PaperBLAST
PaperBLAST Hits for reanno::Burk376:H281DRAFT_01112 deoxynucleoside transporter, permease component 2 (Paraburkholderia bryophila 376MFSha3.1) (364 a.a., MNSRIPSRTD...)
Show query sequence
>reanno::Burk376:H281DRAFT_01112 deoxynucleoside transporter, permease component 2 (Paraburkholderia bryophila 376MFSha3.1)
MNSRIPSRTDPRTDPPSASPMKQTMTTPTVVEIAPSVEAPGLRTRLARNPEWFTVALIVV
TCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAALTMYGIT
KAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQYLYRGLLLTFI
GTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWWLLNRTMMGRAV
YAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFDLVGSELDVIA
AVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGAFILLAGTLFAL
QRKR
Running BLASTp...
Found 250 similar proteins in the literature:
H281DRAFT_01112 deoxynucleoside transporter, permease component 2 from Paraburkholderia bryophila 376MFSha3.1
100% identity, 100% 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.
ECs0377 putative permease of ABC transporter from Escherichia coli O157:H7 str. Sakai
Z0418 putative permease component of transport system, probably ribose specific from Escherichia coli O157:H7 EDL933
35% identity, 88% coverage
Entcl_1205 ABC transporter permease from [Enterobacter] lignolyticus SCF1
39% identity, 88% 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...”
YPTB0800 tRNA-Met from Yersinia pseudotuberculosis IP 32953
36% identity, 82% coverage
BA0668 ribose ABC transporter, permease protein from Bacillus anthracis str. Ames
35% identity, 82% coverage
SCO2747 bifunctional carbohydrate binding and transport protein from Streptomyces coelicolor A3(2)
33% 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...”
BSU35950 ribose ABC transporter (permease) from Bacillus subtilis subsp. subtilis str. 168
34% identity, 84% coverage
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, 85% coverage
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
33% identity, 82% 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...”
BRA0859 ribose ABC transporter, permease protein from Brucella suis 1330
BCAN_B0876 hypothetical protein from Brucella canis ATCC 23365
33% identity, 82% 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...”
BCAL1549 putative sugar ABC transport system, membrane protein from Burkholderia cenocepacia J2315
33% identity, 85% 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
33% identity, 94% coverage
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
31% identity, 93% coverage
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)
31% identity, 84% coverage
LLNZ_RS04080 ABC transporter permease from Lactococcus cremoris subsp. cremoris NZ9000
32% identity, 85% 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...”
RR42_RS03365 fructose ABC transporter, permease component (FrcC) from Cupriavidus basilensis FW507-4G11
33% identity, 84% coverage
- mutant phenotype: Specific phenotype on fructose
SXYL_01519 ABC transporter permease from Staphylococcus xylosus
31% identity, 79% coverage
cg1412 ribose/xylose/arabinose/galactoside ABC-type transporter permease from Corynebacterium glutamicum ATCC 13032
32% identity, 78% 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...”
YPTB3806 ABC ribose transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
YPO3963 sugar transport system permease protein from Yersinia pestis CO92
32% identity, 83% coverage
ABD05_RS24180 ABC transporter permease from Burkholderia pyrrocinia
29% identity, 94% coverage
BTH_II0210 ribose ABC transporter, permease protein from Burkholderia thailandensis E264
33% identity, 85% coverage
Atu4322 ABC transporter, membrane spanning protein (ribose) from Agrobacterium tumefaciens str. C58 (Cereon)
34% identity, 84% coverage
H16_B1499 ABC transporter permease subunit from Cupriavidus necator H16
H16_B1499 ABC-type transporter, permease component: CUT2 family, fructose specific from Ralstonia eutropha H16
32% identity, 95% coverage
BOV_1575 ribose ABC transporter, permease protein from Brucella ovis ATCC 25840
BMEI0392 RIBOSE TRANSPORT SYSTEM PERMEASE PROTEIN RBSC from Brucella melitensis 16M
BR1631 ribose ABC transporter, permease protein from Brucella suis 1330
BCAN_A1668 hypothetical protein from Brucella canis ATCC 23365
32% identity, 81% coverage
- 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 - “...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 - “...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 - “...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...”
BAbS19_II03540 dicarboxylate symporter from Brucella abortus S19
36% identity, 65% coverage
CPE1629 probable ribose ABC transporter from Clostridium perfringens str. 13
29% identity, 87% coverage
HI0503 D-ribose ABC transporter, permease protein (rbsC) from Haemophilus influenzae Rd KW20
32% identity, 80% coverage
Entcl_4081 ABC transporter permease subunit from [Enterobacter] lignolyticus SCF1
33% identity, 92% 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...”
YPTB2205 ABC sugar/ribose transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
29% identity, 100% coverage
MSMEG_3601 ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components from Mycobacterium smegmatis str. MC2 155
30% identity, 98% coverage
MSMEG_4171 ribose transport system permease protein RbsC from Mycobacterium smegmatis str. MC2 155
30% identity, 77% coverage
SAK_RS00825 ABC transporter permease subunit from Streptococcus agalactiae A909
gbs0114 Unknown from Streptococcus agalactiae NEM316
30% identity, 86% coverage
- 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...”
- 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...”
SAK_0167 ribose ABC transporter, permease protein from Streptococcus agalactiae A909
31% identity, 80% coverage
YPTB2535 putative ABC sugar (sorbitol) transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
YPO2499 putative sugar transport system, permease protein from Yersinia pestis CO92
28% identity, 94% coverage
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)
NP_418206 ribose ABC transporter membrane subunit from Escherichia coli str. K-12 substr. MG1655
b3750 ribose ABC transporter permease protein from Escherichia coli str. K-12 substr. MG1655
31% identity, 82% 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) - Cotinine Hydroxylase CotA Initiates Biodegradation of Wastewater Micropollutant Cotinine in Nocardioides sp. Strain JQ2195
Zhao, Applied and environmental microbiology 2021 (secret) - 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.
- 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...”
A7MMV6 Ribose ABC transporter permease from Cronobacter sakazakii (strain ATCC BAA-894)
31% identity, 82% coverage
Z5251 D-ribose high-affinity transport system from Escherichia coli O157:H7 EDL933
31% identity, 82% coverage
Cthe_2448 inner-membrane translocator from Clostridium thermocellum ATCC 27405
30% identity, 83% coverage
Entcl_4403 ribose ABC transporter permease from [Enterobacter] lignolyticus SCF1
31% identity, 82% 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...”
Bbr_1418 ABC transporter permease from Bifidobacterium breve UCC2003
31% identity, 81% coverage
STM3883 ABC superfamily (membrane), D-ribose high-affinity transport protein (1st module, ATP-binding subunit) from Salmonella typhimurium LT2
31% identity, 82% coverage
HSERO_RS11490 D-ribose ABC transporter, permease component RbsC from Herbaspirillum seropedicae SmR1
30% identity, 85% coverage
- mutant phenotype: Specifically important for utilizing D-Ribose.
FTV88_0055 ABC transporter permease from Heliorestis convoluta
31% identity, 79% coverage
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
29% identity, 79% 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...”
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)
30% identity, 88% coverage
HSERO_RS03645 D-mannose ABC transporter, permease component from Herbaspirillum seropedicae SmR1
35% identity, 61% coverage
- mutant phenotype: Specific phenotype on D-mannose
c3068 Hypothetical ABC transporter permease protein yphD from Escherichia coli CFT073
29% identity, 88% coverage
SMb21375 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
30% identity, 82% 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...”
MSMEG_1709 inner membrane ABC transporter permease protein YjfF from Mycobacterium smegmatis str. MC2 155
30% identity, 90% coverage
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
33% identity, 83% coverage
PS417_12060 xylitol ABC transporter, permease component from Pseudomonas simiae WCS417
31% identity, 91% coverage
- mutant phenotype: Specifically important for utilizing xylitol.
YphD / b2546 putative ABC transporter membrane subunit YphD from Escherichia coli K-12 substr. MG1655 (see 4 papers)
29% identity, 88% coverage
SMc02031 PUTATIVE PERMEASE PROTEIN from Sinorhizobium meliloti 1021
30% identity, 76% coverage
ECOLIN_RS18680 ABC transporter permease from Escherichia coli Nissle 1917
c4015 Ribose transport system permease protein rbsC from Escherichia coli CFT073
31% identity, 84% coverage
- 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...”
- 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...”
BTH_II1626 L-arabinose ABC transporter, permease protein from Burkholderia thailandensis E264
31% identity, 92% coverage
SPOA0254 ABC transporter permease from Ruegeria pomeroyi DSS-3
28% identity, 82% 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,...”
BC33_RS14600 autoinducer 2 ABC transporter permease LsrC from Escherichia coli ATCC 700728
32% identity, 80% coverage
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
32% 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...”
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)
29% identity, 81% coverage
- substrates: Xylose, glucose
OKIT_0348 ABC transporter permease subunit from Oenococcus kitaharae DSM 17330
30% identity, 89% coverage
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
30% identity, 87% 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...”
PP_2456 ribose ABC transporter, permease protein from Pseudomonas putida KT2440
29% identity, 82% coverage
ABD05_RS21655 L-arabinose ABC transporter permease AraH from Burkholderia pyrrocinia
29% identity, 99% coverage
S1710 putative transport system permease protein from Shigella flexneri 2a str. 2457T
32% identity, 80% coverage
Entcl_3383 ABC transporter permease from [Enterobacter] lignolyticus SCF1
31% identity, 76% 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 [...”
ECs5208 putative transport system permease protein from Escherichia coli O157:H7 str. Sakai
30% identity, 80% coverage
HSERO_RS05255 ABC transporter for L-fucose, permease component from Herbaspirillum seropedicae SmR1
28% identity, 93% coverage
- mutant phenotype: Specifically important for L-fucose utilization.
Q7UU56 Ribose transport system permease protein rbsC from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
30% identity, 88% coverage
CIBE_5333 galactose/methyl galactoside ABC transporter permease MglC from Clostridium beijerinckii
28% identity, 75% 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_3090 ribose transport system permease protein RbsC from Mycobacterium smegmatis str. MC2 155
30% identity, 88% 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...”
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
32% identity, 85% 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,...”
SC3964 putative ABC superfamily (membrane), sugar transport protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
32% identity, 85% coverage
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
32% identity, 85% coverage
BCAM2796 putative permease component of ABC transporter from Burkholderia cenocepacia J2315
32% identity, 81% coverage
SMc03000 PUTATIVE PERMEASE ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
33% identity, 89% coverage
Entcl_0174 xylose ABC transporter permease XylH from [Enterobacter] lignolyticus SCF1
27% identity, 87% 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...”
H604_RS0100110 ABC transporter permease from Ruminococcus gauvreauii DSM 19829
26% identity, 88% coverage
A8H4W6 Monosaccharide-transporting ATPase from Shewanella pealeana (strain ATCC 700345 / ANG-SQ1)
29% identity, 85% coverage
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
31% identity, 81% 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...”
VK055_1939 ABC transporter permease from Klebsiella pneumoniae subsp. pneumoniae
30% identity, 75% coverage
ML0397 putative transporter protein from Mycobacterium leprae TN
30% identity, 53% coverage
CPE1343 probable galactoside ABC transporter from Clostridium perfringens str. 13
28% identity, 86% 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...”
SMb20854 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
30% identity, 79% coverage
bll2675 sugar ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
28% identity, 83% 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...”
Q7UR04 Ribose transport system permease protein RbsC from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
28% identity, 81% coverage
YPTB3229 ABC sugar transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
YPO0957 putative sugar transport system permease protein from Yersinia pestis CO92
26% identity, 85% coverage
B9Q16_23110 ABC transporter permease from Pantoea ananatis
27% identity, 81% coverage
BCAL1659 putative ribose transport system, permease protein from Burkholderia cenocepacia J2315
28% identity, 82% 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...”
PSPTO_2640 L-arabinose ABC transporter, permease protein from Pseudomonas syringae pv. tomato str. DC3000
28% identity, 76% coverage
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
29% identity, 85% 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...”
STM4076 putative ABC superfamily (membrane), sugar transport protein from Salmonella typhimurium LT2
29% identity, 85% 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...”
BPHYT_RS34240 ABC transporter for L-rhamnose/L-fucose/xylitol, permease component from Burkholderia phytofirmans PsJN
32% identity, 80% coverage
- mutant phenotype: Specifically important for utilizing L-rhamnose, L-fucose, and xylitol.
VK055_3270 ABC transporter permease from Klebsiella pneumoniae subsp. pneumoniae
30% identity, 90% coverage
EfmE4452_1563, EfmE4453_1837 ABC transporter permease from Enterococcus faecium E4452
26% identity, 85% 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...”
BPSL1791 putative membrane protein from Burkholderia pseudomallei K96243
32% identity, 82% coverage
PS417_18395 D-ribose ABC transporter, permease component RbsC from Pseudomonas simiae WCS417
28% identity, 82% coverage
- mutant phenotype: Specifically important for utilizing D-Ribose.
PA1948 membrane protein component of ABC ribose transporter from Pseudomonas aeruginosa PAO1
Q9I2F6 Membrane protein component of ABC ribose transporter from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA14_39320 ribose ABC transporter, permease protein from Pseudomonas aeruginosa UCBPP-PA14
28% identity, 82% 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,...”
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...5153 Q9I7B9 826 Q9I0M1 1908 Q9I2F1 2990 Q9HWL4 4072 Q9I1I4 5154 Q9RQ16 827 Q9I0M4 1909 Q9I2F6 2991 Q9HWL5 4073 Q9I1I5 5155 Q9X6V8 828 Q9I0M6 1910 Q9I2F8 2992 Q9HWL6 4074 Q9I1I7 829 Q9I0Q0 1911 Q9I2G3 2993 Q9HWL7 4075 Q9I1I8 830 Q9I0Q7 1912 Q9I2H6 2994 Q9HWL8 4076 Q9I1J0...”
- 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
26% identity, 80% coverage
C5965_02215 xylose ABC transporter permease XylH from Cronobacter sakazakii
25% identity, 86% coverage
Cphy_2011 Monosaccharide-transporting ATPase from Clostridium phytofermentans ISDg
28% identity, 82% 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...”
LKW31_00160 xylose ABC transporter permease XylH from Pantoea agglomerans
27% identity, 72% coverage
Cthe_0392 inner-membrane translocator from Clostridium thermocellum ATCC 27405
Cthe_0392 ABC transporter permease from Acetivibrio thermocellus ATCC 27405
28% identity, 87% coverage
B2904_orf2671 ABC transporter permease from Brachyspira pilosicoli B2904
28% identity, 84% coverage
PGA1_262p00440 glucose transporter, permease component from Phaeobacter inhibens DSM 17395
37% 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.
RL2450 putative transmembrane component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
31% identity, 79% coverage
H604_RS0100045 ABC transporter permease from Ruminococcus gauvreauii DSM 19829
26% identity, 84% coverage
Pf6N2E2_5970 ABC transporter for D-galactose/L-arabinose, permease component from Pseudomonas fluorescens FW300-N2E2
29% identity, 61% coverage
- mutant phenotype: Specifically important for utilizing D-galactose and L-arabinose
YPTB0550 ABC sugar transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
29% identity, 83% coverage
Pf1N1B4_6033 D-ribose ABC transporter, permease component RbsC from Pseudomonas fluorescens FW300-N1B4
28% identity, 82% 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.
Atu0064 ABC transporter, membrane spanning protein (sugar) from Agrobacterium tumefaciens str. C58 (Cereon)
25% identity, 99% coverage
Pf1N1B4_409 ABC transporter for D-galactose/L-arabinose, permease component from Pseudomonas fluorescens FW300-N1B4
29% identity, 61% coverage
- mutant phenotype: Specifically important for utilizing D-galactose and L-arabinose
YPO0410 putative ABC transporter permease protein from Yersinia pestis CO92
29% identity, 83% coverage
VPA1671 ABC-type arabinose transport system, permease component from Vibrio parahaemolyticus RIMD 2210633
29% identity, 79% 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...”
Shewana3_2076 L-arabinose ABC transporter, permease component 2 AraZ from Shewanella sp. ANA-3
31% identity, 82% coverage
- mutant phenotype: Specifically important for L-arabinose utilization; the gene name is from PMC2996990
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)
Z4993 putative xylose transport, membrane component from Escherichia coli O157:H7 EDL933
SF3612 putative xylose transport, membrane component from Shigella flexneri 2a str. 301
S4157 putative xylose transporter, membrane component from Shigella flexneri 2a str. 2457T
26% identity, 79% coverage
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
30% 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). - 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
KP1_1424 sugar ABC transport system permease component from Klebsiella pneumoniae NTUH-K2044
30% identity, 64% coverage
A4XG53 Monosaccharide-transporting ATPase from Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)
27% identity, 81% coverage
BOV_1300 sugar ABC transporter, permease protein from Brucella ovis ATCC 25840
26% identity, 85% 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...”
Shewana3_2075 L-arabinose ABC transporter, permease component 1 AraW from Shewanella sp. ANA-3
27% identity, 73% coverage
- mutant phenotype: Specifically important for L-arabinose utilization; the gene name is from PMC2996990
BC33_RS14595 autoinducer 2 ABC transporter permease LsrD from Escherichia coli ATCC 700728
ECs2122 putative transport system permease protein from Escherichia coli O157:H7 str. Sakai
30% identity, 88% coverage
AO353_21390 m-Inositol ABC transporter, permease component (iatP) from Pseudomonas fluorescens FW300-N2E3
28% identity, 77% 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.
A7P61_RS11580 ABC transporter permease from Pantoea agglomerans pv. betae
30% identity, 65% coverage
BMEI0664 SUGAR TRANSPORT SYSTEM PERMEASE PROTEIN from Brucella melitensis 16M
24% identity, 91% 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...”
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)
29% identity, 86% 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)
SCO6258 sugar ABC transporter permease protein from Streptomyces coelicolor A3(2)
28% identity, 89% coverage
PS417_11895 Inositol transport system permease protein from Pseudomonas simiae WCS417
28% identity, 77% coverage
- mutant phenotype: specific phenotype on inositol.
BCAN_A1368 Monosaccharide-transporting ATPase from Brucella canis ATCC 23365
BR1340 sugar ABC transporter, permease protein from Brucella suis 1330
24% identity, 94% coverage
- 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...”
- 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...”
RL2720 putative ribose transport system permease protein from Rhizobium leguminosarum bv. viciae 3841
29% identity, 83% 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...”
Gocc_3068 ABC transporter permease from Gaiella occulta
31% identity, 81% coverage
Gocc_0234 ABC transporter permease from Gaiella occulta
28% identity, 81% coverage
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
32% 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...”
Ava_2173 inner-membrane translocator from Anabaena variabilis ATCC 29413
30% identity, 87% 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....”
blr2271 sugar ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
29% identity, 80% coverage
AOT13_11445 multiple monosaccharide ABC transporter permease from Parageobacillus thermoglucosidasius
25% identity, 70% 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-...”
AT5A_19781 ABC transporter permease from Agrobacterium tumefaciens 5A
29% identity, 83% 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...”
RSUY_47250, RSUY_RS22945 sugar ABC transporter permease from Ralstonia solanacearum
32% identity, 36% 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...”
SMb20714 ABC transporter permease from Sinorhizobium meliloti 1021
NP_437961 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
27% identity, 74% 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,...”
Cphy_0582 Monosaccharide-transporting ATPase from Clostridium phytofermentans ISDg
24% identity, 84% coverage
Cphy_0581 Monosaccharide-transporting ATPase from Clostridium phytofermentans ISDg
26% identity, 79% coverage
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
26% identity, 83% 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...”
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
28% identity, 93% 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...”
MSMEG_1706 xylose transport system permease protein XylH from Mycobacterium smegmatis str. MC2 155
28% identity, 85% coverage
BCAL3403 L-arabinose transport system, permease protein from Burkholderia cenocepacia J2315
27% identity, 86% coverage
APECO2_RS16285 arabinose ABC transporter permease AraH from Escherichia coli APEC O2-211
28% identity, 81% 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...”
RSP_3502 ABC sugar transporter, inner membrane subunit from Rhodobacter sphaeroides 2.4.1
31% identity, 85% coverage
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)
26% identity, 71% 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...”
RSp1635 PROBABLE XYLOSE TRANSMEMBRANE ABC TRANSPORTER PROTEIN from Ralstonia solanacearum GMI1000
32% identity, 36% 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...”
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)
30% identity, 75% coverage
SMb21343 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
32% identity, 80% coverage
HI1109 D-xylose ABC transporter permease protein from Haemophilus influenzae Rd KW20
27% identity, 83% coverage
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
28% identity, 81% 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 Escherichia coli
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,...”
S2038 L-arabinose transport system permease protein from Shigella flexneri 2a str. 2457T
28% identity, 81% coverage
BAB2_0300 Bacterial inner-membrane translocator from Brucella melitensis biovar Abortus 2308
25% identity, 74% coverage
BRA0935 sugar ABC transporter, permease protein from Brucella suis 1330
25% identity, 74% 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...”
BCAN_B0955 Monosaccharide-transporting ATPase from Brucella canis ATCC 23365
25% identity, 74% 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...”
BOV_A0877 sugar ABC transporter, permease protein from Brucella ovis ATCC 25840
25% identity, 77% 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...”
pRL90247 putative permease component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
29% identity, 81% coverage
BMEII0362 XYLOSE TRANSPORT SYSTEM PERMEASE PROTEIN XYLH from Brucella melitensis 16M
25% identity, 73% 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...”
FN1167 Galactoside transport system permease protein mglC from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
25% identity, 82% 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,...”
BCAN_B1181 Monosaccharide-transporting ATPase from Brucella canis ATCC 23365
31% identity, 37% 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...”
BOV_A1057 D-xylose ABC transporter, permease protein from Brucella ovis ATCC 25840
31% identity, 29% 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...”
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)
27% identity, 74% coverage
ABD05_RS33475 sugar ABC transporter permease from Burkholderia pyrrocinia
32% identity, 36% coverage
Q7UXV9 Ribose transport system permease protein from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
28% identity, 74% coverage
RLO149_c021960 multiple monosaccharide ABC transporter permease from Roseobacter litoralis Och 149
32% identity, 33% 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...”
SPO0862 sugar ABC transporter permease from Ruegeria pomeroyi DSS-3
36% identity, 31% 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...”
BRA1152 D-xylose ABC transporter, permease protein from Brucella suis 1330
31% identity, 32% 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...”
BPHYT_RS16925 D-galactose ABC transporter, permease component from Burkholderia phytofirmans PsJN
29% identity, 59% coverage
- mutant phenotype: Specifically important for D-galactose utilization
pRL110410 putative permease component of ABC transporter involved in competition for nodulation from Rhizobium leguminosarum bv. viciae 3841
30% identity, 74% coverage
RHA1_ro02906 ABC sugar transporter, permease component from Rhodococcus sp. RHA1
29% identity, 78% coverage
- Unsilencing a cryptic xylose metabolic pathway in Rhodococcus jostii RHA1 for efficient lipid production from lignocellulosic biomass
Acedos, Journal of biological engineering 2025 - “...1188 fumarylacetoacetate hydrolase family protein 5.33 0.00E+00 RHA1_ro02905 penD 717 SDR family oxidoreductase 5.72 0.00E+00 RHA1_ro02906 penC 1050 ABC transporter permease 5.67 0.00E+00 RHA1_ro02907 penB 1551 sugar ABC transporter ATP-binding protein 5.23 0.00E+00 RHA1_ro02908 penA 1047 substrate-binding domain-containing protein 5.41 0.00E+00 RHA1_ro02909 penR 705 FadR/GntR family...”
- “...RHA1 ALE-xyl strain under glucose and xylose growth conditions Locus Name Glucose (counts) Xylose (counts) RHA1_ro02906 ABC transporter permease 211 10,748 RHA1_ro02907 sugar ABC transporter ATP-binding protein 387 14,588. RHA1_ro02908 substrate-binding domain-containing protein 489 20,804 RHA1_ro02804 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC 3800 502 RHA1_ro02805 carbohydrate...”
RL4653 putative transmembrane component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
27% identity, 93% coverage
SMc02772 PUTATIVE SUGAR ABC TRANSPORTER PERMEASE PROTEIN from Sinorhizobium meliloti 1021
27% identity, 78% coverage
ECs5207 putative transport system permease protein from Escherichia coli O157:H7 str. Sakai
30% identity, 76% coverage
SG0965 galactoside ABC transporter permease component from Sodalis glossinidius str. 'morsitans'
27% identity, 85% coverage
SCO6980 ABC transporter membrane protein from Streptomyces coelicolor A3(2)
26% identity, 99% coverage
BMEII0144 XYLOSE TRANSPORT SYSTEM PERMEASE PROTEIN XYLH from Brucella melitensis 16M
30% identity, 32% 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...”
Clocel_2597 ABC transporter permease from Clostridium cellulovorans 743B
28% identity, 68% coverage
SMa0070 putative ABC transporter permease from Sinorhizobium meliloti 1021
28% identity, 74% coverage
SMa1995 Putative ABC transporter, permease protein from Sinorhizobium meliloti 1021
25% identity, 90% coverage
TP0686 methylgalactoside ABC transporter, permease protein (mglC) from Treponema pallidum subsp. pallidum str. Nichols
23% identity, 58% coverage
C289_0765 ABC transporter permease from Anoxybacillus ayderensis
27% identity, 86% 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...”
BCAM0769 ribose transport system permease protein from Burkholderia cenocepacia J2315
30% identity, 93% coverage
Gocc_2300 ABC transporter permease from Gaiella occulta
28% identity, 73% coverage
MSMEG_6803 ribose transport system permease protein RbsC from Mycobacterium smegmatis str. MC2 155
28% identity, 88% coverage
blr4886 ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
27% identity, 90% coverage
MSMEG_1710 ribose transport system permease protein RbsC from Mycobacterium smegmatis str. MC2 155
28% identity, 80% coverage
Csac_2504 Monosaccharide-transporting ATPase from Caldicellulosiruptor saccharolyticus DSM 8903
24% identity, 74% coverage
Z0419 putative permease component of transport system, probably ribose specific from Escherichia coli O157:H7 EDL933
26% identity, 82% coverage
B8809_1448 multiple monosaccharide ABC transporter permease from Bifidobacterium longum subsp. longum
33% identity, 34% coverage
BBMN68_1728 multiple monosaccharide ABC transporter permease from Bifidobacterium longum subsp. longum BBMN68
33% identity, 34% 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...”
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)
33% identity, 34% coverage
MSMEG_4657 ABC transporter membrane protein from Mycobacterium smegmatis str. MC2 155
MSMEG_4657 ABC transporter permease from Mycolicibacterium smegmatis MC2 155
24% identity, 79% coverage
- 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...”
- 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...”
- 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...”
Q7ULN8 Ribose ABC transporter permease protein from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
29% identity, 50% coverage
BMEI1391 RIBOSE TRANSPORT SYSTEM PERMEASE PROTEIN RBSC from Brucella melitensis 16M
26% identity, 75% 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...”
SC2205 ABC superfamily (membrane), methyl-galactoside transport protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
29% identity, 73% coverage
BCAN_A0555 Monosaccharide-transporting ATPase from Brucella canis ATCC 23365
BR0543 ribose ABC transporter, permease protein from Brucella suis 1330
BOV_0545 ribose ABC transporter, permease protein from Brucella ovis ATCC 25840
26% identity, 75% coverage
- 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...”
- 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 - “...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,...”
SCO0810 ABC transporter permease from Streptomyces coelicolor A3(2)
30% identity, 91% coverage
KPHS_36490 beta-methylgalactoside transporter inner membrane protein from Klebsiella pneumoniae subsp. pneumoniae HS11286
VK055_4937 galactose/methyl galactoside ABC transporter permease MglC from Klebsiella pneumoniae subsp. pneumoniae
31% identity, 73% coverage
- Transcriptomic analysis reveals pathways underlying the multi-antibiotic resistance of Klebsiella pneumoniae
Liu, IET systems biology 2025 - “...KPHS_30370, and KPHS_30410, all of which exhibit elevated expression levels. Conversely, genes such as KPHS_34630, KPHS_36490, KPHS_42220, KPHS_34850, KPHS_34790, KPHS_34800, etc., show decreased expression levels (Figure 8 ). Collectively, these findings suggest a mechanism of antibiotic resistance through mutationmediated changes in gene expression. FIGURE 8 Gene...”
- 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...”
ESA_RS04990 galactose/methyl galactoside ABC transporter permease MglC from Cronobacter sakazakii ATCC BAA-894
30% identity, 73% 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...”
MGLC_SALTY / Q56036 Galactose/methyl galactoside import permease protein MglC from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
29% identity, 73% 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).
YPO1295 putative ABC transport integral membrane subunit from Yersinia pestis CO92
30% identity, 82% coverage
YPTB1327 ABC sugar transporter, permease subunit from Yersinia pseudotuberculosis IP 32953
30% identity, 82% coverage
YPK_2564 monosaccharide-transporting ATPase from Yersinia pseudotuberculosis YPIII
27% identity, 85% 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...”
Atu3575 ABC transporter, membrane spanning protein (xylose) from Agrobacterium tumefaciens str. C58 (Cereon)
34% identity, 30% 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...”
PGA1_c07310 Inositol transport system permease protein from Phaeobacter inhibens DSM 17395
25% identity, 71% coverage
- mutant phenotype: Specific phenotype on inositol and cofit with other nearby components
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
25% identity, 78% 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...”
BCAL1433 putative sugar transport system permease protein from Burkholderia cenocepacia J2315
30% identity, 64% 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...”
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
29% identity, 85% 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
- 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:...”
- 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...”
RSP_3501 ABC sugar transporter, inner membrane subunit from Rhodobacter sphaeroides 2.4.1
28% identity, 79% coverage
NCgl0030 ABC transporter permease from Corynebacterium glutamicum ATCC 13032
cg0045 ABC transporter membrane protein from Corynebacterium glutamicum ATCC 13032
22% identity, 89% 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...”
EDL933_3310, EDL933_RS16220 galactose/methyl galactoside ABC transporter permease MglC from Escherichia coli O157:H7 str. EDL933
30% identity, 73% 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...”
Z3403 beta-methylgalactoside transporter inner membrane component from Escherichia coli O157:H7 EDL933
30% identity, 73% coverage
RSc1243 PROBABLE SUGAR TRANSMEMBRANE ABC TRANSPORTER PROTEIN from Ralstonia solanacearum GMI1000
26% identity, 88% coverage
SMb20903 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
30% identity, 29% coverage
RSP_2367 ABC transporter permease from Cereibacter sphaeroides 2.4.1
RSP_2367 ABC sugar (ribose) transporter, inner membrane subunit from Rhodobacter sphaeroides 2.4.1
29% identity, 59% 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....”
PSPTO_4887 branched-chain amino acid ABC transporter, permease protein from Pseudomonas syringae pv. tomato str. DC3000
31% identity, 54% coverage
- Data-Independent Acquisition Proteomics Unravels the Effects of Iron Ions on Coronatine Synthesis in Pseudomonas syringae pv. tomato DC3000
He, Frontiers in microbiology 2020 - “...Buell et al., 2003 ). The expression of ABC transporters responsible for amino acid uptake (PSPTO_4887, PSPTO_4173, PSPTO_4919, PSPTO_1258, PSPTO_1256, and PSPTO_1255), glucose ABC transporter (PSPTO_1294, PSPTO_1293, and gltK), ribose ABC transporters (rbsA-1), iron ABC transporters (PSPTO_5562 and PSPTO_5561), peptide transporters (PSPTO_4562, PSPTO_4559, dppC, PSPTO_4558, and...”
Gocc_1293 sugar ABC transporter permease from Gaiella occulta
34% identity, 34% coverage
BOV_A0935 bacterial inner-membrane translocator:Glucose/ribitol dehydrogenase from Brucella ovis ATCC 25840
BRA0993 ribose ABC transporter, permease protein from Brucella suis 1330
BCAN_B1012 probable sugar ABC transporter, permease protein from Brucella canis ATCC 23365
27% identity, 77% coverage
- 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 - “...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 - “...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...”
blr1450 ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
30% identity, 48% coverage
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)
40% identity, 36% 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
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
31% identity, 66% coverage
SPOA0257 ABC transporter permease from Ruegeria pomeroyi DSS-3
26% 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...”
Entcl_1204 ABC transporter permease from [Enterobacter] lignolyticus SCF1
26% identity, 82% 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....”
VK055_1913 ABC transporter permease from Klebsiella pneumoniae subsp. pneumoniae
24% identity, 82% coverage
Entcl_0166 ABC transporter permease from [Enterobacter] lignolyticus SCF1
25% identity, 85% 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...”
PP_4843 branched-chain amino acid ABC transporter, permease protein, putative from Pseudomonas putida KT2440
32% identity, 68% coverage
blr7869 ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
27% 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...”
MSMEG_6018 xylose transport system permease protein XylH from Mycobacterium smegmatis str. MC2 155
31% 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
31% identity, 32% coverage
SMb20603 putative ureashort-chain amide or branched-chain amino acid uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
29% identity, 55% coverage
- Absence of functional TolC protein causes increased stress response gene expression in Sinorhizobium meliloti
Santos, BMC microbiology 2010 - “...nitrate binding protein -34.8 SMb20436 Probable nitrate transporter -62.2/-63.5 SMb20602 ABC transporter, ATP-binding protein -12.0 SMb20603 ABC transporter, permease -15.7 SMb20604 ABC transporter, permease -25.0 SMb20605 ABC transporter, periplasmic solute-binding protein -22.4 SMb21095 ABC transporter, permease -10.3 SMb21096 ABC transporter, permease -10.7 SMb21097 ABC transporter periplasmic...”
- “...associated with general amino acid transport ( aapJMPQ ) and branched-chain amino acids transport (SMb20602, SMb20603, SMb20604, SMb20605 and SMb21707) also displayed more than 12-fold decreased expression (Table 2 ). Genes encoding another ABC-type transporter putatively involved in the transport of spermidine/putrescine (SMc01963, SMc01964, SMc01965 and...”
- The time course of the transcriptomic response of Sinorhizobium meliloti 1021 following a shift to acidic pH
Hellweg, BMC microbiology 2009 - “...for filtering. Additionally, genes coding for an ABC transport system ( smb21707 , smb20602 , smb20603 , smb20604 and smb20605 ) sharing homologies with amino acid and urea/short chain amide transport systems are present in cluster G. In addition to this transport system genes ( smb20141...”
BMEII0302 RIBOSE TRANSPORT SYSTEM PERMEASE PROTEIN RBSC from Brucella melitensis 16M
27% identity, 77% 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...”
BCAN_B0268 inner-membrane translocator from Brucella canis ATCC 23365
BRA0267 sugar ABC transporter, permease protein from Brucella suis 1330
26% identity, 72% 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...”
H281DRAFT_01115 deoxynucleoside transporter, permease component 1 from Paraburkholderia bryophila 376MFSha3.1
25% identity, 69% 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.
BOV_A0242 sugar ABC transporter, permease protein from Brucella ovis ATCC 25840
26% identity, 72% 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...”
BMEII0981 XYLOSE TRANSPORT SYSTEM PERMEASE PROTEIN XYLH from Brucella melitensis 16M
26% identity, 74% 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...”
DR_A0261 branched-chain amino acid ABC tranpsorter, ATP binding protein from Deinococcus radiodurans R1
31% identity, 26% coverage
- Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans
Wang, Nucleic acids research 2024 - “...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 1.42 A2G07_RS01380 DR_2440 tRNA-dihydrouridine synthase family protein 1.58 NA 1.60 A2G07_RS15955...”
- “...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, directly...”
A2G07_RS14755 ABC transporter permease subunit from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
31% identity, 26% coverage
SMa0198 putative ABC transporter, permease from Sinorhizobium meliloti 1021
25% identity, 79% coverage
Gocc_0079 ABC transporter permease from Gaiella occulta
26% identity, 59% coverage
SY28_RS09865 ABC transporter permease subunit from Meiothermus taiwanensis
37% identity, 18% coverage
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
25% identity, 85% 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...”
slr1201 unknown protein from Synechocystis sp. PCC 6803
26% identity, 55% coverage
- Site-2 Protease Slr1821 Regulates Carbon/Nitrogen Homeostasis during Ammonium Stress Acclimation in Cyanobacterium Synechocystis sp. PCC 6803
Lin, International journal of molecular sciences 2023 - “.../ sll1017 , amt3 / sll0537 ), urea ( urtABC / slr0447 , slr1200 , slr1201 ), nitrate/nitrite ( nrtABCD/sll1450-53 ), arginine and glutamine ( bgtB / sll1270 ) were consistently suppressed two to twenty folds, thus implying the effective attenuation of excess nitrogen influx. Similar...”
- The Signal Transduction Protein PII Controls Ammonium, Nitrate and Urea Uptake in Cyanobacteria
Watzer, Frontiers in microbiology 2019 - “...10 5 2.6 10 5 UrtB Slr1200 41.68 2.4 10 5 1.6 10 6 UrtC Slr1201 45.08 3.5 10 5 4.9 10 6 UrtD Sll0764 41.19 8.1 10 5 3.9 10 6 UrtE Sll0374 27.42 6.5 10 5 6.4 10 6 UreA Slr1256 11.06 4.9 10...”
- Genomics of Urea Transport and Catabolism in Cyanobacteria: Biotechnological Implications
Veaudor, Frontiers in microbiology 2019 - “...urea uptake system permease UrtB/LivH slr1200 urtC ABC high affinity urea uptake system permease UrtC slr1201 urtD/livG ABC high affinity urea uptake system ATPase UrtD sll0764 urtE/braG UrtE branched-chain amino acid transport ATP-binding protein/livF sll0374 Urea carboxylase and allophanate hydrolase uc Urea carboxylase/urea amidolase gll0958 ah...”
- Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803
Giner-Lamia, Nucleic acids research 2017 - “...ABC-type urea transport system 1.48 6.5E-09 slr1200 urtB Urea transport system permease protein 5.19 8.1E-71 slr1201 urtC Urea transport system permease protein 3.33 4.7E-17 Nitrogen in the form of ammonium is incorporated into amino acids by sequential action of GS and glutamate synthase (GOGAT) (Figure 3...”
- Proteomic and metabolomic analyses reveal metabolic responses to 3-hydroxypropionic acid synthesized internally in cyanobacterium Synechocystis sp. PCC 6803
Wang, Biotechnology for biofuels 2016 - “...were found up-regulated, including Slr1247, Sll0540, Sll0679, Sll0680, Sll1598, Sll0385, Sll1699, Sll0374, Sll1270, Slr0559 and Slr1201. Phosphorus is necessary to the ATP and NADPH synthesis, and in Synechocystis transporters with three associated Pi-binding proteins (PBPs) have been identified, they are PstS1 (Sll0680), PstS2 (Slr1247) and SphX...”
- “...worth further investigation. Finally, urea transport system ATP-binding protein Sll0374, urea transport system permease protein Slr1201, arginine/lysine/histidine/glutamine transport system substrate-binding and permease protein Sll1270 and neutral amino acid transport system substrate-binding protein Slr0559 were also up-regulated, although their roles in metabolic responses to 3-HP synthesis is...”
- Comparative analysis of the primary transcriptome of Synechocystis sp. PCC 6803
Kopf, DNA research : an international journal for rapid publication of reports on genes and genomes 2014 - “...for nitrate [e.g. nrtABCD ( sll1450-53 )], urea [e.g. urtABC ( slr0447 , slr1200 , slr1201 )] and ammonium [e.g. amt1 ( sll0108 ), amt2 ( sll1017 ) and amt3 ( sll0537 )] become up-regulated. 38 40 We observed a higher read number for the corresponding...”
- Global gene expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to irradiation with UV-B and white light
Huang, Journal of bacteriology 2002 - “...0.27 sll1017 sll0108 sll0771 slr1200 sll1453 sll1270 sll1762 slr0681 slr1201 0.89 0.15 0.75 0.11 0.65 0.12 0.72 0.15 1.63 0.21 0.57 0.18 0.56 0.16 0.71 0.11...”
- Identification of genes encoding amino acid permeases by inactivation of selected ORFs from the Synechocystis genomic sequence
Quintero, Genome research 2001 - “...are a set of ORFs (slr0447, slr1200, slr1201, sll0764, and sll0374), which have been found to constitute an ABC-type permease for...”
ESA_RS03665 ABC transporter permease from Cronobacter sakazakii ATCC BAA-894
25% identity, 84% 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...”
alr2536 permease protein of branched-chain amino acid ABC transporter from Nostoc sp. PCC 7120
28% identity, 48% 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...”
bll3384 ABC transporter ATP-binding protein from Bradyrhizobium japonicum USDA 110
27% identity, 61% coverage
Q9HUV3 Probable permease of ABC transporter from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
32% identity, 57% coverage
pRL80088 putative permease component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
25% identity, 48% coverage
C0J08_14195 ABC transporter permease subunit from Marinomonas sp. CT5
30% identity, 24% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory