title: Identification of family specific fingerprints in β-lactamase families.
abstract: Beta-lactamases are a superfamily of enzymes which degrade the β-lactam class of antibiotics. They are produced endogenously by the bacterial cells, which when exposed to the β-lactam class of antibiotics inactivate them by cleaving the β-lactam ring. Based on the presence or absence of metallic ligand, β-lactamases have been divided into two broad functional classes. β-Lactamases are a constitutively evolving and expanding superfamily of enzymes, which could be further subdivided on the basis of presence/absence of conserved motifs. In the present study we have used the MEME/MAST suit to identify the patterns/motifs which are specific to a particular family or subfamily of β-lactamases. The family specific patterns/motifs can be also useful in recognizing and assigning newly discovered β-lactamases to one or the other family or subfamily. Cross-validation showed that the proposed method is highly sensitive and specific. We have also designed a webserver, LactFP, for this purpose.
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi 110 021, India.
authors.forename: Abhishikha
authors.initials: A
authors.lastname: Srivastava
authors.affiliation: Department of Microbiology, University of Delhi South Campus, New Delhi 110 021, India.
authors.forename: Neelja
authors.identifier: 0000-0003-0851-6434
authors.initials: N
authors.lastname: Singhal
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi 110 021, India.
authors.forename: Manisha
authors.initials: M
authors.lastname: Goel
authors.affiliation: Department of Microbiology, University of Delhi South Campus, New Delhi 110 021, India.
authors.forename: Jugsharan Singh
authors.initials: JS
authors.lastname: Virdi
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi 110 021, India.
authors.forename: Manish
authors.initials: M
authors.lastname: Kumar
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001419:Bacteria / Q000145:classification* / Q000187:drug effects / Q000235:genetics*; D019295:Computational Biology; D018983:DNA Footprinting; D030541:Databases, Genetic; D024881:Drug Resistance, Bacterial / Q000235:genetics; D056510:Position-Specific Scoring Matrices; D015203:Reproducibility of Results; D064878:Web Browser; D001618:beta-Lactamases / Q000737:chemistry / Q000235:genetics*
chemical_list: D000900:Anti-Bacterial Agents; D001618:beta-Lactamases