Login

Join for Free!
112131 members
table of contents table of contents

Biology Articles » Bioinformatics » Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria » Enterofams: protein families for enterobacteria

Enterofams: protein families for enterobacteria
- Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria

 

The first version of the EnteroFams is a collection of 1579 protein families. Each family is represented by a profile-Hidden Markov Model (HMM) similar to Pfam (4) or TIGRfam (5) protein families. EnteroFams differ from these other databases of protein families in that they contain only full-length alignments of proteins from enterobacterial species. The current collection of EnteroFams consist of proteins that are nearly ubiquitous in enterobacteria. Each HMM was constructed from an alignment of putative orthologous proteins from eight genomes (E. coli MG1655, E. coli EDL933, Salmonella enterica Typhimurium LT2, S. enterica Typhi CT18, Y. pestis CO92, Yersinia pseudotuberculosis 32953, Erwinia chrysanthemi 3937 and Erwinia carotovora atroseptica SCRI1043) and used to scan 11 additional genomes for new members. The threshold for inclusion in a family was defined as the lowest score obtained for a protein from one of the eight seed genomes. The alignment of the seed proteins, the complete alignment of all members and the annotations for each family were manually curated. All members have a link to the associated EnteroFam page that contains alignments, cutoff thresholds and annotations for each family. EnteroFam HMMs will be made available from each EnteroFam page and for bulk download through the ERIC portal. Annotations were selected to be appropriate for all species so that they can be applied to all members of the family enabling the propagation of high-quality annotations across features in related enterobacteria.


rating: 4.00 from 4 votes | updated on: 1 Dec 2007 | views: 11482 |

Rate article:







excellent!bad…