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Domain architecture conservation in orthologs
2011
BMC Bioinformatics
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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
2016
Database: The Journal of Biological Databases and Curation
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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
2018
Genes
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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
2016
Scientific Reports
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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 (http://pfam.xfam.org) 32 . ...
doi:10.1038/srep30700
pmid:27476717
pmcid:PMC4967905
fatcat:3g3pyzqr65gcxflibdlzgbfcxy
Molecular evolution of proteins mediating mitochondrial fission-fusion dynamics
2019
FEBS Letters
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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
2010
BMC Bioinformatics
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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
2007
Cell Cycle
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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
2020
Plants
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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
2019
PLoS ONE
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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
2011
Briefings in Bioinformatics
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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
2013
G3: Genes, Genomes, Genetics
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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
2014
Genome Biology and Evolution
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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
2004
DNA Research
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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
2011
Physical Biology
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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
2011
Small GTPases
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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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