Research Article Identification of Family Specific Fingerprints in -Lactamase Families Abhishikha Srivastava, 1 Neelja Singhal, 2 Manisha Goel, 1 Jugsharan Singh Virdi, 2 and Manish Kumar 1 1 Department of Biophysics, University of Delhi South Campus, New Delhi 110 021, India 2 Department of Microbiology, University of Delhi South Campus, New Delhi 110 021, India Correspondence should be addressed to Manish Kumar; manish@south.du.ac.in Received 31 August 2013; Accepted 14 November 2013; Published 11 February 2014 Academic Editors: I. F. Hung and C. Woods Copyright © 2014 Abhishikha Srivastava et al. his is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Beta-lactamases are a superfamily of enzymes which degrade the -lactam class of antibiotics. hey are produced endogenously by the bacterial cells, which when exposed to the -lactam class of antibiotics inactivate them by cleaving the -lactam ring. Based on the presence or absence of metallic ligand, -lactamases have been divided into two broad functional classes. -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 speciic to a particular family or subfamily of -lactamases. he family speciic patterns/motifs can be also useful in recognizing and assigning newly discovered -lactamases to one or the other family or subfamily. Cross-validation showed that the proposed method is highly sensitive and speciic. We have also designed a webserver, LactFP, for this purpose. 1. Introduction Antibiotics are chemical compounds used to treat bacterial infections. he indiscriminate overuse of antibiotics leads to the evolution of antibiotic resistance in pathogenic microbes. Resistance to antibiotics can be generated by four general mechanisms [1, 2]: (i) inactivation or modiication of the antibiotic; (ii) alteration in the target site of the antibi- otic that reduces its binding capacity; (iii) modiication of metabolic pathways to circumvent the antibiotic efect; (iv) reduced intracellular antibiotic accumulation by decreasing permeability and/or increasing active elux of the antibiotic. -Lactams, the most widely used antibiotics, are rendered inefective by bacteria employing the irst strategy, that is, cleavage of amide bond of the -lactam ring. he extensive overuse of antibiotics exerted selective pres- sure on bacteria, which evolved new variants of -lactamases extending the -lactamase family [3]. he two popular classiication schemes of -lactamase enzymes are Bush- Jacoby scheme which is based on functional characteristics of the enzymes [4] and Ambler’s scheme [5] which is based on the amino acid sequence similarity. According to Ambler’s classiication scheme, -lactamases are divided into four classes. Classes A, C, and D are serine--lactamases which employ an active-site serine to catalyze hydrolysis, while class B -lactamases are metalloenzymes requiring one or two zinc ions for their activity. Although “annotation transfer by homology,” which involves global comparison between two sequences, is the most popular approach for inferring function of a protein, experimental bodies of evidence suggest that protein function can be correlated well with the presence of local patterns of amino acid residues or motifs shared by proteins with similar function. Motifs are a highly conserved set of residues that form similar patterns and oten represent functionally impor- tant regions such as active or binding sites, or regions deining the overall protein fold. hroughout the course of evolution, functionally important parts of proteins like active site residues in case of enzymes have remained conserved. hus, analysis of similarity in local regions of a protein or structural motifs could be useful for predicting protein function and/or identifying functionally signiicant sites. his implies, that Hindawi Publishing Corporation e Scientific World Journal Volume 2014, Article ID 980572, 7 pages http://dx.doi.org/10.1155/2014/980572