PaperBLAST
PaperBLAST Hits for reanno::Burk376:H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component (Paraburkholderia bryophila 376MFSha3.1) (334 a.a., MKLTRLGAAL...)
Show query sequence
>reanno::Burk376:H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component (Paraburkholderia bryophila 376MFSha3.1)
MKLTRLGAALAAAALTVGVIAAAQAATNETIVTVVKVTGINWFNRMDEGVKEFAKDNPGV
TAYQTGPGRADAAQQLKIIEDLIAKKVNAIAVVPYDPPTLEPALKKAMDRGIKVVTHEAD
NAKNTMVDIEAFDNTAYGAGLNERLASCMHNEGKWAVLVGSLGSRSQVQWADGGIGNAKA
KYAKMNLVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQG
KICVYGTGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAKMLVDGKTVENGADLGIPG
YTKVTVAKGPGKGIIVRGQGWVNVDKSNYKQYPF
Running BLASTp...
Found 136 similar proteins in the literature:
H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component from Paraburkholderia bryophila 376MFSha3.1
100% identity, 100% coverage
- mutant phenotype: Important for utilization of dAMP and deoxyinosine. Because the fitness profiles for these compounds are very similar, dAMP is likely hydrolyzed before uptake, but this could also be a transporter for deoxynucleotides.
SMb20316 putative ABC transporter periplasmic sugar-binding protein from Sinorhizobium meliloti 1021
62% identity, 97% coverage
- 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 - “...(1) SMb21652 Lactose, lactulose Polyols (6) SMb20316 Erythritol SMb20072 myo-inositol SMb20712 myo-inositol SMc01628 Xylitol, adonitol, sorbitol, erythritol...”
- “...systems by polyols is summarized in Table 1. ABC-T SMb20316 was induced by erythritol (3-fold) and is located in a 90-kb region that contains seven transport...”
YPO1813 putative sugar-binding periplasmic protein from Yersinia pestis CO92
56% identity, 97% coverage
APY09_02520 substrate-binding domain-containing protein from Schaalia odontolytica
42% identity, 96% coverage
ATU_RS22740 autoinducer 2 ABC transporter substrate-binding protein from Agrobacterium fabrum str. C58
43% identity, 88% coverage
ROD_24811 ABC transporter, substrate-binding protein from Citrobacter rodentium ICC168
43% identity, 92% coverage
Entcl_1207 autoinducer 2 ABC transporter substrate-binding protein from [Enterobacter] lignolyticus SCF1
42% identity, 92% coverage
- Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
Orellana, PloS one 2017 - “...glucose were up-regulated after glucose uptake was stopped ( Fig 2C ) (Entcl_0166, Entcl_0167, Entcl_1205, Entcl_1207, Entcl_3382, Entcl_3383, Entcl_4082, Entcl_4174, and Entcl_4403, S4 Table ). This was presumably a response to the lack of availability of glucose, an effect that has been observed in other fermentative...”
- Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1
Deangelis, Frontiers in microbiology 2013 - “...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 D-xylose ABC transporter, periplasmic substrate-binding protein (complement(183475..184470)) ABC transporters 2.410 1.035...”
- “...transport SBP 4.3 6.2e-20 Entcl_0288 Branched chain polypeptide extracellular SBP ABC transport SBP 3.2 1.9e-02 Entcl_1207 ABC transporter ABC transport 2.9 1.0e-03 All listed were either 2-fold over-expressed or greater (Ratio) or had a significant p-value. Figure 2 Pathways associated with (A) xylose degradation, (B) lignin...”
YPO3633 putative periplasmic binding protein from Yersinia pestis CO92
39% identity, 91% coverage
G5643_21680 autoinducer 2 ABC transporter substrate-binding protein from Serratia marcescens
44% identity, 84% coverage
- Microbial Reduction of Fumonisin B1 by the New Isolate Serratia marcescens 329-2
Keawmanee, Toxins 2021 - “...protein F0335_15805 3.32 A0A6N3ZXZ8 ABC transporter substrate-binding protein G3M84_09620 3.32 A0A6G8TTH4 Autoinducer 2-binding protein LsrB G5643_21680 3.29 A0A656VPU2 Uncharacterized protein AB868_00798 3.26 A0A1C3HHX7 Nitrogen regulatory protein P-II glnB 3.23 A0A1Q5WH71 Thiol:disulfide interchange protein dsbA 3.22 A0A0G8B466 2-dehydro-3-deoxygluconokinase AR325_02155 3.22 A0A0M5K334 Transaldolase tal 3.18 A0A080UWJ0 Peptidyl-prolyl cis-trans...”
YPO3328 putative sugar ABC transporter, periplasmic protein from Yersinia pestis CO92
42% identity, 75% coverage
YPTB0802 putative ABC transporter, periplasmic sugar binding protein from Yersinia pseudotuberculosis IP 32953
42% identity, 82% coverage
pRL80085 putative substrate-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
39% identity, 87% coverage
YE2751 putative periplasmic binding protein from Yersinia enterocolitica subsp. enterocolitica 8081
38% identity, 92% coverage
- The RNA chaperone Hfq impacts growth, metabolism and production of virulence factors in Yersinia enterocolitica
Kakoschke, PloS one 2014 - “...more abundant in the hfq mutant is a putative periplasmic binding protein encoded by gene ye2751 , which flanks the pdu region, and, unlike the pdu genes, is conserved in Y . pseudotuberculosis and Y . pestis . Based on conserved domain CD06302, YE2751 could be...”
- “...catabolic process + 51 YE0741 degP / htrA / gsrA serine endoprotease proteolysis + 38 YE2751 putative periplasmic binding protein transport + 70 YE2730 pduC / pddA putative propanediol utilization protein: dehydratase, large subunit metabolic process + 70 YE2733 pduG / ddrA putative propanediol utilization protein:...”
C6B607 Putative ABC transporter periplasmic sugar-binding protein from Rhizobium leguminosarum bv. trifolii (strain WSM1325)
42% identity, 89% coverage
ECs0374 putative sugar-binding protein from Escherichia coli O157:H7 str. Sakai
Z0415 putative periplasmic binding protein, probable substrate ribose from Escherichia coli O157:H7 EDL933
37% identity, 97% coverage
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...dniR -2.11 1 ECs1710 ychH 4.61 2 ECs0334 O157 -2.07 1 ECs1712 prsA -2.68 1 ECs0374 O157 2.42 2 ECs1859 rnb -2.70 1 ECs0401 mhpR 4.33 3 ECs1954 O157 -2.61 1 ECs0416 O157 3.55 2 ECs1955 O157 -3.22 1 ECs0468 ribH -2.27 1 ECs2011 ynbB 2.34...”
- Metabolism of L-arabinose converges with virulence regulation to promote enteric pathogen fitness
Cottam, Nature communications 2024 - “...the ruminant and human hosts. This locus was predicted to encode a periplasmic binding protein (Z0415), an ATPase (Z0416-7) and two permease subunits comprised of -helices (Z0418/Z0419), characteristic of Type II ABC transporters 33 . In silico modelling of Z0415-9 using AlphaFold2 supported this, by displaying...”
- “...related to pentose monosaccharide substrate specificity and comparison with known E. coli systems supported that Z0415 clustered closely with monosaccharide ABC transporters (Supplementary Fig. 2 ). Presence/absence analysis of Z0415-9 carriage amongst 949 representative E. coli genomes revealed that the locus is not completely conserved across...”
- Metabolism of ʟ -arabinose converges with virulence regulation to promote enteric pathogen fitness
Cottam, 2023 - Transcriptome analysis of Escherichia coli O157:H7 exposed to lysates of lettuce leaves
Kyle, Applied and environmental microbiology 2010 - “...transports monosaccharides exclusively (Z5689, Z5691, and Z0415) (Fig. 4A) (63). The transcription of malE, encoding a maltooligosaccharidebinding protein,...”
SMb20484 putative ABC transporter periplasmic sugar-binding protein from Sinorhizobium meliloti 1021
39% identity, 82% coverage
SMc02324 PUTATIVE PERIPLASMIC BINDING ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
33% identity, 87% 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_0231 autoinducer 2 ABC transporter substrate-binding protein from Gaiella occulta
34% identity, 79% coverage
Atu3487 ABC transporter, substrate binding protein (sugar) from Agrobacterium tumefaciens str. C58 (Cereon)
32% identity, 86% 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)
32% identity, 87% coverage
pRL110413 putative substrate binding protein involved in competition for nodulation from Rhizobium leguminosarum bv. viciae 3841
31% identity, 81% coverage
KPN_04210 putative LACI-type transcriptional regulator from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
32% identity, 85% coverage
B1G1H7 Periplasmic binding protein/LacI transcriptional regulator from Paraburkholderia graminis (strain ATCC 700544 / DSM 17151 / LMG 18924 / NCIMB 13744 / C4D1M)
32% identity, 82% 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...”
Swol_0423 putative sugar ABC transporter, substrate-binding protein from Syntrophomonas wolfei subsp. wolfei str. Goettingen
30% identity, 88% coverage
5hqjA / B1G1H7 Crystal structure of abc transporter solute binding protein b1g1h7 from burkholderia graminis c4d1m, target efi-511179, in complex with d-arabinose
30% identity, 73% coverage
- Ligand: alpha-d-arabinopyranose (5hqjA)
BC2960 Sugar-binding protein from Bacillus cereus ATCC 14579
26% identity, 94% 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...”
4wzzA / A9KIX1 Crystal structure of an abc transporter solute binding protein (ipr025997) from clostridium phytofermentas (cphy_0583, target efi- 511148) with bound l-rhamnose
26% identity, 87% coverage
- Ligand: alpha-l-rhamnopyranose (4wzzA)
Cphy_0583 putative sugar ABC transporter, substrate-binding protein from Clostridium phytofermentans ISDg
26% identity, 79% coverage
C9Z1U7 Putative secreted solute-binding lipoprotein from Streptomyces scabiei (strain 87.22)
27% identity, 80% coverage
C0C300 Periplasmic binding protein domain-containing protein from [Clostridium] hylemonae DSM 15053
26% identity, 88% 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...”
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)
26% identity, 89% coverage
- Ligand: (2r,4s)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran (4pz0A)
TM0114 sugar ABC transporter, periplasmic sugar-binding protein from Thermotoga maritima MSB8
28% identity, 77% 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...”
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2h3hA / Q9WXW9 Crystal structure of the liganded form of thermotoga maritima glucose binding protein (see paper)
28% identity, 77% coverage
- Ligand: beta-d-glucopyranose (2h3hA)
CTN_0576 Sugar ABC transporter, periplasmic sugar-binding protein from Thermotoga neapolitana DSM 4359
28% identity, 77% coverage
6gt9A / W8QN64 Crystal structure of ganp, a glucose-galactose binding protein from geobacillus stearothermophilus, in complex with galactose
27% identity, 75% coverage
- Ligand: beta-d-galactopyranose (6gt9A)
SC3966 putative ABC superfamily (peri_perm), sugar transport protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
26% identity, 98% coverage
LSRB_SALTY / Q8ZKQ1 Autoinducer 2-binding protein LsrB; AI-2-binding protein LsrB from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
STM4077 putative ABC superfamily (peri_perm), sugar transport protein from Salmonella typhimurium LT2
26% identity, 98% coverage
- function: Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. Binds AI-2 and delivers it to the LsrC and LsrD permeases (Probable).
subunit: The complex is composed of two ATP-binding proteins (LsrA), two transmembrane proteins (LsrC and LsrD) and a solute-binding protein (LsrB). - FabR regulates Salmonella biofilm formation via its direct target FabB
Hermans, BMC genomics 2016 - “...yneC/lsrG Isomerase for processing of phospho-AI-2 2.49 7 STM4080 lsrE Putative ribulose-5-phosphate 3-epimerase 2.24 10 STM4077 yneA/lsrB ABC transport protein, solute-binding component 2.13 12 STM4071 Hypothetical protein 2.02 13 STM4072 ydeV/lsrK Sugar kinase 1.87 17 STM4076 ydeZ/lsrD ABC transporter, membrane component 1.75 21 STM4074 ego/lsrA ABC...”
- Intraspecies variation in the emergence of hyperinfectious bacterial strains in nature
Heithoff, PLoS pathogens 2012 - “.... STM0887 artJ 0.78 1.76 2.61 Arginine transport system component [91] . Other virulence-associated genes STM4077 yneA 0.26 1.31 0.96 Involved in quorum sensing; encodes periplasmic receptor for AI-2 [151] ; also called lsrB . STM2084 rfbM 2.03 0.13 0.33 Involved in O-antigen synthesis [152] ;...”
- Identification of functional LsrB-like autoinducer-2 receptors
Pereira, Journal of bacteriology 2009 - “...the protein sequence of LsrB from S. Typhimurium (STM4077). The reciprocal best-hit strategy of sequence similarity comparisons was employed previously for this...”
4wutA / B9K0B2 Crystal structure of an abc transporter solute binding protein (ipr025997) from agrobacterium vitis (avi_5133, target efi-511220) with bound d-fucose
27% identity, 86% coverage
- Ligands: beta-d-fucopyranose; calcium ion (4wutA)
Q8Z2X8 Autoinducer 2-binding protein LsrB from Salmonella typhi
26% identity, 98% coverage
C289_0603 sugar-binding protein from Anoxybacillus ayderensis
25% identity, 81% 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...”
ECs2123 putative LACI-type transcriptional regulator from Escherichia coli O157:H7 str. Sakai
Z2189 putative LACI-type transcriptional regulator from Escherichia coli O157:H7 EDL933
BC33_RS14590 autoinducer 2 ABC transporter substrate-binding protein LsrB from Escherichia coli ATCC 700728
26% identity, 98% coverage
LsrB / b1516 Autoinducer-2 ABC transporter periplasmic binding protein (EC 7.6.2.13) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
LsrB / P76142 Autoinducer-2 ABC transporter periplasmic binding protein (EC 7.6.2.13) from Escherichia coli (strain K12) (see 5 papers)
LSRB_ECOLI / P76142 Autoinducer 2-binding protein LsrB; AI-2-binding protein LsrB from Escherichia coli (strain K12) (see 2 papers)
TC 3.A.1.2.8 / P76142 LsrB(R), component of Autoinducer-2 (AI-2, a furanosyl borate diester: (3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Taga et al., 2001, 2003) from Escherichia coli (see 4 papers)
lsrB autoinducer 2 ABC transporter, periplasmic substrate-binding protein LsrB from Escherichia coli K12 (see paper)
NP_416033 Autoinducer-2 ABC transporter periplasmic binding protein from Escherichia coli str. K-12 substr. MG1655
b1516 AI2 transporter from Escherichia coli str. K-12 substr. MG1655
26% identity, 98% coverage
- function: Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. Binds AI-2 and delivers it to the LsrC and LsrD permeases (Probable).
subunit: The complex is composed of two ATP-binding proteins (LsrA), two transmembrane proteins (LsrC and LsrD) and a solute-binding protein (LsrB). - substrates: Autoinducer-2
- The role of solute binding proteins in signal transduction
Matilla, Computational and structural biotechnology journal 2021 - “...(3.2) 1POY [43] , [131] Tsr P02942 E. coli -Proteobacteria TarH (PF 02203) LsrB/T a P76142 (37) Peripla_BP_4 (PF13407) Autoinducer-2 [45] , [46] TlpB B5Z9N4 Helicobacter pylori -Proteobacteria sCache_2 (PF 17200) AibA/T a AibB/T a B5ZA64 (62) B5Z6J6 (28) SBP_bac_5 (PF00496) ModA (IPR005950) Autoinducer-2 Autoinducer-2 [56]...”
- Impact of chlorhexidine digluconate and temperature on curli production in Escherichia coli-consequence on its adhesion ability
Coquet, AIMS microbiology 2017 - “...Part of the ABC Transporter complex LsrABCD involved in autoinducer 2 (AI-2) import (quorum sensing) P76142 P 48 4 203 3.09 2.29 unknown protein ytfJ (ytfj) Uncharacterized: hypothesized to be involved in temperature stress P39187 P 36 3 122 2.76 2.14 protein yncE (yncE) Uncharacterized: hypothesized...”
- Chemotaxis to the quorum-sensing signal AI-2 requires the Tsr chemoreceptor and the periplasmic LsrB AI-2-binding protein.
Hegde, Journal of bacteriology 2011 - GeneRIF: Both LsrB and Tsr are necessary for sensing AI-2, but AI-2 uptake is not, suggesting that LsrB and Tsr interact directly in the periplasm.
- Vaccine design based on 16 epitopes of SARS-CoV-2 spike protein
He, Journal of medical virology 2021 (secret) - 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
Lee, Applied and environmental microbiology 2009 - “...AI-2 uptake lsrA lsrC lsrD lsrB lsrF lsrG b1513 b1514 b1515 b1516 b1517 b1518 7.0 4.9 5.3 13.9 9.8 7.5 3.0 3.0 3.5 3.2 4.0 3.0 AI-2 uptake AI-2 uptake AI-2...”
- Lack of genomic evidence of AI-2 receptors suggests a non-quorum sensing role for luxS in most bacteria
Rezzonico, BMC microbiology 2008 - “...U07069) and the lsrB gene of E. coli strain K12 (accession number NC_000913, locus tag b1516) were used. The hits were manually checked to confirm that they had the same functional annotation as the query and re-submitted as novel queries until no new relevant positive match...”
- luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling
Wang, Journal of bacteriology 2005 - “...Gene product a Fold change (WT/luxS) b1518 b1515 b1513 b1516 b3829 b1517 b1511 b1520 b2236 b1519 b4308 b1512 b1514 b4395 b3796 b3852 b4017 b2087 b0974 b1127...”
- Regulation of uptake and processing of the quorum-sensing autoinducer AI-2 in Escherichia coli
Xavier, Journal of bacteriology 2005 - “...lsr gene designations are indicated under the annotations. b1516 (lsrB) encodes the periplasmic AI-2 binding protein. b1514 (lsrC) and b1515 (lsrD) encode the...”
- Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects
Tseng, Nucleic acids research 2001 - “...Some unknown genes, such as b1725, b1518, b0598 and b1516, are highly up-regulated in acetate, while others, such as b0905, b2973, b3279 and b1903, are...”
Entcl_0617 autoinducer 2 ABC transporter substrate-binding protein LsrB from [Enterobacter] lignolyticus SCF1
26% identity, 94% coverage
- Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1
Deangelis, Frontiers in microbiology 2013 - “...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 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...”
YPO0409 putative periplasmic solute-binding protein from Yersinia pestis CO92
24% identity, 99% coverage
y3772 putative LACI-type transcriptional regulator from Yersinia pestis KIM
24% identity, 89% coverage
A0R67_09330 sugar ABC transporter substrate-binding protein from Pasteurella multocida subsp. multocida
26% identity, 85% coverage
1tjyA / Q8ZKQ1 Crystal structure of salmonella typhimurium ai-2 receptor lsrb in complex with r-thmf (see paper)
24% identity, 92% coverage
- Ligand: (2r,4s)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran (1tjyA)
PSPTO_2367 ribose ABC transporter, periplasmic ribose-binding protein from Pseudomonas syringae pv. tomato str. DC3000
27% identity, 72% coverage
BBR47_06790 putative ABC transporter substrate binding protein from Brevibacillus brevis NBRC 100599
22% identity, 81% 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
28% identity, 76% 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...”
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
29% identity, 76% coverage
- Ligand: beta-d-allopyranose (5dteB)
RSP_3500 ABC sugar transporter, periplasmic binding protein from Rhodobacter sphaeroides 2.4.1
24% identity, 94% coverage
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
26% identity, 63% 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...”
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
26% identity, 69% 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...”
plu3146 ABC transporter Binding Protein (BP) LsrB from Photorhabdus luminescens subsp. laumondii TTO1
25% identity, 90% coverage
1gudA / P39265 Hinge-bending motion of d-allose binding protein from escherichia coli: three open conformations (see paper)
28% identity, 71% coverage
BCAL1657 putative ribose transport system, substrate-binding protein from Burkholderia cenocepacia J2315
30% identity, 67% 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...”
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component from Herbaspirillum seropedicae SmR1
25% identity, 90% coverage
- mutant phenotype: Specifically important for L-fucose utilization.
HSERO_RS11480 D-ribose ABC transporter, substrate-binding component RbsB from Herbaspirillum seropedicae SmR1
29% identity, 73% coverage
- mutant phenotype: Specifically important for utilizing D-Ribose.
Pf1N1B4_6035 D-ribose ABC transporter, substrate-binding component RbsB from Pseudomonas fluorescens FW300-N1B4
25% identity, 79% coverage
- mutant phenotype: Specifically important for ribose utilization. Also involved in utilization of ribonucleotides, which might be hydrolyzed before uptake.
RHE_RS22400 substrate-binding domain-containing protein from Rhizobium etli CFN 42
27% identity, 70% 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 - “...MM RHE_RS15425 proC; pyrroline-5-carboxylate reductase [EC:1.5.1.2] K00286 Bacteroid RHE_RS28670 proC; pyrroline-5-carboxylate reductase [EC:1.5.1.2] K10439 MM RHE_RS22400 rbsB; ribose transport system substrate-binding protein K10439 MM RHE_RS27555 rbsB; ribose transport system substrate-binding protein K10439 MM RHE_RS30010 rbsB; ribose transport system substrate-binding protein K10439 MM RHE_RS30060 rbsB; ribose transport...”
- “...). The rbsB ; 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...”
CTC_00907 ABC transporter substrate-binding protein from Clostridium tetani E88
Q896U1 D-ribose-binding periplasmic protein from Clostridium tetani (strain Massachusetts / E88)
23% identity, 90% 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...”
3t95A / Q74PW2 Crystal structure of lsrb from yersinia pestis complexed with autoinducer-2 (see paper)
23% identity, 92% coverage
- Ligand: (2r,4s)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran (3t95A)
OKIT_0347 substrate-binding domain-containing protein from Oenococcus kitaharae DSM 17330
26% identity, 60% coverage
Atu3063 ABC transporter, nucleotide binding/ATPase protein from Agrobacterium tumefaciens str. C58 (Cereon)
28% identity, 89% 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...”
blr1123 ABC transporter sugar-binding protein from Bradyrhizobium japonicum USDA 110
26% identity, 49% coverage
Bdiaspc4_05515 sugar-binding protein from Bradyrhizobium diazoefficiens
26% identity, 49% coverage
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
27% identity, 72% 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....”
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...5154 Q9RQ16 827 Q9I0M4 1909 Q9I2F6 2991 Q9HWL5 4073 Q9I1I5 5155 Q9X6V8 828 Q9I0M6 1910 Q9I2F8 2992 Q9HWL6 4074 Q9I1I7 829 Q9I0Q0 1911 Q9I2G3 2993 Q9HWL7 4075 Q9I1I8 830 Q9I0Q7 1912 Q9I2H6 2994 Q9HWL8 4076 Q9I1J0 831 Q9I0Q8 1913 Q9I2I2 2995 Q9HWL9 4077 Q9I1J1 832 Q9I0R2...”
- 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...”
Caur_2286 ABC-type sugar transport system periplasmic component-like protein from Chloroflexus aurantiacus J-10-fl
25% identity, 36% coverage
SMb21016 putative sugar ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
24% identity, 84% coverage
- Sinorhizobium meliloti, a bacterium lacking the autoinducer-2 (AI-2) synthase, responds to AI-2 supplied by other bacteria
Pereira, Molecular microbiology 2008 - “...rather than participating in the conversation. RESULTS S. meliloti contains an AI-2 Binding Protein The SMb21016 hypothetical protein from S. meliloti is 72% identical to the LsrB protein from S. typhimurium and, significantly, the gene SMb21016 is located in an operon that includes orthologs to all...”
- “...S. typhimurium ( Fig. 1B and 1C ). To demonstrate that the protein encoded by SMb21016 , the putative S. meliloti AI-2 receptor gene, is capable of binding AI-2, we cloned and overexpressed the protein in an E. coli strain producing AI-2. The candidate protein was...”
MSMEG_1374 ribose ABC transporter, periplasmic binding protein from Mycobacterium smegmatis str. MC2 155
26% identity, 74% coverage
RL0518 putative solute-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
26% identity, 91% coverage
- Identification of protein secretion systems and novel secreted proteins in Rhizobium leguminosarum bv. viciae
Krehenbrink, BMC genomics 2008 - “...35.4 sugar-binding protein 12d 29.8 36 (51) 4 RL0718 31.0. flagellin 13 27.7 129 10 RL0518 39.4 ribose-binding protein 14 25.0. 113 9 RL2753 27.9 arginine/ornithine-binding protein 15 20.4 57 5 RL1369 24.5 pentapeptide repeat protein 16 17.1 85 6 RL2404 20.5 peptidyl prolyl cis-trans isomerase...”
- “...in length with probabilities between 0.803 and 1.000. One of the predicted signal peptide proteins (RL0518) is also predicted to be a TAT substrate by the TATP 1.0 [ 77 ], but not by the TATFIND [ 78 ] algorithm. The predicted signal peptide of RL0518...”
B2904_orf2673 sugar ABC transporter substrate-binding protein from Brachyspira pilosicoli B2904
28% identity, 62% coverage
PS417_18405 D-ribose ABC transporter, substrate-binding component RbsB from Pseudomonas simiae WCS417
29% identity, 64% coverage
- mutant phenotype: No fitness data for this gene, but data for PS417_18400:18395 confirm this is the ABC transporter for ribose.
llmg_0789 ribose ABC transporter substrate binding protein RbsB from Lactococcus lactis subsp. cremoris MG1363
LLNZ_RS04085 substrate-binding domain-containing protein from Lactococcus cremoris subsp. cremoris NZ9000
23% identity, 69% coverage
CTN_0777 Periplasmic binding protein/LacI transcriptional regulator precursor from Thermotoga neapolitana DSM 4359
TRQ7_RS05225 sugar-binding protein from Thermotoga sp. RQ7
28% identity, 63% coverage
6dspA / U5MRH9 Lsrb from clostridium saccharobutylicum in complex with ai-2 (see paper)
23% identity, 81% coverage
- Ligand: (2r,4s)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran (6dspA)
Cthe_0393 sugar ABC transporter (sugar-binding protein) from Clostridium thermocellum ATCC 27405
Cthe_0393 substrate-binding domain-containing protein from Acetivibrio thermocellus ATCC 27405
33% identity, 41% coverage
- Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution
Ha-Tran, Microorganisms 2021 - “...of ATP-binding protein nbdA (Cthe_0391), inner membrane translocator msdA (Cthe_0392), and ribose ABC transporter cbpA (Cthe_0393) were significantly upregulated in FAs1 and GAs1 ( Figure 4 ). Additionally, the transmembrane sugar transport protein msdB1 (Cthe_1019) in the CbpB operon also exhibited an upregulated expression level. As...”
- Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass
Poudel, Biotechnology for biofuels 2017 - “...cellodextrin ABC transporter components, three (Cthe_1862, Cthe_1020, and Cthe_1019) were classified into cluster 4, whereas Cthe_0393 was a member of cluster 3. This suggests the majority of proteins required for the cellodextrin uptake remain relatively constant, with a modest increase at the transition between growth phases,...”
- Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq
Wei, Frontiers in microbiology 2014 - “...have been characterized for their substrate binding features (Nataf et al., 2009 ). Whereas CbpA (Cthe_0393) binds 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...”
- Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression
Rydzak, BMC microbiology 2012 - “...values (Figure 2a , Additional file 3 ). Characterization of Cbp subunits revealed that CbpA (Cthe_0393) binds only to cellotriose, 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...”
Avi_5339 ABC transporter substrate binding protein (ribose) from Agrobacterium vitis S4
26% identity, 78% coverage
7x0hA / A3DCF2 Crystal structure of sugar binding protein cbpa complexed wtih glucose from clostridium thermocellum (see paper)
33% identity, 41% coverage
- Ligand: beta-d-glucopyranose (7x0hA)
3ejwA / Q926H7 Crystal structure of the sinorhizobium meliloti ai-2 receptor, smlsrb (see paper)
24% identity, 83% coverage
- Ligand: (2r,4s)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran (3ejwA)
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
28% identity, 52% 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...”
BCAM0766 D-ribose-binding periplasmic protein precursor from Burkholderia cenocepacia J2315
28% identity, 51% coverage
4rxtA / B9JKX8 Crystal structure of carbohydrate transporter solute binding protein arad_9553 from agrobacterium radiobacter, target efi-511541, in complex with d-arabinose
26% identity, 83% coverage
- Ligand: alpha-l-arabinopyranose (4rxtA)
5dkvA / B9K0T2 Crystal structure of an abc transporter solute binding protein from agrobacterium vitis(avis_5339, target efi-511225) bound with alpha-d- tagatopyranose
28% identity, 57% coverage
- Ligand: alpha-d-tagatopyranose (5dkvA)
KP1_1422 putative rhizopine uptake ABC transport system periplasmic solute-binding protein precursor from Klebsiella pneumoniae NTUH-K2044
28% identity, 77% coverage
PP_2454 ribose ABC transporter, periplasmic ribose-binding protein from Pseudomonas putida KT2440
24% identity, 69% coverage
SMb21377 putative sugar uptake ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
28% identity, 54% 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...”
SMb20931 putative sugar uptake ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
25% identity, 49% coverage
- Inability to catabolize galactose leads to increased ability to compete for nodule occupancy in Sinorhizobium meliloti
Geddes, Journal of bacteriology 2012 - “...by galactose), SMb21343 (induced 6-fold by galactose), and SMb20931 (induced by - and -galactosides and 2-fold by galactose). Since mutations were previously...”
- Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics
Ramachandran, Genome biology 2011 - “...1) family SBP likely to transport raffinose, melibiose and lactose based on 91% identity to SMb20931 from S. meliloti , whose expression was induced by these sugars [ 5 ]. The second, pRL110281, which encodes a PepT (peptide/opine/nickel transporter) family SBP, is clearly important in the...”
- Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome
Mauchline, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...dulcitol, stachyose Oligosaccharide: galactosides (1) SMb20931 Raffinose, melibiose, lactose, lactulose Oligosaccharide: -galactosides (1) SMb21652 Lactose,...”
- “...We found a previously undescribed second system, ABC-T SMb20931, which was induced not only by -galactosides raffinose and melibiose, but also by the...”
- Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti
Pobigaylo, Applied and environmental microbiology 2006 - “...0.77 0.82 1.67 0.43 0.43 1.50 3-11B 3-5B pSymB.1003846 SMb20931 0.19 0.12 0.43 0.21 1.95 0.94 1.85 0.76 4-12C 4-1H Cluster 4 (highly competitive in stress...”
- “...subunit of an ATP-dependent Clp protease), and SMb20931 (coding for a putative sugar uptake ABC transporter periplasmic solutebinding protein precursor)....”
gbs0113 Unknown from Streptococcus agalactiae NEM316
22% identity, 76% coverage
TTE0206 Periplasmic sugar-binding proteins from Thermoanaerobacter tengcongensis MB4
25% identity, 86% coverage
2ioyA / Q8RD41 Crystal structure of thermoanaerobacter tengcongensis ribose binding protein (see paper)
25% identity, 79% coverage
- Ligand: beta-d-ribopyranose (2ioyA)
RHE_CH00492 probable sugar ABC transporter, substrate-binding protein from Rhizobium etli CFN 42
26% identity, 90% coverage
- Impact of c-di-GMP on the Extracellular Proteome of Rhizobium etli
Lorite, Biology 2022 - “...RHE_PF00186, 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...”
NGR_RS07515 sugar-binding protein from Sinorhizobium fredii NGR234
25% identity, 58% coverage
Entcl_4175 sugar ABC transporter substrate-binding protein from [Enterobacter] lignolyticus SCF1
31% identity, 31% 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...”
SAK_0166 ribose ABC transporter, ribose-binding protein from Streptococcus agalactiae A909
23% identity, 71% coverage
SAN_0145 ribose ABC transporter, periplasmic D-ribose-binding protein from Streptococcus agalactiae COH1
23% identity, 71% coverage
SAG0114 ribose ABC transporter, periplasmic D-ribose-binding protein from Streptococcus agalactiae 2603V/R
24% identity, 75% coverage
7e7mC / Q8E283 Crystal structure analysis of the streptococcus agalactiae ribose binding protein rbsb
24% identity, 75% coverage
- Ligand: beta-d-ribopyranose (7e7mC)
RHE_RS27555 sugar-binding protein from Rhizobium etli CFN 42
27% identity, 74% 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 - “...proC; pyrroline-5-carboxylate reductase [EC:1.5.1.2] K10439 MM RHE_RS22400 rbsB; ribose transport system substrate-binding protein K10439 MM RHE_RS27555 rbsB; ribose 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...”
- “...The rbsB ; 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...”
AOT13_01795 ribose ABC transporter substrate-binding protein RbsB from Parageobacillus thermoglucosidasius
26% identity, 75% coverage
RLV_4716 sugar-binding protein from Rhizobium leguminosarum bv. viciae
27% identity, 74% coverage
TEL01S_RS08670 sugar ABC transporter substrate-binding protein from Pseudothermotoga elfii DSM 9442 = NBRC 107921
30% identity, 42% coverage
GK1896 sugar ABC transporter (sugar-binding protein) from Geobacillus kaustophilus HTA426
24% identity, 75% coverage
SXYL_01518 D-ribose ABC transporter substrate-binding protein from Staphylococcus xylosus
26% identity, 78% coverage
C9ZD81 Putative secreted solute binding protein from Streptomyces scabiei (strain 87.22)
26% identity, 84% coverage
CTN_0240 Sugar binding protein of ABC transporter from Thermotoga neapolitana DSM 4359
25% identity, 64% coverage
CD0300 D-ribose ABC transporter, substrate-binding protein from Clostridium difficile 630
27% identity, 75% 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...”
VCA0130 ribose ABC transporter, periplasmic D-ribose-binding protein from Vibrio cholerae O1 biovar eltor str. N16961
22% identity, 87% coverage
CTN_0364 putative periplasmic binding protein from Thermotoga neapolitana DSM 4359
33% identity, 34% coverage
LBA1481 D-ribose-binding protein precursor from Lactobacillus acidophilus NCFM
26% identity, 53% coverage
RHE_RS30060 substrate-binding domain-containing protein from Rhizobium etli CFN 42
27% identity, 56% 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...”
MSMEG_3999 ABC transporter periplasmic-binding protein YphF from Mycobacterium smegmatis str. MC2 155
23% identity, 67% coverage
Ac3H11_3035 Fructose ABC transporter, substrate-binding component FrcB from Acidovorax sp. GW101-3H11
34% identity, 33% coverage
- mutant phenotype: Specific phenotype: utilization of D-Fructose, D-Mannose, D-Sorbitol
SACE_0943 binding protein/LacI transcriptional regulator from Saccharopolyspora erythraea NRRL 2338
26% identity, 74% coverage
PGA1_262p00430 glucose transporter, periplasmic substrate-binding component from Phaeobacter inhibens DSM 17395
34% identity, 30% coverage
- mutant phenotype: specific phenotype on glucose and cofit with other nearby components. This is similar (65% identity) to gxyS (Atu3576) of Agrobacterium tumefaciens, which is involved in the transport of glucose, glucosamine, and xylose (PMCID: PMC4135649). It is not clear if the Phaeobacter system transports xylose, as it is not required for utilizing xylose, but no other xylose transport system was identified either.
4ry8B / A8F7U7 Crystal structure of 5-methylthioribose transporter solute binding protein tlet_1677 from thermotoga lettingae tmo target efi-511109 in complex with 5-methylthioribose
32% identity, 36% coverage
- Ligand: 5-s-methyl-5-thio-alpha-d-ribofuranose (4ry8B)
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
23% identity, 81% coverage
- Ligands: magnesium ion; 1,2,3,4,5,6-hexahydroxy-cyclohexane (4yo7A)
SPRI_RS32325 sugar ABC transporter substrate-binding protein from Streptomyces pristinaespiralis
23% identity, 76% 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...”
B5S52_21960 ribose ABC transporter substrate-binding protein RbsB from Pectobacterium brasiliense
24% identity, 87% coverage
ECA_RS00065 ribose ABC transporter substrate-binding protein RbsB from Pectobacterium atrosepticum SCRI1043
24% identity, 87% coverage
PFLU_2583 sugar ABC transporter substrate-binding protein from Pseudomonas [fluorescens] SBW25
PFLU2583 putative rhizopine-binding ABC transporter protein from Pseudomonas fluorescens SBW25
23% identity, 84% coverage
- 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...”
- 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...”
OG1RF_0175 possible DNA binding protein from Enterococcus faecalis OG1RF
OG1RF_11789 LacI family DNA-binding transcriptional regulator from Enterococcus faecalis OG1RF
24% identity, 49% coverage
- Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF
Bourgogne, Genome biology 2008 - “...transporter OG1RF_0143 GntR family transcriptional regulator 82745913 236 Probable regulator of the downstream PTS system OG1RF_0175 DNA binding protein 15890504 293 Probable regulator of the iol operon OG1RF_0192 Sensor histidine kinase VanS G 119635646 371 Best homology with Van G and OG1RF_0193 Response regulator VanR G...”
- CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis
Price, mSphere 2016 - “...pLT06 Markerless exchange plasmid; confers chloramphenicol resistance 58 pWH03 Derivative of pLT06 containing OG1RF_11778 and OG1RF_11789 for integration into neutral site on chromosome 43 pVP102 Derivative of pLT06 to create markerless, in-frame deletion of CRISPR3- cas9 in T11RF This study pAS106 Derivative of pLT06 to create...”
- “...pWH03 to integrate OG1SSp OG1RF_11621-OG1RF_11622 and its native promoter into the chromosome between OG1RF_11778 and OG1RF_11789 This study pVP401 Derivative of pGEM-T-Easy with 100-bp insert, including T11 CRISPR2 spacer 1 and the consensus CRISPR2 PAM This study pVP107 Derivative of pLT06 to knock-in the T11 CRISPR2...”
THPA_MYCS2 / A0QYB5 D-threitol-binding protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see paper)
MSMEG_3599 sugar ABC transporter xylitol/D-threitol-binding protein ThpA from Mycolicibacterium smegmatis MC2 155
MSMEG_3599 sugar-binding transcriptional regulator, LacI family protein from Mycobacterium smegmatis str. MC2 155
27% identity, 54% 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...”
Q92TD7 D-fucose, pyruvic acid or L-fucose ABC transporter, periplasmic substrate-binding component from Rhizobium meliloti (strain 1021)
SMc02774 PUTATIVE ABC TRANSPORTER PERIPLASMIC BINDING PROTEIN from Sinorhizobium meliloti 1021
23% identity, 87% coverage
- Quantitative proteomics insights into Chlamydomonas reinhardtii thermal tolerance enhancement by a mutualistic interaction with Sinorhizobium meliloti.
Zhao, Microbiology spectrum 2024 - “...0.89 2.71 1.72 Q92W78 sm_b20485 Putative sugar ABC transporter ATP-binding protein 0.34 1.17 0.71 2.45 Q92TD7 smc02774 Putative D- or L-fucose, or pyruvic acid, periplasmic substrate-binding component of ABC transporter 0.92 0.66 3.1 2.22 Q92RV7 dppD1 Putative amino acid or peptide ABC transporter 1.00 0.65 0.48...”
- Quantitative proteomics insights into Chlamydomonas reinhardtii thermal tolerance enhancement by a mutualistic interaction with Sinorhizobium meliloti
Zhao, Microbiology spectrum 2024 - “...2.71 1.72 Q92W78 sm_b20485 Putative sugar ABC transporter ATP-binding protein 0.34 1.17 0.71 2.45 Q92TD7 smc02774 Putative D- or L-fucose, or pyruvic acid, periplasmic substrate-binding component of ABC transporter 0.92 0.66 3.1 2.22 Q92RV7 dppD1 Putative amino acid or peptide ABC transporter 1.00 0.65 0.48 0.31...”
- Mining the Sinorhizobium meliloti transportome to develop FRET biosensors for sugars, dicarboxylates and cyclic polyols
Bourdès, PloS one 2012 - “...it is thought they are important in binding L-rhamnose. The L-fucose biosensor is based on SMc02774, an SBP of another CUT2 ABC-transporter. This gene was induced by D-fucose (6.7-fold), pyruvate (4.9-fold) and L-fucose (4.2-fold) [9] . SMc02775, contiguous with genes encoding the ABC transporter (SMc02772-4), was...”
- “...between the affinity of SMc02774-CY for L-fucose compared to its affinity for L-rhamnose indicates that SMc02774 encodes a high-affinity L-fucose binding protein. Despite the structural similarity of the two L-deoxy sugar ligands (L-fucose and L-rhamnose).and the fact that both SBPs (SMc02324 and SMc02774) are in the...”
- Regulatable vectors for environmental gene expression in Alphaproteobacteria
Tett, Applied and environmental microbiology 2012 - “...periplasmic solute binding protein from S. meliloti 1021 (SMc02774), including the native leader sequence, to give pLMB548. Although it would be possible to...”
- “...extraction was as previously described (5). Histidine-tagged protein (SMc02774) was purified from the periplasmic extraction using a 1-ml HisTrap FF column at...”
- 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 - “...monosaccharides (8) SMc02324 Rhamnose, erythritol SMc02774 D-()-fucose, pyruvic acid, L-()-fucose SMb21103 D-()-fucose, L-()-fucose SMb21587 D-()-fucose,...”
- “...primarily by the methyl pentose, fucose (Table 1). ABC-T SMc02774 was induced by D-fucose (7-fold) and L-fucose (4fold) as reported by an integrated fusion in...”
- Biotin limitation in Sinorhizobium meliloti strain 1021 alters transcription and translation
Heinz, Applied and environmental microbiology 2003 - “...binding protein SMc03153/Eda2; 2-keto-3-deoxy-6-phosphogluconate aldolase SMc02774; ABC transporter periplasmic sugar binding protein SMb20416/UgpB; ABC...”
- 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 - “...SMc02499 SMc02508 SMc02509 SMc02510 SMc02634 SMc02692 SMc02774 SMc02873 SMc02857 SMc02857 SMc02857 SMc03061 SMa0312 SMc03157 SMc03233 SMc03786 SMc03878 SMc03879...”
RL3840 putative substrate-binding protein component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
25% identity, 58% coverage
- Genome-Scale Metabolic Modelling of Lifestyle Changes in Rhizobium leguminosarum
Schulte, mSystems 2022 - “...factors. The gene encoding the solute-binding protein of a carbohydrate uptake transporter-1 (CUT1) family transporter (RL3840) was 2.6-fold upregulated in the pea rhizosphere compared to free-living cells ( 10 ), which supports the predicted uptake of a di- or oligosaccharide. Ribulose, a monosaccharide metabolized via the...”
- Antioxidant ability of glutaredoxins and their role in symbiotic nitrogen fixation in Rhizobium leguminosarum bv. viciae 3841
Zou, Applied and environmental microbiology 2021 (secret) - Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics
Ramachandran, Genome biology 2011 - “...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) or, in...”
- “...(MtlE, RL4218). Also elevated were genes encoding components of two previously uncharacterized systems. The first, RL3840, encodes a CUT1 (carbohydrate uptake transporter 1) family SBP likely to transport raffinose, melibiose and lactose based on 91% identity to SMb20931 from S. meliloti , whose expression was induced...”
DDA3937_RS00045 ribose ABC transporter substrate-binding protein RbsB from Dickeya dadantii 3937
23% identity, 87% coverage
Q98FL9 Xylose binding protein transport system XylF from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
29% identity, 39% coverage
- Cyclic Isothiocyanate Goitrin Impairs Lotus japonicus Nodulation, Affects the Proteomes of Nodules and Free Mesorhizobium loti, and Induces the Formation of Caffeic Acid Derivatives in Bacterial Cultures
Jeong, Plants (Basel, Switzerland) 2024 - “...]. In F1, 18 identified ABC transporter proteins were down regulated. Most affected proteins were Q98FL9, Q98BA6, Q98FA8, Q98MD4. Seven of these proteins act in amino acid transport, ten in sugar transport. Two transporters/transporter binding proteins were not changed in abundance, one is responsible for thiamine/iron...”
A79_4530 D-ribose-binding periplasmic protein from Vibrio parahaemolyticus AQ3810
VPA1084 ribose ABC transporter, periplasmic D-ribose-binding protein from Vibrio parahaemolyticus RIMD 2210633
24% identity, 70% coverage
- 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...”
- 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...”
RBAM_RS16755 ribose ABC transporter substrate-binding protein RbsB from Bacillus velezensis FZB42
24% identity, 75% coverage
5xssA / A6LW07 Xylfii molecule (see paper)
21% identity, 60% coverage
- Ligand: beta-d-xylopyranose (5xssA)
SMb20856 putative sugar uptake ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
25% identity, 62% coverage
RL3624 putative solute-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
31% identity, 32% coverage
c3070 ABC transporter Periplasmic binding protein yphF precursor from Escherichia coli CFT073
22% identity, 78% 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**...”
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
24% identity, 82% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory