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Domain architecture conservation in orthologs

Kristoffer Forslund, Isabella Pekkari, Erik LL Sonnhammer
2011 BMC Bioinformatics  
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  ...  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  ...  IP participated in the project as a master's student.  ... 
doi:10.1186/1471-2105-12-326 pmid:21819573 pmcid:PMC3215765 fatcat:hno25y2mffcudijlghm7ebdfiq

PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya

Graham L. Cromar, Anthony Zhao, Xuejian Xiong, Lakshmipuram S. Swapna, Noeleen Loughran, Hongyan Song, John Parkinson
2016 Database: The Journal of Biological Databases and Curation  
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya.  ...  In this update article, we present six major new developments in PhyloPro: (i) integration of Pfam-A domain predictions for all proteins; (ii) new summary heatmaps and detailed level views of domain conservation  ...  Domain architectures of target and reference orthologs were compared and classified parsimoniously as having gained or lost domains, having the same (conserved) domain architecture, or having rearrangements  ... 
doi:10.1093/database/baw013 pmid:26980519 pmcid:PMC4792532 fatcat:ijtm26q6cna37ifdxgmi47ouy4

Morphological Stasis and Proteome Innovation in Cephalochordates

László Bányai, Krisztina Kerekes, Mária Trexler, László Patthy
2018 Genes  
These analyses have confirmed that the domain architecture differences of orthologous proteins of the four lancelet species are because of errors of gene prediction, the error rate in the given species  ...  Our earlier studies on a representative sample of proteins have provided evidence suggesting that the differences in the domain architectures of predicted proteins of these two lancelet species reflect  ...  The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.  ... 
doi:10.3390/genes9070353 pmid:30013013 pmcid:PMC6071037 fatcat:yv7l2n23urfitfgoekcoxkam6q

Putative extremely high rate of proteome innovation in lancelets might be explained by high rate of gene prediction errors

László Bányai, László Patthy
2016 Scientific Reports  
Here we show that the conclusion that the rate of proteome innovation is exceptionally high in lancelets may be unjustified: the differences observed in domain architectures of orthologous proteins of  ...  Interestingly, the unusually high rate of domain architecture alteration is not accompanied by a high amino acid substitution rate.  ...  The domain architectures of proteins (defined as the linear sequence of Pfam-A domains) were determined using Pfam ( 32 .  ... 
doi:10.1038/srep30700 pmid:27476717 pmcid:PMC4967905 fatcat:3g3pyzqr65gcxflibdlzgbfcxy

Molecular evolution of proteins mediating mitochondrial fission-fusion dynamics

Sansrity Sinha, Narayanan Manoj
2019 FEBS Letters  
The domain level variations primarily comprise loss-gain of lineage specific domains that are present in the terminal regions of the sequences.  ...  We demonstrate that the three paralogs emerged concurrently in an early mitochondriate eukaryotic ancestor.  ...  We acknowledge Gopalakrishna Aradhyam for fruitful discussions and Infant Sagayaraj Ravhe for help in phylogenetic tree analyses.  ... 
doi:10.1002/1873-3468.13356 pmid:30861107 fatcat:5lv7cvlfgbfavhyertfw2z32pi

DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection

Ting-wen Chen, Timothy H Wu, Wailap V Ng, Wen-chang Lin
2010 BMC Bioinformatics  
Results: An efficient ortholog detection pipeline DODO (DOmain based Detection of Orthologs) is created on the basis of domain architectures in this study.  ...  Starting from domain information, it first assigns protein groups according to their domain architectures and further identifies orthologs within those groups with much reduced complexity.  ...  Acknowledgements This work is supported in part by grant from Academia Sinica and National Science Council. InParanoid code was kindly given by Stockholm Bioinformatics Centre.  ... 
doi:10.1186/1471-2105-11-s7-s6 fatcat:het6rof3lnbirkdmvcrqhsarje

Domain Architectures of the Scm3p Protein Provide Insights into Centromere Function and Evolution

L. Aravind, Lakshminarayan M. Iyer, Carl Wu
2007 Cell Cycle  
Their plant orthologs appear to entirely lack the MYB domains while conserving the SANTA domain.  ...  Furthermore, in plants the monocot and eudicot proteins show considerable differences in their C-terminal architectures.  ...  Diversity of domain architectures of Scm3p across fungal phylogeny The domain architectures of Scm3p proteins have been superimposed on a maximumlikelihood phylogenetic tree of fungi based on six conserved  ... 
doi:10.4161/cc.6.20.4793 pmid:17704645 pmcid:PMC2394858 fatcat:t6ckh5kznnaorgsszebhkhidne

Molecular Evolution and Diversification of Proteins Involved in miRNA Maturation Pathway

Taraka Ramji Moturu, Sansrity Sinha, Hymavathi Salava, Sravankumar Thula, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, Sibu Simon
2020 Plants  
The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which  ...  in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes.  ...  Conservation of Domain Architecture in DDL SE and TGH Orthologs Domain architecture plays a key role in understanding the functionality of proteins along with their evolutionary history.  ... 
doi:10.3390/plants9030299 pmid:32121542 pmcid:PMC7154892 fatcat:dw7gwico4bd73hgxc5sndd3myq

A combined computational strategy of sequence and structural analysis predicts the existence of a functional eicosanoid pathway in Drosophila melanogaster

Michael Scarpati, Yan Qi, Shubha Govind, Shaneen Singh, Claudio M. Soares
2019 PLoS ONE  
Twenty Drosophila candidates were selected based upon (a) sequence identity with human enzymes of the cyclooxygenase and lipoxygenase branches, (b) similar domain architecture and structural conservation  ...  Evaluation of full-length structural models for these 20 top-scoring Drosophila candidates revealed a surprising degree of conservation in their overall folds and potential analogs for functional residues  ...  Domain Architecture FIG. 4. Predicted domain architecture of PTGES and CG1742 determined using Interpro and Pfam.  ... 
doi:10.1371/journal.pone.0211897 pmid:30753230 pmcid:PMC6372189 fatcat:eys2pnpq5rg4taj74hctn4waay

Ortholog identification in the presence of domain architecture rearrangement

K. Sjolander, R. S. Datta, Y. Shen, G. M. Shoffner
2011 Briefings in Bioinformatics  
In this article, we review the issues involved in orthology prediction when data sets include sequences with structurally heterogeneous domain architectures, with particular attention to automated methods  ...  Phylogenetic methods of ortholog identification have also been developed; these methods can be applied to protein data sets sharing a common domain architecture or which share a single functional domain  ...  Individual domains in a multi-domain architecture can have very different evolutionary rates and functional roles, and taxonomic distributions can also vary widely, with some domains being conserved throughout  ... 
doi:10.1093/bib/bbr036 pmid:21712343 pmcid:PMC3178056 fatcat:hgeq2fpmzvd35b2xsusnmnnhqu

Origin and Evolution of Dishevelled

Adler R. Dillman, Paul J. Minor, Paul W. Sternberg
2013 G3: Genes, Genomes, Genetics  
Conservation and diversification of Dsh domain architecture Next, we wanted to assess the protein domains in Dsh and evaluate the conservation of domain structure across animal evolution among orthologs  ...  In no phylum where multiple taxa were examined did we find complete conservation of both domain architecture and number of Dsh orthologs.  ... 
doi:10.1534/g3.112.005314 pmid:23390601 pmcid:PMC3564985 fatcat:vv26tpx4xbgafeux7u3dhxegfm

New Tricks for "Old" Domains: How Novel Architectures and Promiscuous Hubs Contributed to the Organization and Evolution of the ECM

Graham Cromar, Ka-Chun Wong, Noeleen Loughran, Tuan On, Hongyan Song, Xuejian Xiong, Zhaolei Zhang, John Parkinson
2014 Genome Biology and Evolution  
These include the preferential recruitment of novel domains to existing architectures and the utilization of high promiscuity domains in organizing the ECM network around a connected array of structural  ...  Applying a novel framework for identifying potentially important, noncontiguous, conserved arrangements of domains, we find that the distinct biological characteristics of the ECM have arisen through unique  ...  As expected, the protostomes exhibit a drop in conservation of domain architectures (34.3% of orthologs), resulting from an increase in both domain gains and losses in human ECM proteins relative to their  ... 
doi:10.1093/gbe/evu228 pmid:25323955 pmcid:PMC4224354 fatcat:ecpxoc4rn5bkxfnb4eltophc7u

Molecular Evolution of PAS Domain-Containing Proteins of Filamentous Cyanobacteria Through Domain Shuffling and Domain Duplication

R. Narikawa
2004 DNA Research  
Ortholog analysis of PAS-containing proteins showed composite multidomain architecture in some cases of conserved domains and domains of disagreement between the two species.  ...  The conserved PAS domains in the orthologous proteins were analyzed by structural fitting to the known PAS domains.  ...  Conserved PAS domains in orthologous proteins There are 61 pairs of 122 conserved PAS domains in the orthologous proteins between Anabaena and Nostoc.  ... 
doi:10.1093/dnares/11.2.69 pmid:15449540 fatcat:oimbb75qgneynpxlrfgaubd6jm

Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement

Inbar Cohen-Gihon, Roded Sharan, Ruth Nussinov
2011 Physical Biology  
We show that paralogs gaining new domain architectures via duplication tend to adopt new functions compared to paralogs that preserve their domain architectures.  ...  We suggest that in general, new functions are acquired via the integration of gene duplication and domain rearrangements rather than each process acting independently.  ...  This project has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under contract number HHSN261200800001E.  ... 
doi:10.1088/1478-3975/8/3/035009 pmid:21572172 pmcid:PMC3140765 fatcat:7z2de5dgtbaynbtus67gaiz3sq

Evolution of the Ras-like small GTPases and their regulators

Teunis J.P. van Dam, Johannes Bos, Berend Snel
2011 Small GTPases  
We performed an in depth phylogenetic analysis in 64 genomes of diverse eukaryotic species.  ...  We have previously reported on the evolution of cDc25 homology Domain containing proteins, which act as guanine nucleotide exchange factors (GeFs) for Ras-like proteins.  ...  Evolution of the ras Gtpase activating protein domain; conservation of domain architecture.  ... 
doi:10.4161/sgtp.2.1.15113 pmid:21686276 pmcid:PMC3116619 fatcat:q6ee2abpcjc3hip6n3oefwamz4
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