PaperBLAST
PaperBLAST Hits for reanno::pseudo6_N2E2:Pf6N2E2_5402 ABC transporter for D-Alanine, periplasmic substrate-binding component (Pseudomonas fluorescens FW300-N2E2) (343 a.a., MKLLKSTLAV...)
Show query sequence
>reanno::pseudo6_N2E2:Pf6N2E2_5402 ABC transporter for D-Alanine, periplasmic substrate-binding component (Pseudomonas fluorescens FW300-N2E2)
MKLLKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVG
IDADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKF
PGFITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFD
TSDESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEW
LAIVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQI
VKQVGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR
Running BLASTp...
Found 253 similar proteins in the literature:
Pf6N2E2_5402 ABC transporter for D-Alanine, periplasmic substrate-binding component from Pseudomonas fluorescens FW300-N2E2
100% identity, 100% coverage
- mutant phenotype: Very important for D-alanine utilization. This transporter may also uptake L-histidine.
PFLU_1000 amino acid ABC transporter substrate-binding protein from Pseudomonas [fluorescens] SBW25
93% identity, 100% coverage
Q4KHV4 General L-amino acid ABC transporter, periplasmic L-amino acid-binding protein AapJ from Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)
90% identity, 100% coverage
Psyr_1072 extracellular solute-binding protein, family 3 from Pseudomonas syringae pv. syringae B728a
86% identity, 100% coverage
PSPTO_1255 amino acid ABC transporter, periplasmic amino acid-binding protein from Pseudomonas syringae pv. tomato str. DC3000
85% identity, 100% coverage
- Proteomic Profiling Reveals Distinct Bacterial Extracellular Vesicle Subpopulations with Possibly Unique Functionality
McMillan, Applied and environmental microbiology 2023 (secret) - Data-Independent Acquisition Proteomics Unravels the Effects of Iron Ions on Coronatine Synthesis in Pseudomonas syringae pv. tomato DC3000
He, Frontiers in microbiology 2020 - “...expression of ABC transporters responsible for amino acid uptake (PSPTO_4887, PSPTO_4173, PSPTO_4919, PSPTO_1258, PSPTO_1256, and PSPTO_1255), glucose ABC transporter (PSPTO_1294, PSPTO_1293, and gltK), ribose ABC transporters (rbsA-1), iron ABC transporters (PSPTO_5562 and PSPTO_5561), peptide transporters (PSPTO_4562, PSPTO_4559, dppC, PSPTO_4558, and PSPTO_4564), a mannitol ABC transporter (PSPTO_2705),...”
PP1297 general amino acid ABC transporter, periplasmic binding protein from Pseudomonas putida KT2440
PP_1297 amino acid ABC transporter substrate-binding protein from Pseudomonas putida KT2440
86% identity, 100% coverage
- UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - Comparative transcriptomics and proteomics of p-hydroxybenzoate producing Pseudomonas putida S12: novel responses and implications for strain improvement
Verhoef, Applied microbiology and biotechnology 2010 - “...protein PP1273 4.8 10.1 General amino acid ABC transporter, periplasmic binding protein ( aapJ ) PP1297 0.48 d 3.4 0.570.06 c 5.10.6 c General amino acid ABC transporter, permease protein ( aapQ ) PP1298 0.51 d 4.6 General amino acid ABC transporter, permease protein ( aapM...”
- PpoR is a conserved unpaired LuxR solo of Pseudomonas putida which binds N-acyl homoserine lactones
Subramoni, BMC microbiology 2009 - “...PP0999 carbamate kinase 3.475 18. PP0193 hypothetical protein 3.470 19. PP1001 arginine deiminase 3.335 20. PP1297 general amino acid ABC transporter, periplasmic binding protein 3.111 21. PP0764 hypothetical protein 3.100 22. PP4650 ubiquinol oxidase subunit II, cyanide insensitive 3.073 23. PP0751 malate:quinone oxidoreductase 2.972 24. PP0989...”
- Transcriptome analysis of Pseudomonas putida in response to nitrogen availability
Hervás, Journal of bacteriology 2008 - “...transport, including transport of amino acids in general (PP1297 to PP1300), branched-chain amino acids (PP1138 to PP1141, PP4841 to PP4845, and PP4863 to...”
- The AauR-AauS two-component system regulates uptake and metabolism of acidic amino acids in Pseudomonas putida
Sonawane, Applied and environmental microbiology 2006 - “...(PP1141) 6.02 39.4 Amino acid transport 17 aapJ (PP1297) 5.84 36.4 Amino acid transport Branched-chain amino acid ABC transporter, periplasmic amino acid...”
- Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440
Avendaño, Microbial biotechnology 2023 - “...presence of selenite the overexpression of transporters related to the uptake of amino acids (operon PP_1297, PP_1298, PP_1299 and PP_1300) and ribose (PP_2456, PP_2455). The differences in expression patterns in membrane proteins can be explained considering that selenite reduction leads to the accumulation of extracellular selenium...”
Pput_4428 extracellular solute-binding protein from Pseudomonas putida F1
86% identity, 100% coverage
L321_23611 amino acid ABC transporter substrate-binding protein from Pseudomonas plecoglossicida NB2011
86% identity, 100% coverage
W6QUE9 Putative amino-acid ABC transporter-binding protein from Ectopseudomonas oleovorans (strain CECT 5344)
79% identity, 100% coverage
PA3858 probable amino acid-binding protein from Pseudomonas aeruginosa PAO1
64% identity, 100% coverage
PA14_14100 Putative amino-acid ABC transporter binding protei from Pseudomonas aeruginosa UCBPP-PA14
64% identity, 100% coverage
- Dissecting the machinery that introduces disulfide bonds in Pseudomonas aeruginosa
Arts, mBio 2013 - “...periplasmic substrate-binding protein (PA14_67400) 4 P 0.08 Q02S18 Putative amino acid ABC transporter-binding protein YhdW (PA14_14100) 4 P 0.00 Q02TC1 Putative phage-related protein tail component JF1 (PA14_08300) 4 OM 0.38 Q02DR8 Putative uncharacterized protein (PA14_71840) 8 OM 0.06 Q02M97 Chitinase ChiC (PA14_34870) 1 E 0.47 Q02GR5...”
EAMY_0266 putative ABC transport system, periplasmic component from Erwinia amylovora CFBP1430
66% identity, 100% coverage
VV1_2703 ABC-type amino acid transport, signal transduction systems, periplasmic component/domain from Vibrio vulnificus CMCP6
59% identity, 100% coverage
VpaChn25_1613, WU75_14760 amino acid ABC transporter substrate-binding protein from Vibrio parahaemolyticus
Q87P98 Amino acid ABC transporter, periplasmic amino acid-binding protein from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
VP1620 amino acid ABC transporter, periplasmic amino acid-binding protein from Vibrio parahaemolyticus RIMD 2210633
59% identity, 99% coverage
- Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn
Tang, Foods (Basel, Switzerland) 2023 - “...ABC transporter ATP-binding protein WU75_10275 rbsD 0.438 D-ribose pyranase WU75_05845 btuF 0.487 Vitamin B12-binding protein WU75_14760 aapJ 0.491 Amino acid ABC transporter substrate-binding protein WU75_03185 malK 2.175 Maltose/maltodextrin transporter ATP-binding protein WU75_19815 znuA 2.204 Zinc ABC transporter substrate-binding protein WU75_19810 znuC 2.491 Zinc ABC transporter ATPase...”
- Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival
Zhu, BMC genomics 2017 - “...permease VpaChn25_1347 0.3245 Oligopeptide ABC transporter permease VpaChn25_1348 0.3723 Oligopeptide ABC transporter periplasmic oligopeptide-binding protein VpaChn25_1613 2.4584 Amino acid ABC transporter substrate-binding protein VpaChn25_1714 0.4917 Glycine/betaine/proline ABC transporter VpaChn25_1913 2.222 Hypothetical protein VpaChn25_2428 0.4529 Iron (III) ABC transporter permease VpaChn25_2429 0.3234 Iron (III) ABC transporter periplasmic...”
- iTRAQ-based proteomic profiling of Vibrio parahaemolyticus under various culture conditions
Yang, Proteome science 2015 - “...process Q87SB9 ATP-dependent RNA helicase SrmB ATP 2.965 0.048 3.981 0.004 6.081 0.001 ATP-dependent helicaseactivity Q87P98 Amino acid ABC transporter, periplasmic amino acid-binding protein 4.093 0.001 0.191 0.001 9.462 3.95E-06 transporter activity F3RQ38 Diaminobutyrate-pyruvate transaminase and L-2,4-diaminobutyrate decarboxylase 0.217 0.021 2.535 0.001 0.146 0.014 carboxylic acid...”
- Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus
Kalburge, Infection and immunity 2017 - “...acid transport (ORFs VP0008 to VP0006 and VP1620) and thymidine, uridine, serine, aspartate, fumarate, glutarate, arginine, histidine, phenylalanine, tyrosine,...”
BAU10_07410 amino acid ABC transporter substrate-binding protein from Vibrio alginolyticus
58% identity, 99% coverage
- Identification of the global regulatory roles of RraA via the integrative transcriptome and proteome in Vibrio alginolyticus
Chen, mSphere 2024 - “...trends in the rraA mutant, including MppA (BAU10_15390, down 2.52-fold), ArgT (BAU10_04000, down 3.42-fold), AapJ (BAU10_07410, down 3.37-fold), OusX (BAU10_06495, down 3.81-fold), OppA (BAU10_05985, down 24.48-fold), AotP (BAU10_03995, down 2.23-fold), OusV (BAU10_06505, down 3.29-fold), ArtP (BAU10_20535, down 1.78-fold), BAU10_18335(down 17.77-fold), SdaC (BAU10_20390, down 4.55-fold), OppA(BAU10_09280, down...”
AAPJ_RHIJ3 / Q52812 General L-amino acid-binding periplasmic protein AapJ from Rhizobium johnstonii (strain DSM 114642 / LMG 32736 / 3841) (Rhizobium leguminosarum bv. viciae) (see 2 papers)
TC 3.A.1.3.8 / Q52812 AapJ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) from Rhizobium leguminosarum (biovar viciae) (see 2 papers)
aapJ / CAA57933.1 general amino acid ABC type transporter from Rhizobium leguminosarum (see paper)
RL2204 General L-amino acid substrate binding protein from Rhizobium leguminosarum bv. viciae 3841
58% identity, 98% coverage
- function: Part of the ABC transporter complex AapJQMP involved in uptake of L-amino acids (PubMed:19597156, PubMed:8898392). Affects the efflux of these amino acids as well (PubMed:8898392). Essential for the development of bacteroids, the differentiated legume-symbiotic forms of this bacterium, and for the effective N(2) fixation by them (PubMed:19597156).
subunit: The complex is composed of two ATP-binding proteins (AapP), two transmembrane proteins (AapM and AapQ) and a solute-binding protein (AapJ).
disruption phenotype: Reduced uptake of amino acids Glu, Asp, Ala, Leu, Ile and Val by bacteroids that lack this gene and the genes braC and braC3 or braE and braF from another ABC uptake system of branched-chain amino acids. Pea plants inoculated with bacteroids of either triple mutant are defective in symbiosis; the plants are yellow, have increased numbers of small pale pink root nodules, dry weights similar to uninoculated control plants and 30% acetylene reduction compared to plants inoculated with wild-type bacteroids. AapJ/braE/braF triple mutant bacteroids are smaller, have reduced bacteroid protein and cell number per plant compared to wild-type, and have a lower chromosome number of 5 compared with 8 of the wild-type. - substrates: Amino acids
- Antioxidant ability of glutaredoxins and their role in symbiotic nitrogen fixation in Rhizobium leguminosarum bv. viciae 3841
Zou, Applied and environmental microbiology 2021 (secret) - Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis
Wheatley, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret)
VC1362 amino acid ABC transporter, periplasmic amino acid-binding protein from Vibrio cholerae O1 biovar eltor str. N16961
VCV52_1340 amino acid ABC transporter, periplasmic amino acid-binding protein from Vibrio cholerae V52
61% identity, 92% coverage
- Distinct sensory pathways in Vibrio cholerae El Tor and classical biotypes modulate cyclic dimeric GMP levels to control biofilm formation
Hammer, Journal of bacteriology 2009 - “...VCA0025b VCA0939 VCA1070 VC0098 VC0300b VC0402 VC1280b VC1362 Thermoresistant gluconokinase (gntV) GGDEF family protein Transporter (nadC) Sensory box, GGDEF...”
- Differences in gene expression between the classical and El Tor biotypes of Vibrio cholerae O1
Beyhan, Infection and immunity 2006 - “...that encode amino acid ABC transporter components; VCA1039, VC1362, and VCA0978 that each encode for a periplasmic amino acid binding protein; VCA0759 (artI), a...”
- Quorum-sensing regulators control virulence gene expression in Vibrio cholerae
Zhu, Proceedings of the National Academy of Sciences of the United States of America 2002 - “...19.7 16.3 10.5 28.4 40.4 39.5 6.9 VCA0025 VC1318 VCA0687 VC1362 VC1854 6.3 4.5 3.6 4.9 5.5 VC0819 VCA0744 VCA0877 VCA0690 VCA0688 VCA0691 12.7 5.3 6.9 8.1 9.1...”
- Secretome analysis of Vibrio cholerae type VI secretion system reveals a new effector-immunity pair
Altindis, mBio 2015 - “...). Classification of these three proteins, VCV52_1056 (ABC transporter), VCV52_0504 (CysP, thiosulfate ABC transporter), and VCV52_1340 (amino acid ABC transporter) according to their predicted functional categories revealed three new ABC transporters. Whether the occurrence of these proteins in the TseH secretome reflects changes in gene expression...”
SMc02118 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component from Sinorhizobium meliloti 1021
Q92Q71 Probable general L-amino acid-binding periplasmic ABC transporter from Rhizobium meliloti (strain 1021)
SMc02118 PROBABLE GENERAL L-AMINO ACID-BINDING PERIPLASMIC ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
55% identity, 99% coverage
- mutant phenotype: Specific phenotype on L-Histidine; L-Glutamine.
- Comparative Proteomic Analysis Revealing ActJ-Regulated Proteins in Sinorhizobium meliloti.
Albicoro, Journal of proteome research 2023 - A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti
Draghi, Scientific reports 2016 - “...transporter. E-T SMc02873 Q92SZ7 34 102 SVNA 0.41 Multiple sugar-binding protein precursor. G SMc02118 AapJ Q92Q71 48 187 SVNA 2.82 General L-amino acid-binding periplasmic protein. E-T SMc03786 Bfr Q92LA7 55 110 SVNA 1.51 Bacterioferritin (BFR). P SMc02259 Q92S63 46 146 SVNA 1.14 Lysine-arginine-ornithine-binding periplasmic protein precursor....”
- Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti
D'Alessio, mSystems 2017 - “...well as nitrate uptake genes. The amino acid uptake genes include the aap operon ( SMc02118 to SMc02121 ) and the liv ( bra ) operon ( SMc01946 to SMc01951 ), both involved in branched-chain amino acid uptake, as well as the hut ( SMb21163 to...”
- A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti
Draghi, Scientific reports 2016 - “...periplasmic ABC transporter. E-T SMc02873 Q92SZ7 34 102 SVNA 0.41 Multiple sugar-binding protein precursor. G SMc02118 AapJ Q92Q71 48 187 SVNA 2.82 General L-amino acid-binding periplasmic protein. E-T SMc03786 Bfr Q92LA7 55 110 SVNA 1.51 Bacterioferritin (BFR). P SMc02259 Q92S63 46 146 SVNA 1.14 Lysine-arginine-ornithine-binding periplasmic...”
- Quantitative proteomic analysis of the Hfq-regulon in Sinorhizobium meliloti 2011
Sobrero, PloS one 2012 - “...SMc02259), and 4 proteins that were common to all three proteomic studies (SMc00786, SMc01525, SMc01946, SMc02118). Thus, our quantitative proteomic analysis confirmed those hits and significantly expanded the list of candidate genes possibly subject to Hfq-dependent negative riboregulation. As observed for proteins positively regulated by Hfq,...”
- “...[53] ; all proteins encoded by the aap operon ( aapJQMP ; SMc02121, SMc02120, SMc02119, SMc02118), constitute a high affinity transport system for L-amino acids [41] ; and several genes of the liv operon ( livHMGFK ; SMc01946, SMc01948, SMc01949, SMc01950, SMc01951) [41] , are involved...”
- Proteomic alterations explain phenotypic changes in Sinorhizobium meliloti lacking the RNA chaperone Hfq
Barra-Bily, Journal of bacteriology 2010 - “...Overexpression ftsZ1 SMc01946 livK SMc02098 SMc02100 frr tsf SMc02118 SMc02156 SMc02344 SMc02495 SMc02501 Stat (0.48) Expo (2.6); Stat (4.7) Expo (2.6) Expo...”
- “...isoforms (LivK with SMc01946 and SMc00242, AapJ with SMc02118 and SMc02156, and PhoD with SMb21176) (Fig. 2), suggesting that these isoforms could result from...”
- Role of the Sinorhizobium meliloti global regulator Hfq in gene regulation and symbiosis
Gao, Molecular plant-microbe interactions : MPMI 2010 - “...a Relative expression ratio 1021 hfq mutant vs. Rm1021 Gene SymbiosisChip b Real-time PCR c SMc02118 ( aapJ ) 2.2 4.1 0.4 SMc02119 ( aapQ ) 4.1 11.0 0.6 SMc02120 ( aapM ) 4.8 8.4 0.4 SMc01946 ( livK ) 5.5 14.0 0.3 SMc01948 ( livF...”
- 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 - “...SMc01587 SMc01939 SMc02101 SMc02087 SMc02100 SMc02111 SMc02118 SMc02165 Smc02171 SMc02217 SMc02408 SMc02495 SMc02499 SMc02508 SMc02509 SMc02510 SMc02634...”
VSAL_I2057 amino acid ABC transporter substrate-binding protein from Aliivibrio salmonicida LFI1238
VSAL_I2057 general L-amino acid-binding periplasmic protein precursor from Vibrio salmonicida LFI1238
57% identity, 100% coverage
BCAN_A0756 lysine-arginine-ornithine-binding periplasmic protein from Brucella canis ATCC 23365
BR0741 amino acid ABC transporter, periplasmic amino acid-binding protein from Brucella suis 1330
BOV_0736 amino acid ABC transporter, periplasmic amino acid-binding protein from Brucella ovis ATCC 25840
58% identity, 99% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BruAb10760 BR0743 BOV_0737 BCAN_A0758 PAO General L-amino acid import BP BMEI1211, appJ BruAb10761 BR0741 BOV_0738 BCAN_A0756 PAO General L-amino acid import BP BMEII0349, appJ BruAb20285 BRA0948 BOV_0736 BCAN_B0969 92 PAO Arginine BP BMEI1627 BruAb10321 BR0295 BOV_0308 93 PAO Cystine import ABC BMEII0599 BruAb20545 BRA0684 BOV_A0640 BCAN_B0682...”
- Quantitative analysis of the Brucella suis proteome reveals metabolic adaptation to long-term nutrient starvation
Al, BMC microbiology 2013 - “...1293 BRA0953 amino acid ABC transporter, periplasmic amino acid-binding protein, putative 43.3/5.3 1.36 0.0019 1549 BR0741 amino acid ABC transporter, periplasmic amino acid binding protein 37.2/5.3 1.31 0.00014 Protein metabolism Biosynthesis 1783 BR0455 ribosomal protein S6 17.1/8.0 1.69 0.0069 1980 BR0452 ribosomal protein L9 21.0/4.8 1.59...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BMEI1210, appQ BruAb10760 BR0743 BOV_0737 BCAN_A0758 PAO General L-amino acid import BP BMEI1211, appJ BruAb10761 BR0741 BOV_0738 BCAN_A0756 PAO General L-amino acid import BP BMEII0349, appJ BruAb20285 BRA0948 BOV_0736 BCAN_B0969 92 PAO Arginine BP BMEI1627 BruAb10321 BR0295 BOV_0308 93 PAO Cystine import ABC BMEII0599 BruAb20545 BRA0684...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...appJ BruAb10761 BR0741 BOV_0738 BCAN_A0756 PAO General L-amino acid import BP BMEII0349, appJ BruAb20285 BRA0948 BOV_0736 BCAN_B0969 92 PAO Arginine BP BMEI1627 BruAb10321 BR0295 BOV_0308 93 PAO Cystine import ABC BMEII0599 BruAb20545 BRA0684 BOV_A0640 BCAN_B0682 PAO Cystine import IM BMEII0600 BruAb20546 BRA0683 BOV_A0639 BCAN_B0681 PAO Cystine...”
BME_RS06090 amino acid ABC transporter substrate-binding protein from Brucella melitensis bv. 1 str. 16M
Q8YGE8 General l-amino acid-binding periplasmic protein aapj from Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)
BMEI1211 GENERAL L-AMINO ACID-BINDING PERIPLASMIC PROTEIN AAPJ PRECURSOR from Brucella melitensis 16M
58% identity, 99% coverage
- Survival characteristics and transcriptome profiling reveal the adaptive response of the Brucella melitensis 16M biofilm to osmotic stress
Guo, Frontiers in microbiology 2022 - “...involved in the ABC transporter pathways included BME_RS06085, BME_RS12870, BME_RS13630, BME_RS12880, BME_RS1 2875, BME_RS01965, BME_RS02190, BME_RS06090, BME _RS02065, BME_RS02355, BME_RS02180, BME_RS11830. The expressions of these genes using qRT-PCR were in good agreement with the RNA-seq results ( Figures 5AC ). This finding agrees with a previous...”
- Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis
Murugaiyan, Biomolecules 2020 - “...glycine betaine transport system Q8YBF5 Maltose-binding periplasmic protein (Sugar ABC transporter) Q8YCD1 Cystine-binding periplasmic protein Q8YGE8 Cationic amino acid ABC transporter Q2YKN7 Uncharacterized protein Q2YKN9 Uncharacterized protein Q2YQM2 Uncharacterized protein...”
- Transcriptomic Analysis of the Brucella melitensis Rev.1 Vaccine Strain in an Acidic Environment: Insights Into Virulence Attenuation
Salmon-Divon, Frontiers in microbiology 2019 - “...found in the reported proteomic analysis. Gene ID Gene description RNA-seq/proteome BMEI0372 Response regulator Overexpression/overexpression BMEI1211 Amino acid ABC transporter substrate-binding protein Overexpression/overexpression BMEI1390 ABC transporter substrate-binding protein Overexpression/overexpression BMEI1923 Isovaleryl-CoA dehydrogenase Overexpression/overexpression BMEII0203 ABC transporter substrate-binding protein Overexpression/overexpression BMEII0344 ABC transporter permease Overexpression/overexpression BMEII0550 Glycine/betaine...”
- Global analysis of quorum sensing targets in the intracellular pathogen Brucella melitensis 16 M
Uzureau, Journal of proteome research 2010 - “...3 9 193 Q-TOF Unassigned BMEI1201 Hypothetical cytosolic protein AAL52382.1 2.64 6 17 477 Q-TOF BMEI1211 General L-amino acid-binding periplasmic protein AAPJ precursor AAL52392.1 2.07 2 5 151 Q-TOF BMEI1747 aldehyde dehydrogenase AAL52928.1 0.66 5 9 360 Q-TOF BMEI1819 Alcohol dehydrogenase deshydrogenase AAL53000.1 1.44 3 7...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...acid import IM BMEI1210, appQ BruAb10760 BR0743 BOV_0737 BCAN_A0758 PAO General L-amino acid import BP BMEI1211, appJ BruAb10761 BR0741 BOV_0738 BCAN_A0756 PAO General L-amino acid import BP BMEII0349, appJ BruAb20285 BRA0948 BOV_0736 BCAN_B0969 92 PAO Arginine BP BMEI1627 BruAb10321 BR0295 BOV_0308 93 PAO Cystine import ABC...”
- Comparative proteome analysis of Brucella melitensis vaccine strain Rev 1 and a virulent strain, 16M
Eschenbrenner, Journal of bacteriology 2002 - “...periplasmic protein precursor BMEI1945 BMEII0704 BMEI1521 BMEI0755 BMEII0590 BMEI1211 BMEII0344 5.65 4.74 5.42 5.35 4.85 5.06 5.34 6.05 4.74 5.30 5.29 4.97 5.30...”
4z9nB / A0A0M3KL33 Abc transporter / periplasmic binding protein from brucella ovis with glutathione bound
60% identity, 92% coverage
- Ligand: glutathione (4z9nB)
BRA0948 amino acid ABC transporter, periplasmic amino acid-binding protein from Brucella suis 1330
58% identity, 98% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BMEI1211, appJ BruAb10761 BR0741 BOV_0738 BCAN_A0756 PAO General L-amino acid import BP BMEII0349, appJ BruAb20285 BRA0948 BOV_0736 BCAN_B0969 92 PAO Arginine BP BMEI1627 BruAb10321 BR0295 BOV_0308 93 PAO Cystine import ABC BMEII0599 BruAb20545 BRA0684 BOV_A0640 BCAN_B0682 PAO Cystine import IM BMEII0600 BruAb20546 BRA0683 BOV_A0639 BCAN_B0681 PAO...”
BCAN_B0969 amino-acid ABC transporter-binding protein yhdW precursor from Brucella canis ATCC 23365
58% identity, 98% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BruAb10761 BR0741 BOV_0738 BCAN_A0756 PAO General L-amino acid import BP BMEII0349, appJ BruAb20285 BRA0948 BOV_0736 BCAN_B0969 92 PAO Arginine BP BMEI1627 BruAb10321 BR0295 BOV_0308 93 PAO Cystine import ABC BMEII0599 BruAb20545 BRA0684 BOV_A0640 BCAN_B0682 PAO Cystine import IM BMEII0600 BruAb20546 BRA0683 BOV_A0639 BCAN_B0681 PAO Cystine import...”
BOV_A0890 amino acid ABC transporter, periplasmic amino acid-binding protein from Brucella ovis ATCC 25840
58% identity, 98% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BruAb10874 BRA0631 BOV_0945 BCAN_A0967 91 PAO General L-amino acid import ABC BMEI1208, appP BruAb10762 BR0745 BOV_A0890 BCAN_A0760 PAO General L-amino acid import IM BMEI1209, appM BruAb10758 BR0744 BOV_0739 BCAN_A0759 PAO General L-amino acid import IM BMEI1210, appQ BruAb10760 BR0743 BOV_0737 BCAN_A0758 PAO General L-amino acid import...”
BMEII0349 GENERAL L-AMINO ACID-BINDING PERIPLASMIC PROTEIN AAPJ PRECURSOR from Brucella melitensis 16M
59% identity, 94% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...acid import BP BMEI1211, appJ BruAb10761 BR0741 BOV_0738 BCAN_A0756 PAO General L-amino acid import BP BMEII0349, appJ BruAb20285 BRA0948 BOV_0736 BCAN_B0969 92 PAO Arginine BP BMEI1627 BruAb10321 BR0295 BOV_0308 93 PAO Cystine import ABC BMEII0599 BruAb20545 BRA0684 BOV_A0640 BCAN_B0682 PAO Cystine import IM BMEII0600 BruAb20546 BRA0683...”
BAB_RS27735 amino acid ABC transporter substrate-binding protein from Brucella abortus 2308
57% identity, 98% coverage
- The putative amino acid ABC transporter substrate-binding protein AapJ2 is necessary for Brucella virulence at the early stage of infection in a mouse model
Tian, Veterinary research 2018 - “...ability to invade and replicate within host cells. In a previous study, a putative gene bab_RS27735 encoding an amino acid ABC transporter substrate-binding protein homologous to AapJ protein was found to be involved in Brucella abortus virulence. In this study, we successfully constructed a bab_RS27735 deletion...”
- “...which may contribute to the reduced virulence of the mutant. These data elucidated that the bab_RS27735 gene is necessary for B. abortus virulence at the early stage of infection in a mouse model. http://dx.doi.org/10.13039/501100001809 National Natural Science Foundation of China 31602070 Tian Mingxing Shanghai Sailing Program...”
Atu1577 ABC transporter, substrate binding protein (amino acid) from Agrobacterium tumefaciens str. C58 (Cereon)
57% identity, 91% coverage
- Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic conditions (pH 5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions
Yuan, Journal of bacteriology 2008 - “...2017 by University of California, Berkeley Transporter genes Atu1577 Atu1717 Atu2744 Atu3253 Atu3575 Atu3821 Atu4667 Atu4687 Atu5268 Designation 502 YUAN ET AL....”
- “...transporting multidrugs, amino acids, and fatty acids (Atu1577, Atu1717, Atu2744, Atu3253, Atu3575, Atu3821, Atu4667, Atu4768, and Atu5268) (Table 3). The...”
- Secretome analysis uncovers an Hcp-family protein secreted via a type VI secretion system in Agrobacterium tumefaciens
Wu, Journal of bacteriology 2008 - “...6 (13) 6 (14) 5 (20) Atu3576 Atu1789 Atu4489 Atu4345 Atu1577 AGR_L_2505p AGR_C_3292p AGR_L_761p AGR_L_1037 AGR_C_2905p 292 184 115 68 56 5 (15) 4 (13) 2 (9) 1...”
BP0558 amino acid-binding periplasmic protein from Bordetella pertussis Tohama I
Q7VS83 Amino acid-binding periplasmic protein from Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)
56% identity, 93% coverage
- Immuno-proteomics analysis between OMV of vaccine and dominant wild type strains of Bordetella pertussis in Iran
Badamchi, Iranian journal of microbiology 2020 - “...strain tested and OMV of Bp IP91 including (BP2759), (BP2377), (BP2818), (BP3266) (BP0965), (BP0205) and BP0558. ( Figs. 4A and B ). Fig. 3. Functional classes of proteins identified from OMV of Bp. Fig. 4. Protein fingerprint of OMV from Bp both strains by 2-D gel...”
- “...344 Outer membrane 11 smoM 21.7 Putative periplasmic solute-binding protein 40.01 7.36 364 cytoplasm 12 BP0558 14.79 Amino acid-binding periplasmic protein 36.1 6.6 338 periplasm 13 BP3809 20.31 Uncharacterized protein 34.1 6.23 320 cytoplasm 14 BP2891 13.79 Uncharacterized protein 22.641 6 203 cytoplasm 15 BP3465 4.167...”
- Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis
Keidel, RNA (New York, N.Y.) 2018 - “...the Tohama I genome are predicted to encode periplasmic binding proteins of unknown specificity, e.g., BP0558 and BP1529 proteins share 61% sequence identity and 81% sequence positivity with BP3831 transporter. Therefore, it is very well possible that some of these proteins can deliver the glutamate also...”
- Bordetella pertussis Isolates from Argentinean Whooping Cough Patients Display Enhanced Biofilm Formation Capacity Compared to Tohama I Reference Strain
Arnal, Frontiers in microbiology 2015 - “...(branched chain amino acid-) Q7VYN1 - binding protein livJ -, amino acid- binding periplasmic protein Q7VS83 -, ABC transporter ATP binding protein Q7VTG4- ] and four proteins related to stress response and adaptation (putative Zinc protease Q7VVY4 -, antioxidant protein Q7VZE7 -, chaperone protein DnaJ Q7VVY3...”
I6I48_RS29915 amino acid ABC transporter substrate-binding protein from Achromobacter xylosoxidans
55% identity, 94% coverage
- Comprehensive toxicological, metabolomic, and transcriptomic analysis of the biodegradation and adaptation mechanism by Achromobacter xylosoxidans SL-6 to diuron
Hu, Frontiers in microbiology 2024 - “...respectively ( Supplementary Table S1 ). The expressions of nine ABC transporters (I6I48_RS03180, I6I48_RS10650, I6I48_RS28500, I6I48_RS29915, I6I48_RS19805, I6I48_RS18970, I6I48_RS23815 dctP , and pstS ) and one MFS transporters (I6I48_RS22785) were significantly up-regulated ( Supplementary Table S1 ). In summary, we speculate that the strain SL-6 cells...”
BP3831 putative ABC transporter periplasmic amino acid-binding protein from Bordetella pertussis Tohama I
Q7VSU1 ABC transporter periplasmic amino acid-binding protein from Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)
53% identity, 100% coverage
- A new class of binding protein-dependent solute transporter exemplified by the TAXI-GltS system fromBordetella pertussis
Jaques, 2024 - Deep longitudinal multi-omics analysis of Bordetella pertussis cultivated in bioreactors highlights medium starvations and transitory metabolisms, associated to vaccine antigen biosynthesis variations and global virulence regulation
Anziani, Frontiers in microbiology 2023 - “...a sodium/glutamate symporter, increased between 12 and 22 h (log2FC=+0.8). Similarly, while the expression of bp3831 , encoding a putative glutamate transporter ( Keidel et al., 2018 ) decreased between 12 h and 18 h 45 min (Log2FC=1.8), a marked expression increase of this gene was...”
- Identification of BvgA-Dependent and BvgA-Independent Small RNAs (sRNAs) in Bordetella pertussis Using the Prokaryotic sRNA Prediction Toolkit ANNOgesic
Moon, Microbiology spectrum 2021 - “...vrg18 , vrg24 , and vrg73 ) and 4 proteins involved in transport, as follows BP3831 (amino acid ABC transporter substrate-binding protein), BP3862 (peptide ABC transporter substrate-binding protein), vag8 (autotransporter), and sphB1 (autotransporter subtilisin-like protease). Finally, we included 4 flagellar genes, namely, fliA (sigma factor), fliF...”
- “...and the Bvg mode genes vrg24 , vrg73 , BP3871 (cold shock like protein), and BP3831 (encoding an amino acid ABC transporter substrate binding protein) ( Fig.5 ). BP3831 is the Bvg mode gene that has been shown to be a likely target of S18 (RgtA)...”
- Expression of small RNAs of Bordetella pertussis colonizing murine tracheas
Hiramatsu, Microbiology and immunology 2020 - “...r epressor of g lutamate t ransport) that was found to reduce the translation of BP3831, a periplasmic amino acidbinding protein of an ABC transporter, by base pairing with the 5 untranslated region of BP3831 mRNA. 11 , 14 Although this protein is related to the...”
- In Vivo Gene Essentiality and Metabolism in Bordetella pertussis
Gonyar, mSphere 2019 - “...II BP3743 / ctaD Cytochrome c oxidase polypeptide I BP3744 Cytochrome c oxidase subunit II BP3831 Amino acid ABC transporter substrate-binding protein The majority of genes required for infection had metabolic functions. Out of the total 192 genes designated as conditionally essential in vivo , 117...”
- Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis
Keidel, RNA (New York, N.Y.) 2018 - “...abolished RgtA expression. Profiling of the rgtA mutant in the bvgA genetic background identified the BP3831 gene encoding a periplasmic amino acid-binding protein of an ABC transporter as a possible target gene. The results of site-directed mutagenesis and in silico analysis indicate that RgtA base-pairs with...”
- “...the region upstream of the start codon of the BP3831 mRNA and thereby weakens the BP3831 protein production. Furthermore, our data suggest that the function of the BP3831 protein is related to transport of glutamate, an important metabolite in the B. pertussis physiology. We propose that...”
- Modulation of Pertussis and Adenylate Cyclase Toxins by Sigma Factor RpoE in Bordetella pertussis
Barbier, Infection and immunity 2017 - “...Q7TT91 P48210 Q04064 Q7VSU1 BP2497 tuf1, tuf2 groL BP0840 BP3831 BP2497 BP0007; BP3611 BP3495 BP0840 BP3831 892 565 1617 416 356 171 580 1504 445 502 1063...”
- Modulation of Pertussis and Adenylate Cyclase Toxins by Sigma Factor RpoE in Bordetella pertussis
Barbier, Infection and immunity 2017 - “...Total Fold change (PM18/UT25) Q7VVY4 Q7TT91 P48210 Q04064 Q7VSU1 BP2497 tuf1, tuf2 groL BP0840 BP3831 BP2497 BP0007; BP3611 BP3495 BP0840 BP3831 892 565 1617...”
BP1529 putative extracellular solute-binding protein from Bordetella pertussis Tohama I
56% identity, 92% coverage
RSP_1747 ABC glutamate/glutamine/aspartate/asparagine transporter, periplasmic substrate-binding protein from Rhodobacter sphaeroides 2.4.1
54% identity, 92% coverage
PB7211_1204 amino acid ABC transporter substrate-binding protein from Candidatus Pelagibacter sp. HTCC7211
53% identity, 99% coverage
- mdRNA-Seq analysis of marine microbial communities from the northern Red Sea
Hou, Scientific reports 2016 - “...omega subunit gidA PB7211_100 225271 227142 232 74 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA yhdW PB7211_1204 1014159 1015259 215 1791 ABC transporter dnaK PB7211_144 208983 210940 + 189 799 chaperone protein DnaK glcB PB7211_627 61961 64285 + 182.5 86.5 malate synthase atpD PB7211_587 338515 340096 +...”
SAR11_0953 ABC transporter from Candidatus Pelagibacter ubique HTCC1062
53% identity, 93% coverage
- The ultra-high affinity transport proteins of ubiquitous marine bacteria
Clifton, Nature 2024 - “...correctly predicted as taurine, phosphate, citrate and iron( iii ), respectively. The predictions of SAR11_0769, SAR11_0953 and SAR11_1346 as a sugar-binding protein, general amino acid-binding protein and branched-chain amino acid-binding protein were broadly correct, although experimental characterization enabled identification of specific ligands. By contrast, 7 out...”
- “...of these SBP genes across surface stations varied from 310 5 (SAR11_0655) to 310 3 (SAR11_0953); for comparison, the mean total abundance of SBP transcripts across surface stations was estimated to be 2.710 2 , indicating that the SBPs of Ca . P. ubique HTCC1062 and...”
- Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium
Smith, mBio 2013 - “...+INF SAR11_0747 glnA Glutamine synthetase 1.91 5.16 b SAR11_0460 acuC Histone deacetylase-like 1.08 2.65 a SAR11_0953 yhdW Amino acid transporter: periplasmic 1.19 2.35 b SAR11_0279 aspC Aspartate transaminase 1.42 2.04 b SAR11_0433 gltD Glutamate synthase, small subunit 0.44 2.03 b SAR11_0032 ftsZ Cell division protein 1.48...”
YP_165781 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic substrate-binding protein from Silicibacter pomeroyi DSS-3
52% identity, 83% coverage
- In-depth analysis of exoproteomes from marine bacteria by shotgun liquid chromatography-tandem mass spectrometry: the Ruegeria pomeroyi DSS-3 case-study
Christie-Oleza, Marine drugs 2010 - “...Their signal peptides could have been missed in terms of annotation. The three proteins YP_168201, YP_165781 and YP_166898 were re-annotated in terms of N- terminus with the choice as translational start codon of an internal ATG, based on sequence alignments with their closest homologues. The three...”
- “...transporter periplasmic 16 54 presence YP_168201 peptide/nickel/opine uptake ABC transporter periplasmic 10 42 presence * YP_165781 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic 10 39 presence * YP_168669 polyamine ABC trasnporter, periplasmic polyamine-binding protein 6 28 presence YP_165868 sugar ABC transporter, periplasmic sugar-binding protein 7 24 presence YP_167838 TRAP...”
A1B061 L-aspartate-binding protein / L-glutamate-binding protein / L-glutamine-binding protein / L-asparagine-binding protein from Paracoccus denitrificans (strain Pd 1222)
52% identity, 93% coverage
CD16_RS00210 amino acid ABC transporter substrate-binding protein from Candidatus Liberibacter asiaticus
CLIBASIA_00265 cationic amino acid ABC transporter, periplasmic binding protein from Candidatus Liberibacter asiaticus str. psy62
46% identity, 99% coverage
- A Significantly High Abundance of "Candidatus Liberibacter asiaticus" in Citrus Fruit Pith: in planta Transcriptome and Anatomical Analyses
Fang, Frontiers in microbiology 2021 - “...midribs compared with fruit pith ( Supplementary Table 1 ), including five ABC transporter genes (CD16_RS00210, CD16_RS00215, CD16_RS02450, CD16_RS03160, and CD16_RS04765), one glycine betaine transporter gene (CD16_RS01075), and four genes involved in the efflux pumps system (CD16_RS00510, CD16_RS03560, CD16_RS04390, and CD16_RS05425) ( Supplementary Table 1 )....”
- SEC-Translocon Dependent Extracytoplasmic Proteins of Candidatus Liberibacter asiaticus
Prasad, Frontiers in microbiology 2016 - “...3 Common homologs between the seven different species and strains of Liberibacter . ID Annotation CLIBASIA_00265 Cationic amino acid ABC transporter, periplasmic binding protein CLIBASIA_00400 CTP synthetase CLIBASIA_00560 Pyrophosphatefructose-6-phosphate 1 -phosphotransferase CLIBASIA 01020 Large subunit ribosomal protein L35 CLIBASIA_01295 Flagellar basal body L-ring protein CLIBASIA_01305 Flagellar...”
- Global gene expression changes in Candidatus Liberibacter asiaticus during the transmission in distinct hosts between plant and insect
Yan, Molecular plant pathology 2013 (secret) - The ABC transporters in Candidatus Liberibacter asiaticus
Li, Proteins 2012 - “...specificity III(i) PAO CLIBASIA_00280 AapP R . leguminosarum 1e 107 68 CLIBASIA_00275, CLIBASIA_00270 PF00528 (CL0404) CLIBASIA_00265 (PP) General l -amino acid III(i) MOI CLIBASIA_02955 PstB E. coli 7e 75 56 CLIBASIA_02960, CLIBASIA_02965 PF00528 (CL0404) CLIBASIA_02970 (PP) Phosphate III(i) MOI CLIBASIA_02230 ThiQ S. enterica 8e 68 52...”
bll2909 bll2909 from Bradyrhizobium japonicum USDA 110
52% identity, 92% coverage
- Proteomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules
Strodtman, International journal of molecular sciences 2018 - “...include a set involved in nitrogen metabolism: An ABC transporter substrate binding protein for oligopeptides (bll2909, bll5596, bll7921), a peptidyl-dipeptidase (bll7756), a glycine hydroxymethyltransferase (bll5033), a probable amino acid binding protein (bll2909), a glu/leu/phe/val dehydrogenase (blr2146), which causes the reversible oxidative deamination of the substrate to...”
- “...NP_768705 Cytoplasm Nodulate formation efficiency C protein bll2067 NP_768707 Periplasm Probable amino acid binding protein bll2909 NP_769549 Both Glycine hydroxymethyltransferase bll5033 NP_771673 Periplasm ABC transporter substrate-binding protein bll5596 NP_772236 Cytoplasm RecA protein bll5755 NP_772395 Periplasm Hypothetical protein bll6069 NP_772709 Periplasm PQQ-dependent alcohol dehydrogenase bll6220 NP_772860 Cytoplasm...”
Dshi_0318 cationic amino acid ABC transporter, periplasmic binding protein from Dinoroseobacter shibae DFL 12
54% identity, 92% coverage
- Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif
Wang, mSystems 2021 - “...propeller repeat TolB OM-associated/OM -barrel protein Lipid metabolism and cell wall/membrane/envelope biogenesis/integrity 2.24E02 3.07E03 2.24 Dshi_0318 Glutamate/glutamine/aspartate/asparagine ABC transporter Periplasmic protein Transporter 2.20E02 5.41E03 2.20 Dshi_2832 Hypothetical protein OM lipoprotein Hypothetical protein 1.53E02 9.27E04 1.53 Dshi_2784 Hypothetical protein OM lipoprotein Hypothetical protein 1.44E02 4.66E03 1.44 Dshi_0924...”
- “...assigned 1.11E02 1.43E03 1.11 Dshi_1195 TRAP transporter solute receptor Periplasmic protein Transporter 9.51E03 1.98E03 0.95 Dshi_0318 Glutamate/glutamine/aspartate/asparagine ABC transporter Periplasmic protein Transporter 9.23E03 1.33E03 0.92 Dshi_0762 Aminotransferase class I and II Intracellular protein Amino acid metabolism 7.45E03 1.21E03 0.75 Dshi_0273 Translation elongation factor G Intracellular protein...”
ZP_02146891 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic substrate-binding protein from Phaeobacter gallaeciensis BS107
52% identity, 92% coverage
TC 3.A.1.3.7 / Q52663 BztA, component of Glutamate/glutamine/aspartate/asparagine porter from Rhodobacter capsulatus (Rhodopseudomonas capsulata) (see paper)
52% identity, 92% coverage
- substrates: Asparagine, Glutamine, aspartate, glutamate
SPO2364 amino acid ABC transporter substrate-binding protein from Ruegeria pomeroyi DSS-3
50% identity, 92% coverage
- Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium
Chan, Frontiers in microbiology 2012 - “...( glnB-1 ) 9.0 6.6 SPO2295 Glutamine synthetase, type I ( glnA ) 4.7 5.1 SPO2364 Amino acid ABC transporter, periplasmic binding protein 1.3 4.1 SPO3723 Ammonium transporter ( amt-2 ) 28.0 SPO3724 Nitrogen regulatory protein P II ( glnB-2 ) 124.3 39.1 SPOA0300 Branched-chain amino...”
- “...Nitrogen regulatory protein P II 9.0 6.6 SPO2295 glnA Glutamine synthetase, type I 4.7 5.1 SPO2364 Amino acid ABC transporter, periplasmic binding protein 1.3 4.1 SPO2602 RpiR family transcriptional regulator 5.1 2.2 SPO2778 Hypothetical protein 3.0 1.5 SPO2818 Hypothetical protein 4.9 3.0 SPO3607 Hypothetical protein 4.6...”
Rru_A0779 extracellular solute-binding protein, family 3 from Rhodospirillum rubrum ATCC 11170
46% identity, 92% coverage
- Metabolic Regulation as a Consequence of Anaerobic 5-Methylthioadenosine Recycling in Rhodospirillum rubrum
North, mBio 2016 - “...). Additionally, one of the two MetQ orthologues (Rru_A2417), another MetQ-like periplasmic substrate binding protein (Rru_A0779), and an annotated inner membrane lipoprotein (NlpA, Rru_A0791), similar to MetQ in other organisms, were also observed in increased abundance. Chemotaxis is essential for growth on MTA. The role of...”
- “...analyzed by STRING v10 analysis using the following proteins as the query: Rru_A0778, lipoprotein YaeC; Rru_A0779, extracellular solute-binding protein; Rru_A0780, binding-protein-dependent transport system inner membrane protein; Rru_A0781, amino acid ABC transporter permease; Rru_A0788, ABC transporter of MetINQ complex; Rru_A0789, binding-protein-dependent transport system inner membrane protein; Rru_A0791,...”
- A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis
Erb, Nature chemical biology 2012 - “...these were two putative O -acetyl-homoserine sulfhydrylases (Rru_A0774, Rru_A0784). Notably, four of these five proteins (Rru_A0779, Rru_A0792, and the two sulfhydrylases) were encoded by the same genetic region of fourteen different genes presumably involved in thiol metabolism at the level of cysteine and methionine (thiol cluster,...”
OA04_42530 amino acid ABC transporter substrate-binding protein from Pectobacterium versatile
44% identity, 97% coverage
Synpcc7942_0246 extracellular solute-binding protein, family 3 from Synechococcus elongatus PCC 7942
44% identity, 89% coverage
RPA2628 polar amino acid ABC transport substrate-binding protein, aapJ-2 from Rhodopseudomonas palustris CGA009
48% identity, 93% coverage
- Environment sensing and response mediated by ABC transporters
Giuliani, BMC genomics 2011 - “...ligands and inclusion of additional experimental validation methods. Amino acid binding proteins Three proteins (RPA2499, RPA2628, and RPA3810) were identified as amino acid binding proteins via the FTS screening (Table 1). This observation is consistent with the assigned annotation and the general functional prediction of TransportDB...”
- “...acids provide transport capabilities for seven of the individual amino acids. The genes encoding the RPA2628 (PBP), RPA2629 and RPA2630 (integral membrane subunits) (methionine/cysteine/histidine) are orthologs of a verified amino acid transporter in Rhizobium leguminosarum [ 32 ]. They are also localized in a cluster of...”
TC 3.A.1.3.18 / Q8YPM9 NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (see paper)
alr4164 periplasmic amino acid-binding protein of amino acid ABC transporter from Nostoc sp. PCC 7120
43% identity, 87% coverage
- substrates: Amino acids
- β-N-Methylamino-L-Alanine (BMAA) Causes Severe Stress in Nostoc sp. PCC 7120 Cells under Diazotrophic Conditions: A Proteomic Study
Koksharova, Toxins 2021 - “...serine, and threonine metabolism, correspondingly. Moreover, the upregulated periplasmic amino acid-binding protein, ABC transporter ( alr4164 ) ( Table 2 ), is also known to be under NtcA control. This protein is involved in the transport of amino acids Asp, Glu, Asn, Gln, and Met [...”
- “...Figure S7: The scheme shows a protein network of periplasmic amino acid-binding protein, ABC transporter (alr4164) and its protein partners, Figure S8. This scheme presents a protein network of the RNA-binding protein rbpD (asl4022) and its protein partners, Figure S9: This scheme presents a protein network...”
- Amino Acid Transporters and Release of Hydrophobic Amino Acids in the Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120
Pernil, Life (Basel, Switzerland) 2015 - “...Orn, Gln, all1248 natD TM Glu all2912 natE ATPase N-II 3.A.1.3 Asp , Glu, Asn, alr4164 natF PSB [ 28 ] Gln, Met, Thr, alr4165 natG TM Ala, Ser, Gly, alr4166 natH TM His alr4167 bgtA ATPase Bgt 3.A.1.3 Lys , Arg , Orn, alr4167 bgtA...”
- “...27 ]. The system N-II is encoded by a cluster of four genes: natF ( alr4164 ) encodes a periplasmic substrate-binding protein, natG ( alr4165 ) and natH ( alr4166 ) encode transmembrane (permease) proteins, and bgtA ( alr4167 ) encodes an ATPase [ 28 ]....”
- Functional Dependence between Septal Protein SepJ from Anabaena sp. Strain PCC 7120 and an Amino Acid ABC-Type Uptake Transporter
Escudero, Journal of bacteriology 2015 - “...natG natH bgtA bgtB all1046 alr1834 all1047 all1248 all2912 alr4164 alr4165 alr4166 alr4167 alr3187 1893 1861 1894 2177 0815 0246 0247 0248 0249 0248 e96 e109...”
SYNW0840 ABC transporter, substrate binding protein for amino acids from Synechococcus sp. WH 8102
44% identity, 94% coverage
- Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome
Chen, Nucleic acids research 2004 - “...Likelihood score (SYNW0211, (SYNW0319, (SYNW0708, (SYNW0840, (SYNW0969, (SYNW1086, (SYNW1111, (SYNW1168, (SYNW1270, (SYNW1283, (SYNW1340, (SYNW1415, (SYNW1797,...”
- “...found (SYNW0319, 0320, 0321, 0322) Exactly found (SYNW0840, 0841); (SYNW0842, 0843) Exactly found (SYNW1084, 1085, 1086, 1087) (SYNW1109, 1110, 1111, 1112,...”
BL107_14770 extracellular solute-binding protein, family 3 from Synechococcus sp. BL107
45% identity, 84% coverage
EP10_002623 glutamate ABC transporter substrate-binding protein from Geobacillus icigianus
29% identity, 66% coverage
GALLO_1556 Putative ABC transporter, amino acid binding protein from Streptococcus gallolyticus UCN34
33% identity, 52% coverage
IUJ47_RS08610 transporter substrate-binding domain-containing protein from Enterococcus faecalis
32% identity, 54% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...0.447 Multidrug efflux ABC transporter subunit EfrB IUJ47_RS04675 0.451 Energy-coupling factor ABC transporter ATP-binding protein IUJ47_RS08610 0.464 Transporter substrate-binding domain-containing protein IUJ47_RS02640 0.471 Biotin transporter BioY IUJ47_RS04715 0.472 Amino acid ABC transporter ATP-binding protein IUJ47_RS00725 2.036 ABC transporter substrate-binding protein IUJ47_RS07265 2.115 Osmoprotectant ABC transporter substrate-binding...”
Q836J2 Amino acid ABC transporter, amino acid-binding protein from Enterococcus faecalis (strain ATCC 700802 / V583)
EF1119 amino acid ABC transporter, amino acid-binding protein from Enterococcus faecalis V583
OG1RF_10897 transporter substrate-binding domain-containing protein from Enterococcus faecalis OG1RF
32% identity, 54% coverage
- Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion
Downes, Scientific reports 2023 - “...N/A 8 33.5 Q835Q9 Amino acid ABC transporter, amino acid-binding protein Unique N/A 5 28.4 Q836J2 50S ribosomal protein L32-3 Unique N/A 4 37.3 Q836R0 ABC transporter permease Unique N/A 3 13.4 Q837A0 Isopentenyl-diphosphate delta-isomerase Unique N/A 4 15 Q837E2 50S ribosomal protein L36* Unique N/A...”
- Examination of Enterococcus faecalis Toxin-Antitoxin System Toxin Fst Function Utilizing a Pheromone-Inducible Expression Vector with Tight Repression and Broad Dynamic Range
Weaver, Journal of bacteriology 2017 - “...(EF2985) (EF1495) (EF2050) (EF0095) (EF1709) (EF2049) (EF1227) (EF1119) (EF3314) (EF1018) (EF0082) (EF3210) (EF1017) 1 ng/ml 6.28 5.46 5.38 3.51 3.25 3.14...”
- “...(EF0778)c (EF0764/5)c (EF2623)c (EF1307)c (EF2641)c (EF1119) (EF2748)d (EF2746)d (EF3245)d (EF0202)d (EF0118)c (EF2986)d (EF0938)e (EF2985)d Fold change...”
- Global transcriptional analysis of the stringent response in Enterococcus faecalis
Gaca, Microbiology (Reading, England) 2012 - “...EF0807 EF0820 EF0867 EF0891 EF0893 EF0910 EF1117 EF1118 EF1119 EF1120 EF1211 EF1405 EF1413 EF1513 EF1584 EF1585 EF1597 EF1672 EF1681 EF1685 EF1982 EF2075 EF2076...”
- ClpP participates in stress tolerance, biofilm formation, antimicrobial tolerance, and virulence of Enterococcus faecalis
Zheng, BMC microbiology 2020 - “...binding cassette transporter, ABC protein 1.208 AEA93609.1 ( OG1RF_10922 ) hypothetical protein 1.204 AEA93584.1 ( OG1RF_10897 ) glutamine ABC superfamily ATP binding cassette transporter, binding protein 1.200 Abundance-decreased AEA92854.1 ( OG1RF_10167, rplR ) 50S ribosomal protein L18 0.828 AEA93526.1 ( OG1RF_10839 ) universal stress protein 0.826...”
- Surface-Associated Lipoproteins Link Enterococcus faecalis Virulence to Colitogenic Activity in IL-10-Deficient Mice Independent of Their Expression Levels
Ocvirk, PLoS pathogens 2015 - “...traC oligopeptide ABC superfamily ATP binding cassette transporter, binding protein OG1RF_10878 ace collagen adhesin protein OG1RF_10897 - glutamine ABC superfamily ATP binding cassette transporter, binding protein OG1RF_10993 - spermidine/putrescine ABC superfamily ATP binding cassette transporter OG1RF_11130 - pheromone cAM373 lipoprotein OG1RF_11186 modA molybdenum ABC superfamily ATP...”
4zv1A An ancestral arginine-binding protein bound to arginine (see paper)
30% identity, 60% coverage
PA5082 probable binding protein component of ABC transporter from Pseudomonas aeruginosa PAO1
26% identity, 72% coverage
SAG0717 amino acid ABC transporter, amino acid-binding protein from Streptococcus agalactiae 2603V/R
30% identity, 51% coverage
- Protectome analysis: a new selective bioinformatics tool for bacterial vaccine candidate discovery
Altindis, Molecular & cellular proteomics : MCP 2015 - “...aureus: SAOUHSC_01991, SAOUHSC_02699 GBS: SAG0136, SAG0290, SAG0717, SAG0949, SAG1431, SAG1610, SAG1642, SAG1466 S. aureus: SAOUHSC_00634*, SAOUHSC_02690 GBS:...”
- Transcriptional and proteomic profiles of group B Streptococcus type V reveal potential adherence proteins associated with high-level invasion
Johri, Infection and immunity 2007 - “...family 4.3 Transport and binding SAG0715 SAG0716 SAG0717 SAG0769 SAG1007 SAG1085 SAG1394 SAG1466 SAG1739 SAG1796 Amino acid ABC transporter, permease protein...”
5t0wA Crystal structure of the ancestral amino acid-binding protein anccdt- 1, a precursor of cyclohexadienyl dehydratase
28% identity, 70% coverage
BCAL1668 periplasmic solute-binding protein from Burkholderia cenocepacia J2315
27% identity, 71% coverage
OA04_45500 ABC transporter substrate-binding protein from Pectobacterium versatile
27% identity, 74% coverage
CJM1_0885 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein PEB1a from Campylobacter jejuni subsp. jejuni M1
CJJ81176_0928 amino acid ABC transporter, periplasmic amino acid-binding protein PEB1 from Campylobacter jejuni subsp. jejuni 81-176
C8J_0858 amino acid ABC transporter, periplasmic amino acid-binding protein PEB1 from Campylobacter jejuni subsp. jejuni 81116
27% identity, 69% coverage
- Genomic characterization of Campylobacter jejuni strain M1
Friis, PloS one 2010 - “...peb1A , which encodes a 27-kDa putative adhesin [29] were identified as CJM1_1423, CJM1_0958 and CJM1_0885, respectively. In addition porA , which encodes the C. jejuni 43-kDa major outer membrane protein (MOMP), which is a porin and a potential adhesin [30] , was identified as CJM1_1240....”
- Metabolic and fitness determinants for in vitro growth and intestinal colonization of the bacterial pathogen Campylobacter jejuni
Gao, PLoS biology 2017 - “...transporter permease protein CJJ81176_0927 * peb1 7.29 0.00 0.60 amino acid ABC transporter permease protein CJJ81176_0928 * pebA 7.40 0.00 0.83 ABC transporter aspartate/glutamate-binding CJJ81176_1035 livM 6.43 0.04 3.15 high affinity branched-chain aa ABC transporter CJJ81176_1038 livJ 6.70 0.02 5.70 high affinity branched-chain aa ABC transporter...”
- “...layer. 2. Amino acid and peptide catabolism Our INSeq analysis revealed that inactivation of peb1A (CJJ81176_0928), which participates in the utilization of Asp, Glu, Asn, and Gln [ 29 , 57 ], and its downstream genes (CJJ81176_0926, CJJ81176_0927) led to a significant decrease in colonization (...”
- Microbiota-Derived Short-Chain Fatty Acids Modulate Expression of Campylobacter jejuni Determinants Required for Commensalism and Virulence
Luethy, mBio 2017 - “...di-/tripeptide transporter 2.61 Cjj81176_0683 Possible di-/tripeptide transporter 5.90 Cjj81176_0927 peb1a Aspartate/glutamate transporter, permease component 2.74 Cjj81176_0928 peb1b Aspartate/glutamate transporter, solute-binding component 5.48 Cjj81176_0929 peb1c Amino acid transporter, ATP-binding component 5.11 Cjj81176_1615 sdaA l -Serine dehydratase 2.66 Cjj81176_1616 sdaC l -Serine transporter 2.75 Cjj81176_0315 peb3 Glycoprotein; putative...”
- The PAS Domain-Containing Protein HeuR Regulates Heme Uptake in Campylobacter jejuni
Johnson, mBio 2016 - “...ABC transporter, periplasmic 1.11 7.4E08 CJJ81176_0875 Hypothetical protein 1.11 7.2E07 CJJ81176_1622 Hypothetical protein 1.10 6.6E07 CJJ81176_0928 Amino acid ABC transporter, periplasmic 1.10 5.0E05 CJJ81176_0772 Conserved hypothetical protein 1.10 4.6E11 CJJ81176_0067 -Glutamyltransferase 1.04 1.2E03 CJJ81176_0722 Glutamine synthetase, type I 1.04 1.5E05 CJJ81176_1062 Conserved hypothetical protein 1.04 8.5E12...”
- Polyphosphate kinases modulate Campylobacter jejuni outer membrane constituents and alter its capacity to invade and survive in intestinal epithelial cells in vitro
Pina-Mimbela, Emerging microbes & infections 2015 - “...protein 29 16 2 0 CJJ81176_0883 Thiol:disulfide interchange protein DsbA, putative 26 0 0 12 CJJ81176_0928; pebA Bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein 28 135 122 0 CJJ81176_0974 Putative lipoprotein 16 4 1 0 CJJ81176_1002; jlpA Surface-exposed lipoprotein 42 5 0 4 CJJ81176_1016 Hypothetical protein 21 0...”
- Proteomic and genomic analysis reveals novel Campylobacter jejuni outer membrane proteins and potential heterogeneity
Watson, EuPA open proteomics 2014 - “...34.9 46.3 18.4 CJJ81176_0894 Flagellin family protein flgL 5 7 7 10.7 14.8 14.1 81.9 CJJ81176_0928 Amino acid ABC transporter, periplasmic amino acid-binding protein PEB1 pebA 5 4 30.5 23.6 28.1 CJJ81176_0974 Conserved hypothetical protein 6 6 6 53.5 54.2 43.1 16.2 CJJ81176_1001 CjaA protein cjaA...”
- Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis
Banaś, International journal of molecular sciences 2021 - “...their sequences (TupA, LivK, LivJ and C8J_0575), and the others has just one (C8J_0280 and C8J_0858) or none (C8J_1352 and C8J_1291). Out of all these, only proteins containing more than two cysteine residues were identified with statistically significant values; q-value 0.05. We also identified several proteins...”
- Phenotypic and Transcriptomic Responses of Campylobacter jejuni Suspended in an Artificial Freshwater Medium
Trigui, Frontiers in microbiology 2017 - “...3 Select genes differentially expressed in water. Gene Name Product F/B (log2) Amino acid transporter C8J_0858 pebA Amino acid ABC transporter, periplasmic amino 5.08 C8J_0859 pebC Putative polar amino acid transport system 4.82 C8J_0951 livF Branched-chain amino acid transport system 2.01 C8J_0953 livM Branched-chain amino acid...”
Q1GBX1 Amino acid ABC transporter, substrate binding protein from Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14)
26% identity, 69% coverage
TC 3.A.1.3.16 / Q0P9X8 PEB1A, component of Uptake system for glutamate and aspartate from Campylobacter jejuni (see 2 papers)
peb1A / RF|YP_002344319.1 major cell-binding factor from Campylobacter jejuni (see 3 papers)
peb1 / AAA02919.1 major cell-binding factor from Campylobacter jejuni (see paper)
Cj0921c, NP_282073 probable ABC-type amino-acid transporter periplasmic solute-binding protein from Campylobacter jejuni subsp. jejuni NCTC 11168
YP_002344319 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein from Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
27% identity, 69% coverage
- substrates: aspartate, glutamate
- Campylobacter jejuni from no antibiotics ever (NAE) broilers: prevalence, antibiotic resistance, and virulence genes analysis
Poudel, Poultry science 2024 - “...YP_980061 virB9.F429 AAGAACACGCTTTGCAATGGC 21 60.6 535 Poudel et al. (2022) virB9.R964 CGATGATCCTAGTCTCTACTGGAC 24 64.6 pebA NP_282073 pebA.F40 GCTCTAGGTGCTTGTGTTGC 20 62.4 436 Poudel et al. (2022) pebA.R476 GTAGTTGCAGCTTGAGCCAC 20 62.4 porA NP_282406 porA.F740 TCAACTGGACACTTGAAGGTGC 22 62.7 342 Poudel et al. (2022) porA.R1082 CCACCATATACGAAGTCAGCACC 23 64.8 flhB NP_281526...”
- Prevalence, Antimicrobial Resistance, and Molecular Characterization of Campylobacter Isolated from Broilers and Broiler Meat Raised without Antibiotics
Poudel, Microbiology spectrum 2022 - “...62.6 B b virB9 YP_980061 virB9.F429 AAGAACACGCTTTGCAATGGC 21 60.6 535 virB9.R964 CGATGATCCTAGTCTCTACTGGAC 24 64.6 pebA NP_282073 pebA.F40 GCTCTAGGTGCTTGTGTTGC 20 62.4 436 pebA.R476 GTAGTTGCAGCTTGAGCCAC 20 62.4 porA NP_282406 porA.F740 TCAACTGGACACTTGAAGGTGC 22 62.7 342 porA.R1082 CCACCATATACGAAGTCAGCACC 23 64.8 flhB NP_281526 flhB.F531 GGTTGCACAGCTTACTTGGC 20 62.4 257 flhB.R788 ACATCCGCACCTGCAACATC 20...”
- Survival of Campylobacter jejuni 11168H in Acanthamoebae castellanii Provides Mechanistic Insight into Host Pathogen Interactions
Nasher, Microorganisms 2022 - “...antigen C 2.946553 5.82 10 38 Cj0201c imB Integral membrane protein 2.902751 6.00 10 3 Cj0921c peb1A Amino acid transporter 2.902712 2.54 10 24 Cj0865 dsbB Protein-disulfide oxidoreductase 2.727325 9.52 10 11 Cj0030 Uncharacterized protein 2.711549 7.47 10 25 Cj1465 flgN Flagellar hook protein [ 38...”
- Survival of Campylobacter jejuni in Acanthamoebae castellanii provides mechanistic insight into host pathogen interactions
Nasher, 2022 - The role of solute binding proteins in signal transduction
Matilla, Computational and structural biotechnology journal 2021 - “...peptides 4 g/l glucose vs <10 mg/l glucose, fed-batch conditions q 2.2 g [108] PEB1a Cj0921c /T a SBP_bac_3/PF00497 C. jejuni Asp, Glu 7.5% (v/v) O 2 vs 1.9% (v/v) O 2 q 5.6 h /13.3 i [152] Inorganic nutrients and metal ions (complexed and uncomplexed)...”
- Taking Control: Campylobacter jejuni Binding to Fibronectin Sets the Stage for Cellular Adherence and Invasion
Konkel, Frontiers in microbiology 2020 - “...the identified proteins truly act as bacterial adhesins. For example, Cj0268c, Cj0289c (PEB3), Cj0596 (PEB4), Cj0921c (PEB1) are localized in the bacterial periplasmic space, and Cj1349c appears to be localized in the bacterial cytosol ( Supplementary Table S1 ). Moreover, a few of these proteins were...”
- Proteomics of Campylobacter jejuni Growth in Deoxycholate Reveals Cj0025c as a Cystine Transport Protein Required for Wild-type Human Infection Phenotypes
Man, Molecular & cellular proteomics : MCP 2020 - “...to be transported by Cj0903c [1.97-fold/1.49-fold]), Glu (associated with the Peb cluster Cj0920c-Cj0922c [Cj0920c, 1.70-fold/2.18-fold; Cj0921c, down-regulated at 0.34-fold/0.13-fold; and Cj0922c, no change in abundance), Asn and Gln were detected, whereas carbon sources with unknown transporters including pyruvate, were present at significantly decreased intracellular abundances (...”
- “...well as Cys-containing dipeptides ( 76 , 77 ). Other potential Cys transporters including Peb1A (Cj0921c) and CjaC (Cj0734c) have also been reported to not transport Cys or Cys-Cys. Our data correlate with these observations because we saw no change in abundance of CjaA, CjaC or...”
- Campylobacter jejuni Demonstrates Conserved Proteomic and Transcriptomic Responses When Co-cultured With Human INT 407 and Caco-2 Epithelial Cells
Negretti, Frontiers in microbiology 2019 - “...of the four amino acids serine ( sdaC ), aspartate and glutamate [ Cj0919c, Cj0920c, Cj0921c (Peb1A), and Cj0922c (PebC)] ( Stahl et al., 2012 ) and proline ( putA and putP ) were seen to increase from 2.4 to 4 h ( Hofreuter et al.,...”
- More
- Activation of the l-fucose utilization cluster in Campylobacter jejuni induces proteomic changes and enhances Caco-2 cell invasion and fibronectin binding
Middendorf, Heliyon 2024 - “...present 28.4 present Q0P8Q4 CeuE/Cj1355 present present 1.5 present Q0PBE3 CmeA/Cj0367c present present present 1.6 Q0P9X8 Peb1A/Cj0921c present present present 2.1 In isolate C. jejuni 286, three proteins were uniquely significantly downregulated and one significantly upregulated, Peb3 (adhesin), FlgD (basal-body rod modification protein) and Cj1169c (putative...”
- Identification of glutamate ABC-Transporter component in Clostridium perfringens as a putative drug target
Bhatia, Bioinformation 2014 - “...NCTC 11168) [ 9 13 ] were taken from Uniprot Knowledge Base (ID: P37902, Q88NY2, Q0P9X8). The aligned consensus obtained after multiple sequence alignment of these three sequences was used to search Clostridium homologue using BLASTP analysis in C. perfringens Type-A strains. The domain consensus sequence...”
- Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of Campylobacter jejuni
Hoppe, PloS one 2013 - “...clones were screened using HaloLink slides. We used HisJ (UniProt/Swiss-Prot: Q46125), CjaA (Q0P9S0) and Peb1a (Q0P9X8) as positive reference markers, as they have been described previously to be immunodominant [27] [29] . In contrast, ArgC (Q9PIS0) and PyrC (Q0PBP6) were used as negative reference proteins. After...”
- A bacterial virulence factor with a dual role as an adhesin and a solute-binding protein: the crystal structure at 1.5 A resolution of the PEB1a protein from the food-borne human pathogen Campylobacter jejuni.
Müller, Journal of molecular biology 2007 (PubMed)- GeneRIF: A structural basis for understanding both the solute transport and adhesin/virulence functions of PEB1a.
- The Campylobacter jejuni PEB1a adhesin is an aspartate/glutamate-binding protein of an ABC transporter essential for microaerobic growth on dicarboxylic amino acids.
Leon-Kempis, Molecular microbiology 2006 (PubMed)- GeneRIF: Results suggest that in addition to the established role of PEB1a as an adhesin, the PEB1 transport system plays a key role in the utilization of aspartate and glutamate, which may be important in vivo carbon sources for this pathogen.
STM0665 ABC superfamily (bind_prot), glutamate/aspartate transporter from Salmonella typhimurium LT2
25% identity, 85% coverage
SEN0634 ABC transporter periplasmic binding protein from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
25% identity, 85% coverage
- Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis
He, Current research in food science 2022 - “...SEN1291 oppC 2.10 Oligopeptide transport system permease OppC SEN1292 oppD 2.08 Oligopeptide transporter ATP-binding protein SEN0634 gltI 3.30 Glutamate and aspartate transporter subunit SEN0632 gltK 2.44 Glutamate/aspartate transport system permease GltK SEN0633 gltJ 2.31 Glutamate/aspartate transport system permease GltJ SEN0199 fhuB 3.21 Iron-hydroxamate transporter permease subunit...”
Q0P9S0 Amino-acid transporter periplasmic solute-binding protein from Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Cj0982c putative amino-acid transporter periplasmic solute-binding protein from Campylobacter jejuni subsp. jejuni NCTC 11168
26% identity, 69% coverage
- Comprehensive proteomic profiling of outer membrane vesicles from Campylobacter jejuni
Jang, Journal of proteomics 2014 - “...Putative transmembrane protein Cj0404 Membrane M TM Q0PBN7 Putative transmembrane protein Cj0268c Membrane M TM Q0P9S0 Putative amino-acid transporter periplasmic solute-binding protein cjaA Outer membrane E Sec Highly immunogenic [ 54 ] Q9PPD9 Periplasmic nitrate reductase napA Periplasm P Tat Host colonization [ 38 ] Q0PC23...”
- Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of Campylobacter jejuni
Hoppe, PloS one 2013 - “...of 1536 different clones were screened using HaloLink slides. We used HisJ (UniProt/Swiss-Prot: Q46125), CjaA (Q0P9S0) and Peb1a (Q0P9X8) as positive reference markers, as they have been described previously to be immunodominant [27] [29] . In contrast, ArgC (Q9PIS0) and PyrC (Q0PBP6) were used as negative...”
- Proteomics Reveals Multiple Phenotypes Associated with N-linked Glycosylation in Campylobacter jejuni
Cain, Molecular & cellular proteomics : MCP 2019 (secret) - Chicken Anti-Campylobacter Vaccine - Comparison of Various Carriers and Routes of Immunization
Kobierecka, Frontiers in microbiology 2016 - “...and CjaD Proteins Protection Analysis Two highly immunogenic, extracytoplasmic and conserved C. jejuni proteins CjaA (Cj0982c in the genome of C. jejuni NCTC11168) and CjaD (Cj0113 in the genome of C. jejuni NCTC11168), which are often tested as candidates for chicken anti- Campylobacter vaccination were chosen...”
- Cell Wall Anchoring of the Campylobacter Antigens to Lactococcus lactis
Kobierecka, Frontiers in microbiology 2016 - “...ml -1 chloramphenicol. C. jejuni strain 81176 was the source of the cjaA ( cjj81176_1001, cj0982c ) gene. C. jejuni 12/2 strain employed in the protection experiment was a broiler-isolated strain labeled with the pUOA18 plasmid containing a cat gene. Previous experiments have shown that the...”
- Evaluation of the immunogenicity of Campylobacter jejuni CjaA protein delivered by Salmonella enterica sv. Typhimurium strain with regulated delayed attenuation in chickens
Łaniewski, World journal of microbiology & biotechnology 2014 - “...delivered orally by attenuated Salmonella strains have been tested as candidates for subunit chicken vaccine: Cj0982c (CjaA)the solute-binding protein, components of the ABC transport system (Muller et al. 2005 ); Cj0113 (CjaD)the peptidoglycan-associated protein (Pal) anchored in the outer membrane, a component of the Pal-Tol system...”
- “...SS denotes signal sequence Campylobacter jejuni strain 81176 was the source of the cjaA ( cj0982c ) gene. C. jejuni strain Wr1, isolated from a chicken, was employed in animal experiments. C. jejuni strains were routinely grown on Blood Agar Base No. 2 (Merck, Darmstadt, Germany)...”
- Defining the metabolic requirements for the growth and colonization capacity of Campylobacter jejuni
Hofreuter, Frontiers in cellular and infection microbiology 2014 - “...family 3 of solute-binding proteins, which might also facilitate the uptake of amino acids. CjaA (Cj0982c) is an N-glycosylated 30 kDa lipoprotein attached to the inner membrane (Pawelec et al., 1997 ; Wyszynska et al., 2008 ) that binds cysteine (Mller et al., 2005 ). Its...”
- “...Godlewska R. Jagusztyn-Krynicka E. K. ( 2008 ). The Campylobacter jejuni / coli cjaA ( cj0982c ) gene encodes an N-glycosylated lipoprotein localized in the inner membrane . Curr. Microbiol . 57 , 181 188 10.1007/s00284-008-9171-3 18584243 Xu F. Zeng X. Haigh R. D. Ketley J....”
- The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts
Clark, BMC microbiology 2014 - “...0.930.59 Thermonuclease family protein Cj0979c gi|121612563 0.830.38 0.730.68 Amino acid transporter, periplasmic solute-binding protein, putative Cj0982c gi|218562598 1.030.38 0.770.4 Arginyl-tRNA-protein transferase Cj1035c gi|121613462 0.730.29 0.600.26 Flippase Cj1130c gi|218562744 0.270.38 0.670.42 Cytochrome c553 Cj1153 gi|157415419 0.770.25 0.530.38 Cyclopropane fatty acid biosynthesis Cj1183c gi|57238055 1.070.67 0.730.32 NLPA family...”
- Mutational and transcriptomic changes involved in the development of macrolide resistance in Campylobacter jejuni
Hao, Antimicrobial agents and chemotherapy 2013 - “...amino acid transporters, as well as other transporters (Cj0982c, Cj0025c, Cj1389, and Cj1097). Cluster 2 includes genes encoding broad regulators (Cj0448 and...”
- Modification of the Campylobacter jejuni N-linked glycan by EptC protein-mediated addition of phosphoethanolamine
Scott, The Journal of biological chemistry 2012 - “...sequence Da Cj0131 Cj0131 Cj0168c Cj0289c Cj0399 Cj0734c Cj0982c Cj0983 Cj1013cb a b Putative peptidase M23 family protein Putative peptidase M23 family protein...”
- More
cjaA / CAJ20048.1 glutamine-binding protein from Campylobacter jejuni (see paper)
CJJ81176_1001 CjaA protein from Campylobacter jejuni subsp. jejuni 81-176
26% identity, 69% coverage
B6D87_RS01815 transporter substrate-binding domain-containing protein from Pseudomonas fragi
26% identity, 72% coverage
DVU2342, ORF02865 amino acid ABC transporter, periplasmic amino acid-binding protein from Desulfovibrio vulgaris Hildenborough
27% identity, 61% coverage
- Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution
Zhou, The ISME journal 2013 - “...permease protein, His/Glu/ Gln/Arg/opine family DVU2342 Amino-acid ABC transporter, periplasmic amino-acidbinding protein DVU2343 Amino-acid ABC transporter,...”
- Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state
Clark, BMC genomics 2012 - “...genes (DVU2387, DVU2384, DVU0484, and DVU2385) and increased abundances for two transporter proteins (DVU0752 and DVU2342) (Figure 4 , Table 3 ). Differential expression of various ABC transporters has commonly been reported in different biofilms ( e.g., P. aeruginosa, E. coli B. subtilis Thermotoga maritime Streptococcus...”
- Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough
Mukhopadhyay, Journal of bacteriology 2007 - “...DVU0675 DVU0712 DVU0752 DVU0966 DVU1238 DVU1937 DVU2297 DVU2342 DVU3162 dnaK htrA groEL groES zraP potD-1 Polyamine ABC transporter, periplasmic 0.5 (0.84)...”
- Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach
Mukhopadhyay, Journal of bacteriology 2006 - “...amino acid ABC transporter, periplasmic binding protein DVU2342 NA DVU0547 NA Sulfate reduction DVU0847 DVU0848 DVU0849 ApsA QmoA QmoB Adenylylsulfate...”
- Gene expression analysis of energy metabolism mutants of Desulfovibrio vulgaris Hildenborough indicates an important role for alcohol dehydrogenase
Haveman, Journal of bacteriology 2003 - “...ORF04254 ORF02836 ORF02836 ORF00572 ORF00572 ORF00988 ORF02865 ORF00176 ORF04661 ORF04056 ORF00383 ORF00347 ORF00590 ORF01081 ORF01081 ORF03883 ORF02097...”
Q8Z8G8 ABC transporter periplasmic binding protein from Salmonella typhi
24% identity, 85% coverage
Entcl_3149 amino acid ABC transporter substrate-binding protein from [Enterobacter] lignolyticus SCF1
25% identity, 77% coverage
FORC47_RS03370 glutamine ABC transporter substrate-binding protein GlnH from Bacillus cereus
25% identity, 68% coverage
TM0593 amino acid ABC transporter, periplasmic amino acid-binding protein from Thermotoga maritima MSB8
Q9WZ62 Amino acid ABC transporter, periplasmic amino acid-binding protein from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
26% identity, 68% coverage
- Periplasmic Binding Proteins in Thermophiles: Characterization and Potential Application of an Arginine-Binding Protein from Thermotoga maritima: A Brief Thermo-Story
Ausili, Life (Basel, Switzerland) 2013 - “...open reading frames (ORFs) annotated as putative periplasmic binding proteins [ 32 ], among which tm0593 encodes a protein with similar sequence to several polar amino acid-binding protein although from this homology it could not be possible to predict the specific cognate ligand for the protein....”
- “...acid arginine [ 37 ]. 2. TmArgBP Structure Having established that the protein encoded by tm0593 was a specific arginine-binding protein (TmArgBP) with known dissociation constant, its molecular organization, conformational dynamics and structural stability were studied by means of different methods, including low-resolution biophysical techniques, preliminary...”
- Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima
Luchansky, Molecular bioSystems 2010 (PubMed)- “...highly stable and specific periplasmic arginine-binding protein (TM0593). Following signal sequence removal and overexpression in Escherichia coli, TM0593 was...”
- “...across bacterial membranes. Purified and refolded TM0593 was further characterized by fluorescence spectroscopy, mass spectrometry, and circular dichroism...”
- Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools
Kyrpides, Nucleic acids research 2000 - “...regulators TM0186 and TM0842, and the ABC transporters TM0593 and Nucleic Acids Research, 2000, Vol. 28, No. 22 4575 Figure 2. Inferred functional coupling...”
- Development of a Protein Scaffold for Arginine Sensing Generated through the Dissection of the Arginine-Binding Protein from Thermotoga maritima
Smaldone, International journal of molecular sciences 2020 - “...Methods 4.1. Notations Wild-type TmArgBP is a dimeric protein made of 247 residues (UniProtKB - Q9WZ62). Its N -terminal end (residues 119) is the signal peptide responsible for the periplasmic localization of the protein. Since this region is highly hydrophobic, it is typically removed in the...”
- The non-swapped monomeric structure of the arginine-binding protein from Thermotoga maritima
Smaldone, Acta crystallographica. Section F, Structural biology communications 2019 - “...residues 20-246 of the protein sequence (UniProt code Q9WZ62). This region corresponds to the entire protein deprived of the signal sequence for its periplasmic...”
- The characterization of Thermotoga maritima Arginine Binding Protein variants demonstrates that minimal local strains have an important impact on protein stability
Balasco, Scientific reports 2019 - “...C-terminal swapping helix and part of the hinge peptide of the protein sequence (UniProt code Q9WZ62). Mutant of this short form of the protein were designed by replacing Gly52 with Ala or Val. The genes encoding the Gly52Ala and Gly52Val mutations were obtained by site directed...”
- A loose domain swapping organization confers a remarkable stability to the dimeric structure of the arginine binding protein from Thermotoga maritima
Ruggiero, PloS one 2014 - “...protein used in these studies includes the residues 20246 of the protein sequence (UniProt code Q9WZ62). This region corresponds to the entire protein deprived of the signal sequence for its perisplasmic exporting. TmArgBP was expressed by using E. coli Rosetta(DE3)2 cells following the procedure described in...”
- Crystallization and preliminary X-ray crystallographic analysis of ligand-free and arginine-bound forms of Thermotoga maritima arginine-binding protein
Ruggiero, Acta crystallographica. Section F, Structural biology and crystallization communications 2011 - “...20-246 (227 residues) of the protein sequence (UniProt code Q9WZ62). This sequence region was cloned into the NdeI-BamHI site of a pET21a vector. The resulting...”
Q9HWI6 Probable binding protein component of ABC transporter from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA4195 probable binding protein component of ABC transporter from Pseudomonas aeruginosa PAO1
28% identity, 68% coverage
- 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 - 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 - “...transporter 0.01 Q9HVS5 PA4496 Probable binding protein component of ABC transporter 0.396 pae02030 Bacterial chemotaxis Q9HWI6 PA4195 Probable binding protein component of ABC transporter 0.01 Q9I2T4 PA1810 Probable binding protein component of ABC transporter 0.01 Q9I5T6 PA0602 Probable binding protein component of ABC transporter 0.01 Q9I561...”
- 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 - “...0.01 Q9HVS5 PA4496 Probable binding protein component of ABC transporter 0.396 pae02030 Bacterial chemotaxis Q9HWI6 PA4195 Probable binding protein component of ABC transporter 0.01 Q9I2T4 PA1810 Probable binding protein component of ABC transporter 0.01 Q9I5T6 PA0602 Probable binding protein component of ABC transporter 0.01 Q9I561 PA0884...”
- Searching for Biological Function of the Mysterious PA2504 Protein from Pseudomonas aeruginosa
Drabinska, International journal of molecular sciences 2021 - “...the import of cysteine and methionine PA2202 , PA2203 , PA2204 , PA3931 , and PA4195 . The second group related to the conversion of sulphate to sulphite and further to sulphide: cysD, cysN , cysH , and cysI . Furthermore, transcripts coding for enzymes participating...”
- “...Putative methionine-binding protein PA3932 PA3932 0.97 Transcriptional regulator PA4067 oprG 0.49 Outer membrane protein OprG PA4195 PA4195 1.64 Putative amino acid ABC transporter substrate-binding protein/ ABC transporter glutamine-binding protein GlnH precursor PA4442 cysN 1.87 Bifunctional sulphate adenylyltransferase subunit 1/adenylylsulphate kinase PA4443 cysD 2.22 Sulphate adenylyltransferase subunit...”
- The LysR-Type Transcriptional Regulator BsrA (PA2121) Controls Vital Metabolic Pathways in Pseudomonas aeruginosa
Modrzejewska, mSystems 2021 - “...encoding type VI secretion proteins ( PA1657 to PA1671 ) and transporters ( PA4192 to PA4195 , PA2202 , PA2203 , PA5024 ) (see Data Set S2). The altered expression of selected loci in response to BsrA excess was confirmed using RT-qPCR analysis (data not shown)....”
- Involvement of Fe uptake systems and AmpC β-lactamase in susceptibility to the siderophore monosulfactam BAL30072 in Pseudomonas aeruginosa
van, Antimicrobial agents and chemotherapy 2013 - “...Induced PA0263 PA0201 PA0284 PA0191 PA0525 PA3938 PA2204 PA3450 PA4195 PA0283 van Delden et al. TABLE 6 BAL30072 MICs for P. aeruginosa strains with or without...”
- High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
Johnson, PLoS genetics 2008 - “...PAK amino acid ABC transporter membrane protein PA4194 PAK amino acid ABC transporter membrane protein PA4195 PAK amino acid ABC transporter periplasmic binding protein PA4233 PA01 MFS transporter PA4628 PAK lysine APC family transporter PA4804 PAK amino acid APC family transporter PA4909 PA01 branched chain amino...”
- Screening for quorum-sensing inhibitors (QSI) by use of a novel genetic system, the QSI selector
Rasmussen, Journal of bacteriology 2005 - “...PA3444 PA3445 PA3570 PA3720 PA3935 PA3938 PA4067 PA4191 PA4195 PA4710 PA5027 PA5054 PA5083 PA5475 G6 VOL. 187, 2005 SCREENING FOR QS INHIBITORS 1811 phase...”
1xt8B / Q0P9S0 Crystal structure of cysteine-binding protein from campylobacter jejuni at 2.0 a resolution (see paper)
27% identity, 62% coverage
EAM_RS05505 amino acid ABC transporter substrate-binding protein from Erwinia amylovora ATCC 49946
24% identity, 78% coverage
SPO2658 amino acid ABC transporter substrate-binding protein from Ruegeria pomeroyi DSS-3
27% identity, 70% coverage
- Bacterial transcriptional response to labile exometabolites from photosynthetic picoeukaryote Micromonas commoda
Ferrer-González, ISME communications 2023 - “...amino acid ABC transporter, ATP-binding protein SPO1850 AAV95129.1 2 branched-chain amino acid ABC transporter, permease SPO2658 AAV95903.1 2.3 possible sulfonate ABC transporter, substrate binding protein SPO2660 AAV95905.1 2.6 possible sulfonate ABC transporter, permease SPO2661 AAV95906.1 2.1 possible sulfonate ABC transporter, ATP binding protein SPO2802 AAV96043.1 2.3...”
- Diel investments in metabolite production and consumption in a model microbial system
Uchimiya, The ISME journal 2022 - “...4.2 Sulfur compound Choline-O-sulfate SPO1083 betC Choline sulfatase 15.1 [ 75 ] Sulfur compound Cysteate SPO2658 ABC transporter, periplasmic substrate-binding 22.4 [ 41 ] SPO2659 ABC transporter, permease 38.3 SPO2660 ABC transporter, permease 28.0 SPO2661 ABC transporter, ATP-binding 32.7 Sulfur compound Dihydroxypropane-sulfonate (DHPS) SPO0591 hpsK TRAP...”
- Sulfur metabolites that facilitate oceanic phytoplankton-bacteria carbon flux
Landa, The ISME journal 2019 - “...-8.6 This study <0.001 -27.8 This study SPO2658 Cysteate transport sulfolyase ABC transporter, periplasmic SPO2657 Cysteate metabolism -3.0 [28] L-cysteate...”
BTH_I2450 extracellular solute-binding protein from Burkholderia thailandensis E264
27% identity, 63% coverage
PMI0437 glutamate/aspartate ABC transporter, substrate-binding protein from Proteus mirabilis HI4320
25% identity, 76% coverage
- Transcriptome of swarming Proteus mirabilis
Pearson, Infection and immunity 2010 - “...protein PMI1592 PMI0250 PMI2019 PMI3037 PMI2236 PMI2662 PMI0437 PMI3579 PMI1056 PMI2114 PMI1474 PMI1421 PMI1722 PMI1615 PMI2246 PMI2052 PMI2255 PMI2254 PMI3177...”
- “...PMI3037 acs Acetyl coenzyme A 2.91 1.11 0.40 synthetase PMI0437 gltI culture. The lrhA mutant was also recovered in numbers similar to those of the wild-type...”
C3L23_RS03070 transporter substrate-binding domain-containing protein from Nautilia sp. PV-1
26% identity, 66% coverage
LBA1046 glutamine ABC transporter substrate-binding protein from Lactobacillus acidophilus NCFM
25% identity, 76% coverage
2v25A / Q0P9X8 Structure of the campylobacter jejuni antigen peb1a, an aspartate and glutamate receptor with bound aspartate (see paper)
26% identity, 61% coverage
- Ligand: aspartic acid (2v25A)
BPSL2924 glutamate/aspartate periplasmic binding protein precursor from Burkholderia pseudomallei K96243
25% identity, 76% coverage
- Host-Adaptation of Burkholderia pseudomallei Alters Metabolism and Virulence: a Global Proteome Analysis
Mariappan, Scientific reports 2017 - “...acid transport and metabolism / Signal transduction mechanisms Glutamate/aspartate periplasmic binding protein (gltI) 19 0.038 BPSL2924 2.9 33 32699/31300 9.17/9.17 + periplasmic Lysine-arginine-ornithine transport system, binding exported protein (argT) 24 0.044 BPSS0269 2.0 16 27833/28350 7.64/8.61 + periplasmic Secondary metabolites biosynthesis, transport and catabolism / General...”
- “...acid transport and metabolism / Signal transduction mechanisms Glutamate/aspartate periplasmic binding protein (gltI) 21 0.014 BPSL2924 5.6 22 32699/35200 9.17/9.17 + periplasmic Secondary metabolites biosynthesis, transport and catabolism / General function prediction Acetoacetyl-CoA reductase (phbB) 43 0.012 BPSS1916 3.3 14 26408/26298 6.60/6.30 cytoplamic Signal transduction mechanisms...”
APL_1694 antigenic protein, ABC transporter-like protein from Actinobacillus pleuropneumoniae L20
APP7_1755 antigenic protein, ABC transporter-like protein from Actinobacillus pleuropneumoniae serovar 7 str. AP76
26% identity, 71% coverage
HMU03500 putative amino-acid transporter periplasmic solute-binding protein from Helicobacter mustelae 12198
24% identity, 70% coverage
A9497_01790, STER_RS05530 transporter substrate-binding domain-containing protein from Streptococcus thermophilus
29% identity, 52% coverage
AKL23_RS05335 transporter substrate-binding domain-containing protein from Streptococcus thermophilus
29% identity, 52% coverage
- Technological and Genomic Analysis of Roles of the Cell-Envelope Protease PrtS in Yoghurt Starter Development
Tian, International journal of molecular sciences 2018 - “...AKL23_RS08280 AKL23_RS08285 Permease A9497_07905 AKL23_RS01770 ABC transporter substrate-binding protein Glutamine A9497_01790 A9497_06995 A9497_00730 AKL23_RS04225 AKL23_RS00860 AKL23_RS05335 ABC transporter substrate-binding protein A9497_01795 A9497_01800 A9497_09175 AKL23_RS05340 AKL23_RS05345 AKL23_RS03035 ABC transporter permease A9497_03790 A9497_09180 AKL23_RS03040 AKL23_RS07400 ABC transporter ATP-binding protein Methionine A9497_07635 AKL23_RS01505 ABC transporter ATP-binding protein A9497_07640 AKL23_RS01510...”
HZ99_18940 transporter substrate-binding domain-containing protein from Pseudomonas fluorescens
28% identity, 62% coverage
APJL_1726 putative ABC transporter, periplasmic binding protein from Actinobacillus pleuropneumoniae serovar 3 str. JL03
26% identity, 71% coverage
- Genome-wide screening of lipoproteins in Actinobacillus pleuropneumoniae identifies three antigens that confer protection against virulent challenge
Cao, Scientific reports 2020 - “...APP7_1413 APJL_1467 YP_001652463.1 hypothetical protein 42.0 APL_1435 APP7_1497 APJL_1469 YP_001652465.1 hypothetical protein 62.6 APL_1437 APP7_1495 APJL_1726 YP_001652722.1 putative ABC transporter periplasmic binding protein 53.9 APL_1694 APP7_1755 APJL_1919 YP_001652913.1 hypothetical protein 50.9 APL_1875 APP7_1963 APJL_1942 YP_001652936.1 Zn-dependent protease with chaperone function 51.8 APL_1898 APP7_1985 APJL_1976 YP_001652968.1 lipoprotein...”
- “...hypothetical. It is worth noting that a number of hypothetical proteins (APJL_0221, APJL_1318, APJL_1380, APJL_1469, APJL_1726 and APJL_1976) yielded clearly positive reactions with rabbit anti- A. pleuropneumoniae serum in western blotting. Two hypothetical lipoproteins, APJL_1380 and APJL_1976, were selected for further investigation. On the basis of...”
2ia4B / A0A0H2UXX1 Crystal structure of novel amino acid binding protein from shigella flexneri
25% identity, 66% coverage
- Ligand: glutamic acid (2ia4B)
CLP_0371 cysteine ABC transporter substrate-binding protein from Clostridium butyricum E4 str. BoNT E BL5262
25% identity, 75% coverage
UTI89_C0651 glutamate/aspartate periplasmic binding protein precursor from Escherichia coli UTI89
25% identity, 66% coverage
ACINB_20500 amino acid ABC transporter substrate-binding protein from Acidovorax sp. NB1
26% identity, 68% coverage
- Effects of Co-existing Heterotrophs on Physiology of and Nitrogen Metabolism in Autotrophic Nitrite-oxidizing Candidatus Nitrotoga
Ide, Microbes and environments 2023 - “...synthetase glnA gene (ACINB_00240) at a high level, similar to that of amino acid transporters (ACINB_20500 and ACINB_30160), which are periplasmic binding proteins. Furthermore, NB1 in the culture highly expressed nirB (ACINB_14400), nirD (ACINB_14410), D-amino acid dehydrogenase (DAD) (ACINB_23850) and glutamate dehydrogenase (GDH) (ACINB_23490) deaminating glutamate...”
- “...most highly transcribed genes of NB1 were described. AmtB; ammonia/ammonium transporter (W01_00340), Amino acid transporter (ACINB_20500, ACINB_30160), DAD; D-amino acid dehydrogenase (ACINB_23850, ACINB_26800, ACINB_35240), GDH; glutamate dehydrogenase (ACINB_23490), GlnA; glutamine synthetase (W01_14570 for AM1P; ACINB_00240 for NB1), GltB; glutamate synthetase (W01_13290), NirB; nitrite reductase (W01_03820 for...”
HH1481 probable ABC-type amino-acid transporter periplasmic solute-binding protein from Helicobacter hepaticus ATCC 51449
27% identity, 68% coverage
YPTB3957 ABC transporter, periplasmic amino acid binding protein from Yersinia pseudotuberculosis IP 32953
YPO4111 putative periplasmic solute-binding protein from Yersinia pestis CO92
y4125 putative solute-binding periplasmic protein precursor for ABC transporter from Yersinia pestis KIM
26% identity, 67% coverage
- IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
Miller, PLoS pathogens 2014 - “...2.8 YPTB2771 putative ABC iron transporter 2.7 YPTB2772 ABC transporter, periplasmmic iron binding protein 4.1 YPTB3957 ABC transporter, periplasmic amino acid binding protein 4.6 Cell Envelope (5) YPTB1334 pH 6 antigen precursor (antigen 4) (adhesin) psaA 2.5 YPTB2123 putative exported protein ompW 3.3 YPTB2287 putative lipoprotein...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...glutamate dehydrogenase 1.671 (0.005) YPTB3853 (cysM) or2495 pyridoxal-phosphate dependent protein (pseudogene. partial) 0.415 (< 0.001) YPTB3957 YPO4111 putative periplasmic solute-binding protein 1.59 (0.006) F: nucleotide transport and metabolism YPTB0250 (udp) YPO3786 uridine phosphorylase 0.486 (0.005) YPTB0519 (nrdD) YPO3454 anaerobic ribonucleoside-triphosphate reductase 0.614 (0.024) YPTB0584 (deoD) YPO0440...”
- “...A 0.291 (< 0.001) 1.554 (0.038) YPTB3847 (uhpA) YPO4012 two-component system response regulatoR 2.004 (0.006) YPTB3957 YPO4111 putative periplasmic solute-binding protein 1.59 (0.006) YPTB2341 (infC) YPO2432 translation initiation factor IF-3 0.539 (< 0.001) Table 3 Y. pseudotuberculosis IP32953 pYV plasmid-harbored genes that are transcriptionally regulated by...”
- A Rapid Molecular Test for Determining Yersinia pestis Susceptibility to Ciprofloxacin by the Quantification of Differentially Expressed Marker Genes
Steinberger-Levy, Frontiers in microbiology 2016 - “...rumC Putative DNA recombination protein 2.3 YPO3901 ilvG Acetolactate synthase isozyme II large subunit 2.2 YPO4111 YPO4111 Putative periplasmic solute-binding protein 2.2 YPO3900 ilvM Acetolactate synthase isozyme II small subunit 2.2 YPO3899 ilvE Branched-chain amino acid aminotransferase 2.1 YPO0003 asnA Aspartate-ammonia ligase 2.1 2.1 YPO3914 sth...”
- Cell membrane is impaired, accompanied by enhanced type III secretion system expression in Yersinia pestis deficient in RovA regulator
Yang, PloS one 2010 - “...murein peptide-binding protein 4.A Transport/binding proteins YPO4110 2.71 ----- ABC transporter permease 4.A Transport/binding proteins YPO4111 3.77 ----- putative periplasmic solute-binding protein 4.A Transport/binding proteins YPO1937 3.73 ansP L-asparagine permease 4.A.1 Transport/binding proteins YPO4109 4.28 ----- putative amino acid transport system permease 4.A.1 Transport/binding proteins YPO2338...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...dehydrogenase 1.671 (0.005) YPTB3853 (cysM) or2495 pyridoxal-phosphate dependent protein (pseudogene. partial) 0.415 (< 0.001) YPTB3957 YPO4111 putative periplasmic solute-binding protein 1.59 (0.006) F: nucleotide transport and metabolism YPTB0250 (udp) YPO3786 uridine phosphorylase 0.486 (0.005) YPTB0519 (nrdD) YPO3454 anaerobic ribonucleoside-triphosphate reductase 0.614 (0.024) YPTB0584 (deoD) YPO0440 purine...”
- “...0.291 (< 0.001) 1.554 (0.038) YPTB3847 (uhpA) YPO4012 two-component system response regulatoR 2.004 (0.006) YPTB3957 YPO4111 putative periplasmic solute-binding protein 1.59 (0.006) YPTB2341 (infC) YPO2432 translation initiation factor IF-3 0.539 (< 0.001) Table 3 Y. pseudotuberculosis IP32953 pYV plasmid-harbored genes that are transcriptionally regulated by growth...”
- Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation
Pieper, BMC microbiology 2010 - “...fkpA FKBP-type peptidyl-prolyl cis-trans isomerase PP 2031 33670 6.94 5.50 3.45 1.594 0.007 N.D. 93 y4125 - putative solute-binding periplasmic protein precursor for ABC transporter PP 2766 30250 6.27 6.09 3.67 1.661 0.001 2.264 a) spot number as denoted in Figures 1 and 2; b) protein...”
X276_14095 cysteine ABC transporter substrate-binding protein from Clostridium beijerinckii NRRL B-598
26% identity, 63% coverage
6svfA / Q9WZ62 Crystal structure of the p235gk mutant of argbp from t. Maritima (see paper)
26% identity, 63% coverage
BURMUCGD2M_3196 glutamate/aspartate ABC transporter, periplasmic glutamate/aspartate-binding protein from Burkholderia multivorans CGD2M
Bmul_2714 glutamate/aspartate ABC transporter substrate-binding protein from Burkholderia multivorans
25% identity, 76% coverage
YPO2615 putative amino acid-binding protein precursor from Yersinia pestis CO92
y1189 solute-binding periplasmic protein of glutamate/aspartate ABC transporter from Yersinia pestis KIM
YPK_3010 extracellular solute-binding protein from Yersinia pseudotuberculosis YPIII
YPTB1108 ABC transporter, periplasmic glutamate/aspatate binding protein from Yersinia pseudotuberculosis IP 32953
23% identity, 83% coverage
- Differential Gene Expression Patterns of Yersinia pestis and Yersinia pseudotuberculosis during Infection and Biofilm Formation in the Flea Digestive Tract
Chouikha, mSystems 2019 - “...hmsD Diguanylate cyclase, c-di-GMP synthesis 2.3 5.1 YPTB0728 YPO3403 panD Aspartate alpha-decarboxylase 2.5 2.5 YPTB1108 YPO2615 ybeJ Glutamate and aspartate transporter subunit 2.0 2.4 YPTB1923 YPO1925 evg Two-component response regulator 2.6 2.6 YPTB3107 YPO0863 YaeF/YiiX family of permuted papain-like enzymes 2.2 2.4 YPTB3361 YPO0700 Fimbrial protein...”
- “...Aspartate alpha-decarboxylase 2.5 2.5 YPTB1107 YPO2614 gltJ ABC glutamate/aspartate transporter, permease subunit 2.2 2.1 YPTB1108 YPO2615 ybeJ Glutamate and aspartate transporter subunit 2.5 2.5 YPTB1522 YPO1507 mglB Galactose binding periplasmic protein 2.1 2.9 YPTB1923 YPO1925 evg Two-component response regulator 3.2 3.9 YPTB1934 YPO1936 Aminotransferase 2.0 7.8...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPTB0920 (brnQ) YPO3202 branched-chain amino acid transport system II carrier protein 1.481 (0.033) YPTB1108 (glnH) YPO2615 putative amino acid-binding protein precursoR 0.564 (0.005) YPTB1186 YPO1155 putative amino acid transporteR 1.736 (0.017) YPTB1240 YPO1200 putative amino acid permease 0.637 (0.025) YPTB1241 YPO1201 putative amino acid decarboxylase 0.557...”
- “...protein homologue 0.508 (< 0.001) YPTB0789 YPO3343 probable extracellular solute-binding protein 0.462 (0.001) YPTB1108 (glnH) YPO2615 putative amino acid-binding protein precursoR 0.564 (0.005) YPTB1258 (rcsB) YPO1218 probable two component response regulator component B 0.693 (0.016) YPTB1259 YPO1219 putative two component sensor kinase 0.696 (0.041) YPTB1922 YPO1923...”
- Characterization of phagosome trafficking and identification of PhoP-regulated genes important for survival of Yersinia pestis in macrophages
Grabenstein, Infection and immunity 2006 - “...YPO0183 YPO0187 YPO3783 YPO2234 YPO1366 YPO3717 YPO1642 YPO2615 YPO0184 YPO1319 Response regulator protein (phoP) Probable glycosyl transferase (pmrF) Conserved...”
- PspG, a new member of the Yersinia enterocolitica phage shock protein regulon
Green, Journal of bacteriology 2004 - “...84.2 84.2 84.2 83.9 83.5 83.2 83.2 YPO1187 ortholog YPO2615 ortholog EC yhdW ortholog YP astC ortholog YP glnK ortholog YP hisJ ortholog RSp1575 homolog YP fhuC...”
- “...to eliminate the putative promoters upstream of orthologs of YPO2615 and hyfA as members of the Psp regulon, because their expression was unaffected by pspA and...”
- Physiological levels of glucose induce membrane vesicle secretion and affect the lipid and protein composition of Yersinia pestis cell surfaces
Kolodziejek, Applied and environmental microbiology 2013 - “...material). Notably, 44% of proteins (encoded by y0028, y2662, y1189, and y1607) found in the cultures grown without glucose and only one protein (encoded by...”
- Global gene expression profiling of Yersinia pestis replicating inside macrophages reveals the roles of a putative stress-induced operon in regulating type III secretion and intracellular cell division
Fukuto, Infection and immunity 2010 - “...YPO3135 y0740 y2127 y1048 y0946 YPO1366 y1607 y0655 y2882 y1189 y1041 y0310 y1607 YPO1423a y3555 y0509 y0016 y0463 y0655 y1821 y2881 y2125 y3804 y2236 y0015...”
- Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation
Pieper, BMC microbiology 2010 - “...60 y1128 bglX putative beta-glucosidase PP 2324 81506 5.43 3.01 0.52 5.822 0.000 1.740 61 y1189 gltI solute-binding periplasmic protein of glutamate/aspartate ABC transporter PP 2512 35927 7.20 0.41 2.91 0.141 0.005 N.D. 62 y1223 nrdE ribonucleoside-diphosphate reductase 2, alpha subunit U Fur 198 79914 6.32...”
- Characterization of phagosome trafficking and identification of PhoP-regulated genes important for survival of Yersinia pestis in macrophages
Grabenstein, Infection and immunity 2006 - “...y0246 y0244 y3966 y2866 y3964 y3968 y0447 y2076 y0025 y1803 y1189 y3965 y2865 a The 40 genes with greatest positive changes are shown. Locus tag for the KIM...”
- Functional versatility of Zur in metal homeostasis, motility, biofilm formation, and stress resistance in Yersinia pseudotuberculosis
Gu, Microbiology spectrum 2024 - “...(YPK_00570059), ribose (YPK_1161 and YPK_1162), erythritol (YPK_19611963), maltose (YPK_0378 and YPK_0382), simple sugar (YPK_24082411), glutamate/aspartate (YPK_3010), oligopeptide (YPK_2067 and YPK_2068), and nucleoside (YPK_1438 and YPK_3628) transport systems were upregulated by Zur. This suggests Zurs role in nutrient acquisition in Y. pseudotuberculosis . Although similar regulation of...”
- Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
Mahmud, mSystems 2020 - “...TTGGCGTGTTTTTTGCAT + 11.21 54,70 YPK_3001 39 IGS20 3311541 12.6 13.3 10.6 CTGGCACAAACCTTGCAT + 10.73 54,70,38,24 YPK_3010 S 15, 17, 23 IGS20 3311541 12.6 13.3 10.6 ATGGCTGCTTTACTGCCT + 9.24 54,70,38,24 YPK_3010 S 15, 17, 23 IGS20 3311541 12.6 13.3 10.6 CAGGGCTATATTCCGCTT + 8.12 54,70,38,24 YPK_3010 S 15,...”
- “...transcription. Results are shown for expression under virulence-inducing conditions for YPK_0329, YPK_1886, YPK_1894, YPK_2927, YPK_2997, YPK_3010, YPK_3075, YPK_3613, YPK_3887, and YPK_3962 and for expression during stationary phase at 26C for YPK_2908 and YPK_2909. Values represent means SEM of three independent experiments. (Right) Schematic illustration of the...”
- Differential Gene Expression Patterns of Yersinia pestis and Yersinia pseudotuberculosis during Infection and Biofilm Formation in the Flea Digestive Tract
Chouikha, mSystems 2019 - “...YPO0449 hmsD Diguanylate cyclase, c-di-GMP synthesis 2.3 5.1 YPTB0728 YPO3403 panD Aspartate alpha-decarboxylase 2.5 2.5 YPTB1108 YPO2615 ybeJ Glutamate and aspartate transporter subunit 2.0 2.4 YPTB1923 YPO1925 evg Two-component response regulator 2.6 2.6 YPTB3107 YPO0863 YaeF/YiiX family of permuted papain-like enzymes 2.2 2.4 YPTB3361 YPO0700 Fimbrial...”
- “...panD Aspartate alpha-decarboxylase 2.5 2.5 YPTB1107 YPO2614 gltJ ABC glutamate/aspartate transporter, permease subunit 2.2 2.1 YPTB1108 YPO2615 ybeJ Glutamate and aspartate transporter subunit 2.5 2.5 YPTB1522 YPO1507 mglB Galactose binding periplasmic protein 2.1 2.9 YPTB1923 YPO1925 evg Two-component response regulator 3.2 3.9 YPTB1934 YPO1936 Aminotransferase 2.0...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...0.601 (0.03) YPTB0920 (brnQ) YPO3202 branched-chain amino acid transport system II carrier protein 1.481 (0.033) YPTB1108 (glnH) YPO2615 putative amino acid-binding protein precursoR 0.564 (0.005) YPTB1186 YPO1155 putative amino acid transporteR 1.736 (0.017) YPTB1240 YPO1200 putative amino acid permease 0.637 (0.025) YPTB1241 YPO1201 putative amino acid...”
- “...DnaK suppressor protein homologue 0.508 (< 0.001) YPTB0789 YPO3343 probable extracellular solute-binding protein 0.462 (0.001) YPTB1108 (glnH) YPO2615 putative amino acid-binding protein precursoR 0.564 (0.005) YPTB1258 (rcsB) YPO1218 probable two component response regulator component B 0.693 (0.016) YPTB1259 YPO1219 putative two component sensor kinase 0.696 (0.041)...”
ECs0694 putative periplasmic binding transport protein from Escherichia coli O157:H7 str. Sakai
25% identity, 66% coverage
HBZC1_05960 transporter substrate-binding domain-containing protein from Helicobacter bizzozeronii CIII-1
25% identity, 78% coverage
AO353_21710 ABC transporter for D-glucosamine, periplasmic substrate-binding component from Pseudomonas fluorescens FW300-N2E3
26% identity, 69% coverage
- mutant phenotype: # Specifically important in nitrogen source D-Glucosamine Hydrochloride; carbon source D-Glucosamine Hydrochloride
plu1307 Glutamate/aspartate transport system permease protein GltI from Photorhabdus luminescens subsp. laumondii TTO1
24% identity, 77% coverage
NGO2014 putative ABC transporter, periplasmic binding protein, amino acid from Neisseria gonorrhoeae FA 1090
25% identity, 70% coverage
- Huanglongbing Pandemic: Current Challenges and Emerging Management Strategies
Ghosh, Plants (Basel, Switzerland) 2022 - “...0.014 M [ 143 ] Ngo0372 Neisseria gonorrhoeae 2YLN Cystine 0.021 M [ 144 ] Ngo2014 Neisseria gonorrhoeae 2YJP Cysteine 0.026 M [ 144 ] CLasTcyA Candidatus Liberibacter asiaticus 6A80 Cystine 1.26 M [ 145 ] ClasTcyA Mutant (V58W) Candidatus Liberibacter asiaticus - Cystine 0.22 M...”
- Substrate recognition and ATPase activity of the E. coli cysteine/cystine ABC transporter YecSC-FliY
Sabrialabed, The Journal of biological chemistry 2020 - “...84 ) to construct a model of FliY using the 2.26 resolution crystal structure of NGO2014, the l -cysteine SBP of Neisseria gonorrhoeae (PDB code 2YJP , 26% sequence identity to FliY ( 85 )). We then docked l -cysteine to this model (see Experimental procedures...”
- “...which we aligned using MAFFT ( 83 ). Using the 2.26 resolution crystal structure of NGO2014, the cysteine binding protein of N. gonorrhoeae ( 85 ) (PDB code 2YJP , 26% sequence identity to FliY) and the 1.12 resolution crystal structure of NGO0230, the cystine binding...”
- Crystal structures of receptors involved in small molecule transport across membranes
Bulut, European journal of cell biology 2012 (PubMed)- “...of side chains, contrasting the receptors Ngo0372 and Ngo2014 from Neisseria gonorrhaeae that are highly specific for cystine and cysteine, respectively. The...”
- “...the highly specific receptors AcbH, Ngo0372 and Ngo2014. 0 false false Crystallography ABC transporter Acarbose Galactose Arginine Lysine Histidine Cysteine...”
- Crystal structures of two solute receptors for L-cystine and L-cysteine, respectively, of the human pathogen Neisseria gonorrhoeae
Bulut, Journal of molecular biology 2012 (PubMed)- “...crucial for l-cystine binding. The structure of the Ngo2014 receptor was obtained in closed conformation in complex with co-purified l-cysteine. The protein...”
- “...purification, and substrate specificities of Ngo0372 and Ngo2014 Description of overall structures Closure of the venus flytrap fold of Cys-CysRec Binding...”
- MpeR regulates the mtr efflux locus in Neisseria gonorrhoeae and modulates antimicrobial resistance by an iron-responsive mechanism
Mercante, Antimicrobial agents and chemotherapy 2012 - “...NGO1665 NGO1685 NGO1749 NGO1765 NGO1770 NGO1780 NGO1809 NGO2013 NGO2014 NGO2094 NGO0018 lolA NGO0373 NGO0393 NGO0678 leuC mobA bfrB NGO0863 NGO0891 sucB clpB...”
- Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Isabella, BMC genomics 2011 - “...component FarR glnQ NGO2013 -6.3 -11.1 ABC-type amino acid transporter, ATP-binding protein MtrR, FarR apaA NGO2014 -6.3 -16.7 Bacterial extracellular solute-binding proteins, family 3 MtrR, FarR NGO2016 -3.6 -3.3 Predicted permease NGO2096 -6.3 -12.5 SNF family sodium-dependent transporter Energy metabolism/Oxidation-Reduction NGO0108 -4.0 -5.9 NADPH-dependent FMN reductase...”
- MtrR modulates rpoH expression and levels of antimicrobial resistance in Neisseria gonorrhoeae
Folster, Journal of bacteriology 2009 - “...NGO1741 NGO1742 NGO1749 NGO1751 NGO1765 NGO1890 NGO2011 NGO2013 NGO2014 leuS NGO0018 potH rpoH NGO0302 bioA bioD pdxH NGO0756 brfB umpA NGO0863 NGO0891 accB...”
- Two ABC transporter operons and the antimicrobial resistance gene mtrF are pilT responsive in Neisseria gonorrhoeae
Friedrich, Journal of bacteriology 2007 - “...the clusters NGO0372 to NGO0374 and NGO2011 to NGO2014 have highest homology to bacterial transporters that import amino acids, and NGO1368 encodes the protein...”
- “...of putative ABC transporter genes (NGO0372, NGO2011, and NGO2014), mtrF, and farR in strain MS11pilT 4 h postinfection. Transcript levels were measured by...”
SSUBM407_0596 glutamine-binding protein precursor from Streptococcus suis BM407
SSUSC84_RS06430 transporter substrate-binding domain-containing protein from Streptococcus suis SC84
26% identity, 62% coverage
- Proteomic and Bioinformatic Analysis of Streptococcus suis Human Isolates: Combined Prediction of Potential Vaccine Candidates
Prados, Vaccines 2020 - “...Putative exported protein SSUBM407_0299 Streptococcal histidine triad-family protein SSUBM407_0558 Thiol-activated cytolysin (suilysin) SSUBM407_0564 GTPase Era SSUBM407_0596 Putative glutamine-binding protein SSUBM407_0725 Putative gluconate 5-dehydrogenase SSUBM407_1737 Putative D-alanyl-D-alanine carboxypeptidase SSUBM407_2015 Putative exported protein SSUBM407_1318 Putative Mac family protein Secreted proteins SSUBM407_0206 Putative exported protein SSUBM407_0452 Putative exported protein...”
- Transcriptomic Analysis of Streptococcus suis in Response to Ferrous Iron and Cobalt Toxicity
Jia, Genes 2020 - “...of Ferrous Iron Analysis of the transcriptome data revealed that four adjacent genes, i.e., SSUSC84_RS06425, SSUSC84_RS06430, SSUSC84_RS06435, and SSUSC84_RS06440, were among the top 10 up-regulated genes in response to ferrous iron toxicity ( Table S2 ). After treatment with ferrous iron, they were up-regulated approximately 39-,...”
- “...in the DEGs in the presence of cobalt ( Table S3 ). The SSUSC84_RS06425 and SSUSC84_RS06430 genes encode an amino acid ABC transporter ATP-binding protein and glutamine ABC transporter substrate-binding protein, respectively, while the SSUSC84_RS06435 and SSUSC84_RS06440 genes both encode the amino acid ABC transporter permease....”
A9762_17050 glutamate/aspartate ABC transporter substrate-binding protein from Pandoraea sp. ISTKB
26% identity, 67% coverage
8ovoA / P37902,P42212 X-ray structure of the sf-iglusnfr-s72a in complex with l-aspartate
25% identity, 45% coverage
- Ligand: aspartic acid (8ovoA)
Aave_4073 extracellular solute-binding protein, family 3 from Acidovorax avenae subsp. citrulli AAC00-1
27% identity, 64% coverage
I35_RS02685 glutamate/aspartate ABC transporter substrate-binding protein from Burkholderia cenocepacia H111
BCAL3358 periplasmic glutamate/aspartate-binding protein from Burkholderia cenocepacia J2315
26% identity, 70% coverage
- Identification of Key Factors for Anoxic Survival of B. cenocepacia H111
Paszti, International journal of molecular sciences 2022 - “...protein - J 1.7 1.33 I35_RS02485 BCAL3398 competence damage-inducible protein A - S 2.19 1.35 I35_RS02685 BCAL3358 ABC transporter gltI P 1.43 1.12 I35_RS02700 BCAL3354 arginine ABC transporter ATP-binding protein - E 1.88 1.04 I35_RS03285 - tRNA-Lys - - 1.03 1.28 I35_RS04855 - nicotinate phosphoribosyltransferase -...”
- Identification of Key Factors for Anoxic Survival of B. cenocepacia H111
Paszti, International journal of molecular sciences 2022 - “...- J 1.7 1.33 I35_RS02485 BCAL3398 competence damage-inducible protein A - S 2.19 1.35 I35_RS02685 BCAL3358 ABC transporter gltI P 1.43 1.12 I35_RS02700 BCAL3354 arginine ABC transporter ATP-binding protein - E 1.88 1.04 I35_RS03285 - tRNA-Lys - - 1.03 1.28 I35_RS04855 - nicotinate phosphoribosyltransferase - H...”
DVU0752, ORF00176 amino acid ABC transporter, amino acid-binding protein from Desulfovibrio vulgaris Hildenborough
30% identity, 64% coverage
- Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion
Tripathi, Frontiers in microbiology 2021 - “...c553 Electron transfer partner for the formate dehydrogenase in DVH biofilms Clark et al., 2012 DVU0752 DVH ABC transporter Translocation of a wide variety of molecules into or out of biofilm cells Shemesh et al., 2007 ; Clark et al., 2012 DVU0330 DVH Response regulator containing...”
- Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state
Clark, BMC genomics 2012 - “...ABC transporter genes (DVU2387, DVU2384, DVU0484, and DVU2385) and increased abundances for two transporter proteins (DVU0752 and DVU2342) (Figure 4 , Table 3 ). Differential expression of various ABC transporters has commonly been reported in different biofilms ( e.g., P. aeruginosa, E. coli B. subtilis Thermotoga...”
- Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough
Mukhopadhyay, Journal of bacteriology 2007 - “...DVU0095 DVU0107 DVU0169 DVU0386 DVU0547 DVU0675 DVU0712 DVU0752 DVU0966 DVU1238 DVU1937 DVU2297 DVU2342 DVU3162 dnaK htrA groEL groES zraP potD-1 Polyamine...”
- Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis
He, Applied and environmental microbiology 2006 - “...DVU0105 DVU0106 DVU0107 DVU0388 DVU0624 DVU0625 DVU0751 DVU0752 DVU0966 DVU0967 DVU0968 DVU1026 DVU1237 DVU1238 DVU1766 DVU2113 DVU2242 DVU2543 DVU3392...”
- Gene expression analysis of energy metabolism mutants of Desulfovibrio vulgaris Hildenborough indicates an important role for alcohol dehydrogenase
Haveman, Journal of bacteriology 2003 - “...ORF02836 ORF02836 ORF00572 ORF00572 ORF00988 ORF02865 ORF00176 ORF04661 ORF04056 ORF00383 ORF00347 ORF00590 ORF01081 ORF01081 ORF03883 ORF02097 ORF03811...”
CCC13826_0664 surface antigen, CjaA from Campylobacter concisus 13826
25% identity, 69% coverage
H16_A0472 ABC-type transporter, periplasmic component: PAAT family from Ralstonia eutropha H16
26% identity, 68% coverage
alr3429 glutamine-binding protein of glutamine ABC transporter from Nostoc sp. PCC 7120
22% identity, 68% coverage
- Amino Acid Transporters and Release of Hydrophobic Amino Acids in the Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120
Pernil, Life (Basel, Switzerland) 2015 - “...]. 2.2. Plasmid Construction and Genetic Procedures For inactivation of alr2536 , all0342 , and alr3429 , internal fragments of 552 bp, 596 bp, and 469 bp, respectively, were amplified by PCR using DNA from strain PCC 7120 as a template and primers alr2536-7120-1 and alr2536-7120-2...”
- “...vector pGEM-T (Promega) in the case of alr2536 and all0342 or pGEM-T Easy (Promega) for alr3429 , producing pCSR4, pCSR1, and pCSR19, respectively, and then transferred as Bam HI-ended fragments to Bam HI-digested pRL424 [ 36 ] producing pCSR17, pCSR13, and pCSR23, respectively (Nm r )....”
Q8PVM4 Glutamine-binding protein from Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
MM1939 Glutamine-binding protein from Methanosarcina mazei Goe1
27% identity, 59% coverage
2yjpA / Q5F5B5 Crystal structure of the solute receptors for l-cysteine of neisseria gonorrhoeae (see paper)
25% identity, 63% coverage
- Ligands: cysteine; zinc ion (2yjpA)
CAC0380 Periplasmic amino acid-binding protein from Clostridium acetobutylicum ATCC 824
CA_C0380, CEA_G0390 ABC transporter substrate-binding protein from Clostridium acetobutylicum EA 2018
27% identity, 69% coverage
- Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress
Wang, BMC systems biology 2013 - “...novo motif prediction with MOTIFATOR [ 69 ] suggests an ArgR binding site upstream of CAC0380. CAC0380 was previously annotated as a periplasmic amino acid-binding protein, but now with our prediction of ArgR binding site for this gene, we suspect it is an arginine-binding protein with...”
- Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018
Hu, BMC genomics 2011 - “...oligopeptide-binding protein, periplasmic component CEA_G0327 CA_C0316 -4.09229 6.429377 7.957548 6.881528 4.185199 2.037144 ornithine carbomoyltransferase CEA_G0390 CA_C0380 -4.23921 5.06975 5.365591 5.142555 3.394778 2.099342 periplasmic amino acid-binding protein CEA_G0984 CA_C0973 -4.67305 6.390879 8.78089 7.141168 3.889621 2.522783 argininosuccinate synthase CEA_G0985 CA_C0974 -4.03279 6.033303 8.738086 7.66813 4.662246 3.462605 argininosuccinate lyase...”
- “...CEA_G3627 CA_C3620 -2.79225 4.869307 2.77014 4.039679 3.923914 1.658129 amino acid ABC transporter periplasmic-binding protein CEA_G0390 CA_C0380 -4.23921 5.06975 5.365591 5.142555 3.394778 2.099342 periplasmic amino acid-binding protein Energy production and convertion CEA_G1083 CA_C1072 3.271648 3.230747 4.254617 2.59071 2.723209 3.766376 Fe-S oxidoreductase CEA_G2012 CA_C1997 3.052977 3.503142 3.004392 2.8712...”
- “...3.705152 oligopeptide-binding protein, periplasmic component CEA_G0327 CA_C0316 -4.09229 6.429377 7.957548 6.881528 4.185199 2.037144 ornithine carbomoyltransferase CEA_G0390 CA_C0380 -4.23921 5.06975 5.365591 5.142555 3.394778 2.099342 periplasmic amino acid-binding protein CEA_G0984 CA_C0973 -4.67305 6.390879 8.78089 7.141168 3.889621 2.522783 argininosuccinate synthase CEA_G0985 CA_C0974 -4.03279 6.033303 8.738086 7.66813 4.662246 3.462605 argininosuccinate...”
- “...kinase CEA_G3627 CA_C3620 -2.79225 4.869307 2.77014 4.039679 3.923914 1.658129 amino acid ABC transporter periplasmic-binding protein CEA_G0390 CA_C0380 -4.23921 5.06975 5.365591 5.142555 3.394778 2.099342 periplasmic amino acid-binding protein Energy production and convertion CEA_G1083 CA_C1072 3.271648 3.230747 4.254617 2.59071 2.723209 3.766376 Fe-S oxidoreductase CEA_G2012 CA_C1997 3.052977 3.503142 3.004392...”
AO356_00480 ABC transporter for D-Glucosamine, periplasmic substrate-binding component from Pseudomonas fluorescens FW300-N2C3
25% identity, 72% coverage
- mutant phenotype: Specific phenotype on D-Glucosamine Hydrochloride.
SM12261_RS07180 transporter substrate-binding domain-containing protein from Streptococcus mitis NCTC 12261
28% identity, 61% coverage
PPYC1_02025 cysteine ABC transporter substrate-binding protein from Paenibacillus polymyxa
26% identity, 65% coverage
GltI / b0655 glutamate/aspartate ABC transporter periplasmic binding protein (EC 7.4.2.1) from Escherichia coli K-12 substr. MG1655 (see 4 papers)
GltI / P37902 glutamate/aspartate ABC transporter periplasmic binding protein (EC 7.4.2.1) from Escherichia coli (strain K12) (see 3 papers)
GLTI_ECOLI / P37902 Glutamate/aspartate import solute-binding protein from Escherichia coli (strain K12) (see 3 papers)
TC 3.A.1.3.4 / P37902 YBEJ aka GltI aka B0655, component of Glutamate/aspartate porter from Escherichia coli (see 6 papers)
gltI / GB|BAA35307.2 glutamate-aspartate periplasmic-binding protein from Escherichia coli K12 (see 6 papers)
b0655 glutamate and aspartate transporter subunit from Escherichia coli str. K-12 substr. MG1655
NP_415188 glutamate/aspartate ABC transporter periplasmic binding protein from Escherichia coli str. K-12 substr. MG1655
25% identity, 66% coverage
- function: Part of the ABC transporter complex GltIJKL involved in glutamate and aspartate uptake. Binds to both glutamate and aspartate.
subunit: The complex is composed of two ATP-binding proteins (GltL), two transmembrane proteins (GltJ and GltK) and a solute-binding protein (GltI). - substrates: glutamate
tcdb comment: Similar in sequence to 3.A.1.3.19 which is specific for Glu, Asp, Gln and Asn (Singh and Röhm 2008) - 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 - “...enterobactin (enterochelin) transport -3.0 ** cstA f , i b0598 carbon starvation protein 7.6 ybeJ b0655 glutamate/aspartate periplasmic binding transport protein 5.4 artI g b0863 arginine 3rd transport system periplasmic binding protein 4.1 ycaD b0898 putative transport protein 4.4 ompF f , i b0929 outer membrane...”
- Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes
Skippington, Genome biology and evolution 2012 - “...b3576 omrA 22 Variable Incongruent No ompA b0957 micA, rybB 27 Core Incongruent No gltI b0655 gcvB 26 Variable Incongruent Yes dppA b3544 gcvB 25 Variable Incongruent No argT b2310 gcvB 25 Variable Incongruent No sstT b3089 gcvB 27 Core Incongruent Yes oppA b1243 gcvB 27...”
- Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
Kim, Environmental microbiology 2010 - “...1.1 Glutamate/aspartate transport system permease gltJ b0654 6.5 1.1 1.0 Glutamate/aspartate transport system permease gltI b0655 4.9 2.0 1.2 Putative periplasmic binding transport protein putA b1014 2.0 6.1 1.2 Proline dehydrogenase, P5C dehydrogenase putP b1015 4.3 6.1 1.4 Major sodiumproline symporter add b1623 3.5 2.4 1.3...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...b3226 b1759 b4016 b0558 b1503 b1734 b2155 b2361 b2650 b0505 b0655 b0726 b2779 b3732 b0727 b0763 0.01 0.02 0.03 0.03 0.03 0.04 0.04 0.04 0.05 0.05 0.06 0.06 0.06...”
- Construction and optimization of a family of genetically encoded metabolite sensors by semirational protein engineering
Deuschle, Protein science : a publication of the Protein Society 2005 - “...protein accession no. High-sensitivity FRET metabolite sensors NP_415188) without periplasmic leader sequence (as predicted by sequence alignment with closely...”
- Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database.
Pasquali, Electrophoresis 1996 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Structure-based screening of binding affinities via small-angle X-ray scattering.
Chen, IUCrJ 2020 - “...site. The pETMSCIII plasmids for GlnBP (Uniprot entry P0AEQ3, residues 23248) and DEBP (Uniprot entry P37902, residues 28302) were generously provided by Professor Colin Jackson, containing ampicillin resistance and N-terminal His 6 tags. The production and purification of GlnBP and DEBP follow that of previous protocols...”
- Identification of glutamate ABC-Transporter component in Clostridium perfringens as a putative drug target.
Bhatia, Bioinformation 2014 - “...Campylobacter jejuni NCTC 11168) [ 9 13 ] were taken from Uniprot Knowledge Base (ID: P37902, Q88NY2, Q0P9X8). The aligned consensus obtained after multiple sequence alignment of these three sequences was used to search Clostridium homologue using BLASTP analysis in C. perfringens Type-A strains. The domain...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...5.47/52,481 5.40/52,585 5.48/53,050 (5-6) GltI P37902 Glutamate/aspartate periplasmic binding protein 7.82/31,229.49 5.67/15,568 (F) 7.87/36,857 (6-11) GltX...”
WS0279 BINDING COMPONENT OF ABC TRANSPORTER from Wolinella succinogenes DSM 1740
Q7MAG0 BINDING COMPONENT OF ABC TRANSPORTER from Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)
24% identity, 73% coverage
- Enzyme dynamics: Looking beyond a single structure
Agarwal, ChemCatChem 2020 - “...investigators used the approach of ancestral reconstruction to obtain 5 proteins between W. succinogenes AABP (Ws0279) and Pseudomonas aeruginosa CDT (PaCDT), which share the same structural fold (periplasmic binding protein-like II fold) but only show 26% sequence identity. Ancestral reconstruction is based on determining critical branching...”
- The role of oligomerization in the optimization of cyclohexadienyl dehydratase conformational dynamics and catalytic activity.
East, Protein science : a publication of the Protein Society 2022 - “...extant proteins are shown next to the clades in which they are found: Ws0279 (UniProt: Q7MAG0), Pu1068 (UniProt: Q4FLR5), Ea1174 (UniProt: K0ABP5), Ei3690 (UniProt: C5B978), and Mn4388 (UniProt: B8IBK5). (b) A zoomin of the phylogenetic tree shown in (a), highlighting the extant CDT homologs and internal...”
- “...consequence of the GoldenGate assembly method that was used. For oligomeric characterization of Ws0279 (UniProt: Q7MAG0; residues 24258) and Ea1174 (UniProt: K0ABP5; residues 31268), pDOTS7 vectors encoding the proteins were obtained from our previous work. 21 Similarly, AncCDT5(WAG) was characterized by expressing it from a pDOTS7...”
GLNH_BACSU / O34563 ABC transporter glutamine-binding protein GlnH from Bacillus subtilis (strain 168) (see paper)
26% identity, 61% coverage
- function: Part of the ABC transporter complex GlnHMPQ involved in glutamine transport.
subunit: The complex is composed of two ATP-binding proteins (GlnQ), two transmembrane proteins (GlnM and GlnP) and a solute-binding protein (GlnH).
SSA_1567 Polar amino acid ABC transporter, amino acid-binding protein, putative from Streptococcus sanguinis SK36
26% identity, 55% coverage
- Transcriptome, Phenotypic, and Virulence Analysis of Streptococcus sanguinis SK36 Wild Type and Its CcpA-Null Derivative (ΔCcpA)
Bai, Frontiers in cellular and infection microbiology 2019 - “...b , c SSA_0886 a 21,601.58 4,635.68 2.24 0.00000 c242_g1 b , c , m SSA_1567 495.17 111.10 2.08 0.00000 c184_g60 b , c SSA_0687 1,880.60 618.04 1.67 0.00000 c183_g121 SSA_0918 1,791.45 708.64 1.61 0.00000 c307_g1 SSA_2379 375.43 153.25 1.68 0.00000 c185_g39 SSA_2364 2,107.33 1,058.92 1.35...”
- Involvement of signal peptidase I in Streptococcus sanguinis biofilm formation
Aynapudi, Microbiology (Reading, England) 2017 - “...( SSA_0621 ) and a protease-encoding gene ( SSA_2096 ) were significantly up-regulated. Although the SSA_1567 protein is a component of amino acid ABC transporter and a substrate of SPase, the transcriptional up-regulation in SSA_0351 warrants further investigation. Table 1. List of transcripts that are differentially...”
- “...Hypothetical protein No SSA_0819 1.516 6.43E-10 Hypothetical protein No SSA_0618 1.565 6.84E-07 Hypothetical protein No SSA_1567 1.571 8.22E-10 Polar amino acid ABC transporter amino acid-binding protein Yes SSA_0621 1.592 6.52E-14 SOS responce UmuC protein No SSA_0614 1.595 2.34E-09 Transporter No SSA_1569 1.603 9.98E-11 Arginine/histidine ABC transporter...”
SP_0609 amino acid ABC transporter, amino acid-binding protein from Streptococcus pneumoniae TIGR4
28% identity, 57% coverage
- Highly Resistant Serotype 19A Streptococcus pneumoniae of the GPSC1/CC320 Clone from Invasive Infections in Poland Prior to Antipneumococcal Vaccination of Children
Puzia, Infectious diseases and therapy 2023 - “...cbpI SP_0069 Absent 97 cbpJ SP_0378 3/absent 92/1/1/3 SP_0667 SP_0667 5 17/51/26/2/ 1 Lipoproteins glnQ SP_0609 2 96/1 piaA SP_1032 1 97 piuA SP_1872 2 72/24 ppiA SP_0771 1 97 psaA SP_1650 1 97 ppmA SP_0981 1 97 aliA SP_0366 2 96/1 phtA/phtB f SP_1175/SP_1174 4...”
- Corrected and Republished from: "A Novel, Multiple-Antigen Pneumococcal Vaccine Protects against Lethal Streptococcus pneumoniae Challenge"
Chan, Infection and immunity 2022 - “...recognized fewer proteins, with no responses to PspC, LytC, PcsB, PiaA, PiuA, family 1 PspA, SP_0609, SP_2027, Spr0057 (StrH), and StkP. FIG 4 Identification of protein antigens recognized by sera from vaccinated mice. (A) Immunoblots of S. pneumoniae TIGR4, D39, or 19A strain whole-cell lysates probed...”
- Polyamine Synthesis Effects Capsule Expression by Reduction of Precursors in Streptococcus pneumoniae
Ayoola, Frontiers in microbiology 2019 - “...protein synthesis, and carbon utilization pathways. Locus Fold Gene tag Description change Peptidoglycan biosynthesis glnH SP_0609 Amino acid ABC transporter, amino acid-binding protein 1.6 glnP SP_0607 Amino acid ABC transporter, permease protein 1.5 glnQ SP_0610 Amino acid ABC transporter, ATP-binding protein 1.7 Asd SP_1013 Aspartate-semialdehyde dehydrogenase...”
- A Novel, Multiple-Antigen Pneumococcal Vaccine Protects against Lethal Streptococcus pneumoniae Challenge
Chan, Infection and immunity 2019 - “...recognized fewer proteins, with no responses to PspC, LytC, PcsB, PiaA, PiuA, family 1 PspA, SP_0609, SP_2027, Spr0057 (StrH), and StkP. FIG 4 Identification of protein antigens recognized by sera from vaccinated mice. (A) Immunoblots of S. pneumoniae TIGR4, D39, or 19A strain whole-cell lysates probed...”
- Prediction and Validation of Immunogenic Domains of Pneumococcal Proteins Recognized by Human CD4+ T Cells
van, Infection and immunity 2019 - “...35 , 36 SP_1980 TIGR4 Cbf1 308 Cmp-binding factor 1 Unknown 140 6.07 1.9 36 SP_0609 TIGR4 254 Amino acid ABC transporter, amino acid-binding protein Unknown 111 4.71 1.04 36 SP_0613 TIGR4 RnJ 553 Ribonuclease J Cytoplasm 244 4.22 1.31 36 SP_1891 TIGR4 AmiA 659 Oligopeptide...”
- The variome of pneumococcal virulence factors and regulators
Gámez, BMC genomics 2018 - “...18 25 spGH101 sp_0368 / spr0328 5304 1767 348 238 110 18 18 25 glnQ sp_0609 / spr0534 765 254 40 22 18 17 17 25 phtE sp_1004 / spr0908 3120 1039 56 28 28 20 16 25 pbp1B sp_2099 / spr1909 2466 821 81 16...”
SMb21135 putative amino acid uptake ABC transporter periplasmic solute-binding protein precursor from Sinorhizobium meliloti 1021
25% identity, 78% coverage
- Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis
Wheatley, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret) - Temporal expression program of quorum sensing-based transcription regulation in Sinorhizobium meliloti
Charoenpanich, Journal of bacteriology 2013 - “...In contrast, binding sites upstream of cspA3, nesR, SMb21135, SMc01524, SMc04246, and SMc04258 are among the weakest. For the SMc04258 and nesR promoters, a...”
- “...A/T-rich regions appears to weaken the shift, e.g., SMb21543 and SMb21135. Similarly, the presence of As or Ts in the G or C regions may weaken the shift, e.g.,...”
- 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 - “...mannitol, maltitol Sugar amines (3) SMb21135 Galactosamine, glucosamine SMb21221 Glucosamine, galactosamine SMb21151 Galactosamine Sugar phosphates (3)...”
- “...Three systems were induced by sugar amines, ABC-T SMb21135 and ABC-T SMb21221 by both galactosamine and glucosamine, whereas ABC-T SMb21151 was induced weakly...”
HP17_RS11910 transporter substrate-binding domain-containing protein from Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM
25% identity, 62% coverage
- Effect of Temperature on Metronidazole Resistance in Helicobacter pylori
Gong, Frontiers in microbiology 2021 - “...= 0.88) HP17_RS11900 Glucose/galactose MFS transporter 3.067 7.56E25 HP17_RS13150 Nicotinamide riboside transporter PnuC 3.043 6.80E10 HP17_RS11910 Glutamine ABC transporter substrate-binding protein 2.846 3.78E32 HP17_RS16625 ABC transporter permease 2.690 1.28E27 HP17_RS13650 MFS transporter 2.222 2.78E17 HP17_RS15125 Iron chelating transport ATP-binding protein 2.040 1.09E16 HP17_RS14795 MFS transporter 1.935...”
bll7600 ABC transporter amino-acid-binding protein from Bradyrhizobium japonicum USDA 110
25% identity, 75% coverage
- Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence
Yuan, Frontiers in microbiology 2021 - “...two USDA110 protein groups and discovered six same proteins (bll7322, blr1971, blr1091, blr1516, blr0462, and bll7600), which were detected to be expressed in rhizoidal of root nodules during symbiosis in previous studies ( Pessi et al., 2007 ; Delmotte et al., 2010 ; uklina et al.,...”
- “...uklina et al., 2016 blr4473 113-2GL004883 Zhang et al., 2018 bll4736 113-2GL004557 bll5710 113-2GL003508 113-2GL001540 bll7600 Delmotte et al., 2010 Glyma.17G228800 bll7600 113-2GL001540 uklina et al., 2016 Glyma.18G277300 Zhang et al., 2018 Discussion Symbiotic nitrogen fixation system is of great significance in agriculture and ecology, and...”
SPD_0530 amino acid ABC transporter, amino acid-binding protein from Streptococcus pneumoniae D39
spr0534 ABC transporter substrate-binding protein - glutamine transport/Major cell binding factor precursor from Streptococcus pneumoniae R6
27% identity, 60% coverage
- Association of Pneumococcal Protein Antigen Serology With Age and Antigenic Profile of Colonizing Isolates
Azarian, The Journal of infectious diseases 2017 - “...Var-III ATCC 700669 SPN23F16920 151 64.8% Var-I* TIGR4 SPD_0530 161 66.8% Var-II ATCC 700669 SPN23F05490 80 33.2% Var-I Taiwan19F-14 SPT_2213 222 91.7% Var-II*...”
- The variome of pneumococcal virulence factors and regulators
Gámez, BMC genomics 2018 - “...spGH101 sp_0368 / spr0328 5304 1767 348 238 110 18 18 25 glnQ sp_0609 / spr0534 765 254 40 22 18 17 17 25 phtE sp_1004 / spr0908 3120 1039 56 28 28 20 16 25 pbp1B sp_2099 / spr1909 2466 821 81 16 65 17...”
- Penicillin induces alterations in glutamine metabolism in Streptococcus pneumoniae
El, Scientific reports 2017 - “...1.23 1.88 2.18 spr0456 dnaJ molecular chaperone DnaJ 1.23 1.74 1.85 spr0506 bglH 6-phospho-beta-glucosidase 1.24 spr0534 glnH amino acid ABC transporter amino acid-binding protein 1.44 1.65 spr0562 PTS-EII PTS system transporter subunit IIA 1.13 1.23 spr0563 hypothetical protein 1.03 spr0565 bgaA beta-galactosidase 1.11 spr0613 pyrF orotidine...”
- “...(Fig. 2a ) but not in the two other strains. One possible candidate is glnH (spr0534) coding for an ABC transporter that binds glutamine and glutamate 39 . Indeed, glnH remained constant in R6 untreated cells but downregulated in untreated CCRI-8970 and CCRI-21487 (Tables S1 and...”
HMPREF0010_00975 cysteine ABC transporter substrate-binding protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
24% identity, 73% coverage
O25786 Glutamine ABC transporter, periplasmic glutamine-binding protein (GlnH) from Helicobacter pylori (strain ATCC 700392 / 26695)
HP1172 glutamine ABC transporter, periplasmic glutamine-binding protein (glnH) from Helicobacter pylori 26695
25% identity, 62% coverage
- Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
Wei, ACS omega 2022 - “...O25349 HydB 50 O25739 HP_1111 51 P56420 tig 52 O26102 pdxJ 53 O25883 fumC 54 O25786 GlnH 55 O25656 PqqE 56 O25997 HP_1461 57 P56030 rplB 58 P56036 rplJ 59 O25749 HP_1124 60 O25546 HP_0879 61 O25321 HylB 62 O25371 YmxG 63 O24854 ribH 64 P56126...”
- “...O25732 HP_1104 38 O25284 HP_0558 39 O25052 AddB 40 P56008 rpsA 41 O25015 Omp6 42 O25786 GlnH 43 O24925 TlpA 44 P56112 HP_0175 45 O25749 HP_1124 46 O26084 HP_1564 47 P56456 ileS 48 P50610 flgE 49 O25840 Omp28 50 P21762 ahpC 51 P55981 vacA 52 P52093...”
- Identification of an Essential LolD-Like Protein in Helicobacter pylori
McClain, Journal of bacteriology 2023 (secret) - Identification of anti-Helicobacter pylori antibody signatures in gastric intestinal metaplasia
Song, Journal of gastroenterology 2023 - “...0.054 0.57 HP0701 GyrA DNA gyrase subunit A 20 10 16 10 1.71 0.207 0.51 HP1172 GlnH Glutamine ABC transporter substrate-binding protein 26 10 26 18 1.60 0.172 0.52 HP1453 HomD Membrane protein 20 10 16 12 1.40 0.415 0.55 HP0373 Uncharacterized protein 38 10 22...”
- Delineation of the pH-Responsive Regulon Controlled by the Helicobacter pylori ArsRS Two-Component System
Loh, Infection and immunity 2021 (secret) - Human gastric mucins differently regulate Helicobacter pylori proliferation, gene expression and interactions with host cells
Skoog, PloS one 2012 - “...9925 9914 CCUG17874 1007 935* CCUG17875/Le b 1106** 855*** HP201 43627*** nd HP364 8711 nd HP1172 1566 nd Effect of mucins (50 g/mL) on proliferation of different H. pylori strains expressed as percentage of proliferation without mucins. (***p0.001, **p<0.01, *p<0.05, Independent Student's t-test, nd=not determined). Gene...”
- “...provided by Prof. Susann Teneberg, University of Gothenburg, Sweden). The clinically isolated strains HP201 and HP1172, but not HP364, bind mucins positive for Le b and sialyl-Le x [28] (kindly provided by Prof. Lars Engstrand, Swedish Institute for Infectious Disease Control, Sweden). H. pylori binding to...”
- Comparative genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans
Schott, BMC genomics 2011 - “...+ - - HP1461 HBZC1_05960 Putative amino-acid transporter periplasmic solute-binding protein Periplasmic + - + HP1172 HBZC1_06690 Sel1 domain-containing protein repeat-containing protein Extracellular - - - (-) HBZC1_07110 Flagellar hook-associated protein FlgL Extracellular - - - HP0295 HBZC1_07220 Hypothetical protein Extracellular + - + (-) HBZC1_07230...”
- Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants
Thiele, Journal of bacteriology 2005 - “...(GMPS2) HP1169 to HP1172 (GLNabc) .........................................................................................HP0512 (GLNS) HP1174 (GALt2, GLCt2)...”
- Proteomic analysis of the sarcosine-insoluble outer membrane fraction of Helicobacter pylori strain 26695
Baik, Journal of bacteriology 2004 - “...19.0 48 HP1561 37,000 37,552 9.4 9.2 4 16.0 HP1172 31,000 31,222 6.2 6.9 4 16.0 HP1113 HP0127 HP0127 HP0940 31,000 31,000 31,000 30,000 31,896 31,890 31,890...”
- pH-regulated gene expression of the gastric pathogen Helicobacter pylori
Merrell, Infection and immunity 2003 - “...JHP0403 JHP0263 HP0550 HP1203 HP0123 HP1019 HP1171 HP1172 JHP0497 JHP1126 JHP0113 JHP0405 JHP1098 JHP1099 JHP0110 JHP1247 JHP1113 JHP0349 JHP0205 JHP1100...”
- More
MSMEG_0787 Bacterial extracellular solute-binding protein, family protein 3 from Mycobacterium smegmatis str. MC2 155
26% identity, 63% coverage
H7F35_04365 ABC transporter substrate-binding protein from Variovorax sp. PAMC26660
26% identity, 73% coverage
- RNA thermometers are widespread upstream of ABC transporter genes in bacteria
Tong, The Journal of biological chemistry 2024 - “...strain NKZ-259 chromosome D3X13_13420 CP032266.1 Lysinibacillus sp. B2A1 chromosome C3943_02940 CP027224.1 Variovorax sp. PAMC26660 chromosome H7F35_04365 CP060295.1 Figure2 RNA thermometer candidates upstream of ABC transporter genes. A , gene information of the five RNA thermometer candidates tested. B , heat induction factor of all five candidates...”
SGO_0982 amino acid transport protein from Streptococcus gordonii str. Challis substr. CH1
25% identity, 71% coverage
- Streptococcus gordonii Type I Lipoteichoic Acid Contributes to Surface Protein Biogenesis
Lima, mSphere 2019 - “...ButA SGO_1096 Acetoin dehydrogenase SGO_1862 Alkaline shock protein SGO_0578 Amino acid ABC transporter, permease protein SGO_0982 Amino acid ABC transporter, amino acid-binding protein SGO_0104 Arabinogalactan oligomer/maltooligosaccharide transport system substrate-binding protein ArcA SGO_1593 Arginine deiminase SGO_1082 Basic membrane protein A SGO_1630 Branched-chain amino acid transport system substrate-binding...”
- Transcriptome analysis of Streptococcus gordonii Challis DL1 indicates a role for the biofilm-associated fruRBA operon in response to Candida albicans
Jesionowski, Molecular oral microbiology 2016 - “...SGO_1593, SGO_0384), central intermediary metabolism (SGO_0278, SGO_1720, SGO_1757), and transport and binding proteins (SGO_0383, SGO_0630, SGO_0982, SGO_0985, SGO_1216). The shifts in expression generally relate to genes involved in amino acid metabolism and transport. Accordingly, representative genes arcA and arcB , involved in arginine catabolism, and glmS...”
- “...binding proteins/Other 1.7 0.012 SGO_0278 peptide methionine sulfoxide reductase msrA Central intermediary metabolism/Other 1.7 0.01 SGO_0982 amino acid transport protein Transport and binding proteins/Amino acids, peptides and amines 1.6 0.03 SGO_1283 pyridine nucleotide-disulfide oxidoreductase Energy metabolism/Electron transport 1.6 0.043 a Locus tag in S. gordonii genome...”
- Mass Spectrometric Analysis of Whole Secretome and Amylase-precipitated Secretome Proteins from Streptococcus gordonii.
Maddi, Journal of proteomics & bioinformatics 2014 - “...6 14.9 Putative uncharacterized protein SGO_0332 Unknown 53 5 15.6 Amino acid ABC transporter * SGO_0982 Amino acid-binding protein domain 31 5 18.7 Foldase protein prsA * SGO_1572 PPIase domain 34 4 18.8 Penicillin-binding protein 2 pbp2 * SGO_0575 Penicillin binding protein transpeptidase domain 83 4...”
AFA2_00700 ABC transporter substrate-binding protein from Alcaligenes faecalis subsp. faecalis NBRC 13111
27% identity, 74% coverage
- Gene expression analysis of Alcaligenes faecalis during induction of heterotrophic nitrification
Tsujino, Scientific reports 2021 - “...assembly protein SufB 2.35 0.02274 1460.5 287.5 AFA2_00638 Transcriptional regulator SufR 2.36 0.02255 1811.0 354.2 AFA2_00700 Polar amino acid transport system substrate-binding protein 2.28 0.02937 282.6 1374.7 AFA2_00794 yggS family pyridoxal phosphate enzyme 3.30 0.00044 2028.2 207.4 AFA2_00795 Cytoplasmic protein 3.61 0.00012 2262.4 186.1 AFA2_01038 2-Hydroxychromene-2-carboxylate...”
LJ0752 glutamine ABC transporter solute-binding component from Lactobacillus johnsonii NCC 533
29% identity, 53% coverage
HPG27_1116 glutamine ABC transporter, periplasmic glutamine-binding protein from Helicobacter pylori G27
24% identity, 62% coverage
pRL120071 putative substrate-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
23% identity, 85% coverage
- Rhizobium leguminosarum Glutathione Peroxidase Is Essential for Oxidative Stress Resistance and Efficient Nodulation
Hu, Frontiers in microbiology 2021 - “...transporter 32.96 0.82 0.0005 pRL120351 Periplasmic Substrate binding component of ABC transporter 49.96 0.82 0.0001 pRL120071 Periplasmic Substrate-binding component of ABC transporter 30.48 0.78 0.0282 RL4417 Periplasmic Solute-binding component of ABC transporter 70.67 0.76 0.0061 RL1499 ropA2 Outer membrane Porin 36.71 0.74 0.0008 RL2775 ropA1 OuterMembrane...”
- “...down-regulated genes in nodules induced by the gpxA mutant, eight genes RL4665 , pRL120351 , pRL120071 , RL4417 , RL1499 , RL2775 , RL3066 , and RL2554 code for membrane transport proteins, of which four were ABC-type transporters. Four genes RL4392 , pRL90175 , RL0644 ,...”
- Antioxidant ability of glutaredoxins and their role in symbiotic nitrogen fixation in Rhizobium leguminosarum bv. viciae 3841
Zou, Applied and environmental microbiology 2021 (secret) - Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis
Wheatley, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret)
BPSS0153 glutamate/aspartate periplasmic binding protein precursor from Burkholderia pseudomallei K96243
24% identity, 69% coverage
B6D87_RS09955 ABC transporter substrate-binding protein from Pseudomonas fragi
24% identity, 70% coverage
jhp1099 AMINO ACID ABC TRANSPORTER, BINDING PROTEIN PRECURSOR from Helicobacter pylori J99
24% identity, 62% coverage
Pf6N2E2_2053 ABC transporter for D-Glucosamine, periplasmic substrate-binding component from Pseudomonas fluorescens FW300-N2E2
24% identity, 66% coverage
- mutant phenotype: Specific phenotype on D-Glucosamine Hydrochloride.
AO353_16290 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, periplasmic substrate-binding component from Pseudomonas fluorescens FW300-N2E3
26% identity, 69% coverage
- mutant phenotype: # Specifically important in carbon source L-Aspartic Acid; carbon source L-Asparagine; pH ; carbon source L-Glutamic acid monopotassium salt monohydrate; carbon source L-Glutamine
RSUY_41100, RSUY_RS20020 ABC transporter substrate-binding protein from Ralstonia solanacearum
26% identity, 74% coverage
- Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii
Puigvert, Frontiers in plant science 2017 - “...RSUY_01050 RSc3386 3.50 metal ABC transporter substrate-binding protein RSUY_RS17605 RSUY_36050 RSp0429 3.24 MFS transporter RSUY_RS20020 RSUY_41100 RSp0931 2.92 ABC transporter RSUY_RS19045 RSUY_39070 RSp0706 1.77 metal-dependent hydrolase RSUY_RS18205 RSUY_37320 RSp0481 2.03 ABC transporter substrate-binding protein RSUY_RS18195 RSUY_37300 RSp0479 2.09 amino acid ABC transporter ATPase RSUY_RS21220 RSUY_43600 RSp1181...”
- “...RSUY_RS00490 RSUY_01050 RSc3386 3.50 metal ABC transporter substrate-binding protein RSUY_RS17605 RSUY_36050 RSp0429 3.24 MFS transporter RSUY_RS20020 RSUY_41100 RSp0931 2.92 ABC transporter RSUY_RS19045 RSUY_39070 RSp0706 1.77 metal-dependent hydrolase RSUY_RS18205 RSUY_37320 RSp0481 2.03 ABC transporter substrate-binding protein RSUY_RS18195 RSUY_37300 RSp0479 2.09 amino acid ABC transporter ATPase RSUY_RS21220 RSUY_43600...”
9e2bC / A0A101DJ27 Structure of a solute binding protein from desulfonauticus sp. Bound to l-tryptophan
24% identity, 70% coverage
- Ligand: tryptophan (9e2bC)
MAV_4750 Bacterial extracellular solute-binding protein, family protein 3 from Mycobacterium avium 104
26% identity, 53% coverage
bglu_1g05590 Glutamate/aspartate ABC transporter, periplasmic glutamate/aspartate-binding protein from Burkholderia glumae BGR1
25% identity, 71% coverage
- Glutamate uptake is important for osmoregulation and survival in the rice pathogen Burkholderia glumae
Kang, PloS one 2018 - “...the glutamate uptake mutant We mutagenized a cosmid clone pGLT1 carrying the gltI (locus ID: bglu_1g05590) gene encoding a periplasmic substrate binding protein of the glutamate transport system using EZ-Tn 5 TM <KAN-2> (Epicentre, Madison, WI, USA), as described in the manufacturers protocols. Genetic information for...”
- Critical role of quorum sensing-dependent glutamate metabolism in homeostatic osmolality and outer membrane vesiculation in Burkholderia glumae
Kang, Scientific reports 2017 - “...indicated that glutamate uptake is under the control of QS. Expression of gltI (locus ID: bglu_1g05590), which encodes a glutamate transporter, was significantly higher in the QS mutant than in the wild type ( Fig. 1b ), suggesting that glutamate uptake is negatively controlled by QS...”
- “...To obtain B. glumae gltI mutants, we used a cosmid clone (pGLT1) containing the gltI (bglu_1g05590) gene and subjected it to mutagenesis using EZ-Tn 5 TM <KAN-2> (Epicentre, Madison, WI, USA), as described in the manufacturers protocols. A single Tn 5 insertion in the gltI gene...”
AH67_06815 cysteine ABC transporter substrate-binding protein from Bifidobacterium pseudolongum PV8-2
26% identity, 66% coverage
TC 2.A.56.3.1 / P74223 GtrC aka GLNH aka SLL1104, component of Tripartite glutamate:Na+ symporter (see paper)
sll1104 glutamine-binding protein from Synechocystis sp. PCC 6803
24% identity, 76% coverage
- substrates: Na+, glutamate
- Site-2 Protease Slr1821 Regulates Carbon/Nitrogen Homeostasis during Ammonium Stress Acclimation in Cyanobacterium Synechocystis sp. PCC 6803
Lin, International journal of molecular sciences 2023 - “...( slr1596 ), Na + /H + antiporter ( sll0556 ) and ABC transporters ( sll1104, slr1113 ). Knockout of Slr1821 either eliminated the ammonium-induced activation or exaggerated the activation to a much higher level, thus rendering either much lower or much higher level of expression...”
- Functional Dependence between Septal Protein SepJ from Anabaena sp. Strain PCC 7120 and an Amino Acid ABC-Type Uptake Transporter
Escudero, Journal of bacteriology 2015 - “...slr0559 sll0146 slr0949 slr1881 slr1735 slr1270 sll1145 sll1102 sll1103 sll1104 1893 1861 1894 2177 0815 0249 1761 2238 0187 1257 1276 e90 e99 e95 e93 e74 e63...”
- Identification of genes encoding amino acid permeases by inactivation of selected ORFs from the Synechocystis genomic sequence
Quintero, Genome research 2001 - “...TRAP transporter (Forward et al. 1997), whereas ORF sll1104 would encode a polypeptide homologous to glutamine (26.7% identity to E. coli GlnH), glutamate...”
- “...proteins of ABC-type transporters. Because sll1102, sll1103, and sll1104 are tightly clustered in the Synechocystis genome, it has been suggested that they...”
- TRAP transporters: a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse gram-negative bacteria
Forward, Journal of bacteriology 1997 - “...Synechocystis sp. strain PCC6803 cyanobase (www)i 32 Sll1102 Sll1103 Sll1104 Sll1314 24.7 29.7 204 452 7.7 18.0 25.0 368 13.5 (Q) (M) (glnH) (P) H. influenzae...”
TEL01S_RS02380 transporter substrate-binding domain-containing protein from Pseudothermotoga elfii DSM 9442 = NBRC 107921
25% identity, 71% coverage
Psyr_3908 extracellular solute-binding protein, family 3 from Pseudomonas syringae pv. syringae B728a
25% identity, 69% coverage
M9QLL2 Peb1A (Fragment) from Campylobacter jejuni
30% identity, 38% coverage
6h2tA / P96257 Glnh bound to glu, mycobacterium tuberculosis (see paper)
31% identity, 40% coverage
- Ligand: glutamic acid (6h2tA)
MAB_4223 Probable glutamine-binding protein GlnH from Mycobacterium abscessus ATCC 19977
26% identity, 58% coverage
- Virulence-Associated Secretion in Mycobacterium abscessus
Bar-Oz, Frontiers in immunology 2022 - “...MAB_4244 lies between the gene encoding the probable glutamine binding protein H ( glnH , MAB_4223 ) and the gene for acetate kinase A ( ackA , MAB_4225c ), exactly like it does in Mtb ( glnH Rv0411c, ackA Rv0409 ). The close downstream proximity of...”
Mb0419c PROBABLE GLUTAMINE-BINDING LIPOPROTEIN GLNH (GLNBP) from Mycobacterium bovis AF2122/97
P96257 Probable glutamine-binding lipoprotein GlnH (GLNBP) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Rv0411c PROBABLE GLUTAMINE-BINDING LIPOPROTEIN GLNH (GLNBP) from Mycobacterium tuberculosis H37Rv
31% identity, 40% coverage
- Towards Reverse Vaccinology for Bovine TB: High Throughput Expression of Full Length Recombinant Mycobacterium bovis Proteins
Paliwal, Frontiers in molecular biosciences 2022 - “...Insect +++ +++ Mb0485 Iron-regulated heparin binding hemagglutinin hbha E. coli & Insect +++ +++ Mb0419c Probable glutamine-binding lipoprotein glnh (glnbp) E. coli & Insect ++ + Mb3840 Exported repetitive protein precursor PirG E. coli & Insect +++ + Mb0348 Isoniazid inductible gene protein iniB E....”
- The role of solute binding proteins in signal transduction
Matilla, Computational and structural biotechnology journal 2021 - “...[140] Serine/threonine kinase GlnX PknG d P96258 P9WI73 Mycobacterium tuberculosis Actinobacteria 4HB_MCP_1 (PF12729) GlnH/SP a P96257 (35) SBP_bac_3 (PF00497) Asp (5), Glu (15) 6H1U 6H20 6H2T [22] , [23] , [24] a Genes associated with: T: transporter genes; SP: Signaling protein genes. b Size including signal...”
- A potent subset of Mycobacterium tuberculosis glycoproteins as relevant candidates for vaccine and therapeutic target
Yari, Scientific reports 2023 - “...cell processes Rv0583 Lipoprotein LpqN 228 27 (11.8) 2 (0.11) Cell wall and cell processes Rv0411c LipoproteinG GlnH 328 13 (3.96) 2 (0.61) Cell wall and cell processes Rv1418 Lipoprotein LprH 228 15 (96.58) 3 (1.32) Cell wall and cell processes Rv1270c Lipoprotein LprA 244 25...”
- “...9 , 31 . These include proteins like the lipoprotein LprA (Rv1270), LprH (Rv1418), GlnH (Rv0411c), LpqN (Rv05830, Mce lipoprotein Lprk (Rv0173), Mce1A (Rv0169), Mce2E (Rv0593), Mce4A (Rv3499c), Mce1B (Rv0170) and Mce1F (Rv0174) (Table 1 ). Lipoprotein LprA M. tuberculosis is a glycosylated lipoprotein with strong...”
- Virulence-Associated Secretion in Mycobacterium abscessus
Bar-Oz, Frontiers in immunology 2022 - “...kinase A ( ackA , MAB_4225c ), exactly like it does in Mtb ( glnH Rv0411c, ackA Rv0409 ). The close downstream proximity of pknG to glnH is of importance, since these two genes are suggested to be co-expressed in a conserved operon in Actinomycetes (...”
- Single START-domain protein Mtsp17 is involved in transcriptional regulation in Mycobacterium smegmatis
Zhou, PloS one 2021 - “...Rv0164 Yes Mtsp17 Unknown MSMEG_3763 Rv1686c No ABC transporter Cell wall and cell processes MSMEG_0787 Rv0411c No Extracellular solute-binding protein Cell wall and cell processes MSMEG_0788 Rv0412c No Hypothetical protein Cell wall and cell processes MSMEG_2850 Rv3178 No Cell entry related family protein Unknown MSMEG_1769 Rv3288c...”
- ATP-binding cassette (ABC) import systems of Mycobacterium tuberculosis: target for drug and vaccine development
Soni, Emerging microbes & infections 2020 - “...glycine betaine [ 32 ] Glutamine importer (Rv2563, GlnQ/Rv2564, Rv0072, Rv0073, and GlnH/Rv0411c) SBP: GlnH (Rv0411c) TMD: Rv2563 and Rv0072 NBD: GlnQ (Rv2564) and Rv0073 Experimentally not characterized. Sugar importers Glycerophosphocholine importer (UgpABCE /Rv2832c-Rv2835c) SBP: UgpB (Rv2833c) TMD: UgpA (Rv2835c) and UgpE (Rv2834c) NBD: UgpC (Rv2832c)...”
- Physicochemical properties and Mycobacterium tuberculosis transporters: keys to efficacious antitubercular drugs?
Fullam, RSC medicinal chemistry 2020 - “...date only one crystal structure of an amino acid transporter has been determined. 95 GlnH (Rv0411c) is the solute binding domain of an ABC-transporter and appears to have dual functionality in which is acts as an ABC-transporter and a signal sensor. GlnH 95 recognises aspartate, glutamate...”
- The ATP-Binding Cassette (ABC) Transport Systems in Mycobacterium tuberculosis: Structure, Function, and Possible Targets for Therapeutics
Cassio, Biology 2020 - “...development [ 21 ] Rv0072/Rv0073 Lipopolysaccharide export [ECD/TM/NBDr] (2x) Type VII [ 9 ] GlnH (Rv0411c) SBP glutamine/glutamate/aspartate [ 22 ] ProX/ProW/ProZ/ProV (Rv3759/5756/58) SBP-[TM/NBDr] (2x) Glycine/betaine/L-proline/carnitine/ choline [ 23 ] Anions SubI/CysT/CysW/CysA1 (Rv2400/99/98/97) SBP-TM 1 -TM 2 -[NBD] (2x) Sulfate Members of sulfate transporter and sulfate...”
- “...- [ 17 ] Rv3666c (DppA) SBP type II, peptides 6E4D SSVT [ 19 ] Rv0411c (GlnH) SBP type II, amino acids 6H20 6HIU 6H2T Asn Asp Glu [ 22 ] Rv2400c (SubI) SBP type II, anion 6DDN SO 4 - Rv0928 (PstS3) SBP type II,...”
- Characterization of membrane vesicles released by Mycobacterium avium in response to environment mimicking the macrophage phagosome
Chiplunkar, Future microbiology 2019 - “...Rv2320c A0A0H3A0X6 MAV_4750 GluB bacterial extracellular solute-binding protein Cell wall and cell processes 36 2 Rv0411c A0A0H3A326 MAV_4059 Monoxygenase Intermediary metabolism and respiration 95 2 A0A0H3A3W0 MAV_0467 dppD ABC transporter, ATP-binding protein Cell wall and cell processes 60 3 Rv3663c A0QFE1 MAV_2434 SsuB aliphatic sulfonates import...”
- Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig
Kato-Maeda, Clinical and vaccine immunology : CVI 2012 - “...SIFT value Mutations in sublineage RD207 Rv0327c Rv0380c Rv0411c Rv0622 Rv0859 Rv0892 Rv0944 Rv0989c Rv1073 Rv1523 Rv1557 Rv1894c Rv1934c Rv2579 Rv2688c Rv2821c...”
- More
RSp0931 ABC transporter substrate-binding protein from Ralstonia pseudosolanacearum GMI1000
25% identity, 74% coverage
- Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii
Puigvert, Frontiers in plant science 2017 - “...RSc3386 3.50 metal ABC transporter substrate-binding protein RSUY_RS17605 RSUY_36050 RSp0429 3.24 MFS transporter RSUY_RS20020 RSUY_41100 RSp0931 2.92 ABC transporter RSUY_RS19045 RSUY_39070 RSp0706 1.77 metal-dependent hydrolase RSUY_RS18205 RSUY_37320 RSp0481 2.03 ABC transporter substrate-binding protein RSUY_RS18195 RSUY_37300 RSp0479 2.09 amino acid ABC transporter ATPase RSUY_RS21220 RSUY_43600 RSp1181 2.11...”
B2J7D8 Extracellular solute-binding protein, family 3 from Nostoc punctiforme (strain ATCC 29133 / PCC 73102)
30% identity, 18% coverage
PA2204 probable binding protein component of ABC transporter from Pseudomonas aeruginosa PAO1
Q9I1R3 Probable binding protein component of ABC transporter from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
24% identity, 74% coverage
- 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 - “...3.04.E+07 Q9HU31 ABC transporter periplasmic binding protein (PA5153) 63.569 1.26.E+06 1.45.E+07 Q9I1R3 ABC transport protein (PA2204) 62.183 1.02.E+06 5.00.E+06 Q9I6J1 Putrescine-binding protein (SpuD) 61.373 3.67.E+06 5.48.E+06 Q9I5W4 Metalloprotease (ImpA) 61.116 1.17.E+07 9.64.E+06 Q9HW11 UPF0234 protein (PA4395) 59.911 3.33.E+07 1.58.E+06 Q9I457 Glutathione peroxidase (PA1287) 59.694 1.08.E+08 1.14.E+08...”
- Treatment of Pseudomonas aeruginosa infectious biofilms: Challenges and strategies
Yin, Frontiers in microbiology 2022 - “...twitching motility, and inhibiting the expression of various genes involved in biofilm formation, such as PA2204 ( de la Fuente-Nunez et al., 2012 ). Recent studies have found that the anti-biofilm peptide MC1 can inhibit biofilm formation by down-regulating the relative expression levels of pelA ,...”
- Searching for Biological Function of the Mysterious PA2504 Protein from Pseudomonas aeruginosa
Drabinska, International journal of molecular sciences 2021 - “...PA2594 and PA5103 and with the import of cysteine and methionine PA2202 , PA2203 , PA2204 , PA3931 , and PA4195 . The second group related to the conversion of sulphate to sulphite and further to sulphide: cysD, cysN , cysH , and cysI . Furthermore,...”
- “...1.12 Epoxide hydrolase PA2202 PA2202 1.79 Amino acid permease PA2203 PA2203 2.32 Amino acid permease PA2204 PA2204 3.02 ABC transporter PA2328 PA2328 0.86 Hypothetical protein/ nitrate transport protein NrtA precursor PA2329 PA2329 0.72 ABC transporter ATP-binding protein/ nitrate/sulphonate/bicarbonate ABC transporter ATPase PA2330 PA2330 0.74 Hypothetical protein/...”
- Differential transcription profiling of the phage LUZ19 infection process in different growth media
Brandão, RNA biology 2021 (secret) - The MarR-Type Regulator PA3458 Is Involved in Osmoadaptation Control in Pseudomonas aeruginosa
Kotecka, International journal of molecular sciences 2021 - “...in PA3458 and WT P. aeruginosa cells. Analysis of PA3459 , PA3461 , PA5170 , PA2204 , and PA4352 transcripts level in PA3458- deficient cells showed increased expression relatively to WT cells, while the two other tested genes PA1270 and PA2252 exhibited the decreased expression (...”
- Antimicrobial Peptides Derived From Insects Offer a Novel Therapeutic Option to Combat Biofilm: A Review
Sahoo, Frontiers in microbiology 2021 - “...Fuente-Nez et al. (2012) have shown that AMP 1037 stimulates cell proliferation of P. aeruginosa PA2204 but does not affect the motility and biofilm formation ( De La Fuente-Nez et al., 2012 ). Antimicrobial peptides NA-CATH: ATRA1-ATRA1, a synthetic cathelicidin, inhibited S. aureus biofilm form, and...”
- Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways
Gabrielaite, mBio 2020 - “...P40M5-DK43). The 34 genes were orthologs of genes PA2161 to PA2181 and genes PA2189 to PA2204 in the PAO1 reference genome. We noted that three of the lineages (P05F4-DK13, P55M4-DK18, and P40M5-DK43) did not have genes PA2182 to PA2188 (genes flanked by PA2161 to PA2181 and...”
- “...to PA2188 were variable and congregated with genes PA2161 to PA2181 and genes PA2189 to PA2204 in the fourth lineage (P21F4-DK06), so we concluded that the 34 genes were likely lost/acquired together rather than in separate two events ( Fig.4 shows the genetic region of the...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...2.9 + Hydrogen cyanide synthase HcnB PA2195 hcnC 2.4 3 + Hydrogen cyanide synthase HcnC PA2204 1.6 2.1 Probable binding protein component of ABC transporter PA2274 2.2 + Hypothetical protein PA2300 chiC 2.6 4.5 + Chitinase PA2302 ambE 2.1 + AmbE PA2303 ambD 2.1 + AmbD...”
- More
- 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 - 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 - “...protein (PA3302) 66.561 3.27.E+07 3.04.E+07 Q9HU31 ABC transporter periplasmic binding protein (PA5153) 63.569 1.26.E+06 1.45.E+07 Q9I1R3 ABC transport protein (PA2204) 62.183 1.02.E+06 5.00.E+06 Q9I6J1 Putrescine-binding protein (SpuD) 61.373 3.67.E+06 5.48.E+06 Q9I5W4 Metalloprotease (ImpA) 61.116 1.17.E+07 9.64.E+06 Q9HW11 UPF0234 protein (PA4395) 59.911 3.33.E+07 1.58.E+06 Q9I457 Glutathione peroxidase...”
GASBP_PSEAE / Q9I402 L-glutamate/L-aspartate-binding protein from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
TC 3.A.1.3.22 / Q9I402 Probable binding protein component of ABC transporter, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida from Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
PA1342 probable binding protein component of ABC transporter from Pseudomonas aeruginosa PAO1
25% identity, 71% coverage
- function: Binds L-glutamate and L-aspartate.
- substrates: Glutamic Acid, Glutamine, N-acetylglutamic acid
- 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 - “...2.06.E+08 0.00.E+00 P21175 Branched-chain amino acid transport protein (BraC) 176.33 3.10.E+07 1.45.E+08 Q9I402 L-glutamate/L-aspartate-binding protein (PA1342) 161.24 3.78.E+07 6.34.E+07 Q9HXG8 Uncharacterized protein (PA3836) 156.33 8.59.E+07 1.34.E+08 Q9I3D1 Dihydrolipoyl dehydrogenase (IpdG) 155.15 8.33.E+06 2.51.E+07 Q9I047 Transaldolase (Tal) 154.3 4.43.E+07 7.20.E+07 Q9HV43 Chaperone protein (DnaK) 151.49 1.99.E+07 1.07.E+07...”
- “...Aminopeptidase (Lap) 99.454 7.51.E+07 0.00.E+00 Q9I3D1 Dihydrolipoyl dehydrogenase (IpdG) 98.982 1.36.E+07 2.53.E+07 Q9I402 L-Glutamate/L-aspartate-binding protein (PA1342) 98.45 1.49.E+07 2.45.E+07 P21175 Branched-chain amino acid transport protein (BraC) 98.406 2.36.E+06 3.18.E+07 Q9HVA8 Ferric iron-binding protein (HitA) 96.294 2.87.E+06 1.21.E+07 P08308 Ornithine carbamoyltransferase (ArcB) 94.575 1.95.E+06 1.35.E+07 Q9HXL0 Uncharacterized...”
- Utilization of L-glutamate as a preferred or sole nutrient in Pseudomonas aeruginosa PAO1 depends on genes encoding for the enhancer-binding protein AauR, the sigma factor RpoN and the transporter complex AatJQMP
Lundgren, BMC microbiology 2021 - “...on L-glutamate and L-glutamine as sole carbon sources The aauR ( PA1335 ), aatJ ( PA1342 ) and aatQM ( PA1341 PA1340 ) genes were individually deleted from the genome of P. aeruginosa PAO1. The resulting markerless aauR , aatJ , and aatQM mutants, in addition...”
- The role of solute binding proteins in signal transduction
Matilla, Computational and structural biotechnology journal 2021 - “...SBP family/Pfam Species SBP ligands Experimental conditions Fold change Ref. Amino acids and peptides AatJ PA1342 /T a SBP_bac_3/PF00497 Pseudomonas aeruginosa L-Glu 5 mM L-Glu vs 5 mM L-Arg 2.6 b [142] 5 mM D-Glu vs 5 mM L-Arg 2.2 b AliB spd_1357 /T a SBP_bac_5/PF00496...”
- Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Rubio-Gómez, Frontiers in microbiology 2020 - “...most prominent changes were observed for genes involved in: (1) Organic acid transport such as PA1342 ( aatj ), which encodes a C4-dicarboxylate transport protein and PA1183 ( dctA ), (2) Central metabolism, like a PA0795 ( prpC ), which regulates a citrate synthase, PA2008 (...”
- “...lytic transglycolase 0.7 0.010 0.6 0.008 PA1183 dctA C4-dicarboxylate transport protein 1.5 0.000 1.2 0.000 PA1342 aatj Probable binding protein component of ABC transporter 1.0 0.000 1.1 0.000 PA1585 sucA 2-oxoglutarate dehydrogenase 0.5 0.008 0.6 0.001 PA1588 sucC Succinyl-CoA synthetase 0.7 0.000 0.6 0.002 PA1592 nd...”
- Exoproteomics for Better Understanding Pseudomonas aeruginosa Virulence
Sauvage, Toxins 2020 - “...Reaction Monitoring (SRM) was undertaken for ten proteins. Five proteins (LasB, CbpD, PasP, PA4495, and PA1342) were more abundant in the AES-1R cultured in ASMDM in contrast to PAO1, suggesting that abundant virulence factors are important for lung infection. Moreover, 2-DE and LC-MS/MS can be applied...”
- Global reprogramming of virulence and antibiotic resistance in Pseudomonas aeruginosa by a single nucleotide polymorphism in elongation factor, fusA1
Maunders, The Journal of biological chemistry 2020 (secret) - Unraveling Pseudomonas aeruginosa and Candida albicans Communication in Coinfection Scenarios: Insights Through Network Analysis
Grainha, Frontiers in cellular and infection microbiology 2020 - “...48 YNBNP MALDI-TOF MS/MS PAO1 SC5314 ( Purschke et al., 2012 ) Upregulation 3, 6 PA1342 Downregulation Cell Biofilm 1.5, 4.5, 6, 24, 48 YNBNP MALDI-TOF MS/MS PAO1 SC5314 ( Purschke et al., 2012 ) Upregulation 3 PA2453 Downregulation Cell Biofilm 24, 48 YNBNP MALDI-TOF MS/MS...”
- Determination of Ligand Profiles for Pseudomonas aeruginosa Solute Binding Proteins
Fernández, International journal of molecular sciences 2019 - “...l -homoserine also bound with high affinity ( Table 1 ). Different studies suggest that PA1342 (AatJ) belongs to a SBP subfamily that is specific for glutamate and aspartate [ 36 , 59 ]. Previous equilibrium dialysis and competition assays indicated that the protein binds l...”
- “...binding was observed for other amino acids, including l -Gln and l -Asn, indicating that PA1342 is specific for l -Glu and l -Asp ( Table 1 ). Although PA2204 is predicted to bind amino acids, thermal shift assays of exhaustively dialyzed protein using the above...”
- More
- 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 - “...protein (FlgK) 222.17 2.06.E+08 0.00.E+00 P21175 Branched-chain amino acid transport protein (BraC) 176.33 3.10.E+07 1.45.E+08 Q9I402 L-glutamate/L-aspartate-binding protein (PA1342) 161.24 3.78.E+07 6.34.E+07 Q9HXG8 Uncharacterized protein (PA3836) 156.33 8.59.E+07 1.34.E+08 Q9I3D1 Dihydrolipoyl dehydrogenase (IpdG) 155.15 8.33.E+06 2.51.E+07 Q9I047 Transaldolase (Tal) 154.3 4.43.E+07 7.20.E+07 Q9HV43 Chaperone protein (DnaK)...”
- “...4.72.E+07 3.21.E+07 Q9HZQ8 Aminopeptidase (Lap) 99.454 7.51.E+07 0.00.E+00 Q9I3D1 Dihydrolipoyl dehydrogenase (IpdG) 98.982 1.36.E+07 2.53.E+07 Q9I402 L-Glutamate/L-aspartate-binding protein (PA1342) 98.45 1.49.E+07 2.45.E+07 P21175 Branched-chain amino acid transport protein (BraC) 98.406 2.36.E+06 3.18.E+07 Q9HVA8 Ferric iron-binding protein (HitA) 96.294 2.87.E+06 1.21.E+07 P08308 Ornithine carbamoyltransferase (ArcB) 94.575 1.95.E+06...”
3k4uE / Q7MAG0 Crystal structure of putative binding component of abc transporter from wolinella succinogenes dsm 1740 complexed with lysine
25% identity, 65% coverage
BB0329 probable extracellular solute-binding protein from Bordetella bronchiseptica RB50
24% identity, 63% coverage
PA14_46910 putative binding protein component of ABC transporter from Pseudomonas aeruginosa UCBPP-PA14
25% identity, 71% coverage
- Identification of Novel PhoP-PhoQ Regulated Genes That Contribute to Polymyxin B Tolerance in Pseudomonas aeruginosa
Yang, Microorganisms 2021 - “...genes identified via ChIP-seq. Genes Summits in PA14 Chromosome Fold Enrichment oprH 4372078 17.23 PA14_46900, PA14_46910 4177576 15.03 arnB 1578361 6.85 PA14_50740, PA14_50750 4508762 6.24 PA14_21860, PA14_21870 1900312 5.29 PA14_52340, PA14_52350 4644776 4.87 PA14_11970, PA14_11980 1035748 4.17 pilY1 5372861 2.85 microorganisms-09-00344-t002_Table 2 Table 2 Functions of...”
- Pseudomonas aeruginosa Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma Patients
Elmassry, mSystems 2019 - “...amino acids, PA14_15030 and PA14_64870 ; four genes encoding the glutamate and aspartate transport system, PA14_46910 , PA14_46920 , PA14_46930 , and PA14_46950 , plus a fifth gene, ansB , which is involved in glutamate and aspartate metabolism; and six genes related to glycine and serine...”
PMI2898 amino acid ABC transporter, substrate-binding protein from Proteus mirabilis HI4320
PMI_RS14325 ABC transporter substrate-binding protein from Proteus mirabilis HI4320
25% identity, 66% coverage
- Perturbation of FliL interferes with Proteus mirabilis swarmer cell gene expression and differentiation
Cusick, Journal of bacteriology 2012 - “...PMI1645 PMI1648 PMI1644 PMI1617 PMI1359 PMI1637 PMI1636 PMI2898 PMI3460 PMI1660 PMI1646 PMI0842 PMI0833 PMI1647 PMI0992 PMI2149 PMI0291 PMI1623 PMI1622 PMI1442...”
- Transcriptome of swarming Proteus mirabilis
Pearson, Infection and immunity 2010 - “...change PMI1629 PMI1654 PMI1618 PMI1961 PMI1649 PMI1653 PMI2898 PMI1650 PMI1631 PMI1637 PMI1636 PMI1621 PMI1617 PMI1359 PMI0182 PMI1630 PMI1651 PMI1318 PMI1638...”
- “...Annotation Consolidatea Fold change PMI1618 PMI1359 PMI1629 PMI2898 PMI1654 PMI1617 PMI1653 PMI3460 PMI2057 PMI1438 PMI1650 PMI1637 PMI1442 PMI0993 PMI1649...”
- Growth Behavior and Transcriptome Profile Analysis of Proteus mirabilis Strain Under Long- versus Short-Term Simulated Microgravity Environment
Zhang, Polish journal of microbiology 2022 - “...PMI_RS13360 up 2.720 < 0.001 small multidrug resistance pump PMI_RS13370 up 1.424 0.017 putative phosphotransacetylase PMI_RS14325 up 1.473 0.023 amino acid transport system substrate-binding protein PMI_RS17915 up 1.520 < 0.001 Cd 2+ /Zn 2+ -exporting ATPase artP down 1.009 < 0.001 arginine transport system ATP-binding protein...”
- “...msrB , PMI_RS13425 ), membrane transportation ( artP , metI , pstB , ugpABCE , PMI_RS14325 ), metal ion transportation ( feoA , PMI_RS14090 , PMI_RS15035 , PMI_RS17915 ), biological adhesion ( PMI_RS02645 , PMI_RS10955 , PMI_RS14825 , PMI_RS14830 , PMI_ RS14835 , PMI_RS14840 , PMI_RS17135...”
PA14_36200 putative binding protein component of ABC transporter from Pseudomonas aeruginosa UCBPP-PA14
24% identity, 74% coverage
PMA4326_020240 glutamate/aspartate ABC transporter substrate-binding protein from Pseudomonas syringae pv. maculicola str. ES4326
25% identity, 63% coverage
Pf1N1B4_771 ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component from Pseudomonas fluorescens FW300-N1B4
25% identity, 63% coverage
- mutant phenotype: # Specifically important in carbon source L-Asparagine. Also important for glutamate utilization.
cg3045 ABC-type amino acid transport system, secreted component from Corynebacterium glutamicum ATCC 13032
28% identity, 37% coverage
Q9HUA7 Probable binding protein component of ABC transporter from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA5076 probable binding protein component of ABC transporter from Pseudomonas aeruginosa PAO1
26% identity, 68% coverage
- 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 - 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 - “...of ABC sugar transporter 4.538 Q9HU87 PA5096 Probable binding protein component of ABC transporter 100 Q9HUA7 PA5076 Probable binding protein component of ABC transporter 0.01 Q9HVS5 PA4496 Probable binding protein component of ABC transporter 0.396 pae02030 Bacterial chemotaxis Q9HWI6 PA4195 Probable binding protein component of ABC...”
- Phenotypes of a Pseudomonas aeruginosa hypermutator lineage that emerged during prolonged mechanical ventilation in a patient without cystic fibrosis
Nozick, mSystems 2024 - “...repair protein MutL (PA4946) H472L 14 (100%) 0 Putative binding protein component of ABC transporter (PA5076) T104A 14 (100%) 0 Hypothetical protein I62V 14 (100%) 0 Porphobilinogen deaminase (PA5260) D293G 14 (100%) 0 a *, premature stop codon. DISCUSSION Hypermutator strains have been associated with increased...”
- Emergence of a Pseudomonas aeruginosa Hypermutator Strain During the Course of Ventilator-Associated Pneumonia
Nozick, 2022 - The AhR ligand phthiocol and vitamin K analogs as Pseudomonas aeruginosa quorum sensing inhibitors
Jia, Frontiers in microbiology 2022 - “...Up-regulated: PA1224 Probable NAD(P)H dehydrogenase 1.56 fabZ 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ 1.39 ribH 6,7-dimethyl-8-ribityllumazine synthase 1.33 PA5076 Probable binding protein component of ABC transporter 1.32 PA4880 Probable bacterioferritin 1.29 PA4739 BON domain-containing protein 1.25 nalC NalC 1.23 speD S-adenosylmethionine decarboxylase proenzyme 1.22 ihfB Integration host factor subunit...”
- 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 - “...ABC sugar transporter 4.538 Q9HU87 PA5096 Probable binding protein component of ABC transporter 100 Q9HUA7 PA5076 Probable binding protein component of ABC transporter 0.01 Q9HVS5 PA4496 Probable binding protein component of ABC transporter 0.396 pae02030 Bacterial chemotaxis Q9HWI6 PA4195 Probable binding protein component of ABC transporter...”
- Utilization of L-glutamate as a preferred or sole nutrient in Pseudomonas aeruginosa PAO1 depends on genes encoding for the enhancer-binding protein AauR, the sigma factor RpoN and the transporter complex AatJQMP
Lundgren, BMC microbiology 2021 - “...sole source of carbon but not nitrogen (Figs. 2 b and 3 b). The PA5073 PA5076 operon of P. aeruginosa PAO1 encodes for a putative glutamine ABC-transporter complex, but a previous analysis of transposon mutants indicates that this locus is not required for growth on any...”
- “...[ 26 ]. Nonetheless, it is still plausible that L-glutamine enters the cell through PA5073 PA5076 and then undergoes transamination and/or deamidation to yield L-glutamate. Another route for assimilation of L-glutamine involves deamidation in the periplasm catalyzed by the glutaminase-asparaginase AnsB (PA1337) [ 28 ] with...”
- A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1
Lecoutere, MicrobiologyOpen 2012 - “...0.001 155 PA5046 Malic enzyme C CM 45.4 47 5.05 4.99 0.736 0.001 156 * PA5076 Binding component ABC transporter ET P 29.7 27 6.85 6.00 0.770 0.141 157 PA5110 fbp Fructose bisphosphatase G U 37.2 38 5.71 5.75 0.742 0.274 158 * PA5131 pgm Phosphoglycerate...”
- “...2000 ). For some of the proteins with a lowered p I -value (PA1084, PA2800, PA5076, and PA0291), a signal peptide was predicted by SignalP. After excluding these amino acids in the sequences, the proteins theoretical masses and charges are close to the experimental values, suggesting...”
- High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
Johnson, PLoS genetics 2008 - “...PA5074 PAK glutamine ABC transporter ATP binding protein PA5075 PA01 glutamine ABC transporter membrane protein PA5076 PAK glutamine ABC transporter periplasmic binding protein PA5097 PAK proline APC family transporter PA5153 PAK amino acid (lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein PA5155 PAK amino acid (lysine/arginine/ornithine/histidine/octopine) ABC transporter...”
- Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm
Sauer, Journal of bacteriology 2002 - “...5.98 6.41 9 11 3 PA4496 12d 60.08 7.11 13 PA0291 PA5076 12d 12d 49.67 59.74 8.67 6.85 23 7 PA0139 PA4468 PA4671 PA0263 PA0423 PA2395 PA0720 12d 12d 6d 12d 12d...”
- “...for the transport of dipeptides, oligopeptides, and nickel. PA5076, a putative glutamine transporter, belongs to class 3. Class 3 includes proteins that are...”
PSPTO5180 cystine ABC transporter, periplasmic cystine binding protein from Pseudomonas syringae pv. tomato str. DC3000
24% identity, 66% coverage
5eyfB / Q3XZW5 Crystal structure of solute-binding protein from enterococcus faecium with bound glutamate
24% identity, 55% coverage
- Ligand: glutamic acid (5eyfB)
Blon_0747 extracellular solute-binding protein, family 3 from Bifidobacterium longum subsp. infantis ATCC 15697
26% identity, 66% coverage
SPO3040 transporter substrate-binding domain-containing protein from Ruegeria pomeroyi DSS-3
26% identity, 59% coverage
VT47_18645 glutamate/aspartate ABC transporter substrate-binding protein from Pseudomonas syringae CC1543
25% identity, 63% coverage
- Identification of the Genes of the Plant Pathogen Pseudomonas syringae MB03 Required for the Nematicidal Activity Against Caenorhabditis elegans Through an Integrated Approach
Ali, Frontiers in microbiology 2022 - “...hisJ (VT47_18480), which is a part of an ABC transporter for histidine transport; and gltI (VT47_18645), which might be correlated to a shift in nutrient availability. Additionally, pntA (VT47_24115) and scoB (VT47_15125) were up-regulated, whereas scoP (V47_01435), queD (VT47_04670), rpsT (VT47_03545), and two hypothetical proteins (VT47_13300,...”
- “...VT47_18935) and amino acid uptake and metabolism ( aatP VT47_18660, aatM VT47_18655, aatQ VT47_18650, aatJ VT47_18645) were up-regulated during the exponential phase interaction. It has been reported that most of hosts enforce amino acid starvation to the invading bacteria. In response, bacterial pathogens manipulate the host...”
BLGT_RS07135 cysteine ABC transporter substrate-binding protein from Bifidobacterium longum subsp. longum GT15
26% identity, 66% coverage
Cbei_1049 extracellular solute-binding protein from Clostridium beijerincki NCIMB 8052
26% identity, 69% coverage
- Use of proteomic analysis to elucidate the role of calcium in acetone-butanol-ethanol fermentation by Clostridium beijerinckii NCIMB 8052
Han, Applied and environmental microbiology 2013 - “...qRT-PCR. Following protein profiling, four proteins (Cbei_0830, Cbei_1049, Cbei_0829, and Cbei_2831) that showed increased levels and five proteins (Cbei_2110,...”
- “...For qRT-PCR, primers specific for the Cbei_0830, Cbei_1049, Cbei_0829, Cbei_2831, Cbei_2110, Cbei_1273, Cbei_0476, Cbei_0422, Cbei_2146, and 16S rRNA genes were...”
AH68_02785 cysteine ABC transporter substrate-binding protein from Bifidobacterium catenulatum PV20-2
25% identity, 72% coverage
PSPTO_4171 amino acid ABC transporter, periplasmic amino acid-binding protein from Pseudomonas syringae pv. tomato str. DC3000
25% identity, 63% coverage
D9Q9A4 Transporter substrate-binding domain-containing protein from Corynebacterium pseudotuberculosis (strain C231)
CpC231_0647 glutamate ABC transporter substrate-binding protein from Corynebacterium pseudotuberculosis C231
23% identity, 60% coverage
- Changes in protein abundance are observed in bacterial isolates from a natural host
Rees, Frontiers in cellular and infection microbiology 2015 - “...transporter domain-containing ATP-binding protein 1.015 * 2.494 * 1.443 * Amino acid transport and metabolism D9Q9A4 gluB CpC231_0647 Glutamate-binding protein GluB 0.990 * 2.238 * 1.513 * Amino acid transport and metabolism D9Q9H2 gppA2 CpC231_0716 Ppx/GppA phosphatase family 1.726 * 2.633 * 0.665 Inorganic ion transport...”
- Changes in protein abundance are observed in bacterial isolates from a natural host
Rees, Frontiers in cellular and infection microbiology 2015 - “...ATP-binding protein 1.015 * 2.494 * 1.443 * Amino acid transport and metabolism D9Q9A4 gluB CpC231_0647 Glutamate-binding protein GluB 0.990 * 2.238 * 1.513 * Amino acid transport and metabolism D9Q9H2 gppA2 CpC231_0716 Ppx/GppA phosphatase family 1.726 * 2.633 * 0.665 Inorganic ion transport and metabolism...”
MSMEG_2727, MSMEI_2660 glutamate ABC transporter substrate-binding protein from Mycolicibacterium smegmatis MC2 155
A0QVX3 Glutamate binding protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_2727 glutamate binding protein from Mycobacterium smegmatis str. MC2 155
23% identity, 56% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...ATP-binding protein SugC 0.02 0.01 A0QT21 MSMEG_1683, MSMEI_1642 Cytosine/purine/uracil/thiamine/allantoin permease family protein 0.02 0.02 A0QVX3 MSMEG_2727, MSMEI_2660 Glutamate-binding protein 0.22 0.03 0.39 0.03 A0QXB0 MSMEG_3235, MSMEI_3153 ABC-type amino acid transport system, secreted component 0.23 0.09 0.24 0.2 A0R0W7 MSMEG_4533, MSMEI_4420 Sulfate-binding protein 0.16 0.01 0.34 0.23...”
- “...protein SugC 0.02 0.01 A0QT21 MSMEG_1683, MSMEI_1642 Cytosine/purine/uracil/thiamine/allantoin permease family protein 0.02 0.02 A0QVX3 MSMEG_2727, MSMEI_2660 Glutamate-binding protein 0.22 0.03 0.39 0.03 A0QXB0 MSMEG_3235, MSMEI_3153 ABC-type amino acid transport system, secreted component 0.23 0.09 0.24 0.2 A0R0W7 MSMEG_4533, MSMEI_4420 Sulfate-binding protein 0.16 0.01 0.34 0.23 A0QV32...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...transporter, ATP-binding protein SugC 0.02 0.01 A0QT21 MSMEG_1683, MSMEI_1642 Cytosine/purine/uracil/thiamine/allantoin permease family protein 0.02 0.02 A0QVX3 MSMEG_2727, MSMEI_2660 Glutamate-binding protein 0.22 0.03 0.39 0.03 A0QXB0 MSMEG_3235, MSMEI_3153 ABC-type amino acid transport system, secreted component 0.23 0.09 0.24 0.2 A0R0W7 MSMEG_4533, MSMEI_4420 Sulfate-binding protein 0.16 0.01 0.34...”
- Characterization of Conserved and Novel Septal Factors in Mycobacterium smegmatis
Wu, Journal of bacteriology 2018 - “...Rv3802 MSMEG_6942 MSMEG_0030 MSMEG_6725 MSMEG_6282 MSMEG_2727 MSMEG_0736 MSMEG_1353 MSMEG_1930 MSMEG_2391 MSMEG_5042 MSMEG_1252 MSMEG_4484 MSMEG_1285 MSMEG_5798...”
- A Screen for Protein-Protein Interactions in Live Mycobacteria Reveals a Functional Link between the Virulence-Associated Lipid Transporter LprG and the Mycolyltransferase Antigen 85A
Touchette, ACS infectious diseases 2017 - “...MSMEG_2410 Rv2969c Cell Wall & Cell Processes Putative conserved membrane or secreted serine-threonine protein kinase MSMEG_2727 Cell Wall & Cell Processes Periplasmic glutamate-binding periplasmic protein MSMEG_3058 Cell Wall & Cell Processes Lipoprotein MSMEG_3235 Cell Wall & Cell Processes Secreted component of ABC-type amino acid transport system...”
- Functional analyses of mycobacterial lipoprotein diacylglyceryl transferase and comparative secretome analysis of a mycobacterial lgt mutant
Tschumi, Journal of bacteriology 2012 - “...MSMEG_3247d MSMEG_3280 Lipc MSMEG_3598 Lip MSMEG_3235 Lip MSMEG_2727 Lip MSMEG_6804 Lip MSMEG_1704 Lip MSMEG_3636 Lip MSMEG_0643 Lip MSMEG_6524 SPb MSMEG_6047...”
PFLU_0246 cystine ABC transporter substrate-binding protein from Pseudomonas [fluorescens] SBW25
25% identity, 65% coverage
lp_2312 glutamine ABC transporter, substrate binding protein from Lactobacillus plantarum WCFS1
25% identity, 64% coverage
PP_1071 glutamate/aspartate ABC transporter substrate-binding protein from Pseudomonas putida KT2440
24% identity, 61% coverage
CA_C3620, CEA_G3627 ABC transporter substrate-binding protein from Clostridium acetobutylicum EA 2018
23% identity, 68% coverage
- Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018
Hu, BMC genomics 2011 - “...component CEA_G3626 CA_C3619 -2.49499 4.94909 4.797836 4.831871 4.227636 1.349231 amino acid ABC transporter permease CEA_G3627 CA_C3620 -2.79225 4.869307 2.77014 4.039679 3.923914 1.658129 amino acid ABC transporter periplasmic-binding protein CEA_G3629 CA_C3622 3.744723 1.616914 -1.60643 -2.30924 -3.70552 -4.20925 benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase CEA_G3648 CA_C3641 3.877563 5.273677 6.532841 7.05381 6.150331...”
- “...chemotaxis protein CEA_G0334 CA_C0323 3.362504 2.662176 2.652177 3.222052 4.952742 2.037345 sensory transduction histidine kinase CEA_G3627 CA_C3620 -2.79225 4.869307 2.77014 4.039679 3.923914 1.658129 amino acid ABC transporter periplasmic-binding protein CEA_G0390 CA_C0380 -4.23921 5.06975 5.365591 5.142555 3.394778 2.099342 periplasmic amino acid-binding protein Energy production and convertion CEA_G1083 CA_C1072...”
- “...ATPase component CEA_G3626 CA_C3619 -2.49499 4.94909 4.797836 4.831871 4.227636 1.349231 amino acid ABC transporter permease CEA_G3627 CA_C3620 -2.79225 4.869307 2.77014 4.039679 3.923914 1.658129 amino acid ABC transporter periplasmic-binding protein CEA_G3629 CA_C3622 3.744723 1.616914 -1.60643 -2.30924 -3.70552 -4.20925 benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase CEA_G3648 CA_C3641 3.877563 5.273677 6.532841 7.05381...”
- “...methyl-accepting chemotaxis protein CEA_G0334 CA_C0323 3.362504 2.662176 2.652177 3.222052 4.952742 2.037345 sensory transduction histidine kinase CEA_G3627 CA_C3620 -2.79225 4.869307 2.77014 4.039679 3.923914 1.658129 amino acid ABC transporter periplasmic-binding protein CEA_G0390 CA_C0380 -4.23921 5.06975 5.365591 5.142555 3.394778 2.099342 periplasmic amino acid-binding protein Energy production and convertion CEA_G1083...”
A9497_03785, AKL23_RS07395, STER_RS07565, T303_08720 cysteine ABC transporter substrate-binding protein from Streptococcus thermophilus LMD-9
25% identity, 63% coverage
- Cell Proteins Obtained by Peptic Shaving of Two Phenotypically Different Strains of Streptococcus thermophilus as a Source of Anti-Inflammatory Peptides
Allouche, Nutrients 2022 - “...STER_RS01655 DL-methionine transporter subunit; periplasmic-binding component of ABC superfamily 3.89 M 10 33.22 Transport STER_1539|ID:1900277| STER_RS07565 Glutamine-binding protein precursor (GlnBP) 31.30 CS 17 44.91 STHERMOCNRZ21N_v1_10277|ID:59659427|nupN| Lipoprotein involved in guanosine transport 37.64 CS 12 33.33 Energy production and conversion STER_0519|ID:1899133|atpA| STER_RS02545 F1 sector of membrane-bound ATP synthase,...”
- Functional Genomic Analyses of Exopolysaccharide-Producing Streptococcus thermophilus ASCC 1275 in Response to Milk Fermentation Conditions
Wu, Frontiers in microbiology 2019 - “...4.34 Amino acid ABC transporter substrate-binding protein T303_08290 2.47 Amino acid ABC transporter substrate-binding protein T303_08720 1.81 Amino acid ABC transporter substrate-binding protein T303_04105 1.79 Branched-chain amino acid aminotransferase Carbohydrate transport and metabolism T303_04850 0.62 Glucokinase T303_02705 0.53 Transketolase T303_07870 0.49 Lactose/galactose permease T303_06080 5.42 Maltodextrin...”
- Technological and Genomic Analysis of Roles of the Cell-Envelope Protease PrtS in Yoghurt Starter Development
Tian, International journal of molecular sciences 2018 - “...transporter permease A9497_04155 A9497_03360 A9497_03370 A9497_07620 AKL23_RS07765 AKL23_RS06975 AKL23_RS06985 AKL23_RS06990 ABC transporter substrate-binding protein A9497_03375 A9497_03785 A9497_07595 AKL23_RS07395 AKL23_RS01465 AKL23_RS01490 Amino acid A9497_08630 AKL23_RS02545 Transporter A9497_02760 A9497_03620 A9497_09055 AKL23_RS02000 AKL23_RS02915 AKL23_06320 Permease Branched-chain amino acid A9497_00490 A9497_01930 A9497_07910 A9497_07915 AKL23_RS01775 AKL23_RS01780 AKL23_RS05525 AKL23_RS08285 ABC transporter permease...”
- “...A9497_04155 A9497_03360 A9497_03370 A9497_07620 AKL23_RS07765 AKL23_RS06975 AKL23_RS06985 AKL23_RS06990 ABC transporter substrate-binding protein A9497_03375 A9497_03785 A9497_07595 AKL23_RS07395 AKL23_RS01465 AKL23_RS01490 Amino acid A9497_08630 AKL23_RS02545 Transporter A9497_02760 A9497_03620 A9497_09055 AKL23_RS02000 AKL23_RS02915 AKL23_06320 Permease Branched-chain amino acid A9497_00490 A9497_01930 A9497_07910 A9497_07915 AKL23_RS01775 AKL23_RS01780 AKL23_RS05525 AKL23_RS08285 ABC transporter permease A9497_04685 A9497_04690...”
TC 3.A.1.3.19 / Q88NY2 PP1071, component of Acidic amino acid uptake porter, AatJMQP from Pseudomonas putida (strain KT2440) (see paper)
PP1071 amino acid ABC transporter, periplasmic amino acid-binding protein from Pseudomonas putida KT2440
24% identity, 61% coverage
- substrates: Asparagine, Glutamine, aspartate, glutamate
tcdb comment: It is the sole system that transports glutamate and glutamine, but it can also transport aspartate and asparagine (Singh and Röhm 2008) - Enhancing curcumin's solubility and antibiofilm activity via silica surface modification
Barros, Nanoscale advances 2020 - “...Uniprot entry Control 1 Q88K29 Nucleic acid cold-shock chaperone 2 Q88QP8 Elongation factor Tu-A 3 Q88NY2 Glutamate/aspartate ABC transporter-periplasmic binding protein 4 Q88DU2 Chaperone protein DnaK 5 Q88PP2 Putative surface adhesion protein 6 Q88N55 60 kDa chaperonin 7 Q88QN8 Elongation factor G 1 8 Q88FB9 Chaperone...”
- “...Q88QP8 Elongation factor Tu-A 3 Q88N55 60 kDa chaperonin 4 Q88P53 Ornithine carbamoyltransferase, catabolic 5 Q88NY2 Glutamate/aspartate ABC transporter-periplasmic binding protein 6 Q88PP2 Putative surface adhesion protein 7 Q88BX2 ATP synthase subunit alpha 8 Q88P52 Arginine deiminase 9 Q88Q10 50S ribosomal protein L21 10 Q88LL5 Acyl...”
- Identification of glutamate ABC-Transporter component in Clostridium perfringens as a putative drug target
Bhatia, Bioinformation 2014 - “...jejuni NCTC 11168) [ 9 13 ] were taken from Uniprot Knowledge Base (ID: P37902, Q88NY2, Q0P9X8). The aligned consensus obtained after multiple sequence alignment of these three sequences was used to search Clostridium homologue using BLASTP analysis in C. perfringens Type-A strains. The domain consensus...”
- UEG Week 2024 Poster Presentations
, United European gastroenterology journal 2024 - UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - Identification of glutamate ABC-Transporter component in Clostridium perfringens as a putative drug target
Bhatia, Bioinformation 2014 - “...E. coli K 12, Pseudomonas putida KT2440 and Campylobacter jejuni NCTC 11168 are GltI, AatJ (PP1071) and PEB1a (CJ0921c) respectively [ 11 13 ]. The aligned consensus of these three sequences revealed putative gene/ORF for periplasmic glutamate binding protein in C. perfringens Type-A strains Table 2...”
- ATP-dependent RecG helicase is required for the transcriptional regulator OxyR function in Pseudomonas species
Yeom, The Journal of biological chemistry 2012 - “...PP0235 (lsfA) PP3122 PP0885 PP4402 (bkdA2) PP4064 (ivd) PP1071 PP5171 (cysP) PP3123 PP0223 PP2333 PP0252 (hslO) PP4620 PP2337 PP4185 (sucD) 17.39 1.09 14.83...”
- The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
Poblete-Castro, Microbial cell factories 2012 - “...General amino acid ABC transporter PP1300 AapP 4.0 16 1.1 n.s. amino acid ABC transporter PP1071 only in C 23 -2.0 n.s. amino acid ABC transporter PP0282 -33.3 15 -1.2 n.s. Branched-chain amino acid ABC PP4867 -16.7 11 1.8 n.s. Dipeptide ABC transporter PP0885 -5.0 22...”
- Comparative transcriptomics and proteomics of p-hydroxybenzoate producing Pseudomonas putida S12: novel responses and implications for strain improvement
Verhoef, Applied microbiology and biotechnology 2010 - “...acid ABC transporter ATP-binding protein PP1068 2.5 Amino acid ABC transporter, periplasmic amino acid-binding protein PP1071 0.640.01 c Branched-chain amino acid ABC transporter, ATP-binding protein ( braG ) PP1137 2.0 Branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein ( braC ) PP1141 2.10.1 c Multidrug...”
- Characterization of a Pseudomonas putida ABC transporter (AatJMQP) required for acidic amino acid uptake: biochemical properties and regulation by the Aau two-component system
Singh, Microbiology (Reading, England) 2008 (PubMed)- “...a periplasmic solute-binding protein AatJ (encoded by PP1071), two permease domains, AatQ and AatM (PP1070-PP1069), and an ATP-binding subunit, AatP (PP1068)....”
- “...KTaatP and KTaatJ. Genes aatP (PP1068) and aatJ (PP1071) were inactivated by a strategy described previously in detail (Sonawane et al., 2006). Briefly,...”
- The AauR-AauS two-component system regulates uptake and metabolism of acidic amino acids in Pseudomonas putida
Sonawane, Applied and environmental microbiology 2006 - “...the cognate periplasmic solute-binding protein (encoded by PP1071) (17). A BLAST search in the Comprehensive Microbial Resource database (http://cmr.tigr.org...”
- “...indicated that the ABC transporter encoded by PP1071 to PP1068 is most probably involved in the uptake of glutamate and/or aspartate....”
ABUW_2333, FQU82_01778 amino acid ABC transporter substrate-binding protein from Acinetobacter baumannii
D0C807 Glutamate-aspartate periplasmic-binding protein from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)
24% identity, 72% coverage
- Transcriptomic analysis reveals the regulatory role of quorum sensing in the Acinetobacter baumannii ATCC 19606 via RNA-seq
Xiong, BMC microbiology 2022 - “...found to be enriched in the two-component system, including FQU82_00307 ( pilS ), FQU82_01779, FQU82_02017, FQU82_01778, FQU82_01780, FQU82_01752, FQU82_02461 ( kdpA ), and FQU82_02460 ( kdpB ). The downregulated DEGs in this pathway included FQU82_02258 ( cydA ), FQU82_02259 ( cydB ), FQU82_02260 ( cydX ),...”
- Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach
Scribano, International journal of molecular sciences 2019 - “...0.873 SpI score = 19.451 Unknown function 0.143 V5VDN7 Amino acid ABC transporter substrate-binding protein ABUW_2333 gltI Sec SP MLCS: 126 [IQA-AD]. Rs: 0.999 0.958 0.732 SpI score = 12.943 Transport and binding proteins 0.222 A0A077GKV3 Glutaminase-asparaginase ABUW_2359 aspQ Sec SP MLCS: 124 [LYA-KN]. Rs: 0.991...”
- <i>OmpH</i> is Involved in the Decrease of <i>Acinetobacter baumannii</i> Biofilm by the Antimicrobial Peptide Cec4
Qiu, Drug design, development and therapy 2024 - “...log 2 FC P value KEGG-ABC transporter aotQ 1.479873143 0.000332958 glnQ D0C804 1.658356275 0.000395028 gltI D0C807 1.603455392 0.009493657 gltK D0C805 1.45762851 0.000184436 hisM 1.29203391 0.000113647 HMPREF0010_00886 1.189703016 0.001059408 HMPREF0010_01038 1.290063642 0.000108447 HMPREF0010_01713 1.153820896 0.003645927 HMPREF0010_02504 D0CCM4 1.515294175 0.000346461 HMPREF0010_02965 1.034329905 0.001250861 HMPREF0010_03358 1.46539906 0.001734293 HMPREF0010_03359 D0CF29...”
- Loss of Lipooligosaccharide Synthesis in Acinetobacter baumannii Produces Changes in Outer Membrane Vesicle Protein Content
Cano-Castaño, International journal of molecular sciences 2024 - “...HMPREF0010_00209 Translocation and assembly module subunit TamA 3 D0CEK8 atpF ATP synthase subunit b 3 D0C807 gltI Glutamate-aspartate periplasmic-binding protein 2 D0CCD3 HMPREF0010_02413 Uncharacterized protein 6 D0C7Q4 HMPREF0010_00784 Uncharacterized protein 2 Outer membrane vesicles (OMVs). Combined total peptides: total number of peptides (stripped sequences) mapping to...”
- Early and specific targeted mass spectrometry-based identification of bacteria in endotracheal aspirates of patients suspected with ventilator-associated pneumonia
Bardet, European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2021 - “...UniProtKB accession number; retention time: 9.8min); NIGLLAGLPK (A0A059ZM33 UniProtKB accession number; retention time: 20.44min); GQAINVQNIYGK (D0C807 UniProtKB accession number; retention time: 15.56min). * 2 E. coli VVAVGDQVEK: (P75691 UniProtKB accession number; retention time: 11.24min); DYVEGETAAK (P0A9Q7 UniProtKB accession number; retention time: 9.76min); WNGVTVTPK (P0ADU5 UniProtKB accession...”
GLUB_CORGL / P48242 Glutamate-binding protein GluB; Glutamate uptake system protein GluB from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534) (see 2 papers)
TC 3.A.1.3.9 / P48242 GluB aka CGL1951, component of Glutamate porter from Corynebacterium glutamicum (Brevibacterium flavum) (see 2 papers)
cg2137 glutamate secreted binding protein from Corynebacterium glutamicum ATCC 13032
NCgl1876 glutamate ABC transporter substrate-binding protein GluB from Corynebacterium glutamicum ATCC 13032
22% identity, 64% coverage
- function: Part of the ABC transporter complex GluABCD involved in glutamate uptake (PubMed:7868586). Binds glutamate with a high affinity (PubMed:32593757). Also binds aspartate with high affinity, suggesting that GluB could be involved in the transport of both amino acid residues into the cell (PubMed:32593757).
subunit: The complex is composed of two ATP-binding proteins (GluA), two transmembrane proteins (GluC and GluD) and a solute-binding protein (GluB).
disruption phenotype: Deletion of the gluABCD cluster almost abolishes glutamate uptake activity. - substrates: glutamate
- Anaerobic growth of Corynebacterium glutamicum via mixed-acid fermentation
Michel, Applied and environmental microbiology 2015 - “...Category NCgl no. Gene name Annotation Reference(s) Cg2137 NCgl1876 gluB 91 Cg2138 Cg2139 Cg2467 Cg2468 NCgl1877 NCgl1878 NCgl2168 NCgl2169 gluC gluD...”
- The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress
Schelder, PloS one 2011 - “...siderophore ABC transporter, permease protein 0.30 cg2136 NCgl1875 gluA glutamate uptake system ATP-binding protein 0.38 cg2137 NCgl1876 gluB secreted glutamate binding protein 0.37 cg2138 NCgl1877 gluC glutamate permease 0.39 cg2181 NCgl1915 ABC-type peptide transport system, secreted component 0.24 cg2182 NCgl1916 ABC-type peptide transport system, permease component...”
- RosR (Cg1324), a hydrogen peroxide-sensitive MarR-type transcriptional regulator of Corynebacterium glutamicum
Bussmann, The Journal of biological chemistry 2010 - “...cg1344 cg1343 cg1342 cg1341 cg1382 cg1671 cg2136 cg2137 cg2138 cg2139 cg2649 cg2773 Gene H2O2-sensitive Transcriptional Regulator RosR SEPTEMBER 17, 2010 *...”
- Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis
Follmann, BMC genomics 2009 - “...0 -1.36 -0.07 -0.6 -0.5 0.8 1.9 4.3 3.8 2.2 3.4 2.7 GlxR*, AmtR 67 cg2137 aa gluB ABC-type glutamate transporter, substrate binding component 0 -1.38 -0.39 -0.6 2.7 1.3 2.4 3.3 3.5 4.9 5.5 5.1 GlxR*, AmtR 68 cg2138 aa gluC ABC-type glutamate transporter, permease...”
- The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum
Brune, Journal of bacteriology 2007 - “...cg1612 cg3362 cg2565 cg3361 cg1419 cg2610 cg3360 cg2837 cg2137 cg2836 cg0303 cg3047 cg2138 cg2559 cg2136 cg0961 cg3096 cg3022 cg2636 cg2118 cg2630 cg1084 cg1615...”
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...cg0103 cg1061 cg1062 cg1064 cg1065 cg1066 cg1537 cg1785 cg2136 cg2137 cg2138 cg2139 cg2181 cg2183 cg2184 Gene name cmTb urtAc urtBc urtCc urtDc urtEc ptsG amtA...”
- Genome-Scale Mining of Novel Anchor Proteins of Corynebacterium glutamicum
Lin, Frontiers in microbiology 2021 - “...Extracellular @Lipid-anchored 0.33 1 1 FVLSGCG N site 6 WP_011014779.1 glutamate ABC transporter substrate-binding protein NCgl1876 Sec-(SPII) Extracellular @Lipid-anchored 0.33 1 1 VTLTACG N site 7 WP_011265985.1 twin-arginine translocation signal domain-containing protein NCgl2562 Possibly Tat/Sec-(SPII) Extracellular @Lipid-anchored 0.33 1 1 ATLAACA N site 8 WP_011013364.1 sensor...”
- Anaerobic growth of Corynebacterium glutamicum via mixed-acid fermentation
Michel, Applied and environmental microbiology 2015 - “...Category NCgl no. Gene name Annotation Reference(s) Cg2137 NCgl1876 gluB 91 Cg2138 Cg2139 Cg2467 Cg2468 NCgl1877 NCgl1878 NCgl2168 NCgl2169 gluC gluD Cg2470...”
- The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress
Schelder, PloS one 2011 - “...ABC transporter, permease protein 0.30 cg2136 NCgl1875 gluA glutamate uptake system ATP-binding protein 0.38 cg2137 NCgl1876 gluB secreted glutamate binding protein 0.37 cg2138 NCgl1877 gluC glutamate permease 0.39 cg2181 NCgl1915 ABC-type peptide transport system, secreted component 0.24 cg2182 NCgl1916 ABC-type peptide transport system, permease component 0.22...”
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...NCgl0894 NCgl0895 NCgl0896 NCgl0897 NCgl1305 NCgl1521 NCgl1875 NCgl1876 NCgl1877 NCgl1878 NCgl1915 NCgl1917 NCgl1918 Acc. no. 2394 SILBERBACH ET AL. APPL....”
TcyJ / b1920 cystine ABC transporter periplasmic binding protein (EC 7.4.2.12) from Escherichia coli K-12 substr. MG1655 (see 12 papers)
tcyJ / P0AEM9 cystine ABC transporter periplasmic binding protein (EC 7.4.2.12) from Escherichia coli (strain K12) (see 13 papers)
TCYJ_ECOLI / P0AEM9 L-cystine-binding protein TcyJ; CBP; Protein FliY; Sulfate starvation-induced protein 7; SSI7 from Escherichia coli (strain K12) (see 6 papers)
TC 3.A.1.3.10 / P0AEM9 Cystine-binding periplasmic protein FLIY aka CysX aka B1920, component of Cystine/cysteine/diaminopimelate transporter, CysXYZ; these proteins are also designated FliY/YecS/YecC from Escherichia coli (see 7 papers)
NP_416430 cystine ABC transporter periplasmic binding protein from Escherichia coli str. K-12 substr. MG1655
P0AEN0 L-cystine-binding protein TcyJ from Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
b1920 cystine transporter subunit from Escherichia coli str. K-12 substr. MG1655
25% identity, 70% coverage
- function: Part of the ABC transporter complex TcyJLN involved in L- cystine import (PubMed:20351115, PubMed:25139244, PubMed:25837721, PubMed:26350134). This high affinity cystine transporter is involved in resistance to oxidative stress by forming a L-cysteine/L-cystine shuttle system with the EamA transporter, which exports L-cysteine as reducing equivalents to the periplasm to prevent the cells from oxidative stress. Exported L-cysteine can reduce the periplasmic hydrogen peroxide to water, and then generated L-cystine is imported back into the cytoplasm via the TcyJLN complex (PubMed:20351115, PubMed:25837721). Functions at low cystine concentrations (PubMed:26350134). The system can also transport L-cysteine, diaminopimelic acid (DAP), djenkolate, lanthionine, D-cystine, homocystine, and it mediates accumulation of the toxic compounds L- selenaproline (SCA) and L-selenocystine (SeCys) (PubMed:25139244, PubMed:26350134). Binds cystine and DAP (PubMed:4564569, PubMed:8450713).
subunit: The complex is composed of two ATP-binding proteins (TcyN), two transmembrane proteins (TcyL) and a solute-binding protein (TcyJ).
disruption phenotype: Disruption of the gene significantly impairs intracellular uptake of L-cystine (PubMed:20351115, PubMed:25837721). Mutants show a higher sensitivity to H(2)O(2) than wild-type cells (PubMed:20351115). The tcyJ-tcyP double mutant is unable to import cystine and is completely resistant to both L-selenaproline and L- selenocystine (PubMed:25139244, PubMed:26350134). The double disruption of eamA and tcyJ increases cellular levels of lipid peroxides (PubMed:25837721). - substrates: Cystine, DAP
tcdb comment: Note, another transporter is designated CysZ in E. coli (TC# 2.A.121.1.1). CysXYZ also transports the toxic amino acid analogues, L-selenaproline (SCA; L-selenazolidine-4-carboxylic acid) and L-selenocystine (SeCys) (Deutch et al. 2014). FliY binds L-cystine, L-cysteine, and D-cysteine with micromolar affinities, but binding of the L- and D-enantiomers induced different conformational changes in FliY, where the L- enantiomer/SBP complex interacted more efficiently with the YecSC transporter. YecSC has low basal ATPase activity that is moderately stimulated by apo-FliY, more strongly by D-cysteine-bound FliY, and maximally by L-cysteine- or L-cystine-bound FliY (Sabrialabe et al. 2020) - Substrate recognition and ATPase activity of the E. coli cysteine/cystine ABC transporter YecSC-FliY
Sabrialabed, The Journal of biological chemistry 2020 - “...strains and plasmids The genes for yecC (ACC P37774), yecS (ACC P0AFT2), and fliY (ACC P0AEM9) were PCR-amplified from the E. coli K-12 derivative strain BW25113. All restriction sites for subcloning were inserted at this stage. fliY was inserted into the NdeI/XhoI sites of a pET21b...”
- “...( 81 ) to search for homologs of the E. coli cysteine-binding protein (FliY, SWISSPROT P0AEM9). A search against Uniclust30 ( 82 ) yielded 250 homologs, which we aligned using MAFFT ( 83 ). Using the 2.26 resolution crystal structure of NGO2014, the cysteine binding protein...”
- A comparison of asparaginase activity in generic formulations of E.coli derived L- asparaginase: In-vitro study and retrospective analysis of asparaginase monitoring in pediatric patients with leukemia
Sankaran, British journal of clinical pharmacology 2020 (secret) - Escherichia coli flagellar genes as target sites for integration and expression of genetic circuits.
Juhas, PloS one 2014 - GeneRIF: analysis of integration and expression at four candidate loci, fliD, fliS, fliT, and fliY, of the E. coli flagellar region 3a
- Amino acid composition and N-terminal sequence of purified cystine binding protein of Escherichia coli.
Butler, Life sciences 1993 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Impact of chlorhexidine digluconate and temperature on curli production in Escherichia coli-consequence on its adhesion ability
Coquet, AIMS microbiology 2017 - “...several bacteriophages P02943 OM 47 6 428 3.45 Cystine-binding periplasmic protein (fliY) Transport of cyst(e)ine P0AEN0 P 83 6 493 2.84 1.98 Outer-membrane lipoprotein carrier protein (lolA) Transport of proteins P61316 OM 50 4 253 2.79 Arginine-binding periplasmic protein 1 (artI) Transport of arginine P30859 P...”
- Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes
Santos-Zavaleta, BMC genomics 2019 - “...talA- tktB CreB(+) + GEA, IMP [ 11 ] carbohydrate metabolic process, pentose-phosphate shunt tar b1920 tar- tap-cheRBYZ Fnr(+) IMP [ 13 ] chemotaxis, signal transduction tcyJ (fliY) b3116 tcyJ fliA Z -tcyJ H-NS(+), MatA(), SutR(), NsrR(), CsgD(), FlhDC(+) IMP [ 13 ] L-cystine transport tdcC...”
- Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes
Skippington, Genome biology and evolution 2012 - “...btuB b3966 omrA 25 Variable Incongruent No cirA b2155 omrA 21 Variable Incongruent No fliY b1920 omrA 10 Variable Incongruent No fepA b0584 omrA 26 Variable Incongruent No ompT b0565 omrA 3 Variable N < 4 N < 4 folP b3177 omrA 27 Core Incongruent No...”
- The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
Oberto, PloS one 2009 - “...0.23 1.13 1 0.49 0.47 1.55 FRec fumarase A=fumarate hydratase Class I aerobic isozyme fliY b1920 fliAZY 1 1.85 0.69 1.85 1 1.11 0.91 3.26 1 1.42 1.01 0.73 FA putative periplasmic binding transport protein ndk b2518 ndk 1 16.55 0.94 12.98 1 0.67 0.3 8.27...”
- Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses
Gyaneshwar, Journal of bacteriology 2005 - “...a gene encoding a periplasmic cystine binding protein (b1920; misnamed fliY and known to be sulfate starvation induced [18, 37]), the cysteine biosynthetic gene...”
- “...numerically were b0198 and b0199 (metIN), b1919 and b1920 (dcyD-fliY), b2012 and b2013 (yeeDE), b2423 (cysW), b2530 (iscS), and b3207 (yrbL). The genes that...”
- Genome image programs: visualization and interpretation of Escherichia coli microarray experiments
Zimmer, Genetics 2004 - “...of the flagellar and chemotaxis regulon (b1070-1083, b1881-1892, b1920- 1926) and to operons encoding the F1F0 ATPase (b3731- 3739) and the tricarboxylic acid...”
- Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
Wei, Infection and immunity 2003 - “...b0808 b0899 b0934 b1053 b1169 b1170 b1336 b1483 b1543 b1920 b2681 b3514 b3877 b4231 b2117 b1020 b2479 b2090 b3763 b1384 b1892 b1074 b1942 b2365 b1899 b3907...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...Function Name Acetate Propionate NaCl b1918 b1919 b1920 yecC b1919 fliY 1 1 1 Putative transport system permease protein Putative...”
- Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression
Soupene, Journal of bacteriology 2003 - “...4TMTMTMTMTMTMTMTMTMTMTM 4TM 4TMTM cheZYBR-tap-tar/cheWA-motBA/flhCD], b1920 to b1926 [fliYZA/ 4TMTM TMTM3 4TMTM TMTMTMTMTMTM3 TMTMTMTMTMTMTMTMTM...”
CPR_1324 amino acid ABC transporter (binding protein) from Clostridium perfringens SM101
24% identity, 65% coverage
- Identification of glutamate ABC-Transporter component in Clostridium perfringens as a putative drug target
Bhatia, Bioinformation 2014 - “...strains ( http://string-db.org/ ) [ 15 ]. Homology modeling and glutamate binding site prediction of CPR_1324 : The protein sequence of the CPR_1324 from C. perfringens TypeA -SM101 was used for structure prediction based on the availability of the crystal structure of a polar amino acid...”
- “...importer in Clostridium ( Table 2 ). Sequence homology search of C. perfringens TypeA- SM101 CPR_1324 from other species revealed PDB 3HV1 to be the best template for homology modeling of the target sequence as both shared 41% identity ( Figure 2 ). PDB 3HV1 is...”
Pput_1112 extracellular solute-binding protein from Pseudomonas putida F1
24% identity, 61% coverage
SF5M90T_1910 cystine ABC transporter substrate-binding protein from Shigella flexneri 5a str. M90T
25% identity, 70% coverage
- RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Vergara-Irigaray, BMC genomics 2014 - “...PTS system, fructose-specific transport protein -1.99 Aminoacid transport and metabolism SF5M90T_2823 argA N-acetylglutamate synthase 1.94 SF5M90T_1910 fliY putative periplasmic binding transport protein 1.80 SF5M90T_625 ybgH peptide transporter 1.64 -1.60 -1.21 SF5M90T_292 pepD aminoacyl-histidine dipeptidase (peptidase D) 1.54 1.78 1.75 SF5M90T_2879 gcvT aminomethyltransferase 1.53 1.44 SF5M90T_284 proA...”
c2335 Cystine-binding periplasmic protein precursor from Escherichia coli CFT073
25% identity, 70% coverage
WIGMOR_RS02980 transporter substrate-binding domain-containing protein from Wigglesworthia glossinidia endosymbiont of Glossina morsitans
24% identity, 67% coverage
Z3010 putative periplasmic binding transport protein from Escherichia coli O157:H7 EDL933
24% identity, 70% coverage
Pput_0242 cystine transporter subunit from Pseudomonas putida F1
23% identity, 64% coverage
PP0227 cysteine ABC transporter, periplasmic cysteine-binding protein, putative from Pseudomonas putida KT2440
23% identity, 64% coverage
LSA_RS00930 amino acid ABC transporter substrate-binding protein from Fructilactobacillus sanfranciscensis TMW 1.1304
22% identity, 50% coverage
PVLB_05350 glutamate/aspartate ABC transporter substrate-binding protein from Pseudomonas sp. VLB120
24% identity, 61% coverage
PSPTO_1134 amino acid ABC transporter, periplasmic amino acid-binding protein from Pseudomonas syringae pv. tomato str. DC3000
24% identity, 67% coverage
E6B08_RS28125 transporter substrate-binding domain-containing protein from Pseudomonas putida
27% identity, 63% coverage
- A bacterial chemoreceptor that mediates chemotaxis to two different plant hormones
Rico-Jiménez, Environmental microbiology 2022 - “...) that bind both, amino acids and IAA, we purified the SBP of this transporter, E6B08_RS28125, and isothermal titration calorimetry (ITC) assays with IAA revealed no binding (Supp. Fig. S7 ). Subsequently, we used differential scanning fluorimetry (DSF) (MartinMora et al ., 2018a ) and microcalorimetric...”
- “...proteinprotein interaction assays using ITC revealed no evidence of protein complex formation between PcpILBD and E6B08_RS28125 (Supp. Fig. S9 ). To identify ligands that are directly recognized by PcpI, the LBD of PcpI was submitted to highthroughput ligand screening using DSF. We screened ~480 compounds from...”
- The pH Robustness of Bacterial Sensing
Monteagudo-Cascales, mBio 2022 - “...solute binding proteins MBP SBP E. coli K12 SBP_bac_1/PF01547 D-maltose 2.5-11.0 9.0 0.63 This study E6B08_RS28125 SBP P. putida 1290 SBP_bac_3/PF00497 L-ornithine 3.0-11.0 9.0 0.66 ( 50 ) LBDs of cytosolic location TodS-Nter SK P. putida DOT-T1E PAS_4/PF08448 Toluene 5.5-9.5 6.5 0.25 ( 96 ) AdmX-LBD...”
- “...to study SBPs ( 48 , 49 ). We have used E. coli MBP and E6B08_RS28125, an amino acid-sensing SBP of P. putida ( 50 ), as models to study the pH robustness of ligand recognition in solute-binding proteins. Like the periplasmic LBDs, MBP and E6B08_RS28125...”
sll0064 unknown protein from Synechocystis sp. PCC 6803
26% identity, 69% coverage
- Screening and genetic characterization of thermo-tolerant Synechocystis sp. PCC6803 strains created by adaptive evolution
Tillich, BMC biotechnology 2014 - “...change clpC Gac Tac X* 2468031 AA change clpC gTt gCt X* 2579829 AA change sll0064 Ttg Atg X* X* 2717197 Frameshift pyrR - TAATTAACTCCAC X X 3371838 AA change SigF Cgt Tgt X X* X Mutations marked with *indicate mixed reads in Sanger (& NGS),...”
- “...AA change clpC Gac Tac 4.65 2468031* AA change clpC gTt gCt 20.5 2579430 Frameshift sll0064 - CCCTG 61 2717197 Frameshift pyrR AAGGTTAA GTGGCTTTAA 10.9 2717187 Frameshift pyrR - TTAACTCCACTAA 70.4 Positions marked with a *correspond to identical mutation positions for monoclonal strains. Table 4 Mutations...”
- Butanol tolerance regulated by a two-component response regulator Slr1037 in photosynthetic Synechocystis sp. PCC 6803
Chen, Biotechnology for biofuels 2014 - “...and regulator Sll1124 -1.809 2 Two-component sensor histidine kinase, phytochrome-like protein Transport and binding proteins Sll0064 -1.91 15.8 -1.96 15.8 Putative polar amino acid transport system Sll0163 -1.643 5.7 WD-repeat protein Sll0834 -2.36 11.7 -1.944 11.7 Low affinity sulfate transporter Slr0559 -2.07 40.7 Branched chain amino...”
- “...Slr1897 -1.54 18.9 Periplasmic sugar-binding protein of ABC transporter Slr1974 -1.87 26.1 GTP binding protein Sll0064 -1.91 15.8 -1.96 15.8 Putative polar amino acid transport system Circadian rhythms of cyanobacteria are controlled by a cluster of three genes encoding circadian clock proteins ( kaiA , kaiB,...”
- Global transcriptional profiles of the copper responses in the cyanobacterium Synechocystis sp. PCC 6803
Giner-Lamia, PloS one 2014 - “...reductase sll0450 norB 0.12 Cytochrome b subunit of nitric oxide reductase Transport and binding proteins sll0064 0.18 Putative polar amino acid transport system sll1270 bgtB 0.29 ABC-type Bgt permease for basic amino acids and glutamine slr0415 napA 0.29 Na+/H+ antiporter slr0369 envD 0.28 RND multidrug efflux...”
- Proteomic analysis reveals resistance mechanism against biofuel hexane in Synechocystis sp. PCC 6803
Liu, Biotechnology for biofuels 2012 - “...0.64 NAD(P)H-quinone oxidoreductase subunit F Slr077 0.55 NifS protein Slr2005 0.61 Periplasmic protein, function unknown Sll0064 0.65 Putative polar amino acid transport system Slr1410 0.61 Periplasmic WD-repeat protein Slr1615 0.57 Perosamine synthetase Sll0226 0.51 0.56 Photosystem I assembly protein Ycf4 Slr1894 0.60 Probable DNA-binding stress protein...”
- Amino acid transport in taxonomically diverse cyanobacteria and identification of two genes encoding elements of a neutral amino acid permease putatively involved in recapture of leaked hydrophobic amino acids
Montesinos, Journal of bacteriology 1997 - “...the conserved component of ABCtype transport systems; sll0064, a product homologous to periplasmic binding proteins for glutamine; slr0700, a product homologous...”
Teth39_1765 extracellular solute-binding protein from Thermoanaerobacter ethanolicus ATCC 33223
28% identity, 45% coverage
SMb20263 putative ABC transporter periplasmic amino acid-binding protein from Sinorhizobium meliloti 1021
25% identity, 50% coverage
- Transcriptomic Insight in the Control of Legume Root Secondary Infection by the Sinorhizobium meliloti Transcriptional Regulator Clr
Zou, Frontiers in microbiology 2017 - “...smc01848 Conserved hypothetical protein -1,4597 -1,2183 smc03052 FlgD basal body rod modification protein -1,1339 -1,2173 smb20263 Putative ABC transporter periplasmic protein -1,177 -1,1958 smc03046 Putative transcription regulator protein -1,0913 -1,149 smc02588 Putative permease ABC transport protein -1,0468 -1,1399 smc01957 Conserved hypothetical protein -1,0356 -1,0588 smc00330 Putative...”
A9CGZ5 ABC transporter, substrate binding protein (Amino acid) from Agrobacterium fabrum (strain C58 / ATCC 33970)
Atu4678 ABC transporter, substrate binding protein (amino acid) from Agrobacterium tumefaciens str. C58 (Cereon)
26% identity, 54% coverage
- Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks
Zhao, eLife 2014 - “...A5VZY6, A6WW16, A6WXX7, A8H392, A9AKG8, A9AKH1, A9AL52, A9ALD3, A9AQW9, A9CFU8, A9CFU9, A9CFV0, A9CFV4, A9CFW8, A9CGZ4, A9CGZ5, A9CGZ9, A9CH01, A9CH04, A9CKB4, B0VB44, B1KJ76, B3D6W2, B4EHE6, B9J8G8, B9JHU6, B9JQV3, B9K4G4, B9R4E3, C5ZMD2, D2AV87, D2QN44, D5SQS4, D6EJK6, D6EJK7, D6EJK8, D6EJK9, D6EJL0, Q0B950, Q0B953, Q0B9R9, Q0B9S2, Q16D96, Q1QBF3, Q1QU06, Q1QV19,...”
- A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens
Budnick, Scientific reports 2020 - “...of which are components of ABC-type transport systems (e.g., chvE , malE , atu2422 , atu4678 , and atu1879 ) 25 . Indeed, our transcriptomic data largely resembles the proteomic data from that study (Supplementary Table S1 ). However, aside from the ABC-type transport systems, RNA-seq...”
- “...by Overlper and colleagues show differences in expression and regulation of chvE , atu2422 , atu4678 , and atu1879 in abcR1 and vtlR (Supplementary Tables S1 , S3 ) 25 . None of these genes appear to be differentially regulated in the VtlR regulon described previously...”
- Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region
Overlöper, RNA biology 2014 - “...transporter, substrate binding protein (amino acid) 4,50 Atu0157 atu0157 ABC transporter, substrate binding protein 3,87 Atu4678 atu4678 ABC transporter substrate-binding protein (amino acid) 3,85 Atu2422 atu2422 ABC transporter, substrate binding protein (amino acid GABA) 3,66 FrcB atu0063 ABC transporter, substrate binding protein (sugar) 2,13 DppA atu4113...”
- “...1.5) phase. The mRNAs of five periplasmic binding proteins of ABC transporters (Atu4577, MalE, Atu4046, Atu4678, and DppA) showed clear AbcR1-dependent regulation consistent with elevated protein levels in the AbcR1 strain ( Fig.2AE ). The same was true for Atu0857, an annotated oxidoreductase ( Fig.2F )....”
- Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens
Möller, PloS one 2014 - “...number of Hfq-bound mRNAs, many known targets were enriched about 2-fold (e.g. atu2422 , 2.61-fold; atu4678 , 2.2-fold; malE , 2.24-fold; atu4113 , 2.3-fold) [31] , indicating sufficient specificity of the observed interaction with Hfq. The transcript diversity of mRNAs and ncRNAs differed notably between Exp...”
B1745_05195 transporter substrate-binding domain-containing protein from Lactobacillus amylolyticus
23% identity, 82% coverage
- Adaptive mechanism of Lactobacillus amylolyticus L6 in soymilk environment based on metabolism of nutrients and related gene-expression profiles
Fei, Food science & nutrition 2022 - “...B1745_06870 att amino acid permease 1.40 B1745_04855 atpA haloacid dehalogenase 1.40 B1745_00955 pepC aminopeptidase 1.38 B1745_05195 glnH glutamine ABC transporter substratebinding protein 1.32 B1745_01775 groEL chaperonin GroEL 1.23 B1745_06165 metalloprotease 1.18 B1745_05200 GlnP glutamine ABC transporter permease 1.08 B1745_00920 oppA peptide ABC transporter substratebinding protein 1.07...”
- “...amino acid. A glutamate transporter operon (glnQHMP, glnP , B1745_05185; glnM , B1745_05190; glnH , B1745_05195; glnH , B1745_05195) was highly induced in the logarithmic phase to transport the high concentration of free glutamate from the soymilk into the cell (Table 2 and Table 4 )....”
sll0224 hypothetical protein from Synechocystis sp. PCC 6803
24% identity, 71% coverage
MMSR116_20450, MMSR116_RS20185 amino acid ABC transporter substrate-binding protein from Methylobacterium mesophilicum SR1.6/6
24% identity, 62% coverage
- Transcriptome and Secretome Analyses of Endophyte Methylobacterium mesophilicum and Pathogen Xylella fastidiosa Interacting Show Nutrient Competition
Dourado, Microorganisms 2023 - “...43 6 13 - MMSR116_RS13860 MMSR116_14035 Signal peptide protein 19 20 21|22 14 6 MMSR116_RS20185 MMSR116_20450 Extracellular solute-binding protein 33 23 27|28 15 12 MMSR116_RS27490 MMSR116_27830 Multiple sugar-binding periplasmic receptor ChvE 38 15 27|28 16 7 MMSR116_RS07030 MMSR116_07145 Glyceraldehyde-3-phosphate dehydrogenase 36 13 17 4 MMSR116_RS11970 MMSR116_12135...”
- “...Tuf1 43 6 13 - MMSR116_RS13860 MMSR116_14035 Signal peptide protein 19 20 21|22 14 6 MMSR116_RS20185 MMSR116_20450 Extracellular solute-binding protein 33 23 27|28 15 12 MMSR116_RS27490 MMSR116_27830 Multiple sugar-binding periplasmic receptor ChvE 38 15 27|28 16 7 MMSR116_RS07030 MMSR116_07145 Glyceraldehyde-3-phosphate dehydrogenase 36 13 17 4 MMSR116_RS11970...”
AH67_03690 glutamate ABC transporter substrate-binding protein from Bifidobacterium pseudolongum PV8-2
25% identity, 56% coverage
STM1954 putative periplasmic binding transport protein from Salmonella typhimurium LT2
NP_460907 putative periplasmic binding transport protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
24% identity, 70% coverage
- The transcript from the σ(28)-dependent promoter is translationally inert in the expression of the σ(28)-encoding gene fliA in the fliAZ operon of Salmonella enterica serovar Typhimurium
Tanabe, Journal of bacteriology 2011 - “...Downstream of these two genes exists another gene, STM1954, which can be transcribed together with these two genes. However, STM1954 is also expressed from...”
- “...published reports (1, 14, 27, 28, 31, 45, 46). STM1954 has also been called fliY (38). (B) The nucleotide sequence of the regulatory region of the fliAZ...”
- Mass spectrometry-based quantitative proteomic analysis of Salmonella enterica serovar Enteritidis protein expression upon exposure to hydrogen peroxide
Kim, BMC microbiology 2010 - “...STM1886 Glucose-6-phosphate 1-dehydrogenase zwf 55.92 5.52 26% STM1923 Chemotaxis protein motA motA 32.08 5.47 31% STM1954 Cystine-binding periplasmic protein precursor fliY 28.79 8.81 23% STM1959 Flagellin fliC 51.62 4.79 56% STM2104 Phosphomannomutase in colanic acid gene cluster cpsG 50.02 5.18 20% STM2167 NADH independent D-lactate dehydrogenase...”
- “...treA 25 3% STM1886 Glucose-6-phosphate 1-dehydrogenase zwf 0% STM1923 Chemotaxis protein motA motA 14 3% STM1954 Cystine-binding periplasmic protein precursor fliY 9 2% STM1959 Flagellin fliC 0% STM2104 Phosphomannomutase in colanic acid gene cluster cpsG 23 6% STM2167 NADH independent D-lactate dehydrogenase dld 16 5% STM2190...”
- Comparative proteomic analysis of Salmonella enterica serovar Typhimurium ppGpp-deficient mutant to identify a novel virulence protein required for intracellular survival in macrophages
Haneda, BMC microbiology 2010 - “...STM1796 treA 0.7 0.002 EC b 015 STM4403 cpdB 0.6 0.011 0.25 0.06 c 027 STM1954 fliY 0.5 0.033 ND 028 STM2884 sipC 0.1 0.009 ND 029 STM3557 ugpB 0.4 0.019 EC 029-2 STM0748 tolB 0.4 0.019 0.25 0.03 c 037 STM0209 htrA 0.6 0.032 0.60...”
- Genomic comparisons of Salmonella enterica serovar Dublin, Agona, and Typhimurium strains recently isolated from milk filters and bovine samples from Ireland, using a Salmonella microarray
Reen, Applied and environmental microbiology 2005 - “...protein in the flagella. Most of the fli operon (STM1954 to STM1981) was predominantly present in all serovar Agona and Dublin isolates examined; the exception...”
- Multiple promoters contribute to swarming and the coordination of transcription with flagellar assembly in Salmonella.
Wozniak, Journal of bacteriology 2010 - GeneRIF: The fliAZY class 3 promoter lowered class 3 transcription in stationary phase.
Q03PN2 ABC-type amino acid transport/signal transduction system, periplasmic component/domain from Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947)
26% identity, 62% coverage
PfGW456L13_4770 ABC transporter for L-Asparagine and possibly other L-amino acids, periplasmic substrate-binding component from Pseudomonas fluorescens GW456-L13
25% identity, 64% coverage
- mutant phenotype: Specific phenotype on L-Asparagine; Sodium octanoate. Detrimental on glutamine and might leak it. The mild phenotype on octanoate is not explained.
B0D71_08240 glutamate/aspartate ABC transporter substrate-binding protein from Pseudomonas laurylsulfativorans
25% identity, 64% coverage
AH68_03390 glutamate ABC transporter substrate-binding protein from Bifidobacterium catenulatum PV20-2
23% identity, 69% coverage
MMSR116_RS29475 transporter substrate-binding domain-containing protein from Methylobacterium mesophilicum SR1.6/6
24% identity, 54% coverage
LSA1497 Putative glutamine/glutamate ABC transporter, membrane-spanning/substrate-binding subunit precursor from Lactobacillus sakei subsp. sakei 23K
27% identity, 33% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...Putative amino acid:H(+) symporter 1.0 0.8 LSA1496 lsa1496 Putative glutamine/glutamate ABC transporter, ATP-binding subunit 1.2 LSA1497 lsa1497 Putative glutamine/glutamate ABC transporter, membrane-spanning/substrate-binding subunit precursor 0.7 Transport/binding of proteins/peptides LSA0702 oppA Oligopeptide ABC transporter, substrate-binding lipoprotein precursor 1.3 1.0 LSA0703 oppB Oligopeptide ABC transporter, membrane-spanning subunit 0.8...”
SENTW_1129 cystine ABC transporter substrate-binding protein from Salmonella enterica subsp. enterica serovar Weltevreden str.
23% identity, 70% coverage
BP951000_0988 amino acid ABC transporter substrate-binding protein from Brachyspira pilosicoli 95/1000
24% identity, 52% coverage
Blon_0710 extracellular solute-binding protein, family 3 from Bifidobacterium longum subsp. infantis ATCC 15697
24% identity, 69% coverage
HSISS4_01405 ABC transporter substrate-binding protein/permease from Streptococcus salivarius
29% identity, 30% coverage
BLGT_07630 glutamate ABC transporter substrate-binding protein from Bifidobacterium longum subsp. longum GT15
24% identity, 69% coverage
- The Gene Expression Profile Differs in Growth Phases of the Bifidobacterium Longum Culture
Veselovsky, Microorganisms 2022 - “...ABC transporters, quorum sensing, metabolic pathways, homologous recombination, histidine metabolism and glycerolipid metabolism. The transporters (BLGT_07630, BLGT_07625, BLGT_07620, BLGT_07635, BLGT_07350, BLGT_06730, BLGT_06725, BLGT_06720, BLGT_05680, BLGT_04630, BLGT_04635, BLGT_07550, BLGT_01180), Enzymes (BLGT_03450, BLGT_09605, BLGT_07635), DNA repair and recombination proteins (BLGT_07210), Glycosyltransferases (BLGT_03450). The upregulated genes were classified according...”
GSU0800 amino acid ABC transporter, periplasmic amino acid-binding protein from Geobacter sulfurreducens PCA
25% identity, 62% coverage
- Scarless Genome Editing and Stable Inducible Expression Vectors for Geobacter sulfurreducens
Chan, Applied and environmental microbiology 2015 - “...origin, oriT , P acpP -MCS nptI This study pRK2-Geo2i RK2 origin, oriT , P GSU0800 - vanR , P acpP* -MCS nptI This study pRK2-Geo5 RK2 origin, oriT, P taclac -MCS, nptI This study SacB suicide vectors pSMV3 32 pK18mobsacB 31 pDGSU0299 Flanking regions of...”
- “...pRK2-Geo2 to generate pRK2-Geo2-lacZa. pRK2-Geo2i and pRK2-Geo2i-lacZa. Primer PGSU0800-vanR-PacpP-vanA (gBlock) containing the promoter regions of GSU0800 and a modified GSU1604 promoter region with VanR binding sites was digested with NcoI and NdeI and ligated into the same sites in pRVMCS-2 to generate pGVMCS-2. The modified promoter...”
BCAS0291 periplasmic solute-binding protein from Burkholderia cenocepacia J2315
28% identity, 50% coverage
OA04_29520 transporter substrate-binding domain-containing protein from Pectobacterium versatile
23% identity, 74% coverage
OG1RF_10537 amino acid ABC transporter substrate-binding protein from Enterococcus faecalis OG1RF
26% identity, 58% coverage
A1S_1399 ArtI protein from Acinetobacter baumannii ATCC 17978
25% identity, 52% coverage
Swol_0316 extracellular solute-binding protein, family 3 from Syntrophomonas wolfei subsp. wolfei str. Goettingen
26% identity, 62% coverage
RHE_RS11720 transporter substrate-binding domain-containing protein from Rhizobium etli CFN 42
RHE_CH02293 probable amino acid ABC transporter, substrate-binding protein from Rhizobium etli CFN 42
25% identity, 60% 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 regarding ABC.PA. S; the polar amino acid transport system substrate-binding protein, in MM RHE_RS02695, RHE_RS11720, and RHE_RS27400, and in bacteroid RHE_RS07475 and RHE_RS27430 were expressed, potentially regulated by the TFs RHE_RS30745_m3, RHE_RS24110_m2, RHE_RS14135_m3 and RHE_RS18525_m2, RHE_RS26505_m5, respectively. All these data were clustering TF-associated, showing distinct...”
- Impact of c-di-GMP on the Extracellular Proteome of Rhizobium etli
Lorite, Biology 2022 - “...HmuT, OccT, ModA, PotF, MexE1, ZnuA, RHE_CH00971, RHE_PC00008, RHE_PC00118, RHE_PC00160, RHE_CH02418, 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...”
PP_0282 ABC transporter substrate-binding protein from Pseudomonas putida KT2440
PP0282 amino acid ABC transporter, periplasmic amino acid-binding protein from Pseudomonas putida KT2440
26% identity, 66% coverage
- Gene expression reprogramming of Pseudomonas alloputida in response to arginine through the transcriptional regulator ArgR
Molina-Henares, Microbiology (Reading, England) 2024 - “...hisPQM operon, the second most relevant arginine transporter, encoded by the predicted operon PP_0283( aotP )-PP_0282( artJ )-PP_0281-PP_0280 [ 19 ], is positively regulated by ArgR. Other amino acid and dipeptide transporters also show reduced mRNA levels in the argR mutant. Additionally, a set of genes...”
- Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida
Huertas-Rosales, Frontiers in molecular biosciences 2021 - “...antiporter) and hisP (PP_4483; ATP-binding subunit of a histidine/lysine/arginine/ornithine transporter) are targets for RsmE; artJ (PP_0282; L-arginine ABC transporter substrate-binding subunit) and amaD (PP_3596; D-lysine oxidase) are targets for RsmA, and amaB (PP_5258; L-piperidine-6-carboxylate dehydrogenase) is a target for both RsmE and RsmI ( Supplementary Table...”
- Arginine as an environmental and metabolic cue for cyclic diguanylate signalling and biofilm formation in Pseudomonas putida
Barrientos-Moreno, Scientific reports 2020 - “...in c-di-GMP signalling in S. enterica serovar Typhimurium 9 . Two proteins, corresponding to loci PP_0282 and PP_4486, present around 40% identical residues with ArtI of S. enterica , and a third one, encoded by PP_3593, shows 36% identity. The three are periplasmic substrate binding proteins...”
- “...genes are located in clusters encoding predicted amino acid ABC transporters (Supplementary Fig. S5 ). PP_0282 is annotated in the Pseudomonas genome database ( https://www.pseudomonas.com ; 20 ) as ArtJ ( l -arginine ABC transporter substrate-binding subunit) and PP_4486 as ArgT (lysine/arginine/ornithine ABC transporter substrate-binding protein);...”
- The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
Poblete-Castro, Microbial cell factories 2012 - “...and other compounds across the membrane, as well as periplasmic ABC transporters (encoded by PP_1071, PP_0282, PP_0112, PP_0885) (Table 3 ) were clearly downregulated. The dual limitation triggered high induction of only one ABC transporter, LivK (26.4-fold), which is one of the five proteins that form...”
- UEG Week 2024 Poster Presentations
, United European gastroenterology journal 2024 - UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
Poblete-Castro, Microbial cell factories 2012 - “...amino acid ABC transporter PP1071 only in C 23 -2.0 n.s. amino acid ABC transporter PP0282 -33.3 15 -1.2 n.s. Branched-chain amino acid ABC PP4867 -16.7 11 1.8 n.s. Dipeptide ABC transporter PP0885 -5.0 22 1.2 n.s. Amino acid biosynthesis PP0671 GlyA-2 -3.6 20 -1.3 n.s....”
- Comparative transcriptomics and proteomics of p-hydroxybenzoate producing Pseudomonas putida S12: novel responses and implications for strain improvement
Verhoef, Applied microbiology and biotechnology 2010 - “...) PP3433 1.5 d 2.8 Transport systems Amino acid ABC transporter, periplasmic amino acid-binding protein PP0282 1.6 Aromatic amino acid transporter ( aroP2 ) PP0927 3.0 9.0 Amino acid ABC transporter ATP-binding protein PP1068 2.5 Amino acid ABC transporter, periplasmic amino acid-binding protein PP1071 0.640.01 c...”
- Multiple and interconnected pathways for L-lysine catabolism in Pseudomonas putida KT2440
Revelles, Journal of bacteriology 2005 - “...(PP5257) amaB (PP5258) cadA (PP4140) Periplasmic protein (PP0282) Periplasmic protein (PP4486) P. syringae sv.syringae PATHWAYS FOR L-LYSINE CATABOLISM IN P....”
lpg0491 amino acid (glutamine) ABC transporter, periplasmic amino acid binding protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
24% identity, 43% coverage
- Identification of differentially expressed Legionella genes during its intracellular growth in Acanthamoeba
Quan, Heliyon 2020 - “...4.995 DNA binding stress protein lpg1706 4.916 arginine N-succinyltransferase subunit beta lpg1940 4.882 peptide synthetase lpg0491 4.237 amino acid ABC transporter substrate-binding protein lpg0594 4.185 hypothetical protein nuoM 3.971 NADH dehydrogenase I subunit M lpg0797 3.828 tRNA-Met lpg0146 3.807 transposase B, TnpA mutL 3.715 DNA mismatch...”
- Legionella Pneumophila Transcriptome during Intracellular Multiplication in Human Macrophages
Faucher, Frontiers in microbiology 2011 - “...function (lpg2527). Also highly induced intracellularly is a gene encoding a putative glutamine ABC transporter (lpg0491), which is encoded next to the argR gene (lpg0490). The ArgR arginine repressor is required for maximal growth of L. pneumophila in its ameba host Acanthamoeba castellanii (Hovel-Miner et al.,...”
- “...lpg1670 ORF 3.6 2.2 4.9 5.6 lpg1454 Multidrug efflux protein, putative 2.5 4.9 5.4 5.5 lpg0491 Glutamine ABC transporter, putative 2.4 2.3 4.4 5.3 lpg1625 Small ORF (130aa), Icm/Dot effector lem12 0.1 4.6 4.5 5.3 lpg1324 Major facilitator family transporter lbtB 3.1 3.9 5.4 5.2 lpg1420...”
- ArgR-regulated genes are derepressed in the Legionella-containing vacuole
Hovel-Miner, Journal of bacteriology 2010 - “...the most highly ArgR-regulated genes in the genome, lpg0491 to lpg0493 (exponential-phase, log2 ratio of 7.6 to 7.3), which encode a putative amino acid...”
- “...along with a putative amino acid ABC transporter (lpg0491 to lpg0496). The genomic organization of this region is conserved among all sequenced L. pneumophila...”
SCO5776 glutamate binding protein from Streptomyces coelicolor A3(2)
O50494 Glutamate binding protein from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
25% identity, 51% coverage
- Characterization of the Streptomyces coelicolor Glycoproteome Reveals Glycoproteins Important for Cell Wall Biogenesis
Keenan, mBio 2019 - “...DacC, putative d -alanyl- d -alanine carboxypeptidase 1 Y; 0.711 Y; 0.427 SpI; 27.3476 Secreted SCO5776 Glutamate binding protein Y; 0.618 N SpI; 21.8509 Secreted SCO3353 Hypothetical protein N N N Other SCO4307 MurQ, N -acetylmuramic acid-6-phosphate etherase N N N Other SCO5115 BldKD, putative ABC...”
- “...are, or are predicted to be, substrate binding proteins that interact with ABC transporters (SCO0472, SCO5776, SCO7218, SCO4885, and SCO4142). Nearly 50% of the glycoproteins identified in this study are putative membrane proteins with predicted functions, including transport (SCO4141 and SCO5818) and serine/threonine kinases (SCO3848), as...”
- Comparative proteomic analysis of Streptomyces lividans Wild-Type and ppk mutant strains reveals the importance of storage lipids for antibiotic biosynthesis
Le, Applied and environmental microbiology 2013 - “...62/5.3 202 173 55 32 Up Down 4 4 SCO5477 SCO5776 O86572 O50494 62/5.6 27/5.1 174 99 27 32 Down Down 4 4 Phosphate binding protein Phosphate transport system...”
- “...hand, the glutamate binding protein involved in glutamate uptake (SCO5776) was less abundant in the ppk mutant. These results suggest that in the ppk mutant...”
- ArgR of Streptomyces coelicolor is a versatile regulator
Pérez-Redondo, PloS one 2012 - “...metabolism, such as those for serine hydroxymethyltransferase (SCO4837), NAD-dependent glutamate dehydrogenase (SCO2999), glutamate binding protein (SCO5776), and the B 12 -dependent and the B 12 -independent methionine synthases MetH and MetE (SCO1657 and SCO0985, respectively). Two genes involved in sporulation regulation, and five genes for aerial...”
- Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture
Thomas, Molecular & cellular proteomics : MCP 2012 - “...SCO6282 SCO4709 SCO4762 SCO4687 SCO4710 SCO1505 SCO5500 SCO5776 SCO0527 SCO5371 SCO5477 SCO1598 SCO4703 SCO4653 SCO4649 SCO4702 SCO4721 SCO4718 SCO5595 SCO4091...”
- “...acid-binding protein SCO2008 and the glutamatebinding protein GluB SCO5776 were all highly abundant; the first two may be recycling amino acids and peptides...”
- Lack of A-factor production induces the expression of nutrient scavenging and stress-related proteins in Streptomyces griseus
Birkó, Molecular & cellular proteomics : MCP 2009 - “...SCO7020 (78%), SAV5981 (73%) SCO7020 (78%), SAV5981 (73%), SCO5776 (40%), SAV2485 (55%) SCO2231 (48%), SAV5977 (48%) SCO5776 (40%), SAV2485 (55%) SCO1793 (81%),...”
- “...proteins related to ABC transporter systems (including SCO5776, SCO2231, and SCO6009 whose orthologues we found in this study), which was considered...”
- Comparative proteomic analysis of Streptomyces lividans Wild-Type and ppk mutant strains reveals the importance of storage lipids for antibiotic biosynthesis
Le, Applied and environmental microbiology 2013 - “...173 55 32 Up Down 4 4 SCO5477 SCO5776 O86572 O50494 62/5.6 27/5.1 174 99 27 32 Down Down 4 4 Phosphate binding protein Phosphate transport system regulator...”
TC 3.A.1.3.21 / Q9I484 Amino acid ABC transporter periplasmic binding protein, component of Hydroxy L-proline uptake porter, HprABC from Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
PA1260 probable binding protein component of ABC transporter from Pseudomonas aeruginosa PAO1
25% identity, 52% coverage
Q98FA8 Amino acid ABC transporter, periplasmic amino acid-binding protein from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
23% identity, 71% 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 - “...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 transport, the...”
A9497_03405 ABC transporter substrate-binding protein/permease from Streptococcus thermophilus
31% identity, 30% coverage
- Technological and Genomic Analysis of Roles of the Cell-Envelope Protease PrtS in Yoghurt Starter Development
Tian, International journal of molecular sciences 2018 - “...protein Amino acid A9497_00725 A9497_04145 AKL23_RS04220 AKL23_RS07755 ATP-binding cassette (ABC) transporter ATP-binding protein A9497_00720 A9497_04150 A9497_03405 A9497_03795 AKL23_RS04215 AKL23_RS07760 AKL23_RS07020 AKL23_RS07405 ABC transporter permease A9497_04155 A9497_03360 A9497_03370 A9497_07620 AKL23_RS07765 AKL23_RS06975 AKL23_RS06985 AKL23_RS06990 ABC transporter substrate-binding protein A9497_03375 A9497_03785 A9497_07595 AKL23_RS07395 AKL23_RS01465 AKL23_RS01490 Amino acid A9497_08630 AKL23_RS02545...”
IUJ47_RS06845 amino acid ABC transporter substrate-binding protein/permease from Enterococcus faecalis
29% identity, 21% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...protein/permease IUJ47_RS07395 0.116 Amino acid ABC transporter ATP-binding protein IUJ47_RS10590 0.124 ABC transporter ATP-binding protein/permease IUJ47_RS06845 0.129 Amino acid ABC transporter substrate-binding protein/permease IUJ47_RS07470 0.136 Oligopeptide ABC transporter permease Opp1B IUJ47_RS02495 0.157 Peptide ABC transporter substrate-binding protein IUJ47_RS07475 0.198 Oligopeptide ABC transporter permease Opp1C IUJ47_RS01265 0.211...”
AKL23_RS07020 ABC transporter substrate-binding protein/permease from Streptococcus thermophilus
31% identity, 30% coverage
- Technological and Genomic Analysis of Roles of the Cell-Envelope Protease PrtS in Yoghurt Starter Development
Tian, International journal of molecular sciences 2018 - “...A9497_04145 AKL23_RS04220 AKL23_RS07755 ATP-binding cassette (ABC) transporter ATP-binding protein A9497_00720 A9497_04150 A9497_03405 A9497_03795 AKL23_RS04215 AKL23_RS07760 AKL23_RS07020 AKL23_RS07405 ABC transporter permease A9497_04155 A9497_03360 A9497_03370 A9497_07620 AKL23_RS07765 AKL23_RS06975 AKL23_RS06985 AKL23_RS06990 ABC transporter substrate-binding protein A9497_03375 A9497_03785 A9497_07595 AKL23_RS07395 AKL23_RS01465 AKL23_RS01490 Amino acid A9497_08630 AKL23_RS02545 Transporter A9497_02760 A9497_03620 A9497_09055...”
A1S_1490 glutamate/aspartate transport protein from Acinetobacter baumannii ATCC 17978
24% identity, 49% coverage
- Mucin acts as a nutrient source and a signal for the differential expression of genes coding for cellular processes and virulence factors in Acinetobacter baumannii
Ohneck, PloS one 2018 - “...ClpX-ClpP ATP-dependent serine protease Amino acid/peptide transport A1S_1467 2.003213585 0.023546957 Glutamate symport transmembrane protein, GltT/GltP A1S_1490 2.962050012 0.001116133 Glutamate/aspartate periplasmic-binding protein, GltI A1S_1491 3.600540965 5.80563E -05 Glutamate/aspartate transport permease protein, GltJ A1S_1492 3.366102462 0.000230756 Glutamate/aspartate transport permease protein, GltK A1S_1493 3.441857707 9.51136E -05 Glutamate/aspartate transport ATP-binding...”
- Response to Bile Salts in Clinical Strains of Acinetobacter baumannii Lacking the AdeABC Efflux Pump: Virulence Associated with Quorum Sensing
López, Frontiers in cellular and infection microbiology 2017 - “...salts (0.5%) and tigecycline (0.5 mg/L), and (ii) expression of genes determined by microarray analysis (A1S_1490, A1S_0115, A1S_1295, and A1S_1510). The studies were carried out with the Lightcycler 480 RNA MasterHydrolysis Probe (Roche, Germany). The UPL Taqman Probes (Universal Probe Library-Roche, Germany) and primers used are...”
- “...LysR regulator family 2.50 Regulatory Acinetobacter baumannii ATCC 17978 adeB vs. Acinetobacter baumannii ATCC 17978 A1S_1490 Glutamate/Aspartate transporter 1.50 Acid tolerance A1S_0658 Transposase (ISAba1) 2.57 Mobility of genes A1S_0657 Transposase (ISAba2) 2.21 A1S_2218 CsuA/B 1.76 Surface motility/biofilm A1S_1071 Hypothetical protein 1.88 A1S_2652 Hypothetical protein 1.88 A1S_3020...”
SPD_0615 transporter substrate-binding domain-containing protein from Streptococcus pneumoniae D39
26% identity, 37% coverage
- The five homologous CiaR-controlled Ccn sRNAs of Streptococcus pneumoniae modulate Zn-resistance
De, PLoS pathogens 2024 - “...2.91 4.77 SPD_0502 bglF -glucoside PTS transporter subunit 3.07 5.65 SPD_0503 bglA-2 6-phospho--glucosidase 2.57 4.79 SPD_0615 glnH3 degenerate glutamine ABC transporter subunit 11.6 4.05 SPD_0616 glnQ3 glutamine ABC transporter subunit 8.90 3.07 SPD_0617 glnP3b glutamine ABC transporter subunit 11.1 3.63 SPD_0618 glnP3a glutamine ABC transporter subunit...”
- “...transporter subunit 3.07 4.65 SPD_0503 bglA-2 6-phospho--glucosidase 2.57 3.75 SPD_0537 putative Zn-dependent protease 2.07 2.21 SPD_0615 glnH3 degenerate glutamine ABC transporter subunit 11.6 18.0 SPD_0616 glnQ3 glutamine ABC transporter subunit 8.90 16.8 SPD_0617 glnP3b glutamine ABC transporter subunit 11.1 15.8 SPD_0618 glnP3a glutamine ABC transporter subunit...”
- Deletion of the Zinc Transporter Lipoprotein AdcAII Causes Hyperencapsulation of Streptococcus pneumoniae Associated with Distinct Alleles of the Type I Restriction-Modification System
Durmort, mBio 2020 - “...1.00 SPD_0613 Hypothetical protein 1.70 1.83 1.09 SPD_0614 ABC transporter, ATP-binding protein 1.76 1.77 1.11 SPD_0615 ABC transporter substrate binding protein 1.51 2.25 1.25 SPD_0616 glnQ Amino acid ABC transporter ATPase 1.56 2.38 1.13 SPD_0617 glnP Amino acid ABC transporter permease 1.76 2.64 1.25 SPD_0618 glnP...”
- Cysteine-Mediated Gene Expression and Characterization of the CmbR Regulon in Streptococcus pneumoniae
Afzal, Frontiers in microbiology 2016 - “...5,10-methylenetetrahydrofolate reductase, MetF 7.9 spd_0540 Amino acid ABC transporter, amino acid-binding protein, putative, GshT 4.8 spd_0615 ABC transporter substrate-binding protein, authentic truncation 3.2 spd_0616 Amino acid ABC transporter, ATP-binding protein 1.9 spd_0617 Amino acid ABC transporter, permease protein 2.0 spd_0618 Amino acid ABC transporter, permease protein...”
BP0057 amino-acid ABC transporter binding protein precursor from Bordetella pertussis Tohama I
23% identity, 67% coverage
SP_0708 transporter substrate-binding domain-containing protein from Streptococcus pneumoniae TIGR4
26% identity, 37% coverage
4g4pA / Q837S0 Crystal structure of glutamine-binding protein from enterococcus faecalis at 1.5 a (see paper)
29% identity, 44% coverage
- Ligand: glutamine (4g4pA)
2ylnA / Q5F9M1 Crystal structure of the l-cystine solute receptor of neisseria gonorrhoeae in the closed conformation (see paper)
24% identity, 52% coverage
NGO0372 putative ABC transporter, periplasmic binding protein, amino acid from Neisseria gonorrhoeae FA 1090
24% identity, 52% coverage
- Sweet complexity: <i>O</i>-linked protein glycosylation in pathogenic <i>Neisseria</i>
Børud, Frontiers in cellular and infection microbiology 2024 - “...2024 ) NGO0265 NEIS0643, NMB0692 Putative tetrapac protein Membrane, Transmembrane ( Hadjineophytou etal., 2024 ) NGO0372 NEIS0739, NMB0787 Putative ABC transporter, putative amino acid permease substrate-binding protein Periplasmic protein ( Vik etal., 2009 ; Anonsen etal., 2012b ; Hadjineophytou etal., 2024 ) NGO0572 NEIS1270, NMB1332 Putative...”
- Huanglongbing Pandemic: Current Challenges and Emerging Management Strategies
Ghosh, Plants (Basel, Switzerland) 2022 - “...0.030 M [ 143 ] LAO Salmonella typhimurium 1LST Lysine 0.014 M [ 143 ] Ngo0372 Neisseria gonorrhoeae 2YLN Cystine 0.021 M [ 144 ] Ngo2014 Neisseria gonorrhoeae 2YJP Cysteine 0.026 M [ 144 ] CLasTcyA Candidatus Liberibacter asiaticus 6A80 Cystine 1.26 M [ 145 ]...”
- Proteomics-driven Antigen Discovery for Development of Vaccines Against Gonorrhea
Zielke, Molecular & cellular proteomics : MCP 2016 - “...approach (supplemental Table S4, (59)). Within this group only NGO0372 and NGO2012 were downregulated, with average ratios ( S.D.) of 0.4 0.06 and 0.2 0.11,...”
- Quantitative proteomics of the Neisseria gonorrhoeae cell envelope and membrane vesicles for the discovery of potential therapeutic targets
Zielke, Molecular & cellular proteomics : MCP 2014 - “...N NGO2048 azu/NGO0994 NGO1321 NGO0948 NGO0678 NGO0648 mrcA/NGO0099 NGO0238 NGO0372 1.38 0.21 1.09 0.24 1.14 0.25 1.47 0.21 1.08 0.22 1.47 0.12 1.46 0.14 1.1...”
- Crystal structures of two solute receptors for L-cystine and L-cysteine, respectively, of the human pathogen Neisseria gonorrhoeae
Bulut, Journal of molecular biology 2012 (PubMed)- “...structural characterization. The structure of the receptor component Ngo0372 was obtained in a ligand-free open conformation and in a closed conformation when...”
- “...leads to reduction in virulence of N. gonorrhoeae, Ngo0372 might be suited as target for an antimicrobial vaccine. 0 false false ABC transporter l-cystine...”
- Crystal structures of receptors involved in small molecule transport across membranes
Bulut, European journal of cell biology 2012 (PubMed)- “...different sizes of side chains, contrasting the receptors Ngo0372 and Ngo2014 from Neisseria gonorrhaeae that are highly specific for cystine and cysteine,...”
- “...compared with the highly specific receptors AcbH, Ngo0372 and Ngo2014. 0 false false Crystallography ABC transporter Acarbose Galactose Arginine Lysine...”
- Proteomic analysis of Neisseria gonorrhoeae biofilms shows shift to anaerobic respiration and changes in nutrient transport and outermembrane proteins
Phillips, PloS one 2012 - “...NGO0206 putative ABC transporter, periplasmic binding protein, polyamine Amino acids, peptides and amines 1.217 (1) NGO0372 putative ABC transporter, periplasmic binding protein, amino acid Cations and iron carrying compounds 1.109 (1) 0.609 (1) NGO0794 BfrA; bacterioferritin Cations and iron carrying compounds 1.090 (2) NGO0455 hypothetical protein;...”
- Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Isabella, BMC genomics 2011 - “...Transporter Family fbp NGO0217 -4.8 -5.6 ABC-type iron transporter, periplasmic binding protein Fur, Lrp oxiA NGO0372 -6.7 -20.0 Bacterial extracellular solute-binding protein FarR NGO0373 -3.7 -11.1 ABC-type arginine transport system, permease component FarR glnQ NGO0374 -2.9 -11.1 ABC-type amino acid transporter, ATP-binding protein FarR, FNR citT...”
- “...to the genes encoding the iron-binding protein, FbpA (NGO0217), and the solute binding protein, OxiA (NGO0372) confirmed that these genes are anaerobically repressed (Figure 2 H, I ). RT-PCR confirmed that NGO0108, L-lactate dehydrogenase, lldD (NGO0639), thioredoxin, trx1 (NGO0652), heme oxygenase, hemO (NGO1318), and NADH dehydrogenase...”
- More
Q5F9M1 Amino acid ABC transporter substrate-binding protein from Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)
24% identity, 52% coverage
Dtur_1051 extracellular solute-binding protein family 3 from Dictyoglomus turgidum DSM 6724
27% identity, 68% coverage
EF0761 amino acid ABC transporter, amino acid-binding/permease protein from Enterococcus faecalis V583
29% identity, 21% coverage
YPTB1718 putative cystine-binding periplasmic protein from Yersinia pseudotuberculosis IP 32953
26% identity, 56% coverage
- IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
Miller, PLoS pathogens 2014 - “...modulation factor yhbH 2.1 Transport and Binding Proteins (9) YPTB0306 putative sodium:phenylacetate symporter actP 2.4 YPTB1718 putative cystine-binding periplasmic protein fliY 2.4 YPTB2463 PTS system, glucose-specific IIBC component ptsG 2.0 YPTB2682 ABC transporter, periplasmic iron(III)-binding protein sfuA 2.6 YPTB2717 PTS system glucose-specific IIA component, permease crr...”
SUB1152 glutamine ABC transporter, glutamine-binding protein/permease protein from Streptococcus uberis 0140J
31% identity, 21% coverage
PFLU0376 putative ABC transport system, exported protein from Pseudomonas fluorescens SBW25
22% identity, 69% coverage
ECs0946 arginine 3rd transport system periplasmic binding protein from Escherichia coli O157:H7 str. Sakai
24% identity, 67% coverage
PA14_47920 putative binding protein component of ABC transporter from Pseudomonas aeruginosa UCBPP-PA14
24% identity, 52% coverage
SSU1853 amino-acid ABC transporter extracellular-binding protein from Streptococcus suis P1/7
SSUBM407_1923 amino-acid ABC transporter extracellular-binding protein from Streptococcus suis BM407
23% identity, 61% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory