Drosophila, nematode, and fission yeast

    Czech Academy of Sciences Publication Activity Database

    Trachtulec, Zdeněk; Forejt, Jiří

    2001-01-01

    Roč. 12, č. 3 (2001), s. 227-231 ISSN 0938-8990 Institutional research plan: CEZ:AV0Z5052915 Keywords : synteny of orthologous genes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.318, year: 2001

  2. The Princeton Protein Orthology Database (P-POD: a comparative genomics analysis tool for biologists.

    Directory of Open Access Journals (Sweden)

    Sven Heinicke

    2007-08-01

    Full Text Available 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 relationships among predicted orthologs (based on the OrthoMCL method to a query gene from any of eight eukaryotic organisms, and to see the orthologs in a wider evolutionary context (based on the Jaccard clustering method. In addition to the phylogenetic information, the database contains experimental results manually collected from the literature that can be compared to the computational analyses, as well as links to relevant human disease and gene information via the OMIM, model organism, and sequence databases. Our aim is for the P-POD resource to be extremely useful to typical experimental biologists wanting to learn more about the evolutionary context of their favorite genes. P-POD is based on the commonly used Generic Model Organism Database (GMOD schema and can be downloaded in its entirety for installation on one's own system. Thus, bioinformaticians and software developers may also find P-POD useful because they can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools.

  3. In silico mapping of Conserved Ortholog Set (COS) markers in the potato genome

    Science.gov (United States)

    Conserved ortholog set (COS) markers are useful for genetic mapping across diverse taxa, including the Solanaceae. We amplified over 300 COS markers from diverse set of Solanum germplasm, sequenced them and aligned into the whole genome sequence of potato. We also mapped a set of COS markers genetic...

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

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    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.

  5. 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

  6. New Tools in Orthology Analysis: A Brief Review of Promising Perspectives

    Directory of Open Access Journals (Sweden)

    Bruno T. L. Nichio

    2017-10-01

    Full Text Available Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST “all-against-all” methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm; or proteinOrtho (which improves the accuracy of ortholog groups; or ReMark (tackling the integration of the pipeline to turn the entry process automatic; or OrthAgogue (using algorithms developed to

  7. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2007-11-01

    Full Text Available Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs. Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. Results New Archaeal Clusters of Orthologous Genes (arCOGs were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover ~88% of the genes in a genome compared to a ~76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; ~40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile

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

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    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

  9. IONS: Identification of Orthologs by Neighborhood and Similarity—an Automated Method to Identify Orthologs in Chromosomal Regions of Common Evolutionary Ancestry and its Application to Hemiascomycetous Yeasts

    Science.gov (United States)

    Seret, Marie-Line; Baret, Philippe V.

    2011-01-01

    Comparative sequence analysis is widely used to infer gene function and study genome evolution and requires proper ortholog identification across different genomes. We have developed a program for the Identification of Orthologs in one-to-one relationship by Neighborhood and Similarity (IONS) between closely related species. The algorithm combines two levels of evidence to determine co-ancestrality at the genome scale: sequence similarity and shared neighborhood. The method was initially designed to provide anchor points for syntenic blocks within the Génolevures project concerning nine hemiascomycetous yeasts (about 50,000 genes) and is applicable to different input databases. Comparison based on use of a Rand index shows that the results are highly consistent with the pillars of the Yeast Gene Order Browser, a manually curated database. Compared with SYNERGY, another algorithm reporting homology relationships, our method’s main advantages are its automation and the absence of dataset-dependent parameters, facilitating consistent integration of newly released genomes. PMID:21918595

  10. Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs.

    Directory of Open Access Journals (Sweden)

    Nadezda Kryuchkova-Mostacci

    2016-12-01

    Full Text Available The ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide strong evidence of high conservation in tissue-specificity between orthologs, in contrast to low conservation between within-species paralogs. This allows us to shed a new light on the evolution of gene expression patterns. While there have been several studies of the correlation of expression between species, little is known about the evolution of tissue-specificity itself. Ortholog tissue-specificity is strongly conserved between all tetrapod species, with the lowest Pearson correlation between mouse and frog at r = 0.66. Tissue-specificity correlation decreases strongly with divergence time. Paralogs in human show much lower conservation, even for recent Primate-specific paralogs. When both paralogs from ancient whole genome duplication tissue-specific paralogs are tissue-specific, it is often to different tissues, while other tissue-specific paralogs are mostly specific to the same tissue. The same patterns are observed using human or mouse as focal species, and are robust to choices of datasets and of thresholds. Our results support the following model of evolution: in the absence of duplication, tissue-specificity evolves slowly, and tissue-specific genes do not change their main tissue of expression; after small-scale duplication the less expressed paralog loses the ancestral specificity, leading to an immediate difference between paralogs; over time, both paralogs become more broadly expressed, but remain poorly correlated. Finally, there is a small number of paralog pairs which stay tissue-specific with the same main tissue of expression, for at least 300 million years.

  11. Identification of Novel Human Damage Response Proteins Targeted through Yeast Orthology

    OpenAIRE

    Svensson, J. Peter; Fry, Rebecca C.; Wang, Emma; Somoza, Luis A.; Samson, Leona D.

    2012-01-01

    Studies in Saccharomyces cerevisiae show that many proteins influence cellular survival upon exposure to DNA damaging agents. We hypothesized that human orthologs of these S. cerevisiae proteins would also be required for cellular survival after treatment with DNA damaging agents. For this purpose, human homologs of S. cerevisiae proteins were identified and mapped onto the human protein-protein interaction network. The resulting human network was highly modular and a series of selection rule...

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

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    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.

  13. Characterization and expression of a Pinus radiata putative ortholog to the Arabidopsis SHORT-ROOT gene

    OpenAIRE

    Solé, Alicia; Sánchez Fernández, M.ª Concepción; Vielba, Jesús; Valladares, Silvia; Abarca, Dolores; Díaz-Sala, Carmen

    2008-01-01

    We characterized a Pinus radiata D. Don putative ortholog to the Arabidopsis thaliana (L.) Heynh. SHORT-ROOT gene (AtSHR) and analyzed its expression in different organs during vegetative development and in response to exogenous auxin during adventitious rooting. The predicted protein sequence contained domains characteristic of the GRAS protein family and showed a strong similarity to the SHORT-ROOT (SHR) proteins. Quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) and in...

  14. Systematic Functional Characterization of Human 21st Chromosome Orthologs inCaenorhabditis elegans.

    Science.gov (United States)

    Nordquist, Sarah K; Smith, Sofia R; Pierce, Jonathan T

    2018-03-02

    Individuals with Down syndrome have neurological and muscle impairments due to an additional copy of the human 21st chromosome (HSA21). Only a few of ∼200 HSA21 genes encoding proteins have been linked to specific Down syndrome phenotypes, while the remainder are understudied. To identify poorly characterized HSA21 genes required for nervous system function, we studied behavioral phenotypes caused by loss-of-function mutations in conserved HSA21 orthologs in the nematode Caenorhabditis elegans We identified 10 HSA21 orthologs that are required for neuromuscular behaviors: cle-1 ( COL18A1 ), cysl-2 ( CBS ), dnsn-1 ( DONSON ), eva-1 ( EVA1C ), mtq-2 ( N6ATM1 ), ncam-1 ( NCAM2 ), pad-2 ( POFUT2 ), pdxk-1 ( PDXK ), rnt-1 ( RUNX1 ), and unc-26 ( SYNJ1 ). We also found that three of these genes are required for normal release of the neurotransmitter acetylcholine. This includes a known synaptic gene unc-26 ( SYNJ1 ), as well as uncharacterized genes pdxk-1 ( PDXK ) and mtq-2 ( N6ATM1 ). As the first systematic functional analysis of HSA21 orthologs, this study may serve as a platform to understand genes that underlie phenotypes associated with Down syndrome. Copyright © 2018 Nordquist et al.

  15. Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human.

    Science.gov (United States)

    Goodstadt, Leo; Ponting, Chris P

    2006-09-29

    Accurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these relationships have been limited by their use of protein similarity and their failure to take into account multiple splicing events and gene prediction errors. We have developed PhyOP, a new phylogenetic orthology prediction pipeline based on synonymous rate estimates, which accurately predicts orthology and paralogy relationships for transcripts, genes, exons, or genomic segments between closely related genomes. We were able to identify orthologue relationships to human genes for 93% of all dog genes from Ensembl. Among 1:1 orthologues, the alignments covered a median of 97.4% of protein sequences, and 92% of orthologues shared essentially identical gene structures. PhyOP accurately recapitulated genomic maps of conserved synteny. Benchmarking against predictions from Ensembl and Inparanoid showed that PhyOP is more accurate, especially in its predictions of paralogy. Nearly half (46%) of PhyOP paralogy predictions are unique. Using PhyOP to investigate orthologues and paralogues in the human and dog genomes, we found that the human assembly contains 3-fold more gene duplications than the dog. Species-specific duplicate genes, or "in-paralogues," are generally shorter and have fewer exons than 1:1 orthologues, which is consistent with selective constraints and mutation biases based on the sizes of duplicated genes. In-paralogues have experienced elevated amino acid and synonymous nucleotide substitution rates. Duplicates possess similar biological functions for either the dog or human lineages. Having accounted for 2,954 likely pseudogenes and gene fragments, and after separating 346 erroneously merged genes, we estimated that the human genome encodes a minimum of 19,700 protein-coding genes, similar to the gene count of nematode worms. PhyOP is a fast and robust

  16. Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human.

    Directory of Open Access Journals (Sweden)

    Leo Goodstadt

    2006-09-01

    Full Text Available Accurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these relationships have been limited by their use of protein similarity and their failure to take into account multiple splicing events and gene prediction errors. We have developed PhyOP, a new phylogenetic orthology prediction pipeline based on synonymous rate estimates, which accurately predicts orthology and paralogy relationships for transcripts, genes, exons, or genomic segments between closely related genomes. We were able to identify orthologue relationships to human genes for 93% of all dog genes from Ensembl. Among 1:1 orthologues, the alignments covered a median of 97.4% of protein sequences, and 92% of orthologues shared essentially identical gene structures. PhyOP accurately recapitulated genomic maps of conserved synteny. Benchmarking against predictions from Ensembl and Inparanoid showed that PhyOP is more accurate, especially in its predictions of paralogy. Nearly half (46% of PhyOP paralogy predictions are unique. Using PhyOP to investigate orthologues and paralogues in the human and dog genomes, we found that the human assembly contains 3-fold more gene duplications than the dog. Species-specific duplicate genes, or "in-paralogues," are generally shorter and have fewer exons than 1:1 orthologues, which is consistent with selective constraints and mutation biases based on the sizes of duplicated genes. In-paralogues have experienced elevated amino acid and synonymous nucleotide substitution rates. Duplicates possess similar biological functions for either the dog or human lineages. Having accounted for 2,954 likely pseudogenes and gene fragments, and after separating 346 erroneously merged genes, we estimated that the human genome encodes a minimum of 19,700 protein-coding genes, similar to the gene count of nematode worms. PhyOP is a

  17. MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.

    Science.gov (United States)

    Pryszcz, Leszek P; Huerta-Cepas, Jaime; Gabaldón, Toni

    2011-03-01

    Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition of orthology and paralogy and are known to be highly accurate. However, the large computational cost associated to these analyses is a limiting factor that often prevents its use at genomic scales. Recently, several projects have addressed the reconstruction of large collections of high-quality phylogenetic trees from which orthology and paralogy relationships can be inferred. This provides us with the opportunity to infer the evolutionary relationships of genes from multiple, independent, phylogenetic trees. Using such strategy, we combine phylogenetic information derived from different databases, to predict orthology and paralogy relationships for 4.1 million proteins in 829 fully sequenced genomes. We show that the number of independent sources from which a prediction is made, as well as the level of consistency across predictions, can be used as reliable confidence scores. A webserver has been developed to easily access these data (http://orthology.phylomedb.org), which provides users with a global repository of phylogeny-based orthology and paralogy predictions.

  18. Identification and VIGS-based characterization of Bx1 ortholog in rye (Secale cereale L..

    Directory of Open Access Journals (Sweden)

    Jolanta Groszyk

    Full Text Available The first step of the benzoxazinoid (BX synthesis pathway is catalyzed by an enzyme with indole-3-glycerol phosphate lyase activity encoded by 3 genes, Bx1, TSA and Igl. A gene highly homologous to maize and wheat Bx1 has been identified in rye. The goal of the study was to analyze the gene and to experimentally verify its role in the rye BX biosynthesis pathway as a rye ortholog of the Bx1 gene. Expression of the gene showed peak values 3 days after imbibition (dai and at 21 dai it was undetectable. Changes of the BX content in leaves were highly correlated with the expression pattern until 21 dai. In plants older than 21 dai despite the undetectable expression of the analyzed gene there was still low accumulation of BXs. Function of the gene was verified by correlating its native expression and virus-induced silencing with BX accumulation. Barley stripe mosaic virus (BSMV-based vectors were used to induce transcriptional (TGS and posttranscriptional (PTGS silencing of the analyzed gene. Both strategies (PTGS and TGS significantly reduced the transcript level of the analyzed gene, and this was highly correlated with lowered BX content. Inoculation with virus-based vectors specifically induced expression of the analyzed gene, indicating up-regulation by biotic stressors. This is the first report of using the BSMV-based system for functional analysis of rye gene. The findings prove that the analyzed gene is a rye ortholog of the Bx1 gene. Its expression is developmentally regulated and is strongly induced by biotic stress. Stable accumulation of BXs in plants older than 21 dai associated with undetectable expression of ScBx1 indicates that the function of the ScBx1 in the BX biosynthesis is redundant with another gene. We anticipate that the unknown gene is a putative ortholog of the Igl, which still remains to be identified in rye.

  19. Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica.

    Science.gov (United States)

    Jeong, Young-Min; Chung, Won-Hyong; Chung, Hee; Kim, Namshin; Park, Beom-Seok; Lim, Ki-Byung; Yu, Hee-Ju; Mun, Jeong-Hwan

    2014-09-01

    This manuscript provides a Brassica conserved ortholog set (COS) that can be used as diagnostic cross-species markers as well as tools for genetic mapping and genome comparison of the Brassicaceae. A conserved ortholog set (COS) is a collection of genes that are conserved in both sequence and copy number between closely related genomes. COS is a useful resource for developing gene-based markers and is suitable for comparative genome mapping. We developed a COS for Brassica based on proteome comparisons of Arabidopsis thaliana, B. rapa, and B. oleracea to establish a basis for comparative genome analysis of crop species in the Brassicaceae. A total of 1,194 conserved orthologous single-copy genes were identified from the genomes based on whole-genome BLASTP analysis. Gene ontology analysis showed that most of them encoded proteins with unknown function and chloroplast-related genes were enriched. In addition, 152 Brassica COS primer sets were applied to 16 crop and wild species of the Brassicaceae and 57.9-92.8 % of them were successfully amplified across the species representing that a Brassica COS can be used as diagnostic cross-species markers of diverse Brassica species. We constructed a genetic map of Raphanus sativus by analyzing the segregation of 322 COS genes in an F2 population (93 individuals) of Korean cultivars (WK10039 × WK10024). Comparative genome analysis based on the COS genes showed conserved genome structures between R. sativus and B. rapa with lineage-specific rearrangement and fractionation of triplicated subgenome blocks indicating close evolutionary relationship and differentiation of the genomes. The Brassica COS developed in this study will play an important role in genetic, genomic, and breeding studies of crop Brassicaceae species.

  20. 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

  1. Both Hoxc13 orthologs are functionally important for zebrafish tail fin regeneration.

    Science.gov (United States)

    Thummel, Ryan; Ju, Mila; Sarras, Michael P; Godwin, Alan R

    2007-06-01

    Hox genes are re-expressed during regeneration in many species. Given their important role in body plan development, it has been assumed, but not directly shown, that they play a functional role in regeneration. In this paper we show that morpholino-mediated knockdown of either Hoxc13a or Hoxc13b during the process of zebrafish tail fin regeneration results in a significant reduction of regenerative outgrowth. Furthermore, cellular proliferation within the blastema is directly affected in both knockdowns. Hence, similar to the demonstration of unique functions of multiple Hox genes during limb formation, both Hoxc13 orthologs have distinct functions in regeneration.

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

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    Riccardo Rinaldi

    2016-07-01

    Full Text Available 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

  3. Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots.

    Science.gov (United States)

    Cenci, Albero; Guignon, Valentin; Roux, Nicolas; Rouard, Mathieu

    2014-05-01

    Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species.

  4. ORCAN-a web-based meta-server for real-time detection and functional annotation of orthologs.

    Science.gov (United States)

    Zielezinski, Andrzej; Dziubek, Michal; Sliski, Jan; Karlowski, Wojciech M

    2017-04-15

    ORCAN (ORtholog sCANner) is a web-based meta-server for one-click evolutionary and functional annotation of protein sequences. The server combines information from the most popular orthology-prediction resources, including four tools and four online databases. Functional annotation utilizes five additional comparisons between the query and identified homologs, including: sequence similarity, protein domain architectures, functional motifs, Gene Ontology term assignments and a list of associated articles. Furthermore, the server uses a plurality-based rating system to evaluate the orthology relationships and to rank the reference proteins by their evolutionary and functional relevance to the query. Using a dataset of ∼1 million true yeast orthologs as a sample reference set, we show that combining multiple orthology-prediction tools in ORCAN increases the sensitivity and precision by 1-2 percent points. The service is available for free at http://www.combio.pl/orcan/ . wmk@amu.edu.pl. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  5. Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

    Science.gov (United States)

    Huson, Daniel H; Tappu, Rewati; Bazinet, Adam L; Xie, Chao; Cummings, Michael P; Nieselt, Kay; Williams, Rohan

    2017-01-25

    Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes. We present a new method for performing gene-centric assembly, called protein-alignment-guided assembly, and provide an implementation in our metagenome analysis tool MEGAN. Genes are assembled on the fly, based on the alignment of all reads against a protein reference database such as NCBI-nr. Specifically, the user selects a gene family based on a classification such as KEGG and all reads binned to that gene family are assembled. Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered. Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way.

  6. Ortholog-based screening and identification of genes related to intracellular survival.

    Science.gov (United States)

    Yang, Xiaowen; Wang, Jiawei; Bing, Guoxia; Bie, Pengfei; De, Yanyan; Lyu, Yanli; Wu, Qingmin

    2018-04-20

    Bioinformatics and comparative genomics analysis methods were used to predict unknown pathogen genes based on homology with identified or functionally clustered genes. In this study, the genes of common pathogens were analyzed to screen and identify genes associated with intracellular survival through sequence similarity, phylogenetic tree analysis and the λ-Red recombination system test method. The total 38,952 protein-coding genes of common pathogens were divided into 19,775 clusters. As demonstrated through a COG analysis, information storage and processing genes might play an important role intracellular survival. Only 19 clusters were present in facultative intracellular pathogens, and not all were present in extracellular pathogens. Construction of a phylogenetic tree selected 18 of these 19 clusters. Comparisons with the DEG database and previous research revealed that seven other clusters are considered essential gene clusters and that seven other clusters are associated with intracellular survival. Moreover, this study confirmed that clusters screened by orthologs with similar function could be replaced with an approved uvrY gene and its orthologs, and the results revealed that the usg gene is associated with intracellular survival. The study improves the current understanding of intracellular pathogens characteristics and allows further exploration of the intracellular survival-related gene modules in these pathogens. Copyright © 2018. Published by Elsevier B.V.

  7. The Cyclin-Dependent Kinase Ortholog pUL97 of Human Cytomegalovirus Interacts with Cyclins

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    Laura Graf

    2013-12-01

    Full Text Available The human cytomegalovirus (HCMV-encoded protein kinase, pUL97, is considered a cyclin-dependent kinase (CDK ortholog, due to shared structural and functional characteristics. The primary mechanism of CDK activation is binding to corresponding cyclins, including cyclin T1, which is the usual regulatory cofactor of CDK9. This study provides evidence of direct interaction between pUL97 and cyclin T1 using yeast two-hybrid and co-immunoprecipitation analyses. Confocal immunofluorescence revealed partial colocalization of pUL97 with cyclin T1 in subnuclear compartments, most pronounced in viral replication centres. The distribution patterns of pUL97 and cyclin T1 were independent of HCMV strain and host cell type. The sequence domain of pUL97 responsible for the interaction with cyclin T1 was between amino acids 231–280. Additional co-immunoprecipitation analyses showed cyclin B1 and cyclin A as further pUL97 interaction partners. Investigation of the pUL97-cyclin T1 interaction in an ATP consumption assay strongly suggested phosphorylation of pUL97 by the CDK9/cyclin T1 complex in a substrate concentration-dependent manner. This is the first demonstration of interaction between a herpesviral CDK ortholog and cellular cyclins.

  8. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

    Directory of Open Access Journals (Sweden)

    Paul D Thomas

    Full Text Available A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011 has proposed a metric for the "functional similarity" between two genes that uses only the Gene Ontology (GO annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the "ortholog conjecture" (or, more properly, the "ortholog functional conservation hypothesis". First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1 that GO annotations are often incomplete, potentially in a biased manner, and subject to an "open world assumption" (absence of an annotation does not imply absence of a function, and 2 that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the

  9. Drosophila TDP1 Ortholog Important for Longevity and Nervous System Maintenance | Center for Cancer Research

    Science.gov (United States)

    As the molecule responsible for encoding a cell’s hereditary information, DNA must maintain its integrity. However, nucleic acids are vulnerable to damage by a number of endogenous and exogenous insults, such as reactive oxygen species or enzymes that react with DNA. Thus, other enzymes are tasked with repairing damaged DNA, including tyrosyl-DNA phosphodiesterase 1 (TDP1), which frees the 3’ ends of DNA that are blocked by proteins and oxidized bases to allow the ligation of strand breaks. Yeast, mice, and humans that express mutants of TDP1 have a reduced capacity to repair oxidative or topoisomerase-induced damage. A Drosophila TDP1 ortholog, glaikit (gkt), has been reported, but its function in DNA repair has not been evaluated because, surprisingly, gkt knockout flies were not viable.

  10. ATX-2, the C. elegans ortholog of ataxin 2, functions in translational regulation in the germline.

    Science.gov (United States)

    Ciosk, Rafal; DePalma, Michael; Priess, James R

    2004-10-01

    Human ataxin 2 is a protein of unknown function that is implicated in the neurodegenerative disorder spinocerebellar ataxia type 2. We found that the C. elegans ortholog of ataxin 2, ATX-2, forms a complex with PAB-1, a cytoplasmic polyA-binding protein, and that ATX-2 is required for development of the germline. In the absence of ATX-2, proliferation of stem cells is reduced, and the germline is abnormally masculinized. These defects appear to result from inappropriate translational regulation that normally is mediated by the conserved KH-domain protein GLD-1. We find that MEX-3, a second KH-domain protein, exhibits a novel, ATX-2-dependent role in preventing inappropriate translation in the germline stem cells. Together, our results suggest that ATX-2 functions in translational regulation that is mediated by GLD-1 and MEX-3 proteins.

  11. Mutations that Allow SIR2 Orthologs to Function in a NAD+-Depleted Environment

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    Caitlin R. Ondracek

    2017-03-01

    Full Text Available Sirtuin enzymes depend on NAD+ to catalyze protein deacetylation. Therefore, the lowering of NAD+ during aging leads to decreased sirtuin activity and may speed up aging processes in laboratory animals and humans. In this study, we used a genetic screen to identify two mutations in the catalytic domain of yeast Sir2 that allow the enzyme to function in an NAD+-depleted environment. These mutant enzymes give rise to a significant increase of yeast replicative lifespan and increase deacetylation by the Sir2 ortholog, SIRT1, in mammalian cells. Our data suggest that these mutations increase the stability of the conserved catalytic sirtuin domain, thereby increasing the catalytic efficiency of the mutant enzymes. Our approach to identifying sirtuin mutants that permit function in NAD+-limited environments may inform the design of small molecules that can maintain sirtuin activity in aging organisms.

  12. Transcript catalogs of human chromosome 21 and orthologous chimpanzee and mouse regions.

    Science.gov (United States)

    Sturgeon, Xiaolu; Gardiner, Katheleen J

    2011-06-01

    A comprehensive representation of the gene content of the long arm of human chromosome 21 (Hsa21q) remains of interest for the study of Down syndrome, its associated phenotypic features, and mouse models. Here we compare transcript catalogs for Hsa21q, chimpanzee chromosome 21 (Ptr21q), and orthologous regions of mouse chromosomes 16, 17, and 10 for open reading frame (ORF) characteristics and conservation. The Hsa21q and mouse catalogs contain 552 and 444 gene models, respectively, of which only 162 are highly conserved. Hsa21q transcripts were used to identify orthologous exons in Ptr21q and assemble 533 putative transcripts. Transcript catalogs for all three organisms are searchable for nucleotide and amino acid sequence features of ORF length, repeat content, experimental support, gene structure, and conservation. For human and mouse comparisons, three additional summaries are provided: (1) the chromosomal distribution of novel ORF transcripts versus potential functional RNAs, (2) the distribution of species-specific transcripts within Hsa21q and mouse models of Down syndrome, and (3) the organization of sense-antisense and putative sense-antisense structures defining potential regulatory mechanisms. Catalogs, summaries, and nucleotide and amino acid sequences of all composite transcripts are available and searchable at http://gfuncpathdb.ucdenver.edu/iddrc/chr21/home.php. These data sets provide comprehensive information useful for evaluation of candidate genes and mouse models of Down syndrome and for identification of potential functional RNA genes and novel regulatory mechanisms involving Hsa21q genes. These catalogs and search tools complement and extend information available from other gene annotation projects.

  13. Linking the potato genome to the conserved ortholog set (COS) markers.

    Science.gov (United States)

    Lindqvist-Kreuze, Hannele; Cho, Kwangsoo; Portal, Leticia; Rodríguez, Flor; Simon, Reinhard; Mueller, Lukas A; Spooner, David M; Bonierbale, Merideth

    2013-06-08

    Conserved ortholog set (COS) markers are an important functional genomics resource that has greatly improved orthology detection in Asterid species. A comprehensive list of these markers is available at Sol Genomics Network (http://solgenomics.net/) and many of these have been placed on the genetic maps of a number of solanaceous species. We amplified over 300 COS markers from eight potato accessions involving two diploid landraces of Solanum tuberosum Andigenum group (formerly classified as S. goniocalyx, S. phureja), and a dihaploid clone derived from a modern tetraploid cultivar of S. tuberosum and the wild species S. berthaultii, S. chomatophilum, and S. paucissectum. By BLASTn (Basic Local Alignment Search Tool of the NCBI, National Center for Biotechnology Information) algorithm we mapped the DNA sequences of these markers into the potato genome sequence. Additionally, we mapped a subset of these markers genetically in potato and present a comparison between the physical and genetic locations of these markers in potato and in comparison with the genetic location in tomato. We found that most of the COS markers are single-copy in the reference genome of potato and that the genetic location in tomato and physical location in potato sequence are mostly in agreement. However, we did find some COS markers that are present in multiple copies and those that map in unexpected locations. Sequence comparisons between species show that some of these markers may be paralogs. The sequence-based physical map becomes helpful in identification of markers for traits of interest thereby reducing the number of markers to be tested for applications like marker assisted selection, diversity, and phylogenetic studies.

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

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    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.

  15. Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection.

    Science.gov (United States)

    Quraishi, Umar Masood; Abrouk, Michael; Bolot, Stéphanie; Pont, Caroline; Throude, Mickael; Guilhot, Nicolas; Confolent, Carole; Bortolini, Fernanda; Praud, Sébastien; Murigneux, Alain; Charmet, Gilles; Salse, Jerome

    2009-11-01

    Recent updates in comparative genomics among cereals have provided the opportunity to identify conserved orthologous set (COS) DNA sequences for cross-genome map-based cloning of candidate genes underpinning quantitative traits. New tools are described that are applicable to any cereal genome of interest, namely, alignment criterion for orthologous couples identification, as well as the Intron Spanning Marker software to automatically select intron-spanning primer pairs. In order to test the software, it was applied to the bread wheat genome, and 695 COS markers were assigned to 1,535 wheat loci (on average one marker/2.6 cM) based on 827 robust rice-wheat orthologs. Furthermore, 31 of the 695 COS markers were selected to fine map a pentosan viscosity quantitative trait loci (QTL) on wheat chromosome 7A. Among the 31 COS markers, 14 (45%) were polymorphic between the parental lines and 12 were mapped within the QTL confidence interval with one marker every 0.6 cM defining candidate genes among the rice orthologous region.

  16. 6-Pyruvoyltetrahydropterin synthase orthologs of either a single or dual domain structure are responsible for tetrahydrobiopterin synthesis in bacteria.

    Science.gov (United States)

    Kong, Jin Sun; Kang, Ji-Youn; Kim, Hye Lim; Kwon, O-Seob; Lee, Kon Ho; Park, Young Shik

    2006-09-04

    6-Pyruvoyltetrahydropterin synthase (PTPS) catalyzes the second step of tetrahydrobiopterin (BH4) synthesis. We previously identified PTPS orthologs (bPTPS-Is) in bacteria which do not produce BH4. In this study we disrupted the gene encoding bPTPS-I in Synechococcus sp. PCC 7942, which produces BH4-glucoside. The mutant was normal in BH4-glucoside production, demonstrating that bPTPS-I does not participate in BH4 synthesis in vivo and bringing us a new PTPS ortholog (bPTPS-II) of a bimodular polypeptide. The recombinant Synechococcus bPTPS-II was assayed in vitro to show PTPS activity higher than human enzyme. Further computational analysis revealed the presence of mono and bimodular bPTPS-II orthologs mostly in green sulfur bacteria and cyanobacteria, respectively, which are well known for BH4-glycoside production. In summary we found new bacterial PTPS orthologs, having either a single or dual domain structure and being responsible for BH4 synthesis in vivo, thereby disclosing all the bacterial PTPS homologs.

  17. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Morphogenesis of Strongyloides stercoralis infective larvae requires the DAF-16 ortholog FKTF-1.

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    Michelle L Castelletto

    2009-04-01

    Full Text Available Based on metabolic and morphological similarities between infective third-stage larvae of parasitic nematodes and dauer larvae of Caenorhabditis elegans, it is hypothesized that similar genetic mechanisms control the development of these forms. In the parasite Strongyloides stercoralis, FKTF-1 is an ortholog of DAF-16, a forkhead transcription factor that regulates dauer larval development in C. elegans. Using transgenesis, we investigated the role of FKTF-1 in S. stercoralis' infective larval development. In first-stage larvae, GFP-tagged recombinant FKTF-1b localizes to the pharynx and hypodermis, tissues remodeled in infective larvae. Activating and inactivating mutations at predicted AKT phosphorylation sites on FKTF-1b give constitutive cytoplasmic and nuclear localization of the protein, respectively, indicating that its post-translational regulation is similar to other FOXO-class transcription factors. Mutant constructs designed to interfere with endogenous FKTF-1b function altered the intestinal and pharyngeal development of the larvae and resulted in some transgenic larvae failing to arrest in the infective stage. Our findings indicate that FKTF-1b is required for proper morphogenesis of S. stercoralis infective larvae and support the overall hypothesis of similar regulation of dauer development in C. elegans and the formation of infective larvae in parasitic nematodes.

  19. Caroli's Disease: Current Knowledge of Its Biliary Pathogenesis Obtained from an Orthologous Rat Model

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    Yasunori Sato

    2012-01-01

    Full Text Available Caroli's disease belongs to a group of hepatic fibropolycystic diseases and is a hepatic manifestation of autosomal recessive polycystic kidney disease (ARPKD. It is a congenital disorder characterized by segmental saccular dilatations of the large intrahepatic bile duct and is frequently associated with congenital hepatic fibrosis (CHF. The most viable theory explaining its pathogenesis suggests that it is related to ductal plate malformation. The development of the polycystic kidney (PCK rat, an orthologous rodent model of Caroli's disease with CHF as well as ARPKD, has allowed the molecular pathogenesis of the disease and the therapeutic options for its treatment to be examined. The relevance of the findings of studies using PCK rats and/or the cholangiocyte cell line derived from them to the pathogenesis of human Caroli's disease is currently being analyzed. Fibrocystin/polyductin, the gene product responsible for ARPKD, is normally localized to primary cilia, and defects in the fibrocystin from primary cilia are observed in PCK cholangiocytes. Ciliopathies involving PCK cholangiocytes (cholangiociliopathies appear to be associated with decreased intracellular calcium levels and increased cAMP concentrations, causing cholangiocyte hyperproliferation, abnormal cell matrix interactions, and altered fluid secretion, which ultimately result in bile duct dilatation. This article reviews the current knowledge about the pathogenesis of Caroli's disease with CHF, particularly focusing on studies of the mechanism responsible for the biliary dysgenesis observed in PCK rats.

  20. ATX-2, the C. elegans Ortholog of Human Ataxin-2, Regulates Centrosome Size and Microtubule Dynamics.

    Science.gov (United States)

    Stubenvoll, Michael D; Medley, Jeffrey C; Irwin, Miranda; Song, Mi Hye

    2016-09-01

    Centrosomes are critical sites for orchestrating microtubule dynamics, and exhibit dynamic changes in size during the cell cycle. As cells progress to mitosis, centrosomes recruit more microtubules (MT) to form mitotic bipolar spindles that ensure proper chromosome segregation. We report a new role for ATX-2, a C. elegans ortholog of Human Ataxin-2, in regulating centrosome size and MT dynamics. ATX-2, an RNA-binding protein, forms a complex with SZY-20 in an RNA-independent fashion. Depleting ATX-2 results in embryonic lethality and cytokinesis failure, and restores centrosome duplication to zyg-1 mutants. In this pathway, SZY-20 promotes ATX-2 abundance, which inversely correlates with centrosome size. Centrosomes depleted of ATX-2 exhibit elevated levels of centrosome factors (ZYG-1, SPD-5, γ-Tubulin), increasing MT nucleating activity but impeding MT growth. We show that ATX-2 influences MT behavior through γ-Tubulin at the centrosome. Our data suggest that RNA-binding proteins play an active role in controlling MT dynamics and provide insight into the control of proper centrosome size and MT dynamics.

  1. An ortholog of LEAFY in Jatropha curcas regulates flowering time and floral organ development

    Science.gov (United States)

    Tang, Mingyong; Tao, Yan-Bin; Fu, Qiantang; Song, Yaling; Niu, Longjian; Xu, Zeng-Fu

    2016-01-01

    Jatropha curcas seeds are an excellent biofuel feedstock, but seed yields of Jatropha are limited by its poor flowering and fruiting ability. Thus, identifying genes controlling flowering is critical for genetic improvement of seed yield. We isolated the JcLFY, a Jatropha ortholog of Arabidopsis thaliana LEAFY (LFY), and identified JcLFY function by overexpressing it in Arabidopsis and Jatropha. JcLFY is expressed in Jatropha inflorescence buds, flower buds, and carpels, with highest expression in the early developmental stage of flower buds. JcLFY overexpression induced early flowering, solitary flowers, and terminal flowers in Arabidopsis, and also rescued the delayed flowering phenotype of lfy-15, a LFY loss-of-function Arabidopsis mutant. Microarray and qPCR analysis revealed several flower identity and flower organ development genes were upregulated in JcLFY-overexpressing Arabidopsis. JcLFY overexpression in Jatropha also induced early flowering. Significant changes in inflorescence structure, floral organs, and fruit shape occurred in JcLFY co-suppressed plants in which expression of several flower identity and floral organ development genes were changed. This suggests JcLFY is involved in regulating flower identity, floral organ patterns, and fruit shape, although JcLFY function in Jatropha floral meristem determination is not as strong as that of Arabidopsis. PMID:27869146

  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. Identification of novel human damage response proteins targeted through yeast orthology.

    Directory of Open Access Journals (Sweden)

    J Peter Svensson

    Full Text Available Studies in Saccharomyces cerevisiae show that many proteins influence cellular survival upon exposure to DNA damaging agents. We hypothesized that human orthologs of these S. cerevisiae proteins would also be required for cellular survival after treatment with DNA damaging agents. For this purpose, human homologs of S. cerevisiae proteins were identified and mapped onto the human protein-protein interaction network. The resulting human network was highly modular and a series of selection rules were implemented to identify 45 candidates for human toxicity-modulating proteins. The corresponding transcripts were targeted by RNA interference in human cells. The cell lines with depleted target expression were challenged with three DNA damaging agents: the alkylating agents MMS and 4-NQO, and the oxidizing agent t-BuOOH. A comparison of the survival revealed that the majority (74% of proteins conferred either sensitivity or resistance. The identified human toxicity-modulating proteins represent a variety of biological functions: autophagy, chromatin modifications, RNA and protein metabolism, and telomere maintenance. Further studies revealed that MMS-induced autophagy increase the survival of cells treated with DNA damaging agents. In summary, we show that damage recovery proteins in humans can be identified through homology to S. cerevisiae and that many of the same pathways are represented among the toxicity modulators.

  4. Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae).

    Science.gov (United States)

    Zhang, Li-Na; Zhang, Xian-Zhi; Zhang, Yu-Xiao; Zeng, Chun-Xia; Ma, Peng-Fei; Zhao, Lei; Guo, Zhen-Hua; Li, De-Zhu

    2014-09-01

    The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared with nuclear data. In this study, we intended to identify a set of desirable nuclear genes for resolving the phylogeny of the temperate woody bamboos. Using two different methodologies, we identified 209 and 916 genes, respectively, as putative single copy orthologous genes. A total of 112 genes was successfully amplified and sequenced by next-generation sequencing technologies in five species sampled from the tribe. As most of the genes exhibited intra-individual allele heterozygotes, we investigated phylogenetic utility by reconstructing the phylogeny based on individual genes. Discordance among gene trees was observed and, to resolve the conflict, we performed a range of analyses using BUCKy and HybTree. While caution should be taken when inferring a phylogeny from multiple conflicting genes, our analysis indicated that 74 of the 112 investigated genes are potential markers for resolving the phylogeny of the temperate woody bamboos. © 2014 John Wiley & Sons Ltd.

  5. ATX-2, the C. elegans Ortholog of Human Ataxin-2, Regulates Centrosome Size and Microtubule Dynamics.

    Directory of Open Access Journals (Sweden)

    Michael D Stubenvoll

    2016-09-01

    Full Text Available Centrosomes are critical sites for orchestrating microtubule dynamics, and exhibit dynamic changes in size during the cell cycle. As cells progress to mitosis, centrosomes recruit more microtubules (MT to form mitotic bipolar spindles that ensure proper chromosome segregation. We report a new role for ATX-2, a C. elegans ortholog of Human Ataxin-2, in regulating centrosome size and MT dynamics. ATX-2, an RNA-binding protein, forms a complex with SZY-20 in an RNA-independent fashion. Depleting ATX-2 results in embryonic lethality and cytokinesis failure, and restores centrosome duplication to zyg-1 mutants. In this pathway, SZY-20 promotes ATX-2 abundance, which inversely correlates with centrosome size. Centrosomes depleted of ATX-2 exhibit elevated levels of centrosome factors (ZYG-1, SPD-5, γ-Tubulin, increasing MT nucleating activity but impeding MT growth. We show that ATX-2 influences MT behavior through γ-Tubulin at the centrosome. Our data suggest that RNA-binding proteins play an active role in controlling MT dynamics and provide insight into the control of proper centrosome size and MT dynamics.

  6. 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

    2016-02-12

    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. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. LACK, a RACK1 ortholog, facilitates cytochrome c oxidase subunit expression to promote Leishmania major fitness.

    Science.gov (United States)

    Cardenas, Daviel; Carter, Pamela M; Nation, Catherine S; Pizarro, Juan C; Guidry, Jessie; Aiyar, Ashok; Kelly, Ben L

    2015-04-01

    Leishmania are kinetoplastid parasites that cause the sandfly-transmitted disease leishmaniasis. To maintain fitness throughout their infectious life cycle, Leishmania must undergo rapid metabolic adaptations to the dramatically distinct environments encountered during transition between sandfly and vertebrate hosts. We performed proteomic and immunoblot analyses of attenuated L. major strains deficient for LACK, the Leishmania ortholog of the mammalian receptor for activated c kinase (RACK1), that is important for parasite thermotolerance and virulence. This approach identified cytochrome c oxidase (LmCOX) subunit IV as a LACK-dependent fitness protein. Consistent with decreased levels of LmCOX subunit IV at mammalian temperature, and in amastigotes, LmCOX activity and mitochondrial function were also impaired in LACK-deficient L. major under these conditions. Importantly, overexpression of LmCOX subunit IV in LACK-deficient L. major restored thermotolerance and macrophage infectivity. Interestingly, overexpression of LmCOX subunit IV enhanced LmCOX subunit VI expression at mammalian temperature. Collectively, our data suggest LACK promotes Leishmania adaptation to the mammalian host environment by sustaining LmCOX subunit IV expression and hence energy metabolism in response to stress stimuli such as heat. These findings extend the repertoire of RACK1 protein utility to include a role in mitochondrial function. © 2015 John Wiley & Sons Ltd.

  8. Behavioral analysis of the huntingtin-associated protein 1 ortholog trak-1 in Caenorhabditis elegans.

    Science.gov (United States)

    Norflus, Fran; Bu, Jingnan; Guyton, Evon; Gutekunst, Claire-Anne

    2016-09-01

    The precise role of huntingtin-associated protein 1 (HAP1) is not known, but studies have shown that it is important for early development and survival. A Caenorhabditis elegans ortholog of HAP1, T27A3.1 (also called trak-1), has been found and is expressed in a subset of neurons. Potential behavioral functions of three knockout lines of T27A3.1 were examined. From its suspected role in mice we hypothesize that T27A3.1 might be involved in egg hatching and early growth, mechanosensation, chemosensation, sensitivity to osmolarity, and synaptic transmission. Our studies show that the knockout worms are significantly different from the wild-type (WT) worms only in the synaptic transmission test, which was measured by adding aldicarb, an acetylcholinesterase inhibitor. The change in function was determined by measuring the number of worms paralyzed. However, when the T27A3.1 worms were tested for egg hatching and early growth, mechanosensation, chemosensation, and sensitivity to osmolarity, there were no significant differences between the knockout and WT worms. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  9. Characterization and expression of a Pinus radiata putative ortholog to the Arabidopsis SHORT-ROOT gene.

    Science.gov (United States)

    Solé, Alicia; Sánchez, Conchi; Vielba, Jesús M; Valladares, Silvia; Abarca, Dolores; Díaz-Sala, Carmen

    2008-11-01

    We characterized a Pinus radiata D. Don putative ortholog to the Arabidopsis thaliana (L.) Heynh. SHORT--ROOT gene (AtSHR) and analyzed its expression in different organs during vegetative development and in response to exogenous auxin during adventitious rooting. The predicted protein sequence contained domains characteristic of the GRAS protein family and showed a strong similarity to the SHORT--ROOT (SHR) proteins. Quantitative reverse transcriptase--polymerase chain reaction (qRT-PCR) and in situ hybridization showed that the gene is predominantly expressed in roots, root primordia and in the cambial region of hypocotyl cuttings. Increased mRNA levels were observed, independently of the presence or absence of exogenous auxin, in the cambial region and rooting competent cells of hypocotyl cuttings within the first 24 h of adventitious rooting, before the activation of cell divisions and the organization of the adventitious root meristem. The expression pattern in organs and during adventitious rooting was similar to that of a Pinus radiata SCARECROW-LIKE (PrSCL1) gene, except that PrSCL1 is induced in response to exogenous auxin. Results suggest that the Pinus radiata SHORT-ROOT (PrSHR) gene has a role in root meristem formation and maintenance and in the cambial region of hypocotyl cuttings.

  10. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Christiansen, Elisabeth; Tikhonova, Irina G

    2012-01-01

    of the free fatty acid receptor 2 (FFA2) could be developed on the basis of pharmacological variation between species orthologs. For this, bovine FFA2 was characterized, revealing distinct ligand selectivity compared with human FFA2. Homology modeling and mutational analysis demonstrated a single mutation...... ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs....... of activity to endogenous ligands, while responding to the distinct ligand sorbic acid with pEC(50) values for inhibition of cAMP, 5.83 ± 0.11; Ca(2+) mobilization, 4.63 ± 0.05; ERK phosphorylation, 5.61 ± 0.06; and dynamic mass redistribution, 5.35 ± 0.06. This FFA2-RASSL will be useful in future studies...

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

    Directory of Open Access Journals (Sweden)

    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.

  12. 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

  13. 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.

  14. Comparing the evolutionary conservation between human essential genes, human orthologs of mouse essential genes and human housekeeping genes.

    Science.gov (United States)

    Lv, Wenhua; Zheng, Jiajia; Luan, Meiwei; Shi, Miao; Zhu, Hongjie; Zhang, Mingming; Lv, Hongchao; Shang, Zhenwei; Duan, Lian; Zhang, Ruijie; Jiang, Yongshuai

    2015-11-01

    Human housekeeping genes are often confused with essential human genes, and several studies regard both types of genes as having the same level of evolutionary conservation. However, this is not necessarily the case. To clarify this, we compared the differences between human housekeeping genes and essential human genes with respect to four aspects: the evolutionary rate (dN/dS), protein sequence identity, single-nucleotide polymorphism (SNP) density and level of linkage disequilibrium (LD). The results showed that housekeeping genes had lower evolutionary rates, higher sequence identities, lower SNP densities and higher levels of LD compared with essential genes. Together, these findings indicate that housekeeping and essential genes are two distinct types of genes, and that housekeeping genes have a higher level of evolutionary conservation. Therefore, we suggest that researchers should pay careful attention to the distinctions between housekeeping genes and essential genes. Moreover, it is still controversial whether we should substitute human orthologs of mouse essential genes for human essential genes. Therefore, we compared the evolutionary features between human orthologs of mouse essential genes and human housekeeping genes and we got inconsistent results in long-term and short-term evolutionary characteristics implying the irrationality of simply replacing human essential genes with human orthologs of mouse essential genes. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. Caenorhabditis elegans orthologs of human genes differentially expressed with age are enriched for determinants of longevity.

    Science.gov (United States)

    Sutphin, George L; Backer, Grant; Sheehan, Susan; Bean, Shannon; Corban, Caroline; Liu, Teresa; Peters, Marjolein J; van Meurs, Joyce B J; Murabito, Joanne M; Johnson, Andrew D; Korstanje, Ron

    2017-08-01

    We report a systematic RNAi longevity screen of 82 Caenorhabditis elegans genes selected based on orthology to human genes differentially expressed with age. We find substantial enrichment in genes for which knockdown increased lifespan. This enrichment is markedly higher than published genomewide longevity screens in C. elegans and similar to screens that preselected candidates based on longevity-correlated metrics (e.g., stress resistance). Of the 50 genes that affected lifespan, 46 were previously unreported. The five genes with the greatest impact on lifespan (>20% extension) encode the enzyme kynureninase (kynu-1), a neuronal leucine-rich repeat protein (iglr-1), a tetraspanin (tsp-3), a regulator of calcineurin (rcan-1), and a voltage-gated calcium channel subunit (unc-36). Knockdown of each gene extended healthspan without impairing reproduction. kynu-1(RNAi) alone delayed pathology in C. elegans models of Alzheimer's disease and Huntington's disease. Each gene displayed a distinct pattern of interaction with known aging pathways. In the context of published work, kynu-1, tsp-3, and rcan-1 are of particular interest for immediate follow-up. kynu-1 is an understudied member of the kynurenine metabolic pathway with a mechanistically distinct impact on lifespan. Our data suggest that tsp-3 is a novel modulator of hypoxic signaling and rcan-1 is a context-specific calcineurin regulator. Our results validate C. elegans as a comparative tool for prioritizing human candidate aging genes, confirm age-associated gene expression data as valuable source of novel longevity determinants, and prioritize select genes for mechanistic follow-up. © 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

  17. OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies

    Directory of Open Access Journals (Sweden)

    Young Nevin D

    2003-09-01

    Full Text Available Abstract Background In eukaryotic genomes, most genes are members of gene families. When comparing genes from two species, therefore, most genes in one species will be homologous to multiple genes in the second. This often makes it difficult to distinguish orthologs (separated through speciation from paralogs (separated by other types of gene duplication. Combining phylogenetic relationships and genomic position in both genomes helps to distinguish between these scenarios. This kind of comparison can also help to describe how gene families have evolved within a single genome that has undergone polyploidy or other large-scale duplications, as in the case of Arabidopsis thaliana – and probably most plant genomes. Results We describe a suite of programs called OrthoParaMap (OPM that makes genomic comparisons, identifies syntenic regions, determines whether sets of genes in a gene family are related through speciation or internal chromosomal duplications, maps this information onto phylogenetic trees, and infers internal nodes within the phylogenetic tree that may represent local – as opposed to speciation or segmental – duplication. We describe the application of the software using three examples: the melanoma-associated antigen (MAGE gene family on the X chromosomes of mouse and human; the 20S proteasome subunit gene family in Arabidopsis, and the major latex protein gene family in Arabidopsis. Conclusion OPM combines comparative genomic positional information and phylogenetic reconstructions to identify which gene duplications are likely to have arisen through internal genomic duplications (such as polyploidy, through speciation, or through local duplications (such as unequal crossing-over. The software is freely available at http://www.tc.umn.edu/~cann0010/.

  18. The Drosophila Huntington's disease gene ortholog dhtt influences chromatin regulation during development.

    Science.gov (United States)

    Dietz, Kevin N; Di Stefano, Luisa; Maher, Robert C; Zhu, Hui; Macdonald, Marcy E; Gusella, James F; Walker, James A

    2015-01-15

    Huntington's disease is an autosomal dominant neurodegenerative disorder caused by a CAG expansion mutation in HTT, the gene encoding huntingtin. Evidence from both human genotype-phenotype relationships and mouse model systems suggests that the mutation acts by dysregulating some normal activity of huntingtin. Recent work in the mouse has revealed a role for huntingtin in epigenetic regulation during development. Here, we examine the role of the Drosophila huntingtin ortholog (dhtt) in chromatin regulation in the development of the fly. Although null dhtt mutants display no overt phenotype, we found that dhtt acts as a suppressor of position-effect variegation (PEV), suggesting that it influences chromatin organization. We demonstrate that dhtt affects heterochromatin spreading in a PEV model by modulating histone H3K9 methylation levels at the heterochromatin-euchromatin boundary. To gain mechanistic insights into how dhtt influences chromatin function, we conducted a candidate genetic screen using RNAi lines targeting known PEV modifier genes. We found that dhtt modifies phenotypes caused by knockdown of a number of key epigenetic regulators, including chromatin-associated proteins, histone demethylases (HDMs) and methyltransferases. Notably, dhtt strongly modifies phenotypes resulting from loss of the HDM dLsd1, in both the ovary and wing, and we demonstrate that dhtt appears to act as a facilitator of dLsd1 function in regulating global histone H3K4 methylation levels. These findings suggest that a fundamental aspect of huntingtin function in heterochromatin/euchromatin organization is evolutionarily conserved across phyla. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  19. Enhancing the prediction of protein pairings between interacting families using orthology information

    Directory of Open Access Journals (Sweden)

    Pazos Florencio

    2008-01-01

    Full Text Available Abstract Background It has repeatedly been shown that interacting protein families tend to have similar phylogenetic trees. These similarities can be used to predicting the mapping between two families of interacting proteins (i.e. which proteins from one family interact with which members of the other. The correct mapping will be that which maximizes the similarity between the trees. The two families may eventually comprise orthologs and paralogs, if members of the two families are present in more than one organism. This fact can be exploited to restrict the possible mappings, simply by impeding links between proteins of different organisms. We present here an algorithm to predict the mapping between families of interacting proteins which is able to incorporate information regarding orthologues, or any other assignment of proteins to "classes" that may restrict possible mappings. Results For the first time in methods for predicting mappings, we have tested this new approach on a large number of interacting protein domains in order to statistically assess its performance. The method accurately predicts around 80% in the most favourable cases. We also analysed in detail the results of the method for a well defined case of interacting families, the sensor and kinase components of the Ntr-type two-component system, for which up to 98% of the pairings predicted by the method were correct. Conclusion Based on the well established relationship between tree similarity and interactions we developed a method for predicting the mapping between two interacting families using genomic information alone. The program is available through a web interface.

  20. Expression and function of spineless orthologs correlate with distal deutocerebral appendage morphology across Arthropoda.

    Science.gov (United States)

    Setton, Emily V W; March, Logan E; Nolan, Erik D; Jones, Tamsin E; Cho, Holly; Wheeler, Ward C; Extavour, Cassandra G; Sharma, Prashant P

    2017-10-01

    The deutocerebral (second) head segment is putatively homologous across Arthropoda, in spite of remarkable disparity of form and function of deutocerebral appendages. In Mandibulata this segment bears a pair of sensory antennae, whereas in Chelicerata the same segment bears a pair of feeding appendages called chelicerae. Part of the evidence for the homology of deutocerebral appendages is the conserved function of homothorax (hth), which has been shown to specify antennal or cheliceral fate in the absence of Hox signaling, in both mandibulate and chelicerate exemplars. However, the genetic basis for the morphological disparity of antenna and chelicera is not understood. To test whether downstream targets of hth have diverged in a lineage-specific manner, we examined the evolution of the function and expression of spineless (ss), which in two holometabolous insects is known to act as a hth target and distal antennal determinant. Toward expanding phylogenetic representation of gene expression data, here we show that strong expression of ss is observed in developing antennae of a hemimetabolous insect, a centipede, and an amphipod crustacean. By contrast, ss orthologs are not expressed throughout the cheliceral limb buds of spiders or harvestmen during developmental stages when appendage fate is specified. RNA interference-mediated knockdown of ss in Oncopeltus fasciatus, which bears a simple plesiomorphic antenna, resulted in homeotic distal antenna-to-leg transformation, comparable to data from holometabolous insect counterparts. Knockdown of hth in Oncopeltus fasciatus abrogated ss expression, suggesting conservation of upstream regulation. These data suggest that ss may be a flagellar (distal antennal) determinant more broadly, and that this function was acquired at the base of Mandibulata. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. 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

  2. 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.

  3. 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

  4. Identification of Putative Ortholog Gene Blocks Involved in Gestant and Lactating Mammary Gland Development: A Rodent Cross-Species Microarray Transcriptomics Approach

    Science.gov (United States)

    Rodríguez-Cruz, Maricela; Coral-Vázquez, Ramón M.; Hernández-Stengele, Gabriel; Sánchez, Raúl; Salazar, Emmanuel; Sanchez-Muñoz, Fausto; Encarnación-Guevara, Sergio; Ramírez-Salcedo, Jorge

    2013-01-01

    The mammary gland (MG) undergoes functional and metabolic changes during the transition from pregnancy to lactation, possibly by regulation of conserved genes. The objective was to elucidate orthologous genes, chromosome clusters and putative conserved transcriptional modules during MG development. We analyzed expression of 22,000 transcripts using murine microarrays and RNA samples of MG from virgin, pregnant, and lactating rats by cross-species hybridization. We identified 521 transcripts differentially expressed; upregulated in early (78%) and midpregnancy (89%) and early lactation (64%), but downregulated in mid-lactation (61%). Putative orthologous genes were identified. We mapped the altered genes to orthologous chromosomal locations in human and mouse. Eighteen sets of conserved genes associated with key cellular functions were revealed and conserved transcription factor binding site search entailed possible coregulation among all eight block sets of genes. This study demonstrates that the use of heterologous array hybridization for screening of orthologous gene expression from rat revealed sets of conserved genes arranged in chromosomal order implicated in signaling pathways and functional ontology. Results demonstrate the utilization power of comparative genomics and prove the feasibility of using rodent microarrays to identification of putative coexpressed orthologous genes involved in the control of human mammary gland development. PMID:24288657

  5. cdc-25.4, a Caenorhabditis elegans Ortholog of cdc25, Is Required for Male Mating Behavior

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    Sangmi Oh

    2016-12-01

    Full Text Available Cell division cycle 25 (cdc25 is an evolutionarily conserved phosphatase that promotes cell cycle progression. Among the four cdc25 orthologs in Caenorhabditis elegans, we found that cdc-25.4 mutant males failed to produce outcrossed progeny. This was not caused by defects in sperm development, but by defects in male mating behavior. The cdc-25.4 mutant males showed various defects during male mating, including contact response, backing, turning, and vulva location. Aberrant turning behavior was the most prominent defect in the cdc-25.4 mutant males. We also found that cdc-25.4 is expressed in many neuronal cells throughout development. The turning defect in cdc-25.4 mutant males was recovered by cdc-25.4 transgenic expression in neuronal cells, suggesting that cdc-25.4 functions in neurons for male mating. However, the neuronal morphology of cdc-25.4 mutant males appeared to be normal, as examined with several neuronal markers. Also, RNAi depletion of wee-1.3, a C. elegans ortholog of Wee1/Myt1 kinase, failed to suppress the mating defects of cdc-25.4 mutant males. These findings suggest that, for successful male mating, cdc-25.4 does not target cell cycles that are required for neuronal differentiation and development. Rather, cdc-25.4 likely regulates noncanonical substrates in neuronal cells.

  6. 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.

  7. 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.

  8. Efficient Generation of Orthologous Point Mutations in Pigs via CRISPR-assisted ssODN-mediated Homology-directed Repair

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    Kankan Wang

    2016-01-01

    Full Text Available Precise genome editing in livestock is of great value for the fundamental investigation of disease modeling. However, genetically modified pigs carrying subtle point mutations were still seldom reported despite the rapid development of programmable endonucleases. Here, we attempt to investigate single-stranded oligonucleotides (ssODN mediated knockin by introducing two orthologous pathogenic mutations, p.E693G for Alzheimer's disease and p.G2019S for Parkinson's disease, into porcine APP and LRRK2 loci, respectively. Desirable homology-directed repair (HDR efficiency was achieved in porcine fetal fibroblasts (PFFs by optimizing the dosage and length of ssODN templates. Interestingly, incomplete HDR alleles harboring partial point mutations were observed in single-cell colonies, which indicate the complex mechanism of ssODN-mediated HDR. The effect of mutation-to-cut distance on incorporation rate was further analyzed by deep sequencing. We demonstrated that a mutation-to-cut distance of 11 bp resulted in a remarkable difference in HDR efficiency between two point mutations. Finally, we successfully obtained one cloned piglet harboring the orthologous p.C313Y mutation at the MSTN locus via somatic cell nuclear transfer (SCNT. Our proof-of-concept study demonstrated efficient ssODN-mediated incorporation of pathogenic point mutations in porcine somatic cells, thus facilitating further development of disease modeling and genetic breeding in pigs.

  9. 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.

  10. Sequence conservation among orthologous vomeronasal type 1 receptor-like (ora) genes does not support the differential tuning hypothesis in Salmonidae.

    Science.gov (United States)

    Johnson, Marc A; Banks, Michael A

    2011-10-01

    Salmon utilize olfactory cues to guide natal stream homing during spawning migrations. Both inorganic and biogenic chemicals have been proposed as odorants that might be used by salmon during homing. In this study, we used genomic DNA sequence data from nine salmonid species to compare nucleotide identities for orthologous main olfactory receptor (mOR) genes with nucleotide identities for orthologous vomeronasal type 1-like (ora) receptor genes. We found that orthologs for both classes of olfactory receptor genes (mORs and Oras) appear to be highly conserved among species. Our findings do not support the differential tuning hypothesis in Salmonidae, which predicts higher sequence conservation for mORs than ora. We did, however, find convincing evidence for site-specific positive selection acting on paralogous main olfactory receptor genes. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. '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

  12. 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

    Free fatty acid receptors 2 and 3 (FFA2 and FFA3) are G protein-coupled receptors for short chain free fatty acids (SCFAs). They respond to the same set of endogenous ligands but with distinct rank-order of potency such that acetate (C2) has been described as FFA2-selective, whereas propionate (C3...... 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...

  13. Functional evolution of a multigene family: orthologous and paralogous pheromone receptor genes in the turnip moth, Agrotis segetum.

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    Dan-Dan Zhang

    Full Text Available Lepidopteran pheromone receptors (PRs, for which orthologies are evident among closely related species, provide an intriguing example of gene family evolution in terms of how new functions may arise. However, only a limited number of PRs have been functionally characterized so far and thus evolutionary scenarios suffer from elements of speculation. In this study we investigated the turnip moth Agrotis segetum, in which female moths produce a mixture of chemically related pheromone components that elicit specific responses from receptor cells on male antennae. We cloned nine A. segetum PR genes and the Orco gene by degenerate primer based RT-PCR. The nine PR genes, named as AsegOR1 and AsegOR3-10, fall into four distinct orthologous clusters of known lepidopteran PRs, of which one contains six paralogues. The paralogues are under relaxed selective pressure, contrasting with the purifying selection on other clusters. We identified the receptors AsegOR9, AsegOR4 and AsegOR5, specific for the respective homologous pheromone components (Z-5-decenyl, (Z-7-dodecenyl and (Z-9-tetradecenyl acetates, by two-electrode voltage clamp recording from Xenopus laevis oocytes co-expressing Orco and each PR candidate. These receptors occur in three different orthologous clusters. We also found that the six paralogues with high sequence similarity vary dramatically in ligand selectivity and sensitivity. Different from AsegOR9, AsegOR6 showed a relatively large response to the behavioural antagonist (Z-5-decenol, and a small response to (Z-5-decenyl acetate. AsegOR1 was broadly tuned, but most responsive to (Z-5-decenyl acetate, (Z-7-dodecenyl acetate and the behavioural antagonist (Z-8-dodecenyl acetate. AsegOR8 and AsegOR7, which differ from AsegOR6 and AsegOR1 by 7 and 10 aa respectively, showed much lower sensitivities. AsegOR10 showed only small responses to all the tested compounds. These results suggest that new receptors arise through gene duplication, and

  14. The trehalose utilization gene thuA ortholog in Mesorhizobium loti does not influence competitiveness for nodulation on Lotus spp.

    Science.gov (United States)

    Ampomah, Osei Yaw; Jensen, John Beck

    2014-03-01

    Competitiveness for nodulation is a desirable trait in rhizobia strains used as inoculant. In Sinorhizobium meliloti 1021 mutation in either of the trehalose utilization genes thuA or thuB influences its competitiveness for root colonization and nodule occupancy depending on the interacting host. We have therefore investigated whether mutation in the thuA ortholog in Mesorhizobium loti MAFF303099 also leads to a similar competitive phenotype on its hosts. The results show that M. loti thuA mutant Ml7023 was symbiotically effective and was as competitive as the wild type in colonization and nodule occupancy on Lotus corniculatus and Lotus japonicus. The thuA gene in M. loti was not induced during root colonization or in the infection threads unlike in S. meliloti, despite its induction by trehalose and high osmolarity in in vitro assays.

  15. The Roles of AtxA Orthologs in Virulence of Anthrax-like Bacillus cereus G9241

    OpenAIRE

    Scarff, Jennifer M.; Raynor, Malik J.; Seldina, Yuliya I.; Ventura, Christy L.; Koehler, Theresa M.; O’Brien, Alison D.

    2016-01-01

    AtxA is a critical transcriptional regulator of plasmid-encoded virulence genes in Bacillus anthracis. Bacillus cereus G9241, which caused an anthrax-like infection, has two virulence plasmids, pBCXO1 and pBC210, that each harbor toxin genes and a capsule locus. G9241 also produces two orthologs of AtxA: AtxA1, encoded on pBCXO1, and AtxA2, encoded on pBC210. The amino acid sequence of AtxA1 is identical to that of AtxA from B. anthracis, while the sequences of AtxA1 and AtxA2 are 79% identic...

  16. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences

    DEFF Research Database (Denmark)

    Ferreira, Elisa N; Pires, Lilian C; Parmigiani, Raphael B

    2004-01-01

    The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification...... can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within...... the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization...

  17. The C. elegans Ortholog of USP7 controls DAF-16 stability in Insulin/IGF-1-like signaling.

    Science.gov (United States)

    Heimbucher, Thomas; Hunter, Tony

    2015-01-01

    FOXO family transcription factors are downstream effectors of Insulin/IGF-1 signaling (IIS) and are regulated by posttranslational modification and coregulators, including components of the ubiquitin-proteasome system (UPS). Cofactors promoting DAF-16/FOXO protein stability and function in IIS have not been described yet. In a recent study, we have identified the deubiquitylating enzyme MATH-33, the ortholog of mammalian USP7/HAUSP, as an essential DAF-16 coregulator. We found that MATH-33 actively stabilizes DAF-16 protein levels when IIS is downregulated. Here we discuss how DAF-16/FOXO transcription factors are regulated by the UPS, in particular by the interplay of E3-ubiquitin ligases and deubiquitylating enzymes, which is critical for balancing DAF-16/FOXO activity and degradation. Recent findings raise the intriguing possibility that regulated oscillations in DAF-16/FOXO steady state levels play an integral role in mechanisms controlling healthspan and lifespan extension.

  18. 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.

  19. MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales.

    Science.gov (United States)

    Jain, Sourabh; Panda, Arup; Colson, Philippe; Raoult, Didier; Pontarotti, Pierre

    2017-04-07

    With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the major drawback in gene acquisition studies is the focus on few MV families or putative families with large variation in their genetic structure. Thus, here we have tried to develop a methodology by which we can detect horizontal gene transfers (HGTs), taking into consideration orthologous groups of distantly related Megavirale families. Here, we report an automated workflow MimiLook, prepared as a Perl command line program, that deduces orthologous groups (OGs) from ORFomes of Megavirales and constructs phylogenetic trees by performing alignment generation, alignment editing and protein-protein BLAST (BLASTP) searching across the National Center for Biotechnology Information (NCBI) non-redundant (nr) protein sequence database. Finally, this tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detection of HGTs, along with retrieval of information about those OGs that are monophyletic with organisms from cellular domains of life. By implementing MimiLook, we noticed that nine percent of Megavirale gene families (i.e., OGs) have been acquired by HGT, 80% OGs were Megaviralespecific and eight percent were found to be sharing common ancestry with members of cellular domains (Eukaryote, Bacteria, Archaea, Phages or other viruses) and three percent were ambivalent. The results are briefly discussed to emphasize methodology. Also, MimiLook is relevant for detecting evolutionary scenarios in other targeted phyla with user defined modifications. It can be accessed at

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

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    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.

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

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    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.

  2. Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.

    Science.gov (United States)

    Mateos, Julieta L; Tilmes, Vicky; Madrigal, Pedro; Severing, Edouard; Richter, René; Rijkenberg, Colin W M; Krajewski, Paweł; Coupland, George

    2017-12-19

    Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina , respectively. We found that only 14% of their BSs were conserved in both species and that these contained a CArG-box that is recognized by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared with the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets, and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated (COR) genes were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were usually different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared with WT, and this correlated with reduced growth in pep1-1 Therefore, FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution. Copyright © 2017 the Author(s). Published by PNAS.

  3. Isolation and characterization of the Bactrocera oleae genes orthologous to the sex determining Sex-lethal and doublesex genes of Drosophila melanogaster.

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    Lagos, Dimitrios; Ruiz, M Fernanda; Sánchez, Lucas; Komitopoulou, Katia

    2005-03-28

    Here we report the isolation and characterization of the olive fruit fly Bactrocera oleae genes orthologous to the Drosophila melanogaster sex-determining genes Sex-lethal (Sxl) and doublesex (dsx). Fragments of the Sxl and dsx orthologous were isolated with RT-PCR. Genomic and cDNA clones were then obtained by screening a genomic library and separate male and female cDNA adult libraries using the RT-PCR products as probes in both cases. B. oleae Sxl gene (BoSxl) expresses the same pattern of transcripts which encode for a single common polypeptide in both male and female flies. The gene shares a high degree of similarity in sequence and expression to its Ceratitis capitata orthologous and does not appear to play a key regulatory role in the sex-determining cascade. B. oleae dsx gene (Bodsx) expands in a chromosomal region of more than 50 kb, with 6 exons-5 introns, producing different sex-specific mRNAs, according to the Drosophila model. The cDNA sequences are almost identical to the gene orthologous of Bactrocera tryoni. Four repeat elements identical to the D. melanogaster TRA/TRA-2 binding sites have been found in the untranslated region of the female-specific exon 4, predicting a common regulatory splicing mechanism in all studied species of Diptera.

  4. Sina and Sinb genes in triticale do not determine grain hardness contrary to their orthologs Pina and Pinb in wheat

    Science.gov (United States)

    2013-01-01

    Background Secaloindoline a (Sina) and secaloindoline b (Sinb) genes of hexaploid triticale (x Triticosecale Wittmack) are orthologs of puroindoline a (Pina) and puroindoline b (Pinb) in hexaploid wheat (Triticum aestivum L.). It has already been proven that RNA interference (RNAi)-based silencing of Pina and Pinb genes significantly decreased the puroindoline a and puroindoline b proteins in wheat and essentially increased grain hardness (J Exp Bot 62:4025-4036, 2011). The function of Sina and Sinb in triticale was tested by means of RNAi silencing and compared to wheat. Results Novel Sina and Sinb alleles in wild-type plants of cv. Wanad were identified and their expression profiles characterized. Alignment with wheat Pina-D1a and Pinb-D1a alleles showed 95% and 93.3% homology with Sina and Sinb coding sequences. Twenty transgenic lines transformed with two hpRNA silencing cassettes directed to silence Sina or Sinb were obtained by the Agrobacterium-mediated method. A significant decrease of expression of both Sin genes in segregating progeny of tested T1 lines was observed independent of the silencing cassette used. The silencing was transmitted to the T4 kernel generation. The relative transcript level was reduced by up to 99% in T3 progeny with the mean for the sublines being around 90%. Silencing of the Sin genes resulted in a substantial decrease of secaloindoline a and secaloindoline b content. The identity of SIN peptides was confirmed by mass spectrometry. The hardness index, measured by the SKCS (Single Kernel Characterization System) method, ranged from 22 to 56 in silent lines and from 37 to 49 in the control, and the mean values were insignificantly lower in the silent ones, proving increased softness. Additionally, the mean total seed protein content of silenced lines was about 6% lower compared with control lines. Correlation coefficients between hardness and transcript level were weakly positive. Conclusions We documented that RNAi-based silencing

  5. VFL, the Grapevine FLORICAULA/LEAFY Ortholog, Is Expressed in Meristematic Regions Independently of Their Fate1

    Science.gov (United States)

    Carmona, María José; Cubas, Pilar; Martínez-Zapater, José M.

    2002-01-01

    The flowering process in grapevine (Vitis vinifera) takes place in buds and extends for two consecutive growing seasons. To understand the genetic and molecular mechanisms underlying this process, we have characterized grapevine bud development, cloned the grapevine FLORICAULA/LEAFY (FLO/LFY) ortholog, VFL, and analyzed its expression patterns during vegetative and reproductive development. Flowering induction takes place during the first season. Upon induction, the shoot apical meristem begins to produce lateral meristems that will give rise to either inflorescences or tendrils. During the second season, after a winter dormancy period, buds reactivate and inflorescence meristems give rise to flower meristems. VFL is expressed in lateral meristems that give rise to inflorescence and flower meristems, consistent with a role in reproductive development. Furthermore, VFL is also detected in other meristematic regions such as the vegetative shoot apical meristem and the lateral meristems that will give rise to tendrils. VFL is also expressed in leaf primordia and in growing leaf margins until later stages of development. Accumulation of VFL transcripts in cell-proliferating regions suggests a role for VFL not only in flower meristem specification, but also in the maintenance of indeterminacy before the differentiation of derivatives of the apical meristem: flowers, leaves, or tendrils. PMID:12226487

  6. 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

  7. The COP1 ortholog PPS regulates the juvenile-adult and vegetative-reproductive phase changes in rice.

    Science.gov (United States)

    Tanaka, Nobuhiro; Itoh, Hironori; Sentoku, Naoki; Kojima, Mikiko; Sakakibara, Hitoshi; Izawa, Takeshi; Itoh, Jun-Ichi; Nagato, Yasuo

    2011-06-01

    Because plant reproductive development occurs only in adult plants, the juvenile-to-adult phase change is an indispensable part of the plant life cycle. We identified two allelic mutants, peter pan syndrome-1 (pps-1) and pps-2, that prolong the juvenile phase in rice (Oryza sativa) and showed that rice PPS is an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC1. The pps-1 mutant exhibits delayed expression of miR156 and miR172 and the suppression of GA biosynthetic genes, reducing the GA(3) content in this mutant. In spite of its prolonged juvenile phase, the pps-1 mutant flowers early, and this is associated with derepression of RAP1B expression in pps-1 plants independently of the Hd1-Hd3a/RFT1 photoperiodic pathway. PPS is strongly expressed in the fourth and fifth leaves, suggesting that it regulates the onset of the adult phase downstream of MORI1 and upstream of miR156 and miR172. Its ability to regulate the vegetative phase change and the time of flowering suggests that rice PPS acquired novel functions during the evolution of rice/monocots.

  8. 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.

  9. Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway.

    Science.gov (United States)

    McEwan, Deborah L; Feinbaum, Rhonda L; Stroustrup, Nicholas; Haas, Wilhelm; Conery, Annie L; Anselmo, Anthony; Sadreyev, Ruslan; Ausubel, Frederick M

    2016-12-07

    Many pathogens secrete toxins that target key host processes resulting in the activation of immune pathways. The secreted Pseudomonas aeruginosa toxin Exotoxin A (ToxA) disrupts intestinal protein synthesis, which triggers the induction of a subset of P. aeruginosa-response genes in the nematode Caenorhabditis elegans. We show here that one ToxA-induced C. elegans gene, the Tribbles pseudokinase ortholog nipi-3, is essential for host survival following exposure to P. aeruginosa or ToxA. We find that NIPI-3 mediates the post-developmental expression of intestinal immune genes and proteins and primarily functions in parallel to known immune pathways, including p38 MAPK signaling. Through mutagenesis screening, we identify mutants of the bZIP C/EBP transcription factor cebp-1 that suppress the hypersusceptibility defects of nipi-3 mutants. NIPI-3 is a negative regulator of CEBP-1, which in turn negatively regulates protective immune mechanisms. This pathway represents a previously unknown innate immune signaling pathway in intestinal epithelial cells that is involved in the surveillance of cellular homeostasis. Because NIPI-3 and CEBP-1 are also essential for C. elegans development, NIPI-3 is analogous to other key innate immune signaling molecules such as the Toll receptors in Drosophila that have an independent role during development.

  10. 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.

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    Tamio Yamaguchi

    Full Text Available 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.

  11. PTEN Redundancy: Overexpressing lpten, a Homolog of Dictyostelium discoideum ptenA, the Ortholog of Human PTEN, Rescues All Behavioral Defects of the Mutant ptenA−

    OpenAIRE

    Lusche, Daniel F.; Wessels, Deborah; Richardson, Nicole A.; Russell, Kanoe B.; Hanson, Brett M.; Soll, Benjamin A.; Lin, Benjamin H.; Soll, David R.

    2014-01-01

    Mutations in the tumor suppressor gene PTEN are associated with a significant proportion of human cancers. Because the human genome also contains several homologs of PTEN, we considered the hypothesis that if a homolog, functionally redundant with PTEN, can be overexpressed, it may rescue the defects of a PTEN mutant. We have performed an initial test of this hypothesis in the model system Dictyostelium discoideum, which contains an ortholog of human PTEN, ptenA. Deletion of ptenA results in ...

  12. Nuclear Envelope Phosphatase 1-Regulatory Subunit 1 (Formerly TMEM188) Is the Metazoan Spo7p Ortholog and Functions in the Lipin Activation Pathway*

    Science.gov (United States)

    Han, Sungwon; Bahmanyar, Shirin; Zhang, Peixiang; Grishin, Nick; Oegema, Karen; Crooke, Roseann; Graham, Mark; Reue, Karen; Dixon, Jack E.; Goodman, Joel M.

    2012-01-01

    Lipin-1 catalyzes the formation of diacylglycerol from phosphatidic acid. Lipin-1 mutations cause lipodystrophy in mice and acute myopathy in humans. It is heavily phosphorylated, and the yeast ortholog Pah1p becomes membrane-associated and active upon dephosphorylation by the Nem1p-Spo7p membrane complex. A mammalian ortholog of Nem1p is the C-terminal domain nuclear envelope phosphatase 1 (CTDNEP1, formerly “dullard”), but its Spo7p-like partner is unknown, and the need for its existence is debated. Here, we identify the metazoan ortholog of Spo7p, TMEM188, renamed nuclear envelope phosphatase 1-regulatory subunit 1 (NEP1-R1). CTDNEP1 and NEP1-R1 together complement a nem1Δspo7Δ strain to block endoplasmic reticulum proliferation and restore triacylglycerol levels and lipid droplet number. The two human orthologs are in a complex in cells, and the amount of CTDNEP1 is increased in the presence of NEP1-R1. In the Caenorhabditis elegans embryo, expression of nematode CTDNEP1 and NEP1-R1, as well as lipin-1, is required for normal nuclear membrane breakdown after zygote formation. The expression pattern of NEP1-R1 and CTDNEP1 in human and mouse tissues closely mirrors that of lipin-1. CTDNEP1 can dephosphorylate lipins-1a, -1b, and -2 in human cells only in the presence of NEP1-R1. The nuclear fraction of lipin-1b is increased when CTDNEP1 and NEP1-R1 are co-expressed. Therefore, NEP1-R1 is functionally conserved from yeast to humans and functions in the lipin activation pathway. PMID:22134922

  13. The Presence of Phage Orthologous Genes in Helicobacter pylori Correlates with the Presence of the Virulence Factors CagA and VacA.

    Science.gov (United States)

    Kyrillos, Alexandra; Arora, Gaurav; Murray, Bradley; Rosenwald, Anne G

    2016-06-01

    The bacterium Helicobacter pylori is associated with ulcers and the development of gastric cancer. Several genes, including cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA), are associated with increased gastric cancer risk. Some strains of H. pylori also contain sequences related to bacteriophage phiHP33; however, the significance of these phage-related sequences remains unknown. We assessed the extent to which phiHP33-related sequences are present in 335 H. pylori strains using homology searches then mapped shared genes between phiHP33 and H. pylori strains onto an existing phylogeny. One hundred and twenty-one H. pylori strains contain phage orthologous sequences, and the presence of the phage-related sequences correlates with the presence of CagA and VacA. Mapping of the phage orthologs onto a phylogeny of H. pylori is consistent with the hypothesis that these genes were acquired by horizontal gene transfer. phiHP33 phage orthologous sequences might be of significance in understanding virulence of different H. pylori strains. © 2015 John Wiley & Sons Ltd.

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

    Science.gov (United States)

    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

  15. The yeast magmas ortholog pam16 has an essential function in fermentative growth that involves sphingolipid metabolism.

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    Mary K Short

    Full Text Available Magmas is a growth factor responsive gene encoding an essential mitochondrial protein in mammalian cells. Pam16, the Magmas ortholog in Saccharomyces cerevisiae, is a component of the presequence translocase-associated motor. A temperature-sensitive allele (pam16-I61N was used to query an array of non-essential gene-deletion strains for synthetic genetic interactions. The pam16-I61N mutation at ambient temperature caused synthetic lethal or sick phenotypes with genes involved in lipid metabolism, perixosome synthesis, histone deacetylation and mitochondrial protein import. The gene deletion array was also screened for suppressors of the pam16-I61N growth defect to identify compensatory pathways. Five suppressor genes were identified (SUR4, ISC1, IPT1, SKN1, and FEN1 and all are involved in sphingolipid metabolism. pam16-I61N cells cultured in glucose at non-permissive temperatures resulted in rapid growth inhibition and G1 cell cycle arrest, but cell viability was maintained. Altered mitochondria morphology, reduced peroxisome induction in glycerol/ethanol and oleate, and changes in the levels of several sphingolipids including C18 alpha-hydroxy-phytoceramide, were also observed in the temperature sensitive strain. Deletion of SUR4, the strongest suppressor, reversed the temperature sensitive fermentative growth defect, the morphological changes and the elevated levels of C18 alpha-hydroxy phytoceramide in pam16-I61N. Deletion of the other four suppressor genes had similar effects on C18 alpha-hydroxy-phytoceramide levels and restored proliferation to the pam16-I61N strain. In addition, pam16-I61N inhibited respiratory growth, likely by reducing cardiolipin, which is essential for mitochondrial function. Our results suggest that the pleiotropic effects caused by impaired Pam16/Magmas function are mediated in part by changes in lipid metabolism.

  16. 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

  17. Both STING and MAVS fish orthologs contribute to the induction of interferon mediated by RIG-I.

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    Stéphane Biacchesi

    Full Text Available Viral infections are detected in most cases by the host innate immune system through pattern-recognition receptors (PRR, the sensors for pathogen-associated molecular patterns (PAMPs, which induce the production of cytokines, such as type I interferons (IFN. Recent identification in mammalian and teleost fish of cytoplasmic viral RNA sensors, RIG-I-like receptors (RLRs, and their mitochondrial adaptor: the mitochondrial antiviral signaling (MAVS protein, also called IPS-1, highlight their important role in the induction of IFN at the early stage of a virus infection. More recently, an endoplasmic reticulum (ER adaptor: the stimulator of interferon genes (STING protein, also called MITA, ERIS and MPYS, has been shown to play a pivotal role in response to both non-self-cytosolic RNA and dsDNA. In this study, we cloned STING cDNAs from zebrafish and showed that it was an ortholog to mammalian STING. We demonstrated that overexpression of this ER protein in fish cells led to a constitutive induction of IFN and interferon-stimulated genes (ISGs. STING-overexpressing cells were almost fully protected against RNA virus infection with a strong inhibition of both DNA and RNA virus replication. In addition, we found that together with MAVS, STING was an important player in the RIG-I IFN-inducing pathway. This report provides the demonstration that teleost fish possess a functional RLR pathway in which MAVS and STING are downstream signaling molecules of RIG-I. The Sequences presented in this article have been submitted to GenBank under accession numbers: Zebrafish STING (HE856619; EPC STING (HE856620; EPC IRF3 (HE856621; EPC IFN promoter (HE856618.

  18. Saccharomyces cerevisiae Bat1 and Bat2 Aminotransferases Have Functionally Diverged from the Ancestral-Like Kluyveromyces lactis Orthologous Enzyme

    Science.gov (United States)

    Colón, Maritrini; Hernández, Fabiola; López, Karla; Quezada, Héctor; González, James; López, Geovani; Aranda, Cristina; González, Alicia

    2011-01-01

    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 biosynthetic and catabolic

  19. Characterization and Comparative Analysis of Olfactory Receptor Co-Receptor Orco Orthologs Among Five Mirid Bug Species

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    Qi Wang

    2018-03-01

    Full Text Available The phytophagous mirid bugs of Apolygus lucorum, Lygus pratensis as well as three Adelphocoris spp., including Adelphocoris lineolatus, A. suturalis, and A. fasciaticollis are major pests of multiple agricultural crops in China, which have distinct geographical distribution and occurrence ranges. Like many insect species, these bugs heavily rely on olfactory cues to search preferred host plants, thereby investigation on functional co-evolution and divergence of olfactory genes seems to be necessary and is of great interest. In the odorant detection pathway, olfactory receptor co-receptor (Orco plays critical role in the perception of odors. In this study, we identified the full-length cDNA sequences encoding three putative Orcos (AsutOrco, AfasOrco, and LpraOrco in bug species of A. suturalis, A. fasciaticollis, and L. pratensis based on homology cloning method. Next, sequence alignment, membrane topology and gene structure analysis showed that these three Orco orthologs together with previously reported AlinOrco and AlucOrco shared high amino acid identities and similar topology structure, but had different gene structure especially at the length and insertion sites of introns. Furthermore, the evolutional estimation on the ratios of non-synonymous to synonymous (Ka/Ks revealed that Orco genes were under strong purifying selection, but the degrees of variation were significant different between genera. The results of quantitative real-time PCR experiments showed that these five Orco genes had a similar antennae-biased tissue expression pattern. Taking these data together, it is thought that Orco genes in the mirid species could share conserved olfaction roles but had different evolution rates. These findings would lay a foundation to further investigate the molecular mechanisms of evolutionary interactions between mirid bugs and their host plants, which might in turn contribute to the development of pest management strategy for mirid bugs.

  20. 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.

  1. The tailless ortholog nhr-67 regulates patterning of gene expression and morphogenesis in the C. elegans vulva.

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    Jolene S Fernandes

    2007-04-01

    Full Text Available Regulation of spatio-temporal gene expression in diverse cell and tissue types is a critical aspect of development. Progression through Caenorhabditis elegans vulval development leads to the generation of seven distinct vulval cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF, each with its own unique gene expression profile. The mechanisms that establish the precise spatial patterning of these mature cell types are largely unknown. Dissection of the gene regulatory networks involved in vulval patterning and differentiation would help us understand how cells generate a spatially defined pattern of cell fates during organogenesis. We disrupted the activity of 508 transcription factors via RNAi and assayed the expression of ceh-2, a marker for vulB fate during the L4 stage. From this screen, we identified the tailless ortholog nhr-67 as a novel regulator of gene expression in multiple vulval cell types. We find that one way in which nhr-67 maintains cell identity is by restricting inappropriate cell fusion events in specific vulval cells, namely vulE and vulF. nhr-67 exhibits a dynamic expression pattern in the vulval cells and interacts with three other transcriptional regulators cog-1 (Nkx6.1/6.2, lin-11 (LIM, and egl-38 (Pax2/5/8 to generate the composite expression patterns of their downstream targets. We provide evidence that egl-38 regulates gene expression in vulB1, vulC, vulD, vulE, as well as vulF cells. We demonstrate that the pairwise interactions between these regulatory genes are complex and vary among the seven cell types. We also discovered a striking regulatory circuit that affects a subset of the vulval lineages: cog-1 and nhr-67 inhibit both one another and themselves. We postulate that the differential levels and combinatorial patterns of lin-11, cog-1, and nhr-67 expression are a part of a regulatory code for the mature vulval cell types.

  2. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

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    Wolf Yuri I

    2012-12-01

    Full Text Available Abstract Background Collections of Clusters of Orthologous Genes (COGs provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs. Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection

  3. Differences in expression pattern and function between zebrafish hoxc13 orthologs: recruitment of Hoxc13b into an early embryonic role.

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    Thummel, Ryan; Li, Li; Tanase, Carmen; Sarras, Michael P; Godwin, Alan R

    2004-10-15

    Vertebrate Hox genes are generally believed to initiate expression at the primitive streak or early neural plate stages. The timing and spatial restrictions of the Hox expression patterns during these stages correlate well with their demonstrated role in axial patterning. Here we demonstrate that one zebrafish hoxc13 ortholog, hoxc13a, has an expression pattern in the developing tail bud that is consistent with the gene playing a role in axial patterning. However, the second hoxc13 ortholog, hoxc13b, is maternally expressed and is detectable in every cell of early cleavage embryos through gastrulae. In addition, both transcript and protein are detectable at these stages. At 19 h post fertilization (hpf), hoxc13b expression is up-regulated in the tail bud, becoming restricted to the tail bud by 24 hpf. Importantly, by 24 hpf, hoxc13b morphants show a specific developmental delay, which can be rescued by co-injecting synthetic capped hoxc13a or hoxc13b message. These data suggest some functional divergence due to altered expression patterns of the two hoxc13 orthologs after duplication. Further characterization of the hoxc13b morphant delay reveals that it is biphasic in nature, with the first phase of the delay occurring before gastrulation, suggesting a new role for vertebrate Hox genes before their conserved role in axial patterning. The extent of the delay does not change through 20 hpf; however, an additional delay emerges at this time. Notably, this second phase of the delay correlates with hoxc13b expression pattern becoming restricted to the tail bud.

  4. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

    DEFF Research Database (Denmark)

    Muller, J; Szklarczyk, D; Julien, P

    2010-01-01

    clustering. We applied this procedure to 630 complete genomes (529 bacteria, 46 archaea and 55 eukaryotes), which is a 2-fold increase relative to the previous version. The pipeline yielded 224,847 OGs, including 9724 extended versions of the original COG and KOG. We computed OGs for different levels...... of the tree of life; in addition to the species groups included in our first release (i.e. fungi, metazoa, insects, vertebrates and mammals), we have now constructed OGs for archaea, fishes, rodents and primates. We automatically annotate the non-supervised orthologous groups (NOGs) with functional...

  5. Genetic or pharmacological activation of the Drosophila PGC-1α ortholog spargel rescues the disease phenotypes of genetic models of Parkinson's disease.

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    Ng, Chee-Hoe; Basil, Adeline H; Hang, Liting; Tan, Royston; Goh, Kian-Leong; O'Neill, Sharon; Zhang, Xiaodong; Yu, Fengwei; Lim, Kah-Leong

    2017-07-01

    Despite intensive research, the etiology of Parkinson's disease (PD) remains poorly understood and the disease remains incurable. However, compelling evidence gathered over decades of research strongly support a role for mitochondrial dysfunction in PD pathogenesis. Related to this, PGC-1α, a key regulator of mitochondrial biogenesis, has recently been proposed to be an attractive target for intervention in PD. Here, we showed that silencing of expression of the Drosophila PGC-1α ortholog spargel results in PD-related phenotypes in flies and also seem to negate the effects of AMPK activation, which we have previously demonstrated to be neuroprotective, that is, AMPK-mediated neuroprotection appears to require PGC-1α. Importantly, we further showed that genetic or pharmacological activation of the Drosophila PGC-1α ortholog spargel is sufficient to rescue the disease phenotypes of Parkin and LRRK2 genetic fly models of PD, thus supporting the proposed use of PGC-1α-related strategies for neuroprotection in PD. Copyright © 2017 National Neuroscience Institute. Published by Elsevier Inc. All rights reserved.

  6. The Conserved, Disease-Associated RNA Binding Protein dNab2 Interacts with the Fragile X Protein Ortholog in Drosophila Neurons

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    Rick S. Bienkowski

    2017-08-01

    Full Text Available The Drosophila dNab2 protein is an ortholog of human ZC3H14, a poly(A RNA binding protein required for intellectual function. dNab2 supports memory and axon projection, but its molecular role in neurons is undefined. Here, we present a network of interactions that links dNab2 to cytoplasmic control of neuronal mRNAs in conjunction with the fragile X protein ortholog dFMRP. dNab2 and dfmr1 interact genetically in control of neurodevelopment and olfactory memory, and their encoded proteins co-localize in puncta within neuronal processes. dNab2 regulates CaMKII, but not futsch, implying a selective role in control of dFMRP-bound transcripts. Reciprocally, dFMRP and vertebrate FMRP restrict mRNA poly(A tail length, similar to dNab2/ZC3H14. Parallel studies of murine hippocampal neurons indicate that ZC3H14 is also a cytoplasmic regulator of neuronal mRNAs. Altogether, these findings suggest that dNab2 represses expression of a subset of dFMRP-target mRNAs, which could underlie brain-specific defects in patients lacking ZC3H14.

  7. 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)

    Poopanitpan, Napapol; Kobayashi, Satoshi; Fukuda, Ryouichi; Horiuchi, Hiroyuki; Ohta, Akinori

    2010-01-01

    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.

  8. Functional properties of a newly cloned fish ortholog of the neutral amino acid transporter B0AT1 (SLC6A19).

    Science.gov (United States)

    Margheritis, Eleonora; Terova, Genciana; Cinquetti, Raffaella; Peres, Antonio; Bossi, Elena

    2013-10-01

    The functional properties of an ortholog of the B(0)AT1 (SLC6A19) amino acid transporter, cloned from the intestine of the sea bass Dicentrachus labrax, were investigated. The two-electrode voltage-clamp technique was applied to Xenopus laevis oocytes heterologously expressing the transporter in order to measure the currents associated with the transport process in different conditions. In particular the substrate specificity, the ionic requirements, and possible effects of pH were examined. Among the organic substrates, leucine, glycine, serine and valine generated the largest transport currents with apparent affinities in the lower millimolar range. The importance of Na(+) as the driver ion in the transport process is confirmed, although Li(+) is also capable to sustain transport, while K(+) is not. No evidence of a relevant role of Cl(-) in the transport activity was found. Concerning the other two kinds of currents commonly found in electrogenic transporters, very fast pre-steady-state currents were detected in the absence of organic substrate, while lithium-specific leak currents were not observed. The comparison of these properties with those of the mammalian and insect orthologs may give interesting indication for future structure-function studies in this transporter subfamily. © 2013.

  9. The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes.

    Science.gov (United States)

    Atambayeva, Shara; Niyazova, Raigul; Ivashchenko, Anatoliy; Pyrkova, Anna; Pinsky, Ilya; Akimniyazova, Aigul; Labeit, Siegfried

    2017-06-01

    Normally, one miRNA interacts with the mRNA of one gene. However, there are miRNAs that can bind to many mRNAs, and one mRNA can be the target of many miRNAs. This significantly complicates the study of the properties of miRNAs and their diagnostic and medical applications. The search of 2,750 human microRNAs (miRNAs) binding sites in 12,175 mRNAs of human genes using the MirTarget program has been completed. For the binding sites of the miR-619-5p the hybridization free energy of the bonds was equal to 100% of the maximum potential free energy. The mRNAs of 201 human genes have complete complementary binding sites of miR-619-5p in the 3'UTR (214 sites), CDS (3 sites), and 5'UTR (4 sites). The mRNAs of CATAD1, ICA1L, GK5, POLH, and PRR11 genes have six miR-619-5p binding sites, and the mRNAs of OPA3 and CYP20A1 genes have eight and ten binding sites, respectively. All of these miR-619-5p binding sites are located in the 3'UTRs. The miR-619-5p binding site in the 5'UTR of mRNA of human USP29 gene is found in the mRNAs of orthologous genes of primates. Binding sites of miR-619-5p in the coding regions of mRNAs of C8H8orf44, C8orf44, and ISY1 genes encode the WLMPVIP oligopeptide, which is present in the orthologous proteins. Binding sites of miR-619-5p in the mRNAs of transcription factor genes ZNF429 and ZNF429 encode the AHACNP oligopeptide in another reading frame. Binding sites of miR-619-5p in the 3'UTRs of all human target genes are also present in the 3'UTRs of orthologous genes of mammals. The completely complementary binding sites for miR-619-5p are conservative in the orthologous mammalian genes. The majority of miR-619-5p binding sites are located in the 3'UTRs but some genes have miRNA binding sites in the 5'UTRs of mRNAs. Several genes have binding sites for miRNAs in the CDSs that are read in different open reading frames. Identical nucleotide sequences of binding sites encode different amino acids in different proteins. The binding sites of miR-619-5p

  10. 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

  11. 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

  12. Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs

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    Nakai Kenta

    2008-04-01

    Full Text Available Abstract Background Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial. Results We examined promoter conservation as well as protein conservation for 6,901 human and mouse orthologous genes, and observed a very weak correlation between them. We further investigated their relationship by decomposing it based on functional categories, and identified categories with significant tendencies. Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation. Conclusion Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.

  13. A DEF/GLO-like MADS-box gene from a gymnosperm: Pinus radiata contains an ortholog of angiosperm B class floral homeotic genes.

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    Mouradov, A; Hamdorf, B; Teasdale, R D; Kim, J T; Winter, K U; Theissen, G

    1999-09-01

    The specification of floral organ identity during development depends on the function of a limited number of homeotic genes grouped into three classes: A, B, and C. Pairs of paralogous B class genes, such as DEF and GLO in Antirrhinum, and AP3 and PI in Arabidopsis, are required for establishing petal and stamen identity. To gain a better understanding of the evolutionary origin of petals and stamens, we have looked for orthologs of B class genes in conifers. Here we report cDNA cloning of PrDGL (Pinus radiata DEF/GLO-like gene) from radiata pine. We provide phylogenetic evidence that PrDGL is closely related to both DEF- and GLO-like genes of angiosperms, and is thus among the first putative orthologs of floral homeotic B function genes ever reported from a gymnosperm. Expression of PrDGL is restricted to the pollen strobili (male cones) and was not detected in female cones. PrDGL expression was first detected in emergent male cone primordia and persisted through the early stages of pollen cone bud differentiation. Based on the results of our phylogeny reconstructions and expression studies, we suggest that PrDGL could play a role in distinguishing between male (where expression is on) and female reproductive structures (where expression is off) in radiata pine. We speculate that this could be the general function of DEF/GLO-like genes in gymnosperms that may have been recruited for the distinction between stamens and carpels, the male and female reproductive organs of flowering plants, during the evolution of angiosperms out of gymnosperm-like ancestors. Copyright 1999 Wiley-Liss, Inc.

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

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    Melissa eGardiner

    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.

  15. Comparison of orthologous cytochrome P450 genes relative expression patterns in the bark beetles Dendroctonus rhizophagus and Dendroctonus valens (Curculionidae: Scolytinae) during host colonization.

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    Obregón-Molina, G; Cesar-Ayala, A K; López, M F; Cano-Ramírez, C; Zúñiga, G

    2015-12-01

    Bark beetles of the genus Dendroctonus are important components of coniferous forests. During host colonization, they must overcome the chemical defences of their host trees, which are metabolized by cytochrome P450 (CYP or P450) enzymes to compounds that are readily excreted. In this study, we report the relative expression (quantitative real-time PCR) of four orthologous cytochrome P450 genes (CYP6BW5, CYP6DG1, CYP6DJ2 and CYP9Z20) in Dendroctonus rhizophagus and Dendroctonus valens forced to attack host trees at 8 and 24 h following forced attack and in four stages during natural colonization [solitary females boring the bark (T1); both male and female members of couples before oviposition (T2); both male and female members of couples during oviposition (T3), and solitary females inside the gallery containing eggs (T4)]. For both species gene expression was different compared with that observed in insects exposed to single monoterpenes in the laboratory, and the expression patterns were significantly different amongst species, sex, gut region and exposure time or natural colonization stage. The induction of genes (CYP6BW5v1, CYP6DJ2v1 and CYP9Z20v1 from D. rhizophagus, as well as CYP6DG1v3 from D. valens) correlated with colonization stage as well as with the increase in oxygenated monoterpenes in the gut of both species throughout the colonization of the host. Our results point to different functions of these orthologous genes in both species. © 2015 The Royal Entomological Society.

  16. Molecular evolutionary analysis of a gender-limited MID ortholog from the homothallic species Volvox africanus with male and monoecious spheroids.

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    Kayoko Yamamoto

    Full Text Available Volvox is a very interesting oogamous organism that exhibits various types of sexuality and/or sexual spheroids depending upon species or strains. However, molecular bases of such sexual reproduction characteristics have not been studied in this genus. In the model species V. carteri, an ortholog of the minus mating type-determining or minus dominance gene (MID of isogamous Chlamydomonas reinhardtii is male-specific and determines the sperm formation. Male and female genders are genetically determined (heterothallism in V. carteri, whereas in several other species of Volvox both male and female gametes (sperm and eggs are formed within the same clonal culture (homothallism. To resolve the molecular basis of the evolution of Volvox species with monoecious spheroids, we here describe a MID ortholog in the homothallic species V. africanus that produces both monoecious and male spheroids within a single clonal culture. Comparison of synonymous and nonsynonymous nucleotide substitutions in MID genes between V. africanus and heterothallic volvocacean species suggests that the MID gene of V. africanus evolved under the same degree of functional constraint as those of the heterothallic species. Based on semi quantitative reverse transcription polymerase chain reaction analyses using the asexual, male and monoecious spheroids isolated from a sexually induced V. africanus culture, the MID mRNA level was significantly upregulated in the male spheroids, but suppressed in the monoecious spheroids. These results suggest that the monoecious spheroid-specific down regulation of gene expression of the MID homolog correlates with the formation of both eggs and sperm in the same spheroid in V. africanus.

  17. Molecular analysis of Aedes aegypti classical protein tyrosine phosphatases uncovers an ortholog of mammalian PTP-1B implicated in the control of egg production in mosquitoes.

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    Debora Monteiro Moretti

    Full Text Available Protein Tyrosine Phosphatases (PTPs are enzymes that catalyze phosphotyrosine dephosphorylation and modulate cell differentiation, growth and metabolism. In mammals, PTPs play a key role in the modulation of canonical pathways involved in metabolism and immunity. PTP1B is the prototype member of classical PTPs and a major target for treating human diseases, such as cancer, obesity and diabetes. These signaling enzymes are, hence, targets of a wide array of inhibitors. Anautogenous mosquitoes rely on blood meals to lay eggs and are vectors of the most prevalent human diseases. Identifying the mosquito ortholog of PTP1B and determining its involvement in egg production is, therefore, important in the search for a novel and crucial target for vector control.We conducted an analysis to identify the ortholog of mammalian PTP1B in the Aedes aegypti genome. We identified eight genes coding for classical PTPs. In silico structural and functional analyses of proteins coded by such genes revealed that four of these code for catalytically active enzymes. Among the four genes coding for active PTPs, AAEL001919 exhibits the greatest degree of homology with the mammalian PTP1B. Next, we evaluated the role of this enzyme in egg formation. Blood feeding largely affects AAEL001919 expression, especially in the fat body and ovaries. These tissues are critically involved in the synthesis and storage of vitellogenin, the major yolk protein. Including the classical PTP inhibitor sodium orthovanadate or the PTP substrate DiFMUP in the blood meal decreased vitellogenin synthesis and egg production. Similarly, silencing AAEL001919 using RNA interference (RNAi assays resulted in 30% suppression of egg production.The data reported herein implicate, for the first time, a gene that codes for a classical PTP in mosquito egg formation. These findings raise the possibility that this class of enzymes may be used as novel targets to block egg formation in mosquitoes.

  18. Orthology analysis and in vivo complementation studies to elucidate the role of DIR1 during Systemic Acquired Resistance in Arabidopsis thaliana and Cucumis sativus

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    Marisa eIsaacs

    2016-05-01

    Full Text Available AtDIR1 (Defective in Induced Resistance1 is an acidic lipid transfer protein essential for systemic acquired resistance (SAR in Arabidopsis thaliana. Upon SAR induction, DIR1 moves from locally infected to distant uninfected leaves to activate defense priming; however, a molecular function for DIR1 has not been elucidated. Bioinformatic analysis and in silico homology modeling identified putative AtDIR1 orthologs in crop species, revealing conserved protein motifs within and outside of DIR1’s central hydrophobic cavity. In vitro assays to compare the capacity of recombinant AtDIR1 and targeted AtDIR1-variant proteins to bind the lipophilic probe TNS (6,P-toluidinylnaphthalene-2-sulfonate provided evidence that conserved leucine 43 and aspartic acid 39 contribute to the size of the DIR1 hydrophobic cavity and possibly hydrophobic ligand binding. An Arabidopsis-cucumber SAR model was developed to investigate the conservation of DIR1 function in cucumber (Cucumis sativus, and we demonstrated that phloem exudates from SAR-induced cucumber rescued the SAR defect in the Arabidopsis dir1-1 mutant. Additionally, an AtDIR1 antibody detected a protein of the same size as AtDIR1 in SAR-induced cucumber phloem exudates, providing evidence that DIR1 function during SAR is conserved in Arabidopsis and cucumber. In vitro TNS displacement assays demonstrated that recombinant AtDIR1 did not bind the SAR signals azelaic acid, glycerol-3-phosphate or pipecolic acid. However, recombinant CsDIR1 and CsDIR2 interacted weakly with azelaic acid and pipecolic acid. Bioinformatic and functional analyses using the Arabidopsis-cucumber SAR model provide evidence that DIR1 orthologs exist in tobacco, tomato, cucumber and soybean, and that DIR1-mediated SAR signaling is conserved in Arabidopsis and cucumber.

  19. Deciphering the onychophoran 'segmentation gene cascade': Gene expression reveals limited involvement of pair rule gene orthologs in segmentation, but a highly conserved segment polarity gene network.

    Science.gov (United States)

    Janssen, Ralf; Budd, Graham E

    2013-10-01

    The hallmark of the arthropods is their segmented body, although origin of segmentation, however, is unresolved. In order to shed light on the origin of segmentation we investigated orthologs of pair rule genes (PRGs) and segment polarity genes (SPGs) in a member of the closest related sister-group to the arthropods, the onychophorans. Our gene expression data analysis suggests that most of the onychophoran PRGs do not play a role in segmentation. One possible exception is the even-skipped (eve) gene that is expressed in the posterior end of the onychophoran where new segments are likely patterned, and is also expressed in segmentation-gene typical transverse stripes in at least a number of newly formed segments. Other onychophoran PRGs such as runt (run), hairy/Hes (h/Hes) and odd-skipped (odd) do not appear to have a function in segmentation at all. Onychophoran PRGs that act low in the segmentation gene cascade in insects, however, are potentially involved in segment-patterning. Most obvious is that from the expression of the pairberry (pby) gene ortholog that is expressed in a typical SPG-pattern. Since this result suggested possible conservation of the SPG-network we further investigated SPGs (and associated factors) such as Notum in the onychophoran. We find that the expression patterns of SPGs in arthropods and the onychophoran are highly conserved, suggesting a conserved SPG-network in these two clades, and indeed also in an annelid. This may suggest that the common ancestor of lophotrochozoans and ecdysozoans was already segmented utilising the same SPG-network, or that the SPG-network was recruited independently in annelids and onychophorans/arthropods. © 2013 Elsevier Inc. All rights reserved.

  20. Different Principles of ADP-Ribose-Mediated Activation and Opposite Roles of the NUDT9 Homology Domain in the TRPM2 Orthologs of Man and Sea Anemone

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    Frank Kühn

    2017-10-01

    Full Text Available A decisive element in the human cation channel TRPM2 is a region in its cytosolic C-terminus named NUDT9H because of its homology to the NUDT9 enzyme, a pyrophosphatase degrading ADP-ribose (ADPR. In hTRPM2, however, the NUDT9H domain has lost its enzymatic activity but serves as a binding domain for ADPR. As consequence of binding, gating of the channel is initiated. Since ADPR is produced after oxidative DNA damage, hTRPM2 mediates Ca2+ influx in response to oxidative stress which may lead to cell death. In the genome of the sea anemone Nematostella vectensis (nv, a preferred model organism for the evolution of key bilaterian features, a TRPM2 ortholog has been identified that contains a NUDT9H domain as well. Heterologous expression of nvTRPM2 in HEK-293 cells reveals a cation channel with many close similarities to the human counterpart. Most notably, nvTRPM2 is activated by ADPR, and Ca2+ is a co-agonist. However, the intramolecular mechanisms of ADPR gating as well as the role of NUDT9H are strikingly different in the two species. Whereas already subtle changes of NUDT9H abolish ADPR gating in hTRPM2, the region can be completely removed from nvTRPM2 without loss of responses to ADPR. An alternative ADPR binding site seems to be present but has not yet been characterized. The ADP-ribose pyrophosphatase (ADPRase function of nvNUDT9H has been preserved but can be abolished by numerous genetic manipulations. All these manipulations create channels that are sensitive to hydrogen peroxide which fails to induce channel activity in wild-type nvTRPM2. Therefore, the function of NUDT9H in nvTRPM2 is the degradation of ADPR, thereby reducing agonist concentration in the presence of oxidative stress. Thus, the two TRPM2 orthologs have evolved divergently but nevertheless gained analogous functional properties, i.e., gating by ADPR with Ca2+ as co-factor. Opposite roles are played by the respective NUDT9H domains, either binding of ADPR and mediating

  1. Transcriptional activity and nuclear localization of Cabut, the Drosophila ortholog of vertebrate TGF-β-inducible early-response gene (TIEG proteins.

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    Yaiza Belacortu

    Full Text Available BACKGROUND: Cabut (Cbt is a C(2H(2-class zinc finger transcription factor involved in embryonic dorsal closure, epithelial regeneration and other developmental processes in Drosophila melanogaster. Cbt orthologs have been identified in other Drosophila species and insects as well as in vertebrates. Indeed, Cbt is the Drosophila ortholog of the group of vertebrate proteins encoded by the TGF-ß-inducible early-response genes (TIEGs, which belong to Sp1-like/Krüppel-like family of transcription factors. Several functional domains involved in transcriptional control and subcellular localization have been identified in the vertebrate TIEGs. However, little is known of whether these domains and functions are also conserved in the Cbt protein. METHODOLOGY/PRINCIPAL FINDINGS: To determine the transcriptional regulatory activity of the Drosophila Cbt protein, we performed Gal4-based luciferase assays in S2 cells and showed that Cbt is a transcriptional repressor and able to regulate its own expression. Truncated forms of Cbt were then generated to identify its functional domains. This analysis revealed a sequence similar to the mSin3A-interacting repressor domain found in vertebrate TIEGs, although located in a different part of the Cbt protein. Using β-Galactosidase and eGFP fusion proteins, we also showed that Cbt contains the bipartite nuclear localization signal (NLS previously identified in TIEG proteins, although it is non-functional in insect cells. Instead, a monopartite NLS, located at the amino terminus of the protein and conserved across insects, is functional in Drosophila S2 and Spodoptera exigua Sec301 cells. Last but not least, genetic interaction and immunohistochemical assays suggested that Cbt nuclear import is mediated by Importin-α2. CONCLUSIONS/SIGNIFICANCE: Our results constitute the first characterization of the molecular mechanisms of Cbt-mediated transcriptional control as well as of Cbt nuclear import, and demonstrate the

  2. Comparative Genomics of Glossina palpalis gambiensis and G. morsitans morsitans to Reveal Gene Orthologs Involved in Infection by Trypanosoma brucei gambiense.

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    Hamidou Soumana, Illiassou; Tchicaya, Bernadette; Rialle, Stéphanie; Parrinello, Hugues; Geiger, Anne

    2017-01-01

    Blood-feeding Glossina palpalis gambiense (Gpg) fly transmits the single-celled eukaryotic parasite Trypanosoma brucei gambiense (Tbg), the second Glossina fly African trypanosome pair being Glossina morsitans / T .brucei rhodesiense. Whatever the T. brucei subspecies, whereas the onset of their developmental program in the zoo-anthropophilic blood feeding flies does unfold in the fly midgut, its completion is taking place in the fly salivary gland where does emerge a low size metacyclic trypomastigote population displaying features that account for its establishment in mammals-human individuals included. Considering that the two Glossina - T. brucei pairs introduced above share similarity with respect to the developmental program of this African parasite, we were curious to map on the Glossina morsitans morsitans (Gmm), the Differentially Expressed Genes (DEGs) we listed in a previous study. Briefly, using the gut samples collected at days 3, 10, and 20 from Gpg that were fed or not at day 0 on Tbg-hosting mice, these DGE lists were obtained from RNA seq-based approaches. Here, post the mapping on the quality controlled DEGs on the Gmm genome, the identified ortholog genes were further annotated, the resulting datasets being compared. Around 50% of the Gpg DEGs were shown to have orthologs in the Gmm genome. Under one of the three Glossina midgut sampling conditions, the number of DEGs was even higher when mapping on the Gmm genome than initially recorded. Many Gmm genes annotated as "Hypothetical" were mapped and annotated on many distinct databases allowing some of them to be properly identified. We identify Glossina fly candidate genes encoding (a) a broad panel of proteases as well as (b) chitin-binding proteins, (c) antimicrobial peptide production-Pro3 protein, transferrin, mucin, atttacin, cecropin, etc-to further select in functional studies, the objectives being to probe and validated fly genome manipulation that prevents the onset of the developmental

  3. Tomato Cutin Deficient 1 (CD1) and putative orthologs comprise an ancient family of cutin synthase-like (CUS) proteins that are conserved among land plants.

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    Yeats, Trevor H; Huang, Wenlin; Chatterjee, Subhasish; Viart, Hélène M-F; Clausen, Mads H; Stark, Ruth E; Rose, Jocelyn K C

    2014-03-01

    The aerial epidermis of all land plants is covered with a hydrophobic cuticle that provides essential protection from desiccation, and so its evolution is believed to have been prerequisite for terrestrial colonization. A major structural component of apparently all plant cuticles is cutin, a polyester of hydroxy fatty acids; however, despite its ubiquity, the details of cutin polymeric structure and the mechanisms of its formation and remodeling are not well understood. We recently reported that cutin polymerization in tomato (Solanum lycopersicum) fruit occurs via transesterification of hydroxyacylglycerol precursors, catalyzed by the GDSL-motif lipase/hydrolase family protein (GDSL) Cutin Deficient 1 (CD1). Here, we present additional biochemical characterization of CD1 and putative orthologs from Arabidopsis thaliana and the moss Physcomitrella patens, which represent a distinct clade of cutin synthases within the large GDSL superfamily. We demonstrate that members of this ancient and conserved family of cutin synthase-like (CUS) proteins act as polyester synthases with negligible hydrolytic activity. Moreover, solution-state NMR analysis indicates that CD1 catalyzes the formation of primarily linear cutin oligomeric products in vitro. These results reveal a conserved mechanism of cutin polyester synthesis in land plants, and suggest that elaborations of the linear polymer, such as branching or cross-linking, may require additional, as yet unknown, factors. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  4. 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.

  5. X-ray crystallographic studies of the extracellular domain of the first plant ATP receptor, DORN1, and the orthologous protein from Camelina sativa

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    Li, Zhijie; Chakraborty, Sayan; Xu, Guozhou (NCSU)

    2016-10-26

    Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses inArabidopsis thaliana. In order to understand DORN1-mediated ATP sensing and signal transduction, crystallization and preliminary X-ray studies were conducted on the extracellular domain of DORN1 (atDORN1-ECD) and that of an orthologous protein,Camelina sativalectin receptor kinase I.9 (csLecRK-I.9-ECD or csI.9-ECD). A variety of deglycosylation strategies were employed to optimize the glycosylated recombinant atDORN1-ECD for crystallization. In addition, the glycosylated csI.9-ECD protein was crystallized at 291 K. X-ray diffraction data were collected at 4.6 Å resolution from a single crystal. The crystal belonged to space groupC222 orC2221, with unit-cell parametersa= 94.7,b= 191.5,c= 302.8 Å. These preliminary studies have laid the foundation for structural determination of the DORN1 and I.9 receptor proteins, which will lead to a better understanding of the perception and function of extracellular ATP in plants.

  6. A novel DFNA36 mutation in TMC1 orthologous to the Beethoven (Bth) mouse associated with autosomal dominant hearing loss in a Chinese family.

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    Zhao, Yali; Wang, Dayong; Zong, Liang; Zhao, Feifan; Guan, Liping; Zhang, Peng; Shi, Wei; Lan, Lan; Wang, Hongyang; Li, Qian; Han, Bing; Yang, Ling; Jin, Xin; Wang, Jian; Wang, Jun; Wang, Qiuju

    2014-01-01

    Mutations in the transmembrane channel-like gene 1 (TMC1) can cause both DFNA36 and DFNB7/11 hearing loss. More than thirty DFNB7/11 mutations have been reported, but only three DFNA36 mutations were reported previously. In this study, we found a large Chinese family with 222 family members showing post-lingual, progressive sensorineural hearing loss which were consistent with DFNA36 hearing loss. Auditory brainstem response (ABR) test of the youngest patient showed a special result with nearly normal threshold but prolonged latency, decreased amplitude, and the abnormal waveform morphology. Exome sequencing of the proband found four candidate variants in known hearing loss genes. Sanger sequencing in all family members found a novel variant c.1253T>A (p.M418K) in TMC1 at DFNA36 that co-segregated with the phenotype. This mutation in TMC1 is orthologous to the mutation found in the hearing loss mouse model named Bth ten years ago. In another 51 Chinese autosomal dominant hearing loss families, we screened the segments containing the dominant mutations of TMC1 and no functional variants were found. TMC1 is expressed in the hair cells in inner ear. Given the already known roles of TMC1 in the mechanotransduction in the cochlea and its expression in inner ear, our results may provide an interesting perspective into its function in inner ear.

  7. The COP1 Ortholog PPS Regulates the Juvenile–Adult and Vegetative–Reproductive Phase Changes in Rice[C][W

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    Tanaka, Nobuhiro; Itoh, Hironori; Sentoku, Naoki; Kojima, Mikiko; Sakakibara, Hitoshi; Izawa, Takeshi; Itoh, Jun-Ichi; Nagato, Yasuo

    2011-01-01

    Because plant reproductive development occurs only in adult plants, the juvenile-to-adult phase change is an indispensable part of the plant life cycle. We identified two allelic mutants, peter pan syndrome-1 (pps-1) and pps-2, that prolong the juvenile phase in rice (Oryza sativa) and showed that rice PPS is an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC1. The pps-1 mutant exhibits delayed expression of miR156 and miR172 and the suppression of GA biosynthetic genes, reducing the GA3 content in this mutant. In spite of its prolonged juvenile phase, the pps-1 mutant flowers early, and this is associated with derepression of RAP1B expression in pps-1 plants independently of the Hd1-Hd3a/RFT1 photoperiodic pathway. PPS is strongly expressed in the fourth and fifth leaves, suggesting that it regulates the onset of the adult phase downstream of MORI1 and upstream of miR156 and miR172. Its ability to regulate the vegetative phase change and the time of flowering suggests that rice PPS acquired novel functions during the evolution of rice/monocots. PMID:21705640

  8. Monoclonal Antibodies 13A4 and AC133 Do Not Recognize the Canine Ortholog of Mouse and Human Stem Cell Antigen Prominin-1 (CD133.

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    Kristina Thamm

    Full Text Available The pentaspan membrane glycoprotein prominin-1 (CD133 is widely used in medicine as a cell surface marker of stem and cancer stem cells. It has opened new avenues in stem cell-based regenerative therapy and oncology. This molecule is largely used with human samples or the mouse model, and consequently most biological tools including antibodies are directed against human and murine prominin-1. Although the general structure of prominin-1 including its membrane topology is conserved throughout the animal kingdom, its primary sequence is poorly conserved. Thus, it is unclear if anti-human and -mouse prominin-1 antibodies cross-react with their orthologs in other species, especially dog. Answering this issue is imperative in light of the growing number of studies using canine prominin-1 as an antigenic marker. Here, we address this issue by cloning the canine prominin-1 and use its overexpression as a green fluorescent protein fusion protein in Madin-Darby canine kidney cells to determine its immunoreactivity with antibodies against human or mouse prominin-1. We used immunocytochemistry, flow cytometry and immunoblotting techniques and surprisingly found no cross-species immunoreactivity. These results raise some caution in data interpretation when anti-prominin-1 antibodies are used in interspecies studies.

  9. The structure of YqeH: An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition

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    Sudhamsu, J.; Lee, G.I.; Klessig, D.F.; Crane, B.R. (Cornell); (Boyce)

    2009-03-27

    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 {angstrom} 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 but rather hydrolyzes GTP. The YqeH structure reveals a circularly permuted GTPase domain and an unusual C-terminal {beta}-domain. A small N-terminal domain, disordered in the structure, binds zinc. Structural homology among the C-terminal domain, the RNA-binding regulator TRAP, and the hypoxia factor pVHL define a recognition module for peptides and nucleic acids. TRAP residues important for RNA binding are conserved by the YqeH C-terminal domain, whose positioning is coupled to GTP hydrolysis. YqeH and AtNOA1 probably act as G-proteins that regulate nucleic acid recognition and not as nitric-oxide synthases.

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

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    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.

  11. Functional and spatial analysis of C. elegans SYG-1 and SYG-2, orthologs of the Neph/nephrin cell adhesion module directing selective synaptogenesis.

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    Nicola Wanner

    Full Text Available The assembly of specific synaptic connections represents a prime example of cellular recognition. Members of the Ig superfamily are among the most ancient proteins represented in the genomes of both mammalian and invertebrate organisms, where they constitute a trans-synaptic adhesion system. The correct connectivity patterns of the highly conserved immunoglobulin superfamily proteins nephrin and Neph1 are crucial for the assembly of functional neuronal circuits and the formation of the kidney slit diaphragm, a synapse-like structure forming the filtration barrier. Here, we utilize the nematode C. elegans model for studying the requirements of synaptic specificity mediated by nephrin-Neph proteins. In C. elegans, the nephrin/Neph1 orthologs SYG-2 and SYG-1 form intercellular contacts strictly in trans between epithelial guidepost cells and neurons specifying the localization of synapses. We demonstrate a functional conservation between mammalian nephrin and SYG-2. Expression of nephrin effectively compensated loss of syg-2 function in C. elegans and restored defective synaptic connectivity further establishing the C. elegans system as a valuable model for slit diaphragm proteins. Next, we investigated the effect of SYG-1 and SYG-2 trans homodimerization respectively. Strikingly, synapse assembly could be induced by homophilic SYG-1 but not SYG-2 binding indicating a critical role of SYG-1 intracellular signalling for morphogenetic events and pointing toward the dynamic and stochastic nature of extra- and intracellular nephrin-Neph interactions to generate reproducible patterns of synaptic connectivity.

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

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    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.

  13. 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.

  14. Identification and characterization of molluscan caveolin-1 ortholog from Haliotis discus discus: Possible involvement in embryogenesis and host defense mechanism against pathogenic stress.

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    Udayantha, H M V; Bathige, S D N K; Priyathilaka, Thanthrige Thiunuwan; Lee, Sukkyoung; Kim, Myoung-Jin; Lee, Jehee

    2018-01-01

    Caveolins are principal membrane proteins of caveolae that play a central role in signal transduction, substrate transport, and membrane trafficking in various cell types. Numerous studies have reported the crucial role of caveolin-1 (CAV1) in response to invading microbes; yet, very little is known about molluscan CAV1. In this study, we identified and characterized CAV1 ortholog from the disk abalone, Haliotis discus discus (HdCAV1). The cDNA sequence of HdCAV1 is 826 bp long and encodes a 127-amino acid polypeptide. Characteristic caveolin superfamily domain (Glu 3 - Lys 126 ) and two possible transmembrane domains (Cys 48 - Tyr 67 and Ile 103 - Phe 120 ) were identified in the HdCAV1 protein. Homology analysis revealed that HdCAV1 shared higher identity (>47%) with molluscans, but lower identity with other species. Phylogenetic tree constructed by the neighbor-joining (NJ) method revealed a distinct evolutionary pathway for molluscans. Transcriptional analysis by SYBR Green qPCR showed the highest expression of HdCAV1 mRNA in late veliger stage, as compared to that in other embryonic developmental stages of disk abalone. In adult animals, gill tissue showed highest HdCAV1 transcript levels under normal physiological condition. Stimulations with two bacteria (Vibrio parahaemolyticus and Listeria monocytogenes), viral hemorrhagic septicemia virus, and two pathogen-associated molecular patterns (LPS and poly I:C) significantly modulated the expression of HdCAV1 transcripts. Collectively, these data suggest that CAV1 plays an important role in embryogenesis and host immune defense in disk abalone. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Structural and functional characterization of a novel molluskan ortholog of TRAF and TNF receptor-associated protein from disk abalone (Haliotis discus discus).

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    Lee, Youngdeuk; Elvitigala, Don Anushka Sandaruwan; Whang, Ilson; Lee, Sukkyoung; Kim, Hyowon; Zoysa, Mahanama De; Oh, Chulhong; Kang, Do-Hyung; Lee, Jehee

    2014-09-01

    Immune signaling cascades have an indispensable role in the host defense of almost all the organisms. Tumor necrosis factor (TNF) signaling is considered as a prominent signaling pathway in vertebrate as well as invertebrate species. Within the signaling cascade, TNF receptor-associated factor (TRAF) and TNF receptor-associated protein (TTRAP) has been shown to have a crucial role in the modulation of immune signaling in animals. Here, we attempted to characterize a novel molluskan ortholog of TTRAP (AbTTRAP) from disk abalone (Haliotis discus discus) and analyzed its expression levels under pathogenic stress. The complete coding sequence of AbTTRAP consisted of 1071 nucleotides, coding for a 357 amino acid peptide, with a predicted molecular mass of 40 kDa. According to our in-silico analysis, AbTTRAP resembled the typical TTRAP domain architecture, including a 5'-tyrosyl DNA phosphodiesterase domain. Moreover, phylogenetic analysis revealed its common ancestral invertebrate origin, where AbTTRAP was clustered with molluskan counterparts. Quantitative real time PCR showed universally distributed expression of AbTTRAP in selected tissues of abalone, from which more prominent expression was detected in hemocytes. Upon stimulation with two pathogen-derived mitogens, lipopolysaccharide (LPS) and polyinosinic:polycytidylic acid (poly I:C), transcript levels of AbTTRAP in hemocytes and gill tissues were differentially modulated with time. In addition, the recombinant protein of AbTTRAP exhibited prominent endonuclease activity against abalone genomic DNA, which was enhanced by the presence of Mg(2+) in the medium. Collectively, these results reinforce the existence of the TNF signaling cascade in mollusks like disk abalone, further implicating the putative regulatory behavior of TTRAP in invertebrate host pathology. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. 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

  17. Endo-(1,4)-β-glucanase gene families in the grasses: temporal and spatial co-transcription of orthologous genes.

    Science.gov (United States)

    Buchanan, Margaret; Burton, Rachel A; Dhugga, Kanwarpal S; Rafalski, Antoni J; Tingey, Scott V; Shirley, Neil J; Fincher, Geoffrey B

    2012-12-11

    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. 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. The identification of these groups of genes will now allow us to test hypotheses regarding their functions and joint participation in wall synthesis, re-modelling and degradation, together with their potential

  18. The Role of the RACK1 Ortholog Cpc2p in Modulating Pheromone-Induced Cell Cycle Arrest in Fission Yeast

    Science.gov (United States)

    Mos, Magdalena; Esparza-Franco, Manuel A.; Godfrey, Emma L.; Richardson, Kathryn; Davey, John; Ladds, Graham

    2013-01-01

    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. PMID:23843946

  19. SUCROSE NONFERMENTING1-RELATED PROTEIN KINASE2.6, an Ortholog of OPEN STOMATA1, Is a Negative Regulator of Strawberry Fruit Development and Ripening1[OPEN

    Science.gov (United States)

    Dang, Ruihong; Li, Jinxi; Jiang, Jinzhu; Zhang, Ning; Jia, Meiru; Wei, Lingzhi; Li, Ziqiang; Li, Bingbing; Jia, Wensuo

    2015-01-01

    Whereas the regulatory mechanisms that direct fruit ripening have been studied extensively, little is known about the signaling mechanisms underlying this process, especially for nonclimacteric fruits. In this study, we demonstrated that a SUCROSE NONFERMENTING1-RELATED PROTEIN KINASE2, designated as FaSnRK2.6, is a negative regulator of fruit development and ripening in the nonclimacteric fruit strawberry (Fragaria × ananassa) and can also mediate temperature-modulated strawberry fruit ripening. FaSnRK2.6 was identified as an ortholog of OPEN STOMATA1. Levels of FaSnRK2.6 transcript rapidly decreased during strawberry fruit development and ripening. FaSnRK2.6 was found to be capable of physically interacting with strawberry ABSCISIC ACID INSENSITIVE1, a negative regulator in strawberry fruit ripening. RNA interference-induced silencing of FaSnRK2.6 significantly promoted fruit ripening. By contrast, overexpression of FaSnRK2.6 arrested fruit ripening. Strawberry fruit ripening is highly sensitive to temperature, with high temperatures promoting ripening and low temperatures delaying it. As the temperature increased, the level of FaSnRK2.6 expression declined. Furthermore, manipulating the level of FaSnRK2.6 expression altered the expression of a variety of temperature-responsive genes. Taken together, this study demonstrates that FaSnRK2.6 is a negative regulator of strawberry fruit development and ripening and, furthermore, that FaSnRK2.6 mediates temperature-modulated strawberry fruit ripening. PMID:25609556

  20. An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: application to neuroserpin reveals regions that differentially regulate inhibitory activity.

    Science.gov (United States)

    Lee, Tet Woo; Yang, Annie Shu-Ping; Brittain, Thomas; Birch, Nigel P

    2015-01-01

    The analysis of sequence conservation is commonly used to predict functionally important sites in proteins. We have developed an approach that first identifies highly conserved sites in a set of orthologous sequences using a weighted substitution-matrix-based conservation score and then filters these conserved sites based on the pattern of conservation present in a wider alignment of sequences from the same family and structural information to identify surface-exposed sites. This allows us to detect specific functional sites in the target protein and exclude regions that are likely to be generally important for the structure or function of the wider protein family. We applied our method to two members of the serpin family of serine protease inhibitors. We first confirmed that our method successfully detected the known heparin binding site in antithrombin while excluding residues known to be generally important in the serpin family. We next applied our sequence analysis approach to neuroserpin and used our results to guide site-directed polyalanine mutagenesis experiments. The majority of the mutant neuroserpin proteins were found to fold correctly and could still form inhibitory complexes with tissue plasminogen activator (tPA). Kinetic analysis of tPA inhibition, however, revealed altered inhibitory kinetics in several of the mutant proteins, with some mutants showing decreased association with tPA and others showing more rapid dissociation of the covalent complex. Altogether, these results confirm that our sequence analysis approach is a useful tool that can be used to guide mutagenesis experiments for the detection of specific functional sites in proteins. © 2014 Wiley Periodicals, Inc.

  1. Kudoa dianae sp. n. (Myxosporea: Multivalvulida) a new parasite of bullseye puffer, Sphoeroides annulatus (Tetraodontiformes: Tetraodontidae)

    Czech Academy of Sciences Publication Activity Database

    Dyková, Iva; Fajer, E. J.; Fiala, Ivan

    2002-01-01

    Roč. 49, č. 1 (2002), s. 17-23 ISSN 0015-5683 Grant - others: CONACyT (MX) 36621 Institutional research plan: CEZ:AV0Z6022909 Keywords : Myxosporea * Multivalvulida * taxonomy Subject RIV: EA - Cell Biology Impact factor: 0.515, year: 2002

  2. 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

  3. A Homology Model Reveals Novel Structural Features and an Immunodominant Surface Loop/Opsonic Target in the Treponema pallidum BamA Ortholog TP_0326.

    Science.gov (United States)

    Luthra, Amit; Anand, Arvind; Hawley, Kelly L; LeDoyt, Morgan; La Vake, Carson J; Caimano, Melissa J; Cruz, Adriana R; Salazar, Juan C; Radolf, Justin D

    2015-06-01

    We recently demonstrated that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses characteristic BamA bipartite topology. Herein, we used immunofluorescence analysis (IFA) to show that only the β-barrel domain of TP_0326 contains surface-exposed epitopes in intact T. pallidum. Using the solved structure of Neisseria gonorrhoeae BamA, we generated a homology model of full-length TP_0326. Although the model predicts a typical BamA fold, the β-barrel harbors features not described in other BamAs. Structural modeling predicted that a dome comprised of three large extracellular loops, loop 4 (L4), L6, and L7, covers the barrel's extracellular opening. L4, the dome's major surface-accessible loop, contains mainly charged residues, while L7 is largely neutral and contains a polyserine tract in a two-tiered conformation. L6 projects into the β-barrel but lacks the VRGF/Y motif that anchors L6 within other BamAs. IFA and opsonophagocytosis assay revealed that L4 is surface exposed and an opsonic target. Consistent with B cell epitope predictions, immunoblotting and enzyme-linked immunosorbent assay (ELISA) confirmed that L4 is an immunodominant loop in T. pallidum-infected rabbits and humans with secondary syphilis. Antibody capture experiments using Escherichia coli expressing OM-localized TP_0326 as a T. pallidum surrogate further established the surface accessibility of L4. Lastly, we found that a naturally occurring substitution (Leu(593) → Gln(593)) in the L4 sequences of T. pallidum strains affects antibody binding in sera from syphilitic patients. Ours is the first study to employ a "structure-to-pathogenesis" approach to map the surface topology of a T. pallidum OMP within the context of syphilitic infection. Previously, we reported that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses the bipartite topology characteristic of a BamA ortholog. Using a homology

  4. 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

  5. TaFlo2-A1, an ortholog of rice Flo2, is associated with thousand grain weight in bread wheat (Triticum aestivum L.).

    Science.gov (United States)

    Sajjad, Muhammad; Ma, Xiaoling; Habibullah Khan, Sultan; Shoaib, Muhammad; Song, Yanhong; Yang, Wenlong; Zhang, Aimin; Liu, Dongcheng

    2017-10-16

    The Flo2 gene is a member of a conserved gene family in plants. This gene has been found to be related to thousand grain weight (TGW) in rice. Its orthologs in hexaploid wheat were cloned, and the haplotype variation in TaFlo2-A1 was tested for association with TGW. The cloned sequences of TaFlo2-A1, TaFlo2-B1 and TaFlo2-D1 contained 23, 23 and 24 exons, respectively. The deduced proteins of TaFlo2-A1 (1734 aa), TaFlo2-B1 (1698 aa) and TaFlo2-D1 (1682 aa) were highly similar (>94%) and exhibited >77% similarity with the rice FLO2 protein. Like the rice FLO2 protein, four tetratricopeptide repeat (TPR) motifs were observed in the deduced TaFLO2 protein. An 8-bp InDel (-10 to -17 bp) in the promoter region and five SNPs in first intron of TaFlo2-A1 together formed two haplotypes, TaFlo2-A1a and TaFlo2-A1b, in bread wheat. TaFlo2 was located on homeologous group 2 chromosomes. TaFlo2-A1 was inferred to be located on deletion bin '2AL1-0.85-1.00'. The TaFlo2-A1 haplotypes were characterized in the Chinese Micro Core Collection (MCC) and Pakistani wheat collection using the molecular marker TaFlo2-Indel8. TaFlo2-A1 was found to be associated with TGW but not with grain number per spike (GpS) in both the MCC and Pakistani wheat collections. The frequency of TaFlo2-A1b (positive haplotype) was low in commercial wheat cultivars; thus this haplotype can be selected to improve grain weight without negatively affecting GpS. The expression level of TaFlo2-A1 in developing grains at 5 DAF (days after flowering) was positively correlated with TGW in cultivars carrying the positive haplotype. This study will likely lead to additional investigations to understand the regulatory mechanism of the Flo2 gene in hexaploid wheat. Furthermore, the newly developed molecular marker 'TaFlo2-InDel8' could be incorporated into the kit of wheat breeders for use in marker-assisted selection.

  6. Bridge-Induced Translocation between NUP145 and TOP2 Yeast Genes Models the Genetic Fusion between the Human Orthologs Associated With Acute Myeloid Leukemia

    Directory of Open Access Journals (Sweden)

    Valentina Tosato

    2017-09-01

    Full Text Available In mammalian organisms liquid tumors such as acute myeloid leukemia (AML are related to spontaneous chromosomal translocations ensuing in gene fusions. We previously developed a system named bridge-induced translocation (BIT that allows linking together two different chromosomes exploiting the strong endogenous homologous recombination system of the yeast Saccharomyces cerevisiae. The BIT system generates a heterogeneous population of cells with different aneuploidies and severe aberrant phenotypes reminiscent of a cancerogenic transformation. In this work, thanks to a complex pop-out methodology of the marker used for the selection of translocants, we succeeded by BIT technology to precisely reproduce in yeast the peculiar chromosome translocation that has been associated with AML, characterized by the fusion between the human genes NUP98 and TOP2B. To shed light on the origin of the DNA fragility within NUP98, an extensive analysis of the curvature, bending, thermostability, and B-Z transition aptitude of the breakpoint region of NUP98 and of its yeast ortholog NUP145 has been performed. On this basis, a DNA cassette carrying homologous tails to the two genes was amplified by PCR and allowed the targeted fusion between NUP145 and TOP2, leading to reproduce the chimeric transcript in a diploid strain of S. cerevisiae. The resulting translocated yeast obtained through BIT appears characterized by abnormal spherical bodies of nearly 500 nm of diameter, absence of external membrane and defined cytoplasmic localization. Since Nup98 is a well-known regulator of the post-transcriptional modification of P53 target genes, and P53 mutations are occasionally reported in AML, this translocant yeast strain can be used as a model to test the constitutive expression of human P53. Although the abnormal phenotype of the translocant yeast was never rescued by its expression, an exogenous P53 was recognized to confer increased vitality to the translocants, in

  7. Cross-species prophylactic efficacy of Sm-p80-based vaccine and intracellular localization of Sm-p80/Sm-p80 ortholog proteins during development in Schistosoma mansoni, Schistosoma japonicum, and Schistosoma haematobium.

    Science.gov (United States)

    Molehin, Adebayo J; Sennoune, Souad R; Zhang, Weidong; Rojo, Juan U; Siddiqui, Arif J; Herrera, Karlie A; Johnson, Laura; Sudduth, Justin; May, Jordan; Siddiqui, Afzal A

    2017-11-01

    Schistosomiasis remains a major global health problem. Despite large-scale schistosomiasis control efforts, clear limitations such as possible emergence of drug resistance and reinfection rates highlight the need for an effective schistosomiasis vaccine. Schistosoma mansoni large subunit of calpain (Sm-p80)-based vaccine formulations have shown remarkable efficacy in protecting against S. mansoni challenge infections in mice and baboons. In this study, we evaluated the cross-species protective efficacy of Sm-p80 vaccine against S. japonicum and S. haematobium challenge infections in rodent models. We also elucidated the expression of Sm-p80 and Sm-p80 ortholog proteins in different developmental stages of S. mansoni, S. haematobium, and S. japonicum. Immunization with Sm-p80 vaccine reduced worm burden by 46.75% against S. japonicum challenge infection in mice. DNA prime/protein boost (1 + 1 dose administered on a single day) resulted in 26.95% reduction in worm burden in S. haematobium-hamster infection/challenge model. A balanced Th1 (IFN-γ, TNF-α, IL-2, and IL-12) and Th2 (IL-4, IgG1) type of responses were observed following vaccination in both S. japonicum and S. haematobium challenge trials and these are associated with the prophylactic efficacy of Sm-p80 vaccine. Immunohistochemistry demonstrated that Sm-p80/Sm-p80 ortholog proteins are expressed in different life cycle stages of the three major human species of schistosomes studied. The data presented in this study reinforce the potential of Sm-p80-based vaccine for both hepatic/intestinal and urogenital schistosomiasis occurring in different geographical areas of the world. Differential expression of Sm-p80/Sm-p80 protein orthologs in different life cycle makes this vaccine potentially useful in targeting different levels of infection, disease, and transmission.

  8. Caenorhabditis elegans ortholog of the p24/p22 subunit, DNC-3, is essential for the formation of the dynactin complex by bridging DNC-1/p150Glued and DNC-2/dynamitin

    OpenAIRE

    Terasawa, Masahiro; Toya, Mika; Motegi, Fumio; Mana, Miyeko; Nakamura, Kuniaki; Sugimoto, Asako

    2010-01-01

    Dynactin is a multisubunit protein complex required for the activity of cytoplasmic dynein. In Caenorhabditis elegans, although 10 of the 11 dynactin subunits were identified based on the sequence similarities to their orthologs, the p24/p22 subunit has not been detected in the genome. Here, we demonstrate that DNC-3 (W10G11.20) is the functional counterpart of the p24/p22 subunit in C. elegans. RNAi phenotypes and subcellular localization of DNC-3 in early C. elegans embryos were nearly iden...

  9. TaDIR1-2, a Wheat Ortholog of Lipid Transfer Protein AtDIR1 Contributes to Negative Regulation of Wheat Resistance againstPuccinia striiformisf. sp.tritici.

    Science.gov (United States)

    Ahmed, Soyed M; Liu, Peng; Xue, Qinghe; Ji, Changan; Qi, Tuo; Guo, Jia; Guo, Jun; Kang, Zhensheng

    2017-01-01

    Very few LTPs have been shown to act through plasma membrane receptors or to be involved in the hypersensitive response (HR). DIR1, a new type of plant LTP interacts with lipids in vitro , moves to distant tissues during systemic acquired resistance (SAR) and therefore is thought to be involved in long-distance signaling during SAR. However, the exact functions of DIR1 orthologs in cereal species under biotic and abiotic stresses have not been thoroughly defined. In this study, a novel wheat ortholog of the DIR1 gene, TaDIR1-2, was isolated from Suwon11, a Chinese cultivar of wheat and functionally characterized. Phylogenetic analysis indicated that TaDIR1-2 is clustered within the nsLTP-Type II group and shows a closer relationship with DIR1 orthologs from monocots than from eudicots. TaDIR1-2 was localized in the cytoplasm and the cell membrane of wheat mesophyll protoplast. Transcription of TaDIR1-2 was detected in wheat roots, stems and leaves. TaDIR1-2 transcript was significantly induced during the compatible interaction of wheat with the stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst). Treatments with salicylic acid (SA) and low temperature significantly up-regulated the expression of TaDIR1-2. Transient overexpression of TaDIR1-2 did not induce cell death or suppress Bax-induced cell death in tobacco leaves. Knocking down the expression of TaDIR1-2 through virus-induced gene silencing increased wheat resistance to Pst accompanied by HR, increased accumulation of H 2 O 2 and SA, increased expression of TaPR1, TaPR2, TaPAL, and TaNOX, and decreased expression of two reactive oxygen species (ROS) scavenging genes TaCAT and TaSOD. Our results suggest that TaDIR1-2 acts as a negative regulator in wheat resistance to Pst by modulating ROS and/or SA-induced signaling.

  10. Characterization of the expression patterns of LEAFY/FLORICAULA and NEEDLY orthologs in female and male cones of the conifer genera Picea, Podocarpus, and Taxus: implications for current evo-devo hypotheses for gymnosperms.

    Science.gov (United States)

    Vázquez-Lobo, Alejandra; Carlsbecker, Annelie; Vergara-Silva, Francisco; Alvarez-Buylla, Elena R; Piñero, Daniel; Engström, Peter

    2007-01-01

    The identity of genes causally implicated in the development and evolutionary origin of reproductive characters in gymnosperms is largely unknown. Working within the framework of plant evolutionary developmental biology, here we have cloned, sequenced, performed phylogenetic analyses upon and tested the expression patterns of LEAFY/FLORICAULA and NEEDLY orthologs in reproductive structures from selected species of the conifer genera Picea, Podocarpus, and Taxus. Contrary to expectations based on previous assessments, expression of LFY/FLO and NLY in cones of these taxa was found to occur simultaneously in a single reproductive axis, initially overlapping but later in mutually exclusive primordia and/or groups of developing cells in both female and male structures. These observations directly affect the status of the "mostly male theory" for the origin of the angiosperm flower. On the other hand, comparative spatiotemporal patterns of the expression of these genes suggest a complex genetic regulatory network of cone development, as well as a scheme of functional divergence for LFY/FLO with respect to NLY homologs in gymnosperms, both with clear heterochronic aspects. Results presented in this study contribute to the understanding of the molecular-genetic basis of morphological evolution in conifer cones, and may aid in establishing a foundation for gymnosperm-specific, testable evo-devo hypotheses.

  11. Caenorhabditis elegans ortholog of the p24/p22 subunit, DNC-3, is essential for the formation of the dynactin complex by bridging DNC-1/p150(Glued) and DNC-2/dynamitin.

    Science.gov (United States)

    Terasawa, Masahiro; Toya, Mika; Motegi, Fumio; Mana, Miyeko; Nakamura, Kuniaki; Sugimoto, Asako

    2010-11-01

    Dynactin is a multisubunit protein complex required for the activity of cytoplasmic dynein. In Caenorhabditis elegans, although 10 of the 11 dynactin subunits were identified based on the sequence similarities to their orthologs, the p24/p22 subunit has not been detected in the genome. Here, we demonstrate that DNC-3 (W10G11.20) is the functional counterpart of the p24/p22 subunit in C. elegans. RNAi phenotypes and subcellular localization of DNC-3 in early C. elegans embryos were nearly identical to those of the known dynactin components. All other dynactin subunits were co-immunoprecipitated with DNC-3, indicating that DNC-3 is a core component of dynactin. Furthermore, the overall secondary structure of DNC-3 resembles to those of the mammalian and yeast p24/p22. We found that DNC-3 is required for the localization of the DNC-1/p150(Glued) and DNC-2/dynamitin, the two components of the projection arm of dynactin, to the nuclear envelope of meiotic nuclei in the adult gonad. Moreover, DNC-3 physically interacted with DNC-1 and DNC-2 and significantly enhanced the binding ability between DNC-1 and DNC-2 in vitro. These results suggest that DNC-3 is essential for the formation of the projection arm subcomplex of dynactin. © 2010 The Authors. Journal compilation © 2010 by the Molecular Biology Society of Japan/Blackwell Publishing Ltd.

  12. Caenorhabditis elegans ortholog of the p24/p22 subunit, DNC-3, is essential for the formation of the dynactin complex by bridging DNC-1/p150Glued and DNC-2/dynamitin

    Science.gov (United States)

    Terasawa, Masahiro; Toya, Mika; Motegi, Fumio; Mana, Miyeko; Nakamura, Kuniaki; Sugimoto, Asako

    2010-01-01

    Dynactin is a multisubunit protein complex required for the activity of cytoplasmic dynein. In Caenorhabditis elegans, although 10 of the 11 dynactin subunits were identified based on the sequence similarities to their orthologs, the p24/p22 subunit has not been detected in the genome. Here, we demonstrate that DNC-3 (W10G11.20) is the functional counterpart of the p24/p22 subunit in C. elegans. RNAi phenotypes and subcellular localization of DNC-3 in early C. elegans embryos were nearly identical to those of the known dynactin components. All other dynactin subunits were co-immunoprecipitated with DNC-3, indicating that DNC-3 is a core component of dynactin. Furthermore, the overall secondary structure of DNC-3 resembles to those of the mammalian and yeast p24/p22. We found that DNC-3 is required for the localization of the DNC-1/p150Glued and DNC-2/dynamitin, the two components of the projection arm of dynactin, to the nuclear envelope of meiotic nuclei in the adult gonad. Moreover, DNC-3 physically interacted with DNC-1 and DNC-2 and significantly enhanced the binding ability between DNC-1 and DNC-2 in vitro. These results suggest that DNC-3 is essential for the formation of the projection arm subcomplex of dynactin. PMID:20964796

  13. Functional genomics studies of Rhipicephalus (Boophilus) annulatus ticks in response to infection with the cattle protozoan parasite, Babesia bigemina

    Czech Academy of Sciences Publication Activity Database

    Antunes, S.; Galindo, R. C.; Almazán, C.; Rudenko, Natalia; Golovchenko, Maryna; Grubhoffer, Libor; Shkap, V.; do Rosário, A.; de la Fuente, J.; Domingos, A.

    2012-01-01

    Roč. 42, č. 2 (2012), s. 187-195 ISSN 0020-7519 Institutional research plan: CEZ:AV0Z60220518 Keywords : Tick * Genomics * Babesia * Rhipicephalus * Boophilus * RNA interference * Vaccine Subject RIV: EC - Immunology Impact factor: 3.637, year: 2012 http://www.sciencedirect.com/science/article/pii/S0020751912000033

  14. Kin2, the Budding Yeast Ortholog of Animal MARK/PAR-1 Kinases, Localizes to the Sites of Polarized Growth and May Regulate Septin Organization and the Cell Wall.

    Science.gov (United States)

    Yuan, Si-Min; Nie, Wen-Chao; He, Fei; Jia, Zhi-Wen; Gao, Xiang-Dong

    2016-01-01

    MARK/PAR-1 protein kinases play important roles in cell polarization in animals. Kin1 and Kin2 are a pair of MARK/PAR-1 orthologs in the budding yeast Saccharomyces cerevisiae. They participate in the regulation of secretion and ER stress response. However, neither the subcellular localization of these two kinases nor whether they may have other cellular functions is clear. Here, we show that Kin2 localizes to the sites of polarized growth in addition to localization on the plasma membrane. The localization to polarity sites is mediated by two targeting domains-TD1 and TD2. TD1 locates in the N-terminal region that spans the protein kinase domain whereas TD2 locates in the C-terminal end that covers the KA1 domain. We also show that an excess of Kin2 activity impaired growth, septin organization, and chitin deposition in the cell wall. Both TD1 and TD2 contribute to this function. Moreover, we find that the C-terminal region of Kin2 interacts with Cdc11, a septin subunit, and Pea2, a component of the polarisome that is known to play a role in septin organization. These findings suggest that Kin2 may play a role in the regulation of the septin cytoskeleton and the cell wall. Finally, we show that the C-terminal region of Kin2 interacts with Rho3, a Rho GTPase, whereas the N-terminal region of Kin2 interacts with Bmh1, a 14-3-3 protein. We speculate that Kin2 may be regulated by Bmh1, Rho3, or Pea2 in vivo. Our study provides new insight in the localization, function, and regulation of Kin2.

  15. AtHIPM, an ortholog of the apple HrpN-interacting protein, is a negative regulator of plant growth and mediates the growth-enhancing effect of HrpN in Arabidopsis.

    Science.gov (United States)

    Oh, Chang-Sik; Beer, Steven V

    2007-10-01

    HrpN (harpin) protein is critical to the virulence of the fire blight pathogen Erwinia amylovora in host plants like apple (Malus x domestica). Moreover, exogenous treatment of Arabidopsis (Arabidopsis thaliana), a nonhost plant, with partially purified HrpN enhances growth. To address the bases of the effects of HrpN in disease, we sought a HrpN-interacting protein(s) in apple, using a yeast two-hybrid assay. A single positive clone, designated HIPM (HrpN-interacting protein from Malus), was found. HIPM, a 6.5-kD protein, interacted with HrpN in yeast and in vitro. Deletion analysis showed that the N-terminal 198 of 403 amino acids of HrpN are required for interaction with HIPM. HIPM orthologs were found in Arabidopsis (AtHIPM) and rice (Oryza sativa; OsHIPM). HrpN also interacted with AtHIPM in yeast and in vitro. In silico analyses revealed that the three plant proteins contain putative signal peptides and putative transmembrane domains. We showed that both HIPM and AtHIPM have functional signal peptides, and green fluorescent protein-tagged HIPM and AtHIPM associated, in clusters, with plasma membranes. Both HIPM and AtHIPM are expressed constitutively; however, they are expressed more strongly in apple and Arabidopsis flowers than in leaves and stems. The size of AtHIPM knockout mutant plants of Arabidopsis was slightly larger than the wild-type plants. Interestingly, the knockout mutant did not exhibit enhanced plant growth in response to treatment with HrpN. Overexpression of AtHIPM conversely resulted in smaller plants. These results indicate that AtHIPM functions as a negative regulator of plant growth and mediates enhanced growth that results from treatment with HrpN.

  16. AtHIPM, an Ortholog of the Apple HrpN-Interacting Protein, Is a Negative Regulator of Plant Growth and Mediates the Growth-Enhancing Effect of HrpN in Arabidopsis1[C][OA

    Science.gov (United States)

    Oh, Chang-Sik; Beer, Steven V.

    2007-01-01

    HrpN (harpin) protein is critical to the virulence of the fire blight pathogen Erwinia amylovora in host plants like apple (Malus x domestica). Moreover, exogenous treatment of Arabidopsis (Arabidopsis thaliana), a nonhost plant, with partially purified HrpN enhances growth. To address the bases of the effects of HrpN in disease, we sought a HrpN-interacting protein(s) in apple, using a yeast two-hybrid assay. A single positive clone, designated HIPM (HrpN-interacting protein from Malus), was found. HIPM, a 6.5-kD protein, interacted with HrpN in yeast and in vitro. Deletion analysis showed that the N-terminal 198 of 403 amino acids of HrpN are required for interaction with HIPM. HIPM orthologs were found in Arabidopsis (AtHIPM) and rice (Oryza sativa; OsHIPM). HrpN also interacted with AtHIPM in yeast and in vitro. In silico analyses revealed that the three plant proteins contain putative signal peptides and putative transmembrane domains. We showed that both HIPM and AtHIPM have functional signal peptides, and green fluorescent protein-tagged HIPM and AtHIPM associated, in clusters, with plasma membranes. Both HIPM and AtHIPM are expressed constitutively; however, they are expressed more strongly in apple and Arabidopsis flowers than in leaves and stems. The size of AtHIPM knockout mutant plants of Arabidopsis was slightly larger than the wild-type plants. Interestingly, the knockout mutant did not exhibit enhanced plant growth in response to treatment with HrpN. Overexpression of AtHIPM conversely resulted in smaller plants. These results indicate that AtHIPM functions as a negative regulator of plant growth and mediates enhanced growth that results from treatment with HrpN. PMID:17704235

  17. Hd86 mRNA expression profile in Hyalomma scupense life stages, could it contribute to explain anti-tick vaccine effect discrepancy between adult and immature instars?

    Science.gov (United States)

    Ben Said, Mourad; Galaï, Yousr; Ben Ahmed, Melika; Gharbi, Mohamed; de la Fuente, José; Jedidi, Mohamed; Darghouth, Mohamed Aziz

    2013-11-15

    Bm86 midgut protein has been used in order to control ticks of the Hyalomma genus. Previous studies demonstrated the inefficacity of this antigen in the control of Hyalomma scupense, whereas recombinant Hd86 antigen, the Bm86 ortholog in H. scupense produced in Pichia pastoris, was protective against larval H. scupense tick stage infestations but ineffective in the control of the adult stage. One possible explanation for this result is the variation in Hd86 expression levels between these two developmental stages. To test this hypothesis, Hd86 mRNA levels were characterized in H. scupense developmental stages. The expression profile of Hd86 demonstrated a significant variation between tick life stages and showed a significant reduction in the number of transcripts during feeding and, particularly after molting to adults. The most interesting result was noted after molting of engorged nymphs in unfed adults where the expression levels decreased significantly by 12.78 (10.77-17.39) (pstages might explain, in part, the discrepancy of the Hd86 vaccine efficacy against these two life stages of H. scupense. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Protein (Cyanobacteria): 424263 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_723792.1 1117:25190 1150:8925 1205:2560 1206:2560 203124:2560 co-chaperonin GroES Trichodesmium erythrae...um IMS101 MAAVTLSVSTVKPLGERVFVKVSESEEKTAGGILLPDSAKEKPQVGEVVSAGPGKRNDDGTRAEMEVKVGDKVLYSKYAGTDIKLGGDEYVLLAEKDILAIVN ...

  19. Protein (Cyanobacteria): 224923 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_721080.1 1117:4265 1150:1143 1205:18 1206:18 203124:18 putative transposase, orfA Trichodesmium erythrae...um IMS101 MIYCLKTNQVLTRAELAKVLGRHESTITRWLTLYRAGGLKKLLEVKNVPGKTSKISPEILAGLQAKLSETIGFNSLGEIPKWLIEKYQVQLADKTVHKIF ...

  20. Protein (Cyanobacteria): 116376 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n Tery_2812 Trichodesmium erythraeum IMS101 MVNYNKLLNLPSSDELPDSDNKPVDHEIQVIIPNLLKQILNLLWGDRQDWFFGVNMGIYHTTGS...LGIGSEVGNHERCQREWLYWYDSQGNRLMTPEEKTLQQQQRAEQERQRAEQERQRAEQERQRAEKLEQMLRSLGIDPEQL ...

  1. Protein (Cyanobacteria): 493967532 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WP_006910818.1 NZ_DS990557 1117:3961 ... 1118:8120 1301283:24412 ... 167375:439 180281:1513 ... DNA internalizat...ion competence protein, ComEC/Rec2 family protein Cyanobium sp. PCC 7001 MLLGAVLPLG

  2. Protein (Cyanobacteria): 493967295 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WP_006910587.1 NZ_DS990557 1117:3961 ... 1118:8120 1301283:24412 ... 167375:439 180281:1345 ... DNA internalizat...ion competence protein, ComEC/Rec2 family protein Cyanobium sp. PCC 7001 MWGALVLLVL

  3. Protein (Viridiplantae): 968875 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ike Solanum tuberosum MASCIDIASDQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCTNLWSVNMAAAFQSS... 4069:2009 4070:2009 ... 424551:2009 ... 424574:2009 ... 4107:2009 ... 4113:2831 ... PREDICTED: axial regulator YABBY 5-l

  4. Protein (Cyanobacteria): 428215966 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3474 56110:3474 ... hypothetical protein Oscil6304_5715 Oscillatoria acuminata PCC 6304 MEGASIAPLQDQRYAMEGASIAPLQDQRYAMEGASIAPLQDQRFFVMQWRALIGLGYTDKASPARAHQEKLLLTTGLGIKTLFLLFSLHRQASSV

  5. Protein (Viridiplantae): 261309 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YHMFRCVARYGYKDVRKEDHGFFEQLLVESLEKFLRREAQEIALEASTTDAERDDISVVSEVPQSPACEGDLQTPLLSDQRSGDDNRMGTRDGNAPVLPSSSMSAEEDPALEYELEALREAIASGFTYLLAHGDVRARKESFFTKKFIINYFYAFLRRNCRAGTATLKVPHSNIMRVGMTYMV

  6. Protein (Viridiplantae): 531623 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VAQNGKYVICASEDSHVYVWRHDNSSHPSRSRSTVDVTNSYEHFHCHGVTVAVTWPGAEARCSFGPGSSRHSDSDGAVNSGRDLPVENTRHSSDAADIRCNESPACEGVTSRSTSRHPGDGASTSWPDEKLPSAKSSPGHCSSDLCIGAMDVQRRSAWGLVIVTAGRGGEIRVFQNFGFPVQV

  7. Protein (Cyanobacteria): 427729388 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QLLVATILSAQCTDERVNQVTPVLFSRFPDAASLGNADLAELETLVRSTGFYRNKAKNIQAACRMIVSEFDSVVPNTMEQLLKLPGVARKTANVVLAHAYGINAGVTVDTHVKRLSQRLGLTKYADPIHIEKDLMKLLPQPDWENWSIRIIYHGRAVCKARSPACEACELADLCPTAVGAGE

  8. Protein (Cyanobacteria): 428771350 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007163140.1 NC_019776 1117:6802 ... 1118:3108 1301283:18843 ... 102234:1346 379064:2146 755178:2146 ... Salicy...late 1-monooxygenase Cyanobacterium aponinum PCC 10605 MEKEIIIIGGGIGGLTLARALQLKRIDF

  9. Protein (Viridiplantae): 323064 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KSRSRSMSPKRAMSKSMSISPRRSPSRSPSLSPRRSLSRGQGVSRSPPRCPERSVSRSRSPVRSRSRSPARSVSRSPLRGRKSTSFSRSPVRAHSRKSISRS...PVRSRSRRSLSRSPPRSTRKSISRSPVRLSKRSISRSPARSSRRSISRSPVRSPRRSVSRSPVRSSRRSISRSSGRAPPRRSISRSP...RIDRERYSSYRRYSPRRYRSPPRGRTPPRYRGRRSRTRSPSISRSPRYRNRHYSRSHSHSPSRSRTPIRSRSPVDVSRSHSSPKAGRRRSPSQSRSQSESRSSLDSQSPKQASKAGSRSRSRSSSGSPDGKKGLVSYDDGSPDSGR ...LREPSKNYRRSYSRSPARAPPKRSISRSPLREPSRNYRRSYSRSPNPARRVRSPPSNRGRSLSRSISPDASPKRIRRGRGFSERYSYARRYRTPSPDRSSVRSYRYGG

  10. Protein (Viridiplantae): 323433 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EADVVENDGERSPKENGERRSNGVAAVDSKSDRSLERQPDIVDDHPGKSRSRSISPRRTMSKSMSISPRKTHSKSHSVSPKQSMSRSRSVSQSPPQAPLRSKSISRSP...VRNGSRSVSRSPVRNGSRSPGRSISRSPGRGRKGRSISRSPLRSGHQRGISRSPVRSNPQRSPSRSPPRRASRKSISRSPARVSRSVSRSPVRSSRQSLSRSSGRAPSRRSISRS

  11. Protein (Viridiplantae): 323063 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SLSRGQGVSRSPPRCPERSVSRSRSPVRSRSRSPARSVSRSPLRGRKSTSFSRSPVRAHSRKSISRSPVRSRSRRSLSRSPPRSTRKSISRSPVRLSKRSISRSPARSSRRSISRS...PVRSPRRSVSRSPVRSSRRSISRSSGRAPPRRSISRSPLREPSKNYRRSYSRSPARAPPKRSISRSPLREPSR...NYRRSYSRSPNPARRVRSPPSNRGRSLSRSISPDASPKRIRRGRGFSERYSYARRYRTPSPDRSSVRSYRYGGRIDRERYSSYRRYSPRRYRSPPRGRTPPRGRRSRTRSPSISRS

  12. Protein (Viridiplantae): 322964 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KRTVSRSMSISPRRSQSKSPSLSPRRNGGRSPAKGTRQMKNLTNSKRESPVSEEKGRHGRKSPTKSVSRSPARIKRGRDVSRSPSRSISRSPLGIPKRGRDISRSPSRSVSRSPLGIPKRGRDISRS...PSRSISRSPLRIPKRGISRSPSRSISRSPLGIPKRVISRSPVRGRISRSLSKSPVRSASRGSLRRGPLRRSSRRSRSRTPARASRRSLS...RSPIRLSRRSLSRSPIRLSRRSLSRSPIRSPRRSVSRSPVRLSRKSVSRSPVCSSRRSISRSPVRLSRKSVSRSPVRLSRRGISRSPVRGRRRISRS

  13. Protein (Viridiplantae): 323066 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GRRSNGIEEDAQSDRSADRQPDVVDDRPSKSRSRSMSPKRAMSKSMSISPRRSPSRSPSLSPRRSLSRGQGVSRSPPRCPERSVSRSRSPVRSRSRSPARSVSRSPLRGRKSTSFSRSPVRAHSRKSISRS...PVRSRSRRSLSRSPPRSTRKSISRSPVRLSKRSISRSPARSSRRSISRSPVRSPRRSVSRSPVRSSRRSISRSSGRAPPRRSISRS...PLREPSKNYRRSYSRSPARAPPKRSISRSPLREPSRNYRRSYSRSPNPARRVRSPPSNRGRSLSRSISPDASPKRIRRGR...GFSERYSYARRYRTPSPDRSSVRSYRYGGRIDRERYSSYRRYSPRRYRSPPRGRTPPRYRGRRSRTRSPSISRSPRYRNRHYSRSHSHSPSRSRTPIRSRSPVDVSRSHSSPKAGRRRSPSQSRSQSESRSSLDSQSPKQASKAGSRSRSRSSSGSPDGKKGLVSYDDGSPDSGR

  14. Protein (Viridiplantae): 323067 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NGIEEDAQSDRSADRQPDVVDDRPSKSRSRSMSPKRAMSKSMSISPRRSPSRSPSLSPRRSLSRGQGVSRSPPRCPERSVSRSRSPVRSRSRSPARSVSRSPLRGRKSTSFSRSPVRAHSRKSISRS...PVRSRSRRSLSRSPPRSTRKSISRSPVRLSKRSISRSPARSSRRSISRSPVRSPRRSVSRSPVRSSRRSISRSSGRAPPRRSISRSPLREPSKNYRRSYSRSPARAPPKRSISR...RYSYARRYRTPSPDRSSVRSYRYGGRIDRERYSSYRRYSPRRYRSPPRGRTPPRYRGRRSRTRSPSISRSPRYRNRHYSRSHSHSPSRSRTPIRSRSPVDVSRSHSSPKAGRRRSPSQSRSQSESRSSLDSQSPKQASKAGSRSRSRSSSGSPDGKKGLVSYDDGSPDSGR

  15. Protein (Viridiplantae): 323640 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QPDIRDGHPGKSRSQSMSPKRTTGKSISPRRSLSKSPSVSPKRSSSRSHSASRSHPHVSQRSISRSPVRSGSSRSTARSFSRSPVRAKKARSISTSPVRSRSRRSISRSPVRLPPRRSISRS...PVRSRSQSLQKSISRSPVRDSRSISRSPVRSSRRSISRSPVRSSRRSVSRSPVRSSRRSVSRSPVRSLRRSVSKSPVRSSRRSISRSPVRSSRRSISRSSGRAPSRRSISRS

  16. Protein (Viridiplantae): 323065 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RSRSPARSVSRSPLRGRKSTSFSRSPVRAHSRKSISRSPVRSRSRRSLSRSPPRSTRKSISRSPVRLSKRSISRSPARSSRRSISRSPVRSPRRSVSRSPVRSSRRSISRSSGRAPPRRSISRS...PLREPSKNYRRSYSRSPARAPPKRSISRSPLREPSRNYRRSYSRSPNPARRVRSPPSNRGRSLSR...SISPDASPKRIRRGRGFSERYSYARRYRTPSPDRSSVRSYRYGGRIDRERYSSYRRYSPRRYRSPPRGRTPPRYRGRRSRTRSPSISRSPRYRNRHYSRSHSHSPSRS

  17. Protein (Cyanobacteria): 497242523 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2:1902 ... 7-cyano-7-deazaguanine reductase Oscillatoriales cyanobacterium JSC-12 MNRPITESNMKETYGEEKYGERLIAEG... WP_009556745.1 NZ_CM001633 1117:4682 ... 1150:39727 1301283:59529 44887:1731 ... 86470

  18. Protein (Cyanobacteria): 157414062 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_001484928.1 NC_009840 1117:4682 ... 1212:1747 ... 1217:2782 1218:2782 1219:651 9306...0:1440 ... 7-cyano-7-deazaguanine reductase Prochlorococcus marinus str. MIT 9215 MSTAKLDDSTQRPLYGERIIKESKIICF

  19. Protein (Cyanobacteria): 661293060 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :535 ... 7-carboxy-7-deazaguanine synthase, partial Prochlorococcus sp. scB243_498G3 MTNFLPLVEQFHSLQGEGYHAGKSAFFVRLAGCKVGCSWCDTKNS ... WP_029986136.1 NZ_JFMQ01000246 1117:6374 ... 1212:1251 ... 1217:2126 1218:2126 1471492

  20. Protein (Cyanobacteria): 500468482 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available othetical protein Synechococcus sp. RCC307 MRLLCFAVPLAGTLSLLASSSLFAAAKAHPNHHWQNRRAALQEMPVVRDYPDGYGTAAQLPVRRASLRNVARSGQLLDPQAAQRRCNIGRLIGGLAGGGLGYAASRQDGRAWAIPLGALLGSQVGCPVAQGQGPFGGLGY

  1. Protein (Cyanobacteria): 515893735 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 379 ... hypothetical protein Synechococcus sp. PCC 7336 MITENYFEDLHFTECNIGEFSFSDKDLYVNIDSGLYIFGEHPLKGIIQPSDSCIAIFKNVIYSHRILALYSEDRKGFTGEKIVDKNIAQPSEGQNYKRFSIEGVSKNPPAWLTWDIDAASFMLETISS

  2. Protein (Cyanobacteria): 382373 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n DUF1824 Pseudanabaena sp. PCC 7367 MAEPTPEPIAAAQALLNQYVCTEPEIAALDIDQNEVRQATLLLVSFADYCNIGICADNSHQGFRALREYLLALDYEVPFVLEEIPEKNEPVYIKFNARNSTYYQERYTGAYRGVLISCLSDQHEQINGTYGHLPLALFMGES ...

  3. Protein (Cyanobacteria): 8763 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e protein Chroococcidiopsis thermalis PCC 7203 MTDNLTPQDETCKPKDDEALAVCVQALGLPQIQRHVFICADQTLPQCCSKEASLESWDYLKKRLKQLKLDKPTSD...RPSCIFRTKANCLRVCTNGPILVVYPDGVWYRQATPEVIERIIQEHLIGNQIVREYAFLVHPLPEPTSDAIADDN ...

  4. Protein (Viridiplantae): 128879 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 5:248 3803:248 ... 3814:248 ... 163722:3689 ... 3826:3689 ... 3827:3689 ... PREDICTED: uncharacterized protein LOC101515541 Cicer arietinum MNSSTI...CSLFLGLILISQSANAKGHGGGLVVTICKGATDRAACENILGSNSEISHAKSFSQL

  5. Protein (Cyanobacteria): 432519 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available mal protein L18 Prochlorococcus marinus str. MIT 9211 MATLSKKQQTQKRHKRLRRHLNGTNHRPRLAVFRSNNHIYAQVIDDEAQSTICSASTLDKDLREKLKASGGSCDASMAVGALLAQRALAKGIEQVVFDRGGNLYHGRVKALAKSAREAGLKF ...

  6. Protein (Cyanobacteria): 518305272 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 1:947 ... 50S ribosomal protein L18 Prochlorococcus sp. W2 MNTISRKQQTQKRHRRLRRFLVGTKAKPRLSVFRSNNHIYAQVIDDQAQSTICSASTIDKEFKIKDNESTSNCNSSSEVGLLLAKRAIKKGVKEVVFDRGGKIYHGRVKALADAARKAGLKF

  7. Protein (Viridiplantae): 128519 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 9:7 3650:7 ... 1003877:7 ... 3655:7 ... 3656:1095 ... PREDICTED: pectinesterase inhibitor-like Cucumis melo MANNSCLV...IVSLIGVLLFTIILNVASSNYVISTICSKSSNPPFCSSVLKSSGTTYLKGLAVYTLNLAHTNASKSLTLARSLATTTTNPQ

  8. Protein (Cyanobacteria): 74944 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available in tlr1014 Thermosynechococcus elongatus BP-1 MCSVGLLLVPALLPYSLAQTSPRTDVIAPWEITTYARVVLEIEPIRQKYYRQAQAAFQGQVPSNACFGMNPQHIPSGLEAICASYGWEAIQVLKKYNMSLEQFNAITLRAQQDSTLSRRIQAEMLRLQQP ...

  9. Protein (Cyanobacteria): 497473866 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 313612:2918 ... hypothetical protein Lyngbya sp. PCC 8106 MQSEIKHFERHPYLWKIHSAFLAADFWLINKGTKEQLGKPIREYKKGCFGMLAPKYLDPKYSYYLCEFIWQSGLWQTYSCGAITWQHLRISDVRNVFEPGSYLLTSEGNAVLIAPVKLQVSTASLA

  10. Protein (Cyanobacteria): 553734844 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hypothetical protein Lyngbya aestuarii METEYQPHFSRHEYFWKIHSAFLAADFWLISKGSREQLGRPIQEYKKRELATWRFPSRAKFAREGCFGMLTPKCLDPKYSYYLCEFIWQSGLWQTYSCGAITWQHLRINDVRNVFKPGSYFLTTEGNAILIAPVKLQAATAFMD

  11. Protein (Viridiplantae): 108100 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nagariensis YTICKHMPYAICKHMRSASICHYAICKHMPYAICKHIPYAICKHMPYAICKHMRSASICDLQAYAICKHMRSASICNLQAYAICDLQAYAICDLQA...YAICDLQAYAICDLQAYAICKHMQFASIYALQAYYASICNLQAYATCKHMPYAICKHMPYAICKHMPYAICKHMRSASIC

  12. Protein (Viridiplantae): 108113 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_60352, partial Volvox carteri f. nagariensis MRCASIC...DLQPYMICKRMRSASICDVQAYALCKHMRSASICDVQAYAICNHMRPASICALQAYGMCKRMRSTSI

  13. Protein (Viridiplantae): 108085 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available is MRCANICDLQAYAICKHMGCASICDLQPYAICNHMRSASICDLQAYAMCKHMRCASICDLQAYAICKHMRCASICDLQAYAICKHMRSASICDLQAYAMCKHMRSASICDLQAYALCKHMGCASIC...DVQAYAMCKHMRCASICDVQAYAMCKHMRSASICALQAYALCKHMRFASIWDVQAYEICKHMRCASICDLQAYALCKHMRSASIC...DVQAYAMCKHMRSASICDLQAYALCKHMGCASICDVQAYAMCKHMRCASICDVQAYAMCKHMRSASICALQAYALCKHMRFASIWDVQAYEICKHMRCASICDMQTYALCKHMRSASICDVQAYVLCKYM ...065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_71227 Volvox carteri f. nagariens

  14. Protein (Viridiplantae): 108080 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available is MQAYATCDVRSYVICKHIRSASICDLQAYAICKHMPDAICKHMLHSIICDLQAYARCDLQAYATFDVQAYAICKHMRSASICNLQAYAICKHMRSASICHIRCASICDLQAYAICKHMPDAICKRMPHSMCKHMRSASICDLQAYAICKHIPHSMCKHMRYASICDHSYAMLRYATL ...065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_58713 Volvox carteri f. nagariens

  15. Protein (Viridiplantae): 108083 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available is MRSASVCDLQAYAICKHMPDAICKHMPHSMCKHMRSASICDLQAYAICKHMRSASICDLQAYAICKHMPDAICKHMPHPMCKHMRSASICQMRSASICHIRCASIC...DLQAYATSDVQAYAICKHMPDAICKHMPHSMCKHMRSASICDLQAYAICKHMRSASICDLQAYAICKHLPDTICKHMPHSMCKHMRSASIC...DLQAYAICKHMPSASICQMRSASICHIRCASICDLQAYARCDLQAYATFDVQTYAICKHLRSASICDLQAYAICKHMPHSMCKHMRYASLCDLQAYAICKQMQSSVTLQ

  16. Protein (Viridiplantae): 108094 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_71484 Volvox carteri f. nagariensis MRSASIC...DLQAYDKCDLQAYAICKNMPYAICKHMPYAICKHMPYAICKHMHLQAYAVCKHMPYAICKHMPYAICKHMPYAICKHMPYAICKDYNLQAYAICKHMRSASIC...DLQAYAICDLQAYAICDLQAYAICDLQAYAICDLQAYAICDLQAHAICKHMPYAICKHMRSASICHMRSASICSLQAYAVCKHMQSVSICSLQTYAVCKHSNMQAYAVCKHVQSASICSLHAYAICKHMQSASICHM

  17. Protein (Viridiplantae): 788920 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KGPCEHGVKPRSRCKVCSACPHGKWRKQCKECGGASICEHGRIRSVCKECGGASICEHGRQRSQCKECGGSEICEHGRHRSKCKECGGSQICEHGRQRHRCKECGGSSICEHGRHRPQCKECGGASIC...EHGRHRYSCKECGGASICEHGRHRSKCKECGGSQICEHGRQRSRCKECGGGSICEHGRERS...LCKECGGSQICEHGRRRSRCKECGGGSICEHGRIRSQCKECGGASICEHGRQRSQCKECGGSQICEHGRRRSQCKECGGGSICEHGRIRSQCKDCRCERL

  18. Protein (Viridiplantae): 108093 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available is MPYAICKHMQYALCNHMQYAICKHMRSASICHMRPASMCNMRSASICDLQAYDKCDLQAYAICKNMPYAICKHMPYAICKHMPYAICKHMHLQAYAVCKHMPYAI...CKHMPYAICKHMPYAICKHMPYAICKDYNLQAYAICKHMRSASICDLQAYAICDLQACAICDLQAYAICKHMTNAICKHMPSARICHMRSASICHMRSASICHMRYAICDLQAYAVCKHTQSASICSL

  19. Protein (Viridiplantae): 788916 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TKGPCEHGVKPRSRCKVCSACPHGKRRSQCKECGGASICKHSRERFKCKECGGASICEHGRIRSRCKECGGGSICEHGRHRHSCKECGGASICEHGRERRYCKECGGS...GICEHGRHRSFCKECGGSQICEHGRVRSTCKECDGSQICEHGRHRHSCKECGGASICEHGRIRNTCKECGGASICEHGRERSRCKQCGGSQICEHSRVRSRCKECGGSQICEHGRQRSLCKECGGGSICEHSRVRSKCKVCRRGA

  20. Protein (Viridiplantae): 108104 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available is MRSAGICHMLAYAICKHMPYAICKHMPLCDLQAYAIMRSSSICHYAICKHMQSASICHMFAYAICKHMPYAICKHMPCAICKHMPYAICGHMRSASICHMLAYAI...CKHMPYAICKHMPLTICKHMPLCDQQAYAICKHMPYVCICDLQAYAIMRSAGICDLQAYAIMLSAGICDLQAYVICLHMRSASICHMRSASICH

  1. Protein (Viridiplantae): 108095 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_70901, partial Volvox carteri f. nagariensis MQSASIC...NLQAYAICDLQAYAICKHMPYAICKHHMPYAICKHMRSASICDLQAYAICKHMLSASICDLQAYAVCKHMRSASICCLQAYAICKHLRSASICDLQAYVICKHMRSASIC...HMRSASICDLQAYAVCKHMRSASICSLQAYAVCKHMQSASICDLQAYAICKHMRFASMC

  2. Protein (Viridiplantae): 108112 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_68908, partial Volvox carteri f. nagariensis MQYASIC...DLQAYAMCKHMQCASICALQAYGMCKHMRSASICDLQAYAMCKHMQSASVCALQAYAMCKHMRCASI

  3. Protein (Cyanobacteria): 428780101 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 13035:290 ... hypothetical protein Dacsa_1875 Dactylococcopsis salina PCC 8305 MIHTFAPKPPILGACINLPPNPQFWGLASIC...PQTPNSGGLHQFAPKPPILGACINLPPNPQFWGLASICPQTPNSGGLHQFAPKPPILGACINLPPNPQFWGLASICPQTPNSGGLHQFAPKPPILGACINLPPNPQFWGLASIC...PQTPNSGGLHQFAPKPAILGACINLPPNPQFWGLASICPQTRNSGGLHQFAPKPAILGAFINLPPNPQFWGLLSICPQTPNSGGFHQFAPKPPILGAFINLPPNPQFWGLSSICSQTPNSGGFHQFAPKPPILGAFINQFFK

  4. Protein (Viridiplantae): 108109 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nagariensis AICDMQRYVICCDMRYAICDMRPASICDLQAYAICKHMPYAICKHMLCYAMLCYAMLCYAMLCYAMLCYAMLCYAMLCYAMLCYAVLCYAVLCYAMLCYAICKHMQYASIC...DLQAYAMCKHMRSASICNVQAYTLCKHFICDVQAYALCKHMGCASVCDLQAYVICKHMRSASICIMFYVSYLHICICAILCNMRYAAICDMQ

  5. Protein (Cyanobacteria): 129990 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available in Dacsa_1875 Dactylococcopsis salina PCC 8305 MIHTFAPKPPILGACINLPPNPQFWGLASICPQTPNSGGLHQFAPKPPILGACINLPPNPQFWGLASIC...PQTPNSGGLHQFAPKPPILGACINLPPNPQFWGLASICPQTPNSGGLHQFAPKPPILGACINLPPNPQFWGLASICPQTPNSGGLHQFAPKPAILGACINLPPNPQFWGLASIC

  6. Protein (Viridiplantae): 108086 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available is MHLHYASIRSLQAYAICKHMPYAICKHMPYAICKHHMPLCDLQAYAICDLQAYAICKHMRSASICDLQAYALMRPASICDLQAYAICKHMPLCDLQAYAICKHMP...YASVCHMQAYAICKPMPLCDLQAYAICKHMRSASICHYAICKHMQFASICHMQAYAICKHIPYASICDVQAYAICDLQASA...ICKHMPLCDLRAYAICKHIRSASIRNLQTYAICKHMQCASICALQAYVICKRMRCASICDVQAYALCKHMGCASVCDLQAYVICKHMRPASICDVQAYALCKHM

  7. Protein (Viridiplantae): 108078 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available is MQACATCDVQSYVICNHIRSASICDLQAYAICKHMPGAICKHMLHSMCKHMRSASICDLQAYAICKHMPDAICKHMSHSIICDLQAYAICKHMPDAICKHMPHSMCKHMRSASIC...DLQAYAICKHIPHSIICDLQAYAICKHMPDAICKHMPHSMCKHMRSASICDLQAYAICKHIPHSMCKHMRYGSLCDHSYVLCYAMLCYAMLC ...065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_62293 Volvox carteri f. nagariens

  8. Protein (Viridiplantae): 108087 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_32364, partial Volvox carteri f. nagariensis YAICKHMRSASIC...DLQAYAICKHMRSASICDLQAYAICKHLPDTICKHMPHSMCKHMRSASICDLQAYAICKHMPSASICQMRSASICHIRCASICDLQAYARCDLQAYATFDVQTYAICKHLRSASICDLQAYAICKHMPHSMCKHMRYASLCDLQAYAIC

  9. Protein (Viridiplantae): 788917 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PCEHGVKSRSKCKVCSACPHGRKRSQCKECGGASICEHGRIRSKCKECGGASICEHGRRRSQCKECGGASICEHSRIRSKCKECGGSGICEHGRRRFSCKECGGSGICEHGRRRSDCKECGGASIC...VHGRQRSQCKECGGSQICEHGRQRSRCKECGGASICEHGRIRFSCKECGGSQICEHGRRRSRCKECGGSQICEHGRRRHQCKECGGSGICEHGRRRSECKECGGSAICEHGRRRSRCKGCRDNK

  10. Protein (Viridiplantae): 108101 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available is MRSARICDLQAYAICDLQAYAKCKHLPNASICDLQAYAICKHMRSASICDLQAYAICKHMRYAICKHMHYAHMRSASICHLQAYAICDLQAYAICDLQAYAICELQAYAICAIYAICKHMRSASIC...NMQVYAICKHMRSASRCTYAICDLQAYAICKHMRSASICDLQAYAICKHMCCILLNHNWMVASEDTDLEEFHPLK

  11. Protein (Viridiplantae): 788924 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GVKWRSNCKVCSACPHGKQRSRCKECGGSGICEHGRQRHGCKECGGGAICEHGRRRSKCKECGGASICVHARERSKCKECGGASICEHGRERSQCKECGGASICEHGR...RRPQCKECGGVGICVHGRQRHRCKECGGASFCEHGRQRSLCKECGGASICEHGRVRSQCKECGGSQICEHGRRRSKCKECGGASICEHGRVRSQCKECGGSGICEHGRRRSRCKECGGGSISAAAKA

  12. Protein (Viridiplantae): 108090 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_62437, partial Volvox carteri f. nagariensis MRSASIC...HIRCASICELQAYAICKHVRSASICDRQAYAICKHMPDTICKHMPHSMCKHMRSASICQIRPASICHIRCASICDLQAYATCKHMRAASIC...DRQAYAICKHMPDAICKHMPHSMCKHMRSASICQMRSASICHIRCASICDLQAYARCDLQAYAICKHMRSASICQIRCASICDL

  13. Protein (Viridiplantae): 108106 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_39614, partial Volvox carteri f. nagariensis ICKHMRYASIC...QMRCASICHIRCASICDLQAYAICKHMQSASICQMRSASICHIRCARICDMQAYAICKHIRSMLCCDMPYALCYATLCPYATCDVRSYVICKHIRSASICDLQAYAICKHMPDAICKHMLHSMCKHMRSASLCDLQAYTI

  14. Protein (Viridiplantae): 108079 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available is MQAYATCDVQSYVICKHIRPASIYDLQAYAICKHMPDAICKHMPHSMCKHMRSASICDLQAYAICKHMPDAICKHMPPSICDLQAYATFDVQAYAICKHMRSASICNLQAYAICKHMRSASICHIRCASI...CDLQAYAICKHMPDAICKRMPHSMCKHMRSASICDLQAYAICKHIPHSMCKHMRYASICDHSYAMLRYATL

  15. Protein (Viridiplantae): 108088 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_62449 Volvox carteri f. nagariensis MCFIYTNASYASIC...HMRCAIICDLQAYAMCNHIRSASICDVQSYAICKHMPDAICKHMPHSMCKHMRSASICDLQAYAICKHMPDAICKHMPHSICKHFFHLRSASICHIRCASIC...DLQAYAICKHMPDAICKHMPHSMCKHMRSASICDLQAYAICKHIPHSMCKHMRYGSLCDHSYVLCYAMLCYAMLC

  16. Protein (Viridiplantae): 108097 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_70912 Volvox carteri f. nagariensis MRSASIC...DLQAYVICKHIPYAICKHTPYAICKHMPYAICKHIPLCDLQAYAIMRSASICNYAIGKHMPLCDLQAYAICDLQAYTICDLQAYAICDLQAYAICKHMRSASIC...DLQAYMICKHIICDLQAYAICKHMRSASICDLQAYAICDLQAYAICKHMPYAICKHMPYAICKHMRSASICNLQAYAICDLQAYVICKHT

  17. Protein (Viridiplantae): 108099 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_70990, partial Volvox carteri f. nagariensis MRSASIC...DLQAYAICKHLGCASICDAQAYAIWKHMRSASICDLQVYALCKHIGCASVCDLQAYAIICDLQAYAICKHMRCASICALQAYAICKHMRYYMRSASIC...DLQAYATCKHMPYAICKHMPYAICKHMPYAICKHMPYAICKHMRSASICHMRSASICDLQAYAICDLQAYAMLCLLCLL

  18. Protein (Viridiplantae): 108089 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_70544 Volvox carteri f. nagariensis MRSASIC...HYTICKHMPYAICKHMRSASICHYAICKHMPYAICKHIPYAICEHMPYATCKHMRSASICDLQAYAICKHMRSHMPYAICKHMRSASICHYAICKHMP...YAICKHIPYAICEHMPYATCKHMRSASICDLQAYAICKHIRSASICDLQAYAICKHMPSVICKHMRSASICDLQAYAICDLQACAICKHMRSTSICHYAICKHMPSCHLQAYAIMRSASISHYAICKHMPSCDLQAYAIMRSASICHYAICKHMPL

  19. Protein (Viridiplantae): 108084 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:326 ... 3066:326 ... 3067:326 ... 3068:326 ... hypothetical protein VOLCADRAFT_70645, partial Volvox carteri f. nagariensis MRSASIC...HIRCASICDLQAYATSDVQAYAICKHMPDAICKHMPHSMCKHMRSASICDLQAYAICKHMRSASICDLQAYAICKHLPDTICKHMPHSMCKHMRSASIC...DLQAYAICKHMPSASICQMRSASICHIRCASICDLQAYARCDLQAYATFDVQTYAICKHLRSASICDLQAYAICKHMPHSMCKH

  20. Protein (Viridiplantae): 781136 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available g Eutrema salsugineum MSTALINTVTYYLSEHPYIVGFRWGHSQSWGSTWCFLITSISLYIAVSSSLHILLSAVL...836:5711 3699:2519 3700:2519 ... 981100:1661 ... 98005:1661 ... 72664:1661 ... hypothetical protein EUTSA_v10027253m

  1. Protein (Cyanobacteria): 428308225 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AFAQNSQTNSSITSSALKIALIIWLMIALFYVLIFAFNKMIDRDSRNISHYRSIKDSPSNSSSNIPSQSGSQSVSQPASQSVEEISVLYPSSLEFSISISKAWNLRGFDDLNDRLDEQQRTFTNQVNSLISTA...LINLTPEVADRVNILDNSLLHNIALKQLSNVLSENRCEFLKPILIAPYLSLVDETV

  2. Protein (Viridiplantae): 357130763 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VVMDCHEFKYDLHIQIGNDDTLPPSGVALARQARMIQNGVDDPLALSLGSIYSAVPSPPPAPARSIRRRLNNSAPSQQQPEPPSDGAAAAADGSAAPAAPPLPWAT...ERPARHETLEILLSHGVTTVEGEARCKRCNCKATVAYDLAAKFTEVRDYVAAHRHEFNDRAPEAWMNPALPDCAACGEKRCVS

  3. Protein (Viridiplantae): 602846 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SXETTKIFTAEELEKATNNYHESGILGEGGYGIVYKXILAABNNKVVAIKKSKICVXTQKEQFVNELLVLSQINHRNVVRLLGCCLELEVPLLVYEFVAHGTLFEHIH...LLTSKLALDSDRPGADRSLARFFVCLMEEDRLNEILDDDMLNERNIETLKTVANLAKRCVXVKGXDRPTMKEVAMELEGMRITEKHPWGKAEXCSKEXXCLLGPGNSDAYHXDVRADCGPSTGTTIGYDSMXIQFTPYDDGR

  4. Protein (Viridiplantae): 668301 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3065:2755 ... 3066:2755 ... 3067:2755 ... 3068:2755 ... hypothetical protein VOLCADRAFT_32173, partial Volvox carteri f. nagariensis TQRAMP...AMTQRAKPAMTQRAMPAMTQRAKPAMTLRAMPAMTLRAMLEMTQRAKPAMTQRAKPAMTQRAKPAMTQRAKPAMTLRAMPAMTQRAKPAMTQRAMP...AMTQRAKPAMTQRAKPAMTQRAMPAMTQRAKPAMTQRAMPAMTLRAMPAMTQRAKPAMTQRAMPAMTQRAKPAMTQRAMPAMTQRAMP...AMTQRAMPAMTLRAMPAMTQRAMPAMTLRAMPAMTQRAKPVMTLRAMPAMTQRAKPAMTQRAMPAMTLRAMPAMTQRAKPAMTQRAMPAMTQRAMPAMTQ

  5. Protein (Cyanobacteria): 647660116 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :162 ... hypothetical protein, partial Prochlorococcus sp. scB243_496A2 MRILLAAAECAPMIKVGGMGDVVGSLPPSLIKLGHDVRVIIPGYGKLWSLLEVSNEPVFRTNTMGTDFAVYEAKHPIHNYVIYLVGHPTFDSDQIYGGENEDWRFTFFASAT

  6. Protein (Viridiplantae): 409327 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 58 3688:972 ... 238069:972 ... 3689:972 ... 3694:972 ... hypothetical protein POPTR_0019s09290g, partial Populus trichocarpa RESVIDDFRAGKTWVLIATDVLGRGMDFKGVKCVINYDFPDCAASYIHRIGMFLNLWIHSYVYM

  7. Protein (Cyanobacteria): 104398 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PPKHPKITEESKSPNPESIQRQYKSSTSEPISDISLIQRLPETSDSVDVNNAIASHDSTIQRLPETSDSVDVNNAIASHDSPIQRLPETSDSSPIQRLPETSDS...VDINAIASHDSPIQRLPETSDSSPIQRLPETSDSVDVNAIASHDSPSIQRLSETSDSVEDISNAIASHDSPIQRLPETSDSSPIQRLPETSDS...VDVNAIASHDSTIQRLPETSDSSPIQRLPETSDSVDVNAIASHDSPIQRLPETSDSVDVNNAIAFHDSSIQRLPETSDSSPIQRLPETSDSVDVNAIASHDSPIQRLPETSDSSPIQRLPETSDS...VDVNAIASHDSPSIQRLSETSDSVEDISNAIASGDSTIQRLSDTSDSSPIQRLPETSDS...VDVNNAIASHDSPIQRLPETSDSGDVNNAIASHDSPIQRLSETSDSGDVNNAIASHDSPSIQRVSETSDSVEDISNAIASHDSTIQRLSETSDSVEDISNAIASHDSPIQRLPETSDS

  8. Protein (Cyanobacteria): 493719099 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SKSPNPESIQRQYKSSTSEPISDISLIQRLPETSDSVDVNNAIASHDSTIQRLPETSDSVDVNNAIASHDSPIQRLPETSDSSPIQRLPETSDS...VDINAIASHDSPIQRLPETSDSSPIQRLPETSDSVDVNAIASHDSPSIQRLSETSDSVEDISNAIASHDSPIQRLPETSDSSPIQRLPETSDSVDVNAIASHDSTIQRLPETSDS...SPIQRLPETSDSVDVNAIASHDSPIQRLPETSDSVDVNNAIAFHDSSIQRLPETSDSSPIQRLPETSDSVDVNAIASHDSPIQRLPETSDSSPIQRLPETSDS...VDVNAIASHDSPSIQRLSETSDSVEDISNAIASGDSTIQRLSDTSDSSPIQRLPETSDSVDVNNAIASHDSPIQRLPETSDS...GDVNNAIASHDSPIQRLSETSDSGDVNNAIASHDSPSIQRVSETSDSVEDISNAIASHDSTIQRLSETSDSVEDISNAIASHDSPIQRLPETSDS

  9. Protein (Cyanobacteria): 104392 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein SPLC1_S130480 Arthrospira platensis C1 MDVNAIASHDSPIQRLPETSDSSPIQRLPETSDSVDVNAIASHDSPSIQRLSETSDSVEDISNAIASHDSTIQRLPETSDS...VDVNNAIASGNSPSIQRKSDTSDSVEDISNAIASDDSTIQRLPETSDSGDVNNAIAFRDSSIQRVSETSDSSPIQRLPETSDSVGVNNAIASDDSPSIQRLSDTSDS...VEDISNAIASHDSPIQRLPDTSDSSPIQRLPETSDSVDVNNATASHDSPSIQRLSETSDSVEDI...SNAIASHDSPIQRLPETLDSSPIQRLPETSDSGDVNAIASDDSPIQRLPETSDSVGVNNAIASHDSSIQRVSETSDSVDVNAIASHDSPIQRLPETSDSSPIQRLPETSDSVDVNAIASHDSSIQRVSETSDS...VEDISNAIASHDSPIQRLPETLDSSPIQRLPETSDSVDVNAIASDDSSIQRLSETSDWGDVNAIASDDSSIQRLPETSDSGDVNNAIASHDSPIQRLPETSDS

  10. Protein (Viridiplantae): 218421 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SAKKMTPSKSAIKTDLVEMANVYMEARGIKRKLAASDSESDSDSDSDSDSGDEPAAKKAKTAPASSDSSSDSDSSSSDSDSDSGEKKEDENKEPAKPAKSESSSATSSDSDSSDSDSDSDSDS...KPPAEEEKKDEPVAAVKADSSSSSDSDSSSSDSDSDSDSGEKKEEEKAEVKKADSSDSDSSDSDSSSSDSDS...DEKEEEKKDEPKAEVKADSSSSSSSSSSSSDSDSDSDSDEKEEEKKEEKAEVKKADSSDSDSSSSDSDSDSDSDSDSGEKKEEEKAEVKKADSSSSSSSSDSDSDSDSDS...DEKEEEKKDDEPKAEVKADSSSSSSSSDSDSDSDSDSDSKPAAKTMEDKKDDSSSSDSDSDSSSSDSESEEKKEEEKAEVKADSSSSSDSDSSSSDSDSDS...DEKEEEKKDDDKMDVEDAKADSSSSSSSSSSSDSDDDSDSETEPVKMDADAAVAKPESSSSDSDSDSGSDSDSDSDSKPTAMDVDEKQEEAKAAASSDSDSSDS

  11. Protein (Cyanobacteria): 104397 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein AmaxDRAFT_1256 Arthrospira maxima CS-328 MEDISNAIASHDSPIQRLPETSDSVEDISNAIASHDSPIQRLSETSDSGDVNNAIASHDSPSIQRVSETSDS...VEDISNAIASHDSTIQRLSETSDSVEDISNAIASHDSTIQRLSETSDSVEDISNAIASHDSTIQRLSETSDSGDVNDAIDSVEDISNAIASHDSPIQRLPETSDS...GDVNNAIASHDSPIQRLSETSDSSPIQRLSETSDSGDVNNAIASDDSPIQRLPETSDSVGVNNAIASHDSPSIQRVSETSDS...VEDISNAIASHDSPIQRLPETSDSSPIQRLPETSDSVDVNAIASHDSTIQRLPETSDSGDVNNAIASDDSPIQRLSETYDSSPIQRLPETSDSVDVNVIASDDSPIQRLPETSDS...VDVNNAIASHDSPSIQRVSETSDSVEDISNAIASHDSPIQRLPETSDSSPIQRLPETSDSVDVNAITFHDSSIQRLPETSDSSPIQRLPETSVEDISNAIASHDSPIQRLSETSDS

  12. Protein (Viridiplantae): 550181 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 9:1115 3700:1115 ... 981100:441 ... 98005:441 ... 72664:441 ... hypothetical protein EUTSA_v10029206mg Eutrema salsugineum MKRKHPYPSDSDSDSDS...DSHSGSDSDSRTGSDSESDSDSNSHSHSGSDSESDSDSNSHSHSGSDSDSDSDSDSDSDSDS

  13. Protein (Cyanobacteria): 493719093 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available othetical protein Arthrospira maxima MEDISNAIASHDSPIQRLPETSDSVEDISNAIASHDSPIQRLSETSDSGDVNNAIASHDSPSIQRVSETSDSVEDISNAIASHDSTIQRLSETSDS...VEDISNAIASHDSTIQRLSETSDSVEDISNAIASHDSTIQRLSETSDSGDVNDAIDSVEDISNAIASHDSPIQRLPETSDSGDVNNAIASHDSPIQRLSETSDS...SPIQRLSETSDSGDVNNAIASDDSPIQRLPETSDSVGVNNAIASHDSPSIQRVSETSDSVEDISNAIASHDSPIQRLPETSDS...SPIQRLPETSDSVDVNAIASHDSTIQRLPETSDSGDVNNAIASDDSPIQRLSETYDSSPIQRLPETSDSVDVNVIASDDSPIQRLPETSDS...VDVNNAIASHDSPSIQRVSETSDSVEDISNAIASHDSPIQRLPETSDSSPIQRLPETSDSVDVNAITFHDSSIQRLPETSDSSPIQRLPETSVEDISNAIASHDSPIQRLSETSDS

  14. Protein (Viridiplantae): 242039983 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :5312 4558:5312 hypothetical protein SORBIDRAFT_01g026880 Sorghum bicolor MASQTTKMLALVAALLALSTIATATANCLQNIPHVMGMTVMDPCM...QSCMMQQPLAMVMMGMTAMDPCMQSCMMQQPLAMVISSPSLMMRMNSMVSCVQSCMTQQAFSIGGSSLSK

  15. Protein (Viridiplantae): 255557787 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NIGIAISNNTGISDSTQSCCKASEMMLEDLVTNKDACEGEGKSEAELRSFLRATARGSIHSFSHSIVSRSLDMSGGLDQRRDAAVFQSLFSAVLTLLVGTIIWKAEDPCMPLVVALFAVVGMSLKSVVQFFSTIKNKPASDAVALLSLNWFILGTLTYPALPKVARIIAALTLNVLDWTVS ...

  16. Protein (Viridiplantae): 694554 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nsis MQFGGLHGDFILAVAWRGFARGCDVRSLLPQAFCLNVARVRGLRSNEAATYVRRLSTVSCTAFCLNVARVRGLRSNEAATYVRRLSTVSCTAFCLNVARVRGLRSNEAATYVRRLS...TVSCTAFCLKVARVRGLRSNEAATYVRRLSTVSCTAFCLKVARVRGLRSNEAATYVRRLSTVSCTAFCLKVARVRGLRSNEAATYVRRLS...TVSCTAFCLNVARVRGLRSNEAATYVRRLSTVSCTAFCLNVARVRGLRSNEAATYVRRLSTVSCTAFCLNVARVRGLRSNEAATYVRRLSTVSCTAFCLNVARVRGLRSNEAATYVRRLSTVSCTAETGRSA

  17. Protein (Cyanobacteria): 652324638 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available thetical protein Fischerella sp. PCC 9431 MLRDLKKEVFYPYPPQRVWQVLTNRHTLAVWLMENDFEPRVGHKFRFLYSSIPGLAESIDCEVIELDEPKRLS...FTWQDSMMYRPSIVIWTLKPVDGGTQLQLEHKGLSQEPDQTRLSASLHEPMRLSQPWQGRFMHESTALTAHSTMLSPIPVGRYEALNSVILSSFLDGGWDFRLSERMPQVLVSFASNN

  18. Protein (Cyanobacteria): 479132984 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SKSTIFRSILGDYVSPKSNRFYPPKYPESQERSKSHHSESIQRQYESSTSEPISDISPIQRLSETSDSGDINDAIASNDSPSIQRLSETSDSSPIQRLS...EISDSGDINNAIASNDSPSIQRLSETSDSGDINNAIASDDSPSIQRISETSDSGDVNNAIASNDSPSIQRLSETSDSGDLNNAIASDDSP...SIQRISETSDSGDVNNAIASDDSPSIQRLSETSDWGDRNDAIASDDSPSIQRLSETSDSSPIQRLSEISDSGDINNAIASTHDSPSIQRLSETSDSSPIQRLSETSDS...SPIQRISETSDLGDVNNAIASDDSPSIQRISETSDLGDVNNAIASDDSTIQRLSETSDSVGVNNAIASHDSPSIQRLSETSDLGDVNNAIASHDSPSIQRLS...ETSDLGDVNNAIASDDSPSIQRLSETSDYSSPPIQRVSETSDSGDINNAIASDDSTIQRLSETSDSGDVNNAIASTHDSPSIQRLSETSDSSPIQRLS

  19. Protein (Cyanobacteria): 479128382 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :1689 696747:1689 ... hypothetical protein Arthrospira platensis NIES-39 MSFTSSWGHLESSVIATFLHLVDLLRLSHIIVGCDRLSDIFLNRREIYSSDAPPLLLRLS...HIIVGCDRLSDTLLNRREIYSSDAPPLLLRLSHIIVGCDRLSDTFLNQGEIYSSDAPPLLLRLSHIIVGCDRLSDTFLNRREIYSSDAPPLLRLSHIIVGCDRLSDTLLNQGEIVTD

  20. Protein (Cyanobacteria): 327031 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AmaxDRAFT_1930 Arthrospira maxima CS-328 MKPNTNLFVRLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVGLSETQKVGWVKPNTNLFV...GLSETQKVGWVKPNTNLFVGLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVRLS...ETQKVGWVKPNTNLFVGLSETQKVGWVKPNTNLFVGLSETQKVGWVKPNTNLFVGLSETQKVGWVKPNTNLFVRLS...ETQKVGWVKPNTNLFVGLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVRLSETQHESKLLNWDSPGRLGGVDG ...

  1. Protein (Cyanobacteria): 493719463 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hetical protein Arthrospira maxima MKPNTNLFVRLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVGLSETQKVGWVKPNTNLFVGLSETQK...VGWVKPNTNLFVGLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVRLS...ETQKVGWVKPNTNLFVGLSETQKVGWVKPNTNLFVGLSETQKVGWVKPNTNLFVGLSETQKVGWVKPNTNLFVRLSETQ...KVGWVKPNTNLFVGLSETQKVGWVKPNTNLFVRLSETQKVGWVKPNTNLFVRLSETQHESKLLNWDSPGRLGGVDG

  2. Protein (Cyanobacteria): 451051 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein MC7420_1253 Coleofasciculus chthonoplastes PCC 7420 MNPFKRVLAFSRNFSSRLSARLSVYHQWFNIYSKDSATTNLTRHNINPFKRVLAFSRNFSSRLSARLS...VYHQWFNIYSKDSATTNLTGHNMNPFKRVLAFSRNFSSRLSARLSVYHQWFNIYSKDSATTNLTGHNMNPFKRVLAFSRNFSSRLSARLSVYHQWFNIYSKDSATTNLTGHNMNPFKRVLAFSRNFSSRLDARLSVYHQ ...

  3. Protein (Cyanobacteria): 451052 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein MC7420_1362 Coleofasciculus chthonoplastes PCC 7420 MNPFKRVLAFSRNFSSRLSARLSVYHQWFNIYSKDSATTNLTRHNINPFKRVLAFSRNFSSRLSARLSVYHQWFNIYSKDSATTNLTGHNMNPFKRVLAFSRNFSSRLSARLSVYHQ ...

  4. Protein (Cyanobacteria): 493031649 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hypothetical protein Coleofasciculus chthonoplastes MNPFKRVLAFSRNFSSRLSARLSVYHQWFNIYSKDSATTNLTRHNINPFKRVLAFSRNFSSRLSARLS...VYHQWFNIYSKDSATTNLTGHNMNPFKRVLAFSRNFSSRLSARLSVYHQWFNIYSKDSATTNLTGHNMNPFKRVLAFSRNFSSRLSARLSVYHQWFNIYSKDSATTNLTGHNMNPFKRVLAFSRNFSSRLDARLSVYHQ

  5. Protein (Cyanobacteria): 516326988 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8:1709 ... hypothetical protein Oscillatoria sp. PCC 10802 MRDLVRAAGIRPDSASLCIYHGVWIWGELAQLAAQLAAQLAAQLAAQLAAQLAAQLAAQWLSWRLSWRLS...GSAGGSAGGSVGGSVGGSVAHFAAHLAAQWLSWRLSWRLSWRLSWRLSWRLTYFGQMSYHPETNLIT

  6. Protein (Viridiplantae): 302830920 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 058 3068:3058 hypothetical protein VOLCADRAFT_87241 Volvox carteri f. nagariensis MPNPLAEMELLGFWGLKLVATVTDCHMSDSGRVMTAFVFKVVSYRNEAAST...LAEMELLGFWGLKLVATVTDCHMSDSGRVMTAFVFKVVSYRNEAASTMLTPEPLPESLEYLQAQVERALDERRELERVMWA...AREGRGGPSMLSCKQLETIELSTMGEAAELEVKRALEAITVVQYSMPNPLAEMELLGFWGLKLVATVTDCHMSDSGRVMTAFVFKVVSYRNEAASTMLTPEPLPESLEYLQAQVERALDERRELERVMWAAREGRGGPSMLSCKQLETIELSTMGEAAELEVKRALEEMFH ...

  7. Protein (Cyanobacteria): 446030 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein MICAC_1920004 Microcystis aeruginosa PCC 9443 MKLKGKTESNFRSRKAERDTTESSLQEAGLESNSAIDSLVRRVRHRQNRLQVLFLGIKLGIPGSEKALNNALFRYGDEYMALDYLNCGSPELDKGGRQWAYAHGYGVTQSKCGLGTGVECPGGVKWGQF ...

  8. Protein (Cyanobacteria): 428225798 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007109895.1 NC_019703 1117:4682 ... 1150:57546 1301283:79328 ... 63132:2396 1173025...:1855 ... 7-cyano-7-deazaguanine reductase Geitlerinema sp. PCC 7407 MQSEQLAENSTATSETSGVKYGERAIAEGELITFPNPRVG

  9. Protein (Cyanobacteria): 123966873 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 42:1373 ... 7-cyano-7-deazaguanine reductase Prochlorococcus marinus str. MIT 9515 MSTPNLYDSTNKPLYGERLIEESKIIC... YP_001011954.1 NC_008817 1117:4682 ... 1212:1747 ... 1217:2782 1218:2782 1219:651 1675

  10. Protein (Cyanobacteria): 516255382 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WP_017659345.1 NZ_KB235958 1117:4682 ... 1150:57546 1301283:79328 ... 63132:2396 10212...7:713 ... 7-cyano-7-deazaguanine reductase Geitlerinema sp. PCC 7105 MSDLHSVSNSISENETAEAATEVKYGEREIQEGKLITFPN

  11. Protein (Cyanobacteria): 123969195 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 91:1394 ... 7-cyano-7-deazaguanine reductase Prochlorococcus marinus str. AS9601 MSTAKLEDSTQRPLYGERIIEESKIICFD... YP_001010053.1 NC_008816 1117:4682 ... 1212:1747 ... 1217:2782 1218:2782 1219:651 1468

  12. Protein (Cyanobacteria): 654344934 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GGWIGITDKYWMTALVPDQSANSRMSFSDTPLRGQDVYQADYLRDPITVPANGTASITDRLFAGAKVVRIIDAYEGALGIDNFELAIDWGWFYFITKPLFLALLYIQGIVGNFGVAIIVLTILIKLAFFPLAN...TSYVAMSKMKKVQPEMMKLRDRYKDDKQRQQQELMELYRREKVNPLAGCLPILIQIPVFFALYKVLFVTIEMRHAPFFGWIED

  13. Protein (Cyanobacteria): 140213 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VIIHAYSGNIEIESGATIGSGVLLVGKSKIGANVCIGSLATILEQNLESEKVVLPASIIGNSGRQFSDNSTISLPDQDSNQSYLFSNETQESSYSLNLANTASSTEETSTETEKANTQLPLANTS...LPAEETPTETEKANTQLPLANTSLPAEETPTETEKANTQLPLANTSLPVEETPTETEKANTQLPLANTSLPVEETPTETEKANTQLQEESPPNIDAQIYGKEYVNKIMQTLFPYKNSLSSHPDDED ...

  14. Protein (Viridiplantae): 183791 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TQEPFDEELVLSVEQVRLADHVNVSLGTYTTNLNNSNDVDIRFDDVPADDRWVDLNRPGIIENAREVKFASKIHLRISLNGGYHVSDEPLEYSSDFRPSSRDHWPP...SIGVLELGILKATNLMPMKIGGRTDAYCVAKYGPKWVRTRTSVDSREPRWNEQYVWEVYEPFTVITIGVFDNNQLDPESRARG

  15. Protein (Viridiplantae): 242052475 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EERDGRSPRAATRRARSASPTRSPRADRGAFAEPSGPFASASSSSSSSSSSSSSAKNIRRRMSLRDLLSRTGGSDWAGADQQASSGTEVTSRLGFWPPSIWPSRSSKKPCPAPPQPARRSTSSDRPAGAVPTTAKRARPGGGSARRTTSLPYRQGLVLGCLGFGARGYGLAKSMHPLPSR ...

  16. Protein (Viridiplantae): 661740 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LEKLKLHDCSSLVEVHQSIGNLTSLVFLNLKRCWSLKVLPENIGNVKSLKSLNISGCSQLEKLPECMGDMESLTELLADGIKNEQFLSSIGQLKHVKRLSLIGYSFSQDSPSPTSWVSQISSWLSPSSISWPP...SISSFISASVLCLKRSLPTPFIDWRLVKRLDLPDGGLSDCATNCIDFRGSSSLEELDLSGNKFSSLPSGIGSLPTLWVLSVQR

  17. Protein (Viridiplantae): 159466610 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2419 hypothetical protein CHLREDRAFT_123820, partial Chlamydomonas reinhardtii RVQCRLVDMPAPCLPPFLPTCPHKPRRIPMPCTDAH...ELVDMPAPCLPPFLPDNLPARAPQAPHAVTDAHECMQCRLVDMPAPCLPPFLPKCPHKPRRLPMPCTDAHECNMPAPCLPPFLPKCPHKPRRLPMPCTDAHECMQCRLVDMPAPCLPAFLPNCPHKPRRLPMPCTDAHECSAGW ...

  18. Protein (Viridiplantae): 714399 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3051:329 ... 3052:329 ... 3055:329 ... predicted protein Chlamydomonas reinhardtii MAPAALPGRSVKSKQAHLLRTDAHRVKSKQAHLLRTDAHRVKSKQAHLLRTDA...HRVKSKQAHLLRTDAHRVKSKQAHLLRTDAHRVALTTLTGALSLFGGACTATSFVLQVSASAASYAASLRLSCPAVPSLTDVA

  19. Protein (Viridiplantae): 928250 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ... 70447:1749 ... 70448:2455 ... TRAPP 20 K subunit (ISS) Ostreococcus tauri MSASAALTVVNANGRSVYERELGSSADSVDTDAH...VRELIGRAALDFADARSWESSATYLRLVDRFNDADAHGYRTSGGGRFVLTLRGRLRGNAGDETIRQFFTDAHEAYAIAKMNPMRDEDEDLGEAFDRAVRESFRRRLAPLFPFARTDE

  20. Protein (Cyanobacteria): 221991 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ivities AAA_3 Nostoc sp. PCC 7107 MANSQGNTQVISYFAPTLTAASVCLCLSILFIKIMSQNHSVFIDLDQNL...YP_007052429.1 1117:4211 1161:939 1162:431 1177:1722 317936:2662 ATPase associated with various cellular act

  1. Protein (Cyanobacteria): 221973 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007126999.1 1117:4211 1118:2627 102231:1117 1173026:1117 ATPase associated with various cellular activiti...es AAA_3 Gloeocapsa sp. PCC 7428 MKKIEILTQNLSRTIVGKAEPIRLVLVSLLAGGHVLLEDVPGVGKTLLAK

  2. Protein (Viridiplantae): 232868 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3051:4703 ... 3052:4703 ... 3055:4703 ... hypothetical protein CHLREDRAFT_120274, partial Chlamydomonas reinhardtii PPGCRCSSAPPGCRCSSAPP...GCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCS

  3. Protein (Cyanobacteria): 450480 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available CCP_1839 Synechocystis sp. PCC 6803 substr. PCC-P MNIQEIQTIANQLTLTLDSPQSVKLQVKQINLAQKQLRAIKKEINAHIRQINQDASQAYSDSIVSVGLDIFGKNKWAGRVRAETRRMIERNKKDARQPYMELKDYIDQLILKGDKLKLSAEQYLLSRE ...

  4. Protein (Cyanobacteria): 133117 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein Microcystis aeruginosa PCC 7941 MGIVLQPENIVFLDTAPFIYFFEQHPIFFPYMEKLFYDVSIYQVKVITSMITFIEIVTHPARIGNQELVEQYRTYFTPSSQITLLPIDLSIANEAIALRTQYTLKTPDAIQLGTAIAYSATYIITNDRQWKQLTPQNVLLVDEM ...

  5. Protein (Cyanobacteria): 450478 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TI_1840 Synechocystis sp. PCC 6803 substr. GT-I MNIQEIQTIANQLTLTLDSPQSVKLQVKQINLAQKQLRAIKKEINAHIRQINQDASQAYSDSIVSVGLDIFGKNKWAGRVRAETRRMIERNKKDARQPYMELKDYIDQLILKGDKLKLSAEQYLLSRE ...

  6. Protein (Cyanobacteria): 33862119 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 9:1168 59919:1168 hypothetical protein PMM1563 Prochlorococcus marinus subsp. pastoris str. CCMP1986 MGEAKRRKSLGLPPKQKNTKSKSDESPRIFDWLPLTINQRDSLMKMSIKASWYGIGGLVILWVIVRFIGPAAGWWTPADSL

  7. Protein (Cyanobacteria): 155596 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LRVVVFADGREWITGRNLPPNLRERQQQGIMGWVAEDKLFQRSLADHKTGNYLGAWLALEKARQFGAGEAILIDSQGNWLETSTGNLWGWKGGSWWTPVLDESILPGIQRSAIINRLKSQDIFVEENLWTPDFIEELEVIAYSNCVVEIIPFTVILSQKRKLTFNAFHPALKQLRINTFKN ...

  8. Protein (Cyanobacteria): 554637619 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2386 1183438:2386 ... hypothetical protein GKIL_3310 Gloeobacter kilaueensis JS1 MSSHDVDRRLSDILDAASSIQQYTANLSELQFISGQQVVDAVNYNLIKIGEAVANLPEDFKEANPDIPWQAIKRTRNFITIVILWWTPASSGQQSGLICRNL

  9. Protein (Cyanobacteria): 384788 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available oneopterin aldolase Prochlorococcus marinus str. AS9601 METFLKIENIKLWARVGVLDEERELGQLFILDIFLWTHFEKCTIDDDIKKTVDYSKLVQILQNQSKKIYCYTIEKYSNAILEIIDQEFKISKIKIILTKCNPPITGFDGKVSIVRILENK ...

  10. Protein (Cyanobacteria): 384791 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available eopterin aldolase Prochlorococcus marinus str. MIT 9202 METFLKIENIKLWARVGVLDKERELGQLFILDIFLWTDFEKCTVNDDIKKTVDYSKLVQILKDQSNKIYCLTIEKYSNAILEIIDQEFKLSKVKIILTKCNPPITGFDGKVSIVRILENN ...

  11. Protein (Cyanobacteria): 384790 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available neopterin aldolase Prochlorococcus marinus str. MIT 9215 METFLKIENIKLWARVGVLDKERELGQPFILDIFLWTDFEKCTVNDDIKKTVDYSKLVQILKDQSNKIYCFTIEKYSNAILEIIDQEFKLSKVKIILTKCNAPITGFDGKVSIVRILENN ...

  12. Protein (Cyanobacteria): 78213804 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ... hypothetical protein Syncc9605_2296 Synechococcus sp. CC9605 MHRSLLLWIVAMACTTSSVGASQSWKRSLPLQEASQQAVTAANAVINQSGSEECLRGKFSNAILRLSNSCDVSGYSSTECELASKIAGQESKLSMSDMIATSETLLDLLGDSATSN

  13. Protein (Cyanobacteria): 497314923 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ANLLGANLSSSDLVKANLREADLYKANLKDAEVSGAYLSRAHLREACLQRCDLSLANLQGADLTNAYFSGANLSGADLDESDLSNANLNETNLSNAILSNANLTNADL...RRSDLTNANLEYANLSNSNLSDSKICTANLSHANLQECDLSNTTINQSNLSHANLADSILSNANLSNANLSYTNLKNAVLSNAIL

  14. Protein (Cyanobacteria): 657935082 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NIDLTGVTFVAAEMRGANFQGSNLSNAILTKGILLRANLEGANLSYALVDRVTMDEANLKNAIFTEATLTSSRFYGADITGADFTDAIIDRYQVSLLCDRASGVNPVTGISTRESLGCR ...01 ... hypothetical protein [ Scytonema hofmanni] UTEX 2349 MKKILLRFLSLIVSLLLAALWIIFNPHPAFGQVNTINYSNMSLENRDFS

  15. Protein (Cyanobacteria): 414076585 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available pothetical protein ANA_C11310 Anabaena sp. 90 MSVGAKHLEDELSVIAKNSSPNASPVQLLVGGKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVVICPENNPKEQIICAVICGVEEKSNEITAIPELIKVLDMTGCLYSTHLNYLI

  16. Protein (Cyanobacteria): 661286037 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 0:477 ... hypothetical protein, partial Prochlorococcus sp. scB243_498P3 MSTKSDSLKEKLIENFSDFSKLSDYSFMNYLRADPQ...STKDGNDHKPRSVYSGHYVPVLPTAIPEPEYISHSKKLFKELRLSSDLTKDKNFCLFFSGDISVANYPMSPVGWATGYALSIYGTEYTQQCPFGTGNGYGDGIAISVFEGLFNGKRMEMQLKGGGPTPYCRGA

  17. Protein (Cyanobacteria): 208270 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available transferase Halothece sp. PCC 7418 MKIVIARDFNDFARCIMIRTQVFVMEQGISAEIETDEWENHSTHYLAGDGEKALATARSRLINNQTAKIERVAVLKEARSQGVGTELMRYILQEIHSYSNIQTIKLGSQNSAIPFYEKLGFQVIGEEYLDAGIPHHLMMQRINT ...

  18. Protein (Cyanobacteria): 440680211 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available CEAGDVQGAIEDCNQALRINPKLAEAYCNRSNARCESGDVEGAIEDCNQALRINPKLAEAYLNRGNARRESGDIKRAIEDYNQGLRINPNLAQAYRNRGFARCESGDF...KGAIEDFNQAIRINPNLAQAYQNRGFARCESGDFKGAIEDFNQALRINPNYAEAYYNRGLAHNYSGDRQAEIEDFNQALRINPNLAEAYLNRGVTRRESGDVKGAIEDYNQALHINPNLAEAYQNRGFARC

  19. Protein (Cyanobacteria): 310254 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available sp. CC9605 MIAPLPMPAEPLLEQYGQGARLCPCANDQITLVFSQEYPFDLVELEQLLEAVGWSRRPIRRVRKALSHSLLKVGLWRHDPRVPRLVGFARCTGDGVFEATVWDVAVHPLYQGNGLGKQLMAYILEALDQMGTERVSLFADPGVVSFYQGQGWDLEPQGHRCAFWYAN ...

  20. Protein (Cyanobacteria): 324054 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 472DRAFT_2939 Cyanothece sp. ATCC 51472 MKISLIFLTLPLLFLITLLSSCNRSDFSNSIKSQSLIKQNNSQNSINLNQTCTNKKVGYQVNYPQDWQ...TNSGNVMNDCQVFDPTYAKVPEQTESISKAIYLRVEENAPFDLISQENVGEQHLSKQTLTIDSYQAVAVESKSTGRAMLPKGQRNYSYIVDLGDRTLIATTYDVPDNNYAKNKQILDSMLKTIEFNNNELK ...

  1. Protein (Viridiplantae): 784550 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QPYIPENERSGVLDVSNFGNQDHHEALTHSLRFEAYDLPKPVVSSRVPPAAVASSTELVPVXEPSYARETRQPASSPSVSDAGSSELKLRLDGVQKKWGRPTYSSSAS...lon-like, partial Malus domestica ELQAVISLDAXAVESIMPLDASCEDIEIDKNLSFLNGYVQEALEKGA

  2. Protein (Cyanobacteria): 493566136 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 29:4530 ... putative DNA alkylation repair enzyme Leptolyngbya sp. PCC 7375 MTAKDISKILRDLADPVIAEHSQRFFKTGKGEY... WP_006519474.1 NZ_JH993796 1117:18358 ... 1150:46430 1301283:66978 ... 47251:4271 1021

  3. Protein (Cyanobacteria): 428299087 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007137393.1 NC_019751 1117:18359 ... 1161:10603 ... 1185:1278 1186:1626 32054:1873 1170562:1873 ... DNA alkyla...tion repair protein Calothrix sp. PCC 6303 MAQYLITQLQEQLAQADDSKTKEWWEAYLKHSLPFRGLKL

  4. Protein (Cyanobacteria): 427702805 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ylation repair protein Cyanobium gracile PCC 6307 MGMDRASMTPRAPTIPSAPSSIQKGTPLKHLLG... YP_007046027.1 NC_019675 1117:3386 ... 1118:18369 1301283:9302 ... 167375:2211 59930:1253 292564:1253 ... DNA alk

  5. Protein (Cyanobacteria): 553736347 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WP_023070590.1 NZ_AWNH01000001 1117:18358 ... 1150:46430 1301283:66978 ... 47251:4271 1385935:793 ... dna alkyla...tion repair enzyme Leptolyngbya sp. Heron Island J MTADQISKTLRDLADPAIAEHSQRFFKTGKGE

  6. Protein (Cyanobacteria): 428298871 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007137177.1 NC_019751 1117:18359 ... 1161:10603 ... 1185:1278 1186:1626 32054:1873 1170562:1873 ... DNA alkyla...tion repair protein Calothrix sp. PCC 6303 MAQYLITQLQEQLAQAGDSKTKEWWEAYLKHSLPFRGLKL

  7. Protein (Cyanobacteria): 220909747 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 51 ... hypothetical protein Cyan7425_4387 Cyanothece sp. PCC 7425 MIEMKVAGIALDAATRIPIVLLKDATERRALPIWIGQNEARAI...LSALENQKSPRPMTHDLMVNFLKDWDMLLERVVIHSLQDNTYYAVLTVKQGEVKKEIDARPSDAIAIALRVDCPIWVMEEVVADASIPVDREADEAERQAFREFLDSIRPEDFIQRWGTGETSTGS

  8. Protein (Cyanobacteria): 504928995 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WP_015116097.1 ... 1117:4682 ... 1161:4218 ... 1162:3122 1177:1104 317936:3404 ... NADPH-d...ependent 7-cyano-7-deazaguanine reductase Nostoc sp. PCC 7107 MTQDTSEVKYGERNIAEGNLITFPNPRVGRRYDINITLPEFTCKCP

  9. Protein (Viridiplantae): 816755 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e Solanum tuberosum MAQHYKLSSILLLAFIYFIHDHMITTITARRILQTPSFSTPTTPSFSMPTTPSFSKSPGVSKPASPSFSNSPSLSKPET...PSFSKSETLSFSKPETPSFSTSETPSFSKPETPSFSKPETPSFSKPEIPSFSKPETPSSPRLETPIFIKPETPTFSKPETPTFSKPKTPSLLKPETPSSQKPETPTFSKPET...PIFSKSETHSFSKPETPTSPNPETPTFSKPETPSSPKPETPSFSKPETSSFSKPETPTFSKPETPSSPKSETPSFSKPETPTFSKPET...PSSPKSETPTFPKPKIPSSLKPETPSSPNLETPSFLKPETPIFSKPETPSFSKPEMPSSTKPETPIPQSPRPLLSQSLKSQILQTPRPQLETSSFSKPET...PSFSKPETPSSSKPEAPSSPTPEMQSFTKPETPSFSKPETPNSPKPETPSFPKPETSTFSKPQTSNSPKSETSSSPKPETSSFSKSETPSFSKPEMPSSPTPETPNFSKPET

  10. Protein (Cyanobacteria): 504943837 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DTPSSNTLNENPSVNSLVETGQVVSDTERQTSQNNNDNNNVNSQDKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPET...KPPETKPPETKPPETKPPGHKPPETKPPETKPPETKPPGHRPPGHKPPETKPPGHKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETRPPETKPPDTKPPETKPPETRPPETKPPETKPPETKPPETKAPGN

  11. Protein (Cyanobacteria): 427719982 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VVDNPSFLQLSNSSSSSSNASKDTPSSNTLNENPSVNSLVETGQVVSDTERQTSQNNNDNNNVNSQDKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPET...KPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPGHKPPETKPPETKPPETKPPGHRPPGHKPPETKPPGHKPPETKPPETKPPETKPPETKPPETKPPET...KPPETKPPETKPPETRPPETKPPDTKPPETKPPETRPPETKPPETKPPETKPPETKAPGN

  12. Protein (Viridiplantae): 816753 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e Solanum tuberosum MIDEVKEEWPETPSFLNPETPNSQNPETPTFSNPESPTFSKSETPTFSMPETPTFSKPETPSFSKPETPSFSKPET...PSSQKLEASTFSKTETPTFSKLETPSFSKLETPISPNPETPTFSKPKTPSFSKPEIPSFSKPKTPSFSKSETPTLSKPETPSSPKPETPNSPKIEAPSFSKPETPSFSKPET...PTFSNPETLSSPKSETLTFQKPEIPSSPKLETQSSSKPETPSFSKPETPTFSKSKTPSSSKPEMPSSPKPETPSFSKPEILTFSKPKTPSFSKPETPSFSKPETPSFSRPET...PSFSNPETPSSSKPEPETLSSPKPKTPSSAKLETPSFSKLETPSFSKPETPSSLKPETPSFSKPET...PSSPNPKTPSSPKSETPSFSKPKTPSFSKPETPSSSKLETPNFLKPETPSSLKLEAPPTFLKPETSSSTKPKTPSFSTPETPTFSKPETPTFSKSETPSFSKSETPSSFKPETPSFSKPETPSSPKFETPSSPKPETPSSPKT

  13. Protein (Cyanobacteria): 104308 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NASKDTPSSNTLNENPSVNSLVETGQVVSDTERQTSQNNNDNNNVNSQDKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPET...KPPETKPPETKPPETKPPETKPPGHKPPETKPPETKPPETKPPGHRPPGHKPPETKPPGHKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETRPPETKPPDTKPPETKPPETRPPETKPPETKPPETKPPETKAPGN ...

  14. Protein (Viridiplantae): 816751 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 0:266 ... 424551:266 ... 424574:266 ... 4107:266 ... 4113:1088 ... PREDICTED: proteoglycan 4-like Solanum tuberosum MPTLSKLEIPNSPNPET...PGSPKSVTPSISKPKTPSFSKPETPSFSTPETPSFSRPETPSFSKPETPSSSKPEAPSSLTPETPSFSKPETLSFSKPET...PSSPKLEIRNSAKPETPSFSKPETPSFSKPKTPSSPKPETPSFSKPKTPSSPNLKTPTPSSPNSQTPSFSNSRKPEAPTFLKPETPSSPKPKTPSFSTPETPTFSKPET...PNFSKSETPSFSKPETPSSFKPETHSFLKSETPSSPKPETPSSPKFEPPSSPKPETPSSPKTENPSSPNTETPNFSKPETPSSPKPNTPSFPKLDTPSFSNPKTPSYETPSFPKFETTSSQKPETPNSPKFGTPSLPKSKIPSDPIFETISFSKPETSNSSKPKIPTTP

  15. Protein (Cyanobacteria): 52198 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 02412 Synechococcus sp. PCC 7502 MKLTPYLFLTITVTAIIGTSVWQSSAQMNKMMNHNMDEMSMELGAADANLDLRFIDAMIPHHQGAVQMAKEALKK...SKRPEIQKLATAIIKAQQEEIAQLQKWRKLWYPNMSSTPMAWHGEMGHMMTMSASQQKAMMMSMDLGAGDAKFDLRFIDAMIPHHEGALTMAQEALSKSKRPEIQKLAKAIITSQKAEIIEMQKWRKAWY ...

  16. Protein (Viridiplantae): 111158 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available MTRLAASSSPHRAMTSRLVLLAVVAVLCLMASQGVNAQIIIVEGTAEKSPPPKAPQPPSPQPPSPQPPSPQPPSPQPPSPQPPSPQPPSPQPPSPQPPSPQPPSPQPPSPQPPSPKPPSPKPPSPPSPKPPS...PKPPSPKAPYAPRKPEAPKKVKAKGKKFKGKKWNYMISDSMLEFKEADNFCKSAGYVLVSPVEDTSDAVDSACNHSGKGCWLSSDENADPCTYVNSKGGDKAYVNDCKVKNYALCYGPADKPLR

  17. Protein (Viridiplantae): 773137 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FTLLPLQVYDTQITGNLNCSGIGLGAGQCCGLSDSPCSSSDIGSGVCGVMVDLSAISTCRLNPPPPPSPQPPSPEPSPPSPGLPLQPPSPQPSQALPSPPSPATPPQPPSPQPPSPEPSPPSPGLPLQPPS...PQPSQALPSPPSPATPPQPLSPQPPSPEPSPPSPGLPLQPPSPQPTPALPSPPSPATPPQPPSPQPPSPEPSPPS...PGLPLQPPSPQPSQALPSPPSPATPPQPPSPQPPSPEPSPPSPGLPLQPPSPQPSPRCRRRQALQPHHSRRARSHRRQSLHHLAQDSRCSH...PAHSRHQRCRRRQALQPHHSRRARSHRRQSLHHLAQDCRCSHPAHSRHRAAVAAKPCNPTTAAEPAATPPSPQPPSPEPSPPSPGLPLQPPSPQPSQALPSPPSPATPPQPPSPQPPSPEPSPPS...PGLPLQPPSPQPTPALPSPPSPATPPQPPSPQPPSPEPSPPSPGLPLQPPSPQPTPALPSPPSPATPPQPPSPQPPSPEPSPPS

  18. Protein (Viridiplantae): 161468 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NLWPSLVFALAICFIATNVAASDDKPYAYSSPPPPDYYKSSPPWYHHHKTPPYHYKSPPPPSPSPPPPYVYKSPPPPSPSPPPPYIYKSPPPPS...PSPPPPYVYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYMYKSPPPPSPSPPPPYVYKSPPPPSPSPPPRYVYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYVYKSPPPPS...PSPPPPYVYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYIYKSPPPPS...PSPPPPYIYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYIYKSPPPPS...PSPPPPYVYKSPPPPSPSPPPPYIYKSPPPPSPSPPPPYVYKSPPPPSPSPPPPYVYKSPPPPSPSPPPPYVYKSPPPPSPSPPPPYVYKSPPPPSPSPPPPYVYKSPPPPSPSPPKPYDYASPPPPTPY

  19. Protein (Viridiplantae): 779632 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 65:1289 ... 3066:1289 ... 3067:1289 ... 3068:1289 ... hypothetical protein VOLCADRAFT_95759 Volvox carteri f. nagari...ensis MRHGEDTSRHRGNEQKAPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPFLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPFLPPSLPPSLPPSLPPSLPPSLPPSLPPSLPPSPPPSLPPSLPACP

  20. Protein (Viridiplantae): 302844289 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IISDVAKGMDKTAKLSSMLDASAASGHAPSPPPPSPPPPSPPPPQPPPPSPPPPDPPPPSPPPPSPQPPSPPPPYPPRPTLPPLPPRAPRHPPGVLDPPAPVSYGGMY...PGPQESYVAFLTGAASSWLSYYYGYQVRFTVMLIALLSSNDPLGLEYVRVLYSLADMTRLVGLVLKPFIRLQKFEHSSAPPDRFRSRCPPQPSSTTPPS...PPPKQASPPPPLPIVPPPSPPLPPQPPSPTSPSQPPKEAAPPPYSPPSTPPSTPSPPQPPSLTPPSPPPKQAIPPPPSPPFSPPSPPSPPQPPPPTPPSPPPKQASPPPPS...PPFPPPSTPSPPQPPSTIPPSPPPKQATPPPPSPPFPPPSTPSPPQPPPLTPPSPPPKQATPPPPSPPFSPPSPPSPPQPPSPTPPSPPPKQATPPPPSPPFPPPSPPS...PPQPPSTTPPSPAPKQASPPPPSPPFPPPSPPSPPQPPSTTPPSPPPKQASPPPPSPPFSPPSPPSPPQPPS

  1. Protein (Viridiplantae): 674773 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 65:235 ... 3066:235 ... 3067:235 ... 3068:235 ... hypothetical protein VOLCADRAFT_37371, partial Volvox carteri f. nagariensis PSELEADPPS...EWEADPPSELEADPPSELEADPPSELGADPPSELEADPPSELEADPPSELEADPPSELEADPPSGLEADPPSELEADPPSELEADPPSESEADPP

  2. Protein (Viridiplantae): 674776 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 65:235 ... 3066:235 ... 3067:235 ... 3068:235 ... hypothetical protein VOLCADRAFT_56839, partial Volvox carteri f. nagariensis DPPSDWEADPPS...DWEADPPSDWEADPPSDWEADPPSDWEADPPSDWEADPPSDWEADPPSDWEADPPSDWEADPPSDWEADPPSDWEADPPSDWEADPPSDWGADPPSDWEADPPSDWEADPPSDWEADPPSDWKADLPSDWKADPPSD

  3. Protein (Viridiplantae): 674774 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 65:235 ... 3066:235 ... 3067:235 ... 3068:235 ... hypothetical protein VOLCADRAFT_65149, partial Volvox carteri f. nagariensis DPPSDWEADPPS...DWEADPPTIGRLIPPSDWEADPPSDWEADPPSDWKADPPSDWEGDPPSDWEADPPSDWEADPPSDWEADPPSDWEADPPSDWEADPP

  4. Protein (Viridiplantae): 134980 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QPPDGPPGGTILRLTQLGLTAATANGARLCIKLTAGRNGTGCGTLEQMCVPPAGSPPGVCTAAIFDSGNGCCPQVQAGTPSPPSPLPPSPRPPSPKPPS...PPPPPGPPPPSPAPPSPSPPSPPPPSPQPPVPPSPAPPTPPGPPPPSPAPPNPPPPPSPAPPSPKPPSPEPPSPPPPPSPEPPSPKPPSPEPPSPQPPLPPPPPSPYPPSPSPPS...PPPPSPPPPSPAPPSPAPPSPPPPCECLAGERELTCAFLPPSPLPPSPAPPSPQPPLPPPPPSPYPPSPAPPVPPSPPPPSPYPPSPAPPAPPS...PPPPPPPPPPPPPPPPPFPPFPPPPSPPPPSPGPPSPAPPSPPPPPPPPPPSPYPPSPAPPLPPSPPPPSPYPPSPAPPVPPSPAPPSPEPPSPAPPSPPPPPSP

  5. Protein (Viridiplantae): 159472102 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 4474 predicted protein, partial Chlamydomonas reinhardtii PPSPAPPSPEPGSPPPSPAPPSPQPPSPAPPSPEPGSPPPSPAPPSPKPPSPAPPSPEQPGSPPPSPPPPRPQPPSPAPPSPEPGSPPPSPAPPSPQPPSPAPPSPEPGSPPPSPAPTQP ...

  6. Protein (Viridiplantae): 188576 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 65:1947 ... 3066:1947 ... 3067:1947 ... 3068:1947 ... hypothetical protein VOLCADRAFT_62572, partial Volvox carteri f. nagariensis PPS...SVTHTRIPPSSVTHTRIPPSSGTHTRIPPSSGTHTRIPPSSGTHTRIPPSSGTHSRIPPSSGTHSRIPPPSGTHTRIPPPSGTHTRIPPSSVTHTRIPPSSGTHTRIPPS...SGTHTRIPPSSGTHTRIPPSSGTHTRIPPSSGTHTRIPPSSGTHTRIPPSSGTHTRIPPLGRLLLTAAKQHT

  7. Protein (Viridiplantae): 773135 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TPSITYCPNSPFNWGFATLKVSCCPEPPPPSPPPNPPPPSPPPSPPSPSPPSPAPPSPSPPSPAPPSPSPPSPAPPSPSPPSPVPPSPPSPLPPSPTPPSPLPPS...PSPPPPPSPFPPSPPPPPPPPRQTGSPPPPPSPLSTSPPPPATSPAPLSPPPSATQSPPPSATQSPPPSATQSPPPSATQSPPPSATQSPPPSATQSPPPSATQSPPPS...ATQPPPPSATQSPPPSATQSPPPSATQSPPPSATQSPPPSATQSPPPSATQSPPPSPVRFLPPPPSLSPPKTPPIQPKSPKAPKAPKAPKLSSPPPPS

  8. Protein (Viridiplantae): 111171 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available MTSRLVLLAVVAVLCLMAPQGATAAGQTTGIEERFTWNATWDSWDKALASILKKKSPPPSPQPPSPRPPRPSRPPPSPRPPPSPPPPSLPAPPPPSPSPPPPSPPPPSPLPPSPPPPSPFPPSPPPPS...PLPPSPPPPSPPKSSRLISKPNKWKSSATSSQQDPLHQSLLSRDSVPGTDLKAQENDIEL...EAKLSPASHAATITIRNSDDGKEPSPPSPPTSPSPPSPPNSPPQPNPPSPPNPPSPPSPPNPPSPPSPPNPPSPPSPPKAPKSPFAPNAPGKEYEQFKKKKWMYIISN

  9. Protein (Cyanobacteria): 657934340 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FQLEINLSGGTTPRYFYLAQPPRMVIDLPDTKLGYVATQQNYSGAIQRIRVSQLNENVTRIVLDLAPGTSLDPNQVQLQPVSAQNNTRWVLRPLIAGGTYSQQGNYPPPSNLPPSNYNYPAPTNLPPSNLPPS...NYNYPPPSNLPPSNLPPSNYNYPPPSNLPPSNLPPSNYNYPPPSNLPPSNLPPSNYNYPPPSNLPPS...NYNNSQIPLVTVPALNSNNPTQQPGSVLPPPSFPNQPGNFNTAPLSVGAPGFPVQTVPNYPVNVPNSGVFEFGQPFPNSNR

  10. Protein (Viridiplantae): 111164 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available MTRLAASSSPHRAMTSRLVLLAVVAVLCLMAPQGVSAQDVESRNSNKPRPPKAPEAPQPPSPQPPSPKPPRQPKAPKPPSPKPPSPKPPSPKPPSRPPSPKPPSPKPPSPKPPSPKPPSPKPPSPKPPS...PKPPSPKPPSPKPPSPKPPSPKPPSPKPPSPKPPSPKPPSPKPPSPKPPSPKPPSPKPPSPKPPSPKPPSPKPPS

  11. Protein (Viridiplantae): 705809 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SGKMVFQFLTAAVVMVLATPAAAWHGSSSRYTAYPGYIINTPAIACWTGWFTYTTNLTACLTPVEANGINNKADGLASICTNYVPGCLSFHLDTGMFYASNDIALLQASPADNVYLKSLSPPS...PMPPKPSSPPSPTPPSPMPPSPAPPSPAPPSPLPPSPVPPSPAPPSPAPPSPAPPSPAPPSPRPPSPVPPSPAPPSPLPPSPAPPSPAPPS...PEPPSPAPPSPEPPSPEPPSPAPPSPEPPSPEPPSPAPPSPAPPSPVPPSPAPPSPVPPSPPPPSPSPPTPIITNGQGTGQQQ

  12. Protein (Viridiplantae): 302839350 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PPPLKPSNPPPLKPPPLEPSPPPPDFPSVPRHPPSPPPPKPPPPSPPPPSPPPPSPPPPQPPPPSPPPPKPPPPSPRPPSPRPPKPPRPSPPPSPSPPSPLSPPPPPPPPPPPPPSPRPPSPSPPPPS...PRPPKPSPNPPQPPPPNPPPPPPSPPPPSPPPPPSPPPPNPPPPSPPPPNPPPPSPPPPCPPPPSPPPPEPPPPSPPPPSPPPPS...PPPPSPPPPSPPPPSPPPPSPPPPVPPQPPSPFLEPSPPSPRPPRPPPRPPPFATPNVRAGASCIKVLIMGTP ...

  13. Protein (Cyanobacteria): 222097 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available Trichodesmium erythraeum IMS101 MHQTKFWAIAPFGLLTILGKPLLSPALPIHQAVVNFSYVDESSTKSEIFAQDTSFPKVTPSPEMTPTLEDSPSPEMTPTLEDSPSPEMTP...TLEDSPSPEMTPTLEDSPSPEMIPPTQEPEIILQQPGMLSDDDLVLPSDESVYDEHTFEGTEGQVVTVTVESPDFDTYLAVFSPDTKLLGEHDDISKKNTNSQLTITLPMTGKYRVIVNSYDKTGRGEYNLQVIQSGQTSDF ...

  14. Protein (Cyanobacteria): 113477182 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 124:288 ... peptidase-like protein Trichodesmium erythraeum IMS101 MHQTKFWAIAPFGLLTILGKPLLSPALPIHQAVVNFSYVDESSTKSEIFAQDTSFPKVTPSPEMTP...TLEDSPSPEMTPTLEDSPSPEMTPTLEDSPSPEMTPTLEDSPSPEMIPPTQEPEIILQQPGMLSDDDLVLPSDESVYDEHTFEGT

  15. Protein (Viridiplantae): 765946 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available s tolerance to multiple environmental stresses and reduces photooxidative damage ... 41938:10941 3629:10941 ... 214909:10941 ... 3640:10941 ... 3641:10941 ... Encodes a chloroplast protein that induce

  16. Protein (Cyanobacteria): 427702068 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007045290.1 NC_019675 1117:18653 ... 1118:16049 1301283:6725 ... 167375:2724 59930:711 292564:711 ... vancomyc...in resistance protein Cyanobium gracile PCC 6307 MPEGVRFDRSVGDLAAGEVEQRPWIGLIQPILFS

  17. Protein (Cyanobacteria): 158335746 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_001516918.1 NC_009925 1117:18653 ... 1118:16049 1301283:6725 ... 155977:439 155978:2306 329726:2306 ... vancom...ycin B-type resistance protein VanW Acaryochloris marina MBIC11017 MTASSWRTPLRLLKCR

  18. Protein (Cyanobacteria): 158336672 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_001517846.1 NC_009925 1117:18653 ... 1118:16049 1301283:6725 ... 155977:439 155978:2306 329726:2306 ... vancom...ycin B-type resistance protein VanW Acaryochloris marina MBIC11017 MATSQWLPAKQTVRSG

  19. Protein (Cyanobacteria): 158337390 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_001518565.1 NC_009925 1117:18653 ... 1118:16049 1301283:6725 ... 155977:439 155978:2306 329726:2306 ... vancom...ycin B-type resistance protein VanW Acaryochloris marina MBIC11017 MPVNYLQQPQPQQRTR

  20. Protein (Cyanobacteria): 518316762 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available CEKLELNWEDIIELMPNKNLFYRPISQITVLPNLETEQGSVQIITRQILVIDRENQEVISAITLEGEIDSVQSDLSFWQSDFSTKYPNSNIKVIAIKPGSIKIVIEGNQEDIDMLLSD...FESGELTEINGYPVQNIQILTESVEDDESSKRKWRLVEDIRTNKVEGRDLRGVDLSDADLSDAYLVNANLIDADLSDCDLSGANLSD...CDLSGANLSDCDLSGANLSGADLSGADLSGANLSGANLSGANLSGANLSRADLSGADLSGANLSGANLSGANLSGANLSGADLSGADLSGADLSGANLIVANLSD...ANLIVTNLIGADLSGANLSDANLSDANLSGANLSGANLSGANLSGANLSGADLSGADLSGANLIVANLSIANVKKANFSYSNGISKEIKQDLIKRGAIFEDSLGDRSLTTSR

  1. Protein (Cyanobacteria): 158341580 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GESIYLWGADLGGANLSGADLGGATLSGANLWDANLTYADLRGATLIYADLRGATLIGAALIGAALIGAALNGANLSDADLSGADLRNTKISAATKIDAKWKLVHELVNKGGEGKDLSGTDLSGANLSD...ADLSDADLSGADLSDADLSDADLRNTNLRNTKISAETKIDAKWKLVHELVNKGGEGKDLSSTDLSDANLSGTDLSD...ANLSGTDLSDANLSGADLSDADLSGTDLSDTNLSGTDLSDADLSDADLRNTKISAETKIDAKWKLVHELVNKGGEGKDLSGTDLSGADLSGADLSDADLSGADLSDANLSD

  2. Protein (Cyanobacteria): 264858 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LWDANLTYADLRGATLIYADLRGATLIGAALIGAALIGAALNGANLSDADLSGADLRNTKISAATKIDAKWKLVHELVNKGGEGKDLSGTDLSGANLSDADLSDADLSGADLSDADLSD...ADLRNTNLRNTKISAETKIDAKWKLVHELVNKGGEGKDLSSTDLSDANLSGTDLSDANLSGTDLSDANLSGADLSDADLSGTDLSD...TNLSGTDLSDADLSDADLRNTKISAETKIDAKWKLVHELVNKGGEGKDLSGTDLSGADLSGADLSDADLSGADLSDANLSDADLSGADLRNT

  3. Protein (Cyanobacteria): 264168 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available al protein CRC_01598, partial Cylindrospermopsis raciborskii CS-505 MKKFLTLALILILFLVSSFSLGTSPSYAYSQSDLDRLLETRECPECDLSDADLSD...ADLSRDDLRRANLRGAKLKDADLSDADLSDADLRRAKLRHANLRGAKLKDADLSSAYLSGADLTGANLSGADLRDAKLKNADLSGAFLTSADLMRADLTGANLTCAVGADFIVAEIVAE ...

  4. Protein (Cyanobacteria): 359322 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ynechocystis sp. PCC 6803 MYFLLVTLVILVFPLLSIALEWTTSGNSQALVDVLARWFVFWGVGVRLFLAGVVQITKPSFTAEKILGVQSQDSLILVKELGIGNLAIASVALGSIFVNAWVLGAALAGGIFYLLAGINHILQPERNAKENYAMATDLFLGLLLGGILFFAWQP ...

  5. Protein (Cyanobacteria): 652325626 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hetical protein Fischerella sp. PCC 9431 MQRRCERNRKRSKRRAIYCPIHGCYLDSVSQKYPLFADRPGQLQQRGIGRQTALLLVAHKTAVPLEGEWLEAFWCDQCQEKKWYHLKKRDRVYEVSIAAPELWQQAMGVIYPEGNPSVGEFTRRHARMVGCKSSKDFGFIG

  6. Protein (Viridiplantae): 780231 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 401 ... 38832:1362 ... 38833:877 ... 564608:877 predicted protein Micromonas pusilla CCMP1545 MQDSMHDTMHDSIQDSMHDSIQDSMQDSM...AKEEEEPAEPPAKEEEAHAEPPAKEEEAHAEPPAKEEDYAEPPAKEEDYAEPPAKEEAHSMDSMDSMDSMDSMDSMDSMHSMDSMDSMDSMDSMHSMDSMDSMDSM...DSMHSMDSMDSMDSMDSMDSMDSMHSMDTSIDAVDAAANVTDAADTAGAAANVTDAADTAGAAAEEKPPENASVDSLDSLLDG

  7. Protein (Viridiplantae): 746637 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 218 ... 38832:274 ... 38833:414 ... 564608:414 predicted protein Micromonas pusilla CCMP1545 MAQLPSYEVDDGEDSMPGAPGEGPMTDSMQGPPVEVPTSDSM...PGAPGEVPTMDSMHGPPVEVPTMDSMHGAPVEVPMMDSMPGAPVEVPTMDSMQGPPVEVPTMDSMQGAPGEGPMTDSMHGAPGEGPTMDSMNSGNPTKCVVPDWCSTYPPEMQKSKPECQCPDDSHP

  8. Protein (Viridiplantae): 316565 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NXEEKNVETEDRFFRGVGYKRPRLBEESVFGLCDTEMEMNLDIIKEVELDVAAFGSMKSGLNNKPKFYATESEVFADSQKK...SFSSFSVNESKYVTEFGEEVVEGAICLMIISGCGSNWDRISSVTESSDNNSLSLEVQSPGLKNWIMGNKGGVSVCDDTVKFVDCISDGKNVSVXKKVLEFSENNXGFA

  9. Protein (Cyanobacteria): 158340218 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_001521388.1 NC_009927 1117:1153 ... 1118:6712 1301283:22847 ... 155977:4755 155978:4571 329726:4571 ... tyrosi...nase, putative Acaryochloris marina MBIC11017 MFTSKTRREFLISAGAATALFFLPTKVAQAQELRTRK

  10. Protein (Cyanobacteria): 92229 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein Microcystis sp. T1-4 MVRAIIRAASTPNYMSDTSAVKKYLAHWFQLGKKVICPKNQAMLFPLPIFNADRYSSEFEDCWQKMLDPQSGDCYLEGTQQTIQDLLSPQWEFHPCARCTIPVPIEVLGQSGLSCPCHDLSNWPNLELPLPHLPVNSRENLDRIRQRLLKNSPSH ...

  11. Protein (Cyanobacteria): 321817 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ynechococcus sp. WH 8102 MLGRNLGGPRRGWWRWLQWQWWGLDLAWNRWWLSFDQTAQTAWLNQLLGSNPNWIGWLVLAGGALAFALGLRVTRWRAVATPIQRTLRLLETLDVTPQPGESFAALCHRAAASTPSCPCRCWPWPKLTSSLPMHLSPAVSVSCSNGFGSRH ...

  12. Protein (Viridiplantae): 759706 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GEIELETRNGQTYTVGVSKYPDKLVLTAGWGAFVKTYDLQIGDSVVFRYDGDSQFNVIVFDRFGREKASSVVAVADNDPLSPHEQEKNRVSTESLNRSHSYPQRMEVQSPTENVNRSQGHPQAMQMPSPTEN...VNLSQEHPQPMQMPPPTENMDRSQRHPQPMHMQSPTGNVDGFVGLSRHMEVQSPTENMQLSCSHTERQSKLQNDYSNQGDSLPPEDDIEVCEEPRYMLGRKNRLSSAQVKEVDEMVQHIHHENPIFVAVMSKCNVTGSFHLLSVENAILNSLNC

  13. Protein (Cyanobacteria): 428318141 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GNDMICGTNRRGFQPPSHSSSRLKPTENSSDDAAGNDMICGTNRRGFQPPSHSSSRLKPTENSSETDVDQLTLQSSFRGLSL ...10 179408:410 ... hypothetical protein Osc7112_3223 Oscillatoria nigro-viridis PCC 7112 MWWQLLRIMPKFAPNLSPDDAT

  14. Protein (Cyanobacteria): 113478324 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available phorus lyase complex subunit Trichodesmium erythraeum IMS101 MLKVDLPGIWQDEVQQQIFRQL... YP_724385.1 NC_008312 1117:23601 ... 1150:21798 1301283:39608 ... 1205:2820 1206:2820 203124:2820 ... carbon-phos

  15. Protein (Cyanobacteria): 661292839 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2:479 ... chorismate mutase Prochlorococcus sp. scB243_498G3 MNDDYIITFIRGATTASGNSVKEIEVAVVELIDELISRNNLIKTNILSIIFTATKDLNACFPASIARKFNGLDSVAFLDCQQMHVSNDVDFCIRIMAQVLLPPNYEIKHPYLNGAAKLRTDRC

  16. Protein (Cyanobacteria): 470147 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rase III subunit beta Prochlorococcus marinus str. MIT 9313 MEPKMSKDKEFAISKDSLRASWGNVPISAKIYQQIQAYLLQRQSMGLSTDVDELISTATDEFRDFQQRPEVKEALELVCADLASDQAFSGLSKDETTRAIVINFAIANYFNNCIGK ...

  17. Protein (Cyanobacteria): 265138 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_05789486.1 1117:4795 1118:3283 1129:815 166314:333 secreted pentapeptide repeats... protein Synechococcus sp. WH 8109 MASLLAVITLAFSTVVWAESVQAITAPELRGQFAVQEISADMHGLDLKEKEFLKADLREVNLSGTDLRGAVIN

  18. Protein (Cyanobacteria): 265114 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_08955563.1 1117:4795 1118:3283 1129:815 166318:666 pentapeptide repeat protein S...ynechococcus sp. WH 8016 MPLPDLFRKQLLSVLFGLLLTSSLISFPFAAQAITAPELRGQFAVQDISNDMHGRDLKEKEFLKADLRGVDLSDTDLRGAVIN

  19. Protein (Viridiplantae): 357134432 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8024:5377 3398:5377 4447:5981 4734:5981 38820:5981 4479:5981 359160:5029 147368:5115 147385:5115 15367:5115 15368:5115 PREDICTED: bor...on transporter 4-like Brachypodium distachyon MEHKKTLFKGVIEDFRGRAACYKQDWHNGFSSGFRIL

  20. Protein (Viridiplantae): 802013 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ica MASRSITYPGLLLLVVALVLVPSSQAKRSPPRSAPTPAPRIAPSPAPRSAPTPAPRSAPTPAPRAPQALSPTPAPTPAPRTAPTPAPRSAPTPAPRA...PQAPSPTPAPTPAPTPAPRTAPTPAPRSAPTPAPRAPQAPSPTPAPMPAPRTAPTLAPRSAPTPAPRAPQAPSPTPAPRTAPISAPTPAPRSAPTPAPRA...PQAPSPTPAPTPAPRTAPTPAPRSAPTPAQRAPQAPSPTPAPTPPPRTAPTPAPAPAPKSAPTPAPMAPQAPSPTPAPTASPMTAPTPAPTSAPTPAPRAPQAPSPTPAPTPAPMDGSNTCS

  1. Protein (Viridiplantae): 488484 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KLFCKIHREGLRIDGILLSALLGVCANVASIKFGTQIHAYMHKKQPMGDLALDNALVDMYAKSGEYLDSRRAFDEMPSRNV...HYSDALGLFASMLRDGMLPDHFTFGSALKACGAISVIFNVELIHTCIIKLGYWDEKVATASLIDSYAKCRSLSSARVIYDSICEPDLVSSTALISDHSMDRNYSEDAM

  2. Protein (Viridiplantae): 427364 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 803:565 ... 3814:565 ... 163742:102 ... 3877:102 ... 3880:102 ... Aluminum-induced protein Medicago truncatula MKFSPHEKQLDCPRTLRDSGPYPPDQVAKELDGSFAFVVYDSDGSVVISDDLNVIQEGCAKSFAPFSAATMVT

  3. Protein (Viridiplantae): 658913 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GYMPSLLLDPNVKNPSQIQQLKDFGTGIHSQVSQEPSPYTEFYVQQRTSNPRKCKFMGCVKGARGASGLCISHGGGQRCQKPGCNKGAESKTTFCKTHGGGKRCEHLGCTKSAEGKTDFCISH...GGGRRCEFLEGCDKAARGRSGLCIKHGGGKRCNIEDCTRSAEGQAGLCISHGGGKRCQYFSGCEKGAQGSTNYCKAHGGGKRCIFSGCSKGAE

  4. Protein (Viridiplantae): 108125 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:363 ... 3066:363 ... 3067:363 ... 3068:363 ... hypothetical protein VOLCADRAFT_35996, partial Volvox carteri f. nagariensis HIAYCISH...IAYCISHIAYCISHIAYCILHIAYCISHIAYCVSHIAYRILHIAYRILHIAYRILHIAYCILHIAYCILHIAYRISHIAYCISHPYRCIWHIAY

  5. Protein (Viridiplantae): 108124 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:363 ... 3066:363 ... 3067:363 ... 3068:363 ... hypothetical protein VOLCADRAFT_99209 Volvox carteri f. nagariensis MQMHAHTYNISHIVYCISH...IAYCISHIAYRISHIAYRISHIVYRVSHIAYRILHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAYRISHIAAYMAYRISHTAYRISQIAYRCISHIAAYRCILHITYMHIIYAHI

  6. Protein (Viridiplantae): 108120 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:363 ... 3066:363 ... 3067:363 ... 3068:363 ... hypothetical protein VOLCADRAFT_100737 Volvox carteri f. nagariensis MYNISHIVYCISHIAYCISH...IAYRISHIAYRILHIAYCISHIAYCISHIAYCISHIAYRISHIPYRCTISLHMAYRISHTARISHIANCISLHIAYCILHIAYCISHIAYPISLHHIAAYGISHITYRTHIAYRKLHIAAYRISLHIAAYCISHIHICIYAHI

  7. Protein (Viridiplantae): 658914 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KRSGGYMPSLLLDPNVKNPSQIQQLKDFGTGIHSQVSQEPSPYTEFYVQQRTSNPRKCKFMGCVKGARGASGLCISHGGGQRCQKPGCNKGAESKTTFCKTHGGGKRCEHLGCTKSAEGKTDFCISH...GGGRRCEFLEGCDKAARGRSGLCIKHGGGKRCNIEDCTRSAEGQAGLCISHGGGKRCQYFSGCEKGAQGSTNYCKAHGGGKRCIFSGCS

  8. Protein (Cyanobacteria): 218248342 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ... hypothetical protein PCC8801_3595 Cyanothece sp. PCC 8801 MSIQYLLDENLPHLYREQLLRLKSDLTVWIIGDPGVPPKSTLDPEILIWCEQNKFILVTNNRASMPVHLADHLSQNRHIPGIFVLRPKASIGEIIDDLILIDELGNPQDYQDCISHIPFI

  9. Protein (Viridiplantae): 108121 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:363 ... 3066:363 ... 3067:363 ... 3068:363 ... hypothetical protein VOLCADRAFT_90903 Volvox carteri f. nagariensis MQMHIVYCISH...IAYCILHIAYRILHIAYCISHIAYRILHIAYCILHIAYCISHVAYCISHIPYRCIWHIARISHTAYRIPQITYRCISHIAAYRCILHITYTYMYIYAHI

  10. Protein (Viridiplantae): 297811063 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KRSGGYMPSLLLDPTVRNPSQMQQLKDFGTGIHSQVSLEPSPYTALSVQQRTSNPRKCKFMGCLKGARGSSGLCISHGGGQRCQKPGCNKGAESRTTFCKTHGGGKRCEHLGCTKSAEGKTDFCISH...GGGRRCEFLEGCDKAARGKSGLCIKHGGGKRCNIENCTRSAEGQAGLCISHGGGKRCQFSSGCEKGAQGSTNYCKAHGGGKRCIFSGCS

  11. Protein (Viridiplantae): 108123 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 065:363 ... 3066:363 ... 3067:363 ... 3068:363 ... hypothetical protein VOLCADRAFT_71945 Volvox carteri f. nagariensis MRICLHIAYVCISH...IAYRICACLHIAISHIIHIAYRILPIAYCISHIAYCISHIAYCILHIAYCISHIAYRISHIAYCISHIAYCISHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAAYGILHIAYAYRSQHSIA

  12. Protein (Viridiplantae): 276123 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EFEAVASLDIAREKAEARAELLRNERITAKAGDGKITLSSLASAVSSGRLSGIDLHQLNIILKVDVQGSVEAVRQALQVLPQDNVTLKFLLQATGDVSSSDVDLAIAS...QISALKGDNIDDLLETVMLVAELQELKANPHRNAKGTVIEAGLDKSKGPIATFIIQNGTLKRGDVVVCGEAFGKVRALFDDGGKRVDEAGPSIPVQVIGLSNVPKAGD

  13. Protein (Viridiplantae): 357437461 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tioning 1A Medicago truncatula MKEEIHNNPSENKTKVSKFSDQNQPPKLQTTKTTNPNNNNHSKPRLWGAHIV...36 3398:436 71240:66 91827:66 71275:1826 91835:7886 72025:8391 3803:8391 3814:8391 163742:99 3877:99 3880:99 Chloroplast unusual posi

  14. Protein (Cyanobacteria): 281754 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available se with PAS/PAC and GAF sensors Oscillatoria nigro-viridis PCC 7112 MLYNNEILPTLTVESSPRSMNILLYKLLSLRRIEYIAVDR...YP_007115817.1 1117:4890 1150:2464 1158:318 482564:246 179408:246 diguanylate cycla

  15. Protein (Cyanobacteria): 281805 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available se with PAS/PAC and GAF sensors Oscillatoria nigro-viridis PCC 7112 MYLILPDLYANMTYQIDERLNTSPCGFLSFADDGTIVMVN...YP_007118829.1 1117:4890 1150:2464 1158:318 482564:246 179408:246 diguanylate cycla

  16. Protein (Cyanobacteria): 279247 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_09782276.1 1117:4884 1150:2505 35823:234 376219:114 putative Diguanylate cyclase with PAS/PAC and GAF sen...sors Arthrospira sp. PCC 8005 MMDKYLCPCCSEPLLIHIIAHKKIGFCMNCHQEMPLIEQSRQMATVTEPVDVS

  17. Protein (Cyanobacteria): 281377 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_08493855.1 1117:4890 1150:2448 44471:122 119532:63 756067:63 diguanylate cyclase with PAS/PAC and GAF sen...sors Microcoleus vaginatus FGP-2 MIEESKSIKEKFGVLDSVPVGACLLQDDFVVLFWNTCLEEWTKIPRSQIL

  18. Protein (Cyanobacteria): 275943 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007168782.1 1117:4879 1118:3357 92682:39 76023:39 65093:39 diguanylate cyclase with PAS/PAC and GAF senso...rs Halothece sp. PCC 7418 MDKYLARRTQDLRQQAQARLEQRERETDLNEMTPAELAHELEIHQTELEIQYEELQR

  19. Protein (Cyanobacteria): 285307 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ith PAS/PAC and Chase2 sensors Nostoc sp. PCC 7107 MSKQLGKSFVSSNLNLNLKQLLDRKYRQLVVAFSVAVCIILLRSVGMFQSLELAGLD...YP_007048593.1 1117:4890 1161:684 1162:948 1177:381 317936:58 diguanylate cyclase w

  20. Protein (Cyanobacteria): 286149 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007068440.1 1117:4890 1161:684 1185:224 1186:169 99598:92 diguanylate cyclase with PAS/PAC and Chase2 sen...sors Calothrix sp. PCC 7507 MSKQLGKCLVKFIFGLKQSLGRGHRELITASSVVICILFLRSIGLLQFLELAALD

  1. Protein (Cyanobacteria): 281376 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_08491810.1 1117:4890 1150:2448 44471:122 119532:63 756067:63 diguanylate cyclase with PAS/PAC and GAF sen...sors Microcoleus vaginatus FGP-2 MANMTYQIDELLNTSPCGFLSFADDGTILMVNATLLQLLGYETDELRERK

  2. Protein (Cyanobacteria): 279234 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_09781866.1 1117:4884 1150:2505 35823:234 376219:95 putative Diguanylate cyclase with PAS/PAC and GAF sens...ors Arthrospira sp. PCC 8005 MNQLMEDRSKILWIAGNVGNDNHSLPQSILQNNGYEVHLVIGLKPAYNAIQSWP

  3. Protein (Cyanobacteria): 280942 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available se with PAS/PAC and GAF sensors Crinalium epipsammum PCC 9333 MIEQDKTKDQLLAELATMRQLNNFLLFSGMGVQQHLEKLLIEEREF...YP_007141850.1 1117:4890 1150:2445 241421:53 241425:53 1173022:53 diguanylate cycla

  4. Protein (Cyanobacteria): 279248 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available se with PAS/PAC and GAF sensors Arthrospira maxima CS-328 MMDKYLCPCCSEPLLIHIIAHKKIGFCMNCHQEMPLIEQSRQMATVTEPV...ZP_03273626.1 1117:4884 1150:2505 35823:234 129910:158 513049:158 diguanylate cycla

  5. Protein (Cyanobacteria): 307154701 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_003890085.1 NC_014501 1117:8352 ... 1118:3762 1301283:19569 ... 43988:641 497965:226 ... PAS/PAC and GAF sens...ors-containing diguanylate cyclase Cyanothece sp. PCC 7822 MWEFISNFLAPKSYIPHGHCYLWQ

  6. Protein (Cyanobacteria): 281806 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available se with PAS/PAC and GAF sensors Oscillatoria nigro-viridis PCC 7112 MIEESKSIKEKFGVLDSVPVGACLLQDDFVVLFWNTCLEE...YP_007117793.1 1117:4890 1150:2464 1158:318 482564:246 179408:246 diguanylate cycla

  7. Protein (Cyanobacteria): 499307394 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KLGNIGLLRLTFFSNRVSDTVAFKRLTPPVNGNTGTWENIGLVQTTGIEASLNLQLAKNIYAFVNYTANDPRILESANPAEVDKALRFAGADKLNLGASYENPQGWYLGVLMNSLNGYPTNNINTEFLSGYTTFDLKMRVPISDSLVLTGSLDNLFDQRYQLFPGYPDGGRVFQVGLSSRF

  8. Protein (Cyanobacteria): 57689 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GLLRLTFFSNRVSDTVAFKRLTPPVNGNTGTWENIGLVQTTGIEASLNLQLAKNIYAFVNYTANDPRILESANPAEVDKALRFAGADKLNLGASYENPQGWYLGVLMNSLNGYPTNNINTEFLSGYTTFDLKMRVPISDSLVLTGSLDNLFDQRYQLFPGYPDGGRVFQVGLSSRF ...

  9. Protein (Cyanobacteria): 413615 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LMSPALSQELTVENMKEIWQDLITITGPIKKQGDSRVISTVNSDLVSINTEFTNKTEDFIVVFNKEGQVVGIDFPQTKSVEEIAQTVVNAVAQNNFAQARGYLHPFLKTELFPQQIRASWESIQQRNGSFEKIVETEVRSGSSVDKVDVVVVEAQFQKANQKIFFIFDENGRITGIDLTQ ...

  10. Protein (Cyanobacteria): 493499523 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DGSEPEMCGNGIRCLAKFIADLEEEHNEPTLPKSYGVHTLAGIIRPELKPDGQVTVDMGEPILTAREIPTTLGQPDGKVIDETLTVAGENWQVTCVSMGNPHCITFVD...DVEAVPLADIGPRFEHHEAFPARINTEFVEVVRPDFLRMKVWERGAGPTLACGTGTCALVVAAVLNGKCDRQTTVELPGGNLEIEWANNNRVYMTGPATLVFSGDVAVDAAGR

  11. Protein (Cyanobacteria): 5336 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ical protein P9515_09211 Prochlorococcus marinus str. MIT 9515 MEENVDSIGDSYINEKDTFKKDNKNTNKEKVAKEKSNEVNKEINEEKVAKENSNEVNIEINEE...KISEENSKEVNKDINKEKVAKEKSNEVNKEINEEKVAKENSNEVNIEINEEKVAKEKSNEVNKEINEEKISEENSKEVNKDINKEKVSKE

  12. Protein (Cyanobacteria): 123966154 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 42:828 ... hypothetical protein P9515_09211 Prochlorococcus marinus str. MIT 9515 MEENVDSIGDSYINEKDTFKKDNKNTNKEKVAKEKSNEVNKEINEE...KVAKENSNEVNIEINEEKISEENSKEVNKDINKEKVAKEKSNEVNKEINEEKVAKENSNEVNIEINEEKVAKEKSNEVNKEINEEKISEE

  13. Protein (Cyanobacteria): 496702915 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WP_009344458.1 ... 1117:5597 ... 1161:618 ... 1162:884 244599:34 668331:34 ... hypothetica...l protein Raphidiopsis brookii MIEVDHLSKIYGSTLAITDVTFKVEPGEILGFLGPNGAGKTTTMRILAGYLPLVRARLKLLDMMSRIIP

  14. Protein (Viridiplantae): 788919 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available CEHGVKPRSRCKVCGACPHGKQRSRCKECGGSGICEHGRVRSLCKECGGSRICEHGRRRYECKACGGSQICEHGRERCRCKECGGGSICEHGRQRYRCKECGGSSICEHGRQRYRCKECG...GSQICKHGRERSKCKECGGSQICEHGRERCRCKECGGGSICEHGRQRSQCKECGGSAICEHGRHRSYCKECGGSAFCEHGRQRSQCKECG...GSQICEHGRIRSKCKECGGGSICEHGRMRSQCRECGGGSICEHGRRRSRCKECGGPRISTPP

  15. Protein (Viridiplantae): 788911 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EEEEDASNKGTKRKRAPYTKGPCEHGVKYRSKCKVCSACPHGRERRYCKDCGGSKICEHGRQRDYCKECGGGAICEHGRERHRCKECGGSGICEHGRRRSRCKECGGSGICEHGRVRSRCKECG...GGSICEHGRERSRCKECSGSGVCEHGRERSKCKECGGASICEHGRQRSHCKECGGGSTCEHGRERRYCKECGGSGICEHGRIRSQCKECG...GSGICEHGRRRSDCKECGGSQICEHGRIRSTCKECGGSQICEHGRQRSYCKECGGGSICEHGRRRSRCKECGGSQICEHGRERSKCKECGGASICEHGRQRSQCKECG...GSGVCEHGRQRTRCKECGGASICEHGRVRSQCKECGGGGICEHGRQRSKCKECRAAKAGTHS

  16. Protein (Viridiplantae): 788948 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 832:429 ... 296587:152 ... predicted protein Micromonas sp. RCC299 MRARGKVEVELQGVQRLSARCKECGGSQICEHGRQRFHCRECGGSGICEHGRGRHRCKECG...GSQICEHGRVRSQCKECGGSGICEHGRRRSLCKECGGSGICEHGRQRYSCKECGGAGICEHGRERYSCKECRAAKAGTFPDVDVEVGVTEDA...SSKGAKRKRAPYTKGPCEHGVKYRSQCKVCSACPHGRQRNKCKECGGASICVHGRERNKCKECGGASICEHGRQRSHCKECGGASICVHARERNKCKECG...GASFCEHGRQRRYCKECGGSQICEHGRVRRLCKECGGSGICEHGRQRPQCKECGGSQICEHGRQRYSCKECRAAKAKQR

  17. Protein (Viridiplantae): 788910 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GPCEHGVKPRSQCKVCSACPHGKRRRHCKECGGSQICEHGRVRSQCKECGGASICEHGRQRHRCKECGGAGICEHGRQRSVCKECGGSSICEHGRIRSTCKECGGSQICEHGRQRHRCKECG...GGGICEHGRQRSVCKECGGSQICEHGRVRSTCKECGGAGICEHGRQRHRCKECGGASICEHGRQRRYCKECGGSGICVHGRQRHSCKECG...GGGICEHDRQRHRCKECGGSQICEHGRVRSTCKECGGGSICEHGRRRSGCKECGGGGICEHGRQRSRCKECGGGSICEHGRRRCECKECGGSQICEHGRRRSQCKECGGASICEHGRHRHQCKECRAAKAKQSR

  18. Protein (Viridiplantae): 788908 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8832:429 ... 296587:152 ... predicted protein Micromonas sp. RCC299 MPAIWNVSGPLPDVDVEVGVTEDASSKGTKRKRAPPTKGPCEHG...VKPRSKCKVCSACPHGKRRSECKECGGSQICEHGRRRTQCKECGGSQICEHGRVRSTCKECGGSGLCEHGRERSRCKECGGPGICEHGRVRSRCKECGGSQICEHGRQRSKCKECG...GGSICEHGRIRSTCKECGGSQICEHGRERSKCKECGGGAICEHGRIRSTCKECGGGAICEHGRERHRCKECGGSGICEHGRRRSQCKECG...GSAICEHGRHRQYCKECGGGSICEHGRIRSTCKECGGGAICEHGRQRHRCKECGGASFCEHGRQRSRCKECGGSGICEHGRRRSTCKECRAAN

  19. Protein (Viridiplantae): 788912 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8832:429 ... 296587:152 ... predicted protein Micromonas sp. RCC299 MLPDVDVEVGVTEDASSKGTKRKRAPKTKGPCEHGVKRRSNCKVCSACPHGKWRYWCKECG...GAGICEHGRERRRCKECGGASICEHGRQRRYCKECGGGSICEHGRVRYYCKECGGSGICEHGRDRSRCKECGGGSICEHGRERYYCKECGGSQICEHGRRRSECKECG...GSQICEHGRRRSECKECGGSAICEHGRQRYYCKECGGSGICEHGRDRSRCKECGGGSICEHGRERYYCKECG...GAGICEHGRIRSTCKECGGSRICEHDRQRHTCKDCGGSQICEHGRVRSKCKECGGSGICEHGRHRQYCKECGGGSFCEHGRQRRKCKECGGSQI

  20. Protein (Viridiplantae): 788914 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GTKRKRAPYTKGPCEHGVKPRSQCKVCSACPHGKRRRYCKECGGSQICEHGRIRTLCKECGGSRICEHGRERRRCKECGGGSICEHGRQRSYCKECGGSGICEHGRQRHYCKECGGGSICEHGRRRSECKECG...GGSICEHSRVRYTCKECGGSQICAHGRQRSTCKECGGSQICEHGRIRSTCKECGGSQICEHDCIRSTCKECG...GGSICEHGRQRDYCKECGGSRICAHGRERRYCKECGGSGICEHGRQRKQCKECGGSAICEHGRQRHQCKECRGSSVPVGRWVL

  1. Protein (Cyanobacteria): 423018 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HETFSEKKIVQLKIAHPEAEAIAHPECESSVLRHASFIGSTAALLKYCQTSPSQEFIVATEPGIIHQMQKLAPNKHFIPAPPVNNCACNECPFMRLNTLEKLYLAMKNRTPEITMSEDIRVAALRPIQRMLEMSV ... ...TAKILNPDKLVLLPDLNAGCSLADSCPPAEFAAFKAAHPDHVVVSYINCSAEIKAMSDIICTSSNAVKIVQQIPEAQPIIFAPDKNLGRYVMEQTGRDLVLWQGSCIV

  2. Protein (Viridiplantae): 959385 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available othetical protein AMTR_s00062p00178830 Amborella trichopoda MGNCVRKSSSWEGWEDEEWGCDEAEKLVLKPKVEREEEVLSKKKNGGDSKEVKIRISKKQLEELLGKMELHGMSVDQMIEQLMNTNGHKHRGWRPVLQSIPECESWNVGMREKDNCEVADF

  3. Protein (Cyanobacteria): 428210455 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LYTADHRYHRSLYKNILKKSRYFIANRAKIDDANATGDQQEVGARFFEGAAAGTVMLGVPPECESFTRNFDWEDAVIQVAYDAPNIVEILAELDSQPDRLQKIRTNNVVNSLLKHDWVYRWETILATVGLDSTPAMMARKARLQNLVERILTRKNSDRQLITQTGFTSKTERRCQLFESVITD

  4. Protein (Cyanobacteria): 423017 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KILNPEKLVLLPDLNAGCSLADSCPPKEFAAFKAAHPDHLVVSYINCSAEIKAMSDIICTSSNAVKIVQQIPKEQPIIFAPDRNLGRYVMEQTGRDLVLWQGSCLVHETFSEKKIVQLKVAHPQAEAIAHPEC...ESSVLRHASFIGSTAALLQYCQTSPSQEFIVATEPGIIHQMQKLAPNKHFIPAPPINNCACNECPFMRLNTLEKLYWAMKNRTPEITMSEDIRLAALRPMQRMLEMSN ...

  5. Protein (Cyanobacteria): 146367 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ain protein Halothece sp. PCC 7418 MSLVSFSELVTGAKEGKVVSFPTDTVPALAVRPDCAEAIFELKQREATKPLILMGASPEQLWDYVEGTPEEFQ...VWEQTAQQYFPGQLTLVLPSSSLVRPEVNPKTADTIGIRVPDCAIARQVFASTGVLATTSANRSGQPPLTTPEAINQAFPEVLVLADTEPIVSSGLPSTVAKWTGQDWEILRQGNIYLK ...

  6. Protein (Cyanobacteria): 428774810 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 65093:254 ... SUA5/yciO/yrdC domain-containing protein Halothece sp. PCC 7418 MSLVSFSELVTGAKEGKVVSFPTDTVPALAVRPDCA...EAIFELKQREATKPLILMGASPEQLWDYVEGTPEEFQVWEQTAQQYFPGQLTLVLPSSSLVRPEVNPKTADTIGIRVPDCAIARQVFASTGVLATTSANRSGQPPLTTPEAINQAFPEVLVLADTEPIVSSGLPSTVAKWTGQDWEILRQGNIYLK

  7. Protein (Cyanobacteria): 505037159 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ... SUA5/yciO/yrdC domain-containing protein Halothece sp. PCC 7418 MSLVSFSELVTGAKEGKVVSFPTDTVPALAVRPDCAEAIF...ELKQREATKPLILMGASPEQLWDYVEGTPEEFQVWEQTAQQYFPGQLTLVLPSSSLVRPEVNPKTADTIGIRVPDCAIARQVFASTGVLATTSANRSGQPPLTTPEAINQAFPEVLVLADTEPIVSSGLPSTVAKWTGQDWEILRQGNIYLK

  8. Protein (Cyanobacteria): 414077569 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available lasmid addiction system poison protein Anabaena sp. 90 MLINLNENINYTVVIGIDAQDFFESASATLQKKLDRCFEILKIEPRNYPNIKALKGEFSGYYRYRVGDYRVIYEIDDNSKLVTILLIAHRSKVYE ... YP_006996887.1 NC_019440 1117:5824 ... 1161:889 ... 1162:2120 1163:3278 46234:816 ... p

  9. Protein (Viridiplantae): 849056 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IAIVVVLLASVLSPLCAKNGLAVDVPLATEAPSASPQAPFYAPEEAPLPPAFQAPFAAPSPSQAPSQSPGLPDEPPSPSQAPSQSLGEAPS...QNPRPCSCYEPLSPLQAPSQSPGLSYEPLSPSQAPSQSPGLSYEPVSPSQAPSQSPGLSYGPPSPSQAPSQSPGLSYEPLSPSQAPSQSPGLSYEPPSPSQAPSQSPELSYEPSSPSQAPS...QSPGLSYEPPSASQAPSPSPGLSYESLSPSQAPSQNPGLPSKPPSPSLAPPPPKKKSPPKSIPPYMPWGPLPGHRIHPRLPPLREDIYQCWKTLCPIPYCVDRTYWSFYAGKIDVGSFCCKAFERTNDTCFRKMFLAFPNPRLKDALLTYCSKH

  10. Protein (Cyanobacteria): 58265 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PFQYGDQVSCLEWQHGHGEVRAIGPDKLIYVLWADSHQISRHCPSDLIAVREQGLGNNAIASPEVREQGLGNHHTIAPPEV...REQQLGNIELGNNTIAPPEVREQGLGNIELGNNAIASPEVREQQLGNHHTIAPPEVREQQLGNIELGNIELGNNAIASPEVREQGLGNNAIASPEVREQQLGNNAIASP

  11. Protein (Cyanobacteria): 257062007 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PDPDDFDGYWDWIEAWEQWGSSHPDYLIPDSPFQYGDQVSCLEWQHGHGEVRAIGPDKLIYVLWADSHQISRHCPSDLIAVREQGLGNNAIASP...EVREQGLGNHHTIAPPEVREQQLGNIELGNNTIAPPEVREQGLGNIELGNNAIASPEVREQQLGNHHTIAPPEVREQQLGNIELGNIELGNNAIASPEVREQGLGNNAIASP...EVREQQLGNNAIASPEVREQQLGNNAIATPGVREQAVREHPKPTQPPTKVLEKAREFRAKLGNGTIELKKIKSQFYWYFRYRDESRKLKSKYLAKACSISP

  12. Protein (Cyanobacteria): 506264217 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PDYLIPDSPFQYGDQVSCLEWQHGHGEVRAIGPDKLIYVLWADSHQISRHCPSDLIAVREQGLGNNAIASPEVREQGLGNH...HTIAPPEVREQQLGNIELGNNTIAPPEVREQGLGNIELGNNAIASPEVREQQLGNHHTIAPPEVREQQLGNIELGNIELGNNAIASPEVREQGLGNNAIASPEVREQQLGNNAIASP

  13. Protein (Cyanobacteria): 58264 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PFQYGDQVSCLEWQHGHGEVRAIGPDKLIYVLWADSHQISRHCPSDLIAVREQGLGNNAIASPEVREQGLGNHHTIAPPEV...REQQLGNIELGNNTIAPPEVREQGLGNIELGNNAIASPEVREQQLGNHHTIAPPEVREQQLGNIELGNIELGNNAIASPEVREQGLGNNAIASPEVREQQLGNNAIASP

  14. Protein (Cyanobacteria): 257059940 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PDPDDFDGYWDWIEAWEQWGSSHPDYLIPDSPFQYGDQVSCLEWQHGHGEVRAIGPDKLIYVLWADSHQISRHCPSDLIAVREQGLGNNAIASP...EVREQGLGNHHTIAPPEVREQQLGNIELGNNTIAPPEVREQGLGNIELGNNAIASPEVREQQLGNHHTIAPPEVREQQLGNIELGNIELGNNAIASPEVREQGLGNNAIASP...EVREQQLGNNAIASPEVREQQLGNNAIATPGVREQAVREHPKPTQPPTKVLEKAREFRAKLGNGTIELKKIKSQFYWYFRYRDESRKLKSKYLAKACSISP

  15. Protein (Cyanobacteria): 479126449 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_005066409.1 NC_016640 1117:4000 ... 1150:30479 1301283:49254 ... 35823:598 118562:443 696747:443 ... phosphono...pyruvate decarboxylase Arthrospira platensis NIES-39 MIDPQAFYTTLYQAGVHLFAGVPDSLLKDF

  16. Protein (Cyanobacteria): 129527 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ing protein Oscillatoriales cyanobacterium JSC-12 MLLIDTSVWISVFRDRTGQVRQKLETLIDARDIFLTRFTQLKLLQGSLNEKEWTLLSTYLETQDYVEPVGNSWRAAARIYYDLRRRGLTVRSPIDCCIAQAALENDLLLIHNDRDFETIAQVRSLQHFRFQP ...

  17. Protein (Cyanobacteria): 64998 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available syc2491_c Synechococcus elongatus PCC 6301 MRPLTLEPHDQRSVLRLLIGAAWLDGDMQPEERNYLKGLLEKHRLAADPEFQDLMTRTTPISPAVFEQWLTAYLRQHPRREDVEALLEQISSVIYADSLIDAREAAVLCEIEQELEHRPALRLLDRLQTFFHHCLVMS ...

  18. Protein (Cyanobacteria): 394995 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available pothetical protein gll3097 Gloeobacter violaceus PCC 7421 MKYFFLAEGWRVGRVWDSAGVWDDLVQRRKPQLERINLGIIEQGETFWLYRTEEAVVMVEVKRTEQTTNPAVQGIAQVLLKRLIDARETLERLSKAEVIFNACEPRVPLTSSKEESGRMR ...

  19. Protein (Cyanobacteria): 81404 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available _06604 Lyngbya sp. PCC 8106 MNAEVSLFTIGFTRKSAEQFFGILKKAGVTRLIDARLNNSSQLAGFAKKKDLEYFLKVICNIDYIHLLDLSPTKEILDEYKKNGEDWQVYERQFLQLMRDRQVEEKFSPELFYKGCLLCSEATPERCHRRLVAEYLQEKWTTINLNVYHL ...

  20. Protein (Cyanobacteria): 292628 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n Arthrospira sp. PCC 8005 MDDSSAIAHISTRHPHQSSLKPCNFLGVRIIPNVPGINMKFERDTIVKLTIGSGCVLGSLAFPPLAAAEGMVWGNILATALGNVAAGNTANAVDALIDAREGRVSLENQDLTKAVGKAILYETLRERRRYHPRSQTTGRQNPRISRKNRRPSQG ...

  1. Protein (Cyanobacteria): 442135 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rotein MicvaDRAFT_0707 Microcoleus vaginatus FGP-2 MIDFNTVTEFSHTYCIAICAFLVPANLLTTLVTVILTALNRPRIQIWASVVVASLWATAMIFHVFCWFAIGVVMPPTYILLVMGITCLTINVWAIAHPASMMQLIRVAVSVVRGSLQRKKDLVILERRM ...

  2. Protein (Cyanobacteria): 75910043 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QVQLQFYRITAPFEGTVGNIPIKIGDFVNSSTPLLTITQNRPLEVNISVPLERGSQLRQGMPVEIMNTQGQTLGTSRVFFIAPNASNETQSILVKALYNNTNGQLRADQLVRARVIWNQRTGVLIPITAVTRI...AGETFVYVTQTEKTPQGTSQLVARQKRVQLGDIRGNNYQIIKGLQPTDTIVTSGLLNLRDGVPIVPES

  3. Protein (Cyanobacteria): 515884325 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TQLVSITQNQPLEVNIFVPIERGPQLRKGTPVEVMDAQGNSLGMSKVFFIAPSASNNTQSILIKSLYDNSKNQLRADQFARARVIWSQRSGVLVPTTAVTRIAGETFVYVTAQVPSKPPQGEKPQRDQEAFQLVARQKRVRLGTIKGNNYQVLEGLEPGDRVIVSGLLNLKDGVPIAPES

  4. Protein (Cyanobacteria): 427702170 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007045392.1 NC_019675 1117:4830 ... 1118:1420 1301283:4671 ... 167375:1797 59930:341 292564:341 ... copper/sil...ver-translocating P-type ATPase Cyanobium gracile PCC 6307 MSHSTLGSPCCAADPAAAATTGME

  5. Protein (Cyanobacteria): 493577702 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WP_006530817.1 NZ_ALVY01000210 1117:4001 ... 1118:2563 1301283:17370 ... 102231:400 102232:1190 ... putative sil...ver efflux pump Gloeocapsa sp. PCC 73106 MRSQNKPLVKVLLITTLLLSVPKIAISHVGHGDEFQATGGIE

  6. Protein (Cyanobacteria): 427704561 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007047783.1 NC_019675 1117:4830 ... 1118:1420 1301283:4671 ... 167375:1797 59930:341 292564:341 ... copper/sil...ver-translocating P-type ATPase Cyanobium gracile PCC 6307 MDCATEEGEIRHALAGVDGIRGLR

  7. Protein (Cyanobacteria): 414076004 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available pothetical protein ANA_C10715 Anabaena sp. 90 MSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLED...KLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSLNASPVQLSVGRNIPPAPCLFCLLL

  8. Protein (Cyanobacteria): 504891571 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l protein Anabaena sp. 90 MSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLED...KLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSLNASPVQLSVGRNIPPAPCLFCLLL

  9. Protein (Viridiplantae): 444213 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DNTKTADSCDKFKRALENQSNLLAVHSHTGDKINHGREKTPGIESLVNYTSKERPNEENVCETHELELLEDGKGIPLEDLGCDDDSGREDNVCETHELELLEDGKGIPLED...LGCDDDSGREDNVCETHELELLEDGKGIPLEDLGCDDDSGREDNVCETHELELLEDGKGIPLEDLGCDDDSGREDNVCETHELELLEDGKGIPLED...LGCDDDSGREDNVCETHELELLEDGKGIPLEDLGCDDDSGREDNVCETHELELLEDGKGIPLEDLGCDDDSGREDNVCETHELELLEDGKGIPLED...LGCDDDSGREDNVCETHELELLEDGKGIPLEDLGCDDDSGREDNVCETHELELLEDGKGIPLEDLGCDDDSGREDNVCETHELELLEDGKGIPLEDLGCDDDSGREDNVCETHELELLED...GKGIPLEDLGCDDDSGREDNVCETHELELLEDGKGIPLEDLGCDDDSGREDNVCETHELELLEDGKGIPLED

  10. Protein (Cyanobacteria): 259590 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NA_C10715 Anabaena sp. 90 MSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLED...KLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSLNASPVQLSVGRNIPPAPCLFCLLL ...

  11. Protein (Cyanobacteria): 414079227 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available pothetical protein ANA_C20136 Anabaena sp. 90 MVTKFDHNLVVSENVELVNCQLLVGAKHLEDKLSVIAKNSSPNASPVQLLVGAKHLEDKLSVIAKNSSPNASPVQLLVGAKHLED...KLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLSVAKKYFSSLFPVP

  12. Protein (Cyanobacteria): 504896048 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l protein Anabaena sp. 90 MVTKFDHNLVVSENVELVNCQLLVGAKHLEDKLSVIAKNSSPNASPVQLLVGAKHLEDKLSVIAKNSSPNASPVQLLVGAKHLED...KLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLSVAKKYFSSLFPVP

  13. Protein (Cyanobacteria): 259591 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NA_C20136 Anabaena sp. 90 MVTKFDHNLVVSENVELVNCQLLVGAKHLEDKLSVIAKNSSPNASPVQLLVGAKHLEDKLSVIAKNSSPNASPVQLLVGAKHLED...KLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLLVGAKHLEDKLSVIAKNSSANASPVQLSVAKKYFSSLFPVP ...

  14. Protein (Viridiplantae): 102428 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available s domestica MGEEREDPQQLKRVAAAAYDYENDPRWADYWSNILIPTHMSSRSDVIDHFKRKFYQRYIDPELMVDAXSSGSSSQPKRPSXSS...ALQVYFQSIITTKDFIYLIYCITFVTSHLCLKFALIPILCRALEHVAKFLRRNFSXSSLYRKYLEEPCVWVESNTTTLSILSSHAEVGVGFLLIISLFSWQRNIVQAFMYWQLLKLMYHAPATADYHLSVWTKIGRTVHPLIHRYARFLETPLSAVQRWWLR

  15. Protein (Viridiplantae): 251668 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available estica MCYCKGIRDKGGDSKFRKSAXDEEXMVNLYFNRIGWXSSLPTNEKESFVKNVLQKKKMAMDEFLMSEKLTLXPG...VEEFIDDAYKEGIHVVLLTTYSKSGDQIGRSIVEKLGKERISKLKIVGYKEVDLSLYTXLVNDXXLXSSXDKQLAKEAIKVVFAEKQRIAXEVASMLQLSVDIDTSPP...GSFGVQDKSHILEGGKGIYTTTFTSSLLTGRGMMTMXDIGILKHFSSXYVEQRKLDAAFTVAKHIPILEDESSVLGSLLLKLXSSNLIWGASITXLPVMS

  16. Protein (Viridiplantae): 319058 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WCRAMEISLGAKNKIGFINGKVNMPSETKQPDAYAAWQRCNNMLLAWIINSIESDXSBSILYLKTAYEVWEDLXEXFSQSNAPRIFQLQREIASLTQGQQSVAVYYTKLKXLWDELASYXSS...TIXTCGAQHETNRLMQFLMGLNESYSAIRGQILLMNPLPSYRQXYSXIIQEEKQRELGTGSRSLTEPAAMAVRHQQXSSKKQHXQSQTSXNSRP...XLHCSYCDAKYHTVETCWQKNGYXPDHPXHNPNXTXNSKQNGGGSGFSXXSSSAHHVASTPTIKXLQXXVPNLSEKQXADI...FSALTSKNDKSQAANEAPQAHAAJTSPPPSGPDFEGQKAYKLYDLETHKIFTNRDVIFLEDTFPFDPSXTXAPSPPLSDLPHSTPLPIPLDPITLDHSTXTPLDIVXHTSTXLDPPLXPSPPPXSS...SHPPTFHPLTDPPTDPTPDLPJSTQPTXFSTXHKEPNVXLRDYXXSQVMLPPLQSSSXSSXGSTKGTRYPICXXISYHRYSPLHLSXVAH

  17. Protein (Cyanobacteria): 427712179 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LLAGNQRFVQNKSLHPHQDVRQLAVVTETQTPFAAILSCADARVIPEIIFDQGIGDLFVVRVAGNIAITEEIASEEYAVTILKTPLIVVLGHERCGAVTATLSGKNLPGVMSSLTTAIQPAIALAQTEPGDLLTNAIKANVRLQVQRLKNSPVLAEAIRAEALNIVGAYYELASGAVRFLG

  18. Protein (Cyanobacteria): 353150 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available _03407 Synechococcus sp. CB0101 MAACAAPGLVLALPAVAQPVQPCASQQLGLTVDGTGFLLRHQACAPAEQIEPERPAVRRPLLSSPLLKSLLQAHRELGSQVQPRATTFRSEDANIACMAISPGCFTAAEWASCESNPGVAFAQARSCADARQVLAARNASSSGWR ...

  19. Protein (Viridiplantae): 761681 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3688:2831 ... 238069:2831 ... 3689:2831 ... 3694:2831 ... caprice family protein Populus trichocarpa MDRRRKKQAKTTSCCSEQEVSSIEWEFINMSEQEEDLIYRMHNLVGDRWALIAGRIPGRKAEEIERFWLMRHGEGFASRRREQKRCHS

  20. Protein (Cyanobacteria): 661258316 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :556 ... 7-carboxy-7-deazaguanine synthase, partial Prochlorococcus sp. scB241_527E14 RSGVNSISGSYDWITLSPKRHSPPKNYFLKNCNEMKIIINEIEDIEFAIQIKKETLKQYQLSKSEDGL ... WP_029953398.1 NZ_JFKU01000143 1117:6377 ... 1212:1253 ... 1217:2123 1218:2123 1471444

  1. Protein (Cyanobacteria): 493968234 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 1:1983 ... 7-cyano-7-deazaguanine reductase Cyanobium sp. PCC 7001 MTASHPPASSQGAPAAAASQAEPDGATRTPLYGERAIAEASL... WP_006911498.1 NZ_DS990557 1117:4682 ... 1118:6723 1301283:22859 ... 167375:1134 18028

  2. Protein (Cyanobacteria): 517207156 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 27:244 ... 7-cyano-7-deazaguanine reductase filamentous cyanobacterium ESFC-1 MNSMSSETEVAQTPEVKYGERAIADCELITF... WP_018395974.1 NZ_KB904821 1117:4682 ... 1150:39727 1301283:59529 44887:1731 ... 11284

  3. Protein (Cyanobacteria): 440680064 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007154859.1 NC_019775 1117:3991 ... 1161:5387 ... 1162:6232 1163:4927 1165:626 272123:626 ... putative addicti...on module antidote protein Anabaena cylindrica PCC 7122 MALTKDFKETVNARIQRDPDFAIVLLDEAISLFLNGELETARLILRNMLNLSHF

  4. Protein (Viridiplantae): 794323 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SGAALVAPFISYWWPSYPENLLREAFLMLPHSDQWTFRVSHYAPWLFYWWMTQKWFPSLTLTNLLSPDDIEIVKSLSELQNTGQERITQQGEYESLHRDIMSAFGKWEFGPTDITNPFPDNNGSVHIWQGFEDRIIPYTLNRYISHKLPWIRYHELPHAGHLFLFKKNECESIIRALVLT

  5. Protein (Viridiplantae): 794319 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SGAALVAPFISYWWPSYPENLLREAFLMLPHSDQWTFRVSHYAPWLFYWWMTQKWFPSLTLTNLLSPDDIEIVKSLSELQNTGQERITQQGEYESLHRDIMSAFGKWEFGPTDITNPFPDNNGSVHIWQGFEDRIIPYTLNRYISHKLPWIRYHELPHAGHLFLFKKNECESIIRALVLT

  6. Protein (Viridiplantae): 794311 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LSGAALVAPFISYWWPSYPENLLREAFLMLPHSDQWTFRVSHYAPWLFYWWMTQKWFPSLTLTNLLSPDDIEIVKSLSELQNTGQERITQQGEYESLHRDIMSAFGKWEFGPTDITNPFPDNNGSVHIWQGFEDRIIPYTLNRYISHKLPWIRYHELPHAGHLFLFKKNECESIIRALVLT

  7. Protein (Viridiplantae): 879494 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NQEETLLQLANKCLRISPSSEEDENECESSTASTIIHEGGNIIEKRKSDLFDLDAVVDKLYACQYYQCPQSLTGMGFLNKN...LSSLLSALMQHCIPPQRRFPLERGLAPPWWPRGAENWWGEQGFLAHEHGPPPYKKPHDLKKAWKVSLLAAIIKHMSPNLDKLRRLVTQSKTLQDKMTARDTATWSKVM

  8. Protein (Viridiplantae): 794317 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SGAALVAPFISYWWPSYPENLLREAFLMLPHSDQWTFRVSHYAPWLFYWWMTQKWFPSLTLTNLLSPDDIEIVKSLSELQNTGQERITQQGEYESLHRDIMSAFGKWEFGPTDITNPFPDNNGSVHIWQGFEDRIIPYTLNRYISHKLPWIRYHELPHAGHLFLFKKNECESIIRALVLT

  9. Protein (Viridiplantae): 794315 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LSGAALVAPFISYWWPSYPENLLREAFLMLPHSDQWTFRVSHYAPWLFYWWMTQKWFPSLTLTNLLSPDDIEIVKSLSELQNTGQERITQQGEYESLHRDIMSAFGKWEFGPTDITNPFPDNNGSVHIWQGFEDRIIPYTLNRYISHKLPWIRYHELPHAGHLFLFKKNECESIIRALVLT

  10. Protein (Viridiplantae): 794313 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LSGAALVAPFISYWWPSYPENLLREAFLMLPHSDQWTFRVSHYAPWLFYWWMTQKWFPSLTLTNLLSPDDIEIVKSLSELQNTGQERITQQGEYESLHRDIMSAFGKWEFGPTDITNPFPDNNGSVHIWQGFEDRIIPYTLNRYISHKLPWIRYHELPHAGHLFLFKKNECESIIRALVLT

  11. Protein (Viridiplantae): 794321 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SGAALVAPFISYWWPSYPENLLREAFLMLPHSDQWTFRVSHYAPWLFYWWMTQKWFPSLTLTNLLSPDDIEIVKSLSELQNTGQERITQQGEYESLHRDIMSAFGKWEFGPTDITNPFPDNNGSVHIWQGFEDRIIPYTLNRYISHKLPWIRYHELPHAGHLFLFKKNECESIIRALVLT

  12. Protein (Cyanobacteria): 516358569 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tical protein Scytonema hofmanni MEDIVPKQTTLCPSARPESADGVVFGIVGGTATVPRVAYLKQLLPVTNELMAKTGSVKPAEIFRTAASCVESGCQHFDGKDCRLSMRIVEKLPAVVEELPACSIRRNCRWWQQEGKAACMRCPQIVTDNYSSSEQLRQAADPSVYFQT

  13. Protein (Viridiplantae): 694561 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ri f. nagariensis RAWARTYVSVSPSAASPSAASPSAASPSAASPSAASSSAASPSASRRRPPRRRPPRRPRLVVRVSSSASRRPVSPSASRRRGLPVGVSPSASRRQRLAVGMSYVSVSPSAASPSA...ASPSAASPSAASPSAASSSAASPSASRRRPPRRRPPRRPRLVVRVSSSASRRPVSPSASRRRGLPVGVSPSA...SRRQRLAVGMSPSASRRRPPHRPECRVDWLPGLGAYESSGLPAPARRGRPYFYNARLRWVDGWVGDVGVGVVRLGHQPVRPSGTERALLMMGPAE

  14. Protein (Viridiplantae): 653017 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3065:1599 ... 3066:1599 ... 3067:1599 ... 3068:1599 ... hypothetical protein VOLCADRAFT_59909, partial Volvox carter...i f. nagariensis ASVRCTPSASVRRTPSASVRCTPSASVRRTPSASVRCTPSASVRRTPSASVRCTPSASVRRTPSASVRCTPSASVRRTPSASVRCTPSASVRRTPSASVRRT

  15. Protein (Viridiplantae): 792252 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ariensis MYSVKYSASSAFRSPEPSLLGLPDTSVPSAFSLHEASEPEVLGQSGTTVPSAFAQPEPSASSLQEPSAPSAFSPPEASAPSAISPQEASVSSAFSPQEP...STFSLQAPAAFSPQEPAAFSPQEPAAFSPQAPAAFTPPEPSAFSPPEPSAFTPPEPSAFTPPEPSAFTPPEPSAFTPPEPSASSPPSELSAFSPQEPSA...FTPPEPSAFTPPEPSAFSPPEPSASSPQSKPSAFSPQEPSELSAFSPQEPSASSPRLSHRPSPRKSHRPSARLSHRPPACKRHRAIGLQPARAIGAIGLQPARAIGASAIARGAIGLQPARAIGLQPA

  16. Protein (Viridiplantae): 145355221 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:4609 distinct from photosynthetic electron transfer catalyst, CYC6, partial Ostreococcus lucimarinus CCE9901 RDLERNGVATKEDISNLIERGKGKMPGYGESCAPKGACTFGARLDAEEIDALATYVLDRAAVDW ...

  17. Protein (Viridiplantae): 949655 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PASRCCKEVSDFVAANSDPMIPAQRKSRRSCRFWKWLCGPCLSLVSFCCCCQSKCSCHLKKPKCCSCTSCSCIGSKCCDGSCCSNICCCPRPSCPSCPSCPSCSCFRDCCSCPDLSCCIPTCFRSCSCARPSCVSKKKKSSCCSCTCKIRWSSCCFKCPKVRLSSCCFCNCKNPCSNPCCLAF

  18. Protein (Viridiplantae): 949654 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EGVQPASRCCKEVSDFVVANSDPLIPAQRKSRRSCRFWKWLCGPCLSLVSFCCCCQSKCSCHLRKPKCCNCTSCSCIGSKCCDGSCCSNICCCPRPSCPSCSCFRGCCCSCPDMSCCIPSCFRNCSCTRPSCLNKKKSSCCSCNCKIRWSSCFRCPKVRLCSCCFCNCKNLCSNPCCLAF

  19. Protein (Viridiplantae): 389551 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nel, putative Ricinus communis MENDPLLPYHSPRKRTPPQLPPILCPLPEDDEVSLPLSISPSELKERLIFGPSPSPNDSTPVFEALTHSLNSPRP...SCSNQEFNFHDSPRHHQQPQSWLIDPNYSWTKTNLHRSKTAPAMAVINDSLNSSHIPKPQFGSQSIVRQAFVLLILYLSFGVV

  20. Protein (Viridiplantae): 9622 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LLCAASAFLGLAIIMVVEHAYMLIAISNSPPSVLVIWEPDHSGPAKSLKWQAAFFFVATWVSFAVGEILLLIGLSVESGHLRKWSRPRPSCLVLREGVFSAAGVFALTTVLLAAGLYLTALRAQRISLHQETVRREIVEASILYASPPTSPQISTIPRENPIFRETHNIDHQPPAALSKHLNL