Automatic phylogenetic classification of bacterial beta-lactamase sequences including structural and antibiotic substrate preference information

Automatic phylogenetic classification of bacterial beta-lactamase sequences including structural and antibiotic substrate preference information
Title:
Automatic phylogenetic classification of bacterial beta-lactamase sequences including structural and antibiotic substrate preference information
Other Titles:
Journal of Bioinformatics and Computational Biology
DOI:
10.1142/S0219720013430117
Keywords:
Publication Date:
10 December 2013
Citation:
JIANMIN MA, FRANK EISENHABER, and SEBASTIAN MAURER-STROH, J. Bioinform. Comput. Biol. 11, 1343011 (2013)
Abstract:
Beta lactams comprise the largest and still most effective group of antibiotics, but bacteria can gain resistance through different beta lactamases that can degrade these antibiotics. We developed a user friendly tree building web server that allows users to assign beta lactamase sequences to their respective molecular classes and subclasses. Further clinically relevant information includes if the gene is typically chromosomal or transferable through plasmids as well as listing the antibiotics which the most closely related reference sequences are known to target and cause resistance against. This web server can automatically build three phylogenetic trees: the first tree with closely related sequences from a Tachyon search against the NCBI nr database, the second tree with curated reference beta lactamase sequences, and the third tree built specifically from substrate binding pocket residues of the curated reference beta lactamase sequences. We show that the latter is better suited to recover antibiotic substrate assignments through nearest neighbor annotation transfer. The users can also choose to build a structural model for the query sequence and view the binding pocket residues of their query relative to other beta lactamases in the sequence alignment as well as in the 3D structure relative to bound antibiotics. This web server is freely available at http://blac.bii.a-star.edu.sg/.Read More: http://www.worldscientific.com/doi/abs/10.1142/S0219720013430117?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed
License type:
PublisherCopyrights
Funding Info:
Description:
ISSN:
0219-7200
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