PaperBLAST
PaperBLAST Hits for tr|Q9I3H3|Q9I3H3_PSEAE Spermidine export protein MdtI OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA1540 PE=3 SV=1 (109 a.a., MLTLNWIPFA...)
Show query sequence
>tr|Q9I3H3|Q9I3H3_PSEAE Spermidine export protein MdtI OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA1540 PE=3 SV=1
MLTLNWIPFAWLGLAIALEVVANLLLKYSDGFRRRGLGIASILCVMAAFTALAQAVKDIE
LSLAYAIWGGFGILATVAMGWALFGQRLAWRGWLGLLLLLAGMSLLKLA
Running BLASTp...
Found 134 similar proteins in the literature:
PA1540 hypothetical protein from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Non-interchangeable functions of efflux transporters of Pseudomonas aeruginosa in survival under infection-associated stress
Adamiak, Journal of bacteriology 2024 (secret) - Loss of RND-Type Multidrug Efflux Pumps Triggers Iron Starvation and Lipid A Modifications in Pseudomonas aeruginosa
Adamiak, Antimicrobial agents and chemotherapy 2021 (secret) - Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype
Thöming, NPJ biofilms and microbiomes 2020 - “...PA14_28620 PA2746 3.2 PA14_44520 PA1541 ydgF 3.3 PA14_29660 PA2662 2.6 PA14_29350 PA2688 pfeA 2.6 PA14_44530 PA1540 ygdE 2.8 PA14_40850 PA1831 gpmA 2.4 PA14_29480 PA2678 wzm 2.7 PA14_46850 PA1347 2.8 PA14_50520 PA1074 braC 2.5 PA14_32080 PA2518 xylX 3.3 PA14_47380 PA1302 hxuC 2.6 PA14_52660 PA0899 aruB 2.3 PA14_32100...”
- Multidrug Adaptive Resistance of Pseudomonas aeruginosa Swarming Cells
Coleman, Antimicrobial agents and chemotherapy 2020 (secret) - Prevention of siderophore- mediated gut-derived sepsis due to P. aeruginosa can be achieved without iron provision by maintaining local phosphate abundance: role of pH
Romanowski, BMC microbiology 2011 - “...- 3.5-fold increase in the expression of the spermidine export protein mdtJI homolog (PA1541 - PA1540) might also contribute to medium alkalization since production and excretion of polyamines has been shown in E. coli to contribute to an increase in the pH of the extracellular medium...”
- “...(EC 2.6.1.11) Arginine_Biosynthesis_extended PA3865 -2.74 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein Arginine deiminase pathway PA1540 -2.14 Spermidine export protein mdtI Small_Multidrug_Resistance PA1541 -3.44 Spermidine export protein mdtJ Small_Multidrug_Resistance PA0509 nirN -3.39 Nitrite reductase associated c-type cytochorome NirN Dissimilatory_nitrite_reductase PA0510 -4.39 Uroporphyrinogen-III methyltransferase (EC 2.1.1.107) Dissimilatory_nitrite_reductase...”
- Transcriptome analysis of agmatine and putrescine catabolism in Pseudomonas aeruginosa PAO1
Chou, Journal of bacteriology 2008 - “...PA0534 PA0535 PA1178d PA1179d PA1180d PA1409 PA1410 PA1540 PA1541 PA1742 PA2041 PA2268 PA2776 PA3355 PA3356 PA3552d PA3553d PA3554d PA3555d PA3556d PA3557d...”
- Transcriptome analysis of Pseudomonas aeruginosa after interaction with human airway epithelial cells
Frisk, Infection and immunity 2004 - “...in membrane transport (PA2019, PA4770 [lldP], PA2673, PA1540, and PA2437; Table 2). Additional activated genes encode probable transcriptional regulators...”
- “...PA2019 9.4 8.6 8.5 0.044 0.019 0.050 PA4770 PA5412 PA0805 PA1540 PA0674 PA0142 PA0163 PA2673 8.2 7.5 7.0 6.7 6.3 6.2 5.8 5.5 0.027 0.005 0.035 0.013 0.001 0.024...”
PA14_44530 putative membrane transporter of cations and cationic drugs from Pseudomonas aeruginosa UCBPP-PA14
99% identity, 100% coverage
YPTB2052 DMT Superfamily drug efflux pump from Yersinia pseudotuberculosis IP 32953
66% identity, 100% coverage
t1403 putative membrane protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
64% identity, 100% coverage
- Prevalence and Diversity of Staphylococcus aureus and Staphylococcal Enterotoxins in Raw Milk From Northern Portugal
Oliveira, Frontiers in microbiology 2022 - “...Spa typing revealed 62 distinct S. aureus isolates, being t529 (17.7%, 95% CI: 8.227.3%) and t1403 (16.1%, 95% CI: 7.025.3%) the predominant types, commonly associated with livestock infection or carriage. The antimicrobial susceptibility test showed that 35.5% of the S. aureus isolates were resistant to at...”
- “...of prevalence, the most common spa type was t529 (17.7%, 95% CI: 8.227.3%) followed by t1403 (16.1%, 95% CI: 7.025.3%), t337 (9.7%, 95% CI: 2.317.0%), t543 (9.7%, 95% CI: 2.317.0%), and t011 (8.1%, 95% CI: 1.314.8%). Other spa types, such as t528, t571, t2802, and t2873...”
- Susceptibility of Methicillin-Resistant and -Susceptible Staphylococcus aureus Isolates of Various Clonal Lineages from Germany to Eight Biocides
Kernberger-Fischer, Applied and environmental microbiology 2018 - “...(1), t1574 (1), t095 (1) t1181 (2), t6384 (1), t1403 (1) Disease/colonization Poultry (29 colonized), human (12 diseased, 8 colonized, 5 NDb), pet animal (5...”
YPO2069 putative integral membrane protein from Yersinia pestis CO92
70% identity, 88% coverage
NJ56_15780 multidrug/spermidine efflux SMR transporter subunit MdtI from Yersinia ruckeri
62% identity, 100% coverage
MdtI / b1599 multidrug/spermidine efflux pump membrane subunit MdtI from Escherichia coli K-12 substr. MG1655 (see 4 papers)
mdtI / P69210 multidrug/spermidine efflux pump membrane subunit MdtI from Escherichia coli (strain K12) (see 3 papers)
MDTI_ECOLI / P69210 Spermidine export protein MdtI from Escherichia coli (strain K12) (see 2 papers)
TC 2.A.7.1.9 / P69210 MdtI, component of The spermidine exporter, MdtIJ (MdtIJ = YdgEF) from Escherichia coli (strain K12) (see 7 papers)
NP_416116, b1599 multidrug efflux system transporter from Escherichia coli str. K-12 substr. MG1655
SF5M90T_1572 multidrug/spermidine efflux SMR transporter subunit MdtI from Shigella flexneri 5a str. M90T
63% identity, 100% coverage
- function: Catalyzes the excretion of spermidine. Can also confer resistance to deoxycholate and SDS.
subunit: Forms a complex with MdtJ. - substrates: Deoxycholate, SDS, Spermidine
tcdb comment: Catalyzes the export of spermidine and putrescine, and confers resistance to deoxycholate and SDS (Nishino and Yamaguchi 2001). It can be induced by these polyamines and bile salts. Details of the induction mechanism are known (Leuzzi et al. 2015) - Polyamine transporters and polyamines increase furfural tolerance during xylose fermentation with ethanologenic Escherichia coli strain LY180
Geddes, Applied and environmental microbiology 2014 - “...b1296 0.9 1.1 750 590 Spermidine antiporter mdtJ mdtI b4132 b1599 1.3 1.7 1.1 1.5 1.0 1.0 0.3 1.9 Cadaverine symporter cadB b4132 0.6 1.4 0.8 0.7 a Comparisons...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Multidrug Efflux Systems in Helicobacter cinaedi
Morita, Antibiotics (Basel, Switzerland) 2012 - “...(positive), respectively) of B. subtilis , while HCN_1599-HCN_1600 showed significant similarity to MdtJI (NP_416117 and NP_416116; 38% (57%) and 38% (63%) identity (positive), respectively) of E. coli K12. YkkCD is a multidrug efflux pump that gives rise to broad specificity, including to cationic (e.g., streptomycin, tetracycline...”
- Diversity and evolution of the small multidrug resistance protein family
Bay, BMC evolutionary biology 2009 - “...NP_391237 and Bsu-YvaD NP_391236 ) and Escherichia coli (Eco-EmrE NP_415075 ; Eco-SugE NP_418572 ; Eco-YdgE/MdtI NP_416116 and Eco-YdgF/MdtJ NP_416117 ) [ 59 ]. As a result, a total of 685 non-identical SMR sequences (as of March 2008) were identified from the query SMR sequence blasts with...”
- Inactivation of efflux pumps abolishes bacterial biofilm formation
Kvist, Applied and environmental microbiology 2008 - “...mdtI yejA mdtJ b2558 b3240 b0847 b1036 b2211 b2680 b3110 b4148 b1599 b2177 b1600 4.1 12.39 7.63 6.97 4.66 2.78 2.21 3.51 3.59 2.31 2.02 5.31 1.96 2.17 2.83 1.94...”
- A broad-specificity multidrug efflux pump requiring a pair of homologous SMR-type proteins
Jack, Journal of bacteriology 2000 - “...and yvdS, and ykkC and ykkD in B. subtilis as well as b1599 and b1600 in E. coli (Table 1). One member of each B. subtilis protein pair is short (105 to 106...”
- “...Bsu YvdR Bsu YvdS Bsu YvaE Bsu SugE Eco b1599 Eco b1600 Eco EmrE Eco subtilis subtilis subtilis subtilis subtilis subtilis subtilis No. of residues VOL. 182,...”
- Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli
Jindal, BMC microbiology 2019 - “...Putative oligopeptide ABC transporter periplasmic binding protein P33913 [ 131 ] mdtI Spermidine export protein P69210 [ 132 , 133 ] mdtJ Spermidine export protein P69212 [ 133 ] mdtL Multidrug resistance protein (e.g. vs chloramphenicol) P31462 [ 133 ] mdtA Multidrug resistance protein (e.g. vs...”
- The de novo design of a biocompatible and functional integral membrane protein using minimal sequence complexity
Lalaurie, Scientific reports 2018 - “...loops. We identified eight particular SMR proteins (accession numbers P23895, Q2FD83, P69937, P14319, P69926, B0R6K7, P69210, P69213) which are among those to have been characterised and so are validated as authentic gene products. We reasoned that this deliberately restricted dataset, featuring diverse and functionally distinct proteins...”
- RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Vergara-Irigaray, BMC genomics 2014 - “...membrane receptor for ferric iron uptake -2.46 SF5M90T_1483 ydiE hemin uptake protein -2.93 -2.20 -1.55 SF5M90T_1572 mdtI spermidine export protein -3.61 Secondary metabolites biosynthesis, transport and catabolism SF5M90T_1184 putative SAM-dependent methyltransferase 2.12 SF5M90T_331 tauD taurine dioxygenase, 2-oxoglutarate-dependent -2.97 1.94 Cellular processes and signalling Cell cycle control,...”
LHK_01385 Putative membrane transporter of cations and cationic drugs from Laribacter hongkongensis HLHK9
62% identity, 87% coverage
- Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis
Lau, Cell & bioscience 2011 - “...MarC LHK_01384 mdtJ Multidrug efflux system protein MdtJ Klebsiella pneumoniae 3e-20 52/119 (43%) 3 SMR LHK_01385 mdtI Multidrug efflux system protein MdtI Salmonella enterica 6e-21 63/109 (57%) 4 SMR LHK_01424 RND efflux system, outer membrane lipoprotein, NodT family Syntrophobacter fumaroxidans 7e-108 223/446 (50%) -- OMP LHK_01425...”
- “...91 ]. Small Multidrug Resistance (SMR) family Two adjacently located multidrug efflux genes (LHK_01384 and LHK_01385) of the SMR family were identified in the genome of L. hongkongensis . They are homologous to mdtJI (also named ydgEF ) genes in E. coli which confers resistance to...”
DVU3326 multidrug resistance protein, Smr family from Desulfovibrio vulgaris Hildenborough
58% identity, 88% coverage
- Prediction and Characterization of Missing Proteomic Data in Desulfovibrio vulgaris
Li, Comparative and functional genomics 2011 - “...x Multidrug resistance protein DVU2893 4.59 9413.30 x 6.78 9241.60 x Flagellar basal-body rod protein DVU3326 3.13 782.67 x 3.68 2732.60 x Multidrug resistance protein, Smr family DVUA0002 5.53 2257.50 x 12.96 6384.00 x ParA family protein DNA metabolism DVU0878 3.20 1967.30 x 7.13 11149.00 x...”
- Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation
He, Applied and environmental microbiology 2010 - “...operons (DVU0060 to DVU0063, DVU2815 to DVU2817, and DVU3326 and DVU3327) exhibited a trend toward upregulation under both salt adaptation and salt shock...”
- “...encodes an efflux transporter; DVU0061, DVU2816, DVU2817, DVU3326, and DVU3327 encode multidrug resistance proteins; and DVU0062 and DVU2815 encode outer...”
- Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach
Mukhopadhyay, Journal of bacteriology 2006 - “...well as genes in a two-gene multidrug efflux operon (DVU3326 and DVU3327), were highly up-regulated upon salt stress (Fig. 2). Transcripts of a putative acrAB...”
VP0061 putative multidrug transmembrane resistance signal peptide protein from Vibrio parahaemolyticus RIMD 2210633
FORC22_0046 SMR family transporter from Vibrio parahaemolyticus
44% identity, 94% coverage
ECSP_2972 EmrE SMR transporter from Escherichia coli O157:H7 str. TW14359
41% identity, 92% coverage
- Genomic analysis of shiga toxin-containing Escherichia coli O157:H7 isolated from Argentinean cattle
Amadio, PloS one 2021 - “...ren protein ren protein 1837225 ECSP_2973 RafaelaII_01813 multidrug efflux protein SMR multidrug resistance protein 1840145 ECSP_2972 RafaelaII_01814 DLP12 prophage recombinase Recombinase family protein 1840734 ECSP_2971 RafaelaII_01815 kinase inhibitor Far kinase inhibitor ybcL 1842725 ECSP_2970 RafaelaII_01816 DNA-binding transcriptional regulator helix-turn-helix transcriptional regulator 1843286 ECSP_2969 RafaelaII_01817 hypothetical protein...”
MvrC / b0543 DLP12 prophage; multidrug/betaine/choline efflux transporter EmrE from Escherichia coli K-12 substr. MG1655 (see 8 papers)
emrE / P23895 DLP12 prophage; multidrug/betaine/choline efflux transporter EmrE from Escherichia coli (strain K12) (see 107 papers)
EMRE_ECOLI / P23895 Multidrug transporter EmrE; Efflux-multidrug resistance protein EmrE; Ethidium resistance protein; Methyl viologen resistance protein C from Escherichia coli (strain K12) (see 25 papers)
TC 2.A.7.1.3 / P23895 Small cationic multidrug efflux pump (substrates: cationic lipophilic drugs), EmrE. This pump confers resistance to a wide range of disinfectants and dyes known as quaternary cation compounds (QCCs). The 3-D structure of the dimeric EmrE shows opposite orientation of the two subunits in the membrane (Chen et al., 2007), and this conclusion has been confirmed (Fleishman et al. 2006; Lehner et al. 2008; Lloris-Garcerá et al. 2013). There may be a single intermediate state in which the substrate is occluded and immobile from Escherichia coli (see 24 papers)
8uozA / P23895 Emre structure in the tpp-bound state (wt/e14q heterodimer) (see paper)
emrE / PDB|1S7B_A multidrug transporter EmrE from Escherichia coli K12 (see 26 papers)
EB / CAA77936.1 ethidium resistance from Escherichia coli (see paper)
b0543 multidrug efflux protein from Escherichia coli str. K-12 substr. MG1655
NP_415075 multidrug/betaine/choline efflux transporter EmrE from Escherichia coli str. K-12 substr. MG1655
40% identity, 92% coverage
- function: Multidrug efflux protein that confers resistance to a wide range of toxic compounds, including ethidium, methyl viologen, acriflavine, tetraphenylphosphonium (TPP(+)), benzalkonium, propidium, dequalinium and the aminoglycoside antibiotics streptomycin and tobramycin (PubMed:10681497, PubMed:11574548, PubMed:15371426, PubMed:18024586, PubMed:18295794, PubMed:23042996, PubMed:24448799, PubMed:7896833, PubMed:9050242). Can also transport the osmoprotectants betaine and choline (PubMed:22942246). The drug efflux is coupled to an influx of protons (PubMed:15371426, PubMed:29114048, PubMed:7896833). Can couple antiport of a drug to either one or two protons, performing both electrogenic and electroneutral transport of a single substrate (PubMed:29114048). Simultaneously binds and cotransports proton and drug (PubMed:29114048, PubMed:30287687).
subunit: Homodimer (PubMed:14633977, PubMed:14755055, PubMed:15111102, PubMed:15882076, PubMed:17003034, PubMed:18024586, PubMed:20551331, PubMed:22178925, PubMed:23920359). Forms an antiparallel dimeric structure (PubMed:17005200, PubMed:18024586, PubMed:20551331, PubMed:22178925, PubMed:23920359). Also forms dimers of homodimers (PubMed:14755055). - substrates: Cationic lipophilic drugs, TPP, cationic dyes, ethidium, quaternary cationic compounds, tetraphenylphosphonium
tcdb comment: Direct interaction between substrates (tetraphenylphosphonium, TPP+ and MTP+) and Glu14 in TMS1 has been demonstrated using solid state NMR (Ong et al. 2013). A Gly90X6Gly97 motif is important for dimer formation (Elbaz et al., 2008). Two models may account for the opposite (inverted) orientations of the two identical subunits. A post-translational model posits that topology remains malleable after synthesis and becomes fixed once the dimer forms. A second, co-translational model, posits that the protein inserts in both topologies in equal proportions (Woodall et al. 2015). Protonation of E14 leads to rotation and tilt of transmembrane helices 1-3 in conjunction with repacking of loops, conformational changes that alter the coordination of the bound substrate and modulate its access to the binding site from the lipid bilayer. The transport model that emerges posits a proton-bound, but occluded, resting state. Substrate binding from the inner leaflet of the bilayer releases the protons and triggers alternating access between inward- and outward-facing conformations of the substrate-loaded transporter, thus enabling antiport without dissipation of the proton gradient (Dastvan et al. 2016). TMS4 is the known dimerization domain of EmrE (Julius et al. 2017). Few conserved residues are essential for drug polyselectivity. Aromatic QCC selection involves a greater portion of conserved residues compared to other QCCs (Saleh et al. 2018). The topologies of helical membrane proteins are generally defined during insertion of the transmembrane helices, yet topology can change after insertion. In EmrE, topology flipping occurs so that the populations in both orientations equalize. Woodall et al. 2017 demonstrated that when EmrE is forced to insert in a distorted topology, topology flipping of the first TMS can occur, and topological malleability also extends to the C-terminal helix; even complete inversion of the entire EmrE protein can occur after the full protein is translated and inserted. Thus, topological rearrangements appear to be possible during biogenesis. Subtle but significant differences in the sizes of EmrE with different QCC ligands bound has been reported (Qazi and Turner 2018) - Ligand: tetraphenylphosphonium (8uozA)
- The two-component system histidine kinase EnvZ contributes to Avian pathogenic Escherichia coli pathogenicity by regulating biofilm formation and stress responses
Fu, Poultry science 2023 - “...b4337 mdtM Multidrug efflux pump/bile salt:H (+) antiporter/Na (+):H (+) antiporter/K (+):H (+) antiporter 5.15 b0543 emrE Multidrug/betaine/choline efflux transporter EmrE 2.61 PTS system b2703 srlE PTS system, glucitol/sorbitol-specific IIBC component 2.21 b3947 ptsA Putative PTS multi-phosphoryl transfer protein PtsA 2.20 b2704 srlB PTS system, glucitol/sorbitol-specific...”
- Biocide Selective TolC-Independent Efflux Pumps in Enterobacteriaceae
Slipski, The Journal of membrane biology 2018 - “...Entcl_2273; WP_013366261 BK ND BW25113 Hassan et al. ( 2015b ) Escherichia coli SMR EmrE b0543; NP_415075 MV ACR ET CV BK R6G TPP TMP ERY CHL KAM3; JM109 Nishino and Yamaguchi ( 2001 ) SMR SugE b4148; NP_418572 CTP CTAB CET ND DH5alpha Chung and...”
- Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis
Wu, mSystems 2016 - “...tag Entcl_2352) ( 13 ), E.coli K-12 sugE (locus tag b4148) and emrE (locus tag b0543) ( 38 , 39 ), Salmonella enterica smvA (locus tag STM1574) ( 40 , 41 ), and Bacillus cereus ykkC and ykkD ( 21 ), were downloaded, from the NCBI...”
- Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
Bonocora, PLoS genetics 2015 - “...- b0517 allD 5500 7.934 IS05 567582 2 G TGG TGCAATAC TTGC A 567568 + b0543 emrE + b0544 ybcK 543 10.546 IS06 655861 1 T TGG TAAAGTTT TTGC T 655846 + b0622 pagP + b0623 cspE 654 10.387 IS07 769197 2 CC GG TATGGAATA TGC...”
- Characterization of Escherichia coli MG1655 grown in a low-shear modeled microgravity environment
Tucker, BMC microbiology 2007 - “...inner mem. present renD b0542 yes -2.02 0.0005 orf, phage ren gene homolog lysis emrE b0543 yes -2.02 0.0001 multidrug resistance pump, methylviologen resistance inner mem. orthologue essD b0554 yes -2.57 0.0001 orf, phage lambda S lysis protein homolog mem. lysis ybcS b0555 yes -2.19 0.0001...”
- Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions
Mariño-Ramírez, Journal of bacteriology 2004 - “...b0339 b2751 b0840 b3639 b4362 b0470 b0812 b2364 b3075 b0543 b0596 b2927 b2439 b2457 b2459 b3963 b0180 b0730 b1385 b0587 b1940 b1946 b2303 b0080 b0825 b2800...”
- Contributions of MexAB-OprM and an EmrE homolog to intrinsic resistance of Pseudomonas aeruginosa to aminoglycosides and dyes
Li, Antimicrobial agents and chemotherapy 2003 - “...aeruginosa genome with the well-characterized EmrEEco protein (b0543; GenBank accession number AE000160) revealed the presence of six genes coding for...”
- Charge neutralization of the active site glutamates does not limit substrate binding and transport by small multidrug resistance transporter EmrE.
Spreacker, The Journal of biological chemistry 2023 - GeneRIF: Charge neutralization of the active site glutamates does not limit substrate binding and transport by small multidrug resistance transporter EmrE.
- High-pH structure of EmrE reveals the mechanism of proton-coupled substrate transport.
Shcherbakov, Nature communications 2022 - GeneRIF: High-pH structure of EmrE reveals the mechanism of proton-coupled substrate transport.
- Cotranslational folding and assembly of the dimeric Escherichia coli inner membrane protein EmrE.
Mermans, Proceedings of the National Academy of Sciences of the United States of America 2022 - GeneRIF: Cotranslational folding and assembly of the dimeric Escherichia coli inner membrane protein EmrE.
- Activating alternative transport modes in a multidrug resistance efflux pump to confer chemical susceptibility.
Spreacker, Nature communications 2022 - GeneRIF: Activating alternative transport modes in a multidrug resistance efflux pump to confer chemical susceptibility.
- Small multidrug resistance protein EmrE phenotypically associates with OmpW, DcrB and YggM for osmotic stress protection by betaine in Escherichia coli.
Pushpker, Microbiology (Reading, England) 2022 (PubMed)- GeneRIF: Small multidrug resistance protein EmrE phenotypically associates with OmpW, DcrB and YggM for osmotic stress protection by betaine in Escherichia coli.
- Characterization of Proteobacterial Plasmid Integron-Encoded qac Efflux Pump Sequence Diversity and Quaternary Ammonium Compound Antiseptic Selection in Escherichia coli Grown Planktonically and as Biofilms
Slipski, Antimicrobial agents and chemotherapy 2021 - “...using an approximate likelihood ratio testing method. Sequences of archetypical E. coli SMR members EmrE (NP_415075) and Gdx/SugE (NP_418572.4) are highlighted in bold. Other sequences shown in bold indicate qac genes that were selected for AST based on their detection frequency in various plasmids. The taxonomic...”
- Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE.
Jurasz, PLoS computational biology 2021 - GeneRIF: Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE.
- Inducing conformational preference of the membrane protein transporter EmrE through conservative mutations.
Leninger, eLife 2019 - GeneRIF: Inducing conformational preference of the membrane protein transporter EmrE through conservative mutations.
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- Long-Range PCR Reveals the Genetic Cargo of IncP-1 Plasmids in the Complex Microbial Community of an On-Farm Biopurification System Treating Pesticide-Contaminated Wastewater
Dunon, Applied and environmental microbiology 2022 (secret) - Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates
Kermani, eLife 2022 - “...Designation Source or reference Identifiers Additional information Gene ( Escherichia coli ) EmrE 3 Uniprot P23895 Bears mutations E25N, W31I, V34M to bind monobody(this paper see Figure 1 ) Gene ( Clostridiales bacterium oral taxon 876) Gdx-Clo GenBank ERI95081.1 PMID: 33247110 Recombinant DNA reagent EmrE 3...”
- Clostridioides difficile as a Dynamic Vehicle for the Dissemination of Antimicrobial-Resistance Determinants: Review and In Silico Analysis
Kartalidis, Microorganisms 2021 - “...protein length), as well as with the multidrug efflux transporter EmrE of E. coli (UniProt P23895; 40% identity over 90% of the C. difficile protein length). Apart from the TetTR-family, regulator pCD-SMR contained a MobA/MobL mobilization protein (IPR005053; ORF8) and a winged helix-like DNA-binding domain superfamily...”
- An in silico survey of Clostridioides difficile extrachromosomal elements
Hornung, Microbial genomics 2019 - “...C. difficile protein length) and to the multidrug efflux transporter EmrE of E. coli (UniProt P23895; 40% identity over 90% of the C. difficile protein length). It also contains a MobA/MobL mobilization protein (IPR005053; ORF8), and a winged helix-like DNA-binding domain superfamily protein (IPR036388; ORF3). A...”
- “...Table S1. PDB: 1L5I, 4CWC, 4CIJ, 3DKX, 2NRA, 2Z9O, 3H25, 3H20, 2R2A. UniProt: P38442, P0CW82, P23895, P06107. Supplementary Data Supplementary File 1 Click here for additional data file. Supplementary File 2 Click here for additional data file. Funding information Work in the group of W. K....”
- Inducing conformational preference of the membrane protein transporter EmrE through conservative mutations
Leninger, eLife 2019 - “...out . The L51I and I62L constructs are single site mutants of wild-type EmrE (UniProt P23895). Luria-Bertani (LB) media and Luria agar powder for resistance assay were purchased from Research Products International. Each construct in the pET Duet-1 vector was transformed into BL21(DE3) and grown at...”
- The de novo design of a biocompatible and functional integral membrane protein using minimal sequence complexity
Lalaurie, Scientific reports 2018 - “...TM helices connected by short extramembrane loops. We identified eight particular SMR proteins (accession numbers P23895, Q2FD83, P69937, P14319, P69926, B0R6K7, P69210, P69213) which are among those to have been characterised and so are validated as authentic gene products. We reasoned that this deliberately restricted dataset,...”
- Members of the conserved DedA family are likely membrane transporters and are required for drug resistance in Escherichia coli
Kumar, Antimicrobial agents and chemotherapy 2014 - “...LIWLCILSFFSVLNEMVLNVSLP NPYIYLGGAILAEVIGTTLMKFS NP417566 NP417482 NP212384 P0AEZ0 AAB09024 P23895 DedA DedA DedA 12-TMS family of the MFS 14-TMS family of the...”
- Genome-scale identification and characterization of moonlighting proteins
Khan, Biology direct 2014 - “...with very different functions (the bar at =1.0 in Figure 9 B). This protein is P23895, a third category/weak moonlighting protein identified to function as a multidrug transporter and in DNA damage response. It interacts with P77368 (UPF0098 family protein inferred by homology) and P75719 (endopeptidase...”
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LF82_0556 multidrug efflux SMR transporter EmrE from Escherichia coli LF82
40% identity, 92% coverage
Z1870 methylviologen resistance protein encoded within prophage CP-933X from Escherichia coli O157:H7 EDL933
40% identity, 92% coverage
LF82_0557 multidrug efflux SMR transporter EmrE from Escherichia coli LF82
SF1980 methylviologen resistance from Shigella flexneri 2a str. 301
S4821 resistance protein from Shigella flexneri 2a str. 2457T
40% identity, 92% coverage
- A multi-phenotypic imaging screen to identify bacterial effectors by exogenous expression in a HeLa cell line
Collins, Scientific data 2018 - “...LF82_394 1.57 0.04 Set3_Part1 C08 LF82_356 1.57 0.06 Set4 E02 LF82_759 1.57 0.07 Set2_Part1 F10 LF82_0557 1.57 0.12 Set1_Part2 E04 LF82_314 1.56 0.17...”
- The extant World War 1 dysentery bacillus NCTC1: a genomic analysis
Baker, Lancet (London, England) 2014 - “...SF3098 SFXv_3402 bcr NCTC1_02492 S2398 SF2269 SFXv_2504 bl1_ec NCTC1_04677 S4573 SF4308 SFXv_4697 emrE NCTC1_02153 S4821 SF1980 SFXv_2210 ksgA NCTC1_00048 S0050 SF0048 SFxv_0050 macB NCTC1_00837 S0879 SF0839 SFxv_0909 mdfA .. S0838 SF0795 SFxv_0864 mdtE NCTC1_03830, NCTC1_03893 S4169 SF3599, SF3547 SFXv_3923, SFXv_3866 mdtF NCTC1_03891, NCTC1_03892 .. SF3598, SF3597...”
- The extant World War 1 dysentery bacillus NCTC1: a genomic analysis
Baker, Lancet (London, England) 2014 - “...S3303 SF3098 SFXv_3402 bcr NCTC1_02492 S2398 SF2269 SFXv_2504 bl1_ec NCTC1_04677 S4573 SF4308 SFXv_4697 emrE NCTC1_02153 S4821 SF1980 SFXv_2210 ksgA NCTC1_00048 S0050 SF0048 SFxv_0050 macB NCTC1_00837 S0879 SF0839 SFxv_0909 mdfA .. S0838 SF0795 SFxv_0864 mdtE NCTC1_03830, NCTC1_03893 S4169 SF3599, SF3547 SFXv_3923, SFXv_3866 mdtF NCTC1_03891, NCTC1_03892 .. SF3598,...”
WP_001304280 multidrug efflux SMR transporter EmrE from Escherichia coli
40% identity, 86% coverage
- Four novel algal virus genomes discovered from Yellowstone Lake metagenomes
Zhang, Scientific reports 2015 - “...hispanica (WP_014039315), Haloferax (WP_004045282), Sphingobacterium spiritivorum (WP_002995628), Escherichia coli (WP_032285312), Escherichia coli O104:H4 str. C227-11 (WP_001304280), Wigglesworthia glossinidia endosymbiont (WP_011070390), Elizabethkingia anophelis (CDN79378), Prevotella bergensis (WP_007174771), Bacteroides sp.3_1_33FAA (WP_008654963), Ostreococcus tauri (XP_003082847), Coccomyxa subellipsoidea c-169 (XP_005651632), Bathycoccus prasinos (XP_007513508), and Micromonas pusilla CCMP1545 (XP_003063730). Figure 9...”
WP_032285312 multidrug efflux SMR transporter EmrE from Escherichia coli O119:H4 str. 03-3458
39% identity, 92% coverage
- Four novel algal virus genomes discovered from Yellowstone Lake metagenomes
Zhang, Scientific reports 2015 - “...sequences used are as follows: Haloarcula hispanica (WP_014039315), Haloferax (WP_004045282), Sphingobacterium spiritivorum (WP_002995628), Escherichia coli (WP_032285312), Escherichia coli O104:H4 str. C227-11 (WP_001304280), Wigglesworthia glossinidia endosymbiont (WP_011070390), Elizabethkingia anophelis (CDN79378), Prevotella bergensis (WP_007174771), Bacteroides sp.3_1_33FAA (WP_008654963), Ostreococcus tauri (XP_003082847), Coccomyxa subellipsoidea c-169 (XP_005651632), Bathycoccus prasinos (XP_007513508), and...”
ECA2982 EmrE family multidrug efflux SMR transporter from Pectobacterium atrosepticum SCRI1043
41% identity, 88% coverage
HCN_1599 DMT family transporter from Helicobacter cinaedi PAGU611
40% identity, 80% coverage
- Multidrug Efflux Systems in Helicobacter cinaedi
Morita, Antibiotics (Basel, Switzerland) 2012 - “...ABC HH1856 (87 (93)) Cj0607 (32 (57)) HCN_1563 RND HH0174 (88 (95)) CmeB (53 (73)) HCN_1599 SMR HH0508 (59 (74)) Cj1174 (54 (76)) HCN_1600 SMR HH0509 (61 (73)) Cj1173 (40 (64)) HCN_2016 SMR HH1452 (61 (73)) Cj0309c (57 (73)) HCN_2017 SMR HH1451 (56 (69)) Cj0309c (57...”
Smal_2304 small multidrug resistance protein from Stenotrophomonas maltophilia R551-3
42% identity, 84% coverage
- The DSF quorum sensing system controls the positive influence of Stenotrophomonas maltophilia on plants
Alavi, PloS one 2013 - “...6.3 Smal_1855 chemotaxis signal transducer 2.7 Smal_1845 CheR-type chemotaxis methyltransferase 2.7 direct plant growth promoting Smal_2304 putative spermidine export protein * 43.8 Smal_2305 putative spermidine export protein * 5.4 Smal_3769 spermidine synthase 1.5 Smal_1341 spermidine/putrescine-binding periplasmic protein 1.5 LPS biosynthesis Smal_0537 permease 2.1 Smal_1400 3-deoxy-manno-octulosonate cytidylyltransferase...”
- “...polysaccharide deacetylase -5.5 iron transport Smal_1803 iron transport protein 1.8 antibiotic resistance and multidrug pumps Smal_2304 multidrug resistance protein 43.8 Smal_2305 small multidrug resistance protein 5.4 Smal_2146 beta-lactamase 2.3 Smal_1568 multidrug efflux transporter (SmeW) 2.7 chaperone synthesis Smal_1891 flagellin-specific chaperone 50.2 Smal_1916 DnaJ class molecular chaperone...”
Smlt2851 putative transmembrane efflux protein from Stenotrophomonas maltophilia K279a
41% identity, 84% coverage
WP_010661279 DMT family transporter from Brucella lupini
38% identity, 91% coverage
BME_RS05230 SMR family transporter from Brucella melitensis bv. 1 str. 16M
38% identity, 91% coverage
MXAN_5186 transporter, small multidrug resistance (SMR) family from Myxococcus xanthus DK 1622
42% identity, 88% coverage
y2000 methylviologen resistance from Yersinia pestis KIM
YPO2333 quaternary ammonium compound-resistance protein from Yersinia pestis CO92
37% identity, 89% coverage
Cj1174 putative efflux protein from Campylobacter jejuni subsp. jejuni NCTC 11168
45% identity, 65% coverage
- Transcriptomic response of Campylobacter jejuni following exposure to acidified sodium chlorite
Weerasooriya, NPJ science of food 2021 - “...of genes involved in DNA damage and repair ( recR and Cj0198c) and efflux protein (Cj1174) indicated the cellular response mechanism in bacterial cell death. Activation of genes involved in DNA damage and repair has been noted in other bacteria treated with SH and hydrogen peroxide...”
- Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations
Pascoe, Molecular ecology 2017 - “...etal., 2010 ; Smid etal., 2013 ). Three efflux pump genes ( Cj0034c, Cj0619 and Cj1174 ) which have been implicated in fluoroquinolone resistance, showed elevated recombination and phylogeographical variation (Table S3 ; Ge, McDermott, White, & Meng, 2005 ; Luangtongkum etal., 2009 ). Clinical and...”
- Mutational and transcriptomic changes involved in the development of macrolide resistance in Campylobacter jejuni
Hao, Antimicrobial agents and chemotherapy 2013 - “...study (34) found that insertional inactivation of Cj1687, Cj1257c, Cj1174, and Cj0035c did not alter the susceptibility of C. jejuni to Ery, the upregulation of...”
- Identification of immunogenic and virulence-associated Campylobacter jejuni proteins
Nielsen, Clinical and vaccine immunology : CVI 2012 - “...processes Macromolecule Cj0917c Cj0965c Cj1092c Cj1094c Cj1163c (4) Cj1174 (3) Cj1292 Cj1364c Cj1371 (2) Cj1382c (4) Cj1529c (5) Cj1628 Cj1632c cstA, carbon...”
- “...Cj0645 Cj0774c Cj0811 Cj0917c Cj0965c Cj1092c Cj1094c Cj1163c Cj1174 Cj1292 Cj1364c Cj1371 Cj1382c Cj1529c Cj1628 Cj1632c Inside and outside Inside and outside...”
- Multidrug Efflux Systems in Helicobacter cinaedi
Morita, Antibiotics (Basel, Switzerland) 2012 - “...(32 (57)) HCN_1563 RND HH0174 (88 (95)) CmeB (53 (73)) HCN_1599 SMR HH0508 (59 (74)) Cj1174 (54 (76)) HCN_1600 SMR HH0509 (61 (73)) Cj1173 (40 (64)) HCN_2016 SMR HH1452 (61 (73)) Cj0309c (57 (73)) HCN_2017 SMR HH1451 (56 (69)) Cj0309c (57 (73)) HCN_1563, with a calculated...”
- Role of efflux pumps and topoisomerase mutations in fluoroquinolone resistance in Campylobacter jejuni and Campylobacter coli
Ge, Antimicrobial agents and chemotherapy 2005 - “...DMT MFS MFS MFS 342/309 1,200 1,185 1,272 381 on Cj1174 537 556 679 data for C. jejuni NCTC11168 indicates the presence of multiple putative drug efflux pumps...”
- “...on E. coli (21). Cj0309c, Cj0310c, Cj1173, and Cj1174 were similar (27 to 38% similarity) to an ethidium bromide resistance protein in Staphylococcus aureus...”
TC 2.A.7.1.11 / Q2FD83 Small MDR pump, AbeS (53% identical to EmrE of E. coli; TC# 2.A.7.1.3). Exports chloramphenicol, ciprofloxacin, erythromycin, novobiocin, acridine orange, acriflavine, benzalkonium chloride, DAPI, deoxycholate, ethidium bromide, sodium dodecyl sulfate (SDS), tetraphenylphosphonium and others from Acinetobacter baumannii (see paper)
ABAYE1181 putative multidrug resistance efflux protein from Acinetobacter baumannii AYE
36% identity, 92% coverage
- substrates: Acridine orange, Benzalkonium chloride, Chloramphenicol, DAPI, Deoxycholate, Novobiocin, SDS, TPP, acriflavine, erythromycin, ethidium bromide
tcdb comment: Purified AbeS binds tetraphenylphosphonium with nanomolar affinity and exhibits electrogenic transport of 1-methyl-4-phenylpyridinium after reconstitution into liposomes (Lytvynenko et al. 2016) - Functional Characterization of AbeD, an RND-Type Membrane Transporter in Antimicrobial Resistance in Acinetobacter baumannii
Srinivasan, PloS one 2015 - “...2.32 ABAYE3381 norM ; multidrug ABC transporter; K03327 multidrug resistance protein, MATE family 1.52 0.87 ABAYE1181 multidrug resistance efflux protein; K03297 small multidrug resistance family protein 1.15 0.74 ABAYE3515 hypothetical protein; K03298 drug/metabolite transporter, DME family 3.48 0.98 ABAYE3514 tolC ; channel-tunnel spanning the outer membrane...”
- AbuO, a TolC-like outer membrane protein of Acinetobacter baumannii, is involved in antimicrobial and oxidative stress resistance
Srinivasan, Antimicrobial agents and chemotherapy 2015 - “...ABAYE0747 ABAYE0746 ABAYE1796 ABAYE3381 ABAYE3248 ABAYE0728 ABAYE1181 ABAYE3515 ABAYE0008 ABAYE0010 ABAYE0827 ABAYE0640 ABAYE0924 adeB; RND protein; K18146...”
- Role of AbeS, a novel efflux pump of the SMR family of transporters, in resistance to antimicrobial agents in Acinetobacter baumannii
Srinivasan, Antimicrobial agents and chemotherapy 2009 - “...used as a host (5). The protein encoded by ORF ABAYE1181 in the AYE genome is annotated as a putative multidrug efflux protein. It exhibits 51.8% identity (E...”
- “...well-characterized member of the SMR family (34). Thus, the ABAYE1181 ORF was selected as the putative SMR-typepump gene to be investigated in this study. The...”
- The de novo design of a biocompatible and functional integral membrane protein using minimal sequence complexity.
Lalaurie, Scientific reports 2018 - “...helices connected by short extramembrane loops. We identified eight particular SMR proteins (accession numbers P23895, Q2FD83, P69937, P14319, P69926, B0R6K7, P69210, P69213) which are among those to have been characterised and so are validated as authentic gene products. We reasoned that this deliberately restricted dataset, featuring...”
- The putative drug efflux systems of the Bacillus cereus group.
Hassan, PloS one 2017 - “...BC0358 92.9 NepA of Arthrobacter nicotinovorans probably exports methylamine Q8GAI5 2.A.7.1.8 (2e-20); P14319 2.A.7.1.1 (6e-20); Q2FD83 2.A.7.1.11 (1e-18) BC0852 93.5 YkkC of Bacillus subtilis Multidrug efflux P49856 2.A.7.1.5 (1e-14); D5CES3 2.A.7.1.10 (2e-13); P69937 2.A.7.1.4 (3e-12) BC0853 92.3 YkkD of Bacillus subtilis Multidrug efflux P49857 2.A.7.1.5 (7e-21);...”
TC 2.A.7.1.6 / O31791 EbrB, component of The heterooligomeric drug resistance efflux pump, EbrAB (substrates: ethidium bromide, acriflavin, pyronin Y, and safranin O) from Bacillus subtilis (see 2 papers)
P0CW82 Multidrug resistance protein EbrB from Bacillus subtilis (strain 168)
NP_389611 small multidrug efflux transporter from Bacillus subtilis subsp. subtilis str. 168
39% identity, 83% coverage
- substrates: acriflavin, ethidium bromide, pyronin Y, safranin O
- Clostridioides difficile as a Dynamic Vehicle for the Dissemination of Antimicrobial-Resistance Determinants: Review and In Silico Analysis
Kartalidis, Microorganisms 2021 - “...mentioned transporter presents similarity to the multidrug efflux transporter EbrB found in B. subtilis (UniProt P0CW82; 46% identity over 89% of the C. difficile protein length), as well as with the multidrug efflux transporter EmrE of E. coli (UniProt P23895; 40% identity over 90% of the...”
- An in silico survey of Clostridioides difficile extrachromosomal elements
Hornung, Microbial genomics 2019 - “...however, the transporter shows homology to the multidrug efflux transporter EbrB from B. subtilis (UniProt P0CW82; 46% identity over 89% of the C. difficile protein length) and to the multidrug efflux transporter EmrE of E. coli (UniProt P23895; 40% identity over 90% of the C. difficile...”
- “...in Table S1. PDB: 1L5I, 4CWC, 4CIJ, 3DKX, 2NRA, 2Z9O, 3H25, 3H20, 2R2A. UniProt: P38442, P0CW82, P23895, P06107. Supplementary Data Supplementary File 1 Click here for additional data file. Supplementary File 2 Click here for additional data file. Funding information Work in the group of W....”
- Diversity and evolution of the small multidrug resistance protein family
Bay, BMC evolutionary biology 2009 - “...Archaeal and Bacterial species using query SMR sequences from Bacillus subtilis (Bsu-EbrA NP_389612 and Bsu-EbrB NP_389611 ; Bsu-YkkC NP_389192 and Bsu-YkkD NP_389193 ; Bsu-YvdR NP_391330 and Bsu-YvdS NP_391329 ; Bsu-YvaE NP_391237 and Bsu-YvaD NP_391236 ) and Escherichia coli (Eco-EmrE NP_415075 ; Eco-SugE NP_418572 ; Eco-YdgE/MdtI NP_416116...”
AOLE_05535 multidrug efflux SMR transporter AbeS from Acinetobacter oleivorans DR1
36% identity, 92% coverage
Smal_2787 small multidrug resistance protein from Stenotrophomonas maltophilia R551-3
38% identity, 92% coverage
- Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles
Youenou, Genome biology and evolution 2015 - “...emr E smlt3363 SmBFE_300027 99.1 ALOG_130569 99.1 SMBUR_120032 98.2 AGRB_680070 92.3 BurJV3_2811 92.3 SMD_2935 93.6 Smal_2787 96.4 SmPIER_460115 90.9 Methyl viologen, tetraphenylphosphonium, benzalkonium, CTAB, cetylpyridinium chloride, EtBr, acriflavin/proflavin, crystal violet, pyronine, safranine, ampicillin, erythromycin, tetracycline sug E smlt4304 SmBFE_380178 100 ALOG_160482 100 SMBUR_10170 99.1 AGRB_470010 100...”
D727_p1037 quaternary ammonium compound efflux SMR transporter QacG2 from Enterobacter cloacae
36% identity, 95% coverage
BurJV3_2811 SMR family transporter from Stenotrophomonas maltophilia JV3
38% identity, 92% coverage
- Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles
Youenou, Genome biology and evolution 2015 - “...bromide, cetyldimethylethyl ammonium bromide emr E smlt3363 SmBFE_300027 99.1 ALOG_130569 99.1 SMBUR_120032 98.2 AGRB_680070 92.3 BurJV3_2811 92.3 SMD_2935 93.6 Smal_2787 96.4 SmPIER_460115 90.9 Methyl viologen, tetraphenylphosphonium, benzalkonium, CTAB, cetylpyridinium chloride, EtBr, acriflavin/proflavin, crystal violet, pyronine, safranine, ampicillin, erythromycin, tetracycline sug E smlt4304 SmBFE_380178 100 ALOG_160482 100...”
EBRB_BACAT / P0CW83 Multidrug resistance protein EbrB from Bacillus atrophaeus (see paper)
41% identity, 83% coverage
WP_008654963 DMT family transporter from Bacteroides fragilis str. 2-F-2 #4
36% identity, 88% coverage
- Four novel algal virus genomes discovered from Yellowstone Lake metagenomes
Zhang, Scientific reports 2015 - “...str. C227-11 (WP_001304280), Wigglesworthia glossinidia endosymbiont (WP_011070390), Elizabethkingia anophelis (CDN79378), Prevotella bergensis (WP_007174771), Bacteroides sp.3_1_33FAA (WP_008654963), Ostreococcus tauri (XP_003082847), Coccomyxa subellipsoidea c-169 (XP_005651632), Bathycoccus prasinos (XP_007513508), and Micromonas pusilla CCMP1545 (XP_003063730). Figure 9 Unrooted phylogenetic tree reconstructed using amino acid sequences of OLV2 and its homolog...”
HH0508 predicted efflux protein from Helicobacter hepaticus ATCC 51449
37% identity, 91% coverage
- Multidrug Efflux Systems in Helicobacter cinaedi
Morita, Antibiotics (Basel, Switzerland) 2012 - “...(87 (93)) Cj0607 (32 (57)) HCN_1563 RND HH0174 (88 (95)) CmeB (53 (73)) HCN_1599 SMR HH0508 (59 (74)) Cj1174 (54 (76)) HCN_1600 SMR HH0509 (61 (73)) Cj1173 (40 (64)) HCN_2016 SMR HH1452 (61 (73)) Cj0309c (57 (73)) HCN_2017 SMR HH1451 (56 (69)) Cj0309c (57 (73)) HCN_1563,...”
Smlt3363 putative transmebrane small multidrug resistance transport protein from Stenotrophomonas maltophilia K279a
37% identity, 92% coverage
- Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles
Youenou, Genome biology and evolution 2015 - “...98.1 Smal_0853 98.1 SmPIER_90108 98.1 CTAB, cetylpyridinium chloride, cetylpyridinium bromide, cetyldimethylethyl ammonium bromide emr E smlt3363 SmBFE_300027 99.1 ALOG_130569 99.1 SMBUR_120032 98.2 AGRB_680070 92.3 BurJV3_2811 92.3 SMD_2935 93.6 Smal_2787 96.4 SmPIER_460115 90.9 Methyl viologen, tetraphenylphosphonium, benzalkonium, CTAB, cetylpyridinium chloride, EtBr, acriflavin/proflavin, crystal violet, pyronine, safranine, ampicillin,...”
- An inducible fusaric acid tripartite efflux pump contributes to the fusaric acid resistance in Stenotrophomonas maltophilia
Hu, PloS one 2012 - “..., and Smlt4191 of S. maltophilia ), two SMR-type transporters (EmrE of E. coli and Smlt3363 of S. maltophilia ), and FuaA of S. maltophilia. Discussion The classification of bacterial efflux pumps has been well described and includes the RND, MFS, ABC, MATE, and SMR families...”
Q9X2N9 Quaternary ammonium compound-resistance protein QacF from Klebsiella aerogenes
36% identity, 95% coverage
SEN1399 Putative multi-drug transporter from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
SC1647 putative membrane transporter of cations from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
35% identity, 88% coverage
WP_002995628 DMT family transporter from Sphingobacterium spiritivorum
34% identity, 91% coverage
- Four novel algal virus genomes discovered from Yellowstone Lake metagenomes
Zhang, Scientific reports 2015 - “...numbers of the sequences used are as follows: Haloarcula hispanica (WP_014039315), Haloferax (WP_004045282), Sphingobacterium spiritivorum (WP_002995628), Escherichia coli (WP_032285312), Escherichia coli O104:H4 str. C227-11 (WP_001304280), Wigglesworthia glossinidia endosymbiont (WP_011070390), Elizabethkingia anophelis (CDN79378), Prevotella bergensis (WP_007174771), Bacteroides sp.3_1_33FAA (WP_008654963), Ostreococcus tauri (XP_003082847), Coccomyxa subellipsoidea c-169 (XP_005651632), Bathycoccus...”
D616_p71007 quaternary ammonium compound efflux SMR transporter QacL from Escherichia coli
38% identity, 89% coverage
- Biocide Selective TolC-Independent Efflux Pumps in Enterobacteriaceae
Slipski, The Journal of membrane biology 2018 - “...et al. ( 2005 ) SMR QacG D727_p1037; YP_006965429.1 ND ND ND ND SMR QacH D616_p71007; YP_006953609.1 ND ND ND ND MFS CmlA2 KPN_RS28175; WP_011152976.1 ND CHL AMP JM83 Ploy et al. ( 1998 ) CDF CepA/FieF D647_p28113; YP_008110862.1, ECL_A245; YP_003602738.1 ND ND ND Ren et...”
LM5578_1862 small multidrug resistance protein, SMR family from Listeria monocytogenes 08-5578
39% identity, 96% coverage
NEPA_PAENI / Q8GAI5 Nicotine metabolites export pump subunit NepA; SMR efflux pump subunit NepA from Paenarthrobacter nicotinovorans (Arthrobacter nicotinovorans) (see paper)
36% identity, 82% coverage
- function: Component of an efflux pump responsible for the transport of nicotine breakdown products, in particular methylamine, out of the cell. This pump apparently serves as a metabolic valve for nicotine catabolites and may protect the bacteria from the potentially toxic side effects of these compounds.
subunit: The efflux pump is composed of NepA and NepB. - The putative drug efflux systems of the Bacillus cereus group.
Hassan, PloS one 2017 - “...best match Top blastp hit(s) b BC0358 92.9 NepA of Arthrobacter nicotinovorans probably exports methylamine Q8GAI5 2.A.7.1.8 (2e-20); P14319 2.A.7.1.1 (6e-20); Q2FD83 2.A.7.1.11 (1e-18) BC0852 93.5 YkkC of Bacillus subtilis Multidrug efflux P49856 2.A.7.1.5 (1e-14); D5CES3 2.A.7.1.10 (2e-13); P69937 2.A.7.1.4 (3e-12) BC0853 92.3 YkkD of Bacillus...”
JD965_RS09240 DMT family transporter from Bacillus siamensis
36% identity, 82% coverage
qacE / CAA48311.1 multiresistance protein from Klebsiella aerogenes (see paper)
P0AGC9 Quaternary ammonium compound-resistance protein QacE from Escherichia coli
37% identity, 89% coverage
SMc01523 PUTATIVE METHYL VIOLOGEN/ETHIDIUM RESISTANCE TRANSMEMBRANE PROTEIN from Sinorhizobium meliloti 1021
34% identity, 88% coverage
TZ05_0853 quaternary ammonium compound efflux SMR transporter SugE2 from Listeria monocytogenes
lmo0854 similar to E. coli SugE protein (transmembrane chaperone) from Listeria monocytogenes EGD-e
35% identity, 97% coverage
EBRA_BACAT / P0CW81 Multidrug resistance protein EbrA from Bacillus atrophaeus (see paper)
34% identity, 91% coverage
- function: Part of a multidrug efflux pump. Confers resistance to cationic lipophilic dyes such as ethidium bromide, acriflavine, pyronine Y and safranin O. The efflux is probably coupled to an influx of protons.
subunit: The efflux pump is composed of EbrA and EbrB.
LM6179_1166 quaternary ammonium compound efflux SMR transporter SugE2 from Listeria monocytogenes 6179
34% identity, 97% coverage
U876_RS03760 SMR family transporter from Aeromonas hydrophila NJ-35
45% identity, 84% coverage
- In Vitro Antibiofilm Activity of Resveratrol against Aeromonas hydrophila
Qin, Antibiotics (Basel, Switzerland) 2023 - “...subunit TssG U876_RS13155 - 1.81 Type VI secretion system tip protein VgrG Small drug resistance U876_RS03760 3.43 - SMR family multidrug efflux pump U876_RS03765 2.91 2.21 SMR family multidrug efflux pump Others U876_RS01620 1.93 3.42 Helix-turn-helix transcriptional regulator U876_RS08385 - 2.26 OmpA family protein antibiotics-12-00686-t002_Table 2...”
EFA0010 multidrug resistance protein from Enterococcus faecalis V583
Q82YU7 Multidrug resistance protein from Enterococcus faecalis (strain ATCC 700802 / V583)
32% identity, 74% coverage
- Involvement, and dissemination, of the enterococcal small multidrug resistance transporter QacZ in resistance to quaternary ammonium compounds
Braga, The Journal of antimicrobial chemotherapy 2011 (PubMed)- “...transporter, annotated in Enterococcus faecalis V583 genome as EFA0010 (we will refer to this gene as qacZ), in decreased susceptibility to biocides. Methods: A...”
- “...e-mail: journals.permissions@oup.com 283 Braga et al. reading frame, EFA0010, annotated as a putative SMR transporter. In this work we provide evidence that...”
- The Response of Enterococcus faecalis V583 to Chloramphenicol Treatment
Aakra, International journal of microbiology 2010 - “...the differentially transcribed (downregulated) plasmid genes was one gene coding for drug resistance or transport (EFA0010). 4. Discussion In this paper, we report the transcriptional patterns of E. faecalis V583 treated with chloramphenicol. E. faecalis V583 is able to grow in media containing chloramphenicol, but compared...”
- “...are several genes coding for putative drug transporters. One of these genes were down regulated, (EFA0010). The EF1732 and EF1733 genes, however, which encode ABC transporters in the MDR family, were upregulated (t90 (EF1732); all time points (EF1733)). These two genes were induced in V583 cells...”
- Survey of genomic diversity among Enterococcus faecalis strains by microarray-based comparative genomic hybridization
Aakra, Applied and environmental microbiology 2007 - “...for the rRNA adenine dimethylase family protein; EFA0010; and Downloaded from http://aem.asm.org/ on February 11, 2017 by University of California, Berkeley...”
- “...EFA0007 was divergent in all of the test strains; EFA0010 was present in EF BRIDGE and unclassified in JH2SS, NCDO642, and 170Vet; and EFA0061 was present in...”
- Biocide-Tolerant Listeria monocytogenes Isolates from German Food Production Plants Do Not Show Cross-Resistance to Clinically Relevant Antibiotics
Roedel, Applied and environmental microbiology 2019 - “...- x - - - - - - - - Multidrug resistance protein Enterococcus faecalis Q82YU7 emrC LT732640.1 100 100 - - x x - - - - - - - - - - - QAC resistance protein QacC S. aureus P14319 qacH HG329628.1 100 92100...”
YP_019986 multidrug resistance protein, Smr family from Bacillus anthracis str. 'Ames Ancestor'
31% identity, 88% coverage
- Draft Genome Sequences of Two Bulgarian Bacillus anthracis Strains
Birdsell, Genome announcements 2013 - “...beta-lactam antibiotic acylase (accession no. YP_019964) and a sulfamethoxypyridazine (SMPR) multidrug efflux pump (accession no. YP_019986). Nucleotide sequence accession numbers. The draft genome sequences of B.anthracis strains 3154 and 3166 have been included in the GenBank WGS database under accession no. ANFF00000000 and ANFG00000000 , respectively....”
qacEdelta1 / AAB60005.1 QacEdelta1 from Pseudomonas aeruginosa (see 6 papers)
ABAYE3642 ethidium bromide resistance protein (E1 protein) from Acinetobacter baumannii AYE
ACICU_00227 membrane transporter from Acinetobacter baumannii ACICU
A1J85_26675, A1Q75_26335, A7J11_00271, AW170_27110, AYK88_26875, D647_p51049, IAU57_09095 quaternary ammonium compound efflux SMR transporter QacE delta 1 from Escherichia coli
38% identity, 79% coverage
- Binding of Tetracyclines to Acinetobacter baumannii TetR Involves Two Arginines as Specificity Determinants
Sumyk, Frontiers in microbiology 2021 - “...when AbTetR was incubated with an amplified 96-bp non-binding DNA sequence between the downstream genes ABAYE3642 and ABAYE3644 ( Figure 2C ). These results indicated that AbTetR binds to the intercistronic region between tetA and tetR of A. baumannii AYE. FIGURE 2 Intercistronic region of tetR...”
- Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group
Iacono, Antimicrobial agents and chemotherapy 2008 - “...CAJ77829 (99, 100) qacE1, SMR family efflux pump ACICU_00227 Negative Negative CAJ77030 CAJ77049 CAJ77052 CAJ77088 Quaternary ammonium a b c (100, (100, (100,...”
- Complete Genome Sequence of Pseudomonas aeruginosa CMC-097, Isolated from a Ventilator-Associated Pneumonia Patient, Containing a Novel Carbapenem Resistance Class 1 Integron
Rao, Microbiology resource announcements 2021 - “...-like element In 2020 IAU57_09085 N -Acetyltransferase GNAT family protein IAU57_09090 sul1 Sulfonamide-resistant dihydropteroate synthase IAU57_09095 qacE 1 Quaternary ammonium compound efflux SMR (truncated) transporter IAU57_09100 bla OXA-2 Oxacillin-hydrolyzing class D -lactamase IAU57_09105 aacA27 Aminoglycoside N -acetyltransferase AAC(6)-IIc IAU57_09110 intI1 e Class 1 integron integrase IntI1...”
- Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics
Khaledi, EMBO molecular medicine 2020 - “...types Drug Data type PA14/CARD gene_id PA14/CARD gene_acc Prokka/Roary gene_id SNP position TOB (GPA_EXPR) GPA A7J11_00271 qacEdelta1 emrE GPA A7J11_02078 sul1 folP_2_indel GPA PA14_04410 ptsP ptsP GPA group_282 GPA PA14_20840 group_14073 GPA group_20477 EXPR PA14_15450 traJ GPA PA14_15100 mepM_1 GPA A7J11_02078 sul1 folP_2 GPA group_8948 GPA...”
- Biocide Selective TolC-Independent Efflux Pumps in Enterobacteriaceae
Slipski, The Journal of membrane biology 2018 - “...), Kazama et al. ( 1999 ), Kcken et al. ( 2000 ) SMR QacED1 D647_p51049; NC_025134.1 NR NR BHB2600; C600 Paulsen et al. ( 1993 ), Kazama et al. ( 1999 ), Kcken et al. ( 2000 ) SMR QacF D733_p4; YP_006961976.1 CTAB BK AMP...”
- Genome Sequencing of Four Multidrug-Resistant Enterobacter aerogenes Isolates from Hospitalized Patients in Brazil
Grazziotin, Frontiers in microbiology 2016 - “...AYK88_15075 A1Q75_15485 A1J85_02150 QacE family quaternary ammonium compound efflux SMR transporter WP_000679416.1 AW170_27110 AYK88_26875 A1Q75_26335 A1J85_26675 Quaternary ammonium compound-resistance protein SugE WP_001597468.1 AW170_19990 AYK88_18310 A1Q75_19995 A1J85_18375 Tetracycline efflux MFS transporter Tet(D) WP_001039466.1 A1Q75_26055 - Although the four isolates showed carbapenem-resistance, no carbapenemase gene was identified using...”
- “...AW170_16750 AYK88_15075 A1Q75_15485 A1J85_02150 QacE family quaternary ammonium compound efflux SMR transporter WP_000679416.1 AW170_27110 AYK88_26875 A1Q75_26335 A1J85_26675 Quaternary ammonium compound-resistance protein SugE WP_001597468.1 AW170_19990 AYK88_18310 A1Q75_19995 A1J85_18375 Tetracycline efflux MFS transporter Tet(D) WP_001039466.1 A1Q75_26055 - Although the four isolates showed carbapenem-resistance, no carbapenemase gene was identified...”
- “...MdtP WP_015369857.1 AW170_16750 AYK88_15075 A1Q75_15485 A1J85_02150 QacE family quaternary ammonium compound efflux SMR transporter WP_000679416.1 AW170_27110 AYK88_26875 A1Q75_26335 A1J85_26675 Quaternary ammonium compound-resistance protein SugE WP_001597468.1 AW170_19990 AYK88_18310 A1Q75_19995 A1J85_18375 Tetracycline efflux MFS transporter Tet(D) WP_001039466.1 A1Q75_26055 - Although the four isolates showed carbapenem-resistance, no carbapenemase gene...”
- “...WP_015369857.1 AW170_16750 AYK88_15075 A1Q75_15485 A1J85_02150 QacE family quaternary ammonium compound efflux SMR transporter WP_000679416.1 AW170_27110 AYK88_26875 A1Q75_26335 A1J85_26675 Quaternary ammonium compound-resistance protein SugE WP_001597468.1 AW170_19990 AYK88_18310 A1Q75_19995 A1J85_18375 Tetracycline efflux MFS transporter Tet(D) WP_001039466.1 A1Q75_26055 - Although the four isolates showed carbapenem-resistance, no carbapenemase gene was...”
H5F64_RS00010 DMT family transporter from Psychrobacter sp.
32% identity, 87% coverage
APL_1607 putative drug resistance protein from Actinobacillus pleuropneumoniae L20
30% identity, 93% coverage
LM6179_2296 quaternary ammonium compound efflux SMR transporter QacH from Listeria monocytogenes 6179
32% identity, 81% coverage
T2KSX9 Multidrug efflux SMR transporter from Listeria monocytogenes
33% identity, 81% coverage
- Food for Thought: Proteomics for Meat Safety
Tarbeeva, Life (Basel, Switzerland) 2023 - “...resistance [ 61 ] bcrA, bcrB, bcrC, qacH, qacA A0A5Y1L6S6 *, I6ZWK8 *, I7B1C4 *, T2KSX9 *, T1YPL4 * Quaternary ammonium compounds [ 69 ] Pseudomonas aeruginosa gyrB P13364 Aminocoumarin [ 70 ] aadA, rpsL A0A844NVA2 *, Q9HWD0 Aminoglycosides [ 71 , 72 ] blaCTXM, PBP1a,...”
y0613 suppresses groEL, may be chaperone from Yersinia pestis KIM
39% identity, 67% coverage
7sztA / U2EQ00 Crystal structure of gdx-clo from small multidrug resistance family of transporters in low ph (protonated state) (see paper)
39% identity, 90% coverage
- Ligand: dodecyldimethylphosphine oxide (7sztA)
lp_3284 quaternary ammonium compound-resistance protein from Lactobacillus plantarum WCFS1
37% identity, 79% coverage
WP_019467894 QacCGHJ group quaternary ammonium compound efflux SMR transporter from Staphylococcus cohnii
32% identity, 75% coverage
CU052_15655 DMT family transporter from Vibrio harveyi
32% identity, 92% coverage
YPO0355 putative chaperone from Yersinia pestis CO92
40% identity, 93% coverage
QACC_STAAU / P14319 Quaternary ammonium compound-resistance protein QacC; Ethidium bromide resistance protein; Multidrug resistance protein; Quaternary ammonium determinant C from Staphylococcus aureus (see 2 papers)
TC 2.A.7.1.1 / P14319 Small multidrug efflux pump, Smr (QacC, QacD, Ebr) from Staphylococcus aureus (see 6 papers)
qacD / AAA26666.1 resistance protein from Staphylococcus aureus (see paper)
qacC / AAB02114.1 resistance protein from Staphylococcus aureus (see paper)
VRA0026 quaternary ammonium compound-resistance protein QacC from Staphylococcus aureus
25% identity, 93% coverage
- function: Multidrug exporter. Is implicated for the resistance to bacteriocidal quaternary ammonium compounds and ethidium bromide.
- substrates: Aromatic dyes, Quaternary amines, TPP derivatives
tcdb comment: Substrates: (1) aromatic dyes (e.g., ethidium bromide), (2) quaternary amines (e.g., the disinfectant benzalkonium) and (3) derivatives of tetraphenylphosphonium (TPP) (Fuentes et al. 2005). Unassembled monomers of the SMR family exist in a dynamic equilibrium where the N-terminal TMS flips in and out of the membrane, with rates that depend on dimerization and the polypeptide sequence (Seurig et al. 2019) - The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated
McCarthy, BMC microbiology 2012 - “...Mercury Resistance mphBM SAP052A_035 Macrolide Resistance mupA SAP082A_042 Mupirocin Resistance qacA SAP066A_020 Biocide Resistance qacC VRA0026 Biocide Resistance qacJ pNVH01_p2 Biocide Resistance sat SAP049A_002 Streptothricin Resistance str pS194_p1 Streptomycin Resistance tcaA SAP082A_032 Teichoplanin Resistance tetK pKH17_02 Tetracycline Resistance tetL FN377602 Tetracycline Resistance tetM SAPIG0957 Tetracycline &...”
- Genomic analysis of Listeria monocytogenes from US food processing environments reveals a high prevalence of QAC efflux genes but limited evidence of their contribution to environmental persistence.
Daeschel, BMC genomics 2022 - “...response P31473 1192 0 bin Tn522 DNA invertase P20384 1264 120 qacC Multidrug efflux pump P14319 2290 1 cwlO Peptidoglycan endopeptidase P40767 1044 14 qorB Quinone oxidoreductase P39315 1390 5 cadA Cadmium transporting ATPase P20021 1212 141 cadC Cadmium resistance transcriptional regulatory protein P20047 1192 141...”
- Biocide-Tolerant Listeria monocytogenes Isolates from German Food Production Plants Do Not Show Cross-Resistance to Clinically Relevant Antibiotics
Roedel, Applied and environmental microbiology 2019 - “...- - - - - - - - - QAC resistance protein QacC S. aureus P14319 qacH HG329628.1 100 92100 x - - - x x - - x x x x x x x a QAC, quaternary ammonium compound. b ID, identification. x, present; -,...”
- The de novo design of a biocompatible and functional integral membrane protein using minimal sequence complexity.
Lalaurie, Scientific reports 2018 - “...by short extramembrane loops. We identified eight particular SMR proteins (accession numbers P23895, Q2FD83, P69937, P14319, P69926, B0R6K7, P69210, P69213) which are among those to have been characterised and so are validated as authentic gene products. We reasoned that this deliberately restricted dataset, featuring diverse and...”
- The putative drug efflux systems of the Bacillus cereus group
Hassan, PloS one 2017 - “...blastp hit(s) b BC0358 92.9 NepA of Arthrobacter nicotinovorans probably exports methylamine Q8GAI5 2.A.7.1.8 (2e-20); P14319 2.A.7.1.1 (6e-20); Q2FD83 2.A.7.1.11 (1e-18) BC0852 93.5 YkkC of Bacillus subtilis Multidrug efflux P49856 2.A.7.1.5 (1e-14); D5CES3 2.A.7.1.10 (2e-13); P69937 2.A.7.1.4 (3e-12) BC0853 92.3 YkkD of Bacillus subtilis Multidrug efflux...”
- Tn6188 - a novel transposon in Listeria monocytogenes responsible for tolerance to benzalkonium chloride
Müller, PloS one 2013 - “...L. monocytogenes K15, HG329628), QacH_LMHPB2262 ( L. monocytogenes HPB2262, EFF95069), QACC_STAAU ( Staphylococcus aureus , P14319), QACH_STASA ( Staphylococcus saprophyticus , O87868), QACJ_STAAU ( Staphylococcus aureus , NP_783299), EMRE_ECOLI ( E. coli , P23895). Notably, Tn 554 and related transposons (Tn 558 , Tn 559 ,...”
- Proton-dependent multidrug efflux systems
Paulsen, Microbiological reviews 1996 - “...P23895 149, 177, 228 CV, EB Smr Smr SW P14319 PR S25583 GB L06418 91, 155, 256 208 33, 208, 284 Staphylococcus aureus Klebsiella pneumonia Gram-negative...”
FTN_0799 putative membrane transporter of cations and cationic drugs, multidrug resistance protein from Francisella tularensis subsp. novicida U112
32% identity, 87% coverage
- Genetic Determinants of Antibiotic Resistance in Francisella
Kassinger, Frontiers in microbiology 2021 - “...protein ErmE multidrug resistance antiporter of cations and cationic drugs, small multidrug resistance family proteins FTN_0799 ArsB (arsenite-antimonite efflux family protein) FTT_0853 Not found FTN_0382 (A0Q4X0) FTN_0800 ArsR family transcriptional regulator K03892, arsenate/arsenite/antimonite-responsive transcriptional repressor ( Xu et al., 1996 ) FTT_0868c FTL_0370 FTN_0395 FTN_0801 The...”
- “...by a computational approach, but not in all strains of Francisella. This locus includes emrE (FTN_0799), a gene which is annotated to be encoding a multidrug resistance antiporter of cations and cationic drugs; and arsRB (FTN_0800 and FTN_0801), two arsenite resistance genes, with arsB potentially being...”
- Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources
Siddaramappa, BMC genomics 2012 - “...arsRB loci or emrE . The occurrence of an ortholog of emrE in strains U112 (FTN_0799, 109 aa) and TX07-7308 (F7308_1297, 109 aa) suggests that arsRB and emrE loci are ancestral and evolutionarily conserved among some environmental lineages of the genus Francisella . Summary of important...”
- Common ancestry and novel genetic traits of Francisella novicida-like isolates from North America and Australia as revealed by comparative genomic analyses
Siddaramappa, Applied and environmental microbiology 2011 - “...hypothetical proteins; T2, ISFtu2 transposase; emrE (FTN_0799), multidrug resistance antiporter; arsRB (FTN_0800 and FTN_0801), arsenite resistance proteins....”
- “...U112 also contained a gene encoding a putative protein (FTN_0799, 109 aa) that was 44% identical to the small multidrug resistance antiporter EmrE of E. coli....”
- Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
Asare, Environmental microbiology 2010 - “...# tnfn1_pw060328p08q153 FTN_0739 potG ATP-binding cassette putrescine uptake system, ATP-binding protein 2 5 # tnfn1_pw060510p04q103 FTN_0799 emrE putative membrane transporter of cations and cationic drugs, multidrug resistance protein 2 2 tnfn1_pw060323p01q177 FTN_0799 emrE putative membrane transporter of cations and cationic drugs, multidrug resistance protein 4 3...”
- “...C IglC 88 6 Selected Mutants tnfn1_pw060328p05q136 FTN_0384 20 2 tnfn1_pw060323p07q141 FTN_0788 75 4 tnfn1_pw060323p01q177 FTN_0799 emrE 26 3 tnfn1_pw060510p01q158 FTN_0988 prmA 84 4 tnfn1_pw060420p02q179 FTN_1263 comL 78 5 tnfn1_pw060323p01q113 FTN_1343 72 2 Table 4 Classification of metabolic genes according to metabolic pathways Amino acid metabolism...”
- Exploitation of host cell biology and evasion of immunity by francisella tularensis
Asare, Frontiers in microbiology 2010 - “...protein FTN_0728 Predicted Co/Zn/Cd cation transporter FTN_0739 potG ATP-binding cassette putrescine uptake system, ATP-binding protein FTN_0799 emrE Putative membrane transporter of cations and cationic drugs, multidrug resistance protein FTN_0800 ArsB arsenite/antimonite exporter FTN_0848 Amino acid antiporter FTN_0885 Proton-dependent oligopeptide transporter (POT) family protein, di-, or tripeptide:...”
- Molecular bases of proliferation of Francisella tularensis in arthropod vectors
Asare, Environmental microbiology 2010 - “...# tnfn1_pw060328p08q153 FTN_0739 potG ATP-binding cassette putrescine uptake system, ATP-binding protein 2 5 # tnfn1_pw060510p04q103 FTN_0799 emrE putative membrane transporter of cations and cationic drugs, multidrug resistance protein 2 2 tnfn1_pw060323p01q177 FTN_0799 emrE putative membrane transporter of cations and cationic drugs, multidrug resistance protein 4 3...”
HCN_1600 DMT family transporter from Helicobacter cinaedi PAGU611
32% identity, 68% coverage
- Multidrug Efflux Systems in Helicobacter cinaedi
Morita, Antibiotics (Basel, Switzerland) 2012 - “...RND HH0174 (88 (95)) CmeB (53 (73)) HCN_1599 SMR HH0508 (59 (74)) Cj1174 (54 (76)) HCN_1600 SMR HH0509 (61 (73)) Cj1173 (40 (64)) HCN_2016 SMR HH1452 (61 (73)) Cj0309c (57 (73)) HCN_2017 SMR HH1451 (56 (69)) Cj0309c (57 (73)) HCN_1563, with a calculated molecular mass of...”
QACC_STASS / Q55339 Quaternary ammonium compound-resistance protein QacC; Quaternary ammonium determinant C from Staphylococcus sp. (strain ST827) (see paper)
AXY41_12200 quaternary ammonium compound efflux SMR transporter QacC from Staphylococcus saprophyticus
24% identity, 93% coverage
O87868 Quaternary ammonium compound-resistance protein QacH from Staphylococcus saprophyticus
30% identity, 74% coverage
- Tn6188 - a novel transposon in Listeria monocytogenes responsible for tolerance to benzalkonium chloride
Müller, PloS one 2013 - “...L. monocytogenes HPB2262, EFF95069), QACC_STAAU ( Staphylococcus aureus , P14319), QACH_STASA ( Staphylococcus saprophyticus , O87868), QACJ_STAAU ( Staphylococcus aureus , NP_783299), EMRE_ECOLI ( E. coli , P23895). Notably, Tn 554 and related transposons (Tn 558 , Tn 559 , Tn 5406 ) show a strong...”
rrnAC0240 quaternary ammonium compound-resistance protein from Haloarcula marismortui ATCC 43049
29% identity, 78% coverage
- Genome information management and integrated data analysis with HaloLex
Pfeiffer, Archives of microbiology 2008 - “...Extended HQ1261A rrnAC0215 723 522 Extended NP0356A, HQ2398A, OE1636F rrnAC0239 999 1,110 Shortened NP1902A, OE2918F rrnAC0240 333 372 Shortened OE3652F, HQ2230A rrnAC0249 879 1,017 Shortened OE3606R, NP3184A rrnAC0261 267 300 Shortened HQ2898A, NP3686A, OE3683R rrnAC0280 333 381 Shortened NP2580A, HQ2722A rrnAC0284 447 225 Extended NP2596A, HQ2724A...”
Mvan_0339 small multidrug resistance protein from Mycobacterium vanbaalenii PYR-1
35% identity, 87% coverage
SOA0159 multidrug efflux transporter from Shewanella oneidensis MR-1
29% identity, 97% coverage
IM712_RS15090 DMT family transporter from Bacillus velezensis
34% identity, 82% coverage
PH197_06315 DMT family transporter from Leuconostoc lactis
34% identity, 83% coverage
WP_014039315 DMT family transporter from Haloarcula hispanica
28% identity, 92% coverage
- Four novel algal virus genomes discovered from Yellowstone Lake metagenomes
Zhang, Scientific reports 2015 - “...using Archaea emrE. The accession numbers of the sequences used are as follows: Haloarcula hispanica (WP_014039315), Haloferax (WP_004045282), Sphingobacterium spiritivorum (WP_002995628), Escherichia coli (WP_032285312), Escherichia coli O104:H4 str. C227-11 (WP_001304280), Wigglesworthia glossinidia endosymbiont (WP_011070390), Elizabethkingia anophelis (CDN79378), Prevotella bergensis (WP_007174771), Bacteroides sp.3_1_33FAA (WP_008654963), Ostreococcus tauri (XP_003082847),...”
WP_037996453 quaternary ammonium compound efflux SMR transporter SugE from Thermoactinomyces vulgaris
37% identity, 92% coverage
- Identification of the Biosynthetic Gene Cluster of Thermoactinoamides and Discovery of New Congeners by Integrated Genome Mining and MS-Based Molecular Networking
Della, Frontiers in chemistry 2020 - “...75 hypothetical protein WP_037996451, Thermoactinomyces 3e45 100/100 ORF5 RMB00108 28,97929,302 107 multidrug efflux SMR transporter WP_037996453, Thermoactinomyces 9e68 100/100 ThdA RMB00109 29,71941,271 3,850 NRPS (C*-A-PCP-C-A-PCP-E-C-A-PCP-E) WP_049720208, Thermoactinomyces sp. CDF 0.0 99/99 ThdB KYQ85937 41,34751,942 3531 NRPS (C-A-PCP-C-A-PCP-C-A-PCP-E) WP_138614946, Thermoactinomyces vulgaris 0.0 99/99 ORF8 RMB00111 51,98852,482 164...”
Q7UJY5 SugE protein-putative transmembrane protein from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
36% identity, 69% coverage
KAR41_06800 SMR family transporter from Periweissella fabalis
34% identity, 88% coverage
- Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species
Fanelli, Microbiology spectrum 2023 - “...KAR27_06420 KAR41_04745, KAR41_07660 KAR50_07235, KAR50_01360 KAR53_01010, KAR53_04580 KAR63_04340 Multidrug Multidrug transporter EmrE emrE NA NA KAR41_06800 KAR50_05895 KAR53_09040 NA Multidrug Multidrug efflux MFS transporter EmrY emrY NA KAR27_02805 KAR41_07550 KAR50_07345 KAR53_02530 NA Multidrug MFS transporter mdrP NA KAR27_02725 KAR41_05095 NA KAR53_04955 KAR63_00455/KAR63_00830 Fosfomycin HAD family hydrolase...”
RUO99_13645 DMT family transporter from Lactiplantibacillus plantarum
36% identity, 79% coverage
CSK29544_03219 SMR family transporter from Cronobacter sakazakii
35% identity, 88% coverage
FD24_GL003284 DMT family transporter from Lactiplantibacillus pentosus DSM 20314
37% identity, 77% coverage
ESA_01940 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
ESA_01940 SMR family transporter from Cronobacter sakazakii ATCC BAA-894
34% identity, 89% coverage
KAR50_05895 DMT family transporter from Periweissella fabaria
34% identity, 91% coverage
- Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species
Fanelli, Microbiology spectrum 2023 - “...KAR41_04745, KAR41_07660 KAR50_07235, KAR50_01360 KAR53_01010, KAR53_04580 KAR63_04340 Multidrug Multidrug transporter EmrE emrE NA NA KAR41_06800 KAR50_05895 KAR53_09040 NA Multidrug Multidrug efflux MFS transporter EmrY emrY NA KAR27_02805 KAR41_07550 KAR50_07345 KAR53_02530 NA Multidrug MFS transporter mdrP NA KAR27_02725 KAR41_05095 NA KAR53_04955 KAR63_00455/KAR63_00830 Fosfomycin HAD family hydrolase mupP...”
SUB0162 quaternary ammonium compound-resistance protein from Streptococcus uberis 0140J
38% identity, 62% coverage
- A dominant clonal lineage of Streptococcus uberis in cattle in Germany
Fenske, Antonie van Leeuwenhoek 2022 - “...gene tetS , coding for tetracycline resistance, was also confirmed. Furthermore, the gene qacH ( SUB0162 ), which may leads to resistance to quaternary ammonium compounds, was found in all isolates with a coverage ranging from at least 50% to as high as 100% in the...”
- “...in vitro, which means that functional resistance cannot be confirmed here. The gene qacH ( SUB0162 ) has been described in previous studies with 41% identity to the gene QACH_STASA in Staphylococcus saprophyticus, which codes for a quaternary ammonium compound-resistance protein (Ward et al. 2009 )....”
- Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis
Ward, BMC genomics 2009 - “...a hygiene measure. The S. uberis 0140J genome contains a putative quaternary ammonium compound-resistance protein (SUB0162) that has 41% identity with QACH_STASA the quaternary ammonium compound-resistance protein QacH from Staphylococcus saprophyticus plasmid pST2H6 [ 40 ]. Downstream of this CDS there are two other CDSs that...”
KJR89_14975 quaternary ammonium compound efflux SMR transporter BcrC from Listeria monocytogenes
I6ZWM1 BcrC from Listeria monocytogenes
31% identity, 87% coverage
- Comparative analysis of Listeria monocytogenes plasmid transcriptomes reveals common and plasmid-specific gene expression patterns and high expression of noncoding RNAs
Anast, MicrobiologyOpen 2022 - “...(Table 3 ). Additionally, pLM5446 harbors several annotated stressassociated genes, including bcrABC (Locus_tags: KJR89_14985, KJR89_14980, KJR89_14975), cadA2 and cadC2 (Locus_tags: KJR89_14955 and KJR89_14960), npr (Locus_tag: KJR89_15095), and an mco identical to the pLM7802 mco (Locus_tag: KJR89_15410). Similar to pLM7802, two genes encode proteins annotated as heavy...”
- Biocide-Tolerant Listeria monocytogenes Isolates from German Food Production Plants Do Not Show Cross-Resistance to Clinically Relevant Antibiotics
Roedel, Applied and environmental microbiology 2019 - “...- - - x - - - - - - - - BcrC L. monocytogenes I6ZWM1 bcrC JX023284.1 100 99 - - - - - - x - - - - - - - - Multidrug resistance protein Enterococcus faecalis Q82YU7 emrC LT732640.1 100 100 -...”
PP1701 sugE protein from Pseudomonas putida KT2440
35% identity, 77% coverage
AAU60_03380 quaternary ammonium compound efflux SMR transporter SugE from Acinetobacter johnsonii
32% identity, 84% coverage
- Genome-sequence analysis of Acinetobacter johnsonii MB44 reveals potential nematode-virulent factors
Tian, SpringerPlus 2016 - “...AAU60_15305 AAU60_13180 AAU60_06585 MFS transporter AAU60_15825 AAU60_07305 AAU60_08870 AAU60_07850 AAU60_07470 AAU60_15415 Resistance Drug/multi-drug resistance AAU60_03375 AAU60_03380 AAU60_01105 AAU60_00855 a HS: predictions from both HMM (hidden markov model) and SVM (hybrid support vector machines) modules are in consensus Acinetobacter baumannii is the most prevalent nosocomial pathogen of...”
Fisuc_1215 small multidrug resistance protein from Fibrobacter succinogenes subsp. succinogenes S85
31% identity, 95% coverage
- Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85
Wu, Scientific reports 2017 - “...HPr Fisuc_1095 1.8 0.02141 Pyridoxal-5-phosphate-dependent protein beta subunit (Cysteine synthase) Fisuc_1133 1.4 8.92E-08 YidE/YbjL duplication Fisuc_1215 1.6 0.0242 small multidrug resistance protein (Membrane transporters of cations and cationic drugs) Fisuc_1277 3.1 7.56E-36 preprotein translocase, SecE subunit Fisuc_1362 1.4 1.18E-05 lipoprotein (TIGR02167 bacterial surface protein 26-residue repeat)...”
JD965_RS02265 DMT family transporter from Bacillus siamensis
30% identity, 83% coverage
PMI2710 multidrug resistance protein from Proteus mirabilis HI4320
27% identity, 86% coverage
- Anaerobic choline metabolism in microcompartments promotes growth and swarming of Proteus mirabilis
Jameson, Environmental microbiology 2016 - “...emrE homologue 8.6639517 7.24E13 Quaternary ammonium compound resistance protein PMI2717 cutO 9.6507023 1.08E10 Alcohol dehydrogenase PMI2710 emrE homologue 9.2090116 2.81E06 Multidrug resistance protein, EmrE homologue PMI0695 trxB 1.9182025 0.000123 Thioredoxin reductase PMI2713 cutH 5.5647202 0.000259 Phosphate acetyltransferase PMI0501 1.8393886 0.000698 Uncharacterized conserved protein YjdB, phage protein...”
MdtJ / b1600 multidrug/spermidine efflux pump membrane subunit MdtJ from Escherichia coli K-12 substr. MG1655 (see 6 papers)
mdtJ / P69212 multidrug/spermidine efflux pump membrane subunit MdtJ from Escherichia coli (strain K12) (see 9 papers)
MDTJ_ECOLI / P69212 Spermidine export protein MdtJ from Escherichia coli (strain K12) (see 2 papers)
TC 2.A.7.1.9 / P69213 MdtJ, component of The spermidine exporter, MdtIJ (MdtIJ = YdgEF) from Escherichia coli O157:H7 (see 2 papers)
NP_416117 multidrug/spermidine efflux pump membrane subunit MdtJ from Escherichia coli str. K-12 substr. MG1655
b1600 multidrug efflux system transporter from Escherichia coli str. K-12 substr. MG1655
ECs2306 possible chaperone from Escherichia coli O157:H7 str. Sakai
36% identity, 79% coverage
- function: Catalyzes the excretion of spermidine. Can also confer resistance to deoxycholate and SDS.
subunit: Forms a complex with MdtI. - substrates: Deoxycholate, SDS, Spermidine
tcdb comment: Catalyzes the export of spermidine and putrescine, and confers resistance to deoxycholate and SDS (Nishino and Yamaguchi 2001). It can be induced by these polyamines and bile salts. Details of the induction mechanism are known (Leuzzi et al. 2015) - Co-translational protein aggregation and ribosome stalling as a broad-spectrum antibacterial mechanism
Khodaparast, Nature communications 2025 (no snippet) - Functional Prediction of Biological Profile During Eutrophication in Marine Environment
Sbaoui, Bioinformatics and biology insights 2022 - “...protein YdeP P77561 Putative formate dehydrogenase, related to acid resistance with formate dehydrogenase/DMSO reductase YdgF P69212 Multidrug/spermidine efflux pump membrane subunit YdiJ P77748 Putative FAD-linked oxidoreductase YdiL P76196 Conserved hypothetical protein YdjX P76219 DedA family protein YehT P0AFT5 DNA-binding transcriptional dual regulator yfaL P45508 Serine protease...”
- Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli
Jindal, BMC microbiology 2019 - “...] mdtI Spermidine export protein P69210 [ 132 , 133 ] mdtJ Spermidine export protein P69212 [ 133 ] mdtL Multidrug resistance protein (e.g. vs chloramphenicol) P31462 [ 133 ] mdtA Multidrug resistance protein (e.g. vs novobiocin) P76397 [ 134 ] acrA Multidrug efflux pump subunit...”
- Multidrug Efflux Systems in Helicobacter cinaedi
Morita, Antibiotics (Basel, Switzerland) 2012 - “...(68%) identity (positive), respectively) of B. subtilis , while HCN_1599-HCN_1600 showed significant similarity to MdtJI (NP_416117 and NP_416116; 38% (57%) and 38% (63%) identity (positive), respectively) of E. coli K12. YkkCD is a multidrug efflux pump that gives rise to broad specificity, including to cationic (e.g.,...”
- Diversity and evolution of the small multidrug resistance protein family
Bay, BMC evolutionary biology 2009 - “...NP_391236 ) and Escherichia coli (Eco-EmrE NP_415075 ; Eco-SugE NP_418572 ; Eco-YdgE/MdtI NP_416116 and Eco-YdgF/MdtJ NP_416117 ) [ 59 ]. As a result, a total of 685 non-identical SMR sequences (as of March 2008) were identified from the query SMR sequence blasts with e-values of 1...”
- Scorpion species of medical importance in the Brazilian Amazon: a review to identify knowledge gaps.
Martins, The journal of venomous animals and toxins including tropical diseases 2021 - “...To2 (Tc48a) P60212 7318 NKDGYLMEGDGCKMGCLTRKASYCVDQCKEVGGKDGYCYAWLSCYCYNMPDSVEIWDSKNNKCGK NaTx Na + -channel Changes Na + -channel To3 (Tc48b) P69213 7385 KDGYLVGNDG ... NaTx - - To3 (Tc49a) P69213 7152 KDGYLVGNDG ... NaTx - - To1 (Tc49b) P60214 7405 KKEGYLVGND ... NaTx - - Tc50 P84688 7073 LDGYPLSKIN ... -...”
- “...- - - Tc83 P84694 25402 NDQCLVIEIL ... - - - Tityus obscurus To3 (Tc48b) P69213 7385 KDGYLVGNDGCKYNCLTRPGHYCANECSRVKGKDGYCYAWMACYCYSMPDWVKTWSRSTNRCGR -toxin Na + -currents of cultured rat pituitary GH3 cells Changes Na + -currents of cultured rat pituitary GH3 cells [ 43 ] Tityus obscurus To1 (Tc49b) P60214...”
- The de novo design of a biocompatible and functional integral membrane protein using minimal sequence complexity
Lalaurie, Scientific reports 2018 - “...We identified eight particular SMR proteins (accession numbers P23895, Q2FD83, P69937, P14319, P69926, B0R6K7, P69210, P69213) which are among those to have been characterised and so are validated as authentic gene products. We reasoned that this deliberately restricted dataset, featuring diverse and functionally distinct proteins from...”
- Identification and phylogenetic analysis of Tityus pachyurus and Tityus obscurus novel putative Na+-channel scorpion toxins
Guerrero-Vargas, PloS one 2012 - “..., this work Tc48a Tc48a (P60212) 7319.3 7318.3 35.1 [25] , this work Tc48b/Tc49a Tc48b/Tc49a (P69213) 7385.4 7385.2 36.6 [29] , this work To4 Tc54 (P60215) 7254.6 7253.2 40.0 [28] , this work To5 - 6937.7 6937.1 45.4 This work To6 Tc43 (P84685.1) 7266.3 7266.0 34.3...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
Kim, Environmental microbiology 2010 - “...phnE b4104 1.4 4.3 1.4 Membrane channel protein component of Pn transporter Transport related ydgF b1600 1.2 1.4 2.1 Multidrug resistance efflux protein, with MdtI tdcC b3116 1.8 1.5 2.1 Serine/threonine:H + symport permease malP b3417 1.7 1.1 2.6 Maltodextrin phosphorylase malG b4032 1.6 1.5 2.0...”
- Inactivation of efflux pumps abolishes bacterial biofilm formation
Kvist, Applied and environmental microbiology 2008 - “...mdtJ b2558 b3240 b0847 b1036 b2211 b2680 b3110 b4148 b1599 b2177 b1600 4.1 12.39 7.63 6.97 4.66 2.78 2.21 3.51 3.59 2.31 2.02 5.31 1.96 2.17 2.83 1.94 3.79 7.66...”
- Transient erythromycin resistance phenotype associated with peptidyl-tRNA drop-off on early UGG and GGG codons
Macvanin, Journal of bacteriology 2007 - “...xylB astD yaiI ygfX argH ytfN lldP hycA Blattner no. b1600 b1958 b1186 b1193 b2524 b3354 b3824 b0654 b2258 b4539 b1317 b2277 b0638 b3564 b1746 b0387 b2896 b3960...”
- Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli
Bausch, Journal of bacteriology 2004 - “...flhA ymfL rimJ ymfO b2459 yggC narJ narU yjiW yiaC thiM b1600 ycal b1152 hyaF b2460 ymfA nrfE yibK aceE evgS ycjV queA idnR idnT yafV yi21-2 cynT yhgG b1565...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...yhcR yhaI celC rpmJ b0011 b1447 rpmD b1451 menC yagS b1600 yaeS b2534 hemL rpmC b1400 b4013 b1029 b2783 b0651 b1832 b1129 b3666 b1444 b1601 b0696 b4017 b0188...”
- “...b2578 b1749 b3242 b3104 b1736 b3299 b0011 b1447 b3302 b1451 b2261 b0285 b1600 b0174 b2534 b0154 b3312 b1400 82 77 59 28 27 24 24 20 19 17 16 15 13 12 12 11 9.6...”
- A broad-specificity multidrug efflux pump requiring a pair of homologous SMR-type proteins
Jack, Journal of bacteriology 2000 - “...including resistance to cationic, anionic, and neutral drugs. b1600 pair, and possibly also for the E. coli SugE-Ebr pair (Table 1). Interestingly, sugE and...”
- “...ykkC and ykkD in B. subtilis as well as b1599 and b1600 in E. coli (Table 1). One member of each B. subtilis protein pair is short (105 to 106 aminoacyl...”
- Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
Bergholz, Applied and environmental microbiology 2009 - “...2.98 0.89 Cell envelope ECs0100 ECs1428 ECs2001 ECs2306 ECs2348 ECs2515 ECs2690 ECs2859 ECs2914 ECs3151 ECs3669 ECs3860 ECs4321 ECs4493 ECs4666 ECs4884 ECs5011...”
QU35_18255 DMT family transporter from Bacillus subtilis subsp. subtilis str. 168
NP_391237 putative metabolite-efflux transporter from Bacillus subtilis subsp. subtilis str. 168
31% identity, 88% coverage
NEPB_PAENI / Q8GAI6 Nicotine metabolites export pump subunit NepB; SMR efflux pump subunit NepB from Paenarthrobacter nicotinovorans (Arthrobacter nicotinovorans) (see paper)
29% identity, 60% coverage
- function: Component of an efflux pump responsible for the transport of nicotine breakdown products, in particular methylamine, out of the cell. This pump apparently serves as a metabolic valve for nicotine catabolites and may protect the bacteria from the potentially toxic side effects of these compounds.
subunit: The efflux pump is composed of NepA and NepB.
KJS00_15095 quaternary ammonium compound efflux SMR transporter BcrC from Listeria monocytogenes
31% identity, 87% coverage
I7B1C4 BcrC from Listeria monocytogenes
31% identity, 87% coverage
- Food for Thought: Proteomics for Meat Safety
Tarbeeva, Life (Basel, Switzerland) 2023 - “...* Mercury resistance [ 61 ] bcrA, bcrB, bcrC, qacH, qacA A0A5Y1L6S6 *, I6ZWK8 *, I7B1C4 *, T2KSX9 *, T1YPL4 * Quaternary ammonium compounds [ 69 ] Pseudomonas aeruginosa gyrB P13364 Aminocoumarin [ 70 ] aadA, rpsL A0A844NVA2 *, Q9HWD0 Aminoglycosides [ 71 , 72 ]...”
IM712_RS02140 DMT family transporter from Bacillus velezensis
30% identity, 83% coverage
BurJV3_3746 quaternary ammonium compound efflux SMR transporter SugE from Stenotrophomonas maltophilia JV3
34% identity, 94% coverage
DR1005 sugE protein from Deinococcus radiodurans R1
47% identity, 54% coverage
Smal_0853 small multidrug resistance protein from Stenotrophomonas maltophilia R551-3
31% identity, 92% coverage
VC1393 sugE protein from Vibrio cholerae O1 biovar eltor str. N16961
33% identity, 77% coverage
I6ZWK8 BcrC from Listeria monocytogenes
31% identity, 87% coverage
- Food for Thought: Proteomics for Meat Safety
Tarbeeva, Life (Basel, Switzerland) 2023 - “...MerR A0A3T2B4E2 * Mercury resistance [ 61 ] bcrA, bcrB, bcrC, qacH, qacA A0A5Y1L6S6 *, I6ZWK8 *, I7B1C4 *, T2KSX9 *, T1YPL4 * Quaternary ammonium compounds [ 69 ] Pseudomonas aeruginosa gyrB P13364 Aminocoumarin [ 70 ] aadA, rpsL A0A844NVA2 *, Q9HWD0 Aminoglycosides [ 71 ,...”
PMI_RS13360 DMT family transporter from Proteus mirabilis HI4320
PMI2711 quaternary ammonium compound resistance protein from Proteus mirabilis HI4320
33% identity, 50% coverage
PA1882 probable transporter from Pseudomonas aeruginosa PAO1
35% identity, 91% coverage
- Metallo-sideromycin as a dual functional complex for combating antimicrobial resistance
Wang, Nature communications 2023 - “..., we first generated five CEF-resistant strains, including three PAO1 strains and two clinical isolates PA1882 by treatment of these bacteria with a sub-inhibitory concentration of CEF (started from 0.5M) over a period of 12 consecutive passages, and the MICs after 12 passages were measured to...”
- The Art of War with Pseudomonas aeruginosa: Targeting Mex Efflux Pumps Directly to Strategically Enhance Antipseudomonal Drug Efficacy
Avakh, Antibiotics (Basel, Switzerland) 2023 - “...PASmr/EmrEPae PA4990 ACR, EtBr, GEN, KAN, NEO [ 90 , 91 ] SugE subfamily SMR PA1882 Further research is needed [ 92 ] MATE PmpM PA1361 ACR, BZK, CIP, EtBr, NOR, OFX, TPPCL [ 93 ] PACE PA2880 PA2880 CHX [ 94 ] RND MexAB-OprM PA0425-PA0426-PA0427...”
- Role of Efflux Pumps on Antimicrobial Resistance in Pseudomonas aeruginosa
Lorusso, International journal of molecular sciences 2022 - “...Pae PA4990 ACR, EtBr, GEN, KAN, NEO [ 73 , 74 ] SugE subfamily SMR PA1882 Further research is needed [ 75 ] MATE PmpM PA1361 ACR, BZK, CIP, EtBr, NOR, OFX, TPPCL [ 76 ] PACE PA2880 PA2880 CHX [ 77 ] RND MexAB-OprM PA0425-PA0426-PA0427...”
- Membrane proteases and aminoglycoside antibiotic resistance
Hinz, Journal of bacteriology 2011 - “...identified previously (24). Mutations in two AmgRS-dependent genes (PA1882 and PA2549) were not included, because they were not represented or were not...”
- Targeting a bacterial stress response to enhance antibiotic action
Lee, Proceedings of the National Academy of Sciences of the United States of America 2009 - “...requires AmgRS Gene* PA2830 PA1331 PA2549 PA3712 PA5528 PA3575 PA1882 PA3787 PA2604 E. coli homologue htpX yegH ygjT yebE None yceJ sugE nlpD yccA Tob/-Tob...”
- Effect of anaerobiosis and nitrate on gene expression in Pseudomonas aeruginosa
Filiatrault, Infection and immunity 2005 - “...PA1518 PA1523 PA1546 PA1556 PA1561 PA1673 PA1789 PA1806 PA1882 PA1883 PA1939 PA2012 PA2013 PA2014 PA2015 PA2016 PA2024 PA2026 PA2073 PA2110 PA2112 PA2113 hemF...”
DR1004 sugE protein from Deinococcus radiodurans R1
38% identity, 75% coverage
GU3_13795 DMT family transporter from Oceanimonas sp. GK1
34% identity, 82% coverage
- Genome-Wide Analysis of Oceanimonas sp. GK1 Isolated from Gavkhouni Wetland (Iran) Demonstrates Presence of Genes for Virulence and Pathogenicity
Parsa, Cell journal 2015 - “...drug resistance Multidrug efflux pumps and proteins GU3_02680, GU3_09445 GU3_09470,GU3_09475 GU3_10125, GU3_10715 GU3_11340, GU3_13155 GU3_13675, GU3_13795 GU3_14635, GU3_14865 GU3_15950, Bicyclomycin resistance protein GU3_10430 Iron acquisition TonB-dependent siderophore receptor (GU3_ 15315) TonB-dependent receptor (GU3_13825),(GU3_10775), (GU3_ 00520) Putative virulence factors Adhesins In silico analysis of the O. sp....”
Smlt1007 putative multidrug resistance protein/chaperone from Stenotrophomonas maltophilia K279a
30% identity, 92% coverage
BurJV3_0859 quaternary ammonium compound efflux SMR transporter SugE from Stenotrophomonas maltophilia JV3
30% identity, 92% coverage
WP_004045282 DMT family transporter from Haloferax volcanii
30% identity, 87% coverage
- Four novel algal virus genomes discovered from Yellowstone Lake metagenomes
Zhang, Scientific reports 2015 - “...emrE. The accession numbers of the sequences used are as follows: Haloarcula hispanica (WP_014039315), Haloferax (WP_004045282), Sphingobacterium spiritivorum (WP_002995628), Escherichia coli (WP_032285312), Escherichia coli O104:H4 str. C227-11 (WP_001304280), Wigglesworthia glossinidia endosymbiont (WP_011070390), Elizabethkingia anophelis (CDN79378), Prevotella bergensis (WP_007174771), Bacteroides sp.3_1_33FAA (WP_008654963), Ostreococcus tauri (XP_003082847), Coccomyxa subellipsoidea...”
E5Y90_15705, FSC09_15345 DMT family transporter from Acinetobacter indicus
28% identity, 87% coverage
- Characterization of Virulent T4-Like Acinetobacter baumannii Bacteriophages DLP1 and DLP2
Peters, Viruses 2023 - “...hit is also to a quaternary ammonium transporter (A0A6N0LIZ1; AFDB) from Acinetobacter sp. 10FS3-1 (gene: E5Y90_15705) with an E-value of 3.3 10 19 ( Supplementary Figure S8 ). Both phages encode the putative virulence factor YbiA (ADLP1_205 and ADLP2_205), which has been shown to cause defects...”
- “...EmrE top hit is to a quaternary ammonium transporter (A0A6C0Y7S0; AFDB) from Acinetobacter indicus (gene: FSC09_15345) with an E-value of 2.9 10 19 ( Supplementary Figure S7 ). For DLP2, EmrE top hit is also to a quaternary ammonium transporter (A0A6N0LIZ1; AFDB) from Acinetobacter sp. 10FS3-1...”
PMI3584 quaternary ammonium compound-resistance protein from Proteus mirabilis HI4320
35% identity, 84% coverage
YPO2068 putative integral membrane protein from Yersinia pestis CO92
y2242 possible chaperone from Yersinia pestis KIM
33% identity, 63% coverage
STY4698 SugE protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
36% identity, 93% coverage
SMc01278 PROBABLE CHAPERONE HOMOLOGUE TRANSMEMBRANE PROTEIN from Sinorhizobium meliloti 1021
38% identity, 76% coverage
Smlt4304 putative chaperone protein from Stenotrophomonas maltophilia K279a
Smal_3713 small multidrug resistance protein from Stenotrophomonas maltophilia R551-3
34% identity, 94% coverage
- Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles
Youenou, Genome biology and evolution 2015 - “...benzalkonium, CTAB, cetylpyridinium chloride, EtBr, acriflavin/proflavin, crystal violet, pyronine, safranine, ampicillin, erythromycin, tetracycline sug E smlt4304 SmBFE_380178 100 ALOG_160482 100 SMBUR_10170 99.1 AGRB_470010 100 BurJV3_3746 100 SMD_3898 99.1 Smal_3713 99.1 SmPIER_550005 96.2 CTAB, cetylpyridinium chloride, cetylpyridinium bromide and cetyldimethylethyl ammonium bromide MFS emr A smlt1529 SmBFE_180083...”
- Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles
Youenou, Genome biology and evolution 2015 - “...sug E smlt4304 SmBFE_380178 100 ALOG_160482 100 SMBUR_10170 99.1 AGRB_470010 100 BurJV3_3746 100 SMD_3898 99.1 Smal_3713 99.1 SmPIER_550005 96.2 CTAB, cetylpyridinium chloride, cetylpyridinium bromide and cetyldimethylethyl ammonium bromide MFS emr A smlt1529 SmBFE_180083 100 ALOG_60096 100 SMBUR_80146 99.5 AGRB_730022 99 BurJV3_1279 98.7 SMD_1360 99.5 Smal_1288 98.5...”
NP_391330 hypothetical protein from Bacillus subtilis subsp. subtilis str. 168
33% identity, 92% coverage
- Diversity and evolution of the small multidrug resistance protein family
Bay, BMC evolutionary biology 2009 - “...Bacillus subtilis (Bsu-EbrA NP_389612 and Bsu-EbrB NP_389611 ; Bsu-YkkC NP_389192 and Bsu-YkkD NP_389193 ; Bsu-YvdR NP_391330 and Bsu-YvdS NP_391329 ; Bsu-YvaE NP_391237 and Bsu-YvaD NP_391236 ) and Escherichia coli (Eco-EmrE NP_415075 ; Eco-SugE NP_418572 ; Eco-YdgE/MdtI NP_416116 and Eco-YdgF/MdtJ NP_416117 ) [ 59 ]. As a...”
A1S_2298 SMR family efflux pump from Acinetobacter baumannii ATCC 17978
38% identity, 56% coverage
lp_3285 DMT family transporter from Lactiplantibacillus plantarum WCFS1
lp_3285 quaternary ammonium compound-resistance protein from Lactobacillus plantarum WCFS1
30% identity, 85% coverage
- Butanol Tolerance of Lactiplantibacillus plantarum: A Transcriptome Study
Petrov, Genes 2021 - “...showed the presence of multidrug efflux transporters that are probably involved in butanol efflux: SMR (lp_3285), about twelve members of the MFS and DHA2 families, and an MMPL family transporter (lp_0295). All multidrug transporters were found to be from two- to sixfold overexpressed in both strains,...”
GDX_CITFR / O69279 Guanidinium exporter from Citrobacter freundii (see paper)
34% identity, 93% coverage
- function: Guanidinium ion exporter. Couples guanidinium export to the proton motive force, exchanging one guanidinium ion for two protons.
YP_209396 SugE protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
34% identity, 69% coverage
SAR11_0786 multidrug resistance protein from Candidatus Pelagibacter ubique HTCC1062
26% identity, 91% coverage
NMB0393 multidrug resistance protein from Neisseria meningitidis MC58
33% identity, 74% coverage
- Interplay Between Virulence and Variability Factors as a Potential Driver of Invasive Meningococcal Disease
Siena, Computational and structural biotechnology journal 2018 - “...[ 15 , 43 ] Capsule Immune evasion synE ND Drug resistance Immune evasion ermE NMB0393 Yes [ 15 ] Protease Immune evasion NEIS2103 NMB2127 T-cell stimulating protein Immune evasion tspB NMB1548 Factor H binding protein Immune modulator fHbp NMB1870 Neisserial surface protein A Immune modulator...”
- Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence
Ampattu, BMC genomics 2017 - “...for anorganic ion transport and metabolism proteins (COG P) including a putative multidrug resistance protein (NMB0393), the lactoferrin-binding protein A (LbpA) and the putative ammonium transporter AmtB, as well as six genes involved in cell envelope biogenesis (COG M) including genes for the two sialic acid...”
- Transcriptional profiling of serogroup B Neisseria meningitidis growing in human blood: an approach to vaccine antigen discovery
Hedman, PloS one 2012 - “...0.596 0.614 NMB0199 lpxB Lipid-A-disaccharide synthase 0.691 0.657 NMB0216 katA Catalase 2.656 2.750 3.301 2.483 NMB0393 Multidrug resistance protein 0.816 NMB0586 Putative adhesin 0.649 NMB0922 lst Alpha-2,3-sialyltransferase 1.159 0.809 0.913 0.686 NMB0926 Opacity protein 0.673 0.884 NMB0995 mip Macrophage infectivity potentiator 1.337 0.958 0.741 0.734 0.729...”
- Identification of iron-activated and -repressed Fur-dependent genes by transcriptome analysis of Neisseria meningitidis group B
Grifantini, Proceedings of the National Academy of Sciences of the United States of America 2003 - “...several virulence-associated genes are overexpressed. These include NMB0393, NMB0977, and NMB1857, which are homologous to E. coli genes involved in toxin...”
TC 2.A.7.1.7 / B0R6K7 The drug resistance efflux pump, Hsmr (Ninio and Schuldiner, 2003) (exports ethidium, acriflavin tetraphenylphosphonium (TPP) and other cationic drugs) from Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1) (see paper)
27% identity, 75% coverage
- substrates: Cationic drugs, TPP, ethidium bromide
tcdb comment: Inhibited by a peptide with the sequence of TMS4 (Poulsen and Deber 2012). TMS4-TMS4 interactions may constitute the highest affinity locus for dimerization (Poulsen et al. 2009) - The de novo design of a biocompatible and functional integral membrane protein using minimal sequence complexity.
Lalaurie, Scientific reports 2018 - “...extramembrane loops. We identified eight particular SMR proteins (accession numbers P23895, Q2FD83, P69937, P14319, P69926, B0R6K7, P69210, P69213) which are among those to have been characterised and so are validated as authentic gene products. We reasoned that this deliberately restricted dataset, featuring diverse and functionally distinct...”
YPTB2051 DMT Superfamily drug efflux pump from Yersinia pseudotuberculosis IP 32953
32% identity, 63% coverage
KAR53_09040 DMT family transporter from Periweissella ghanensis
31% identity, 91% coverage
- Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species
Fanelli, Microbiology spectrum 2023 - “...KAR41_07660 KAR50_07235, KAR50_01360 KAR53_01010, KAR53_04580 KAR63_04340 Multidrug Multidrug transporter EmrE emrE NA NA KAR41_06800 KAR50_05895 KAR53_09040 NA Multidrug Multidrug efflux MFS transporter EmrY emrY NA KAR27_02805 KAR41_07550 KAR50_07345 KAR53_02530 NA Multidrug MFS transporter mdrP NA KAR27_02725 KAR41_05095 NA KAR53_04955 KAR63_00455/KAR63_00830 Fosfomycin HAD family hydrolase mupP NA...”
PPYC1_00515 DMT family transporter from Paenibacillus polymyxa
29% identity, 80% coverage
PP4930 multidrug efflux SMR transporter from Pseudomonas putida KT2440
PP_4930 DMT family transporter from Pseudomonas putida KT2440
29% identity, 91% coverage
MAB_2640c Putative multidrug resistance protein from Mycobacterium abscessus ATCC 19977
38% identity, 91% coverage
I7A797 BcrB from Listeria monocytogenes
KJR89_14980, KJS00_15100 quaternary ammonium compound efflux SMR transporter BcrB from Listeria monocytogenes
33% identity, 94% coverage
- Biocide-Tolerant Listeria monocytogenes Isolates from German Food Production Plants Do Not Show Cross-Resistance to Clinically Relevant Antibiotics
Roedel, Applied and environmental microbiology 2019 - “...- x x x - x x x x x x x BcrB L. monocytogenes I7A797 bcrB JX023284.1 100 100 - - - - - - x - - - - - - - - BcrC L. monocytogenes I6ZWM1 bcrC JX023284.1 100 99 - - -...”
- Comparative analysis of Listeria monocytogenes plasmid transcriptomes reveals common and plasmid-specific gene expression patterns and high expression of noncoding RNAs
Anast, MicrobiologyOpen 2022 - “...KJR89_15050) (Table 3 ). Additionally, pLM5446 harbors several annotated stressassociated genes, including bcrABC (Locus_tags: KJR89_14985, KJR89_14980, KJR89_14975), cadA2 and cadC2 (Locus_tags: KJR89_14955 and KJR89_14960), npr (Locus_tag: KJR89_15095), and an mco identical to the pLM7802 mco (Locus_tag: KJR89_15410). Similar to pLM7802, two genes encode proteins annotated as...”
- “...acid identity to the pLM80 proteins) copies of CadA2C2 (Locus_tags: KJS00_15155; KJS00_15150), BcrABC (Locus_tags: KJS00_15105; KJS00_15100; and KJS00_15095), Tmr (Locus_tag: KJS00_15080), and a Group 2 RepA (Locus_tag: KJS00_15040). Four putative UvrX proteins are encoded on four separate small contigs (6092441bp in size) contained in pLM7802. However,...”
ECWSU1_RS01760, WP_014168291 quaternary ammonium compound efflux SMR transporter SugE from Enterobacter ludwigii
32% identity, 93% coverage
- Biocide Selective TolC-Independent Efflux Pumps in Enterobacteriaceae
Slipski, The Journal of membrane biology 2018 - “...NOR CIP LEV TMP ERY FOS KAM32 He et al. ( 2011a ) SMR SugE ECWSU1_RS01760; WP_014168291 BK CTAB CTP TPP ET FOS KAM32 He et al. ( 2011b ) PACE AceI Entcl_2273; WP_013366261 BK ND BW25113 Hassan et al. ( 2015b ) Escherichia coli SMR...”
- “...CIP LEV TMP ERY FOS KAM32 He et al. ( 2011a ) SMR SugE ECWSU1_RS01760; WP_014168291 BK CTAB CTP TPP ET FOS KAM32 He et al. ( 2011b ) PACE AceI Entcl_2273; WP_013366261 BK ND BW25113 Hassan et al. ( 2015b ) Escherichia coli SMR EmrE...”
RL2561 putative transmembrane efflux/ MDR protein from Rhizobium leguminosarum bv. viciae 3841
32% identity, 77% coverage
MSMEG_3672 transporter, small multidrug resistance (SMR) family protein from Mycobacterium smegmatis str. MC2 155
35% identity, 91% coverage
SMc01179 PUTATIVE MULTIDRUG TRANSMEMBRANE RESISTANCE SIGNAL PEPTIDE PROTEIN from Sinorhizobium meliloti 1021
34% identity, 85% coverage
TC 2.A.7.1.6 / O31792 EbrA, component of The heterooligomeric drug resistance efflux pump, EbrAB (substrates: ethidium bromide, acriflavin, pyronin Y, and safranin O) from Bacillus subtilis (see 2 papers)
NP_389612 small multidrug resistance efflux transporter from Bacillus subtilis subsp. subtilis str. 168
QU35_09520 multidrug efflux SMR transporter subunit EbrA from Bacillus subtilis subsp. subtilis str. 168
33% identity, 75% coverage
DR76_2220, DR76_RS11510 quaternary ammonium compound efflux SMR transporter SugE from Escherichia coli ATCC 25922
33% identity, 72% coverage
SugE / b4148 guanidinium exporter from Escherichia coli K-12 substr. MG1655 (see 3 papers)
gdx / P69937 guanidinium exporter from Escherichia coli (strain K12) (see 13 papers)
GDX_ECOLI / P69937 Guanidinium exporter; Quaternary ammonium compound-resistance protein SugE from Escherichia coli (strain K12) (see 5 papers)
TC 2.A.7.1.4 / P69937 Quaternary ammonium compound (cetylpyridinium, cetyldimethyl ethylammonium, hexadecyltrimethyl ammonium) efflux pump from Escherichia coli (see 8 papers)
NP_418572 suppresses groEL, may be chaperone from Escherichia coli str. K-12 substr. MG1655
NP_418572, b4148 guanidinium exporter from Escherichia coli str. K-12 substr. MG1655
33% identity, 72% coverage
- function: Guanidinium ion exporter. Couples guanidinium export to the proton motive force, exchanging one guanidinium ion for two protons (PubMed:29507227). Overexpression leads to resistance to a subset of toxic quaternary ammonium compounds such as cetylpyridinium, cetyldimethylethyl ammonium and cetrimide cations (PubMed:11948170).
subunit: Homodimer. The subunits assemble with antiparallel topology. - substrates: Cetyldimethyl ethylammonium, Cetylpyridinium, Hexadecyltrimethyl ammonium
- Biocide Selective TolC-Independent Efflux Pumps in Enterobacteriaceae
Slipski, The Journal of membrane biology 2018 - “...TPP TMP ERY CHL KAM3; JM109 Nishino and Yamaguchi ( 2001 ) SMR SugE b4148; NP_418572 CTP CTAB CET ND DH5alpha Chung and Saier Jr. ( 2002 ) MATE MdtK/YdhE/NorM b1663; YP_025307 BK TPP DOC CHL DOX NOR ENO FOS TMP KAM3 Nishino and Yamaguchi (...”
- Diversity and evolution of the small multidrug resistance protein family
Bay, BMC evolutionary biology 2009 - “...NP_391329 ; Bsu-YvaE NP_391237 and Bsu-YvaD NP_391236 ) and Escherichia coli (Eco-EmrE NP_415075 ; Eco-SugE NP_418572 ; Eco-YdgE/MdtI NP_416116 and Eco-YdgF/MdtJ NP_416117 ) [ 59 ]. As a result, a total of 685 non-identical SMR sequences (as of March 2008) were identified from the query SMR...”
- Biocide Selective TolC-Independent Efflux Pumps in Enterobacteriaceae
Slipski, The Journal of membrane biology 2018 - “...R6G TPP TMP ERY CHL KAM3; JM109 Nishino and Yamaguchi ( 2001 ) SMR SugE b4148; NP_418572 CTP CTAB CET ND DH5alpha Chung and Saier Jr. ( 2002 ) MATE MdtK/YdhE/NorM b1663; YP_025307 BK TPP DOC CHL DOX NOR ENO FOS TMP KAM3 Nishino and Yamaguchi...”
- 5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms
Militello, BMC microbiology 2016 - “...mglB D-galactose-, D-glucose-binding protein, periplasmic; substrate recognition for transport and chemotaxis; binds calcium 1.45 2.24E-03 b4148 sugE Multidrug efflux pump; overexpression resistance to cetylpyridinium 1.44 1.22E-03 b3983 rplK 50S ribosomal subunit protein L11; kasugamycin sensitivity 1.44 2.33E-03 b0118 acnB Aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase;...”
- Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis
Wu, mSystems 2016 - “...including Enterobacter lignolyticus eilA (locus tag Entcl_2352) ( 13 ), E.coli K-12 sugE (locus tag b4148) and emrE (locus tag b0543) ( 38 , 39 ), Salmonella enterica smvA (locus tag STM1574) ( 40 , 41 ), and Bacillus cereus ykkC and ykkD ( 21 ),...”
- Spectroscopic analysis of the intrinsic chromophores within small multidrug resistance protein SugE.
Bay, Biochimica et biophysica acta 2011 (PubMed)- GeneRIF: Spectroscopic analysis of the intrinsic chromophores within small multidrug resistance protein SugE
- Inactivation of efflux pumps abolishes bacterial biofilm formation
Kvist, Applied and environmental microbiology 2008 - “...sugE mdtI yejA mdtJ b2558 b3240 b0847 b1036 b2211 b2680 b3110 b4148 b1599 b2177 b1600 4.1 12.39 7.63 6.97 4.66 2.78 2.21 3.51 3.59 2.31 2.02 5.31 1.96 2.17 2.83...”
- Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
Smulski, Journal of bacteriology 2001 - “...b4396 b3461 b1814 b3506 b1642 b3349 b3129 b4062 b2521 b4148 b3616 b3706 b0004 b0001 b0738 b0998 b3519 b1421 b1610 b3453 b1183 b3495 b1521 b0422 b4031 b2605...”
- Endotoxin shock in the rat: reduction of arterial blood pressure fall by the bradykinin antagonist B4148
Weipert, Progress in clinical and biological research 1989 (PubMed) (secret) - The de novo design of a biocompatible and functional integral membrane protein using minimal sequence complexity
Lalaurie, Scientific reports 2018 - “...connected by short extramembrane loops. We identified eight particular SMR proteins (accession numbers P23895, Q2FD83, P69937, P14319, P69926, B0R6K7, P69210, P69213) which are among those to have been characterised and so are validated as authentic gene products. We reasoned that this deliberately restricted dataset, featuring diverse...”
- The putative drug efflux systems of the Bacillus cereus group
Hassan, PloS one 2017 - “...(1e-18) BC0852 93.5 YkkC of Bacillus subtilis Multidrug efflux P49856 2.A.7.1.5 (1e-14); D5CES3 2.A.7.1.10 (2e-13); P69937 2.A.7.1.4 (3e-12) BC0853 92.3 YkkD of Bacillus subtilis Multidrug efflux P49857 2.A.7.1.5 (7e-21); D5CES3 2.A.7.1.10 (3e-20); P69937 2.A.7.1.4 (1e-17) BC4213 88.2 YkkC of Bacillus subtilis Multidrug efflux P49856 2.A.7.1.5 (4e-27);...”
- “...(3e-21 BC4214 95.3 YkkD of Bacillus subtilis Multidrug efflux P49857 2.A.7.1.5 (4e-32); D5CES3 2.A.7.1.10 (4e-27); P69937 2.A.7.1.4 (6e-25) a . Numbers show the percent conservation of the protein in the predicted proteomes of 169 B . cereus group isolates according to comparative BLASTP searches (see Fig...”
- Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.
Paparoditis, Biochimica et biophysica acta 2014 - “...Q7ULN1 11 2.A.6.7.1 O29039 12 unknown unknown Q7UF33 14 2.A.7 Drug/Metabolite Transporter (DMT) Superfamily 2.A.7.1.4 P69937 4 multiple drugs cetylpyridinium, cetyldimethyl ethylammonium, hexadecyltrimethyl ammonium Q7UJY5 4 2.A.7.2.1 P29939 5 unknown unknown Q7UHH1 5 2.A.7.7.2 P27844 10 multiple drugs antibiotic Q7UQ61 10 2.A.7.21.4 Q3SAW5 10 nucleobases orotate...”
- Decoding HMMs using the k best paths: algorithms and applications.
Brown, BMC bioinformatics 2010 - “.... [ 11 ]: the five proteins identified are EmrE [Swiss-Prot: P23895 ], SugE [Swiss-Prot: P69937 ], CrcB [Swiss-Prot: P37002 ], YdgC [Swiss-Prot: P0ACX0 ], and YnfA [Swiss-Prot: P76169 ]. For all of these proteins, the two topologies differ only in their sidedness : they all...”
PMI1158 multidrug resistance protein from Proteus mirabilis HI4320
36% identity, 66% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory