PaperBLAST
PaperBLAST Hits for tr|Q9HT72|Q9HT72_PSEAE High-affinity zinc uptake system membrane protein ZnuB OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=znuB PE=3 SV=1 (262 a.a., MADFLLNALL...)
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>tr|Q9HT72|Q9HT72_PSEAE High-affinity zinc uptake system membrane protein ZnuB OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=znuB PE=3 SV=1
MADFLLNALLAGLALALVAGPLGSFVVWRRMAYFGDTLSHAALLGVALGFLLDVSPTLAV
TVGCVLLAVLLVTLQQRQPLAADTLLGILAHSTLSLGLVTLSFMKEVRVDLMAYLFGDLL
AVSASDLLWIIAGSALVLALICFLWRPLLAITVHEELAKVEGLPVGAIRLALMLLIAIVI
AVAMKIVGVLLITSLLIIPAAAAQRHARSPEQMAVGASLLGLVAVCAGLALSWFKDTPAG
PSIVVSAAGLFLLSFVLPRRTV
Running BLASTp...
Found 205 similar proteins in the literature:
Q9HT72 High-affinity zinc uptake system membrane protein ZnuB from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA14_72590 permease of ABC zinc transporter ZnuB from Pseudomonas aeruginosa UCBPP-PA14
PA5501 permease of ABC zinc transporter ZnuB from Pseudomonas aeruginosa PAO1
IS492_31610 zinc ABC transporter permease subunit ZnuB from Pseudomonas aeruginosa
100% identity, 100% 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 - 3-Benzyl-Hexahydro-Pyrrolo[1,2-a]Pyrazine-1,4-Dione Extracted From Exiguobacterium indicum Showed Anti-biofilm Activity Against Pseudomonas aeruginosa by Attenuating Quorum Sensing
Singh, Frontiers in microbiology 2019 - “...-5.23 PA3824_queA queA S-adenosylmethionine:trna ribosyltransferase-isomerase Q9HXH8 -5.15 PA5501_znuB znuB permease of ABC zinc transporter ZnuB Q9HT72 -4.97 PA2236 pslF hypothetical protein Q9I1N3 -4.76 PA1082_flgG flgG flagellar basal-body rod protein FlgG Q9I4P7 -4.75 PA4309_pctA pctA chemotactic transducer PctA G3XD24 -4.35 PA4224 pchG pyochelin biosynthetic protein PchG G3XCL0...”
- Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
Valzano, Microbiology spectrum 2022 - “...PA14_72580 znuC Zinc ABC transporter, ATP-binding protein ZnuC (zinc uptake) + 1.2E07 0.9 IS492_31610 PA5501 PA14_72590 znuB Zinc ABC transporter, ZnuB permease (zinc uptake) + 1.9E03 0.6 IS492_31780 PA5534 PA14_73000 Hypothetical protein (unknown function, DUF1826 domain-containing protein) + 9.8E23 1.5 IS492_31785 PA5535 PA14_73010 zigA Zinc metallochaperone...”
- Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
Valzano, Microbiology spectrum 2022 - “...PA5500 PA14_72580 znuC Zinc ABC transporter, ATP-binding protein ZnuC (zinc uptake) + 1.2E07 0.9 IS492_31610 PA5501 PA14_72590 znuB Zinc ABC transporter, ZnuB permease (zinc uptake) + 1.9E03 0.6 IS492_31780 PA5534 PA14_73000 Hypothetical protein (unknown function, DUF1826 domain-containing protein) + 9.8E23 1.5 IS492_31785 PA5535 PA14_73010 zigA Zinc...”
- Strategies for Zinc Uptake in Pseudomonas aeruginosa at the Host-Pathogen Interface
Wang, Frontiers in microbiology 2021 - “...homologous to E. coli znuABC , PA5498 ( znuA ), PA5500 ( znuB ), and PA5501 ( znuC ). ZnuA is a zinc-specific solute-binding protein (SBP) with high affinity that exists in the periplasmic space ( Luo and Liu, 2019 ). P. aeruginosa ZnuA has two...”
- Global Analysis of the Zinc Homeostasis Network in Pseudomonas aeruginosa and Its Gene Expression Dynamics
Ducret, Frontiers in microbiology 2021 - “...PA4065 PA4065 Permease of ABC transporter PA4066 PA4066 Solute-binding protein znuA PA5498 Solute-binding protein znuB PA5501 Permease of ABC transporter znuD PA0781 TonB-dependent receptor zrmA PA4837 TonB-dependent receptor zrmD PA4834 Nicotianamine synthase C+/C paralogs dksA PA4723 Supressor protein dksA2 PA5536 Supressor protein rpmE PA5049 Ribosomal protein...”
- ZnuA and zinc homeostasis in Pseudomonas aeruginosa
Pederick, Scientific reports 2015 - “...homologous to E. coli znuABC : PA5498 ( znuA ), PA5500 ( znuB ), and PA5501 ( znuC ), which have also been shown to be under the control of the Zur transcriptional regulator 16 26 . The putative znuA gene is present in a separate...”
- The transcriptional regulator Np20 is the zinc uptake regulator in Pseudomonas aeruginosa
Ellison, PloS one 2013 - “...(PA5498), 40 to 223 (80%) of znuB (PA5500), and 38 to 226 (70%) of znuC (PA5501). The oligonucleotide primers used to produce the mutant alleles added an XbaI site to the ends of the mutant zur allele, EcoRI sites to the end of znuA , and...”
- Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
Valzano, Microbiology spectrum 2022 - “...IS492_31605 PA5500 PA14_72580 znuC Zinc ABC transporter, ATP-binding protein ZnuC (zinc uptake) + 1.2E07 0.9 IS492_31610 PA5501 PA14_72590 znuB Zinc ABC transporter, ZnuB permease (zinc uptake) + 1.9E03 0.6 IS492_31780 PA5534 PA14_73000 Hypothetical protein (unknown function, DUF1826 domain-containing protein) + 9.8E23 1.5 IS492_31785 PA5535 PA14_73010 zigA...”
T1E_4763 zinc ABC transporter permease subunit ZnuB from Pseudomonas putida DOT-T1E
85% identity, 99% coverage
PP0117, PP_0117 zinc ABC transporter, permease protein ZnuB from Pseudomonas putida KT2440
85% identity, 99% coverage
WP_039607122 zinc ABC transporter permease subunit ZnuB from Pseudomonas flexibilis
79% identity, 99% coverage
VF_0828 zinc ABC transporter membrane protein from Vibrio fischeri ES114
VF_0828 zinc ABC transporter permease subunit ZnuB from Aliivibrio fischeri ES114
65% identity, 89% coverage
VP_RS04150, WU75_19805 zinc ABC transporter permease subunit ZnuB from Vibrio parahaemolyticus RIMD 2210633
62% identity, 99% coverage
- ZrgA contributes to zinc acquisition in Vibrio parahaemolyticus
Zheng, Virulence 2023 - “...21 ], was among the most highly upregulated genes ( Table 1 ). The genes VP_RS04150 to VP_RS04160 , which encode the conserved Zn transporter ZnuABC, were upregulated approximately 8- to 16-fold ( Table 1 ). Notably, the operon VP_RS01455 to VP_RS01475 , which encodes the...”
- “...protein VP_RS01470 205.8130005 zrgA DUF2796 domain-containing protein/Predicted zinc-binding protein VP_RS01475 147.2656093 zrgD DUF2607 domain-containing protein VP_RS04150 8.2713958 znuB zinc ABC transporter permease subunit ZnuB VP_RS04155 7.959515461 znuC zinc ABC transporter ATP-binding protein ZnuC VP_RS04160 16.16829765 znuA zinc ABC transporter substrate-binding protein ZnuA VP_RS09335 2.1031618 ribA GTP...”
- 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 - “...WU75_19810 znuC 2.491 Zinc ABC transporter ATPase WU75_02265 artP 2.617 Arginine ABC transporter ATP-binding protein WU75_19805 znuB 2.666 Membrane protein WU75_00425 macB 14.353 Macrolide transporter Two-component system WU75_07480 glnG 0.186 Nitrogen regulation protein NR(I) WU75_13735 mcp 0.218 Chemotaxis protein WU75_15795 tctB 0.237 TctB WU75_21750 dctD 0.288...”
VpaChn25_0846 zinc ABC transporter permease subunit ZnuB from Vibrio parahaemolyticus
62% identity, 99% coverage
BC33_RS12920 zinc ABC transporter permease subunit ZnuB from Escherichia coli ATCC 700728
ECs2569 hypothetical protein from Escherichia coli O157:H7 str. Sakai
60% identity, 97% coverage
STM1893 ABC superfamily (atp_bind) high affinity Zn transport protein from Salmonella typhimurium LT2
60% identity, 97% coverage
CUC46_10485 zinc ABC transporter permease subunit ZnuB from Citrobacter freundii
60% identity, 97% coverage
- Citrobacter freundii fitness during bloodstream infection
Anderson, Scientific reports 2018 - “...cell division protein 3.3 (1.210 7 ) pfkA CUC46_21195 6-phosphofructokinase 2.0 (3.210 2 ) znuB CUC46_10485 zinc ABC transporter permease 1.1 (9.010 1 ) a Decrease in fitness as determined by the abundance of transposon mutants recovered from murine spleens relative to inputs as fold-change (FC)...”
ZnuB / b1859 Zn2+ ABC transporter membrane subunit (EC 7.2.2.20) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
ZnuB / P39832 Zn2+ ABC transporter membrane subunit (EC 7.2.2.20) from Escherichia coli (strain K12) (see paper)
TC 3.A.1.15.5 / P39832 ZnuB aka B1859, component of Zinc (Zn2+) porter of E. coli, ZnuABC from Escherichia coli (see 7 papers)
b1859 high-affinity zinc transporter membrane component from Escherichia coli str. K-12 substr. MG1655
NP_416373 Zn(2(+)) ABC transporter membrane subunit from Escherichia coli str. K-12 substr. MG1655
60% identity, 97% coverage
- substrates: Zn2+
tcdb comment: Required for Zn2+ homeostasis and virulence in the close E. coli relative, Salmonella enterica (Ammendola et al., 2007) - NfiS, a species-specific regulatory noncoding RNA of Pseudomonas stutzeri, enhances oxidative stress tolerance in Escherichia coli
Hu, AMB Express 2019 - “...b0089 ftsW 1.48 Putative lipid II flippase integral membrane protein FtsZ ring stabilizer 4.60E03 26.51 b1859 znuB 1.00 Zinc ABC transporter permease 4.87E03 26.39 b2832 ygdQ 1.84 UPF0053 family inner membrane protein 4.89E03 26.38 The impact of NfiS on oweS and xanP gene expression was less...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
King, Applied and environmental microbiology 2010 - “...ECs5321 ECs0206 ECs3395 ECs0055 ECs2569 b4361 b0210 b2529 b0050 b1859 bcsE (yhjS) yecJ yhcN yheO yaiZ ybeD ydcX yebG yohJ yieP rrmJ yiaU zntR xseA nudE pdhR...”
- Severe zinc depletion of Escherichia coli: roles for high affinity zinc binding by ZinT, zinc transport and zinc-independent proteins
Graham, The Journal of biological chemistry 2009 - “...b4046 2.38 1.37 0.0725 0.9578 znuC znuB zntR zraS b1858 b1859 b3292 b4003 1.36 1.34 1.34 1.32 0.2294 zraP b4002 1.25 0.9322 yiiP b3915 1.17 0.2742 zitB zntA...”
- SoxS increases the expression of the zinc uptake system ZnuACB in an Escherichia coli murine pyelonephritis model.
Warner, Journal of bacteriology 2012 - GeneRIF: This work implicates SoxS control of znuCB expression as a key factor in persistence of Escherichia coli in murine pyelonephritis.
EW045_RS10010 zinc ABC transporter permease subunit ZnuB from Klebsiella pneumoniae
60% identity, 97% coverage
- Zinc acquisition and its contribution to Klebsiella pneumoniae virulence
Maunders, Frontiers in cellular and infection microbiology 2023 - “...WP_004890185.1 56.97 n/a EW045_RS05295 ZniA AAC74927.2 WP_023286807.1 54.68 n/a EW045_RS05545 ZnuB AAC74929.1 WP_004212745.1 98.8 b1859 EW045_RS10010 78.4 ZnuC AAC74928.1 WP_002911449.1 98.85 b1858 EW045_RS10015 76.8 ZinT AAC75039.1 WP_048269641.1 86.11 b1973 EW045_RS26395 59.0 ZupT AAC76076.1 WP_038808242.1 96.89 b3040 EW045_RS03460 71.7 PitA AAC76518.1 WP_002921200.1 97.6 b3493 EW045_RS01375 81.7 MntH...”
PMI1150 high-affinity zinc uptake system membrane protein from Proteus mirabilis HI4320
56% identity, 99% coverage
BCAN_B1152 29 kDa membrane protein in psaA 5'region from Brucella canis ATCC 23365
BAB2_1081 ABC transporter, family 3:Sodium:dicarboxylate symporter from Brucella melitensis biovar Abortus 2308
58% identity, 88% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BRA0675 BOV_A0632 BCAN_B0674 35 MET Zinc import IM BMEII0176, ZnuB BruAb21061, ZnuB BRA1124, ZnuB BOV_A1029 BCAN_B1152 MET Zinc import ABC BMEII0177, ZnuC BruAb21060, ZnuC BRA1123, ZnuC BOV_A1028 BCAN_B1151 MET Zinc import BP BMEII0178, ZnuA BruAb21059, ZnuA BRA1122, ZnuA BOV_A1027 BCAN_B1150 36 MKL Involved in toluene tolerance...”
- Transposon Sequencing of Brucella abortus Uncovers Essential Genes for Growth In Vitro and Inside Macrophages
Sternon, Infection and immunity 2018 - “...storage BAB1_0386 BAB1_0387 BAB2_1079 BAB2_1080 BAB2_1081 BAB2_0411 BAB2_0412 BAB1_1589 BAB1_1045 Metabolism BAB2_0366 BAB2_0367 BAB2_0370 BAB2_1013 BAB1_1761...”
- Metal acquisition and virulence in Brucella
Roop, Animal health research reviews 2012 - “...BAB2_0837 MntH Mn 2+ transport BAB1_1460 ZnuA Zn 2+ transport BAB2_1079 ZnuB Zn 2+ transport BAB2_1081 ZnuC Zn 2+ transport BAB2_1080 NikA Ni 2+ transport BAB2_0433/0434 a NikB Ni 2+ transport BAB2_0435 NikC Ni 2+ transport BAB2_0436 NikD Ni 2+ transport BAB2_0437 NikE Ni 2+ transport...”
BMEII0176 HIGH-AFFINITY ZINC UPTAKE SYSTEM MEMBRANE PROTEIN ZNUB from Brucella melitensis 16M
58% identity, 89% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BCAN_B0676 ISVH Iron(III) import BP BMEII0607 BruAb20553 BRA0675 BOV_A0632 BCAN_B0674 35 MET Zinc import IM BMEII0176, ZnuB BruAb21061, ZnuB BRA1124, ZnuB BOV_A1029 BCAN_B1152 MET Zinc import ABC BMEII0177, ZnuC BruAb21060, ZnuC BRA1123, ZnuC BOV_A1028 BCAN_B1151 MET Zinc import BP BMEII0178, ZnuA BruAb21059, ZnuA BRA1122, ZnuA BOV_A1027...”
BRA1124 zinc ABC transporter, permease protein from Brucella suis 1330
58% identity, 88% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BP BMEII0607 BruAb20553 BRA0675 BOV_A0632 BCAN_B0674 35 MET Zinc import IM BMEII0176, ZnuB BruAb21061, ZnuB BRA1124, ZnuB BOV_A1029 BCAN_B1152 MET Zinc import ABC BMEII0177, ZnuC BruAb21060, ZnuC BRA1123, ZnuC BOV_A1028 BCAN_B1151 MET Zinc import BP BMEII0178, ZnuA BruAb21059, ZnuA BRA1122, ZnuA BOV_A1027 BCAN_B1150 36 MKL Involved...”
HI0407 conserved hypothetical integral membrane protein from Haemophilus influenzae Rd KW20
P44691 High-affinity zinc uptake system membrane protein ZnuB from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
53% identity, 99% coverage
- Structural determinants of the interaction between the TpsA and TpsB proteins in the Haemophilus influenzae HMW1 two-partner secretion system
Grass, Journal of bacteriology 2015 - “...laboratory strains that have been described previously. E. coli HI0407 is an enterotoxigenic E. coli strain that was generously provided by M. Keuhn and has...”
- Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
Shahbaaz, PloS one 2013 - “...HP HI0396 950708 P44683 RmlC-like cupins 63. HP HI0398 949499 P44684 ADP-ribose pyrophosphatase 64. HP HI0407 949507 P44691 ABC transporter involved in vitamin B12 uptake, BtuC family protein 65. HP HI0409 949412 P44693 Endopeptidases (Peptidase, M23/M37 family) 66. HP HI0414 949402 Q57392 Porin, opacity type 67....”
- Genome-scale approaches to identify genes essential for Haemophilus influenzae pathogenesis
Wong, Frontiers in cellular and infection microbiology 2012 - “...protein a e NUTRIENT ACQUISITION ZINC HI0119 znuA High-affinity zinc transporter periplasmic component a f HI0407 znuB Zinc transport system permease protein a HI0408 znuC Zinc transport system ATP-binding protein a HI1249 zevA ABC transporter periplasmic component (zinc binding system) a HI1248 zevB ABC transporter permease...”
- Identification of the znuA-encoded periplasmic zinc transport protein of Haemophilus ducreyi
Lewis, Infection and immunity 1999 - “...of this hypothesis, the predicted protein products of ORFs HI0407 and HI0408 identified in the H. influenzae Rd genome (23) have 60 and 48% identity to the...”
- Topology prediction for helical transmembrane proteins at 86% accuracy
Rost, Protein science : a publication of the Protein Society 1996 - “...11 MLLVNLAIFI HI0687 in 10 MNNENMVRVF HI1241 HI0359 HI0392 HI0407 HI0825 HI1248 HI0188 HI1122 HI1 178 HI1187 HI 1307 HI 1548 HI1621 HI1452 HI1620 HI0238 HI03 18...”
- Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
Shahbaaz, PloS one 2013 - “...950708 P44683 RmlC-like cupins 63. HP HI0398 949499 P44684 ADP-ribose pyrophosphatase 64. HP HI0407 949507 P44691 ABC transporter involved in vitamin B12 uptake, BtuC family protein 65. HP HI0409 949412 P44693 Endopeptidases (Peptidase, M23/M37 family) 66. HP HI0414 949402 Q57392 Porin, opacity type 67. HP HI0420...”
- “...be involved in virulence and essential for intracellular survival of pathogens [92] . The protein P44691 was predicted to be a member of ABC 3 transporter family, presumably involved in virulence because they are associated with the uptake of metal ions, such as iron, zinc, and...”
SMc04243 PROBABLE HIGH-AFFINITY ZINC UPTAKE SYSTEM MEMBRANE ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
59% identity, 92% coverage
YPK_2142 ABC-3 protein from Yersinia pseudotuberculosis YPIII
y2251 inner membrane permease of zinc ABC transporter from Yersinia pestis KIM
58% identity, 99% coverage
- Functional versatility of Zur in metal homeostasis, motility, biofilm formation, and stress resistance in Yersinia pseudotuberculosis
Gu, Microbiology spectrum 2024 - “...the 41 DEGs classified under the membrane transport pathway, znuA ( ypk_2140 ), znuB ( ypk_2142 ), and znuC ( ypk_2141 ) were observed to be downregulated by Zur with fold-changes of 3.67, 1.54, and 1.60, respectively. This finding aligns with previous studies ( 30 )....”
- Type VI Secretion System Transports Zn2+ to Combat Multiple Stresses and Host Immunity
Wang, PLoS pathogens 2015 - “...; hcp2 , ypk_0803 ; hcp3 , ypk_1481 ; oxyR , ypk_4079 ; znuB , ypk_2142 ; znuC , ypk_2141 ; fur , ypk_2991 ; katG , ypk_3388; sod ( Fe/Mn ), ypk_1863; sod ( Cu/Zn ), ypk_3445 . Supporting Information S1 Table Bacterial strains and...”
- Znu is the predominant zinc importer in Yersinia pestis during in vitro growth but is not essential for virulence
Desrosiers, Infection and immunity 2010 - “...pestis KIM10. Y. pestis KIM10 locus tags y2249, y2250, y2251, and y3862 were annotated as znuA, znuC, and znuB (Fig. 1A) and pitA, respectively, based on...”
PM0241 unknown from Pasteurella multocida subsp. multocida str. Pm70
PmVP161_0986 zinc ABC transporter permease subunit ZnuB from Pasteurella multocida
54% identity, 97% coverage
VC2083 zinc ABC transporter, permease protein from Vibrio cholerae O1 biovar eltor str. N16961
61% identity, 92% coverage
BOV_A1029 zinc ABC transporter, permease protein from Brucella ovis ATCC 25840
58% identity, 88% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BruAb20553 BRA0675 BOV_A0632 BCAN_B0674 35 MET Zinc import IM BMEII0176, ZnuB BruAb21061, ZnuB BRA1124, ZnuB BOV_A1029 BCAN_B1152 MET Zinc import ABC BMEII0177, ZnuC BruAb21060, ZnuC BRA1123, ZnuC BOV_A1028 BCAN_B1151 MET Zinc import BP BMEII0178, ZnuA BruAb21059, ZnuA BRA1122, ZnuA BOV_A1027 BCAN_B1150 36 MKL Involved in toluene...”
CD16_RS02450, NKF51_02430 metal ABC transporter permease from Candidatus Liberibacter asiaticus
CLIBASIA_03030 zinc uptake ABC transporter, permease protein from Candidatus Liberibacter asiaticus str. psy62
43% identity, 98% coverage
- Pathogenicity and Transcriptomic Analyses of Two "Candidatus Liberibacter asiaticus" Strains Harboring Different Types of Phages
Zheng, Microbiology spectrum 2023 - “...lolC , and mlaF ) were upregulated in strain PGD (Table S6). The gene znuB (NKF51_02430 [2.4-fold]), a member of the Znu system involved in zinc import, was significantly upregulated in strain PGD ( Fig.5 ; Table S6). Previous studies found that Ca . Liberibacter asiaticus...”
- A Significantly High Abundance of "Candidatus Liberibacter asiaticus" in Citrus Fruit Pith: in planta Transcriptome and Anatomical Analyses
Fang, Frontiers in microbiology 2021 - “...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 ). The expression...”
- The ABC transporters in Candidatus Liberibacter asiaticus
Li, Proteins 2012 - “...TauB E. coli 3e 39 42 III(i) MET CLIBASIA_03025 ZnuC E. coli 3e 59 45 CLIBASIA_03030 PF00950 (CL0142) CLIBASIA_03020 (PP) Zinc III(i) MET CLIBASIA_02125 SitB S. typhimurium 6e 71 52 CLIBASIA_02130, CLIBASIA_02135 PF00950 (CL0142) CLIBASIA_02120 (PP) Manganese and iron III(i) MKL CLIBASIA_00090 LinL S. japonicum 6e...”
RSP_3567 ABC zinc tranporter, inner membrane subunit ZnuB from Rhodobacter sphaeroides 2.4.1
55% identity, 92% coverage
ECH_0517 putative cation ABC transporter, permease protein from Ehrlichia chaffeensis str. Arkansas
35% identity, 97% coverage
- Impact of Three Different Mutations in Ehrlichia chaffeensis in Altering the Global Gene Expression Patterns
Kondethimmanahalli, Scientific reports 2018 - “...addition, transcripts for two membrane transporters: cation ABC transporter permease protein transcript of the gene ECH_0517 and another ABC transporter permease protein transcript of the gene ECH_0972 were downregulated. Three genes coding for phage-like proteins {phage prohead protease (ECH_0032), phage portal protein (ECH_0033), and phage major...”
- “...uroporphyrinogen-III synthase ECH_0485 537 172 3.14 diaminopimelate decarboxylase ECH_0504 859 288 3.03 GTP-binding protein EngA ECH_0517 503 52 10 putative cation ABC transporter, permease protein ECH_0523 1525 159 10 conserved domain protein ECH_0541 251 124 2 5-formyltetrahydrofolate cyclo-ligase family protein ECH_0602 84 24 3.57 formamidopyrimidine-DNA glycosylase...”
TC 3.A.1.15.6 / Q9RNI8 MtsC aka SPY0456, component of Iron (Fe2+)/Zinc (Zn2+)/Copper (Cu2+) porter from Streptococcus pyogenes (see paper)
mtsC / GB|AAX71473.1 metal ion ABC transporter, permease protein from Streptococcus pyogenes MGAS9429 (see paper)
SPy0456 ABC transporter (permease protein) from Streptococcus pyogenes M1 GAS
38% identity, 91% coverage
- substrates: Cu2+, Fe2+, Zn2+
- Peroxide stimulon and role of PerR in group A Streptococcus
Grifantini, Journal of bacteriology 2011 - “...iron transport system (SPy0453, SPy0454, and SPy0456), the FhuGBDA or FtsDCBA (SPy0383-SPy0386) heme/ferrichrome transport system, and Shr/Shp/SiaABCD...”
- Identification and characterization of HtsA, a second heme-binding protein made by Streptococcus pyogenes
Lei, Infection and immunity 2003 - “...spy0386 (28); and mtsA (spy0453), mtsB (spy0454), and mtsC (spy0456) (18). The MtsA protein has been shown to have broad specificity for metal ions (18). shp is...”
- Identification and characterization of a novel heme-associated cell surface protein made by Streptococcus pyogenes
Lei, Infection and immunity 2002 - “...spy0386 (not yet characterized); and spy0453, spy0454, and spy0456. Proteins encoded by spy0383 to spy0386 are homologous to a ferrichrome ABC transporter, and...”
- Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica
Paparoditis, Biochimica et biophysica acta 2014 - “...P0AGH8 6 anions Phosphate Q7UP19 6 3.A.1.10.1 P21408 1 cations Fe 3+ Q7UYK9 1 3.A.1.15.6 Q9RNI8 7 cations Cu 2+ , Zn 2+ , Fe 2+ Q7UIM9 9 3.A.1.15.8 P96116 1 cations Mn 2+ , Zn 2+ , Fe 2+ Q7UIM5 1 3.A.1.15.8 P96118 7 cations...”
Spy49_0383 Integral membrane protein MtsC, ABC transporter from Streptococcus pyogenes NZ131
38% identity, 91% coverage
7kypF / A0A0H2ZPI2 Psabc from streptococcus pneumoniae in complex with fab (see paper)
36% identity, 89% coverage
- Ligand: cyclohexyl-hexyl-beta-d-maltoside (7kypF)
TC 3.A.1.15.14 / Q2MGF9 Putative manganese ABC transporter, permease protein, component of High affinity Mn2+ uptake complex, PsaABC from Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
SPD_1462 manganese ABC transporter, permease protein, putative from Streptococcus pneumoniae D39
SP_1649 putative manganese ABC transporter permease from Streptococcus pneumoniae TIGR4
36% identity, 91% coverage
- substrates: Mn2+
- Inactivation of Transcriptional Regulator FabT Influences Colony Phase Variation of Streptococcus pneumoniae
Zhang, mBio 2021 - “...gtrB Bactoprenol glucosyl transferase 0.80 0.007 SPD_1461 psaB Manganese ABC transporter, ATP-binding protein 1.98 0.009 SPD_1462 psaC Manganese ABC transporter, permease protein, putative 1.97 0.006 SPD_1463 psaA Metal ABC transporter substrate-binding lipoprotein/adhesin PsaA 1.88 0.022 SPD_1468 gpmA Phosphoglycerate mutase 0.98 0.001 SPD_1483 murF UDP- N -acetylmuramoyl-tripeptide...”
- The structural basis of bacterial manganese import
Neville, Science advances 2021 - “...genome to determine the presence, amino acid sequence, and alignment of spd_1461 ( psaB ), spd_1462 ( psaC ), and spd_1463 ( psaA ) across the 20,020 clinical isolates using the screen_assembly script ( 53 ) and BLASTN v2.9.0 with parameters of 80% coverage and 80%...”
- S1 Domain RNA-Binding Protein CvfD Is a New Posttranscriptional Regulator That Mediates Cold Sensitivity, Phosphate Transport, and Virulence in Streptococcus pneumoniae D39
Sinha, Journal of bacteriology 2020 (secret) - Cysteine-Mediated Gene Expression and Characterization of the CmbR Regulon in Streptococcus pneumoniae
Afzal, Frontiers in microbiology 2016 - “...GlnQ -2.0 spd_1402 Non-heme iron-containing ferritin -2.6 spd_1461 Manganese ABC transporter, ATP-binding protein, PsaB -4.0 spd_1462 Manganese ABC transporter, permease protein, putative, PsaC -4.0 spd_1463 ABC transporter, substrate binding lipoprotein -4.0 a Gene numbers refer to D39 locus tags. b D39 annotation/TIGR4 annotation ( Lanie et...”
- Ni2+-Dependent and PsaR-Mediated Regulation of the Virulence Genes pcpA, psaBCA, and prtA in Streptococcus pneumoniae
Manzoor, PloS one 2015 - “...wall-associated serine protease PrtA 4.53 (1.22) spd_1461 Manganese ABC transporter, ATP-binding protein, PsaB 2.83 (0.24) spd_1462 Manganese ABC transporter, permease protein, PsaC 3.15 (0.30) spd_1463 Manganese ABC transporter, ATP-binding protein, PsaA 5.88 (1.55) spd_1965 Choline binding protein PcpA 10.53 (3.09) a Gene numbers refer to D39...”
- “...Cell wall-associated serine protease PrtA 3.02 6.65E-05 spd_1461 Manganese ABC transporter, ATP-binding protein 2.39 7.47E-05 spd_1462 Manganese ABC transporter, permease protein, putative 2.52 1.46E-04 spd_1450 Iron-dependent transcriptional regulator (PsaR) -4.43 7.45E-07 spd_1632 Hypothetical protein -2.22 9.00E-04 spd_1965 Choline binding protein PcpA 14.42 2.65E-09 a Gene numbers...”
- A random six-phase switch regulates pneumococcal virulence via global epigenetic changes
Manso, Nature communications 2014 - “...Uncharacterized protein 2.4 2.3 2.4 SPD_1461 psaB Manganese ABC transporter, ATP binding 2.8 2.9 2.6 SPD_1462 psaC Manganese ABC transporter, permease 3.0 3.0 2.7 SPD_1463 psaA Manganese, substrate-binding lipoprotein 2.6 2.9 2.7 SPD_1535 scrR Sucrose operon repressor 2.2 2.1 2.4 SPD_1992 PTS system, IIA component 2.7...”
- The Two-Component System YesMN Promotes Pneumococcal Host-to-Host Transmission and Regulates Genes Involved in Zinc Homeostasis
Zafar, Infection and immunity 2023 (secret) - The Effect of Impaired Polyamine Transport on Pneumococcal Transcriptome
Nakamya, Pathogens (Basel, Switzerland) 2021 - “...3.2 <0.0001 Manganese ABC transporter substrate-binding SP_1648 psaB 3.4 <0.0001 Metal ABC transporter ATP-binding protein SP_1649 psaC 3.5 <0.0001 Metal ABC transporter permease SP_0502 glnA 4.2 <0.0001 Glutamine synthetase SP_2148 arcA 4.6 <0.0001 Arginine deiminase SP_2151 arcC 3.7 <0.0001 Carbamate kinase SP_0798 ciaR 3.0 <0.0001 DNA-binding...”
- Electronic Cigarette (E-Cigarette) Vapor Exposure Alters the Streptococcus pneumoniae Transcriptome in a Nicotine-Dependent Manner without Affecting Pneumococcal Virulence
Bagale, Applied and environmental microbiology 2020 (secret) - Polyamine Synthesis Effects Capsule Expression by Reduction of Precursors in Streptococcus pneumoniae
Ayoola, Frontiers in microbiology 2019 - “...Trehalose PTS system, IIABC components 26.2 psaB SP_1648 Manganese ABC transporter, ATP-binding protein 2.7 psaC SP_1649 Putative manganese ABC transporter, permease protein 2.7 psaA SP_1650 Manganese ABC transporter substrate-binding lipoprotein 2.7 Polyamine biosynthesis aguA SP_0921 Putative agmatine deiminase 25.7 aguB SP_0922 Carbonnitrogen hydrolase family protein 19.7...”
- Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
Jiménez-Munguía, PeerJ 2018 - “...gene SP_1872 coding for the iron-compound ABC transporter, the manganese ABC transporter system (genes SP_1648, SP_1649 and SP_1650), the ATP synthase complex (genes SP_1509 to SP_1513), and others including several transporter systems. Also, an operon containing genes for the riboflavin biosynthetic system (genes SP_0175 to SP_0178)...”
- “...SP_1513 5/8 Upregulated 38789 SP_1566, SP_1569 2/6 Upregulated 38795 SP_1591, SP_1592 2/2 Upregulated 38805 SP_1648, SP_1649, SP_1650 3/3 Upregulated 38808 SP_1662, SP_1665 2/8 Upregulated 38809 SP_1669, SP_1670 2/3 Upregulated 38833 SP_1774, SP_1775 2/3 Upregulated 38839 SP_1802, SP_1803, SP_1804 3/4 Upregulated 38854 SP_1860, SP_1861, SP_1862, SP_1863 4/4...”
- The roles of transition metals in the physiology and pathogenesis of Streptococcus pneumoniae
Honsa, Frontiers in cellular and infection microbiology 2013 - “...Mn 2+ in growth media. Berry and Paton, 1996 ; Johnston et al., 2006 psaC SP_1649 Manganese ABC transporter permease Absolute requirement for Mn 2+ in growth media. Berry and Paton, 1996 ; Johnston et al., 2006 psaR SP_1638 Manganese-dependent regulator Essential for murine systemic infection....”
spr1493 ABC transporter membrane-spanning permease - manganese transport from Streptococcus pneumoniae R6
36% identity, 91% coverage
Spaf_0348 metal ABC transporter permease from Streptococcus parasanguinis FW213
36% identity, 92% coverage
SAG1531 manganese ABC transporter, permease protein from Streptococcus agalactiae 2603V/R
SAK_1554 metal ABC transporter, permease protein from Streptococcus agalactiae A909
gbs1587 Unknown from Streptococcus agalactiae NEM316
ID870_02020 metal ABC transporter permease from Streptococcus agalactiae CJB111
35% identity, 94% coverage
- CsrRS regulates group B Streptococcus virulence gene expression in response to environmental pH: a new perspective on vaccine development
Santi, Journal of bacteriology 2009 - “...uptake and transport (1); mtsC (SAG1532) and mtsB (SAG1531), homologous to the GAS mtsABC operon; and SAG0745, coding for a putative NRAMP family transporter...”
- Identification of Zinc-Dependent Mechanisms Used by Group B Streptococcus To Overcome Calprotectin-Mediated Stress
Burcham, mBio 2020 - “.../Fe 2+ transporter, NRAMP family 0.006823 0.04543 SAK_1539 nikE Nickel ABC transporter, ATP-binding protein 0.04795 SAK_1554 mtsC Metal ABC transporter, permease protein 9.914E12 SAK_1555 mtsB Metal ABC transporter, ATP-binding protein 2.325E10 SAK_1556 mtsA Metal ABC transporter, metal-binding lipoprotein 1.381E11 0.003134 SAK_1897 shtII Streptococcal histidine triad family...”
- “...systems of interest that were underrepresented in our calprotectin transposon library screen were mtsABC ( SAK_1554 to 1556 ), mntH ( SAK_0871 ), sczA ( SAK_0515 ), czcD ( SAK_0514 ), and cadD ( SAK_2051 ). mtsABC encodes the manganese/iron-dependent ABC transporter, and mtsA is a...”
- Transcriptomic Analysis of Streptococcus pyogenes Colonizing the Vaginal Mucosa Identifies hupY, an MtsR-Regulated Adhesin Involved in Heme Utilization
Cook, mBio 2019 - “...data shows that GBS homologs of genes in the GAS MtsR regulon, including mstABC ( sak_1554 to - 1556 ) and nrdF.2IE.2 ( sak_499 to - 501 ), were similarly upregulated during vaginal colonization and contain putative MtsR promoter DNA binding sites ( Fig.2B ) (...”
- A Vaginal Tract Signal Detected by the Group B Streptococcus SaeRS System Elicits Transcriptomic Changes and Enhances Murine Colonization
Cook, Infection and immunity 2018 - “...sak_1427 sak_1476 sak_1477 sak_1538 sak_1539 sak_1540 sak_1541 sak_1542 sak_1554 sak_1555 sak_1556 Gene name rbsB rbsC rbsA rbsD oppD oppD oppF cylA cylB fhuD...”
- Extensive adaptive changes occur in the transcriptome of Streptococcus agalactiae (group B streptococcus) in response to incubation with human blood
Mereghetti, PloS one 2008 - “...after contact with blood. For example, fhuA and fhuG (gbs1462 and gbs1465), mtsC and mtsB (gbs1587 and gbs1588), and another putative operon (gbs1043gbs1045), all involved in iron metabolism, were down-regulated from 2.2- to 5.8-fold. Similarly, the genes adcC and adcB (gbs0151 and gbs0152) involved in zinc...”
- Identification of a DNA-cytosine methyltransferase that impacts global transcription to promote group B streptococcal vaginal colonization
Manzer, mBio 2023 - “...ABC transporter substrate-binding protein 1.14 18.30 ID870_02015 mtsB Metal ABC transporter ATP-binding protein 1.33 17.77 ID870_02020 mtsC Metal ABC transporter permease 1.72 16.42 ID870_07400 copA Copper-translocating P-type ATPase 1.32 11.26 ID870_07395 copZ Heavy-metal-associated domain-containing protein 1.21 10.28 Adhesins ID870_06030 PI-1 major pilin 1.75 5.66 ID870_02595 pilA...”
TC 3.A.1.15.13 / B2IWT1 ABC-3 protein, component of The ZnuA18/ZnuA08/ZnuB/ZnuC zinc (Zn2+) uptake system from Nostoc punctiforme (strain ATCC 29133 / PCC 73102)
33% identity, 88% coverage
- substrates: Zn2+
tcdb comment: ZnuB (M) and ZnuC (C) can function with either of two zinc ion receptors, ZnuA18 (R) which is encoded in the znuACB operon, and ZnuA08 (R) which is encoded elsewhere on the chromosome. ZnuA18 is more efficient that ZnuA08 in promoting uptake (Hudek et al. 2013)
SGO_1801 ABC transporter membrane-spanning permease - manganese transport from Streptococcus gordonii str. Challis substr. CH1
38% identity, 93% coverage
- Proteomics of Streptococcus gordonii within a model developing oral microbial community
Hendrickson, BMC microbiology 2012 - “...nd SGO_1073 0.8 2.1 nd 1.3 nd nd SGO_1800 nd 2.2 2.8 nd nd 0.7 SGO_1801 nd nd nd nd nd nd SGO_1802 6.2 2.7 3.4 3.4 2.8 0.6 SGO_1816 0.9 0.1 nd 0.7 nd nd Bold: statistically significant difference, all ratios are log 2 ....”
- “...Sca actually refers to streptococcal coaggregation adherence because one of the regulated transporter proteins, ScaA, SGO_1801, was originally identified as an adhesin important for aggregation with A. neaslundii [ 29 ]. ScaA was not detected in any of the samples, though that is not unusual for...”
MTSB_STRGN / P42361 Manganese import system permease protein ScaB; ORF2 from Streptococcus gordonii (see paper)
TC 3.A.1.15.2 / P42361 P29K aka ScaB, component of Manganese (Mn2+) and zinc (Zn2+) porter from Streptococcus gordonii challis (see paper)
38% identity, 93% coverage
- function: Part of the high-affinity ABC transporter complex ScaABC involved in manganese import. Probably responsible for the translocation of the substrate across the membrane. Essential for growth under Mn(2+)-limiting conditions.
subunit: The complex is composed of two ATP-binding proteins (ScaC), two transmembrane proteins (ScaB) and a solute-binding protein (ScaA). - substrates: Mn2+, Zn2+
I872_09650 metal ABC transporter permease from Streptococcus cristatus AS 1.3089
37% identity, 93% coverage
A3CKL5 ABC-type Mn2+/Zn2+ transport systems, permease component, putative from Streptococcus sanguinis (strain SK36)
SSA_0261 ABC-type Mn2+/Zn2+ transport systems, permease component, putative from Streptococcus sanguinis SK36
37% identity, 90% coverage
FD24_GL000107 metal ABC transporter permease from Lactiplantibacillus pentosus DSM 20314
33% identity, 89% coverage
- Dual effects of a bacteriocin-producing Lactiplantibacillus pentosus CF-6HA, isolated from fermented aloreña table olives, as potential probiotic and antimicrobial agent
Abriouel, Heliyon 2024 - “...Gene length Protein description Ontology term (Ontology ID) COG class description (COG class) Adhesion gene_267 FD24_GL000107 151284152156 + 873 Metal ABC transporter permease Plasma membrane, integral component of membrane, ATP binding, ATPase activity, coupled to transmembrane movement of substances, transmembrane transport (GO:0005886, GO:0016021, GO:0005524, GO:0042626, GO:0055085)...”
A8A08_02205, CHQ89_16650, CHQ90_08460 zinc ABC transporter permease subunit ZnuB from Acinetobacter baumannii
35% identity, 96% coverage
- Genotypic and Phenotypic Characterization of Novel Sequence Types of Carbapenem-Resistant Acinetobacter baumannii, With Heterogeneous Resistance Determinants and Targeted Variations in Efflux Operons
Bharathi, Frontiers in microbiology 2021 - “...in A. baumannii strains DR1 (CHQ89_16635, CHQ89_16650, CHQ89_16645), DR2 (CHQ90_08475, CHQ90_08460, CHQ90_08465), and AB067 (A8A08_02190, A8A08_02205, A8A08_02200). Although copper is required by bacteria for cuproenzyme activity, it uses the copABCRS efflux pump as the stress responsive system to combat its toxicity. This entire operon was found...”
- “...the presence of the high-affinity ABC-type transporter (100% identity) in A. baumannii strains DR1 (CHQ89_16635, CHQ89_16650, CHQ89_16645), DR2 (CHQ90_08475, CHQ90_08460, CHQ90_08465), and AB067 (A8A08_02190, A8A08_02205, A8A08_02200). Although copper is required by bacteria for cuproenzyme activity, it uses the copABCRS efflux pump as the stress responsive system...”
- “...high-affinity ABC-type transporter (100% identity) in A. baumannii strains DR1 (CHQ89_16635, CHQ89_16650, CHQ89_16645), DR2 (CHQ90_08475, CHQ90_08460, CHQ90_08465), and AB067 (A8A08_02190, A8A08_02205, A8A08_02200). Although copper is required by bacteria for cuproenzyme activity, it uses the copABCRS efflux pump as the stress responsive system to combat its toxicity....”
ABUW_3743 zinc ABC transporter permease subunit ZnuB from Acinetobacter baumannii
35% identity, 96% coverage
Gocc_1486 metal ABC transporter permease from Gaiella occulta
36% identity, 94% coverage
LLKF_1406 manganese ABC transporter permease from Lactococcus lactis subsp. lactis KF147
32% identity, 91% coverage
LSA0181 Manganese ABC transporter, membrane-spanning subunit from Lactobacillus sakei subsp. sakei 23K
32% identity, 90% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...-0.7 LSA0134 lsa0134 Putative Na(+)/H(+) antiporter -0.6 LSA0180 mtsC Manganese ABC transporter, ATP-binding subunit -0.8 LSA0181 mtsB Manganese ABC transporter, membrane-spanning subunit -0.8 -1.0 LSA0182 mtsA Manganese ABC transporter, substrate-binding lipoprotein precursor -0.7 -0.6 LSA0246 mntH1 Mn(2+)/Fe(2+) transport protein -0.9 -1.3 LSA0283 lsa0283 Putative zinc/iron ABC...”
LMOf2365_1465 zinc ABC transporter, permease protein from Listeria monocytogenes str. 4b F2365
33% identity, 82% coverage
lmo1446 metal (zinc) transport protein (ABC transporter, permease protein) from Listeria monocytogenes EGD-e
NP_464971 metal (zinc) transport protein (ABC transporter, permease) from Listeria monocytogenes EGD-e
33% identity, 83% coverage
llmg_1137 manganese transport system membrane protein from Lactococcus lactis subsp. cremoris MG1363
32% identity, 92% coverage
L149891 manganese ABC transporter permease protein from Lactococcus lactis subsp. lactis Il1403
32% identity, 92% coverage
PPYC1_13110 metal ABC transporter permease from Paenibacillus polymyxa
35% identity, 85% coverage
LACR_1439 ABC-type Mn2+/Zn2+ transport system, permease component from Lactococcus lactis subsp. cremoris SK11
31% identity, 92% coverage
SYNW2479 ABC transporter component, possibly Zn transport. from Synechococcus sp. WH 8102
35% identity, 93% coverage
- A single sensor controls large variations in zinc quotas in a marine cyanobacterium
Mikhaylina, Nature chemical biology 2022 - “...neighborhoods, WH8102 harbors two putative ABC (ATP-binding-cassette)-type zinc-uptake transporter systems (ZnuABC), encoded by the genes synw2479 synw2481 and synw0969 synw0971 . A Zur-binding site (Zur box; Fig. 1a,b ) is predicted in the intergenic region between synw0970 ( znuC ) and synw0971 ( znuA ) 26...”
- “...fourfold with respect to replete media. A second putative znuABC system in this strain ( synw2479 synw2481 ) was neither zinc- nor Zur-regulated. However, the periplasmic binding protein SYNW2481 was previously identified in the proteome of WH8102 cultured at 80nM Zn 28 , and our transcriptomic...”
- Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species
Tetu, Frontiers in microbiology 2013 - “...function. Those few with functional predictions include an encoded ribosomal protein SYNW2091, ABC transporter component SYNW2479 and CpeT homolog SYNW2003. While there were overlaps in the transcriptional response between the two shock treatments, there were also clear differences in the response to each chemical, many of...”
- “...SYNW2485-2487, annotated as putative zinc and cyanate transporters respectively. All but one of these genes (SYNW2479) were not significantly upregulated in the MC treatment. Only two of these genes have homologs in CC9311 (sync_1497/SYNW2479 and sync1498/SYNW2480) and in CC9311 these genes were not significantly affected by...”
- Statistical analysis of microarray data with replicated spots: a case study with synechococcus WH8102
Thomas, Comparative and functional genomics 2009 - “...SYNW1305 2.03 11.34 Hypothetical SYNW0947 2.03 12.86 Two-component response regulator, phosphate SYNW1463 2.02 32.03 Hypothetical SYNW2479 1.96 9.04 ABC transporter component, possibly Zn transport SYNW1654 1.95 13.34 Conserved hypothetical protein SYNW2486 1.91 15.10 Putative cyanate ABC transporter SYNW0454 1.84 12.43 Possible glycosyltransferase SYNW1947 1.81 14.14 Conserved...”
- A suppression subtractive hybridization approach reveals niche-specific genes that may be involved in predator avoidance in marine Synechococcus isolates
Jones, Applied and environmental microbiology 2006 - “...NP_898568 SYNW1112 SYNW0886 SYNW0355 SYNW2453 SYNW2479 NP_897305 NP_897365 SYNW1212 SYNW1270 NP_896965 NP_897416 NP_897024 NP_898277 NP_898531 SYNW0872...”
- Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome
Chen, Nucleic acids research 2004 - “...(SYNW1415, (SYNW1797, (SYNW1857, (SYNW1915, (SYNW2393, (SYNW2438, (SYNW2479, (SYNW2485, Exactly found (SYNW0319, 0320, 0321, 0322) Exactly found (SYNW0840,...”
- “...found Exactly found (SYNW2438, 2439, 2440, 2441, 2442, 2443) (SYNW2479, 2480) Exactly found 0.31 0.39 1.68 1.34; 1.03 1.03 0.31 0.00 0.08; 0.39 1.61 1.03 1.68...”
LACR_2417 ABC-type Mn2+/Zn2+ transport system, permease component from Lactococcus lactis subsp. cremoris SK11
35% identity, 96% coverage
SSA_0137 ABC transporter (permease), Zn porter, putative from Streptococcus sanguinis SK36
32% identity, 94% coverage
slr2045 hypothetical protein from Synechocystis sp. PCC 6803
32% identity, 91% coverage
SCO2507 metal transport ABC transporter from Streptomyces coelicolor A3(2)
35% identity, 83% coverage
- The zinc-responsive regulator Zur controls expression of the coelibactin gene cluster in Streptomyces coelicolor
Kallifidas, Journal of bacteriology 2010 - “...SCO2506 znuC; putative metal transport ABC transporter SCO2507 znuB; putative metal transport ABC transporter SCO3426 YciC homologue; zinc metallochaperone...”
- Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR
Owen, Journal of bacteriology 2007 - “...of a ZnuABC high-affinity zinc uptake system (SCO2505 to SCO2507, or znuACB) (44). The zur reading frame was deleted in M145 to generate a strain designated...”
- The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2)
Shin, Journal of bacteriology 2007 - “...a probable ATPase of 256 aa), and ZnuB (the SCO2507 gene product, a probable membrane permease of 300 aa) show 26.5, 34.8, and 27.3% identity, respectively, to...”
gbs0152 unknown from Streptococcus agalactiae NEM316
SAK_0219 zinc ABC transporter, permease protein from Streptococcus agalactiae A909
SAG0156 zinc ABC transporter, permease protein from Streptococcus agalactiae 2603V/R
ID870_08640 metal ABC transporter permease from Streptococcus agalactiae CJB111
33% identity, 93% coverage
- Extensive adaptive changes occur in the transcriptome of Streptococcus agalactiae (group B streptococcus) in response to incubation with human blood
Mereghetti, PloS one 2008 - “...metabolism, were down-regulated from 2.2- to 5.8-fold. Similarly, the genes adcC and adcB (gbs0151 and gbs0152) involved in zinc uptake, and gbs1679gbs1680 encoding cobalt transport proteins, were also down-regulated. However, mts , pts, and gbs1043gbs1045 subsequently were up-regulated at 90 min relative to 30 min. Differential...”
- The Adc/Lmb System Mediates Zinc Acquisition in Streptococcus agalactiae and Contributes to Bacterial Growth and Survival
Moulin, Journal of bacteriology 2016 - “...an AdcCB tanslocon, consisting of a permease, called AdcB (SAK_0219), and an ATPase, AdcC (SAK_0218), to form an ABC transporter. In all sequenced S. agalactiae...”
- Transcriptomic analysis of Streptococcus agalactiae periprosthetic joint infection
Cho, MicrobiologyOpen 2021 - “...(SAG0535) and AdcAII (SAG1938), redundant binding proteins that combine with the AdcCB translocon (SAG0155 and SAG0156) form a zincABC transporter, with their expression controlled by zincdependent regulator AdcR (SAG0154) (Moulin et al., 2016 ). In this study, sag0535 and sag01540156 were highly expressed in sonicate fluid...”
- Genomic Analyses Identify Manganese Homeostasis as a Driver of Group B Streptococcal Vaginal Colonization
Burcham, mBio 2022 - “...16.55 18.27 31.92 40.23 ID870_08465 ABC transporter ATP-binding protein 4.34 ID870_08470 ABC transporter permease 6.77 ID870_08640 adcB Zinc ABC transporter permease 6.37 ID870_08780 Putative metal homeostasis protein 10.07 Transport systems Phosphotransferase systems ID870_00140 PTS transporter subunit EIIC 4.92 ID870_00190 PTS sugar transporter subunit IIB 9.85 ID870_00265...”
SGO_1937 ABC transporter permease, Mn from Streptococcus gordonii str. Challis substr. CH1
31% identity, 93% coverage
EF0576 cation ABC transporter, permease protein from Enterococcus faecalis V583
34% identity, 92% coverage
Q832Z3 ABC-type Mn2+ transporter (subunit 2/3) (EC 7.2.2.5) from Enterococcus faecalis (see paper)
EF2075 ABC transporter, permease protein from Enterococcus faecalis V583
31% identity, 84% coverage
- EfaR is a major regulator of Enterococcus faecalis manganese transporters and influences processes involved in host colonization and infection
Abrantes, Infection and immunity 2013 - “...EF0577 EF0578 EF0579 EF1057 EF1058 EF1901 EF2074 EF2075 EF2076 TAGGCTTGACTAAA Cationic ABC transporter, ATP-binding protein Cationic ABC transporter, permease...”
- Characterization of the effects of an rpoC mutation that confers resistance to the Fst peptide toxin-antitoxin system toxin
Brinkman, Journal of bacteriology 2013 - “...2226c 20.7 16.4, 11.1 EF1400 11.6 EF0759, 0758 10.0, 8.7 EF2075, 2074 EF2067, 2068 EF1673, 1672 8.8, 7.1 8.6, 7.1 8.4, 6.7 EF1351, 1352 8.2, 6.3 EF2699 7.8...”
- Global transcriptional analysis of the stringent response in Enterococcus faecalis
Gaca, Microbiology (Reading, England) 2012 - “...EF1584 EF1585 EF1597 EF1672 EF1681 EF1685 EF1982 EF2075 EF2076 EF2355 EF2509 EF2678 EF3015 EF3164 EF3233 EF3282 EF3283 Oligopeptide ABC transporter General...”
- Impact of manganese, copper and zinc ions on the transcriptome of the nosocomial pathogen Enterococcus faecalis V583
Abrantes, PloS one 2011 - “...5.80 3.78 universal stress protein family ef2074 (efaC) 2.94 16.58 2.24 ABC transporter, ATP-binding protein ef2075 (efaB) 4.10 13.14 2.01 ABC transporter, permease protein ef2076 (efaA) 4.02 11.54 2.03 endocarditis specific antigen a Metals used (added-metal concentrations in GM17): 4 mM ZnSO 4 , 0.4 mM...”
- The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood
Vebø, PloS one 2009 - “...ABC transporter, ATP-binding protein ( efaC ) Transport and binding proteins 3.6 [9] , [12] EF2075 ABC transporter, permease protein ( efaB ) Transport and binding proteins 2.4 [9] , [12] EF2076 endocarditis specific antigen ( efaA ) Cellular processes 1.4 * [9] , [12] EF2167...”
- Comparison of OG1RF and an isogenic fsrB deletion mutant by transcriptional analysis: the Fsr system of Enterococcus faecalis is more than the activator of gelatinase and serine protease
Bourgogne, Journal of bacteriology 2006 - “...efaA is the third gene of the efaCBA operon. efaB (ef2075) and efaA (ef2076) expression was activated in OG1RF three- to eightfold (P 0.05) compared to the fsrB...”
- Comparative proteomics analysis of biofilms and planktonic cells of Enterococcus faecalis and Staphylococcus lugdunensis with contrasting biofilm-forming ability
Cho, PloS one 2024 - “...0.89 Q839V4 mrnC Mini-ribonuclease 3 18.24 20.50 0.89 Q839A9 EF_3207 tRNA-dihydrouridine synthase 19.22 21.65 0.89 Q832Z3 EF_0180 ABC transporter, permease protein 17.04 19.20 0.89 Q835M8 EF_1349 Alpha-amylase 16.73 18.92 0.88 Q835M9 EF_1348 Glucan 1,6-alpha-glucosidase, putative 17.35 19.66 0.88 S . lugdunensis A0A292DIE8 EQ812_06280 Cold shock protein...”
IUJ47_RS12790 metal ABC transporter permease from Enterococcus faecalis
31% identity, 84% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...Ribosome small subunit-dependent GTPase A ABC transporters IUJ47_RS12795 0.002 substrate-binding protein IUJ47_RS12785 0.003 ATP-binding protein IUJ47_RS12790 0.008 ABC transporter permease IUJ47_RS07400 0.012 ABC transporter permease subunit IUJ47_RS13490 0.036 Carbohydrate ABC transporter permease IUJ47_RS13485 0.05 ABC transporter substrate-binding protein IUJ47_RS07460 0.097 Oligopeptide ABC transporter substrate-binding protein Opp1A...”
ACIAD0174 high affinity Zn transport protein (ABC superfamily, membrane) from Acinetobacter sp. ADP1
34% identity, 95% coverage
SM12261_RS09035 metal ABC transporter permease from Streptococcus mitis NCTC 12261
32% identity, 94% coverage
TC 3.A.1.15.3 / O33704 AdcB aka SP2170, component of Zinc (Zn2+) porter, AdcABC/AII from Streptococcus pneumoniae (see 3 papers)
SPD_1998 zinc ABC transporter, permease protein from Streptococcus pneumoniae D39
SP_2170 zinc ABC transporter, permease protein from Streptococcus pneumoniae TIGR4
32% identity, 94% coverage
- substrates: Zn2+
- A Tn-seq Screen of Streptococcus pneumoniae Uncovers DNA Repair as the Major Pathway for Desiccation Tolerance and Transmission
Matthews, Infection and immunity 2021 (secret) - The metalloregulatory zinc site in Streptococcus pneumoniae AdcR, a zinc-activated MarR family repressor
Reyes-Caballero, Journal of molecular biology 2010 - “...pyogenes 45 , each of the genes encoding the Zn(II)-specific ABC uptake system adcCBA (SPD_1999, SPD_1998, SPD_1997, respectively) increased in transcript abundance in the adcR strain. In addition, as was predicted in a genomic analysis 4 and shown by RT-PCR analysis, 26 transcript amounts of the...”
- Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster
Valentino, Nature communications 2014 - “...arginine metabolism (SP_2148 to SP_2151), and a fucose binding, uptake, and catabolic pathway (SP_2158 to SP_2170) ( Supplementary Data 5 ). This block of metabolic functions has been displaced in ECC genomes with a 12.7 kb sequence that encodes, among other things, ZmpC2. Some ECC (ST448,...”
- The roles of transition metals in the physiology and pathogenesis of Streptococcus pneumoniae
Honsa, Frontiers in cellular and infection microbiology 2013 - “...2011 adcAII SP_1002 Zinc Importer (Redundant with AdcA) No effect McDevitt et al., 2011 adcB SP_2170 Transmembrane permease Significantly more sensitive than wild type McDevitt et al., 2011 adcC SP_2171 ATPase No effect Hava and Camilli, 2002 ; van Opijnen and Camilli, 2012 ; Kimaro Mlacha...”
- Microarray analysis of Streptococcus pneumoniae gene expression changes to human lung epithelial cells
Song, Canadian journal of microbiology 2008 (PubMed)- “...strain R6. We demonstrated that 2 genetic loci, SP_2170 (AdcB, zinc ABC transporter) and SP_0157 (hypothetical protein), were involved in adherence to A549...”
- “...R6. Nous avons demontre que deux loci genetiques, SP_2170 (transporteur ABC de zinc AdcB) et SP_0157 (proteine hypothetique), sont impliques dans l'adherence...”
BAS4182 cation ABC transporter, permease protein, putative from Bacillus anthracis str. Sterne
34% identity, 88% coverage
- Identification, Functional Characterization, and Regulon Prediction of the Zinc Uptake Regulator (zur) of Bacillus anthracis - An Insight Into the Zinc Homeostasis of the Pathogen
Kandari, Frontiers in microbiology 2018 - “...that there is no transcriptional coupling with the gene downstream of ba zur . BAS4183, BAS4182, and BAS4181 encode 256, 277, and 137 aa proteins, respectively. BAS4183 when used as a query in BLASTP screen against the NCBI non-redundant (nr) database revealed high similarities with ATP-binding...”
- “...Patzer and Hantke, 1998 ; Hantke, 2001 ). Next, in the BLASTP screen of the BAS4182 sequence against the NCBI nr database, it was observed that it exhibits high similarity with the permease of the metal ABC transporter and belongs to ZnuB superfamily (Supplementary Table S3...”
SMU_1993 metal ABC transporter permease from Streptococcus mutans UA159
34% identity, 89% coverage
- Cnm of Streptococcus mutans is important for cell surface structure and membrane permeability
Naka, Frontiers in cellular and infection microbiology 2022 - “...2.125 SMU_1078c ABC transporter ATP-binding protein 1028403 SMU_1078c 2.039 adcB ABC transporter zinc permease 1029187 SMU_1993 2.014 SMU_2035 Bacteriocin immunity protein 1029223 SMU_2035 2.007 Signal transmission-related genes Gene name Description NCBI gene ID Locus tag Fold-change SMU_626 Competence protein 1028064 SMU_626 10.558 comEA Competence protein 1029564...”
GQY01_RS11400 metal ABC transporter permease from Staphylococcus epidermidis
30% identity, 92% coverage
EF0057 ABC transporter, permease protein from Enterococcus faecalis V583
31% identity, 93% coverage
SSU05_0111 ABC-type Mn2+/Zn2+ transport system, permease component from Streptococcus suis 05ZYH33
SSU98_0114 ABC-type Mn2+/Zn2+ transport system, permease component from Streptococcus suis 98HAH33
30% identity, 89% coverage
- In vitro transcriptome analysis of two Chinese isolates of Streptococcus suis serotype 2
Zhang, Genomics, proteomics & bioinformatics 2014 - “...listed in the order of 05ZYH33, 98HAH33 and P1/7. For example, Gene ID SSU05_0111/SSU98_0114/SSU0114 represent SSU05_0111 in 05ZYH33, SSU98_0114 in 98HAH33 and SSU0114 in P1/7, which all encode ORF 46, and their expression level in terms of RPKM is 152.6 in 05ZYH33, 292.4 in 98HAH33 and...”
- In vitro transcriptome analysis of two Chinese isolates of Streptococcus suis serotype 2
Zhang, Genomics, proteomics & bioinformatics 2014 - “...order of 05ZYH33, 98HAH33 and P1/7. For example, Gene ID SSU05_0111/SSU98_0114/SSU0114 represent SSU05_0111 in 05ZYH33, SSU98_0114 in 98HAH33 and SSU0114 in P1/7, which all encode ORF 46, and their expression level in terms of RPKM is 152.6 in 05ZYH33, 292.4 in 98HAH33 and 79.3 in P1/7,...”
SSU0114 ABC transporter permease protein from Streptococcus suis P1/7
30% identity, 95% coverage
- Identification of conditionally essential genes for Streptococcus suis infection in pigs
Arenas, Virulence 2020 - “...functional enrichment. Generation of directed mutants To obtain knockout mutants in S. suis strain 10 (SSU0114, glA , SSU0469, fhs , SSU0883, penA , SSU1501, SSU1869, SSU1940), DNA fragments corresponding to flanking regions of the genes of interest and a spectinomycin-resistance cassette were amplified from chromosomal...”
- “...synthetase 4.5 SSU0262 Threonine synthase 9.4 8.3 3.6 SSU1634 acoL Dihydrolipoamide dehydrogenase 4.9 3.6 Transporters SSU0114 Metal cation ABC transporter (Permease) 7.4 6.3 8.1 SSU1865 Metal cation ABC transporter membrane protein 4.2 2.8 4.5 SSU0883 Glutamine ABC transporter, glutamine-binding protein/permease protein 2.2 SSU1675 Glutamine ABC transporter,...”
- In vitro transcriptome analysis of two Chinese isolates of Streptococcus suis serotype 2
Zhang, Genomics, proteomics & bioinformatics 2014 - “...and P1/7. For example, Gene ID SSU05_0111/SSU98_0114/SSU0114 represent SSU05_0111 in 05ZYH33, SSU98_0114 in 98HAH33 and SSU0114 in P1/7, which all encode ORF 46, and their expression level in terms of RPKM is 152.6 in 05ZYH33, 292.4 in 98HAH33 and 79.3 in P1/7, respectively. Mixed means that...”
A1S_0143 high affinity Zn transport protein from Acinetobacter baumannii ATCC 17978
35% identity, 89% coverage
- Identification of an Acinetobacter baumannii zinc acquisition system that facilitates resistance to calprotectin-mediated zinc sequestration
Hood, PLoS pathogens 2012 - “...intragenic PDL31A9 A1S_0118 hypothetical protein resistant intragenic PDL11C6 A1S_3142 putative membrane protein resistant intragenic PDL04G7 A1S_0143 high affinity Zn transport protein sensitive intragenic PDL06H4 A1S_2477 isocitrate dehydrogenase sensitive intragenic PDL09F4 A1S_0076 aconitate hydratase sensitive intragenic PDL05A7 A1S_0430 Putative glycosyltransferase sensitive intragenic PDL19C1 A1S_2588 Holliday junction DNA...”
- “...of a Zn uptake system in A. baumannii In one mutant, 4G7, the transposon disrupts A1S_0143, which is annotated as encoding the permease component of a previously unstudied ABC family Zn transporter. Consistent with a role for A1S_0143 in Zn transport, disruption of this gene by...”
TC 3.A.1.15.15 / G0LRW8 ABC transporter permease protein, component of High affinity Mn2+ uptake complex, MntABC from Staphylococcus aureus subsp. aureus LGA251
29% identity, 93% coverage
- substrates: Mn2+
tcdb comment: The 3-d structure of MntC has been solved to 2.2Å resolution (Gribenko et al. 2013)
SACOL0689 ABC transporter, permease protein from Staphylococcus aureus subsp. aureus COL
SA0588 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV0632 similar to ABC transporter, permease protein from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_00636 iron (chelated) ABC transporter, permease protein, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0619 ABC transporter, permease protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_0602 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
SAR0642 ABC transporter permease protein from Staphylococcus aureus subsp. aureus MRSA252
B7H15_03550 metal ABC transporter permease from Staphylococcus aureus
29% identity, 93% coverage
- Staphylococcus aureus gene expression in a rat model of infective endocarditis
Hanses, Genome medicine 2014 - “...-4.3 -4.4 hypothetical protein mntC SACOL0688 3.7 -5.8 3.5 -6.3 ABC transporter substrate-binding protein mntB SACOL0689 4.1 -5.7 4.5 -4.7 ABC transporter permease mntA SACOL0690 8.5 -2.7 5.6 -4.4 ABC transporter ATP-binding protein SACOL0157 -11.4 -12.0 -12.9 -12.8 conserved hypothetical protein SACOL0158 -6.8 -15.2 -6.1 -13.4...”
- An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus
Campbell, Antimicrobial agents and chemotherapy 2012 - “...-4.0 SAV1199 SAV0189 SAS0665 pyrP glcA NA SAV0389 SACOL0689 pbuX NA Glucose-specific PTS transporter protein, IIABC component Uracil permease PTS enzyme II PTS...”
- “...April 2012 Volume 56 Number 4 porter; SACOL0689 (metal cation ABC transporter permease); and nhaC (Na/H antiporter). Genes encoding the phosphotransferase...”
- The C-terminal region of the RNA helicase CshA is required for the interaction with the degradosome and turnover of bulk RNA in the opportunistic pathogen Staphylococcus aureus
Giraud, RNA biology 2015 - “...Uncharacterized protein, similar to Manganese ABC transporter substrate-binding lipoprotein precursor SA0587 1.8 2.0 2.1 2.3 SA0588 SA0587-SA0589 Uncharacterized protein, similar to Manganese transport system membrane protein MntC SA0588 1.7 2.0 2.1 2.6 SA0589 SA0587-SA0589 Uncharacterized protein, similar to Manganese transport system ATP-binding protein MntB SA0589 1.7...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...sa_c4796s4102_at * 2.7 15 stable rpoA SA2213 RNA polymerase, sa_c7633s6648_a_at * 3.3 5 stable rpoB SA0588 RNA polymerase, sa_c2650s2225_a_at * 3.5 2.5 15 rpoD SA1618 RNA polymerase sigma factor sa_c8190s7169_at 4.5 2.5 2.5 saeR SA0766 response regulator sa_c5056s4355_a_at 4.9 2.5 ND sarY SA2289 staphylococcal accessory regulator...”
- “...sa_c4796s4102_at * 4.9 15 15 rpoA SA2213 RNA polymerase sa_c7633s6648_a_at * 3.2 5 2.5 rpoB SA0588 RNA polymerase sa_c2650s2225_a_at * 2.4 2.5 2.5 rpoD SA1618 RNA polymerase sigma factor sa_c9811s8552_a_at 3.6 2.5 2.5 rpoE SA2120 RNA polymerase sa_c1187s970_at 2.0 2.5 2.5 rpoZ SA1222 RNA polymerase sa_c9851s9296_a_at...”
- Characterization of the oxygen-responsive NreABC regulon of Staphylococcus aureus
Schlag, Journal of bacteriology 2008 - “...Upregulated genes SA0143 SA0183 SA0232 SA0477 SA0478 SA0562 SA0588 SA0589 SA1140 SA1149 SA1150 SA1183 SA1269 SA1270 SA1271 SA1506 SA1709 SA2007 SA2008 SA2142...”
- Overexpression of genes of the cell wall stimulon in clinical isolates of Staphylococcus aureus exhibiting vancomycin-intermediate- S. aureus-type resistance to vancomycin
McAleese, Journal of bacteriology 2006 - “...SA0109 SA0110 SA0111 SA0217 SA0420 SA0421 SA0566 SA0587 SA0588 SA0589 SA0690 SA0769 SA0770 SA0927 SA0928 SA1016 SA2228 SA0270 SA0295 SA1777 SA1852 SA2097 SA2120...”
- “...ORF no. SA0231 SA0938 SA0113 SA2410 SA2336 SA2409 SA0587 SA0588 SA0589 SA2149 SA2150 SA0101 SA0102 SA0114 SA0221a SAS007 a Gene nrdD clpC nrdG Product or...”
- Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype
Seggewiss, Journal of bacteriology 2006 - “...proteins SA0175 SA1702 SA0412 SA0213 SA2220 SA0413 SA0212 SA0588 SA2329 SA1712 SA0908 SA2146 SA0919 SA0725 SA1021 SA1031 SA1032 SA0824 SA1433 SA0301 SA0962...”
- Differential gene expression profiling of Staphylococcus aureus cultivated under biofilm and planktonic conditions
Resch, Applied and environmental microbiology 2005 - “...0.796 6.461 4.89 SA0271 SA0292 SA0609 SA0890 SA1403 SA0588 SA1053 SA1472 SA1419 SA2133 SA1944 SA1056 SA0412 SA1402 SA0291 SA1971 SAS048 SA2378 SA2143 SA1293...”
- “...Tn554 0.096 0.047 0.087 1.805 1.799 3.357 SA2268 SA0588 SA1985 SA0271 SA1986 SA0227 SA0929 SA1403 SA0412 SA2133 SA1912 SA0371 SA1925 SA1402 SA0292 SA1916 SA0609...”
- Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci
Dunman, Journal of bacteriology 2001 - “...SA2251 Transport 2.4 2.3 SA1214 SA0953 Transport Transport 2.5 2.7 SA0588 SA0589 Transport Transport 2.7 12.6 14.3 7.0 2.2 3.0 3.4 7.0 2.3 2.4 3.0 2.2 3.4 2.0...”
- Transcriptional Analysis of the Effects of Gambogic Acid and Neogambogic Acid on Methicillin-Resistant Staphylococcus aureus
Hua, Frontiers in pharmacology 2019 - “...50S ribosomal protein L10 1.39 2 SAV0631 None manganese ABC transporter substrate-binding protein 2.14 2.16 SAV0632 None membrane protein ABC transporter permease 1.96 2.14 SAV0633 None phosphonate ABC transporter ATP-binding protein 1.9 2.09 SAV0705 saeS histidine protein kinase 2.9 3.41 SAV0706 saeR response regulator saeR 1.82...”
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...biosynthetic type SAOUHSC_02281 0.331 Dihydroxy-acid dehydratase ABC transporters SAOUHSC_00634 0.012 ABC transporter substrate-binding protein putative SAOUHSC_00636 0.014 Iron (chelated) ABC transporter permease protein putative SAOUHSC_00637 0.015 Conserved hypothetical protein SAOUHSC_01945 0.095 Membrane protein putative SAOUHSC_00927 0.133 Oligopeptide ABC transporter substrate-binding protein putative SAOUHSC_00926 0.147 Oligopeptide ABC...”
- The Polycyclic Polyprenylated Acylphloroglucinol Antibiotic PPAP 23 Targets the Membrane and Iron Metabolism in Staphylococcus aureus
Wang, Frontiers in microbiology 2019 - “...PPAP 23 challenged S. aureus HG001. ORF Gene description Fold change Down-regulated a Iron metabolism SAOUHSC_00636 Ironmanganese ABC transporter MntABC (SitABC) system permease protein ( mntB ) -4 SAOUHSC_00637 Ironmanganese ABC transporter MntABC (SitABC) system ATP-binding protein ( mntA ) -4 SAOUHSC_00746 Iron ABC transporter SstABCD...”
- Genome-wide screen for genes involved in eDNA release during biofilm formation by Staphylococcus aureus
DeFrancesco, Proceedings of the National Academy of Sciences of the United States of America 2017 - “...SAOUHSC_00880 SAOUHSC_02699 SAOUHSC_00670 SAOUHSC_03037 SAOUHSC_00636 SAOUHSC_01979 SAOUHSC_00620 SAOUHSC_01586 SAOUHSC_00034 SAOUHSC_01850 SAOUHSC_02273...”
- The Staphylococcus aureus KdpDE two-component system couples extracellular K+ sensing and Agr signaling to infection programming
Xue, Infection and immunity 2011 - “...SAOUHSC_01385 SAOUHSC_01386 SAOUHSC_02311 SAOUHSC_02310 SAOUHSC_01990 SAOUHSC_00636 SAOUHSC_00637 SAOUHSC_02661 PstB product phosphate ABC transporter Similar...”
- Investigation of the Staphylococcus aureus GraSR regulon reveals novel links to virulence, stress response and cell wall signal transduction pathways
Falord, PloS one 2011 - “...dehydrogenase iron-sulfur subunit 1.8 1.99E09 Stress SAOUHSC_00634 mntC Putative ABC transporter substrate-binding protein 3.9 <1.0E16 SAOUHSC_00636 mntB Putative iron (chelated) ABC transporter permease 4.3 <1.0E-16 SAOUHSC_00637 mntA Putative manganese/iron ABC transporter ATP-binding protein 2.5 <1.0E16 SAOUHSC_03045 cspB Cold shock protein CspB 2.3 <1.0E16 SAOUHSC_01730 csbD Sigma-B...”
- Staphylococcus aureus lacking a functional MntABC manganese import system has increased resistance to copper
Al-Tameemi, Molecular microbiology 2021 - “...ermB ) rsaC::tetR This study JMB 9201 cop- mntA::tetR This study JMB 9208 cop- mntB::tetR (SAUSA300_0619) This study JMB 9325 cop- mntABC::tetR (SAUSA300_061921) This study JMB 9151 cop- mntR:tetR (SAUSA300_0621) This study JMB 9244 cop- mntR:tetR mntA1::Tn ( ermB ) This study JMB 8625 cop- sufD*...”
- Genetic requirements for Staphylococcus aureus nitric oxide resistance and virulence
Grosser, PLoS pathogens 2018 - “...genes encoding the F 1 F 0 ATPase (SAUSA300_2057 through SAUSA300_2064), SodA (SAUSA300_1513), MntABC (SAUSA300_0618, SAUSA300_0619 SAUSA300_0620), UvrA (SAUSA300_0742), UvrC (SAUSA300_1045), MprF (SAUSA300_1255) and RpoZ (SAUSA300_1103). Other genes important for fitness specifically during NO stress included genes associated with carbohydrate utilization ( ptsI /SAUSA300_0984 and gpmI/...”
- Differential gene expression in Staphylococcus aureus exposed to Orange II and Sudan III azo dyes
Pan, Journal of industrial microbiology & biotechnology 2015 - “...CCGCCATTGCTTTCTCTTT SAUSA300_1679 (acsA) SAUSA300_1005 SAUSA300_1897 SAUSA300_0619 SAUSA300_0545 (azo1) Table 3Summary of differentially expressed genes in S....”
- “...SAUSA300_1673 I SAUSA300_2176 SAUSA300_1005 P P SAUSA300_1897 SAUSA300_0619 SAUSA300_1899 Poorly characterized SAUSA300_1700 SAUSA300_2268 P P Q 13 R R...”
- Identifying potential therapeutic targets of methicillin-resistant Staphylococcus aureus through in vivo proteomic analysis
Diep, The Journal of infectious diseases 2014 - “...changed to TAA and 12th codon from TTA changed to TAA SAUSA300_0619 gene: 34th codon TTA changed to TAA and 37th codon TTA changed to TAA This study This study...”
- Inactivation of the Ecs ABC transporter of Staphylococcus aureus attenuates virulence by altering composition and function of bacterial wall
Jonsson, PloS one 2010 - “...ATP-binding protein 1.9 NWMN_0343 ABC transporter ATP-binding protein 0.5 NWMN_0601 ABC transporter substrate-binding protein 1.8 NWMN_0602 iron (chelated) ABC transporter permease protein 1.8 NWMN_0688 ABC transporter ATP-binding protein 0.5 NWMN_0690 ABC transporter 1.9 NWMN_0691 amino acid ABC transporter permease protein 1.9 NWMN_0696 di-/tripeptide ABC transporter 1.9...”
- Impact of Bacterial and Human Genetic Variation on Staphylococcus aureus Infections
Messina, PLoS pathogens 2016 - “..., pyrC , pyrR , pyrE , and pyrF ), iron repressible ABC transport (SAR0641, SAR0642, and SAR0643), and an azoreductase ( acpD ) [ 9 ]. Recently, CC30 was also shown to express an allelic variant of the key toxin Phenol-Soluble Modulin 3 that conferred...”
- The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
Kenny, PloS one 2009 - “...kinase protein 2.17 2.64E-02 SAR0563 putative deaminase 2.50 3.75E-03 SAR0569 putative glycosyl transferase 2.13 4.40E-03 SAR0642 ABC transporter permease protein 2.56 9.65E-03 SAR0643 ABC transporter ATP-binding protein 3.70 9.25E-03 SAR0655 putative Na+ dependent nucleoside transporter 2.17 2.25E-03 SAR0743 putative sodium:sulfate symporter protein 2.22 4.39E-04 SAR0847 nuc...”
- Staphylococcus aureus Stress Response to Bicarbonate Depletion
Liberini, International journal of molecular sciences 2024 - “...6 B7H15_00420 YdhK family protein, lipoprotein, putative 13.5 29 B7H15_00415 Copper-translocating P-type ATPase 11.2 21.6 B7H15_03550 Metal ABC transporter permease 11.2 176 Toxins B7H15_02365 PSM-3, phenol-soluble modulin 479 6360 B7H15_11280 -lysin, phenol-soluble modulin 336 11,215 B7H15_06120 PSM-, phenol-soluble modulin 235 5200 B7H15_06050 Hla, -hemolysin 61 2408...”
SPy0094, SPy_0094 putative ABC transporter (permease) from Streptococcus pyogenes M1 GAS
31% identity, 93% coverage
- Genomic Landscape of Intrahost Variation in Group A Streptococcus: Repeated and Abundant Mutational Inactivation of the fabT Gene Encoding a Regulator of Fatty Acid Synthesis
Eraso, Infection and immunity 2016 - “...Spy_1397 Spy_1398 Spy_1632 Spy_1635 Spy_1636 Spy_1637 Spy_1638 Spy_0094 Spy_0851 sdaD2 adh2 adhA dexB dexS lacD.1 lacC.1 lacB.1 lacA.1 lacG lacD.2 lacC.2...”
- “...encode enzymes of the tagatose pathway cluster 2; Spy_0094 encodes acetate kinase. Spy_0851 encodes phosphotransacetylase. The shaded rows indicate genes in the...”
- Distinct structural features of the peroxide response regulator from group A Streptococcus drive DNA binding
Lin, PloS one 2014 - “.... A PerR-deficient mutant shows hyper-resistant to zinc toxicity [8] . AdcRCB ( SPy0092 - SPy0094 ) was identified as a transport complex for streptococcal Mn 2+ /Zn 2+ import [44] , [45] . PerR-dependent expression of AdcR regulon is important in metal homeostasis [43] ....”
- The metal homeostasis protein, Lsp, of Streptococcus pyogenes is necessary for acquisition of zinc and virulence
Weston, Infection and immunity 2009 - “...and the structural components of the transporter (SPy_0093 and SPy_0094), but unlike in S. pneumoniae, it lacks the gene for the cluster 9 family ligand-binding...”
- PerR confers phagocytic killing resistance and allows pharyngeal colonization by group A Streptococcus
Gryllos, PLoS pathogens 2008 - “...four loci differentially regulated in perR mutant strain 003Sm perR D: adcRCB ( SPy0092 - SPy0094 ), adcA ( SPy0714 ), rpsN.2 ( SPy1871 ) and phtD ( SPy2006 ). Our results of AdcR motif search in M-type 3 GAS are in line with those reported...”
- MtsABC is important for manganese and iron transport, oxidative stress resistance, and virulence of Streptococcus pyogenes
Janulczyk, Infection and immunity 2003 - “...is encoded by the genome of S. pyogenes (spy0093, spy0094, and spy0714) but differs from its S. pneumoniae counterpart in that the gene encoding the lipoprotein...”
DIP0441 Putative membrane protein from Corynebacterium diphtheriae NCTC 13129
34% identity, 88% coverage
- Identification of zinc and Zur-regulated genes in Corynebacterium diphtheriae
Peng, PloS one 2019 - “...dip0439 putative membrane protein -2.54 2.71 dip0440 anchored repeat-type ABC transporter ATP-binding subunit -2.42 2.65 dip0441 anchored repeat-type ABC transporter permease subunit -2.43 2.95 dip0442 ABC transporter permease -3.42 3.51 dip0443 putative surface-anchored protein -3.18 3.3 dip0444 putative membrane protein -2.9 3.38 dip0445 DUF3068 domain-containing protein...”
- “...regions may contain a Zur binding site, and the absence of an intergenic region between dip0441 and dip0442 indicates that the promoter for dip0442 is within the dip0441 coding region. The presence of a promoter in a coding region in C . diphtheriae has not been...”
- Iron and Zinc Regulate Expression of a Putative ABC Metal Transporter in Corynebacterium diphtheriae
Peng, Journal of bacteriology 2018 - “...encoded by mnt (mntABCD) and tro (dip0438 to dip0441). Nonpolar deletions of these two uptake systems were constructed in C. diphtheriae, and these mutations...”
- Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation
Wittchen, BMC genomics 2018 - “...Post-translational modification, protein turnover, and chaperones DIP0438 - DIP0445 8 + detected DIP0438, DIP0439, DIP0440, DIP0441, DIP0442, DIP0443, DIP0444, DIP0445.Inorganic ion transport and metabolism; Function unknown DIP0719 - DIP0726 8 + detected DIP0719, DIP0720, DIP0721, DIP0722, DIP0723, DIP0724, DIP0725, uvrD . Function unknown; Replication, recombination and...”
GBAA3190 ABC transporter, permease protein from Bacillus anthracis str. 'Ames Ancestor'
30% identity, 85% coverage
lmo0155 similar to high-affinity zinc ABC transporter (membrane protein) from Listeria monocytogenes EGD-e
33% identity, 96% coverage
LMRG_00995 manganese ABC transporter, permease protein from Listeria monocytogenes 10403S
lmo1848 similar metal cations ABC transporter (permease protein) from Listeria monocytogenes EGD-e
30% identity, 92% coverage
- Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
Oliver, BMC genomics 2009 - “...to cold shock protein 679.4 LMRG_01081 hup lmo1934 similar to non-specific DNA-binding protein HU 631.8 LMRG_00995 lmo1848 lmo1848 similar metal cations ABC transporter (permease protein) 621.2 LMRG_00922 rpsU lmo1469 30S ribosomal protein S21 609 LMRG_02619 lmo0197 lmo0197 similar to B. subtilis SpoVG protein 577.3 Noncoding NGN...”
- Transcriptome Sequencing of Listeria monocytogenes Reveals Major Gene Expression Changes in Response to Lactic Acid Stress Exposure but a Less Pronounced Response to Oxidative Stress
Cortes, Frontiers in microbiology 2019 - “...lactic acid exposure. In both 6179 and R479a, high upregulation of mntABC ( lmo1847, lmo1849, lmo1848 ), a set of genes encoding a putative manganese transporter, was observed; the log2fold expression change ranged from 7.93 to 8.32 in 6179 and from 6.65 to 9.89 in R479a...”
- Listeria monocytogenes shows temperature-dependent and -independent responses to salt stress, including responses that induce cross-protection against other stresses
Bergholz, Applied and environmental microbiology 2012 - “...and iron-carrying compounds lmo0803, lmo1424, lmo1516, lmo1848, lmo1960, lmo2689); lmaDCBA and A118 bacteriophage-like protein operon lmo0119-lmo0128; agrBCD...”
- “...during the short-term response (lmo0803, lmo1424, lmo1516, lmo1848, and lmo2689), and 3 genes had elevated transcript levels during the long-term response...”
- The transcriptional response of Listeria monocytogenes during adaptation to growth on lactate and diacetate includes synergistic changes that increase fermentative acetoin production
Stasiewicz, Applied and environmental microbiology 2011 - “...lmo0818 LMOH7858 _0876 lmo0990 lmo1073 lmo1100 lmo1846 lmo1848 lmo1852 lmo2087 lmo2088 lmo2105 lmo2378 lmo2379 lmo2382 lmo2575 lmo2600 lmo2601 lmo2680 lmo2725...”
- Listeria monocytogenes 6-Phosphogluconolactonase mutants induce increased activation of a host cytosolic surveillance pathway
Crimmins, Infection and immunity 2009 - “...lmo1912 lmo1911 lmo2161 lmo0179 lmo0027 lmo1407 lmo1849 lmo1847 lmo1848 lmo0997 lmo2785 lmo2648 lmo2651 lmo2650 lmo2647 lmo0558 Fold changeb 71.6 9.8 8.1 7.2...”
- Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
Oliver, BMC genomics 2009 - “...cold shock protein 679.4 LMRG_01081 hup lmo1934 similar to non-specific DNA-binding protein HU 631.8 LMRG_00995 lmo1848 lmo1848 similar metal cations ABC transporter (permease protein) 621.2 LMRG_00922 rpsU lmo1469 30S ribosomal protein S21 609 LMRG_02619 lmo0197 lmo0197 similar to B. subtilis SpoVG protein 577.3 Noncoding NGN NL...”
- Genomic and proteomic analysis of the Alkali-Tolerance Response (AlTR) in Listeria monocytogenes 10403S
Giotis, BMC microbiology 2008 - “...protein LMOf2365_1877 NA -7.45 0.003 Cations and iron carrying compounds Manganese ABC transporter, ATP-binding protein lmo1848 NA -6.13 0.003 Similar metal cations ABC transporter lmo2087 NA 4.03 0.004 Similar to unknown proteins lmo2507 ftsE -4.06 0.002 Cell division Highly similar to cell-division ATP-binding protein FtsE lmo0582...”
- Glycerol metabolism and PrfA activity in Listeria monocytogenes
Joseph, Journal of bacteriology 2008 - “...purC purB purK purE lmo1778 rncS lmo1827 pyrP lmo1847 lmo1848 lmo1849 lmo1884 lmo1885 aroE tyrA hisC lmo1926 aroB aroF gpsA lysA fhuC lmo1976 lmo1978 ilvD ilvB...”
- Overexpression of PrfA leads to growth inhibition of Listeria monocytogenes in glucose-containing culture media by interfering with glucose uptake
Marr, Journal of bacteriology 2006 - “...for glycine betaine (lmo1015 and lmo1016) and for metal cations (lmo1848 and lmo1849). Again, none of the group III genes have a putative PrfA box in the 5...”
Dde_2210 permease component of zinc ABC transporter from Desulfovibrio desulfuricans G20
33% identity, 86% coverage
- System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions
Bosak, PloS one 2016 - “...Dde_1329 ABC-type dipeptide transport system, periplasmic component -0.92 -1.33 -0.51 -2.86 -2.01 -0.86 -3.05 transport Dde_2210 permease component of zinc ABC transporter -1.68 -2.43 -0.99 -3.93 -3.72 -1.61 -5.30 transport Dde_2201 geranyltranstransferase -2.42 -2.24 -1.57 -2.81 -2.13 -1.25 -2.86 lipid biosynthesis Dde_3782 multi-sensor signal transduction histidine...”
- “...limitation and starvation depended on the periplasmic component of ABC-type Mn 2+ /Zn 2+ transporter (Dde_2210) ( Table 1 ). Based on the large fitness defects of Dde_2210 in the presence of O 2 , the uncoupler FCCP and SDS ( Fig 3 ), lignin, during...”
SERP0291 ABC transporter, permease protein from Staphylococcus epidermidis RP62A
30% identity, 92% coverage
HISP_05845 metal ABC transporter permease from Haloarcula hispanica N601
32% identity, 77% coverage
- Insights into gene regulation of the halovirus His2 infecting Haloarcula hispanica
Lee, MicrobiologyOpen 2020 - “...ion transport and metabolism ABCtype Mn/Zn transport systems, ATPase component 1.509 0.652 0.653 0.203 E HISP_05845 METABOLISM Inorganic ion transport and metabolism ABCtype Mn2+/Zn2+ transport systems, permease components 1.389 0.716 0.557 0.115 E HISP_10570 METABOLISM Inorganic ion transport and metabolism ABCtype phosphate transport system, ATPase component...”
LMOf2365_1876 manganese ABC transporter, permease protein from Listeria monocytogenes str. 4b F2365
30% identity, 92% coverage
CJJ81176_0177 cation ABC transporter, permease protein from Campylobacter jejuni subsp. jejuni 81-176
28% identity, 94% coverage
SACOL1612 ABC transporter, permease protein from Staphylococcus aureus subsp. aureus COL
SAOUHSC_01656 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1515 ABC transporter, permease protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_1458 ABC transporter permease from Staphylococcus aureus subsp. aureus str. Newman
30% identity, 83% coverage
- Virulence and Metabolism
Richardson, Microbiology spectrum 2019 (secret) - Changes in the Staphylococcus aureus transcriptome during early adaptation to the lung
Chaffin, PloS one 2012 - “...fold increased expression compared to stationary phase cells. ABC-type Mn2+/Zn2+ transport system permease component znuB (SACOL1612) was expressed 6.2 fold higher after 30 in vivo and the ATP binding component znuC (SACOL1613) 3.0 fold higher compared to stationary phase conditions. This operon is divergently transcribed from...”
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...protein putative SAOUHSC_00423 3.536 Conserved hypothetical protein SAOUHSC_02430 3.658 ABC transporter periplasmic binding protein putative SAOUHSC_01656 4.262 Conserved hypothetical protein SAOUHSC_01657 4.964 ABC transporter putative SAOUHSC_00175 10.497 Multiple sugar-binding transport ATP-binding protein putative SAOUHSC_02640 22.861 Conserved hypothetical protein SAOUHSC_02641 37.417 Permease putative domain protein Carotenoid biosynthesis...”
- Human Urine Alters Methicillin-Resistant Staphylococcus aureus Virulence and Transcriptome
Paudel, Applied and environmental microbiology 2021 (secret) - Short and Robust Anti-Infective Lipopeptides Engineered Based on the Minimal Antimicrobial Peptide KR12 of Human LL-37
Lakshmaiah, ACS infectious diseases 2021 - “...No SAUSA300_0988 trkA Potassium uptake protein 1.6 Yes SAUSA300_1089 lspA lipoprotein signal peptidase 1.6 Yes SAUSA300_1515 ABC transporter permease 1.6-3.1 Yes SAUSA300_1967 conserved hypothetical phage protein 3.1 No SAUSA300_1228 thrB homoserine kinase 1.6-3.1 Yes SAUSA300_0394 FAD/NAD(P)-binding Rossmann fold superfamily protein 3.1 No SAUSA300_0646 graS Sensor histidine...”
- Resistome of Staphylococcus aureus in Response to Human Cathelicidin LL-37 and Its Engineered Antimicrobial Peptides
Golla, ACS infectious diseases 2020 - “...and resistance are known 46 48 . We found the disruption of the ABC transporter (SAUSA300_1515) of S. aureus JE2 did not show growth defect. Like the WT JE2, it showed similar membrane permeation to LL-37, but increased permeation to its engineered peptide 17BIPHE2. However, this...”
- “...to a limited Zn 2+ supply. Additional studies are required to understand the role of SAUSA300_1515 in Zn 2+ resistance, infection and immunity. Bacterial lipoproteins have many important functions, including substrate binding and transport, adherence, protein export and folding, cell signaling, sporulation, and antibiotic resistance 49...”
- The Metallophore Staphylopine Enables Staphylococcus aureus To Compete with the Host for Zinc and Overcome Nutritional Immunity
Grim, mBio 2017 - “...S.pneumoniae ( 38 ). The ABC transporter AdcBC is comprised of a transmembrane component, AdcB (NWMN_1458), and a nucleotide-binding domain, AdcC (NWMN_1459). Unusually, the gene encoding S.aureus AdcA was not clustered with the ABC transporter. Initially, we examined the role of the putative AdcABC permease in...”
- Inactivation of the Ecs ABC transporter of Staphylococcus aureus attenuates virulence by altering composition and function of bacterial wall
Jonsson, PloS one 2010 - “...ABC transporter ATP-binding protein 0.6 NWMN_1292 oligopeptide transporter permease 0.5 NWMN_1293 oligopeptide transporter permease 0.6 NWMN_1458 ABC transporter permease 0.5 NWMN_1540 preprotein translocase YajC subunit 2.7 NWMN_1728 ABC transporter ATP-binding protein 2.2 7.0 NWMN_1749 amino acid ABC transporter ATP-binding protein 3.1 NWMN_1763 ABC transporter ATP-binding protein...”
all0830 ABC transporter permease protein from Nostoc sp. PCC 7120
33% identity, 79% coverage
Cj0141c ABC transporter integral membrane protein from Campylobacter jejuni subsp. jejuni NCTC 11168
28% identity, 93% coverage
- Efficient inference of recombination hot regions in bacterial genomes
Yahara, Molecular biology and evolution 2014 - “...Cj0038c 5656457211 Hypothetical protein (possible membrane protein, containing two possible transmembrane domains at the N-terminus) Cj0141c 143953144756 znuB , integral membrane protein in ZnuABC system b Cj0142c 144749145603 znuC , ATPase component in ZnuABC system b Cj0143c 145616146506 znuA , zinc-binding protein in ZnuABC system b...”
- Multi-omics approaches to deciphering a hypervirulent strain of Campylobacter jejuni
Wu, Genome biology and evolution 2013 - “...functional class. Besides three ABC transporter genes cjsa_0132 , cjsa_0134 , and cjsa_0730 (corresponding to cj0141c , cj0143c , and cj0774c in NCTC11168, respectively), this group mainly included the iron transport genes. In Campylobacter , several iron-acquisition systems have been identified. Both IA3902 and NCTC11168 encode...”
- A Campylobacter jejuni znuA orthologue is essential for growth in low-zinc environments and chick colonization
Davis, Journal of bacteriology 2009 - “...is encoded on a zinc-dependent operon with Cj0142c and Cj0141c, which encode the other two likely components of the transport system of C. jejuni. Transcription...”
- “...residues 43 to 47. (B) Genetic organization of Cj0141c, Cj0142c, and Cj0143c with consensus promoter sequences (black lines above sequence) and ribosome binding...”
KAR41_05155 metal ABC transporter permease from Periweissella fabalis
30% identity, 98% coverage
- Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species
Fanelli, Microbiology spectrum 2023 - “...ZnuA-like ZnuC KAK10_06935 KAR27_02770 KAR41_05160 KAR50_00880 KAR53_05015 KAR63_00520 Multidrug ABC transporter, TroCD-like ZnuB KAK10_06940 KAR27_02775 KAR41_05155 KAR50_00885 KAR53_05010 KAR63_00525 Multidrug ABC-transporter extension domain YbiT KAK10_05380 KAR27_02780 KAR41_08250 KAR50_09450 KAR53_08895 KAR63_00530 a T , type strain; NA, not annotated. Phenotypic analysis. (i) Assessment of the probiotic and...”
cg0042 ABC transporter protein membrane protein from Corynebacterium glutamicum ATCC 13032
33% identity, 88% coverage
E6P09_14780 metal ABC transporter permease from Haloferax mediterranei ATCC 33500
31% identity, 78% coverage
- Transcriptomic profiling of haloarchaeal denitrification through RNA-Seq analysis
Miralles-Robledillo, Applied and environmental microbiology 2024 - “...denitrifying conditions (oxic vs denitrifying conditions) NCBI locus tag Gene product Log 2 FC Operon E6P09_14780 Metal ABC transporter permease (ZnuB) 4.63 E6P09_14785 Metal ABC transporter ATP-binding protein (ZnuC) 4.35 E6P09_14790 Metal ABC transporter substrate-binding protein (ZnuA) 4.34 Operon E6P09_18045 Multicopper oxidase domain-containing protein 7.66 E6P09_18050...”
DVU1341 permease component of zinc ABC transporter from Desulfovibrio vulgaris Hildenborough
33% identity, 85% coverage
Sant_3721 metal ABC transporter permease from Sodalis praecaptivus
34% identity, 87% coverage
- Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria
Boyd, Nature communications 2024 - “...tan. Regarding the latter, several genes predicted to function as ATP-powered transporters ( znuABC , Sant_3721, Sant_3722, tbpA and thiPQ ), along with genes encoding other proteins known to influence energy homeostasis ( cutA , cpdA, pgm and djlA ). Abbreviations: C . = Columbicola ,...”
SA1384 hypothetical protein from Staphylococcus aureus subsp. aureus N315
29% identity, 83% coverage
HVO_2399 ABC-type transport system permease protein (probable substrate zinc) from Haloferax volcanii DS2
30% identity, 77% coverage
- Extracellular vesicle formation in Euryarchaeota is driven by a small GTPase
Mills, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...proteins identified as enriched by differential expression analysis were also present in this list, except HVO_2399 identified as enriched only in EVs from UV-treated cells, suggesting that the protein composition slightly changes upon UV exposure. The most abundant protein was cytoskeletal protein, CetZ1 (HVO_2204), followed by...”
- A Small RNA Is Linking CRISPR-Cas and Zinc Transport
Märkle, Frontiers in molecular biosciences 2021 - “...znu C1 2.11 1.6E-07 Putative zinc ABC transporter ATP-binding protein HVO_2400 2.08 1.7E-08 Hypothetical protein HVO_2399; znu B1 1.98 3.2E-07 Putative zinc ABC transporter permease The log 2 fold change (column log 2 ) deletion vs. wild type is given alongside the HVOgene number (column gene),...”
- “...we further concentrated our analysis on the znu operon comprising znu A1 (HVO_2397), znu B1 (HVO_2399), and znu C1 (HVO_2398). TSS analyses ( Babski et al., 2016 ) show that expression is governed by a single TSS four nucleotides upstream of the znu A1 start codon,...”
KAR50_00885 metal ABC transporter permease from Periweissella fabaria
29% identity, 98% coverage
- Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species
Fanelli, Microbiology spectrum 2023 - “...ZnuC KAK10_06935 KAR27_02770 KAR41_05160 KAR50_00880 KAR53_05015 KAR63_00520 Multidrug ABC transporter, TroCD-like ZnuB KAK10_06940 KAR27_02775 KAR41_05155 KAR50_00885 KAR53_05010 KAR63_00525 Multidrug ABC-transporter extension domain YbiT KAK10_05380 KAR27_02780 KAR41_08250 KAR50_09450 KAR53_08895 KAR63_00530 a T , type strain; NA, not annotated. Phenotypic analysis. (i) Assessment of the probiotic and biotechnological...”
PA2409 probable permease of ABC transporter from Pseudomonas aeruginosa PAO1
PA14_33540 putative permease of ABC transporter from Pseudomonas aeruginosa UCBPP-PA14
35% identity, 81% coverage
- Phage Resistance Evolution Induces the Sensitivity of Specific Antibiotics in Pseudomonas aeruginosa PAO1
Xuan, Microbiology spectrum 2022 - “...in PAO1-R1-associated ORFS Function cluster Annotation No. of genes Gene name Cluster 1 Membrane 20 PA2409, PA2541, PA1923, lepA , fliF , kefB , PA0801, PA0847, PA4394, PA1108, PA1361, pyoS5 , pntB , PA3522, PA1611, cysW , tolA , pcrD , mtr , pilQ Cluster 2...”
- Plant growth-promoting effect and genomic analysis of the P. putida LWPZF isolated from C. japonicum rhizosphere
Jin, AMB Express 2022 - “...34.7% ( LWPZF JNO42_02130 to PAO1 PA2398 ) to 85.4% ( LWPZF JNO42_04035 to PAO1 PA2409 ). Two opening reading frames (ORFs) of JNO42_04020 and JNO42_04025 , upstream of the membrane protein gene cluster JNO42_04030 JNO42_04065 were unique and had no homologs among the PVD genes...”
- ECF Sigma Factor HxuI Is Critical for In Vivo Fitness of Pseudomonas aeruginosa during Infection
Cai, Microbiology spectrum 2022 - “...4.65E-38 PA2407 fpvC Periplasmic binding protein 5.52 7.38E-15 PA2408 fpvD ABC transporter ATPase 5.65 2.14E-15 PA2409 fpvE ABC transporter permease 5.98 5.47E-17 PA2410 fpvF Periplasmic binding protein 4.99 4.89E-18 PA2467 foxR Anti-sigma factor FoxR Fur box 2 2.52E-05 PA3530 bfd Bacterioferritin-associated ferredoxin Fur box 2.26 3.94E-05...”
- Pf4 Phage Variant Infection Reduces Virulence-Associated Traits in Pseudomonas aeruginosa
Tortuel, Microbiology spectrum 2022 - “...5.13 PA2407 fpvC FpvC PvdS, SigX, FpvI 5.71 PA2408 fpvD FpvD PvdS, SigX, FpvI 5.46 PA2409 fpvE FpvE PvdS, SigX, FpvI 5.99 PA2410 fpvF FpvF PvdS, SigX, FpvI 4.65 PA2411 Probable thioesterase PvdS 5.10 PA2412 mbtH Conserved hypothetical protein PvdS 5.26 PA2413 pvdH l -2,4-Diaminobutyrate:2-ketoglutarate 4-aminotransferase,...”
- Loss of RND-Type Multidrug Efflux Pumps Triggers Iron Starvation and Lipid A Modifications in Pseudomonas aeruginosa
Adamiak, Antimicrobial agents and chemotherapy 2021 (secret) - PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia
Chen, BioData mining 2018 - “...binding protein, as well as other components of an ABC transporter (genes PA2407, PA2408, and PA2409 at https://goo.gl/bfqOk8 ) [ 40 ]. PathCORE-T suggested a relationship between zinc and iron pathways in P. aeruginosa transcriptional data though such a relationship has not yet been described. Structural...”
- Increased ParB level affects expression of stress response, adaptation and virulence operons and potentiates repression of promoters adjacent to the high affinity binding sites parS3 and parS4 in Pseudomonas aeruginosa
Kawalek, PloS one 2017 - “...-3,0 6 transcriptional regulator PA2403 -3,1 6 hypothetical protein PA2406 -2,7 -3,2 6 hypothetical protein PA2409 -3,0 -2,8 6 probable permease of ABC transporter PA2410 -3,0 -3,2 6 hypothetical protein PA2411 -2,2 5 probable thioesterase Transcriptional regulators PA0515 3,1 3,0 4 probable transcriptional regulator PA1196 3,7...”
- “...seems to be negatively affected by ParB excess as the genes PA2403 , PA2406 , PA2409 and PA2410 (Cluster 6) from the pyoverdine biosynthesis operon are significantly downregulated in ParB-overproducing cells ( Table 4 ). Analysis of ParB-related transcriptional silencing around parS sites Analysis of the...”
- The HigB/HigA toxin/antitoxin system of Pseudomonas aeruginosa influences the virulence factors pyochelin, pyocyanin, and biofilm formation
Wood, MicrobiologyOpen 2016 - “...of ABC transporter, membrane proteins PA2403 5.7 Hypothetical protein; membrane proteins PA2406 5.3 Hypothetical protein PA2409 4.0 Probable permease of ABC transporter, membrane proteins/transport of small molecules PA2407 3.5 Probable adhesion protein, motility and attachment PA2410 3.5 Hypothetical protein Related to pyoverdine and iron transportation PA2398_...”
- More
- The horizontal transfer of Pseudomonas aeruginosa PA14 ICE PAPI-1 is controlled by a transcriptional triad between TprA, NdpA2 and MvaT
Dangla-Pélissier, Nucleic acids research 2021 - “...two different loci are regulated by TprA. These loci are an ABC transporter permease ( PA14_33540 ) and a putative reverse transcriptase ( PA14_07480 ) in an operon with a tRNA-Met ( PA14_07470 ). The PA14_07480 gene was most strongly regulated by TprA, with a 95-fold...”
ZNUB_BACSU / O34610 High-affinity zinc uptake system membrane protein ZnuB from Bacillus subtilis (strain 168) (see 3 papers)
TC 3.A.1.15.11 / O34610 Probable zinc transport system permease protein adcB, component of The zinc uptake porter, YcdHI-YceA; AdcA/AdcC/AdcB from Bacillus subtilis (see 3 papers)
BSU02870 high affinity Zn(II) ABC transporter (permease) from Bacillus subtilis subsp. subtilis str. 168
34% identity, 86% coverage
- function: Part of the high-affinity ABC transporter complex ZnuABC involved in zinc import (Probable). Responsible for the translocation of the substrate across the membrane (By similarity). ZnuABC-mediated zinc transport is required for comF expression and competence development.
subunit: The complex is composed of two ATP-binding proteins (ZnuC), two transmembrane proteins (ZnuB) and a solute-binding protein (ZnuA).
disruption phenotype: Disruption results in low transformability. - substrates: Zn2+
- The Blueprint of a Minimal Cell: MiniBacillus
Reuß, Microbiology and molecular biology reviews : MMBR 2016 - “...Fe-S cluster sufB sufU sufD sufS sufC fra yutI BSU02870 No BSU03950 No BSU32670 BSU32680 BSU32700 BSU32690 BSU32710 BSU05750 BSU32220 Yes Yes Yes Yes Yes No No...”
SE1242 ABC transporter from Staphylococcus epidermidis ATCC 12228
29% identity, 84% coverage
TC 3.A.1.15.4 / Q56955 YfeD aka YPO2442 aka Y1894, component of Iron and manganese porter from Yersinia pestis (see 4 papers)
YPTB2350 ABC chelated iron transporter, permease subunit yfeD from Yersinia pseudotuberculosis IP 32953
YPO2442 chelated iron transport system membrane protein from Yersinia pestis CO92
y1894 permease for iron and manganese ABC transporter from Yersinia pestis KIM
31% identity, 85% coverage
RT0612 zinc/manganese ABC transporter permease protein from Rickettsia typhi str. wilmington
26% identity, 87% coverage
- Genome-wide screen for temperature-regulated genes of the obligate intracellular bacterium, Rickettsia typhi
Dreher-Lesnick, BMC microbiology 2008 - “...chaperone DnaK [Rickettsia typhi str. Wilmington] 0.6 (0.4, 0.6, 1.1) Inorganic ion transport and metabolism RT0612 zinc/manganese ABC transporter permease protein [Rickettsia typhi str. Wilmington] 0.6 (0.3, 1.1, 0.6) RT0258 hypothetical protein RT0258 [Rickettsia typhi str. Wilmington] 0.6 (0.5, 0.9, 0.6) General function prediction only RT0320*...”
- Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae
McLeod, Journal of bacteriology 2004 - “...a potential zinc/manganese transporter (RT0013 and RT0612), a magnesium transporter (RT0572), potassium transporter (RT0798), a glutamine transporter (RT0118,...”
EW045_RS05540, VK055_4482 metal ABC transporter permease from Klebsiella pneumoniae
34% identity, 90% coverage
- Zinc acquisition and its contribution to Klebsiella pneumoniae virulence
Maunders, Frontiers in cellular and infection microbiology 2023 - “...SBP gene within a putative operon that also encodes an ABC transporter (transmembrane domain (TMD), EW045_RS05540; nucleotide-binding domain (NBD), EW045_RS05535). This operon structure is frequently observed for ABC importers and their associated ligand-recruiting SBPs. Taken together, these data strongly suggest that K. pneumoniae AJ218 encodes a...”
- Two-Component Response Regulator OmpR Regulates Mucoviscosity through Energy Metabolism in Klebsiella pneumoniae
Wang, Microbiology spectrum 2023 - “...protein 93.2 20.01 2.39 4.94E-28 VK055_4481 4481 ATP-binding cassette domain-containing protein 201.03 69.63 1.70 2.62E-14 VK055_4482 4482 metal ABC transporter permease 82.72 21.67 2.1 1.49E-11 VK055_4483 4483 metal ABC transporter substrate-binding protein 67.12 18.80 2.00 4.13E-10 VK055_1148 pspC envelope stress response membrane protein PspC 221.79 73.53...”
KAR63_00525 metal ABC transporter permease from Weissella uvarum
28% identity, 97% coverage
- Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species
Fanelli, Microbiology spectrum 2023 - “...KAR27_02770 KAR41_05160 KAR50_00880 KAR53_05015 KAR63_00520 Multidrug ABC transporter, TroCD-like ZnuB KAK10_06940 KAR27_02775 KAR41_05155 KAR50_00885 KAR53_05010 KAR63_00525 Multidrug ABC-transporter extension domain YbiT KAK10_05380 KAR27_02780 KAR41_08250 KAR50_09450 KAR53_08895 KAR63_00530 a T , type strain; NA, not annotated. Phenotypic analysis. (i) Assessment of the probiotic and biotechnological potential. (a)...”
BBW69_00880 metal ABC transporter permease from Neisseria sp. RH3002v2f
31% identity, 89% coverage
BIF_01817 metal ABC transporter permease from Bifidobacterium animalis subsp. lactis BB-12
34% identity, 86% coverage
- Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12
Jensen, Microbiology resource announcements 2021 - “...1759026 GT Intergenic(70/+66) BIF_tRNA49 / BIF_00125 1759057 +C Intergenic(101/+35) BIF_tRNA49 / BIF_00125 1770206 7bp20bp Intergenic(+28/+64) BIF_01817 / BIF_01834 1770224 GC Intergenic(+46/+52) BIF_01817 / BIF_01834 1787741 18bp50bp Intergenic(+6/+30) BIF_02258 / BIF_00170 1790308 1bp Intergenic(+24/+44) BIF_01753 / BIF_01191 1790315 + GGGCCCGCGAACAC Intergenic(+31/+37) BIF_01753 / BIF_01191 1790322 1bp Intergenic(+38/+30)...”
DR_2283 metal ABC transporter permease from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
DR2283 manganese ABC transporter, permease protein, putative from Deinococcus radiodurans R1
33% identity, 96% coverage
- Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species
Lim, FEMS microbiology reviews 2019 - “...Nramp H-dependent Mn 2+ transporter MntH (DR_1709) and the ATP-binding cassette (ABC)-type Mn 2+ transporter (DR_2283, DR2284 and DR_2523 encoding transmembrane subunit/permease component MntB, ATPase component MntC and solute-binding component MntA, respectively) (Sun etal. 2010 ; Ul Hussain Shah etal. 2014 ,). The D . radiodurans...”
- Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of deinococcus radiodurans R1
Luan, PloS one 2014 - “...also protect proteins from the ROS produced during irradiation [9] . Our data showed that DR_2283 and DR_2284 (manganese ABC transporter permease) functioning as Mn 2+ transporters were induced in the early stages of irradiation and recovery. An overview of components of the irradiation protection network...”
- DR1440 is a potential iron efflux protein involved in maintenance of iron homeostasis and resistance of Deinococcus radiodurans to oxidative stress
Dai, PloS one 2018 - “...regulator of a Fe-dependent transporter gene ( dr1219 ) and a Mn transporter gene ( dr2283 ) [ 30 ]. However, the exact regulation of DR1440 and co-regulation of Mn and Fe transporters to increase the intracellular Mn/Fe ratio in D . radiodurans requires further studies....”
- A Mur regulator protein in the extremophilic bacterium Deinococcus radiodurans
Ul, PloS one 2014 - “...( dr1236 ), and as a negative regulator of Mn ABC transporter genes, such as dr2283 , dr2284 and dr2523 . Therefore, it plays an important role in maintaining the homoeostasis of intracellular Mn (II), and also other Mn 2+ , zinc (Zn 2+ ) and...”
- “...(Mn 2+ efflux genes) [17] , dr1709 (Nramp family transporters) and three ATP-dependent transporters ( dr2283 , dr2284 and dr2523 ). The genes that are involved in Fe 2+ -dependent transport encode an ABC-type hemin transporter ( drb0016 ), an ABC-type Fe(III)-siderophore transporter ( drb0017 ),...”
- Extracellular dGMP enhances Deinococcus radiodurans tolerance to oxidative stress
Li, PloS one 2013 - “...0.18 DR1546 Cu/Zn superoxide dismutase 0.95 0.29 DRA0202 Cu/Zn superoxide dismutase 0.73 0.78 other genes DR2283 manganese ABC transporter permease 2.98 1.79E-05 DR2523 Manganese/iron transport system substrate-binding protein 1.36 0.0003 DR2539 Mn-dependent transcriptional regulator 2.25 0.00014 DRB0016 iron complex transport system ATP-binding protein 2.79 0.0047 DRB0092...”
- Regulation of MntH by a dual Mn(II)- and Fe(II)-dependent transcriptional repressor (DR2539) in Deinococcus radiodurans
Sun, PloS one 2012 - “...mntABC promoters Because DR0865 cannot regulate MntH transcription, we turned our attention to dr2523 , dr2283 , and dr2284 , which encode the other putative Mn(II) acquisition transporters. The EMSA results indicate that DR0865 binds to the promoters of dr2523 , dr2283 , and dr2284 (...”
- “...On the other hand, we found that DR2539 protein cannot bind to the promoters of dr2283 , dr2284 , or dr2523 (data not shown). The manganese resistance assay showed that the dr0865 null mutant is comparable to the wild strain while the manganese resistance of the...”
- Oxidative stress resistance in Deinococcus radiodurans
Slade, Microbiology and molecular biology reviews : MMBR 2011 - “...is regulated by an ABC-type Mn transporter (DR2283), an NRAMP family Mn transporter (DR1709), and an Mn-dependent transcriptional regulator, TroR/DtxR (DR2539)...”
- “...desiccation (602). DR2539 is a negative regulator of DR2283 and a positive regulator of Fe-dependent transporter genes (DR1219 and DRB0125) (93). D. deserti has...”
- DR2539 is a novel DtxR-like regulator of Mn/Fe ion homeostasis and antioxidant enzyme in Deinococcus radiodurans
Chen, Biochemical and biophysical research communications 2010 (PubMed)- “...as a negative regulator of a Mn transporter gene (dr2283) and as a positive regulator of Fe-dependent transporter genes (dr1219, drb0125) in D. radiodurans. 0...”
- “...wild-type and mutant dtxR . The expression of dr2283 was upregulated 11.43-fold, whereas the expression of dr1219 and drb0125 was downregulated 3.5-fold and...”
- Disruption of manganese ions [Mn(II)] transporter genes DR1709 or DR2523 in extremely radio-resistant bacterium Deinococcus radiodurans
Chang, Wei sheng wu xue bao = Acta microbiologica Sinica 2009 (PubMed)- “...possibly controlled by several different steps. The roles of DR2523 might be partially substituted by DR2283 and/or DR2284, while no other genes could exercise the similar function as DR1709....”
I35_RS13380 metal ABC transporter permease from Burkholderia cenocepacia H111
34% identity, 90% coverage
- Transcriptional Response of Burkholderia cenocepacia H111 to Severe Zinc Starvation
Barnett, British journal of biomedical science 2023 - “...Phenol degradation protein 2.320499563 2.27E28 I35_RS22340 Hypothetical protein 2.300982216 0.00000167 I35_RS20825 Alpha/beta hydrolase 2.246852811 0.035832439 I35_RS13380 ABC transporter permease 2.238628283 5.97E30 I35_RS10865 Hypothetical protein 2.099694274 0.022469745 I35_RS16595 DNA-binding protein 2.091617711 0.000362322 I35_RS29435 Hypothetical protein 2.072176035 0.022280782 I35_RS27035 2,2-Dialkylglycine decarboxylase 2.047152459 0.00024177 I35_RS16045 Hypothetical protein 2.046747087 1.75E09...”
TC 3.A.1.15.7 / Q9XCR9 SitD aka STM2864, component of Manganese (Mn2+) (Km=0.1 μM) and iron (Fe2+) (5 μM) porter (inhibited by Cd2+ > Co2+ > Ni2+, Cu2+) (most similar to YfeABCD of Yersinia pestis (TC #3.A.1.15.4)). Important for virulence in Salmonella from Salmonella typhimurium (see 2 papers)
STM2864 Salmonella iron transporter: fur regulated from Salmonella typhimurium LT2
H9L416 Fur regulated Salmonella iron transporter from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
32% identity, 90% coverage
- substrates: Fe2+, Mn2+
- Mass spectrometry-based quantitative proteomic analysis of Salmonella enterica serovar Enteritidis protein expression upon exposure to hydrogen peroxide
Kim, BMC microbiology 2010 - “...ung 25.48 6.56 67% STM2829 DNA strand exchange and recombinant protein recA 37.94 5.08 28% STM2864 Iron transporter protein, fur regulated sitD 33.7 7.84 41% STM2882 Secretory Effector Protein sipA 73.94 6.41 35% STM2884 Translocation Machinery Component sipC 42.98 8.88 38% STM2924 RNA polymerase sigma factor...”
- “...Uracil-DNA glycosylase ung 27 2% STM2829 DNA strand exchange and recombinant protein recA 24 2% STM2864 Iron transporter protein, fur regulated sitD -45 8% STM2882 Secretory Effector Protein sipA 0% STM2884 Translocation Machinery Component sipC 301 30% STM2924 RNA polymerase sigma factor rpoS rpoS 13 2%...”
- Whole genome sequencing reveals widespread distribution of typhoidal toxin genes and VirB/D4 plasmids in bovine-associated nontyphoidal Salmonella
Delgado-Suárez, Scientific reports 2018 - “...the CD database 18 . However, further review of the structure of the reference protein (H9L416) in Uniprot showed the untranslated fragment contains the functional domain, as well as 6 out 8 transmembrane-spanning regions. Therefore, most likely the truncated sitD gene is not encoding a fully...”
- “...2+ /Zn 2+ transport system component. Since it did, we then analysed the reference protein (H9L416) structure at Uniprot ( http://www.uniprot.org/ ) to check if the untranslated fragment contains regions that are required for a fully functional protein. Finally, since the virulence profile showed a widespread...”
MSMEG_6045 metal ABC transporter permease from Mycolicibacterium smegmatis MC2 155
MSMEG_6045 ABC heavy metal transporter, inner membrane subunit from Mycobacterium smegmatis str. MC2 155
32% identity, 83% coverage
NGO_0169 metal ABC transporter permease from Neisseria gonorrhoeae FA 1090
30% identity, 89% coverage
KAR27_02775 metal ABC transporter permease from Weissella diestrammenae
28% identity, 98% coverage
- Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species
Fanelli, Microbiology spectrum 2023 - “...protein, ZnuA-like ZnuC KAK10_06935 KAR27_02770 KAR41_05160 KAR50_00880 KAR53_05015 KAR63_00520 Multidrug ABC transporter, TroCD-like ZnuB KAK10_06940 KAR27_02775 KAR41_05155 KAR50_00885 KAR53_05010 KAR63_00525 Multidrug ABC-transporter extension domain YbiT KAK10_05380 KAR27_02780 KAR41_08250 KAR50_09450 KAR53_08895 KAR63_00530 a T , type strain; NA, not annotated. Phenotypic analysis. (i) Assessment of the probiotic...”
TTHA0454 Mn2+/Zn2+ ABC transporter, permease protein from Thermus thermophilus HB8
38% identity, 87% coverage
JNO42_04035, T1E_2577 metal ABC transporter permease from Pseudomonas putida DOT-T1E
35% identity, 82% coverage
NTHI0477 putative ABC-type chelated iron transport system, permease component from Haemophilus influenzae 86-028NP
Q4QNI3 ABC-type chelated iron transport system, permease component from Haemophilus influenzae (strain 86-028NP)
26% identity, 96% coverage
I6G91_01720 metal ABC transporter permease from Fannyhessea vaginae
26% identity, 95% coverage
- Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia Strongly Influence Each Other's Transcriptome in Triple-Species Biofilms
Sousa, Microbial ecology 2024 - “...RimM 11.49 8.4510 3 F. vaginae upregulated genes I6G91_04240 HlyC/CorC family transporter 3.14 9.6810 6 I6G91_01720 Metal ABC transporter permease 3.04 0.00 I6G91_01715 ATP-binding cassette domaincontaining protein 2.80 0.00 I6G91_01120 PTS sugar transporter subunit IIA 2.80 2.4510 7 I6G91_01725 Hypothetical protein 2.71 0.00 rpoD RNA polymerase...”
- “...top 10 most upregulated and downregulated genes, several associated with membrane transport (including I6G91_04240 and I6G91_01720) were upregulated on the triple-species biofilms while several associated with transcriptional regulation were downregulated (namely I6G91_05895, I6G91_05165, and I6G91_05185). Despite not having any enrichment detected for the DEGs of F....”
NMB0587 membrane protein from Neisseria meningitidis MC58
30% identity, 89% coverage
- Subversion of nutritional immunity by the pathogenic Neisseriae
Cornelissen, Pathogens and disease 2018 - “...tag in NGO FA1090 NMB1728 NMB1729 NMB1730 NMB0586 NMB0587 NMB1497 (CbpA) NMB0964 (ZnuD) NMB0634 NMB0633 NMB0632 NMB0588 None NMB1882 NMB1988 None NMB0461/...”
- Interplay Between Virulence and Variability Factors as a Potential Driver of Invasive Meningococcal Disease
Siena, Computational and structural biotechnology journal 2018 - “...nth NMB0533 Manganese transport system Stress response mntA NMB0588 Manganese transport system Stress response mntB NMB0587 Manganese transport system Stress response mntC NMB0586 Methionine sulphoxide reductase Stress response msrA / B ( pilB ) NMB0044 Nitrite reductase Stress response pan1 NMB1623 Recombinational repair protein Stress response...”
- Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence
Ampattu, BMC genomics 2017 - “...1.74 NMB0294 dsbA-2 Thiol:disulfide interchange protein DsbA n.s. 1.38 n.s. n.s. n.s. n.s. n.s. n.s. NMB0587 znuB ABC-type Mn2+/Zn2+ transporter, permease n.s. n.s. n.s. n.s. 3.06 n.s. 1.94 2.49 NMB0588 znuC ABC-type Mn2+/Zn2+ transporer, ATPase n.s. n.s. n.s. 1.53 2.26 n.s. n.s. n.s. NMB1398 sodC Superoxide...”
- The zinc-responsive regulon of Neisseria meningitidis comprises 17 genes under control of a Zur element
Pawlik, Journal of bacteriology 2012 - “...469 qRT-PCR nmb0317 nmb0525 nmb0546 nmb0577 nmb0586 nmb0587 nmb0588 nmb0817 nmb0819 nmb0820 nmb0942 nmb0964 nmb0990 nmb1475 nmb1497 nmb2142 MP141 MP143 MP165...”
- “...paralogues of 50S ribosomal proteins; and nmb0588 and nmb0587, together with one single gene, nmb0586, encode the components of the putative ABC transporter for...”
- An outer membrane receptor of Neisseria meningitidis involved in zinc acquisition with vaccine potential
Stork, PLoS pathogens 2010 - “...the E. coli zur gene, i.e. NMB1266, and of a putative znuCBA operon, i.e. NMB0588, NMB0587, and NMB0586. In addition, we found sequences resembling the E. coli Zur binding sequence in the regions upstream of the znuD ( GtAATGTTATATaATAACAaact ) and znuC ( cAAAcGTTATACagTAtCATaTC ) (identical...”
- “...proteins described in this study in Genbank are: ZnuD (NMB0964), AAF62323; ZnuA (NMB0586), AAF41014; ZnuB (NMB0587), AAF41015; ZnuC (NMB0588), AAF41016; Zur (NMB1266), AAF41643; TonB (NMB1730), AAF42075. Other accession numbers are provided in Table 1 . Supporting Information Figure S1 Alignment of meningococcal ZnuD homologs. Aligned is...”
- Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536
Dobrindt, Infection and immunity 2002 - “...amino acid sequences are homologous to proteins (NMB0586, NMB0587, and NMB0588) encoded by three adjacent genes in Neisseria meningitidis strain MC58. Other...”
Hflu203001647 COG1108: ABC-type Mn2+/Zn2+ transport systems, permease components from Haemophilus influenzae R2866
HI0359 iron (chelated) ABC transporter, permease protein (yfeD) from Haemophilus influenzae Rd KW20
26% identity, 95% coverage
- A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae
Atack, Nature communications 2015 - “...protein hitB 1.75 4.39 723_01328 Hflu203001648 Iron chelated ABC transporter permease yfeC 1.90 1.69 723_01329 Hflu203001647 Iron chelated ABC transporter permease yfeD 2.08 3.98 723_00591 Hflu203000516 Anaerobic DMSO chain C dmsC 2.09 1.26 723_01434 Hflu103000469 Haem/haemopexin-binding hxuB 2.14 1.15 723_01326 Hflu203001650 Iron chelated ABC transporter yfeA...”
- Haemophilus influenzae responds to glucocorticoids used in asthma therapy by modulation of biofilm formation and antibiotic resistance
Earl, EMBO molecular medicine 2015 - “...asthma patients. Inorder to test this hypothesis, the transcript level of three corticosteroid-responsive genes ( HI0359, HI0628 and HI0994 ) was established by qRTPCR on sputum samples collected from twenty-four asthma patients. A comparison of the demographics and asthma characteristics of these patients are shown in...”
- “...(y) and sex FEV1% Inhaled steroid treatment a Detected bacterial strains b mRNA level c HI0359 HI0628 HI0994 S1 27 (M) 26 Bec Hi, Sp 24.9 (0.4) 4.4 (0.9) 7.1 (0.2) S2 26 (F) 32 Bec Hi, Pa, Sa, MRSA, Ko, Sm 18.9 (0.4) 4.3 (0.6)...”
- Comparison of transcription of the Haemophilus influenzae iron/heme modulon genes in vitro and in vivo in the chinchilla middle ear
Whitby, BMC genomics 2013 - “...-29.31 -3.29 -9.20 -2.92 -3.93 HI0264 Heme-hemopexin utilization protein HxuA -18.55 -2.86 -7.44 -2.55 -2.11 HI0359 Fe/Mn/Zn ABC transporter, permease protein YfeD -2.92 ns -4.35 -1.31 -1.66 HI0360 Fe/Mn/Zn ABC transporter, permease protein YfeC -3.54 ns -6.90 -1.34 -1.81 HI0361 Fe/Mn/Zn ABC transporter, ATP-binding protein YfeB...”
- An ABC transporter system of Yersinia pestis allows utilization of chelated iron by Escherichia coli SAB11
Bearden, Journal of bacteriology 1998 - “...and as-yetuncharacterized region of the H. influenzae genome (HI0359 to HI0362) whose genetic organization is identical to that of yfeABCD and whose ORFs have...”
- “...(83%), YfeC and MntB (72%), or YfeD and HI0359 (80%). Identification of putative yfe-encoded proteins. To determine the polypeptides necessary for promoting...”
- Molecular cloning of a 32-kilodalton lipoprotein component of a novel iron-regulated Staphylococcus epidermidis ABC transporter
Cockayne, Infection and immunity 1998 - “...membrane protein/? ScaA-associated membrane protein/? HI0359 membrane protein/? MntB membrane protein/Mn transport YfeC membrane protein/Fe transport?...”
- Topology prediction for helical transmembrane proteins at 86% accuracy
Rost, Protein science : a publication of the Protein Society 1996 - “...HI1154 in 11 MLLVNLAIFI HI0687 in 10 MNNENMVRVF HI1241 HI0359 HI0392 HI0407 HI0825 HI1248 HI0188 HI1122 HI1 178 HI1187 HI 1307 HI 1548 HI1621 HI1452 HI1620...”
TC 3.A.1.15.10 / A1IQK4 MntB (M), component of The Mn2+/Zn2+ transporter MntABC (KB of Mn2+ and Zn2+ is 0.1μM which bind with equal affinity to the same site from Neisseria meningitidis serogroup A (see paper)
NMA0790 putative ABC-transporter membrane protein from Neisseria meningitidis Z2491
30% identity, 89% coverage
Atu3179 ABC transporter, membrane spanning protein from Agrobacterium tumefaciens str. C58 (Cereon)
33% identity, 90% coverage
- Activation of ChvG-ChvI regulon by cell wall stress confers resistance to β-lactam antibiotics and initiates surface spreading in Agrobacterium tumefaciens
Williams, PLoS genetics 2022 - “...the exception of mrcA , encoding PBP1a, were yciC (Atu3181), zinT (Atu1049), troC (Atu3180), troB (Atu3179), troA (Atu3179), and Atu3184, all of which are major components of cytoplasmic zinc uptake in A . tumefaciens ( Fig 2A , bottom) [ 22 ]. We also observed large...”
- Agrobacterium tumefaciens Zur Regulates the High-Affinity Zinc Uptake System TroCBA and the Putative Metal Chaperone YciC, along with ZinT and ZnuABC, for Survival under Zinc-Limiting Conditions
Chaoprasid, Applied and environmental microbiology 2016 - “...tumefaciens has a cluster of genes (Atu3178, Atu3179, and Atu3180) encoding an ABC-type transporter, here named troA, troB, and troC, respectively,...”
- “...contains a cluster of genes consisting of Atu3178, Atu3179, and Atu3180 that are annotated as a putative zinc/manganese ABC transport system (http://www...”
- Dual control of quorum sensing by two TraM-type antiactivators in Agrobacterium tumefaciens octopine strain A6
Wang, Journal of bacteriology 2006 - “...contains two truncated open reading frames (Atu3178, Atu3179) (http://www.ncbi.nlm.nih.gov/), but none of them showed homology to traM (data not shown)....”
jpw_15965 metal ABC transporter permease from Pseudomonas asiatica
36% identity, 69% coverage
- Genomic Analysis of Pseudomonas asiatica JP233: An Efficient Phosphate-Solubilizing Bacterium
Wang, Genes 2022 - “...protein jpw_15955 fpvC zinc ABC transporter substrate-binding protein jpw_15960 fpvD metal ABC transporter ATP-binding protein jpw_15965 fpvE metal ABC transporter permease jpw_15970 fpvF zinc ABC transporter substrate-binding protein jpw_17705 pvdS extracytoplasmic-function sigma-70 factor jpw_17575 fpvI sigma-70 family RNA polymerase sigma factor jpw_17710 acetyltransferase Trehalose jpw_16785 treS...”
mll8314 ABC transporter, permease protein from Mesorhizobium loti MAFF303099
32% identity, 89% coverage
C645_RS02300 metal ABC transporter permease from Haemophilus influenzae 2019
26% identity, 95% coverage
- Hfe Permease and <i>Haemophilus influenzae</i> Manganese Homeostasis
Ganio, ACS infectious diseases 2024 - “...amino acid sequences of HfeA (C645_RS02315; WP_005656358.1), HfeB (C645_RS02310; WP_005630123.1), HfeC (C645_RS02305; WP_005666620.1), and HfeD (C645_RS02300; WP_005666622.1) as reference sequences to screen the H. influenzae genome database. The HfeA protein was present in 100% of genomes analyzed, with high levels of amino acid sequence conservation (99.0%...”
lp_0464 zinc/iron ABC transporter, permease protein from Lactobacillus plantarum WCFS1
30% identity, 88% coverage
lp_0464 metal ABC transporter permease from Lactiplantibacillus plantarum WCFS1
30% identity, 89% coverage
- Molecular Responses of Lactobacilli to Plant Phenolic Compounds: A Comparative Review of the Mechanisms Involved
López, Antioxidants (Basel, Switzerland) 2021 - “...a metal that competes with and antagonizes copper. One of these L. plantarum transporters ( lp_0464 ) was also induced by OLE [ 28 ], and the corresponding L. brevis homologous permease ( lvis_0472 ) was induced in cells exposed to ferulic acid [ 23 ]...”
- “...ABC transporters) [ 27 ] Oleuropein npr2 pox5 (lp_3589) gshR2 msrA4 lexA CBS, CSE lp_0463, lp_0464 (zinc ABC transporter) [ 28 ] Hydroxytyrosol npr2 kat (lp_3578) pox4 (lp_3587) msrA3 gshR4 lp_0858 CBS, CSE lp_2992 (mntH3) (iron transporter) [ 29 ] Black font: upregulated genes or proteins....”
LF82_184 iron/manganese ABC transporter permease subunit SitD from Escherichia coli LF82
UTI89_C1336 SitD protein from Escherichia coli UTI89
29% identity, 88% coverage
BH01900 ABC transporter, permease protein from Bartonella henselae str. Houston-1
29% identity, 88% coverage
- A family of genus-specific RNAs in tandem with DNA-binding proteins control expression of the badA major virulence factor gene in Bartonella henselae
Tu, MicrobiologyOpen 2017 - “...copies of the filamentous hemagglutinin genes (BH06670 and BH07150) and four ABC transporter genes (BH00170, BH01900, BH12230, and BH15040). In addition, genes encoding VirB type IV secretion system components VirB6 (BH13300) and VirB9 (BH13330) were predicted targets of Brt1 (Table 3 ). Three histidine kinases including...”
- “...Gene locus Gene name/annotation Function Algorithm G kcal/mol BH13400 BepC Pathogenesis, T4SS effector IntaRNA 11.1 BH01900 ABC transporter Ferric uptake IntaRNA 10.0 BH16450 PhaC antiporter pH adaptation, H+/K+ efflux IntaRNA 9.7 b BH13330 VirB9 Pathogenesis, T4SS IntaRNA 9.7 BH05790 LipA Lipoic acid metabolism IntaRNA 9.7 b...”
MAP3774c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
33% identity, 81% coverage
- The Fur-like regulatory protein MAP3773c modulates key metabolic pathways in Mycobacterium avium subsp. paratuberculosis under in-vitro iron starvation
Thapa, Scientific reports 2024 - “...is predicted to encode several metal uptake systems, an ATP-binding cassette (ABC) transporter ( MAP3776c- MAP3774c ), a ferric uptake regulator ( MAP3773c ) and a cobalamin (vitamin B12) synthesis ( MAP3772c ) 8 . LSP15 was likely acquired via horizontal gene transfer from an unrelated...”
- “...lipid transport (Fig. 5 d). MAP3773c upregulated ATP-binding cassette (ABC) type metal transporters genes , MAP3774c (metal ABC transporter permease), MAP3775c (ATP-binding cassette domain-containing protein) and MAP3776c (zinc ABC transporter substrate-binding protein) at 30min iron stress. MAP3173c (ABC type transporter, mptF) gene was also upregulated. Putative...”
- Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis
Goethe, mSystems 2020 - “...(61.3) <0.0001 4.0 Glyoxalase/bleomycin resistance protein/dioxygenase MSMEG_5617 <0.0001 4.45 Immunogenic protein MPT63 MSMEG_6045 Rv2060 (43.7) MAP3774c (70.1) <0.0001 21.29 Heavy metal ABC transporter inner membrane protein MSMEG_6046 MAP3775c (61.2) <0.0001 19.04 ABC transporter ATP-binding protein MSMEG_6047 MAP3776c (56.4) <0.0001 43.8 Cation ABC transporter periplasmic cation-binding protein...”
- “...Zn b *MSMEG_1123 MAP1730c (43.1) <0.0001 8.64 7.56 7.50 Cobalamin synthesis protein MSMEG_6045 Rv2060 (43.7) MAP3774c (70.1) <0.0001 24.62 21.29 24.42 Heavy metal ABC transporter inner membrane protein MSMEG_6046 MAP3775c (61.2) <0.0001 20.65 19.04 19.90 ABC transporter ATP-binding protein **MSMEG_6047 MAP3776c (56.4) <0.0001 26.24 43.8 25.50...”
- Diagnostic Sequences That Distinguish M. avium Subspecies Strains
Bannantine, Frontiers in veterinary science 2020 - “...B 97 NA MAP_RS19330 WP_003879173.1 ANTAR domain-containing protein 87 MAP3772c MAP_RS19335 WP_003873951.1 GTP-binding protein 380 MAP3774c MAP_RS19345 WP_003879175.1 Metal ABC transporter permease 285 MAP3775c MAP_RS19350 WP_003873948.1 ABC transporter 262 MAP3776c MAP_RS19355 WP_019305700.1 ABC transporter substrate-binding protein 263 MAP3815 MAP_RS19565 WP_019305842.1 Hypothetical protein 254 NA MAP_RS19570 WP_003873898.1...”
- Iron Acquisition in Mycobacterium avium subsp. paratuberculosis
Wang, Journal of bacteriology 2015 - “...flanking the junction of neighboring genes produced amplicons for MAP3776c and MAP3775c , MAP3775c and MAP3774c , MAP3774c and MAP3773c , and MAP3773c and MAP3772c , consistent with a single transcript spanning these multiple genes ( Fig. 3D ). In addition, for wild-type M. avium subsp....”
- “...data indicated overexpression of other genes in the operon, we then hypothesized that MAP3775c and MAP3774c , predicted to encode the ATP-binding and transmembrane domains of an ABC transporter, respectively, could function without MAP3776c, the solute-binding protein, when free ferric ions were present in the environment....”
- Identification of a lineage specific zinc responsive genomic island in Mycobacterium avium ssp. paratuberculosis
Eckelt, BMC genomics 2014 - “...MAP3775c Rv2397c (52.38) MAV_0582 (55.5) <0.0001 15.26 ATPase component of Mn/Zn ABC-type transporter P - MAP3774c Rv2060 (37.0) MAV_0581 (51.89) <0.0001 17.58 ABC-type Mn2+/Zn2+ transport system, permease component P - MAP3773c Rv2359 (56.8) MAV_2036 (58.06) <0.0001 16.92 Fe2+/Zn2+ uptake regulation protein, Fur family protein P -...”
- Primary transcriptomes of Mycobacterium avium subsp. paratuberculosis reveal proprietary pathways in tissue and macrophages
Janagama, BMC genomics 2010 - “...synthase (MAP3763c) belonging to LSP14 were all upregulated in macrophage infections. An ABC transporter operon (MAP3774c - MAP3776c), which is located on LSP 15, was downregulated in infected tissues. Interestingly, MAP3773c, a probable Ferric Uptake Regulator protein on LSP 15, was downregulated in the tissues and...”
KAR53_05010 metal ABC transporter permease from Periweissella ghanensis
29% identity, 98% coverage
- Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species
Fanelli, Microbiology spectrum 2023 - “...KAK10_06935 KAR27_02770 KAR41_05160 KAR50_00880 KAR53_05015 KAR63_00520 Multidrug ABC transporter, TroCD-like ZnuB KAK10_06940 KAR27_02775 KAR41_05155 KAR50_00885 KAR53_05010 KAR63_00525 Multidrug ABC-transporter extension domain YbiT KAK10_05380 KAR27_02780 KAR41_08250 KAR50_09450 KAR53_08895 KAR63_00530 a T , type strain; NA, not annotated. Phenotypic analysis. (i) Assessment of the probiotic and biotechnological potential....”
jk1488 manganese ABC transport system, permease protein from Corynebacterium jeikeium K411
29% identity, 91% coverage
APJL_0128 iron (chelated) transport system membrane protein from Actinobacillus pleuropneumoniae serovar 3 str. JL03
APL_0127 putative iron transport system membrane protein from Actinobacillus pleuropneumoniae L20
28% identity, 91% coverage
O2ColV4 SitD from Escherichia coli
28% identity, 88% coverage
HD1024 iron (chelated) transport system membrane protein from Haemophilus ducreyi 35000HP
28% identity, 91% coverage
PGN_1876 putative ABC transporter membrane protein from Porphyromonas gingivalis ATCC 33277
27% identity, 90% coverage
- Gene expression of Porphyromonas gingivalis ATCC 33277 when growing in an in vitro multispecies biofilm
Romero-Lastra, PloS one 2019 - “..., as ABC transporters PG_0912 [-2.36 (SD = 0.05)], PGN_1898 MgtE [-2.24 (SD = 0.27)], PGN_1876 [-2.41 (SD = 0.18)], PG_1010 [-2.57 (SD = 0.23)], PGN_1343 [-2.81 (SD = 0.71)], PGN_1734 [-3.09 (SD = 0.43)]; aerotolerance , as ( BatA-E ), PGN_0529 [-5.86 (SD = 1.09)],...”
sitD / SP|Q6J5N7 iron/manganese ABC transporter, permease protein from Escherichia coli (see paper)
28% identity, 88% coverage
Halsa_0275 metal ABC transporter permease from Halanaerobium hydrogeniformans
27% identity, 89% coverage
NGO0169 putative ABC transporter, membrane protein from Neisseria gonorrhoeae FA 1090
30% identity, 92% coverage
EY04_RS29155 metal ABC transporter permease from Pseudomonas chlororaphis
34% identity, 88% coverage
UTI89_C1337 SitC protein from Escherichia coli UTI89
27% identity, 89% coverage
- Glycosuria Alters Uropathogenic Escherichia coli Global Gene Expression and Virulence
Islam, mSphere 2022 - “...1.2711 3.1580* 1.9088* Glycosyltransferase UTI89_C1336 sitD 1.376* 3.355* 1.997* Iron/manganese ABC transporter permease subunit SitD UTI89_C1337 sitC 0.959 2.552* 1.612* Iron/manganese ABC transporter permease subunit SitC UTI89_C1338 sitB 0.816 2.338* 1.543* Iron/manganese ABC transporter ATP-binding protein SitB UTI89_C1339 sitA 0.960 2.363* 1.423* Iron/manganese ABC transporter substrate-binding...”
MAP_RS19345 metal ABC transporter permease from Mycobacterium avium subsp. paratuberculosis K-10
33% identity, 87% coverage
LF82_185 iron/manganese ABC transporter permease subunit SitC from Escherichia coli
27% identity, 89% coverage
Atu4469 ABC transporter, membrane spanning protein (iron) from Agrobacterium tumefaciens str. C58 (Cereon)
29% identity, 90% coverage
SG1519 iron ABC transporter permease component from Sodalis glossinidius str. 'morsitans'
30% identity, 84% coverage
- Regulation of high-affinity iron acquisition homologues in the tsetse fly symbiont Sodalis glossinidius
Runyen-Janecky, Journal of bacteriology 2010 - “...21, 39, 54), are present in Sodalis (SG1516 to SG1519). The sit and yfe genes have been found in numerous pathogenic bacteria, and among the enteric species,...”
- “...Y Y Y Y SG1431 to SG1436 Y SG1505 Y SG1516 to SG1519 Y SG1526 Y SG1538 to SG1540 Y SG1674 SG1998 SG2280 SG2322 SGP1_0035 to SGP1_0045 Y N N Y Y Inner membrane...”
- Quorum sensing primes the oxidative stress response in the insect endosymbiont, Sodalis glossinidius
Pontes, PloS one 2008 - “...damaged cellular components (SG1106 and SG1348), transport of iron and manganese (SG1516, SG1517, SG1518 and SG1519) and protein folding (e.g., SG0409, SG0584, SG0692 and SG2325; Supplementary Table S2 ). The addition of OHHL also increased the expression of bacterioferritin (SG2280) and genes involved in iron siderophore...”
KAK10_06940 metal ABC transporter permease from Periweissella beninensis
31% identity, 95% coverage
- Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species
Fanelli, Microbiology spectrum 2023 - “...binding protein, ZnuA-like ZnuC KAK10_06935 KAR27_02770 KAR41_05160 KAR50_00880 KAR53_05015 KAR63_00520 Multidrug ABC transporter, TroCD-like ZnuB KAK10_06940 KAR27_02775 KAR41_05155 KAR50_00885 KAR53_05010 KAR63_00525 Multidrug ABC-transporter extension domain YbiT KAK10_05380 KAR27_02780 KAR41_08250 KAR50_09450 KAR53_08895 KAR63_00530 a T , type strain; NA, not annotated. Phenotypic analysis. (i) Assessment of the...”
BTH_I0688 cation ABC transporter, permease protein, putative from Burkholderia thailandensis E264
31% identity, 90% coverage
D11S_1643 AfeC from Aggregatibacter actinomycetemcomitans D11S-1
28% identity, 91% coverage
SP68_09585 iron/manganese ABC transporter permease subunit SitC from Klebsiella variicola
26% identity, 91% coverage
B488_10160 metal ABC transporter permease from Liberibacter crescens BT-1
23% identity, 96% coverage
PMI1024 iron ABC transporter, membrane protein from Proteus mirabilis HI4320
26% identity, 82% coverage
TC 3.A.1.15.9 / Q92LL2 PUTATIVE IRON TRANSPORT SYSTEM MEMBRANE ABC TRANSPORTER PROTEIN aka SitD, component of Manganese (Mn2+) and Iron (Fe2+) porter, SitABCD from Rhizobium meliloti (Sinorhizobium meliloti) (see paper)
SMc02506 PUTATIVE IRON TRANSPORT SYSTEM MEMBRANE ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
28% identity, 89% coverage
TP0036 ABC transporter, permease protein from Treponema pallidum subsp. pallidum str. Nichols
29% identity, 89% coverage
CT417 (Metal Transport Protein) from Chlamydia trachomatis D/UW-3/CX
25% identity, 87% coverage
CTL0674 metal transporter, membrane permease component from Chlamydia trachomatis 434/Bu
25% identity, 87% coverage
- Requirement of GrgA for Chlamydia infectious progeny production, optimal growth, and efficient plasmid maintenance
Lu, mBio 2024 - “...ctrR12_n 2.59 6.4E-15 tRNA-Leu tRNA-Leu 2.48 3.9E-04 ctl0339 Phosphatidylcholine-hydrolyzing phospholipase D (PLD) Protein 2.43 1.8E-12 ctl0674 Metal ABC transporter permease 2.38 1.0E-29 nth Transcription termination/antitermination protein NusA 2.37 1.5E-14 tRNA-Ile tRNA-Ile 2.36 9.6E-10 oppF Oligopeptide ABC transporter ATP-binding protein 2.26 1.9E-15 ctl0016 Putative membrane protein 2.25...”
- “...L2/cgad-peig cultures during the midcycle, oppD and oppF encode oligopeptide ABC transporter ATP-binding proteins, while ctl0674 encodes a metal ABC transporter, and trpB encodes tryptophan synthase B. These changes suggest that GrgA promotes RB growth by upregulating both nutrient acquisition from host cells and de novo...”
- Identification of the alternative sigma factor regulons of Chlamydia trachomatis using multiplexed CRISPR interference
Hatch, mSphere 2023 - “...2.32 CT489 CTL0750 glgC Glucose-1-phosphate adenylyltransferase 2.55 2.59 S CT055 CTL0311 sucB_1 Succinyltransferase 2.54 CT417 CTL0674 CTL0674 Metal ABC transporter permease 2.35 CT821 CTL0193 sucC Succinyl-CoA ligase subunit beta 2.27 2.10 CT628 CTL0892 ispA Farnesyl diphosphate synthase 2.07 Membrane organization associated CT444 CTL0703 omcA Outer membrane...”
- A Reverse Genetic Approach for Studying sRNAs in Chlamydia trachomatis
Wang, mBio 2022 - “...region ( TableS1 ). We focused on four of these mRNAs, YtgB, CTL0389, CTL0015 and CTL0674, because they contained predicted CtrR3-interacting sequences located at their RBS, which is the site where sRNAs frequently bind to regulate protein expression ( Fig.6 , Table1 ). TABLE1 List of...”
- “...ctl0389 a (16)C GGGAGGA GAG(6) ytgB a (17)A UUGGGAGG GA(7) ctl0015 a (12)A GGGAGG GGAU(2) ctl0674 a (9)U UUUGGGAG A(+1) gatA b (51)G UUGGGAGGA UU(40) rpsT b (13)A UUGGGAG AGAUU(1) rpsM b (15)A GGGAGG C(8) ctl0190 b (10)G GGGAGGA GGA(+1) hctB b (+9)G UUGGGAG U AC...”
BQ01780 ABC transporter, permease protein from Bartonella quintana str. Toulouse
28% identity, 89% coverage
Q7UIM8 Manganese ABC transporter permease protein from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
31% identity, 55% coverage
O2ColV3 SitC from Escherichia coli
26% identity, 92% coverage
sitC / SP|Q6J5N8 iron/manganese ABC transporter, permease protein from Escherichia coli (see paper)
26% identity, 89% coverage
MNTC_BACSU / O35024 Manganese transport system membrane protein MntC from Bacillus subtilis (strain 168) (see paper)
BSU30750 manganese ABC transporter (permease) from Bacillus subtilis subsp. subtilis str. 168
31% identity, 58% coverage
- function: Probably part of the ABC transporter complex MntABCD involved in manganese import. Probably responsible for the translocation of the substrate across the membrane.
subunit: The complex is probably composed of two ATP-binding proteins (MntB), two transmembrane proteins (MntC and MntD) and a solute-binding protein (MntA). - In Silico Safety Assessment of <i>Bacillus</i> Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates
Bin, International journal of molecular sciences 2024 - “...MntH P96593 mntD Manganese transport system membrane protein O34500 mntC Manganese transport system membrane protein O35024 mntB Manganese transport system ATP-binding protein O34338 mntA Manganese-binding lipoprotein O34385 ahpF NADH dehydrogenase P42974 tpx Thiol peroxidase P80864 trxA Thioredoxin P14949 trxB Thioredoxin reductase P80880 msrA Peptide methionine sulfoxide...”
- Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station
Morrison, NPJ microgravity 2019 - “...2.41 6-carboxyhexanoateCoA ligase BirA BSU30740 mntD 3.95 4.11 3.13 3.32 Manganese ABC transporter (permease) MntR BSU30750 mntC 3.97 4.12 2.98 3.31 Manganese ABC transporter (membrane protein) MntR BSU30760 mntB 3.83 3.98 2.82 3.15 Manganese ABC transporter (ATP-binding protein) MntR BSU30770 mntA 3.12 3.32 2.70 2.76 Manganese...”
RL3886 putative Fur regulated salmonella iron ABC transporter component from Rhizobium leguminosarum bv. viciae 3841
25% identity, 90% coverage
Nmar_0330 ABC-3 protein from Nitrosopumilus maritimus SCM1
28% identity, 83% coverage
SPO3364, YP_168560 zinc/manganese/iron ABC transporter, permease protein from Silicibacter pomeroyi DSS-3
SPO3364 metal ABC transporter permease from Ruegeria pomeroyi DSS-3
34% identity, 62% coverage
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...SPO3307 Lysine-ketoglutarate reductase lkr Function YP_168559 SPO3363 Manganese ABC transporter, permease protein sitD Function YP_168560 SPO3364 Manganese ABC transporter, permease protein sitC Function YP_168561 SPO3365 Manganese ABC transporter, ATP-binding protein sitB Function YP_168562 SPO3366 Manganese ABC transporter, periplasmic protein sitA Function YP_168752 SPO3557 Sulfite dehydrogenase subunit...”
- “...YP_168503 SPO3307 Lysine-ketoglutarate reductase lkr Function YP_168559 SPO3363 Manganese ABC transporter, permease protein sitD Function YP_168560 SPO3364 Manganese ABC transporter, permease protein sitC Function YP_168561 SPO3365 Manganese ABC transporter, ATP-binding protein sitB Function YP_168562 SPO3366 Manganese ABC transporter, periplasmic protein sitA Function YP_168752 SPO3557 Sulfite dehydrogenase...”
- Manganese uptake in marine bacteria; the novel MntX transporter is widespread in Roseobacters, Vibrios, Alteromonadales and the SAR11 and SAR116 clades
Green, The ISME journal 2013 - “...et al., 2006). The consecutive genes SPO3366, SPO3365, SPO3364 and SPO3363 are predicted to encode the ABC-class Mn2 transporter SitABCD (Figure 1a); sitA...”
- “...operon, the corresponding gene tags being SPO3366, SPO3365, SPO3364 and SPO3363, respectively. Numbers of base pairs in intergenic spaces are shown, ` 4'...”
RTCIAT899_RS04615 metal ABC transporter permease from Rhizobium tropici CIAT 899
29% identity, 84% coverage
- Dissecting the Acid Stress Response of Rhizobium tropici CIAT 899
Guerrero-Castro, Frontiers in microbiology 2018 - “...predicted functions of the encoded proteins. We identified several genes associated with metal transport (like RTCIAT899_RS04615, RTCIAT899_RS04620, RTCIAT899_RS04610, RTCIAT899_RS17535, RTCIAT899_RS10385, or RTCIAT899_RS14255). It is known that in tropical acid soils high concentrations of metals like Zn 2+ , Co 2+ , Cd 2+ , Ni 2+...”
- “...or repression. Locus tag Location Log2FC COG Function UP-REGULATED GENES pH 4.5 vs. pH 6.8 RTCIAT899_RS04615 Chromosome 5.7363999 P Mn/Zn ABC transporter permease RTCIAT899_RS04620 Chromosome 5.5273566 P Mn/Zn ABC transporter ATP-binding protein RTCIAT899_RS26115 pRtrCIAT899c 5.2777315 P Potassium-transporting ATPase subunit A RTCIAT899_RS27660 pRtrCIAT899c 5.1789806 Q L-lysine 6-monooxygenase...”
B488_10170, B488_RS04935 metal ABC transporter permease from Liberibacter crescens BT-1
28% identity, 88% coverage
plu2675 Chelated iron transport system membrane protein yfeD homolog from Photorhabdus luminescens subsp. laumondii TTO1
26% identity, 86% coverage
HBB05_RS21090 iron/manganese ABC transporter permease subunit SitC from Pantoea agglomerans
26% identity, 90% coverage
PG1946 ABC 3 transporter family protein from Porphyromonas gingivalis W83
27% identity, 90% coverage
APL_0128 putative iron transport system membrane protein from Actinobacillus pleuropneumoniae L20
26% identity, 91% coverage
TC 3.A.1.15.9 / Q92LL3 PUTATIVE IRON TRANSPORT SYSTEM MEMBRANE ABC TRANSPORTER PROTEIN aka SitC, component of Manganese (Mn2+) and Iron (Fe2+) porter, SitABCD from Rhizobium meliloti (Sinorhizobium meliloti) (see paper)
SMc02507 PUTATIVE IRON TRANSPORT SYSTEM MEMBRANE ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
25% identity, 91% coverage
TC 3.A.1.15.7 / Q9XCS0 SitC aka STM2863, component of Manganese (Mn2+) (Km=0.1 μM) and iron (Fe2+) (5 μM) porter (inhibited by Cd2+ > Co2+ > Ni2+, Cu2+) (most similar to YfeABCD of Yersinia pestis (TC #3.A.1.15.4)). Important for virulence in Salmonella from Salmonella typhimurium (see 2 papers)
SEN2705 Iron transport protein, inner membrane component from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
STM2863 Salmonella iron transporter: fur regulated from Salmonella typhimurium LT2
25% identity, 90% coverage
RSP_0906 ABC Mn+2/Fe+2 transporter, inner membrane subunit SitC from Rhodobacter sphaeroides 2.4.1
26% identity, 90% coverage
TC 3.A.1.15.1 / Q55282 MntB aka SLL1600, component of Manganese (Mn2+) porter (see 3 papers)
sll1600 Mn transporter; MntB from Synechocystis sp. PCC 6803
24% identity, 83% coverage
- substrates: Mn2+
- Ethylene causes transcriptomic changes in Synechocystis during phototaxis
Lacey, Plant direct 2018 - “...several are annotated as either transporters ( slr0753 , slr0559 , sll1598 , sll1599 , sll1600 ) or transcriptional regulators ( slr0895 , sll1392 ) with the remainder being annotated for other processes. By contrast, the largest groups of downregulated gene transcripts with annotation are glycosyltransferases...”
- “...ethylene (Slr0146, Slr0949, Slr0467, Slr1881) to transport amino acids, Sll1598 that interacts with Sll11599 and Sll1600 (both also altered by ethylene) in response to manganese starvation, and Slr1452 that interacts with Slr1453 (also altered by ethylene), Slr1454, and Slr1455 to regulate sulfur uptake. Table 1 Synechocystis...”
- Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining
Kreula, PeerJ 2018 - “...al., 1998 ), suggesting the possible involvement of electron-transfer. Interestingly, a manganese transport component (MntB, sll1600) was also part of the script-based cluster which is relevant given that ChlH is Mg 2+ -dependent. In comparison, we also searched for candidate genes to SigE using STRING-db (...”
- Complete Genome Sequence of Cyanobium sp. NIES-981, a Marine Strain Potentially Useful for Ecotoxicological Bioassays
Yamaguchi, Genome announcements 2016 (no snippet) - SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803
Kim, BMC bioinformatics 2008 - “...subunit 4 (Slr0343), respectively. Furthermore, the experimentally-verified nine transmembrane helices of MntB protein encoded by sll1600 [ 29 ] was also confirmed by the Phobius result provided in SynechoNET even though one of the nine transmembrane helices showed a weak signal in the probability profile of...”
- Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns
De, Genome research 2002 - “...groES 0.0400 slr1808 hemA 0.0400 sll1599 mntA 0.0400 sll1600 mntB 0.0400 sll0622 nadA 0.0400 slr2034 ycf 0.0400 slr2073 ycf 0.0400 slr0181 ycf 0.0400 slr1552...”
Atu4468 ABC transporter, membrane spanning protein (iron transport) from Agrobacterium tumefaciens str. C58 (Cereon)
26% identity, 91% coverage
- Discrete Responses to Limitation for Iron and Manganese in Agrobacterium tumefaciens: Influence on Attachment and Biofilm Formation
Heindl, Journal of bacteriology 2015 - “...genes are the sitABCD manganese-specific ABC transporter (Atu4468 to Atu4471) and the manganese transporter mntH (Atu1736). The most highly downregulated...”
- “...uptake systems, the ABC transporter sitABCD (Atu4471 to Atu4468) and the Nramp1 Mn2/H symporter mntH (Atu1736) (19, 20), and both of these were upregulated...”
- Agrobacterium tumefaciens fur has important physiological roles in iron and manganese homeostasis, the oxidative stress response, and full virulence
Kitphati, Applied and environmental microbiology 2007 - “...a putative sitABCD operon (Atu4471, Atu4470, Atu4469, and Atu4468, respectively). To determine the role of FurAt in the regulation of sitABCD expression, RT-PCR...”
PMT9312_RS03095 metal ABC transporter permease from Prochlorococcus marinus str. MIT 9312
27% identity, 84% coverage
CLIBASIA_02130 ABC transporter, membrane spanning protein (iron) from Candidatus Liberibacter asiaticus str. psy62
22% identity, 89% coverage
SYNPCC7002_A1733 ABC 3 transport family protein from Synechococcus sp. PCC 7002
23% identity, 90% coverage
- An organic acid based counter selection system for cyanobacteria
Begemann, PloS one 2013 - “...factor 2.89 2.75E-12 SYNPCC7002_A0782 conserved hypothetical membrane protein 2.89 0 SYNPCC7002_G0109 hypothetical protein 2.79 0 SYNPCC7002_A1733 ABC 3 transport family protein (Mn 2+ ) 2.78 2.44E-15 rubA rubredoxin (photosynthesis lipid) 2.77 0 SYNPCC7002_A2433 galactosyl-1-phosphate transferase 2.68 0.06 SYNPCC7002_A2086 conserved hypothetical protein 2.66 0.02 rpaB two-component response...”
C645_RS02305 metal ABC transporter permease from Haemophilus influenzae 2019
28% identity, 91% coverage
- Hfe Permease and <i>Haemophilus influenzae</i> Manganese Homeostasis
Ganio, ACS infectious diseases 2024 - “...performed using the Hi2019 amino acid sequences of HfeA (C645_RS02315; WP_005656358.1), HfeB (C645_RS02310; WP_005630123.1), HfeC (C645_RS02305; WP_005666620.1), and HfeD (C645_RS02300; WP_005666622.1) as reference sequences to screen the H. influenzae genome database. The HfeA protein was present in 100% of genomes analyzed, with high levels of amino...”
Nmar_0331 ABC-3 protein from Nitrosopumilus maritimus SCM1
27% identity, 65% coverage
NTHI0478 putative ABC-type chelated iron transport system, permease component from Haemophilus influenzae 86-028NP
28% identity, 91% coverage
TC 3.A.1.15.8 / P96118 TroC, component of Manganese (Mn2+), zinc (Zn2+) and possibly iron (Fe2+) uptake porter, TroABCD from Treponema pallidum (see 2 papers)
TP0165 ABC transporter, permease protein (troC) from Treponema pallidum subsp. pallidum str. Nichols
28% identity, 88% coverage
- substrates: Fe2+, Mn2+, Zn2+
tcdb comment: Transcription of the operon is controlled by the Mn2+-activated (not Zn2+- or Fe2+-activated) repressor, TroR (153 aas, acc# F7IW50;) TroR contains a metal-binding domain homologous to the YtgC-R protein (3.A.1.15.12) which has the membrane domain of this ABC transporter (N-terminus) fused to the repressor domain (C-terminus) (Liu et al. 2013). TroA (Tromp1), the periplasmic metal binding protein, was originally reported to be an outer membrane porin (Zhang et al. 1999), but this proved to be incorrect - Whole genome sequence of the Treponema pallidum subsp. endemicum strain Iraq B: A subpopulation of bejel treponemes contains full-length tprF and tprG genes similar to those present in T. p. subsp. pertenue strains
Mikalová, PloS one 2020 - “...1433 R/K 136528 C T 151 E/K 136542 C T 137 R/H 188037 G T TP0165 477 TroC L/L 203271 G A TP0186 368 HemN G/E 230525 C A TP0225 241 hypothetical protein P/T 320541 A G TP0304 1580 hypothetical protein M/T 330101 G A TP0313...”
- Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum
Subramanian, Infection and immunity 2000 - “...-- operon including regulator PhoU -- TP0163, TP0165, TP0166; Tro iron transport operon BB0610; one FKBP-type peptidyl prolyl isomerase (Trigger TP0506,...”
- Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.
Paparoditis, Biochimica et biophysica acta 2014 - “...3.A.1.15.8 P96116 1 cations Mn 2+ , Zn 2+ , Fe 2+ Q7UIM5 1 3.A.1.15.8 P96118 7 cations Mn 2+ , Zn 2+ , Fe 2+ Q7UIM8 9 3.A.1.16.2 Q7BW13 6 anions bispecific cyanate/nitrite Q7UYV0 6 3.A.1.17.6 Q9CLG9 6 nucleobases hydroxymethylpyrimi dine, N-formyl-4- amino-5- (aminomethyl)-2- methylpyrimidine...”
MAP0487c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
30% identity, 76% coverage
MAV_0581 ABC-type Mn2+/Zn2+ transport system, permease component from Mycobacterium avium 104
30% identity, 76% coverage
- Identification of a lineage specific zinc responsive genomic island in Mycobacterium avium ssp. paratuberculosis
Eckelt, BMC genomics 2014 - “...MAV_0582 (55.5) <0.0001 15.26 ATPase component of Mn/Zn ABC-type transporter P - MAP3774c Rv2060 (37.0) MAV_0581 (51.89) <0.0001 17.58 ABC-type Mn2+/Zn2+ transport system, permease component P - MAP3773c Rv2359 (56.8) MAV_2036 (58.06) <0.0001 16.92 Fe2+/Zn2+ uptake regulation protein, Fur family protein P - *MAP3772c - -...”
- “...(99.3) <0.0001 30.0 putative Zinc ABC transporter, ATP-binding protein ZnuC P - MAP0487c Rv2060 (84.2) MAV_0581 (99.7) <0.0001 10.07 putative Zinc ABC transporter, transmembrane protein ZnuB P a Reference Common Name. b q-value of differentially expressed genes MAPwt standard culture vs. MAPwt TPEN culture calculated by...”
RradSPS_2222 metal ABC transporter permease from Rubrobacter radiotolerans
28% identity, 63% coverage
HD1025 iron (chelated) transport system membrane protein from Haemophilus ducreyi 35000HP
25% identity, 91% coverage
LSA0284 Putative zinc/iron ABC transporter, membrane-spanning subunit from Lactobacillus sakei subsp. sakei 23K
28% identity, 80% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...mntH1 Mn(2+)/Fe(2+) transport protein -0.9 -1.3 LSA0283 lsa0283 Putative zinc/iron ABC transporter, ATP-binding subunit -0.5 LSA0284 lsa0284 Putative zinc/iron ABC transporter, membrane-spanning subunit -0.6 LSA0399 lsa0399 Iron(III)-compound ABC transporter, substrate-binding lipoprotein precursor 1.1 0.9 LSA0400 lsa0400 Iron(III)-compound ABC transporter, ATP-binding subunit 0.7 LSA0401 lsa0401 Iron(III)-compound ABC...”
plu2674 Chelated iron transport system membrane protein YfeC from Photorhabdus luminescens subsp. laumondii TTO1
24% identity, 88% coverage
PPYC1_17630 metal ABC transporter permease from Paenibacillus polymyxa
27% identity, 78% coverage
PMI1025 iron ABC transporter, membrane protein from Proteus mirabilis HI4320
24% identity, 80% coverage
HI0360 iron (chelated) ABC transporter, permease protein (yfeC) from Haemophilus influenzae Rd KW20
Hflu203001648 COG1108: ABC-type Mn2+/Zn2+ transport systems, permease components from Haemophilus influenzae R2866
25% identity, 91% coverage
- Comparison of transcription of the Haemophilus influenzae iron/heme modulon genes in vitro and in vivo in the chinchilla middle ear
Whitby, BMC genomics 2013 - “...-7.44 -2.55 -2.11 HI0359 Fe/Mn/Zn ABC transporter, permease protein YfeD -2.92 ns -4.35 -1.31 -1.66 HI0360 Fe/Mn/Zn ABC transporter, permease protein YfeC -3.54 ns -6.90 -1.34 -1.81 HI0361 Fe/Mn/Zn ABC transporter, ATP-binding protein YfeB -7.89 ns -8.91 -1.74 -2.12 HI0362 Fe/Mn/Zn ABC transporter, periplasmic binding protein...”
- An ABC transporter system of Yersinia pestis allows utilization of chelated iron by Escherichia coli SAB11
Bearden, Journal of bacteriology 1998 - “...of similarity (60%) than is indicated for YfeC and HI0360 (83%), YfeC and MntB (72%), or YfeD and HI0359 (80%). Identification of putative yfe-encoded proteins....”
- “...from a putative ABC transporter from H. influenzae (HI0360, HI0361, and HI0362). Amino acids in boldface represent ATP-binding motifs (Walker A and Walker B)....”
- A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae
Atack, Nature communications 2015 - “...pckA 1.69 1.00 723_01614 ORF00565 Iron (III) ABC transporter, permease protein hitB 1.75 4.39 723_01328 Hflu203001648 Iron chelated ABC transporter permease yfeC 1.90 1.69 723_01329 Hflu203001647 Iron chelated ABC transporter permease yfeD 2.08 3.98 723_00591 Hflu203000516 Anaerobic DMSO chain C dmsC 2.09 1.26 723_01434 Hflu103000469 Haem/haemopexin-binding...”
FTN_0181 manganese/zinc/iron chelate uptake transporter (MZT) family protein from Francisella tularensis subsp. novicida U112
27% identity, 90% coverage
SCO0475 ABC transporter protein, integral membrane subunit from Streptomyces coelicolor A3(2)
35% identity, 89% coverage
- Identification and Characterization of Mycobacterium smegmatis and Mycobacterium avium subsp. paratuberculosis Zinc Transporters
Goethe, Journal of bacteriology 2021 (secret) - The frontline antibiotic vancomycin induces a zinc starvation response in bacteria by binding to Zn(II)
Zarkan, Scientific reports 2016 - “...analysis of the transcriptional response to vancomycin of ( a ) the six Zur-regulated genes SCO0475, SCO2505, SCO7676, SCO7677, SCO7681 and SCO7682 in S. coelicolor ( b ) the putative Zur regulated genes SGR5019 (SCO2505 orthologue), SGR0545 (SCO3429 orthologue) and SGR0546 (SCO3428 orthologue) in S. griseus...”
- The zinc-responsive regulator Zur controls expression of the coelibactin gene cluster in Streptomyces coelicolor
Kallifidas, Journal of bacteriology 2010 - “...Indeed, SCO0473 is homologous to ZnuA (42% similarity), SCO0475 is homologous to ZnuB (46% similarity), and SCO0476 is homologous to ZnuC (50% similarity)....”
- The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2)
Shin, Journal of bacteriology 2007 - “...protein L32; a putative zinc transporter gene (SCO0475); a solute-binding lipoprotein gene (SCO6644); and a putative efflux protein gene (SCO6751). The...”
PPYC1_17625 metal ABC transporter permease from Paenibacillus polymyxa
26% identity, 78% coverage
OTBS_1909 Zinc/manganese ABC transporter permease protein from Orientia tsutsugamushi Boryong
24% identity, 100% coverage
SG1518 iron ABC transporter permease component from Sodalis glossinidius str. 'morsitans'
24% identity, 85% coverage
CLIBASIA_02135 ABC transporter, membrane spanning protein (iron transport) from Candidatus Liberibacter asiaticus str. psy62
19% identity, 87% coverage
Q7UIM9 Manganese ABC transporter permease protein from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
30% identity, 52% coverage
YPTB2349 ABC chelated iron transporter, permease subunit yfeC from Yersinia pseudotuberculosis IP 32953
24% identity, 88% coverage
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPTB2348 YPO2440 yfeB ABC chelated iron transporter, ATP-binding subunit YfeB 3.141 (< 0.001) 2.772 (0.001) YPTB2349 YPO2441 yfeC ABC chelated iron transporter, permease subunit YfeC 4.375 (< 0.001) 1.817 (0.017) YPTB2350 YPO2442 yfeD ABC chelated iron transporter, permease subunit YfeD 2.103 (< 0.001) 1.369 (0.195) YPTB2353...”
- “...YPO2439 periplasmic-binding protein 11.88 (< 0.001) YPTB2348 (yfeB) YPO2440 ATP-binding transport protein 3.141 (< 0.001) YPTB2349 (yfeC) YPO2441 chelated iron transport system membrane protein 4.375 (< 0.001) YPTB2350 (yfeD) YPO2442 chelated iron transport system membrane protein 2.104 (< 0.001) YPTB2546 (dps) YPO2509 putative DNA-binding protein 0.566...”
MAB_0575c Putative ABC-transporter transmembrane protein from Mycobacterium abscessus ATCC 19977
29% identity, 85% coverage
- 2-Aminoimidazoles Inhibit Mycobacterium abscessus Biofilms in a Zinc-Dependent Manner
Belardinelli, International journal of molecular sciences 2022 - “...biosynthesis 7.95 10.46 MAB_0336 50S ribosomal protein L31 type B Zn-independent ribosomal protein 8.52 9.38 MAB_0575c Putative ABC-transporter transmembrane protein ZnuABC transporter (Zn import) 2.91 2.39 MAB_0576c Putative ABC-transporter ATP-binding protein 4.05 2.89 MAB_0577c * Putative ABC-transporter solute binding protein 5.54 5.40 MAB_0809c * Conserved hypothetical...”
B9H01_RS10005 metal ABC transporter permease from Streptococcus suis
SSU1866 metal cation ABC transporter membrane protein from Streptococcus suis P1/7
29% identity, 86% coverage
RradSPS_1136 metal ABC transporter permease from Rubrobacter radiotolerans
31% identity, 80% coverage
Q6NK66 ABC-type Mn2+ transporter (subunit 2/3) (EC 7.2.2.5) from Corynebacterium diphtheriae (see paper)
DIP0171 Putative membrane protein from Corynebacterium diphtheriae NCTC 13129
27% identity, 85% coverage
TC 3.A.1.15.4 / Q56954 YfeC aka YPO2441 aka Y1895, component of Iron and manganese porter from Yersinia pestis (see 4 papers)
YPO2441 chelated iron transport system membrane protein from Yersinia pestis CO92
y1895 permease for iron and manganese ABC transporter from Yersinia pestis KIM
23% identity, 88% coverage
- substrates: Fe2+, Mn2+
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPO2440 yfeB ABC chelated iron transporter, ATP-binding subunit YfeB 3.141 (< 0.001) 2.772 (0.001) YPTB2349 YPO2441 yfeC ABC chelated iron transporter, permease subunit YfeC 4.375 (< 0.001) 1.817 (0.017) YPTB2350 YPO2442 yfeD ABC chelated iron transporter, permease subunit YfeD 2.103 (< 0.001) 1.369 (0.195) YPTB2353 YPO2445...”
- “...protein 11.88 (< 0.001) YPTB2348 (yfeB) YPO2440 ATP-binding transport protein 3.141 (< 0.001) YPTB2349 (yfeC) YPO2441 chelated iron transport system membrane protein 4.375 (< 0.001) YPTB2350 (yfeD) YPO2442 chelated iron transport system membrane protein 2.104 (< 0.001) YPTB2546 (dps) YPO2509 putative DNA-binding protein 0.566 (< 0.001)...”
- 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 - “...Y0052 (yopB), y0464 (fadB), y0509, y0655, y0850, y1895 (yfeC), y2316, y3120, and y3553 were determined by quantitative reverse transcription-PCR (qRT-PCR). The...”
- “...y3911 y3912 y0539 y0540 y0541 y0543 y0544 y1891 y1894 y1895 y1896 y1897 y1524 y1525 y1526 y2872 y2873 y2874 y2875 Ferric uptake regulator Ferrous iron transport...”
cg2913 ABC-type Mn2+/Zn2+ transport system, permease component from Corynebacterium glutamicum ATCC 13032
28% identity, 78% coverage
- The Zur regulon of Corynebacterium glutamicum ATCC 13032
Schröder, BMC genomics 2010 - “...potential zinc ABC-type transporters ( cg0041 - cg0042 / cg0043 ; cg2911 - cg2912 - cg2913 ), a putative secreted protein ( cg0040 ), a putative oxidoreductase ( cg0795 ), and a putative P-loop GTPase of the COG0523 protein family ( cg0794 ). Enhanced transcript levels...”
- “...substrate-binding protein TGTTGACATCCTTTTTCAATA 3.52 43.8 cg2912 znuC1 ABC-type Zn/Mn transporter, ATPase subunit - 2.79 75.8 cg2913 znuB1 ABC-type Zn/Mn transporter, permease subunit - 1.29 29.0 1 Genes listed without 21-bp motif (-) belong to predicted operons. 2 The gene expression in C. glutamicum JS2502 was compared...”
- Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway
Mormann, BMC genomics 2006 - “...51C02 2,537,800 cg2661 Putative dithiol-disulfide isomerase involved in polyketide biosynthesis ACTGGACT 53.6 + 51A01 2,772,437 cg2913 ABC-type Mn 2+ /Zn 2+ transport system, permease component TTGCTGAT 57.2 + 97B06 2,913,169 cg3049_3050 upstream acyltransferase ( cg3050 ) CTCGACTG 57.1 + 02A09 2,958,982 cg3100 dnaK Heat shock protein...”
MNTD_BACSU / O34500 Manganese transport system membrane protein MntD from Bacillus subtilis (strain 168) (see paper)
BSU30740 manganese ABC transporter (permease) from Bacillus subtilis subsp. subtilis str. 168
27% identity, 65% coverage
- function: Probably part of the ABC transporter complex MntABCD involved in manganese import. Probably responsible for the translocation of the substrate across the membrane.
subunit: The complex is probably composed of two ATP-binding proteins (MntB), two transmembrane proteins (MntC and MntD) and a solute-binding protein (MntA). - In Silico Safety Assessment of <i>Bacillus</i> Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates
Bin, International journal of molecular sciences 2024 - “...BsaA P52035 mntH Divalent metal cation transporter MntH P96593 mntD Manganese transport system membrane protein O34500 mntC Manganese transport system membrane protein O35024 mntB Manganese transport system ATP-binding protein O34338 mntA Manganese-binding lipoprotein O34385 ahpF NADH dehydrogenase P42974 tpx Thiol peroxidase P80864 trxA Thioredoxin P14949 trxB...”
- Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station
Morrison, NPJ microgravity 2019 - “...4.75 1.36 1.31 Lysine-8-amino-7-oxononanoate aminotransferase BirA BSU30240 bioW 5.63 5.94 2.31 2.41 6-carboxyhexanoateCoA ligase BirA BSU30740 mntD 3.95 4.11 3.13 3.32 Manganese ABC transporter (permease) MntR BSU30750 mntC 3.97 4.12 2.98 3.31 Manganese ABC transporter (membrane protein) MntR BSU30760 mntB 3.83 3.98 2.82 3.15 Manganese ABC...”
LBA1771 ABC transporter permease protein from Lactobacillus acidophilus NCFM
26% identity, 89% coverage
SYNW0969 ABC transporter component, possibly Mn transport from Synechococcus sp. WH 8102
27% identity, 68% coverage
- A single sensor controls large variations in zinc quotas in a marine cyanobacterium
Mikhaylina, Nature chemical biology 2022 - “...two putative ABC (ATP-binding-cassette)-type zinc-uptake transporter systems (ZnuABC), encoded by the genes synw2479 synw2481 and synw0969 synw0971 . A Zur-binding site (Zur box; Fig. 1a,b ) is predicted in the intergenic region between synw0970 ( znuC ) and synw0971 ( znuA ) 26 , but none...”
- “...affinity 20 . In fact, the entire gene cluster synw0968 synw0973 , including znuB ( synw0969 ; encoding the permease component of the ABC transporter) and znuC ( synw0970 ; encoding the ATPase component of the ABC transporter), was upregulated, suggesting that all six of these...”
- Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome
Chen, Nucleic acids research 2004 - “...score (SYNW0211, (SYNW0319, (SYNW0708, (SYNW0840, (SYNW0969, (SYNW1086, (SYNW1111, (SYNW1168, (SYNW1270, (SYNW1283, (SYNW1340, (SYNW1415, (SYNW1797, (SYNW1857,...”
Amuc_0056 ABC-3 protein from Akkermansia muciniphila ATCC BAA-835
28% identity, 74% coverage
- Omics-based analysis of <i>Akkermansia muciniphila</i> cultivation in food-grade media
Geerlings, Microbiome research reports 2024 - “...as peptide, aliphatic sulfonate, nitrate/sulfonate/bicarbonate, cobalt and manganese ABC transporters (Amuc_0672, AMUC_1297, Amuc_0408, Amuc_1198, Amuc_1199, Amuc_0056, Amuc_1380 and Amuc_1186) with an increase > 5-fold. In addition, genes involved in oxygen stress response were found to be higher in soy medium including rubrerythrin (Amuc_2055 and Amuc_2056), peroxidase...”
Q6NK65 ABC-type Mn2+ transporter (subunit 1/3) (EC 7.2.2.5) from Corynebacterium diphtheriae (see paper)
DIP0172 Putative membrane protein from Corynebacterium diphtheriae NCTC 13129
27% identity, 85% coverage
DIP0617 Putative ABC transport system membrane protein from Corynebacterium diphtheriae NCTC 13129
28% identity, 78% coverage
MXAN_2948 cation ABC transporter, permease protein from Myxococcus xanthus DK 1622
29% identity, 83% coverage
Rv2060 Possible conserved integral membrane protein from Mycobacterium tuberculosis H37Rv
36% identity, 46% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...EET03_RS01545 Salvage pathway and transport bacA Cobalamin transporter Rv1819c btuB btuC Iron ABC transporter permease Rv2060 btuD btuF Anaerobic pathway cbiA CbiA domain-containing protein cbiB cbiC Precorrin-8X methylmutase AWC07_17765 cbiD cbiE Precorrin-6Y C(5,15)-methyltransferase MCNS_30630 AWC07_17805 H0P51_RS16435 cbiF Precorrin-4 C(11)-methyltransferase AWC07_17800 cbiG - cbiH ATP-binding protein AWC07_17770...”
- “...bacA Cobalamin transporter Rv1819c 112.5766667 3.598373089 27.63 21.66365312 82.66333333 59.02668455 btuC Iron ABC transporter permease Rv2060 191.76 5.638421765 296.6266667 162.4777085 106.7166667 150.9201573 Anaerobic pathway cbiX Sirohydrochlorin ferrochelatase Rv0259c 12.73 1.498465882 0 0 0 0 Urpoporfirynogen III pathway cysG Multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase Rv2847c 68.92 5.318890862 36.77...”
- Zinc limitation triggers anticipatory adaptations in Mycobacterium tuberculosis
Dow, PLoS pathogens 2021 - “...CP in vitro . As expected, we saw significant upregulation of the Zur regulon (except Rv2060 for which we did not detect gene expression), including the altRP operon (Rv2055c-Rv2058c), which was one of the most highly expressed features in response to CP ( Fig 1A )....”
- Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis
Goethe, mSystems 2020 - “...MSMEG_5616 Rv0911 (61.3) <0.0001 4.0 Glyoxalase/bleomycin resistance protein/dioxygenase MSMEG_5617 <0.0001 4.45 Immunogenic protein MPT63 MSMEG_6045 Rv2060 (43.7) MAP3774c (70.1) <0.0001 21.29 Heavy metal ABC transporter inner membrane protein MSMEG_6046 MAP3775c (61.2) <0.0001 19.04 ABC transporter ATP-binding protein MSMEG_6047 MAP3776c (56.4) <0.0001 43.8 Cation ABC transporter periplasmic...”
- “...zur TPEN Zn b *MSMEG_1123 MAP1730c (43.1) <0.0001 8.64 7.56 7.50 Cobalamin synthesis protein MSMEG_6045 Rv2060 (43.7) MAP3774c (70.1) <0.0001 24.62 21.29 24.42 Heavy metal ABC transporter inner membrane protein MSMEG_6046 MAP3775c (61.2) <0.0001 20.65 19.04 19.90 ABC transporter ATP-binding protein **MSMEG_6047 MAP3776c (56.4) <0.0001 26.24...”
- A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance
Sheen, BMC genomics 2017 - “...M. tuberculosis included Rv2059 and Rv0106 . As metal ion transporters we included the metalloproteins: Rv2060 , Rv0106 , nicT , nurA , furB, SBP , mntH , and the cation transporter ATPase family: CtpI , CtpE , CtpC , CtpG and CtpV . Special attention...”
- Identification of a lineage specific zinc responsive genomic island in Mycobacterium avium ssp. paratuberculosis
Eckelt, BMC genomics 2014 - “...Rv2397c (52.38) MAV_0582 (55.5) <0.0001 15.26 ATPase component of Mn/Zn ABC-type transporter P - MAP3774c Rv2060 (37.0) MAV_0581 (51.89) <0.0001 17.58 ABC-type Mn2+/Zn2+ transport system, permease component P - MAP3773c Rv2359 (56.8) MAV_2036 (58.06) <0.0001 16.92 Fe2+/Zn2+ uptake regulation protein, Fur family protein P - *MAP3772c...”
- “...- MAV_0582 (99.3) <0.0001 30.0 putative Zinc ABC transporter, ATP-binding protein ZnuC P - MAP0487c Rv2060 (84.2) MAV_0581 (99.7) <0.0001 10.07 putative Zinc ABC transporter, transmembrane protein ZnuB P a Reference Common Name. b q-value of differentially expressed genes MAPwt standard culture vs. MAPwt TPEN culture...”
- The ESX-3 secretion system is necessary for iron and zinc homeostasis in Mycobacterium tuberculosis
Serafini, PloS one 2013 - “...) encoding an incomplete putative ABC transporter. Interestingly, the final part of rv2059 totally overlaps rv2060 , even if using a different reading frame due to a deletion leading to the fusion of the terminal part of rv2059 with a sequence internal to rv2060 . This...”
- “...the structure of the ABC transporter system is intact [ 27 ]. Whether Rv2059 and Rv2060 are still functional is unknown, but seems unlikely given the large extent of the lesion. We can hypothesize that while the transport of zinc across the plasma membrane is due...”
- The zinc-responsive regulator Zur controls expression of the coelibactin gene cluster in Streptomyces coelicolor
Kallifidas, Journal of bacteriology 2010 - “...and SCO475 are also related to Rv2059 and Rv2060, respectively, which were shown to be controlled by Zur in Mycobacterium tuberculosis (10). The SCO7676-92...”
- The Metal-Dependent Regulators FurA and FurB from Mycobacterium Tuberculosis
Lucarelli, International journal of molecular sciences 2008 - “...encodes for two components of an ABC-transport system, Rv2059 shows homology with the TroA superfamily, Rv2060 is similar to a membrane protein part of an ABC-type Mn 2+ /Zn 2+ transport system [ 42 , 43 ]. However, since the two reading frames of Rv2059 and...”
- More
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