- Meeting abstract
- Open Access
Ab Initio prediction of mycobacteriophages protein structure and function
© Kapadia and Rinehart; licensee BioMed Central Ltd. 2013
- Published: 22 October 2013
- Structural Family
- Genome Organization
- Combinatorial Library
- Soil Bacterium
Mycobacterium smegmatis is a soil bacterium. Over 448 mycobacteriophages specific for M. smegmatis have been sequenced and grouped into clusters of related genomes based on the similarity of their products and genome organization. Only 20% of mycobacteriophage genes have known function, as predicted by protein sequence level alignments .
Genes that are grouped together using BLAST at the protein sequence level have been assembled into loose groupings called phams . The phagesdb.org/phams database contains the protein sequences organized by phams. From these data we used ab initio folding, using I-TASSER , to predict the structure of multiple phams across numerous mycobacteriophage clusters. Predicted models were grouped into structural families based upon RMSD scores from pairwise comparisons. Models from two structural families per pham were submitted to COFACTOR , which finds the best structural homologies to proteins in the PDB library and returns the matching structures along with GO terms, EC numbers and active site information.
- Hatfull GF: Mycobacteriophages: genes and genomes. Annu Rev Microbiol. 2010, 64: 331-356. 10.1146/annurev.micro.112408.134233.View ArticlePubMedGoogle Scholar
- Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF: Phamerator: a bioinformatics tool for comparative bacteriophage genomics. BMC Bioinformatics. 2011, 12: 395-10.1186/1471-2105-12-395.PubMed CentralView ArticlePubMedGoogle Scholar
- Roy A, Kucukural A, Zhang Y: I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols. 2010, 5 (4): 725-738. 10.1038/nprot.2010.5.PubMed CentralView ArticlePubMedGoogle Scholar
- Roy A, Yang J, Zhang Y: COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res. 2012, 40 (Web Server issue): W471-W477.PubMed CentralView ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.