PaperBLAST
PaperBLAST Hits for TCDB::Q9X0U6 TM1219, component of Probable cellobiose porter. Induced by barley, glucomannan () (315 a.a., MSLLKVQNLT...)
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>TCDB::Q9X0U6 TM1219, component of Probable cellobiose porter. Induced by barley, glucomannan ()
MSLLKVQNLTKEFPLGFFGKERLKAVDDVSFEIERSRIVSLIGESGSGKTTVGKLILKLI
RPSSGQILLNGRDITQIKGRELREYYRKVQGVFQDPFSSFNPIYKIDRVLDMVFEEFFPD
TPASERRTKMEEVIASVGMNPREILGKYPHQLSGGQLQRILIARTLLLNVELLIADEIIS
MLDASTRVDILNLLGDLRERGMSVIFITHDLSLGYYISDETFIMYRGNIVEMGDTEKVFH
NPIHPYTKMLLESVPEIDRKWDLSKRFIPELVSSSNAPCKYYDRCPIRDERCLVQKPAMV
EVEENHKVLCLKAGD
Running BLASTp...
Found 302 similar proteins in the literature:
TC 3.A.1.5.14 / Q9X0U6 TM1219, component of Probable cellobiose porter. Induced by barley, glucomannan (see paper)
TM1219 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
TM_1219 ABC transporter ATP-binding protein from Thermotoga maritima MSB8
100% identity, 100% coverage
- substrates: Cellobiose
- Duplication of genes in an ATP-binding cassette transport system increases dynamic range while maintaining ligand specificity
Ghimire-Rijal, The Journal of biological chemistry 2014 - “...Inner Membrane TM1223 Outer Membrane TM1226 tmMnBP6 TM1221 TM1219 TM1218 ATP TM1222 TM1220 ADP TM1224 PBPs are the specificity-determining unit of ABC transport...”
- “...and TM1222) in addition to two ATP-hydrolyzing subunits (TM1219 and TM1220). Binding of ligand by the PBPs stimulates an interaction with the ABC transporter,...”
- Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases
Frock, Applied and environmental microbiology 2012 - “...endoglucanases (TM1524 and TM1525), a mannobiose transporter (TM1219 to TM1223), a transporter of oligosaccharides derived from xyloglucans (TM0300 to TM0304),...”
- “...extracellular endo1,4--mannanase (TM1227) and a mannobiose transporter (TM1219 to TM1223) (33), which may be sufficient for mannan consumption. Assuming that...”
- In silico method for modelling metabolism and gene product expression at genome scale
Lerman, Nature communications 2012 - “...with cellobiose metabolism were identified. Interestingly, the promoter region of the TU-containing TM1222, TM1221, TM1220, TM1219 and TM1218 did not contain a CelR motif ( Fig. 6c,d ). TM1222, TM1221, TM1220 and TM1219 encode for a cellobiose ABC transporter, while TM1218 is annotated as a LacI...”
- Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales
Noll, BMC evolutionary biology 2008 - “...TM1204 TM1204 TM1204 TM1578 TM1205 TM1217 TM1205 TM0372 X TM1206 TM1218 TM1206 X TM1581 TM1207 TM1219 TM1207 TM0945 TM0009 TM1875 TM1208 TM1220 TM1208 TM1851 TM1581 TM1209 TM1221 TM1209 TM1836 TM1836 TM1203 TM1203 TM1204 TM1839 mal2 TM1829 TM1681 TM1391 TM1830 TM1678 X TM0781 TM1831 2 TM1679 X...”
- Responses of wild-type and resistant strains of the hyperthermophilic bacterium Thermotoga maritima to chloramphenicol challenge
Montero, Applied and environmental microbiology 2007 - “...as was down-regulation of the cellobiose uptake transporter (TM1219 to TM1223); cellobiose was the primary carbon and energy source used here. The purine...”
- Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
Nanavati, Applied and environmental microbiology 2006 - “...acquisition by HGT. These genes and the adjoining ORFs (TM1219 to TM1222) appear to encode a mannoside (man) transporter. These two SBPs have diverged in...”
- “...malE1 Maltose transportc Annotated by TIGR (34) malG1 malF1 malE1 TM1219 TM1220 TM1221 TM1222 TM1223 TM1226 ABP ABP MSP MSP SBP SBP 1 manL manK manG manF manE...”
- An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
Conners, Journal of bacteriology 2005 - “...and the Opp/Dpp family ABC transporter subunits encoded by TM1219 to TM1223 (36) (Fig. 5A). In keeping with the designation of the related P. furiosus...”
- Regulation of endo-acting glycosyl hydrolases in the hyperthermophilic bacterium Thermotoga maritima grown on glucan- and mannan-based polysaccharides
Chhabra, Applied and environmental microbiology 2002 - “...in addition to multiple oligopeptide ABC transporter subunits (TM1219 to TM1223) downstream of the gene, there are also a number of sugar ABC transporter...”
- Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85
Raut, Scientific reports 2019 - “...transporters C9RQJ3 FSU_1687 Oligopeptide/dipeptide ABC transporter 1.32 **** na ABC Cellobiose/cellodextrin import 40.9% to (TM_0027, TM_1219) and cbtF 22 , 23 , 55 C9RLQ8 FSU_3055 ABC transporter 1.21 * na ABC TM_1028 31.8% 56 C9RQJ4 FSU_1688 Oligopeptide/dipeptide ABC transporter 1.15 ** na ABC TM_1220 (36%) and...”
TK1756 ABC-type dipeptide/oligopeptide transport system, ATPase component from Thermococcus kodakaraensis KOD1
57% identity, 96% coverage
PAB0631 OLIGOPEPTIDE TRANSPORT ATP-BINDING PROTEIN APPF from Pyrococcus abyssi GE5
59% identity, 96% coverage
- Cellobiose uptake in the hyperthermophilic archaeon Pyrococcus furiosus is mediated by an inducible, high-affinity ABC transporter
Koning, Journal of bacteriology 2001 - “...P. furiosus. ORFs PAB0627, PAB0628, PAB2363, PAB0630, and PAB0631 of the P. abyssi GE5 chromosome resemble cbtA, cbtB, cbtC, cbtD, and cbtF, respectively. The...”
PF0361 oligopeptide ABC transporter (ATP-binding protein) from Pyrococcus furiosus DSM 3638
58% identity, 96% coverage
PF1213 oligopeptide ABC transporter (ATP-binding protein) from Pyrococcus furiosus DSM 3638
58% identity, 97% coverage
N186_RS00315 ABC transporter ATP-binding protein from Thermofilum adornatum
43% identity, 97% coverage
- Novel Hyperthermophilic Crenarchaeon Thermofilum adornatum sp. nov. Uses GH1, GH3, and Two Novel Glycosidases for Cellulose Hydrolysis
Zayulina, Frontiers in microbiology 2019 - “...( N186_RS00340 , Cel40 ) which gene was clustered with ABC transporters and permease genes N186_RS00315 , N186_RS00320 , N186_RS00325 , and N186_RS00330 . Another GH1 ( N186_RS06555 , putative beta-galactosidase) gene was co-located with the genes, encoding a PTS transporter ( N186_RS06510 ), a sugar-phosphate...”
TC 3.A.1.5.16 / Q9WXN4 TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (see paper)
TM_0027 ABC transporter ATP-binding protein from Thermotoga maritima MSB8
TM0027 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
52% identity, 83% coverage
- substrates: beta-glucosides
- Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85
Raut, Scientific reports 2019 - “...(ABC) transporters C9RQJ3 FSU_1687 Oligopeptide/dipeptide ABC transporter 1.32 **** na ABC Cellobiose/cellodextrin import 40.9% to (TM_0027, TM_1219) and cbtF 22 , 23 , 55 C9RLQ8 FSU_3055 ABC transporter 1.21 * na ABC TM_1028 31.8% 56 C9RQJ4 FSU_1688 Oligopeptide/dipeptide ABC transporter 1.15 ** na ABC TM_1220 (36%)...”
- Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases
Frock, Applied and environmental microbiology 2012 - “...a -glucosidase (TM0025), and a cellobiose/ laminaribiose transporter (TM0027 to TM0031) (33, 38). The XylR regulon is composed of xylan utilization genes and...”
- “...BglR operon TM0023 TM0024 TM0025 TM0026 TM0027 TM0028 TM0029 TM0031 TM0032 Methyl-accepting chemotaxis protein Laminarinase -Glucosidase Hypothetical protein...”
- Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
Nanavati, Applied and environmental microbiology 2006 - “...found to be bound by these SBPs. The ORFs TM0027 to TM0031 appear to encode a -glucoside transporter (bgl, abbreviation of the glucoside substrates and name of...”
- “...February 13, 2017 by University of California, Berkeley TM0027 TM0028 TM0029 TM0030 TM0031 VOL. 72, 2006 T. MARITIMA OLIGOPEPTIDE-BINDING PROTEINS BIND SUGARS...”
- Whole-genome expression profiling of Thermotoga maritima in response to growth on sugars in a chemostat
Nguyen, Journal of bacteriology 2004 - “...(TM0071 to TM0075, TM1194, TM1196 to TM1199, and TM0027 to TM0031) were reported to be most closely related to those encoding archaeal transporters (17)....”
TC 3.A.1.5.13 / Q9WXT0 TM0075, component of Probable xylan oligosaccharide porter (Conners et al., 2005). Induced by xylan and xylose. Regulated by xylose-responsive regulator XylR (see paper)
TM0075 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
46% identity, 95% coverage
- substrates: Xylanoligosaccharides
- Understanding the structural and functional properties of carbohydrate esterases with a special focus on hemicellulose deacetylating acetyl xylan esterases
Sista, Mycology 2018 - “...no predicted signal. The gene organisation analysis has shown that TM0077 gene co-localises with xylanase (TM0075) and -xylosidase encoding genes. The complete structure of TM0077-SeMet (TM0077 seleno-methionine incorporated) and the native apo model of TM0077 consists of native hexamer where calcium ion of each monomer is...”
- Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases
Frock, Applied and environmental microbiology 2012 - “...and TM0070), a xylobiose/xylotriose transporter (TM0071 to TM0075), a transporter of unknown xylan degradation products (TM0056 to TM0060), the xylose/ glucose...”
- “...5.7 5.7 4.7 8.2 2.2 19.4 10.6 13.8 4.8 3.6 5.8 TM0075 TM0076 TM0077 TM0110 TM0111 TM0113 TM0114 TM0115 TM0309 TM0310 TM1667 9.7 6.2 3.5 11.7 5.9 Absent 2.7 2.6...”
- Hyperthermostable acetyl xylan esterase
Drzewiecki, Microbial biotechnology 2010 - “...periplasmic binding protein; TM0072(), ABCtransporter permease protein; TM0073(), ABCtransporter permease protein; TM0074(), ABCtransporter ATPbinding protein; TM0075(), ABCtransporter ATPbinding protein; TM0076(), xylosidase ( bxlA ); TM0077(), acetyl xylan esterase ( axeA ). It is stressed that the proposed intracellular localization of AxeA has not been proven experimentally....”
- Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
Nanavati, Applied and environmental microbiology 2006 - “...encoded enzymes. The transporters encoded by TM0071 to TM0075 (xlo, abbreviation of the xylose oligosaccharide substrate and the adjacent xloA gene) and TM0112,...”
- “...bgtpE ABP ABP MSP MSP SBP TM0071 SBP TM0072 TM0073 TM0074 TM0075 MSP MSP ABP ABP 1 2 TM0112 TM0114 TM0115 MSP SBP ABP 2 xylF xylE xylK Xylose transport...”
- An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
Conners, Journal of bacteriology 2005 - “...and acetyl xylan esterase colocalize with TM0071 to TM0075, and an -glucuronidase colocalizes with TM0056 to TM0060. Although no regulatory proteins are located...”
- “...differs (Fig. 6). We propose to designate TM0071 to TM0075 as XtpABCDF in keeping with the names assigned to orthologous proteins found in an unpublished...”
- Whole-genome expression profiling of Thermotoga maritima in response to growth on sugars in a chemostat
Nguyen, Journal of bacteriology 2004 - “...ORFs in three of these apparent operons (TM0071 to TM0075, TM1194, TM1196 to TM1199, and TM0027 to TM0031) were reported to be most closely related to those...”
Dtur_1719 oligopeptide/dipeptide ABC transporter, ATPase subunit from Dictyoglomus turgidum DSM 6724
48% identity, 91% coverage
Dtur_0158 oligopeptide/dipeptide ABC transporter, ATPase subunit from Dictyoglomus turgidum DSM 6724
44% identity, 95% coverage
PF0194 dipeptide ABC transporter, ATP-binding protein from Pyrococcus furiosus DSM 3638
43% identity, 93% coverage
- Impact of substrate glycoside linkage and elemental sulfur on bioenergetics of and hydrogen production by the hyperthermophilic archaeon Pyrococcus furiosus
Chou, Applied and environmental microbiology 2007 - “...Alanine aminotransferase Oligopeptide ABC transporter PF0191 PF0192 PF0193 PF0194 PF0195 5.4 4.7 4.5 3.6 5.6 11.2 9.6 10.6 8.1 8.6 Acyl-CoA synthetase II PF0233...”
- Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins
Weinberg, Journal of bacteriology 2005 - “...are each upstream of a cluster of four ORFs (PF0191 to PF0194 for CipA and PF1409 to PF1412 for CipB). The two nearest ORFs in each cluster are annotated as...”
- “...do CipA and CipB to OppA. For example, for PF0191 to PF0194, the sequence similarities range from 33 to 59% (19 to 44% identity). In addition, not only is OppA...”
- Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides
Schut, Journal of bacteriology 2003 - “...peptide transporters of one type or another (PF0191 to PF0194, PF0357 to PF0361, PF0999 to PF1001, and PF1408 to PF1412). However, none of them are up-regulated...”
TON_1768 ABC-type dipeptide/oligopeptide transport system, ATPase component from Thermococcus onnurineus NA1
42% identity, 93% coverage
YP_184213 ABC-type dipeptide/oligopeptide transport system, ATPase component from Thermococcus kodakaraensis KOD1
44% identity, 93% coverage
Q73NS6 ABC-type dipeptide transporter (EC 7.4.2.9) from Treponema denticola (see paper)
TDE_1076 ABC transporter ATP-binding protein from Treponema denticola ATCC 35405
43% identity, 85% coverage
- Characterization of a Treponema denticola ATCC 35405 mutant strain with mutation accumulation, including a lack of phage-derived genes
Yokogawa, PloS one 2022 - “...investigate the function of the TDE_1072 protein in nutrient uptake. Moreover, the genes TDE_1073 to TDE_1076, also annotated with a transporter, were also upregulated in the transcription, suggesting that these genes (TDE_1072 to TDE_1076) form an operon, and proteins encoded by these genes might function cooperatively...”
- Characterization of a novel potential peptide import system in Treponema denticola
Asai, Microbial pathogenesis 2018 (PubMed)- “...encoded by TDE_1072, TDE_1073, TDE_1074, TDE_1075, and TDE_1076 shared respective similarities to the substrate-binding domain (DppA) of an ABC-type...”
DV713_01770 dipeptide ABC transporter ATP-binding protein from Parageobacillus thermoglucosidasius
40% identity, 45% coverage
TC 3.A.1.5.15 / Q9X272 TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (see paper)
TM1750 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
42% identity, 94% coverage
- substrates: Mannose, Mannosides
- Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases
Frock, Applied and environmental microbiology 2012 - “...into the cell by the products of TM1746 to TM1750, before being further hydrolyzed by two intracellular glucomannanases (TM1751 and TM1752) (8), which are only...”
- “...Mannan utilization TM1746 TM1747 TM1748 TM1749 TM1750 TM1751 Mannan ABC transporter, periplasmic oligopeptide-binding protein Mannan ABC transporter, permease...”
- Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
Nanavati, Applied and environmental microbiology 2006 - “...et al., the ABC transporter encoded by TM1746 to TM1750 was proposed to transport galactomannans (9, 12). That transporter was originally assigned a role as a...”
- An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
Conners, Journal of bacteriology 2005 - “...xylose, other components of the transporter (TM1747 to TM1750), two endoglucanases (Cel5A TM1751 and Cel5B TM1752), and a -mannosidase (TM1624) are highest...”
- “...propose to designate the transporter components TM1746 to TM1750 as MtpABCDF (Table 2). The third substrate-binding protein of group 1 (TM0031) is located...”
- Substrate specificities and expression patterns reflect the evolutionary divergence of maltose ABC transporters in Thermotoga maritima
Nanavati, Journal of bacteriology 2005 - “...that the ABC transporter encoded by TM1746 to TM1750 transports galactomannans (3). Those microarrays did not include malE1 and malE2, so the patterns we...”
- “...found. The transporter encoded by TM1746 to TM1750 may transport mannobiose and mannotriose. The archaeal hyperthermophile Thermococcus litoralis has a...”
- Regulation of endo-acting glycosyl hydrolases in the hyperthermophilic bacterium Thermotoga maritima grown on glucan- and mannan-based polysaccharides
Chhabra, Applied and environmental microbiology 2002 - “...indicates that multiple oligopeptide ABC transporters (TM1746 to TM1750 and TM0300 to TM0304) are present (39). In the case of man5 (TM1227), in addition...”
Dtur_0668 oligopeptide/dipeptide ABC transporter, ATPase subunit from Dictyoglomus turgidum DSM 6724
42% identity, 98% coverage
TM1196 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
45% identity, 94% coverage
- Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales
Noll, BMC evolutionary biology 2008 - “...lettingae Ts. melanesiensis F. nodosum mal1 TM1192 TM0972 TM1193 TM1044 2 TM1194 TM1190 TM1195 TM1191 TM1196 TM1192 TM1197 TM1193 TM1198 TM1194 TM0431 TM1199 TM1195 TM0810 TM1193 TM1200 TM1200 TM1200 TM1200 TM1201 TM1201 TM1201 TM1201 TM1202 TM1202 TM1202 TM1202 TM1203 TM1203 TM1203 TM1203 TM1204 TM1204 TM1204 TM1204...”
- Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species
Mongodin, Journal of bacteriology 2005 - “...endoglucanase (TM1201), oligopeptide ABC transporter (TM1194 and TM1196 to TM1199), a maltose transporter (TM1202 to TM1204), and 6 putative NADH dehydrogenases...”
- Whole-genome expression profiling of Thermotoga maritima in response to growth on sugars in a chemostat
Nguyen, Journal of bacteriology 2004 - “...of an oligopeptide ABC transporter (TM1199, TM1197, and TM1196) (Table 1). Except for the transcript of galK (TM1190), which showed very weak signal...”
- “...TM0381, TM1190, TM1191, TM1192, TM1193, TM1194 TM1195, TM1196 TM1197 TM1198 TM1199 TM1200 TM1201 TM1202, TM1203, TM1204, TM1216 TM1837, TM1839, TM1840, Maltose...”
PF1412 dipeptide transport ATP-binding protein from Pyrococcus furiosus DSM 3638
42% identity, 94% coverage
BH3645 oligopeptide ABC transporter (ATP-binding protein) from Bacillus halodurans C-125
40% identity, 96% coverage
- Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis
Takami, Nucleic acids research 2000 - “...BH570, BH571, BH1799, BH1800, BH2077, BH2078, BH3639, BH3640, BH3645, BH3646, AppD and AppF) are distributed throughout the C-125 genome. We speculate that...”
TM0304 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
45% identity, 90% coverage
TC 3.A.1.5.20 / P42065 AppF, component of 5-6 amino acyl oligopeptide transporter AppA-F from Bacillus subtilis (see 3 papers)
40% identity, 94% coverage
- substrates: Oligopeptides
NWMN_0863 oligopeptide ABC transporter, ATP-binding protein from Staphylococcus aureus subsp. aureus str. Newman
39% identity, 96% coverage
- Inactivation of the Ecs ABC transporter of Staphylococcus aureus attenuates virulence by altering composition and function of bacterial wall
Jonsson, PloS one 2010 - “...permease protein 1.9 NWMN_0696 di-/tripeptide ABC transporter 1.9 NWMN_0861 oligopeptide ABC transporter substrate-binding protein 0.4 NWMN_0863 oligopeptide ABC transporter ATP-binding protein 0.2 NWMN_0903 ABC transporter ATP-binding protein 2.3 0.1 NWMN_0943 cobalt transport 2.2 NWMN_0968 spermidine/putrescine ABC transporter binding protein 1.8 NWMN_1231 ABC transporter ATP-binding protein 0.4...”
- “...transferase group 1 0.2 NWMN_0353 ParB family chromosome partioning protein 4.1 NWMN_0542 VraX (SAS016) 0.2 NWMN_0863 oligopeptide ABC transporter ATP-binding protein 0.2 NWMN_0903 ABC transporter ATP-binding protein 2.3 0.1 NWMN_0995 bacteriophage L54a antirepressor 0.2 NWMN_1223 hypothetical protein 0.1 NWMN_1252 hypothetical protein 0.2 NWMN_1445 hypothetical protein 0.2...”
Dtur_1061 oligopeptide/dipeptide ABC transporter, ATPase subunit from Dictyoglomus turgidum DSM 6724
42% identity, 94% coverage
APL_0068 dipeptide transport ATP-binding protein DppF from Actinobacillus pleuropneumoniae L20
39% identity, 94% coverage
- Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
Labrie, Veterinary research 2010 - “...transport protein 3.168 APL_0869 abgB Aminobenzoyl-glutamate utilization-like protein 3.004 APL_1857 merP Copper chaperone MerP 2.911 APL_0068 dppF Dipeptide transport ATP-binding protein DppF 2.860 APL_1665 gntP_1 Gluconate permease 2.723 APL_0066 dppC Dipeptide transport system permease protein DppC 2.640 APL_1440 znuA High-affinity zinc uptake system protein ZnuA precursor...”
TC 3.A.1.5.37 / B1W1L8 Putative peptide ABC transporter ATP-binding protein, component of The ABC BldKA-E (SGR_2418-2414) oligopeptide transport system. It controls aerial mycelium formation on glucose media. Probably involved in extracellular peptide signalling (Akanuma et al. 2011). Probably orthologous to 3.A.1.5.35 from Streptomyces griseus subsp. griseus (strain JCM 4626 / NBRC 13350)
39% identity, 80% coverage
- substrates: Oligopeptides
CA_C3641, CEA_G3648 ABC transporter ATP-binding protein from Clostridium acetobutylicum EA 2018
40% identity, 94% coverage
- Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018
Hu, BMC genomics 2011 - “...transporter periplasmic-binding protein CEA_G3629 CA_C3622 3.744723 1.616914 -1.60643 -2.30924 -3.70552 -4.20925 benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase CEA_G3648 CA_C3641 3.877563 5.273677 6.532841 7.05381 6.150331 2.645978 oligopeptide ABC transporter, ATPase component CEA_G3649 CA_C3642 3.862767 5.064748 6.213521 7.100308 6.123778 2.328286 oligopeptide ABC transporter, ATPase component CEA_G3651 CA_C3644 3.540737 4.731217 4.796332 6.751584...”
- “...ABC transporter periplasmic-binding protein CEA_G3629 CA_C3622 3.744723 1.616914 -1.60643 -2.30924 -3.70552 -4.20925 benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase CEA_G3648 CA_C3641 3.877563 5.273677 6.532841 7.05381 6.150331 2.645978 oligopeptide ABC transporter, ATPase component CEA_G3649 CA_C3642 3.862767 5.064748 6.213521 7.100308 6.123778 2.328286 oligopeptide ABC transporter, ATPase component CEA_G3651 CA_C3644 3.540737 4.731217 4.796332...”
VC0616 peptide ABC transporter, ATP-binding protein from Vibrio cholerae O1 biovar eltor str. N16961
38% identity, 93% coverage
- TsrA Regulates Virulence and Intestinal Colonization in Vibrio cholerae
DuPai, mSphere 2020 - “...VC0800 1.43 2.00E42 2.74 5.90E147 1.13 VC0801 citG 1.57 9.80E42 2.80 1.20E127 1.09 Chitin utilization VC0616 1.64 3.20E29 0.50 1.10E03 1.03 VC0617 2.10 3.40E55 1.04 3.30E14 1.02 VC0618 2.92 3.80E62 1.74 1.40E22 1.08 VC0619 1.86 1.20E24 0.88 2.40E06 1.01 a The indicated genes showed significant differences...”
- Species-Specific Quorum Sensing Represses the Chitobiose Utilization Locus in Vibrio cholerae
Klancher, Applied and environmental microbiology 2020 (secret) - Quorum sensing-regulated chitin metabolism provides grazing resistance to Vibrio cholerae biofilms
Sun, The ISME journal 2015 - “...et al. , 2008 ). Indeed, it has been reported that six genes (VC0613, VC0614, VC0616, VC0619, VC1284 and VC2424) involved in chitin utilisation are also induced during colonisation of the infant mice small intestine ( Mandlik et al. , 2011 ). Therefore, the QS-regulated chitin...”
- “...Cellobiose/cellodextrin-phosphorylase 1.92 VC0613 Beta- N -acetylhexosaminidase 1.54 VC0614 Hypothetical protein 1.55 VC0615 Endoglucanase-like protein 1.01 VC0616 Peptide ABC transporter ATP-binding protein 1.63 VC0617 Peptide ABC transporter ATP-binding protein 1.78 VC0618 Peptide ABC transporter permease 1.42 VC0619 Peptide ABC transporter permease 1.96 VC0620 Peptide ABC transporter substrate-binding...”
- An in vivo expression technology screen for Vibrio cholerae genes expressed in human volunteers
Lombardo, Proceedings of the National Academy of Sciences of the United States of America 2007 - “...caused attenuation in vivo. Deletion of VC0616 -VC0617 (chitobiose transport), VC1275 (hypothetical), VCA0629 (conserved hypothetical), or VC1687 (inorganic...”
- “...3 4 2 3 VC0300 VC0488 VC0613 VC0614 VC0616 VC1034 VC1072 VC1173 VC1275 VC1658 VC1687 VC2363 VC2373 VC2411 VC2419 VC2539 VC0291-301 1 VC0611-620 VC0611-620...”
- The chitinolytic cascade in Vibrios is regulated by chitin oligosaccharides and a two-component chitin catabolic sensor/kinase
Li, Proceedings of the National Academy of Sciences of the United States of America 2004 - “...is encoded by the first, VC0620, whereas VC0619 -VC0616 encode a (GlcNAc)2 ABC-type permease. Regulation of chiS requires expression of CBP but not (GlcNAc)2...”
- “...cbp as the recipient. (iii) CBP-positive, permease deletion strain (VC0616- VC0619): The mutant contains 311 bp of the N terminus of VC0619, a BglII site,...”
TC 3.A.1.5.29 / Q9WXR3 Oligopeptide ABC transporter, ATP-binding protein, component of Probable xylan oligosaccharide porter (Conners et al. 2005). Induced by cylan and xylose. Regulated by xylose-responsive regulator XylR from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
TM0057 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
42% identity, 92% coverage
WU75_11610 ABC transporter ATP-binding protein from Vibrio parahaemolyticus
VP2483 peptide ABC transporter, ATP-binding protein from Vibrio parahaemolyticus RIMD 2210633
38% identity, 93% coverage
N646_1580 ABC transporter ATP-binding protein from Vibrio alginolyticus NBRC 15630 = ATCC 17749
38% identity, 93% coverage
BC0245 Oligopeptide transport ATP-binding protein oppF from Bacillus cereus ATCC 14579
41% identity, 96% coverage
- Effects of Insect-Resistant Maize 2A-7 Expressing mCry1Ab and mCry2Ab on the Soil Ecosystem
Yang, Plants (Basel, Switzerland) 2022 - “...China). The soil sucrase activities (S-SC) were determined with soil sucrase (S-SC) activity detection kits (BC0245, Solerbio, Beijing, China). The soil alkaline phosphatase activities (S-AKP/ALP) were determined with soil alkaline phosphatase (S-AKP/ALP) activity detection kits (BC0285, Solerbio, Beijing, China). The soil acid phosphate activities (S-ACP) were...”
- PlcRa, a new quorum-sensing regulator from Bacillus cereus, plays a role in oxidative stress responses and cysteine metabolism in stationary phase
Huillet, PloS one 2012 - “...system permease protein oppC-like 1 4 BC0244 Oligopeptide transport ATP-binding protein oppD-like 1 5 3 BC0245 Oligopeptide transport ATP-binding protein oppF-like 1 3 Iron transport/metabolism BC5380 Ferrichrome-binding protein 3 1 BC5381 Ferrichrome transport ATP-binding protein fhuC 2 1 BC5382 Ferrichrome transport system permease protein fhuG 3...”
BA4734 oligopeptide ABC transporter, ATP-binding protein from Bacillus anthracis str. Ames
38% identity, 94% coverage
BAS4394 oligopeptide ABC transporter, ATP-binding protein from Bacillus anthracis str. Sterne
38% identity, 71% coverage
VDA_001636 murein tripeptide/oligopeptide ABC transporter ATP binding protein OppF from Photobacterium damselae subsp. damselae CIP 102761
39% identity, 88% coverage
CPR_2254 oligopeptide ABC transporter, ATPase component from Clostridium perfringens SM101
40% identity, 96% coverage
MA4253 oligopeptide ABC transporter, ATP-binding protein from Methanosarcina acetivorans C2A
39% identity, 98% coverage
SCO5480 oligopeptide ABC transporter ATP-binding protein from Streptomyces coelicolor A3(2)
36% identity, 62% coverage
CV1101 dipeptide transport system ATP-binding protein from Chromobacterium violaceum ATCC 12472
38% identity, 96% coverage
Q5V9R8 ABC-type oligopeptide transporter (EC 7.4.2.6) from Vibrio fluvialis (see paper)
TC 3.A.1.5.22 / Q5V9R8 OppF, component of The peptide transporter OppA,B,C,D,F (influences biofilm formation; Lee et al., 2004). Similar to 3.A.1.5.1, OppA is similar to the Vibrio furnissii OppA that provides several functions: hemolysis, antibiotic resistance, and virulence from Vibrio fluvialis (see paper)
36% identity, 94% coverage
BAU10_09575 murein tripeptide/oligopeptide ABC transporter ATP binding protein OppF from Vibrio alginolyticus
38% identity, 86% coverage
RPA0758 putative oligopeptide ABC transporter, ATP-binding component from Rhodopseudomonas palustris CGA009
37% identity, 88% coverage
AHA_2609 oligopeptide ABC transporter, ATP-binding protein OppF from Aeromonas hydrophila subsp. hydrophila ATCC 7966
A0KLG7 Oligopeptide ABC transporter, ATP-binding protein OppF from Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049)
38% identity, 88% coverage
- Quantitative Proteomics Analysis Reveals the Effect of a MarR Family Transcriptional Regulator AHA_2124 on Aeromonas hydrophila
Li, Biology 2023 - “...1 ( Figure 6 A). A total of seven peptide transport proteins ( AHA_2001 , AHA_2609 , AHA_2611 , AHA_3324 , AHA_3325 , AHA_3428 , and AHA_3431 ) were significantly enriched and most of them showed decreased abundances in MCODE 2, except for A0KJT1 ( AHA_2001...”
- The LysR-Type Transcriptional Regulator YeeY Plays Important Roles in the Regulatory of Furazolidone Resistance in Aeromonas hydrophila
Fu, Frontiers in microbiology 2020 - “...Transcriptional regulator 10 0.036697 1.818 A0KLG5 bsr Broad specificity amino-acid racemase 18 4.43E-06 2.302 A0KLG7 AHA_2609 Oligopeptide ABC transporter, ATP-binding protein OppF 19 1.4E-05 1.330 A0KLG8 AHA_2610 Oligopeptide ABC transporter, ATP-binding protein OppD 14 0.000151 1.074 A0KLT0 carB Carbamoyl-phosphate synthase large chain 52 9.59E-06 1.054 A0KLY2...”
- The LysR-Type Transcriptional Regulator YeeY Plays Important Roles in the Regulatory of Furazolidone Resistance in Aeromonas hydrophila
Fu, Frontiers in microbiology 2020 - “...AHA_2561 Transcriptional regulator 10 0.036697 1.818 A0KLG5 bsr Broad specificity amino-acid racemase 18 4.43E-06 2.302 A0KLG7 AHA_2609 Oligopeptide ABC transporter, ATP-binding protein OppF 19 1.4E-05 1.330 A0KLG8 AHA_2610 Oligopeptide ABC transporter, ATP-binding protein OppD 14 0.000151 1.074 A0KLT0 carB Carbamoyl-phosphate synthase large chain 52 9.59E-06 1.054...”
WU75_12785 murein tripeptide/oligopeptide ABC transporter ATP binding protein OppF from Vibrio parahaemolyticus
38% identity, 88% coverage
- Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn
Tang, Foods (Basel, Switzerland) 2023 - “...0.138-fold). The DEGs ( oppABCDF , WU75_12765 , WU75_12770 , WU75_12775 , WU75_12780 , and WU75_12785 ) encoding a peptide ABC transporter substrate-binding protein, an oligopeptide transporter permease, a peptide ABC transporter permease, an oligopeptide transporter ATP-binding component, and a peptide ABC transporter ATP-binding protein, respectively,...”
- “...Hypothetical protein WU75_07215 yejE 0.221 Peptide ABC transporter permease WU75_09670 aotP 0.228 Amino acid transporter WU75_12785 oppF 0.228 Peptide ABC transporter ATP-binding protein WU75_04720 oppA 0.341 Peptide ABC transporter substrate-binding protein WU75_16165 proV 0.343 Glycine/betaine ABC transporter ATP-binding protein WU75_14765 aapQ 0.377 Amino acid ABC transporter...”
SPO0664 ABC transporter ATP-binding protein from Ruegeria pomeroyi DSS-3
SPO0664, YP_165919 peptide ABC transporter, ATP-binding protein from Silicibacter pomeroyi DSS-3
39% identity, 94% coverage
- Diel investments in metabolite production and consumption in a model microbial system
Uchimiya, The ISME journal 2022 - “...transporter, permease 32.3 SPO0662 naaB' ABC transporter, permease 42.7 SPO0663 naaC ABC transporter, ATP-binding 58.2 SPO0664 naaC' ABC transporter, ATP-binding 28.2 Sulfur compound Taurine SPO0674 tauA ABC transporter, periplasmic substrate-binding 1.8 (n.s.) [ 41 ] SPO0675 tauB ABC transporter, ATP-binding 3.7 SPO0676 tauC ABC transporter, permease...”
- Sulfur metabolites that facilitate oceanic phytoplankton-bacteria carbon flux
Landa, The ISME journal 2019 - “...SPO0674 naaT SPO0657 SPO0658 naaC naaC' SPO0663 SPO0664 SPO0676 Taurine transport N-acetyltaurine metabolism naaB naaB' SPO0661 SPO0662 SPO0660 naaR naaA...”
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...transporter, permease protein naaB' Function YP_165918 SPO0663 N-acetyltaurine ABC transporter, ATP-binding protein naaC Function YP_165919 SPO0664 N-acetyltaurine ABC transporter, ATP-binding protein naaC' Function YP_165928 SPO0673 Taurine-pyruvate aminotransferase tpa Function YP_165929 SPO0674 Taurine ABC transporter, periplasmic taurine-binding protein tauA Function YP_165930 SPO0675 Taurine ABC transporter, ATP-binding protein...”
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...ABC transporter, permease protein naaB' Function YP_165918 SPO0663 N-acetyltaurine ABC transporter, ATP-binding protein naaC Function YP_165919 SPO0664 N-acetyltaurine ABC transporter, ATP-binding protein naaC' Function YP_165928 SPO0673 Taurine-pyruvate aminotransferase tpa Function YP_165929 SPO0674 Taurine ABC transporter, periplasmic taurine-binding protein tauA Function YP_165930 SPO0675 Taurine ABC transporter, ATP-binding...”
AHA_3428 oligopeptide transport ATP-binding protein AppF from Aeromonas hydrophila subsp. hydrophila ATCC 7966
37% identity, 93% coverage
HI1120 oligopeptide ABC transporter, ATP-binding protein (oppF) from Haemophilus influenzae Rd KW20
P45051 Oligopeptide transport ATP-binding protein OppF from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
37% identity, 93% coverage
- Identification of new genetic regions more prevalent in nontypeable Haemophilus influenzae otitis media strains than in throat strains
Xie, Journal of clinical microbiology 2006 - “...NT H. influenzae gene not found in strain Rd) HI0631 Unknown HI1120, HI1121 sJPX163 sJPX161 sJPX176 46 (100) 46 (100) 46 (100) 16 (70) 19 (83) 19 (83) 1.44 1.21...”
- Old and new strategies in therapy and diagnosis against fungal infections.
Vanzolini, Applied microbiology and biotechnology 2024 - “...al. 2020 ), and VT-1129 and VT-1161 are potent selective inhibitors of the fungal cytochrome P45051 (CYP51). In addition, several antibacterial drugs have demonstrated antifungal properties. Most of them inhibit protein synthesis by binding the ribosome subunits but it seems that the inhibition of particular mitochondrial...”
- “...electron transport chain Fluconazole Histatin 5 Natural ATP synthesis machinery Amphotericin B VT-1129 Synthetic Cytochrome P45051 (CYP51) VT-1161 Synthetic Cytochrome P45051 (CYP51) Protein synthesis Linezolid Synthetic Inhibition of protein synthesis Fluconazole, itraconezole, voriconazole, amphotericin B Azithromycin Synthetic Inhibition of protein synthesis Terbinafine, amphotericin B, itraconazole, voriconazole,...”
- The adherence-associated lipoprotein P100, encoded by an opp operon structure, functions as the oligopeptide-binding domain OppA of a putative oligopeptide transport system in Mycoplasma hominis
Henrich, Journal of bacteriology 1999 - “...Haemophilus influenzae, P44572, P45054, P45053, P45052, and P45051. Fluorescence spectroscopy. The P100 protein was solubilized from the membrane with 0.5%...”
Cthe_2962 oligopeptide/dipeptide ABC transporter, ATPase subunit from Clostridium thermocellum ATCC 27405
37% identity, 91% coverage
MSMEG_0639 oligopeptide transport ATP-binding protein AppF from Mycobacterium smegmatis str. MC2 155
38% identity, 92% coverage
- Differentiating the roles of Mycobacterium tuberculosis substrate binding proteins, FecB and FecB2, in iron uptake
de, PLoS pathogens 2023 - “...MSMEG_0438 Rv0265c 95% 590 FecB MSMEG_1039/2319 Rv3044 54.9% 68 OppA MSMEG_0643 Rv1280c 12.6% 10 OppD-2 MSMEG_0639 Rv1281c - 2 nd half 17.3% 6 OppD-1 MSMEG_0640 Rv1281c 1 st half 6.7% 2 To corroborate our co-IP results for FecB, we performed reverse co-IPs with the small periplasmic...”
- Aggregation of Nontuberculous Mycobacteria Is Regulated by Carbon-Nitrogen Balance
DePas, mBio 2019 - “...Missense Ser21Pro MSMEG_6430 Hypothetical protein Missense Thr371Lys MSMEG_6821 NLP/P60 family protein Missense Gln2017Arg Passage 60 MSMEG_0639 Oligopeptide transport ATP-binding protein OppF Frameshift Lys12fs b MSMEG_0640 Oligopeptide transport ATP-binding protein OppD Missense Phe96Leu MSMEG_2148 HNH endonuclease domain-containing protein Missense Pro380Arg MSMEG_2148 HNH endonuclease domain-containing protein Frameshift Ser534fs...”
- “...Ser534 frameshift hypothetically replaces the 8 C-terminal amino acids with a different 23-amino-acid sequence. b MSMEG_0639 is 336 amino acids. Lys12 frameshift hypothetically replaces the 325 C-terminal amino acids with a different 24-amino-acid sequence. c MSMEG_5061 is 465 amino acids. Glu225 frameshift hypothetically replaces the 241...”
- Protein Composition of Mycobacterium smegmatis Differs Significantly Between Active Cells and Dormant Cells With Ovoid Morphology
Trutneva, Frontiers in microbiology 2018 - “...were more abundant than in the active cell proteome [extracellular solute-binding protein (MSMEG_0643), oligopeptide transport (MSMEG_0639), ABC transporter (MSMEG_1954), unique and porin (MSMEG_5483)]. Discussion Comparison of protein profiles of active and dormant Msm cells revealed significant differences in protein abundance. Thus, 180 proteins (51%) were found...”
- Characterization of Conserved and Novel Septal Factors in Mycobacterium smegmatis
Wu, Journal of bacteriology 2018 - “...MSMEG_4484 MSMEG_1285 MSMEG_5798 oxaA pknA MSMEG_2974 MSMEG_0035 MSMEG_0639 MSMEG_4692 MSMEG_5086 MSMEG_1945 MSMEG_4504 ppiB rhlE ppk deaD purM fadD6 dnaJ...”
Dtur_1704 oligopeptide/dipeptide ABC transporter, ATPase subunit from Dictyoglomus turgidum DSM 6724
40% identity, 92% coverage
OPPF_SALTY / P08007 Oligopeptide transport ATP-binding protein OppF; EC 7.4.2.6 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 3 papers)
TC 3.A.1.5.1 / P08007 OppF aka STM1742, component of Oligopeptide porter (also takes up amino glycoside antibiotics such as kanamycin, streptomycin and neomycin as well as cell wall-derived peptides such as murein tripeptide). It transports substrate peptides of 2-5 amino acids with highest affinity for tripeptides. Also transports δ-aminolevulinic acid (ALA). [May be regulated by PTS Enzyme INtr-aspartokinase.] ATP-binding to OppDF may result in donation of peptide to OppBC and simultaneous release of OppA from Salmonella typhimurium (see 2 papers)
STM1742 ABC superfamily (atp-binding), oligopeptide transport protein from Salmonella typhimurium LT2
STM14_2106 murein tripeptide/oligopeptide ABC transporter ATP-binding protein OppF from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
38% identity, 93% coverage
- function: Part of the ABC transporter complex OppABCDF involved in the uptake of oligopeptides, including the cell wall murein tripeptide L- alanyl-gamma-D-glutamyl-meso-diaminopimelate (PubMed:2821267, PubMed:3301822). Probably responsible for energy coupling to the transport system (PubMed:2651120). Plays an important nutritional role and is involved in the recycling of cell wall peptides (PubMed:2821267, PubMed:3301822).
catalytic activity: a [peptide](out) + ATP + H2O = a [peptide](in) + ADP + phosphate + H(+) (RHEA:78459)
catalytic activity: L-alanyl-gamma-D-glutamyl-meso-diaminoheptanedioate(out) + ATP + H2O = L-alanyl-gamma-D-glutamyl-meso-diaminoheptanedioate(in) + ADP + phosphate + H(+) (RHEA:29763)
subunit: The complex is composed of two ATP-binding proteins (OppD and OppF), two transmembrane proteins (OppB and OppC) and a solute-binding protein (OppA). - substrates: Oligopeptides
- The adherence-associated lipoprotein P100, encoded by an opp operon structure, functions as the oligopeptide-binding domain OppA of a putative oligopeptide transport system in Mycoplasma hominis
Henrich, Journal of bacteriology 1999 - “...S. typhimurium, P06202, P08006, P08066, P04285, and P08007; and Haemophilus influenzae, P44572, P45054, P45053, P45052, and P45051. Fluorescence spectroscopy....”
- Repression of Salmonella enterica phoP expression by small molecules from physiological bile
Antunes, Journal of bacteriology 2012 - “...STM0738 STM1744 PSLT046 STM2190 STM2799 STM1292 STM0730 STM3321 STM1742 STM3033 STM4274 STM4126 ORF04918 Fold regulation cyoC cyoE dppA phoH fimI lpdA acnB...”
- Utilizing nutrient type compounds as anti-bacterial compounds: arginine and cysteine inhibit Salmonella survival in egg white
Ben-Porat, Frontiers in bioengineering and biotechnology 2024 - “...involved in the purine transport process - Purine metabolism 7.94 0.00094 0.01627 7.70 0.00077 0.01780 STM14_2106 oppF oligopeptide transport protein 6.64 0.00305 0.03249 6.19 0.00369 0.03830 STM14_1100 focA formate transporter 7.89 0.00064 0.01585 7.67 0.00051 0.01780 STM14_1781 ydgI putative arginine:ornithine antiporter 8.88 0.00113 0.01666 6.34 0.00374...”
BMEII0223 OLIGOPEPTIDE TRANSPORT ATP-BINDING PROTEIN OPPF from Brucella melitensis 16M
38% identity, 77% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BCAN_B1103 OPN Dipeptide/ Oligopeptide import ABC BMEII0222 BruAb21018 BRA1079 BCAN_B1102 OPN Dipeptide/ Oligopeptide import ABC BMEII0223 BruAb21019 BRA1078 BCAN_B1101 69 OPN Dipeptide import BP BMEII0284 BruAb20952 BRA1012 BOV_A0504 BCAN_B1032 OPN Dipeptide import IM BMEII0285 BruAb20950 BRA1009 BOV_A0501 BCAN_B1031 OPN Dipeptide import IM BMEII0286 BruAb20951 BRA1008 BOV_A0502...”
SPO2551 ABC transporter ATP-binding protein from Ruegeria pomeroyi DSS-3
38% identity, 97% coverage
- Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3
Rivers, Frontiers in microbiology 2016 - “...protein 0.001 SPO2911 Thioesterase family protein 0.003 SPO2543 GntR family transcriptional regulator Transcriptional regulation 0.004 SPO2551 Peptide/opine/nickel uptake ATP-binding protein Transport 0.008 SPO0919 MarR family transcriptional regulator Transcriptional regulation 0.009 trans66 130 SPO0164 Oxidoreductase, FMN nucleotide-disulfide 0.003 SPO1125 Hypothetical protein 0.006 SPO1226 Putative lipoprotein Lipid metabolism...”
EAMY_3609 putative ABC transport system, ATP-binding component from Erwinia amylovora CFBP1430
40% identity, 89% coverage
Pdsh_05675 ABC transporter ATP-binding protein from Pyrodictium delaneyi
37% identity, 85% coverage
- The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction
Demey, Standards in genomic sciences 2017 - “...transporters (Pdsh_0567005665 and Pdsh_0763507620), and each oligopeptide transport cluster had dipeptide transport subunits directly upstream (Pdsh_05675 and Pdsh_0764007645). We also identified in the genome 13 putative peptidases, including a metallocarboxypeptidase (M32) (Pdsh_06240), three aminopeptidases (Pdsh_04150, Pdsh_05315, and Pdsh_07085), a metalloprotease (M50) (Pdsh_05275), and several omega peptidases...”
HVO_0058 ABC-type transport system ATP-binding protein (probable substrate dipeptides/oligopeptides) from Haloferax volcanii DS2
40% identity, 65% coverage
BRA1101 oligopeptide ABC transporter, ATP-binding protein, putative from Brucella suis 1330
38% identity, 95% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...OPN Oligopeptide import ABC BMEII0199, oppF BruAb21039 BRA1100 OPN Oligopeptide import ABC BMEII0200, oppD BruAb21040 BRA1101 BCAN_B1123 OPN Oligopeptide import IM BMEII0201, oppC BruAb21037 BRA0099 BCAN_B1122 OPN Oligopeptide import IM BMEII0202, oppB BruAb21038 BRA0098 BCAN_B1121 OPN Oligopeptide import BP BMEII01203 BruAb21036 BRA0097 BCAN_B1119 67 OPN Dipeptide...”
BMEII0199 OLIGOPEPTIDE TRANSPORT ATP-BINDING PROTEIN OPPF from Brucella melitensis 16M
38% identity, 84% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...OPN Oligopeptide import IM BMEI1937, oppC BruAb10010 BR0010 BOV_0007 BCAN_A0007 66 OPN Oligopeptide import ABC BMEII0199, oppF BruAb21039 BRA1100 OPN Oligopeptide import ABC BMEII0200, oppD BruAb21040 BRA1101 BCAN_B1123 OPN Oligopeptide import IM BMEII0201, oppC BruAb21037 BRA0099 BCAN_B1122 OPN Oligopeptide import IM BMEII0202, oppB BruAb21038 BRA0098 BCAN_B1121...”
PMI1471 oligopeptide ABC transporter, ATP-binding protein from Proteus mirabilis HI4320
38% identity, 87% coverage
RL3547 putative ATP-binding component of ABC transporter protein from Rhizobium leguminosarum bv. viciae 3841
38% identity, 94% coverage
BCAN_B1101 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain from Brucella canis ATCC 23365
38% identity, 92% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...Oligopeptide import ABC BMEII0222 BruAb21018 BRA1079 BCAN_B1102 OPN Dipeptide/ Oligopeptide import ABC BMEII0223 BruAb21019 BRA1078 BCAN_B1101 69 OPN Dipeptide import BP BMEII0284 BruAb20952 BRA1012 BOV_A0504 BCAN_B1032 OPN Dipeptide import IM BMEII0285 BruAb20950 BRA1009 BOV_A0501 BCAN_B1031 OPN Dipeptide import IM BMEII0286 BruAb20951 BRA1008 BOV_A0502 BCAN_B1030 OPN Dipeptide...”
TC 3.A.1.5.36 / Q8CJS2 Putative peptide transport system ATP-binding subunit, component of Peptide transporter encoded adjacent to the putative transport system with TC#3.A.1.5.35 (Akanuma et al. 2011). Induced by exogenous S-adenosylmethionine (SAM) at a concentration of 2muM which also enhanced antibiotic production and inhibited morphological development (Park et al. 2005). SAM can be imported into cells. Mutants in the bldK genes confer resistance to the toxic tripeptide, bialaphos from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
SCO5116 peptide transport system ATP-binding subunit from Streptomyces coelicolor A3(2)
37% identity, 81% coverage
- substrates: peptides
- The evolution of morphological development is congruent with the species phylogeny in the genus Streptomyces
Wang, Frontiers in microbiology 2023 - “...Q93IU0 ABC transporter intracellular ATPase subUT BldKD S. coelicolor Bentley et al., 2002 BldKE 381 Q8CJS2 Peptide transport system ATP-binding subUT S. coelicolor Bentley et al., 2002 BldM 203 Q7AKI8 Putative two-component regulator (isolation response regulatory proteins) S. coelicolor Bentley et al., 2002 BldN 177 Q9WX11...”
- Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor
Getsin, BMC microbiology 2013 - “...uptake porter. BldKA-D and Sco5116; Sco5112-6 (M, R, M, C, C) [ 112 ] Q93IU3-0; Q8CJS2 3.A.1.5.36 BldKA-D and Sco5116; peptide uptake porter induced by S-adenosylmethionine. DesABC; Sco7499-8, Sco7400 (R, M-M, C) [ 113 ] Q9L177-9 3.A.1.14.12 Desferrioxamine B uptake porter. CchCDEF; Sco0497-4 (M, M, C,...”
- A terD domain-encoding gene (SCO2368) is involved in calcium homeostasis and participates in calcium regulation of a DosR-like regulon in Streptomyces coelicolor
Daigle, Journal of bacteriology 2015 - “...SCO2717 SCO3323 SCO3324 SCO3579 SCO4768 SCO5112 SCO5113 SCO5114 SCO5116 SCO5147 SCO7647 Daigle et al. TABLE 4 Characteristics of a gene cluster possibly...”
- Insights into naturally minimised Streptomyces albus J1074 genome
Zaburannyi, BMC genomics 2014 - “...spore pigment [ 19 ]. Additionally, we found that the bldK genes ( SCO5112 to SCO5116 ), which encode a peptide transporter involved in morphological development in S. coelicolor A3(2) [ 20 ], are not present in S. albus . However, S. albus contains multiple other...”
- Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor
Getsin, BMC microbiology 2013 - “...M, M, C, C) [ 111 ] Q9F353-49 3.A.1.5.35 Probable oligopeptide uptake porter. BldKA-D and Sco5116; Sco5112-6 (M, R, M, C, C) [ 112 ] Q93IU3-0; Q8CJS2 3.A.1.5.36 BldKA-D and Sco5116; peptide uptake porter induced by S-adenosylmethionine. DesABC; Sco7499-8, Sco7400 (R, M-M, C) [ 113 ]...”
- Diverse control of metabolism and other cellular processes in Streptomyces coelicolor by the PhoP transcription factor: genome-wide identification of in vivo targets
Allenby, Nucleic acids research 2012 - “...( D ) SCO5477SCO5480 (ABC transporter). Two other operons negatively targeted by PhoP include SCO5112 SCO5116 ( bldK ) and SCO5476 SCO5480 which both encode putative oligopeptide ABC transporter systems ( Figure 4 and Supplementary Figure S8 ). Both are implicated in antibiotic production and development...”
- Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350
Ohnishi, Journal of bacteriology 2008 - “...developmental genes, the bldK genes (SCO5112 to SCO5116) (31), which encode a peptide transporter involved in morphological development in S. coelicolor...”
- Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
Hsiao, Antonie van Leeuwenhoek 2008 - “...0.92 0.75 0.51 SCO5114 BldKC 0.39 0.08 1.23 0.23 SCO5115 BldKD 0.01 0.18 0.89 0.15 SCO5116 bldKE putative peptide transport system ATP-binding protein 0.04 0.22 0.70 0.03 SCO5314 whiE protein VII 1.24 0.23 0.03 0.67 SCO5315 polyketide cyclase 0.39 0.82 0.31 0.25 SCO5316 acyl carrier protein...”
TC 3.A.1.5.27 / P45094 Dipeptide transport ATP-binding protein DppF, component of The glutathione uptake porter, DppBCDF with the glutathione binding protein, DppA (GbpA; HbpA). Takes up reduced (GSH) and oxidized (GSSG) but not bulky glutathione S conjugates or glutathione derivatives with C-terminal modifications from Haemophilus influenzae (see 2 papers)
38% identity, 94% coverage
STM3626 ABC superfamily (atp_bind), dipeptide transport protein from Salmonella typhimurium LT2
39% identity, 89% coverage
- Novel Two-Step Hierarchical Screening of Mutant Pools Reveals Mutants under Selection in Chicks
Yang, Infection and immunity 2016 - “...mapped to two MGD regions, STM0102 to STM0092 and STM3626 to STM3650. Confirmation of candidate phenotypes and complementation analysis. We retested 9 of the 12...”
- Effects of indole on drug resistance and virulence of Salmonella enterica serovar Typhimurium revealed by genome-wide analyses
Nikaido, Gut pathogens 2012 - “...of tdc operon (LysR family) 0.18 0.095 STM3577 tcp Methyl-accepting transmembrane citrate/phenol chemoreceptor 0.13 0.041 STM3626 dppF ABC superfamily (atp_bind), dipeptide transport protein 0.31 0.036 STM3628 dppC ABC superfamily (membrane), dipeptide transport protein 2 0.33 0.088 STM4258 Putative methyl-accepting chemotaxis protein 0.08 0.088 STM4300 fumB Fumarase...”
- Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes
Soyer, BMC evolutionary biology 2009 - “...putative 1914 TO (0.0035) - STM3258 - 462 Ty# (0.0157) 124, 139, 143, 144, 147 STM3626 oppF Oligopeptide ABC transporter, ATP-binding protein 1011 Ty# (0.0157) - Genes in JCVI role category "Unclassified and unknown function" STM3592 - Proton/peptide symporter family protein 1470 TO (0.0104) - STM1088...”
BRA1078 peptide ABC transporter, ATP-binding protein from Brucella suis 1330
37% identity, 92% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...Dipeptide/ Oligopeptide import ABC BMEII0222 BruAb21018 BRA1079 BCAN_B1102 OPN Dipeptide/ Oligopeptide import ABC BMEII0223 BruAb21019 BRA1078 BCAN_B1101 69 OPN Dipeptide import BP BMEII0284 BruAb20952 BRA1012 BOV_A0504 BCAN_B1032 OPN Dipeptide import IM BMEII0285 BruAb20950 BRA1009 BOV_A0501 BCAN_B1031 OPN Dipeptide import IM BMEII0286 BruAb20951 BRA1008 BOV_A0502 BCAN_B1030 OPN...”
FN0400 Dipeptide transport ATP-binding protein dppF from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
35% identity, 98% coverage
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...FN0236, FN0258, FN0276, FN0308, FN0309, FN0310, FN0332, FN0341, FN0352, FN0375, FN0376, FN0377, FN0397, FN0398, FN0399, FN0400, FN0450, FN0598, FN0658, FN0660, FN0685, FN0695, FN0793, FN0800, FN0801, FN0827, FN0828, FN1022, FN1080, FN1086, FN1135, FN1136, FN1166, FN1167, FN1187, FN1190, FN1198, FN1256, FN1301, FN1348, FN1349, FN1352, FN1353, FN1354, FN1362, FN1363,...”
- “...Covers FN0660, FN0793, FN0800, FN0801, FN1187, FN1398, FN1432, FN1801. 4 Covers FN0192, FN0396, FN0397, FN0399, FN0400, FN0998, FN1111, FN1359, FN1362, FN1363, FN1523, FN1525. 5 Covers FN0308, FN0309, FN0310, FN0375, FN0376, FN0377. In contrast to FnSg, FnPg and FnPgSg displayed predominantly unchanged and reduced transporter protein levels...”
TDE1271 oligopeptide/dipeptide ABC transporter, ATP-binding protein from Treponema denticola ATCC 35405
36% identity, 96% coverage
- Transcriptional responses of Treponema denticola to other oral bacterial species
Sarkar, PloS one 2014 - “...TDE1072 lipoprotein, putative 2.72 2.67 2.64 TDE1238 secG preprotein translocase, SecG subunit 1.83 2.38 3.05 TDE1271 oligopeptide/dipeptide ABC transporter, ATP-binding protein 1.56 TDE1272 oligopeptide/dipeptide ABC transporter, ATP-binding protein 2.00 1.80 1.62 TDE1273 oligopeptide/dipeptide ABC transporter, peptide-binding protein 2.25 1.89 - TDE1274 oligopeptide/dipeptide ABC transporter, permease protein...”
Z4957 putative ATP-binding component of dipeptide transport system from Escherichia coli O157:H7 EDL933
40% identity, 89% coverage
CD630_26700 ABC transporter ATP-binding protein from Clostridioides difficile 630
CD2670 oligopeptide ABC transporter, ATP-binding protein from Clostridium difficile 630
39% identity, 96% coverage
- sRNARFTarget: a fast machine-learning-based approach for transcriptome-wide sRNA target prediction
Naskulwar, RNA biology 2022 - “...spo0A Stage 0 sporulation protein A 114 CD630_08560 oppD ABC-type transport system, ATP-binding component 125 CD630_26700 ABC-type transport system, ATP-binding protein 138 CD630_15110 cotB Spore coat protein 163 CD630_13860 Putative allophanate hydrolase subunit 1 187 CD630_24920 Two-component sensor histidine kinase, sporulation-associated spo0A 205 CD630_35690 Sporulation-specific protease...”
- The repertoire of ABC proteins in Clostridioides difficile
Pipatthana, Computational and structural biotechnology journal 2021 - “...Unknown 227 cd630_25330 TMD-NBD Unknown Exporter 74 cd630_25930 NBD/NBD 3 550 NBD/NBD Pristinamycin/macrolide/multidrug N/A 75 cd630_26700 NBD 2 323 cd630_26720 cd630_26710 cd630_26730 cd630_26740 NBD-NBD-SBD-TMD-TMD Peptide/nickel Importer 76 cd630_26710 NBD 2 325 cd630_26720 cd630_26700 cd630_26730 cd630_26740 77 cd630_28170 TMD/NBD 6 596 cd630_28180 TMD/NBD-TMD/NBD Multidrug Exporter 78 cd630_28180...”
- “...of catabolizable carbohydrates in C. difficile [45] . Sub-family 2: peptide/nickel importer Three NPs (cd630_08560, cd630_26700, and cd630_26710) were grouped into sub-family 2, which is functionally verified as a peptide/nickel importer [46] , [47] . It was noted that NPs of sub-family 2 specifically associated with...”
- Conserved oligopeptide permeases modulate sporulation initiation in Clostridium difficile
Edwards, Infection and immunity 2014 - “...oppF qPCR (CD0857) oppF qPCR (CD0857) appF qPCR (CD2670) appF qPCR (CD2670) (Continued on following page) October 2014 Volume 82 Number 10 iai.asm.org 4279...”
- “...of sequenced strain 630 as CD0853 to CD0857 and CD2670 to CD2674, respectively (53, 54). The app genes are arranged in two apparently divergently transcribed...”
ACT74_06165 murein tripeptide/oligopeptide ABC transporter ATP binding protein OppF from Aggregatibacter actinomycetemcomitans
36% identity, 93% coverage
- Identification of a glutathione transporter in A. actinomycetemcomitans
Klementiev, Microbiology spectrum 2024 - “...percent identity to OppABCDF from E. coli MG1655. Operon gttABCDE corresponds to loci ACT74_06145 to ACT74_06165 in strain VT1169. (C) Extracellular glutathione produced by wild-type A. actinomycetemcomitans ( Aa ) , the gttD transposon mutant ( Aa gttD - ), and the genetically complemented Aa gttD...”
- “...coli . This analysis yielded a putative five-gene A. actinomycetemcomitans operon containing genes ACT74_06145 to ACT74_06165, which putatively encode proteins with homology to E. coli OppABCDF ( Fig. 2B ). OppABCDF is an ATP-dependent oligopeptide permease that has been well characterized in Salmonella typhimurium ( 16...”
EAMY_1933 Oligopeptide ABC transport system, ATP-binding protein oppF from Erwinia amylovora CFBP1430
37% identity, 93% coverage
OG1RF_10639, OG1RF_RS03325 oligopeptide ABC transporter ATP-binding protein Opp1F from Enterococcus faecalis OG1RF
EF0912 peptide ABC transporter, ATP-binding protein from Enterococcus faecalis V583
41% identity, 84% coverage
- Radezolid Is More Effective Than Linezolid Against Planktonic Cells and Inhibits Enterococcus faecalis Biofilm Formation
Zheng, Frontiers in microbiology 2020 - “...ABC/membrane protein 2.145 1.672 OG1RF_RS04555 OG1RF_10870 Cell wall surface anchor family protein 2.127 1.021 OG1RF_RS03325 OG1RF_10639 (oppF) ABC superfamily ATP-binding cassette transporter, ABC protein 2.004 1.969 OG1RF_RS05110 OG1RF_10982 Response regulator 0.357 0.527 OG1RF_RS03235 OG1RF_10620 ABC superfamily ATP-binding cassette transporter, ABC protein 0.222 0.369 OG1RF_RS11320 OG1RF_12207 ABC...”
- “...transporter, ABC/membrane protein 2.145 1.672 OG1RF_RS04555 OG1RF_10870 Cell wall surface anchor family protein 2.127 1.021 OG1RF_RS03325 OG1RF_10639 (oppF) ABC superfamily ATP-binding cassette transporter, ABC protein 2.004 1.969 OG1RF_RS05110 OG1RF_10982 Response regulator 0.357 0.527 OG1RF_RS03235 OG1RF_10620 ABC superfamily ATP-binding cassette transporter, ABC protein 0.222 0.369 OG1RF_RS11320 OG1RF_12207...”
- Identification of proteins related to the stress response in Enterococcus faecalis V583 caused by bovine bile
Bøhle, Proteome science 2010 - “...components EF0020 35.5 5.11 50 22 1.62 3.06 0.90 8 peptide ABC transporter, ATP-binding protein EF0912 35.9 5.97 20 7 1.10 1,00 0.46 9 e Amino acid biosynthesis Ornithine carbamoyltransferase EF0105 38.1 5.02 18 5 1.03 0.64 3.48 10 e Decarboxylase, putative EF0634 71.96 5.14 47...”
- “...synthesis towards generation of ATP. Three transporter and binding proteins were identified (EF0020, EF0709 and EF0912). The IIAB component of a mannose-specific phosphotransferase system (PTS; EF0020) was strongly up-regulated. Interestingly, there are studies showing that this type of transporter is important for the survival of saprophytic...”
- Characterization of the pheromone response of the Enterococcus faecalis conjugative plasmid pCF10: complete sequence and comparative analysis of the transcriptional and phenotypic responses of pCF10-containing cells to pheromone induction
Hirt, Journal of bacteriology 2005 - “...EF0224 EF0775 tufA rplF rpsE ebsG EF0782 EF0909 EF0912 EF0997 EF1045 EF1046 EF1727 EF1728 EF1730 EF1821 EF1822 EF1891 EF1974 EF2076 EF2326 EF2403 EF2496 EF3106...”
DppF / b3540 dipeptide ABC transporter ATP binding subunit DppF (EC 7.4.2.9) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
DppF / P37313 dipeptide ABC transporter ATP binding subunit DppF (EC 7.4.2.9) from Escherichia coli (strain K12) (see 2 papers)
DPPF_ECOLI / P37313 Dipeptide transport ATP-binding protein DppF; EC 7.4.2.9 from Escherichia coli (strain K12) (see 3 papers)
b3540 dipeptide transporter from Escherichia coli str. K-12 substr. MG1655
ECB_03391 dipeptide transporter from Escherichia coli B str. REL606
40% identity, 89% coverage
- function: Part of the ABC transporter DppABCDF involved in dipeptide transport (PubMed:7536291). Responsible for energy coupling to the transport system (Probable).
function: When a foreign outer membrane heme receptor is expressed in E.coli, DppABCDF can also transport heme and its precursor, 5- aminolevulinic acid (ALA), from the periplasm into the cytoplasm.
catalytic activity: a dipeptide(out) + ATP + H2O = a dipeptide(in) + ADP + phosphate + H(+) (RHEA:23120)
subunit: The complex is composed of two ATP-binding proteins (DppD and DppF), two transmembrane proteins (DppB and DppC) and a solute-binding protein (DppA) (PubMed:16905647, PubMed:7536291). MppA can replace DppA as binding protein for heme and ALA transport (PubMed:16905647).
disruption phenotype: Inactivation of the gene abolishes use of heme as an iron source. - Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind's AlphaFold2 Program Dramatically Expands the Metalloproteome
Wehrspan, Journal of molecular biology 2022 - “...Fe-S cluster-containing proteins. Two of these 14 proteins (TrhP ( P76403 ) and DppF ( P37313 )) were explicitly tested and confirmed by the authors, and encouragingly, both of these proteins are also identified here as binding Fe-S clusters: TrhP is identified here as containing a...”
- Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium
Cortés-Tolalpa, Microbial cell factories 2014 - “...Transport 43.4944 dppB b3543 Polypeptide: dipeptide ABC transporter - putative membrane subunit Transport 23.0830 dppF b3540 Polypeptide: dipeptide ABC transporter - putative ABC binding subunit Transport 32.6107 fecA b4291 Polypeptide: ferric citrate OMP FecA Transport 23.6130 malE b4034 Maltose ABC transporter - periplasmic binding protein Transport...”
- Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes
Skippington, Genome biology and evolution 2012 - “...dppB b3543 omrA 27 Core Incongruent No yjcH b4068 omrA 24 Variable Congruent No dppF b3540 omrA 27 Core Incongruent No fimA b4314 omrA 2 Variable N < 4 N < 4 ykgC b0304 omrA 21 Variable Incongruent No csgF b1038 omrA 23 Variable Incongruent No...”
- Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli
Hensley, Journal of inorganic biochemistry 2012 - “...ATP-binding component of dipeptide transport system 2.0E-05 4.7 Fnr or IHF [ 65 ] dppF b3540 putative ATP-binding component of dipeptide transport system 5.1E-05 4.4 Fnr or IHF [ 65 ] napG b2205 ferredoxin-type protein: electron transfer 4.7E-05 4.3 FlhDC [ 69 ] fumC b1611 Type...”
- Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
Lee, Applied and environmental microbiology 2009 - “...b3012 b3049 b3175 b3230 b3311 b3426 b3447 b3453 b1488 b3540 b3541 b3542 b3588 b3704 b3722 b4051 b4067 b4069 b4119 b4149 b4187 b4227 b1197 b4239 b4240 5.3 6.1...”
- Transcriptome analysis of Pseudomonas putida in response to nitrogen availability
Hervás, Journal of bacteriology 2008 - “...PP0878; homologues of E. coli b1243 to b1247 and b3540 to b3544). We observed 2.5-fold upregulation in the presence of serine of codA (PP3189), which is...”
- Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses
Gyaneshwar, Journal of bacteriology 2005 - “...We failed to detect genes in the dpp operon (b3540 to b3544) which were detected in mutant comparisons. Apart from glnHPQ and dpp, the results for strain...”
- Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions
Brown, BMC genomics 2017 - “...P. aeruginosa Peptide Description Locus Tag Locus Tag ECB_00686 sucB SSVDILVPDLPESVADATVATWHKK PA14_44000 MAIEIK Dihydrolipoamide Succinyltransferase ECB_03391 dppF STQEATLQQPLLQAIDLKK PA14_58490 METVLTAR Dipeptide transporter ATP-binding subunit ECB_00915 rpsA TESFAQLFEESLKE PA14_23330 SESFAELFEESLK 30S ribosomal protein S1 ECB_00155 yadR SDDVALPLEFTDAAANKV PA14_08510 SIETFTPTPLLFTPGAANK Iron-sulfur cluster insertion protein ErpA ECB_00183 accA SLNFLDFEQPIAELEAKI...”
ABLAC_24450 ABC transporter ATP-binding protein from Acinetobacter baumannii LAC-4
42% identity, 44% coverage
LSEI_2061 ABC-type oligopeptide transport system, ATPase component from Lactobacillus casei ATCC 334
LSEI_2061 ABC transporter ATP-binding protein from Lacticaseibacillus paracasei ATCC 334
40% identity, 82% coverage
BOV_A0950 peptide ABC transporter, ATP-binding protein from Brucella ovis ATCC 25840
42% identity, 81% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...import BP BMEII01203 BruAb21036 BRA0097 BCAN_B1119 67 OPN Dipeptide import ABC BMEII0205, dppF BruAb21033 BRA1095 BOV_A0950 BCAN_B1117 OPN Dipeptide import ABC BMEII0206, dppD BruAb21034 BRA1094 BOV_A0951 BCAN_B1116 OPN Dipeptide import IM BMEII0207, dppC BruAb21031 BRA1093 BCAN_B1115, dppC OPN Dipeptide import IM BruAb21032 BRA1092 BOV_A0952 OPN Dipeptide...”
SpyM3_0219 putative oligopeptide ABC transporter, ATP-binding protein from Streptococcus pyogenes MGAS315
SPy0297 oligopeptidepermease from Streptococcus pyogenes M1 GAS
M28_Spy0248 oligopeptide transport ATP-binding protein from Streptococcus pyogenes MGAS6180
41% identity, 94% coverage
- Novel regulatory small RNAs in Streptococcus pyogenes
Tesorero, PloS one 2013 - “...dehydrogenase >>> SPyM3_0202 putative amino acid ABC transporter ATP-binding protein <<< Q, Z SSRC 7 SPyM3_0219 putative oligopeptide ABC transporter >>> rRNA rRNA >>> Q, P SSRC 8 * SPyM3_0298 putative cell envelope proteinase >>> SPyM3_0299 hypothetical protein >>> Q, Z, P SSRC 9 SPyM3_0300 methionyl-tRNA...”
- Adaptation of group A Streptococcus to human amniotic fluid
Sitkiewicz, PloS one 2010 - “...SPy0295 oppC 2.01 Oligopeptide transport system permease M28_Spy0247 SPy0296 oppD 1.75 Oligopeptide transport ATP-binding M28_Spy0248 SPy0297 oppF 1.89 Oligopeptide transport ATP-binding Values represent fold change in expression in AF at ML, LL, and S growth phases compared to expression in THY medium. The most dramatic changes...”
- Adaptation of group A Streptococcus to human amniotic fluid
Sitkiewicz, PloS one 2010 - “...M28_Spy0246 SPy0295 oppC 2.01 Oligopeptide transport system permease M28_Spy0247 SPy0296 oppD 1.75 Oligopeptide transport ATP-binding M28_Spy0248 SPy0297 oppF 1.89 Oligopeptide transport ATP-binding Values represent fold change in expression in AF at ML, LL, and S growth phases compared to expression in THY medium. The most dramatic...”
HTZ92_1663 ABC transporter ATP-binding protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
42% identity, 44% coverage
- Genome diversity of domesticated Acinetobacter baumannii ATCC 19606T strains
Artuso, Microbial genomics 2022 - “...C ->CT N62E 67/181/181 GO593_15095/FQU82_1785 HTZ92_1775 Acyltransferase DMO12_04716 (181) 3271196 T ->TG R380Q 381/576/576 GO593_15665/FQU82_01898 HTZ92_1663 Dipeptide ABC transporter ATP-binding protein DMO12_05028 (576) 3974985 T ->TC F157I 172/212/212 GO593_18930/FQU82_02556 HTZ92_1005 TetR family transcriptional regulator DMO12_07332 (212) 3976370 G ->GA E45R 75/300/300 GO593_18945/FQU82_02559 HTZ92_1002 ATPase AAA DMO12_07341...”
A1S_1613 putative ABC transporter ATP-binding protein from Acinetobacter baumannii ATCC 17978
42% identity, 49% coverage
- Genetic Determinants of Acinetobacter baumannii Serum-Associated Adaptive Efflux-Mediated Antibiotic Resistance
Young, Antibiotics (Basel, Switzerland) 2023 - “...proteins (2.18.2; A1S_0801, A1S_0802, A1S_2326 and A1S_2327), four ATP-binding cassette pump proteins (34.2; loci A1S_1611, A1S_1613, A1S_1786, and A1S_2299), and ammonium transporters (4.85.2; loci A1S_021 and A1S_2748; ref. [ 49 ]). In a second possibility, YhaK may be responsible for activating cellular efflux capability post-translationally. Indeed,...”
DMO12_05028, DMO12_RS08470 ABC transporter ATP-binding protein from Acinetobacter baumannii ACICU
ACICU_01639 ATPase component of various ABC-type transport systems from Acinetobacter baumannii ACICU
42% identity, 44% coverage
ECs1747 oligopeptide ABC transport system ATP-binding protein OppF from Escherichia coli O157:H7 str. Sakai
BC33_RS15820 murein tripeptide/oligopeptide ABC transporter ATP-binding protein OppF from Escherichia coli ATCC 700728
38% identity, 87% coverage
OppF / b1247 murein tripeptide ABC transporter / oligopeptide ABC transporter ATP binding subunit OppF (EC 7.4.2.6) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
oppF / P77737 murein tripeptide ABC transporter / oligopeptide ABC transporter ATP binding subunit OppF (EC 7.4.2.6) from Escherichia coli (strain K12) (see 2 papers)
OPPF_ECOLI / P77737 Oligopeptide transport ATP-binding protein OppF; EC 7.4.2.6 from Escherichia coli (strain K12) (see paper)
TC 3.A.1.5.41 / P77737 Oligopeptide transport ATP-binding protein OppF, component of Oligopeptide transporter, OppABCDF/MppA/YgiS from Escherichia coli (strain K12)
b1247 oligopeptide transporter subunit from Escherichia coli str. K-12 substr. MG1655
38% identity, 87% coverage
- function: Part of the ABC transporter complex OppABCDF involved in the uptake of oligopeptides and of the ABC transporter complex MppA-OppBCDF involved in the uptake of the cell wall murein tripeptide L-alanyl- gamma-D-glutamyl-meso-diaminopimelate (PubMed:9495761). Probably responsible for energy coupling to the transport system (Probable). Plays an important nutritional role and is involved in the recycling of cell wall peptides (PubMed:9495761).
catalytic activity: a [peptide](out) + ATP + H2O = a [peptide](in) + ADP + phosphate + H(+) (RHEA:78459)
catalytic activity: L-alanyl-gamma-D-glutamyl-meso-diaminoheptanedioate(out) + ATP + H2O = L-alanyl-gamma-D-glutamyl-meso-diaminoheptanedioate(in) + ADP + phosphate + H(+) (RHEA:29763)
subunit: The complex is composed of two ATP-binding proteins (OppD and OppF), two transmembrane proteins (OppB and OppC) and a solute-binding protein (OppA or MppA). - substrates: Oligopeptides
tcdb comment: MppA is a murein peptide receptor, and YgiS is a bile acid (e.g., cholate, deoxycholate) receptor that may use the Opp system for uptake. YgiS mRNA is degraded by the toxin MgsR which is regulated by the antitoxin, MgsA and this loss of the mRNA protects the cell against bile acid stress (Kwan et al. 2015) - Toxicity and inhibition mechanism of gallic acid on physiology and fermentation performance of Escherichia coli
Liu, Bioresources and bioprocessing 2022 - “...Outer membrane porin C 3 b1243 oppA 3.8 Oligopeptide ABC transporter periplasmic binding protein 4 b1247 oppF 3.6 Murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF 5 b1245 oppC 2.4 Murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppC 6 b0463 acrA 3.2...”
- Improving membrane protein expression and function using genomic edits
Jensen, Scientific reports 2017 - “...the corresponding gene disruption benefits IMP expression (for example, the R High/Low for oppF , b1247 for CyoB-GFP at 200M IPTG is 5.615, Table S1 ). The relatively small number of cells sequenced in each experiment meant that a large number of genes had very few...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Transcriptome analysis of Pseudomonas putida in response to nitrogen availability
Hervás, Journal of bacteriology 2008 - “...(PP0885 to PP0878; homologues of E. coli b1243 to b1247 and b3540 to b3544). We observed 2.5-fold upregulation in the presence of serine of codA (PP3189), which...”
- Effect of RyhB small RNA on global iron use in Escherichia coli
Massé, Journal of bacteriology 2005 - “...b2297 b2832 b0401 b1905 b2587 b1186 b0814 b1243 b1244 b1245 b1246 b1247 b1981 b0481 2.0 1.8 4.0 2.4 4.2 2.2 2.2 2.8 2.3 1.8 1.6 1.4 1.4 5.1 3.3 1.4 1.2 1.9...”
BCAN_B1028 Oligopeptide transport ATP-binding protein oppF from Brucella canis ATCC 23365
BRA1008 peptide ABC transporter, ATP-binding protein from Brucella suis 1330
42% identity, 81% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...import ABC BMEII0287 BruAb20948 BRA1011 BOV_A0500 BCAN_B1029 OPN Dipeptide import ABC BMEII0288 BruAb20949 BRA1010 BOV_A0501 BCAN_B1028 70 OPN Nickel import BP BMEII0487 BruAb20428 BRA0804 BOV_A0754 BCAN_B0818, NikA OPN Nickel import IM BMEII0488, nikB BruAb20429, nikB BRA0802, nikC BOV_A0752 BCAN_B0817, NikB OPN Nickel import IM BMEII0489, nikC...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...OPN Dipeptide import IM BMEII0285 BruAb20950 BRA1009 BOV_A0501 BCAN_B1031 OPN Dipeptide import IM BMEII0286 BruAb20951 BRA1008 BOV_A0502 BCAN_B1030 OPN Dipeptide import ABC BMEII0287 BruAb20948 BRA1011 BOV_A0500 BCAN_B1029 OPN Dipeptide import ABC BMEII0288 BruAb20949 BRA1010 BOV_A0501 BCAN_B1028 70 OPN Nickel import BP BMEII0487 BruAb20428 BRA0804 BOV_A0754 BCAN_B0818,...”
NJ56_15445 murein tripeptide/oligopeptide ABC transporter ATP binding protein OppF from Yersinia ruckeri
38% identity, 87% coverage
8z1wD / P37313 Cryo-em structure of escherichia coli dppbcdf complex bound to atpgammas
39% identity, 91% coverage
- Ligands: iron/sulfur cluster; phosphothiophosphoric acid-adenylate ester (8z1wD)
BAS1105 oligopeptide ABC transporter, ATP-binding protein from Bacillus anthracis str. Sterne
BA1195 oligopeptide ABC transporter, ATP-binding protein from Bacillus anthracis str. Ames
37% identity, 99% coverage
TDE1067 oligopeptide/dipeptide ABC transporter, ATP-binding protein from Treponema denticola ATCC 35405
39% identity, 75% coverage
- Porphyromonas gingivalis and Treponema denticola exhibit metabolic symbioses
Tan, PLoS pathogens 2014 - “...(GcvP1, GcvP2 and GcvH), the glycine reductase system (Protein B2) and oligopeptide/dipeptide/amino acid transporters (OppA, TDE1067, TDE0985) were up-regulated suggesting an increased glycine catabolism by T. denticola . The increased expression of genes encoding components of the glycine cleavage and glycine reductase systems was confirmed by...”
BMEII0288 DIPEPTIDE TRANSPORT ATP-BINDING PROTEIN DPPF from Brucella melitensis 16M
41% identity, 81% coverage
- Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network
Hur, BMC immunology 2011 - “...partitioning BMEII0470 crcB crcB family protein 5 1 (0) CM (10.00) General function prediction only BMEII0288 oppF peptide ABC transporter, ATP-binding protein 6 3 (2) CM (9.99) BMEI1081 surE stationary phase survival protein SurE 8 5 (2) C (8.96) BMEI0215 ialA dinucleoside polyphosphate hydrolase 1 1...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BOV_A0502 BCAN_B1030 OPN Dipeptide import ABC BMEII0287 BruAb20948 BRA1011 BOV_A0500 BCAN_B1029 OPN Dipeptide import ABC BMEII0288 BruAb20949 BRA1010 BOV_A0501 BCAN_B1028 70 OPN Nickel import BP BMEII0487 BruAb20428 BRA0804 BOV_A0754 BCAN_B0818, NikA OPN Nickel import IM BMEII0488, nikB BruAb20429, nikB BRA0802, nikC BOV_A0752 BCAN_B0817, NikB OPN Nickel...”
TDE0397 oligopeptide/dipeptide ABC transporter, ATP-binding protein from Treponema denticola ATCC 35405
36% identity, 95% coverage
TDE0987 oligopeptide/dipeptide ABC transporter, ATP-binding protein from Treponema denticola ATCC 35405
35% identity, 97% coverage
- Localization and pathogenic role of the cysteine protease dentipain in Treponema denticola
Miyai-Murai, Molecular oral microbiology 2023 - “...protein 2.45 TDE2676 threonine synthase 2.44 TDE0437 HEAT repeat-containing PBS lyase 2.37 TDE0418 lipoprotein 2.27 TDE0987 oligopeptide/dipeptide ABC transporter ATP-binding protein 2.25 TDE0806 hypothetical protein 2.18 TDE1618 hypothetical protein 2.17 TDE2752 hypothetical protein 2.13 TDE2451 S-adenosylmethioninetRNA ribosyltransferase-isomerase 2.09 TDE0345 methyl-accepting chemotaxis protein DmcB 2.07 TDE2372 hypothetical...”
SMa1646 ABC transporter, ATP-binding protein from Sinorhizobium meliloti 1021
38% identity, 91% coverage
TC 3.A.1.5.39 / W0WLZ8 Dipeptide transport ATP-binding protein DppF, component of Di- and tri-peptide transporter, DppBCDF with periplasmic substrate binding receptors, A1, A3, A5, A7 and A9, each with differing specificities for peptides from Pseudomonas aeruginosa MH38
PA4506 probable ATP-binding component of ABC dipeptide transporter from Pseudomonas aeruginosa PAO1
35% identity, 97% coverage
- substrates: dipeptides, tripeptides
- The development of a new parameter for tracking post-transcriptional regulation allows the detailed map of the Pseudomonas aeruginosa Crc regulon
Corona, Scientific reports 2018 - “...4,85 2,37 1,88 Transport PA4505 Dipeptide ABC transporter ATP-binding protein DppD 4,61 2,35 2,08 Transport PA4506 Dipeptide ABC transporter ATP-binding protein DppF 4,55 2,16 1,59 Iron piuB PA4513 Probable oxidoreductase 0,66 0,84 1,73 Iron piuA PA4514 Probable outer membrane receptor for iron transport 0,87 1,99 4,8...”
- Sarcosine Catabolism in Pseudomonas aeruginosa Is Transcriptionally Regulated by SouR
Willsey, Journal of bacteriology 2016 - “...PA3629 PA4385 PA4386 PA4498 PA4501 PA4502 PA4504 PA4505 PA4506 PA4761 PA5415 PA5416 PA5417 PA5418 PA5419 PA5420 PA5421 Gene name aprE aprI antB adhC groEL...”
- “...also revealed that the dipeptide transport system (PA4501 to PA4506) was induced by sarcosine in the gbdR souR strain but not in the gbdR strain. Regulation of...”
- Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria
Browne, BMC microbiology 2010 - “...component of ABC transporter 3.48 PA4502 c probable binding protein component of ABC transporter 3.35 PA4506 c probable ATP-binding component of ABC dipeptide transporter 8.43 dadA PA5304 D-amino acid dehydrogenase, small subunit 2.36 Genes differentially regulated, based on proteome data, in rich media in a crc...”
- “...PA2553 is proximal to PA2555, (b) PA3187 is proximal to PA3186 and (c) PA4502 and PA4506 are proximal to PA4501. A proteomic analysis comparing the wild type strain P. aeruginosa PAO1 to an isogenic crc mutant in LB broth was also recently performed [ 27 ]....”
- Transcriptome analysis of Pseudomonas aeruginosa growth: comparison of gene expression in planktonic cultures and developing and mature biofilms
Waite, Journal of bacteriology 2005 - “...PA2782 PA3221 PA4501 PA4502 PA4503 PA4504 PA4505 PA4506 PA4526 PA4555 PA4697 PA5033 PA5041 PA5139 Hypothetical protein Conserved hypothetical protein...”
- “...(a probable major facilitator superfamily transporter), PA4501 through PA4506 (six genes in a region associated with the transport of small molecules), and...”
T1E_1824 peptide ABC transporter ATP-binding protein from Pseudomonas putida DOT-T1E
36% identity, 96% coverage
pRL110054 putative ATP-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
43% identity, 41% coverage
B6D87_RS04090 peptide ABC transporter ATP-binding protein from Pseudomonas fragi
36% identity, 96% coverage
PP0878 dipeptide ABC transporter, ATP-binding protein from Pseudomonas putida KT2440
36% identity, 96% coverage
GALLO_0328 putative oligopeptide ABC transporter, ATP-binding protein from Streptococcus gallolyticus UCN34
SGGBAA2069_c03160, SGGB_0356 ABC transporter ATP-binding protein from Streptococcus gallolyticus subsp. gallolyticus ATCC BAA-2069
39% identity, 99% coverage
- Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex
Papadimitriou, BMC genomics 2014 - “...protein oppD GALLO_0327 SGGB_0355 SGGBAA2069_c03150 SGPB_0279 SMA_0356 Sinf_0308 Sinf_1822 Oligopeptide ABC transporter, ATP-binding protein oppF GALLO_0328 SGGB_0356 SGGBAA2069_c03160 SGPB_0280 SMA_0357 Sinf_0309 Sinf_1821 Dipeptide/tripeptide permease dtpT GALLO_0638 SGGB_0613 SGGBAA2069_c05810 SGPB_0507 SMA_0600 Sinf_0519 Cysteine aminopeptidase C pepC GALLO_0478 SGGB_0452 SGGBAA2069_c04140 SGPB_0379 SMA_0442 Sinf_0388 Aminopeptidase N pepN GALLO_1143 SGGB_1134...”
- Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex
Papadimitriou, BMC genomics 2014 - “...GALLO_0327 SGGB_0355 SGGBAA2069_c03150 SGPB_0279 SMA_0356 Sinf_0308 Sinf_1822 Oligopeptide ABC transporter, ATP-binding protein oppF GALLO_0328 SGGB_0356 SGGBAA2069_c03160 SGPB_0280 SMA_0357 Sinf_0309 Sinf_1821 Dipeptide/tripeptide permease dtpT GALLO_0638 SGGB_0613 SGGBAA2069_c05810 SGPB_0507 SMA_0600 Sinf_0519 Cysteine aminopeptidase C pepC GALLO_0478 SGGB_0452 SGGBAA2069_c04140 SGPB_0379 SMA_0442 Sinf_0388 Aminopeptidase N pepN GALLO_1143 SGGB_1134 SGGBAA2069_c11310 SGPB_1002...”
- “...oppD GALLO_0327 SGGB_0355 SGGBAA2069_c03150 SGPB_0279 SMA_0356 Sinf_0308 Sinf_1822 Oligopeptide ABC transporter, ATP-binding protein oppF GALLO_0328 SGGB_0356 SGGBAA2069_c03160 SGPB_0280 SMA_0357 Sinf_0309 Sinf_1821 Dipeptide/tripeptide permease dtpT GALLO_0638 SGGB_0613 SGGBAA2069_c05810 SGPB_0507 SMA_0600 Sinf_0519 Cysteine aminopeptidase C pepC GALLO_0478 SGGB_0452 SGGBAA2069_c04140 SGPB_0379 SMA_0442 Sinf_0388 Aminopeptidase N pepN GALLO_1143 SGGB_1134 SGGBAA2069_c11310...”
SGPB_0280 ABC transporter ATP-binding protein from Streptococcus pasteurianus ATCC 43144
39% identity, 99% coverage
RHE_RS25825 ABC transporter ATP-binding protein from Rhizobium etli CFN 42
37% identity, 46% coverage
DPPF_PSEAB / A0A0H2ZH52 Di/tripeptide transport ATP-binding protein DppF; EC 7.4.2.9 from Pseudomonas aeruginosa (strain UCBPP-PA14) (see paper)
PA14_58490 putative dipeptide transport system ATP-binding pr from Pseudomonas aeruginosa UCBPP-PA14
35% identity, 97% coverage
- function: Part of the ABC transporter DppABCDF involved in the uptake of various di/tripeptides (PubMed:25338022). Is also involved in the uptake of phaseolotoxin, a toxic tripeptide inhibiting the enzyme ornithine carbamoyltransferase (PubMed:25338022). Responsible for energy coupling to the transport system (Probable).
catalytic activity: a dipeptide(out) + ATP + H2O = a dipeptide(in) + ADP + phosphate + H(+) (RHEA:23120)
subunit: The complex is composed of two ATP-binding proteins (DppD and DppF), two transmembrane proteins (DppB and DppC) and a solute-binding protein (DppA1-A5) (PubMed:25338022). Five orthologous SBPs (DppA1-A5) are present in P.aeruginosa, which increases the substrate specificity of the DppBCDF transporter (PubMed:25338022).
disruption phenotype: Deletion of the dppBCDF operon leads to reduced ability to utilize di/tripeptides as nitrogen source. - Gene Expression Profiling of <i>Pseudomonas aeruginosa</i> Upon Exposure to Colistin and Tobramycin
Cianciulli, Frontiers in microbiology 2021 - “...permease DppC 13.03 3.55 dppD PA14_58470 Dipeptide ABC transporter ATP-binding protein DppD 34.43 10.45 dppF PA14_58490 Dipeptide ABC transporter ATP-binding protein DppF 21.5 4.19 Transcription and translation tufB PA14_08680 Elongation factor Tu 92.01 3.09 rplC PA14_08850 50S ribosomal protein L3 27.97 ND rplD PA14_08860 50S ribosomal...”
- Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions
Brown, BMC genomics 2017 - “...Description Locus Tag Locus Tag ECB_00686 sucB SSVDILVPDLPESVADATVATWHKK PA14_44000 MAIEIK Dihydrolipoamide Succinyltransferase ECB_03391 dppF STQEATLQQPLLQAIDLKK PA14_58490 METVLTAR Dipeptide transporter ATP-binding subunit ECB_00915 rpsA TESFAQLFEESLKE PA14_23330 SESFAELFEESLK 30S ribosomal protein S1 ECB_00155 yadR SDDVALPLEFTDAAANKV PA14_08510 SIETFTPTPLLFTPGAANK Iron-sulfur cluster insertion protein ErpA ECB_00183 accA SLNFLDFEQPIAELEAKI PA14_23860 SNWLVDKLIPSIMR Acetyl-CoA...”
- High-throughput screening of dipeptide utilization mediated by the ABC transporter DppBCDF and its substrate-binding proteins DppA1-A5 in Pseudomonas aeruginosa
Pletzer, PloS one 2014 - “...), and two encoding the hydrophilic nucleotide- and ATP-binding proteins PA14_58470 ( dppD ) and PA14_58490 ( dppF ) ( Figure 1A ). Using the protein sequence of PA14_58440, we identified orthologs of the dipeptide permease in Haemophilus influenzae (61% identity), E. coli (66% identity) and...”
RHE_RS24230 ABC transporter ATP-binding protein from Rhizobium etli CFN 42
43% identity, 42% coverage
BRA0404 peptide ABC transporter, ATP-binding protein from Brucella suis 1330
BOV_A0347 peptide ABC transporter, ATP-binding protein from Brucella ovis ATCC 25840
BCAN_B0407 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain from Brucella canis ATCC 23365
37% identity, 98% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...OPN Oligopeptide import ABC BMEII0863 BruAb20796 BRA0405 BOV_A0347 BCAN_B0408 OPN Oligopeptide import ABC BMEII0864 BruAb20797 BRA0404 BOV_A0348 BCAN_B0407 75 OSP Maltose import ABC BMEI1713, malK BruAb10233 BR0238 BOV_0231 BCAN_A0241 OSP Maltose import IM BMEI1714, malG BruAb10231 BR0237 BOV_0230 BCAN_A0240 OSP Maltose import IM BMEI1715, malF BruAb10232...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...Oligopeptide import IM BMEII0861 BruAb20794 BRA0407 BOV_A0350 BCAN_B0410 OPN Oligopeptide import ABC BMEII0863 BruAb20796 BRA0405 BOV_A0347 BCAN_B0408 OPN Oligopeptide import ABC BMEII0864 BruAb20797 BRA0404 BOV_A0348 BCAN_B0407 75 OSP Maltose import ABC BMEI1713, malK BruAb10233 BR0238 BOV_0231 BCAN_A0241 OSP Maltose import IM BMEI1714, malG BruAb10231 BR0237 BOV_0230...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...import ABC BMEII0863 BruAb20796 BRA0405 BOV_A0347 BCAN_B0408 OPN Oligopeptide import ABC BMEII0864 BruAb20797 BRA0404 BOV_A0348 BCAN_B0407 75 OSP Maltose import ABC BMEI1713, malK BruAb10233 BR0238 BOV_0231 BCAN_A0241 OSP Maltose import IM BMEI1714, malG BruAb10231 BR0237 BOV_0230 BCAN_A0240 OSP Maltose import IM BMEI1715, malF BruAb10232 BR0236 BOV_0229...”
BMEII0864 OLIGOPEPTIDE TRANSPORT ATP-BINDING PROTEIN APPF from Brucella melitensis 16M
37% identity, 90% coverage
YPK_2066 oligopeptide/dipeptide ABC transporter, ATPase subunit from Yersinia pseudotuberculosis YPIII
37% identity, 87% coverage
PputUW4_00739 peptide ABC transporter ATP-binding protein from Pseudomonas sp. UW4
35% identity, 94% coverage
ILP77_RS14160 ABC transporter ATP-binding protein from Staphylococcus aureus
MW0871 ORFID:MW0871~oligopeptide transport system ATP-binding protein OppF homologue from Staphylococcus aureus subsp. aureus MW2
43% identity, 84% coverage
TC 3.A.1.5.19 / Q2FZR4 OppF, component of The major oligopeptide uptake porter, Opp-3 (of four paralogues, this is the only one that mediates nitrogen nutrition from Staphylococcus aureus (strain NCTC 8325)
SAKOR_00906, USA300HOU_RS04905 ABC transporter ATP-binding protein from Staphylococcus aureus subsp. aureus USA300_TCH1516
SA0848 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV0989 oligopeptide transport system ATP-binding protein OppF homolog from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_00926 oligopeptide ABC transporter, ATP-binding protein, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0890 oligopeptide ABC transporter, ATP-binding protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
43% identity, 84% coverage
- substrates: Oligopeptides
- Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells
Tsuchiya, The Biochemical journal 2018 - “...152.32 ST398NM01_1322 Uncharacterized protein 28.118 SELEELC*K 118.23 recG ATP-dependent DNA helicase RecG 78.343 C*IFFNQPYLK 125.72 SAKOR_00906 Oligopeptide transport ATP-binding protein oppF 16.074 GETLGLVGESGC*GK 102.03 murD MURD 29.82 NQTEEDYLIC*NYHQR 92.151 SA0315 Uncharacterized protein 20.923 C*DAPMEVNK 73.435 HMPREF0776_0655 3-Demethylubiquinone-9 3-methyltransferase domain protein 16.768 VLC*SDSFGR 132.03 SAOUHSC_02324 Uncharacterized protein...”
- Absence of Protoheme IX Farnesyltransferase CtaB Causes Virulence Attenuation but Enhances Pigment Production and Persister Survival in MRSA
Xu, Frontiers in microbiology 2016 - “...USA300HOU_RS02375 gltB1 1.63 2.23E-02 Glutamate synthase (NADPH), large subunit USA300HOU_RS06050 pyrF 1.62 3.08E-02 Orotidine-5'-phosphate decarboxylase USA300HOU_RS04905 oppF1 1.58 1.92E-02 Oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein USA300HOU_RS01935 rpsF 1.56 2.29E-02 Ribosomal protein S6 USA300HOU_RS04620 dltA 1.55 2.45E-02 Long-chain-fatty-acidCoA ligase USA300HOU_RS07105 dapA 1.52 4.99E-02 dihydrodipicolinate...”
- Comparative genomic analysis of European and Middle Eastern community-associated methicillin-resistant Staphylococcus aureus (CC80:ST80-IV) isolates by high-density microarray
Goering, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2009 - “...1198 did not contain the epidermin immunity factor ( epiG ) gene or hypothetical protein SA0848, found in all other isolates. Isolate 1201 lacked hypothetical protein SA0406, the SAA0001 replication initiation protein repC , the SA0002 tetracycline resistance protein, the SAA0003 plasmid recombination-mobilization protein pre ,...”
- “...+ + USA300+ USA400+ SA0753 Conserved hypothetical protein + + + + + USA300+ USA400+ SA0848 Hypothetical protein + + + + + USA300+ USA400 SA0865 Hypothetical protein + + + USA300+ USA400+ SA0871 Putatative acetyltransferase + + + USA300+ USA400+ SA0881 Putative thioredoxin + +...”
- Transcriptional signature following inhibition of early-stage cell wall biosynthesis in Staphylococcus aureus
O'Neill, Antimicrobial agents and chemotherapy 2009 - “...SA0482 SA0612 SA0707 SA0818 SA0835 SA0845 SA0846 SA0847 SA0848 SA0849 SA0871 SA0883 SA0886 SA0958 SA1019 SA1163 SA1164 SA1165 SA1166 SA1170 SA1226 SA1227 SA1228...”
- Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
Donat, Journal of bacteriology 2009 - “...transporter/transporter proteins SA0255 SA0616 SA0617 SA0845 SA0847 SA0848 SA0849 SA1960 SA2079 SA2132 SA2143 SA2200 SA2202 SA2253 SA2302 SA2434 vraF vraG oppB...”
- Microarray analysis of toxicogenomic effects of ortho-phenylphenol in Staphylococcus aureus
Jang, BMC genomics 2008 - “...transporter protein opp D Amino acid transport and metabolism, Inorganic ion transport and metabolism sa_c332s172_a_at SA0848 9.13E-05 2.2 probable peptide ABC transporter ATP-binding ABC transporter protein opp F Amino acid transport and metabolism sa_c5349s4625_a_at SA0950 0.0022 2.2 ABC transporter ATP-binding protein spermidine:putrescine transport pot A Amino...”
- Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome
Ben, Journal of bacteriology 2008 - “...SA0294 Membrane/SP SA0655 Membrane SA1156 Membrane SA0848 Cytoplasm SAR1761 Membrane/SP SA1592 Membrane SA1958 Cytoplasm SA1960 Membrane SAR2268 Secreted/SP...”
- 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 - “...SA1140 SA1960 SA0293 SA2156 SA0589 SA2303 SA0208 SA2302 SA0111 SA0848 SA2167 SA0207 SA0849 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00...”
- Two novel point mutations in clinical Staphylococcus aureus reduce linezolid susceptibility and switch on the stringent response to promote persistent infection
Gao, PLoS pathogens 2010 - “...SAV0987 opp3C oligopeptide transport permease, Opp3C 4.94 SAV0988 opp3D oligopeptide transport ATP-binding protein, Opp3D 7.27 SAV0989 opp3F oligopeptide transport ATP-binding protein, Opp3F 7.36 SAV0990 opp3A oligopeptide binding protein, Opp3A 6.06 SAV0994 oligopeptide transport system permease 3.19 SAV1023 htrA Serine protease HtrA 3.34 SAV1083 argJ bifunctional ornithine...”
- Staphylococcus aureus virulence expression is impaired by Lactococcus lactis in mixed cultures
Even, Applied and environmental microbiology 2009 - “...MW0868 oppB SAV1380 SAV1382 MW1268 MW1270 SAV0727 SAV0989 MW0689 MW0871 Energetic metabolism genes SAV2607 SAV1116 SAV0623 SAV0625 SAV1832 SAV0627 Nitrogen...”
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...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 transporter ATP-binding protein putative SAOUHSC_00925 0.168 Conserved hypothetical protein SAOUHSC_02741 0.228 Amino acid ABC transporter permease protein putative SAOUHSC_00924 0.266 Conserved hypothetical protein SAOUHSC_02742 0.312 ABC transporter...”
- Proteomics and Transcriptomics Uncover Key Processes for Elasnin Tolerance in Methicillin-Resistant Staphylococcus aureus
Sulaiman, mSystems 2022 - “...instance, transporters such as phosphate-binding protein PstS, amino acid ABC transporter SAOUHSC_02697, oligopeptide ABC transporter SAOUHSC_00926, and magnesium transport protein CorA, proteins involved in S. aureus infection and pathogenesis such as response regulator ArlR, immunoglobulin G-binding protein A (Spa), and iron-regulated surface determinant protein H (IsdH),...”
- Human Urine Alters Methicillin-Resistant Staphylococcus aureus Virulence and Transcriptome
Paudel, Applied and environmental microbiology 2021 (secret)
NWMN_0859 oligopeptide ABC transporter, ATP-binding protein from Staphylococcus aureus subsp. aureus str. Newman
SACOL0994 oligopeptide ABC transporter, ATP-binding protein from Staphylococcus aureus subsp. aureus COL
43% identity, 84% coverage
- CodY in Staphylococcus aureus: a regulatory link between metabolism and virulence gene expression
Pohl, Journal of bacteriology 2009 - “...NWMN_0348 NWMN_2573 NWMN_2574 NWMN_2577 NWMN_2370 NWMN_0859 NWMN_0428 NWMN_1950 NWMN_0423 NWMN_2288 NWMN_0016 NWMN_0379 NWMN_1110 NWMN_1111 NWMN_1112 NWMN_1249...”
- Mutations in mmpL and in the cell wall stress stimulon contribute to resistance to oxadiazole antibiotics in methicillin-resistant Staphylococcus aureus
Xiao, Antimicrobial agents and chemotherapy 2014 - “...(xanthine phosphoribosyltransferase) Intergenic region between sacol0994 (oligopeptide ABC transporter ATP-binding protein) and sacol0995 (oligopeptide ABC...”
- In vitro and in vivo models of Staphylococcus aureus endophthalmitis implicate specific nutrients in ocular infection
Sadaka, PloS one 2014 - “...Oligopeptide ABC transporter permease 11.5 (1.4) SACOL0993 oppD Oligopeptide ABC transporter ATP-binding protein 8.3 (1.3) SACOL0994 oppF Oligopeptide ABC transporter ATP-binding protein 7.9 (1.2) SACOL0995 Oligopeptide ABC transporter oligopeptide-binding protein 8.3 (1.2) SACOL1018 Sodium:alanine symporter family protein 21.9 (1.2) 9.9 (3.4) 15.7 (1.7) ig_SACOL1018-9 Intergenic region...”
- Mode-of-action studies of the novel bisquaternary bisnaphthalimide MT02 against Staphylococcus aureus
Menzel, Antimicrobial agents and chemotherapy 2011 - “...SACOL0079 SACOL0480 SACOL0682 SACOL0684 SACOL0991 SACOL0994 SACOL1193 SACOL1195 SACOL1196 SACOL1319 SACOL2450 SACOL2452 SACOL2453 SACOL2475 Nucleotide...”
- A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome
Becher, PloS one 2009 - “...acids or oligopeptides [from left to right: SACOL2451, SACOL2309, SACOL2452, SACOL2453, SACOL0993 (OppD), SACOL0992 (OppC), SACOL0994 (OppF), SACOL0995, SACOL1963, SACOL2450, SACOL0991 (OppB)], CPS (capsular polysaccharide) biosynthesis [SACOL0151 (Cap5P), SACOL0138 (Cap5C), SACOL0143 (Cap5H), SACOL0137 (Cap5B), SACOL0136 (Cap5A), SACOL0142 (Cap5G), SACOL0150 (Cap5O), SACOL0145 (Cap5J), glycerol utilization [SACOL0805, SACOL1514...”
A9497_03140, AKL23_RS06725, T303_08070 ATP-binding cassette domain-containing protein from Streptococcus thermophilus
40% identity, 94% coverage
- Technological and Genomic Analysis of Roles of the Cell-Envelope Protease PrtS in Yoghurt Starter Development
Tian, International journal of molecular sciences 2018 - “...A9497_03155 AKL23_RS06740 OppB; Permease protein A9497_03150 AKL23_RS06735 OppC; Permease protein A9497_03145 AKL23_RS06730 OppD; ATP-binding protein A9497_03140 AKL23_RS06725 OppF; ATP-binding protein Amino acid A9497_00725 A9497_04145 AKL23_RS04220 AKL23_RS07755 ATP-binding cassette (ABC) transporter ATP-binding protein A9497_00720 A9497_04150 A9497_03405 A9497_03795 AKL23_RS04215 AKL23_RS07760 AKL23_RS07020 AKL23_RS07405 ABC transporter permease A9497_04155 A9497_03360 A9497_03370...”
- “...AKL23_RS06740 OppB; Permease protein A9497_03150 AKL23_RS06735 OppC; Permease protein A9497_03145 AKL23_RS06730 OppD; ATP-binding protein A9497_03140 AKL23_RS06725 OppF; ATP-binding protein Amino acid A9497_00725 A9497_04145 AKL23_RS04220 AKL23_RS07755 ATP-binding cassette (ABC) transporter ATP-binding protein A9497_00720 A9497_04150 A9497_03405 A9497_03795 AKL23_RS04215 AKL23_RS07760 AKL23_RS07020 AKL23_RS07405 ABC transporter permease A9497_04155 A9497_03360 A9497_03370 A9497_07620...”
- Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275
Padmanabhan, Frontiers in microbiology 2018 - “...2.21 T303_03155 6-phosphofructokinase 124 GACAAGGTAGAGATTGGTGAAG TGAAGCCCGTAGCAGTAT 3.39 2.96 T303_06085 4-alpha-glucanotransferase 156 CGTCAAGGTGAACCAATCA CATACGCCATCTCCAGTTTC 3.90 3.37 T303_08070 Peptide ABC transporter ATP-binding protein 162 CTGCGGCTAGTTTGAATGA CGTGAGGGTAACGTGTTAAG 0.73 0.58 T303_08085 Peptide ABC transporter permease 158 CAGCTACCAAGAGTCGTTATC GACACCTGTTGACACACTATC 1.22 0.96 a Mean log2fold change value of triplicates, b -Ct value...”
pRL120330 putative ATP-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
35% identity, 98% coverage
Q8E7K6 ABC transporter domain-containing protein from Streptococcus agalactiae serotype III (strain NEM316)
SAK_0210 oligopeptide ABC transporter, ATP-binding protein from Streptococcus agalactiae A909
SAG0152 oligopeptide ABC transporter, ATP-binding protein from Streptococcus agalactiae 2603V/R
gbs0148 Unknown from Streptococcus agalactiae NEM316
42% identity, 81% coverage
- Relevance of peptide uptake systems to the physiology and virulence of Streptococcus agalactiae
Samen, Journal of bacteriology 2004 - “...Q8E5L7; OppB, Q8E7K9; OppC, Q8E7K8; OppD, Q8E7K7; OppF, Q8E7K6; DpsA, Q8E489. The genome of S. agalactiae possesses several putative peptide permease genes. The...”
- 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_0167 sak_0168 sak_0169 sak_0207 sak_0208 sak_0209 sak_0210 sak_0302 sak_0303 sak_0472 sak_0561 sak_0562 sak_0795 sak_0796 sak_0899 sak_0900 sak_0901...”
- Genomic characterisation of perinatal Western Australian Streptococcus agalactiae isolates
Furfaro, PloS one 2019 - “...only represented by capsular genotypes IaVI. Eleven surface protein genes were assessed, with fibrinogen-binding protein (SAG0152), laminin-binding protein (SAG01234), and serine peptidase (SAG1236) detected in 98% of all sequences. To a lesser extent, bac (SAG2195) was detected in 15.7% and rib (SAG0433) in 27.8% of isolates....”
- RovS and its associated signaling peptide form a cell-to-cell communication system required for Streptococcus agalactiae pathogenesis
Pérez-Pascual, mBio 2015 - “...uptake is undertaken by a single oligopeptide ABC transporter system: oppA1-F (encoded by gbs0144 to gbs0148 in strain NEM316) ( 22 , 28 ). We inactivated the Opp system by deleting the oppB gene and then transferred the plasmid P shp into this strain, thus producing...”
- Transcriptome adaptation of group B Streptococcus to growth in human amniotic fluid
Sitkiewicz, PloS one 2009 - “...system gbs0146 oppC 8.0 Oligopeptide transport system gbs0147 oppD 2.2 9.0 4.1 Oligopeptide transport system gbs0148 oppF 2.1 9.7 2.6 Oligopeptide transport system gbs0966 oppA 23.2 Oligopeptide-binding protein oppA gbs1513 2.5 Di- tripeptide transporter Branched chains amino acids gbs1627 16.3 319.3 gbs1628 14.5 502.1 ATP-binding protein...”
- Relevance of peptide uptake systems to the physiology and virulence of Streptococcus agalactiae
Samen, Journal of bacteriology 2004 - “...transporters are encoded by the genes gbs0144 to gbs0148, gbs0184 to gbs0188, and gbs1573 to gbs1577. According to the functional analysis of these genes...”
SSO2615 Dipeptide ABC transporter ATP binding protein (dppF-3) from Sulfolobus solfataricus P2
36% identity, 94% coverage
VK055_1971 ABC transporter ATP-binding protein from Klebsiella pneumoniae subsp. pneumoniae
36% identity, 90% coverage
- A Serendipitous Mutation Reveals the Severe Virulence Defect of a Klebsiella pneumoniae fepB Mutant
Palacios, mSphere 2017 - “...protein VK055_1973 Binding-protein-dependent transport system inner membrane component VK055_1972 Binding-protein-dependent transport system inner membrane component VK055_1971 Oligopeptide/dipeptide ABC transporter, ATP binding VK055_1970 Oligopeptide/dipeptide ABC transporter, ATP binding VK055_1969 Amidase. Hydatoinase/carbamoylase family protein VK055_1968 EamA-like transporter family protein VK055_1967 Bacterial transcriptional regulator, GntR family protein VK055_1966 Bacterial...”
TC 3.A.1.5.18 / O31310 OppF, component of The oligopeptide transporter OppA1-5, B1, C1, DF (functions with five binding proteins of differing induction properties and peptide specificities; OppA1-3 are chromosomally encoded; OppA4 and 5 are plasmid encoded.) from Borrelia burgdorferi (Lyme disease spirochete) (see 2 papers)
BB0335 oligopeptide ABC transporter, ATP-binding protein (oppF) from Borrelia burgdorferi B31
BB_0335 ATP-binding cassette domain-containing protein from Borreliella burgdorferi B31
40% identity, 95% coverage
- substrates: Oligopeptides
- Peptide Uptake Is Essential for Borrelia burgdorferi Viability and Involves Structural and Regulatory Complexity of its Oligopeptide Transporter
Groshong, mBio 2017 - “...F and pless Erm R); Erm r -positive clones were subsequently screened using bb0334 and bb0335 flanking primers 5 bb0334-35 null F1 and 3 bb0334-35 null F2. A positive clone with wild-type plasmid content ( Bb AG132) was further confirmed to carry p Ec AG137 by...”
- Correction: Characterization of the RelBbu regulon in Borrelia burgdorferi reveals modulation of glycerol metabolism by (p)ppGpp
PLOS, PloS one 2015 - “...-4.07 0.015 BB0334 oligopeptide ABC transporter, ATP-binding protein ( oppD ) -3.25 0.006 -1.21 0.002 BB0335 oligopeptide ABC transporter, ATP-binding protein ( oppF ) -1.51 <0.001 BBB04 chitobiose transporter protein ( chbC ) 1.83 0.004 2.11 <0.001 BBB05 chitobiose transporter protein ( chbA ) 4.05 0.013...”
- Characterization of the RelBbu Regulon in Borrelia burgdorferi Reveals Modulation of Glycerol Metabolism by (p)ppGpp
Bugrysheva, PloS one 2015 - “...-4.07 0.015 BB0334 oligopeptide ABC transporter, ATP-binding protein ( oppD ) -3.25 0.006 -1.21 0.002 BB0335 oligopeptide ABC transporter, ATP-binding protein ( oppF ) -1.51 <0.001 BBB04 chitobiose transporter protein ( chbC ) 1.83 0.004 2.11 <0.001 BBB05 chitobiose transporter protein ( chbA ) 4.05 0.013...”
- “...during the exponential phase, while many more of the genes of this transporter (BB0328-BB330, BB0334, BB0335) decreased in the mutant during stationary phase ( Table 1 , S1 Table , S2 Table ). Expression of HMG-CoA synthase ( hmgs , BB0683) was increased in the rel...”
- Stage-specific global alterations in the transcriptomes of Lyme disease spirochetes during tick feeding and following mammalian host adaptation
Iyer, Molecular microbiology 2015 - “...(OppB1 [BB0332]/OppC1 [BB0333] and OppB2 [BB0747]/OppC2 [BB0746]) and two ATP-binding proteins OppD (BB0334) and OppF (BB0335). The system also contains five distinct oligopeptide-binding lipoproteins (OppA1-OppA5). The genes encoding OppA1-A3 ( bb0328, bb0329, bb0330 ) are immediately upstream of oppB1 and oppC1 , while those for OppA4...”
- BosR (BB0647) governs virulence expression in Borrelia burgdorferi
Ouyang, Molecular microbiology 2009 - “..., encodes a glucosamine-6-phosphate isomerase), and oligopeptide ABC transporter encoding genes bb0333 (oppC-1 ) and bb0335 ( oppF ). BosR controls the expression of OspC and DbpA in Bb The above microarray analysis suggested that ospC, dbp A and rpoS were regulated by BosR. To further...”
- Identification of Borrelia burgdorferi ribosomal protein L25 by the phage surface display method and evaluation of the protein's value for serodiagnosis
Mueller, Journal of clinical microbiology 2006 - “...sequences of B. burgdorferi B31, namely, BB0182, BB0272, BB0335, BB0371, BB0713, BB0786, BBA26, BBK32, and BBL38. One sequence encoded the fibronectin binding...”
- Comparative transcriptional profiling of Borrelia burgdorferi clinical isolates differing in capacities for hematogenous dissemination
Ojaimi, Infection and immunity 2005 - “...as operons. The chromosomal region between BB0328 and BB0335 contains genes encoding components of an oligopeptide permease (Opp). These ABC transporter systems...”
- “...OppA-1, OppA-2, and OppA-3, respectively; BB0332 to BB0335 encode the transmembrane and ATP-binding components of the transporter. BBB16 (on plasmid cp26)...”
- Combined effects of blood and temperature shift on Borrelia burgdorferi gene expression as determined by whole genome DNA array
Tokarz, Infection and immunity 2004 - “...BB0562 hypothetical protein BBG18 hypothetical protein BB0335 ABC transporter, ATP-binding protein (OppF) BBK22 conserved hypothetical protein BB116...”
- More
- The Functional and Molecular Effects of Doxycycline Treatment on Borrelia burgdorferi Phenotype
Caskey, Frontiers in microbiology 2019 - “...65.4991 -2.049111687 0.65 -3 0.001751913 0.044454875 BB_0417 Adenylate kinase 112.5984 -2.048758137 0.62 -3 0.000994892 0.032295719 BB_0335 Peptide ABC transporter ATP-binding protein (OppF) 143.0424 -2.046159104 0.63 -3 0.001064589 0.033694243 BB_0843 Arginine-ornithine antiporter 351.7582 -1.950882657 0.64 -3 0.002298966 0.048508182 BB_0729 Dicarboxylate/amino acid:cation symporter 214.2514 -1.912156352 0.62 -3 0.002113701...”
- “...10027.5 2.016905 0.60385 -3.34008 0.000838 0.054598 BB_0839 Hypothetical protein 66.6184 2.004598 0.587771 -3.41051 0.000648 0.045087 BB_0335 Peptide ABC transporter ATP-binding protein (OppF) 133.4096 1.94966 0.550044 -3.54455 0.000393 0.029299 BB_0334 Peptide ABC transporter ATP-binding protein (OppD) 174.8033 1.828725 0.554848 -3.2959 0.000981 0.060191 Down-regulated in Regrown versus Treated...”
LS25_0754 ABC transporter ATP-binding protein from Latilactobacillus sakei subsp. sakei 23K
LSA0706 Oligopeptide ABC transporter, ATP-binding subunit from Lactobacillus sakei subsp. sakei 23K
39% identity, 83% coverage
- Effects of glucose availability in Lactobacillus sakei; metabolic change and regulation of the proteome and transcriptome
McLeod, PloS one 2017 - “...Oligopeptide ABC transporter ATP-binding subunit ( oppD ) -4.10 -3.91 0.70 -0.71 -0.79 -0.68 LCA_0706 LS25_0754 Oligopeptide ABC transporter ATP-binding subunit ( oppF ) -4.31 -4.11 0.69 -0.71 -0.79 -0.66 LCA_0788 LS25_0881 Putative MIP family facilitator protein -3.81 -1.91 0.61 -0.63 -0.70 -0.61 LCA_0790 LS25_0883 Hypothetical...”
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...ABC transporter, membrane-spanning subunit 1.8 1.0 LSA0705 oppD Oligopeptide ABC transporter, ATP-binding subunit 1.2 1.1 LSA0706 oppF Oligopeptide ABC transporter, ATP-binding subunit 1.2 1.2 Protein fate LSA0053 pepO Endopeptidase O 0.6 LSA0133 pepR Prolyl aminopeptidase 1.5 LSA0226 pepN Aminopeptidase N (lysyl-aminopeptidase-alanyl aminopeptidase) -0.7 LSA0285 pepF1 Oligoendopeptidase...”
- Analysis of Lactobacillus sakei mutants selected after adaptation to the gastrointestinal tracts of axenic mice
Chiaramonte, Applied and environmental microbiology 2010 - “...the response to oxidative stresses. Five proteins (LSA0705, LSA0706, LSA0938, LSA0616, and LSA1366) are components of ABC TABLE 2. Growth characteristics of L....”
- “...RNA methyltransferase LSA0836 LSA0705 0.004 0.022 2.1 3.5 LSA0706 0.007 3.4 LSA0938 0.026 3.3 LSA0616 0.023 3.1 LSA0104 LSA0030 LSA1712 LSA1779 LSA1134 LSA1426...”
PF0193 putative ABC transport ATP binding protein from Pyrococcus furiosus DSM 3638
36% identity, 97% coverage
VP_RS15290 ATP-binding cassette domain-containing protein from Vibrio parahaemolyticus RIMD 2210633
41% identity, 81% coverage
- Comparative Transcriptome Analysis Reveals Regulatory Factors Involved in Vibrio Parahaemolyticus Biofilm Formation
Wang, Frontiers in cellular and infection microbiology 2022 - “...transporter substrate-binding protein VP_RS06515 4.77 ATP-binding cassette domain-containing protein VP_RS06520 4.32 ATP-binding cassette domain-containing protein VP_RS15290 3.21 ABC transporter ATP-binding protein ribA 2.91 GTP cyclohydrolase II VP_RS02600 2.87 3-deoxy-7-phosphoheptulonate synthase lepB 2.35 signal peptidase I VP_RS16920 2.34 ABC transporter ATP-binding protein VP_RS20695 2.30 ABC transporter ATP-binding...”
LGG_01940 oligopeptide ABC transporter, ATPase component, oppF from Lactobacillus rhamnosus GG
LGG_01940 ATP-binding cassette domain-containing protein from Lacticaseibacillus rhamnosus GG
38% identity, 93% coverage
Q03PP1 ABC-type oligopeptide transport system, ATPase component from Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947)
38% identity, 86% coverage
NCgl1918 ABC transporter ATP-binding protein from Corynebacterium glutamicum ATCC 13032
cg2184 peptide ABC transporter ATPase from Corynebacterium glutamicum ATCC 13032
42% identity, 44% coverage
- Anaerobic growth of Corynebacterium glutamicum via mixed-acid fermentation
Michel, Applied and environmental microbiology 2015 - “...transporters Cg2181 Cg2182 Cg2183 Cg2184 NCgl1915 NCgl1916 NCgl1917 NCgl1918 77 77 77 77 Cg2549 NCgl2238 Cg2550 NCgl2239 Cg2551 NCgl2240 Cg2552 NCgl2241 Cg2675...”
- The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress
Schelder, PloS one 2011 - “...transport system, permease component 0.22 cg2183 NCgl1917 ABC-type peptide transport system, permease component 0.20 cg2184 NCgl1918 ABC-type peptide transport system, ATPase component 0.19 cg2610 NCgl2294 ABC-type transport system, secreted component 0.34 cg3320 NCgl2891 ABC-type transporter, permease component 0.20 cg3404 NCgl2970 secreted siderophore-binding lipoprotein 0.26 Other cg0414...”
- Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA
Brocker, Journal of bacteriology 2009 - “...NCgl0524 NCgl2808 NCgl2201 NCgl1915 NCgl1916 NCgl1917 NCgl1918 NCgl2131 NCgl0629 NCgl0630 NCgl2563 NCgl2565 NCgl2476 NCgl2477 NCgl2656 NCgl2657 NCgl0805...”
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...NCgl1521 NCgl1875 NCgl1876 NCgl1877 NCgl1878 NCgl1915 NCgl1917 NCgl1918 Acc. no. 2394 SILBERBACH ET AL. APPL. ENVIRON. MICROBIOL. TABLE 1--Continued NCBI no....”
- Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine
Lange, Applied and environmental microbiology 2003 - “...NCgl1916 2095b NCgl1917 2096b 2280b 2281b 2425 2453b NCgl1918 NCgl2086 (2274263-2274442) NCgl1482 NCgl1502 2455b NCgl1503 b 2456 NCgl1504 2736 2790b 2791b 2792b...”
- Adaptive evolution and metabolic engineering of a cellobiose- and xylose- negative Corynebacterium glutamicum that co-utilizes cellobiose and xylose
Lee, Microbial cell factories 2016 - “...found in genes encoding for putative proteins, phage integrase, ATPase component of ABC-type transport system (Cg2184), GTPase, tranposase (Cg2461), and intergentic regions. Thus, we searched the identical genetic variants in between Cg - Cello01(evo) and Cg - Cello02(evo) strains. Finally, 10 identical genetic variants were identified...”
- Anaerobic growth of Corynebacterium glutamicum via mixed-acid fermentation
Michel, Applied and environmental microbiology 2015 - “...77 Putative peptide ABC transporters Cg2181 Cg2182 Cg2183 Cg2184 NCgl1915 NCgl1916 NCgl1917 NCgl1918 77 77 77 77 Cg2549 NCgl2238 Cg2550 NCgl2239 Cg2551 NCgl2240...”
- Maltose uptake by the novel ABC transport system MusEFGK2I causes increased expression of ptsG in Corynebacterium glutamicum
Henrich, Journal of bacteriology 2013 - “...criteria and identified two clusters of genes, cg2181 to cg2184 and cg2703 to cg2708, which indeed encode putative ABC transporters and which were repressed in...”
- “...when cultivated with glucose. As the cluster cg2181 to cg2184 is annotated as a peptide uptake system (25), we focused on the investigation of the cluster...”
- IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria
Baumgart, BMC biology 2013 - “...(cg3195), a hypothetical endoglucanase (cg2896), and two further transporters (cg0621 to cg0623 and cg2181 to cg2184) (Additional file 1 : Table S3). Among the strongly upregulated genes was a cluster encoding enzymes for inositol catabolism (cg3389 to cg3392), an operon encoding both menE and a putative...”
- Transcriptional regulation of the operon encoding stress-responsive ECF sigma factor SigH and its anti-sigma factor RshA, and control of its regulatory network in Corynebacterium glutamicum
Busche, BMC genomics 2012 - “...Putative secondary C4-dicarboxylate transporter, tripartite ATP-independent transporter (TRAP-T) family 1.58 cg0699 guaB2 IMP dehydrogenase 1.56 cg2184 ABC-type putative dipeptide/oligopeptide transporter, ATPase subunit 1.56 cg3077 Putative membrane protein 1.56 cg1410* rbsR Transcriptional repressor of ribose importer RbsACBD, LacI-family 1.54 cg1464 Putative transcriptional regulator, HTH_3-family 1.52 a Genes...”
- The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress
Schelder, PloS one 2011 - “...peptide transport system, permease component 0.22 cg2183 NCgl1917 ABC-type peptide transport system, permease component 0.20 cg2184 NCgl1918 ABC-type peptide transport system, ATPase component 0.19 cg2610 NCgl2294 ABC-type transport system, secreted component 0.34 cg3320 NCgl2891 ABC-type transporter, permease component 0.20 cg3404 NCgl2970 secreted siderophore-binding lipoprotein 0.26 Other...”
- Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA
Brocker, Journal of bacteriology 2009 - “...cg2966 cg1255 cg0638 cg3216 cg2504 cg2181 cg2182 cg2183 cg2184 cg3151 cg0759 cg0760 cg0762 cg2938 cg2940 cg2836 cg2837 cg3047 cg3048 cg0961 cg2426 cg1612 cg2610...”
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...cg1066 cg1537 cg1785 cg2136 cg2137 cg2138 cg2139 cg2181 cg2183 cg2184 Gene name cmTb urtAc urtBc urtCc urtDc urtEc ptsG amtA gluA gluB gluC gluD b vs clow...”
HVO_RS20010 ABC transporter ATP-binding protein from Haloferax volcanii DS2
39% identity, 84% coverage
- Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii
Gelsinger, Journal of bacteriology 2018 - “...transposase/pseudoregion (HVO_RS19935), an IS 4 family transposase (HVO_RS03870), (HVO_RS07060), and an ABC transporter ATP-binding protein (HVO_RS20010). Of these most highly expressed sRNAs, 3 asRNAs (STRG.2050.2, STRG.3974.5, and STRG.4700.1) targeted the same mRNAs, and 3 intergenic sRNAs (STRG.3072.1, STRG.2702.1, and STRG.2983.4) were expressed under both the no-challenge...”
Bbr_1202 dipeptide ABC transporter ATP-binding protein from Bifidobacterium breve UCC2003
41% identity, 38% coverage
- Bifidobacterial biofilm formation is a multifactorial adaptive phenomenon in response to bile exposure
Kelly, Scientific reports 2020 - “...0.000906418 Bbr_0329 ATP synthase beta chain 1.42 0.000860229 Bbr_0328 ATP synthase gamma chain 1.41 0.000351287 Bbr_1202 Oligopeptide transport ATP-binding protein oppD 1.28 0.001120451 Bbr_0371 Polyribonucleotide nucleotidyltransferase 1.23 0.000351287 Bbr_0776 Xylulose-5-phosphate/Fructose-6-phosphate phosphoketolase 1.13 0.00154578 Locus tag Putative function Fold change in expression (downregulation) P-value Bbr_0579 Solute binding...”
- “...production (Bbr_328/329), iron-sulfur metabolism (Bbr_0911) and an ATP component of the oligopeptide nucleotide transporter OppD (Bbr_1202). Whether or not the genes involved in bile resistance and genes involved in biofilm formation are interconnected remains to be seen. Therefore, we decided to investigate which genes are involved...”
Bd1221 ABC-type dipeptide transport system, ATPase component from Bdellovibrio bacteriovorus HD100
41% identity, 45% coverage
- The first bite--profiling the predatosome in the bacterial pathogen Bdellovibrio
Lambert, PloS one 2010 - “...and export and solute uptake via, in some cases ATP-dependent ABC transporters such as Bd0995, Bd1221 and Bd3637. GroES- EL chaperone and Bd3764 trigger factor [18] genes are up-regulated to assist with the waves of protein synthesis that occur and a few genes associated with cell...”
- “...in the genome were up-regulated in both HI and predatory datasets, Bd2512 for glycerol-3-phosphate transport, Bd1221 for dipeptide transport and two other ABC transporters. It seems likely that many more will be up-regulated in the predatory state soon after the 30 minute point as breakdown products...”
NP_387225 PUTATIVE PEPTIDE TRANSPORT SYSTEM ATP-BINDING ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
37% identity, 49% coverage
OPPF_BACSU / P24137 Oligopeptide transport ATP-binding protein OppF; Stage 0 sporulation protein KE; EC 7.4.2.6 from Bacillus subtilis (strain 168) (see 3 papers)
39% identity, 83% coverage
- function: Part of the ABC transporter complex OppABCDF involved in the uptake of oligopeptides (PubMed:1901616). Probably responsible for energy coupling to the transport system (Probable). Required for genetic competence but not for peptide transport or for sporulation (PubMed:1899858, PubMed:1901616).
catalytic activity: a [peptide](out) + ATP + H2O = a [peptide](in) + ADP + phosphate + H(+) (RHEA:78459)
subunit: The complex is composed of two ATP-binding proteins (OppD and OppF), two transmembrane proteins (OppB and OppC) and a solute-binding protein (OppA).
disruption phenotype: Inactivation of the gene does not affect the sporulation process but causes a defect in competence (PubMed:1899858, PubMed:1901616). Disruption does not affect resistance to bialaphos (PubMed:1901616). - Lipoproteins in Gram-Positive Bacteria: Abundance, Function, Fitness
Nguyen, Frontiers in microbiology 2020 - “...and OppD. 3D crystal model of OppF was downloaded from protein data bank (SMR ID: P24137) and visualized in PyMoL software ( DeLano, 2009 ). The Phyre2 predition showed 6 transmembrane motifs in both OppB and OppC ranging from 6 to 297 amino acids in OppB...”
- Membrane Proteomes and Ion Transporters in Bacillus anthracis and Bacillus subtilis Dormant and Germinating Spores
Chen, Journal of bacteriology 2019 - “...P16450 O32167 Q01625 P94360 P24141 P24138 P24139 P24136 P24137 P38050 Q45064 P39793 P24327 P20166 P46911 P46912 P34957 P36947 P35160 O32047 P16336 P40868 P40869...”
- Extracellular vesicle proteomes reflect developmental phases of Bacillus subtilis
Kim, Clinical proteomics 2016 - “...R sc a FDR Biological process annotation P19405 Alkaline phosphatase 3 7.1 2.32E38 Metabolic process P24137 Oligopeptide transport ATP-binding protein OppF (Stage 0 sporulation protein KE spo0KE) 5.8 9.84E16 Sporulation P71021 Septum site-determining protein DivIVA c 3.8 3.88E10 Sporulation P54375 Superoxide dismutase 2.2 2.63E04 Stress response...”
- The adherence-associated lipoprotein P100, encoded by an opp operon structure, functions as the oligopeptide-binding domain OppA of a putative oligopeptide transport system in Mycoplasma hominis
Henrich, Journal of bacteriology 1999 - “...B. subtilis, P24141, P24138, P24139, P24136, and P24137; S. typhimurium, P06202, P08006, P08066, P04285, and P08007; and Haemophilus influenzae, P44572, P45054,...”
lmo2192 similar to oligopeptide ABC transporter (ATP-binding protein) from Listeria monocytogenes EGD-e
LMON_2268 ABC transporter ATP-binding protein from Listeria monocytogenes EGD
39% identity, 82% coverage
- Listeria monocytogenes utilizes glutathione and limited inorganic sulfur compounds as sources of essential cysteine
Berude, Infection and immunity 2024 (secret) - Transcriptomic analysis of Listeria monocytogenes biofilm formation at different times
Gou, Canadian journal of veterinary research = Revue canadienne de recherche veterinaire 2023 - “...upregulated DEGs were lmo0024, lmo0374, lmo0544, hly, and lmo2434. The top 5 downregulated DEGs were lmo2192, lmo1211, cheY, lmo0689, and secY. After real-time quantitative polymerase chain reaction, the expression of these 10 DEGs were consistent with the results of the transcriptomic sequence. This research lays the...”
- A comprehensive investigation of protein expression profiles in L. monocytogenes exposed to thermal abuse, mild acid, and salt stress conditions
D'Onofrio, Frontiers in microbiology 2023 - “...OppA ( lmo2196 ), OppC ( lmo2194 ), OppD ( lmo2193 ), and OppF ( lmo2192 ): they are peptide transporter subunits implicated in virulence gene expression as part of cell-to-cell signaling regulation. In fact, OppD seems to be involved in biofilm formation and virulence pathways....”
- Deletion of the oligopeptide transporter Lmo2193 decreases the virulence of Listeria monocytogenes
Li, Journal of veterinary science 2020 - “...15 new putative virulence factors, including Opp that is potentially coded in 2 putative genes: lmo2192 and lmo2193 . The RAST annotation of Lmo2192 is OppF, however the function of lmo2193 is unknown, as no RAST annotation exists [ 10 ]. Studies indicate that Opp in...”
- “...transporter [ 22 ], however, research on pathogenicity has not been reported. Maury assumed the lmo2192 gene function as OppF [ 10 ]. The OppD gene in L. monocytogenes has not yet been described or reported. The oligopeptide transport system OppABCDF is one of the main...”
- Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
Hingston, PloS one 2017 - “...opuCA lmo1428 10 2.63 5.54 3.94 1.30 -0.01 LMON_2268 Oligopeptide transport ATP-binding protein OppF oppF lmo2192 2 -0.56 -0.61 -0.43 -0.39 1.39 LMON_2269 Oligopeptide transport ATP-binding protein OppD oppD lmo2193 2 -0.59 -0.74 -0.38 -0.30 0.91 LMON_2270 Oligopeptide transport system permease protein OppC oppC lmo2194 15*...”
- Characterisation of the transcriptomes of genetically diverse Listeria monocytogenes exposed to hyperosmotic and low temperature conditions reveal global stress-adaptation mechanisms
Durack, PloS one 2013 - “...1.47 *** 1.66 *** 1.48 *** 1.44 *** 1.51 *** similar to uncharacterized conserved proteins lmo2192 oppE 2.11 *** 1.18* 2.26 *** 1.15 * 1.63 *** 1.85 *** similar to oligopeptide ABC transporter, ATP binding protein lmo2194 oppC 1.44 ** 1.82 * 1.46 *** 1.31 *...”
- 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 - “...gene (lmo2163 gfo), ATP-binding ABC component gene (lmo2192 oppF), glucose-6phosphate isomerase gene (lmo2367 pgi) lmo0001 (dnaA), lmo0243 (sigH), bkd operon...”
- “...negative enrichment for the Hpr gene set (lmo2192 oppF, lmo0593) codY, branched-chain amino acid biosynthesis genes (ilvBN, leuA) lmo0002 (dnaN), lmo0890...”
- Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling
Schauer, BMC genomics 2010 - “...rf 3.4 0 5 lmo0221 hypothetical type III pantothenate kinase possible 6.9 1.0 1,3 oppF (lmo2192) oligopeptide ABC-transporter, ATP-binding protein no 21.0 8.0/4.0 1,3 pdxK (lmo0662) pyridoxine kinase no 13.1 1/4.0 lmo2227 ABC transporter, ATP-binding protein possible 5.8 1.3 lmo1043 molybdopterin-guanine dinucleotide biosynthesis MobB rf 7.9...”
- “...gene This study EGD oppF in-frame deletion mutant of the putative oligopeptide ABC transporter gene lmo2192 This study EGDlmo2734 in-frame deletion mutant of lmo2734 encoding a putative sugar hydrolase This study EGDlmo2781 in-frame deletion mutant of lmo2781 involved in cellobiose metabolism This study pLSV101 Temperature-sensitive shuttle...”
- Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
Hingston, PloS one 2017 - “...activated L-carnitine/choline ABC transporter, ATP-binding protein OpuCA opuCA lmo1428 10 2.63 5.54 3.94 1.30 -0.01 LMON_2268 Oligopeptide transport ATP-binding protein OppF oppF lmo2192 2 -0.56 -0.61 -0.43 -0.39 1.39 LMON_2269 Oligopeptide transport ATP-binding protein OppD oppD lmo2193 2 -0.59 -0.74 -0.38 -0.30 0.91 LMON_2270 Oligopeptide transport...”
OENOO_30005 ABC-type oligopeptide transport system, ATP-binding cassette from Oenococcus oeni ATCC BAA-1163
39% identity, 82% coverage
APZ00_22975 ABC transporter ATP-binding protein from Pannonibacter phragmitetus
38% identity, 50% coverage
BBMN68_280 dipeptide ABC transporter ATP-binding protein from Bifidobacterium longum subsp. longum BBMN68
BL1390 DppD from Bifidobacterium longum NCC2705
41% identity, 38% coverage
HP0302 dipeptide ABC transporter, ATP-binding protein (dppF) from Helicobacter pylori 26695
O25073 Dipeptide ABC transporter, ATP-binding protein (DppF) from Helicobacter pylori (strain ATCC 700392 / 26695)
40% identity, 82% coverage
- Identification of an Essential LolD-Like Protein in Helicobacter pylori
McClain, Journal of bacteriology 2023 (secret) - The Role of a Dipeptide Transporter in the Virulence of Human Pathogen, Helicobacter pylori
Xu, Frontiers in microbiology 2021 - “...HP0297 rpmA 1.4635 HP0298 dppA 4.9784 HP0299 dppB 1.4717 HP0300 dppC 2.088 HP0301 dppD 2.4619 HP0302 dppF 2.0374 HP0303 obgE A-3.1174 HP0304 Predicted gene 2.0838 HP0318 Predicted gene 1.2903 HP0364 nrdF 1.1763 HP0377 dsbC 1.3781 HP0378 ycf5 1.1151 HP0390 tagD 2.3061 HP0415 Predicted gene 2.9304 HP0514...”
- Delineation of the pH-Responsive Regulon Controlled by the Helicobacter pylori ArsRS Two-Component System
Loh, Infection and immunity 2021 (secret) - The orphan response regulator HP1021 of Helicobacter pylori regulates transcription of a gene cluster presumably involved in acetone metabolism
Pflock, Journal of bacteriology 2007 - “...JHP0285 JHP1235 JHP1236 JHP1238 JHP1239 JHP1445 JHP1444 HP0302 Transport and binding proteins HP0140 HP0299 HP0300 HP1315 HP1316 HP1318 HP1319 HP1554 HP1555...”
- Acid-adaptive genes of Helicobacter pylori
Wen, Infection and immunity 2003 - “...1.41 1.00 4.04 HP0301 0.93 0.94 0.96 1.01 1.09 1.00 2.84 HP0302 0.99 1.06 0.97 0.95 1.16 0.93 1.04 1.56 1.04 1.01 1.23 1.33 1.32 1.82 2.03 1.10 1.67 2.20 4.02...”
- “...chemotaxis protein gene; trbB (HP1421), a virB11 homolog; dppF (HP0302), a dipeptide transporter gene; and ureI (HP0071), the urea channel, were all found to be...”
- Metabolism and genetics of Helicobacter pylori: the genome era
Marais, Microbiology and molecular biology reviews : MMBR 1999 - “...orthologues are HP0301 to dppD from B. subtilis, and HP0302 and HP0298 to dppF and dppA from E. coli; the genes encoding dipeptide ABC transporter permease...”
- Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
Wei, ACS omega 2022 - “...O25762 HP_1143 252 P66637 HP_1143 253 O26039 plsY 254 O24864 CheV 255 O26052 HP_1524 256 O25073 DppF 257 O24999 mrp 258 O25684 HP_1043 259 P56041 rplP 260 O25288 HP_0564 261 P56039 rplN 262 O25930 BamD 263 O24951 HP_0139 264 O25089 HP_0322 265 O25426 HP_0726 266 O25116...”
HPG27_RS01515 ABC transporter ATP-binding protein from Helicobacter pylori G27
jhp0287 DIPEPTIDE TRANSPORT SYSTEM ATP-BINDING PROTEIN from Helicobacter pylori J99
40% identity, 82% coverage
PIB40_08925 dipeptide ABC transporter ATP-binding protein from Bifidobacterium longum
41% identity, 38% coverage
OENOO_31006 ABC-type oligopeptide transport system, ATP-binding cassette from Oenococcus oeni ATCC BAA-1163
40% identity, 84% coverage
IMZ28_RS09850 ABC transporter ATP-binding protein from Sulfurovum indicum
44% identity, 47% coverage
SSU1662 oligopeptide transport ATP-binding protein OppF from Streptococcus suis P1/7
SSU05_1866 ABC-type oligopeptide transport system, ATPase component from Streptococcus suis 05ZYH33
40% identity, 90% coverage
spr1703 ABC transporter ATP-binding protein - oligopeptide transport from Streptococcus pneumoniae R6
40% identity, 91% coverage
WP_186292434 ABC transporter ATP-binding protein from Cardinium endosymbiont of Dermatophagoides farinae
33% identity, 96% coverage
IYO_RS15145 ABC transporter ATP-binding protein from Pseudomonas syringae pv. actinidiae ICMP 18884
37% identity, 85% coverage
F9UN55 Oligopeptide ABC transporter, ATP-binding protein from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
lp_1265 oligopeptide ABC transporter, ATP-binding protein from Lactobacillus plantarum WCFS1
37% identity, 83% coverage
SPD_1667 oligopeptide ABC transporter, ATP-binding protein AmiF from Streptococcus pneumoniae D39
40% identity, 94% coverage
SP_RS09375 ATP-binding cassette domain-containing protein from Streptococcus pneumoniae TIGR4
SP_1887 oligopeptide ABC transporter, ATP-binding protein AmiF from Streptococcus pneumoniae TIGR4
40% identity, 94% coverage
- Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci
Alcorlo, PLoS pathogens 2024 - “...substrates across the membrane. In addition, two ATPases, namely AmiE (SP_1881/ SP_RS09380) and AmiF (SP_1887/ SP_RS09375), are positioned at the cytosolic face of the membrane, orchestrating substrate transport through the ATP hydrolysis. The Ami system is completed by the presence of the SBP AmiA (SP_1891/ SP_RS09395),...”
- Molecular and Structural Basis of Oligopeptide Recognition and Transport by the Ami Transporter System in Pneumococci
Alcorlo, 2023 - The Streptococcus pneumoniae transcriptome in patient cerebrospinal fluid identifies novel virulence factors required for meningitis
Wall, 2024 - Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae
Nishimoto, Cell reports 2022 - “...a tool for other strain backgrounds, more of the transposase between treR (Sp_1885) and amiF (Sp_1887) was excluded than in previous publications in order to increase the homology shared in other strains (D39, BHN97). 52 , 56 These amplicons were spliced with the PhunSweetErm cassette with...”
- Genome-wide identification of Streptococcus pneumoniae genes essential for bacterial replication during experimental meningitis
Molzen, Infection and immunity 2011 - “...protein 0.8ns 2.3 0.2 Transport and binding SP_0321 SP_1715 SP_1887 SP_2037 amiF a ns , not significant; NA, not available. genes, respectively (Fig. 3A). Genes...”
- Site-specific contributions of glutamine-dependent regulator GlnR and GlnR-regulated genes to virulence of Streptococcus pneumoniae
Hendriksen, Infection and immunity 2008 - “...SP_1817 SP_1869 SP_1870 SP_1871 SP_1872 SP_1887 SP_1888 SP_1889 SP_1890 Gene name Annotation Ratiob purC Phosphoribosylaminoimidazole-succinocarboxamide...”
SPSF3K_00634 ATP-binding cassette domain-containing protein from Streptococcus parauberis
39% identity, 93% coverage
TC 3.A.1.5.8 / Q97UG5 MalK, component of Maltose and maltooligosaccharide porter from Sulfolobus solfataricus (see paper)
SSO3055 Maltose ABC transporter, ATP-binding protein from Sulfolobus solfataricus P2
40% identity, 41% coverage
TC 3.A.1.5.12 / Q9X0F3 TM1063, component of Probable rhamnose oligosaccharide porter. Induced by rhamnose (see paper)
TM1063 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
39% identity, 91% coverage
SSO1276 Oligo/dipeptide transport, ATP binding protein (dppD-1) from Sulfolobus solfataricus P2
39% identity, 97% coverage
MCA1268 peptide ABC transporter, ATP-binding protein from Methylococcus capsulatus str. Bath
42% identity, 47% coverage
SSO1277 Oligo/dipeptide transport, ATP binding protein (dppF-1) from Sulfolobus solfataricus P2
37% identity, 95% coverage
RL3798 putative ATP-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
44% identity, 45% coverage
SERP0573 oligopeptide ABC transporter, ATP-binding protein OppF from Staphylococcus epidermidis RP62A
42% identity, 81% coverage
BMEI0438 DIPEPTIDE TRANSPORT ATP-BINDING PROTEIN DPPF from Brucella melitensis 16M
42% identity, 81% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...system IM BMEI1139, LolE BruAb10837, LolE BR0823, LolE BOV_0817 BCAN_A0838 64 OPN Dipeptide import ABC BMEI0438, dppF BruAb11569 BR1582 BOV_1527 BCAN_A1617 OPN Dipeptide import ABC BMEI0437, dppD BruAb11570 BR1583 BOV_1528 BCAN_A1618 OPN Dipeptide import IM BMEI0435, dppC BruAb11571 BR1584 BOV_1530 BCAN_A1620 OPN Dipeptide import IM BMEI0436,...”
SMc02424 PUTATIVE OLIGOPEPTIDE TRANSPORT ATP-BINDING ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
37% identity, 89% coverage
Fphi_1029 peptide/opine/nickel uptake transporter (PepT) family protein from Francisella philomiragia subsp. philomiragia ATCC 25017
34% identity, 96% coverage
- Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources
Siddaramappa, BMC genomics 2012 - “...2e-84 Fphi_1027 (219 aa) Oligopeptide transport system permease protein (OppD) CV_4326, 333 aa, 61%, 3e-137 Fphi_1029 (324 aa) Oligopeptide transport ATP-binding protein (OppF) NT05HA_1387, 332 aa, 58%, 5e-105 Glucuronate metabolism 3 F7308_1388 (520 aa) Rhamnogalacturonide transporter (RhiT) KPK_1307, 502 aa, 44%, 2e-116 F7308_1389 (776 aa) Alpha-glucosidase...”
HSISS4_01361 ATP-binding cassette domain-containing protein from Streptococcus salivarius
40% identity, 94% coverage
BR1582 dipeptide ABC transporter, ATP-binding protein, putative from Brucella suis 1330
BCAN_A1617 hypothetical protein from Brucella canis ATCC 23365
42% identity, 81% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...LolE BruAb10837, LolE BR0823, LolE BOV_0817 BCAN_A0838 64 OPN Dipeptide import ABC BMEI0438, dppF BruAb11569 BR1582 BOV_1527 BCAN_A1617 OPN Dipeptide import ABC BMEI0437, dppD BruAb11570 BR1583 BOV_1528 BCAN_A1618 OPN Dipeptide import IM BMEI0435, dppC BruAb11571 BR1584 BOV_1530 BCAN_A1620 OPN Dipeptide import IM BMEI0436, dppC BruAb11572 BR1585...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...LolE BR0823, LolE BOV_0817 BCAN_A0838 64 OPN Dipeptide import ABC BMEI0438, dppF BruAb11569 BR1582 BOV_1527 BCAN_A1617 OPN Dipeptide import ABC BMEI0437, dppD BruAb11570 BR1583 BOV_1528 BCAN_A1618 OPN Dipeptide import IM BMEI0435, dppC BruAb11571 BR1584 BOV_1530 BCAN_A1620 OPN Dipeptide import IM BMEI0436, dppC BruAb11572 BR1585 BOV_1529 BCAN_A1619...”
NP_881029 putative ABC transporter ATP-binding subunit from Bordetella pertussis Tohama I
BP2397 dipeptide ABC transporter ATP-binding protein from Bordetella pertussis Tohama I
41% identity, 40% coverage
VV1_2972 ABC-type oligopeptide transport system, ATPase component from Vibrio vulnificus CMCP6
40% identity, 86% coverage
- A consensus sequence for binding of SmcR, a Vibrio vulnificus LuxR homologue, and genome-wide identification of the SmcR regulon
Lee, The Journal of biological chemistry 2008 - “...VV1_2358, VV1_2976b VV1_2975 VV1_2974 VV1_2973 VV1_2972, VV2_0856, VV2_0970, VV2_1270, VV2_1527 VV1_0842b VV1_0843 VV1_0844 VV1_0845, VV1_2805, VV2_1106...”
- “...VV1_2358 VV1_2976 VV1_2975 VV1_2974 VV1_2973 VV1_2972 DNA/RNA endonuclease G Hypoxanthine phosphoribosyltransferase Hypoxanthine phosphoribosyltransferase 3...”
SMb20479 putative dipeptide ABC transporter ATP-binding protein from Sinorhizobium meliloti 1021
39% identity, 82% coverage
NP_386055 PUTATIVE PEPTIDE TRANSPORT ATP-BINDING ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
39% identity, 48% coverage
SPD_1167 ABC transporter, ATP-binding protein from Streptococcus pneumoniae D39
DQM66_RS06230, spr1191 ABC transporter ATP-binding protein from Streptococcus pneumoniae
35% identity, 47% coverage
BH3639 oligopeptide ABC transporter (ATP-binding protein) from Bacillus halodurans C-125
41% identity, 83% coverage
- Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis
Takami, Nucleic acids research 2000 - “...(BH27, BH28, BH570, BH571, BH1799, BH1800, BH2077, BH2078, BH3639, BH3640, BH3645, BH3646, AppD and AppF) are distributed throughout the C-125 genome. We...”
LBA0203 ATP binding protein ( oligopeptide ABC transporter ) from Lactobacillus acidophilus NCFM
38% identity, 85% coverage
- Use of Mass Spectrometry to Profile Peptides in Whey Protein Isolate Medium Fermented by Lactobacillus helveticus LH-2 and Lactobacillus acidophilus La-5
Ali, Frontiers in nutrition 2019 - “...protein oppD1 ( LBA0202 ) 352/352 (100%) Oligopeptide ABC transporter, ATP binding protein oppF1 ( LBA0203 ) 313/314 (99%) Oligopeptide ABC transporter, substrate binding protein oppA3 ( LBA1216 ) 527/527 (100%) Oligopeptide ABC transporter, substrate binding protein oppA2 ( LBA1300 ) 584/585 (99%) Oligopeptide ABC transporter,...”
- Microarray analysis of a two-component regulatory system involved in acid resistance and proteolytic activity in Lactobacillus acidophilus
Azcarate-Peril, Applied and environmental microbiology 2005 - “...L. acidophilus genome (Fig. 4): opp1 (ORFs LBA0197 to LBA0203) and opp2 (ORFs LBA1300 to LBA1306). Each consists of six genes, opp1 consists of oppD1, oppF1,...”
- “...ABC transporter, ATP-binding protein oppD1 LBA0203 oligopeptide ABC transporter, ATP-binding protein oppF1 LBA0849 diaminopimelate epimerase LBA0850...”
DPPF_LACLM / A2RI78 Dipeptide transport ATP-binding protein DppF; EC 7.4.2.9 from Lactococcus lactis subsp. cremoris (strain MG1363) (see paper)
42% identity, 81% coverage
- function: Part of the ABC transporter DppABCDF involved in dipeptide transport (PubMed:11409543). Responsible for energy coupling to the transport system (Probable).
catalytic activity: a dipeptide(out) + ATP + H2O = a dipeptide(in) + ADP + phosphate + H(+) (RHEA:23120)
subunit: The complex is composed of two ATP-binding proteins (DppD and DppF), two transmembrane proteins (DppB and DppC) and a solute-binding protein (DppA).
disruption phenotype: Inactivation of the gene impairs growth on low concentrations of di-valine.
Ldb1385 Oligopeptide ABC transporter, ATP-binding protein from Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842
36% identity, 88% coverage
BTH_II2215 peptide ABC transporter, ATP-binding protein from Burkholderia thailandensis E264
35% identity, 83% coverage
EF3109 peptide ABC transporter, ATP-binding protein from Enterococcus faecalis V583
OG1RF_RS12140 oligopeptide ABC transporter ATP-binding protein Opp2F from Enterococcus faecalis OG1RF
40% identity, 81% coverage
- Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids
Repoila, Scientific reports 2022 - “...ef0581 and ef0583 (operon ef0581/84) , ef0634 and ef0636 (operon ef0634/36 ), and ef3107, ef3108, ef3109 and ef3110 (operon ef3106/10 ) , predicted to encode transport systems for vitamins, metal ions, amino-acids or peptides 50 , 51 , 66 , 67 . RT-qPCR analyses for those...”
- Characterization of the pheromone response of the Enterococcus faecalis conjugative plasmid pCF10: complete sequence and comparative analysis of the transcriptional and phenotypic responses of pCF10-containing cells to pheromone induction
Hirt, Journal of bacteriology 2005 - “...EF1822 EF1891 EF1974 EF2076 EF2326 EF2403 EF2496 EF3106 EF3108 EF3109 EF3331 rpoN oppB2 oppF2 ftsZ pfkA pykA ebsA ebsB ebsC fsrB fsrA relA efaA cpdA cobA oppA...”
- Transcriptional response of Enterococcus faecalis V583 to erythromycin
Aakra, Antimicrobial agents and chemotherapy 2005 - “...EF2394 EF2647 EF2769 EF2959 EF2960 EF3106 EF3107 EF3108 EF3109 EF3110 EF3277 EF0452 EF0453 EF0678 EF0877 EF0905 EF1062 EF1075 EF1077 EF1110 EF1138 EF1329 EF2440...”
- Omadacycline Efficacy against Enterococcus faecalis Isolated in China: In Vitro Activity, Heteroresistance, and Resistance Mechanisms
Lin, Antimicrobial agents and chemotherapy 2020 - “...OMC-induced resistance ( Fig. 2 and Fig. S4). Overexpression of six candidate genes, namely, OG1RF_RS00630, OG1RF_RS12140, OG1RF_RS02205, OG1RF_RS06145, OG1RF_RS06880, and OG1RF_RS11485, was correlated with the occurrence of OMC heteroresistance or resistance ( Fig. 2 ). TABLE 5 Transcriptional expression levels of 12 candidate differentially expressed genes...”
- “...ribosomal protection protein Lsa(A) 2.77 (0.011) 2.16 0.14 OG1RF_RS06880 CoA-binding protein 3.37 (0.0003) 2.67 0.35 OG1RF_RS12140 ABC transporter ATP-binding protein 3.75 (<0.0001) 15.70 2.48 OG1RF_RS02205 ABC transporter ATP-binding protein 3.84 (<0.0001) 3.22 0.49 OG1RF_RS05865 Sulfate ABC transporter ATP-binding protein 4.21 (<0.0001) 8.54 1.24 OG1RF_RS06145 Molybdate ABC...”
- Mechanism of Eravacycline Resistance in Clinical Enterococcus faecalis Isolates From China
Wen, Frontiers in microbiology 2020 - “...the parent isolate. In addition, overexpression of OG1RF_RS06145 encoding a molybdate ABC transporter substrate-binding protein, OG1RF_RS12140 encoding an ABC transporter ATP-binding protein, and OG1RF_RS06880 encoding a coenzyme A-binding protein conferred heteroresistance to Tige but not Erava. TABLE 5 Tige and Erava MICs in E. faecalis derivatives...”
- Examination of Enterococcus faecalis Toxin-Antitoxin System Toxin Fst Function Utilizing a Pheromone-Inducible Expression Vector with Tight Repression and Broad Dynamic Range
Weaver, Journal of bacteriology 2017 - “...OG1RF_RS02610 OG1RF_RS02615 OG1RF_RS06160 OG1RF_RS12145 OG1RF_RS12140 OG1RF_RS12135 OG1RF_RS08565 OG1RF_RS08570 OG1RF_RS12130 OG1RF_RS02900 OG1RF_RS04695...”
HVO_B0024 ABC-type transport system ATP-binding protein (probable substrate dipeptides/oligopeptides) from Haloferax volcanii DS2
36% identity, 41% coverage
- D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii
Johnsen, The Journal of biological chemistry 2009 - “...HVO_B0020-B0021 HVO_B0021 HVO_B0021-B0022 HVO_B0023-B0024 HVO_B0024 HVO_B0024 HVO_B0027-B0028 HVO_B0032-B0034 HVO_B0032-B0034 HVO_B0034 HVO_B0034-B0035...”
- “...transcribed into polycistronic mRNAs, e.g. HVO_B0021 to HVO_B0024, HVO_B0027 to HVO_B0029, HVO_B0034 to HVO_B0038, and HVO_B0228 to HVO_B0231. Cotranscription...”
DdpF / b1483 putative D,D-dipeptide ABC transporter ATP-binding subunit DdpF from Escherichia coli K-12 substr. MG1655 (see 2 papers)
DDPF_ECOLI / P77622 Probable D,D-dipeptide transport ATP-binding protein DdpF from Escherichia coli (strain K12) (see paper)
b1483 D-ala-D-ala transporter subunit from Escherichia coli str. K-12 substr. MG1655
35% identity, 99% coverage
- function: Part of the ABC transporter complex DdpABCDF, which is probably involved in D,D-dipeptide transport (PubMed:9097039). Probably responsible for energy coupling to the transport system.
subunit: The complex is composed of two ATP-binding proteins (DdpD and DdpF), two transmembrane proteins (DdpB and DdpC) and a solute-binding protein (DdpA). - 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
Wei, Infection and immunity 2003 - “...b1948 b2259 b0808 b0899 b0934 b1053 b1169 b1170 b1336 b1483 b1543 b1920 b2681 b3514 b3877 b4231 b2117 b1020 b2479 b2090 b3763 b1384 b1892 b1074 b1942 b2365...”
- Transcriptional profile of the Escherichia coli response to the antimicrobial insect peptide cecropin A
Hong, Antimicrobial agents and chemotherapy 2003 - “...from unnamed clusters of seven genes ahead of ydd (b1483 to b1489) and nine genes following ydd (b1498 to b1506) were broadly decreased up to 3.6-fold. Several...”
- Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression
Soupene, Journal of bacteriology 2003 - “...(b1006 to b1012), ydcSTUVW (b1440 to b1444), ddpXABCDE (b1483 to b1488), yeaGH (b1783 to b1784), yedL (b1932), cbl (b1987), nac (b1988), argT (b2310), ygjG...”
- Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation
Zimmer, Proceedings of the National Academy of Sciences of the United States of America 2000 - “...genes of the b1440 - 44 operon and the ddp (b1483- 88) operon and adjacent genes in experiments a-k. (B) Profiles (log ratios) for these genes visualized as red...”
- Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi
McClelland, Nucleic acids research 2000 - “...674 Phage Rac (31) ydbA_1 1 463 416 1 480 225 16 809 ? b1483 1 555 136 1 596 110 40 974 xasA, gadB, pqqL ydfK 1 631 063 1 650 732 19 669 Phage Qin molR_1 2 194...”
- Functional Prediction of Biological Profile During Eutrophication in Marine Environment
Sbaoui, Bioinformatics and biology insights 2022 - “...P0ACZ8 DNA-binding transcriptional activator CutA P69488 Copper binding protein CysH P17854 Phosphoadenosine phosphosulfate reductase DdpF P77622 Putative dipeptide transport protein (ABC superfamily, atp_bind) DgcZ P31129 Enzyme diguanylate cyclase DsbB P0A6M2 Disulfide bond formation proteins (oxidoreductase) with quinone as electron acceptor, reoxidizes DsbA DsrB P0AEG8 Dissimilatory sulfate...”
TC 3.A.1.5.25 / Q9CIK8 Oligopeptide ABC trasporter ATP binding protein, component of The ABC peptide/signalling peptide transporter. OptA binds peptides of 3-6 aas; OptS binds dipeptides. OptB,C,D are most similar to 3.A.1.5.19 from Lactococcus lactis subsp. lactis (see paper)
42% identity, 81% coverage
- substrates: Oligopeptides, peptides
DU507_08650 ABC transporter ATP-binding protein from Lacticaseibacillus rhamnosus GG
40% identity, 81% coverage
Q8ZQM4 ABC-type glutathione transporter (EC 7.4.2.10) from Salmonella enterica subsp. enterica serovar Typhimurium (see paper)
STM0848 putative ATPase components of ABC-type transport system, contain duplicated ATPase domain from Salmonella typhimurium LT2
40% identity, 41% coverage
- Purification and Characterization of an ATPase GsiA from Salmonella enterica
Wang, BioMed research international 2017 - “...by Professor Lynne Regan of Yale University. The Salmonella enterica subsp. enterica serovar Typhimurium LT2: STM0848 and E. coli strains BL21(DE3) and DH5 were preserved in our laboratory. KOD-FX polymerase was bought from ToYoBo, and T4 DNA ligase and restriction enzymes were got from NEB. Other...”
- “...sequence of the gsiA gene was amplified from Salmonella enterica subsp. enterica serovar Typhimurium LT2: STM0848 genome and cloned into pMAL-c2X derived plou3 vector. To facilitate protein purification, a 6His tag was added before MBP and a TEV protease cleavage site was added between MBP and...”
Q03TX9 ABC-type oligopeptide transport system, ATPase component from Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947)
37% identity, 87% coverage
Pyrde_0356 ABC transporter ATP-binding protein from Pyrodictium delaneyi
36% identity, 88% coverage
SSO2616 Dipeptide ABC transporter ATP binding protein (dppD-3) from Sulfolobus solfataricus P2
36% identity, 89% coverage
TON_1767 ABC-type dipeptide/oligopeptide transport system, ATPase component from Thermococcus onnurineus NA1
35% identity, 97% coverage
AB395_0000388 ABC transporter ATP-binding protein from Sinorhizobium fredii CCBAU 45436
40% identity, 81% coverage
BCAN_B1117 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain from Brucella canis ATCC 23365
35% identity, 92% coverage
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BP BMEII01203 BruAb21036 BRA0097 BCAN_B1119 67 OPN Dipeptide import ABC BMEII0205, dppF BruAb21033 BRA1095 BOV_A0950 BCAN_B1117 OPN Dipeptide import ABC BMEII0206, dppD BruAb21034 BRA1094 BOV_A0951 BCAN_B1116 OPN Dipeptide import IM BMEII0207, dppC BruAb21031 BRA1093 BCAN_B1115, dppC OPN Dipeptide import IM BruAb21032 BRA1092 BOV_A0952 OPN Dipeptide import...”
BMEII0205 DIPEPTIDE TRANSPORT ATP-BINDING PROTEIN DPPF from Brucella melitensis 16M
36% identity, 76% coverage
- Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network
Hur, BMC immunology 2011 - “...3 (2) C (9.12) BMEII1054 hisG ATP phosphoribosyltransferase catalytic subunit 2 1 (0) C (9.97) BMEII0205 dppF ABC transporter 6 3 (2) CM (7.88) BMEI1324 pepN aminopeptidase N 5 1 (1) V C (9.12) BMEII0407 asd aspartate-semialdehyde dehydrogenase 6 1 (0) C (9.97) BMEI1652 ureC-1 urease...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...BRA0098 BCAN_B1121 OPN Oligopeptide import BP BMEII01203 BruAb21036 BRA0097 BCAN_B1119 67 OPN Dipeptide import ABC BMEII0205, dppF BruAb21033 BRA1095 BOV_A0950 BCAN_B1117 OPN Dipeptide import ABC BMEII0206, dppD BruAb21034 BRA1094 BOV_A0951 BCAN_B1116 OPN Dipeptide import IM BMEII0207, dppC BruAb21031 BRA1093 BCAN_B1115, dppC OPN Dipeptide import IM BruAb21032...”
BAU10_05965 ABC transporter ATP-binding protein from Vibrio alginolyticus
35% identity, 92% coverage
- Identification of the global regulatory roles of RraA via the integrative transcriptome and proteome in Vibrio alginolyticus
Chen, mSphere 2024 - “...3.29-fold), ArtP (BAU10_20535, down 1.78-fold), BAU10_18335(down 17.77-fold), SdaC (BAU10_20390, down 4.55-fold), OppA(BAU10_09280, down 1.86-fold), OppF (BAU10_05965, down 12.57-fold), and GlnQ (BAU10_07585, down 1.54-fold), suggesting that RraA may play a role in positively regulating the uptake of amino acids and maintaining the balance between carbon and nitrogen...”
CpC231_0361 ABC transporter ATP-binding protein from Corynebacterium pseudotuberculosis C231
D9QED0 Oligopeptide ABC transporter ATP-binding protein OppD from Corynebacterium pseudotuberculosis (strain C231)
36% identity, 45% coverage
- Changes in protein abundance are observed in bacterial isolates from a natural host
Rees, Frontiers in cellular and infection microbiology 2015 - “...* 0.001 D9QEB4 CpC231_0345 CpC231_0345 Uncharacterized protein 0.209 2.552 * 0.381 Function unknown D9QED0 oppDF1 CpC231_0361 Oligopeptide transport ATP-binding protein 0.309 1.187 * 1.416 * Posttranslational modification D9QEP1 pyc CpC231_0477 Pyruvate carboxylase 1.120 * 1.723 * 1.611 * Energy production and conversion D9QEQ2 rbsR CpC231_0488 Ribose...”
- Changes in protein abundance are observed in bacterial isolates from a natural host
Rees, Frontiers in cellular and infection microbiology 2015 - “...0.406 1.297 * 0.001 D9QEB4 CpC231_0345 CpC231_0345 Uncharacterized protein 0.209 2.552 * 0.381 Function unknown D9QED0 oppDF1 CpC231_0361 Oligopeptide transport ATP-binding protein 0.309 1.187 * 1.416 * Posttranslational modification D9QEP1 pyc CpC231_0477 Pyruvate carboxylase 1.120 * 1.723 * 1.611 * Energy production and conversion D9QEQ2 rbsR...”
TC 3.A.1.5.9 / Q97VF4 CbtF, component of Cellobiose and cellooligosaccharide porter from Sulfolobus solfataricus (see paper)
34% identity, 97% coverage
- substrates: Cellobiose, Cellooligosaccharide
GsiA / b0829 glutathione ABC transporter ATP binding subunit GsiA (EC 7.4.2.10) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
gsiA / P75796 glutathione ABC transporter ATP binding subunit GsiA (EC 7.4.2.10) from Escherichia coli (strain K12) (see 3 papers)
GSIA_ECOLI / P75796 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 from Escherichia coli (strain K12) (see paper)
P75796 ABC-type glutathione transporter (EC 7.4.2.10) from Escherichia coli (see paper)
TC 3.A.1.5.11 / P75796 Hypothetical ABC transporter ATP-binding protein yliA, component of Glutathione porter, YliABCD or GsiABCD from Escherichia coli (see 4 papers)
NP_415350 glutathione ABC transporter ATP binding subunit GsiA from Escherichia coli str. K-12 substr. MG1655
b0829 fused predicted peptide transport subunits of ABC superfamily: ATP-binding components from Escherichia coli str. K-12 substr. MG1655
42% identity, 41% coverage
- function: Part of the ABC transporter complex GsiABCD involved in glutathione import. Responsible for energy coupling to the transport system.
catalytic activity: glutathione(out) + ATP + H2O = glutathione(in) + ADP + phosphate + H(+) (RHEA:29791)
subunit: The complex is composed of two ATP-binding proteins (GsiA), two transmembrane proteins (GsiC and GsiD) and a solute-binding protein (GsiB). - substrates: Glutathione
- The yliA, -B, -C, and -D genes of Escherichia coli K-12 encode a novel glutathione importer with an ATP-binding cassette.
Suzuki, Journal of bacteriology 2005 - GeneRIF: Imports extracellular glutathione into the cytoplasm in an ATP-dependent manner.
- Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli
Jindal, BMC microbiology 2019 - “...yifK probable transport protein (possibly amino acid) P27837 [ 128 ] yliA/gsiA ATP-driven Glutathione importer P75796 [ 129 ] ybiR Inner membrane protein P75788 (none) yccS Inner membrane protein P75870 (none) phoR Phosphate sensor regulon P08400 [ 130 ] yejA Putative oligopeptide ABC transporter periplasmic binding...”
- SATIN: a micro and mini satellite mining tool of total genome and coding regions with analysis of perfect repeats polymorphism in coding regions
Dantas, BMC bioinformatics 2024 - “...Escherichia coli groups of the K12 and O157 strains using SATIN. Note that the gene b0829 was identified by the name gsiA SSR Gene AOV AOV AOV AOV AOV SHAPIROWILK SHAPIROWILK KRUSKALWALLIS KRUSKALWALLIS Pr(>F) F_value Mean_Sq Sum_Sq Df W P-value chi_squared p_value (A)9 yibA 1.4510 72...”
- Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
Ren, Applied and environmental microbiology 2005 - “...with unknown functions b0309 b0309 b0484 b0484 b0485 b0485 b0829 b0829 b1729 b1729 b2379 b2379 hdeA b3510 hdeB b3509 yeeD b2012 yeeE b2013 yjeB b4178 ybhG b0795...”
- Amplified intergenic locus polymorphism as a basis for bacterial typing of Listeria spp. and Escherichia coli
Somer, Applied and environmental microbiology 2005 - “...b1688 aidB b1284 yaiN ycgW caiF yacA serW dsrB yaaH molR-1 yjiD b0829 yibA b1031 mhpR folA pyrD b2345 ykgE osmB gutP b1248 galS uvrB yafY pepD 1 1 4 1 1 1 1 1...”
- Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses
Gyaneshwar, Journal of bacteriology 2005 - “...cysI (b2763), and genes coding for glutathione transport components (b0829 to b0830) (34) (Fig. 1, row 4). For genes detected on both taurine and glutathione,...”
- “...clusters were b0197 (metQ), b0606 (ahpF), b0801 (ybiC), b0829 and b0830 (yliAB), b1654 (ydhD), b1677 (lpp), b1823 (cspC), b1987 (cbl), b2528 and b2529 (iscAU),...”
- Aspartic peptide hydrolases in Salmonella enterica serovar typhimurium
Larsen, Journal of bacteriology 2001 - “...and moeB) and three genes of unknown function (ybiK, b0829, and b0830). A Blast search of the GenBank database using the amino acid sequence corresponding to...”
- Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism
Gur-Arie, Genome research 2000 (secret)
N646_0377 ABC transporter ATP-binding protein from Vibrio alginolyticus NBRC 15630 = ATCC 17749
35% identity, 92% coverage
BP3858 putative transport ATP-binding protein from Bordetella pertussis Tohama I
36% identity, 85% coverage
Q938E4 Putative oligopeptide permease OppF from Mycolicibacterium smegmatis
39% identity, 81% coverage
Amuc_0672 ABC transporter related from Akkermansia muciniphila ATCC BAA-835
39% identity, 82% coverage
- Omics-based analysis of <i>Akkermansia muciniphila</i> cultivation in food-grade media
Geerlings, Microbiome research reports 2024 - “...Amuc_0221 and Amuc_0037), as well 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...”
SF5M90T_807 glutathione ABC transporter ATP-binding protein GsiA from Shigella flexneri 5a str. M90T
42% identity, 41% coverage
- RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Vergara-Irigaray, BMC genomics 2014 - “...serine hydroxymethyltransferase 1.16 SF5M90T_2967 gsp glutathionylspermidine synthetase/amidase 1.16 0.70 SF5M90T_1806 edd 6-phosphogluconate dehydratase 1.15 -0.72 SF5M90T_807 glutathione transporter ATP-binding protein 1.08 SF5M90T_2317 hisJ histidine-binding periplasmic protein of high-affinity histidine transport system 1.05 SF5M90T_806 ybiK putative asparaginase 1.02 SF5M90T_1122 potC spermidine/putrescine transport system permease 0.97 -1.09 -0.92...”
pRL110513 putative ATP-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
36% identity, 85% coverage
TC 3.A.1.5.32 / F0TFS9 Oligopeptide ABC transporter ATP-binding protein, component of ABC α-galactoside uptake porter from Lactobacillus acidophilus (strain 30SC)
37% identity, 78% coverage
- substrates: Alpha-galactosides
tcdb comment: Most highly induced by stachyose (Andersen et al. 2012)
LBA1305 oligopeptide ABC transporter (ATP-binding protein) from Lactobacillus acidophilus NCFM
37% identity, 78% coverage
Q73NS7 ABC-type dipeptide transporter (EC 7.4.2.9) from Treponema denticola (see paper)
TDE_1075 ABC transporter ATP-binding protein from Treponema denticola ATCC 35405
37% identity, 90% coverage
IYO_RS01165 ABC transporter ATP-binding protein from Pseudomonas syringae pv. actinidiae ICMP 18884
32% identity, 51% coverage
TM0501 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
35% identity, 88% coverage
VV1_0837 ABC-type oligopeptide transport system, ATPase component from Vibrio vulnificus CMCP6
40% identity, 84% coverage
TDE1272 oligopeptide/dipeptide ABC transporter, ATP-binding protein from Treponema denticola ATCC 35405
36% identity, 90% coverage
Bbr_1815 ABC transporter ATP-binding protein from Bifidobacterium breve UCC2003
36% identity, 43% coverage
- Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation
Lanigan, Frontiers in microbiology 2017 - “...ferric iron/siderophore uptake 1.7 Bbr_0224 sifB , permease protein ABC transporter ferric iron/siderophore uptake 1.7 Bbr_1815 oppD , ATP-binding protein of iron siderophore uptake system 1.7 Locus tag Gene name and/or predicted Function Downregulation Bbr_1898 nrdF , Ribonucleoside-diphosphate reductase beta chain 4.8 Bbr_1899 nrdE , Ribonucleoside-diphosphate...”
C9RQJ3 Putative oligopeptide/dipeptide ABC transporter, ATP-binding protein from Fibrobacter succinogenes (strain ATCC 19169 / S85)
Fisuc_1226 ABC transporter related protein from Fibrobacter succinogenes subsp. succinogenes S85
FSU_1687 ABC transporter ATP-binding protein from Fibrobacter succinogenes subsp. succinogenes S85
39% identity, 82% coverage
- Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85
Raut, Scientific reports 2019 - “...p-value Signal peptide (Residues) COG motif Predicted activity Sequence homology ATP binding cassette (ABC) transporters C9RQJ3 FSU_1687 Oligopeptide/dipeptide ABC transporter 1.32 **** na ABC Cellobiose/cellodextrin import 40.9% to (TM_0027, TM_1219) and cbtF 22 , 23 , 55 C9RLQ8 FSU_3055 ABC transporter 1.21 * na ABC TM_1028...”
- Influence of Substrates on the Surface Characteristics and Membrane Proteome of Fibrobacter succinogenes S85
Raut, PloS one 2015 - “...- Fisuc_1897 FSU_2403 TonB family protein - 8 3 Unknown -0.393 32.452 9.84 No - Fisuc_1226 FSU_1687 ABC transporter related protein - 4 3 Cytoplasmic membrane -0.323 30.503 8.6 No - Fisuc_1895 FSU_2401 Biopolymer transport protein ExbD/TolR - 3 2 Unknown -0.2 32.44 4.72 No -...”
- Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85
Raut, Scientific reports 2019 - “...Signal peptide (Residues) COG motif Predicted activity Sequence homology ATP binding cassette (ABC) transporters C9RQJ3 FSU_1687 Oligopeptide/dipeptide ABC transporter 1.32 **** na ABC Cellobiose/cellodextrin import 40.9% to (TM_0027, TM_1219) and cbtF 22 , 23 , 55 C9RLQ8 FSU_3055 ABC transporter 1.21 * na ABC TM_1028 31.8%...”
- Influence of Substrates on the Surface Characteristics and Membrane Proteome of Fibrobacter succinogenes S85
Raut, PloS one 2015 - “...Fisuc_1897 FSU_2403 TonB family protein - 8 3 Unknown -0.393 32.452 9.84 No - Fisuc_1226 FSU_1687 ABC transporter related protein - 4 3 Cytoplasmic membrane -0.323 30.503 8.6 No - Fisuc_1895 FSU_2401 Biopolymer transport protein ExbD/TolR - 3 2 Unknown -0.2 32.44 4.72 No - Fisuc_0149...”
SMc02829 ABC transporter ATP-binding protein from Sinorhizobium meliloti 1021
43% identity, 47% coverage
VP_RS06515, VpaChn25_1344 ABC transporter ATP-binding protein from Vibrio parahaemolyticus
VP1343 oligopeptide ABC transporter, ATP-binding protein from Vibrio parahaemolyticus RIMD 2210633
34% identity, 93% coverage
- Comparative Transcriptome Analysis Reveals Regulatory Factors Involved in Vibrio Parahaemolyticus Biofilm Formation
Wang, Frontiers in cellular and infection microbiology 2022 - “...permease OppB VP_RS06525 7.51 ABC transporter permease subunit VP_RS06535 5.56 peptide ABC transporter substrate-binding protein VP_RS06515 4.77 ATP-binding cassette domain-containing protein VP_RS06520 4.32 ATP-binding cassette domain-containing protein VP_RS15290 3.21 ABC transporter ATP-binding protein ribA 2.91 GTP cyclohydrolase II VP_RS02600 2.87 3-deoxy-7-phosphoheptulonate synthase lepB 2.35 signal peptidase...”
- Identification of Antibacterial Components in the Methanol-Phase Extract from Edible Herbaceous Plant Rumex madaio Makino and Their Antibacterial Action Modes
Liu, Molecules (Basel, Switzerland) 2022 - “...transporter permease OppB VP_RS06520 0.256 ATP-binding cassette domain-containing protein VP_RS06525 0.265 ABC transporter permease subunit VP_RS06515 0.297 ATP-binding cassette domain-containing protein VP_RS06485 0.310 ABC transporter ATP-binding protein VP_RS06495 0.346 ABC transporter permease VP_RS06535 0.362 Peptide ABC transporter substrate-binding protein VP_RS20670 0.368 ABC transporter ATP-binding protein VP_RS06490...”
- Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival
Zhu, BMC genomics 2017 - “...protein VpaChn25_0846 0.4129 Zinc ABC transporter permease VpaChn25_0848 0.4556 Zinc ABC transporter periplasmic zinc-binding protein VpaChn25_1344 0.2076 Oligopeptide ABC transporter ATP-binding protein VpaChn25_1345 0.2716 Oligopeptide ABC transporter ATP-binding protein VpaChn25_1346 0.2355 Oligopeptide ABC transporter permease VpaChn25_1347 0.3245 Oligopeptide ABC transporter permease VpaChn25_1348 0.3723 Oligopeptide ABC transporter...”
- The release of a distinct cell type from swarm colonies facilitates dissemination of Vibrio parahaemolyticus in the environment
Freitas, The ISME journal 2020 - “...flagellum proteins. Highlight in green indicates the protein VP1343, which is significantly downregulated in cells from the periphery. b Fluorescence and DIC...”
- “...in order to monitor lafA expression, and the promoter of vp1343 was fused to T7 polymerase and the promotor of T7 polymerase was fused to sfGFP (Pvp1343::T7 and...”
- Two regulators of Vibrio parahaemolyticus play important roles in enterotoxicity by controlling the expression of genes in the Vp-PAI region
Kodama, PloS one 2010 - “...the same operon as the vscC2 gene was also regulated by VtrB. Production of the VP1343 protein, which was expected to be co-transcribed with vscC2 ( Fig. 2C ), was examined by immunoblotting. VP1343 protein was not detected in bacterial pellets from vtrA and/or vtrB deletion...”
APZ00_12920 ABC transporter ATP-binding protein from Pannonibacter phragmitetus
40% identity, 42% coverage
- Genomic insights of Pannonibacter phragmitetus strain 31801 isolated from a patient with a liver abscess
Zhou, MicrobiologyOpen 2017 - “...transporter ATPbinding protein APZ00_20870 fliI Flagellumspecific ATP synthase FliI APZ00_19800 algB Twocomponent response regulator AlgB APZ00_12920; APZ00_19550; APZ00_21280 fliP Flagellar biosynthetic protein FliP APZ00_09865 pchF Pyochelin synthetase PchF APZ00_05615 pchH ABC transporter ATPbinding protein APZ00_02420 fha1 Type VI secretion system forkheadassociated protein Fha1 APZ00_12570 waaG Bband...”
ECs2087 putative ATP-binding component of a transport system from Escherichia coli O157:H7 str. Sakai
34% identity, 99% coverage
FSDG_RS10175 ABC transporter ATP-binding protein from Fusobacterium animalis 7_1
35% identity, 94% coverage
- A survey of Fusobacterium nucleatum genes modulated by host cell infection
Cochrane, Microbial genomics 2020 - “...(LPS) biosynthesis protein); FSDG_RS08715 (haemolysin III); FSDG_RS09645 (UDP- N -acetylenolpyruvoylglucosamine reductase); FSDG_RS10170 (ATP binding protein); FSDG_RS10175 (ABC transporter ATP binding protein)] (File S1). Infection with CRC-associated strain F. nucleatum 7-3 results in similar activation of fusobacterial genes Given the substantial genetic, antigenic and pathogenic diversity among...”
Teth514_1792 oligopeptide/dipeptide ABC transporter, ATPase subunit from Thermoanaerobacter ethanolicus X514
33% identity, 94% coverage
- Discovery of two β-1,2-mannoside phosphorylases showing different chain-length specificities from Thermoanaerobacter sp. X-514
Chiku, PloS one 2014 - “...is an extracellular solute-binding protein; Teth514_1795 and Teth514_1794, which are permease proteins; and Teth514_1793 and Teth514_1792, which are ATP-binding proteins), two hypothetical proteins (Teth514_1791 and Teth514_1785), a GH5 -glycoside hydrolase (Teth514_1790), a mannose-1-phosphate guanylyltransferase (Teth514_1787), a GDP-mannose-dependent -mannosyltransferase (Teth514_1786), and two GH130 -1,2-mannoside phosphorylases (Teth514_1788 and...”
- “...( Fig. 7 ): 1,2--oligomannan is transported into the cytoplasmic space by an ABC transporter (Teth514_1792 to Teth514_1796) and is sequentially phosphorolyzed by 1,2--oligomannan phosphorylases (Teth514_1788) and -1,2-mannobiose phosphorylases (Teth514_1789). Then, the resultant -Man1 P is converted into GDP- d -mannose by mannose-1-phosphate guanylyltransferase (Teth514_1787). In...”
TC 3.A.1.5.12 / Q9X0F4 TM1064, component of Probable rhamnose oligosaccharide porter. Induced by rhamnose (see paper)
TM1064 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
35% identity, 94% coverage
sll1927 ABC transporter from Synechocystis sp. PCC 6803
38% identity, 39% coverage
SPO0098 ABC transporter ATP-binding protein from Ruegeria pomeroyi DSS-3
42% identity, 44% coverage
TC 3.A.1.5.15 / Q9X271 TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (see paper)
TM1749 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
36% identity, 96% coverage
Q82ZF0 Peptide ABC transporter, ATP-binding protein from Enterococcus faecalis (strain ATCC 700802 / V583)
EF3110 peptide ABC transporter, ATP-binding protein from Enterococcus faecalis V583
34% identity, 92% coverage
- Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion
Downes, Scientific reports 2023 - “...(adcABC) 2.61741 0.00538351 8 44.8 Q839U5 Peptide ABC transporter, ATP-binding protein 1.28554 0.00946214 12 70.7 Q82ZF0 5'-nucleotidase family protein 0.948218 0.011422 23 26.9 Q839U0 LemA family protein 0.664767 0.00432472 6 40.7 Q838I0 Phage portal protein 0.64703 0.0486542 16 56 Q835K9 ABC transporter, ATP-binding protein 0.643841 0.0456337...”
- Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids
Repoila, Scientific reports 2022 - “...ef0583 (operon ef0581/84) , ef0634 and ef0636 (operon ef0634/36 ), and ef3107, ef3108, ef3109 and ef3110 (operon ef3106/10 ) , predicted to encode transport systems for vitamins, metal ions, amino-acids or peptides 50 , 51 , 66 , 67 . RT-qPCR analyses for those three operons...”
- “...of the TCA response, and had similar expression levels to RNAs probed ef0581, ef0634 and ef3110 (Table S5 ). The normalization was done using the geNorm program 91 . Primer sequences are reported Table S6 . Cluster of Orthologous Groups and assignment categories based on expression...”
- Examination of Enterococcus faecalis Toxin-Antitoxin System Toxin Fst Function Utilizing a Pheromone-Inducible Expression Vector with Tight Repression and Broad Dynamic Range
Weaver, Journal of bacteriology 2017 - “...EF0409 REV par-pAD1 FWD par-pAD1 REV EF1017 FWD EF1017 REV EF3110 FWD EF3110 REV EF0417 FWD EF0417 REV EF1117 FWD EF1117 REV EF1304 FWD EF1304 REV EF0758 FWD...”
- Transcriptional response of Enterococcus faecalis V583 to erythromycin
Aakra, Antimicrobial agents and chemotherapy 2005 - “...EF2647 EF2769 EF2959 EF2960 EF3106 EF3107 EF3108 EF3109 EF3110 EF3277 EF0452 EF0453 EF0678 EF0877 EF0905 EF1062 EF1075 EF1077 EF1110 EF1138 EF1329 EF2440 EF2450...”
CAC3182 Oligopeptide ABC transporter, ATPase component from Clostridium acetobutylicum ATCC 824
37% identity, 95% coverage
SPO1213 ABC transporter ATP-binding protein from Ruegeria pomeroyi DSS-3
40% identity, 44% coverage
- A mutant fitness assay identifies bacterial interactions in a model ocean hot spot
Schreier, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...protein ( phnM ) Phosphate acquisition 0.11 SPO1727 polyphosphate kinase 2, putative Phosphate storage 2.2 SPO1213 oligopeptide ABC transporter, ATP-binding Transporter peptide 0.12 SPO2815 peptide/nickel/opine ABC transporter, permease Transporter 0.12 SPO2816 peptide/nickel/opine ABC transporter, permease Transporter 0.14 SPO1814 TRAP dicarboxylate transporter ( dctP ) Transporter organic...”
FN0399 Dipeptide transport ATP-binding protein dppD from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
37% identity, 87% coverage
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...FN0130, FN0236, FN0258, FN0276, FN0308, FN0309, FN0310, FN0332, FN0341, FN0352, FN0375, FN0376, FN0377, FN0397, FN0398, FN0399, FN0400, FN0450, FN0598, FN0658, FN0660, FN0685, FN0695, FN0793, FN0800, FN0801, FN0827, FN0828, FN1022, FN1080, FN1086, FN1135, FN1136, FN1166, FN1167, FN1187, FN1190, FN1198, FN1256, FN1301, FN1348, FN1349, FN1352, FN1353, FN1354, FN1362,...”
- “...3 Covers FN0660, FN0793, FN0800, FN0801, FN1187, FN1398, FN1432, FN1801. 4 Covers FN0192, FN0396, FN0397, FN0399, FN0400, FN0998, FN1111, FN1359, FN1362, FN1363, FN1523, FN1525. 5 Covers FN0308, FN0309, FN0310, FN0375, FN0376, FN0377. In contrast to FnSg, FnPg and FnPgSg displayed predominantly unchanged and reduced transporter protein...”
BOV_A0500 ABC transporter ATP-binding protein from Brucella ovis ATCC 25840
41% identity, 77% coverage
- Identification of Brucella ovis exclusive genes in field isolates from Argentina
Alvarez, Veterinary journal (London, England : 1997) 2016 (PubMed)- “...10.1016/j.tvjl.2015.12.005 Elsevier Ltd Fig. 1 Presence of the BOV_A0500 (a) and BOV_0198 (b) genes in Brucella spp. Agarose gel showing the PCR...”
- The predicted ABC transporter AbcEDCBA is required for type IV secretion system expression and lysosomal evasion by Brucella ovis
Silva, PloS one 2014 - “...sequence to sequences available at the NCBI protein database (BLASTx). Two proteins encoded by abcA (BOV_A0500) and abcB (BOV_A0501), which were deleted in the abcBA mutant strain, are predicted to be ATPases of ABC systems, with conserved Walker A and B motifs. Therefore, deletion of abcA...”
- ATP-Binding Cassette Systems of Brucella
Jenner, Comparative and functional genomics 2009 - “...Dipeptide import IM BMEII0286 BruAb20951 BRA1008 BOV_A0502 BCAN_B1030 OPN Dipeptide import ABC BMEII0287 BruAb20948 BRA1011 BOV_A0500 BCAN_B1029 OPN Dipeptide import ABC BMEII0288 BruAb20949 BRA1010 BOV_A0501 BCAN_B1028 70 OPN Nickel import BP BMEII0487 BruAb20428 BRA0804 BOV_A0754 BCAN_B0818, NikA OPN Nickel import IM BMEII0488, nikB BruAb20429, nikB BRA0802,...”
OG1RF_12370 oligopeptide ABC transporter ATP-binding protein Opp2D from Enterococcus faecalis OG1RF
34% identity, 89% coverage
- Enterococcal quorum-controlled protease alters phage infection
Sheriff, FEMS microbes 2024 - “...No, not present OG1RF_10750 PTS sugar transporter subunit IIB 0.11 No, not present opp2D ( OG1RF_12370 ) ABC transporter ATP-binding protein 0.12 Yes OG1RF_10751 PTS lactose/cellobiose transporter subunit IIA 0.13 No, not present OG1RF_11463 PspC domain-containing protein 0.16 No, not present OG1RF_10660 AAA family ATPase 0.16...”
MSMEG_0640 oligopeptide transport ATP-binding protein OppD from Mycobacterium smegmatis str. MC2 155
MSMEG_0640 ABC transporter ATP-binding protein from Mycolicibacterium smegmatis MC2 155
37% identity, 84% coverage
- Differentiating the roles of Mycobacterium tuberculosis substrate binding proteins, FecB and FecB2, in iron uptake
de, PLoS pathogens 2023 - “...OppA MSMEG_0643 Rv1280c 12.6% 10 OppD-2 MSMEG_0639 Rv1281c - 2 nd half 17.3% 6 OppD-1 MSMEG_0640 Rv1281c 1 st half 6.7% 2 To corroborate our co-IP results for FecB, we performed reverse co-IPs with the small periplasmic proteins, MmpS4 and MmpS5. As Msm has several homologs...”
- Multi-Omics Profiling Specifies Involvement of Alternative Ribosomal Proteins in Response to Zinc Limitation in Mycobacterium smegmatis
Dow, Frontiers in microbiology 2022 - “...DE MSMEG_6895 rpsR ribosomal protein S18 not DE 2.94 not DE not DE Over-represented protein MSMEG_0640 oligopeptide transport ATP-binding protein OppD 1.64 4.36 1.31 not DE MSMEG_3044 dihydroorotase 2.07 not DE 2.28 3.75 MSMEG_3599 sugar-binding transcriptional regulator, LacI family protein 1.65 not DE 1.31 1.69 MSMEG_3630...”
- “...not in the altRP mutant, and the gene encoding the oligopeptide transport ATP-binding protein OppD (MSMEG_0640), showing strong upregulation at the protein level only in the wild type. Interestingly, these proteins that are significantly overrepresented only in the wild type background are involved in transporting molecules...”
- Aggregation of Nontuberculous Mycobacteria Is Regulated by Carbon-Nitrogen Balance
DePas, mBio 2019 - “...family protein Missense Gln2017Arg Passage 60 MSMEG_0639 Oligopeptide transport ATP-binding protein OppF Frameshift Lys12fs b MSMEG_0640 Oligopeptide transport ATP-binding protein OppD Missense Phe96Leu MSMEG_2148 HNH endonuclease domain-containing protein Missense Pro380Arg MSMEG_2148 HNH endonuclease domain-containing protein Frameshift Ser534fs a MSMEG_3677 Serine/threonine protein kinase Silent Val320Val MSMEG_4217 DivIVA...”
Cthe_2963 oligopeptide/dipeptide ABC transporter, ATPase subunit from Clostridium thermocellum ATCC 27405
33% identity, 91% coverage
CSP5_0340 ABC transporter ATP-binding protein from Cuniculiplasma divulgatum
33% identity, 36% coverage
- Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum
Bargiela, Microorganisms 2020 - “...dehydrogenase (CSP5_0454), PepT family ABC transporter substrate-binding component (CSP5_1067) and PepT family ABC transporter ATPase (CSP5_0340), amino acid-binding ACT domain protein (CSP5_0205) and prolyl endopeptidase (CSP5_0260). Moreover, in the Carbohydrate transport and metabolism category, the glycogen debranching enzyme (alpha-1,6-glucosidase; CSP5_1243) was expressed. Additionally, ABC-type transporters from...”
C173_26182 ABC transporter ATP-binding protein from Paenibacillus sp. FSL R7-277
35% identity, 91% coverage
- Genomic comparison of sporeforming bacilli isolated from milk
Moreno, BMC genomics 2014 - “...II 4 C171_31256 82% [ Paenibacillus sp.=WP_018755215.1] R7-277 P. sp . Lasso_peptide 4 C173_26127 to C173_26182 78% [ Paenibacillus sp.=WP_019913509.1] Sactipeptides 4 C173_26762 to C173_26742 93% [ Paenibacillus sp.=WP_017690652.1] R7-269 P. sp . Lasso_peptide 4 C162_11816 to C162_11871 78% [ Paenibacillus sp.=WP_019913509.1] Sactipeptides 4 C162_32049 to...”
CDR20291_0787 oligopeptide ABC transporter, ATP-binding protein from Clostridium difficile R20291
CD196_0806 oligopeptide ABC transporter, ATP-binding protein from Clostridium difficile CD196
CD196_0806 ABC transporter ATP-binding protein from Clostridioides difficile CD196
36% identity, 99% coverage
B1745_00950 ABC transporter ATP-binding protein from Lactobacillus amylolyticus
40% identity, 80% coverage
VIBHAR_00643 ABC oligopeptide transporter ATPase component from Vibrio harveyi ATCC BAA-1116
39% identity, 84% coverage
SPO1656 ABC transporter ATP-binding protein from Ruegeria pomeroyi DSS-3
35% identity, 44% coverage
- Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3
Rivers, Frontiers in microbiology 2016 - “...Yes SPO3650 Adenylate/guanylate cyclase Signal transduction 0.009 trans79 436 SPO3223 Response regulator Transcriptional regulation 0.002 SPO1656 Oligopeptide/dipeptide ABC, ATP-binding Transport 0.003 SPO0310 Molybdopterin biosynthesis protein MoeA Coenzyme metabolism 0.004 SPO1432 Rhodanese domain-containing protein 0.006 SPO0078 Ribosomal subunit interface protein, putative Translation and biogenesis 0.007 SPO2314 DsbE...”
PF1212 putative peptide ABC uptake protein from Pyrococcus furiosus DSM 3638
37% identity, 96% coverage
bgla_2g29570 ABC transporter ATP-binding protein from Burkholderia gladioli BSR3
39% identity, 43% coverage
RHE_RS27625 ABC transporter ATP-binding protein from Rhizobium etli CFN 42
39% identity, 46% coverage
Bphyt_3178 oligopeptide/dipeptide ABC transporter, ATPase subunit from Burkholderia phytofirmans PsJN
34% identity, 42% coverage
- Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species
Nguyen, The plant pathology journal 2017 - “...WP_012433975.1 Cytidylate kinase Bphyt_3002 WP_012434114.1 50S ribosomal protein L28 Bphyt_3149 WP_012434141.1 ABC transporter ATP-binding protein Bphyt_3178 WP_012434224.1 Hypothetical protein Bphyt_3263 WP_012434453.1 FMN-dependent NADH-azoreductase Bphyt_3502 WP_041759656.1 Propionate catabolism operon regulatory protein PrpR - Burkholderia sp. KJ006 WP_011880598.1 MS: DNA-binding response regulator MYA_5939 WP_011881944.1 MS: peroxiredoxin MYA_4577 WP_011882749.1...”
Rv3663c PROBABLE DIPEPTIDE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER DPPD from Mycobacterium tuberculosis H37Rv
39% identity, 42% coverage
- Molecular basis for substrate transport of Mycobacterium tuberculosis ABC importer DppABCD
Hu, Science advances 2024 - “...mechanism of DppABCD transport. RESULTS Characterization of the DppABCD complex Rv3666c ( DppA ) to Rv3663c ( DppD ) coding for Dpp transporter are located on the same operon of Mtb ( 22 ). To examine whether the lipoprotein DppA and its translocator DppBCD could form...”
- Metabolic switching and cell wall remodelling of Mycobacterium tuberculosis during bone tuberculosis
Kaur, The Journal of infection 2023 (PubMed)- “...two of these virulence proteins (Rv1046c and Rv3663c) significantly inhibited osteoblast differentiation. Conclusion M.tb alters its transcriptome to establish...”
- “...bone TB Role of virulence factors (Rv1046c and Rv3663c) in bone TB pathogenesis Effect of recombinant Rv1046c or Rv3663c on osteoblast proliferation and...”
- Transporters Involved in the Biogenesis and Functionalization of the Mycobacterial Cell Envelope
Jackson, Chemical reviews 2021 - “...transporter consisting of DppA (R3666c; substrate-binding protein), DppB/C (R3665c/Rv3664c, integral membrane permease proteins), and DppD (Rv3663c, ATPase) is essential for heme uptake 262 , and cobalamin is taken up through the Rv1819c transporter 258 , 263 . On the basis of the heme-binding property of their...”
- ATP-binding cassette (ABC) import systems of Mycobacterium tuberculosis: target for drug and vaccine development
Soni, Emerging microbes & infections 2020 - “...] Dipeptide importer (DppABCD/Rv3666c-Rv3663c) SBP: DppA (Rv3666c) TMD: DppB (Rv3665c) and DppC (Rv3664c) NBD: DppD (Rv3663c) (two copies) dppD mutant shows decreased survival in mice [ 14 ] dppC mutant attenuated for virulence in mice [ 31 ] dppABCD knockout strain shows reduced survival in mice...”
- “...Rv1281c decreased apoptosis-inducing ability and production of cytokines IL-1b, IL-6, and TNF-. The deletion of Rv3663c in H37Rv strain showed decreased survival at the early stage of mice infection [ 14 ]. Likewise, the disruption of Rv3664c in BCG strain resulted in most attenuating mutations [...”
- Heme and hemoglobin utilization by Mycobacterium tuberculosis
Mitra, Nature communications 2019 - “...Dpp transporter include DppA (R3666c; substrate-binding protein), DppB/C (R3665c/Rv3664c, integral membrane permease proteins), and DppD (Rv3663c, ATPase). To examine whether the Mtb Dpp transporter is involved in heme utilization, we deleted the entire dpp operon in the avirulent Mtb strain mc 2 6206 by homologous recombination...”
- Characterization of membrane vesicles released by Mycobacterium avium in response to environment mimicking the macrophage phagosome
Chiplunkar, Future microbiology 2019 - “...2 A0A0H3A3W0 MAV_0467 dppD ABC transporter, ATP-binding protein Cell wall and cell processes 60 3 Rv3663c A0QFE1 MAV_2434 SsuB aliphatic sulfonates import ATP-binding protein Cell wall and cell processes 28 3 A0QHM5 MAV_3231 lspA lipoprotein signal peptidase Cell wall and cell processes 20 2 Rv1539 A0QK47...”
- TASmania: A bacterial Toxin-Antitoxin Systems database
Akarsu, PLoS computational biology 2019 - “...guilt_by_association x 1324 xT Rv3662c a Conserved hypothetical protein 256 interpro_only interpro_only T 1914 xxxT Rv3663c Probable dipeptide-transport ATP-binding protein ABC transporter DppD 548 guilt_by_association guilt_by_association x 1914 xxxT a toxin genes that have been tested experimentally b toxin genes that have been tested experimentally and...”
- ORBIT: a New Paradigm for Genetic Engineering of Mycobacterial Chromosomes
Murphy, mBio 2018 - “...3,5-epimerase Rv3484 cpsA Possible conserved protein CpsA Rv3581c ispF Probable 2C-methyl- d -erythritol 2,4-cyclodiphosphate synthase Rv3663c dppD Probable dipeptide transport ATP-binding protein Rv3910 Rv3910 Probable conserved transmembrane protein a CoA, coenzyme A. In order to cure recombinants of the RecT-Int-producing plasmid following modification, pKM461, a sacB...”
- More
BCAS0451 ABC transporter ATP-binding protein from Burkholderia cenocepacia J2315
38% identity, 46% coverage
- Response of Burkholderia cenocepacia H111 to micro-oxia
Pessi, PloS one 2013 - “...). Among them, 139 genes/proteins (78%) were up-regulated in micro-oxia, including several transporters (BCAL0447, BCAS0081, BCAS0451, BCAS0602) and outer membrane proteins, genes involved in synthesis of the EPS cepacian (BCAM1004-1005 and BCAM1010), several proteases ( Table 2 ) and an isocitrate lyase (ICL, BCAL2118). Several genes/proteins...”
- “...protein nd 15.1 CCE47595 BCAM2482 Agmatinase nd 19.8 CCE51862 BCAS0081 ABC transporter nd 27.9 CCE52306 BCAS0451 ABC transporter ATP-binding protein nd 19.4 CCE52596 BCAS0602 Permease of the metabolite transporter (DMT) superfamily TM nd M only Energy production and conversion CCE49315 BCAL0052 D-2-hydroxyglutarate dehydrogenase nd 15.0 CCE48192...”
Teth514_1793 oligopeptide/dipeptide ABC transporter, ATPase subunit from Thermoanaerobacter ethanolicus X514
35% identity, 95% coverage
- Discovery of two β-1,2-mannoside phosphorylases showing different chain-length specificities from Thermoanaerobacter sp. X-514
Chiku, PloS one 2014 - “...(Teth514_1796, which is an extracellular solute-binding protein; Teth514_1795 and Teth514_1794, which are permease proteins; and Teth514_1793 and Teth514_1792, which are ATP-binding proteins), two hypothetical proteins (Teth514_1791 and Teth514_1785), a GH5 -glycoside hydrolase (Teth514_1790), a mannose-1-phosphate guanylyltransferase (Teth514_1787), a GDP-mannose-dependent -mannosyltransferase (Teth514_1786), and two GH130 -1,2-mannoside phosphorylases...”
NRBB52_0582 ABC transporter ATP-binding protein from Bifidobacterium breve
39% identity, 83% coverage
- Comparative genomics and genotype-phenotype associations in Bifidobacterium breve
Bottacini, Scientific reports 2018 - “...ABC transporter system for peptides PF00528 Uncharacterized NRBB52_0581 Oligopeptide transport ATP-binding protein oppD PF00005 Uncharacterized NRBB52_0582 Oligopeptide transport ATP-binding protein oppF PF00005 Uncharacterized NRBB52_0583 Beta-galactosidase PF00005 Uncharacterized NRBB52_0584 Transcriptional regulator PF13377 Uncharacterized Sucrose Bbr_0018 Hypothetical membrane spanning protein PF04854 Uncharacterized Bbr_0019 Transcriptional regulator, LacI family PF13377...”
TC 3.A.1.5.20 / P42064 AppD, component of 5-6 amino acyl oligopeptide transporter AppA-F from Bacillus subtilis (see 2 papers)
34% identity, 95% coverage
- substrates: Oligopeptides
8xfcD / I6Y482 Cryo-em structure of the atp-bound mtb dppabcd with the d445a mutation of dppa
39% identity, 45% coverage
- Ligand: adenosine-5'-triphosphate (8xfcD)
FN1525 Dipeptide transport ATP-binding protein dppF from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
33% identity, 90% coverage
- Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
Hendrickson, MicrobiologyOpen 2014 - “...FN1190, FN1198, FN1256, FN1301, FN1348, FN1349, FN1352, FN1353, FN1354, FN1362, FN1363, FN1398, FN1420, FN1432, FN1480, FN1525, FN1701, FN1734, FN1735, FN1737, FN1738, FN1739, FN1740, FN1741, FN1797, FN1798, FN1801, FN1811, FN1833, FN1834, FN1858, FN1860, FN1898, FN1989, FN2008, FN2009, FN2102, FN2105, FN2106. 2 Covers FN0130, FN0236, FN0450, FN0598, FN0658,...”
- “...FN1432, FN1801. 4 Covers FN0192, FN0396, FN0397, FN0399, FN0400, FN0998, FN1111, FN1359, FN1362, FN1363, FN1523, FN1525. 5 Covers FN0308, FN0309, FN0310, FN0375, FN0376, FN0377. In contrast to FnSg, FnPg and FnPgSg displayed predominantly unchanged and reduced transporter protein levels in all categories when compared to Fn...”
- The Fusobacterium nucleatum outer membrane protein RadD is an arginine-inhibitable adhesin required for inter-species adherence and the structured architecture of multispecies biofilm
Kaplan, Molecular microbiology 2009 - “...genomic DNA contamination. Amplification from the 3 end of Fn1526 to the 5 end of Fn1525 produced a product from genomic DNA, but not from cDNA confirming that Fn1526 is the last gene transcribed in the operon ( Fig. 6 ). The relationship between the proteins...”
- “...Fn1529 are transcribed as a single unit. No fragments were amplified using primers spanning gene Fn1525 (1525R) and Fn1526 (Fn1526-3F). RNA was used as a negative control for genomic DNA contamination. Black arrowheads indicate the position of primers used in this analysis. Table 1 Effect of...”
C162_11871 ABC transporter ATP-binding protein from Paenibacillus sp. FSL R7-269
35% identity, 91% coverage
- Genomic comparison of sporeforming bacilli isolated from milk
Moreno, BMC genomics 2014 - “...C173_26762 to C173_26742 93% [ Paenibacillus sp.=WP_017690652.1] R7-269 P. sp . Lasso_peptide 4 C162_11816 to C162_11871 78% [ Paenibacillus sp.=WP_019913509.1] Sactipeptides 4 C162_32049 to C162_32089 48% [ Dorea sp.=WP_005337554.1] R5-192 P. amylolyticus Lantibiotic mersacidin C161_23334 to C161_23344 38.0% [ B. cereus =ZP_17590371] Lasso_peptide 4 C161_09323 to...”
CPR_2255 oligopeptide ABC transporter, ATPase component from Clostridium perfringens SM101
34% identity, 95% coverage
OPPF_LACLA / P0A2V4 Oligopeptide transport ATP-binding protein OppF; EC 7.4.2.6 from Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis) (see paper)
TC 3.A.1.5.10 / P0A2V4 OppF, component of Oligopeptide porter (transports peptides of 4-35) amino acyl residues; di- and tripeptides are not transported; hydrophobic basic peptides are preferred). OppA determines the specificity of the system (Doeven et al., 2004). A large cavity in OppA binds proline-rich peptides preferentially (Berntsson et al., 2009). Two crystal structures of OppA with different nonapeptides show binding in different registers from Lactococcus lactis subsp. lactis (Streptococcus lactis) (see 2 papers)
LLNZ_03630 murein tripeptide/oligopeptide ABC transporter ATP-binding protein OppF from Lactococcus cremoris subsp. cremoris NZ9000
llmg_0698 oligopeptide transport ATP-binding protein oppF from Lactococcus lactis subsp. cremoris MG1363
38% identity, 80% coverage
- function: Part of the ABC transporter complex OppABCDF involved in the uptake of oligopeptides (PubMed:8244921). Probably responsible for energy coupling to the transport system (Probable). Essential for uptake of peptides larger than three amino acids and for growth in milk (PubMed:8244921).
catalytic activity: a [peptide](out) + ATP + H2O = a [peptide](in) + ADP + phosphate + H(+) (RHEA:78459)
subunit: The complex is composed of two ATP-binding proteins (OppD and OppF), two transmembrane proteins (OppB and OppC) and a solute-binding protein (OppA). - substrates: Oligopeptides
- Genomics and transcriptomics analysis reveals the mechanism of isobutanol tolerance of a laboratory evolved Lactococcus lactis strain
Gupta, Scientific reports 2020 - “...P 4.12 Peptide degradation 8 LLNZ_02900 Phosphoserine aminotransferase 3.35 Glycine, serine and threonine metabolism 9 LLNZ_03630 Oligopeptide transport ATP-binding protein oppF 3 Peptide uptake 10 LLNZ_04835 Dihydrodipicolinate reductase 2.1 Lysine biosynthesis The PadR transcriptional regulator (LLNZ_01700) that is involved in the regulation of genes required for...”
- Transcriptional response of Lactococcus lactis during bacterial emulsification
Tarazanova, PloS one 2019 - “...transport system permease oppB2 5.3 2.1e-6 llmg_0697 oppD oligopeptide transport ATP-binding protein oppD 5.3 4.2e-5 llmg_0698 oppF oligopeptide transport ATP-binding protein oppF 5.6 5.2e-6 llmg_0699 oppB peptide transport system permease oppB 5.3 2.2e-5 llmg_0700 oppC oligopeptide transport system permease oppC 5.3 1.9e-5 llmg_0096 llmg_0096 glyoxylase 4.9...”
TM0500 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
33% identity, 82% coverage
- The genus Thermotoga: recent developments
Frock, Environmental technology 2010 - “...4B,C ). In the T. maritima genome, the permeases (TM0503, TM0502) and ATP-binding subunits (TM0501, TM0500) ( Fig. 4C ), comprising an oligopeptide ABC transporter, are located immediately upstream of gene encoding for TM0504; anti-microbial peptide transporter domains existed in both TM0500 and TM0501 (COG4167 and...”
- Colocation of genes encoding a tRNA-mRNA hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium Thermotoga maritima
Montero, Journal of bacteriology 2006 - “...subunits of a putative oligopeptide transporter system, while TM0500 and TM0501 are putative ABC transporter ATPases. Unlike other ABC transporter operons of...”
- An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
Conners, Journal of bacteriology 2005 - “...However, transcripts of an Opp/Dpp family transporter operon (TM0500 to TM0503) which lacks a substrate-binding protein are detected at higher levels in high...”
Blon_0650 ABC transporter related from Bifidobacterium longum subsp. infantis ATCC 15697
39% identity, 77% coverage
TC 3.A.1.5.14 / Q9X0U7 TM1220, component of Probable cellobiose porter. Induced by barley, glucomannan (see paper)
TM_1220 ABC transporter ATP-binding protein from Thermotoga maritima MSB8
TM1220 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
35% identity, 88% coverage
- substrates: Cellobiose
- Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85
Raut, Scientific reports 2019 - “...* na ABC TM_1028 31.8% 56 C9RQJ4 FSU_1688 Oligopeptide/dipeptide ABC transporter 1.15 ** na ABC TM_1220 (36%) and cbtD 23 , 55 , 57 Solute binding protein ( SBP ) D9S9B3 FSU_1047 Extracellular solute-binding protein 1.25 **** na SBP Cellobiose/cellodextrin import 31.3% to (cbpB) A3DE73 58...”
- Duplication of genes in an ATP-binding cassette transport system increases dynamic range while maintaining ligand specificity
Ghimire-Rijal, The Journal of biological chemistry 2014 - “...Membrane TM1226 tmMnBP6 TM1221 TM1219 TM1218 ATP TM1222 TM1220 ADP TM1224 PBPs are the specificity-determining unit of ABC transport systems (4, 5)....”
- “...in addition to two ATP-hydrolyzing subunits (TM1219 and TM1220). Binding of ligand by the PBPs stimulates an interaction with the ABC transporter, which couples...”
- In silico method for modelling metabolism and gene product expression at genome scale
Lerman, Nature communications 2012 - “...associated with cellobiose metabolism were identified. Interestingly, the promoter region of the TU-containing TM1222, TM1221, TM1220, TM1219 and TM1218 did not contain a CelR motif ( Fig. 6c,d ). TM1222, TM1221, TM1220 and TM1219 encode for a cellobiose ABC transporter, while TM1218 is annotated as a...”
- Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences
Vanfossen, Applied and environmental microbiology 2009 - “...proteins TM1839 (maltose, maltotriose, trehalose) TM1220 (cellobiose, barley) TM0810 (N-acetylglucosamine or GlcNAc polysaccharide) TM1120...”
- Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales
Noll, BMC evolutionary biology 2008 - “...TM1205 TM0372 X TM1206 TM1218 TM1206 X TM1581 TM1207 TM1219 TM1207 TM0945 TM0009 TM1875 TM1208 TM1220 TM1208 TM1851 TM1581 TM1209 TM1221 TM1209 TM1836 TM1836 TM1203 TM1203 TM1204 TM1839 mal2 TM1829 TM1681 TM1391 TM1830 TM1678 X TM0781 TM1831 2 TM1679 X X TM1832 2 TM1677 2 TM1826...”
- Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
Nanavati, Applied and environmental microbiology 2006 - “...Maltose transportc Annotated by TIGR (34) malG1 malF1 malE1 TM1219 TM1220 TM1221 TM1222 TM1223 TM1226 ABP ABP MSP MSP SBP SBP 1 manL manK manG manF manE manD...”
TC 3.A.1.5.29 / Q9WXR4 Oligopeptide ABC transporter, ATP-binding protein, component of Probable xylan oligosaccharide porter (Conners et al. 2005). Induced by cylan and xylose. Regulated by xylose-responsive regulator XylR from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
TM0058 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
36% identity, 88% coverage
BPSL2200 putative ABC transport system, ATP-binding protein from Burkholderia pseudomallei K96243
40% identity, 44% coverage
ABD05_RS14560 ABC transporter ATP-binding protein from Burkholderia pyrrocinia
37% identity, 46% coverage
TC 3.A.1.5.13 / Q9WXS9 TM0074, component of Probable xylan oligosaccharide porter (Conners et al., 2005). Induced by xylan and xylose. Regulated by xylose-responsive regulator XylR (see paper)
TM0074 oligopeptide ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
34% identity, 93% coverage
- substrates: Xylanoligosaccharides
- Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases
Frock, Applied and environmental microbiology 2012 - “...13, 2017 by University of California, Berkeley TM0072 TM0073 TM0074 Thermotoga sp. strain RQ2 Frock et al. 1986 aem.asm.org 37. 38. 39. 40. 41. 42. 43. 44....”
- Hyperthermostable acetyl xylan esterase
Drzewiecki, Microbial biotechnology 2010 - “...2008 )]; TM0071(), ABCtransporter periplasmic binding protein; TM0072(), ABCtransporter permease protein; TM0073(), ABCtransporter permease protein; TM0074(), ABCtransporter ATPbinding protein; TM0075(), ABCtransporter ATPbinding protein; TM0076(), xylosidase ( bxlA ); TM0077(), acetyl xylan esterase ( axeA ). It is stressed that the proposed intracellular localization of AxeA has...”
- Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
Nanavati, Applied and environmental microbiology 2006 - “...(12) bgtpE ABP ABP MSP MSP SBP TM0071 SBP TM0072 TM0073 TM0074 TM0075 MSP MSP ABP ABP 1 2 TM0112 TM0114 TM0115 MSP SBP ABP 2 xylF xylE xylK Xylose transport...”
TDE0986 oligopeptide/dipeptide ABC transporter, ATP-binding protein from Treponema denticola ATCC 35405
TDE_0986 ABC transporter ATP-binding protein from Treponema denticola ATCC 35405
32% identity, 95% coverage
- Localization and pathogenic role of the cysteine protease dentipain in Treponema denticola
Miyai-Murai, Molecular oral microbiology 2023 - “...chemotaxis protein 2.73 TDE0205 adenylate/guanylate cyclase catalytic 2.69 TDE2054 hypothetical protein 2.59 TDE0421 lipoprotein 2.57 TDE0986 oligopeptide/dipeptide ABC transporter ATP-binding protein 2.56 TDE0423 hypothetical protein 2.50 TDE2270 methyl-accepting chemotaxis protein 2.45 TDE2676 threonine synthase 2.44 TDE0437 HEAT repeat-containing PBS lyase 2.37 TDE0418 lipoprotein 2.27 TDE0987 oligopeptide/dipeptide...”
- Investigation of the potential regulator proteins associated with the expression of major surface protein and dentilisin in Treponema denticola
Arai, Journal of oral microbiology 2020 - “...protein 11.78 TDE0688 Hypothetical protein 11.01 TDE0689 Methylthioribose kinase 10.96 TDE0043 TPR (tetratricopeptide repeats) 10.85 TDE0986 Oligopeptide/dipeptide ABC transporter ATP-binding protein 9.56 TDE0985 Oligopeptide/dipeptide ABC transporter periplasmic peptide-binding protein 8.83 TDE1020 Dicarboxylate transporter periplasmic dicarboxylate-binding protein 6.58 TDE0687 Phosphoribosylaminoimidazole carboxylase catalytic subunit PurE 5.80 TDE0250 Sodium-dependent...”
- The Role of Treponema denticola Motility in Synergistic Biofilm Formation With Porphyromonas gingivalis
Ng, Frontiers in cellular and infection microbiology 2019 - “...8.79 0.00 P TDE0985 Oligopeptide/dipeptide ABC transporter, periplasmic peptide-binding protein, putative 3.22E+08 5.20 0.33 E TDE0986 Oligopeptide/dipeptide ABC transporter, ATP-binding protein 2.92E+06 12.92 0.00 P TDE1004 Flagellar filament core protein (FlaB) 5.28E+08 0.24 0.01 N TDE1208 DNA topoisomerase I (TopA) 6.03E+07 1.93 1.79 L TDE1234 Hypothetical...”
- Localization and pathogenic role of the cysteine protease dentipain in Treponema denticola
Miyai-Murai, Molecular oral microbiology 2023 - “...glycosyl transferase, a sensor histidine kinase, a methyl-accepting chemotaxis protein, three oligopeptide/dipeptide ABC transporters (TDE_0984, TDE_0986, and TDE_087), and an adenylate/guanylate cyclase (TDE_0205) were downregulated ( Table 3 ). Among the differentially expressed genes presented in Tables 2 and 3 , genes encoding membrane-associated proteins, potential...”
PF0360 oligopeptide ABC transporter (ATP-binding protein) from Pyrococcus furiosus DSM 3638
37% identity, 96% coverage
Tfu_0913 oligopeptide/dipeptide ABC transporter, ATP-binding protein from Thermobifida fusca YX
36% identity, 92% coverage
OA04_05160 dipeptide ABC transporter ATP-binding protein from Pectobacterium versatile
39% identity, 41% coverage
bglu_1g12300 hypothetical protein from Burkholderia glumae BGR1
39% identity, 41% coverage
- Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species
Nguyen, The plant pathology journal 2017 - “...ribosomal protein L28 bglu_1g28680 WP_012734522.1 FMN-dependent NADH-azoreductase bglu_1g04330 WP_012734950.1 Cytidylate kinase bglu_1g08790 WP_015875283.1 ABC transporter bglu_1g12300 WP_015875291.1 AraC family transcriptional regulator bglu_1g12380 WP_012734097.1 Sigma-54-dependent Fis family transcriptional regulator bglu_1p1190 WP_012733828.1 AraC family transcriptional regulator bglu_2g10410 WP_012733977.1 Protocatechuate 3,4-dioxygenase subunit beta bglu_2g12060 WP_015877421.1 Alkyl hydroperoxide reductase subunit...”
C9Z5D2 Putative oligopeptide ABC transporter component from Streptomyces scabiei (strain 87.22)
36% identity, 85% coverage
MSMEG_4997 ABC transporter, ATP-binding protein OppD from Mycobacterium smegmatis str. MC2 155
40% identity, 42% coverage
PAB0630 OLIGOPEPTIDE TRANSPORT ATP-BINDING PROTEIN APPF from Pyrococcus abyssi GE5
37% identity, 96% coverage
- Cellobiose uptake in the hyperthermophilic archaeon Pyrococcus furiosus is mediated by an inducible, high-affinity ABC transporter
Koning, Journal of bacteriology 2001 - “...cbt cluster of P. furiosus. ORFs PAB0627, PAB0628, PAB2363, PAB0630, and PAB0631 of the P. abyssi GE5 chromosome resemble cbtA, cbtB, cbtC, cbtD, and cbtF,...”
YEJF_AGRFC / A9CKL2 Peptidoglycan transport ATP-binding protein YejF; EC 7.4.2.- from Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58)) (see paper)
Atu0190 ABC transporter, nucleotide binding/ATPase protein (peptide) from Agrobacterium tumefaciens str. C58 (Cereon)
40% identity, 47% coverage
- function: Part of the ABC transporter complex YejBEF-YepA involved in the uptake of muropeptides, the breakdown products of cell wall peptidoglycan (PubMed:36566216). The import of muropeptides into the cell enables peptidoglycan recycling, which is vital for cell wall integrity in this bacterium (PubMed:36566216). Is also probably part of the ABC transporter complex YejABEF, which is likely involved in broad- spectrum peptide import (Probable). Responsible for energy coupling to the transport system (Probable).
subunit: The complex is composed of one ATP-binding protein (YejF), two transmembrane proteins (YejB and YejE) and a solute-binding protein (YepA or YejA).
disruption phenotype: The deletion mutant is hypersensitive to ampicillin, in a manner only partly dependent on the beta-lactamase AmpC (PubMed:36566216). Deletion of the yejABEF operon leads to the accumulation of anhydromuramyl tri-, tetra- and pentapeptides in large quantities in the extracellular milieu (PubMed:36566216). The yejABEF mutant displays cell swelling and lysis as well as a severe growth defect (PubMed:36566216). - Peptidoglycan recycling mediated by an ABC transporter in the plant pathogen Agrobacterium tumefaciens
Gilmore, Nature communications 2022 - “...consisting of two membrane-spanning proteins yejB and yejE (Atu0188 and Atu0189) and an ATPase yejF (Atu0190). Interestingly, these genes form an operon with a periplasmic SBP, yejA (Atu0187) which was not affected in Tn insertions under Fosfomycin treatment. Instead, our screen identified an alternative peptide-binding SBP...”
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