EvoProDom: Evolutionary modeling of protein families by assessing translocations of protein domains

Abstract Illuminating the role of specific gene duplications within the human lineage can provide insights into human-specific adaptations. The so-called human core duplicon gene families have received particular attention in this respect, due to special features, such as expansion along single chromosomes, newly acquired protein domains and signatures of positive selection. Here, we summarize the data available for 10 such families and include some new analyses. A picture emerges that suggests broad functions for these protein families, possibly through modification of core cellular pathways. Still, more dedicated studies are required to elucidate the function of core-duplicons gene families and how they have shaped adaptations and evolution of humans.

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InterPro (The Integrated Resource of Protein Domains and Functional Sites)

Yeast ◽

10.1155/2000/604642 ◽

2000 ◽

Vol 1 (4) ◽

pp. 327-334

Author(s):

Christopher Southan

Keyword(s):

Comparative Genomics ◽

Protein Domains ◽

Protein Family ◽

European Bioinformatics Institute ◽

Protein Families ◽

Functional Sites ◽

The Family ◽

Graphic Displays

The family and motif databases, PROSITE, PRINTS, Pfam and ProDom, have been integrated into a powerful resource for protein secondary annotation. As of June 2000, InterPro had processed 384 572 proteins in SWISS-PROT and TrEMBL. Because the contributing databases have different clustering principles and scoring sensitivities, the combined assignments compliment each other for grouping protein families and delineating domains. The graphic displays of all matches above the scoring thresholds enables judgements to be made on the concordances or differences between the assignments. The website links can be used to analyse novel sequences and for queries across the proteomes of 32 organisms, including the partial human set, by domain and/or protein family. An analysis of selected HtrA/DegQ proteases demonstrates the utility of this website for detailed comparative genomics. Further information on the project can be found at the European Bioinformatics Institute at http://www.ebi.ac.uk/interpro/.

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EvoProDom: Evolutionary model of protein families by means of translocations of protein domains

10.1101/2020.02.23.961532 ◽

2020 ◽

Author(s):

Gon Carmi ◽

Alessandro Gorohovski ◽

Milana Frenkel-Morgenstern

Keyword(s):

Protein Design ◽

Protein Domains ◽

Evolutionary Model ◽

Protein Domain ◽

Protein Families ◽

Orthologous Protein ◽

Search Tool ◽

Host Virus Interactions ◽

Virus Interactions ◽

Evolution Of Proteins

AbstractHere, we developed a novel evolution of protein domains (EvoProDom) model for evolution of proteins, which was based on mix and merge of protein domains. We collected and integrated genomic and proteome data for 109 organisms. These data include protein domain content and orthologous protein families. In EvoProDom, we defined evolutionary events, such as translocations, as reciprocal exchanges of protein domains between orthologous proteins of different organisms. We found that protein domains, which frequently appear in translocation events, were enriched in trans-splicing events, i.e., producing novel transcripts fused from two distinct genes. We presented in EvoProDom, a general method to obtain protein domain content and orthologous protein annotation, by predicting these data from protein sequences using the Pfam search tool and KoFamKOALA, respectively. This method can be implemented in other research such as proteomics, protein design and host-virus interactions.

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