PaperBLAST
PaperBLAST Hits for TCDB::Q9X053 Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)) (323 a.a., MKKSLFVVLV...)
Show query sequence
>TCDB::Q9X053 Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
MKKSLFVVLVLVGLLLVSFTGLAQEQQKPKGKMAIVISTLNNPWFVVLAETAKQRAEQLG
YEATIFDSQNDTAKESAHFDAIIAAGYDAIIFNPTDADGSIANVKRAKEAGIPVFCVDRG
INARGLAVAQIYSDNYYGGVLMGEYFVKFLKEKYPDAKEIPYAELLGILSAQPTWDRSNG
FHSVVDQYPEFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALGAMKACEA
AGRTDIYIFGFDGAEDVINAIKEGKQIVATIMQFPKLMARLAVEWADQYLRGERSFPEIV
PVTVELVTRENIDKYTAYGRKEE
Running BLASTp...
Found 250 similar proteins in the literature:
TC 3.A.1.2.19 / Q9X053 Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
TM0958 ribose ABC transporter, periplasmic ribose-binding protein from Thermotoga maritima MSB8
TM_0958 D-ribose ABC transporter substrate-binding protein from Thermotoga maritima MSB8
100% identity, 100% coverage
- substrates: Ribose
- Retracing the evolution of a modern periplasmic binding protein
Michel, 2023 - Retracing the evolution of a modern periplasmic binding protein
Michel, Protein science : a publication of the Protein Society 2023 - “...being observable between residues 30155 and 156310 of the RBP (numbering consistent with Uniprot entry Q9X053). To compare this with the alignment of the proposed progenitor flavodoxinlike proteins, the same alignment was generated within the Fuzzle database (Ferruz et al., 2021 ), which automatically excludes sequences...”
- “...HHsuite (Gabler et al., 2020 ) (Figure S1 ). The sequence of fulllength RBP (UniProtID: Q9X053) excluding the extracellular transport signal was run with standard parameters, but disabling secondary structure scoring and increasing the number of maximal hits to 10,000 to also obtain sequences with lower...”
- myo-inositol and D-ribose ligand discrimination in an ABC periplasmic binding protein
Herrou, Journal of bacteriology 2013 - “...Thermoanaerobacter tengcongensis Q8RD41 (32), and Thermotoga maritima Q9X053 (30), were used to construct a BIONJ neighbor-joining phylogenetic tree with the...”
- “...(49), T. tengcongensis (Q8RD41) (32), and T. maritima (Q9X053) (30), were aligned in order to calculate evolutionary protein distances and construct a...”
- Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases
Frock, Applied and environmental microbiology 2012 - “...TM1235 TM0595 TM1199 xylE2 TM1855 TM0418 TM0432 TM0958 CTN_0408 CTN_0664 CTN_1767 CTN_1367 CTN_0765 CTN_1348 CTN_1502-3 CTN_0780 CTN_0638 CTN_0622 CTN_0576...”
- Ligand-induced conformational changes in a thermophilic ribose-binding protein
Cuneo, BMC structural biology 2008 - “...identified in the T. maritima genome sequence [ 17 ] as open reading frame (ORF) tm0958 , based on sequence similarity to the E. coli RBP, and genetic linkage of this ORF within a putative operon that contains sequences for ABC transporters characteristic of a ribose...”
- “...one truncated copy of tmRBP. Neither full-length, nor truncated homodimers were observed. Analysis of the tm0958 DNA sequence suggests that this truncation may result from translation initiation at methionine 142 (numbering according to NCBI NP 228766 ), which is preceded by a ribosome binding site (Figure...”
- Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
Nanavati, Applied and environmental microbiology 2006 - “...TM0418 (InoE), myo-inositol; TM0432 (AguE), -1,4-digalactouronic acid; and TM0958 (RbsB), ribose. We found that T. maritima does not grow on several complex...”
- “...The affinity of the putative ribose-binding protein TM0958 for radiolabeled ribose was measured by precipitating the protein-ligand complex with ammonium...”
- The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture
Johnson, Applied and environmental microbiology 2006 - “...TM0433 TM0533 TM0624 TM0627 TM0633 TM0752 TM0767 TM0958 TM1064 TM1068 TM1199 TM1223 TM1227 TM1231 TM1232-35 TM1524 TM1525 TM1650 TM1746-49 TM1751 TM1752...”
- An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
Conners, Journal of bacteriology 2005 - “...the putative binding protein of this transport set (TM0958) was more highly upregulated than other transporter components. Expression results shown here suggest...”
- Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species
Mongodin, Journal of bacteriology 2005 - “...for subunits of a ribose ABC transporter (TM0955, TM0956, TM0958, and TM0959). Thermotoga strains LA10, LA4, RQ7, and VMA1/ L12B are closely related to T....”
- The role of solute binding proteins in signal transduction
Matilla, Computational and structural biotechnology journal 2021 - “...cellopentaose, xylopentaose, laminaripentaose, mannohexaose 0.25% (w/v) mannose vs 0.25% (w/v) arabinose Up-regulated b [195] RBP TM_0958 /T a Peripla_BP_4/PF13407 T. maritima D-ribose 10 mM D-ribose vs 10 mM L-arabinose 22 b [186] 10 mM D-ribose vs 10 mM L-trehalose 42 b RbsB rbsB /T a Peripla_BP_4/PF13407...”
CTN_1618 Ribose ABC transporter, periplasmic ribose-binding protein from Thermotoga neapolitana DSM 4359
100% identity, 99% coverage
2fn8A / Q9X053 Thermotoga maritima ribose binding protein ribose bound form (see paper)
100% identity, 90% coverage
- Ligand: beta-d-ribopyranose (2fn8A)
TTE0206 Periplasmic sugar-binding proteins from Thermoanaerobacter tengcongensis MB4
42% identity, 97% coverage
2ioyA / Q8RD41 Crystal structure of thermoanaerobacter tengcongensis ribose binding protein (see paper)
45% identity, 87% coverage
- Ligand: beta-d-ribopyranose (2ioyA)
APIBP_PARG4 / B1G898 D-apiose import binding protein; D-apiose binding SBP from Paraburkholderia graminis (strain ATCC 700544 / DSM 17151 / LMG 18924 / NCIMB 13744 / C4D1M) (see paper)
42% identity, 97% coverage
- function: Part of an ABC transporter complex involved in D-apiose import (Probable). Binds D-apiose, D-ribose and D-ribulose (PubMed:29867142).
- Functional assignment of multiple catabolic pathways for D-apiose.
Carter, Nature chemical biology 2018 - “...in red; located in a single cluster): UniProt ID A6VKQ8 from Actinobacillus succinogenes ATCC 55618, B1G898 from Burkholderia graminis C4D1M, and Q2JZQ5 from Rhizobium etli CFN42) ( Supplementary Table 1 ). We determined that D-apiose is the physiological ligand for the SBPs. The SBP from Rhizobium...”
- “...binding SBP), A6X3G3 (D-apionate lactonase), A7IJG7 (3-oxo-isoapionate 4-phosphate transcarboxylase), B1G889 (3-oxo-isoapionate kinase), B1G894 (D-apiose dehydrogenase), B1G898 (D-apiose binding SBP), B9JK73 (3-oxo-isoapionate 4-phosphate decarboxylase), B9JK75 (D-apionate oxidoisomerase), B9JK80 (D-apiose dehydrogenase), B9JN19 (D-erythrulose 4-phosphate isomerase), B9JN20 (L-eythrulose 1-phosphate isomerase), C0CMQ5/C0CMQ6 (3-oxo-isoapionate transketolase), C0CMQ7 (D-apionate oxidoisomerase), C0CMQ8 (hydroxypyruvate reductase),...”
5ibqA / Q2JZQ5 Crystal structure of an abc solute binding protein from rhizobium etli cfn 42 (rhe_pf00037,target efi-511357) in complex with alpha-d-apiose
45% identity, 82% coverage
- Ligands: 3-c-(hydroxylmethyl)-alpha-d-erythrofuranose; calcium ion (5ibqA)
APIBP_RHIEC / Q2JZQ5 D-apiose import binding protein; D-apiose binding SBP from Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42) (see paper)
45% identity, 82% coverage
- function: Part of an ABC transporter complex involved in D-apiose import (Probable). Binds D-apiose, D-ribose and D-ribulose (PubMed:29867142).
- Functional assignment of multiple catabolic pathways for D-apiose
Carter, Nature chemical biology 2018 - “...cluster): UniProt ID A6VKQ8 from Actinobacillus succinogenes ATCC 55618, B1G898 from Burkholderia graminis C4D1M, and Q2JZQ5 from Rhizobium etli CFN42) ( Supplementary Table 1 ). We determined that D-apiose is the physiological ligand for the SBPs. The SBP from Rhizobium etli CFN42 (UniProt ID Q2JZQ5) was...”
- “...Agrobacterium radiobacter K84 that encodes an SBP (UniProt ID B9JK76) sharing 92% sequence identity with Q2JZQ5; we also disrupted four proximal genes encoding putative pathway enzymes. For all mutants, growth with D-ribose and D-ribulose as carbon source was unaffected; however, growth with D-apiose was reduced or...”
AOT13_01795 ribose ABC transporter substrate-binding protein RbsB from Parageobacillus thermoglucosidasius
40% identity, 94% coverage
VPA1084 ribose ABC transporter, periplasmic D-ribose-binding protein from Vibrio parahaemolyticus RIMD 2210633
A79_4530 D-ribose-binding periplasmic protein from Vibrio parahaemolyticus AQ3810
40% identity, 96% coverage
- Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus
Kalburge, Infection and immunity 2017 - “...regions (mannitol, VPA0500 to VPA0501; ribose, VPA1087 to VPA1084), and a promoter region for a mannose transport and metabolism cluster (VPA1424 to VPA1425)....”
- “...transporter (VP0008 to VP0006), ribose (VPA1087 to VPA1084), and mannose (VPA1424 to VPA1425) metabolism and transporter, mannitol (VPA0500 to VPA0501), and...”
- Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis
Sun, International journal of molecular sciences 2014 - “...transporter ATP binding protein VPA1086 ( rbsC ) Chn25A_0595 8.678 Ribose ABC transporter permease protein VPA1084 Chn25A_0596 7.7049 d -ribose transporter subunit RbsB Maltose transport VPA1399 ( malG ) Chn25A_1076 2.0352 Maltose transporter permease VPA1400 ( malF ) Chn25A_1077 2.8009 Maltose transporter membrane protein VPA1401( malE...”
- Comparative Proteomics and Secretomics Revealed Virulence and Antibiotic Resistance-Associated Factors in Vibrio parahaemolyticus Recovered From Commonly Consumed Aquatic Products
Zhu, Frontiers in microbiology 2020 - “...TSBP H323_16900 30,690.84 4.98 62.67 Hydrolase activity, kinase activity S16 A6AZB7 D -Ribose-binding periplasmic protein A79_4530 30,676.77 4.91 65.07 ATPase-coupled monosaccharide transmembrane transporter activity, hydrolase activity S17 A0A0D1F2I1 Succinate dehydrogenase ironsulfur subunit H323_04040 27,500.27 4.94 31.30 2 Iron, 2 sulfur cluster binding, 3 iron, 4 sulfur...”
DDA3937_RS00045 ribose ABC transporter substrate-binding protein RbsB from Dickeya dadantii 3937
40% identity, 87% coverage
B5S52_21960 ribose ABC transporter substrate-binding protein RbsB from Pectobacterium brasiliense
39% identity, 87% coverage
HM1_2420 ribose abc transporter, ribose-binding protein from Heliobacterium modesticaldum Ice1
38% identity, 95% coverage
ECA_RS00065 ribose ABC transporter substrate-binding protein RbsB from Pectobacterium atrosepticum SCRI1043
39% identity, 87% coverage
TC 3.A.1.2.11 / Q92WK4 EryG aka RB0335, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) from Rhizobium meliloti (Sinorhizobium meliloti) (see paper)
41% identity, 89% coverage
APIBP_RHIR8 / B9JK76 D-apiose import binding protein; D-apiose binding SBP from Rhizobium rhizogenes (strain K84 / ATCC BAA-868) (Agrobacterium radiobacter) (see paper)
41% identity, 90% coverage
- function: Part of an ABC transporter complex involved in D-apiose import.
disruption phenotype: Disruption of the gene does not affect growth on D-ribose and D-ribulose as a carbon source but decreases growth with D- apiose. - Functional assignment of multiple catabolic pathways for D-apiose
Carter, Nature chemical biology 2018 - “...We then disrupted the gene in Agrobacterium radiobacter K84 that encodes an SBP (UniProt ID B9JK76) sharing 92% sequence identity with Q2JZQ5; we also disrupted four proximal genes encoding putative pathway enzymes. For all mutants, growth with D-ribose and D-ribulose as carbon source was unaffected; however,...”
Entcl_4402 ribose ABC transporter substrate-binding protein RbsB from [Enterobacter] lignolyticus SCF1
40% identity, 87% coverage
- Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1
Deangelis, Frontiers in microbiology 2013 - “...Pyruvate metabolism 3.770 2.490 Entcl_0617 AI-2 transport system substrate-binding protein (642484..643485) ABC transporters 3.180 1.780 Entcl_4402 Periplasmic binding protein/LacI transcriptional regulator (complement(4764359..4765249)) ABC transporters 2.020 1.704 Entcl_1207 ABC transporter, substrate-binding protein (complement(1260320..1261303)) ABC transporters 2.380 1.564 Entcl_2658 Isocitrate dehydrogenase, NADP-dependent (complement(2808830..2810080)) Glutathione metabolism 2.010 1.091 Entcl_0176...”
APIBP_ACTSZ / A6VKQ8 D-apiose import binding protein; D-apiose binding SBP from Actinobacillus succinogenes (strain ATCC 55618 / DSM 22257 / CCUG 43843 / 130Z) (see paper)
42% identity, 81% coverage
- function: Part of an ABC transporter complex involved in D-apiose import (Probable). Binds D-apiose, D-ribose and D-ribulose (PubMed:29867142).
- Cotinine Hydroxylase CotA Initiates Biodegradation of Wastewater Micropollutant Cotinine in Nocardioides sp. Strain JQ2195.
Zhao, Applied and environmental microbiology 2021 (no snippet) - Functional assignment of multiple catabolic pathways for D-apiose
Carter, Nature chemical biology 2018 - “...bound D-apiose, D-ribose, and D-ribulose (highlighted in red; located in a single cluster): UniProt ID A6VKQ8 from Actinobacillus succinogenes ATCC 55618, B1G898 from Burkholderia graminis C4D1M, and Q2JZQ5 from Rhizobium etli CFN42) ( Supplementary Table 1 ). We determined that D-apiose is the physiological ligand for...”
- “...to proteins with following UniProt IDs ( Supplementary Table 7 ): A6VKQ3/A6VKQ4 (D-apulose 4-phosphate transketolase), A6VKQ8 (D-apiose binding SBP), A6X3G3 (D-apionate lactonase), A7IJG7 (3-oxo-isoapionate 4-phosphate transcarboxylase), B1G889 (3-oxo-isoapionate kinase), B1G894 (D-apiose dehydrogenase), B1G898 (D-apiose binding SBP), B9JK73 (3-oxo-isoapionate 4-phosphate decarboxylase), B9JK75 (D-apionate oxidoisomerase), B9JK80 (D-apiose dehydrogenase),...”
STM3884 ABC superfamily (peri_perm), D-ribose transport protein from Salmonella typhimurium LT2
P0A2C6 Ribose import binding protein RbsB from Salmonella typhi
40% identity, 87% coverage
Q8XAW6 D-ribose transporter subunit RbsB from Escherichia coli O157:H7
Z5252 D-ribose periplasmic binding protein from Escherichia coli O157:H7 EDL933
40% identity, 87% coverage
GM298_22990 ribose ABC transporter substrate-binding protein RbsB from Enterobacter sp. HSTU-ASh6
40% identity, 87% coverage
VCA0130 ribose ABC transporter, periplasmic D-ribose-binding protein from Vibrio cholerae O1 biovar eltor str. N16961
36% identity, 96% coverage
RbsB / b3751 ribose ABC transporter periplasmic binding protein from Escherichia coli K-12 substr. MG1655 (see 25 papers)
RbsB / P02925 ribose ABC transporter periplasmic binding protein from Escherichia coli (strain K12) (see 25 papers)
RBSB_ECOLI / P02925 Ribose import binding protein RbsB from Escherichia coli (strain K12) (see 5 papers)
TC 3.A.1.2.1 / P02925 RbsB aka RBSP aka PRLB aka B3751, component of Ribose porter from Escherichia coli (see 11 papers)
rbsB / GB|AAC76774.1 D-ribose-binding periplasmic protein; EC 3.6.3.17 from Escherichia coli K12 (see 11 papers)
b3751 D-ribose transporter subunit from Escherichia coli str. K-12 substr. MG1655
NP_418207 ribose ABC transporter periplasmic binding protein from Escherichia coli str. K-12 substr. MG1655
40% identity, 87% coverage
- function: Part of the ABC transporter complex RbsABC involved in ribose import. Binds ribose. Also serves as the primary chemoreceptor for chemotaxis.
subunit: The complex is composed of an ATP-binding protein (RbsA), two transmembrane proteins (RbsC) and a solute-binding protein (RbsB). - 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) - Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth
Franchini, PloS one 2015 - “...11.9 rbsD g , i b3748 D-ribose high-affinity transport system, membrane-associated protein 3.6 rbsB g b3751 D-ribose periplasmic binding protein 9.4 glpF c , f , i b3927 facilitated diffusion of glycerol 9.6 yjbB i b4020 putative alpha helix protein -3.6 malG f , g ,...”
- Time-dependent translational response of E. coli to excess Zn(II)
Easton, Journal of biomolecular techniques : JBT 2006 (secret) - DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...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 high-affinity...”
- 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.
- Analysis of conformational motions and residue fluctuations for Escherichia coli ribose-binding protein revealed with elastic network models.
Li, International journal of molecular sciences 2013 - GeneRIF: Data indicate the molecular motion of ribose-binding protein (RBP).
- The amino acid sequence of D-ribose-binding protein from Escherichia coli K12.
Groarke, The Journal of biological chemistry 1983 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Optimized Signal Peptide for Secretory Expression of Human Recombinant Somatropin in E. coli
Ahmadi, Advanced pharmaceutical bulletin 2023 - “...Escherichia coli (strain K12) P0AEG6 MKKGFMLFTLLAAFSGFAQA D-ribose-binding periplasmic protein rbsB 25 Escherichia coli (strain K12) P02925 MNMKKLATLVSAVALSATVSANAMA Cyclic di-GMP-binding protein bcsB 25 Escherichia coli (strain K12) P37652 MKRKLFWICAVAMGMSAFPSFMTQA Threonine-rich inner membrane protein GfcA gfcA 21 Escherichia coli (strain K12) P75885 MKHKLSAILMAFMLTTPAAFA Salivary acidic proline -rich phosphoprotein...”
- Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...conversion Periplasm 10 P0AAX3 YBIJ Function unknown Periplasm 11 P0AES9 HDEA Function unknown Periplasm 12 P02925 RBSB Carbohydrate transport and metabolism Periplasm 13 P0A862 TPX Posttranslational modification, protein turnover, chaperones Periplasm 14 P64534 RCNB Function unknown Periplasm 15 P0AFM2 PROX Amino acid transport and metabolism Periplasm...”
- FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts
Jeong, Nature communications 2022 - “...Out of them, 12 were FI90 dataset exclusive, containing ribose import binding protein RbsB (UniProtKB: P02925) with known signal peptide cleavage. In total, 600 unmodified and truncated proteoforms have been identified from the FI90 dataset while 375 have been identified from the ST90 dataset. Thus we...”
- The role of solute binding proteins in signal transduction
Matilla, Computational and structural biotechnology journal 2021 - “...[38] , [39] , [42] , [128] , [129] , [130] RBP Ribose-binding protein/T a P02925 (31) Peripla_BP_4 (PF13407) D-ribose (0.13) 2DRI PotD spermidine binding protein/T a P0AFK9 (39) SBP_bac_8 (PF13416) Spermidine (3.2) 1POY [43] , [131] Tsr P02942 E. coli -Proteobacteria TarH (PF 02203) LsrB/T...”
- Identification of Functional Interactome of Colistin Resistance Protein MCR-1 in Escherichia coli
Li, Frontiers in microbiology 2020 - “...P0AG30 Transcription termination factor Rho 47,032 rho 28 P0AGE0 Single-stranded DNA-binding protein 18,963 ssb 29 P02925 Ribose import binding protein RbsB 30,931 rbsB 30 P0A7J7 50S ribosomal protein L11 14,923 rplK 31 P64596 Uncharacterized protein YraP 20,073 yraP 32 Q0TCG0 50S ribosomal protein L15 14,957 rplO...”
- 129Xe NMR-Protein Sensor Reveals Cellular Ribose Concentration
Zemerov, Analytical chemistry 2020 - “...preparation. The codon-optimized gene for ribose binding protein (RBP) from Escherichia coli (UniProt accession no. P02925) incorporating a L19A mutation was synthesized and cloned into a pJ411 vector by ATUM. The RBP(L19A) gene was amplified using the primers listed in Table S1 and cloned into a...”
- Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli
Jindal, BMC microbiology 2019 - “...Broad-specificity pyrimidine permease P75892 [ 123 125 ] rbsB Ribose ABC transporter periplasmic binding protein P02925 [ 126 ] ybiO mechanosensitive ion channel P75783 [ 127 ] yifK probable transport protein (possibly amino acid) P27837 [ 128 ] yliA/gsiA ATP-driven Glutathione importer P75796 [ 129 ]...”
- Impact of chlorhexidine digluconate and temperature on curli production in Escherichia coli-consequence on its adhesion ability
Coquet, AIMS microbiology 2017 - “...5 228 2.98 D-ribose-binding periplasmic protein (rbsB) Transport of carbohydrateServe as primary receptor for chemotaxis P02925 P 70 9 716 2.27 DcrB protein (dcrB) Required for phage C1 adsorption P0AEE1 P 66 4 181 4.18 Vitamin B12 transport periplasmic protein (btuE) Part of btuCED operon. the...”
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1dbpA / P02925 Identical mutations at corresponding positions in two homologous proteins with non-identical effects (see paper)
40% identity, 87% coverage
- Ligand: beta-d-ribopyranose (1dbpA)
RBAM_RS16755 ribose ABC transporter substrate-binding protein RbsB from Bacillus velezensis FZB42
37% identity, 91% coverage
HMPREF0389_00295 ribose ABC transporter substrate-binding protein RbsB from Filifactor alocis ATCC 35896
41% identity, 88% coverage
- Proteome variation among Filifactor alocis strains
Aruni, Proteomics 2012 - “...HMPREF0389_01476 Hypothetical protein 20.1/20 48/0.42 4 1.973 M DUF 1836 uncharacterized domain 0.78 Nonsecretory 45. HMPREF0389_00295 Ribose ABC transporter, periplasmic ribose binding protein 32/32.4 65/0.56 6 0.300 M Periplasmic binding fold domain 2.84 N terminal signal peptide sequence 46. HMPREF0389_01217 Hypothetical protein 37.3/37 21/0.09 4 3.837...”
RBSB_BACSU / P36949 Ribose import binding protein RbsB from Bacillus subtilis (strain 168) (see 2 papers)
BSU35960 ribose ABC transporter (ribose-binding lipoprotein) from Bacillus subtilis subsp. subtilis str. 168
36% identity, 91% coverage
- function: Part of the ABC transporter complex RbsABC involved in ribose import. Binds ribose.
subunit: The complex is composed of an ATP-binding protein (RbsA), two transmembrane proteins (RbsC) and a solute-binding protein (RbsB) (By similarity). Interacts with FloT (PubMed:23651456). - myo-inositol and D-ribose ligand discrimination in an ABC periplasmic binding protein
Herrou, Journal of bacteriology 2013 - “...enterica serovar Typhimurium F5ZWH0 (48), Bacillus subtilis P36949 (49), Thermoanaerobacter tengcongensis Q8RD41 (32), and Thermotoga maritima Q9X053 (30), were...”
- “...S. enterica serovar Typhimurium (F5ZWH0) (48), B. subtilis (P36949) (49), T. tengcongensis (Q8RD41) (32), and T. maritima (Q9X053) (30), were aligned in order...”
- ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow
Wu, Microorganisms 2023 - “...GPR relationship of the ribose ABC transport system is BSU35930 and BSU35940 and BSU35950 and BSU35960 in the model, but the GPRuler tool did not include BSU35930 . By searching UniProt, we found that BSU35930 encodes D-ribose pyranase, which catalyzes the interconversion of beta-pyran and beta-furan...”
TC 3.A.1.2.13 / A6VKT0 RbsB, 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)
37% identity, 95% coverage
- substrates: Autoinducer-2
NTHI0632 D-ribose transporter subunit RbsB from Haemophilus influenzae 86-028NP
38% identity, 95% coverage
4zjpA / A6VKT0 Structure of an abc-transporter solute binding protein (sbp_ipr025997) from actinobacillus succinogenes (asuc_0197, target efi-511067) with bound beta-d-ribopyranose
38% identity, 85% coverage
- Ligand: beta-d-ribopyranose (4zjpA)
HI0504 D-ribose ABC transporter, periplasmic-binding protein (rbsB) from Haemophilus influenzae Rd KW20
38% identity, 95% coverage
TC 3.A.1.2.16 / Q1M4Q9 Periplasmic erythritol binding protein, 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)
pRL120200 putative substrate binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
38% identity, 89% coverage
- substrates: Erythritol
- Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis
Wheatley, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret) - Metabolic Adaptation of a C-Terminal Protease A-Deficient Rhizobium leguminosarum in Response to Loss of Nutrient Transport
Jun, Frontiers in microbiology 2017 - “...Ile, Leu, and Val biosynthesis 36/311 3.14 Predicted erythritol ABC transporter 2, substrate-binding component VBIRhiLeg32091_0201 pRL120200 13 Solute binding component of ABC transporter 36/262 1.95 Fumarylpyruvate hydrolase VBIRhiLeg32091_4442 RL3169 14 Tyrosine metabolism 36/706 1.57 groEL f VBIRhiLeg32091_2042 RL0883 46 Protein folding 36/485 2.79 Leu, Ile, Val,...”
- “...a delayed chemotactic response to sugars ( Shimoda et al., 1993 ). EryG encoded by pRL120200 is a periplasmic-binding protein for the erythritol ABC transporter ( Yost et al., 2006 ) and its reduced abundance could impact the net transport of erythritol. The gene products of...”
VK055_1936 D-ribose ABC transporter substrate-binding protein from Klebsiella pneumoniae subsp. pneumoniae
37% identity, 92% coverage
- A Serendipitous Mutation Reveals the Severe Virulence Defect of a Klebsiella pneumoniae fepB Mutant
Palacios, mSphere 2017 - “...transport system/permease component family protein VK055_1938 Heme ABC exporter, ATP-binding protein CcmA VK055_1937 Hypothetical protein VK055_1936 Periplasmic binding and sugar binding domain of LacI family protein VK055_1935 4-Phosphopantetheinyl transferase superfamily protein, EntD VK055_1934 TonB-dependent siderophore receptor family protein, FepA smr_C mutant VK055_1933 Fes VK055_1932 MbtH-like family...”
eryG / Q2YIY2 putative erythritol ABC transporter substrate-binding protein from Brucella abortus (strain 2308) (see 3 papers)
BAW_20365 D-ribose ABC transporter substrate-binding protein from Brucella abortus
BAB2_0377 Periplasmic binding protein/LacI transcriptional regulator from Brucella melitensis biovar Abortus 2308
BruAb2_0373 RbsB-2, ribose ABC transporter, periplasmic D-ribose-binding protein from Brucella abortus biovar 1 str. 9-941
37% identity, 89% coverage
- The regulon of Brucella abortus two-component system BvrR/BvrS reveals the coordination of metabolic pathways required for intracellular life
Rivas-Solano, PloS one 2022 - “...] BAW_20116 BAB2_0118 vjbR LuxR family regulatory protein VjbR, important for virulence [ 64 ] BAW_20365 BAB2_0377 eryG; rbsB-2 Erythritol periplasmic binding protein, important for virulence [ 65 ] BAW_20366 BAB2_0378 deoR DeoR family regulatory protein, erythritol regulator [ 66 ] BAW_20415 BAB2_0432 nikR Nickel-responsive regulator...”
- The regulon of Brucella abortus two-component system BvrR/BvrS reveals the coordination of metabolic pathways required for intracellular life
Rivas-Solano, PloS one 2022 - “...BAW_20116 BAB2_0118 vjbR LuxR family regulatory protein VjbR, important for virulence [ 64 ] BAW_20365 BAB2_0377 eryG; rbsB-2 Erythritol periplasmic binding protein, important for virulence [ 65 ] BAW_20366 BAB2_0378 deoR DeoR family regulatory protein, erythritol regulator [ 66 ] BAW_20415 BAB2_0432 nikR Nickel-responsive regulator of...”
- Proteomics of Brucella
Poetsch, Proteomes 2020 - “...protein/glutamate receptor: bacterial extracellular solute-binding protein, family 3 (BAB2_0558); RbsB-2: periplasmic binding protein/LacI transcriptional regulator (BAB2_0377); DnaK: chaperone protein (BAB1_2129); SurA: trigger factor-peptidyl prolyl cis-trans isomerase (BAB1_0917); AspC: aminotransferase (BAB1_1514); CHG: choloylglycine hydrolase (BAB1_1488); SerC: phosphoserine transaminase (BAB1_1699); GroES: 10 kDa chaperonin (BAB2_0190); IalB: invasion protein...”
- Evaluation of the effects of erythritol on gene expression in Brucella abortus
Rodríguez, PloS one 2012 - “...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 2.48 Phosphoglycerate kinase COG0126G BAB1_0448 -...”
- Intracellular adaptation of Brucella abortus
Lamontagne, Journal of proteome research 2009 - “...24 hours after infection, as were other sugar metabolism enzymes and several sugar ABC transporters (BAB2_0377, BAB2_0938, BAB2_0547, BAB1_0238). Interestingly, the decline of the Omp2b porin (BAB1_0660) was clearly evident at 20 hours. Two proteins (BAB1_1645 and BAB1_1646) that are part of the phosphoenolpyruvate carbohydrate phosphotransferase...”
- “...of the infection. This interpretation is supported by the uniform reduction of 5 sugar transporters (BAB2_0377, BAB2_0938, BAB2_0547, BAB1_0238, BAB1_0660) during this period, suggesting a limited availability of sugar substrates throughout the intracellular infection period. Alternative routes that bypass some steps of the TCA cycle, such...”
- Adhesins of Brucella: Their Roles in the Interaction with the Host
Bialer, Pathogens (Basel, Switzerland) 2020 - “...peptic digestion suggested that SP29 is a D-ribose-binding periplasmic protein precursor found in B. melitensis (BruAb2_0373) ( Figure 1 ). No further characterization of this protein or its importance for Brucella pathogenesis has been reported despite the demonstration that B. melitensis is able to invade erythrocytes...”
- “...Host Ligands Detected Cellular Adhesion Role In Vivo Infection Role Reference SP29 B. abortus 9-941 BruAb2_0373 WP_002965789.1 D-ribose ABC transporter substrate-binding protein Sialic acid-containing proteins Erythrocytes ND [ 60 ] SP41 B. abortus 9-941 BruAb2_0571 WP_002965982.1 ATP-binding cassette transporter Sialic acid-containing proteins Epithelial (HeLa) No role...”
BRA0858 ribose ABC transporter, periplasmic D-ribose-binding protein from Brucella suis 1330
BCAN_B0875 rhizopine-binding protein precursor from Brucella canis ATCC 23365
37% identity, 89% coverage
- RegA Plays a Key Role in Oxygen-Dependent Establishment of Persistence and in Isocitrate Lyase Activity, a Critical Determinant of In vivo Brucella suis Pathogenicity
Abdou, Frontiers in cellular and infection microbiology 2017 - “...glycolysis in Brucella devoid of phosphofructokinase (Figure 6B ). In agreement, ABC-transporter periplasmic binding proteins (BRA0858 and BRA1150) specific for erythritol and xylose (Table S2 ), whose respective metabolites erythrose-4-P and xylulose-5-P can be used in carbohydrate metabolism solely via the PPC, were repressed by RegA....”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 IM BMEII0700 BruAb20655 BRA0568 BOV_A0535 MOS Galactoside/Ribose import...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 IM BMEII0700 BruAb20655 BRA0568 BOV_A0535 MOS Galactoside/Ribose import IM BMEII0701 BruAb20656...”
LBA1481 D-ribose-binding protein precursor from Lactobacillus acidophilus NCFM
37% identity, 94% coverage
SXYL_01518 D-ribose ABC transporter substrate-binding protein from Staphylococcus xylosus
39% identity, 81% coverage
BA0669 ribose ABC transporter, ribose-binding protein from Bacillus anthracis str. Ames
36% identity, 96% coverage
- Role of luxS in Bacillus anthracis growth and virulence factor expression
Jones, Virulence 2010 - “...permease protein (rbsC) -1.42 -14.42 -12.91 -7.94 BA0669 ribose ABC transporter, ribose-binding protein (rbsB) -1.58 -15.89 -11.88 -6.96 BA0887 S-layer protein...”
- Application of in vivo induced antigen technology (IVIAT) to Bacillus anthracis
Rollins, PloS one 2008 - “...ABC transporter Membrane associated Chromosome 1/1 Predicted ABC metal ion transporter; contains lipoprotein domain Transport BA0669 ( rbsB ) Ribose binding protein of a ribose ABC transporter Membrane associated Chromosome 1/1 Contains membrane-associated signal peptide sequence Metabolism BA2125 ( narG ) Respiratory nitrate reductase, alpha subunit...”
- “...grown B. anthracis . Gene Upstream primer Downstream primer 16S TAGGTGGCAAGCGTTATC GGTGTTCCTCCATATCTCTAC BA0314 TAGGGGTTTCAGCATTAAG GTGTAATCAGAGAACTCAAC BA0669 TGTTCAATGGAACCACCAGA ATCAATTCAATGCCGCTTTC BA0698 GCAGAAATACTCGTTGCCATT GCTAGCAGTTCCGAGAAGGA BA2125 GTGGTAAAGGGGGATTCGTT GCCTGCAGCATGACTTAACA BA2748 ATCGGGCGAAGATGTTATTG ACGAGCATTTGCTTCGTTTT BA4073 ATTGCCCACATAGAATGC TATAATCGCCTTACCTGTC BA4074 GGTGGTGCTTTTTCTTTTGG GTTAAAGCCTGTGGGAGTGG BA4606 TTAATTGGCAATGTGGGTGA GCCGGTCCACTTGATACAAT BA5474 GGCGAATTCGTATCTGGTGT TGAGAAGTGCTAGGGCCTGT pXO1-110 ( pagA ) GCATGCGTCGTTCTTTGATA CCATTGTTTCAGCCCAAGTT pXO2-08...”
Bbr_1417 D-ribose ABC transporter substrate-binding protein from Bifidobacterium breve UCC2003
34% identity, 98% coverage
7e7mC / Q8E283 Crystal structure analysis of the streptococcus agalactiae ribose binding protein rbsb
36% identity, 88% coverage
- Ligand: beta-d-ribopyranose (7e7mC)
SAK_0166 ribose ABC transporter, ribose-binding protein from Streptococcus agalactiae A909
36% identity, 88% coverage
HMPREF0424_1336 periplasmic binding protein and sugar binding domain of the LacI family protein from Gardnerella vaginalis 409-05
38% identity, 88% coverage
- Comparative transcriptomic analysis of Gardnerella vaginalis biofilms vs. planktonic cultures using RNA-seq
Castro, NPJ biofilms and microbiomes 2017 - “...showed decreased transcript levels of genes encoding several factors involved in energy production, such as HMPREF0424_1336, a gene encoding primary receptors for chemotaxis and transport of many sugar based solutes. In addition, the expression levels of genes associated with glucose metabolic pathways were also lower in...”
- “...HMPREF0424_0429 (xseA) Exodeoxyribonuclease VII large subunit 6.73 4 HMPREF0424_0260 30S ribosomal protein S3 5.43 5 HMPREF0424_1336 Periplasmic-binding protein and sugar-binding domain of the LacI family protein 5.39 6 HMPREF0424_0259 50S ribosomal protein L22 5.36 7 HMPREF0424_0258 50S ribosomal protein L2 4.93 8 HMPREF0424_0471 (gap) Glyceraldehyde 3-phosphate...”
SAG0114 ribose ABC transporter, periplasmic D-ribose-binding protein from Streptococcus agalactiae 2603V/R
36% identity, 88% coverage
SAN_0145 ribose ABC transporter, periplasmic D-ribose-binding protein from Streptococcus agalactiae COH1
35% identity, 88% coverage
gbs0113 Unknown from Streptococcus agalactiae NEM316
35% identity, 88% coverage
CKS_3355 D-ribose ABC transporter substrate-binding protein from Pantoea stewartii subsp. stewartii DC283
33% identity, 90% coverage
BMEII0435 D-RIBOSE-BINDING PERIPLASMIC PROTEIN PRECURSOR from Brucella melitensis 16M
37% identity, 85% coverage
- Immuno-profiling of Brucella proteins for developing improved vaccines and DIVA capable serodiagnostic assays for brucellosis
Nandini, Frontiers in microbiology 2023 - “...translocase component YidC BMEII0275 Flagellar basal body rod modification protein BMEII0164 D-ribose-binding periplasmic protein precursor BMEII0435 Hypothetical protein BMEII0989 COML competence lipoprotein BMEI0587 Periplasmic protein of efflux system BMEI0653 ABC transporter substrate-binding protein BMEI0015 DNA mismatch repair protein MutS BMEI1801 Translocation protein TolB BMEI0339 Hypothetical protein...”
- Genomic analysis of the original Elberg Brucella melitensis Rev.1 vaccine strain reveals insights into virulence attenuation
Salmon-Divon, Virulence 2018 - “...p.His277Arg Missense variant BMEI1923 isovaleryl-CoA dehydrogenase p.Pro273Ser Missense variant BMEII0268 succinyl-diaminopimelate desuccinylase p.Cys224Tyr Missense variant BMEII0435 D-ribose ABC transporter substrate-binding protein p.Ala45fs Frameshift variant BMEII1048 60 kDa chaperonin groEL p.Cys284Arg Missense variant Virulence associated genes with differences between the Rev.1 and 16M strains To identify genes...”
- Impact of Hfq on global gene expression and intracellular survival in Brucella melitensis
Cui, PloS one 2013 - “...of the transporters involved in the uptake of different sugars (BMEI1716, BMEII0086, BMEII0114, BMEII0360, BMEII0361, BMEII0435, BMEII0590, and BMEII1053) were also less abundant in the mutant, indicating a reduced efficiency in the import of primary carbon substrates. Additionally, the lack of Hfq led to the dysregulation...”
- Characterization of outer membrane vesicles from Brucella melitensis and protection induced in mice
Avila-Calderón, Clinical & developmental immunology 2012 - “...OM Probable heat-resistant agglutinin 1 protein Rhizobium leguminosarum bv. viciae, (54.9%) D-Ribose-binding periplasmic protein precursor BMEII0435 30.99 Periplasmic binding protein and sugar-binding domain of LacI family, P Porin Rhizobium leguminosarum bv. trifolii, (59.2%) Hypothetical protein BMEI0542 BMEI0542 30.04 Unknown, EC Hypothetical protein Rhizobium sp ., (48.3%)...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 IM BMEII0700 BruAb20655 BRA0568 BOV_A0535...”
- Role in virulence of a Brucella abortus protein exhibiting lectin-like activity
Vemulapalli, Infection and immunity 2006 - “...INFECT. IMMUN. of the B. melitensis gene BMEII0435, which encodes a putative ribose-binding periplasmic protein (8). Disruption of the 14-kDa protein-encoding...”
- Comparative proteome analysis of Brucella melitensis vaccine strain Rev 1 and a virulent strain, 16M
Eschenbrenner, Journal of bacteriology 2002 - “...were also underexpressed (i.e., products of ORFs BMEII0983, BMEII0435, BMEI0755, and BMEI0742). Of the 45 underexpressed proteins, 31 were identified with high...”
- “...dehydrogenase BMEI0251 BMEI0124 BMEI0536 BMEII0844 BMEI0755 BMEII0983 BMEII0435 BMEI1923 BMEI1923 BMEII0607 BMEI1708 5.16 5.39 5.28 5.11 5.34 4.98 4.77 5.41...”
LLNZ_RS04085 substrate-binding domain-containing protein from Lactococcus cremoris subsp. cremoris NZ9000
llmg_0789 ribose ABC transporter substrate binding protein RbsB from Lactococcus lactis subsp. cremoris MG1363
33% identity, 87% coverage
SCO2747 bifunctional carbohydrate binding and transport protein from Streptomyces coelicolor A3(2)
36% identity, 39% 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...”
OKIT_0347 substrate-binding domain-containing protein from Oenococcus kitaharae DSM 17330
35% identity, 81% coverage
cg1413 secreted sugar-binding protein from Corynebacterium glutamicum ATCC 13032
34% identity, 85% 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 - “...transporter, ATPase subunit (TC 3.A.1.2.1) 1.92 cg2636 catA Catechol 1,2-dioxygenase 1.88 cg1780 pgl 6-Phosphogluconolactonase 1.87 cg1413 rbsB ABC-type ribose transporter, substrate-binding lipoprotein (TC 3.A.1.2.1) 1.85 cg0498 hemC Porphobilinogen deaminase 1.84 cg2665 Hypothetical protein 1.82 cg2181* ABC-type putative dipeptide/oligopeptide transporter, substrate-binding lipoprotein 1.80 cg1128 Hypothetical protein, similar...”
- 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 - “...2017 by University of California, Berkeley cg1488 cg1487 cg1413 cg1412 cg1658 cg1453 cg1411 cg1129 cg2893 cg1410 cg2391 cg3359 cg2894 cg1612 cg3362 cg2565...”
- 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 - “...cg0957 cg1120 cg1121 cg1343 cg1344 cg1405 cg1412 cg1413 cg1418 cg1419 cg1447 NCgl0777 NCgl0778 NCgl0779 NCgl0802 NCgl0943 NCgl0944 NCgl1141 NCgl1142 NCgl1200...”
MSMEG_3095 D-ribose-binding periplasmic protein from Mycobacterium smegmatis str. MC2 155
33% identity, 92% coverage
SMb20856 putative sugar uptake ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
32% identity, 98% coverage
B2904_orf2673 sugar ABC transporter substrate-binding protein from Brachyspira pilosicoli B2904
30% identity, 98% coverage
KP1_1422 putative rhizopine uptake ABC transport system periplasmic solute-binding protein precursor from Klebsiella pneumoniae NTUH-K2044
30% identity, 89% coverage
4ry9A / A1WJM2 Crystal structure of carbohydrate transporter solute binding protein veis_2079 from verminephrobacter eiseniae ef01-2, target efi-511009, a complex with d-talitol
29% identity, 88% coverage
- Ligand: d-altritol (4ry9A)
C9ZD81 Putative secreted solute binding protein from Streptomyces scabiei (strain 87.22)
31% identity, 81% coverage
A0R67_09330 sugar ABC transporter substrate-binding protein from Pasteurella multocida subsp. multocida
30% identity, 90% coverage
SMb21345 putative sugar uptake ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
33% identity, 87% coverage
- Genetic and computational identification of a conserved bacterial metabolic module
Boutte, PLoS genetics 2008 - “...(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 1.1e-34 SMb21377 (sugar binding protein) 5.5e-13 2.7e-6 SMb21376...”
- 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 - “...D-()-fucose, L-()-arabinose, glucose, D-()-arabinose, L-()-fucose SMb21345 Galactose SMa2305 Tagatose SMb21421 Tagatose SMb20410 Mannose, dulcitol SMb20902...”
- “...A second system was induced by galactose: ABC-T SMb21345, albeit to a lesser extent (6-fold) than ABC-T SMa0203. Tagatose induced ABC-T SMa2305 (CUT1) (5-fold)...”
4irxA / A0A0H3C834 Crystal structure of caulobacter myo-inositol binding protein bound to myo-inositol (see paper)
30% identity, 90% coverage
- Ligand: 1,2,3,4,5,6-hexahydroxy-cyclohexane (4irxA)
CD0300 D-ribose ABC transporter, substrate-binding protein from Clostridium difficile 630
30% identity, 86% coverage
- Temporal differential proteomes of Clostridium difficile in the pig ileal-ligated loop model
Janvilisri, PloS one 2012 - “...host response to CDI. For the transport and binding functional category, the expression of RbsB (CD0300), RbsA (CD0301), PotA (CD1024), FeoB1 (CD1479), MetQ (CD1491), CD1618, CD2365 were elevated whereas the expression of proteins in the gene cluster CD0873, CD0874, and CD0875 were suppressed. Interestingly, CD2169 was...”
4yo7A / Q9KAG4 Crystal structure of an abc transporter solute binding protein (ipr025997) from bacillus halodurans c-125 (bh2323, target efi- 511484) with bound myo-inositol
31% identity, 89% coverage
- Ligands: magnesium ion; 1,2,3,4,5,6-hexahydroxy-cyclohexane (4yo7A)
GK1896 sugar ABC transporter (sugar-binding protein) from Geobacillus kaustophilus HTA426
30% identity, 93% coverage
RHE_CH01210 probable sugar ABC transporter, substrate-binding protein from Rhizobium etli CFN 42
34% identity, 79% coverage
- Impact of c-di-GMP on the Extracellular Proteome of Rhizobium etli
Lorite, Biology 2022 - “...RHE_CH01465, RHE_CH04006, RHE_PF00410, RHE_CH02293, RHE_CH03027, RHE_CH03963, RHE_CH03445, RHE_PB00126, RHE_CH00175, RHE_PF00269, RHE_CH02683, RHE_CH02890, RHE_PE00259, RHE_PF00068, RHE_CH00492, RHE_CH01210, RHE_CH02898, RHE_PF00091, RHE_PB00025, RHE_PF00321, RHE_PB00139, RHE_PF00395, RHE_CH00485, RHE_PC00167, RHE_CH03866, RHE_CH02084 Bold letters indicate proteins reported as moonlighting in other organisms (see http://www.moonlightingproteins.org/proteins/ accessed on 22 November 2022). Underlined are proteins...”
PFLU3996 putative sugar-binding exported protein from Pseudomonas fluorescens SBW25
32% identity, 83% coverage
TC 3.A.1.2.21 / B8H228 Inositol ABC transporter, periplasmic inositol-binding protein IbpA, 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)
Q9A9V2 Sugar ABC transporter, periplasmic sugar-binding protein from Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)
CC0859, CC_0859 sugar ABC transporter, periplasmic sugar-binding protein from Caulobacter crescentus CB15
29% identity, 86% coverage
- substrates: myo-inositol
- Conserved ABC Transport System Regulated by the General Stress Response Pathways of Alpha- and Gammaproteobacteria
Herrou, Journal of bacteriology 2017 - “...B. burgdorferi ProX (O51169), C. crescentus 250 IbpA (Q9A9V2). Sequences without the signal peptide were aligned with Geneious 251 software, using the MUSCLE...”
- myo-inositol and D-ribose ligand discrimination in an ABC periplasmic binding protein
Herrou, Journal of bacteriology 2013 - “...to 327 of myo-inositol-binding protein (IBP; ibpA gene number CC_0859) was amplified by PCR from C. crescentus NA1000 genomic DNA. The PCR product was isolated...”
- Genetic and computational identification of a conserved bacterial metabolic module
Boutte, PLoS genetics 2008 - “...of iolR (CC1297) left the first and last 6 codons intact. The deletion of ibpA (CC0859) left the first 45 and last 38 codons intact. The deletion of iatA (CC0860) left the first 12 and last 9 codons intact. The deletion of iatP (CC0861) left the...”
- “...with in-frame deletions of each of these genes individually: C. crescentus strains CB15N ibpA ( CC0859 , i nositol b inding p rotein, NP_419676), CB15N iatA ( CC0860 , i nositol A BC t ransporter A TPase, NP_419677), and CB15N iatP ( CC0861 , i nositol...”
RALBP_PSEAE / Q9I2F8 D-ribose/D-allose-binding protein from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
PA1946 binding protein component precursor of ABC ribose transporter from Pseudomonas aeruginosa PAO1
29% identity, 89% coverage
- function: Binds specifically both D-ribose and D-allose, with affinities in the lower micromolar range.
- A Shaving Proteomic Approach to Unveil Surface Proteins Modulation of Multi-Drug Resistant Pseudomonas aeruginosa Strains Isolated From Cystic Fibrosis Patients
Montemari, Frontiers in medicine 2022 - “...= PA0176, Q9I6V6, Aerotaxis transducer Aer2; Aer = PA1561, Q9I3F6, Aerotaxis receptor Aer; RbsB = PA1946, Q9I2F8, Binding protein component of ABC ribose transporter; DppA = PA4496, Q9HVS5, Probable binding protein component of ABC transporter. Green box = P. aeruginosa -specific pathway. Click here for additional...”
- Determination of Ligand Profiles for Pseudomonas aeruginosa Solute Binding Proteins
Fernández, International journal of molecular sciences 2019 - “...including spermidine and histamine, did not reveal any binding. 2.4. Proteins Predicted to Bind Sugars PA1946 is homologous to the E.coli RbsB ribose binding protein [ 48 ] and the study of Johnson et al. [ 36 ] also predicted this ligand to interact with PA1946...”
- “...( Figure 4 A). Microcalorimetric titrations showed that d -ribose and d -allose binding to PA1946 was characterized by K D values of 2.1 and 6.6 M, respectively ( Figure 4 B). The interaction with d -arabinose is likely to occur with a much lower affinity...”
- A temporal examination of the planktonic and biofilm proteome of whole cell Pseudomonas aeruginosa PAO1 using quantitative mass spectrometry
Park, Molecular & cellular proteomics : MCP 2014 - “...samples were detected at all three time points: PA1946 (rbsB, binding the protein component of ABC ribose transporter), PA3236 (a probable glycine...”
- Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms
Amini, PLoS pathogens 2011 - “...mexE ), SAH124 (PA3844), SAH127 (PA1723, pscJ ), SAH128 (PA3222), SAH129 (PA3966), SAH130 (PA5207), SAH318 (PA1946, rbsB ), SAH320 (PA3751, purT ), and SAH328 (PA4175). NPN (final concentration of 50 M) and tobramycin (final concentration of 8 g/ml) were added after 60 and 180 seconds, respectively....”
- A Shaving Proteomic Approach to Unveil Surface Proteins Modulation of Multi-Drug Resistant Pseudomonas aeruginosa Strains Isolated From Cystic Fibrosis Patients
Montemari, Frontiers in medicine 2022 - “...AlgF Periplasmic 0.01 Q06749 algL Alginate lyase 100 G3XD47 aotJ Arginine/ornithine binding protein AotJ 0.344 Q9I2F8 rbsB Binding protein component of ABC ribose transporter 100 pae02030 Bacterial chemotaxis Q9HV60 PA4739 BON domain-containing protein 0.134 Q59635 katB Catalase 0.01 Q9I6M0 PA0270 Cupin_2 domain-containing protein 0.01 P00099 nirM...”
- “...was over-expressed in MDR vs. WT; and the Binding protein component of ABC ribose transporter (Q9I2F8) was over-expressed in PDR vs. WT ( Supplementary Figure 1B ). Aer in PA is a family of receptors able to sense cellular energy. Its transducer Aer2, a soluble receptor,...”
- Adsorption of extracellular proteases and pyocyanin produced by Pseudomonas aeruginosa using a macroporous magnesium oxide-templated carbon decreases cytotoxicity
Hirakawa, Current research in microbial sciences 2022 - “...1.02.E+07 Q9I5D1 AmpDh3 128.06 2.78.E+07 1.02.E+08 P13794 Outer membrane porin F (OprF) 126.26 8.62.E+07 1.23.E+08 Q9I2F8 D-Ribose/D-allose-binding protein (RbsB) 120.15 6.37.E+06 4.19.E+07 G3XD47 Arginine/ornithine binding protein (AotJ) 107.83 2.10.E+07 2.55.E+07 Q9I4Y4 Pyocin S5 (PyoS5) 106.84 3.93.E+07 0.00.E+00 Q9HTM5 Uncharacterized protein (PA5330) 101.42 4.72.E+07 3.21.E+07 Q9HZQ8 Aminopeptidase...”
PSPTO_2367 ribose ABC transporter, periplasmic ribose-binding protein from Pseudomonas syringae pv. tomato str. DC3000
28% identity, 89% coverage
5dteB / A6VKG5 Crystal structure of an abc transporter periplasmic solute binding protein (ipr025997) from actinobacillus succinogenes 130z(asuc_0081, target efi-511065) with bound d-allose
31% identity, 80% coverage
- Ligand: beta-d-allopyranose (5dteB)
YPTB3231 putative sugar ABC transporter periplasmic binding protein from Yersinia pseudotuberculosis IP 32953
28% identity, 94% coverage
Pf1N1B4_6035 D-ribose ABC transporter, substrate-binding component RbsB from Pseudomonas fluorescens FW300-N1B4
28% identity, 89% coverage
- mutant phenotype: Specifically important for ribose utilization. Also involved in utilization of ribonucleotides, which might be hydrolyzed before uptake.
YPO2501 sugar binding protein precursor from Yersinia pestis CO92
YPK_1611 monosaccharide-transporting ATPase from Yersinia pseudotuberculosis YPIII
32% identity, 86% coverage
- Cell membrane is impaired, accompanied by enhanced type III secretion system expression in Yersinia pestis deficient in RovA regulator
Yang, PloS one 2010 - “...Transport/binding proteins YPO1757 2.30 manY, ptsP, pel PTS system, mannose-specific IIC component 4.A.3 Transport/binding proteins YPO2501 2.51 rbsB sugar binding protein precursor 4.A.3 Transport/binding proteins YPCD1.05c 2.44 sycE putative yopE chaperone sycE, yerA, yopE targeting protein YPCD1.16c 3.36 hypothetical protein YPCD1.17c 2.60 ylpA putative lipoprotein precursor...”
- Functional versatility of Zur in metal homeostasis, motility, biofilm formation, and stress resistance in Yersinia pseudotuberculosis
Gu, Microbiology spectrum 2024 - “...conducted to verify the transcriptional regulation by Zur of ypk_0057 (coding for D-xylose transporter, XylF), ypk_1611 (coding for ribose transporter, RbsB), and ypk_2067 (coding for oligopeptide transporter, OppD) ( Fig. 3A and B ). The data revealed that Zur directly upregulates the transcription of these genes...”
- “...( A ) qRT-PCR analysis of mRNA levels of xylF ( ypk_0057 ), rbsB ( ypk_1611 ), and oppD ( ypk_2067 ). ( B ) EMSA was performed to analyze the interactions between His6-Zur and the promoters of nutrient transporter genes ( ypk_0057 p, ypk_1611 p,...”
MSMEG_4172 D-ribose-binding periplasmic protein RbsB from Mycobacterium smegmatis str. MC2 155
29% identity, 76% coverage
y3346 periplasmic binding protein for ABC transporter from Yersinia pestis KIM
YPO0959 putative sugar ABC transporter periplasmic binding protein from Yersinia pestis CO92
27% identity, 94% coverage
- The Diverse Roles of the Global Transcriptional Regulator PhoP in the Lifecycle of Yersinia pestis
Fukuto, Pathogens (Basel, Switzerland) 2020 - “...]. In addition, genes encoding ribose ABC transporter proteins ( y3243/rbsA , y3345 , and y3346 in KIM strain) are down-regulated in the phoP mutant infecting fleas [ 64 ]. These results are consistent with a role of PhoP in mediating Crp-dependent regulation of alternate sugar...”
- Cell membrane is impaired, accompanied by enhanced type III secretion system expression in Yersinia pestis deficient in RovA regulator
Yang, PloS one 2010 - “...transport ATP-binding protein 4.A.3 Transport/binding proteins YPO0860 2.28 ----- sugar-binding periplasmic protein 4.A.3 Transport/binding proteins YPO0959 1.88 ----- putative sugar ABC transporter periplasmic binding protein 4.A.3 Transport/binding proteins YPO1757 2.30 manY, ptsP, pel PTS system, mannose-specific IIC component 4.A.3 Transport/binding proteins YPO2501 2.51 rbsB sugar binding...”
HSERO_RS11480 D-ribose ABC transporter, substrate-binding component RbsB from Herbaspirillum seropedicae SmR1
29% identity, 93% coverage
- mutant phenotype: Specifically important for utilizing D-Ribose.
Shewana3_2073 L-arabinose ABC transporter, substrate-binding component AraU from Shewanella sp. ANA-3
Shewana3_2073 periplasmic binding protein/LacI transcriptional regulator from Shewanella sp ANA-3
33% identity, 83% coverage
5ocpA / A0KWY4 The periplasmic binding protein component of the arabinose abc transporter from shewanella sp. Ana-3 bound to alpha and beta-l- arabinofuranose
33% identity, 83% coverage
- Ligands: alpha-l-arabinofuranose; beta-l-arabinofuranose (5ocpA)
Psyr_3265 Periplasmic binding protein/LacI transcriptional regulator from Pseudomonas syringae pv. syringae B728a
27% identity, 97% coverage
- Gene Expression Profiling in Viable but Nonculturable (VBNC) Cells of Pseudomonas syringae pv. syringae
Postnikova, Frontiers in microbiology 2015 - “...uptake of nutrients or efflux of toxins, remain operational. One of the up-regulated ABC transporters, Psyr_3265 represents periplasmic binding proteins, which are the primary receptors for chemotaxis and mediate solute uptake. Polyamines are required for growth of bacterial cells. In Escherichia coli , approximately half of...”
- “...genes in each of the overrepresented functional categories . Log 2 fold change Annotation Category Psyr_3265 3.50 Periplasmic binding protein Carbohydrate metabolism and transport Psyr_3138 3.97 Major facilitator transporter Carbohydrate metabolism and transport Psyr_2440 3.21 Extracellular solute-binding protein Carbohydrate metabolism and transport Psyr_1737 3.71 ABC transporter...”
NP_437959 putative rhizopine uptake ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
SMb20712 sugar ABC transporter substrate-binding protein from Sinorhizobium meliloti 1021
31% identity, 88% coverage
- Genetic and computational identification of a conserved bacterial metabolic module
Boutte, PLoS genetics 2008 - “...of Cross-Species 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...”
- Mining the Sinorhizobium meliloti transportome to develop FRET biosensors for sugars, dicarboxylates and cyclic polyols
Bourdès, PloS one 2012 - “...are important for binding between D-quinic acid and SMb20036. The inositol biosensor is based on SMb20712, a SBP of an ABC-transporter of the carbohydrate uptake transporter (CUT) 2 sub-family, the gene of which was induced 6.4-fold by myo -inositol [9] . The ABC transporter operon (SMb20712...”
- “...inositol, but with phosphate groups replacing hydroxyl groups. SWISS-MODEL threaded the tertiary structure of core SMb20712 on two ribose binding proteins (which show 55% id to each other). The first is a ribose SBP from Thermoanaerobacter tengcongensis (PDB: 2IOY; 34% id) [36] and the second from...”
- Genetic and computational identification of a conserved bacterial metabolic module
Boutte, PLoS genetics 2008 - “...Candidate operon in S. meliloti C. crescentus A. tumefaciens B. japonicum B. melitensis M. loti SMb20712 (sugar 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...”
- “...in either iolA (NP_384832 ) or in the predicted ABC transporter periplasmic binding protein gene, Smb20712 [24] , on GTS minimal medium [25] supplemented with either glucose or myo -inositol as the sole carbon source. Both Tn5 mutant strains grew normally in GTS-glucose and in Luria-Bertani...”
- 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 - “...(6) SMb20316 Erythritol SMb20072 myo-inositol SMb20712 myo-inositol SMc01628 Xylitol, adonitol, sorbitol, erythritol SMb21377 Dulcitol, tagatose, galactose,...”
- “...Two systems were induced by myo-inositol. The first is ABC-T SMb20712, the SBP of which has high identity (77%) to the rhizopine SBP of S. meliloti L5-30 (MocB)...”
- sinI- and expR-dependent quorum sensing in Sinorhizobium meliloti
Gao, Journal of bacteriology 2005 - “...SMa1296 SMa1450 SMa1993 SMa2037 SMa2041 SMb20170 SMb20712 SMb20899 SMb21121 SMb21133 SMb21309 SMb21321 SMb21652 SMc00153 SMc00154 SMc00242 SMc00361 SMc00365...”
- Proteomic analysis of wild-type Sinorhizobium meliloti responses to N-acyl homoserine lactone quorum-sensing signals and the transition to stationary phase
Chen, Journal of bacteriology 2003 - “...Ratingc SMa0241 SMa0947 SMa1169 SMa1438 SMa1450 SMa1450 SMb20019 SMb20325 SMb20442 SMb20712 SMb20895 SMb21010 SMb21181 SMb21221 SMb21652 3 1 1 2 3 3 2 3 3 3 2 3...”
PFLU3117 putative sugar ABC transport system, lipoprotein from Pseudomonas fluorescens SBW25
29% identity, 99% coverage
PP_2454 ribose ABC transporter, periplasmic ribose-binding protein from Pseudomonas putida KT2440
27% identity, 87% coverage
ECOLIN_RS18690 substrate-binding domain-containing protein from Escherichia coli Nissle 1917
30% identity, 91% coverage
- Identification of a gene cluster for D-tagatose utilization in Escherichia coli B2 phylogroup
Ha, iScience 2022 - “...annotated to encode tagatose bisphosphate family class II aldolase (encoded 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...”
- “...gene cluster increased significantly (>40-fold, p value <0.01), especially for the first three genes (ECOLIN_RS18685, ECOLIN_RS18690, and ECOLIN_RS18695) (>1000-fold). Growth on D-tagatose also resulted in higher transcriptional levels of ECOLIN_RS18700 and ECOLIN_RS18705 in the latter gene cluster, but to a much lesser extent (around two-fold, p...”
c4017 Putative ribose ABC transporter from Escherichia coli CFT073
30% identity, 91% coverage
SSA_0215 Periplasmic sugar-binding protein (ribose porter), putative from Streptococcus sanguinis SK36
27% identity, 88% coverage
- Systematic study of genes influencing cellular chain length in Streptococcus sanguinis
Evans, Microbiology (Reading, England) 2014 - “...mutants (SSA_0142, SSA_0222, SSA_0393, SSA_1907, SSA_2077, SSA_2250) and upregulated genes showing longer chain mutants (SSA_0191, SSA_0215, SSA_0217, SSA_0678, SSA_0758, SSA_1218, SSA_1266, SSA_1900, SSA_2224, SSA_2233). This complicated result suggests that the longer chain of Ssx_1972 might be a comprehensive result of multiple gene regulations. This information again...”
Pden_4851 periplasmic binding protein/LacI transcriptional regulator from Paracoccus denitrificans PD1222
32% identity, 81% coverage
6hbdA / A0QT50 Crystal structure of msmeg_1712 from mycobacterium smegmatis in complex with beta-d-galactofuranose (see paper)
31% identity, 69% coverage
- Ligands: zinc ion; beta-d-galactofuranose (6hbdA)
PSPTO_3049 sugar ABC transporter, periplasmic sugar-binding, putative from Pseudomonas syringae pv. tomato str. DC3000
34% identity, 81% coverage
MSMEG_1712 ABC transporter periplasmic-binding protein YtfQ from Mycobacterium smegmatis str. MC2 155
31% identity, 68% coverage
- Characterization of the l-arabinofuranose-specific GafABCD ABC transporter essential for l-arabinose-dependent growth of the lignocellulose-degrading bacterium Shewanella sp. ANA-3
Drousiotis, Microbiology (Reading, England) 2023 - “...be of physiological significance and we noted that the YtfQ homologue in Mycobacterium smegmatis , MSMEG_1712, was encoded with l -arabinose-degrading genes [ 11 ]. This hypothesis has been supported in an elegant study that demonstrated that MSMEG_1712 is an l -Ara f and d -Gal...”
- Genome-wide Phenotypic Profiling Identifies and Categorizes Genes Required for Mycobacterial Low Iron Fitness
Dragset, Scientific reports 2019 - “...gene ywbN of Bacillus subtilis 47 . Genes within a region spanning from msmeg_1701 to msmeg_1712 are under-represented in the fxbA ( msmeg_1701 / deoD , msmeg_1703 / amiA1 ), mbtD ( msmeg_1705 ) and fxbA mbtD -screens ( msmeg_1712 ). msmeg_1704-1712 encode a putative ABC...”
- Functional analyses of mycobacterial lipoprotein diacylglyceryl transferase and comparative secretome analysis of a mycobacterial lgt mutant
Tschumi, Journal of bacteriology 2012 - “...PstS (MSMEG_5782) Lip EhuB (MSMEG_5368) Lip MSMEG_4533 Lip MSMEG_1712 Lip MSMEG_5574 Lip MSMEG_4999 Lip Tschumi et al. MSMEG_3493) and a 28-kDa antigen...”
- A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
McKenzie, Journal of bacteriology 2012 - “...D-Xylose Arabinose MSMEG_1707 MSMEG_1708 MSMEG_1709 MSMEG_1710 MSMEG_1711 MSMEG_1712 MSMEG_1713 MSMEG_1714 MSMEG_1715 pho araR araG araF araK araE araB araD...”
- “...xylose (MSMEG_1704 and MSMEG_6018), arabinose (MSMEG_1711 and MSMEG_1712), ribose (MSMEG_3090, -3095, and -3601), sugar alcohol (MSMEG_5571 to 2196 jb.asm.org...”
- Lipoglycans contribute to innate immune detection of mycobacteria
Krishna, PloS one 2011 - “...Miriam Braunstein (University of North Carolina at Chapel Hill). Msmeg1712-HA was expressed from the native MSMEG_1712 promoter. The plasmid pHSG84, carrying a Km resistance gene, was electrotransformed in Msmeg / lspAres strain and its complemented counterpart. The transformants were selected on 7H11 agar plates containing kanamycin...”
- A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis
Titgemeyer, Journal of bacteriology 2007 - “...B. subtilis. The adjacent ABC permease (msmeg_1709 to msmeg_1712) could be the uptake system for arabinose. Its gene products, including the juxtaposed...”
- “...msmeg_0505 msmeg_0515 msmeg_0553 msmeg_1374 msmeg_1704 msmeg_1712 msmeg_3095 msmeg_3111 msmeg_3266 msmeg_3599 msmeg_3999 msmeg_4172 msmeg_4658 msmeg_5061...”
W1DEX1 Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1) from Klebsiella pneumoniae IS43
37% identity, 46% coverage
BPSL1793 putative sugar-binding exported protein from Burkholderia pseudomallei K96243
27% identity, 88% coverage
CAC1453 Ribose ABC transporter (ribose-binding periplasmic component) from Clostridium acetobutylicum ATCC 824
27% identity, 97% coverage
4rs3A / A0QYB3 Crystal structure of carbohydrate transporter a0qyb3 from mycobacterium smegmatis str. Mc2 155, target efi-510969, in complex with xylitol (see paper)
32% identity, 76% coverage
- Ligands: xylitol; zinc ion (4rs3A)
XYPA_MYCS2 / A0QYB3 Xylitol-binding protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see paper)
MSMEG_3598 periplasmic sugar-binding proteins from Mycobacterium smegmatis str. MC2 155
32% identity, 70% coverage
THPA_MYCS2 / A0QYB5 D-threitol-binding protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see paper)
MSMEG_3599 sugar-binding transcriptional regulator, LacI family protein from Mycobacterium smegmatis str. MC2 155
MSMEG_3599 sugar ABC transporter xylitol/D-threitol-binding protein ThpA from Mycolicibacterium smegmatis MC2 155
32% identity, 71% coverage
- function: Part of an ABC transporter complex involved in D-threitol import. Binds D-threitol. Functions in the transport for the degradation pathway of D-threitol, that allows M.smegmatis to grow on this compound as the sole carbon source.
disruption phenotype: Cells lacking this gene are defective for growth with D-threitol. - Multi-Omics Profiling Specifies Involvement of Alternative Ribosomal Proteins in Response to Zinc Limitation in Mycobacterium smegmatis
Dow, Frontiers in microbiology 2022 - “...ATP-binding protein OppD 1.64 4.36 1.31 not DE MSMEG_3044 dihydroorotase 2.07 not DE 2.28 3.75 MSMEG_3599 sugar-binding transcriptional regulator, LacI family protein 1.65 not DE 1.31 1.69 MSMEG_3630 transcriptional repressor, CopY family protein 2.05 not DE 2.65 2.14 MSMEG_1812 conserved hypothetical protein 1.74 not DE 1.58...”
- Protein Composition of Mycobacterium smegmatis Differs Significantly Between Active Cells and Dormant Cells With Ovoid Morphology
Trutneva, Frontiers in microbiology 2018 - “...were found in both types of cells (TetR MSMEG_0859; MoxR MSMEG_3147; NusG MSMEG_1345; and LacI MSMEG_3599). However, some of them were represented in the active cell proteome only (Gre A MSMEG_5263; Crp/Fnr family protein MSMEG_0539; PhoP MSMEG_5872; MSMEG_3264; Supplementary Table S2 ). In ovoid cells, transcription...”
- Functional analyses of mycobacterial lipoprotein diacylglyceryl transferase and comparative secretome analysis of a mycobacterial lgt mutant
Tschumi, Journal of bacteriology 2012 - “...and unknown function MSMEG_5617 SP MSMEG_1051 SP MSMEG_3599 Lip MSMEG_2408 MSMEG_1038 tuf (MSMEG_1401) MSMEG_0233 SP MSMEG_3528 SP MSMEG_2381 MSMEG_6078 Lip...”
- A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
McKenzie, Journal of bacteriology 2012 - “...n-fold changea P value Descriptionb Ribose MSMEG_3598 MSMEG_3599 MSMEG_3600 MSMEG_3601 rbsB3 rbsR3 rbsC3 1.28 1.42 (1.02) 1.53 4.65E03 1.01E02 7.80E01 6.94E03...”
- A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis
Titgemeyer, Journal of bacteriology 2007 - “...msmeg_1704 msmeg_1712 msmeg_3095 msmeg_3111 msmeg_3266 msmeg_3599 msmeg_3999 msmeg_4172 msmeg_4658 msmeg_5061 msmeg_5145 msmeg_5574 msmeg_6020 msmeg_6804...”
4rsmA / A0QYB5 Crystal structure of carbohydrate transporter msmeg_3599 from mycobacterium smegmatis str. Mc2 155, target efi-510970, in complex with d-threitol (see paper)
32% identity, 77% coverage
- Ligand: d-threitol (4rsmA)
BCAL1657 putative ribose transport system, substrate-binding protein from Burkholderia cenocepacia J2315
28% identity, 88% coverage
- Burkholderia cenocepacia transcriptome during the early contacts with giant plasma membrane vesicles derived from live bronchial epithelial cells
Pimenta, Scientific reports 2021 - “...in bacterial chemotaxis, namely flagellar motor switch protein coding genes fliG and fliM ; and BCAL1657 (putative ribose transport system) and BCAM0766 (D-ribose-binding periplasmic protein precursor) which appear to be associated with ribose-related pathways (Table S1 ). In contrast, several metabolic pathways are down-regulated, namely oxidative...”
- The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia
Sass, The ISME journal 2013 - “...stress protein 55 BCAM1500 Universal stress protein 14 BCAM1829 Universal stress protein 44 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...”
- Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
O'Grady, Frontiers in cellular and infection microbiology 2011 - “...BCAS0449 Nickle ion binding-protein-dependent transport 1.6 CARBOHYDRATE TRANSPORT AND METABOLISM BCAL0804 N -acetylglucosamine transferase 1.5 BCAL1657 Putative ribose transport system 1.8 BCAL1658 Putative ribose ABC transporter ATP-binding 1.5 BCAL1754 Major facilitator superfamily protein, carbohydrate transport 3.5 BCAL2040 Polysaccharide deacetylase, carbohydrate transport 1.5 BCAL3038 ABC transporter ATP-binding...”
- “...Putative electron transport protein 1.51 BCAL1499 Putative exported protein 1.79 BCAL1539 Putative exported protein 2.30 BCAL1657 Putative ribose transport system 1.77 BCAL1658 Putative ribose ABC transporter ATP-binding 1.56 BCAL1671 Metallo peptidase, subfamily M23B 1.61 BCAL1678 Putative outer membrane usher protein precursor 2.40 BCAL1699 Putative l -ornithine...”
SMb21377 putative sugar uptake ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
30% identity, 81% coverage
- Galactitol catabolism in Sinorhizobium meliloti is dependent on a chromosomally encoded sorbitol dehydrogenase and a pSymB-encoded operon necessary for tagatose catabolism
Kohlmeier, Molecular genetics and genomics : MGG 2019 (PubMed)- “...pRK7813/gatZ codon optimized SMc01500 expressing plasmid SMb21377 and upstream promoter region Broad host range vector Gateway compatible expression...”
- “...al. (1986) Clark et al. (2001) SMb21373, SMb21375, and SMb21377 was amplified using the primers listed in Table S1, cloned into the suicide vector pTH1360 (Yuan...”
- Genetic and computational identification of a conserved bacterial metabolic module
Boutte, PLoS genetics 2008 - “...(ATP-binding protein) 8.7e-113 7.0e-98 1.5e-104 8e-98 6.6e-102 SMb21343 (permease protein) 6.4e-30 3.7e-32 4.2e-31 2.3e-35 1.1e-34 SMb21377 (sugar binding protein) 5.5e-13 2.7e-6 SMb21376 (ATP-binding protein) 2.8e-103 2e-118 1e-103 1.4e-112 1.7e-105 SMb21375 (permease protein) 1.8e-48 7.5e-41 1.1e-44 2.5e-58 4.1e-37 SMb20856 (sugar binding protein) 2.6e-18 3.4e-13 1.6e-17 4.2e-11 4.9e-22...”
- 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 - “...SMc01628 Xylitol, adonitol, sorbitol, erythritol SMb21377 Dulcitol, tagatose, galactose, sorbose, L-()-lyxose SMc01496 Dulcitol, sorbitol, mannitol, maltitol...”
- “...Two systems were primarily induced by dulcitol. ABC-T SMb21377 (CUT2) was induced by dulcitol (C6, galactitol) but also by C6 monosaccharides; galactose (an...”
PSPTO_3490 sugar ABC transporter, periplasmic sugar-binding protein from Pseudomonas syringae pv. tomato str. DC3000
26% identity, 98% coverage
YP_3140 putative periplasmic protein precursor from Yersinia pestis biovar Medievalis str. 91001
32% identity, 69% coverage
PS417_11885 Inositol transport system sugar-binding protein from Pseudomonas simiae WCS417
28% identity, 88% coverage
- mutant phenotype: specific phenotype on inositol.
Z5689 putative periplasmic ribose-binding protein of ABC transport system from Escherichia coli O157:H7 EDL933
30% identity, 89% coverage
BPSS0140 putative sugar ABC transport system, lipoprotein from Burkholderia pseudomallei K96243
27% identity, 90% coverage
- Burkholderia pseudomallei transcriptional adaptation in macrophages
Chieng, BMC genomics 2012 - “...5.93 5.61 BPSL2945 Allantoicase 27.90 9.57 8.83 7.41 BPSL3354 Putative cytochrome 18.66 11.70 8.64 7.62 BPSS0140 Sugar ABC transport system, lipoprotein 7.80 16.62 13.56 13.94 BPSS0142 * Sugar ABC transport system, ATP-binding protein 4.62 10.04 11.34 18.79 BPSS0143 ROK family transcriptional regulator 4.78 9.97 11.80 18.64...”
- Human immune responses to Burkholderia pseudomallei characterized by protein microarray analysis
Suwannasaen, The Journal of infectious diseases 2011 - “...proteins (BPSL3222, BPSL2298, BPSL1600, BPSS0908, BPSL2827, BPSS2053, BPSS0140, and BPSL1913) increased after treatment (r-values were between 0.3573 and 0...”
- “...7 BPSS2053 Putative cell surface protein 0.389 .03 8 BPSS0140 Putative sugar ABC transport system 0.3812 .03 -0.3701 .04 0.3573 .048 9 BPSL0326 Putative outer...”
2vk2A / P39325 Crystal structure of a galactofuranose binding protein (see paper)
30% identity, 80% coverage
- Ligand: beta-d-galactofuranose (2vk2A)
ECs5205 putative LACI-type transcriptional regulator from Escherichia coli O157:H7 str. Sakai
Z5838 putative LACI-type transcriptional regulator from Escherichia coli O157:H7 EDL933
30% identity, 80% coverage
YtfQ / b4227 galactofuranose ABC transporter periplasmic binding protein (EC 7.5.2.9) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
YtfQ / P39325 galactofuranose ABC transporter periplasmic binding protein (EC 7.5.2.9) from Escherichia coli (strain K12) (see 3 papers)
YTFQ_ECOLI / P39325 Galactofuranose-binding protein YtfQ from Escherichia coli (strain K12) (see paper)
P39325 ABC-type D-galactofuranose transporter (EC 7.5.2.9) from Escherichia coli (see paper)
NP_418648 galactofuranose ABC transporter periplasmic binding protein from Escherichia coli str. K-12 substr. MG1655
b4227 predicted sugar transporter subunit: periplasmic-binding component of ABC superfamily from Escherichia coli str. K-12 substr. MG1655
30% identity, 80% coverage
- function: Part of the ABC transporter complex YtfQRT-YjfF involved in galactofuranose transport (Probable). Binds to both alpha- and beta- galactofuranose (PubMed:19744923).
subunit: The complex is composed of two ATP-binding proteins (YtfR), two transmembrane proteins (YtfT and YjfF) and a solute-binding protein (YtfQ). - Quantitative Shotgun Proteomic Analysis of Bacteria after Overexpression of Recombinant Spider Miniature Spidroin, MaSp1
Randene, International journal of molecular sciences 2024 - “...FKBP-type peptidyl-prolyl cis-trans isomerase SlyD P0A9K9 +1.52 2.52 10 3 Chaperone ytfQ Galactofuranose-binding protein YtfQ P39325 1.64 1.04 10 8 Sugar transport gatB PTS system galactitol-specific EIIB component P37188 1.82 1.87 10 4 Sugar transport pliG Inhibitor of g-type lysozyme P76002 3.33 4.28 10 4 Inhibitor...”
- Impact of chlorhexidine digluconate and temperature on curli production in Escherichia coli-consequence on its adhesion ability
Coquet, AIMS microbiology 2017 - “...391 3.41 3.15 ABC Transporter periplasmic-binding protein (ytfQ) Binding component of a galactose ABC transporter P39325 P 38 6 386 2.37 Molybdate-binding periplasmic protein (modA) Binding component of the molybdate ABC transporter P37329 P 48 4 254 2.60 Probable phospholipid-binding protein MlaC (mlaC) Binding protein of...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...YrdC P0A9W9 P45748 YrfE YtfJ YtfQ P39187 P39325 ZnuA P39172 Zwf P0AC53 5.66/22,341.86 5.34/20,685.91 5.72/42,097.02 6.31/26,951.84 Hypothetical protein Inner...”
- Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
Link, Electrophoresis 1997 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Multicenter Preparedness Exercise Enables Rapid Development of Cluster-Specific PCR-Based Screening Assays from Bacterial Genomic Data
Treffon, Journal of clinical microbiology 2023 (secret) - Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth
Franchini, PloS one 2015 - “...D-allose-binding periplasmic protein -3.2 ** cycA b4208 transport of D-alanine, D-serine, and glycine 4.0 ytfQ b4227 putative D-ribose transport protein, ABC superfamily 3.6 ytfR b4228 putative ATP-binding component of a transport system 5.2 idnT f , g b4265 L-idonate transporter -3.3 * -3.0 sgcX b4305 putative...”
- Furfural inhibits growth by limiting sulfur assimilation in ethanologenic Escherichia coli strain LY180
Miller, Applied and environmental microbiology 2009 - “...b1650 b1783 b1987 b2148 b2149 b2150 b3011 b3012 b3917 b4116 b4227 b4354 b4485 tauA* tauB* tauC tauD cstA ycgB ynaE* ydfK* nemR nemA yeaG cbl mglC mglA mglB yqhD...”
- 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 - “...b3541 b3542 b3588 b3704 b3722 b4051 b4067 b4069 b4119 b4149 b4187 b4227 b1197 b4239 b4240 5.3 6.1 8.0 4.0 8.6 12.1 8.0 13.9 12.1 1.4 8.6 5.7 6.5 13.0 13.0 8.6...”
- Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
Wei, Infection and immunity 2003 - “...b2070 b2372 b3837 b1377 b2074 b2337 b0900 b2118 b2491 b4227 b4365 b0535 b0663 b0135 b0938 b1031 b1502 b1835 b2108 b2333 b2335 b4364 b1948 b2259 b0808 b0899...”
Entcl_4082 ABC transporter substrate-binding protein from [Enterobacter] lignolyticus SCF1
30% identity, 89% coverage
- Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
Orellana, PloS one 2017 - “...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 [ 32...”
AT5A_00215 galactofuranose ABC transporter, galactofuranose-binding protein YtfQ from Agrobacterium tumefaciens 5A
28% identity, 96% coverage
- Introducing the ArsR-Regulated Arsenic Stimulon
Rawle, Frontiers in microbiology 2021 - “...M 100 M 0 100 M 0 50 M 0 75 M 0 75 M AT5A_00215 Ribose ABC transporter substrate binding 2.3 2.2 3.1 2.6 AT5A_00220 Ribose ABC transporter nucleotide binding 2.0 2.4 2.1 AT5A_01015 Monosaccharide-transporting ATPase 2.3 AT5A_03235 Putative multiple sugar transport system 2.3 AT5A_03250...”
J2ZWP7 ABC-type sugar transport system, periplasmic component from Pseudomonas sp. GM48
27% identity, 88% coverage
B21_04060 galactofuranose ABC transporter substrate-binding protein YtfQ from Escherichia coli BL21(DE3)
30% identity, 80% coverage
SACE_0943 binding protein/LacI transcriptional regulator from Saccharopolyspora erythraea NRRL 2338
29% identity, 87% coverage
PS417_18405 D-ribose ABC transporter, substrate-binding component RbsB from Pseudomonas simiae WCS417
28% identity, 89% coverage
- mutant phenotype: No fitness data for this gene, but data for PS417_18400:18395 confirm this is the ABC transporter for ribose.
Entcl_4175 sugar ABC transporter substrate-binding protein from [Enterobacter] lignolyticus SCF1
27% identity, 95% coverage
- Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1
Deangelis, Frontiers in microbiology 2013 - “...Citrate cycle (TCA cycle) 2.670 3.102 Entcl_3179 UspA domain-containing protein (3394773..3395201) None given 3.080 2.953 Entcl_4175 Periplasmic binding protein/LacI transcriptional regulator (complement(4503494..4504456)) ABC transporters 2.170 2.796 Entcl_3779 Carbon starvation protein CstA (4066791..4068944) None given 2.670 2.701 Entcl_1304 Malic protein NAD-binding (1376647..1378926) Pyruvate metabolism 3.770 2.490 Entcl_0617...”
C9ZDX0 Putative secreted solute-binding protein from Streptomyces scabiei (strain 87.22)
30% identity, 69% coverage
A0R773 Sugar ABC transporter substrate-binding protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_6804 sugar ABC transporter substrate-binding protein from Mycobacterium smegmatis str. MC2 155
MSMEG_6804 substrate-binding domain-containing protein from Mycolicibacterium smegmatis MC2 155
29% identity, 76% coverage
- Mycobacterium tuberculosis Small RNA MTS1338 Confers Pathogenic Properties to Non-Pathogenic Mycobacterium smegmatis
Bychenko, Microorganisms 2021 - “...(Penicillin-binding protein) MSMEG_2433 Rv2911 Cell wall and cell processes A0QRU0 3 Uncharacterized protein MSMEG_1237 no A0R773 2,7 Sugar ABC transporter substrate-binding protein MSMEG_6804 no A0QQ67 2,7 GH16 domain-containing protein MSMEG_0645 no A0R639 2,3 Septum_form domain-containing protein MSMEG_6414 Rv3835 Cell wall and cell processes A0R445 2,3 Secreted...”
- Mycobacterium tuberculosis Small RNA MTS1338 Confers Pathogenic Properties to Non-Pathogenic Mycobacterium smegmatis
Bychenko, Microorganisms 2021 - “...cell processes A0QRU0 3 Uncharacterized protein MSMEG_1237 no A0R773 2,7 Sugar ABC transporter substrate-binding protein MSMEG_6804 no A0QQ67 2,7 GH16 domain-containing protein MSMEG_0645 no A0R639 2,3 Septum_form domain-containing protein MSMEG_6414 Rv3835 Cell wall and cell processes A0R445 2,3 Secreted protein MSMEG_5700 Rv0867c Cell wall and cell...”
- Identifying feasible metabolic routes in Mycobacterium smegmatis and possible alterations under diverse nutrient conditions
Baloni, BMC microbiology 2014 - “...to MSMEG_2124) permeases which are expressed. The transporters for fructose such as MSMEG_6802, MSMEG_6803 and MSMEG_6804 seem to be expressed in the reference condition itself. Msm has glucose-6-phosphate isomerase (MSMEG_5541) for its utilization. Fructose is also known to have another mechanism of utilization via the expression...”
- Functional analyses of mycobacterial lipoprotein diacylglyceryl transferase and comparative secretome analysis of a mycobacterial lgt mutant
Tschumi, Journal of bacteriology 2012 - “...Lipc MSMEG_3598 Lip MSMEG_3235 Lip MSMEG_2727 Lip MSMEG_6804 Lip MSMEG_1704 Lip MSMEG_3636 Lip MSMEG_0643 Lip MSMEG_6524 SPb MSMEG_6047 Lip PstS (MSMEG_5782)...”
- A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
McKenzie, Journal of bacteriology 2012 - “...ABC transporter substrate-binding protein Ribose MSMEG_6802 MSMEG_6803 MSMEG_6804 Boldface values indicate a downregulation of 1.5-fold or greater in gene...”
- A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis
Titgemeyer, Journal of bacteriology 2007 - “...to msmeg_3602, msmeg_4170 to msmeg_4174, and msmeg_6798 to msmeg_6804). Several of the analyzed ABC systems of M. smegmatis revealed similarities to the ribose...”
- “...msmeg_5061 msmeg_5145 msmeg_5574 msmeg_6020 msmeg_6804 N-terminal sequence (no. of residues) * ---------------MTRTRLFRFGSAVASTLTVAALALSACAPGPSGDSGSSPAPTGEVSKDI...”
PFLU2583 putative rhizopine-binding ABC transporter protein from Pseudomonas fluorescens SBW25
PFLU_2583 sugar ABC transporter substrate-binding protein from Pseudomonas [fluorescens] SBW25
27% identity, 96% coverage
- The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion
Pacheco-Moreno, PLoS biology 2024 - “...tested genes with one another. Using this approach, we identified 3 new barley cultivar-discrimination genes: PFLU2583 , a sugar transporter, PFLU6072 , a transcription factor predicted to play a role in carbon metabolism control, and PFLU5080 , an uncharacterised protein with a putative role in prophage...”
- The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion
Pacheco-Moreno, PLoS biology 2024 - “...abundant in Tipple isolates but scarce in Chevallier strains, e.g., the sugar ABC transporter gene PFLU_2583 . Likewise, others were found at higher rates in Chevallier isolates, such as PFLU_0315 , encoding a GABA transporter. 10.1371/journal.pbio.3002232.g005 Fig 5 Cultivar-driven gene selection within the barley rhizosphere Pseudomonas...”
- “...PFLU_1533 LysR-family transcriptional regulator Chevallier PFLU_2414 Iron siderophore sensor Chevallier PFLU_6072 LysR-family transcriptional regulator Chevallier PFLU_2583 Putative rhizopine-binding protein Tipple PFLU_3295 GntR family transcriptional regulato r : vanR Tipple PFLU_3500 C4-dicarboxylate transporter Tipple PFLU_5080 Hypothetical protein Tipple Chevallier and Tipple rhizosphere competition assays were then carried...”
- Adaptive Remodeling of the Bacterial Proteome by Specific Ribosomal Modification Regulates Pseudomonas Infection and Niche Colonisation
Little, PLoS genetics 2016 - “...Putative amino-acid transport system, substrate-binding protein PFLU_1311 6.10 5.29 5.69 Putative rhizopine-binding ABC transporter protein PFLU_2583 5.85 5.59 5.72 Aromatic-amino-acid aminotransferase PFLU_4209 8.00 3.73 5.87 Putative ubiquinolcytochrome C reductase, cytochrome C1 PFLU_0843 9.26 3.00 6.13 Biopolymer transport membrane protein exbB 9.43 3.12 6.27 Putative branched amino-acid...”
PFLU3727 putative D-ribose-binding protein component of ABC transporter from Pseudomonas fluorescens SBW25
29% identity, 88% coverage
Q1MM20 Solute-binding component of ABC transporter from Rhizobium johnstonii (strain DSM 114642 / LMG 32736 / 3841)
RL0489 putative solute-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
28% identity, 85% coverage
Atu0063 ABC transporter, substrate binding protein (sugar) from Agrobacterium tumefaciens str. C58 (Cereon)
28% identity, 78% coverage
- Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens
Kraus, Journal of bacteriology 2020 (secret) - Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region
Overlöper, RNA biology 2014 - “...(amino acid) 3,85 Atu2422 atu2422 ABC transporter, substrate binding protein (amino acid GABA) 3,66 FrcB atu0063 ABC transporter, substrate binding protein (sugar) 2,13 DppA atu4113 ABC transporter substrate-binding protein (dipeptide) 2,07 Atu3259 atu3259 dehydrogenase 0,20 RplI atu1088 50S ribosomal protein L9 0,18 AtpH atu2625 ATP Synthase...”
CTN_0364 putative periplasmic binding protein from Thermotoga neapolitana DSM 4359
29% identity, 72% coverage
RL2376 putative periplasmic-binding protein component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
29% identity, 78% coverage
- Characterization of the l-arabinofuranose-specific GafABCD ABC transporter essential for l-arabinose-dependent growth of the lignocellulose-degrading bacterium Shewanella sp. ANA-3
Drousiotis, Microbiology (Reading, England) 2023 - “...d -galactose binding. Interestingy, the GafA Sm orthologue from Rhizobium leguminosarum bv. viciae 3841, namely RL2376, was found to bind d -galactose and its use as a biosensor was proposed [ 55 ], although it is highly likely to also bind l -arabinose and might not...”
- Mining the Sinorhizobium meliloti transportome to develop FRET biosensors for sugars, dicarboxylates and cyclic polyols
Bourdès, PloS one 2012 - “...and the other detecting dicarboxylates using a protein from R. capsulatus . D-galactose FRET biosensor RL2376, a SBP of an ABC-transporter of the CUT2 sub-family, shows 68% id with the D-galactose SBP YtfQ from E. coli for which a crystal structure and precise ligand has been...”
- “...from E. coli [28] . SWISS-MODEL used YtfQ (PDB: 2VK2) as a template for threading RL2376 core. Given the high amino acid identity (68%) between these two SBPs, it is not surprising that all the hydrogen bond-forming amino acids are conserved in RL2376 (Glu13; Arg17; Asp90;...”
FTV88_0053 substrate-binding domain-containing protein from Heliorestis convoluta
29% identity, 83% coverage
RL4655 putative rhizopine-binding ABC transporter protein from Rhizobium leguminosarum bv. viciae 3841
28% identity, 88% coverage
- Rhizobium leguminosarum Glutathione Peroxidase Is Essential for Oxidative Stress Resistance and Efficient Nodulation
Hu, Frontiers in microbiology 2021 - “...0.0036 RL2820 Cytoplasmic Uncharacterized protein 8.97 1.26 0.0121 RL1124 Cytoplasmic Uncharacterized protein 12.33 1.22 0.0136 RL4655 intA Periplasmic Solute binding protein of inositol ABC transporter 32.96 0.82 0.0005 pRL120351 Periplasmic Substrate binding component of ABC transporter 49.96 0.82 0.0001 pRL120071 Periplasmic Substrate-binding component of ABC transporter...”
- Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics
Ramachandran, Genome biology 2011 - “...amine transporter. Classification of 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)...”
- “...). Common to all rhizospheres was induction of genes for uptake systems for inositol (IntA, RL4655) [ 8 , 14 ] and sorbitol/mannitol/dulcitol (MtlE, RL4218). Also elevated were genes encoding components of two previously uncharacterized systems. The first, RL3840, encodes a CUT1 (carbohydrate uptake transporter 1)...”
- Transcriptomic analysis of Rhizobium leguminosarum biovar viciae in symbiosis with host plants Pisum sativum and Vicia cracca
Karunakaran, Journal of bacteriology 2009 - “...characterized inositol ABC transporter (20); expression of RL4655 (intA, encoding a solute-binding protein) and RL4653 (intC, encoding an integral membrane...”
- “...immediately downstream of the massively induced (70-fold) intA (RL4655). Central metabolism of bacteroids. A comparison of 28-day bacteroids from P. sativum to...”
CPE1627 probable ribose ABC transporter from Clostridium perfringens str. 13
36% identity, 41% coverage
RL4172 putative solute-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
26% identity, 93% coverage
AlsB / b4088 D-allose ABC transporter periplasmic binding protein (EC 7.5.2.8) from Escherichia coli K-12 substr. MG1655 (see 5 papers)
AlsB / P39265 D-allose ABC transporter periplasmic binding protein (EC 7.5.2.8) from Escherichia coli (strain K12) (see 5 papers)
ALSB_ECOLI / P39265 D-allose-binding periplasmic protein; ALBP from Escherichia coli (strain K12) (see paper)
P39265 ABC-type D-allose transporter (EC 7.5.2.8) from Escherichia coli (see paper)
TC 3.A.1.2.6 / P39265 AlsB aka B4088, component of D-allose porter from Escherichia coli (see 6 papers)
alsB / GB|AAC77049.1 D-allose-binding periplasmic protein; EC 3.6.3.17 from Escherichia coli K12 (see 6 papers)
b4088 D-allose transporter subunit from Escherichia coli str. K-12 substr. MG1655
30% identity, 82% coverage
- function: Part of the binding-protein-dependent transport system AlsBAC for D-allose.
- 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) - Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth
Franchini, PloS one 2015 - “...i b4037 periplasmic protein of mal regulon 12.5 actP f b4067 acetate permease 10.7 alsB b4088 D-allose-binding periplasmic protein -3.2 ** cycA b4208 transport of D-alanine, D-serine, and glycine 4.0 ytfQ b4227 putative D-ribose transport protein, ABC superfamily 3.6 ytfR b4228 putative ATP-binding component of a...”
YPK_3045 monosaccharide-transporting ATPase from Yersinia pseudotuberculosis YPIII
25% identity, 97% coverage
- Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
Mahmud, mSystems 2020 - “...YPK_2997 YPK_2996 E 168, 189, 199 IrGAs15 3347078 3.5 NA NA TTGGCAAGAAATCTGCAC + 10.7 38,70,54,28 YPK_3045 NA 5, 7, 3 IrGAs16 3383005 13.6 11.8 9.3 ATGGCACGGATTTTGCCC 10.8 38,24,54,70 YPK_3075 YPK_3074 43, 50, 72 IrGAs17 3435112 5.4 3.7 NA AAGGCACGATAGTTGCGT 10.5 54,28,32,38 YPK_3144 NA 52, 104, 119...”
B9Q16_23105 substrate-binding domain-containing protein from Pantoea ananatis
25% identity, 87% coverage
Atu3063 ABC transporter, nucleotide binding/ATPase protein from Agrobacterium tumefaciens str. C58 (Cereon)
28% identity, 95% coverage
- Comparative Transcriptome Analysis of Agrobacterium tumefaciens Reveals the Molecular Basis for the Recalcitrant Genetic Transformation of Camellia sinensis L
Jin, Biomolecules 2022 - “...mcp genes ( mcpV , mcpG , atu5442 ), cheA , cheW , cheY , atu3063 , atu3533 and dppA were down-regulated in the tea group on day 0 ( Figure 4 B and Table S5 ). On day 3, six mcp genes ( mcpA ,...”
- The RNase YbeY Is Vital for Ribosome Maturation, Stress Resistance, and Virulence of the Natural Genetic Engineer Agrobacterium tumefaciens
Möller, Journal of bacteriology 2019 - “...e00730-18 Annotation Atu4447 Atu3165 Atu3472 Atu0542 Atu4577 Atu3063 Atu4695 Atu2391 Atu4719 Atu5343 Atu5237 Atu4312 SoxA DppA BkdA2 Fla Protein Function...”
SMb20671 putative sugar uptake ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
28% identity, 88% coverage
MSMEG_1374 ribose ABC transporter, periplasmic binding protein from Mycobacterium smegmatis str. MC2 155
27% identity, 81% coverage
YP1134 putative sugar-binding periplasmic protein from Yersinia pestis biovar Medievalis str. 91001
25% identity, 97% coverage
- Evidence for two evolutionary lineages of highly pathogenic Yersinia species
Rakin, Journal of bacteriology 1995 - “...Z35457, Y. pseudotuberculosis YP200 irp2; Z35477, Y. pseudotuberculosis YP1134 irp2; Z35488, E. coli K49 irp2; Z46919, E. coli K235 irp2. a S, sensitive; I,...”
- “...O3 Y. pseudotuberculosis YP714, O3 Y. pseudotuberculosis YP1134, O3 Y. pseudotuberculosis YPIII, O3 Y. pseudotuberculosis YP3813, O4A Y. pseudotuberculosis K86,...”
MHJ_0227 periplasmic sugar-binding proteins from Mycoplasma hyopneumoniae J
Q4AAA3 Periplasmic sugar-binding protein from Mesomycoplasma hyopneumoniae (strain J / ATCC 25934 / NCTC 10110)
mhp145 putative D-ribose-binding protein mutant from Mycoplasma hyopneumoniae 232
MHP7448_0234 periplasmic sugar-binding proteins from Mycoplasma hyopneumoniae 7448
27% identity, 73% coverage
- Pathogenicity & virulence of Mycoplasma hyopneumoniae
Leal, Virulence 2020 - “...MHJ_0263 Fibronectin, plasminogen, porcine epithelial cilia Y [ 110 ] Periplasmic sugar-binding protein mhp145 MHP7448_0234 MHJ_0227 Fibronectin, heparin Y [ 78 ] Putative MgpA like-protein d mhp005 MHP7448_0005 MHJ_0005 ND NR [ 19 , 172 ] Putative P76 membrane protein (P159) mhp494 MHP7448_0497 MHJ_0494 Fibronectin, heparin,...”
- N-terminomics identifies widespread endoproteolysis and novel methionine excision in a genome-reduced bacterial pathogen
Berry, Scientific reports 2017 - “...DNA-binding protein 1 NC Transporter MHJ_0611 Phosphocarrier protein HPr 1 MHJ_0469 Phosphoenolpyruvate-protein phosphotransferase 2 Membrane MHJ_0227 Periplasmic sugar-binding protein 1 NC Protein Folding MHJ_0524 Elongation factor Tu 26 MHJ_0071 Elongation factor G 3 MHJ_0064 Chaperone protein DnaJ 3 NC MHJ_0063 Chaperone protein DnaK 20 MHJ_0052 Elongation...”
- Post-translational processing targets functionally diverse proteins in Mycoplasma hyopneumoniae
Tacchi, Open biology 2016 (no snippet) - Pathogenicity & virulence of Mycoplasma hyopneumoniae
Leal, Virulence 2020 - “...mhp108 MHP7448_0271 MHJ_0263 Fibronectin, plasminogen, porcine epithelial cilia Y [ 110 ] Periplasmic sugar-binding protein mhp145 MHP7448_0234 MHJ_0227 Fibronectin, heparin Y [ 78 ] Putative MgpA like-protein d mhp005 MHP7448_0005 MHJ_0005 ND NR [ 19 , 172 ] Putative P76 membrane protein (P159) mhp494 MHP7448_0497 MHJ_0494...”
- Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays
Madsen, Infection and immunity 2006 - “...mhp064 mhp069 mhp071 mhp072 mhp073 mhp078 mhp128 mhp144 mhp145 mhp147 mhp148 mhp149 mhp150 mhp151 mhp152 mhp153 mhp171 mhp172 mhp209 mhp211 mhp212 mhp214 mhp221...”
- Pathogenicity & virulence of Mycoplasma hyopneumoniae
Leal, Virulence 2020 - “...MHP7448_0271 MHJ_0263 Fibronectin, plasminogen, porcine epithelial cilia Y [ 110 ] Periplasmic sugar-binding protein mhp145 MHP7448_0234 MHJ_0227 Fibronectin, heparin Y [ 78 ] Putative MgpA like-protein d mhp005 MHP7448_0005 MHJ_0005 ND NR [ 19 , 172 ] Putative P76 membrane protein (P159) mhp494 MHP7448_0497 MHJ_0494 Fibronectin,...”
- Survey of surface proteins from the pathogenic Mycoplasma hyopneumoniae strain 7448 using a biotin cell surface labeling approach
Reolon, PloS one 2014 - “...Studies suggested a surfacelocalization 5 MHP7448_0088 YP_287488.1 Hypothetical protein MHP7448_0088 MHP7448_0138 YP_287535.1 Hypothetical protein MHP7448_0138 MHP7448_0234 YP_287631.1 Periplasmic sugar-binding protein [46] MHP7448_0309 YP_287705.1 NADH-dependent flavin oxidoreductase [48] , [49] , [50] MHP7448_0324 YP_287719.1 Hypothetical protein MHP7448_0324 MHP7448_0333 YP_287728.1 Hypothetical protein MHP7448_0333 MHP7448_0352 YP_287746.1 Hypothetical protein MHP7448_0352...”
H16_B1500 ABC-type transporter, periplasmic component: CUT2 family, fructose specific from Ralstonia eutropha H16
29% identity, 90% coverage
CAC1351 Periplasmic sugar-binding protein from Clostridium acetobutylicum ATCC 824
CEA_G1365 sugar ABC transporter substrate-binding protein from Clostridium acetobutylicum EA 2018
27% identity, 78% coverage
H16_B1500 ABC transporter substrate-binding protein from Cupriavidus necator H16
29% identity, 91% coverage
1gudA / P39265 Hinge-bending motion of d-allose binding protein from escherichia coli: three open conformations (see paper)
30% identity, 75% coverage
BCAL1548 putative sugar ABC transport system, lipoprotein from Burkholderia cenocepacia J2315
28% identity, 90% coverage
- The Small RNA ncS35 Regulates Growth in Burkholderia cenocepacia J2315
Kiekens, mSphere 2018 - “...2.3 Succinylglutamate desuccinylase BCAL2933 4.0 4.0 2.4 d -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...”
BCAN_A0557 hypothetical protein from Brucella canis ATCC 23365
25% identity, 88% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BP BMEI0662 BruAb11335 52 MOS 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...”
SMb21587 putative sugar uptake ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
28% identity, 86% coverage
- Characterization of the l-arabinofuranose-specific GafABCD ABC transporter essential for l-arabinose-dependent growth of the lignocellulose-degrading bacterium Shewanella sp. ANA-3
Drousiotis, Microbiology (Reading, England) 2023 - “...produced by IDT. The synthetic gene was cloned into pET20b vector using Gibson assembly. The smb21587 gene sequence was amplified from genomic DNA of S. meliloti 1021 using Q5 DNA polymerase (NEB) with the following primers: GafASmF CATGCCATGGCCGAACTCGTCGTCGGCTTT and GafASmR CCGCTCGAGGTAGCCGAGGCCTTTCTTTTCTTCG. The PCR product was digested...”
- 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 - “...acid, L-()-fucose SMb21103 D-()-fucose, L-()-fucose SMb21587 D-()-fucose, L-()-arabinose, talose SMb20442 D-()-fucose, mannose, L-()-fucose SMa0252...”
- “...promoter directly in front of SMb21103. ABC-T SMb21587 was induced by D-fucose (5-methyl-Larabinose) (40-fold), L-arabinose (10-33-fold), and talose (11-fold)....”
SMc02171 PUTATIVE PERIPLASMIC BINDING ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
26% identity, 93% coverage
- The Sinorhizobium meliloti SyrM regulon: effects on global gene expression are mediated by syrA and nodD3
Barnett, Journal of bacteriology 2015 - “...SMc00252 SMc00712 SMc00809 SMc01016 SMc01216 SMc01557 SMc01586 SMc02171 SMc02388 SMc02389 SMc02669 SMc03900 SMc04336 SMc04434 a Decrease in nodD3 expression may...”
- Antimicrobial nodule-specific cysteine-rich peptides induce membrane depolarization-associated changes in the transcriptome of Sinorhizobium meliloti
Tiricz, Applied and environmental microbiology 2013 - “...SMc02515 SMc02516 SMc02517 SMc02518 SMc02519 SMc00265 SMc02171 SMc02219 SMc02616 SMc02873 SMc03121 SMc03167 SMc04202 SM_b20117 SM_b20611 SM_b20633 SM_b21604...”
- Quantitative proteomic analysis of the Hfq-regulon in Sinorhizobium meliloti 2011
Sobrero, PloS one 2012 - “...SMc00770, SMc00784, SMc02884 and SMc03786), 3 proteins shared with Torres-Quesada et al . [38] (SMc02121, SMc02171, SMc02259), and 4 proteins that were common to all three proteomic studies (SMc00786, SMc01525, SMc01946, SMc02118). Thus, our quantitative proteomic analysis confirmed those hits and significantly expanded the list of...”
- An extracytoplasmic function sigma factor acts as a general stress response regulator in Sinorhizobium meliloti
Sauviac, Journal of bacteriology 2007 - “...smc01758 smc01814 smc01815 smc01820 smc01933 smc01977 smc02171 smc02172 smc02461 smc02645 smc02769 smc02885 smc03780 smc03844 smc03999 smc04118 smc04194...”
- Identification of Sinorhizobium meliloti early symbiotic genes by use of a positive functional screen
Zhang, Applied and environmental microbiology 2006 - “...J) promoters of the lsrA, dgkA, ppe, SMc02171, SMc02773R, and SMc03205R open reading frames, respectively. Downloaded from http://aem.asm.org/ on February 12,...”
- “...epimerase SMc02171 .............................................................................................................................ABC transporter...”
- 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 - “...this study both plasmid and integrated fusions to frcB (SMc02171 SBP), which is upstream of frcC, were constitutive. These data suggest that the 352-bp and...”
- Proteomic analysis of wild-type Sinorhizobium meliloti responses to N-acyl homoserine lactone quorum-sensing signals and the transition to stationary phase
Chen, Journal of bacteriology 2003 - “...SMc01732 SMc02049 SMc02101 SMc02111 SMc02122 SMc02165 SMc02171 SMc02217 SMc02436 SMc02495 SMc02562 SMc02720 SMc02720 SMc02737 SMc02838 SMc02852 SMc02873...”
- “...SMc02101 SMc02087 SMc02100 SMc02111 SMc02118 SMc02165 Smc02171 SMc02217 SMc02408 SMc02495 SMc02499 SMc02508 SMc02509 SMc02510 SMc02634 SMc02692 SMc02774...”
BAB1_1648 Periplasmic binding protein/LacI transcriptional regulator from Brucella melitensis biovar Abortus 2308
30% identity, 86% coverage
- Iron-dependent reconfiguration of the proteome underlies the intracellular lifestyle of Brucella abortus
Roset, Scientific reports 2017 - “...0.60 0.09 GI:82699145 BAB1_0241 ABC-type sugar transport systems, ATPase comp. U NO 0.60 0.06 GI:82700425 BAB1_1648 ABC-type sugar transport system, periplasmic comp U NO 0.55 0.07 GI:83269394 BAB2_0491 ABC-type sugar transport system, periplasmic comp. U NO 1.62 0.21 GI:82939718 BAB2_0547 Probable sugar-binding periplasmic protein precursor U...”
- Intracellular adaptation of Brucella abortus
Lamontagne, Journal of proteome research 2009 - “...dependent on the dihydroxyacetone kinase complex (Dha) and the putative periplasmic rhizopine-related ABC transporter RbsB (BAB1_1648) were reduced 3 hours post-infection and remained reduced throughout the infection period. Since the PTS energy-transducing systems are involved in carbohydrate uptake and control of carbon metabolism, reduced functional activity...”
- “...arrangements. For example BAB1_1922, BAB1_1923, BAB1_1925, as well as BAB1_1149, BAB1_1150, BAB1_1151, and BAB1_1645, BAB1_1646, BAB1_1648. These proteins may be transcribed as a single message and subsequently translated as has been observed in other systems 47 . The latter trio of genes defines a putative phosphoenolpyruvate...”
A9CF36 ABC transporter, substrate binding protein (Sugar) from Agrobacterium fabrum (strain C58 / ATCC 33970)
29% identity, 80% coverage
- myo-inositol and D-ribose ligand discrimination in an ABC periplasmic binding protein
Herrou, Journal of bacteriology 2013 - “...meliloti Q926E6, Mesorhizobium loti Q98CU7, Agrobacterium tumefaciens A9CF36, Brucella melitensis Q8YIQ0 (14), and Pseudomonas sp. strain GM48 J2ZWP7 (46), and...”
- “...meliloti (Q926E6), M. loti (Q98CU7), A. tumefaciens (A9CF36), B. Journal of Bacteriology Downloaded from http://jb.asm.org/ on February 19, 2017 by University...”
HSERO_RS03635 D-mannose ABC transporter, substrate-binding component from Herbaspirillum seropedicae SmR1
28% identity, 90% coverage
- mutant phenotype: Specific phenotype on D-mannose
C289_0603 sugar-binding protein from Anoxybacillus ayderensis
26% identity, 95% coverage
- A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization
Kahar, International journal of molecular sciences 2013 - “...glycosidase (C289_2139), and 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...”
FRCB_RHIML / Q9F9B2 Fructose import binding protein FrcB from Rhizobium meliloti (Ensifer meliloti) (Sinorhizobium meliloti) (see paper)
TC 3.A.1.2.7 / Q9F9B2 FrcB, component of Fructose/mannose/ribose porter from Rhizobium meliloti (Sinorhizobium meliloti) (see paper)
26% identity, 93% 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. Binds fructose, ribose and mannose.
subunit: The complex is composed of two ATP-binding proteins (FrcA), two transmembrane proteins (FrcC) and a solute-binding protein (FrcB). - substrates: Mannose, Ribose, fructose
BR0544 ribose ABC transporter, periplasmic D-ribose-binding protein from Brucella suis 1330
25% identity, 88% coverage
- Quantitative analysis of the Brucella suis proteome reveals metabolic adaptation to long-term nutrient starvation
Al, BMC microbiology 2013 - “...Degradation 1881 BR1510 long-chain acyl-CoA thioester hydrolase, putative 14.25/6.6 1.67 * Sugar metabolism Transport 1642 BR0544 ribose ABC transporter, periplasmic D-ribose-binding 34.6/4.8 1.46 * Regulation 1743 BR0569 transcriptional regulator, Ros/MucR family 16.10/7.8 1.73 0.021 1843 BR2159 transcriptional regulator, Cro/Cl family 15.1/9.0 1.6 * 1813 BR1502 leucine-responsive...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 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,...”
mlr7582 sugar ABC transporter, periplasmic sugar-binding protein from Mesorhizobium loti MAFF303099
28% identity, 73% coverage
PsgRace4_17419 substrate-binding domain-containing protein from Pseudomonas savastanoi pv. glycinea str. race 4
30% identity, 70% coverage
Pden_4771 ABC ribose transporter, periplasmic solute-binding protein from Paracoccus denitrificans PD1222
25% identity, 78% coverage
BOV_0546 ribose ABC transporter, periplasmic D-ribose-binding protein from Brucella ovis ATCC 25840
25% identity, 88% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...Ribose Import BP BMEI0662 BruAb11335 52 MOS 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...”
BCAM0766 D-ribose-binding periplasmic protein precursor from Burkholderia cenocepacia J2315
29% identity, 65% coverage
RbsR / VIMSS66308 RbsR regulator of Ribose utilization, effector Ribose (repressor) from Bacillus halodurans C-125
28% identity, 69% coverage
Q8YIQ0 D-ribose-binding periplasmic protein from Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)
BMEI0393 D-RIBOSE-BINDING PERIPLASMIC PROTEIN PRECURSOR from Brucella melitensis 16M
31% identity, 69% coverage
- myo-inositol and D-ribose ligand discrimination in an ABC periplasmic binding protein
Herrou, Journal of bacteriology 2013 - “...loti Q98CU7, Agrobacterium tumefaciens A9CF36, Brucella melitensis Q8YIQ0 (14), and Pseudomonas sp. strain GM48 J2ZWP7 (46), and five sequences jb.asm.org 2381...”
- “...(B) Structure of Caulobacter myo-Inositol-Binding Protein melitensis (Q8YIQ0) (14), and Pseudomonas sp. strain GM48 (J2ZWP7) (46), and five sequences...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 Import BP BMEI0663 BruAb11340 BR1342...”
BOV_1574 sugar-binding transcriptional regulator, LacI family from Brucella ovis ATCC 25840
31% identity, 68% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 Import BP BMEI0663 BruAb11340 BR1342 BOV_1301 BCAN_A1369 MOS...”
BCAN_A1667 rhizopine-binding protein precursor from Brucella canis ATCC 23365
BR1630 sugar-binding transcriptional regulator, LacI family from Brucella suis 1330
BME_RS01965 substrate-binding domain-containing protein from Brucella melitensis bv. 1 str. 16M
31% identity, 68% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 Import BP BMEI0663 BruAb11340 BR1342 BOV_1301 BCAN_A1369 MOS Ribose...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 Import BP BMEI0663 BruAb11340 BR1342 BOV_1301 BCAN_A1369...”
- Survival characteristics and transcriptome profiling reveal the adaptive response of the Brucella melitensis 16M biofilm to osmotic stress
Guo, Frontiers in microbiology 2022 - “...upregulated genes involved in the ABC transporter pathways included BME_RS06085, BME_RS12870, BME_RS13630, BME_RS12880, BME_RS1 2875, BME_RS01965, BME_RS02190, BME_RS06090, BME _RS02065, BME_RS02355, BME_RS02180, BME_RS11830. The expressions of these genes using qRT-PCR were in good agreement with the RNA-seq results ( Figures 5AC ). This finding agrees with...”
- Transcriptome Landscape of Intracellular Brucella ovis Surviving in RAW264.7 Macrophage Immune System
Jiao, Inflammation 2020 - “...predict_RNA519 F: TCTGAAGTTCGGCGAGTTCC R: GAAGACGACAAGCCGCAATC predict_RNA1099 F: CTTGCGTTTCGGTAGATGCG R: GACGGTTGATGATTGCGAGC BME_RS12005 F: GGATTTTGCGCCGATCTTCC R: CCATGCAATTGTACGAGGCG BME_RS01965 F: CCCGTTTGGAAGGCAACAAG R: CAGATATCGGACTGCGGCTT BME_RS08185 F: ATGAGGTCATCGACGCATCC R: CAGGACGAAATCGACCACCA BME_RS14785 F: ACGGAAGCGACAAAGGATGT R: CGCCTCTATGGTCGGAAGAC BME_RS08160 F: ACGTCACCATCGTCTATCGC R: AAGAACGGCTTCGGCAAAAC predict_RNA1390 F: GCGGGCCGGATGGATAATAA R: CATGCGCTTAACTCGCAGAC predict_RNA953 F: CGTCGAGTGTCTGATAGCCC R: GAGTTTATCGCGCTTGGCTG BME_RS01160...”
SCAB_5351 putative substrate-binding component of ABC transporter from Streptomyces scabiei 87.22
C9YUG2 Putative substrate-binding component of ABC transporter from Streptomyces scabiei (strain 87.22)
28% identity, 84% coverage
- Suberin Regulates the Production of Cellulolytic Enzymes in Streptomyces scabiei, the Causal Agent of Potato Common Scab
Padilla-Reynaud, Microbes and environments 2015 - “...or SCAB_22931 Arabinofuranosidase GH62, CBM13 ND 0.68 C9YUC5 SCAB_4961 Glucuronoarabinoxylan endo-1,4--xylanase GH30 ND 0.49 C9YUG2 SCAB_5351 ABC-type sugar transport system NF 1.27 0.71 C9YVN3 SCAB_5851 Glycosyl hydrolase CBM32 ND 0.17 C9YVP9 SCAB_6021 Endo -1,4-xylanase GH10 0.25 1.37 C9YYN8 SCAB_7551 Glycosyl hydrolase NF 0.62 D C9Z1T6 SCAB_9291...”
- Suberin Regulates the Production of Cellulolytic Enzymes in Streptomyces scabiei, the Causal Agent of Potato Common Scab
Padilla-Reynaud, Microbes and environments 2015 - “...SCAB_3881 or SCAB_22931 Arabinofuranosidase GH62, CBM13 ND 0.68 C9YUC5 SCAB_4961 Glucuronoarabinoxylan endo-1,4--xylanase GH30 ND 0.49 C9YUG2 SCAB_5351 ABC-type sugar transport system NF 1.27 0.71 C9YVN3 SCAB_5851 Glycosyl hydrolase CBM32 ND 0.17 C9YVP9 SCAB_6021 Endo -1,4-xylanase GH10 0.25 1.37 C9YYN8 SCAB_7551 Glycosyl hydrolase NF 0.62 D C9Z1T6...”
PS417_12055 xylitol ABC transporter, substrate-binding component from Pseudomonas simiae WCS417
28% identity, 71% coverage
- mutant phenotype: Specifically important for utilizing xylitol.
Q2YMQ4 Periplasmic binding protein/LacI transcriptional regulator from Brucella abortus (strain 2308)
Q57EI7 RbsB-1, ribose ABC transporter from Brucella abortus biovar 1 (strain 9-941)
25% identity, 88% coverage
- Brucella abortus Encodes an Active Rhomboid Protease: Proteome Response after Rhomboid Gene Deletion
Marchesini, Microorganisms 2022 - “...TSB-grown bacteria, four proteins exhibited lower p values: Q2YJW2 (Nitrous-oxide reductase NosZ); Q2YP89 (Fumarylacetoacetate hydrolase); Q2YMQ4 (Periplasmic binding protein/LacI transcriptional regulator) and Q2YRV5 (immunogenic 31 KDa TRAP transporter solute receptor, TAXI family protein). In the membrane fraction of TSB-grown bacteria Q2YNA5 (DNA topoisomerase 4 subunit A),...”
- Evaluation of the differences between biofilm and planktonic Brucella abortus via metabolomics and proteomics
Tang, Functional & integrative genomics 2021 (PubMed)- “...cytosine. Both metabolites correlated with the protein Q57EI7 (RbsB-1, ribose ABC transporter). One common pathway, fatty acid biosynthesis, was identified by...”
- “...These two metabolites all correlated with the protein Q57EI7 (RbsB-1, ribose ABC transporter). In the enrichment analysis, 17 pathways were found in the...”
BMEI1390 D-RIBOSE-BINDING PERIPLASMIC PROTEIN PRECURSOR from Brucella melitensis 16M
25% identity, 88% coverage
- Immuno-profiling of Brucella proteins for developing improved vaccines and DIVA capable serodiagnostic assays for brucellosis
Nandini, Frontiers in microbiology 2023 - “...of open reading frames of 10 serodominant proteins. Gene ID Primer sequence BMEI1980 F-5CGCGGATCCGTGCGATCGCCATTT-3 R-5CCGCTCGAGATTGCTTTCCTGCACA-3 BMEI1390 F-5CGCGGATCCATGACGGCGGGCGC-3 R-5CCGCTCGAGGAATGGAGAATCTGGGA-3 BMEI1513 F-5CGCGGATCCATGCGCGATCCCTAT-3 R-5CCGCTCGAGCACAACCCTGCGTTT-3 BMEI0063 F-5CGCGGATCCGTGGGGCAGGGG-3 R-5CCGCTCGAGTGTAAAATTAAAGTTTC-3 BMEI0856 F-5CGCGGATCCATGCCGATCAATATCACC-3 R-5CCGCTCGAGGACCAGCATACCCATC-3 BMEI0916 F-5CGCGGATCCATGCGCGACGGCGTA-3 R-5CCGCTCGAGGTCGACAATGTCATCG-3 BMEII1048 F-5CGCGGATCCATGGCTGCAAAAGAC-3 R-5CCGCTCGAGGAAGTCCATGCCGCC-3 BMEI0855 F-5ATTTGCGGCCGCATGCCCATAGAAAT-3 R-5CCGCTCGAGAGCGGTATAGGTAACG-3 BMEII0154 F-5ATTTGCGGCCGCATGAACATTGAG-3 R-5CCGCTCGAGTGGCTTGGACTTGAT-3 BMEI0748 F-5CGCGGATCCATGGCTGATCTCGCA-3 R-5CCGCTCGAGCTTGAGTTCAACCTTGG-3 Purification of His-tagged serodominant...”
- “...biogenesis GTP-binding protein YsxC BMEII0274 Membrane metalloprotease BMEI0829 Cytoplasmic protein BMEII0772 D-ribose-binding periplasmic protein precursor BMEI1390 Molecular chaperone GroEL BMEII1048 Flagellar motor switch protein FLIM BMEII1110 ABC transporter periplasmic-binding protein BMEII0702 Sugar-binding protein BMEII0590 Hypothetical protein BMEI1514 Invasion protein B BMEI1584 Hypothetical protein BMEI0060 MarR family...”
- Transcriptomic Analysis of the Brucella melitensis Rev.1 Vaccine Strain in an Acidic Environment: Insights Into Virulence Attenuation
Salmon-Divon, Frontiers in microbiology 2019 - “...Gene description RNA-seq/proteome BMEI0372 Response regulator Overexpression/overexpression BMEI1211 Amino acid ABC transporter substrate-binding protein Overexpression/overexpression BMEI1390 ABC transporter substrate-binding protein Overexpression/overexpression BMEI1923 Isovaleryl-CoA dehydrogenase Overexpression/overexpression BMEII0203 ABC transporter substrate-binding protein Overexpression/overexpression BMEII0344 ABC transporter permease Overexpression/overexpression BMEII0550 Glycine/betaine ABC transporter substrate-binding protein Overexpression/overexpression BMEII0590 Sugar-binding periplasmic...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 import IM BMEI1391, rbsC BruAb10565, rbsC1 BR0543, rbsC1 BOV_0545 rbsC1 BCAN_A0555 MOS Ribose import ABC2 BMEI1392, rbsA BruAb10564, rbsA1 BR0542, rbsA1...”
- Comparative proteome analysis of Brucella melitensis vaccine strain Rev 1 and a virulent strain, 16M
Eschenbrenner, Journal of bacteriology 2002 - “...protein 2-Oxoisovalerate dehydrogenase beta subunit BMEII0590 BMEI1551 BMEI1390 BMEII0590 BMEII1120 BMEI1551 BMEII0747 4.85 4.63 4.48 4.80 4.77 4.85 4.83 4.97...”
- “...74 75 76 BMEII0747 BMEI0372 BMEII0105 BMEII0103 BMEI0754 BMEI1390 BMEI0340 BMEI1819 BMEII0633 BMEI1746 BMEI0899 BMEII0023 5.50 4.76 5.71 5.66 5.05 4.61 9.92...”
MSMEG_3999 ABC transporter periplasmic-binding protein YphF from Mycobacterium smegmatis str. MC2 155
26% identity, 93% coverage
BT1754 two-component system sensor histidine kinase/response regulator, hybrid ('one component system') from Bacteroides thetaiotaomicron VPI-5482
27% identity, 29% coverage
- Determinants of raffinose family oligosaccharide use in <i>Bacteroides</i> species
Basu, Journal of bacteriology 2024 - “...( 28 ). This PUL is induced by fructose through a hybrid two-component sensor kinase BT1754 and contains genes encoding an inner membrane fructose transporter ( BT1758 ) , a fructokinase ( BT1757 ), and three GH32 family enzymes, which include some with sucrase activity (...”
- “...sucrases cleave the glucose-fructose bond in RFOs, thus liberating free fructose and activating PUL22 through BT1754 . Fig 4 PUL22 is important for RFO utilization in B. thetaiotaomicron and its GH32 family sucrases act redundantly to promote RFO utilization. ( A ) Genomic organization of B....”
- A conserved inhibitory interdomain interaction regulates DNA-binding activities of hybrid two-component systems in Bacteroides
Gao, mBio 2024 - “...substrates, including BT4124 ( 25 ), BT4663 ( 19 ), BT3334 ( 26 ), and BT1754 ( 27 ), were selected for in vitro phosphorylation analyses. Phosphorylation of purified RR fragments (REC + DBD) and REC domains upon addition of PAM was analyzed using Phos-tag gels...”
- Harnessing gut microbes for glycan detection and quantification
Modesto, Nature communications 2023 - “...( BT1763 , blue), 4 levanases ( BT1760-1759 BT3082 BT1765 , purple), fructan sensor ( BT1754 , red), or a putative inner-membrane fructose importer ( BT1758 , orange) were measured during anaerobic culture in minimal media containing levan as a sole carbon source. Values are the...”
- “...required for levan utilization. Reporter activation requires levan-derived fructose detection by the PUL sensor protein, BT1754, because a mutant lacking BT1754 displays only 1.4- or 1.7-fold increased reporter activity following the introduction of either levan (Fig. 4b ) or fructose (Fig. 4c ), respectively 19 ....”
- Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions
Feng, Cell host & microbe 2022 - “...levan strain The B. thetaiotaomicron ATCC 29148 (VPI-5482) wild-type and B. thetaiotamicron levan (deletion of BT1754 - BT1765 ) strains were grown at 37 C anaerobically in ABB media for 1216 hr. Cultures were diluted by 20-fold into ABB media and then incubated at 37 C...”
- Insights into SusCD-mediated glycan import by a prominent gut symbiont
Gray, Nature communications 2021 - “...a predicted fructokinase and Bt1758 is a predictedinner membrane (IM) major facilitator superfamily (MFS) transporter. Bt1754 is a hybrid two-component system that binds directly to fructose in the periplasm to upregulate expression of the PUL ( b ) 19 . c Cartoon representation of the Bt1762-63...”
- “..., 24 . The fructose is recognised by the periplasmic domain of the PUL sensorregulator BT1754, which upregulates expression of the PUL 19 . Thus, by growing B. theta on fructose, large amounts of the Bt1762-63 transporter can be obtained for structural work 15 . A...”
- Metagenomic reconstructions of gut microbial metabolism in weanling pigs
Wang, Microbiome 2019 - “...BT1760 (extracellular), BT3082 (periplasmic), and BT1765 (intracellular), as well as hybrid two-component (HTC) signaling system, BT1754 are required for fructan utilization in B . thetaiotaomicron and related Bacteroides spp. [ 41 ]. B . thetaiotaomicron utilized levan while Bacteroides caccae ferments inulin [ 41 , 69...”
- Genetic Variation of the SusC/SusD Homologs from a Polysaccharide Utilization Locus Underlies Divergent Fructan Specificities and Functional Adaptation in Bacteroides thetaiotaomicron Strains
Joglekar, mSphere 2018 - “...VPI-5482 mutant ( 7 ), lacking the native hybrid two-component sensor regulator (HTCS) gene ( BT1754 ), prevented growth on inulin (and other fructans; data not shown) ( Fig.2B ). 10.1128/mSphereDirect.00185-18.3 FIGS3 Fructose-induced expression of susC / susD homologs from Bt-8736 fructan PUL upon transfer into...”
- Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut
Lim, Cell 2017 - “...multiple, or undefined operons; repeating or low-complexity sequences recalcitrant to amplification). The hybrid two-component sensor BT1754 regulates a multi-gene polysaccharide utilization locus required for growth on fructose. We replaced the 200 base pairs upstream of BT1754 with the 200 base pair P1T DP promoter ( Figure...”
- “...::tetR (designated Bt ::tetR P1T DP GH023 -BT1754). Growth of Bt ::tetR P1T DP GH023 -BT1754 is entirely dependent on the addition of aTC in fructose but not glucose ( Figure 3A ). Additionally, cell doubling rates in fructose can be readily tuned by varying aTC...”
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RR42_RS03370 fructose ABC transporter, substrate-binding component (FrcB) from Cupriavidus basilensis FW507-4G11
28% identity, 90% coverage
- mutant phenotype: Specific phenotype on fructose
2x7xA / Q8A6X1 Fructose binding periplasmic domain of hybrid two component system bt1754 (see paper)
30% identity, 60% coverage
- Ligand: beta-d-fructofuranose (2x7xA)
CMM_0423 putative sugar ABC transporter, binding protein from Clavibacter michiganensis subsp. michiganensis NCPPB 382
28% identity, 70% coverage
- A Proteomic Study of Clavibacter Michiganensis Subsp. Michiganensis Culture Supernatants
Hiery, Proteomes 2015 - “...putative sugar ABC transporter substrate-binding protein +/+ CMM_0363 putative iron-siderophore ABC transporter substrate-binding protein +/+ CMM_0423 putative sugar ABC transporter substrate-binding protein +/+ CMM_0430 putative cell surface protein +/+ CMM_0431 putative hemagglutinin/hemolysin-related protein +/+ CMM_0435 putative iron-siderophore ABC transporter substrate-binding protein +/+ CMM_0613 levanase +/+ CMM_0667...”
Q98CU7 Mll4996 protein from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
28% identity, 93% coverage
- myo-inositol and D-ribose ligand discrimination in an ABC periplasmic binding protein
Herrou, Journal of bacteriology 2013 - “...B8H228), Sinorhizobium meliloti Q926E6, Mesorhizobium loti Q98CU7, Agrobacterium tumefaciens A9CF36, Brucella melitensis Q8YIQ0 (14), and Pseudomonas sp. strain...”
- “...no. B8H228), S. meliloti (Q926E6), M. loti (Q98CU7), A. tumefaciens (A9CF36), B. Journal of Bacteriology Downloaded from http://jb.asm.org/ on February 19,...”
BACOVA_04496 hypothetical protein from Bacteroides ovatus ATCC 8483
30% identity, 20% coverage
- Harnessing gut microbes for glycan detection and quantification
Modesto, Nature communications 2023 - “...7a ) 3 , 11 , 19 . Bo inulin utilization requires the PUL-sensor protein, BACOVA_04496, because a mutant lacking the corresponding gene is unable to grow on inulin as a sole carbon source (Supplementary Fig. 7a ) and exhibits reduced growth rates on fructose (Supplementary...”
- “...wild-type Bt (gray) and Bo (black) or a strain lacking the Bo inulin sensor ( BACOVA_04496 , red) were measured during anaerobic culture in minimal media containing inulin as a sole carbon source. b Relative luminescence from wild-type Bo harboring p Bolux (black) or a plasmid...”
blr3200 ABC transporter sugar-binding protein from Bradyrhizobium japonicum USDA 110
27% identity, 72% coverage
SMb20072 putative rhizopine binding protein from Sinorhizobium meliloti 1021
27% identity, 95% coverage
- ExoS/ChvI Two-Component Signal-Transduction System Activated in the Absence of Bacterial Phosphatidylcholine
Geiger, Frontiers in plant science 2021 - “...(iatA) putative myo -inositol transporter, ATP-binding protein 1.20 SMa2408 (rhbE) rhizobactin siderophore biosynthesis protein 1.33 SMb20072 putative rhizopine binding protein 1.62 SMc02726 (shmR) hemin-binding outer membrane receptor 1.92 M-values describe the log 2 ratio between mutant signal/wild type signal as described in section Materials and Methods....”
- “...catabolism are reduced ( Figure 4 ), among them transcripts for a periplasmic rhizopine-binding protein (SMb20072), a scyllo -inositol oxidase IolY (SMc01163), a myo -inositol transporter (SMb20713), and myo -inositol catabolism proteins IolBCD (SMc00432, SMc01165, SMc01166), suggesting that regulation involving the IolR repressor (SMc01164) ( Kohler...”
- The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon metabolism and the symbiotic interaction with alfalfa
Torres-Quesada, BMC microbiology 2010 - “...), and other organic acids/alcohols ( SMb20144 ) [ 34 ]. An additional gene ( SMb20072 ), displaying more than 32-fold reduction (M value -5.87) in transcript abundance in the hfq mutant has been annotated as coding for a putative myo -inositol-induced periplasmic solute-binding protein [...”
- Identification of direct transcriptional target genes of ExoS/ChvI two-component signaling in Sinorhizobium meliloti
Chen, Journal of bacteriology 2009 - “...(0.99) 3.22 (0.32) 0.70 (0.16) SMa1587 SMa1705 SMb20072 SMb20329 SMb20943 SMb20944 SMb20945 SMb20946 SMb20948 SMb20949 SMb20954 SMb20955 SMb20956 SMb20957...”
- Genetic and computational identification of a conserved bacterial metabolic module
Boutte, PLoS genetics 2008 - “...periplasmic binding protein of the Smb20712-4 operon as the top hit, but rather another protein, Smb20072, that is also annotated as a periplasmic rhizopine-binding protein. Indeed, a simple BLAST search revealed several different ABC transporter operons in S. meliloti with high probability scores to the experimentally-defined...”
- 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 - “...lactulose Polyols (6) SMb20316 Erythritol SMb20072 myo-inositol SMb20712 myo-inositol SMc01628 Xylitol, adonitol, sorbitol, erythritol SMb21377 Dulcitol,...”
- “...(IntABC) (2, 27). The second SBP induced by myo-inositol (SMb20072) has high identity to SMb20712 (54%), MocB (52%), and IntA (60%) but is not part of an...”
- Role of the regulatory gene rirA in the transcriptional response of Sinorhizobium meliloti to iron limitation
Chao, Applied and environmental microbiology 2005 - “...SMa2406 SMa2408 SMa2410 SMa2412 SMa2414 SMb20022 SMb20072 SMb20099 SMb20127 SMb20203 SMb20545 SMb20600 SMb20755 SMb20757 SMb20924 SMb20946 SMb20949 SMb20959...”
Ac3H11_3035 Fructose ABC transporter, substrate-binding component FrcB from Acidovorax sp. GW101-3H11
27% identity, 89% coverage
- mutant phenotype: Specific phenotype: utilization of D-Fructose, D-Mannose, D-Sorbitol
YPO0860 sugar-binding periplasmic protein from Yersinia pestis CO92
28% identity, 89% coverage
SPRI_RS32325 sugar ABC transporter substrate-binding protein from Streptomyces pristinaespiralis
26% identity, 85% coverage
- Diversity and prevalence of ANTAR RNAs across actinobacteria
Mehta, BMC microbiology 2021 - “..., one of which lies in the transcript of a sugar (fructose) transporter protein ( SPRI_RS32325 ). The uptake of complex sugars by Streptomyces favors development (sporulation) and production of antibiotics [ 56 58 ]. In fact, perturbation of glycolysis/ gluconeogenesis pathways is a standard method...”
- “...65 , 66 ]. The discovery of these ANTAR-target RNAs in Streptomyces thus implicates gene SPRI_RS32325 and SPRI_RS23705 as possible candidates that might be investigated to understand the observed phenotype. Our comprehensive description of ANTAR-target RNAs and ANTAR proteins in actinobacteria now provides a resource for...”
4rxmA Crystal structure of periplasmic abc transporter solute binding protein a7jw62 from mannheimia haemolytica phl213, target efi-511105, in complex with myo-inositol
26% identity, 77% coverage
- Ligands: 1,2,3,4,5,6-hexahydroxy-cyclohexane; beta-d-glucopyranose (4rxmA)
BPSS0257 putative ribose ABC transport system, substrate-binding exported protein from Burkholderia pseudomallei K96243
27% identity, 70% coverage
PP_2758 ribose ABC transporter, periplasmic ribose-binding protein, putative from Pseudomonas putida KT2440
26% identity, 83% coverage
YphF / b2548 putative ABC transporter periplasmic binding protein YphF from Escherichia coli K-12 substr. MG1655 (see 4 papers)
P77269 ABC transporter periplasmic-binding protein YphF from Escherichia coli (strain K12)
NP_417043 putative ABC transporter periplasmic binding protein YphF from Escherichia coli str. K-12 substr. MG1655
27% identity, 74% coverage
C289_0763 sugar ABC transporter substrate-binding protein from Anoxybacillus ayderensis
28% identity, 70% coverage
- A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization
Kahar, International journal of molecular sciences 2013 - “...(C289_2139), and 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...”
A0A140N593 Periplasmic binding protein/LacI transcriptional regulator from Escherichia coli (strain B / BL21-DE3)
27% identity, 74% coverage
- Omics analysis coupled with gene editing revealed potential transporters and regulators related to levoglucosan metabolism efficiency of the engineered Escherichia coli
Chang, Biotechnology for biofuels and bioproducts 2022 - “...and metabolismrelated proteins Maltodextrin-binding protein A0A140NCD0 malE 2.34 3.34 ABC-type sugar transport system periplasmic component A0A140N593 yphF 1.57 2.21 ABC transporter related A0A140NAC2 mglA 1.44 1.21 Extracellular solute-binding protein family 1 A0A140N4W8 ugpB 2.16 1.77 Phosphoenolpyruvate synthase A0A140NB77 ppsA 2.25 1.87 d -Xylose ABC transporter, periplasmic...”
- “...ABC transporters such as XylF (A0A140N4K7), MalE (A0A140NCD0), UgpB (A0A140N4W8), UgpC (A0A140N2F0), YtfQ (A0A140NEX7), YphF (A0A140N593), and MglA (A0A140NAC2) were upregulated at both the early- and mid-log phases of levoglucosan consumption compared to those of fructose consumption (Table 1 ). The d -xylose ABC transporter substrate-binding...”
c3070 ABC transporter Periplasmic binding protein yphF precursor from Escherichia coli CFT073
27% identity, 74% coverage
- Sequence validation of candidates for selectively important genes in sunflower
Chapman, PloS one 2013 - “...0.0000 0.3002 0.5340 0.0450** I c2588 ATIDD11 (INDETERMINATE-DOMAIN11) 0.0053 0.0087 0.0000 0.3958 0.8769 0.0017** I c3070 Gly-rich RNA binding protein 0.0088 0.0067 0.0077 0.9702 0.7709 0.7452 I c5666 Peroxidase 0.0237 0.0057 0.0000 0.3859 0.4254 0.0192 ** I J22O06 Unknown protein 0.0264 0.0031 0.0000 0.3104 0.3827 0.0010**...”
FRUE_BIFLO / Q8G848 Fructose import binding protein FruE from Bifidobacterium longum (strain NCC 2705) (see paper)
BLD_0045 ABC-type sugar transport system periplasmic component from Bifidobacterium longum DJO10A
BL0033 probable solute binding protein of ABC transporter system possibly for sugars from Bifidobacterium longum NCC2705
28% identity, 74% coverage
- function: Part of the high-affinity ABC transporter complex FruEKFG involved in fructose uptake. Can also transport ribose and xylose, with lower affinity. Binds fructose, ribose and xylose, with fructose as the preferred substrate.
subunit: The complex is composed of an ATP-binding protein (FruK), two transmembrane proteins (FruF and FruG) and a solute-binding protein (FruE).
disruption phenotype: Mutant is unable to grow on fructose as sole carbon source. - Intraspecies Genomic Diversity and Long-Term Persistence of Bifidobacterium longum
Chaplin, PloS one 2015 - “...+ + + + + + + Gene of fructose transporter protecting from Shiga-like toxin BLD_0045 (DJO10A) + + + + + + + + + + + + + + + + + + + + + + + + + + Serpin gene BLD_0126...”
- The Pleiotropic Effects of Carbohydrate-Mediated Growth Rate Modifications in Bifidobacterium longum NCC 2705
Duboux, Microorganisms 2023 - “...the import of various carbohydrates were induced, including the transporters for fructose and FOS ( BL0033 ), maltose and arabinose ( BL00141 , BL0146 ), raffinose ( BL1521 , BL1524 , BL1526 ), xylans and arabinans ( BL0426 ), and xylosides ( BL1710 ) ( Figure...”
- Probiotic Bifidobacterium longum subsp. longum Protects against Cigarette Smoke-Induced Inflammation in Mice
Budden, International journal of molecular sciences 2022 - “...modified strain B. longum subsp. longum NCC9036 (MUT), where the sugar ABC transporter solute-binding protein BL0033 was disrupted by insertional mutagenesis, causing a significantly reduced capacity to produce acetate [ 5 ]. All of the experiments were approved by the University of Newcastle Animal Care and...”
- Carbohydrate-controlled serine protease inhibitor (serpin) production in Bifidobacterium longum subsp. longum
Duboux, Scientific reports 2021 - “...of acetate, which depends on the gene encoding the sugar ABC transporter solute-binding protein ( BL0033 ) 11 . Moreover, B. longum NCC 2705 produces a serine protease inhibitor (serpin) encoded by the BL0108 gene, which forms covalent products with pancreatic and neutrophil elastases thereby inhibiting...”
- Bifidobacteria and Their Role as Members of the Human Gut Microbiota
O'Callaghan, Frontiers in microbiology 2016 - “...GENE DELETION Non-replicative plasmid insertion Stable mutation Successful knock-outs left with antibiotic marker Disruption of BL0033 in B. longum NCC2705 (Fukuda et al., 2011 ) Double crossover homologous recombination Gene target is deleted Time-consuming and laborious- multiple transformations and extensive screening of transformants 5 and 3...”
- “...B. longum NCC2705, this approach allows for the successful deletion of (part of) the gene BL0033, a solute binding protein of an ABC transporter that is highly induced when B. longum NCC2705 is grown on fructose (Fukuda et al., 2011 ). The double-crossover marker-less strategy has...”
- Tough nuts to crack: site-directed mutagenesis of bifidobacteria remains a challenge
Brancaccio, Bioengineered 2013 - “...in Bifidobacteria In B. longum NCC2705, the bl0033 gene encoding the substrate-binding protein of a fructose-specific ABC-type sugar transporter6 has been...”
- “...increased acetate production.7 For the targeted disruption of bl0033, two 1-kb fragments flanking the gene were cloned up- and downstream of a spectinomycin...”
- A targeted gene knockout method using a newly constructed temperature-sensitive plasmid mediated homologous recombination in Bifidobacterium longum
Sakaguchi, Applied microbiology and biotechnology 2012 (PubMed)- “...%. This knockout method also worked for the BL0033 gene in B. longum NCC2705. Keywords Temperature-sensitive plasmid . Bifidobacteria . Mutagenesis . Gene...”
- “...Cmr gene 7.7 kb plasmid for gene knockout of the BL0033 gene pKO403 containing 0.25 kb sequences of upstream of pyrE gene pKO403 containing 0.5 kb sequences of...”
- Fructose uptake in Bifidobacterium longum NCC2705 is mediated by an ATP-binding cassette transporter
Wei, The Journal of biological chemistry 2012 - “...Cloning and expression of the corresponding ORFs (bl0033- 0036) result in efficient fructose uptake by bacteria. Sequence analysis reveals high similarity...”
- “...as the preferred substrate. Our data suggest that BL0033- 0036 constitute a high affinity fructose-specific ABC transporter of B. longum NCC2705. We thus...”
- Technological advances in bifidobacterial molecular genetics: application to functional genomics and medical treatments
Fukiya, Bioscience of microbiota, food and health 2012 - “...This strategy was first applied in bifidobacteria for inactivation of an ABC-type carbohydrate transporter gene, BL0033, in B. longum subsp. longum NCC2705 [ 42 ]. c) Double-crossover markerless gene deletion Double crossover was applied to introduction of markerless gene deletion in the bifidobacterial chromosome ( Fig....”
- “...mice from the mortal effect of E. coli O157. A gene knockout mutant of the BL0033 was constructed by inactivation strategy b, double-crossover gene disruption. The knockout mutant was not able to protect mice from the lethal effect of E. coli O157 infection due to a...”
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HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component from Herbaspirillum seropedicae SmR1
28% identity, 74% coverage
- mutant phenotype: Specifically important for L-fucose utilization.
CTN_0777 Periplasmic binding protein/LacI transcriptional regulator precursor from Thermotoga neapolitana DSM 4359
TRQ7_RS05225 sugar-binding protein from Thermotoga sp. RQ7
26% identity, 83% coverage
CTC_00907 ABC transporter substrate-binding protein from Clostridium tetani E88
Q896U1 D-ribose-binding periplasmic protein from Clostridium tetani (strain Massachusetts / E88)
26% identity, 70% coverage
- More than a Toxin: Protein Inventory of Clostridium tetani Toxoid Vaccines
Möller, Proteomes 2019 - “...potential. Especially antibodies directed against surface-exposed proteins such ABC (ATP-binding cassette) transporter components (CTC_02340, CTC_01379, CTC_00907, CTC_00860), putative S-layer proteins (CTC_02093, CTC_00691, CTC_00465, CTC_00462), flagellar components (CTC_01724) and putative adhesins (CTC_00777, CTC_00774, CTC_00771, CTC_00770, CTC_00769, CTC_00749, CTC_00747) may have an influence on host colonization by the...”
- “...Electron transport complex subunit G M Q896J5 CTC_01009 Conserved protein, putative N-acetylmuramoyl-L-alanine amidase M Q896U1 CTC_00907 D-ribose-binding periplasmic protein U Q896W4 CTC_00882 Carboxyl-terminal protease M, C Q896W8 CTC_00878 50S ribosomal protein L25 U Q896Y3 CTC_00860 D-galactose-binding periplasmic protein U Q896Y6 CTC_00856 Uncharacterized protein M, C Q897C9...”
- More than a Toxin: Protein Inventory of Clostridium tetani Toxoid Vaccines
Möller, Proteomes 2019 - “...CTC_01021 Electron transport complex subunit G M Q896J5 CTC_01009 Conserved protein, putative N-acetylmuramoyl-L-alanine amidase M Q896U1 CTC_00907 D-ribose-binding periplasmic protein U Q896W4 CTC_00882 Carboxyl-terminal protease M, C Q896W8 CTC_00878 50S ribosomal protein L25 U Q896Y3 CTC_00860 D-galactose-binding periplasmic protein U Q896Y6 CTC_00856 Uncharacterized protein M, C...”
pRL90085 putative periplasmic substrate binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
26% identity, 87% coverage
4wutA / B9K0B2 Crystal structure of an abc transporter solute binding protein (ipr025997) from agrobacterium vitis (avi_5133, target efi-511220) with bound d-fucose
25% identity, 88% coverage
- Ligands: beta-d-fucopyranose; calcium ion (4wutA)
AW20_2081 ribose operon transcriptional repressor RbsR from Bacillus anthracis str. Sterne
BAS0631 ribose operon repressor from Bacillus anthracis str. Sterne
27% identity, 68% coverage
TC 3.A.1.2.20 / G4FGN5 LacI family transcriptional regulator, 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)
Tmari_1858 sugar-binding protein from Thermotoga maritima MSB8
26% identity, 84% coverage
- substrates: Xylose, glucose
- Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network
Latif, Applied and environmental microbiology 2015 - “...the entire glucose ABC transporter cassette (gluEFK, Tmari_1858 to Tmari_1856) and gluR are contained within a large gene duplication-amplification mutation...”
- “...of the solute binding protein of the gluEFK transporter (Tmari_1858, gluE). One of these mutations occurs in the GluR operator sequence, and the second is...”
- Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima
Rodionov, Frontiers in microbiology 2013 - “...four genes from the ATCC-derived strain of T. maritima MSB8: cbpA (Tmari_1862), treE (Tmari_1861), gluE (Tmari_1858) , and gluR (Tmari_1855) (Genbank Accession CP004077). Genomic RNA was isolated from cells grown on minimal medium supplied with either trehalose, D-glucose, or D-ribose and collected at the same optical...”
ML0398 putative D-ribose-binding protein from Mycobacterium leprae TN
25% identity, 90% coverage
KPN_04210 putative LACI-type transcriptional regulator from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
27% identity, 80% coverage
B9K0Q5 ABC-type D-galactose transporter (EC 7.5.2.11) from Agrobacterium vitis (see paper)
Avi_5305 ABC transporter, binding protein from Agrobacterium vitis S4
21% identity, 91% coverage
RbsR / VIMSS358011 RbsR regulator of Ribose utilization, effector Ribose (repressor) from Bacillus cereus ATCC 14579
BC0659 Ribose operon repressor from Bacillus cereus ATCC 14579
25% identity, 86% coverage
EF0172 sugar-binding transcriptional regulator, LacI family from Enterococcus faecalis V583
27% identity, 67% coverage
RT761_02219 sugar ABC transporter substrate-binding protein from Atribacter laminatus
27% identity, 98% coverage
5hqjA / B1G1H7 Crystal structure of abc transporter solute binding protein b1g1h7 from burkholderia graminis c4d1m, target efi-511179, in complex with d-arabinose
26% identity, 87% coverage
- Ligand: alpha-d-arabinopyranose (5hqjA)
B1G1H7 Periplasmic binding protein/LacI transcriptional regulator from Paraburkholderia graminis (strain ATCC 700544 / DSM 17151 / LMG 18924 / NCIMB 13744 / C4D1M)
26% identity, 87% coverage
- Deciphering Cellodextrin and Glucose Uptake in Clostridium thermocellum.
Yan, mBio 2022 - “...blue), which connect the two domains. (D) Overlay of CbpD (pink) and the sugar-binding protein B1G1H7 (gray) from Burkholderia graminis (PDB ID 5HQJ , arabinose complex). Arabinose is shown as cyan sticks. Inset shows that CbpD has a similar substrate-binding pocket for an as-yet-unidentified monosaccharide. Download...”
BBR47_06790 putative ABC transporter substrate binding protein from Brevibacillus brevis NBRC 100599
26% identity, 80% coverage
CTN_0576 Sugar ABC transporter, periplasmic sugar-binding protein from Thermotoga neapolitana DSM 4359
27% identity, 95% coverage
4wt7A / B9K0E0 Crystal structure of an abc transporter solute binding protein (ipr025997) from agrobacterium vitis (avi_5165, target efi-511223) with bound allitol
27% identity, 89% coverage
- Ligand: d-allitol (4wt7A)
BCAL1431 putative ribose ABC transport system, substrate-binding exported protein from Burkholderia cenocepacia J2315
25% identity, 72% coverage
- Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
Fang, BMC systems biology 2011 - “...is required 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...”
- “...of MglA, MglB, and MglC, 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...”
CMM_2842 putative sugar ABC transporter, substrate binding protein from Clavibacter michiganensis subsp. michiganensis NCPPB 382
25% identity, 69% coverage
- A Proteomic Study of Clavibacter Michiganensis Subsp. Michiganensis Culture Supernatants
Hiery, Proteomes 2015 - “...putative sugar ABC transporter substrate-binding protein +/+ CMM_2733 putative sugar ABC transporter substrate-binding protein +/+ CMM_2842 putative sugar ABC transporter substrate-binding protein +/+ CMM_2941 putative metal ABC transporter substrate-binding protein +/+ pCM1_0018 putative secreted protein +/+ pCM1_0020 CelA +/+ pCM1_0023 putative extracellular serine protease pCM2_0025 putative...”
2h3hA / Q9WXW9 Crystal structure of the liganded form of thermotoga maritima glucose binding protein (see paper)
27% identity, 87% coverage
- Ligand: beta-d-glucopyranose (2h3hA)
TM0114 sugar ABC transporter, periplasmic sugar-binding protein from Thermotoga maritima MSB8
27% identity, 84% coverage
- Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases
Frock, Applied and environmental microbiology 2012 - “...TM0060), the xylose/ glucose transporter XylE1F1K1 (TM0112, TM0114, and TM0115), a -xylosidase (TM0076), a xylose isomerase (TM1667), and a xylulokinase...”
- “...TM0810 TM1204 TM1839 TM1223 TM1067 treE TM0056 TM0071 TM0114 TM0309 TM1235 TM0595 TM1199 xylE2 TM1855 TM0418 TM0432 TM0958 CTN_0408 CTN_0664 CTN_1767 CTN_1367...”
- Structure of a periplasmic glucose-binding protein from Thermotoga maritima
Palani, Acta crystallographica. Section F, Structural biology and crystallization communications 2012 - “...rights reserved 1460 doi:10.1107/S1744309112045241 The target gene (tm0114) for NYSGXRC target 11013q was cloned using polymerase chain reaction from T....”
- Ligands of thermophilic ABC transporters encoded in a newly sequenced genomic region of Thermotoga maritima MSB8 screened by differential scanning fluorimetry
Boucher, Applied and environmental microbiology 2011 - “...of this ABC transporter system is homologous to TM0114 (XylE1), a substrate-binding protein that binds both glucose and xylose (12, 20). This suggests that...”
- Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences
Vanfossen, Applied and environmental microbiology 2009 - “...4 TM0810 (N-acetylglucosamine or GlcNAc polysaccharide) TM0114 (monosaccharides) TM1223 (cellobiose, barley) None None--proximate to two xylose isomerase-like...”
- “...TM1839 (maltose, maltotriose, trehalose) None TM0114 (monosaccharides) TM0595 (N-acetylglucosamine or GlcNAc polysaccharide) None--proximate to multidomain GHs...”
- Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein
Tian, Protein science : a publication of the Protein Society 2007 - “...as putative periplasmic sugar-binding proteins, among which tm0114 encodes a protein showing the highest sequence homology with E. coli...”
- “...for the 201 residues that can be aligned). The tm0114 ORF from the genomic DNA of T. maritima with its N-terminal signal peptide predicted (the first 31...”
- Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
Nanavati, Applied and environmental microbiology 2006 - “...The ligands for these bacterial SBPs are TM0114 (XylE), xylose; TM0418 (InoE), myo-inositol; TM0432 (AguE), -1,4-digalactouronic acid; and TM0958 (RbsB),...”
- “...-1,4-Mannotriose -1,4-Mannotetraose -1,4-Galactosyl mannobiose Cellobiose TM0114 (xylE) Xylose TM0418 (inoE) myo-Inositol 24.0 1 None TM0432 (aguE)...”
- The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture
Johnson, Applied and environmental microbiology 2006 - “...M. jannaschii a Gene(s) TM0024 TM0030-31 TM0070 TM0071 TM0114 TM0123 TM0300-302 TM0310 TM0418 TM0430-432 TM0433 TM0533 TM0624 TM0627 TM0633 TM0752 TM0767 TM0958...”
- 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 in...”
- More
6gt9A / W8QN64 Crystal structure of ganp, a glucose-galactose binding protein from geobacillus stearothermophilus, in complex with galactose
24% identity, 89% coverage
- Ligand: beta-d-galactopyranose (6gt9A)
4y9tA / B9K0Q5 Crystal structure of an abc transporter solute binding protein (ipr025997) from agrobacterium vitis s4 (avi_5305, target efi-511224) with bound alpha-d-glucosamine (see paper)
22% identity, 81% coverage
- Ligand: 2-amino-2-deoxy-alpha-d-glucopyranose (4y9tA)
Gocc_2298 sugar ABC transporter substrate-binding protein from Gaiella occulta
24% identity, 81% coverage
BC2960 Sugar-binding protein from Bacillus cereus ATCC 14579
24% identity, 79% coverage
- SinR controls enterotoxin expression in Bacillus thuringiensis biofilms
Fagerlund, PloS one 2014 - “...on motility. Genes possibly involved in detoxification processes (BC2230, BC3076, BC3078, BC4272), in sugar metabolism (BC2960, BC2854, BC3759), in DNA recombination (BC2556) or degradation (BC1072), in peptidoglycan turnover (BC5234), and in energy production (BC3142) were also identified as being regulated by SinR in strain 407 at...”
- “...4.4 BC3078 aminoglycoside 3-phosphotransferase NH 5.4 BC4272 superoxide dismutase NH 2.7 BC2854 aldo-keto-oxidoreductase NH 6.2 BC2960 Glycosyl transferase NH 2.9 BC3759 6-phospho-beta-glucosidase NH 3.0 BC2410 TetR family transcriptional regulator NH 2.2 BC3142 NADPH-dependent oxidoreductase NH 2.2 BC5234 N-acetylmuramoyl-L-alanine amidase NH 2.2 BC2450 macrolide-efflux protein MFS-1 family...”
Atu3487 ABC transporter, substrate binding protein (sugar) from Agrobacterium tumefaciens str. C58 (Cereon)
25% identity, 78% coverage
pRL110413 putative substrate binding protein involved in competition for nodulation from Rhizobium leguminosarum bv. viciae 3841
26% identity, 69% coverage
ruthe_01818 LacI family DNA-binding transcriptional regulator from Rubellimicrobium thermophilum DSM 16684
25% identity, 64% coverage
TC 3.A.1.2.9 / Q7BSH5 RhaS, 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) (see paper)
25% identity, 70% coverage
Avi_5339 ABC transporter substrate binding protein (ribose) from Agrobacterium vitis S4
25% identity, 71% coverage
5dkvA / B9K0T2 Crystal structure of an abc transporter solute binding protein from agrobacterium vitis(avis_5339, target efi-511225) bound with alpha-d- tagatopyranose
25% identity, 72% coverage
- Ligand: alpha-d-tagatopyranose (5dkvA)
SMc02324 PUTATIVE PERIPLASMIC BINDING ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
23% identity, 74% coverage
- Mining the Sinorhizobium meliloti transportome to develop FRET biosensors for sugars, dicarboxylates and cyclic polyols
Bourdès, PloS one 2012 - “...) was made. This plasmid has RFP (mKate2) and YFP (Aphrodite) cloned either side of SMc02324 which binds L-rhamnose. It was hoped that FRET between mKate2 and Aphrodite could be detected, but initial results with pLMB634 showed that this was not the case. The FRET vector...”
- “...the opposite properties showing a greater response to L-fucose. The L-rhamnose biosensor is based on SMc02324, the SBP of a CUT2 ABC-transporter. The gene encoding SMc02324 was induced more than 6.2-fold by both L-rhamnose and erythritol [9] ( Table 1 ). The rhamnose uptake and catabolic...”
- Characterization of a two-component regulatory system that regulates succinate-mediated catabolite repression in Sinorhizobium meliloti
Garcia, Journal of bacteriology 2010 - “...the genes into the rhamnose-binding protein gene (smc02324) Downloaded from http://jb.asm.org/ on February 12, 2017 by University of California, Berkeley they...”
- “...cloning PCR products (Apr) Suicide vector pMB438 containing smc02324 with trp terminator (Kmr Nmr) Suicide vector pMB438 containing smc02324 with trp terminator...”
- HPrK regulates succinate-mediated catabolite repression in the gram-negative symbiont Sinorhizobium meliloti
Pinedo, Journal of bacteriology 2009 - “...the rhamnose utilization operon in S. meliloti Rm1021, SMc02324 (36). Suicide plasmids with the mutant alleles were then delivered into the chromosome of...”
- “...that carries a wild-type copy of hpr in SMc02324, was used Downloaded from http://jb.asm.org/ on February 12, 2017 by University of California, Berkeley...”
- Sinorhizobium meliloti mutants lacking phosphotransferase system enzyme HPr or EIIA are altered in diverse processes, including carbon metabolism, cobalt requirements, and succinoglycan production
Pinedo, Journal of bacteriology 2008 - “...(5) that contains a fragment of the S. meliloti smc02324 gene followed by a trp terminator upstream of a multiple cloning site. This plasmid recombines into...”
- “...manX and hpr mutant strains, respectively. Insertion into the smc02324 gene was confirmed by the inability of the strains to grow on M9 medium plates containing...”
- 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 - “...Inducer Sugars (33): Pentose monosaccharides (8) SMc02324 Rhamnose, erythritol SMc02774 D-()-fucose, pyruvic acid, L-()-fucose SMb21103 D-()-fucose, L-()-fucose...”
- “...operons by the gene for the SBP (e.g., ABC-T SMc02324 and TRAP-T SMb20442) and routinely refer to the classification system of Saier (15). This system is based...”
Gocc_3071 sugar ABC transporter substrate-binding protein from Gaiella occulta
25% identity, 79% coverage
Swol_0423 putative sugar ABC transporter, substrate-binding protein from Syntrophomonas wolfei subsp. wolfei str. Goettingen
26% identity, 89% coverage
orf7 sugar-binding sensor histidine kinase/response r egulator hybrid from Gramella forsetii KT0803
25% identity, 21% coverage
- Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family
Silverio, The Journal of membrane biology 2011 - “...(Sac2 and Dvu1), one -proteobacterial protein (Mfe1) and three putative crenarcheaotal proteins (Nma1, Orf4 and Orf7) at the bottom of the tree. In view of the fact that two of the latter proteins were obtained from uncultured and unclassified Crenarchaeota, little can be said about orthologous...”
- “...maritimus SCM1 161527883 Crenarchaeota Archaea 210 Orf4 Uncultured marine crenarchaeote HF4000_APKG3E18 167043871 Crenarchaeota Archaea 203 Orf7 Uncultured crenarchaeote 42557779 Crenarchaeota Archaea 210 Average protein size (amino acids) 215 SD 20 Cluster 14 Cbo1 Clostridium bolteae ATCC BAA-613 160938401 Firmicutes Bacteria 219 Cph1 Clostridium phytofermentans ISDg 160879149...”
A6T653 Periplasmic binding protein/LacI transcriptional regulator from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
KPN_00624 putative periplasmic binding protein/LacI transcriptional regulator from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
28% identity, 68% coverage
VK055_1912 sugar ABC transporter substrate-binding protein from Klebsiella pneumoniae subsp. pneumoniae
28% identity, 68% coverage
2rjoA / B2TEP5 Crystal structure of twin-arginine translocation pathway signal protein from burkholderia phytofirmans
25% identity, 74% coverage
- Ligand: beta-d-galactopyranose (2rjoA)
Atu3821 ABC transporter, substrate binding protein (ribose) from Agrobacterium tumefaciens str. C58 (Cereon)
24% identity, 97% coverage
- Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region
Overlöper, RNA biology 2014 - “...AbcR1/WT Atu4577 atu4577 ABC transporter substrate binding protein 66,90 PykA atu3762 pyruvate kinase 36,86 RbsB atu3821 ABC transporter substrate-binding protein (ribose) 25,64 Atu0857 atu0857 oxidoreductase 13,45 Atu2188 atu2188 oxidoreductase 9,42 MalE atu2601 ABC transporter, substrate binding protein (maltose) 8,05 Pgi atu0404 glucose-6-phosphate isomerase 6,64 Atu4046 atu4046...”
- 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 - “...Transporter genes Atu1577 Atu1717 Atu2744 Atu3253 Atu3575 Atu3821 Atu4667 Atu4687 Atu5268 Designation 502 YUAN ET AL. ribonucleotide reduction were also...”
- “...and fatty acids (Atu1577, Atu1717, Atu2744, Atu3253, Atu3575, Atu3821, Atu4667, Atu4768, and Atu5268) (Table 3). The reduced uptake of multidrugs might be...”
YPTS_1642 hypothetical protein from Yersinia pseudotuberculosis PB1/+
27% identity, 68% coverage
- Impact of MgtC on the Fitness of Yersinia pseudotuberculosis
Li, Pathogens (Basel, Switzerland) 2023 - “...Fold Change mgtC/ PB1+ p -Value YPTS_0907 Transporter substrate-binding domain-containing protein 6.494781 1.04 10 8 YPTS_1642 Sugar ABC transporter substrate-binding protein 6.125791 1.59 10 6 YPTS_3843 Malate synthase A 5.255804 1.16 10 10 YPTS_2011 Aspartate aminotransferase family protein 5.083721 1.85 10 7 YPTS_3842 Isocitrate lyase 5.081315...”
BOV_A0938 ribose ABC transporter, periplasmic D-ribose-binding protein from Brucella ovis ATCC 25840
25% identity, 84% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 Monosaccharide import IM BMEII0362 BruAb20298 BRA0935 BOV_A0877 BCAN_B0955...”
BRA0996 ribose ABC transporter, periplasmic D-ribose-binding protein from Brucella suis 1330
BCAN_B1015 rhizopine-binding protein precursor from Brucella canis ATCC 23365
25% identity, 78% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 Monosaccharide import IM BMEII0362 BruAb20298 BRA0935...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...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 Monosaccharide import IM BMEII0362 BruAb20298 BRA0935 BOV_A0877 BCAN_B0955 57...”
NJ56_RS14540 HTH-type transcriptional repressor PurR from Yersinia ruckeri
23% identity, 82% coverage
4pz0A / A0A6H3AKG3 The crystal structure of a solute binding protein from bacillus anthracis str. Ames in complex with quorum-sensing signal autoinducer-2 (ai-2)
23% identity, 72% coverage
- Ligand: (2r,4s)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran (4pz0A)
RbsR / VIMSS7180207 RbsR regulator of Ribose utilization, effector Ribose (repressor) from Ralstonia pickettii 12J
22% identity, 64% coverage
ESA_RS03670 sugar ABC transporter substrate-binding protein from Cronobacter sakazakii ATCC BAA-894
27% identity, 68% coverage
- The Global Response of Cronobacter sakazakii Cells to Amino Acid Deficiency
Chen, Frontiers in microbiology 2018 - “...artJ 6.46 Arginine ABC transporter substrate-binding protein ESA_RS13095 glnK 6.45 Nitrogen regulatory protein P-II 2 ESA_RS03670 N/A 6.43 Sugar ABC transporter substrate-binding protein ESA_RS04175 yfcG 6.4 Thiol:disulfide oxidoreductase ESA_RS16950 thiG 6.30 Thiazole synthase ESA_RS05615 cbl 6.30 CysB family transcriptional regulator ESA_RS03660 N/A 6.30 Sugar ABC transporter...”
8fxuA / D9TSJ1 Thermoanaerobacter thermosaccharolyticum periplasmic glucose-binding protein glucose complex: badan conjugate attached at f17c (see paper)
27% identity, 67% coverage
- Ligands: beta-d-glucopyranose; calcium ion; 2-bromo-1-[6-(dimethylamino)naphthalen-2-yl]ethan-1-one (8fxuA)
A4XG54 Periplasmic binding protein/LacI transcriptional regulator from Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)
Csac_0242 periplasmic binding protein/LacI transcriptional regulator from Caldicellulosiruptor saccharolyticus DSM 8903
25% identity, 72% coverage
- Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2
Andrews, Analytical and bioanalytical chemistry 2010 - “...54 58 Total Proteins Identified 17 50 28 A4XFY3 Putative, probable polyprotein 6 29 17 A4XG54 Periplasmic binding protein/Lacl transcriptional regulator precursor 10 2 1 A4XG90 Putative, probable ISOPREN_C2_like protein 9 2 A4XG91 Putative, probable transglutaminase domain protein 14 A4XGB3 5-methyltetrahydropteroyltriglutamatehomocysteine S-methyltransferase 1 3 A4XGF7 D-isomer...”
- “...1 precursor Yes Yes 1 A4XJP0 Cell wall hydrolase autolysin precursor Yes Yes 1 Yes A4XG54 Periplasmic binding protein Lacl transcriptional regulator precursor Yes Yes 1 Yes A4XJ27 Ig domain protein, group 2 domain protein precursor Yes Yes 1 Yes A4XJH6 Thiamine pyrophosphate enzyme domain protein...”
- Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting
Andrews, Analytical and bioanalytical chemistry 2010 - “...I and II data shown here) Protein Sequence ID and Function PS PTD Intracellular Extracellular A4XG54 Periplasmic binding protein/Laci transcriptional regulator precursor x A4XG54 Pulative, probable transglutaminase domain protein x A4XGB3 5-methyttetrahydropteroyttriglutamate-homocysteine S-methyttransferase A4XGF7 d -isomer specific 2-hydroxyacid dehydrogenase, NAD-binding Not C-terminus C-terminus A4XGF5 Extracellular solute-binding...”
- Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences
Vanfossen, Applied and environmental microbiology 2009 - “...saccharolyticus genome, (i) Csac_0238 and Csac_0240 to Csac_0242 (Csac_0238,0240-0242) and (ii) Csac_2504 to Csac_2506 (Csac_2504-2506). These may have broad...”
- Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus
van, Applied and environmental microbiology 2008 - “...in carbohydrate utilization. Putative SBPs encoded by Csac_0242, Csac_0391, Csac_2326, and Csac_2507 belong to COG1879. Csac_2506 and Csac_2510 are associated...”
- “...were upregulated (Csac0692 to Csac_0696, Csac0240 to Csac_0242, and Csac2416 to Csac_ 2419). These clusters encode ABC transport systems, transcriptional...”
O68456 D-xylose-binding protein from Thermoanaerobacter ethanolicus
27% identity, 66% coverage
Cbei_2377 periplasmic binding protein/LacI transcriptional regulator from Clostridium beijerincki NCIMB 8052
A6LW07 Periplasmic binding protein/LacI transcriptional regulator from Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)
22% identity, 95% coverage
Tcur_1732 transcriptional regulator, LacI family from Thermomonospora curvata DSM 43183
25% identity, 59% coverage
- Genomics of aerobic cellulose utilization systems in actinobacteria
Anderson, PloS one 2012 - “...S. roseum . A phylogenetic cluster is formed by T. fusca CelR, Ndas_0809, Sros_3304, Tbis_1895, Tcur_1732, and Snas_6278. With the exception of Ndas_0809, these transcriptional regulators are found in operons with putative cellobiose ABC transporters ( Figure 2 ). N. dassonvillei does not have an ABC...”
EXUR_BACSU / Q9JMQ1 Probable HTH-type transcriptional repressor ExuR; Probable galacturonate locus repressor from Bacillus subtilis (strain 168) (see paper)
BSU12370 transcriptional regulator (LacI family) from Bacillus subtilis subsp. subtilis str. 168
27% identity, 53% coverage
- function: Transcriptional repressor for the exu locus which is required for galacturonate utilization.
disruption phenotype: Cells lacking this gene express the exu locus genes (required for hexuronate utilization) constitutively. Its absence additionally confers the ability to grow on minimal medium plus glucuronate, which cells cannot do in the presence of ExuR. - The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis
Eichenberger, PLoS biology 2004 - “...cypA (BSU26740), cysC (BSU15600), cysH (BSU15570), cysK (BSU00730), cysP (BSU15580), dctP (BSU04470), dctR (BSU04460), exuR (BSU12370), exuT (BSU12360), gerE (BSU28410), gerM (BSU28380), gerPA (BSU10720), gltR (BSU26670), goxB (BSU11670), kapD (BSU31470), lip (BSU31470), mpr (BSU02240), phoB (BSU05740), proH (BSU18480), proJ (BSU18470), racA/ywkC (BSU37030), safA (BSU27840), sat (BSU15590),...”
C0C300 Periplasmic binding protein domain-containing protein from [Clostridium] hylemonae DSM 15053
24% identity, 69% coverage
- Machine learning aided construction of the quorum sensing communication network for human gut microbiota
Wu, Nature communications 2022 - “...annotations Halococcus morrhuae 931277 M0MA34 WP_004054989.1 100% 100% ArsR subfamily of regulator Clostridium hylemonae 553973 C0C300 WP_006443816.1 100% 100% Autoinducer 2 ABC transporter Prevotella bivia 868129 I4Z9V6 WP_036847997.1 80% 80.39% Beta-ketoacyl-ACP synthase III Enterococcus caccae 1158612 R3TYZ5 WP_069646785.1 100% 80.80% Histidine kinase Lactobacillus ruminis 525362 E7FSN7...”
Cthe_2446 substrate-binding domain-containing protein from Acetivibrio thermocellus DSM 1313
Cthe_2446 ABC-type sugar transport system periplasmic component-like protein from Clostridium thermocellum ATCC 27405
27% identity, 67% coverage
- Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution
Ha-Tran, Microorganisms 2021 - “...was used as the sole carbon source, two sugar transporter genes cbpC (Cthe_2128) and cbpD (Cthe_2446) were found to be upregulated. Interestingly, in our study, after numerous generations, these genes of the CbpD operon still maintained their highly expressed activities in FAs8 and GAs8, thus indicating...”
- Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq
Wei, Frontiers in microbiology 2014 - “...only to cellotriose (G3), CbpB (Cthe_1020) binds to G2-G5 cellodextrins, and CbpC (Cthe_2128) and D (Cthe_2446) bind to G3-G5 cellodextrins (Nataf et al., 2009 ; Rydzak et al., 2012 ). Several transcripts of these annotated genes have been detected in the transcriptome of C. thermocellum (Raman...”
- Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression
Rydzak, BMC microbiology 2012 - “...CbpB (Cthe_1020) binds to cellodextrins of different lengths (G2-G5), while CbpC and CbpD (Cthe_2128 and Cthe_2446, respectively) preferentially bind to G3-G5 cellodextrins [ 34 ]. Given the absence of cellodextrins longer than cellobiose (G2) in our growth medium, the absence of the latter transporters Cthe_2125-2128 and...”
Pat9b_3290 sugar ABC transporter substrate-binding protein from Pantoea sp. At-9b
28% identity, 60% coverage
CPE1341 probable galactoside ABC transporter from Clostridium perfringens str. 13
26% identity, 66% coverage
- RNA-seq analysis of virR and revR mutants of Clostridium perfringens
Low, BMC genomics 2016 - “...sigG sporulation sigma factor 2.73 2.06 cpe1753 spoIVA sporulation protein A 2.73 2.44 Galactoside 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...”
pRL100415 putative substrate-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
25% identity, 77% coverage
YPTB1325 ABC transporter, periplasmic sugar-binding protein from Yersinia pseudotuberculosis IP 32953
23% identity, 81% coverage
ManR2 / VIMSS6936097 ManR2 regulator of Mannose utilization; Mannosides utilization, effector Mannose (repressor) from Shewanella amazonensis SB2B
24% identity, 66% coverage
TC 3.A.1.2.24 / O50503 Solute-binding 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)
SCO6009 solute-binding protein from Streptomyces coelicolor A3(2)
26% identity, 68% coverage
- substrates: Sugars
- Functional connexion of bacterioferritin in antibiotic production and morphological differentiation in Streptomyces coelicolor
García-Martín, Microbial cell factories 2024 - “...to carbohydrate transport and degradation were more abundant in bfr (Additional File S12 A): XylF (SCO6009) and BxlE1 (SCO7028), which are involved in the binding and import of xylose [ 142 ] and xylobiose [ 143 ], respectively, and CsnB (SCO2024) and DagB (SCO3487), a chitosanase...”
- Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor
Romero-Rodríguez, BMC microbiology 2016 - “...due to 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...”
- Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism
Guyet, BMC microbiology 2014 - “...tgtcccgatc 5.99 -170 2.246 u. f. SCO5862 SLI6134 SGR1670 cutR tggccgaaaa 7.69 -99 1.927 r. SCO6009 SLI6398 SGR1498 cttccagcca 6.53 -52 1.736 c. p. a Orthologs of S. lividans AdpA-dependent genes (listed in Additional file 2 : Table S2) were analysed in silico using the S....”
- The ROK family regulator Rok7B7 pleiotropically affects xylose utilization, carbon catabolite repression, and antibiotic production in streptomyces coelicolor
Świątek, Journal of bacteriology 2013 - “...(upstream) and the xylose transporter operon xylFGH (SCO6009 to SCO6011; downstream), with its gene synteny highly conserved in streptomycetes. Rok7B7 exhibits...”
- “...in the secretome, with the xylose binding protein SCO6009 in both lists) whose expression changed with statistical significance in the rok7B7 null mutant (Fig....”
- Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor
Getsin, BMC microbiology 2013 - “...]. XylFGH. O50503-5 3.A.1.2.24 Xylose uptake porter; transcriptionally regulated by a GntR-type 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) [...”
- Lack of A-factor production induces the expression of nutrient scavenging and stress-related proteins in Streptomyces griseus
Birkó, Molecular & cellular proteomics : MCP 2009 - “...SCO1793 (81%), SAV6485 (83%) SCO5260 (58%), SAV2982 (58%) SCO6009 (78%), SAV2247 (77%) SCO6009 (78%), SAV2247 (77%) SCO6531 (83%), SAV1862 (84%) SCO5254 (87%),...”
- “...SCO4366 (87%), SAV3883 (87%) SCO4366 (87%), SAV3883 (87%) SCO6009 (78%), SAV2247 (77%) SCO6009 (78%), SAV2247 (77%) Orthologue in SCO/SAV TABLE I Proteins with...”
- The twin-arginine translocation pathway is a major route of protein export in Streptomyces coelicolor
Widdick, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...SCO4142, SCO4152, SCO4884, SCO4885, SCO5074, SCO5113, SCO5447, SCO5461, SCO6009, SCO6644, SCO6738, and SCO7399. *, two versions of each of these signal peptides...”
UriR / VIMSS300374 UriR regulator of Pyrimidine utilization; Uridine utilization, effector New effector (repressor) from Corynebacterium efficiens YS-314
24% identity, 67% coverage
3ksmA / Q2S7D2 Crystal structure of abc-type sugar transport system, periplasmic component from hahella chejuensis
28% identity, 68% coverage
- Ligand: beta-d-ribofuranose (3ksmA)
OA04_14870 sugar ABC transporter substrate-binding protein from Pectobacterium versatile
24% identity, 67% coverage
ExuR / VIMSS3427925 ExuR regulator of Glucuronate utilization; Galacturonate utilization, effector Glucuronate; Galacturonate (repressor) from Bacillus pumilus SAFR-032
26% identity, 49% coverage
RbsR / VIMSS2859848 RbsR regulator of Ribose utilization, effector Ribose (repressor) from Psychromonas sp. CNPT3
22% identity, 73% coverage
RHE_RS30060 substrate-binding domain-containing protein from Rhizobium etli CFN 42
25% identity, 49% coverage
- Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network
Taboada-Castro, Frontiers in microbiology 2022 - “...transport system substrate-binding protein K10439 MM RHE_RS30010 rbsB; ribose transport system substrate-binding protein K10439 MM RHE_RS30060 rbsB; ribose transport system substrate-binding protein K10439 MM RHE_RS09135 rbsB; ribose transport system substrate-binding protein K10439 Bacteroid RHE_RS29865 rbsB; ribose transport system substrate-binding protein K02968 MM RHE_RS01805 RP-S20, rpsT; small...”
- “...; ribose transport system substrate-binding protein is represented by the isoenzymes RHE_RS09135, RHE_RS22400, RHE_RS27555, RHE_RS30010, RHE_RS30060 in MM, and RHE_RS29865 was expressed in bacteroid ( Table 1 ). For the nupA , general nucleoside transport system ATP-binding protein in MM RHE_RS10660 and in bacteroid RHE_RS00955 were...”
ScrR / VIMSS1100825 ScrR regulator of Sucrose utilization, effector Sucrose-6-phosphate (repressor) from Lactobacillus sakei subsp. sakei 23K
22% identity, 80% coverage
RbsR / VIMSS547489 RbsR regulator of Ribose utilization, effector Ribose (repressor) from Photorhabdus luminescens TTO1
22% identity, 85% coverage
Q2S7D2 ABC-type sugar transport system, periplasmic component from Hahella chejuensis (strain KCTC 2396)
28% identity, 68% coverage
5ulbA / A1JTX8 Crystal structure of sugar abc transporter from yersinia enterocolitica subsp. Enterocolitica 8081
26% identity, 73% coverage
- Ligands: 5-se-methyl-5-seleno-alpha-d-ribofuranose; 5-se-methyl-5-seleno-beta-d-ribofuranose (5ulbA)
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory