BacEffluxPred: A two-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteins.

Scientific Reports
Deeksha PandeyManish Kumar

Abstract

Efflux proteins are transport proteins, which are involved in transporting different substrates from the cell to the external environment, including antibiotics. The efflux mechanism and efflux pumps are a major reason underlying emerging rampant antibiotic resistance (AR) in microbes. To reduce the resources required and time of identification, characterization and classification of bacterial efflux proteins, we have developed a fast and accurate support vector machine based two-tier prediction system, BacEffluxPred, which can predict bacterial efflux proteins responsible for AR and identify their corresponding families. A leave-one-out cross-validation also called jackknife procedure was used for performance evaluation. The accuracy to discriminate bacterial AR efflux from non-AR efflux was obtained as 85.81% (at tier-I) while accuracies for prediction of efflux pump families like ABC, MFS, RND and MATE family were found 92.13%, 85.39%, 91.01% and 99.44%, respectively (at tier-II). Benchmarking on an independent dataset also showed that BacEffluxPred had comparable accuracy for prediction of bacterial AR efflux pumps and their families. This is the first in-silico tool for predicting bacterial AR efflux proteins and their fam...Continue Reading

References

Oct 20, 1975·Biochimica Et Biophysica Acta·B W Matthews
Dec 21, 2002·The Journal of Antimicrobial Chemotherapy·M A Webber, L J V Piddock
Sep 19, 2003·The Biochemical Journal·M Ines Borges-WalmsleyAdrian R Walmsley
Jun 14, 2005·Biochimie·Béatrice Marquez
Jul 26, 2005·Academic Radiology·John Eng
Feb 6, 2007·Nature Reviews. Microbiology·Gerard D Wright
Sep 7, 2007·Microbiology and Molecular Biology Reviews : MMBR·Jacek LubelskiArnold J M Driessen
Nov 29, 2007·BMC Bioinformatics·Manish KumarGajendra P S Raghava
Jun 10, 2008·Annual Review of Microbiology·Christopher J LawDa-Neng Wang
Dec 23, 2008·Biochimica Et Biophysica Acta·Teruo Kuroda, Tomofusa Tsuchiya
Aug 15, 2009·Drugs·Xian-Zhi Li, Hiroshi Nikaido
Dec 21, 2010·Journal of Theoretical Biology·Kuo-Chen Chou
Jun 29, 2011·FEMS Microbiology Reviews·Hiroshi Nikaido, Jean-Marie Pagès
Jul 12, 2012·The Journal of Antimicrobial Chemotherapy·Ea ZankariMette Voldby Larsen
May 8, 2013·Antimicrobial Agents and Chemotherapy·Andrew G McArthurGerard D Wright
Dec 6, 2014·Database : the Journal of Biological Databases and Curation·Abhishikha SrivastavaManish Kumar
Dec 3, 2016·Nucleic Acids Research·Alice R WattamRick L Stevens
Jun 3, 2017·PloS One·Sabri BoughorbelMohammed El-Anbari
Dec 16, 2017·Journal of Biomolecular Structure & Dynamics·Abhishikha Srivastava, Manish Kumar
Jul 14, 2018·Nature Reviews. Microbiology·Dijun DuBen F Luisi
Aug 24, 2018·Journal of Theoretical Biology·Abhishikha SrivastavaManish Kumar
Nov 6, 2018·Nucleic Acids Research·UNKNOWN UniProt Consortium
Oct 11, 2019·Scientific Reports·Abu Sayed ChowdhuryShira L Broschat

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Software Mentioned

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SVM
BacEffluxPred
DeepARG
BLAST
ResFinder
VAMPr
Resfams
LOOCV

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