Seq2Enz: An application of mask BLAST methodology with a new chemical logic of amino acids for improved enzyme function prediction

Amita Pathak; B Jayaram

doi:10.1016/j.bbapap.2021.140721

Seq2Enz: An application of mask BLAST methodology with a new chemical logic of amino acids for improved enzyme function prediction

Biochim Biophys Acta Proteins Proteom. 2022 Jan;1870(1):140721. doi: 10.1016/j.bbapap.2021.140721. Epub 2021 Oct 6.

Authors

Amita Pathak¹, B Jayaram²

Affiliations

¹ Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India.
² Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India; Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India. Electronic address: bjayaram@chemistry.iitd.ac.in.

PMID: 34624539
DOI: 10.1016/j.bbapap.2021.140721

Abstract

Seq2Enz method is a new way to identify whether a query protein sequence is an enzyme and to assign an enzyme class to the protein sequence. The method is based on mask BLAST fortified with some novel structural-chemical properties (NCL) of the building blocks of proteins. All available reviewed enyme sequences (267,276 in number) in Uniprot/SwissProt and most recent depositions (7062) not used for training in ECPred, a state of the art software for enzyme class prediction, are taken for assessment and the results are compared with those from conventional BLAST and ECPred respectively. Seq2Enz is seen to perform consistently better for all the enzyme classes to all the four levels. Seq2Enz methodology is converted into an easy to use web-server and made freely accessible at http://www.scfbio-iitd.res.in Seq2Enz/.

Keywords: Enzyme class; Enzyme levels; Protein annotation; Protein function.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Catalytic Domain*
Enzymes / chemistry
Enzymes / metabolism
Humans
Sequence Analysis, Protein / methods*
Software*

Substances

Enzymes