Vol 42: LenVarDB: database of length-variant protein domains.Report as inadecuate



 Vol 42: LenVarDB: database of length-variant protein domains.


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This article is from Nucleic Acids Research, volume 42.AbstractProtein domains are functionally and structurally independent modules, which add to the functional variety of proteins. This array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. Length variations indels can introduce changes at structural, functional and interaction levels. LenVarDB freely available at http:-caps.ncbs.res.in-lenvardb- traces these length variations, starting from structure-based sequence alignments in our Protein Alignments organized as Structural Superfamilies PASS2 database, across 731 structural classification of proteins SCOP-based protein domain superfamilies connected to 2 730 625 sequence homologues. Alignment of sequence homologues corresponding to a structural domain is available, starting from a structure-based sequence alignment of the superfamily. Orientation of the length-variant indel regions in protein domains can be visualized by mapping them on the structure and on the alignment. Knowledge about location of length variations within protein domains and their visual representation will be useful in predicting changes within structurally or functionally relevant sites, which may ultimately regulate protein function. Non-technical summary: Evolutionary changes bring about natural changes to proteins that may be found in many organisms. Such changes could be reflected as amino acid substitutions or insertions–deletions indels in protein sequences. LenVarDB is a database that provides an early overview of observed length variations that were set among 731 protein families and after examining 2 million sequences. Indels are followed up to observe if they are close to the active site such that they can affect the activity of proteins. Inclusion of such information can aid the design of bioengineering experiments.



Author: Mutt, Eshita; Mathew, Oommen K.; Sowdhamini, Ramanathan

Source: https://archive.org/







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