ECOD: Identification of distant homology among multidomain and transmembrane domain proteins

Richard Dustin Schaeffer, Lisa Kinch, Kirill E. Medvedev, Jimin Pei, Hua Cheng, Nick V Grishin

Research output: Contribution to journalArticle

Abstract

The manual classification of protein domains is approaching its 20th anniversary. ECOD is our mixed manual-automatic domain classification. Over time, the types of proteins which require manual curation has changed. Depositions with complex multidomain and multichain arrangements are commonplace. Transmembrane domains are regularly classified. Repeatedly, domains which are initially believed to be novel are found to have homologous links to existing classified domains. Here we present a brief summary of recent manual curation efforts in ECOD generally combined with specific case studies of transmembrane and multidomain proteins wherein manual curation was useful for discovering new homologous relationships. We present a new taxonomy for the classification of ABC transporter transmembrane domains. We examine alternate topologies of the leucine-specific (LS) domain of Leucine tRNA-synthetase. Finally, we elaborate on a distant homologous links between two helical dimerization domains.

Original languageEnglish (US)
Article number18
JournalBMC Molecular and Cell Biology
Volume20
Issue number1
DOIs
StatePublished - Jun 21 2019

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Leucine-tRNA Ligase
ATP-Binding Cassette Transporters
Dimerization
Anniversaries and Special Events
Leucine
Proteins
Protein Domains

ASJC Scopus subject areas

  • Cell Biology
  • Molecular Biology

Cite this

ECOD : Identification of distant homology among multidomain and transmembrane domain proteins. / Schaeffer, Richard Dustin; Kinch, Lisa; Medvedev, Kirill E.; Pei, Jimin; Cheng, Hua; Grishin, Nick V.

In: BMC Molecular and Cell Biology, Vol. 20, No. 1, 18, 21.06.2019.

Research output: Contribution to journalArticle

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