Premium
Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043
Author(s) -
Chen LingLing,
Ma BinGuang,
Gao Na
Publication year - 2008
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2007.06190.x
Subject(s) - erwinia , orfs , biology , pathogen , microbiology and biotechnology , botany , bacteria , gene , genetics , open reading frame , peptide sequence
Over‐annotation of hypothetical ORFs is a common phenomenon in bacterial genomes, which necessitates confirming the coding reliability of hypothetical ORFs and then predicting their functions. The important plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043 ( Eca 1043) is a typical case because more than a quarter of its annotated ORFs are hypothetical. Our analysis focuses on annotation of Eca 1043 hypothetical ORFs, and comprises two efforts: (a) based on the Z‐curve method, 49 originally annotated hypothetical ORFs are recognized as noncoding, this is further supported by principal components analysis and other evidence; and (b) using sequence‐alignment tools and some functional resources, more than a half of the hypothetical genes were assigned functions. The potential functions of 427 hypothetical genes are summarized according to the cluster of orthologous groups functional category. Moreover, 114 and 86 hypothetical genes are recognized as putative ‘membrane proteins’ and ‘exported proteins’, respectively. Reannotation of Eca 1043 hypothetical ORFs will benefit research into the lifestyle, metabolism and pathogenicity of the important plant pathogen. Also, our study proffers a model for the reannotation of hypothetical ORFs in microbial genomes.