PaperBLAST

PaperBLAST Hits for TCDB::Q9WXW7 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)) (317 a.a., MASKFKKRTF...)

Show query sequence

>TCDB::Q9WXW7 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
MASKFKKRTFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVI
ISGGGAIDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVP
AFIITLGTLTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFF
LRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGV
GSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIV
IVVAVTLDILRRRLASK

Running BLASTp...

Found 274 similar proteins in the literature:

TC 3.A.1.2.18 / Q9WXW7 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
TM0112 sugar ABC transporter, permease protein from Thermotoga maritima MSB8
100% identity, 100% coverage

• substrates: Xylose
• Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases
  Frock, Applied and environmental microbiology 2012
  • “...to TM0060), the xylose/ glucose transporter XylE1F1K1 (TM0112, TM0114, and TM0115), a -xylosidase (TM0076), a xylose isomerase (TM1667), and a xylulokinase...”
• Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
  Nanavati, Applied and environmental microbiology 2006
  • “...oligosaccharide substrate and the adjacent xloA gene) and TM0112, TM0114, and TM0115 (xyl, xylose, as named for E. coli [49]) transport similar substrates. The...”
  • “...TM0072 TM0073 TM0074 TM0075 MSP MSP ABP ABP 1 2 TM0112 TM0114 TM0115 MSP SBP ABP 2 xylF xylE xylK Xylose transport Abbreviation of substrate rbsC2b rbsA2 rbsB2...”
• An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
  Conners, Journal of bacteriology 2005
  • “...This study 47, 80 Unknown rbsC2A2B2a rbsDB1A1C1a TM0112, TM0114, TM0115 TM0955-6, TM0958-9 TM0102-TM0105 This study This study Unknown a Designation proposed...”

Q7UU56 Ribose transport system permease protein rbsC from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
42% identity, 95% coverage

• Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica
  Paparoditis, Biochimica et biophysica acta 2014
  • “...Cassette (ABC) Superfamily 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7ULN8 8 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UU56 8 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UR04 8 3.A.1.2.15 A8H4W6 9 sugar xylitol Q7UXV9 10 3.A.1.5.22 Q5V9S0 6 peptide peptide Q7UHZ2 6 3.A.1.5.22 Q5V9S1 6 peptide peptide Q7UHZ1 6 3.A.1.7.1...”

SCO2747 bifunctional carbohydrate binding and transport protein from Streptomyces coelicolor A3(2)
43% identity, 47% coverage

• A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis
  Titgemeyer, Journal of bacteriology 2007
  • “...xylFGH E. coli ytf operon, B. subtilis araABD rbsH (SCO2747), rbsA (SCO2746), E. coli rbsB 6, S, C 6, S, C 5058-5061 5142-5147 5571-5574 6018-6022 6798-6805...”
  • “...to many ABC permease genes, SCO0580, rpiB E. coli SCO2747, B. subtilis ribose operon yph operon E. coli E. coli ribose operon rbsCBR M. tuberculosis usp operon...”

CPE1629 probable ribose ABC transporter from Clostridium perfringens str. 13
42% identity, 97% coverage

• Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces
  Soncini, BMC genomics 2020
  • “...3.087 0.0276 rbsB Probable ribose ABC transporter CPE1627 3.103 0.0276 rbsC Probable ribose ABC transporter CPE1629 2.619 0.0405 rbsA Probable ribose ABC transporter CPE1630 2.403 0.0276 trmU Probable tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase CPE1783 2.530 0.0276 nifU Probable nitrogen fixation protein CPE1784 2.309 0.0276 dacF Serine-type D-Ala-D-Ala carboxypeptidase CPE1806...”

gbs0114 Unknown from Streptococcus agalactiae NEM316
SAK_RS00825 ABC transporter permease subunit from Streptococcus agalactiae A909
44% identity, 96% coverage

• Transcriptome adaptation of group B Streptococcus to growth in human amniotic fluid
  Sitkiewicz, PloS one 2009
  • “...to amniotic fluid. Locus Name ML LL S Putative function gbs0113 2.5 9.5 D-ribose-binding protein gbs0114 2.3 2.1 9.7 Ribose transport system permease protein rbsC gbs0115 2.7 5.7 Ribose transport ATP-binding protein rbsA gbs0116 2.4 6.2 D-ribose mutarotase gbs0117 2.5 3.0 Ribokinase gbs0316 - 3.4 10.8...”
• Gestational diabetes augments group B Streptococcus infection by disrupting maternal immunity and the vaginal microbiota
  Mercado-Evans, Nature communications 2024
  • “..., Supplementary Table 2 ). Uterine GBS and placental GBS shared 5 DEGs (SAK_RS07995, SAK_RS00885, SAK_RS00825, SAK_RS08150, SAK_RS00940) which include an acetyltransferase, L-lactate dehydrogenase, ribose transporter, YneF family protein, and a transcription factor respectively. Fig. 2 GBS transcriptional profiling in control and gestational diabetic pregnancy identifies...”
  • “...identified 60 DEGs between vaginal, uterine, and placental sites. A gene associated with ribose metabolism (SAK_RS00825) was upregulated in vaginal tissue in our study in line with a previous study comparing GBS transcriptional profiles in vaginal tissues versus chemically defined medium 17 . Several DEGs overlapped...”

SAK_0167 ribose ABC transporter, permease protein from Streptococcus agalactiae A909
44% identity, 95% coverage

• A Vaginal Tract Signal Detected by the Group B Streptococcus SaeRS System Elicits Transcriptomic Changes and Enhances Murine Colonization
  Cook, Infection and immunity 2018
  • “...sak_1910 sak_1911 sak_1920 ABC transporters sak_0166 sak_0167 sak_0168 sak_0169 sak_0207 sak_0208 sak_0209 sak_0210 sak_0302 sak_0303 sak_0472 sak_0561 sak_0562...”

BSU35950 ribose ABC transporter (permease) from Bacillus subtilis subsp. subtilis str. 168
43% identity, 95% coverage

• ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow
  Wu, Microorganisms 2023
  • “...example, the GPR relationship of the ribose ABC transport system is BSU35930 and BSU35940 and BSU35950 and BSU35960 in the model, but the GPRuler tool did not include BSU35930 . By searching UniProt, we found that BSU35930 encodes D-ribose pyranase, which catalyzes the interconversion of beta-pyran...”

YPTB2535 putative ABC sugar (sorbitol) transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
YPO2499 putative sugar transport system, permease protein from Yersinia pestis CO92
41% identity, 91% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(0.002) YPTB2515 YPO2474 conserved hypothetical protein 0.593 (0.036) YPTB2518 YPO2477 putative solute-binding protein 0.62 (0.029) YPTB2535 (rbsC) YPO2499 putative sugar transport system. permease protein 1.7 (0.013) YPTB2715 (ptsH) YPO2993 PTS system. phosphocarrier protein 1.697 (0.001) YPTB2716 (ptsI) YPO2994 PTS sytem. enzyme I component 1.945 (< 0.001)...”
• Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high-mountain plague foci of Kyrgyzstan
  Eroshenko, PloS one 2017
  • “...SNPs were selected ( S2B Table ). The marker SNPs for the 3.ANT1 in the YPO2499 locus, and the marker SNPs for the 3.ANT2 in the YPO1708 locus were not found. Therefore, all 42 strains of antique biovar from Tien Shan and Alai high-mountain foci must...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPO2474 conserved hypothetical protein 0.593 (0.036) YPTB2518 YPO2477 putative solute-binding protein 0.62 (0.029) YPTB2535 (rbsC) YPO2499 putative sugar transport system. permease protein 1.7 (0.013) YPTB2715 (ptsH) YPO2993 PTS system. phosphocarrier protein 1.697 (0.001) YPTB2716 (ptsI) YPO2994 PTS sytem. enzyme I component 1.945 (< 0.001) YPTB2717 (crr)...”

TC 3.A.1.2.19 / Q9X050 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
TM0955 ribose ABC transporter, permease protein from Thermotoga maritima MSB8
44% identity, 89% coverage

• substrates: Ribose
• Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
  Nanavati, Applied and environmental microbiology 2006
  • “...transport TM0434, agu (-glucuronidase [53]) ugpBb ugpA ugpE TM0955 TM0956 TM0958 TM0959 MSP ABP SBP MSP 1 rbsC rbsA rbsB rbsD Ribose transport Annotated...”
• Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species
  Mongodin, Journal of bacteriology 2005
  • “...ORFs coding for subunits of a ribose ABC transporter (TM0955, TM0956, TM0958, and TM0959). Thermotoga strains LA10, LA4, RQ7, and VMA1/ L12B are closely related...”
• Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima
  Nesbø, Journal of bacteriology 2002
  • “...MSB8 2.7E20 80 430 TM0595 sugar ABC transporter 335 TM0955 ribose ABC transporter 263 TM1066 oligopeptide ABC 167 transporter T. maritima MSB8 T. maritima MSB8...”

SXYL_01519 ABC transporter permease from Staphylococcus xylosus
42% identity, 97% coverage

• Transcriptomic analysis of Staphylococcus xylosus in the presence of nitrate and nitrite in meat reveals its response to nitrosative stress
  Vermassen, Frontiers in microbiology 2014
  • “...SXYL_00221 fda Fructose-bisphosphate aldolase class 1 2.5 SXYL_01518 rbsB Ribose ABC transporter substrate-binding protein 2.2 SXYL_01519 rbsC Ribose ABC transporter permease 2.3 SXYL_01521 rbsD D-ribose pyranase 2.1 SXYL_00125 araA L-arabinose isomerase 0.4 SXYL_00124 araD L-ribulose-5-phosphate 4-epimerase 0.4 SXYL_00126 araT Arabinose-proton symporter 0.6 SXYL_00607 araB1 Ribulokinase 2.0...”

HI0503 D-ribose ABC transporter, permease protein (rbsC) from Haemophilus influenzae Rd KW20
43% identity, 87% coverage

• Genome-scale approaches to identify genes essential for Haemophilus influenzae pathogenesis
  Wong, Frontiers in cellular and infection microbiology 2012
  • “...afuB Ferric transport system permease-like protein d HEME HI0263 hxuB Heme/hemopexin-binding protein B f RIBOSE HI0503 ribsC Ribose ABC transporter permease e TRANSPORTERS HI0561 Putative oligopeptide transporter (OPT) family d HI1218 lctP l -lactate permease d HI0898 emrA Multidrug resistance protein A d METABOLIC PROCESSES/ELECTRON TRANSPORT...”
• Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis
  Gmuender, Genome research 2001
  • “...hi0537 hi1661 hi0425 hi0863 hi1434.1 hi1186 hi1676 hi1040 hi0503 hi1152 hi1193 hi0538 hi1033 hi1632 hi1227 hi1041 hi1163 hi0117 hi1022 hi0563 hi0539 hi1201...”

BA0668 ribose ABC transporter, permease protein from Bacillus anthracis str. Ames
42% identity, 98% coverage

• Role of luxS in Bacillus anthracis growth and virulence factor expression
  Jones, Virulence 2010
  • “...pyruvate formate-lyase-activating enzyme (pflA) -1.26 -23.26 -36.00 BA0668 ribose ABC transporter, permease protein (rbsC) -1.42 -14.42 -12.91 -7.94 BA0669...”

ABD05_RS24180 ABC transporter permease from Burkholderia pyrrocinia
40% identity, 90% coverage

• The peanut root exudate increases the transport and metabolism of nutrients and enhances the plant growth-promoting effects of burkholderia pyrrocinia strain P10
  Han, BMC microbiology 2023
  • “...cyoD Cytochrome o ubiquinol oxidase 1.25 ABD05_RS21580 malK Multiple sugar transport system ATP-binding protein 1.89 ABD05_RS24180 rbsC Ribose transport system permease protein 1.15 ABD05_RS21645 araF L-arabinose transport system substrate-binding protein 1.15 ABD05_RS21655 araH L-arabinose transport system permease protein 2.24 ABD05_RS33475 xylH D-xylose transport system permease protein...”

SMc02772 PUTATIVE SUGAR ABC TRANSPORTER PERMEASE PROTEIN from Sinorhizobium meliloti 1021
43% identity, 87% coverage

• Identification of Sinorhizobium meliloti early symbiotic genes by use of a positive functional screen
  Zhang, Applied and environmental microbiology 2006
  • “...by University of California, Berkeley ering most of the SMc02772 open reading frame (Fig. 7) (24). But the direction of the fragment showing promoter activities...”
  • “...this region opposite to that of the SMc02772 and SMc02773 open reading frames, using prokaryotic promoter predicting software (http://www.fruitfly.org). Both...”

LLNZ_RS04080 ABC transporter permease from Lactococcus cremoris subsp. cremoris NZ9000
39% identity, 99% coverage

• Enhanced acid-stress tolerance in Lactococcus lactis NZ9000 by overexpression of ABC transporters
  Zhu, Microbial cell factories 2019
  • “...expression of genes involved in sugar transport ( ptcA , malFG , fruA , and LLNZ_RS04080 ). Moreover, several genes implicated in pyrimidine metabolism ( pyrCBDEK ) were up-regulated during acid stress (Fig. 3 a). Interestingly, the cspABCD2 genes and multiple transcriptional regulators were also consistently...”
  • “...survival and colonization [ 33 ]. Interestingly, two sugar ABC transporters ( malG , and LLNZ_RS04080 ) were downregulated in L. lactis (MsmK). Therefore, we speculate that L. lactis may have developed a self-regulatory mechanism to achieve optimal flow of metabolism and transport of carbohydrates, and...”

BR1631 ribose ABC transporter, permease protein from Brucella suis 1330
BMEI0392 RIBOSE TRANSPORT SYSTEM PERMEASE PROTEIN RBSC from Brucella melitensis 16M
BOV_1575 ribose ABC transporter, permease protein from Brucella ovis ATCC 25840
BCAN_A1668 hypothetical protein from Brucella canis ATCC 23365
41% identity, 93% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...ABC2 BMEI0391 BruAB11620, rbsA-2 BR1632, rbsA-2 BOV_1576 BCAN_A1669 MOS Ribose import IM BMEI0392 BruAB11619, rbsC-2 BR1631, rbsC-2 BOV_1575, rbsC2 BCAN_A1668 MOS Ribose import BP BMEI0393 BruAB11618 BR1630 BOV_1574 BCAN_A1667 51 MOS Ribose Import ABC BMEI0665 BruAb11337 BR1339 BOV_1299 BCAN_A1367 MOS Ribose Import IM BMEI0664 BruAb11338 BR1340...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...MOS Ribose import ABC2 BMEI0391 BruAB11620, rbsA-2 BR1632, rbsA-2 BOV_1576 BCAN_A1669 MOS Ribose import IM BMEI0392 BruAB11619, rbsC-2 BR1631, rbsC-2 BOV_1575, rbsC2 BCAN_A1668 MOS Ribose import BP BMEI0393 BruAB11618 BR1630 BOV_1574 BCAN_A1667 51 MOS Ribose Import ABC BMEI0665 BruAb11337 BR1339 BOV_1299 BCAN_A1367 MOS Ribose Import IM...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BruAB11620, rbsA-2 BR1632, rbsA-2 BOV_1576 BCAN_A1669 MOS Ribose import IM BMEI0392 BruAB11619, rbsC-2 BR1631, rbsC-2 BOV_1575, rbsC2 BCAN_A1668 MOS Ribose import BP BMEI0393 BruAB11618 BR1630 BOV_1574 BCAN_A1667 51 MOS Ribose Import ABC BMEI0665 BruAb11337 BR1339 BOV_1299 BCAN_A1367 MOS Ribose Import IM BMEI0664 BruAb11338 BR1340 BOV_1300 BCAN_A1368...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BR1632, rbsA-2 BOV_1576 BCAN_A1669 MOS Ribose import IM BMEI0392 BruAB11619, rbsC-2 BR1631, rbsC-2 BOV_1575, rbsC2 BCAN_A1668 MOS Ribose import BP BMEI0393 BruAB11618 BR1630 BOV_1574 BCAN_A1667 51 MOS Ribose Import ABC BMEI0665 BruAb11337 BR1339 BOV_1299 BCAN_A1367 MOS Ribose Import IM BMEI0664 BruAb11338 BR1340 BOV_1300 BCAN_A1368 MOS Ribose...”

TC 3.A.1.2.13 / A6VKS9 RbsC, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) from Actinobacillus succinogenes (strain ATCC 55618 / 130Z)
39% identity, 94% coverage

• substrates: Autoinducer-2
• Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.
  Paparoditis, Biochimica et biophysica acta 2014
  • “...organo-sulfur- containing compound Q7UEN7 8 3.A P-P-Bond Hydrolysis-driven Transporters 3.A.1 ATP-binding Cassette (ABC) Superfamily 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7ULN8 8 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UU56 8 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UR04 8 3.A.1.2.15 A8H4W6 9 sugar xylitol Q7UXV9 10 3.A.1.5.22 Q5V9S0 6 peptide...”

c4015 Ribose transport system permease protein rbsC from Escherichia coli CFT073
ECOLIN_RS18680 ABC transporter permease from Escherichia coli Nissle 1917
40% identity, 96% coverage

• The Analysis of Multiple Genome Comparisons in Genus Escherichia and Its Application to the Discovery of Uncharacterised Metabolic Genes in Uropathogenic Escherichia coli CFT073
  Bryant, Comparative and functional genomics 2009
  • “...the genes. SAC No. 8 (genes c4013 to c4018) has several genes annotated putatively already, c4015 to c4017 as part of a ribose ABC transporter, and c4018 as a tagatose 1,6-diphosphate aldolase. The hypothetical genes bear similarities to other sugar metabolism encoding genes: c4013 to a...”
• Identification of a gene cluster for D-tagatose utilization in Escherichia coli B2 phylogroup
  Ha, iScience 2022
  • “...by ECOLIN_RS18695), substrate-binding domain-containing protein (ECOLIN_RS18690), sugar ABC transporter ATP-binding protein (ECOLIN_RS18685), ABC transporter permease (ECOLIN_RS18680), sugar kinase (ECOLIN_RS18675), and aldose 1-epimerase family protein (ECOLIN_RS18670). The latter gene cluster on the forward strand contained the remaining two genes, encoding the DeoR/GlpR transcriptional regulator (ECOLIN_RS18700) and sugar...”
  • “...gene cluster containing at least four homologs of tagatose kinase (ECOLIN_RS18675) and ABC transport subunits (ECOLIN_RS18680, ECOLIN_RS18685, and ECOLIN_RS18690) ( Figure6 ). The cladogram describing the phylogenetic relationships among them was constructed based on the NCBI Taxonomy database and the phylogenetic tree of each phylum. 31...”

TC 3.A.1.2.20 / G4FGN4 Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
40% identity, 90% coverage

• substrates: Xylose, glucose

cg1412 ribose/xylose/arabinose/galactoside ABC-type transporter permease from Corynebacterium glutamicum ATCC 13032
40% identity, 93% coverage

• Transcriptional regulation of the operon encoding stress-responsive ECF sigma factor SigH and its anti-sigma factor RshA, and control of its regulatory network in Corynebacterium glutamicum
  Busche, BMC genomics 2012
  • “...putative manganese/zinc transporter, ATPase subunit 1.65 cg0228 Two-component system, sensory histidine kinase, putative pseudogene 1.65 cg1412 rbsC ABC-type ribose transporter, permease subunit (TC 3.A.1.2.1) 1.65 cg1778 zwf Glucose-6-phosphate 1-dehydrogenase 1.65 cg1686 Putative transcriptional regulatory protein 1.61 cg1482 Putative Zn-dependent hydrolase 1.61 cg2514 Conserved hypothetical protein 1.59...”
• The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum
  Brune, Journal of bacteriology 2007
  • “...by University of California, Berkeley cg1488 cg1487 cg1413 cg1412 cg1658 cg1453 cg1411 cg1129 cg2893 cg1410 cg2391 cg3359 cg2894 cg1612 cg3362 cg2565 cg3361...”
  • “...observed when 40-mer sequences present upstream of the cg1412 (rbsC), cg1486, cg1617, cg2391 (aroG), and cg2545 genes were used (Fig. 4B). The specificity of...”
• Two-component systems of Corynebacterium glutamicum: deletion analysis and involvement of the PhoS-PhoR system in the phosphate starvation response
  Kocan, Journal of bacteriology 2006
  • “...cg0928 cg0957 cg1120 cg1121 cg1343 cg1344 cg1405 cg1412 cg1413 cg1418 cg1419 cg1447 NCgl0777 NCgl0778 NCgl0779 NCgl0802 NCgl0943 NCgl0944 NCgl1141 NCgl1142...”

FTV88_0055 ABC transporter permease from Heliorestis convoluta
38% identity, 97% coverage

• Analysis of the Complete Genome of the Alkaliphilic and Phototrophic Firmicute Heliorestis convoluta Strain HH^T
  Dewey, Microorganisms 2020
  • “...was annotated in the Hrs. convoluta genome, a putative ribose ABC transporter complex (FTV88_0053, FTV88_0054, FTV88_0055) was identified and may allow for carbohydrate transport [ 41 ]. As genes encoding glycolytic pathway enzymes are present in the Hrs. convoluta genome, it is tempting to speculate that...”

eryF / Q2YIY3 putative erythritol ABC transporter membrane protein from Brucella abortus (strain 2308) (see 3 papers)
BAB2_0376 Bacterial inner-membrane translocator:Sodium:dicarboxylate symporter from Brucella melitensis biovar Abortus 2308
BMEII0433 RIBOSE TRANSPORT SYSTEM PERMEASE PROTEIN RBSC from Brucella melitensis 16M
BruAb2_0372 ribose ABC transporter, permease protein from Brucella abortus biovar 1 str. 9-941
39% identity, 86% coverage

• Evaluation of the effects of erythritol on gene expression in Brucella abortus
  Rodríguez, PloS one 2012
  • “...BAB2_0372 2.58 3.85 Erythritol kinase, EryA COG1070G BAB2_0375 2.78 2.23 Phosphoribulokinase ABC transporter ATPase COG1129G BAB2_0376 1.96 2.38 Inner-membrane translocator COG1172G BAB2_0377 2.16 2.05 Periplasmic protein/LacI transcrip. regulator COG1879G BAB2_0378 - 2.30 DeoR family regulatory protein COG1349GK BAB1_1741 1.59 - Glyceraldehyde 3-phosphate dehydrogenase COG0057G BAB1_1742 1.75...”
  • “...Crasta et al . [9] . The fact that in B. abortus strain S19 the BAB2_0376 ortholog (BAbS19_II03540) is affected by a 68 bp deletion and probably inactivated suggests the existence of alternative erythritol uptake systems in Brucella . The end product of erythritol catabolism would...”
• Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes
  Crasta, PloS one 2008
  • “...the ribose transporter protein, S19 BAbS19_II03540; A. with the homologs from strain 9941 (BruAb2_0372), 2308 (BAB2_0376) and B. suis (BRA0859); B. Protein alignment of the ribose transporter protein from strain 2308 (BAB2_0376) with the putative Rhizobium leguminosarum eryF protein. The sequence deleted in S19 BAbS19_II03540 is...”
  • “...virulence in mice. S19 also contains a 68 nucleotide deletion in the ORF corresponding to BAB2_0376 of B. abortus 2308, which results in a 114 aa N terminal truncation ( Figure 4 AB ). BAB2_0376 encodes a putative inner-membrane translocator sodium dicarboxylate symporter, which is highly...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...import ABC2 BMEII0432, rbsA BruAb20371, rbsA3 BRA0860, rbsA3 BOV_A0807, rsbA3 BCAN_B0877 MOS Erythritol import IM BMEII0433, rbsC BruAb20372, rbsC3 BRA0859, rbsC3 BCAN_B0876 MOS Erythritol import BP BMEII0435 BruAb20373, rbsB2 BRA0858, rbsB2 BOV_A0805 BCAN_B0875 58 MOS Galactoside/Ribose import ABC2 BMEII0698 BruAb20654 BRA0570 BOV_A0533 BCAN_B0570 MOS Galactoside/Ribose import...”
• Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes
  Crasta, PloS one 2008
  • “...shown in Table 7 . Four of the 45 OCDs (ORFs BruAb1_0072, BruAb2_0365, BruAb2_0366, and BruAb2_0372 in 9941) showed more than 60 bp differences between the attenuated and the virulent strains and were considered as Major Virulence Associated Differences (priority 0 in Table 7 ). The...”
  • “...247 247 K_erythritol transcriptional regulator 3 0 BruAb2_0366 423 423 -_EryC, D-erythrulose-1-phosphate dehydrogenase 4 0 BruAb2_0372 68 68 G_ribose ABC transporter, permease protein 5 1 BruAb1_0019 7 7 FS I_carboxyl transferase family protein 6 1 BruAb1_0443 2 2 FS I_enoyl-(acyl carrier protein) reductase 7 2 BAB1_0967...”

MSMEG_4171 ribose transport system permease protein RbsC from Mycobacterium smegmatis str. MC2 155
43% identity, 88% coverage

• Nitrogen starvation-induced transcriptome alterations and influence of transcription regulator mutants in Mycobacterium smegmatis
  Jeßberger, BMC research notes 2013
  • “...amidolyase msmeg_4569 3.48 Conserved hypothetical protein msmeg_1292 3.48 FAD binding domain in molybdopterin dehydrogenase protein msmeg_4171 3.58 Ribose transport system permease protein RbsC msmeg_3994 3.64 Short chain dehydrogenase msmeg_5648 3.68 Hypothetical protein msmeg_2189 3.68 Allophanate hydrolase ( atF ) msmeg_0393 3.73 Fmt protein msmeg_1153 3.73 FAD...”
• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...1.53 4.65E03 1.01E02 7.80E01 6.94E03 MSMEG_3602 MSMEG_4170 MSMEG_4171 MSMEG_4172 MSMEG_4173 rbsA3 rbsA4 rbsC4 rbsB4 rbsR4 1.22 (1.08) 1.21 1.46 (1.13) 2.29E01...”

YPTB2205 ABC sugar/ribose transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
41% identity, 85% coverage

• Characterization of chromosomal regions conserved in Yersinia pseudotuberculosis and lost by Yersinia pestis
  Pouillot, Infection and immunity 2008
  • “...of 3,608 bp and is composed of three genes: YPTB2205 to YPTB2207 (Fig. 1B and see Table S4 in the supplemental material). YPTB2207 encodes a hypothetical...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...hypothetical protein 1.297 (0.041) YPTB2190 (mlc) YPO2268 putative ROK family transcriptional regulatory protein 1.417 (0.037) YPTB2205 or3894 ABC sugar/ribose transporter. permease subunit 1.61 (0.036) YPTB2306 (pykF) YPO2393 pyruvate kinase I 2.282 (< 0.001) YPTB2318 (ppsA) YPO2409 phosphoenolpyruvate synthase 0.463 (0.008) YPTB2356 (kduI) YPO1725 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1.444...”

Entcl_3383 ABC transporter permease from [Enterobacter] lignolyticus SCF1
42% identity, 95% coverage

• Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
  Orellana, PloS one 2017
  • “...up-regulated after glucose uptake was stopped ( Fig 2C ) (Entcl_0166, Entcl_0167, Entcl_1205, Entcl_1207, Entcl_3382, Entcl_3383, Entcl_4082, Entcl_4174, and Entcl_4403, S4 Table ). This was presumably a response to the lack of availability of glucose, an effect that has been observed in other fermentative anaerobes [...”

BRA0859 ribose ABC transporter, permease protein from Brucella suis 1330
BCAN_B0876 hypothetical protein from Brucella canis ATCC 23365
39% identity, 86% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BruAb20371, rbsA3 BRA0860, rbsA3 BOV_A0807, rsbA3 BCAN_B0877 MOS Erythritol import IM BMEII0433, rbsC BruAb20372, rbsC3 BRA0859, rbsC3 BCAN_B0876 MOS Erythritol import BP BMEII0435 BruAb20373, rbsB2 BRA0858, rbsB2 BOV_A0805 BCAN_B0875 58 MOS Galactoside/Ribose import ABC2 BMEII0698 BruAb20654 BRA0570 BOV_A0533 BCAN_B0570 MOS Galactoside/Ribose import IM BOV_A0534 BCAN_B0567 MOS...”
• Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes
  Crasta, PloS one 2008
  • “...S19 BAbS19_II03540; A. with the homologs from strain 9941 (BruAb2_0372), 2308 (BAB2_0376) and B. suis (BRA0859); B. Protein alignment of the ribose transporter protein from strain 2308 (BAB2_0376) with the putative Rhizobium leguminosarum eryF protein. The sequence deleted in S19 BAbS19_II03540 is indicated by the strike-through...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BRA0860, rbsA3 BOV_A0807, rsbA3 BCAN_B0877 MOS Erythritol import IM BMEII0433, rbsC BruAb20372, rbsC3 BRA0859, rbsC3 BCAN_B0876 MOS Erythritol import BP BMEII0435 BruAb20373, rbsB2 BRA0858, rbsB2 BOV_A0805 BCAN_B0875 58 MOS Galactoside/Ribose import ABC2 BMEII0698 BruAb20654 BRA0570 BOV_A0533 BCAN_B0570 MOS Galactoside/Ribose import IM BOV_A0534 BCAN_B0567 MOS Galactoside/Ribose import...”

TC 3.A.1.2.16 / Q1M4Q8 Erythritol permease, component of ABC transporter, component of The erythritol uptake permease, EryEFG (Yost et al., 2006) (probably orthologous to 3.A.1.2.11) from Rhizobium leguminosarum bv. viciae (strain 3841) (see paper)
pRL120201 putative permease component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
39% identity, 85% coverage

• substrates: Erythritol
• Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes
  Crasta, PloS one 2008
  • “...eryF abolished erythritol uptake. Because BAB2_0376 has 85% sequence similarity with the predicted eryF ORF (pRL120201) and the conservation of gene order with the eryEFG operon, it is very likely that BAB2-0376 also encodes a putative erythritol transporter. Hence, we hypothesize that mutation of the gene...”

OKIT_0348 ABC transporter permease subunit from Oenococcus kitaharae DSM 17330
42% identity, 96% coverage

• Functional divergence in the genus Oenococcus as predicted by genome sequencing of the newly-described species, Oenococcus kitaharae
  Borneman, PloS one 2012
  • “...ribose-binding protein RbsB (TC 3.A.1.2.1) OKIT_0347 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1) OKIT_0348 O. kitaharae Fructose utilization PTS system, fructose-specific IIA component (EC 2.7.1.69) OKIT_0249 PTS system, fructose-specific IIB component (EC 2.7.1.69) OKIT_0248 PTS system, fructose-specific IIC component (EC 2.7.1.69) OKIT_0250 O. oeni...”

SMc02031 PUTATIVE PERMEASE PROTEIN from Sinorhizobium meliloti 1021
39% identity, 90% coverage

• The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon metabolism and the symbiotic interaction with alfalfa
  Torres-Quesada, BMC microbiology 2010
  • “...genes), -glucosides ( aglE and aglF ), fructose ( frcB and frcK ), ribose ( SMc02031 ), glycerol ( SMc02514 and SMc02519 ), and other organic acids/alcohols ( SMb20144 ) [ 34 ]. An additional gene ( SMb20072 ), displaying more than 32-fold reduction (M value...”

TC 3.A.1.2.11 / Q92WK1 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) from Rhizobium meliloti (Sinorhizobium meliloti) (see paper)
41% identity, 87% coverage

• substrates: Erythritol

SMb21375 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
36% identity, 96% coverage

• Genetic and computational identification of a conserved bacterial metabolic module
  Boutte, PLoS genetics 2008
  • “...1.1e-34 SMb21377 (sugar binding protein) 5.5e-13 2.7e-6 SMb21376 (ATP-binding protein) 2.8e-103 2e-118 1e-103 1.4e-112 1.7e-105 SMb21375 (permease protein) 1.8e-48 7.5e-41 1.1e-44 2.5e-58 4.1e-37 SMb20856 (sugar binding protein) 2.6e-18 3.4e-13 1.6e-17 4.2e-11 4.9e-22 SMb20855 (ATP-binding protein) 1.3e-108 1.5e-114 5.7e-112 8.5e-92 2.4e-80 SMb20854 (permease protein) 2.0e-52 1.9e-29 1.7e-35...”

VK055_1939 ABC transporter permease from Klebsiella pneumoniae subsp. pneumoniae
38% identity, 86% coverage

• A Serendipitous Mutation Reveals the Severe Virulence Defect of a Klebsiella pneumoniae fepB Mutant
  Palacios, mSphere 2017
  • “...pyrophosphate enzyme, C-terminal TPP b binding domain protein VK055_1941 Hypothetical protein VK055_1940 Putative transcriptional regulator VK055_1939 Branched-chain amino acid transport system/permease component family protein VK055_1938 Heme ABC exporter, ATP-binding protein CcmA VK055_1937 Hypothetical protein VK055_1936 Periplasmic binding and sugar binding domain of LacI family protein VK055_1935...”

RbsC / b3750 ribose ABC transporter membrane subunit from Escherichia coli K-12 substr. MG1655 (see 5 papers)
RbsC / P0AGI1 ribose ABC transporter membrane subunit from Escherichia coli (strain K12) (see 4 papers)
RBSC_ECOLI / P0AGI1 Ribose import permease protein RbsC from Escherichia coli (strain K12) (see 5 papers)
TC 3.A.1.2.1 / P0AGI1 Ribose transport system permease protein RbsC aka B3750, component of Ribose porter from Escherichia coli (see 6 papers)
b3750 ribose ABC transporter permease protein from Escherichia coli str. K-12 substr. MG1655
NP_418206 ribose ABC transporter membrane subunit from Escherichia coli str. K-12 substr. MG1655
41% identity, 95% coverage

• function: Part of the ABC transporter complex RbsABC involved in ribose import. Probably responsible for the translocation of the substrate across the membrane.
  function: (Microbial infection) Probably transports the toxic C- terminal region of CdiA from D.dadantii strain 3937 across the inner membrane to the cytoplasm, where CdiA has a toxic effect. Toxin transport is strain-specific, mutations in this gene do not confer resistance to several other tested CdiA toxins.
  subunit: The complex is composed of an ATP-binding protein (RbsA), two transmembrane proteins (RbsC) and a solute-binding protein (RbsB).
  disruption phenotype: Disruption confers resistance to cellular contact-dependent growth inhibition (CDI) CdiA of D.dadantii strain 3937, but not to several other tested CdiA toxins.
• substrates: Ribose
  tcdb comment: RbsA has two ATPase domains fused together; RbsB is the substrate receptor; RbsC has 10 TMSs with N- and C-termini in the cytoplasm and forms a dimer (Stewart and Hermodson, 2003). ABC importers can be divided into two classes. Type I importers follow an alternating access mechanism driven by the presence of the substrate. Type II importers accept substrates in a nucleotide-free state, with hydrolysis driving an inward-facing conformation. RbsABC2 seems to share functional traits with both type I and type II importers, as well as possessing unique features, and employs a distinct mechanism relative to other ABC transporters (Clifton et al. 2014)
• Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
  Kim, Environmental microbiology 2010
  • “...Tryptophanase rbsA b3749 3.7 1.3 1.3 ATP-binding component of d -ribose high-affinity transport system rbsC b3750 3.0 1.0 1.3 d -ribose high-affinity transport system ptsA b3947 1.6 4.0 1.2 PEP-protein phosphotransferase system enzyme I phnM b4095 1.5 4.6 1.6 Phosphonate metabolism phnL b4096 1.8 4.0 1.6...”
• YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
  Zhang, Journal of bacteriology 2007
  • “...b2094 b2093 b2092 b2091 b0553 b1015 b3748 b3749 b3750 b2796 b1256 Membrane-bound ATP synthase, F0 sector, subunit A Membrane-bound ATP synthase, F0 sector,...”
• Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022)
  González, Journal of bacteriology 2006
  • “...yhjS rbsC b2365 b2809 b3254 b3555 b0372 b3536 b3750 Hypothetical protein Transcriptional regulator of cryptic csgA gene for curli surface fibers Regulator of...”
• Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR
  Herring, Journal of bacteriology 2004
  • “...1.02 12.62 1.93 b2396 alaX 2.36 2.31 10.97 0.83 13.33 1.48 b3750 rbsC 1.73 0.75 9.75 0.43 11.48 0.43 b3534 yhjQ 1.68 0.63 5.96 0.30 7.64 0.42 b3748 rbsD 1.42...”
• DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
  Polen, Applied and environmental microbiology 2003
  • “...2 2 D-Ribose 0.49* 0.41 0.73* 0.62 0.97 0.75 b3750 b3751 b3752 rbsC rbsB rbsK 2 2 2 high-affinity transport system ATP-binding component of D-ribose...”
• In vitro reassembly of the ribose ATP-binding cassette transporter reveals a distinct set of transport complexes.
  Clifton, The Journal of biological chemistry 2015
  • GeneRIF: Data suggest that complex RbsABC2 shares functional traits with both type I and type II importers.
• Cotinine Hydroxylase CotA Initiates Biodegradation of Wastewater Micropollutant Cotinine in Nocardioides sp. Strain JQ2195
  Zhao, Applied and environmental microbiology 2021 (secret)

Entcl_4403 ribose ABC transporter permease from [Enterobacter] lignolyticus SCF1
41% identity, 95% coverage

• Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
  Orellana, PloS one 2017
  • “...was stopped ( Fig 2C ) (Entcl_0166, Entcl_0167, Entcl_1205, Entcl_1207, Entcl_3382, Entcl_3383, Entcl_4082, Entcl_4174, and Entcl_4403, S4 Table ). This was presumably a response to the lack of availability of glucose, an effect that has been observed in other fermentative anaerobes [ 32 ]. Enterobacteriaceae is...”

A4XG53 Monosaccharide-transporting ATPase from Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)
40% identity, 96% coverage

• Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting
  Andrews, Analytical and bioanalytical chemistry 2010
  • “...0.08850 A4XI39 NUDIX hydrolase 16.0 6 0.12612 A4XHT6 Putative, probable YjbQ-like protein 15.9 5 0.10662 A4XG53 Monosaccharide-transporting ATPase 34.1 5 0.04486 A4XLT3 Putative, probable beta-lactamase-like protein 5.9 4 0.22209 A4XHL3 Lipolytic enzyme, G-D-S-L family 26.9 4 0.05052 A4XFT4 phage-shock protein A, PspA 25.6 4 0.05302 (...”

Z5251 D-ribose high-affinity transport system from Escherichia coli O157:H7 EDL933
41% identity, 95% coverage

• Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
  Segura, BMC genomics 2018
  • “...Z5252 rbsB Ribose transport system substrate-binding protein 4.23 1.81E-08 2.16 9.34E-03 NDE 2.59 1.10E-03 NDE Z5251 rbsC Ribose transport system permease protein 6.49 5.50E-29 5.18 2.95E-18 4.04 1.99E-11 6.28 1.33E-26 5.00 3.27E-17 Z5249 rbsD D-ribose pyranase 6.17 2.40E-23 5.28 5.82E-17 3.40 1.91E-07 6.10 2.29E-22 4.81 3.25E-14...”

B9Q16_23110 ABC transporter permease from Pantoea ananatis
39% identity, 83% coverage

• Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity
  Stice, Frontiers in microbiology 2018
  • “...xylB Xylulose kinase B9Q16_23115 Xylulokinase CDS 1,449 rbsC Tr Ribose transport system permease protein RbsC B9Q16_23110 Sugar ABC transporter permease CDS 1,026 rbsB D-ribose-binding periplasmic protein precursor B9Q16_23105 LacI family transcriptional regulator CDS 981 rbsA Ribose import ATP-binding protein RbsA B9Q16_23100 ABS transporter CDS 1,503 Hypothetical...”

AO353_21390 m-Inositol ABC transporter, permease component (iatP) from Pseudomonas fluorescens FW300-N2E3
42% identity, 79% coverage

• mutant phenotype: Specific phenotype on m-Inositol and 71% identical to SMb20174 or itaP, which also has this function (see PMC2597717). The periplasmic substrate-binding component (AO353_21380) is not included in this table because it was annotated correclty in both resources.

PS417_11895 Inositol transport system permease protein from Pseudomonas simiae WCS417
42% identity, 79% coverage

• mutant phenotype: specific phenotype on inositol.

RL2720 putative ribose transport system permease protein from Rhizobium leguminosarum bv. viciae 3841
43% identity, 96% coverage

• Competitiveness for Nodule Colonization in Sinorhizobium meliloti: Combined In Vitro-Tagged Strain Competition and Genome-Wide Association Analysis
  Bellabarba, mSystems 2021
  • “...an ABC-type ribose import system. In Rhizobium leguminosarum , a putative ribose ABC transporter (RbsA, RL2720) was induced by the presence of arabinogalactan, and it was specifically overexpressed in the alfalfa rhizosphere ( 50 ). The COG1172, detected by both association analyses, contains a ribose/xylose/arabinose/galactoside ABC-type...”
• Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics
  Ramachandran, Genome biology 2011
  • “...ABC transporters is as follows: MolT, RL3040; CUT1, RL2418 (MtlE); CUT2, RL4655 (IntA), RL3840 and RL2720; PepT, pRL110281 and pRL110243; PAAT, pRL80060 and pRL80064; POPT, pRL100248; NitT, RL3721. Asterisks indicate a compound metabolized by an enzyme whose expression is elevated (Figure 2) or, in the case...”
  • “...to deal with toxic canavanine may enable selection of MsiA-producing bacteria by these leguminous plants. RL2720 encodes a CUT2 family SBP specifically induced in the alfalfa rhizosphere (Figure 1 ). From the up-regulation of expression of RL2720-2 (4- to 25-fold) in microarrays of cells grown in...”

MSMEG_3601 ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components from Mycobacterium smegmatis str. MC2 155
40% identity, 82% coverage

• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...P value Descriptionb Ribose MSMEG_3598 MSMEG_3599 MSMEG_3600 MSMEG_3601 rbsB3 rbsR3 rbsC3 1.28 1.42 (1.02) 1.53 4.65E03 1.01E02 7.80E01 6.94E03 MSMEG_3602...”

Bbr_1418 ABC transporter permease from Bifidobacterium breve UCC2003
40% identity, 86% coverage

• Comparative genomics and genotype-phenotype associations in Bifidobacterium breve
  Bottacini, Scientific reports 2018
  • “...Pokusaeva et al . 26 Bbr_1417 D-ribose-binding protein rbsB PF13407 Pokusaeva et al . 26 Bbr_1418 Ribose transport system permease protein rbsC PF02653 Pokusaeva et al . 26 Bbr_1419 Ribose transport ATP-binding protein rbsA PF00005 Pokusaeva et al . 26 Bbr_1420 Transcriptional regulator, LacI family PF13377...”

YPO0957 putative sugar transport system permease protein from Yersinia pestis CO92
YPTB3229 ABC sugar transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
37% identity, 84% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...aldolase class II 1.325 (0.048) 0.699 (0.015) YPTB3196 (pgk) YPO0921 phosphoglycerate kinase 1.366 (0.024) YPTB3229 YPO0957 putative sugar transport system permease protein 0.626 (0.018) YPTB3230 (mglA) YPO0958 putative sugar transport ATP-binding protein 0.624 (0.005) YPTB3262 YPO0988 putative membrane protein 2.167 (< 0.001) YPTB3268 YPO0995 Sodium:galactoside symporter...”
• Characterization of chromosomal regions conserved in Yersinia pseudotuberculosis and lost by Yersinia pestis
  Pouillot, Infection and immunity 2008
  • “...sugar/ribose transporters. Since another ABC sugar transporter operon (YPTB3229 to YPTB3231) is present on the IP32953 genome, it may fulfill the same function...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...fructose-bisphosphate aldolase class II 1.325 (0.048) 0.699 (0.015) YPTB3196 (pgk) YPO0921 phosphoglycerate kinase 1.366 (0.024) YPTB3229 YPO0957 putative sugar transport system permease protein 0.626 (0.018) YPTB3230 (mglA) YPO0958 putative sugar transport ATP-binding protein 0.624 (0.005) YPTB3262 YPO0988 putative membrane protein 2.167 (< 0.001) YPTB3268 YPO0995 Sodium:galactoside...”

A7MMV6 Ribose ABC transporter permease from Cronobacter sakazakii (strain ATCC BAA-894)
40% identity, 95% coverage

• Subtractive genomics study for the identification of therapeutic targets against Cronobacter sakazakii: A threat to infants
  Ahammad, Heliyon 2024
  • “...glycosyltransferase MrdB 62.0 Novel target 4 WP_007848259.1 A7MQS9 Apolipoprotein N-acyltransferase 60.0 Novel target 5 AKE93920.1 A7MMV6 ribose ABC transporter permease 58.0 Novel target 6 WP_012126359.1 A7MGF9 sn-glycerol-3-phosphate transport system permease protein UgpE 56.0 Novel target 7 AKE96704.1 A7MES4 ATP-binding protein CydC 54.0 Terbinafine drug target 8...”

HSERO_RS05255 ABC transporter for L-fucose, permease component from Herbaspirillum seropedicae SmR1
40% identity, 90% coverage

• mutant phenotype: Specifically important for L-fucose utilization.

c3068 Hypothetical ABC transporter permease protein yphD from Escherichia coli CFT073
37% identity, 95% coverage

• Identification of in vivo-induced antigens including an RTX family exoprotein required for uropathogenic Escherichia coli virulence
  Vigil, Infection and immunity 2011
  • “...c0743 c1770 c2105-c2106 c5007-c5006 c3625 c0186 c4487 c2179 c3068 c2085 c4682 c2051 c0875 c4901 c0537 c2661 Function of gene product Hypothetical dipeptide ABC...”

STM3883 ABC superfamily (membrane), D-ribose high-affinity transport protein (1st module, ATP-binding subunit) from Salmonella typhimurium LT2
40% identity, 95% coverage

• Mapping and regulation of genes within Salmonella pathogenicity island 12 that contribute to in vivo fitness of Salmonella enterica Serovar Typhimurium
  Tomljenovic-Berube, Infection and immunity 2013
  • “...fepA 2.32 2.31 2.25 1.48E36 1.31E02 3.44E57 STM0587 STM3883 ybdZ rbsC 2.25 2.24 1.45E06 1.57E22 STM3808.S STM2068 STM0586 STM0509 STM0700 STM1424 STM3830...”
• DNA amplification and rearrangements in archival Salmonella enterica serovar Typhimurium LT2 cultures
  Porwollik, Journal of bacteriology 2004
  • “...STM1842-1844, including the htpX heat shock protein, and STM3883 (rbsC) to STM3886 (rbsR), a ribose transport operon Amplification between STM2154 (mrp) and...”

A8H4W6 Monosaccharide-transporting ATPase from Shewanella pealeana (strain ATCC 700345 / ANG-SQ1)
40% identity, 81% coverage

• Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.
  Paparoditis, Biochimica et biophysica acta 2014
  • “...3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UU56 8 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UR04 8 3.A.1.2.15 A8H4W6 9 sugar xylitol Q7UXV9 10 3.A.1.5.22 Q5V9S0 6 peptide peptide Q7UHZ2 6 3.A.1.5.22 Q5V9S1 6 peptide peptide Q7UHZ1 6 3.A.1.7.1 P07654 6 anions Phosphate Q7UP20 6 3.A.1.7.1 P0AGH8 6 anions...”

VPA1671 ABC-type arabinose transport system, permease component from Vibrio parahaemolyticus RIMD 2210633
37% identity, 92% coverage

• L-arabinose affects the growth, biofilm formation, motility, c-di-GMP metabolism, and global gene expression of Vibrio parahaemolyticus
  Zhang, Journal of bacteriology 2023 (secret)
• Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus
  Kalburge, Infection and immunity 2017
  • “...(VP2397 to VP2400), and L-arabinose transport and metabolism (VPA1671 to VPA1677) (Table S4). qPCR analysis confirmed the downregulation of VPA1674 (araB), an...”
  • “...included mannose (VPA1424 to VPA1425), arabinose (VPA1673 to VPA1671), and glycogen (VPA1620) transport and/or metabolism genes (Table S6). In order to validate...”

BPSL1791 putative membrane protein from Burkholderia pseudomallei K96243
39% identity, 88% coverage

• Molecular basis of rare aminoglycoside susceptibility and pathogenesis of Burkholderia pseudomallei clinical isolates from Thailand
  Trunck, PLoS neglected tropical diseases 2009
  • “...mbaS MbaS, extracytoplasmic sigma factor BPSL1788 Pseudogene BPSL1789 Short chain dehydrogenase BPSL1790 Putative zinc-binding dehydrogenase BPSL1791 Hypothetical protein BPSL1792 Hypothetical protein BPSL1793 Putative sugar-binding exported protein BPSL1794 Putative AraC-family transcriptional regulator BPSL1795 Hypothetical protein BPSL1796 Hypothetical protein BPSL1797 Putative ABC transport system, membrane protein BPSL1798 Hypothetical...”

S2038 L-arabinose transport system permease protein from Shigella flexneri 2a str. 2457T
36% identity, 93% coverage

• Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
  Wei, Infection and immunity 2003
  • “...S1092 S2672 S2276 S3922 S1455 S2032 S1158 S2081 S2569 S2038 S3764 Gene 2784 INFECT. IMMUN. WEI ET AL. proteins, which includes members from bacteria, plants,...”

AraH / b4460 arabinose ABC transporter membrane subunit (EC 7.5.2.13; EC 7.5.2.12) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
araH / P0AE26 arabinose ABC transporter membrane subunit (EC 7.5.2.13) from Escherichia coli (strain K12) (see paper)
ARAH_ECOLI / P0AE26 L-arabinose transport system permease protein AraH from Escherichia coli (strain K12) (see 2 papers)
TC 3.A.1.2.2 / P0AE26 L-arabinose transport system permease protein araH aka b4460, component of Arabinose porter from Escherichia coli (see 7 papers)
araH / GB|AAN43497.1 L-arabinose ABC transporter, permease protein AraH from Escherichia coli K12 (see 2 papers)
EcolC_1736 monosaccharide-transporting ATPase from Escherichia coli C str. ATCC 8739
b4460 fused L-arabinose transporter subunits of ABC superfamily: membrane components from Escherichia coli str. K-12 substr. MG1655
36% identity, 93% coverage

• function: Part of the binding-protein-dependent transport system for L- arabinose. Probably responsible for the translocation of the substrate across the membrane
• substrates: Arabinose
• New xylose transporters support the simultaneous consumption of glucose and xylose in <i>Escherichia coli</i>
  Zhu, mLife 2022
  • “...EcolC_1734 araF Larabinosebinding periplasmic protein 2.3 2 EcolC_1735 araG Arabinose import ATPbinding protein 9 4.8 EcolC_1736 araH Arabinose ABC transporter permease 3.9 3.5 EcolC_3593 araC Arabinose operon regulatory protein 3.3 6.6 EcolC_3594 araB Ribulokinase 200 117 EcolC_3595 araA Larabinose isomerase 181 88 EcolC_3596 araD Lribulose5phosphate4epimerase 250...”
• Furfural inhibits growth by limiting sulfur assimilation in ethanologenic Escherichia coli strain LY180
  Miller, Applied and environmental microbiology 2009
  • “...pstA, pstC, glpT, glpF, argT, ssuA, pstB, gltK, gltI, b4460, mtlA, pstS, narU, mdtM, sufA, dctA, mglC, mglA, sbp, mglB, tauA, tauB, tauC ssuD, ssuE, ybdL yccT,...”

APECO2_RS16285 arabinose ABC transporter permease AraH from Escherichia coli APEC O2-211
36% identity, 93% coverage

• Role of LsrR in the regulation of antibiotic sensitivity in avian pathogenic Escherichia coli
  Yu, Poultry science 2020
  • “...compared with the WT strain. Gene Product log 2 FC APECO2_RS03445 prpB Methylisocitrate lyase 1.30 APECO2_RS16285 ygaF Hydroxyglutarate oxidase 1.25 APECO2_RS03310 - LuxR family transcriptional regulator 1.57 APECO2_RS03450 prpCz 2-methylcitrate synthase 1.03 APECO2_RS17500 xanQ MULTISPECIES: xanthine permease XanQ 1.60 APECO2_RS07530 flgH MULTISPECIES: flagellar L-ring protein 2.25...”

RR42_RS03365 fructose ABC transporter, permease component (FrcC) from Cupriavidus basilensis FW507-4G11
41% identity, 94% coverage

• mutant phenotype: Specific phenotype on fructose

YphD / b2546 putative ABC transporter membrane subunit YphD from Escherichia coli K-12 substr. MG1655 (see 4 papers)
37% identity, 95% coverage

HSERO_RS03645 D-mannose ABC transporter, permease component from Herbaspirillum seropedicae SmR1
41% identity, 85% coverage

• mutant phenotype: Specific phenotype on D-mannose

Atu4322 ABC transporter, membrane spanning protein (ribose) from Agrobacterium tumefaciens str. C58 (Cereon)
38% identity, 90% coverage

• Agrobacterium tumefaciens exoR controls acid response genes and impacts exopolysaccharide synthesis, horizontal gene transfer, and virulence gene expression
  Heckel, Journal of bacteriology 2014
  • “...Heckel et al. 3226 jb.asm.org (atu4321) and rbsC (atu4322), involved in ribose transport (59), which are upregulated in both comparisons (consistent with ribose...”
• Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic conditions (pH 5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions
  Yuan, Journal of bacteriology 2008
  • “...genes Atu2055 Atu2470 Atu2471 Atu3273 Atu3274 Atu4017 Atu4322 Atu4334 Atu4335 Atu4337 Atu4338 Atu4340 Atu4341 Atu4342 Atu4343 1.14 1.23 1.57 1.03 2.47...”

PSPTO_2640 L-arabinose ABC transporter, permease protein from Pseudomonas syringae pv. tomato str. DC3000
33% identity, 91% coverage

• Identification of Indole-3-Acetic Acid-Regulated Genes in Pseudomonas syringae pv. tomato Strain DC3000
  Djami-Tchatchou, Journal of bacteriology 2022 (secret)
• CrcZ and CrcX regulate carbon source utilization in Pseudomonas syringae pathovar tomato strain DC3000
  Filiatrault, RNA biology 2013
  • “...DC3000 are the L-arabinose transporter permease protein (PSPTO_2640) and a myo-inositol 2-dehydrogenase (PSPTO_3494).9 Therefore, we tested whether deletion of...”

B2904_orf2671 ABC transporter permease from Brachyspira pilosicoli B2904
41% identity, 95% coverage

• Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity
  Mappley, BMC genomics 2012
  • “...to an insertion between genes encoding OrfE and Hvp53, containing genes for a monosaccharide-transporting ATPase (B2904_orf2671; wesB_2628), an ABC transporter-related protein (B2904_orf2672; wesB_2629), a ROK family protein (B2904_orf2674; wesB_2631), an integrase in B2904 only (B2904_orf2675), and a periplasmic binding protein/LacI transcriptional regulator (B2904_orf2673; wesB_2627 and wesB_2630)....”

BCAL1549 putative sugar ABC transport system, membrane protein from Burkholderia cenocepacia J2315
40% identity, 89% coverage

• The Small RNA ncS35 Regulates Growth in Burkholderia cenocepacia J2315
  Kiekens, mSphere 2018
  • “...-Amino acid dehydrogenase Carbohydrate transport and metabolism BCAL1548 2.2 3.3 2.2 Sugar ABC transport system BCAL1549 2.4 3.0 Sugar ABC transport system BCAL1550 2.3 Sugar ABC transport system BCAL1661 2.0 Ribokinase BCAL3038 2.0 ABC-type glycerol-3-phosphate transport BCAL3039 2.0 ABC-type glycerol-3-phosphate transport Ornibactin biosynthesis BCAL1696 2.3 Ornibactin...”

AK34_1628 ABC transporter permease subunit from Burkholderia dolosa AU0158
40% identity, 90% coverage

• An Oxygen-Sensing Two-Component System in the Burkholderia cepacia Complex Regulates Biofilm, Intracellular Invasion, and Pathogenicity
  Schaefers, PLoS pathogens 2017
  • “...system histidine kinase -10.5 Other rbsK (AK34_5286) Ribokinase -9.1 AK34_4362 Putative cytochrome P450 hydroxylase -44.7 AK34_1628 ABC-type sugar transport system, permease protein -9.4 AK34_1627 ABC-type sugar transport system, ATP-binding protein -9.9 AK34_5433 Outer membrane protein (porin) -3.6 AK34_3420 Major facilitator family transporter -3.6 AK34_1355 Outer membrane...”

Cthe_2448 inner-membrane translocator from Clostridium thermocellum ATCC 27405
33% identity, 96% coverage

• Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress
  Wilson, Biotechnology for biofuels 2013
  • “...1.99 2.98 1.82 D Cthe_1851 Protein of unknown function DUF1113 0.30 2.84 2.29 1.76 D Cthe_2448 ABC-type transporter, integral membrane subunit 0.40 2.82 2.19 1.66 A Cthe_2449 Phosphoglycerate mutase 0.03 2.44 2.04 1.84 A Cthe_3054 Hypothetical protein 0.01 2.75 2.03 2.33 B Cthe_3112 Glycosidase related protein...”

TC 3.A.1.2.21 / B8H230 Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved from Caulobacter crescentus (strain NA1000 / CB15N)
CC0861 sugar ABC transporter, permease protein from Caulobacter crescentus CB15
43% identity, 88% coverage

• substrates: myo-inositol
• Genetic and computational identification of a conserved bacterial metabolic module
  Boutte, PLoS genetics 2008
  • “...iatA (CC0860) left the first 12 and last 9 codons intact. The deletion of iatP (CC0861) left the first 30 and last 13 codons intact. A transporter complementation plasmid was generated by cloning the full transporter locus plus promoter region into the Kpn I and Nde...”
  • “...CC0860 , i nositol A BC t ransporter A TPase, NP_419677), and CB15N iatP ( CC0861 , i nositol A BC t ransporter p ermease, NP_419678). Individual in-frame deletions of each of these genes abolished growth on defined medium containing myo -inositol as the sole carbon...”

Pf6N2E2_5970 ABC transporter for D-galactose/L-arabinose, permease component from Pseudomonas fluorescens FW300-N2E2
34% identity, 95% coverage

• mutant phenotype: Specifically important for utilizing D-galactose and L-arabinose

PS417_12060 xylitol ABC transporter, permease component from Pseudomonas simiae WCS417
42% identity, 92% coverage

• mutant phenotype: Specifically important for utilizing xylitol.

Pf1N1B4_409 ABC transporter for D-galactose/L-arabinose, permease component from Pseudomonas fluorescens FW300-N1B4
35% identity, 93% coverage

• mutant phenotype: Specifically important for utilizing D-galactose and L-arabinose

YPO3963 sugar transport system permease protein from Yersinia pestis CO92
YPTB3806 ABC ribose transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
40% identity, 95% coverage

• A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim
  Feldman, Molecular biology and evolution 2016
  • “...to GTG A to V YPO3839 4460688 C T CGG to CAG R to Q YPO3963 Sugar transport system permease pCD1 29959 A G AAC to AGC N to S YPCD1.41 yscO Type III secretion apparatus component 50462 T C AAA to GAA K to E...”
• Lipopolysaccharide Biosynthesis Genes of Yersinia pseudotuberculosis Promote Resistance to Antimicrobial Chemokines
  Erickson, PloS one 2016
  • “...genes are predicted to encode a phosphoribulokinase/uridine kinase (YPTB3726) and an ABC-ribose transport permease subunit (YPTB3806). These genes have not previously been implicated in the evasion of host defense peptides. Two additional mutants had insertions that mapped to intergenic regions. These mutants displayed more moderate increases...”

RL4653 putative transmembrane component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
35% identity, 91% coverage

• Transcriptomic analysis of Rhizobium leguminosarum biovar viciae in symbiosis with host plants Pisum sativum and Vicia cracca
  Karunakaran, Journal of bacteriology 2009
  • “...of RL4655 (intA, encoding a solute-binding protein) and RL4653 (intC, encoding an integral membrane protein) was elevated 71- and 33fold, respectively. A second...”

bll2675 sugar ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
36% identity, 97% coverage

• Transcriptomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules
  Franck, International journal of molecular sciences 2018
  • “...genes shown in the figure are: bll0116, bll0195, bll0776, bll0979, bll1109, bll1422, bll2116, bll2410, bll2494, bll2675, bll3374, bll3444, bll3470, bll3505, bll3783, bll4141, bll4201, bll4403, bll4596, bll4793, bll5240, bll5296, bll5959, bll6302, bll6471, bll6498, bll6891, bll7298, bll7311, bll7402, bll7610, bll7835, bll7964, blr0310, blr0925, blr1457, blr2533, blr2715, blr2809, blr3324,...”
  • “...Ribose 5-phosphate isomerase Blr3755 BAC49020 Cytoplasm 3-Deoxy-manno-octulosonate cytidylyltransferase Bll1422 BAC46687 Cytoplasm Sugar ABC transporter permease Bll2675 BAC47940 Cytoplasmic membrane Flagellar protein Bll6868 BAC52133 Extracellular 3-Oxoacyl-(acyl-carrier-protein) synthase II Bll3809 BAC49074 Unknown Branched-chain amino acid ABC transporter substrate-binding protein Bll0979 BAC46244 Periplasm Cytochrome O ubiquinol oxidase Blr2715 AND93893...”

AT5A_19781 ABC transporter permease from Agrobacterium tumefaciens 5A
43% identity, 92% coverage

• Introducing the ArsR-Regulated Arsenic Stimulon
  Rawle, Frontiers in microbiology 2021
  • “...3.7 3.5 3.0 AT5A_19386 Sugar ABC transporter ATP-binding protein 2.2 2.5 17.2 33.6 2.1 2.0 AT5A_19781 Ribose ABC transporter transmembrane protein AT5A_22281 Sugar ABC transporter permease 2.4 AT5A_22286 Sugar ABC transporter substrate-binding protein 2.4 AT5A_24025 Sugar ABC transporter substrate-binding protein 2.3 2.6 2.2 AT5A_24035 Sugar ABC...”

BTH_II0210 ribose ABC transporter, permease protein from Burkholderia thailandensis E264
40% identity, 91% coverage

• Characterization of the Burkholderia thailandensis SOS response by using whole-transcriptome shotgun sequencing
  Ulrich, Applied and environmental microbiology 2013
  • “...BTH_I1771 BTH_I1772 BTH_I1821 BTH_I1825 BTH_I3010 BTH_II0210 BTH_II0475 BTH_II1444 BTH_II1817 BTH_II2215 BTH_II2217 HAD-superfamily hydrolase FscRII...”

Cthe_0392 inner-membrane translocator from Clostridium thermocellum ATCC 27405
Cthe_0392 ABC transporter permease from Acetivibrio thermocellus ATCC 27405
36% identity, 88% coverage

• Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution
  Ha-Tran, Microorganisms 2021
  • “...present study. The mRNA expression levels of ATP-binding protein nbdA (Cthe_0391), inner membrane translocator msdA (Cthe_0392), and ribose ABC transporter cbpA (Cthe_0393) were significantly upregulated in FAs1 and GAs1 ( Figure 4 ). Additionally, the transmembrane sugar transport protein msdB1 (Cthe_1019) in the CbpB operon also...”
  • “...an indel mutation (deletion of GG at position 19/1050) was observed in the msdA gene (Cthe_0392) of FAs8 and GAs8. Both indel and stop-gain events occurred in the nbdA gene (Cthe_0391) of FAs8. The cbpB gene (Cthe_1020) in GAs8 had a non-syn mutation (Ala was replaced...”
• Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass
  Wilson, Biotechnology for biofuels 2013
  • “...96.4 68.4 88.1 67.9 87.9 Cthe_0271 CBM_3 99.1 88.3 99.8 92.3 99.8 83.8 99.9 89.2 Cthe_0392 Transport 100 98.5 99.8 95.3 99.9 97.5 99.7 96.8 Cthe_0624 Dockerin 81.8 96.1 78.2 96.5 91.5 98.6 65.8 93.7 Cthe_0736 Scaffoldin 59.1 86.7 53.6 85.0 72.8 96.6 42.4 75.2 Cthe_1890...”

Csac_2504 Monosaccharide-transporting ATPase from Caldicellulosiruptor saccharolyticus DSM 8903
35% identity, 77% coverage

• Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences
  Vanfossen, Applied and environmental microbiology 2009
  • “...and Csac_0240 to Csac_0242 (Csac_0238,0240-0242) and (ii) Csac_2504 to Csac_2506 (Csac_2504-2506). These may have broad specificity for mon- VOL. 75, 2009...”

MSMEG_3090 ribose transport system permease protein RbsC from Mycobacterium smegmatis str. MC2 155
35% identity, 92% coverage

• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...operon regulatory protein Ribose, ribonucleosides MSMEG_3089 MSMEG_3090 MSMEG_3091 MSMEG_3092 MSMEG_3093 MSMEG_3094 MSMEG_3095 deoC rbsC2 rbsA2 rbsR2 sugK sugD...”
  • “...and MSMEG_6018), arabinose (MSMEG_1711 and MSMEG_1712), ribose (MSMEG_3090, -3095, and -3601), sugar alcohol (MSMEG_5571 to 2196 jb.asm.org Journal of...”
• A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis
  Titgemeyer, Journal of bacteriology 2007
  • “...Ribose and ribose-like carbohydrates (msmeg_1372 to msmeg_1378, msmeg_3090 to msmeg_3095, msmeg_3598 to msmeg_3602, msmeg_4170 to msmeg_4174, and msmeg_6798 to...”
  • “...for a ribose-specific ABC permease seem to be msmeg_3090, msmeg_3091, and msmeg_3095. The latter one is the substrate binding protein that shares the highest...”

Cphy_2011 Monosaccharide-transporting ATPase from Clostridium phytofermentans ISDg
34% identity, 97% coverage

• Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans
  Petit, PloS one 2013
  • “...ATP-binding cassette (ABC) transporter, likely to mediate fucose uptake. Both the ATP-binding (Cphy_2010) and permease (Cphy_2011) subunits of the transporter contain domains that are characteristic of hexose and pentose-importing ABC transporters; i.e. two similar ATP-binding domains (cd03215 and cd03216) in Cphy_2011 and a permease (cd06579) in...”
  • “...Fucose transport Cphy_2010 Fucose ABC transport system, ATPase subunit E. coli FucP (n.d.) 58.4 1.3 Cphy_2011 Fucose ABC transport system, permease subunit E. coli FucP (n.d.) 82.3 1.9 Cphy_2012 Fucose ABC transport system,periplasmic solute binding protein E. coli FucP (n.d.) 64.9 1.6 Rhamnose dissimilation Cphy_1146 Rhamnulose...”

H16_B1499 ABC-type transporter, permease component: CUT2 family, fructose specific from Ralstonia eutropha H16
38% identity, 91% coverage

• Implications of various phosphoenolpyruvate-carbohydrate phosphotransferase system mutations on glycerol utilization and poly(3-hydroxybutyrate) accumulation in Ralstonia eutropha H16
  Kaddor, AMB Express 2011
  • “...frcA H16_B1498 Fructose-specific ABC-type transporter, ATPase component frcB H16_B1500 Fructose-specific ABC-type transporter, periplasmic component frcC H16_B1499 Fructose-specific ABC-type transporter, permease component Data were obtained using the KEGG (Kyoto encyclopedia of genes and genomes) database at GenomeNet ( Kanehisa et al. 2002 ). The CDS designations specify...”
• Effects of homologous phosphoenolpyruvate-carbohydrate phosphotransferase system proteins on carbohydrate uptake and poly(3-Hydroxybutyrate) accumulation in Ralstonia eutropha H16
  Kaddor, Applied and environmental microbiology 2011
  • “...specific ABC-type transporter, periplasmic component, fructose specific H16_B1499 H16_B1500 nagE frcA frcC frcB 12% EIIABMan (manX) 33% HPr (ptsH)b 33% NPr...”

Entcl_0174 xylose ABC transporter permease XylH from [Enterobacter] lignolyticus SCF1
33% identity, 74% coverage

• Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
  Orellana, PloS one 2017
  • “...uptake of mannose (Entcl_3690, Entcl_3691, Entcl_3692, Entcl_3811 and Entcl_3812), xylose (Entcl_0175 and Entcl_0176) and ribose (Entcl_0174, Entcl_1204, Entcl_1206, Entcl_4081) were down-regulated in early exponential phase. However, after glucose was made unavailable due to concentrations dipping below its half-saturation constant for uptake, they were transcribed in higher...”
  • “...(29) Gluconokinase, EC 2.7.1.12, encoded by Entcl_0304, and Entcl_3682; (30) Gluconolactonase, EC 3.1.1.17, encoded by Entcl_0174; and (31) 2-dehydro-3-deoxy-phosphogluconate aldolase, EC 4.1.2.14, encoded by Entcl_1940. (DOCX) Click here for additional data file. S2 Fig Optical density measured at 600 nm (OD 600 ) as a metric...”

KP1_1424 sugar ABC transport system permease component from Klebsiella pneumoniae NTUH-K2044
39% identity, 78% coverage

• YjcC, a c-di-GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43
  Huang, PloS one 2013
  • “...Maltose/maltodextrin transporter ATP binding protein malK 4.2 KP1_0276 Sugar ABC transport system permease component 4.1 KP1_1424 Putative ABC transporter mocB 3.7 KP1_1423 Putative rhizopine uptake ABC transporter proY 3.7 KP1_1422 Permease Putative PTS permease 6.5 KP1_0760 Putative amino acid permease 4.3 KP1_1204 Amino acid biosynthesis Arginine...”

BAbS19_II03540 dicarboxylate symporter from Brucella abortus S19
40% identity, 70% coverage

• Evaluation of the effects of erythritol on gene expression in Brucella abortus
  Rodríguez, PloS one 2012
  • “...al . [9] . The fact that in B. abortus strain S19 the BAB2_0376 ortholog (BAbS19_II03540) is affected by a 68 bp deletion and probably inactivated suggests the existence of alternative erythritol uptake systems in Brucella . The end product of erythritol catabolism would be DHAP,...”
• Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes
  Crasta, PloS one 2008
  • “...mouse model [18] . 10.1371/journal.pone.0002193.g004 Figure 4 Protein alignment of the ribose transporter protein, S19 BAbS19_II03540; A. with the homologs from strain 9941 (BruAb2_0372), 2308 (BAB2_0376) and B. suis (BRA0859); B. Protein alignment of the ribose transporter protein from strain 2308 (BAB2_0376) with the putative Rhizobium...”

SPOA0254 ABC transporter permease from Ruegeria pomeroyi DSS-3
34% identity, 79% coverage

• Diel investments in metabolite production and consumption in a model microbial system
  Uchimiya, The ISME journal 2022
  • “...transporter, ATP-binding protein 29.2 Sugar Ribose SPOA0253 ABC transporter, periplasmic substrate-binding 30.9 [ 47 ] SPOA0254 rbsC-1 ABC transporter, permease 54.9 SPOA0256 ABC transporter, periplasmic substrate-binding protein 21.4 SPOA0257 rbsC-2 ABC transporter, permease 50.4 SPOA0258 rbsA ABC transporter, ATP-binding 55.7 Sugar Glucose SPO0861 xylF ABC transporter,...”

RL2450 putative transmembrane component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
37% identity, 85% coverage

• Antioxidant ability of glutaredoxins and their role in symbiotic nitrogen fixation in Rhizobium leguminosarum bv. viciae 3841
  Zou, Applied and environmental microbiology 2021 (secret)

ABD05_RS21655 L-arabinose ABC transporter permease AraH from Burkholderia pyrrocinia
34% identity, 83% coverage

• The peanut root exudate increases the transport and metabolism of nutrients and enhances the plant growth-promoting effects of burkholderia pyrrocinia strain P10
  Han, BMC microbiology 2023
  • “...rbsC Ribose transport system permease protein 1.15 ABD05_RS21645 araF L-arabinose transport system substrate-binding protein 1.15 ABD05_RS21655 araH L-arabinose transport system permease protein 2.24 ABD05_RS33475 xylH D-xylose transport system permease protein 2.20 ABD05_RS33480 xylG D-xylose transport system ATP-binding protein 1.76 ABD05_RS31300 fabH 3- Oxoacyl-[acyl- carrier-protein] synthase III...”

AlsC / b4086 D-allose ABC transporter membrane subunit (EC 7.5.2.8) from Escherichia coli K-12 substr. MG1655 (see paper)
AlsC / P32720 D-allose ABC transporter membrane subunit (EC 7.5.2.8) from Escherichia coli (strain K12) (see paper)
ALSC_ECOLI / P32720 D-allose transport system permease protein AlsC from Escherichia coli (strain K12) (see paper)
TC 3.A.1.2.6 / P32720 AlsC aka B4086, component of D-allose porter from Escherichia coli (see 6 papers)
37% identity, 91% coverage

• function: Part of the binding-protein-dependent transport system AlsBAC for D-allose; probably responsible for the translocation of the substrate across the membrane.
• substrates: Allose
  tcdb comment: The structure of AlsB has been solved at 1.8 Å resolution (Chaudhuri et al. 1999). Ten residues from both the domains form 14 hydrogen bonds with the sugar. 6-Deoxy-allose, 3-deoxy-glucose and ribose bind with reduced affinity so AlbP can function as a low affinity transporter for D-ribose (Chaudhuri et al. 1999)

BCAM2796 putative permease component of ABC transporter from Burkholderia cenocepacia J2315
34% identity, 87% coverage

• Burkholderia cenocepacia ShvR-regulated genes that influence colony morphology, biofilm formation, and virulence
  Subramoni, Infection and immunity 2011
  • “...for L-arabinose: AraF (BCAL3405, BCAM2798), AraH (BCAL3403, BCAM2796), and AraG (BCAL3404, BCAM2797) (30). The BCAS0204 protein sequence shows 45% similarity to...”

BTH_II1626 L-arabinose ABC transporter, permease protein from Burkholderia thailandensis E264
33% identity, 89% coverage

• Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis
  Yu, BMC microbiology 2006
  • “...57.1 BPSS1412 (TTS1)* BTH_II0072 proteins BTH_I1335 biosynthesis + BPSL2806 proteins* BPSL2848- Phosphonate utilization 12 70.9 BTH_II1626- L-arabinose assimilation 10.4 71 BTH_II0431- Transposase 6.8 62.4 BPSS1940- Signal transduction; 4.4 69.4 BPSL2860 operon + BTH_II1633 operon * BTH_II0436 BPSS1941 chemotaxis * genes associated with this functional difference have...”

Ava_2173 inner-membrane translocator from Anabaena variabilis ATCC 29413
43% identity, 89% coverage

• In vivo Inhibition of the 3-Dehydroquinate Synthase by 7-Deoxysedoheptulose Depends on Promiscuous Uptake by Sugar Transporters in Cyanobacteria
  Rapp, Frontiers in microbiology 2021
  • “...wildtype was isolated and the genomic environment of the fructose ABC-transporter operon ( Ava_2170 - Ava_2173 ) was investigated (see Supplementary Figure 2 ). Gene specific primers were designed for each single gene of the operon, but also for the whole operon. A PCR with a...”
  • “...Anabaena sp. (pRL1049- frtRABC ) The fructose transporter operon from A. variabilis ( Ava_2170 - Ava_2173 ) was amplified from genomic DNA with the Gibson primers 3+4 (sequence in Table 2 ), adding overlapping fragments to the operon. Vector pRL1049, which is self-replicating in Anabaena sp....”

LKW31_00160 xylose ABC transporter permease XylH from Pantoea agglomerans
33% identity, 73% coverage

• Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.)
  Patakova, Frontiers in microbiology 2024
  • “...Gluconokinase LKW31_01605 Gluconate transporter 6-phosphogluconate dehydrogenase (5) LKW31_07145 NADP-dependent phosphogluconate dehydrogenase Glucose non-PTS transport (6) LKW31_00160 Sugar ABC transporter permease Glucose dehydrogenase (7)/NADH oxidoreductase (8) LKW31_09960 Glucose 1-dehydrogenase gdh LKW31_09965 NADH:flavin oxidoreductase/NADH oxidase Catalase (9)/glucose dehydrogenase (10) LKW31_10630 Manganese catalase family protein LKW31_10635 Glucose 1-dehydrogenase gdh...”

A7P61_RS11580 ABC transporter permease from Pantoea agglomerans pv. betae
40% identity, 79% coverage

• Synergistic interaction between the type III secretion system of the endophytic bacterium Pantoea agglomerans DAPP-PG 734 and the virulence of the causal agent of olive knot Pseudomonas savastanoi pv. savastanoi DAPP-PG 722
  Moretti, Molecular plant pathology 2021
  • “...+ + + + + + hopQ1 A7P61_RS08055 + + hopD1 A7P62_RS10595 + + hopAY1 A7P61_RS11580 + + hopAF1 A7P62_RS00640 + + hopAK1 A7P62_RS00650 + + hopV1 A7P62_RS00655 + + xopE2 A7P62_RS10630 + + hsvG A7P62_RS10725 + + hsvB A7P62_RS10575 + + pthG A7P62_RS18080 + +...”

Entcl_4081 ABC transporter permease subunit from [Enterobacter] lignolyticus SCF1
39% identity, 89% coverage

• Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
  Orellana, PloS one 2017
  • “...(Entcl_3690, Entcl_3691, Entcl_3692, Entcl_3811 and Entcl_3812), xylose (Entcl_0175 and Entcl_0176) and ribose (Entcl_0174, Entcl_1204, Entcl_1206, Entcl_4081) were down-regulated in early exponential phase. However, after glucose was made unavailable due to concentrations dipping below its half-saturation constant for uptake, they were transcribed in higher abundance. The initial...”

Gocc_2300 ABC transporter permease from Gaiella occulta
39% identity, 79% coverage

• High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria
  Severino, MicrobiologyOpen 2019
  • “...2011 ). The genes for ABC transport systems for ribose (Gocc_0079 to Gocc_0081; Gocc_2298 to Gocc_2300; Gocc_3068, Gocc_3069 and Gocc_3071), rhamnose (Gocc_0123 to Gocc_0125; Gocc_0231 to Gocc_0234), Dxylose (Gocc_1293 to Gocc_1295), and raffinose/stachyose/melibiose (Gocc_1613 to Gocc_1616) were identified in G. occulta genome. Four unspecific sugar transport...”

SMb20854 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
37% identity, 84% coverage

• Genetic and computational identification of a conserved bacterial metabolic module
  Boutte, PLoS genetics 2008
  • “...binding protein) 2.6e-18 3.4e-13 1.6e-17 4.2e-11 4.9e-22 SMb20855 (ATP-binding protein) 1.3e-108 1.5e-114 5.7e-112 8.5e-92 2.4e-80 SMb20854 (permease protein) 2.0e-52 1.9e-29 1.7e-35 3.4e-60 1.1e-50 The BLAST score of each of the three protein subunits encoded in these candidate transporter operons was calculated against the equivalent protein subunits...”
• Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome
  Mauchline, Proceedings of the National Academy of Sciences of the United States of America 2006
  • “...by galactose. The other pentose-induced systems include ABC-T SMb20854 induced by deoxyribose (7-fold) and ABC-T SMa0067, which is induced 4-fold by both ribose...”

HSERO_RS11490 D-ribose ABC transporter, permease component RbsC from Herbaspirillum seropedicae SmR1
36% identity, 92% coverage

• mutant phenotype: Specifically important for utilizing D-Ribose.

BCAL3403 L-arabinose transport system, permease protein from Burkholderia cenocepacia J2315
31% identity, 84% coverage

• Burkholderia cenocepacia ShvR-regulated genes that influence colony morphology, biofilm formation, and virulence
  Subramoni, Infection and immunity 2011
  • “...transporters for L-arabinose: AraF (BCAL3405, BCAM2798), AraH (BCAL3403, BCAM2796), and AraG (BCAL3404, BCAM2797) (30). The BCAS0204 protein sequence shows 45%...”

blr2271 sugar ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
40% identity, 82% coverage

• Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress
  Cytryn, Journal of bacteriology 2007
  • “...blr6760 blr6761 blr6762 bll0324 blr3200 blr3201 bll3208 blr2271 blr0725 blr4948 blr0612 blr8148 blr3575 blr8147 bll2362 bll7574 blr1499 bll2752 blr2358...”

BPHYT_RS16925 D-galactose ABC transporter, permease component from Burkholderia phytofirmans PsJN
31% identity, 84% coverage

• mutant phenotype: Specifically important for D-galactose utilization

SMb20714 ABC transporter permease from Sinorhizobium meliloti 1021
NP_437961 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
37% identity, 92% coverage

• Mining the Sinorhizobium meliloti transportome to develop FRET biosensors for sugars, dicarboxylates and cyclic polyols
  Bourdès, PloS one 2012
  • “...myo -inositol [9] . The ABC transporter operon (SMb20712 (SBP), SMb20713 (ATP binding cassette) and SMb20714 (permeases)) is preceded by SMb20711 which was identified as a putative inosose isomerase. A wide range of bacteria, including R. leguminosarum and S. meliloti , can catabolise myo -inositol, via...”
• Genetic and computational identification of a conserved bacterial metabolic module
  Boutte, PLoS genetics 2008
  • “...binding protein) 2.0e-22 3.8e-129 1.1e-21 3.3e-34 2.6e-23 SMb20713 (ATP-binding protein) 7.1e-197 2.3e-246 1.3e-108 2e-117 8.3e-113 SMb20714 (permease protein) 4.3e-34 3.0e-122 8.8e-29 7e-37 3.7e-38 SMb21345 (sugar binding protein) 1.1e-26 3.0e-16 4.4e-18 7.0e-29 SMb21344 (ATP-binding protein) 8.7e-113 7.0e-98 1.5e-104 8e-98 6.6e-102 SMb21343 (permease protein) 6.4e-30 3.7e-32 4.2e-31 2.3e-35...”
  • “...IbpA. As such, we have annotated Smb20712 as ibpA , Smb20713 as iatA , and Smb20714 as iatP . 10.1371/journal.pgen.1000310.t004 Table 4 Doubling times, in minutes, of S. meliloti strains grown in Luria-Bertani (LB) broth, and minimal GTS medium supplemented with either glucose (GTS-G) or myo...”
• Genetic and computational identification of a conserved bacterial metabolic module
  Boutte, PLoS genetics 2008
  • “...Functional Predictions in Sinorhizobium meliloti The cross-species network predicted that the operon Smb20712-4 (NP_437959, NP_437960, NP_437961) in S. meliloti 1021 is a myo -inositol transporter ( Figure 6A ). This ABC transporter operon in S. meliloti 1021 is annotated in GenBank as a putative rhizopine transporter,...”

C289_0765 ABC transporter permease from Anoxybacillus ayderensis
33% identity, 95% coverage

• A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization
  Kahar, International journal of molecular sciences 2013
  • “...oligo-1,6-glucosidase (C289_0857, C289_1909, and C289_2139). Several putative sugar transporters (C289_0465, C289_0466, C289_0467, C289_0603, C289_0763, C289_0764, C289_0765, C289_0778, C289_0779, C289_0780, C289_1015, C289_1174, C289_1392, C289_1394, C289_1910, C289_1911, and C289_1912) were also found in the Blast2GO annotation. The draft genome was submitted to the National Center for Biotechnology Information...”

H604_RS0100045 ABC transporter permease from Ruminococcus gauvreauii DSM 19829
29% identity, 93% coverage

• Analysis of Temporal Changes in Growth and Gene Expression for Commensal Gut Microbes in Response to the Polyphenol Naringenin
  Firrman, Microbiology insights 2018
  • “...description Fold Function H604_RS0100855 Hypothetical protein 1.6 Unknown H604_RS0100345 Iron transporter FeoA 1.4 Iron uptake H604_RS0100045 Hypothetical protein 1.4 Unknown H604_RS0100920 Proton-coupled thiamine transporter YuaJ 1.3 Thiamine transport H604_RS0100110 Ribose ABC transporter permease 1.3 Molecular translocation H604_RS0100455 Hypothetical protein 1.3 Unknown H604_RS19840 Hypothetical protein 1.3 Unknown...”

Gocc_3068 ABC transporter permease from Gaiella occulta
36% identity, 91% coverage

• High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria
  Severino, MicrobiologyOpen 2019
  • “...). The genes for ABC transport systems for ribose (Gocc_0079 to Gocc_0081; Gocc_2298 to Gocc_2300; Gocc_3068, Gocc_3069 and Gocc_3071), rhamnose (Gocc_0123 to Gocc_0125; Gocc_0231 to Gocc_0234), Dxylose (Gocc_1293 to Gocc_1295), and raffinose/stachyose/melibiose (Gocc_1613 to Gocc_1616) were identified in G. occulta genome. Four unspecific sugar transport systems...”

Z5690 putative permease of ribose ABC transport system from Escherichia coli O157:H7 EDL933
ECs5072 putative carbohydrate ABC transport system permease from Escherichia coli O157:H7 str. Sakai
39% identity, 92% coverage

• Rapid determination of Escherichia coli O157:H7 lineage types and molecular subtypes by using comparative genomic fingerprinting
  Laing, Applied and environmental microbiology 2008
  • “...Z1963 Z2400 Z2386-Z2387 Z3358 Z3939 Z4188 NA Z5690 ECs4955-ECs4956 ECs0020 ECs0275 ECs1184 ECs1386 ECs1506 ECs1695 ECs1941 ECs1954 ECs2990 ECs3507 ECs3724...”
• Genetic diversity among Escherichia coli O157:H7 isolates and identification of genes linked to human infections
  Wu, Infection and immunity 2008
  • “...heme/hemoglobin transporter (chuS), a putative ribose-specific transporter (Z5690 and ECs5072), and a putative antibiotic efflux pump (Z3494 and ECs3132). Among...”
• Rapid determination of Escherichia coli O157:H7 lineage types and molecular subtypes by using comparative genomic fingerprinting
  Laing, Applied and environmental microbiology 2008
  • “...ECs1954 ECs2990 ECs3507 ECs3724 ECs4954 ECs5072 S-loop#274 OI#1/S-loop#1 OI#8/S-loop#16 S-loop#69 OI#43/S-loop#72 OI#50/S-loop#77 OI#55/S-loop#83 S-loop#91...”
• Genetic diversity among Escherichia coli O157:H7 isolates and identification of genes linked to human infections
  Wu, Infection and immunity 2008
  • “...transporter (chuS), a putative ribose-specific transporter (Z5690 and ECs5072), and a putative antibiotic efflux pump (Z3494 and ECs3132). Among the E. coli...”

YPO0411 putative ABC transporter permease protein from Yersinia pestis CO92
YP_3770 putative ABC transporter permease protein from Yersinia pestis biovar Medievalis str. 91001
32% identity, 87% coverage

• The cyclic AMP receptor protein, CRP, is required for both virulence and expression of the minimal CRP regulon in Yersinia pestis biovar microtus
  Zhan, Infection and immunity 2008
  • “...AAAACGTGATCTAGATT GAACTT YPO0409 1 2.14 MD YPO0410 1 g YPO0411 1 3.27 7.43 A AAATTGTGATCTTGGTT ACGCCA D/118/8.76 YPO0412 1 sdaC 4.84 3.20 B D/308/9.19 YPO1321...”
• Marmots and Yersinia pestis Strains in Two Plague Endemic Areas of Tien Shan Mountains
  Sariyeva, Frontiers in veterinary science 2019
  • “...293 240 155 Genotype 9 YP_EV_76 210 230 606 184 252 222 155 Genotype 10 YP_3770 210 179 547 174 245 285 119 Genotype 11 YP_Angola 210 162 362 134 259 276 137 Genotype 12 YP_91001 210 196 303 184 252 258 128 Genotype 13 YP_Antiqua...”

HI1109 D-xylose ABC transporter permease protein from Haemophilus influenzae Rd KW20
34% identity, 83% coverage

• Antibiotic Susceptibility and Molecular Typing of Invasive Haemophilus influenzae Isolates, with Emergence of Ciprofloxacin Resistance, 2017-2021, Italy
  Giufrè, Microorganisms 2023
  • “...949 17 IIb * * * * Hi1108 2 4 919 48 IIb * * Hi1109 1.5 2 57 57 113 IIc T * BLPACR Hi854 256 8 836 836 33 III-like * * * * * * Hi1031 256 4 422 422 43 m *...”

BCAL1659 putative ribose transport system, permease protein from Burkholderia cenocepacia J2315
36% identity, 88% coverage

• The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia
  Sass, The ISME journal 2013
  • “...Pentose turnover BCAL1657 Ribose transport substrate-binding protein 7.5 BCAL1658 Ribose ABC transporter ATP-binding protein 8.8 BCAL1659 Ribose transport system, permease protein 2.9 BCAL1660 Ribose operon repressor 3.1 BCAL1661 Ribokinase 8.9 BCAM0310 a Ribonucleotide reductase, class II 15 BCAM0311 a Ribokinase 89 Amino-acid turnover BCAL1796 Saccharopine dehydrogenase...”
• Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species
  Van, PloS one 2013
  • “...synthase ATCATCCAGCAGGGTCTGAAGA GCCATTTCCTCGCGATAGAA BCAL0421 DNA gyrase B subunit GTTCCACTGCATCGCGACTT GGGCTTCGTCGAATTCATCA BCAL1459 Calcineurin-like phosphoesterase ATCCCTTGAAATCGAGCATCA TACGCTCGACAACGTGCATTA BCAL1659 Ribose transport permease ACCGTGTTCGGACGCTATCT CATCAGTGCGAATACGAGAATTTT BCAL1861 Acetoacetyl-CoA reductase GATCACCTGCTTCGTGACGTT GACGTCGTGTTCCGCAAGAT BCAL2694 Dehydrogenase CTTGCCGTGATCCTCGAGAT GAGATCAGCGAGGCCGAGTA BCAM0991 Tryptophane synthase beta chain GCCAACGTCTACCGGATGAA GACCGTGCCGATGATGTAGAA BCAM2784 Aminotransferase CCCCGTTCTCGCTCTACGT GTGTCGCCGAGGCAGAAAT BCAS0175 Hydrolase ATGGCCAGTTCGCTCATCA ACGCGATGTCGATACTCGAAT Flow...”
• Transcriptional response of Burkholderia cenocepacia J2315 sessile cells to treatments with high doses of hydrogen peroxide and sodium hypochlorite
  Peeters, BMC genomics 2010
  • “...candidate reference genes (Additional file 6 ). These ten genes included (i) five genes (BCAL1459, BCAL1659, BCAL2694, BCAM2784 and BCAS0175), which encode functionally diverse proteins and which showed a moderate and stable expression under all test conditions in the microarray experiments (fold difference between test conditions...”
  • “...test conditions. Pairwise variation analysis (data not shown) resulted in the selection of five genes (BCAL1659, BCAL2694, BCAL1459, BCAS0175 and BCAL1861) necessary for an accurate normalization of our data. Lipase activity in biofilm supernatant In order to determine the lipase activity in the supernatant of untreated...”

blr4886 ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
29% identity, 92% coverage

• Soybean-mediated suppression of BjaI/BjaR₁ quorum sensing in Bradyrhizobium diazoefficiens impacts symbiotic nitrogen fixation
  Han, Applied and environmental microbiology 2024 (secret)

Q7ULN8 Ribose ABC transporter permease protein from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
39% identity, 50% coverage

• Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica
  Paparoditis, Biochimica et biophysica acta 2014
  • “...8 3.A P-P-Bond Hydrolysis-driven Transporters 3.A.1 ATP-binding Cassette (ABC) Superfamily 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7ULN8 8 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UU56 8 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UR04 8 3.A.1.2.15 A8H4W6 9 sugar xylitol Q7UXV9 10 3.A.1.5.22 Q5V9S0 6 peptide peptide Q7UHZ2 6 3.A.1.5.22...”

EfmE4452_1563, EfmE4453_1837 ABC transporter permease from Enterococcus faecium E4453
29% identity, 97% coverage

• Hospital and community ampicillin-resistant Enterococcus faecium are evolutionarily closely linked but have diversified through niche adaptation
  de, PloS one 2012
  • “...EfmE4453_1842 Resolvase/integrase Bin EfmE4452_1560 EfmE4453_1840 toxin-antitoxin system, toxin component, MazF family EfmE4452_1561 EfmE4453_1839 D-xylulose kinase EfmE4452_1563 EfmE4453_1837 transporter permease EfmE4452_1564 EfmE4453_1836 ABC transporter EfmE4452_1565 EfmE4453_1835 beta-1,4-xylosidase EfmE4452_1566 EfmE4453_1834 xylose isomerase EfmE4452_1567 EfmE4453_2638 xylose operon repressor EfmE4452_1568 EfmE4453_2637 conserved hypothetical protein EfmE4452_1773 EfmE4453_0609 heavy metal translocating P-type...”
  • “...Resolvase/integrase Bin EfmE4452_1560 EfmE4453_1840 toxin-antitoxin system, toxin component, MazF family EfmE4452_1561 EfmE4453_1839 D-xylulose kinase EfmE4452_1563 EfmE4453_1837 transporter permease EfmE4452_1564 EfmE4453_1836 ABC transporter EfmE4452_1565 EfmE4453_1835 beta-1,4-xylosidase EfmE4452_1566 EfmE4453_1834 xylose isomerase EfmE4452_1567 EfmE4453_2638 xylose operon repressor EfmE4452_1568 EfmE4453_2637 conserved hypothetical protein EfmE4452_1773 EfmE4453_0609 heavy metal translocating P-type ATPase...”

Gocc_0234 ABC transporter permease from Gaiella occulta
37% identity, 79% coverage

• High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria
  Severino, MicrobiologyOpen 2019
  • “...to Gocc_0081; Gocc_2298 to Gocc_2300; Gocc_3068, Gocc_3069 and Gocc_3071), rhamnose (Gocc_0123 to Gocc_0125; Gocc_0231 to Gocc_0234), Dxylose (Gocc_1293 to Gocc_1295), and raffinose/stachyose/melibiose (Gocc_1613 to Gocc_1616) were identified in G. occulta genome. Four unspecific sugar transport systems (Gocc_0123 to Gocc_0125, Gocc_0222 to Gocc_0224, Gocc_2321 to Gocc_2323 and...”

RSUY_47250, RSUY_RS22945 sugar ABC transporter permease from Ralstonia solanacearum
34% identity, 72% coverage

• Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii
  Puigvert, Frontiers in plant science 2017
  • “...3.44342 isoaspartyl peptidase Carbohydrate metabolism RSUY_RS22935 RSUY_47230 RSp1633 1.90617 xylF D-xylose ABC transporter substrate-bindingprotein RSUY_RS22945 RSUY_47250 RSp1635 2.40016 xylH xylose ABC transporter permease RSUY_RS21965 RSUY_45140 RSp1270 2.4781 glycosyl hydrolase RSUY_RS22940 RSUY_47240 RSp1634 2.98048 xylG D-xylose ABC transporter ATP-binding protein RSUY_RS17060 RSUY_34910 RSp0423 3.65067 aldolase RSUY_RS22950 RSUY_47260...”
  • “...RSc1378 3.44342 isoaspartyl peptidase Carbohydrate metabolism RSUY_RS22935 RSUY_47230 RSp1633 1.90617 xylF D-xylose ABC transporter substrate-bindingprotein RSUY_RS22945 RSUY_47250 RSp1635 2.40016 xylH xylose ABC transporter permease RSUY_RS21965 RSUY_45140 RSp1270 2.4781 glycosyl hydrolase RSUY_RS22940 RSUY_47240 RSp1634 2.98048 xylG D-xylose ABC transporter ATP-binding protein RSUY_RS17060 RSUY_34910 RSp0423 3.65067 aldolase RSUY_RS22950...”

BOV_0545 ribose ABC transporter, permease protein from Brucella ovis ATCC 25840
BR0543 ribose ABC transporter, permease protein from Brucella suis 1330
BCAN_A0555 Monosaccharide-transporting ATPase from Brucella canis ATCC 23365
35% identity, 87% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BR0544, rbsB1 BOV_0546 rbsB1 BCAN_A0557 MOS Ribose import IM BMEI1391, rbsC BruAb10565, rbsC1 BR0543, rbsC1 BOV_0545 rbsC1 BCAN_A0555 MOS Ribose import ABC2 BMEI1392, rbsA BruAb10564, rbsA1 BR0542, rbsA1 BOV_0544 rbsA1 BCAN_A0554, rsbA 53 MOS Possibly galactoside BP BMEII0083 BruAb20010 BRA0010 BOV_A0007 MOS Possibly galactoside ABC2 BMEII0085,...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BruAb10566, rbsB1 BR0544, rbsB1 BOV_0546 rbsB1 BCAN_A0557 MOS Ribose import IM BMEI1391, rbsC BruAb10565, rbsC1 BR0543, rbsC1 BOV_0545 rbsC1 BCAN_A0555 MOS Ribose import ABC2 BMEI1392, rbsA BruAb10564, rbsA1 BR0542, rbsA1 BOV_0544 rbsA1 BCAN_A0554, rsbA 53 MOS Possibly galactoside BP BMEII0083 BruAb20010 BRA0010 BOV_A0007 MOS Possibly galactoside...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BOV_0546 rbsB1 BCAN_A0557 MOS Ribose import IM BMEI1391, rbsC BruAb10565, rbsC1 BR0543, rbsC1 BOV_0545 rbsC1 BCAN_A0555 MOS Ribose import ABC2 BMEI1392, rbsA BruAb10564, rbsA1 BR0542, rbsA1 BOV_0544 rbsA1 BCAN_A0554, rsbA 53 MOS Possibly galactoside BP BMEII0083 BruAb20010 BRA0010 BOV_A0007 MOS Possibly galactoside ABC2 BMEII0085, mglA BruAb20009...”

BMEI1391 RIBOSE TRANSPORT SYSTEM PERMEASE PROTEIN RBSC from Brucella melitensis 16M
35% identity, 85% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...Ribose import BP BMEI1390 BruAb10566, rbsB1 BR0544, rbsB1 BOV_0546 rbsB1 BCAN_A0557 MOS Ribose import IM BMEI1391, rbsC BruAb10565, rbsC1 BR0543, rbsC1 BOV_0545 rbsC1 BCAN_A0555 MOS Ribose import ABC2 BMEI1392, rbsA BruAb10564, rbsA1 BR0542, rbsA1 BOV_0544 rbsA1 BCAN_A0554, rsbA 53 MOS Possibly galactoside BP BMEII0083 BruAb20010 BRA0010...”

Q7UR04 Ribose transport system permease protein RbsC from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
33% identity, 88% coverage

• Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica
  Paparoditis, Biochimica et biophysica acta 2014
  • “...autoinducer-2 Q7ULN8 8 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UU56 8 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UR04 8 3.A.1.2.15 A8H4W6 9 sugar xylitol Q7UXV9 10 3.A.1.5.22 Q5V9S0 6 peptide peptide Q7UHZ2 6 3.A.1.5.22 Q5V9S1 6 peptide peptide Q7UHZ1 6 3.A.1.7.1 P07654 6 anions Phosphate Q7UP20 6 3.A.1.7.1...”

TC 3.A.1.2.9 / Q7BSH3 RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) from Rhizobium leguminosarum (biovar trifolii)
33% identity, 94% coverage

• substrates: Rhamnose

PP_2456 ribose ABC transporter, permease protein from Pseudomonas putida KT2440
35% identity, 91% coverage

• Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440
  Avendaño, Microbial biotechnology 2023
  • “...related to the uptake of amino acids (operon PP_1297, PP_1298, PP_1299 and PP_1300) and ribose (PP_2456, PP_2455). The differences in expression patterns in membrane proteins can be explained considering that selenite reduction leads to the accumulation of extracellular selenium nanoparticles, which could lead to a significant...”

Atu0064 ABC transporter, membrane spanning protein (sugar) from Agrobacterium tumefaciens str. C58 (Cereon)
32% identity, 84% coverage

• Sibling rivalry: related bacterial small RNAs and their redundant and non-redundant roles
  Caswell, Frontiers in cellular and infection microbiology 2014
  • “...In Agrobacterium , AbcR1, but not AbcR2, controls the expression of the ABC transporter-associated genes atu0064 ( frcC ), atu1879 , and atu2422 by altering the stability of the mRNA messages, resulting in a negative impact on the expression of these genes, Atu2422 is a periplasmic-binding...”

TC 3.A.1.2.26 / A6LW12 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas from Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)
X276_14750 sugar ABC transporter permease from Clostridium beijerinckii NRRL B-598
Cbei_2382 monosaccharide-transporting ATPase from Clostridium beijerincki NCIMB 8052
33% identity, 75% coverage

• substrates: Xylose
  tcdb comment: Controlled by a 3 component sensor kinase/response regulator system (XylFII, sensor, A6LW07; LytS, SK, A6LW08; YesN, RR, A6LW09) (Sun et al. 2015). The XylFII-LytS complex provides the molecular basis for D-xylose utilization and metabolic modification (Li et al. 2017)
• Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol-producing Clostridium beijerinckii NRRL B-598
  Vasylkivska, PloS one 2019
  • “...D-xylose transporter found in C . beijerinckii NCIMB 8052 [ 78 ], coded by X276_14760- X276_14750, were identified in the C . beijerinckii NRRL B-598 genome. None of these non-PTS systems were differentially expressed during fermentation ( S6 File ), however, these genes may be of...”
• Reconstruction of xylose utilization pathway and regulons in Firmicutes
  Gu, BMC genomics 2010
  • “...xylose utilization genes in several Clostridiales, Thermoanaerobacterales, and Bacillales species ( e.g . Cbei_2380 - Cbei_2382 in C. beijerinckii ; see Figure 3 ). Another xylose transporter belonging to the MFS transporter family, XylT, was described in Bacillus megaterium [ 27 ] and L. brevis [...”

BCAN_B1181 Monosaccharide-transporting ATPase from Brucella canis ATCC 23365
47% identity, 39% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BruAb20008 BRA0008 BOV_A0004 54 MOS Xylose import IM BMEII0144, xylH BruAb21089, xylH BRA1152, xylH BOV_A1057 BCAN_B1181 MOS Xylose import ABC2 BMEII0145, xylG BruAb21088, xylG BRA1151, xylG BOV_A1056 BCAN_B1180, xylG MOS Xylose import BP BMEII0146, xylF BruAb21087, xylF BRA1150, xylF BOV_A1055 BCAN_B1179, xylF 55 MOS Ribose import...”

VK055_3270 ABC transporter permease from Klebsiella pneumoniae subsp. pneumoniae
31% identity, 89% coverage

• A systematic analysis of hypermucoviscosity and capsule reveals distinct and overlapping genes that impact Klebsiella pneumoniae fitness
  Mike, PLoS pathogens 2021
  • “...3C ). The ten transporters identified include five sugar transporters ( VK055_0865 , VK055_2628 , VK055_3270 , xylH , VK055_1895 ), a C4-dicarboxylate transporter ( dctA ), two amino acid transporters ( VK055_1956 and VK055_2661 ), a nucleoside transporter ( VK055_4768 ), and an osmoprotectant transporter...”

PS417_18395 D-ribose ABC transporter, permease component RbsC from Pseudomonas simiae WCS417
36% identity, 92% coverage

• mutant phenotype: Specifically important for utilizing D-Ribose.

Entcl_1205 ABC transporter permease from [Enterobacter] lignolyticus SCF1
33% identity, 93% coverage

• Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
  Orellana, PloS one 2017
  • “...beside glucose were up-regulated after glucose uptake was stopped ( Fig 2C ) (Entcl_0166, Entcl_0167, Entcl_1205, Entcl_1207, Entcl_3382, Entcl_3383, Entcl_4082, Entcl_4174, and Entcl_4403, S4 Table ). This was presumably a response to the lack of availability of glucose, an effect that has been observed in other...”

Q7UXV9 Ribose transport system permease protein from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
33% identity, 86% coverage

• Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica
  Paparoditis, Biochimica et biophysica acta 2014
  • “...autoinducer-2 Q7UU56 8 3.A.1.2.13 A6VKS9 9 organoanions autoinducer-2 Q7UR04 8 3.A.1.2.15 A8H4W6 9 sugar xylitol Q7UXV9 10 3.A.1.5.22 Q5V9S0 6 peptide peptide Q7UHZ2 6 3.A.1.5.22 Q5V9S1 6 peptide peptide Q7UHZ1 6 3.A.1.7.1 P07654 6 anions Phosphate Q7UP20 6 3.A.1.7.1 P0AGH8 6 anions Phosphate Q7UP19 6 3.A.1.10.1...”

STY3795 putative ABC transporter permease protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
t3543 putative ABC transporter permease protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
34% identity, 88% coverage

• The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi
  Carey, 2024
• The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi
  Carey, 2022
• A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi
  Perkins, PLoS genetics 2009
  • “...lyase is crucial for macrophage persistence in Mycobacterium tuberculosis [47] . Three genes t3544 , t3543 and t3538 that are predicted components of a ribose/arabinose transport operon were also increased in expression. Furthermore, predicted genes t1788 - 90 were greatly increased in expression in the ompR...”

LSRC_SALTY / Q8ZKQ3 Autoinducer 2 import system permease protein LsrC; AI-2 import system permease protein LsrC from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
STM4075 putative ABC superfamily (membrane), sugar transport protein from Salmonella typhimurium LT2
34% identity, 88% coverage

• function: Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. Probably responsible for the translocation of the substrate across the membrane (Probable).
  subunit: The complex is composed of two ATP-binding proteins (LsrA), two transmembrane proteins (LsrC and LsrD) and a solute-binding protein (LsrB).
• FabR regulates Salmonella biofilm formation via its direct target FabB
  Hermans, BMC genomics 2016
  • “...ydeZ/lsrD ABC transporter, membrane component 1.75 21 STM4074 ego/lsrA ABC transporter ATP-binding protein 1.66 23 STM4075 ydeY/lsrC ABC transporter permease protein 1.64 4 STM4184 aceA Isocitrate lyase 2.50 Glyoxylate metabolism 11 STM4183 aceB Malate synthase A 2.07 14 STM4185 aceK Isocitrate dehydrogenase kinase/phosphatase 1.86 9 STM3195...”
• Comparing the presence of different genes in Salmonella subspecies I-IV and development of a diagnostic multiplex PCR method for identification of Salmonella subspecies
  Münch, Berliner und Munchener tierarztliche Wochenschrift 2013 (PubMed)
  • “...IIIb and IV. In the present study, the occurrence of the genes invA, ttrCA, iroB, STM4075, sciA, STM3690, sadA, gatD, foxA, pagN, fljB, iucD, spvB, lacZ, iutA, mdcA and irp2 was examined in 41 Salmonella strains from Middle Eastern animals (mainly reptiles) by monoplex PCR. According...”
• Salmonella serovar identification using PCR-based detection of gene presence and absence
  Arrach, Journal of clinical microbiology 2008
  • “...STM4046, STM4052, STM4067, STM4068, STM4072, STM4074, STM4075, STM4078, STM4102, STM4113, STM4115, STM4205, STM4261, STM4279, STM4306, STM4319, STM4373,...”

ML0397 putative transporter protein from Mycobacterium leprae TN
34% identity, 52% coverage

• Antigen discovery: a postgenomic approach to leprosy diagnosis
  Aráoz, Infection and immunity 2006
  • “...8 8 8 8 8 8 8 10 ML0333 10 ML0336 3 ML0394 ML0397 ML0398 ML0447 7 3 3 10 ML0458 ML0578 7 7 ML1419 ML1553 ML2177 ML2341 9 2 7 9 ML2346 10 ML2498 ML2649 ML0376...”

CPE1343 probable galactoside ABC transporter from Clostridium perfringens str. 13
33% identity, 88% coverage

• RNA-seq analysis of virR and revR mutants of Clostridium perfringens
  Low, BMC genomics 2016
  • “...transporters cpe1341 mglB galactoside ABC transporter 2.42 3.90 cpe1342 mglA galactoside ABC transporter 2.70 3.71 cpe1343 mglC galactoside ABC transporter 2.69 4.36 Fibronectin III domain proteins cpe1875 cpe1875 fibronectin/fucosidase 1.40 1.84 cpe0818 cpe0818 endo-beta-N-acetylglucosaminidase 1.63 2.26 Hypothetical proteins cpe1257 ugpB ABC transporter substrate binding protein 1.47...”

TC 3.A.1.2.24 / O50505 Probable ABC-type transmembrane transport protein, component of XylFGH downstream of characterized transcriptional regulator, ROK7B7 (Sco6008); XylF (Sco6009); XylG (Sco6010); XylH (Sco6011)) from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
SCO6011 probable ABC-type transmembrane transport protein from Streptomyces coelicolor A3(2)
30% identity, 72% coverage

• substrates: Sugars
• Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor
  Romero-Rodríguez, BMC microbiology 2016
  • “...the lack of specific inducers in the system. Interestingly, the xylose transporter, ( SCO6009 - SCO6011 ) showed 10-fold stimulation, just after the GlcP transporter (Fig. 4a and b ). This oddly up-regulation of the xylose transporter was also accompanied by changes in its transcriptional regulator...”
• The ROK family regulator Rok7B7 pleiotropically affects xylose utilization, carbon catabolite repression, and antibiotic production in streptomyces coelicolor
  Świątek, Journal of bacteriology 2013
  • “...and the xylose transporter operon xylFGH (SCO6009 to SCO6011; downstream), with its gene synteny highly conserved in streptomycetes. Rok7B7 exhibits 27% amino...”
  • “...Rok7B7 controls the downstream-located xylose operon SCO6009 to SCO6011 (xylFGH), SCO6009 and SCO6010 were strongly upregulated (9- to 11-fold) in the rok7B7...”
• Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor
  Getsin, BMC microbiology 2013
  • “...protein, ROK7B7. XylF, Sco6009 (R; 1 N-terminal TMS); XylG, Sco6010 (C; ATP-binding, no TMSs); XylH, Sco6011 (M; 12 TMSs); [ 109 ] Probable ABC peptide uptake porter; Sco5476-80 (M, R, M, C, C) [ 110 ] O86571-5 3.A.1.5.34 Probably takes up a peptide involved in the...”

SC3964 putative ABC superfamily (membrane), sugar transport protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
34% identity, 88% coverage

• Identification and characterization of the ilvR gene encoding a LysR-type regulator of Caulobacter crescentus
  Malakooti, Journal of bacteriology 1994
  • “...CB15 SC3428 SC3429 SC3430 SC3431 SC3844 SC3950 SC3951 SC3964 SC3965 SC3966 SC3967 E. coli XLI-Blue Relevant genotype or characteristic THE C. CRESCENTUS ilvR...”
  • “...L4 Cm R chromo: some -v 7 Phenotype Kan 3 Q SC3964 I X 3 1279 FIG. 5. Schematic representation of the genetic manipulations of the ilvD and ilvR chromosomal...”

C5965_02215 xylose ABC transporter permease XylH from Cronobacter sakazakii
41% identity, 40% coverage

• Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains
  Jang, Standards in genomic sciences 2018
  • “...binding protein , locus tag C5965_02220), xylH (a sugar ABC transporter permease , locus tag C5965_02215), which is part of the ABC transporter complex XylFGH. This latter complex is involved in D-xylose uptake, xylR (an Ara C-like xylose operon transcription regulator , locus tag C5965_02210), bax...”

H604_RS0100110 ABC transporter permease from Ruminococcus gauvreauii DSM 19829
32% identity, 96% coverage

• Analysis of Temporal Changes in Growth and Gene Expression for Commensal Gut Microbes in Response to the Polyphenol Naringenin
  Firrman, Microbiology insights 2018
  • “...Iron uptake H604_RS0100045 Hypothetical protein 1.4 Unknown H604_RS0100920 Proton-coupled thiamine transporter YuaJ 1.3 Thiamine transport H604_RS0100110 Ribose ABC transporter permease 1.3 Molecular translocation H604_RS0100455 Hypothetical protein 1.3 Unknown H604_RS19840 Hypothetical protein 1.3 Unknown H604_RS0100765 Hypothetical protein 1.3 Unknown H604_RS0100350 Iron transporter FeoA 1.3 Iron uptake H604_RS0100290...”

Cphy_0582 Monosaccharide-transporting ATPase from Clostridium phytofermentans ISDg
31% identity, 73% coverage

• Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans
  Petit, PloS one 2013
  • “...8.1 34.9 Cphy_0581 Rhamnose ABC transport system, permease subunit R. leguminosarum RhaP (57) 9.3 37.6 Cphy_0582 Rhamnose ABC transport system, permease subunit R. leguminosarum RhaQ (57) 10.8 51.5 Cphy_0583 Rhamnose ABC transport system, periplasmic solute-binding subunit R. leguminosarum RhaS (53) 10.7 62.4 Cphy_0584 Isomerase n.i. n.i....”

SMb21343 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
35% identity, 83% coverage

• Inability to catabolize galactose leads to increased ability to compete for nodule occupancy in Sinorhizobium meliloti
  Geddes, Journal of bacteriology 2012
  • “...transporters that carry SMa0203 (induced 19-fold by galactose), SMb21343 (induced 6-fold by galactose), and SMb20931 (induced by - and -galactosides and 2-fold...”
• Genetic and computational identification of a conserved bacterial metabolic module
  Boutte, PLoS genetics 2008
  • “...(sugar binding protein) 1.1e-26 3.0e-16 4.4e-18 7.0e-29 SMb21344 (ATP-binding protein) 8.7e-113 7.0e-98 1.5e-104 8e-98 6.6e-102 SMb21343 (permease protein) 6.4e-30 3.7e-32 4.2e-31 2.3e-35 1.1e-34 SMb21377 (sugar binding protein) 5.5e-13 2.7e-6 SMb21376 (ATP-binding protein) 2.8e-103 2e-118 1e-103 1.4e-112 1.7e-105 SMb21375 (permease protein) 1.8e-48 7.5e-41 1.1e-44 2.5e-58 4.1e-37 SMb20856...”

Pf1N1B4_6033 D-ribose ABC transporter, permease component RbsC from Pseudomonas fluorescens FW300-N1B4
35% identity, 92% coverage

• mutant phenotype: No fitness data for this gene, but the other putative components are upstream (Pf1N1B4_6035:Pf1N1B4_6034) and are specifically important for ribose utilization.

BOV_A1057 D-xylose ABC transporter, permease protein from Brucella ovis ATCC 25840
47% identity, 36% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BMEII0087 BruAb20008 BRA0008 BOV_A0004 54 MOS Xylose import IM BMEII0144, xylH BruAb21089, xylH BRA1152, xylH BOV_A1057 BCAN_B1181 MOS Xylose import ABC2 BMEII0145, xylG BruAb21088, xylG BRA1151, xylG BOV_A1056 BCAN_B1180, xylG MOS Xylose import BP BMEII0146, xylF BruAb21087, xylF BRA1150, xylF BOV_A1055 BCAN_B1179, xylF 55 MOS Ribose...”

SMa0070 putative ABC transporter permease from Sinorhizobium meliloti 1021
37% identity, 82% coverage

• Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti
  Pobigaylo, Applied and environmental microbiology 2006
  • “...0.72 0.35 0.42 0.50 0.21 0.13 0.03 0.15 0.13 0.13 SMa0070 0.75 0.46 0.13 0.08 SMc01219 0.64 0.35 0.74 0.19 SMc01700 SMc02050 SMc02144 0.72 0.74 1.17 0.31 0.70...”
  • “...clones with mutations in transporter genes (chrA and SMa0070), a sodC (coding for a superoxide dismutase) mutant, and an SMa0091 (encoding a hypothetical...”

BRA1152 D-xylose ABC transporter, permease protein from Brucella suis 1330
50% identity, 33% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...galactoside IM BMEII0087 BruAb20008 BRA0008 BOV_A0004 54 MOS Xylose import IM BMEII0144, xylH BruAb21089, xylH BRA1152, xylH BOV_A1057 BCAN_B1181 MOS Xylose import ABC2 BMEII0145, xylG BruAb21088, xylG BRA1151, xylG BOV_A1056 BCAN_B1180, xylG MOS Xylose import BP BMEII0146, xylF BruAb21087, xylF BRA1150, xylF BOV_A1055 BCAN_B1179, xylF 55...”

CIBE_5333 galactose/methyl galactoside ABC transporter permease MglC from Clostridium beijerinckii
33% identity, 76% coverage

• l-Rhamnose Metabolism in Clostridium beijerinckii Strain DSM 6423
  Diallo, Applied and environmental microbiology 2019
  • “...(% similarity) 3 h 6.5 h 10 h l - Rhamnose transport into the cell CIBE_5333 Rhamnose ABC transporter, permease subunit Rhizobium leguminosarum bv. Trifolii RhaP (51) ND 4.18 3.96 CIBE_5334 Rhamnose ABC transporter, ATPase subunit R. leguminosarum bv. Trifolii RhaT (62) 1.26 4.47 4.11 CIBE_5335...”

MSMEG_1709 inner membrane ABC transporter permease protein YjfF from Mycobacterium smegmatis str. MC2 155
34% identity, 84% coverage

• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...2.52E02 1.76E02 D-Xylose Arabinose MSMEG_1707 MSMEG_1708 MSMEG_1709 MSMEG_1710 MSMEG_1711 MSMEG_1712 MSMEG_1713 MSMEG_1714 MSMEG_1715 pho araR araG araF araK...”
• A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis
  Titgemeyer, Journal of bacteriology 2007
  • “...proteins of B. subtilis. The adjacent ABC permease (msmeg_1709 to msmeg_1712) could be the uptake system for arabinose. Its gene products, including the...”

PA1948 membrane protein component of ABC ribose transporter from Pseudomonas aeruginosa PAO1
PA14_39320 ribose ABC transporter, permease protein from Pseudomonas aeruginosa UCBPP-PA14
36% identity, 92% coverage

• Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics
  Salvà-Serra, Frontiers in microbiology 2022
  • “...amino acid permease 3 7 1.09 0.06 1.25 0.00 4.78 0.00 Down 1.35 0.00 WP_003088303.1 PA1948 RbsC Membrane protein component of ABC ribose transporter 3 14 1.05 0.43 1.11 0.08 5.66 0.00 Down 1.04 0.52 WP_003088580.1 PA2006 - Probable major facilitator superfamily (MFS) transporter 3 6...”
  • “...amino acid permease 4 6 1.00 0.90 1.16 0.04 1.72 0.00 Down 1.18 0.02 WP_003088303.1 PA1948 RbsC Membrane protein component of ABC ribose transporter 3 14 1.10 0.19 1.10 0.22 1.81 0.00 Down 1.66 0.00 Higher WP_023464954.1 PA2252 - Probable AGCS sodium/alanine/glycine symporter 3 5 1.08...”
• Putative RNA Ligase RtcB Affects the Switch between T6SS and T3SS in Pseudomonas aeruginosa
  Dadashi, International journal of molecular sciences 2021
  • “...21 1.18 10 19 1.6 PA1249 T2SS AprA 5.56 10 6 4.76 10 5 1.2 PA1948 T2SS ToxA 5.76 10 6 4.91 10 5 1.1 PA2862 T2SS LipA 1.08 10 7 1.17 10 6 4.8 PA2939 T2SS PaAP 3.42 10 17 7.92 10 16 1.5 PA2676...”
• Protein Secretion Systems in Pseudomonas aeruginosa: An Essay on Diversity, Evolution, and Function
  Filloux, Frontiers in microbiology 2011
  • “...et al. ( 2010 ) PrpL (PA4175) Protease Fox et al. ( 2008 ) ToxA (PA1948) Exotoxin A-ADP ribosyltransferase Lu et al. ( 1993 ) T2SS (Hxc) HxcPHxcZ, HxcQ (PA0685) HxcR (PA0686) LapA (PA0688) Low-molecular weight alkaline phosphatase Ball et al. ( 2002 ) T3SS PscBL,...”
• Structural genome variants of Pseudomonas aeruginosa clone C and PA14 strains
  Klockgether, Frontiers in microbiology 2023
  • “...in HCF324 in inverted area Before 3,500,638 IS 6100 + 25.5 kbp spec. DNA ORF PA14_39320 ( rbsC ) disrupted by add. DNA K4 Keratitis (2003/2004) 6.859 4.512 1,002,329ff. 7.3 kbp spec. DNA No duplicated sequence, strain-spec. insertions at both breakpoints Before 5,514,000 52 kbp spec....”
  • “...respective sites, but in HCF324 one copy had inserted into the 1 kbp ORF rbsC (PA14_39320). Due to this disruption and the inversion, 185 bp of the ORFs 5 end were present in the right breakpoint area, while 814 bp of the 3 end were found...”

VC1328 galactoside ABC transporter, permease protein from Vibrio cholerae O1 biovar eltor str. N16961
30% identity, 92% coverage

• L-arabinose induces the formation of viable non-proliferating spheroplasts in Vibrio cholerae
  Espinosa, Applied and environmental microbiology 2021 (secret)
• The Cpx system regulates virulence gene expression in Vibrio cholerae
  Acosta, Infection and immunity 2015
  • “...the genes involved in galactose uptake (VC1325, VC1327, and VC1328) and utilization (VC1594, VC1595, and VC1596) (54). Based on these data, a plausible model is...”

BCAL1433 putative sugar transport system permease protein from Burkholderia cenocepacia J2315
33% identity, 90% coverage

• Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
  Fang, BMC systems biology 2011
  • “...for the first step of ornithine-derived lipid biosynthesis; BLAST E value of 1E-29 BCAL1431, BCAL1432, BCAL1433 Putative sugar transport system Galactose transport MglB, MglA, MglC TC-3.A.1.2.3 BIOLOG assays indicated growth on galactose; and BLAST E values (< 2E-23) BCAL1933, BCAL1934 Putative formyltransferase, NAD-dependent epimerase/dehydratase family protein...”
  • “...which are galactose-binding proteins conveying galactose into the cell, gene BCAL1431 (mglB), BCAL1432 (mglA), and BCAL1433 (mglC) were identified and they had been annotated as a putative sugar ABC transporter ATP-binding protein, a putative ribose ABC transport system, and a putative sugar transport system permease protein...”

RSc1243 PROBABLE SUGAR TRANSMEMBRANE ABC TRANSPORTER PROTEIN from Ralstonia solanacearum GMI1000
33% identity, 91% coverage

• The population genetic test Tajima's D identifies genes encoding pathogen-associated molecular patterns and other virulence-related genes in Ralstonia solanacearum
  Eckshtain-Levi, Molecular plant pathology 2018 (secret)

BMEII0144 XYLOSE TRANSPORT SYSTEM PERMEASE PROTEIN XYLH from Brucella melitensis 16M
50% identity, 33% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BRA0007 BOV_A0005 MOS Possibly galactoside IM BMEII0087 BruAb20008 BRA0008 BOV_A0004 54 MOS Xylose import IM BMEII0144, xylH BruAb21089, xylH BRA1152, xylH BOV_A1057 BCAN_B1181 MOS Xylose import ABC2 BMEII0145, xylG BruAb21088, xylG BRA1151, xylG BOV_A1056 BCAN_B1180, xylG MOS Xylose import BP BMEII0146, xylF BruAb21087, xylF BRA1150, xylF...”

FN1167 Galactoside transport system permease protein mglC from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
31% identity, 90% coverage

• Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
  Hendrickson, MicrobiologyOpen 2014
  • “...FN0658, FN0660, FN0685, FN0695, FN0793, FN0800, FN0801, FN0827, FN0828, FN1022, FN1080, FN1086, FN1135, FN1136, FN1166, FN1167, FN1187, FN1190, FN1198, FN1256, FN1301, FN1348, FN1349, FN1352, FN1353, FN1354, FN1362, FN1363, FN1398, FN1420, FN1432, FN1480, FN1525, FN1701, FN1734, FN1735, FN1737, FN1738, FN1739, FN1740, FN1741, FN1797, FN1798, FN1801, FN1811, FN1833,...”

RSp1635 PROBABLE XYLOSE TRANSMEMBRANE ABC TRANSPORTER PROTEIN from Ralstonia solanacearum GMI1000
43% identity, 37% coverage

• Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii
  Puigvert, Frontiers in plant science 2017
  • “...isoaspartyl peptidase Carbohydrate metabolism RSUY_RS22935 RSUY_47230 RSp1633 1.90617 xylF D-xylose ABC transporter substrate-bindingprotein RSUY_RS22945 RSUY_47250 RSp1635 2.40016 xylH xylose ABC transporter permease RSUY_RS21965 RSUY_45140 RSp1270 2.4781 glycosyl hydrolase RSUY_RS22940 RSUY_47240 RSp1634 2.98048 xylG D-xylose ABC transporter ATP-binding protein RSUY_RS17060 RSUY_34910 RSp0423 3.65067 aldolase RSUY_RS22950 RSUY_47260 RSp1636...”

ABD05_RS33475 sugar ABC transporter permease from Burkholderia pyrrocinia
43% identity, 38% coverage

• The peanut root exudate increases the transport and metabolism of nutrients and enhances the plant growth-promoting effects of burkholderia pyrrocinia strain P10
  Han, BMC microbiology 2023
  • “...araF L-arabinose transport system substrate-binding protein 1.15 ABD05_RS21655 araH L-arabinose transport system permease protein 2.24 ABD05_RS33475 xylH D-xylose transport system permease protein 2.20 ABD05_RS33480 xylG D-xylose transport system ATP-binding protein 1.76 ABD05_RS31300 fabH 3- Oxoacyl-[acyl- carrier-protein] synthase III 3.04 ABD05_RS30960 fadD Long-chain acyl-CoA synthetase 1.61 Note:...”

YjfF / b4231 galactofuranose ABC transporter putative membrane subunit YjtF (EC 7.5.2.9) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
YjfF / P37772 galactofuranose ABC transporter putative membrane subunit YjtF (EC 7.5.2.9) from Escherichia coli (strain K12) (see 3 papers)
YJFF_ECOLI / P37772 Inner membrane ABC transporter permease protein YjfF from Escherichia coli (strain K12) (see paper)
b4231 putative transport system permease protein from Escherichia coli str. K-12 substr. MG1655
34% identity, 79% coverage

• function: Part of the ABC transporter complex YtfQRT-YjfF involved in galactofuranose transport (Probable). Probably responsible for the translocation of the substrate across the membrane (Probable).
  subunit: The complex is composed of two ATP-binding proteins (YtfR), two transmembrane proteins (YtfT and YjfF) and a solute-binding protein (YtfQ).
• Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
  Kim, Environmental microbiology 2010
  • “...Fumarate reductase membrane anchor polypeptide frdA b4154 1.3 1.8 2.3 Fumarate reductase flavoprotein subunit yjfF b4231 1.8 3.0 2.1 Putative ABC transporter permease protein, function unknown fecE b4287 2.5 2.1 2.5 ATP-binding component of citrate-dependent iron(III) transport protein fecD b4288 2.1 3.2 2.3 Citrate-dependent iron transport,...”
• Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
  Wei, Infection and immunity 2003
  • “...b1169 b1170 b1336 b1483 b1543 b1920 b2681 b3514 b3877 b4231 b2117 b1020 b2479 b2090 b3763 b1384 b1892 b1074 b1942 b2365 b1899 b3907 Putative replicase Putative...”

SMc03000 PUTATIVE PERMEASE ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
33% identity, 93% coverage

• Characterization of Sinorhizobium meliloti triose phosphate isomerase genes
  Poysti, Journal of bacteriology 2007
  • “...chromosomal locus (systematic identifiers SMc02321 to SMc02325 and SMc03000 to SMc03003) (data not shown). This locus was found to be homologous to a rhamnose...”

XylH / b3568 xylose ABC transporter membrane subunit (EC 7.5.2.13; EC 7.5.2.10) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
XylH / P0AGI4 xylose ABC transporter membrane subunit (EC 7.5.2.13) from Escherichia coli (strain K12) (see paper)
TC 3.A.1.2.4 / P0AGI4 Xylose transport system permease protein XylH aka B3568, component of Xylose porter from Escherichia coli (see 4 papers)
xylH / RF|NP_418025 D-xylose ABC transporter, permease protein from Escherichia coli K12 (see 7 papers)
S4157 putative xylose transporter, membrane component from Shigella flexneri 2a str. 2457T
SF3612 putative xylose transport, membrane component from Shigella flexneri 2a str. 301
Z4993 putative xylose transport, membrane component from Escherichia coli O157:H7 EDL933
42% identity, 34% coverage

• substrates: Xylose
• Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery
  Yang, Nucleic acids research 2005
  • “...transport system ATP-binding protein SF3611 S4158 SBO3575 xylH d -xylose transport system permease protein SF3612 S4157 SBO3576 a Pseudogenes....”
• Toward Single Bacterium Proteomics
  Végvári, Journal of the American Society for Mass Spectrometry 2023
  • “...[R].DIDVAR.[Q] 917.53 459.27 +2 41.97 1 206.14 6.25% xyle transport system permease protein XylH xylH P0AGI4 [268279] [R].IYAIGGNLEAAR.[L] 1477.82 739.41 +2 61.15 1 190.99 6.25% uncharacterized protein YmfJ ymfJ P75973 [27] [M].NEQNLK.[H] 974.55 487.77 +2 55.13 1 184.83 6.25% putative DNA repair helicase RadD radD P33919...”
• Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery
  Yang, Nucleic acids research 2005
  • “...-xylose transport system ATP-binding protein SF3611 S4158 SBO3575 xylH d -xylose transport system permease protein SF3612 S4157 SBO3576 a Pseudogenes....”
• Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
  Segura, BMC genomics 2018
  • “...2.54 3.06E-03 Z4992 xylG D-xylose transport system (ATP-binding protein) NDE NDE NDE 2.08 4.14E-03 NDE Z4993 xylH D-xylose transport system (permease protein) NDE NDE 2.03 1.36E-03 2.07 1.01E-03 NDE Z5717 yjdE Arginine:agmatine antiporter 2.43 8.29E-03 NDE 3.76 1.94E-05 NDE 3.19 3.64E-04 Z0461 z0461 Fucose transporter (optimal...”

ECs5208 putative transport system permease protein from Escherichia coli O157:H7 str. Sakai
34% identity, 81% coverage

• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...- 2.57 3 ECs4991 O157 2.12 2 ECs5207 ytfT 3.32 2 ECs5007 lysC -3.43 1 ECs5208 yjfF 2.59 2 ECs5038 pfkA 2.14 2 ECs5211 yjgA 2.20 2 ECs5039 yjbR 2.21 2 ECs5213 cybC 2.20 2 ECs5049 actP 4.17 2 ECs5222 pyrB -2.95 1 ECs5050 yjcH 3.78...”

YPTB0800 tRNA-Met from Yersinia pseudotuberculosis IP 32953
33% identity, 89% coverage

• Genome-wide evaluation of the interplay between Caenorhabditis elegans and Yersinia pseudotuberculosis during in vivo biofilm formation
  Joshua, Infection and immunity 2015
  • “...Y. pestis), a putative sugar transporter permease subunit Yptb0800 (YPO3330 in Y. pestis), and a putative exported protein (YPO3050 in Y. pestis). Mutation of...”

VK055_1913 ABC transporter permease from Klebsiella pneumoniae subsp. pneumoniae
32% identity, 86% coverage

• A Serendipitous Mutation Reveals the Severe Virulence Defect of a Klebsiella pneumoniae fepB Mutant
  Palacios, mSphere 2017
  • “...Short-chain dehydrogenase family protein VK055_1915 Iron-containing alcohol dehydrogenase family protein VK055_1914 ABC transporter family protein VK055_1913 Branched-chain amino acid transport system/permease component family protein VK055_1912 Periplasmic binding and sugar binding domain of LacI family protein VK055_1911 LVIVD repeat family protein a HAD, haloacid dehalogenase. b TPP,...”

Shewana3_2075 L-arabinose ABC transporter, permease component 1 AraW from Shewanella sp. ANA-3
33% identity, 66% coverage

• mutant phenotype: Specifically important for L-arabinose utilization; the gene name is from PMC2996990

BOV_1300 sugar ABC transporter, permease protein from Brucella ovis ATCC 25840
31% identity, 84% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...Ribose Import ABC BMEI0665 BruAb11337 BR1339 BOV_1299 BCAN_A1367 MOS Ribose Import IM BMEI0664 BruAb11338 BR1340 BOV_1300 BCAN_A1368 MOS Ribose Import BP BMEI0663 BruAb11340 BR1342 BOV_1301 BCAN_A1369 MOS Ribose Import BP BMEI0662 BruAb11335 52 MOS Ribose import BP BMEI1390 BruAb10566, rbsB1 BR0544, rbsB1 BOV_0546 rbsB1 BCAN_A0557 MOS...”

Z0418 putative permease component of transport system, probably ribose specific from Escherichia coli O157:H7 EDL933
ECs0377 putative permease of ABC transporter from Escherichia coli O157:H7 str. Sakai
30% identity, 94% coverage

• Metabolism of ʟ -arabinose converges with virulence regulation to promote enteric pathogen fitness
  Cottam, 2023
• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...0.65 0.71 0.87 Transport and binding proteins ECs0377 ECs0505 ECs0537 ECs0624 ECs0694 ECs0780 ECs0887 ECs0888 ECs0889 ECs1746 ECs2087 ECs2103 ECs2302 ECs2443...”
• Identification of Escherichia coli O157:H7 genomic regions conserved in strains with a genotype associated with human infection
  Steele, Applied and environmental microbiology 2007
  • “...katP pO157, etpF pOSAK1 ECs0238 and -9 ECS0281 ECs0377 ECs0760 ECs1120 ECs1164 ECs1191 ECs1223 ECS1382 ECs1425 ECs1588 and -9 ECs1698 ECs1954 ECs1998 ECs2775...”

BMEI0664 SUGAR TRANSPORT SYSTEM PERMEASE PROTEIN from Brucella melitensis 16M
31% identity, 81% coverage

• High-Resolution Melting PCR as Rapid Genotyping Tool for Brucella Species
  Girault, Microorganisms 2022
  • “...ggcccggcaattgctcctga 375225-375244 NR NR 81 C T B. suis-B. canis 687223 ctggcggaaaaggatttgat 687162-687181 aatcacgacaaaccacagca 687232-687251 BMEI0664 sugar transport system permease protein 90 T C B. suis biovar 1 656162 tgacatggaccctgttttcc 656196-656215 cagcgtgacactgaacatgg 656138-656157 BMEI0629 hypothetical protein 78 G A B. suis biovar 2 221777 agaccttgcgcttgaacg 221821-221838...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BCAN_A1667 51 MOS Ribose Import ABC BMEI0665 BruAb11337 BR1339 BOV_1299 BCAN_A1367 MOS Ribose Import IM BMEI0664 BruAb11338 BR1340 BOV_1300 BCAN_A1368 MOS Ribose Import BP BMEI0663 BruAb11340 BR1342 BOV_1301 BCAN_A1369 MOS Ribose Import BP BMEI0662 BruAb11335 52 MOS Ribose import BP BMEI1390 BruAb10566, rbsB1 BR0544, rbsB1 BOV_0546...”

MSMEG_6803 ribose transport system permease protein RbsC from Mycobacterium smegmatis str. MC2 155
35% identity, 90% coverage

• Identifying feasible metabolic routes in Mycobacterium smegmatis and possible alterations under diverse nutrient conditions
  Baloni, BMC microbiology 2014
  • “...dihydroxyacetone (MSMEG_2121 to MSMEG_2124) permeases which are expressed. The transporters for fructose such as MSMEG_6802, MSMEG_6803 and MSMEG_6804 seem to be expressed in the reference condition itself. Msm has glucose-6-phosphate isomerase (MSMEG_5541) for its utilization. Fructose is also known to have another mechanism of utilization via...”
• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...Sugar ABC transporter substrate-binding protein Ribose MSMEG_6802 MSMEG_6803 MSMEG_6804 Boldface values indicate a downregulation of 1.5-fold or greater in gene...”

XYLH_SULAC / Q4J711 Xylose/arabinose import permease protein XylH from Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (see paper)
Q4J711 ABC-type D-xylose/L-arabinose transporter (subunit 2/2) (EC 7.5.2.13) from Sulfolobus acidocaldarius (see paper)
Saci_2121 membrane protein from Sulfolobus acidocaldarius DSM 639
31% identity, 84% coverage

• function: Part of the ABC transporter complex XylFGH involved in the uptake of xylose and arabinose (PubMed:29150511). Responsible for the translocation of the substrate across the membrane (Probable).
  subunit: The complex is composed of two ATP-binding proteins (XylG), two transmembrane proteins (XylH) and a solute-binding protein (XylF).
  disruption phenotype: Deletion of the gene results in a growth defect on D-xylose and L-arabinose.
• Identification of XylR, the Activator of Arabinose/Xylose Inducible Regulon in Sulfolobus acidocaldarius and Its Application for Homologous Protein Expression
  van, Frontiers in microbiology 2020
  • “...responsible for pentose uptake in S. acidocaldarius was identified: XylF ( saci_2122 ), XylG ( saci_2121 ), XylH ( saci_2120 ) ( Wagner et al., 2018 ). Also, the pentose metabolizing genes involved in the aldolase independent Weimberg pathway were characterized. The promiscuous glucose dehydrogenase 1...”
• Sulfolobus acidocaldarius Transports Pentoses via a Carbohydrate Uptake Transporter 2 (CUT2)-Type ABC Transporter and Metabolizes Them through the Aldolase-Independent Weimberg Pathway
  Wagner, Applied and environmental microbiology 2018
  • “...was observed for the four genes saci_2122, saci_2121, saci_1938, and saci_1939. Bioinformatic analysis of saci_2121 and saci_2122 using BLASTP 2.3.0 (34)...”
  • “....gov/orffinder/) in the nearby genomic region of saci_2121 and saci_2122 revealed the presence of a gene located downstream of saci_2121. This...”

BPHYT_RS34240 ABC transporter for L-rhamnose/L-fucose/xylitol, permease component from Burkholderia phytofirmans PsJN
31% identity, 79% coverage

• mutant phenotype: Specifically important for utilizing L-rhamnose, L-fucose, and xylitol.

YdeY / b1514 Autoinducer-2 ABC transporter membrane subunit LsrC (EC 7.6.2.13) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
lsrC / P77672 Autoinducer-2 ABC transporter membrane subunit LsrC (EC 7.6.2.13) from Escherichia coli (strain K12) (see 2 papers)
LSRC_ECOLI / P77672 Autoinducer 2 import system permease protein LsrC; AI-2 import system permease protein LsrC from Escherichia coli (strain K12) (see 2 papers)
TC 3.A.1.2.8 / P77672 LsrC(M), component of Autoinducer-2 (AI-2, a furanosyl borate diester: (3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Taga et al., 2001, 2003) from Escherichia coli (see 6 papers)
lsrC / RF|NP_416031.1 autoinducer 2 ABC transporter, permease protein LsrC from Escherichia coli (see paper)
b1514 AI2 transporter from Escherichia coli str. K-12 substr. MG1655
31% identity, 82% coverage

• function: Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. Probably responsible for the translocation of the substrate across the membrane (Probable).
  subunit: The complex is composed of two ATP-binding proteins (LsrA), two transmembrane proteins (LsrC and LsrD) and a solute-binding protein (LsrB).
• substrates: Autoinducer-2
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...fimbria-like protein AI-2 uptake lsrA lsrC lsrD lsrB lsrF lsrG b1513 b1514 b1515 b1516 b1517 b1518 7.0 4.9 5.3 13.9 9.8 7.5 3.0 3.0 3.5 3.2 4.0 3.0 AI-2 uptake...”
• luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling
  Wang, Journal of bacteriology 2005
  • “...b1516 b3829 b1517 b1511 b1520 b2236 b1519 b4308 b1512 b1514 b4395 b3796 b3852 b4017 b2087 b0974 b1127 b1019 b1550 b4196 b0630 b1022 b1437 b4186 b2406 b3939...”
• Regulation of uptake and processing of the quorum-sensing autoinducer AI-2 in Escherichia coli
  Xavier, Journal of bacteriology 2005
  • “...b1516 (lsrB) encodes the periplasmic AI-2 binding protein. b1514 (lsrC) and b1515 (lsrD) encode the channel proteins, and b1513 (lsrA) encodes the ATPase that...”

BC33_RS14600 autoinducer 2 ABC transporter permease LsrC from Escherichia coli ATCC 700728
31% identity, 82% coverage

• Transcriptomic analysis reveal differential gene expressions of Escherichia coli O157:H7 under ultrasonic stress
  Li, Ultrasonics sonochemistry 2021
  • “...lysine/arginine/ornithine transport system substrate-binding protein Quorum sensing BC33_RS14590 lsrB 1.7 AI-2 transport system substrate-binding protein BC33_RS14600 lsrC 1.8 AI-2 transport system permease protein BC33_RS14595 lsrD 1.7 AI-2 transport system permease protein BC33_RS14615 lsrK 1.5 autoinducer-2 kinase BC33_RS14610 lsrR 1.4 lsr operon transcriptional repressor BC33_RS14585 lsrF 1.6...”

S1710 putative transport system permease protein from Shigella flexneri 2a str. 2457T
31% identity, 82% coverage

• Selective Isolation of Bifidobacterium From Human Faeces Using Pangenomics, Metagenomics, and Enzymology
  Yang, Frontiers in microbiology 2021
  • “...1.60 S1708 10040 257 924 120 27.58 2.81 S1709 12317 713 935 96 23.30 3.80 S1710 12932 343 2329 230 53.95 1.22 S1711 10758 264 1151 233 31.79 4.50 S1712 8298 165 496 45 17.90 0.58 S2001 8618 442 894 235 30.65 3.45 S2002 6396141 134...”

PGA1_c07310 Inositol transport system permease protein from Phaeobacter inhibens DSM 17395
31% identity, 84% coverage

• mutant phenotype: Specific phenotype on inositol and cofit with other nearby components

YPTB0799 putative ABC sugar transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
29% identity, 85% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...0.001) YPTB0583 (deoB) YPO0439 phosphopentomutase 1.651 (0.03) YPTB0782 (dhaK) YPO3350 putative dihydroxyacetone kinase 0.683 (0.028) YPTB0799 YPO3332 putative sugar ABC transporter. permease protein 1.787 (0.018) 1.912 (0.01) YPTB0803 (fucR) YPO3327 putative deoR-family regulatory protein 0.435 (< 0.001) 1.521 (0.007) YPTB0804 (araD) YPO3326 L-ribulose-5-phosphate 4-epimerase 0.537 (<...”

YPO3332 putative sugar ABC transporter, permease protein from Yersinia pestis CO92
29% identity, 87% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB0583 (deoB) YPO0439 phosphopentomutase 1.651 (0.03) YPTB0782 (dhaK) YPO3350 putative dihydroxyacetone kinase 0.683 (0.028) YPTB0799 YPO3332 putative sugar ABC transporter. permease protein 1.787 (0.018) 1.912 (0.01) YPTB0803 (fucR) YPO3327 putative deoR-family regulatory protein 0.435 (< 0.001) 1.521 (0.007) YPTB0804 (araD) YPO3326 L-ribulose-5-phosphate 4-epimerase 0.537 (< 0.001)...”

Z0419 putative permease component of transport system, probably ribose specific from Escherichia coli O157:H7 EDL933
29% identity, 89% coverage

• Metabolism of ʟ -arabinose converges with virulence regulation to promote enteric pathogen fitness
  Cottam, 2023

BR1340 sugar ABC transporter, permease protein from Brucella suis 1330
BCAN_A1368 Monosaccharide-transporting ATPase from Brucella canis ATCC 23365
31% identity, 84% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...MOS Ribose Import ABC BMEI0665 BruAb11337 BR1339 BOV_1299 BCAN_A1367 MOS Ribose Import IM BMEI0664 BruAb11338 BR1340 BOV_1300 BCAN_A1368 MOS Ribose Import BP BMEI0663 BruAb11340 BR1342 BOV_1301 BCAN_A1369 MOS Ribose Import BP BMEI0662 BruAb11335 52 MOS Ribose import BP BMEI1390 BruAb10566, rbsB1 BR0544, rbsB1 BOV_0546 rbsB1 BCAN_A0557...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...Import ABC BMEI0665 BruAb11337 BR1339 BOV_1299 BCAN_A1367 MOS Ribose Import IM BMEI0664 BruAb11338 BR1340 BOV_1300 BCAN_A1368 MOS Ribose Import BP BMEI0663 BruAb11340 BR1342 BOV_1301 BCAN_A1369 MOS Ribose Import BP BMEI0662 BruAb11335 52 MOS Ribose import BP BMEI1390 BruAb10566, rbsB1 BR0544, rbsB1 BOV_0546 rbsB1 BCAN_A0557 MOS Ribose...”

SG0965 galactoside ABC transporter permease component from Sodalis glossinidius str. 'morsitans'
32% identity, 92% coverage

• Heme-induced genes facilitate endosymbiont (Sodalis glossinidius) colonization of the tsetse fly (Glossina morsitans) midgut
  Runyen-Janecky, PLoS neglected tropical diseases 2022
  • “...to import or bind to fucose might help Sgm colonize tsetses gut. Additionally, SG0963 - SG0965 , which constitute an operon that encodes a putative galactose ABC transporter, were inducted 2 to 3.7-fold by heme. Galactose present in the blood as a result of human digestion...”

PGA1_262p00440 glucose transporter, permease component from Phaeobacter inhibens DSM 17395
40% identity, 35% coverage

• mutant phenotype: specific phenotype on glucose and cofit with nearby xylF (PGA1_262p00430) and xylG (PGA1_262p00450). This is similar to the gxyB (Atu3575) of Agrobacterium tumefaciens, which is involved in the transport of glucose, glucosamine, and xylose (PMCID: PMC4135649). It is not clear if the Phaeobacter system transports xylose, as it is not required for utilizing xylose, but no other xylose transport system was identified either.

Clocel_2597 ABC transporter permease from Clostridium cellulovorans 743B
33% identity, 90% coverage

• Elucidation of the recognition mechanisms for hemicellulose and pectin in Clostridium cellulovorans using intracellular quantitative proteome analysis
  Aburaya, AMB Express 2015
  • “...4.70 4.53E06 Clocel_2596 Sugar ABC transporter periplasmic protein Ribose transport system substrate-binding protein 4.62 1.06E03 Clocel_2597 Inner-membrane translocator Ribose transport system permease protein 4.01 7.36E05 Clocel_2598 ABC transporter Ribose transport system ATP-binding protein 4.34 1.89E05 Clocel_2881 PTS system lactose/cellobiose-specific transporter subunit IIB PTS system, cellobiose-specific IIB...”

YPTB1327 ABC sugar transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
32% identity, 89% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB1166 (gpmA) YPO1133 phosphoglycerate mutase 1 3.178 (< 0.001) YPTB1290 (bglA) YPO1254 6-phospho-beta-glucosidase 1.802 (0.008) YPTB1327 YPO1295 putative ABC transport integral membrane subunit 1.976 (0.009) YPTB1381 YPO1355 conserved hypothetical protein 0.683 (0.031) YPTB1522 (mglB) YPO1507 galactose-binding protein 0.56 (0.002) 1.47 (0.029) YPTB1581 YPO1572 putative sugar transporteR...”

YPO1295 putative ABC transport integral membrane subunit from Yersinia pestis CO92
32% identity, 89% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(gpmA) YPO1133 phosphoglycerate mutase 1 3.178 (< 0.001) YPTB1290 (bglA) YPO1254 6-phospho-beta-glucosidase 1.802 (0.008) YPTB1327 YPO1295 putative ABC transport integral membrane subunit 1.976 (0.009) YPTB1381 YPO1355 conserved hypothetical protein 0.683 (0.031) YPTB1522 (mglB) YPO1507 galactose-binding protein 0.56 (0.002) 1.47 (0.029) YPTB1581 YPO1572 putative sugar transporteR 0.587...”

BCAM0769 ribose transport system permease protein from Burkholderia cenocepacia J2315
36% identity, 90% coverage

• Comparative transcriptomic analysis of the Burkholderia cepacia tyrosine kinase bceF mutant reveals a role in tolerance to stress, biofilm formation, and virulence
  Ferreira, Applied and environmental microbiology 2013
  • “...BCAL0340 BCAL0341 BCAL0343 BCAL0348 BCAL0350 BCAL0742 BCAL1646 BCAL3099 BCAM0760 BCAM0769 1.2 1.2 1.4 1.3 1.3 1.2 1.4 1.3 1.5 1.3 1.6 1.6 1.7 1.5 1.9 1.5 2.0...”

FRCC_RHIML / Q9F9B1 Fructose import permease protein FrcC from Rhizobium meliloti (Ensifer meliloti) (Sinorhizobium meliloti) (see paper)
TC 3.A.1.2.7 / Q9F9B1 FrcC, component of Fructose/mannose/ribose porter from Rhizobium meliloti (Sinorhizobium meliloti) (see 2 papers)
SMc02170 PUTATIVE PERMEASE ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
30% identity, 84% coverage

• function: Part of the high-affinity ABC transporter complex FrcBCA involved in fructose uptake. Is also a high-affinity transporter for ribose and mannose (PubMed:11466273). Responsible for the translocation of the substrate across the membrane (Probable).
  subunit: The complex is composed of two ATP-binding proteins (FrcA), two transmembrane proteins (FrcC) and a solute-binding protein (FrcB).
  disruption phenotype: Disruption mutant is unable to grow on fructose as sole carbon source, but can still grow with ribose and mannose as sole carbon source.
• substrates: Mannose, Ribose, fructose
• Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis
  Taboada-Castro, Frontiers in bioinformatics 2024
  • “...487; it contains ABC transporter permease SMc02160, glucose-6-phosphate isomerase SMc02163, dihydroorotase SMc02166, ABC transporter permease SMc02170, TF SMc02172, hypothetical gene SMc02174, and TF SMc02175 ( Supplementary Table 5 g, column CO). Moreover, the bacteroid S. meliloti 1021 network contains 54 neighbor groups, and it is the...”
• Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome
  Mauchline, Proceedings of the National Academy of Sciences of the United States of America 2006
  • “...Frc system. Lambert et al. (17) showed that frcC (SMc02170 integral membrane domain) was induced by fructose and mannose. However, in this study both plasmid...”

Entcl_1204 ABC transporter permease from [Enterobacter] lignolyticus SCF1
29% identity, 90% coverage

• Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
  Orellana, PloS one 2017
  • “...of mannose (Entcl_3690, Entcl_3691, Entcl_3692, Entcl_3811 and Entcl_3812), xylose (Entcl_0175 and Entcl_0176) and ribose (Entcl_0174, Entcl_1204, Entcl_1206, Entcl_4081) were down-regulated in early exponential phase. However, after glucose was made unavailable due to concentrations dipping below its half-saturation constant for uptake, they were transcribed in higher abundance....”

SCO6258 sugar ABC transporter permease protein from Streptomyces coelicolor A3(2)
33% identity, 91% coverage

• Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures
  Yagüe, PloS one 2014
  • “...Predicted permease 0.5 1.4 SCO6104 Possible secreted protein 0.7 3.2 SCO2780 Secreted protein 2 0.3 SCO6258 Sugar ABC transporter permease 0.4 1.4 SCO2905 Putative sugar permease 1.5 0.2 SCO6417 Integral membrane transporter 1.5 0.3 SCO3402 Possible secreted protein 1.1 0.1 ( Fig. 4B, E, H, K,...”

H281DRAFT_01115 deoxynucleoside transporter, permease component 1 from Paraburkholderia bryophila 376MFSha3.1
30% identity, 75% coverage

• mutant phenotype: Important for utilization of dAMP and deoxyinosine. Because the fitness profiles for these compounds are very similar, dAMP is likely hydrolyzed before uptake, but this could also be a transporter for deoxynucleotides.

ESA_RS03665 ABC transporter permease from Cronobacter sakazakii ATCC BAA-894
30% identity, 92% coverage

• The Global Response of Cronobacter sakazakii Cells to Amino Acid Deficiency
  Chen, Frontiers in microbiology 2018
  • “...Function BAA-894 MG1655 ESA_RS12970 ykgM 8.13 50S ribosomal protein L31 ESA_RS19300 zinT 7.68 Metal-binding protein ESA_RS03665 rbsC 6.97 ABC transporter permease ESA_RS13555 tauA 6.97 Taurine ABC transporter substrate-binding protein ESA_RS16935 thiE 6.88 Thiamine phosphate synthase ESA_RS02415 cysD 6.83 Sulfate adenylyltransferase subunit 2 ESA_RS13090 amtB 6.79 Ammonium...”

MSMEG_1710 ribose transport system permease protein RbsC from Mycobacterium smegmatis str. MC2 155
33% identity, 74% coverage

• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...1.76E02 D-Xylose Arabinose MSMEG_1707 MSMEG_1708 MSMEG_1709 MSMEG_1710 MSMEG_1711 MSMEG_1712 MSMEG_1713 MSMEG_1714 MSMEG_1715 pho araR araG araF araK araE...”

SCO6980 ABC transporter membrane protein from Streptomyces coelicolor A3(2)
30% identity, 85% coverage

• Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures
  Yagüe, PloS one 2014
  • “...protein 2.3 0.6 SCO6665 Probable secreted glucosidase 0.4 1 SCO3286 Putative secreted protin 3.1 0.5 SCO6980 ABC transporter membrane protein 1.4 0 SCO3366 Exporter 1.8 0.4 SCO7453 Putative secreted protein 3.4 0.6 Average log2 abundance values from three biological replicates of the MII with respect to...”

Cphy_0581 Monosaccharide-transporting ATPase from Clostridium phytofermentans ISDg
30% identity, 95% coverage

• Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans
  Petit, PloS one 2013
  • “...Rhamnose transport Cphy_0580 Rhamnose ABC transport system, ATPase component Rhizobium leguminosarum RhaT (62) 8.1 34.9 Cphy_0581 Rhamnose ABC transport system, permease subunit R. leguminosarum RhaP (57) 9.3 37.6 Cphy_0582 Rhamnose ABC transport system, permease subunit R. leguminosarum RhaQ (57) 10.8 51.5 Cphy_0583 Rhamnose ABC transport system,...”

MSMEG_4657 ABC transporter permease from Mycolicibacterium smegmatis MC2 155
MSMEG_4657 ABC transporter membrane protein from Mycobacterium smegmatis str. MC2 155
29% identity, 89% coverage

• Elucidating the role of c-di-AMP in Mycobacterium smegmatis: Phenotypic characterization and functional analysis
  Chaudhary, Heliyon 2023
  • “...ATP-binding protein 1.21 0.047 8 Plasma membrane MSMEG_0549 ABC transporter, permease protein 1.35 0.040 9 MSMEG_4657 ABC transporter membrane protein 1.11 0.057 10 MSMEG_5060 ABC transporter, permease protein SugA 1.51 0.0361 11 MSMEG_0642 Hypothetical ABC transporter permease protein YliD 1.32 0.044 12 MSMEG_0549 ABC transporter, permease...”
• Azido Inositol Probes Enable Metabolic Labeling of Inositol-Containing Glycans and Reveal an Inositol Importer in Mycobacteria
  Hodges, ACS chemical biology 2023
  • “...the gene encoding the transmembrane subunit of the adjacent ABC transporter. To silence MSMEG_4659 and MSMEG_4657 , plasmids encoding guide RNAs to target these genes were designed according to reported PAM strength guidelines 47 ( Table S3 ) and transformed into Msmeg ino1 and wild-type Msmeg...”
  • “...and subsequent enhanced expression of genes involved in inositol importation and/or utilization. In contrast, when MSMEG_4657 , the gene encoding the transmembrane protein of the MSMEG_46564658 ABC transporter, was silenced in Msmeg ino1 ( Msmegino1(MSMEG_4657()) ), there was a lack of growth on 1 mM inositol...”
• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...protein Unknown sugar MSMEG_4655 MSMEG_4656 MSMEG_4657 MSMEG_4658 MSMEG_4659 MSMEG_4660 MSMEG_4661 MSMEG_4662 MSMEG_4663 MSMEG_4664 MSMEG_4665 MSMEG_4666...”

AOT13_11445 multiple monosaccharide ABC transporter permease from Parageobacillus thermoglucosidasius
40% identity, 34% coverage

• Development of a xylose-inducible and glucose-insensitive expression system for Parageobacillus thermoglucosidasius
  Wang, Applied microbiology and biotechnology 2024
  • “...AOT13_16590 ) and a set of sugar ABC transporter ( AOT13_11435 , AOT13_11440 , and AOT13_11445 ) in P. thermoglucosidasius DSM 2542. We introduced a highly adaptable xylose-inducible expression system, denoted as IExyl*, developed based on the xylA promoter and its associated regulator XylR. IExyl* exhibited...”
  • “...xylA5 p- sfgfp , respectively. To assess the contribution of AOT13_11435 , AOT13_11440 , and AOT13_11445 genes to the uptake of xylose, the knockout plasmid pUB31-transporter- mCherry - sfgfp was constructed. This was achieved by assembly of the vector pUB31 backbone with three segments, including pLdh-...”

pRL110410 putative permease component of ABC transporter involved in competition for nodulation from Rhizobium leguminosarum bv. viciae 3841
29% identity, 79% coverage

• Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis
  Wheatley, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret)

pRL90247 putative permease component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
31% identity, 79% coverage

• Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis
  Wheatley, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret)

FRUF_BIFLO / Q8G846 Fructose import permease protein FruF from Bifidobacterium longum (strain NCC 2705) (see paper)
BL0035 probable ABC transport system permease protein for sugars from Bifidobacterium longum NCC2705
32% identity, 73% coverage

• function: Part of the high-affinity ABC transporter complex FruEKFG involved in fructose uptake. Can also transport ribose and xylose, with lower affinity. Probably responsible for the translocation of the substrate across the membrane.
  subunit: The complex is composed of an ATP-binding protein (FruK), two transmembrane proteins (FruF and FruG) and a solute-binding protein (FruE).
• Fructose uptake in Bifidobacterium longum NCC2705 is mediated by an ATP-binding cassette transporter
  Wei, The Journal of biological chemistry 2012
  • “...generate polyclonal antibodies, purified His-tagged BL0033, BL0034, BL0035, and BL0036 proteins were injected subcutaneously into BALB/c female mice. Sera from...”
  • “...of the identified ABC transporter system (bl0033, bl0034, bl0035, and bl0036), primers were designed (Table 1) to amplify these genes by PCR. The amplified...”
• Proteomics analysis of Bifidobacterium longum NCC2705 growing on glucose, fructose, mannose, xylose, ribose, and galactose
  Liu, Proteomics 2011 (PubMed)
  • “...of these sugars suggesting that BL0033, BL0034, BL0035, and BL0036 constitute an ABC transporter with fructose as preferred substrate. Received: January...”
  • “...the other components of this ABC transporter (BL0034, BL0035, Proteomics 2011, 11, 2628-2638 and BL0036) by 2-D PAGE and MS. These components are...”

B8809_1448 multiple monosaccharide ABC transporter permease from Bifidobacterium longum subsp. longum
37% identity, 38% coverage

• Two extracellular α-arabinofuranosidases are required for cereal-derived arabinoxylan metabolism by Bifidobacterium longum subsp. longum
  Friess, Gut microbes 2024
  • “...gene cluster that is upregulated (consisting of four genes with the locus tags B8809_1436, B8809_1437, B8809_1448 and B8809_1449) is predicted to encode a pentose sugar ABC transporter, which may be responsible for xylose/XOS uptake. Gene-trait matching based on genes identified by transcriptome analysis and AX growth...”

BRA0993 ribose ABC transporter, permease protein from Brucella suis 1330
BOV_A0935 bacterial inner-membrane translocator:Glucose/ribitol dehydrogenase from Brucella ovis ATCC 25840
BCAN_B1012 probable sugar ABC transporter, permease protein from Brucella canis ATCC 23365
32% identity, 84% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...ABC2 BMEII0300, rbsA BruAb20239rbsA4 BRA0995, rbsA4 BOV_A0937 BCAN_B1014 MOS Ribose import IM BMEII0301 rbsC BruAb20240,rbsC5 BRA0993, rbsC5 BCAN_B1013 MOS Ribose import IM BMEII0302 rbsC BruAb20239, rbsC4 BRA0994, rbsC5 BOV_A0935 BCAN_B1012 MOS Ribose import BP BruAb20238 BRA0996, rbsB3 BOV_A0938 BCAN_B1015 56 MOS Monosaccharide import BP BMEII0360, chvE...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...rbsC BruAb20240,rbsC5 BRA0993, rbsC5 BCAN_B1013 MOS Ribose import IM BMEII0302 rbsC BruAb20239, rbsC4 BRA0994, rbsC5 BOV_A0935 BCAN_B1012 MOS Ribose import BP BruAb20238 BRA0996, rbsB3 BOV_A0938 BCAN_B1015 56 MOS Monosaccharide import BP BMEII0360, chvE BruAb20296 BRA0937 BOV_A0879 BCAN_B0957 MOS Monosaccharide import ABC2 BMEII0361 BruAb20297 BRA0936 BOV_A0878 BCAN_B0956...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BruAb20240,rbsC5 BRA0993, rbsC5 BCAN_B1013 MOS Ribose import IM BMEII0302 rbsC BruAb20239, rbsC4 BRA0994, rbsC5 BOV_A0935 BCAN_B1012 MOS Ribose import BP BruAb20238 BRA0996, rbsB3 BOV_A0938 BCAN_B1015 56 MOS Monosaccharide import BP BMEII0360, chvE BruAb20296 BRA0937 BOV_A0879 BCAN_B0957 MOS Monosaccharide import ABC2 BMEII0361 BruAb20297 BRA0936 BOV_A0878 BCAN_B0956 MOS...”

TC 3.A.1.2.22 / Q8G3Q9 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production from Bifidobacterium longum (strain NCC 2705)
37% identity, 38% coverage

• substrates: Sugars

BBMN68_1728 multiple monosaccharide ABC transporter permease from Bifidobacterium longum subsp. longum BBMN68
37% identity, 38% coverage

• Transcriptomic analysis of Bifidobacterium longum subsp. longum BBMN68 in response to oxidative shock
  Zuo, Scientific reports 2018
  • “...protein mglA3 NS 1.10 BBMN68_1727 Putative multiple sugar transport system permease protein xylH 1.75 1.59 BBMN68_1728 MalE-type ABC sugar transport system periplasmic component 2.03 1.98 BBMN68_217 MalF-type ABC sugar transport systems permease component 2.66 1.62 BBMN68_218 MalG-type ABC sugar transport system permease component 1.74 1.49 BBMN68_219...”
  • “...the ABC transporter system and predicted to be a putative transporter for oligofructose 50 ; BBMN68_1728 encoding a putative multiple sugar transport system permease protein and suggested to be involved in the transport of multiple sugars with fructose and mannose moieties 50 ; BBMN68_217219 encoding proteins...”
• Mechanism analysis of acid tolerance response of bifidobacterium longum subsp. longum BBMN 68 by gene expression profile using RNA-sequencing
  Jin, PloS one 2012
  • “...BBMN68_114 CACACCCCGACCGAACACCG GGTGAGGGTTTCGGCCTCGC 165 1.96 BBMN68_1694 GCGAGGACGCCGTCATGGAG CGACCACGGGAGCCGACAAC 175 1.95 BBMN68_270 GTGCTGTACGCCGTGACCCC GGCGACGCAGGCGATGATGA 195 1.95 BBMN68_1728 GAGGTCCTGACCGGAGGCGT GTTGACTCCGGCGCGTTCCA 195 1.93 BBMN68_195 GTGCCGCTCGTTGGCCGTAT TGGCCTCGTCGTCCAGCAGA 235 1.97 BBMN68_1099 GCACATTGCAACGCGACCCC ATGGCCAGCACGGCCACATC 160 1.93 BBMN68_1100 CAAGCAGGCCATCCCCACCG GGCCTTGGCCACTTCCTCGG 166 1.95 BBMN68_933 ACTACGTGCGCCTGTTGGGC GCGCCGTACACGAAACCCCA 226 2.01 BBMN68_1816 GCCGTGCCACCGACATCGAA CGATGCGGGCACGATCGACA 222 1.92 Determination...”
  • “...protein BBMN68_1727 322.43 63.43 5.08 G COG1129 K10548, putative multiple sugar transport system ATP-binding protein BBMN68_1728 294.8 71.37 4.13 * G COG1172 K10547, putative multiple sugar transport system permease protein BBMN68_335 96.32 47.34 2.03 * G COG0395 Sugar permeases BBMN68_919 61.44 26.66 2.30 * R COG1123...”

BMEII0302 RIBOSE TRANSPORT SYSTEM PERMEASE PROTEIN RBSC from Brucella melitensis 16M
32% identity, 84% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BCAN_B1014 MOS Ribose import IM BMEII0301 rbsC BruAb20240,rbsC5 BRA0993, rbsC5 BCAN_B1013 MOS Ribose import IM BMEII0302 rbsC BruAb20239, rbsC4 BRA0994, rbsC5 BOV_A0935 BCAN_B1012 MOS Ribose import BP BruAb20238 BRA0996, rbsB3 BOV_A0938 BCAN_B1015 56 MOS Monosaccharide import BP BMEII0360, chvE BruAb20296 BRA0937 BOV_A0879 BCAN_B0957 MOS Monosaccharide import...”

MSMEG_6018 xylose transport system permease protein XylH from Mycobacterium smegmatis str. MC2 155
42% identity, 31% coverage

• D-Xylose Blocks the Broad Negative Regulation of XylR on Lipid Metabolism and Affects Multiple Physiological Characteristics in Mycobacteria
  Wang, International journal of molecular sciences 2023
  • “...cell wall in the bacterium. MSMEG_6021 (XylA) is a xylose isomerase involved in xylose metabolism; MSMEG_6018 (XylH), MSMEG_6019 (XylF), and MSMEG_6020 (XylE) are associated with the transport of xylose in M. smegmatis . Recently, it was found that D-xylose could act as a signaling molecule and...”
• Elucidating the role of c-di-AMP in Mycobacterium smegmatis: Phenotypic characterization and functional analysis
  Chaudhary, Heliyon 2023
  • “...Cysteine synthase B 1.39 0.04 5 MSMEG_4533 Sulfate-binding protein 1.35 0.044 6 Monosaccharide-transporting ATPase activity MSMEG_6018 Xylose transport system permease 1.39 0.038 7 MSMEG_4656 Sugar ABC transporter ATP-binding protein 1.21 0.047 8 Plasma membrane MSMEG_0549 ABC transporter, permease protein 1.35 0.040 9 MSMEG_4657 ABC transporter membrane...”
• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...permease protein Substrate-binding protein Repressor Xylose MSMEG_6018 MSMEG_6019 MSMEG_6020 MSMEG_6021 MSMEG_6022 xylG1 xylF1 xylE1 xylA1 xylR1 1.60 (1.20)...”
  • “...family whose substrates include xylose (MSMEG_1704 and MSMEG_6018), arabinose (MSMEG_1711 and MSMEG_1712), ribose (MSMEG_3090, -3095, and -3601), sugar alcohol...”
• A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis
  Titgemeyer, Journal of bacteriology 2007
  • “...-xylosides (msmeg_1704 to msmeg_1706, msmeg_5142 to msmeg_5147, and msmeg_6018 to msmeg_6022). Xylose is usually taken up by an ABC permease and further...”
  • “...to enter the pentose-phosphate shunt. The region msmeg_6018 to msmeg_6022 was designated the xylGFEAR1 regulon since it encodes proteins sharing identities...”

MSMEG_6018 sugar ABC transporter permease from Mycolicibacterium smegmatis MC2 155
42% identity, 32% coverage

• Elucidating the role of c-di-AMP in Mycobacterium smegmatis: Phenotypic characterization and functional analysis
  Chaudhary, Heliyon 2023
  • “...Cysteine synthase B 1.39 0.04 5 MSMEG_4533 Sulfate-binding protein 1.35 0.044 6 Monosaccharide-transporting ATPase activity MSMEG_6018 Xylose transport system permease 1.39 0.038 7 MSMEG_4656 Sugar ABC transporter ATP-binding protein 1.21 0.047 8 Plasma membrane MSMEG_0549 ABC transporter, permease protein 1.35 0.040 9 MSMEG_4657 ABC transporter membrane...”

pRL80088 putative permease component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
29% identity, 79% coverage

• Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis
  Wheatley, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret)

RLO149_c021960 multiple monosaccharide ABC transporter permease from Roseobacter litoralis Och 149
26% identity, 75% coverage

• Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis
  Kalhoefer, BMC genomics 2011
  • “...protein regulator) RLO149_c021940 SbpA: multiple sugar-binding periplasmic protein RLO149_c021950 putative multiple sugar transport ATP-binding protein RLO149_c021960 putative multiple sugar transport permease protein RLO149_c021970 AraC: L-arabonate dehydratase (EC 4.2.1.25) RLO149_c021980 Gal: D-galactose 1-dehydrogenase (EC 1.1.1.48) Glycogen R. litoralis was not able to grow with glycogen as a...”

RSP_2367 ABC sugar (ribose) transporter, inner membrane subunit from Rhodobacter sphaeroides 2.4.1
RSP_2367 ABC transporter permease from Cereibacter sphaeroides 2.4.1
28% identity, 95% coverage

• Ribonuclease E strongly impacts bacterial adaptation to different growth conditions
  Börner, RNA biology 2023
  • “...pqqACD) , several proteins involved in metal transport ( sitACD, znuABC, zur ), sugar transport (RSP_2367, 2368), subunits of a TRAP-T transporter (RSP_14181420), and two predicted transcriptional regulators (RSP_2950 and RSP_3448). Under phototrophic conditions cluster 4, 5, and 6 are strongly induced in the wild type....”

BCAN_B0955 Monosaccharide-transporting ATPase from Brucella canis ATCC 23365
39% identity, 37% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...import ABC2 BMEII0361 BruAb20297 BRA0936 BOV_A0878 BCAN_B0956 MOS Monosaccharide import IM BMEII0362 BruAb20298 BRA0935 BOV_A0877 BCAN_B0955 57 MOS Erythritol import ABC2 BMEII0432, rbsA BruAb20371, rbsA3 BRA0860, rbsA3 BOV_A0807, rsbA3 BCAN_B0877 MOS Erythritol import IM BMEII0433, rbsC BruAb20372, rbsC3 BRA0859, rbsC3 BCAN_B0876 MOS Erythritol import BP BMEII0435...”

BAB2_0300 Bacterial inner-membrane translocator from Brucella melitensis biovar Abortus 2308
39% identity, 37% coverage

• Endoribonuclease YbeY Is Linked to Proper Cellular Morphology and Virulence in Brucella abortus
  Budnick, Journal of bacteriology 2018
  • “...BAB2_0278 BAB2_0279 BAB2_0280 BAB2_0281 BAB2_0282 BAB2_0300 BAB2_0519 BAB2_0547 BAB2_0548 BAB2_0583 BAB2_0584 BAB2_0585 BAB2_0593 BAB2_0700 BAB2_0822 BAB2_0827...”

BOV_A0877 sugar ABC transporter, permease protein from Brucella ovis ATCC 25840
39% identity, 38% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...Monosaccharide import ABC2 BMEII0361 BruAb20297 BRA0936 BOV_A0878 BCAN_B0956 MOS Monosaccharide import IM BMEII0362 BruAb20298 BRA0935 BOV_A0877 BCAN_B0955 57 MOS Erythritol import ABC2 BMEII0432, rbsA BruAb20371, rbsA3 BRA0860, rbsA3 BOV_A0807, rsbA3 BCAN_B0877 MOS Erythritol import IM BMEII0433, rbsC BruAb20372, rbsC3 BRA0859, rbsC3 BCAN_B0876 MOS Erythritol import BP...”

BRA0935 sugar ABC transporter, permease protein from Brucella suis 1330
39% identity, 37% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...MOS Monosaccharide import ABC2 BMEII0361 BruAb20297 BRA0936 BOV_A0878 BCAN_B0956 MOS Monosaccharide import IM BMEII0362 BruAb20298 BRA0935 BOV_A0877 BCAN_B0955 57 MOS Erythritol import ABC2 BMEII0432, rbsA BruAb20371, rbsA3 BRA0860, rbsA3 BOV_A0807, rsbA3 BCAN_B0877 MOS Erythritol import IM BMEII0433, rbsC BruAb20372, rbsC3 BRA0859, rbsC3 BCAN_B0876 MOS Erythritol import...”

BMEII0362 XYLOSE TRANSPORT SYSTEM PERMEASE PROTEIN XYLH from Brucella melitensis 16M
39% identity, 37% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BOV_A0879 BCAN_B0957 MOS Monosaccharide import ABC2 BMEII0361 BruAb20297 BRA0936 BOV_A0878 BCAN_B0956 MOS Monosaccharide import IM BMEII0362 BruAb20298 BRA0935 BOV_A0877 BCAN_B0955 57 MOS Erythritol import ABC2 BMEII0432, rbsA BruAb20371, rbsA3 BRA0860, rbsA3 BOV_A0807, rsbA3 BCAN_B0877 MOS Erythritol import IM BMEII0433, rbsC BruAb20372, rbsC3 BRA0859, rbsC3 BCAN_B0876 MOS...”

SCO0810 ABC transporter permease from Streptomyces coelicolor A3(2)
33% identity, 89% coverage

• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...SCO0800 putative TetR-family transcriptional regulatory protein SCO0142 hypothetical protein SCO0802 hypothetical protein SCO0150 hypothetical protein SCO0810 putative ABC transporter permease SCO0201 putative integral membrane protein SCO0830 putative penicillin-binding protein SCO0232 hypothetical protein SCO0839 putative transmembrane transport protein SCO0415 hypothetical protein SCO0840 putative marR-family transcriptional regulator SCO0443...”

Entcl_0166 ABC transporter permease from [Enterobacter] lignolyticus SCF1
31% identity, 74% coverage

• Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
  Orellana, PloS one 2017
  • “...other sugars beside glucose were up-regulated after glucose uptake was stopped ( Fig 2C ) (Entcl_0166, Entcl_0167, Entcl_1205, Entcl_1207, Entcl_3382, Entcl_3383, Entcl_4082, Entcl_4174, and Entcl_4403, S4 Table ). This was presumably a response to the lack of availability of glucose, an effect that has been observed...”

Gocc_1293 sugar ABC transporter permease from Gaiella occulta
44% identity, 34% coverage

• High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria
  Severino, MicrobiologyOpen 2019
  • “...Gocc_2298 to Gocc_2300; Gocc_3068, Gocc_3069 and Gocc_3071), rhamnose (Gocc_0123 to Gocc_0125; Gocc_0231 to Gocc_0234), Dxylose (Gocc_1293 to Gocc_1295), and raffinose/stachyose/melibiose (Gocc_1613 to Gocc_1616) were identified in G. occulta genome. Four unspecific sugar transport systems (Gocc_0123 to Gocc_0125, Gocc_0222 to Gocc_0224, Gocc_2321 to Gocc_2323 and Gocc_3042 to...”

SMa1995 Putative ABC transporter, permease protein from Sinorhizobium meliloti 1021
29% identity, 93% coverage

• The LuxR homolog ExpR, in combination with the Sin quorum sensing system, plays a central role in Sinorhizobium meliloti gene expression
  Hoang, Journal of bacteriology 2004
  • “...SMa1226 (fixT1) SMc02877 SMa1266 SMa0667 SMa1169 SMa1231 SMa1995 SMa1335 SMa1136 SMa0748 SMc01855 SMc04081 (sqdD) SMa0765 (fixN2) SMc01525 (dppA2) SMa1615...”

TP0686 methylgalactoside ABC transporter, permease protein (mglC) from Treponema pallidum subsp. pallidum str. Nichols
31% identity, 56% coverage

• Crystal stuctures of MglB-2 (TP0684), a topologically variant d-glucose-binding protein from Treponema pallidum, reveal a ligand-induced conformational change
  Brautigam, Protein science : a publication of the Protein Society 2018
  • “...namely tp0685 (mglA; the ATP-binding component) and tp0686 (mglC; the permease).15 Materials and Methods Protein purification The procedure for expression and...”
• The Tp0684 (MglB-2) Lipoprotein of Treponema pallidum: A Glucose-Binding Protein with Divergent Topology
  Brautigam, PloS one 2016
  • “...pathogens and commensal bacteria. We also searched for sequence homologues to the gene product of tp0686 , which is the putative permease for the TpMglB-2s cognate transporter. The distribution of homologs was similar to that of TpMglB-2, with close homologs appearing in other treponemes and slightly...”

VK055_1895 ABC transporter permease from Klebsiella pneumoniae subsp. pneumoniae
32% identity, 85% coverage

• A systematic analysis of hypermucoviscosity and capsule reveals distinct and overlapping genes that impact Klebsiella pneumoniae fitness
  Mike, PLoS pathogens 2021
  • “...transporters identified include five sugar transporters ( VK055_0865 , VK055_2628 , VK055_3270 , xylH , VK055_1895 ), a C4-dicarboxylate transporter ( dctA ), two amino acid transporters ( VK055_1956 and VK055_2661 ), a nucleoside transporter ( VK055_4768 ), and an osmoprotectant transporter ( VK055_4957 ) [...”

LSRD_SALTY / Q8ZKQ2 Autoinducer 2 import system permease protein LsrD; AI-2 import system permease protein LsrD from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
SC3965 putative ABC superfamily (membrane), sugar transport protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
25% identity, 90% coverage

• function: Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. Probably responsible for the translocation of the substrate across the membrane (Probable).
  subunit: The complex is composed of two ATP-binding proteins (LsrA), two transmembrane proteins (LsrC and LsrD) and a solute-binding protein (LsrB).
• Identification and characterization of the ilvR gene encoding a LysR-type regulator of Caulobacter crescentus
  Malakooti, Journal of bacteriology 1994
  • “...SC3428 SC3429 SC3430 SC3431 SC3844 SC3950 SC3951 SC3964 SC3965 SC3966 SC3967 E. coli XLI-Blue Relevant genotype or characteristic THE C. CRESCENTUS ilvR GENE, A...”
  • “...18, 2017 by University of California, Berkeley A Strain Cro6ss CB15 . iX SC3965 2 X3 S R R S R R S R R - p ,~~~~~~~~~~~~~~~~~~~~~~. .. W2e ~- _ ilv D p I cat...”

RSP_3501 ABC sugar transporter, inner membrane subunit from Rhodobacter sphaeroides 2.4.1
31% identity, 86% coverage

• A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions
  Billenkamp, Journal of bacteriology 2015
  • “...transcriptional regulator 0.15 0.11 RSP_3503, 1 RSP_3502, 2 RSP_3501, 3 0.06 0.12 0.02 RSP_3949 (ansB) 22.4 RSP_1576 (trxB) 22 19.59 1 Thioredoxin reductase...”

STM4076 putative ABC superfamily (membrane), sugar transport protein from Salmonella typhimurium LT2
25% identity, 89% coverage

• FabR regulates Salmonella biofilm formation via its direct target FabB
  Hermans, BMC genomics 2016
  • “...solute-binding component 2.13 12 STM4071 Hypothetical protein 2.02 13 STM4072 ydeV/lsrK Sugar kinase 1.87 17 STM4076 ydeZ/lsrD ABC transporter, membrane component 1.75 21 STM4074 ego/lsrA ABC transporter ATP-binding protein 1.66 23 STM4075 ydeY/lsrC ABC transporter permease protein 1.64 4 STM4184 aceA Isocitrate lyase 2.50 Glyoxylate metabolism...”

SPOA0257 ABC transporter permease from Ruegeria pomeroyi DSS-3
30% identity, 84% coverage

• Diel investments in metabolite production and consumption in a model microbial system
  Uchimiya, The ISME journal 2022
  • “...47 ] SPOA0254 rbsC-1 ABC transporter, permease 54.9 SPOA0256 ABC transporter, periplasmic substrate-binding protein 21.4 SPOA0257 rbsC-2 ABC transporter, permease 50.4 SPOA0258 rbsA ABC transporter, ATP-binding 55.7 Sugar Glucose SPO0861 xylF ABC transporter, periplasmic substrate-binding 2.7 (n.s.) [ 47 ] SPO0862 xylH ABC transporter, permease 6.2...”

MglC / b2148 D-galactose/methyl-galactoside ABC transporter membrane subunit from Escherichia coli K-12 substr. MG1655 (see 4 papers)
MglC / P23200 D-galactose/methyl-galactoside ABC transporter membrane subunit from Escherichia coli (strain K12) (see paper)
MGLC_ECOLI / P23200 Galactose/methyl galactoside import permease protein MglC from Escherichia coli (strain K12) (see paper)
TC 3.A.1.2.3 / P23200 MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter from Escherichia coli (see 4 papers)
b2148 beta-methylgalactoside transporter inner membrane component from Escherichia coli str. K-12 substr. MG1655
33% identity, 92% coverage

• function: Part of the ABC transporter complex MglABC involved in galactose/methyl galactoside import. Probably responsible for the translocation of the substrate across the membrane.
  subunit: The complex is composed of one ATP-binding protein (MglA), two transmembrane proteins (MglC) and a solute-binding protein (MglB).
• substrates: Galactose, glucose
• Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms
  Wang, The ISME journal 2009
  • “...aceB b4014 1.5 Malate synthetase A mglA b2149 1.6 Alactoside transport and galactose taxis mglC b2148 1.7 Alactoside transport and galactose taxis gltA b0720 2.1 Citrate synthetase fumA b1612 1.6 Fumarate hydratase class I fumC b1611 1.7 SoxRS regulon, fumarate hydratase class II acs b4069 1.7...”
• Furfural inhibits growth by limiting sulfur assimilation in ethanologenic Escherichia coli strain LY180
  Miller, Applied and environmental microbiology 2009
  • “...b0368 b0598 b1188 b1375 b1544 b1649 b1650 b1783 b1987 b2148 b2149 b2150 b3011 b3012 b3917 b4116 b4227 b4354 b4485 tauA* tauB* tauC tauD cstA ycgB ynaE* ydfK*...”
• Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
  Stepanova, Journal of bacteriology 2007
  • “...class I; aerobic isozyme mglC mglA mglB IG galS glpQ b2148 b2149 b2150 3.0 3.2 4.1 5.0 1.5 2.2 2.6 2.8 4.6 4.3 1.9 3.2 Methyl-galactoside transport and...”
• Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12
  White-Ziegler, Journal of bacteriology 2007
  • “...b2150 Galactose transport protein (ABC superfamily, peri_bind) b2148 Methyl-galactoside transport and galactose taxis b0679 PTS family enzyme IIC (N terminal);...”
• Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression
  Soupene, Journal of bacteriology 2003
  • “...galactose transporter; the mglBAC operon (b2150 to b2148), which codes for a high-affinity transporter for -methylgalactosides; galS (b2151), the regulator of...”
  • “...1.5 1.4 b2151 galS 1.3 3.3 b2943 galP 2.8 3.9 b2150 b2149 b2148 mglB mglA mglC 3.6 2.6 0.8 13 7.3 4.9 b4120 b4119 b4118 melB melA melR 1.0 1.3 1.1 2.3 4.5 1.1...”
• DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
  Polen, Applied and environmental microbiology 2003
  • “...oxidoreductase Putative oxidoreductase 0.27 0.47* 0.69* 0.87 0.67 b2148 b2149 b2150 mgIC mgIA mgIB 1 1 1 Methyl-galactoside transport and galactose taxis...”
• Biodistribution of ⁸⁹Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
  Li, Poultry science 2023
  • “...Cell inner membrane 536 P0AFK4 POTB Amino acid transport and metabolism Cell inner membrane 537 P23200 MGLC Carbohydrate transport and metabolism Cell inner membrane 538 P30844 BASS Signal transduction mechanisms Cell inner membrane 539 P31064 YEDE General function prediction only Cell inner membrane 540 P31119 AAS...”
• Comparative genomics of the transportome of Ten Treponema species.
  Buyuktimkin, Microbial pathogenesis 2019
  • “...2.A.25.1.9 W0WFC6 Uptake of amino acids Galactose/glucose (methyl galactoside) porter (3 components) 3.A.1.2.3 P0AAG8, P0AEE5, P23200 Transport of glucose and galactose Purine nucleoside permease (PnrABCDE) (5 components) 3.A.1.2.10 083340-43, P29724 Uptake of nucleosides; assists in replication Manganese (Mn2+), zinc (Zn2+) and possibly iron (Fe2+) uptake porter:...”

SC2205 ABC superfamily (membrane), methyl-galactoside transport protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
33% identity, 92% coverage

• Use of pulsed field gel electrophoresis and transposon mutagenesis to estimate the minimal number of genes required for motility in Caulobacter crescentus
  Ely, Genetics 1989
  • “..., (flu-662) flbK 3900 320 D 1100 A 600 S SC2205 (flbK640),SC2207 (flbK641) flaYG cluster flbM 48 motA a Abbreviations: D, DtuI; A, ASE AseI; S, SpeI. Flagellar...”

FRUG_BIFLO / Q8G845 Fructose import permease protein FruG from Bifidobacterium longum (strain NCC 2705) (see paper)
BL0036 probable ABC transporter permease protein for sugars from Bifidobacterium longum NCC2705
34% identity, 76% coverage

• function: Part of the high-affinity ABC transporter complex FruEKFG involved in fructose uptake. Can also transport ribose and xylose, with lower affinity. Probably responsible for the translocation of the substrate across the membrane.
  subunit: The complex is composed of an ATP-binding protein (FruK), two transmembrane proteins (FruF and FruG) and a solute-binding protein (FruE).
• Fructose uptake in Bifidobacterium longum NCC2705 is mediated by an ATP-binding cassette transporter
  Wei, The Journal of biological chemistry 2012
  • “...antibodies, purified His-tagged BL0033, BL0034, BL0035, and BL0036 proteins were injected subcutaneously into BALB/c female mice. Sera from the immunized mice...”
  • “...identified ABC transporter system (bl0033, bl0034, bl0035, and bl0036), primers were designed (Table 1) to amplify these genes by PCR. The amplified PCR...”
• Proteomics analysis of Bifidobacterium longum NCC2705 growing on glucose, fructose, mannose, xylose, ribose, and galactose
  Liu, Proteomics 2011 (PubMed)
  • “...these sugars suggesting that BL0033, BL0034, BL0035, and BL0036 constitute an ABC transporter with fructose as preferred substrate. Received: January 21, 2011...”
  • “...transporter (BL0034, BL0035, Proteomics 2011, 11, 2628-2638 and BL0036) by 2-D PAGE and MS. These components are membrane-associated components of the ABC...”

Z3403 beta-methylgalactoside transporter inner membrane component from Escherichia coli O157:H7 EDL933
33% identity, 92% coverage

• Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
  Segura, BMC genomics 2018
  • “...mglB Methyl-galactoside transport system (substrate-binding protein) 3.75 1.06E-06 4.77 4.85E-10 2.76 6.21E-04 4.09 1.00E-07 NDE Z3403 mglC Methyl-galactoside transport system (permease protein) 3.02 4.18E-05 3.33 7.49E-06 3.06 4.16E-05 2.85 1.52E-04 NDE Z0824 nagA N-acetylglucosamine 6-phosphate deacetylase 2.37 7.39E-06 2.95 2.19E-08 NDE NDE NDE Z0825 nagB Glucosamine...”

MGLC_SALTY / Q56036 Galactose/methyl galactoside import permease protein MglC from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
33% identity, 92% coverage

• function: Part of the ABC transporter complex MglABC involved in galactose/methyl galactoside import. Probably responsible for the translocation of the substrate across the membrane.
  subunit: The complex is composed of one ATP-binding protein (MglA), two transmembrane proteins (MglC) and a solute-binding protein (MglB).

EDL933_3310, EDL933_RS16220 galactose/methyl galactoside ABC transporter permease MglC from Escherichia coli O157:H7 str. EDL933
33% identity, 92% coverage

• Genomic Island-Encoded Histidine Kinase and Response Regulator Coordinate Mannose Utilization with Virulence in Enterohemorrhagic Escherichia coli
  Yang, mBio 2023
  • “...PutP EDL933_RS12005 EDL933_2451 2293529 2294854 2293532 1.23 2.7 Type III secretion system effector NleA EDL933_RS16220 EDL933_3310 3061066 3060056 3061296 1.27 2.6 Galactose/methyl galactoside ABC transporter permease MglC EDL933_RS19525 EDL933_3982 3744261 3745577 3744540 1.8 2.04 l -Fucose:H + symporter permease EDL933_RS24320 EDL933_4948 4686886 4684082 4686880 1.64 3.2...”
  • “...symporter PutP EDL933_RS12005 EDL933_2451 2293529 2294854 2293532 1.23 2.7 Type III secretion system effector NleA EDL933_RS16220 EDL933_3310 3061066 3060056 3061296 1.27 2.6 Galactose/methyl galactoside ABC transporter permease MglC EDL933_RS19525 EDL933_3982 3744261 3745577 3744540 1.8 2.04 l -Fucose:H + symporter permease EDL933_RS24320 EDL933_4948 4686886 4684082 4686880 1.64...”

VK055_4937 galactose/methyl galactoside ABC transporter permease MglC from Klebsiella pneumoniae subsp. pneumoniae
32% identity, 92% coverage

• A novel esterase regulates Klebsiella pneumoniae hypermucoviscosity and virulence
  Wang, PLoS pathogens 2024
  • “...to overexpress either the VK055_3347 locus or VK055_4943. Unfortunately, the construction of a plasmid overexpressing VK055_4937 ( mglA ), another top-upregulated gene, failed several times for unknown reasons, so its impact on mucoviscosity could not be further studied. Our current study thus focuses on investigating the...”

SPO0862 sugar ABC transporter permease from Ruegeria pomeroyi DSS-3
38% identity, 37% coverage

• Diel investments in metabolite production and consumption in a model microbial system
  Uchimiya, The ISME journal 2022
  • “...ATP-binding 55.7 Sugar Glucose SPO0861 xylF ABC transporter, periplasmic substrate-binding 2.7 (n.s.) [ 47 ] SPO0862 xylH ABC transporter, permease 6.2 SPO0863 xylG ABC transporter, ATP-binding 4.2 Sulfur compound Choline-O-sulfate SPO1083 betC Choline sulfatase 15.1 [ 75 ] Sulfur compound Cysteate SPO2658 ABC transporter, periplasmic substrate-binding...”
• Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium
  Chan, Frontiers in microbiology 2012
  • “...( glnB-2 ) 124.3 39.1 SPOA0300 Branched-chain amino acid ABC transporter, periplasmic binding protein 6.6 SPO0862 Xylose ABC transporter, permease protein ( xylH ) 0.3 0.3 SPO1079 Lysine exporter, putative 0.1 2.0 SPO1743 Glutamate dehydrogenase 0.2 0.2 SPO3156 l -threonine aldolase, low-specificity, putative 1.3 0.3 SPO3712...”
  • “...(34 GENES) SPO0227 PaxA, putative 0.3 0.2 SPO0406 rpoH-2 RNA polymerase factor sigma-32 0.6 0.3 SPO0862 xylH Xylose ABC transporter, permease protein 0.3 0.3 SPO1060 Hypothetical protein 0.1 SPO1079 Lysine exporter, putative 0.1 2.0 SPO1308 Hypothetical protein 0.3 SPO1336 ispZ Intracellular septation protein A 0.6 0.3...”

ESA_RS04990 galactose/methyl galactoside ABC transporter permease MglC from Cronobacter sakazakii ATCC BAA-894
33% identity, 92% coverage

• The Global Response of Cronobacter sakazakii Cells to Amino Acid Deficiency
  Chen, Frontiers in microbiology 2018
  • “...L -serine ammonia-lyase ESA_RS17695 lldP -5.55 L -lactate permease ESA_RS04410 glpQ -5.83 Glycerophosphoryl diester phosphodiesterase ESA_RS04990 mglC -5.98 Galactoside ABC transporter permease ESA_RS04980 mglB -5.99 Galactose ABC transporter substrate-binding protein ESA_RS04985 mglA -6.05 Galactose/methyl galactoside ABC transporter ATP-binding protein ESA_RS04405 uhpC -6.65 MFS transporter ESA_RS17675 glpK...”

ECs5207 putative transport system permease protein from Escherichia coli O157:H7 str. Sakai
38% identity, 67% coverage

• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...ytfQ 6.29 2 ECs4990 O157 2.13 2 ECs5206 - 2.57 3 ECs4991 O157 2.12 2 ECs5207 ytfT 3.32 2 ECs5007 lysC -3.43 1 ECs5208 yjfF 2.59 2 ECs5038 pfkA 2.14 2 ECs5211 yjgA 2.20 2 ECs5039 yjbR 2.21 2 ECs5213 cybC 2.20 2 ECs5049 actP 4.17...”

YPK_2564 monosaccharide-transporting ATPase from Yersinia pseudotuberculosis YPIII
33% identity, 90% coverage

• Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
  Mahmud, mSystems 2020
  • “...9.25 54,24,32 YPK_2519 YPK_2517, YPK_2518 69, 120 IrGS24 2815385 3.0 NA NA ACGGTATAATTATTGCGT 10 28,54,70 YPK_2564 NA 1, 70 IrGS25 2870433 3.2 NA NA ATGGTATAAAAATTGCGC 9.85 NA YPK_2615 NA NA IrGS26 2978162 15.7 8.2 7.7 TTGGCACGATTGATGCTC 10.9 70,28,38,54 YPK_2696 YPK_2695 26, 53, 86 IrGS27 3075166 4.1...”

YtfT / b4230 galactofuranose ABC transporter putative membrane subunit YtfT (EC 7.5.2.9) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
YtfT / P39328 galactofuranose ABC transporter putative membrane subunit YtfT (EC 7.5.2.9) from Escherichia coli (strain K12) (see 2 papers)
YTFT_ECOLI / P39328 Galactofuranose transporter permease protein YtfT from Escherichia coli (strain K12) (see paper)
b4230 predicted sugar transporter subunit: membrane component of ABC superfamily from Escherichia coli str. K-12 substr. MG1655
38% identity, 67% coverage

• function: Part of the ABC transporter complex YtfQRT-YjfF involved in galactofuranose transport (Probable). Probably responsible for the translocation of the substrate across the membrane (Probable).
  subunit: The complex is composed of two ATP-binding proteins (YtfR), two transmembrane proteins (YtfT and YjfF) and a solute-binding protein (YtfQ).
• Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements
  Ge, Journal of biosciences 2011
  • “...1552733 3.14 maeA b1478 12 3103916 3104517 1.83 nupG b2964 12 4449949 4450142 3.14 ytfR b4230 13 48080 48753 1.77 kefC b0047 13 94377 94642 3.08 murE b0086 14 500178 500563 1.77 gsk b0477 14 2443970 2444451 3.08 mepA b2328 15 2052323 2052876 1.77 amn b1982...”
• In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements
  Maciag, Nucleic acids research 2011
  • “...treF Trehalase b3519 1.53 S ( 9 , 19 ) ytfT Putative galactose ABC transporter b4230 1.55 S ( 19 ) otsB Trehalose-6-phosphate phosphatise b1897 1.56 S ( 7 ) araF Arabinose transporter, component of an ABC transport system b1901 1.57 CRP, AraC ( 69 );...”

blr7869 ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
32% identity, 43% coverage

• Transcriptomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules
  Franck, International journal of molecular sciences 2018
  • “...DAP include the regulatory proteins blr2424, blr5109, and blr0155, the ABC permease proteins blr5304 and blr7869, the potassium uptake protein blr3802, the small heat shock protein blr5220, and the metabolic proteins, including the phospholipid N-methytransferase blr0681, the acetyl CoA synthase blr3924, the indolepyruvate ferredoxin oxidoreductase, alpha...”

YdeZ / b1515 Autoinducer-2 ABC transporter membrane subunit LsrD (EC 7.6.2.13) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
lsrD / P0AFS1 Autoinducer-2 ABC transporter membrane subunit LsrD (EC 7.6.2.13) from Escherichia coli (strain K12) (see 2 papers)
LSRD_ECOLI / P0AFS1 Autoinducer 2 import system permease protein LsrD; AI-2 import system permease protein LsrD from Escherichia coli (strain K12) (see 2 papers)
TC 3.A.1.2.8 / P0AFS1 LsrD(M)AKA Inner membrane ABC transporter permease protein ydeZ, component of Autoinducer-2 (AI-2, a furanosyl borate diester: (3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Taga et al., 2001, 2003) from Escherichia coli (see 6 papers)
lsrD autoinducer 2 ABC transporter, permease protein LsrD from Escherichia coli K12 (see paper)
b1515 AI2 transporter from Escherichia coli str. K-12 substr. MG1655
S1711 putative transport system permease protein from Shigella flexneri 2a str. 2457T
27% identity, 89% coverage

• function: Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. Probably responsible for the translocation of the substrate across the membrane (Probable).
  subunit: The complex is composed of two ATP-binding proteins (LsrA), two transmembrane proteins (LsrC and LsrD) and a solute-binding protein (LsrB).
• substrates: Autoinducer-2
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...protein AI-2 uptake lsrA lsrC lsrD lsrB lsrF lsrG b1513 b1514 b1515 b1516 b1517 b1518 7.0 4.9 5.3 13.9 9.8 7.5 3.0 3.0 3.5 3.2 4.0 3.0 AI-2 uptake AI-2 uptake...”
• luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling
  Wang, Journal of bacteriology 2005
  • “...LB Gene Gene product a Fold change (WT/luxS) b1518 b1515 b1513 b1516 b3829 b1517 b1511 b1520 b2236 b1519 b4308 b1512 b1514 b4395 b3796 b3852 b4017 b2087 b0974...”
• Regulation of uptake and processing of the quorum-sensing autoinducer AI-2 in Escherichia coli
  Xavier, Journal of bacteriology 2005
  • “...the periplasmic AI-2 binding protein. b1514 (lsrC) and b1515 (lsrD) encode the channel proteins, and b1513 (lsrA) encodes the ATPase that provides energy for...”
• Selective Isolation of Bifidobacterium From Human Faeces Using Pangenomics, Metagenomics, and Enzymology
  Yang, Frontiers in microbiology 2021
  • “...2.81 S1709 12317 713 935 96 23.30 3.80 S1710 12932 343 2329 230 53.95 1.22 S1711 10758 264 1151 233 31.79 4.50 S1712 8298 165 496 45 17.90 0.58 S2001 8618 442 894 235 30.65 3.45 S2002 6396141 134 71 6.08 3.08 S2003 6352 276 186...”
• Monday: Poster Sessions, Pt.I
  , Molecular biology of the cell 1994

YPTB0550 ABC sugar transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
25% identity, 89% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(0.001) YPTB0542 YPO0402 PTS system. IIB component 0.565 (0.023) YPTB0548 YPO0408 putative aldolase 1.968 (0.021) YPTB0550 YPO0410 putative ABC transporter permease protein 0.573 (0.033) YPTB0569 YPO0424 putative pectinesterase 0.268 (< 0.001) YPTB0583 (deoB) YPO0439 phosphopentomutase 1.651 (0.03) YPTB0782 (dhaK) YPO3350 putative dihydroxyacetone kinase 0.683 (0.028) YPTB0799...”

SMb20903 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
37% identity, 38% coverage

• Transcriptome analysis of the role of GlnD/GlnBK in nitrogen stress adaptation by Sinorhizobium meliloti Rm1021
  Yurgel, PloS one 2013
  • “...because of the difference in carbon sources used for cell growth. However, sugar transporters SMb20902, SMb20903, SMc02514 and a lipoic acid related gene, lpdA2 (2-oxoglutarate dehydrogenase E3 component), were differentially expressed in both studies. Glutamine synthetase II (glnII) was upregulated under nitrogen limitation, which was consistent...”
• Resistance to organic hydroperoxides requires ohr and ohrR genes in Sinorhizobium meliloti
  Fontenelle, BMC microbiology 2011
  • “...bands were observed in the presence of OhrR (Figure 3B ). The intergenic region between SMb20903 and SMb20964 (this latter gene encoding the putative AhpC protein of S. meliloti ) was used as a negative control. No specific binding of OhrR protein to this DNA fragment...”

Atu3575 ABC transporter, membrane spanning protein (xylose) from Agrobacterium tumefaciens str. C58 (Cereon)
37% identity, 43% coverage

• GxySBA ABC transporter of Agrobacterium tumefaciens and its role in sugar utilization and vir gene expression
  Zhao, Journal of bacteriology 2014
  • “...encoded by the downstream gene loci Atu3574 and Atu3575 are predicted to be an ATP-binding protein and a transmembrane protein, respectively (Fig. 1). Together,...”
  • “...xylose utilization and therefore gene loci Atu3576, Atu3575, and Atu3574 were renamed gxyS, gxyB, and gxyA, respectively, for glucose/xylose transport. Directly...”
• Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic conditions (pH 5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions
  Yuan, Journal of bacteriology 2008
  • “...Berkeley Transporter genes Atu1577 Atu1717 Atu2744 Atu3253 Atu3575 Atu3821 Atu4667 Atu4687 Atu5268 Designation 502 YUAN ET AL. ribonucleotide reduction were...”
  • “...acids, and fatty acids (Atu1577, Atu1717, Atu2744, Atu3253, Atu3575, Atu3821, Atu4667, Atu4768, and Atu5268) (Table 3). The reduced uptake of multidrugs might...”

YPO0410 putative ABC transporter permease protein from Yersinia pestis CO92
25% identity, 89% coverage

• The cyclic AMP receptor protein, CRP, is required for both virulence and expression of the minimal CRP regulon in Yersinia pestis biovar microtus
  Zhan, Infection and immunity 2008
  • “...AATGTATGATCGAGATC ACTTTT AAAACGTGATCTAGATT GAACTT YPO0409 1 2.14 MD YPO0410 1 g YPO0411 1 3.27 7.43 A AAATTGTGATCTTGGTT ACGCCA D/118/8.76 YPO0412 1 sdaC 4.84...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB0542 YPO0402 PTS system. IIB component 0.565 (0.023) YPTB0548 YPO0408 putative aldolase 1.968 (0.021) YPTB0550 YPO0410 putative ABC transporter permease protein 0.573 (0.033) YPTB0569 YPO0424 putative pectinesterase 0.268 (< 0.001) YPTB0583 (deoB) YPO0439 phosphopentomutase 1.651 (0.03) YPTB0782 (dhaK) YPO3350 putative dihydroxyacetone kinase 0.683 (0.028) YPTB0799 YPO3332...”

NCgl0030 ABC transporter permease from Corynebacterium glutamicum ATCC 13032
cg0045 ABC transporter membrane protein from Corynebacterium glutamicum ATCC 13032
31% identity, 69% coverage

• Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function
  Selengut, BMC bioinformatics 2010
  • “...a BLAST query succeeds in recovering the pattern of urea utilizing species. One of these, NCgl0030 (GenBank: BAB97424 ], is shown as a triangle plot at exaggerated scale in Figure 3C and as a direct comparison of the size-30 subsequences in Figure 3D . Figure 3...”
  • “...C. glutamicum UrtC protein (NCgl0895). C) A heat map for the non-urea transporting C. glutamicum NCgl0030 permease at exaggerated scale illustrating negligible response. D) SIMBAL score plot of UrtB (blue) and NCgl0030 (green) at a window size of 30 amino acids. Although no crystal structures have...”
• Ciprofloxacin triggered glutamate production by Corynebacterium glutamicum
  Lubitz, BMC microbiology 2016
  • “...0.000 cg2080 - Conserved hypothetical protein -1.74 0.012 cg2952 - Putative secreted protein -1.58 0.002 cg0045 - ABC-type putative sugar transporter, permease subunit -1.36 0.025 cg1884 - Putative membrane protein -1.30 0.038 cg1340 - Conserved hypothetical protein -1.27 0.001 cg3226 - Putative MFS-type L-lactate permease -1.15...”
• Adaptive evolution and metabolic engineering of a cellobiose- and xylose- negative Corynebacterium glutamicum that co-utilizes cellobiose and xylose
  Lee, Microbial cell factories 2016
  • “...Gene name Type Reference nucleotide Allele nucleotide Coding region change Amino acid change Annotation 32227 cg0045 MISSENSE A T 551A>T Asn184Ile Probable ABC transport protein, membrane component 364912 cg0414 MISSENSE A C 1089A>C Glu363Asp Wzz, cell surface polysaccharide biosynthesis/chain length determinant protein 1689677 cg1796 MISSENSE C...”
• IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria
  Baumgart, BMC biology 2013
  • “...cg3323 ino1 Myo -inositol phosphate synthase 0.047 cg0044 rbsB ABC transporter/periplasmic d -ribose-binding protein 0.082 cg0045 - Probable ABC transport protein, membrane component 0.138 cg2910 - Transcriptional regulator, LacI family 0.173 cg3195 - Flavin-containing monooxygenase 0.178 cg0046 - Probable ABC transport protein, ATP-binding component 0.323 cg3210...”
• Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate
  Kato, BMC microbiology 2010
  • “...CgXII DL-lactate and CgXII L-lactate respectively. Gene a Annotation a mRNA level b LB CgXII cg0045 ABC-type transporter, permease component 0,1 n.d. cg0594 ribosomal protein L3 1,3 0,2 cg0598 ribosomal protein L2 1,7 0,2 cg0652 ribosomal protein S13 0,9 0,2 cg0653 ribosomal protein S11 1,6 0,2...”
• The Zur regulon of Corynebacterium glutamicum ATCC 13032
  Schröder, BMC genomics 2010
  • “...lacking candidate Zur-binding sites. CDS Gene Predicted function Differential gene expression 1 Array RT-PCR 2 cg0045 - ABC-type transporter, permease subunit - 1.12 n.s. cg0215 cspA cold-shock protein A 1.24 n.s. cg0793 - putative secreted protein 1.67 4.01 cg0796 prpD1 citrate dehydratase 1 6.68 cg1109 porB...”

ECs2122 putative transport system permease protein from Escherichia coli O157:H7 str. Sakai
BC33_RS14595 autoinducer 2 ABC transporter permease LsrD from Escherichia coli ATCC 700728
26% identity, 87% coverage

• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...ybbV 3.27 2 ECs0733 phrB 2.15 2 ECs2095 yddV 4.27 2 ECs0769 cydB -2.03 4 ECs2122 ydeZ 4.88 2 ECs0957 poxB 2.47 2 ECs2123 yneA 5.14 2 ECs0973 trxB -2.25 1 ECs2124 yneB 4.46 2 ECs1155 cbpA 2.26 2 ECs2705 yedU 4.54 2 ECs1236 lomW 2.21...”
• Transcriptomic analysis reveal differential gene expressions of Escherichia coli O157:H7 under ultrasonic stress
  Li, Ultrasonics sonochemistry 2021
  • “...lsrB 1.7 AI-2 transport system substrate-binding protein BC33_RS14600 lsrC 1.8 AI-2 transport system permease protein BC33_RS14595 lsrD 1.7 AI-2 transport system permease protein BC33_RS14615 lsrK 1.5 autoinducer-2 kinase BC33_RS14610 lsrR 1.4 lsr operon transcriptional repressor BC33_RS14585 lsrF 1.6 hydroxy-5-phosphonooxypentane-2,4-dione thiolase Transcription and translation BC33_RS02870 rpoA 2.1...”

TC 3.A.1.2.5 / O05177 GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter from Agrobacterium radiobacter (see paper)
Atu2346 ABC transporter, membrane spanning protein (sugar) from Agrobacterium tumefaciens str. C58 (Cereon)
33% identity, 41% coverage

• substrates: Arabinose, Fucose, Galactose, Xylose, glucose
• Discrete Responses to Limitation for Iron and Manganese in Agrobacterium tumefaciens: Influence on Attachment and Biofilm Formation
  Heindl, Journal of bacteriology 2015
  • “...(Atu4606), and sugar transporter subunits (Atu2345 and Atu2346). Genes coding for the transcriptional regulator SinR and the diguanylate cyclase homologue DgcC...”

WP_024839148 sugar ABC transporter permease from Cellulosimicrobium composti
39% identity, 32% coverage

• Biosynthesis of akaeolide and lorneic acids and annotation of type I polyketide synthase gene clusters in the genome of Streptomyces sp. NPS554
  Zhou, Marine drugs 2015
  • “...C. cellulans , WP_024839149 79/86 248 418 ABC transporter ABC transporter permease, C. cellulans , WP_024839148 74/82 249 138 unknown hypothetical protein AOR_1_82014, Aspergillus oryzae , XP_003189833 50/60 250 c 185 unknown hypothetical protein, Streptomyces sp. CNQ766, WP_018834862 24/43 251 c 158 unknown hypothetical protein, Jiangella...”

MSMEG_1706 xylose transport system permease protein XylH from Mycobacterium smegmatis str. MC2 155
34% identity, 47% coverage

• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...result of sequencing error Xylose MSMEG_1704 MSMEG_1705 MSMEG_1706 xylF2 xylG2 xylH2 1.63 1.47 1.41 2.66E02 2.52E02 1.76E02 D-Xylose Arabinose MSMEG_1707...”
• A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis
  Titgemeyer, Journal of bacteriology 2007
  • “...(Table 1). (iv) Xylose and -xylosides (msmeg_1704 to msmeg_1706, msmeg_5142 to msmeg_5147, and msmeg_6018 to msmeg_6022). Xylose is usually taken up by an ABC...”
  • “...a xylose ABC transporter is encoded by msmeg_1704 to msmeg_1706 (xylFGH2). XylF2, XylG2, and XylH2 share 38% to 48% identity to the corresponding E. coli...”

BCAN_B1013 permease component of ABC transporter from Brucella canis ATCC 23365
BMEA_RS14825 ABC transporter permease from Brucella melitensis ATCC 23457
31% identity, 95% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...rbsA BruAb20239rbsA4 BRA0995, rbsA4 BOV_A0937 BCAN_B1014 MOS Ribose import IM BMEII0301 rbsC BruAb20240,rbsC5 BRA0993, rbsC5 BCAN_B1013 MOS Ribose import IM BMEII0302 rbsC BruAb20239, rbsC4 BRA0994, rbsC5 BOV_A0935 BCAN_B1012 MOS Ribose import BP BruAb20238 BRA0996, rbsB3 BOV_A0938 BCAN_B1015 56 MOS Monosaccharide import BP BMEII0360, chvE BruAb20296 BRA0937...”
• Genetic Characterization and Comparative Genome Analysis of Brucella melitensis Isolates from India
  Azam, International journal of genomics 2016
  • “...nucleotide-disulfide oxidoreductase 20 BMEA_RS13580 AGGGGGGGGG AGGGGGGGGGG N-formylglutamate amidohydrolase 21 BMEA_RS13730 CTTTTTTT CTTTTTTTT Hypothetical protein 22 BMEA_RS14825 GAAAACGCCAAAA GAAA ABC transporter permease 23 BMEA_RS14895 TCCCCCCCCC TCCCCCCCCCCCC Amidase 24 BMEA_RS15830 CAAA CAAAA Amino acid ABC transporter substrate-binding protein...”

BMEII0301 RIBOSE TRANSPORT SYSTEM PERMEASE PROTEIN RBSC from Brucella melitensis 16M
30% identity, 96% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...MOS Ribose import ABC2 BMEII0300, rbsA BruAb20239rbsA4 BRA0995, rbsA4 BOV_A0937 BCAN_B1014 MOS Ribose import IM BMEII0301 rbsC BruAb20240,rbsC5 BRA0993, rbsC5 BCAN_B1013 MOS Ribose import IM BMEII0302 rbsC BruAb20239, rbsC4 BRA0994, rbsC5 BOV_A0935 BCAN_B1012 MOS Ribose import BP BruAb20238 BRA0996, rbsB3 BOV_A0938 BCAN_B1015 56 MOS Monosaccharide import...”

BRA0994 ribose ABC transporter, permease protein from Brucella suis 1330
31% identity, 95% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...IM BMEII0301 rbsC BruAb20240,rbsC5 BRA0993, rbsC5 BCAN_B1013 MOS Ribose import IM BMEII0302 rbsC BruAb20239, rbsC4 BRA0994, rbsC5 BOV_A0935 BCAN_B1012 MOS Ribose import BP BruAb20238 BRA0996, rbsB3 BOV_A0938 BCAN_B1015 56 MOS Monosaccharide import BP BMEII0360, chvE BruAb20296 BRA0937 BOV_A0879 BCAN_B0957 MOS Monosaccharide import ABC2 BMEII0361 BruAb20297 BRA0936...”

H281DRAFT_01112 deoxynucleoside transporter, permease component 2 from Paraburkholderia bryophila 376MFSha3.1
31% identity, 78% coverage

• mutant phenotype: Important for utilization of dAMP and deoxyinosine. Because the fitness profiles for these compounds are very similar, dAMP is likely hydrolyzed before uptake, but this could also be a transporter for deoxynucleotides.

D2S417 Xylose transport system permease protein XylH from Geodermatophilus obscurus (strain ATCC 25078 / DSM 43160 / JCM 3152 / CCUG 61914 / KCC A-0152 / KCTC 9177 / NBRC 13315 / NRRL B-3577 / G-20)
30% identity, 73% coverage

• Three novel polymorphic microsatellite markers for the glaucoma locus GLC1B by datamining tetranucleotide repeats on chromosome 2p12-q12.
  Murga-Zamalloa, Genetics and molecular biology 2009
  • “...affected relatives, regarding markers D2S2264, D2S1897 and D2S176 , but not sharing the alleles at D2S417 and D2S2161 ( Fujita et al. , 2002 ; Guevara-Fujita et al. , 2003 ). The segment delimited by D2S176 and D2S2264 was discarded for GLC1B , thus narrowing down...”
  • “...In order to refine the location of GLC1B , we sought markers between D2S2264 and D2S417 which were about 15 Mb apart. However, the reported microsatellite markers did not evenly cover this region, neither were informative in the family we were studying. This prompted us to...”
• The variant inv(2)(p11.2q13) is a genuinely recurrent rearrangement but displays some breakpoint heterogeneity.
  Fickelscher, American journal of human genetics 2007

RSP_3502 ABC sugar transporter, inner membrane subunit from Rhodobacter sphaeroides 2.4.1
30% identity, 92% coverage

• A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions
  Billenkamp, Journal of bacteriology 2015
  • “...GntR family transcriptional regulator 0.15 0.11 RSP_3503, 1 RSP_3502, 2 RSP_3501, 3 0.06 0.12 0.02 RSP_3949 (ansB) 22.4 RSP_1576 (trxB) 22 19.59 1 Thioredoxin...”

BMEII0981 XYLOSE TRANSPORT SYSTEM PERMEASE PROTEIN XYLH from Brucella melitensis 16M
38% identity, 42% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BRA0569 BCAN_B0568 MOS Galactoside/Ribose import BP BMEII0702 BRA0567 BOV_A0532 BCAN_B0567 59 MOS Monosaccharide import IM BMEII0981 BruAb20913 BRA0267 BOV_A0242 BCAN_B0268 MOS Monosaccharide import ABC2 BMEII0982 BruAb20914 BRA0266 BOV_A0241 BCAN_B0267 MOS Monosaccharide import BP BMEII0983 BruAb20916 BRA0265 BOV_A0240 BCAN_B0266 60 o228 Unknown IM BMEI0361 O228 Unknown MFP...”

BOV_A0242 sugar ABC transporter, permease protein from Brucella ovis ATCC 25840
38% identity, 41% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...Galactoside/Ribose import BP BMEII0702 BRA0567 BOV_A0532 BCAN_B0567 59 MOS Monosaccharide import IM BMEII0981 BruAb20913 BRA0267 BOV_A0242 BCAN_B0268 MOS Monosaccharide import ABC2 BMEII0982 BruAb20914 BRA0266 BOV_A0241 BCAN_B0267 MOS Monosaccharide import BP BMEII0983 BruAb20916 BRA0265 BOV_A0240 BCAN_B0266 60 o228 Unknown IM BMEI0361 O228 Unknown MFP BMEI0359 o228 Unknown...”

BCAN_B0268 inner-membrane translocator from Brucella canis ATCC 23365
BRA0267 sugar ABC transporter, permease protein from Brucella suis 1330
38% identity, 41% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...import BP BMEII0702 BRA0567 BOV_A0532 BCAN_B0567 59 MOS Monosaccharide import IM BMEII0981 BruAb20913 BRA0267 BOV_A0242 BCAN_B0268 MOS Monosaccharide import ABC2 BMEII0982 BruAb20914 BRA0266 BOV_A0241 BCAN_B0267 MOS Monosaccharide import BP BMEII0983 BruAb20916 BRA0265 BOV_A0240 BCAN_B0266 60 o228 Unknown IM BMEI0361 O228 Unknown MFP BMEI0359 o228 Unknown ABC...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...MOS Galactoside/Ribose import BP BMEII0702 BRA0567 BOV_A0532 BCAN_B0567 59 MOS Monosaccharide import IM BMEII0981 BruAb20913 BRA0267 BOV_A0242 BCAN_B0268 MOS Monosaccharide import ABC2 BMEII0982 BruAb20914 BRA0266 BOV_A0241 BCAN_B0267 MOS Monosaccharide import BP BMEII0983 BruAb20916 BRA0265 BOV_A0240 BCAN_B0266 60 o228 Unknown IM BMEI0361 O228 Unknown MFP BMEI0359 o228...”

Shewana3_2076 L-arabinose ABC transporter, permease component 2 AraZ from Shewanella sp. ANA-3
32% identity, 80% coverage

• mutant phenotype: Specifically important for L-arabinose utilization; the gene name is from PMC2996990

Gocc_0079 ABC transporter permease from Gaiella occulta
27% identity, 74% coverage

• High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria
  Severino, MicrobiologyOpen 2019
  • “...for growth (Albuquerque et al., 2011 ). The genes for ABC transport systems for ribose (Gocc_0079 to Gocc_0081; Gocc_2298 to Gocc_2300; Gocc_3068, Gocc_3069 and Gocc_3071), rhamnose (Gocc_0123 to Gocc_0125; Gocc_0231 to Gocc_0234), Dxylose (Gocc_1293 to Gocc_1295), and raffinose/stachyose/melibiose (Gocc_1613 to Gocc_1616) were identified in G. occulta...”

PFREUD_06660 ABC transporter permease from Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1
30% identity, 61% coverage

• A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment
  Saraoui, BMC genomics 2013
  • “...3,1E-01 CUST_254_PI426428742 PFREUD_02700 glpT Glycerol-3-phosphate transporter 1.2.4 Transport/binding of carbohydrates 3,1 4,1E-07 1,1 2,6E-01 CUST_267_PI426428742 PFREUD_06660 IM protein of ribose/xylose/arabinose/galactoside ABC transporter 1.2.4 Transport/binding of carbohydrates 5,2 1,1E-08 1,2 1,3E-01 CUST_650_PI426428742 PFREUD_12690 ydaO IM protein of branched-chain amino acids ABC transporter (HAA: undef: Branched-chain amino acids)...”

alr2536 permease protein of branched-chain amino acid ABC transporter from Nostoc sp. PCC 7120
32% identity, 50% coverage

• Amino Acid Transporters and Release of Hydrophobic Amino Acids in the Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120
  Pernil, Life (Basel, Switzerland) 2015
  • “...TM N-III 3.A.1.4 Gly , Pro, Glu, alr2535 natI PSB This work Phe, Leu, Ala, alr2536 natJ TM Gln alr2538 natK TM alr2539 natL ATPase alr2541 natM ATPase Some cyanobacterial mutants have been reported to accumulate amino acids in the culture medium [ 6 , 23...”
  • “...at standard concentrations [ 35 ]. 2.2. Plasmid Construction and Genetic Procedures For inactivation of alr2536 , all0342 , and alr3429 , internal fragments of 552 bp, 596 bp, and 469 bp, respectively, were amplified by PCR using DNA from strain PCC 7120 as a template...”

DR_2121 branched-chain amino acid ABC transporter, permease protein from Deinococcus radiodurans R1
33% identity, 36% coverage

• Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans
  Wang, Nucleic acids research 2024
  • “...1.53 NA 1.53 A2G07_RS14760 DR_A0262 branched-chain amino acid ABC transporter permease 1.86 NA 1.52 A2G07_RS02995 DR_2121 branched-chain amino acid ABC transporter permease 1.50 NA 1.43 A2G07_RS14755 DR_A0261 branched-chain amino acid ABC transporter ATP-binding protein/permease 1.88 NA 1.43 A2G07_RS14725 DR_A0255 N-acyl homoserine lactone acylase QqaR 1.58 NA...”
  • “...the N-acetyltransferase (DR_1917), the peptidoglycan endopeptidase (DR_1749), Siderophore-interacting protein (DR_B0124), ABC transporters related proteins (DR_B0125, DR_2121, DR_A0261, DR_A0262), and N -acetylmuramoyl- l -alanine amidase (DR_C0013) (Table 1 ; Supplementary Table S3 ), which are related to the cell wall or the cell membrane synthesis or transportation,...”

A2G07_RS02995 branched-chain amino acid ABC transporter permease from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
34% identity, 37% coverage

• Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans
  Wang, Nucleic acids research 2024
  • “...ligase 1.53 NA 1.53 A2G07_RS14760 DR_A0262 branched-chain amino acid ABC transporter permease 1.86 NA 1.52 A2G07_RS02995 DR_2121 branched-chain amino acid ABC transporter permease 1.50 NA 1.43 A2G07_RS14755 DR_A0261 branched-chain amino acid ABC transporter ATP-binding protein/permease 1.88 NA 1.43 A2G07_RS14725 DR_A0255 N-acyl homoserine lactone acylase QqaR 1.58...”

SMa0198 putative ABC transporter, permease from Sinorhizobium meliloti 1021
26% identity, 44% coverage

• Biogeography of a Novel Ensifer meliloti Clade Associated with the Australian Legume Trigonella suavissima
  Eardly, Applied and environmental microbiology 2017
  • “...12 3 2 6 6 51 6 nodCc 3 3 32 4 4 15 4 22 7 7 7 7 sma0198 13 32 3 14 6 4 6 3 33 34 33 3 E. medicae A321T M1 M3 M102 M161 M205 M254 M280 2 2 2 2 2 16 2 2 2 9 2 2...”
  • “...420 bp; nodC, acetylglucosaminyltransferase, 348 bp; and SMa0198, ABC transporter permease, 312 bp (19). Similarly, three chromid (pSymB) loci were selected...”
• Application of multilocus sequence typing to study the genetic structure of megaplasmids in medicago-nodulating rhizobia
  van, Applied and environmental microbiology 2010
  • “...5-CGCGCGTGCTCATCCKGAAGT-3 1,958 479009-480289 1144475-1145977 SMa0198 F: 5-CCKCGSGCSATGAGCTAT-3 R: 5-ACGCCGGCGATCGACAGCAG-3 647 108822-109769 275441-276388 F:...”
  • “...5-CCGGCGATCGACAGCAGCGTG-3 429 PCR primers adeC3 Sequence primers adeC3 SMa0198 Full 207-227 714-734 a The genes listed code for the following products: adeC3,...”

EF1254 ABC transporter, permease protein from Enterococcus faecalis V583
25% identity, 78% coverage

• Functional studies of E. faecalis RNase J2 and its role in virulence and fitness
  Gao, PloS one 2017
  • “...ef1094 SrtC -4.24 0.026 ef1096 conserved hypothetical protein -6.44 0.072 ef1097 Enterococcin V583 -34.64 0.005 ef1254 ABC transporter, permease protein -7.72 0.038 ef1260 DNA-binding response regulator -5.49 0.040 ef1261 sensor histidine kinase -3.97 0.035 ef1268 cation-transporting Pase, E1-E2 family -5.60 0.068 ef1288 conserved hypothetical protein -3.28...”
• Transcriptional response of Enterococcus faecalis V583 to erythromycin
  Aakra, Antimicrobial agents and chemotherapy 2005
  • “...EF0576 EF0793 EF0892 EF0907 EF0938 EF1057 EF1100 EF1128 EF1254 EF1268 EF1304 EF1331 EF1344 EF1345 EF1352 EF1492 EF1673 EF1720 EF1759 EF2049 EF2050 EF2074 EF2081...”

FN1431 Branched-chain amino acid transport system permease protein livH from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
33% identity, 32% coverage

• Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics
  Mira, BMC evolutionary biology 2004
  • “...amino acid transport system liv G-M operon; biased and homogeneous codon usage 5062 FN1428 to FN1431 Bifidobacterium longum 1 "Split" indicates a cluster separated by a long intergenic spacer, the two parts of the cluster generally coding for different functions. 2 Range of sequence similarity among...”

New Search

Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.