PaperBLAST

PaperBLAST Hits for reanno::pseudo6_N2E2:Pf6N2E2_1961 ABC transporter for D-sorbitol, permease component 2 (Pseudomonas fluorescens FW300-N2E2) (277 a.a., MMTLKQSRSL...)

Show query sequence

>reanno::pseudo6_N2E2:Pf6N2E2_1961 ABC transporter for D-sorbitol, permease component 2 (Pseudomonas fluorescens FW300-N2E2)
MMTLKQSRSLQSLLLGTLAWVAALLLFFPIFWMVLTSFKTEIDAFATPPQFIFMPTLENY
LHIQERSDYFHFAWNSVLISFSATALCMLIAVPAAYSMAFYETKRTKQTLLWMLSTKMLP
PVGVLMPIYLLAKGAGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPREILEAARLDGA
TLGQEMLRVLLPISKGGLASTMLLSMILCWNEAFWSLNLTSSSAAPLTALIASYSSPEGL
FWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK

Running BLASTp...

Found 250 similar proteins in the literature:

Pf6N2E2_1961 ABC transporter for D-sorbitol, permease component 2 from Pseudomonas fluorescens FW300-N2E2
100% identity, 100% coverage

• mutant phenotype: # Specifically important in carbon source D-Sorbitol. We do not have fitness data for the putative first subunit Pf6N2E2_1962.

AO356_00015 ABC transporter for D-Sorbitol, permease component 1 from Pseudomonas fluorescens FW300-N2C3
99% identity, 100% coverage

• mutant phenotype: Specific phenotypes on D-Sorbitol; D-Sorbitol. (no phenotype on mannitol)

TC 3.A.1.1.49 / O30493 MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK from Pseudomonas fluorescens
91% identity, 100% coverage

• substrates: Arabitinol, glucitol, mannitol

PS417_12705 ABC transporter for D-Mannitol and D-Sorbitol, permease component 1 from Pseudomonas simiae WCS417
91% identity, 100% coverage

• mutant phenotype: Specific phenotypes on D-Mannitol; D-Sorbitol. Also important for D-mannose utilization, but closely related to a P. aeruginosa system that is apparently not a mannose transporter (the substrate-binding component PA2338 does not bind mannose, see PMC6829864).

CPH89_RS23690 carbohydrate ABC transporter permease from Pseudomonas fluorescens
90% identity, 100% coverage

• Transcriptome Reveals Regulation of Quorum Sensing of <i>Hafnia alvei</i> H4 on the Coculture System of <i>Hafnia alvei</i> H4 and <i>Pseudomonas fluorescens</i> ATCC13525
  Wang, Foods (Basel, Switzerland) 2024
  • “...transporter permease CPH89_RS19375 1.480685108 ABC transporter ATP-binding protein CPH89_RS16095 1.459658475 amino acid ABC transporter permease CPH89_RS23690 2.876670285 carbohydrate ABC transporter permease urtD 2.872150064 urea ABC transporter ATP-binding protein UrtD CPH89_RS08665 1.314199994 sulfonate ABC transporter substrate-binding protein ssuB 0.972531529 aliphatic sulfonates ABC transporter ATP-binding protein CPH89_RS15185 0.63533128...”

mtlG / Q4KC55 polyol ABC-type transporter permease component MtlG from Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (see paper)
90% identity, 100% coverage

PSPTO_2705 mannitol ABC transporter, permease protein from Pseudomonas syringae pv. tomato str. DC3000
89% identity, 100% coverage

• Identification of Indole-3-Acetic Acid-Regulated Genes in Pseudomonas syringae pv. tomato Strain DC3000
  Djami-Tchatchou, Journal of bacteriology 2022 (secret)
• Data-Independent Acquisition Proteomics Unravels the Effects of Iron Ions on Coronatine Synthesis in Pseudomonas syringae pv. tomato DC3000
  He, Frontiers in microbiology 2020
  • “...(PSPTO_5562 and PSPTO_5561), peptide transporters (PSPTO_4562, PSPTO_4559, dppC, PSPTO_4558, and PSPTO_4564), a mannitol ABC transporter (PSPTO_2705), dipeptide ABC transporters (PSPTO_4562, PSPTO_4559, dpc, and PSPTO_4564), a D -xylose ABC transporter (xylH), and several other proteins were upregulated in the study. The presence of these ABC transporters showed...”

PA2340 probable binding-protein-dependent maltose/mannitol transport protein from Pseudomonas aeruginosa PAO1
84% identity, 100% coverage

• Catabolite repression control protein antagonist, a novel player in Pseudomonas aeruginosa carbon catabolite repression control
  Sonnleitner, Frontiers in microbiology 2023
  • “...component of ABC maltose/mannitol transporter PA2339 4.97 3.00E-07 PA 2339 Probable binding-protein-dependent maltose/mannitol transport protein PA2340 3.98 1.94E-04 PA 2340 Probable binding-protein-dependent maltose/mannitol transport protein PA2341 5.09 6.80E-13 PA 2341 Probable ATP-binding component of ABC maltose/mannitol transporter PA2342 4.43 3.10E-09 mtlD Mannitol dehydrogenase PA2343 5.74 1.23E-04...”
• Genome-wide association study of signature genetic alterations among pseudomonas aeruginosa cystic fibrosis isolates
  Hwang, PLoS pathogens 2021
  • “...patients may be the background from which the mutations arose in the gene cassette (PA2338, PA2340, PA2341, and PA2342). These large-scale mutations are highlighted in bold in Table 1 . 10.1371/journal.ppat.1009681.t001 Table 1 KEGG annotation of candidate proteins with large-scale mutation. All large-scale mutations were annotated...”
  • “...iron complex outer membrane recepter protein PA2338 K10227 sorbitol/mannitol transport system substrate-binding protein ABC transporters PA2340 K10229 sorbitol/mannitol transport system permease protein ABC transporters PA2341 K10111 multiple sugar transport system ATP-binding protein ABC transporters PA2342 K00045 mannitol 2-dehydrogenase Fructose and mannose metabolism PA2343 K00854 xylulokinase PA2344...”
• Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis
  Schuster, Journal of bacteriology 2003
  • “...PA0887 PA1559 PA2007 PA2008 PA2009 PA2250 PA2338 PA2339 PA2340 PA2341 PA2343 PA3038 PA3174 PA3205 PA3233 PA3234 PA3235 PA3281 PA3282 PA3283 PA3284 PA3364 PA3365...”

PA14_34390 putative binding-protein-dependent maltose/mannitol transport protein from Pseudomonas aeruginosa UCBPP-PA14
84% identity, 100% coverage

• Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates
  Jeske, NPJ biofilms and microbiomes 2022
  • “...PA14_09970 fpvB 1.05 PA14_10600 hpaX 1.48 PA14_34370 mtlK 0.86 PA14_10170 fepB 1.39 PA14_10610 hpcD 1.08 PA14_34390 mtlG 1.45 PA14_13430 fecA 1.15 PA14_10630 hpcC 0.87 PA14_34410 mtlF 1.48 PA14_20010 hasR 1.46 PA14_10640 hpaG2 1.07 PA14_34420 mtlE 1.01 PA14_20030 hasD 1.13 PA14_10650 hpaG1 1.23 PA14_42080 fadB 1.00 PA14_20040...”
• Pseudomonas aeruginosa Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma Patients
  Elmassry, mSystems 2019
  • “...upregulated. The highest level of upregulation was detected with the genes PA14_34370 (10-fold change) and PA14_34390 (34-fold change), which encode orthologs to MtlK and MtlG, respectively. Found in P. protegens , P. syringae , and P. fluorescens , these proteins transport polyols (sugar alcohols) such as...”

RL4216 putative mannitol transmembrane permease component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
63% identity, 99% coverage

• The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum
  Perry, Frontiers in microbiology 2016
  • “...transporter CUT1 mannitol transporter (S. Mel SBP homolog smc01496 induced by dulcitol, sorbitol, mannitol) 1.0 RL4216 mtlG Mannitol transmembrane permease component of ABC transporter VGI 0.56 3.2 GD 1 34.11 NE 1.5.3 Putative permease component of ABC transporter CUT1 mannitol transporter (S. Mel SBP homolog smc01496...”

BPHYT_RS16105 ABC transporter for D-Sorbitol, permease component 1 from Burkholderia phytofirmans PsJN
66% identity, 90% coverage

• mutant phenotype: Specific phenotypes on D-Sorbitol.

PGA1_c13190 ABC transporter for D-Sorbitol, permease component 1 from Phaeobacter inhibens DSM 17395
68% identity, 94% coverage

• mutant phenotype: Specific phenotypes on D-Sorbitol; D-Sorbitol.

TC 3.A.1.1.5 / O30833 SmoG, component of Hexitol (glucitol; mannitol) porter from Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides) (see paper)
61% identity, 99% coverage

• substrates: Hexitols

Ac3H11_2942 ABC transporter for D-Sorbitol, permease component 1 from Acidovorax sp. GW101-3H11
64% identity, 93% coverage

• mutant phenotype: Specific phenotypes on D-Sorbitol. The homolog in P. simiae WCS417 is probably a mannitol transporter as well.

MSMEG_5572 sugar ABC transporter permease protein from Mycobacterium smegmatis str. MC2 155
42% identity, 90% coverage

• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...Aerobic C4-dicarboxylate transport protein Sugar alcohol MSMEG_5571 MSMEG_5572 MSMEG_5573 MSMEG_5574 MSMEG_5575 smoK smoG smoF somE smoR 1.80 1.76 1.99 1.92...”

Dshi_0549 ABC transporter for Xylitol, permease component 2 from Dinoroseobacter shibae DFL-12
41% identity, 90% coverage

• mutant phenotype: Specific phenotypes on Xylitol; Xylitol. Phenotype is very specific

SCO1900 integral membrane sugar transport protein from Streptomyces coelicolor A3(2)
38% identity, 93% coverage

• The DeoR-like pleiotropic regulator SCO1897 controls specialised metabolism, sporulation, spore germination, and phosphorus accumulation in Streptomyces coelicolor
  Fernández-García, Communications biology 2024
  • “...amino acid similarity of 92.2%, 88.2%, 86.1%, 89.1%, 91.6%, and 86.8% with SCO1897, SCO1898, SCO1899, SCO1900, SCO1901, and SCO1903 respectively (Fig. 1a ). SCO1902 was less conserved, showing an average similarity of 58.4% in these model Streptomyces strains. Fig. 1 The sco1897::Tn5 mutant phenotype and genotype,...”
  • “...). The overexpression of sco1901 did not affect the cytosolic phosphorus content, whereas that of sco1900 alone led to a statistically significant decrease in cytosolic phosphorus content (Fig. 3b ). Fig. 3 Phosphorus accumulation in S. coelicolor spores . a Phosphorus accumulation in the sco1897::Tn5 mutant...”
• From waste to health-supporting molecules: biosynthesis of natural products from lignin-, plastic- and seaweed-based monomers using metabolically engineered Streptomyces lividans
  Seo, Microbial cell factories 2023
  • “...Hypothetical protein SCO1902 100/99.0 SLYA8N_28210 Zinc-binding dehydrogenase, smoD SCO1901 100/99.6 SLYA8N_28215 Membrane sugar transporter, smoG SCO1900 100/99.8 SLYA8N_28220 Membrane sugar transport protein, smoF SCO1899 100/100 SLYA8N_28225 Substrate binding protein, smoE SCO1898 100/99.3 SLYA8N_28230 Transcriptional regulator deoR-type, smoR SCO1897 100/99.7 In terms of metabolic adjustment, the use...”

HAH_5144 carbohydrate ABC transporter permease from Haloarcula hispanica ATCC 33960
37% identity, 87% coverage

• Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica
  Ortjohann, Extremophiles : life under extreme conditions 2024
  • “...mscE gene (HAH_5146), this cluster encodes two transmembrane domains (TMDs; mscF , mscG ; HAH_5145, HAH_5144) and one nucleotide-binding domain (NBD; mscK , HAH_5143). Directly up- and downstream of the ABC gene cluster, two dehydrogenase genes and one gene encoding a transcriptional regulator were identified. Together,...”

blr3568 ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
33% identity, 81% coverage

• Growth Rate of and Gene Expression in Bradyrhizobium diazoefficiens USDA110 due to a Mutation in blr7984, a TetR Family Transcriptional Regulator Gene
  Ohkama-Ohtsu, Microbes and environments 2016
  • “...blr7984 mutant cells ( Table 2 ). Five genes induced in the cluster, blr3566, blr3567, blr3568, blr3570, and blr3571, encoded proteins for ABC transport systems, which uptake substances in cells using energy from ATP hydrolysis. Three genes, blr3573, blr3574, and blr3575, induced in the cluster encode...”
  • “...transporter substrate-binding protein 24.3 B blr3567 ABC transporter permease 22.2 B bll7982 hypothetical protein 20.3 blr3568 ABC transporter permease 19.5 B bll7981 dehydrogenase 18.2 blr3571 ABC transporter ATP-binding protein 17.4 B bsr3569 hypothetical protein 16.7 B blr3575 phosphoenolpyruvate-protein phosphotransferase 12.6 B blr3570 ABC transporter ATP-binding protein...”

SACE_0926 binding-protein-dependent transport systems membrane component from Saccharopolyspora erythraea NRRL 2338
32% identity, 87% coverage

• Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain
  Peano, Microbial cell factories 2012
  • “...264; -G 273) Extracellular solute binding protein SACE_0925 337 1PM ABC-type transport system, permease component SACE_0926 284 Missense (V18M, A89T) ABC-type sugar transport system, permease component SACE_0991 300 Frameshift (-G 370) Dipeptide transport system permease SACE_1587 297 Frameshift (-C 585) Sugar transport system permease SACE_1969 152...”

AT5A_09945 carbohydrate ABC transporter permease from Agrobacterium tumefaciens 5A
34% identity, 98% coverage

• Introducing the ArsR-Regulated Arsenic Stimulon
  Rawle, Frontiers in microbiology 2021
  • “...2.6 AT5A_09935 Sugar ABC transporter substrate-binding protein 2.6 AT5A_09940 Sugar ABC transporter transmembrane protein 2.3 AT5A_09945 Sugar ABC transporter transmembrane protein 2.1 AT5A_09950 Sugar ABC transporter nucleotide-binding ATPase 2.2 AT5A_18906 Maltose ABC transporter transmembrane protein 2.4 AT5A_18911 Maltose ABC transporter transmembrane protein 2.4 AT5A_18916 Maltose ABC...”

blr1891 ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
32% identity, 93% coverage

• DNA Microarray-Based Identification of Genes Regulated by NtrC in Bradyrhizobium japonicum
  Franck, Applied and environmental microbiology 2015
  • “...Hypothetical protein Unknown protein bll5155 blr5803 blr1893 blr1891 blr1890 bsr2847 bll3639 blr1895 bll7395 blr4988 blr5556 bll2292 blr2344 bsr5172 blr8273...”

TM0279 sugar ABC transporter, permease protein from Thermotoga maritima MSB8
33% identity, 89% coverage

• In silico method for modelling metabolism and gene product expression at genome scale
  Lerman, Nature communications 2012
  • “...single additional instance in an intergenic region upstream of the TU-containing genes TM0277, TM0278 and TM0279 ( Fig. 6d ). These genes were induced when L -Arab was the carbon source, but not when cellobiose or maltose serves as the carbon source ( Supplementary Fig. S3...”
  • “...known. When we examined these genes using the SEED RAST server 37 , TM0278 and TM0279 were classified as permeases of an ABC transporter putatively involved in L -Arab utilization, whereas TM0277 was not classified because it was annotated as containing an authentic frameshift 38 ....”
• An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
  Conners, Journal of bacteriology 2005
  • “...material). Sugar ABC permease subunits TM0278 and TM0279 do not show strong differential regulation and, together with a frameshifted substrate-binding protein...”

TC 3.A.1.1.25 / Q72H66 Maltose transport system permease protein malG aka TT_C1629, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose from Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (see paper)
WP_011173998 carbohydrate ABC transporter permease from Thermus thermophilus
TTC1629 No description from Thermus thermophilus HB27
34% identity, 89% coverage

• substrates: Maltose, Palatinose, Sucrose, Trehalose
  tcdb comment: The structures have been solved to a resolution range of 1.6-2.0 Å (Chandravanshi et al. 2019). D
• An ArsR/SmtB family member regulates arsenic resistance genes unusually arranged in Thermus thermophilus HB27.
  Antonucci, Microbial biotechnology 2017
  • GeneRIF: TtSmtB is the arsenate sensor responsible for the induction of TtArsC which generates arsenite exported by TTC0354 efflux protein to detoxify cells.
• The high-affinity maltose/trehalose ABC transporter in the extremely thermophilic bacterium Thermus thermophilus HB27 also recognizes sucrose and palatinose
  Silva, Journal of bacteriology 2005
  • “...coli 429 291 280 398 442 439 TTC1627 TTC1628 TTC1629 TTC1288 TTC1287 TTC1286 50/36 60/41 47/34 40/26 48/28 49/31 38/22 56/27 36/27 47/31 55/36 57/41 MalEs show...”

BR0237 sugar ABC transporter, permease protein from Brucella suis 1330
BOV_0230 sugar ABC transporter, permease protein from Brucella ovis ATCC 25840
29% identity, 89% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...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 BCAN_A0239 OSP Maltose import BP BMEI1716 BruAb10230 BR0235 BOV_0228 BCAN_A0238 76 OSP Oligosaccharide or polyol import ABC BMEII0112, ugpC...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...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 BCAN_A0239 OSP Maltose import BP BMEI1716 BruAb10230 BR0235 BOV_0228 BCAN_A0238 76 OSP Oligosaccharide or polyol import ABC BMEII0112, ugpC BruAb21119...”

BAB1_0240 Binding-protein-dependent transport systems inner membrane component from Brucella melitensis biovar Abortus 2308
29% identity, 89% coverage

• Characterization of Three Small Proteins in Brucella abortus Linked to Fucose Utilization
  Budnick, Journal of bacteriology 2018
  • “...guest BAB designation BAB1_0238 BAB1_0239 BAB1_0241 BAB1_0240 BAB1_0242 BAB1_0244 BAB1_0246 BAB1_0247 BAB1_0248 BAB1_0243 BAB1_0237 BAB1_0236 Small Proteins in...”

BMEI1714 MALTOSE TRANSPORT SYSTEM PERMEASE PROTEIN MALG from Brucella melitensis 16M
29% identity, 88% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...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 BCAN_A0239 OSP Maltose import BP BMEI1716 BruAb10230 BR0235 BOV_0228 BCAN_A0238 76 OSP Oligosaccharide or polyol import...”

BCAN_A0240 binding-protein-dependent transport systems inner membrane component from Brucella canis ATCC 23365
28% identity, 89% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...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 BCAN_A0239 OSP Maltose import BP BMEI1716 BruAb10230 BR0235 BOV_0228 BCAN_A0238 76 OSP Oligosaccharide or polyol import ABC BMEII0112, ugpC BruAb21119 BRA1183...”

Ac3H11_794 ABC transporter for Glycerol, permease component 2 from Acidovorax sp. GW101-3H11
32% identity, 92% coverage

• mutant phenotype: Specific phenotype on Glycerol.

HSERO_RS17010 ABC transporter for D-sorbitol/xylitol, permease component 2 from Herbaspirillum seropedicae SmR1
35% identity, 86% coverage

• mutant phenotype: Specifically important for utilization of D-sorbitol and xylitol.

RPA1397 putative sugar ABC transporter, permease protein from Rhodopseudomonas palustris CGA009
33% identity, 94% coverage

• Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris
  Oda, Journal of bacteriology 2005
  • “...RPA1390 RPA1391 RPA1392 RPA1393 RPA1394 RPA1395 RPA1396 RPA1397 RPA1398 RPA1399 RPA1400 glnAIII Genes adjacent to iron nitrogenase gene cluster 1431 1432...”

TC 3.A.1.1.41 / G4FGN6 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
30% identity, 97% coverage

• substrates: Trehalose

PP_2263 sugar ABC transporter, permease protein from Pseudomonas putida KT2440
29% identity, 90% coverage

• Transcriptome Changes in Pseudomonas putida KT2440 during Medium-Chain-Length Polyhydroxyalkanoate Synthesis Induced by Nitrogen Limitation
  Dabrowska, International journal of molecular sciences 2020
  • “...for the nitrogen metabolism pathway (NirB, NirD, CobA, and NasA), ABC transporters (PP_2260, PP_2261, PP_2262, PP_2263, UrtA, UrtB, UrtC, UrtD), and chemotaxis (PP_0779, PP_4888). Other genes code flagellar hook protein (FlgE), transglutaminase (PP_2686), and undetermined, hypothetical proteins (PP_2687, PP_2688, PP_3007, and PP_4331). 2.4. Validation of Illumina...”
  • “...protein 39.87 7.93 8.01 PP_2259 PP_2262 nd sugar ABC transporter permease 11.31 6.05 6.29 PP_2259 PP_2263 nd sugar ABC transporter permease 9.75 4.34 7.6 PP_2259 PP_5047 glnL ntrB 1.00* 5.82* 1.16 * PP_5048 glnG ntrC 1.00* 4.84* 1.23 * PP_2685 nd hypothetical protein 1.12 4.81 1.45...”

TP0076 sugar ABC transporter, permease protein (y4oR) from Treponema pallidum subsp. pallidum str. Nichols
29% identity, 98% coverage

• Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry
  Osbak, PLoS neglected tropical diseases 2016
  • “...filament outer layer protein FlaA; Tromp-2 27 7.5 13.9 Bacterial-type flagellum-dependent cell motility Flagellum none TP0076 R9UUX9 Sugar ABC superfamily ATP binding cassette transporter, membrane protein 30 7.4 0.4 Transport Inner membrane G TP1029 R9UY97 Uncharacterized protein 25 7.4 0.9 Unknown none TP0249 R9UVD9 Flagellar filament...”
• Footprint of positive selection in Treponema pallidum subsp. pallidum genome sequences suggests adaptive microevolution of the syphilis pathogen
  Giacani, PLoS neglected tropical diseases 2012
  • “...chain release factor 1, PrfA F S (104)P (104) T (59887)C (59897) 351 351 TPChic0076 TP0076 Sugar ABC transporter, permease protein F L (198)V (198) C (83983)G (83994) 276 273 TPChic0265 TP0265 Branched-chain amino acid transport system II carrier protein, BrnQ R P (230)L (230) G...”
  • “...release factor 1 (PrfA)/Transcriptional regulator- DNA binding protein S (104)P (104) C C N TPChic0076 TP0076 Sugar ABC transporter, permease protein/Membrane-Transport L (198)V (198) C C N TPChic0265 TP0265 Amino acid ABC transporter, permease protein (BfnQ)/Membrane-Transport P (230)L (230) C C N TPChic0299 TP0300 Ribose, galactose...”
• Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays
  Matejková, BMC microbiology 2008
  • “...this region b 1 TP0012 37 390 12322 12711 3 nt deletion - - 2 TP0076 29 529 83788 84316 - 1 solitary SNP - 3 TP0117 86 699 134808 135506 7 clustered SNPs - - 4 TP0117 86 3 clustered SNPs - - 5 TP0126...”

SM_b21105 ABC transporter for L-Fucose, permease component 2 from Sinorhizobium meliloti 1021
29% identity, 90% coverage

• mutant phenotype: Specific phenotypes on L-Fucose.

BRA0306 sugar ABC transporter, permease protein from Brucella suis 1330
BCAN_B0307 hypothetical protein from Brucella canis ATCC 23365
33% identity, 90% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...OSP Maltose import ABC BMEII0940 BruAb20874 BRA0307 BOV_A0282 BCAN_B0308 OSP Maltose import IM BMEII0942 BruAb20875 BRA0306 BOV_A0281 BCAN_B0307 OSP Maltose import IM BMEII0943 BruAb20876 BRA0305 BOV_A0280 BCAN_B0306 OSP Maltose import BP BMEII0944 BOV_A0279 OSP Maltose import BP BMEII0945 BruAb20877 BRA0304 BCAN_B0305 82 OTCN Glycine betaine/L-proline import...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...import ABC BMEII0940 BruAb20874 BRA0307 BOV_A0282 BCAN_B0308 OSP Maltose import IM BMEII0942 BruAb20875 BRA0306 BOV_A0281 BCAN_B0307 OSP Maltose import IM BMEII0943 BruAb20876 BRA0305 BOV_A0280 BCAN_B0306 OSP Maltose import BP BMEII0944 BOV_A0279 OSP Maltose import BP BMEII0945 BruAb20877 BRA0304 BCAN_B0305 82 OTCN Glycine betaine/L-proline import ABC BMEI0439,...”

SMc02516 PUTATIVE TRANSPORT SYSTEM PERMEASE ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
30% identity, 100% coverage

• Antimicrobial nodule-specific cysteine-rich peptides induce membrane depolarization-associated changes in the transcriptome of Sinorhizobium meliloti
  Tiricz, Applied and environmental microbiology 2013
  • “...SMc03807 SMc03900 SMc04350 SMc04351 SMc02514 SMc02515 SMc02516 SMc02517 SMc02518 SMc02519 SMc00265 SMc02171 SMc02219 SMc02616 SMc02873 SMc03121 SMc03167...”

RUMGNA_02696 hypothetical protein from Ruminococcus gnavus ATCC 29149
31% identity, 92% coverage

• Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut
  Bell, Nature microbiology 2019
  • “...single ABC transporter, orthologous to the uncharacterised Steptococcus pneumoniae SAT2 system (Sp_1690-2), including two permeases (RUMGNA_02696 and 02697) and Rg SBP (RUMNGA_02698). R. gnavus SAT2 transporter is expected to be coupled with an MsiK-like ATPase encoded elsewhere in the genome, with RUMGNA_03040 sharing 59% identity with...”
• The mucin-degradation strategy of Ruminococcus gnavus: The importance of intramolecular trans-sialidases
  Crost, Gut microbes 2016
  • “...transporter composed of a solute-binding protein (RUMGNA_02698 or RGNV35913_01296) and two putative permeases (RUMGNA_02697 and RUMGNA_02696, or RGNV35913_01295 and RGNV35913_01294) ( Fig.5A ). It is not known whether this transporter is specific of the 2,7-anhydro-Neu5Ac or could also transport Neu5Ac. Once inside the cell, 2,7-anhydro-Neu5Ac could...”
  • “...solute-binding protein (RUMGNA_02698 in ATCC 29149;RGNV35913_01296 in ATCC 35913) and two putative permeases (RUMGNA_02697 and RUMGNA_02696 in ATCC 29149; RGNV35913_01295 and RGNV35913_01294 in ATCC 35913) and then hydrolyzed into Neu5Ac, possibly by the action of RUMGNA_02701 or RGNV35913_01299, before being catabolized into GlcNAc-6-P following the traditional...”
• Utilisation of mucin glycans by the human gut symbiont Ruminococcus gnavus is strain-dependent
  Crost, PloS one 2013
  • “...following 3 genes code for a predicted solute-binding protein (RUMGNA_02698) and two putative permeases (RUMGNA_02697, RUMGNA_02696), components of a sugar ABC transporter; RUMGNA_02696gp has specific homology with putative sialic acid transporters of the SAT2 family [54] . The following gene has no known function. The sialidase...”
  • “...pairs). To confirm this bioinformatics analysis, RT-PCR analysis using primer sets encompassing the neighboring ORFs (RUMGNA_02696 to RUMGNA_02691) was performed on total RNA extracted from a mid-logarithmic phase culture of R. gnavus ATCC 29149 grown with mucins or 3SL as sole carbon source. The data showed...”

NGR_c30980 carbohydrate ABC transporter permease from Sinorhizobium fredii NGR234
NGR_c30980 putative permease component of ABC transporter from Rhizobium sp. NGR234
30% identity, 100% coverage

• Calcium Induces the Cleavage of NopA and Regulates the Expression of Nodulation Genes and Secretion of T3SS Effectors in Sinorhizobium fredii NGR234
  Kim, International journal of molecular sciences 2024
  • “...putative ATP-binding protein of sugar ABC transporter NGR_c30970 4.03463148 putative permease component of ABC transporter NGR_c30980 3.840488791 putative permease component of ABC transporter NGR_c30990 3.026543595 putative transmembrane protein thuE 3.61249158 ABC transporter sugar-binding protein Energy production and conversion/Protein turnover, chaperones glpD2 5.238406536 glycerol-3-phosphate dehydrogenase glpR 4.505200318...”

RPPS3_43670, RPYSC3_44090 carbohydrate ABC transporter permease from Rhodopseudomonas palustris
30% identity, 91% coverage

• Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3)
  Lo, Scientific reports 2018
  • “...there are genes encoding multiple sugar ABC transport systems (RPPS3_01220, RPPS3_01230, RPPS3_033890, RPPS3_35020, RPPS3_35050, RPPS3_35450, RPPS3_43670, RPPS3_45360, RPYSC3_01220, RPYSC3_01230, RPYSC3_35200, RPYSC3_35230, RPYSC3_35650, RPYSC3_44090 and RPYSC3_45830) and TonB-dependent transporters in the R. palustris genomes (Supplementary Tables S5 and S6 ). TonB-dependent transporters have been considered to be...”
  • “...transport systems (RPPS3_01220, RPPS3_01230, RPPS3_033890, RPPS3_35020, RPPS3_35050, RPPS3_35450, RPPS3_43670, RPPS3_45360, RPYSC3_01220, RPYSC3_01230, RPYSC3_35200, RPYSC3_35230, RPYSC3_35650, RPYSC3_44090 and RPYSC3_45830) and TonB-dependent transporters in the R. palustris genomes (Supplementary Tables S5 and S6 ). TonB-dependent transporters have been considered to be involved in dietary polysaccharide processing in bacteria...”

BMEII0942 MALTOSE TRANSPORT SYSTEM PERMEASE PROTEIN MALG from Brucella melitensis 16M
33% identity, 90% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BMEII0755 81 OSP Maltose import ABC BMEII0940 BruAb20874 BRA0307 BOV_A0282 BCAN_B0308 OSP Maltose import IM BMEII0942 BruAb20875 BRA0306 BOV_A0281 BCAN_B0307 OSP Maltose import IM BMEII0943 BruAb20876 BRA0305 BOV_A0280 BCAN_B0306 OSP Maltose import BP BMEII0944 BOV_A0279 OSP Maltose import BP BMEII0945 BruAb20877 BRA0304 BCAN_B0305 82 OTCN Glycine...”

RL3860 putative transmembrane component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
30% identity, 84% coverage

• Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics
  Ramachandran, Genome biology 2011
  • “...is unknown, it clearly has a role in the pea rhizosphere as a mutation in RL3860 led to a RCI of 0.58 (Additional file 8 ). The transporter genes are surrounded by genes encoding predicted mandelate racemase/muconate lactonising proteins (RL3858, RL3864-66), a family of enzymes involved...”

MSMEG_3268 ABC transporter, permease protein from Mycobacterium smegmatis str. MC2 155
33% identity, 86% coverage

• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...periplasmic protein Unknown MSMEG_3264 MSMEG_3265 MSMEG_3266 MSMEG_3267 MSMEG_3268 MSMEG_3269 MSMEG_3270 MSMEG_3271 abcR sugK abcE abcF abcG abcK1 abcK2 sugK...”

Pf1N1B4_5114 sucrose ABC transporter, permease component 2 from Pseudomonas fluorescens FW300-N1B4
31% identity, 92% coverage

• mutant phenotype: Specific phenotype on sucrose

TT_P0041 No description from Thermus thermophilus HB27
32% identity, 88% coverage

• Engineering the genome of Thermus thermophilus using a counterselectable marker
  Carr, Journal of bacteriology 2015
  • “...of p-Cl- A Counterselectable Marker for T. thermophilus TT_P0041, without deleting any chromosomal sequence, to produce strain MD132 (Fig. 2A; see also Fig. S4...”
  • “...Number 6 surrounding open reading frames, walking outward from TT_P0041 to map the limits of each deletion. From these analyses, we determined that the MD156...”

SSGG_01377 sugar ABC transporter permease from Streptomyces filamentosus NRRL 15998
31% identity, 94% coverage

• Transcriptional analysis of the effect of exogenous decanoic acid stress on Streptomyces roseosporus
  Liao, Microbial cell factories 2013
  • “...of trehalose (Table 3 ). Expression of genes coding for the putative maltose ABC transporter (SSGG_01377), and Tres (SSGG_05057) which catalyzes the conversion of maltose into Trehalose was elevated. In addition, gene expression of alpha-amylase (SSGG_05058) was induced, which degrade starch to provide the maltose for...”
  • “...significant change in expression in DA-stress relative to control Locus Gene description Log 2 stress/control SSGG_01377 putative maltose ABC transporter permease 2.46 SSGG_05057 trehalose synthase 3.09 SSGG_05058 alpha-amylase 2.12 SSGG_03685 fructose-bisphosphate aldolase 1.37 SSGG_06343 phosphopyruvate hydratase 1.63 SSGG_01114 pyruvate kinase 1.30 SSGG_02477 phosphopyruvate hydratase 1.53 Genes...”

cg0831 sugar ABC transporter, permease protein from Corynebacterium glutamicum ATCC 13032
29% identity, 90% coverage

• HrrSA orchestrates a systemic response to heme and determines prioritization of terminal cytochrome oxidase expression
  Keppel, Nucleic acids research 2020
  • “...metabolism, LuxR-family 10 2.1 0.5 0.6 Oxidative stress cg0310 katA Catalase 132 19 0.7 1.2 cg0831 tusG Trehalose uptake system, ABC-type, permease protein 30 1.8 0.0 0.2 cg1791 gapA Glyceraldehyde-3-phos. dehydrogenase, glycolysis 86 3.9 0.3 0.4 cg1069 gapB Glyceraldehyde-3-phos. dehydrogenase, gluconeogenesis 175 2.4 1.6 0.1 Cell...”

Pden_4440 binding-protein-dependent transport systems inner membrane component from Paracoccus denitrificans PD1222
30% identity, 95% coverage

• H-NOX Influences Biofilm Formation, Central Metabolism, and Quorum Sensing in Paracoccus denitrificans
  Islam, Journal of proteome research 2024
  • “...denitrificans , we observe significant downregulation for an entire operon of the CUT1 family (Pden_4439, Pden_4440, and Pden_4442) as well as several monosaccharide SBPs of the CUT2 family (Pden_4771, Pden_4845, and Pden_4851) and an amino acid SBP of the HAAT family (Pden_4797). This indicates a disruption...”

smoH / Q7CS31 ABC-type 3-(6-sulfo-α-D-quinovosyl)-sn-glycerol transporter permease subunit from Agrobacterium fabrum (strain C58 / ATCC 33970) (see paper)
Atu3284 ABC transporter, membrane spanning protein (sugar) from Agrobacterium tumefaciens str. C58 (Cereon)
31% identity, 97% coverage

• Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria
  Sharma, Proceedings of the National Academy of Sciences of the United States of America 2022
  • “...( Atu3277 - Atu3285 ) for cells grown on SQ. Proteins encoded by Atu3283 and Atu3284 were not observed; however, they are predicted to be integral membrane proteins that can be difficult to detect using conventional proteomic workflows ( 14 ). Thus, the gene cluster Atu3277-Atu3285...”
  • “...the gene cluster identified through proteomics, Atu3281 ( smoE ), Atu3283 ( smoG ), and Atu3284 ( smoH ) were annotated as an ABC transporter system, with Atu3282 ( smoF ) encoding an associated periplasmic solute-binding protein. The substrate preferences of solute-binding proteins are useful for...”

AT5A_19376 carbohydrate ABC transporter permease from Agrobacterium tumefaciens 5A
33% identity, 78% coverage

• Introducing the ArsR-Regulated Arsenic Stimulon
  Rawle, Frontiers in microbiology 2021
  • “...5.9 5.1 AT5A_19371 Sugar ABC transporter permease 5.7 6.3 6.1 4.3 25.4 5.4 4.7 4.0 AT5A_19376 Multiple sugar transport system permease protein 4.2 4.6 9.1 3.1 30.9 3.7 3.5 3.0 AT5A_19386 Sugar ABC transporter ATP-binding protein 2.2 2.5 17.2 33.6 2.1 2.0 AT5A_19781 Ribose ABC transporter...”
  • “...upon As(III) exposure. An example of this pattern is the sugar transporter system (AT5A_19366, AT5A_19371, AT5A_19376, AT5A_19386) in the arsR1 mutant ( Supplementary Table 3 ). The third pattern involved no deviation from wild type in the absence of As(III), followed by a significant change in...”

SPO0612 carbohydrate ABC transporter permease from Ruegeria pomeroyi DSS-3
29% identity, 91% coverage

• Bacterial transcriptional response to labile exometabolites from photosynthetic picoeukaryote Micromonas commoda
  Ferrer-González, ISME communications 2023
  • “...AAV93925.1 8.5 glycerol ABC transporter, ATP binding protein SPO0611 AAV93926.1 12.6 glycerol ABC transporter, permease SPO0612 AAV93927.1 10.5 glycerol ABC transporter, permease SPO1017 AAV94321.1 5.7 lactic acid ABC transporter ATP-binding protein SPO1018 AAV94322.1 6.6 lactic acid ABC transporter ATP-binding protein SPO1019 AAV94323.1 4.5 lactic acid ABC...”

SSA_0076 ABC sugar transporter, permease protein, putative from Streptococcus sanguinis SK36
30% identity, 93% coverage

• Glucose Phosphotransferase System Modulates Pyruvate Metabolism, Bacterial Fitness, and Microbial Ecology in Oral Streptococci
  Zeng, Journal of bacteriology 2023 (secret)
• Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut
  Bell, Nature microbiology 2019
  • “...(72% identity/86% similarity) with the SBP from the putative sialic transporters in Streptococcus sanguinis SK36 (SSA_0076) and Streptococcus gordonii str. Challis substr. CH1 (SGO_0122) 12 . It would therefore be of interest to determine the specificity of Streptococcus SBPs towards 2,7-anhydro-Neu5Ac. Once inside the cell, 2,7-anhydro-Neu5Ac...”
• Insights into the evolution of sialic acid catabolism among bacteria
  Almagro-Moreno, BMC evolutionary biology 2009
  • “...SP_1328 8.00E-59 Streptococcus pyogenes M1 GAS SAT 3 Spy_254 seed Streptococcus sanguinis SK36 SAT 2 SSA_0076 seed Vibrio cholerae N16961 TRAP VC1777 seed Vibrio fischeri ES114 SSS VF0668 seed Vibrio vulnificus YJ016 TRAP VVA1200 0 Yersinia bercovieri ATCC 43970 NanT YberA_01002486 1.00E-91 Yersinia enterocolitica subsp. enterocolitica...”
  • “...(VC1777) Tripartite ATP-independent periplasmic C4-dicarboxylate transport system SAT (HD1670) ATP binding cassette transporter SAT 2 (SSA_0076) ATP binding cassette transporter SAT 3 (Spy_254) ATP binding cassette transporter N-acetylneuraminate transport system permease SSS (VF0668) Sodium-glucose/galactose cotransporter/SSS family Sym (SSP0376) Na+/proline symporter All the Gamma-Proteobacteria that contained the...”

SCO2944 sugar transporter membrane protein from Streptomyces coelicolor A3(2)
30% identity, 91% coverage

• SepG coordinates sporulation-specific cell division and nucleoid organization in Streptomyces coelicolor
  Zhang, Open biology 2016 (no snippet)
• The dasABC gene cluster, adjacent to dasR, encodes a novel ABC transporter for the uptake of N,N'-diacetylchitobiose in Streptomyces coelicolor A3(2)
  Saito, Applied and environmental microbiology 2007
  • “...of the signature sequence SCO0532 SCO0533 SCO2945 SCO2944 SCO5233 (DasB) SCO5234 (DasC) 302 285 316 281 328 276 ESARMDGAGAARVERSVTFP EAAQVDGCTRAGAFRRVAFP...”

BF29_RS14610 carbohydrate ABC transporter permease from Heyndrickxia coagulans DSM 1 = ATCC 7050
30% identity, 99% coverage

• Time-resolved transcriptomic and proteomic profiling of <i>Heyndrickxia coagulans</i> during NaOH-buffered L-lactic acid production
  Huang, Frontiers in microbiology 2023
  • “...coagulans DSM1-mediated L-LA production. ThuEFG constitutes a trehalose/maltose transport system; with ThuF (BF29_RS14615) and ThuG (BF29_RS14610) serve as permease proteins, and ThuE (BF29_RS14620) acts as the substrate-binding protein ( Jensen et al., 2002 ). Trehalose is widely recognized as a universal stress molecule and osmoprotectant, safeguarding...”

DJ458_RS02925 carbohydrate ABC transporter permease from Staphylococcus pseudintermedius
29% identity, 90% coverage

• Staphylococcal Protein A (spa) Locus Is a Hot Spot for Recombination and Horizontal Gene Transfer in Staphylococcus pseudintermedius
  Zukancic, mSphere 2020
  • “...also shown. DJ458_RS02915 encodes a sn -glycerol-3-phosphate ABC transporter; DJ458_RS02920 encodes a Gfo/Idh/MocA family oxidoreductase; DJ458_RS02925 encodes a carbohydrate ABC transporter permease; DJ458_RS02930 encodes a sugar ABC transporter permease; DJ458_RS02935 encodes a sugar ABC transporter substrate-binding protein; DJ458_RS02940 encodes a helix-turn-helix domain-containing protein. The lineage-specific genes...”

OB3121 sugar ABC transporter permease from Oceanobacillus iheyensis HTE831
31% identity, 93% coverage

• Reconstruction of xylose utilization pathway and regulons in Firmicutes
  Gu, BMC genomics 2010
  • “...xyloside transport via a committed ABC cassette was predicted for Oceanobacillus iheyensis ( OB3123 - OB3121 ) and several other species. The Xyn ABC transport system is homologous to an oligosaccharide ABC transporter from the Streptococcus mutans (~24% identity; [ 25 ]). The functional prediction is...”

PM1760 unknown from Pasteurella multocida subsp. multocida str. Pm70
28% identity, 99% coverage

• Using genomics to understand inter- and intra- outbreak diversity of Pasteurella multocida isolates associated with fowl cholera in meat chickens
  Omaleki, Microbial genomics 2020
  • “...the isolates from each group (PM1333 and PM1352 in the LPS type 3 isolates and PM1760 and PM17644 in the LPS type 1 isolates) had their LPS outer core biosynthesis loci over 2 contigs (broken natC gene and broken pcgD gene, respectively). A review of the...”
• Screening of Streptococcus pneumoniae ABC transporter mutants demonstrates that LivJHMGF, a branched-chain amino acid ABC transporter, is necessary for disease pathogenesis
  Basavanna, Infection and immunity 2009
  • “...SsuiDRAFT_0078 SsuiDRAFT_0077 Spy1227 SAK_1051 Spy0928 PM1760 PM1761 PM1762 SsuiDRAFT_0524 SsuiDRAFT_0525 SsuiDRAFT_0526 Lxx14070 STH2752 Lxx14040 RUMOBE_00498...”

Csac_2491 binding-protein-dependent transport systems inner membrane component from Caldicellulosiruptor saccharolyticus DSM 8903
26% identity, 88% coverage

• Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus
  van, Applied and environmental microbiology 2008
  • “...to Csac_0784), a maltose ABC transport system (Csac_2491 to Csac_2493), and a second pullulanase (Csac_0671). Thus, C. saccharolyticus is well equipped...”
  • “...and Csac_0431) and the maltose ABC transport system (Csac_2491 to Csac_2493). As observed for certain T. maritima maltose transporters, both sets of transport...”

SM_b20327 ABC transporter for D-trehalose/D-maltose/sucrose, permease component 2 (ThuG) from Sinorhizobium meliloti 1021
TC 3.A.1.1.17 / Q9R9Q5 ThuG aka RB0313 aka SMB20327, component of Trehalose/maltose/sucrose porter (trehalose inducible) from Rhizobium meliloti (Sinorhizobium meliloti) (see 3 papers)
32% identity, 92% coverage

• mutant phenotype: Specific phenotype on trehalose, but also reported to transport maltose and sucrose (PMID:12003938; also PMC1635973)
• substrates: Maltose, Sucrose, Trehalose

pRL90234 putative permease component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
29% identity, 93% coverage

• Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere
  Garcia-Fraile, Plant and soil 2015
  • “...study X376 (H2K2B08-1C04) 3841 carrying mTn5 in RL0634 This study X377(H2K2C06-1B06) 3841 carrying mTn5 in pRL90234 This study X378H5K5F04-1A10) 3841 carrying mTn5 in RL1109 This study X379 (H2K2B02-1B05) 3841 carrying mTn5 in RL0811A This study X380 (H2K2C07-1C07) 3841 carrying mTn5 in RL4123 This study X382 (H3K3G11-1E05)...”
  • “...This study A1398 300 carrying mTn5 in RL0634 This study A1399 300 carrying mTn5 in pRL90234 This study A1401 300 carrying mTn5 in RL0811A This study A1402 300 carrying mTn5 in RL4123 This study A1404 300 carrying mTn5 in RL3613 This study A1405 300 carrying mTn5...”

C289_1910 carbohydrate ABC transporter permease from Anoxybacillus ayderensis
31% identity, 89% coverage

• A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization
  Kahar, International journal of molecular sciences 2013
  • “...transporters (C289_0465, C289_0466, C289_0467, C289_0603, C289_0763, C289_0764, C289_0765, C289_0778, C289_0779, C289_0780, C289_1015, C289_1174, C289_1392, C289_1394, C289_1910, C289_1911, and C289_1912) were also found in the Blast2GO annotation. The draft genome was submitted to the National Center for Biotechnology Information (NCBI) Bioproject with accession no. PRJNA174378. 2.2. Analysis...”

blr3920 ABC transporter permease protein from Bradyrhizobium japonicum USDA 110
29% identity, 84% coverage

• Genome-wide transcriptional and physiological responses of Bradyrhizobium japonicum to paraquat-mediated oxidative stress
  Donati, Applied and environmental microbiology 2011
  • “...bll6833 bll6834 blr1601 blr1602 blr1604 blr3917 blr3920 ABC transporter ATP-binding protein ABC transporter substrate-binding protein Probable ABC transporter...”

TC 3.A.1.1.33 / Q8KN17 Putative sugar transporter integral membrane protein, component of The N,N'-diacetylchitobiose uptake transporter, DasABC/MsiK (MsiK energizes several ABC transporters (see 3.A.1.1.23)) from Streptomyces sp. 139 (see 2 papers)
31% identity, 90% coverage

• substrates: N,N'-diacetylchitobiose

CGSSp3BS71_10423 sugar ABC transporter permease from Streptococcus pneumoniae SP3-BS71
29% identity, 90% coverage

• Blood group antigen recognition by a solute-binding protein from a serotype 3 strain of Streptococcus pneumoniae
  Higgins, Journal of molecular biology 2009
  • “...gene ( Fig. 1B ). Downstream of fcssbp are two contiguous genes (Locus tags: CGSSp3BS71_10428 CGSSp3BS71_10423) ( Fig. 1B ) that are distantly related to each other (18% identity at the DNA level) and encode proteins with predicted topologies of six and five transmembrane segments, respectively....”

TC 3.A.1.1.44 / Q9KZ08 Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
SCO2229 maltose permease from Streptomyces coelicolor A3(2)
27% identity, 90% coverage

• substrates: Maltodextrin, Maltose
  tcdb comment: The MalK protein may be the MsiK (Sco4240; Q9L0Q1; see 3.A.1.1.33) protein
• Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor
  Romero-Rodríguez, BMC microbiology 2016
  • “...4a ). Glucose repression was detected over the maltose transporter malG and malF genes ( SCO2229 - SCO2230 ) and the putative operon SCO3482 - SCO3484 (coding for a sugar permease, an integral membrane transport protein and a sugar-binding protein) were repressed (Fig. 4b ). It...”

DASC_STRCO / Q9K489 Diacetylchitobiose uptake system permease protein DasC from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (see paper)
SCO5234 sugar transporter integral membrane protein from Streptomyces coelicolor A3(2)
29% identity, 93% coverage

• function: Part of the ABC transporter complex DasABC-MsiK involved in N,N'-diacetylchitobiose ((GlcNAc)2) uptake. Responsible for the translocation of the substrate across the membrane.
  subunit: The complex is composed of two ATP-binding proteins (MsiK), two transmembrane proteins (DasB and DasC) and a solute-binding protein (DasA).
• The dasABC gene cluster, adjacent to dasR, encodes a novel ABC transporter for the uptake of N,N'-diacetylchitobiose in Streptomyces coelicolor A3(2)
  Saito, Applied and environmental microbiology 2007
  • “...SCO0532 SCO0533 SCO2945 SCO2944 SCO5233 (DasB) SCO5234 (DasC) 302 285 316 281 328 276 ESARMDGAGAARVERSVTFP EAAQVDGCTRAGAFRRVAFP EAAALDGASQWRIWRSVLAP...”
  • “...is divergently located, whereas two ORFs (SCO5233 and SCO5234) encoding putative integral membrane proteins are present downstream of dasA (see Fig. 2B). On the...”
• Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships
  Rigali, Nucleic acids research 2004
  • “...observed in S.griseus with orfs SCO5232, SCO5233 and SCO5234 that are homologous Table 1. Best HutC/GntR candidates for the PTSNag regulon HutC members (name)...”

SPO3786 carbohydrate ABC transporter permease from Ruegeria pomeroyi DSS-3
29% identity, 90% coverage

• Bacterial transcriptional response to labile exometabolites from photosynthetic picoeukaryote Micromonas commoda
  Ferrer-González, ISME communications 2023
  • “...SPO3784 AAV97004.1 4.6 sugar ABC transporter, ATP-binding protein SPO3785 AAV97005.1 3.9 sugar ABC transporter, permease SPO3786 AAV97006.1 5.6 sugar ABC transporter, permease SPO3787 AAV97007.1 5.2 sugar ABC transporter, substrate-binding protein SPOA0278 AAV97412.1 7.5 TRAP dicarboxylate transporter, large permease dctM SPOA0279 AAV97413.1 7.8 TRAP dicarboxylate transporter, small...”

TEL01S_RS00535 carbohydrate ABC transporter permease from Pseudothermotoga elfii DSM 9442 = NBRC 107921
28% identity, 99% coverage

• Adaptation Strategies to High Hydrostatic Pressures in Pseudothermotoga species Revealed by Transcriptional Analyses
  Fenouil, Microorganisms 2023
  • “...Figure 1 ). Among the over-expressed genes, 14 (locus tags TEL01S_RS00165 to TEL01S_RS00175, TEL01S_RS00525 to TEL01S_RS00535, and TEL01S_RS08670 to TEL01S_RS08705) encode proteins of sugar transport and metabolism, while two genes (locus tags TEL01S_RS06345 and TEL01S_RS06350) encode an ABC-2 type transporter system. Furthermore, five of the under-expressed...”

TC 3.A.1.1.35 / G3LHZ1 GlpQ, component of Glycerol uptake porter, GlpSTPQV from Rhizobium leguminosarum bv. viciae
28% identity, 94% coverage

• substrates: glycerol

ML1088 probable ABC-transport protein, inner membrane component from Mycobacterium leprae TN
31% identity, 87% coverage

• Mycobacterium leprae Transcriptome During In Vivo Growth and Ex Vivo Stationary Phases
  Ojo, Frontiers in cellular and infection microbiology 2021
  • “...compared to MFP5 ( Figure3E ). Many of the sugar transporters like sugA (ML1087), sugB (ML1088) and sugC (ML1089) were down regulated in ML96 along with uspE (ML1769), uspC (ML1770) and mmpL10 (ML1231). ML0283, a possible cation-efflux transporter was significantly upregulated at 96 hr in axenic...”

Blon_0460 binding-protein-dependent transport systems inner membrane component from Bifidobacterium longum subsp. infantis ATCC 15697
27% identity, 94% coverage

• Exposure of Bifidobacterium longum subsp. infantis to Milk Oligosaccharides Increases Adhesion to Epithelial Cells and Induces a Substantial Transcriptional Response
  Kavanaugh, PloS one 2013
  • “...0.017 1.26 0.036 1.78 0.0001 Blon_0392 Cation efflux protein 1.66 0.006 1.84 0.0001 3.04 0.00001 Blon_0460 Binding-protein-dependent transport systems inner membrane component 1.32 0.037 1.38 0.02 1.81 0.001 Blon_0617 Glutamate-cysteine ligase, GCS2 1.32 0.022 1.63 0.0009 1.37 0.014 Blon_0758 Glutaredoxin-like protein 1.45 0.004 1.45 0.004 1.99...”

RPPS3_35020 carbohydrate ABC transporter permease from Rhodopseudomonas palustris
27% identity, 84% coverage

• Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3)
  Lo, Scientific reports 2018
  • “...glucose. In addition, there are genes encoding multiple sugar ABC transport systems (RPPS3_01220, RPPS3_01230, RPPS3_033890, RPPS3_35020, RPPS3_35050, RPPS3_35450, RPPS3_43670, RPPS3_45360, RPYSC3_01220, RPYSC3_01230, RPYSC3_35200, RPYSC3_35230, RPYSC3_35650, RPYSC3_44090 and RPYSC3_45830) and TonB-dependent transporters in the R. palustris genomes (Supplementary Tables S5 and S6 ). TonB-dependent transporters have been...”

AT5A_18911 carbohydrate ABC transporter permease from Agrobacterium tumefaciens 5A
32% identity, 73% coverage

• Introducing the ArsR-Regulated Arsenic Stimulon
  Rawle, Frontiers in microbiology 2021
  • “...2.1 AT5A_09950 Sugar ABC transporter nucleotide-binding ATPase 2.2 AT5A_18906 Maltose ABC transporter transmembrane protein 2.4 AT5A_18911 Maltose ABC transporter transmembrane protein 2.4 AT5A_18916 Maltose ABC transporter substrate-binding protein 2.7 AT5A_18921 Maltose/maltodextrin ABC transporter 2.7 AT5A_19366 Sugar ABC transporter periplasmic sugar-binding protein 7.2 7.8 5.5 5.7 26.5...”

SGO_0122 ABC transporter permease protein SP1688 from Streptococcus gordonii str. Challis substr. CH1
28% identity, 92% coverage

• Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut
  Bell, Nature microbiology 2019
  • “...putative sialic transporters in Streptococcus sanguinis SK36 (SSA_0076) and Streptococcus gordonii str. Challis substr. CH1 (SGO_0122) 12 . It would therefore be of interest to determine the specificity of Streptococcus SBPs towards 2,7-anhydro-Neu5Ac. Once inside the cell, 2,7-anhydro-Neu5Ac needs to be converted back into Neu5Ac to...”
• Effect of starch and amylase on the expression of amylase-binding protein A in Streptococcus gordonii
  Nikitkova, Molecular oral microbiology 2012
  • “...SGO_1304, and msmG SGO_1303 with transcriptional regulator msmR SGO_1306; another Msm-like ABC transporter SGO_0120, SGO_0121, SGO_0122 with each gene having up to 54% amino acid identity with Msm proteins of S. mutans and closely positioned on the chromosome phosphosugar-binding transcriptional regulator SGO_0127; and yet another sugar...”
• Insights into the evolution of sialic acid catabolism among bacteria
  Almagro-Moreno, BMC evolutionary biology 2009
  • “...agalactiae 2603V/R SAT 3 SAG0035 4.00E-121 Streptococcus gordonii str . Challis substr. CH1 SAT 2 SGO_0122 1.00E-130 Streptococcus pneumoniae TIGR4 a SAT 2/3 SP_1688 SP_1682 3.00E-131 Streptococcus pneumoniae TIGR4 b Sym SP_1328 8.00E-59 Streptococcus pyogenes M1 GAS SAT 3 Spy_254 seed Streptococcus sanguinis SK36 SAT 2...”

RPYSC3_35200 carbohydrate ABC transporter permease from Rhodopseudomonas palustris
27% identity, 84% coverage

• Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3)
  Lo, Scientific reports 2018
  • “...multiple sugar ABC transport systems (RPPS3_01220, RPPS3_01230, RPPS3_033890, RPPS3_35020, RPPS3_35050, RPPS3_35450, RPPS3_43670, RPPS3_45360, RPYSC3_01220, RPYSC3_01230, RPYSC3_35200, RPYSC3_35230, RPYSC3_35650, RPYSC3_44090 and RPYSC3_45830) and TonB-dependent transporters in the R. palustris genomes (Supplementary Tables S5 and S6 ). TonB-dependent transporters have been considered to be involved in dietary polysaccharide...”

DR_1436 ABC transporter, permease protein, MalFG family from Deinococcus radiodurans R1
32% identity, 96% coverage

• Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species
  Lim, FEMS microbiology reviews 2019
  • “...and in vitro binding of DqsR to three selected regions has been observed: upstream of DR_1436 (ABC transporter), DR_A0158 (phosphate ABC transporter) and DR_B0067 (extracellular nuclease) (Lin etal. 2016a ). The DqsI and DqsR proteins involved in the AHL-mediated QS system are conserved in the other...”

SCO0533 sugar transporter membrane protein from Streptomyces coelicolor A3(2)
31% identity, 93% coverage

• The dasABC gene cluster, adjacent to dasR, encodes a novel ABC transporter for the uptake of N,N'-diacetylchitobiose in Streptomyces coelicolor A3(2)
  Saito, Applied and environmental microbiology 2007
  • “...acid sequencea Position of the signature sequence SCO0532 SCO0533 SCO2945 SCO2944 SCO5233 (DasB) SCO5234 (DasC) 302 285 316 281 328 276 ESARMDGAGAARVERSVTFP...”

RC1_3731 maltose transport system permease protein malG, putative from Rhodospirillum centenum SW
31% identity, 93% coverage

• Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development
  Dong, BMC genomics 2015
  • “...expression during cyst development. This includes; a variety of sugar transporters coded by RC1_2705, RC1_3730, RC1_3731, RC1_3732, and RC1_3734 ; two TonB homologs ( RC1_0278 and RC1_3723) and several TonB dependent transporters ( RC1_0403 , RC1_0945 ); an outer membrane efflux protein ( RC1_3821); a B...”

LMRG_01861 ABC transporter, permease protein from Listeria monocytogenes 10403S
29% identity, 88% coverage

• The Listeria monocytogenes Bile Stimulon under Acidic Conditions Is Characterized by Strain-Specific Patterns and the Upregulation of Motility, Cell Wall Modification Functions, and the PrfA Regulon
  Guariglia-Oropeza, Frontiers in microbiology 2018
  • “...to include (i) a gene classified as encoding a chemotaxis protein, (ii) the ycjPQRS operon (LMRG_01861 - LMRG_01864; peg_2641 - peg_2644), which is involved in sugar utilization, and (iii) a number of genes encoding proteins similar to internalins (see Tables 6 , 7 for details). One...”

Cthe_1018 binding-protein-dependent transport systems inner membrane component from Clostridium thermocellum ATCC 27405
26% identity, 95% coverage

• A blue native-PAGE analysis of membrane protein complexes in Clostridium thermocellum
  Peng, BMC microbiology 2011
  • “...48 17 Cthe_1557 125974066 ABC transporter related protein ATP-binding protein 30203.7 175 21 47 18 Cthe_1018 125973533 binding-protein-dependent transport systems inner membrane component 31919.9 67 13 23 6 19 Cthe_1840 125974344 cysteine synthase 33392 469 25 57 20 Cthe_1104 125713844 prepilin-type cleavage/methylation 19233.2 183 21 65...”
  • “...C10 14 Cthe_3148 ABC transporter related protein 140 C11 16 Cthe_1020 solute-binding protein 190 18 Cthe_1018 binding-protein-dependent transport systems inner membrane component 21 Cthe_1862 ABC transporter related protein C12 17 Cthe_1557 ABC transporter related protein ATP-binding protein 140 C13 22 Cthe_1754 solute-binding protein 170 C14 12...”

SAG0036 sugar ABC transporter, permease protein from Streptococcus agalactiae 2603V/R
28% identity, 99% coverage

• Maltose uptake by the novel ABC transport system MusEFGK2I causes increased expression of ptsG in Corynebacterium glutamicum
  Henrich, Journal of bacteriology 2013
  • “...further hypothetical protein, from the ORFs sag0034, sag0035, and sag0036, which encode the SBP and the TMDs of the NanT ABC importer for sialic acid (78)....”

MALG_THELN / Q7LYX6 Trehalose/maltose transport system permease protein MalG from Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C) (see 3 papers)
TC 3.A.1.1.7 / O51925 MalG aka PF1741, component of Maltose/trehalose porter (see paper)
PF1741 trehalose/maltose transport inner membrane protein from Pyrococcus furiosus DSM 3638
29% identity, 98% coverage

• function: Part of the ABC transporter complex MalEFGK involved in trehalose/maltose import. Responsible for the translocation of the substrate across the membrane.
  subunit: The complex is composed of two ATP-binding proteins (MalK), two transmembrane proteins (MalG and MalF) and a solute-binding protein (MalE).
• substrates: Maltose, Trehalose
• Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation
  Bräsen, Microbiology and molecular biology reviews : MMBR 2014
  • “...transporters, specific for trehalose/maltose (TM system [PF1739 to PF1741 and PF1744]) and maltodextrins (MD system [PF1933 and PF1936 to PF1938]), were found...”
• 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
  • “...6845 6846 CHOU ET AL. ose transporter (PF1739 to PF1741) and a TrmB homolog (PF1743) known to regulate maltose uptake (30), was minimally affected by the...”
  • “...binding module Membrane protein, DUF835 Mal I operon PF1739 PF1740 PF1741 PF1742 PF1743 PF1744 PF1745 PF1746 PF1747 PF1748 PF1749 1.6 NC NC 1.7 1.8 1.6 NC NC NC...”
• Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus
  Lee, Journal of bacteriology 2006
  • “...phosphorylase Maltose/trehalose-binding protein (Mal-I) PF1740 PF1741 PF1742 PF1743 PF1744 PF1933 PF1935*d PF1936 PF1937 PF1938 Maltose/trehalose transport...”
  • “...E. coli. One is the Mal-I transporter (PF1739 to PF1741, PF1744), which in P. furiosus has been shown to recognize and transport maltose and trehalose but not...”
• Metabolic and evolutionary relationships among Pyrococcus Species: genetic exchange within a hydrothermal vent environment
  Hamilton-Brehm, Journal of bacteriology 2005
  • “...transporter (malEFG and malK, represented by PF1739 to PF1741 and PF1744, respectively), as well as a trehalose-degrading enzyme (PF1742) (1, 32, 36, 37, 44,...”
  • “...PF0796 PF0797 PF0798 PF1337 PF1339 PF1340 PF1737 PF1738 PF1339 PF1740 PF1741 PF1742 PF1743 PF1744 PF1745 PF1746 PF1747 PF1748 PF1749 PF1750 PF1751 * * * * * * *...”
• Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides
  Schut, Journal of bacteriology 2003
  • “...PF1710 PF1711 PF1713 PF1739 [Maltose transport] PF1740 PF1741 PF1742 PF1784 PF1852 PF1870 [Maltose transport] PF1935 PF1936 PF1937 PF1938 PF1951 PF1975 Mean...”
• Biochemical evidence for the presence of two alpha-glucoside ABC-transport systems in the hyperthermophilic archaeon Pyrococcus furiosus
  Koning, Archaea (Vancouver, B.C.) 2002
  • “...furiosus Escherichia coli MalE PF1938 PF1937 PF1936 PF1933 PF1739 PF1740 PF1741 PF1744 1 2 Identity. Similarity. 1 MalF MalG MalK 2 28 (46) 35 (56) 33 (55) 47...”

SPD_1493 sugar ABC transporter, permease protein from Streptococcus pneumoniae D39
SPD_RS07935 carbohydrate ABC transporter permease from Streptococcus pneumoniae D39
30% identity, 89% coverage

• N-acetylglucosamine-Mediated Expression of nagA and nagB in Streptococcus pneumoniae
  Afzal, Frontiers in cellular and infection microbiology 2016
  • “...PTS system, mannose/fructose/sorbose family protein, IID component 3.0 spd_1494 Sugar ABC transporter, permease protein 2.7 spd_1493 Sugar ABC transporter, permease protein 2.4 spd_1866 N-acetylglucosamine-6-phosphate deacetylase, NagA 2.4 spd_1846 PTS system, IIB component 2.3 spd_1246 glucosamine-6-phosphate isomerase, NagB 2.3 spd_0264 PTS system, mannose-specific IIAB components, ManL 2.1...”
• N-acetylgalatosamine-Mediated Regulation of the aga Operon by AgaR in Streptococcus pneumoniae
  Afzal, Frontiers in cellular and infection microbiology 2016
  • “...lyase, NanA2 3.7 spd_1490 Hypothetical protein 3.5 spd_1491 Hypothetical protein 7.4 spd_1492 Hypothetical protein 3.9 spd_1493 Sugar ABC transporter, permease protein, NanW 4.8 spd_1494 Sugar ABC transporter, permease protein, NanV 2.5 spd_1495 Sugar ABC transporter, sugar-binding protein, NanU 6.4 spd_1496 PTS system, IIBC components, NanP 3.2...”
• Sialic acid-mediated gene expression in Streptococcus pneumoniae and role of NanR as a transcriptional activator of the nan gene cluster
  Afzal, Applied and environmental microbiology 2015
  • “...(NanP) (spd_1496), three ABC transporters (NanUVW) (spd_1493 to spd_1495), three hypothetical proteins (spd_1490 to spd_1492), an N-acetylneuraminate lyase...”
  • “...spd_1330 spd_1488 spd_1489 spd_1490 spd_1491 spd_1492 spd_1493 spd_1494 spd_1495 spd_1496 spd_1497 spd_1504 spd_1505 spd_1800 spd_2012 spd_2013 Downregulated...”
• Transcriptional and metabolic effects of glucose on Streptococcus pneumoniae sugar metabolism
  Paixão, Frontiers in microbiology 2015
  • “...0.78 SPD_1057 PTS system, IIB component, putative 1.48 SPD_1409 Sugar ABC transporter, ATP-binding protein 0.52 SPD_1493 Sugar ABC transporter, permease protein 0.61 SPD_1494 Sugar ABC transporter, permease protein 0.54 SPD_1495 Sugar ABC transporter, sugar-binding protein 0.56 SPD_1496 PTS system, IIBC components 0.48 0.72 SPD_1832 PTS system,...”
• SPD_0410 negatively regulates capsule polysaccharide synthesis and virulence in <i>Streptococcus pneumoniae</i> D39
  Tao, Frontiers in microbiology 2024
  • “...SPD_RS00485 spd_0090 ABC transporter substrate-binding 2.16055 2.30E-07 SPD_RS05200 spd_0966 Sugar ABC transporter permease 1.05367 2.61E-07 SPD_RS07935 satC Carbohydrate ABC transporter 1.25945 2.60E-06 SPD_RS07940 satB Sugar ABC transporter permease 1.20096 0.000206 Phosphotransferase system SPD_RS00335 gadV PTS system mannose/fructose/N-acetylgalactosamine-transporter subunit IIB 1.76673 9.74E-06 SPD_RS00340 gadW PTSmannose/fructose/sorbose/N- PTS system...”
• Intracellular replication of Streptococcus pneumoniae inside splenic macrophages serves as a reservoir for septicaemia
  Ercoli, Nature microbiology 2018
  • “...strain D39 (serotype 2), its non-encapsulated derivative R6 51 , 52 , a sialidase/neuraminidase nanA (SPD_RS07935) deletion mutant 53 , the serotype 4 strain TIGR4 54 , and GFP and RFP fluorescent D39 (kindly provided by Jan Willem Veening, Groningen) 17 , were used in this...”

TC 3.A.1.1.12 / Q9AI66 PalG, component of Palatinose (isomaltulose; 6-O-α-D-glucopyranosyl-D-fructose) uptake porter from Erwinia rhapontici (see paper)
28% identity, 95% coverage

• substrates: Palatinose

SP_1688 ABC transporter, permease protein from Streptococcus pneumoniae TIGR4
28% identity, 99% coverage

• Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
  Jiménez-Munguía, PeerJ 2018
  • “...3/3 Downregulated 38765 SP_1465, SP_1466 2/2 Downregulated 38778 SP_1522, SP_1523 2/7 Downregulated 38815 SP_1686, SP_1687, SP_1688, SP_1689 4/4 Downregulated 38822 SP_1724, SP_1725 2/2 Downregulated 38840 SP_1809, SP_1810 2/2 Downregulated 38867 SP_1920, SP_1922 2/3 Downregulated 38868 SP_1923, SP_1924, SP_1925, SP_1926 4/4 Downregulated 38873 SP_1948, SP_1949 2/2 Downregulated...”
• Insights into the evolution of sialic acid catabolism among bacteria
  Almagro-Moreno, BMC evolutionary biology 2009
  • “...str . Challis substr. CH1 SAT 2 SGO_0122 1.00E-130 Streptococcus pneumoniae TIGR4 a SAT 2/3 SP_1688 SP_1682 3.00E-131 Streptococcus pneumoniae TIGR4 b Sym SP_1328 8.00E-59 Streptococcus pyogenes M1 GAS SAT 3 Spy_254 seed Streptococcus sanguinis SK36 SAT 2 SSA_0076 seed Vibrio cholerae N16961 TRAP VC1777 seed...”
• Site-specific contributions of glutamine-dependent regulator GlnR and GlnR-regulated genes to virulence of Streptococcus pneumoniae
  Hendriksen, Infection and immunity 2008
  • “...SP_1306 SP_1356 SP_1357 SP_1358 spr1302 SP_1651 SP_1659 SP_1688 spr1598 SP_1754 spr1620 SP_1811 SP_1817 SP_1869 SP_1870 SP_1871 SP_1872 SP_1887 SP_1888 SP_1889...”

LMOf2365_2828 ABC transporter, permease protein from Listeria monocytogenes str. 4b F2365
29% identity, 88% coverage

• Catabolite control protein C contributes to virulence and hydrogen peroxide-induced oxidative stress responses in <i>Listeria monocytogenes</i>
  Ogunleye, Frontiers in microbiology 2024
  • “...protein 2.7 1.1E-05 LMOf2365_2553 Putative hemin transport system permease protein: FtsX-like permease family 1.7 4.3E-03 LMOf2365_2828 Inner membrane ABC transporter permease protein 1.7 3.2E-02 Pentose phosphate pathway (PPP) LMOf2365_0363 Fructose-6-phosphate aldolase 2.1 8.2E-03 LMOf2365_0379 D-tagatose-1,6-bisphosphate aldolase class-II 1.5 6.2E-03 LMOf2365_0528 Ribulose-phosphate 3 epimerase family 2.1 9.3E-03...”
• Contributions of a LysR Transcriptional Regulator to Listeria monocytogenes Virulence and Identification of Its Regulons
  Abdelhamed, Journal of bacteriology 2020 (secret)

SPD_1500 ABC transporter, permease protein from Streptococcus pneumoniae D39
SPCG_RS08595 carbohydrate ABC transporter permease from Streptococcus pneumoniae CGSP14
28% identity, 99% coverage

• Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination
  Campo, eLife 2018
  • “...0.088 (0.0430.340) 0.226 (0.1940.504) Linear mixed effects CLS01446 Sialic acid and N-acetylmannosamine ABC transporter permease SPD_1500 0.033 (0.0860.080) 0.118 (0.175 - 0.074) 0.074 (0.0390.175) 0.073 (0.0620.126) 0.187 (0.0040.259) Linear mixed effects CLS01563 ROK-family transcriptional repressor protein - 1.502 (1.0301.894) 0.098 (0.141 - 0.039) 0.049 (0.0450.499) 0.028...”
• Sialic acid-mediated gene expression in Streptococcus pneumoniae and role of NanR as a transcriptional activator of the nan gene cluster
  Afzal, Applied and environmental microbiology 2015
  • “...a hypothetical protein (spd_1503), three ABC transporters (spd_1500 to spd_ 1502), a neuraminidase nanB (spd_1499), and an oxidoreductase (spd_1498). The gene...”
• Site-specific contributions of glutamine-dependent regulator GlnR and GlnR-regulated genes to virulence of Streptococcus pneumoniae
  Hendriksen, Infection and immunity 2008
  • “...SPD_1190 SPD_1191 SPD_1192 SPD_1276 SPD_1464 SPD_1472 SPD_1500 SPD_1563 SPD_1564 SPD_1585 SPD_1596 SPD_1602 SPD_1649 SPD_1650 SPD_1651 SPD_1652 SPD_1667...”
• The transcriptomic response of Streptococcus pneumoniae following exposure to cigarette smoke extract
  Manna, Scientific reports 2018
  • “...SPCG_RS00515 Glycosyltransferase 1.64 0.042 SPCG_RS00520 Polysaccharide biosynthesis protein 1.48 0.037 SPCG_RS04895 Endo-beta-N-acetylglucosaminidase LytB 1.40 0.004 SPCG_RS08595 Carbohydrate ABC transporter permease 1.13 0.044 SPCG_RS09625 Phosphotransferase system trehalose transporter subunit IIABC TreP 1.07 0.014 Cell wall/membrane biogenesis SPCG_RS00545 Peptidoglycan-binding protein LysM 1.76 0.004 SPCG_RS04610 ABC-type lipoprotein export system,...”

BRA0750 sugar ABC transporter, permease protein, putative from Brucella suis 1330
28% identity, 92% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...polyol import IM BMEII0541 BruAb20483 BRA0749 BOV_A0700 BCAN_B0757 OSP Oligosaccharide or polyol import IM BruAb20482 BRA0750 BOV_A0699 BCAN_B0756 OSP Oligosaccharide or polyol import BP BMEII0542 BruAb20484 BRA0748 BOV_A0698 BCAN_B0755 OSP Oligosaccharide or polyol import ABC BMEII0544 BruAb20487 BRA0745 BOV_A0696 BCAN_B0753 78 OSP Oligosaccharide or polyol import...”
• The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts
  Paulsen, Proceedings of the National Academy of Sciences of the United States of America 2002
  • “...BR0404 BR0391 BR0355 BR0389, BR0390 BR0221 BRA0631-BRA0635 BRA0749, BRA0750 BRA0907 BRA1080 BRA1096 Unique B. melitensis regions 107 764 276 238 845 105 194 339...”

BMEII0541 SUGAR TRANSPORT SYSTEM PERMEASE PROTEIN from Brucella melitensis 16M
28% identity, 86% coverage

• Differential expression of iron acquisition genes by Brucella melitensis and Brucella canis during macrophage infection
  Eskra, PloS one 2012
  • “...regulatory protein, LYSR family - NC 2.25 BMEII0539 BCAN_B0760 hypothetical cytosolic protein - NC 2.37 BMEII0541 BCAN_B0757 sugar transport system permease protein - NC 2.57 BMEII0542 BCAN_B0755 sugar-binding protein - NC 5.25 BMEII0544 BCAN_B0753 SN-glycerol-3-phosphate transport ATP-binding protein ugpC NC 4.46 BMEII0548 BCAN_B0748 glycine betaine/L-proline transport...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...or polyol import BP BMEII0115 BruAb21116 BRA1180 BCAN_B1211 77 OSP Oligosaccharide or polyol import IM BMEII0541 BruAb20483 BRA0749 BOV_A0700 BCAN_B0757 OSP Oligosaccharide or polyol import IM BruAb20482 BRA0750 BOV_A0699 BCAN_B0756 OSP Oligosaccharide or polyol import BP BMEII0542 BruAb20484 BRA0748 BOV_A0698 BCAN_B0755 OSP Oligosaccharide or polyol import...”

AOT13_11485 carbohydrate ABC transporter permease from Parageobacillus thermoglucosidasius
29% identity, 97% coverage

• Development of a xylose-inducible and glucose-insensitive expression system for Parageobacillus thermoglucosidasius
  Wang, Applied microbiology and biotechnology 2024
  • “...permease, respectively), were found to be directly upstream of the ara operon ( AOT13_11450 to AOT13_11485 ) (Liang et al. 2022a ), which showed moderate sequence identities to XylF, XylG, and XylH of G. kaustophilus HTA426 (35.8%, 54.6%, and 43.1%, respectively, Fig. S3 and Table S4...”

BCAN_B0757 hypothetical protein from Brucella canis ATCC 23365
28% identity, 92% coverage

• Differential expression of iron acquisition genes by Brucella melitensis and Brucella canis during macrophage infection
  Eskra, PloS one 2012
  • “...protein, LYSR family - NC 2.25 BMEII0539 BCAN_B0760 hypothetical cytosolic protein - NC 2.37 BMEII0541 BCAN_B0757 sugar transport system permease protein - NC 2.57 BMEII0542 BCAN_B0755 sugar-binding protein - NC 5.25 BMEII0544 BCAN_B0753 SN-glycerol-3-phosphate transport ATP-binding protein ugpC NC 4.46 BMEII0548 BCAN_B0748 glycine betaine/L-proline transport ATP-binding...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BMEII0115 BruAb21116 BRA1180 BCAN_B1211 77 OSP Oligosaccharide or polyol import IM BMEII0541 BruAb20483 BRA0749 BOV_A0700 BCAN_B0757 OSP Oligosaccharide or polyol import IM BruAb20482 BRA0750 BOV_A0699 BCAN_B0756 OSP Oligosaccharide or polyol import BP BMEII0542 BruAb20484 BRA0748 BOV_A0698 BCAN_B0755 OSP Oligosaccharide or polyol import ABC BMEII0544 BruAb20487 BRA0745...”

sugB / P9WG01 ABC-type trehalose transporter integral membrane protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
SUGB_MYCTU / P9WG01 Trehalose transport system permease protein SugB from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
TC 3.A.1.1.31 / O50453 PROBABLE SUGAR-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER SUGB, component of The trehalose-recycling ABC transporter, LpqY-SugA-SugB-SugC (essential for virulence) from Mycobacterium tuberculosis (see 3 papers)
Rv1237 PROBABLE SUGAR-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER SUGB from Mycobacterium tuberculosis H37Rv
NP_215753 sugar ABC transporter permease SugB from Mycobacterium tuberculosis H37Rv
31% identity, 80% coverage

• function: Part of the ABC transporter complex LpqY-SugA-SugB-SugC, which is highly specific for uptake of trehalose. Involved in the recycling of extracellular trehalose released from trehalose-containing molecules synthesized by M.tuberculosis. Trehalose uptake is essential for virulence. Probably responsible for the translocation of the substrate across the membrane.
  subunit: The complex is composed of two ATP-binding proteins (SugC), two transmembrane proteins (Suga and SugB) and a solute-binding protein (LpqY).
• substrates: Trehalose
• Genomic analysis of Mycobacterium brumae sustains its nonpathogenic and immunogenic phenotype
  Renau-Mínguez, Frontiers in microbiology 2022
  • “...Other virulence factors 72.4 100 Rv1236 sugA 1,378,927 1,379,850 Forward Protein ABC transporter 73.1 93.8 Rv1237 sugB 1,379,855 1,380,679 Forward Protein ABC transporter 81.1 98.9 Rv1238 sugC 1,380,684 1,381,865 Forward Protein ABC transporter 78.7 100 Rv1293 lysA 1,448,028 1,449,371 Forward Other virulence factors 76.1 99.6 Rv1346...”
• Shotgun proteomic profiling of dormant, 'non-culturable' Mycobacterium tuberculosis
  Nikitushkin, PloS one 2022
  • “...behaviour of proteins of the ABC trehalose transporter complex LpqYSugASugBSugC ( Rv1235 , Rv1236 , Rv1237 , Rv1238 ): out of four annotated in the Mtb genome only Rv1235 and Rv1238 were detected in the current study, albeit with a different sign of FC in dormancy,...”
• Heat-killed Mycolicibacterium aurum Aogashima: An environmental nonpathogenic actinobacteria under development as a safe novel food ingredient
  Nouioui, Food science & nutrition 2021
  • “...orf03429 Rv1235 28.3 <60% 2E53 sug A orf03428 Rv1236 53.0 <60% 3E91 sug B orf03427 Rv1237 57.1 <60% 3E109 sug C orf03426 Rv1238 53.9 <60% 8E142 Copper uptake Copper exporter ctp V orf03576 Rv0969 54.3 <60% 0 fad D33 orf02653 Rv1345 61.7 <95% 0 Mbt A...”
• ATP-binding cassette (ABC) import systems of Mycobacterium tuberculosis: target for drug and vaccine development
  Soni, Emerging microbes & infections 2020
  • “...maltose [ 39 ] Trehalose importer (LpqY-SugABC/Rv1235-Rv1238) SBP: LpqY (Rv1235) TMD: SugA (Rv1236) and SugB (Rv1237) NBD: SugC (Rv1238) (two copies) LpqY-SugABC mutant shows reduced virulence in mice [ 43 ] Uptake and recycle disaccharide trehalose [ 43 ] Involved in biofilm formation [ 43 ]...”
• Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection
  Anand, Scientific reports 2014
  • “...HIV-1 strains resistant to multiple protease inhibitors Ritonavir (DB00503;RIT) 0.68 Rv0511; Rv0627; Rv0904c; Rv1092c; Rv1220c; Rv1237; Rv1663; Rv1843c; Rv2026c.; Rv2335; Rv2388c; Rv2678c; Rv2689c; Rv2842c; Rv2935; Rv3303c; Rv3509c; Rv3582c; Rv3825c; Rv3886c; Indicated in combination with other antiretroviral agents for the treatment of HIV-infection. Rosiglitazone (DB00412;BRL) 0.66 Rv0755c;...”
  • “...the treatment of Type II diabetes mellitus Amprenavir (DB00701;478) 0.64 Rv0085; Rv0237; Rv0478; Rv0635; Rv1127c; Rv1237; Rv1505c; Rv1542c; Rv1655; Rv1663.2; Rv1843c; Rv1850; Rv2153c; Rv2524c; Rv2524c; Rv2613c; Rv2689c; Rv2931; Rv2938; Rv2939; Rv3135; Rv3245c; Rv3804c; Rv3882c; Rv3883c; Rv3886c; Rv3887c; For the treatment of HIV-1 infection in combination with...”
• A systematic assessment of mature MBP in membrane protein production: overexpression, membrane targeting and purification
  Hu, Protein expression and purification 2011
  • “...Rv1236 5 33.0 o + Rv1337 6 25.7 o o Rv1457c 6 27.3 o o Rv1237 6 29.1 o o Rv2398c 6 29.3 o o Rv2938 6 29.6 o o Rv2399c 6 29.7 o o Rv2093c 6 33.8 o o Rv0929 6 34.2 o o Rv2881c...”
• Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis
  Fang, BMC systems biology 2010
  • “...phthiocerol dimycocerosate to the biomass objective function [ 62 ] 27 32 33 34 Rv1236 Rv1237 Rv1238 sugA sugB sugC FN Transport Transport of glucose, maltoheptaose, maltose, ribose, trehalose, and xylose into cell (1) Allowed xylose uptake and added xylose to the biomass objective function 28...”
• In vivo inactivation of the mycobacterial integral membrane stearoyl coenzyme A desaturase DesA3 by a C-terminus-specific degradation process
  Chang, Journal of bacteriology 2008
  • “...in sugar transport Rv1237 .....................................Sugar (maltose) transporter Rv1244 .....................................Unknown lipoprotein...”
• Trehalose-recycling ABC transporter LpqY-SugA-SugB-SugC is essential for virulence of Mycobacterium tuberculosis.
  Kalscheuer, Proceedings of the National Academy of Sciences of the United States of America 2010
  • GeneRIF: Data show that the LpqY-SugA-SugB-SugC ATP-binding cassette transporter is a recycling system mediating the retrograde transport of released trehalose.

CPE0373 probable suger ABC transporter from Clostridium perfringens str. 13
28% identity, 88% coverage

• Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces
  Soncini, BMC genomics 2020
  • “...component CPE0371 3.351 0.0405 ugpA Probable ABC transporter CPE0372 3.083 0.0405 ugpE Probable ABC transporter CPE0373 3.126 0.0405 aga Alpha-galactosidase CPE0374 3.251 0.0276 skn1 Endo-beta-galactosidase C CPE0375 3.511 0.0276 arcD Probable amino acid permease CPE0389 3.325 0.0276 dchS Histidine decarboxylase CPE0390 3.404 0.0276 Conserved hypothetical protein,...”

PGA1_c27950 N-Acetyl-D-glucosamine ABC transport system, permease component 2 from Phaeobacter inhibens DSM 17395
26% identity, 99% coverage

• mutant phenotype: Specific phenotypes on N-Acetyl-D-Glucosamine.

BH1866 sugar transport system (permease) (binding protein dependent transporter) from Bacillus halodurans C-125
27% identity, 95% coverage

• Widespread occurrence and genomic context of unusually small polyketide synthase genes in microbial consortia associated with marine sponges
  Fieseler, Applied and environmental microbiology 2007
  • “...baltica BH1865 (BAB05584), Bacillus halodurans BH1866 (BAB05585), B. halodurans ABC1215 (BAD63753), Bacillus clausii SAV6951 (BAC74662), Streptomyces...”

BOV_A0700 putative sugar ABC transporter, permease protein from Brucella ovis ATCC 25840
28% identity, 79% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BP BMEII0115 BruAb21116 BRA1180 BCAN_B1211 77 OSP Oligosaccharide or polyol import IM BMEII0541 BruAb20483 BRA0749 BOV_A0700 BCAN_B0757 OSP Oligosaccharide or polyol import IM BruAb20482 BRA0750 BOV_A0699 BCAN_B0756 OSP Oligosaccharide or polyol import BP BMEII0542 BruAb20484 BRA0748 BOV_A0698 BCAN_B0755 OSP Oligosaccharide or polyol import ABC BMEII0544 BruAb20487...”

CAC0428 Sugar permease from Clostridium acetobutylicum ATCC 824
29% identity, 94% coverage

• Small RNAs in the genus Clostridium
  Chen, mBio 2011
  • “...37 to 42) based on microarray data (34) include the following: CAC3313 (37), CAP0060 (38), CAC0428 (39), CAC1094 (40), CAC2614 (41), and CAC2179 (42). The negative controls (genes 43 to 47) include the following intergenic region (IR) sequences (Ig stands for intergenic): IgCAC_1350 (43), IgCAC_232 (44),...”
• A proteomic and transcriptional view of acidogenic and solventogenic steady-state cells of Clostridium acetobutylicum in a chemostat culture
  Janssen, Applied microbiology and biotechnology 2010
  • “...1.8 R CAC0427 Glycerol-3-phosphate ABC transporter, permease component 3.1 3.1 5.7 2.9 3.7 1.3 G CAC0428 Sugar permease 4.2 2.7 11.2 3.5 5.4 3.9 G CAC0429 Glycerol-3-phosphate ABC transporter, periplasmic component 4.6 3.3 9.2 5.7 5.7 2.5 G CAC0430 Glycerophosphoryl diester phosphodiesterase 2.2 3.5 7.1 6.8...”
  • “...binding protein involved in sugar transport ( msmX , CAC3237) and the genes cac0427 , cac0428 , and cac0429 of a glycerol-3-phosphate ABC transporter system which are organized in a common operon together with glycerophosphoryl diester phosphodiesterase ( cac0430 ; Karp et al. 2005 ). Additionally,...”

MSMEG_0555 ABC transporter permease protein from Mycobacterium smegmatis str. MC2 155
26% identity, 80% coverage

• The Biological Characteristics of Mycobacterium Phage Henu3 and the Fitness Cost Associated with Its Resistant Strains
  Li, International journal of molecular sciences 2024
  • “...factors might influence the antibiotic stress response, further experiments are required for confirmation. Additionally, genes MSMEG_0555, MSMEG_4468, MSMEG_2004 and MSMEG_6758 encode a sugar ABC transporter protease, a substrate-binding protein, an MFS family membrane transporter protein, and an aquaporin, respectively. Research has indicated that the absence of...”
  • “...Henu3-resistant bacteria. Strain Mutation Location Mutant Genes Type of Mutation REF ALT Function 2E1 632863 MSMEG_0555 INDEL C CACACTGTTCTGCGCGTTGTAGACGCGGTTCGACGACGCCGACAGCTCTTTGT Carbohydrate ABC transporter permease 0G102E1 1000473 MSMEG_0916 INDEL GCC G TetR/AcrR family transcriptional regulator 0G10, 2E1 1127759 MSMEG_1060 INDEL CCTG C Lsr2 family protein 0G10, 2E1 2085173...”

lmo0180 similar to sugar ABC transporter, permease protein from Listeria monocytogenes EGD-e
29% identity, 95% coverage

• Listeria monocytogenes grown at 7° C shows reduced acid survival and an altered transcriptional response to acid shock compared to L. monocytogenes grown at 37° C
  Ivy, Applied and environmental microbiology 2012
  • “...b Gene function lmo0113 lmo0114 lmo0136 lmo0137 lmo0180 lmo0181 lmo0230 lmo0231 lmo0232 (clpC) lmo0680 lmo0681 lmo0683 lmo0806 lmo0808 lmo0809 lmo0810 lmo0811...”
• Glycerol metabolism and PrfA activity in Listeria monocytogenes
  Joseph, Journal of bacteriology 2008
  • “...lmo0105b lmo0130b lmo0135 lmo0153 lmo0154 lmo0155 lmo0169 lmo0180 lmo0181 lmo0182a lmo0183 lmo0184 prfAb,d plcAb,d hlyb,d mplb,d actAb,d plcBb,d lmo0206 lmo0207...”

YcjP / b1312 putative ABC transporter membrane subunit YcjP from Escherichia coli K-12 substr. MG1655 (see 2 papers)
TC 3.A.1.1.46 / P77716 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV from Escherichia coli (strain K12)
b1312 predicted sugar transporter subunit: membrane component of ABC superfamily from Escherichia coli str. K-12 substr. MG1655
30% identity, 89% coverage

• substrates: Glucosides
  tcdb comment: Encoded in an operon or gene cluster with a glucosyl hydrolase and two oxidoreductases (Moussatova et al. 2008)
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
  Ren, Applied and environmental microbiology 2005
  • “...b4208 b4138 1.5 0.0005 1.6 0.0074 1.4 0.0170 1.5 0.0004 b1312 bglF fhuD b1312 b3722 b0152 1.0 1.0000 1.4 0.0546 1.1 0.8560 1.6 0.0319 1.6 0.0053 1.6 0.0032 nikE...”
• Biochemistry and regulation of a novel Escherichia coli K-12 porin protein, OmpG, which produces unusually large channels
  Fajardo, Journal of bacteriology 1998
  • “...blot analysis using three different probes, specific to pspA, b1312 to 1313, and ompG (Fig. 6). The data revealed that in the cog-192 strain, regions...”

Rv2834c PROBABLE Sn-GLYCEROL-3-PHOSPHATE TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER UGPE from Mycobacterium tuberculosis H37Rv
29% identity, 90% coverage

• ATP-binding cassette (ABC) import systems of Mycobacterium tuberculosis: target for drug and vaccine development
  Soni, Emerging microbes & infections 2020
  • “...characterized. Sugar importers Glycerophosphocholine importer (UgpABCE /Rv2832c-Rv2835c) SBP: UgpB (Rv2833c) TMD: UgpA (Rv2835c) and UgpE (Rv2834c) NBD: UgpC (Rv2832c) (two copies) UgpB is a substrate of the twin-arginine translocation (Tat) pathway [ 39 ] Import glycerophosphocholine instead of sn-glycerol-3-phosphate and maltose [ 39 ] Trehalose importer...”
• Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread
  Coscolla, The Journal of infectious diseases 2015
  • “...... A G Rv2702 K197E 3 017 446 ppgK C G G A Rv2763c Rv2834c D70H T269I 3 073 402 3 140 509 dfrA ugpE C G Rv3201c V399L 3 575 842 ... G G A A Rv3308 Rv3415c...”
• From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet
  Krawczyk, Nucleic acids research 2009
  • “...( pstA1 ), Rv2220 ( glnA1 ) Rv2832c ( ugpC ), Rv2833c ( ugpB ), Rv2834c ( ugpE ), Rv2835c ( ugpA ), Rv2918c ( glnD ) Rv2919c ( glnB ), Rv2920c ( amt ), Rv3859c ( gltB ) SOS and stress response Rv0867c ( rpfA...”
  • “...( pstA1 ), Rv1095 ( phoH2 ) Rv2832c ( ugpC ), Rv2833c ( ugpB ), Rv2834c ( ugpE ), Rv2835c ( ugpA ) Rv0827c Macroelement and metal homeostasis Rv0827c (-) Rv1994c Macroelement and metal homeostasis Rv1994c (-) IdeR Carbohydrate metabolism Rv0247c (-), Rv3318 ( sdhA )...”

NGCG_STRCO / O50501 Diacetylchitobiose uptake system permease protein NgcG from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (see paper)
SCO6007 probable transmembrane transport protein from Streptomyces coelicolor A3(2)
27% identity, 72% coverage

• function: Part of the ABC transporter complex NgcEFG-MsiK involved in N,N'-diacetylchitobiose ((GlcNAc)2) uptake. Responsible for the translocation of the substrate across the membrane.
  subunit: The complex is composed of two ATP-binding proteins (MsiK), two transmembrane proteins (NgcF and NgcG) and a solute-binding protein (NgcE).
• NgcE^Sco Acts as a Lower-Affinity Binding Protein of an ABC Transporter for the Uptake of N,N'-Diacetylchitobiose in Streptomyces coelicolor A3(2)
  Iinuma, Microbes and environments 2018
  • “...cluster includes two additional ORFs encoding the putative ABC-type integral membrane proteins ( SCO6006 and SCO6007 ) that form a transporter permease ( Fig. S1 ). Regarding most streptomycetes sugar ABC transporters, the gene for the ATPase component was not included in the cluster and energy...”
  • “...identity for the SCO6005 protein and NgcE, 44% for SCO6006 and NgcF, and 50% between SCO6007 and NgcG ( Fig. S1 ). In contrast, the other streptomycetes NgcE orthologues share between 80 to 91% amino acid identities throughout the full-length sequence. These low amino acid identities...”
• The ROK family regulator Rok7B7 pleiotropically affects xylose utilization, carbon catabolite repression, and antibiotic production in streptomyces coelicolor
  Świątek, Journal of bacteriology 2013
  • “...by two sugar transport operons, namely, SCO6005 to SCO6007 (upstream) and the xylose transporter operon xylFGH (SCO6009 to SCO6011; downstream), with its gene...”
  • “...is transported via DasABC (51). Since SCO6005 to SCO6007 shows limited sequence similarity to NgcEFG (around 35% amino acid identity), it likely transports a...”
• The dasABC gene cluster, adjacent to dasR, encodes a novel ABC transporter for the uptake of N,N'-diacetylchitobiose in Streptomyces coelicolor A3(2)
  Saito, Applied and environmental microbiology 2007
  • “...occurred (Fig. 5B). Putative ORFs (SCO6005, SCO6006, and SCO6007) corresponding to the ngcEFG genes of S. olivaceoviridis are present in the S. coelicolor A3(2)...”

SMc02871 ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 from Sinorhizobium meliloti 1021
28% identity, 91% coverage

• mutant phenotype: Specific phenotypes on N-Acetyl-D-Glucosamine; N-Acetyl-D-Glucosamine.

SM_b21219 ABC transporter for D-Glucosamine, permease component 1 from Sinorhizobium meliloti 1021
SMb21219 putative sugar uptake ABC transporter permease protein from Sinorhizobium meliloti 1021
31% identity, 98% coverage

• mutant phenotype: Specific phenotypes on D-Glucosamine Hydrochloride.
• Response of Sinorhizobium meliloti to elevated concentrations of cadmium and zinc
  Rossbach, Applied and environmental microbiology 2008
  • “...putative transporters, mainly of the ABC type (SMa0270, SMb21219, and SMb21344), and those putatively involved in the transport of C4 dicarboxylates (SMa0157),...”
  • “...but genes that encode putative ABC-type transporters (SMa0270, SMb21219, and SMb21344) were induced. The analysis of mutant strains revealed that ExoK and CcsA...”

TC 3.A.1.1.20 / Q7WWQ8 Transmembrane permease MsmG, component of The fructooligosaccharide porter, MsmEFGK from Lactobacillus acidophilus (see 2 papers)
msmG / GI|33149340 transmembrane permease MsmG from Lactobacillus acidophilus (see paper)
27% identity, 95% coverage

• substrates: Fructooligosaccharides

SGO_1303 transmembrane permease MsmG from Streptococcus gordonii str. Challis substr. CH1
26% identity, 86% coverage

• Effect of starch and amylase on the expression of amylase-binding protein A in Streptococcus gordonii
  Nikitkova, Molecular oral microbiology 2012
  • “...Msm transporter candidate in S. gordonii is annotated as: msmE SGO_1305, msmF SGO_1304, and msmG SGO_1303 with transcriptional regulator msmR SGO_1306; another Msm-like ABC transporter SGO_0120, SGO_0121, SGO_0122 with each gene having up to 54% amino acid identity with Msm proteins of S. mutans and closely...”

TC 3.A.1.1.39 / Q9WYR1 Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
TM0430 sugar ABC transporter, permease protein from Thermotoga maritima MSB8
28% identity, 96% coverage

• substrates: Alpha-1,4-digalacturonate
• Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars
  Nanavati, Applied and environmental microbiology 2006
  • “...TM1419, ino1 (myo-inositol-1-P-synthase [1]) malE3b malF3 ugpE malK2 TM0430 TM0431 TM0432 MSP MSP SBP 1 aguG aguF aguE -Galactouronate transport TM0434, agu...”
  • “...has a similarly complex evolutionary history. The ORFs TM0430 to TM0432 encode an apparent -galacturonate (agu, as used for TM0434 [53]) transporter. AguE...”
• Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima
  Nesbø, Journal of bacteriology 2002
  • “...MSB8 5.5E19 7.0E22 Thermotoga neapolitana 1.0E-104 (DNA) 215 TM0430 sugar ABC transporter T. maritima MSB8 5.5E16 52 197 TM0432 sugar ABC transporter T....”

TC 3.A.1.1.18 / Q8RJU8 NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) from Streptomyces olivaceoviridis (Streptomyces corchorusii) (see paper)
27% identity, 83% coverage

• substrates: N,N'-diacetyl chitobiose, N-acetylglucosamine

TEL01S_RS00165 carbohydrate ABC transporter permease from Pseudothermotoga elfii DSM 9442 = NBRC 107921
32% identity, 55% coverage

• Adaptation Strategies to High Hydrostatic Pressures in Pseudothermotoga species Revealed by Transcriptional Analyses
  Fenouil, Microorganisms 2023
  • “...under-expressed at 20 MPa ( Figure 1 ). Among the over-expressed genes, 14 (locus tags TEL01S_RS00165 to TEL01S_RS00175, TEL01S_RS00525 to TEL01S_RS00535, and TEL01S_RS08670 to TEL01S_RS08705) encode proteins of sugar transport and metabolism, while two genes (locus tags TEL01S_RS06345 and TEL01S_RS06350) encode an ABC-2 type transporter system....”

Atu3132 ABC transporter, membrane spanning protein (sugar) from Agrobacterium tumefaciens str. C58 (Cereon)
28% identity, 88% coverage

• Comparative Transcriptome Analysis of Agrobacterium tumefaciens Reveals the Molecular Basis for the Recalcitrant Genetic Transformation of Camellia sinensis L
  Jin, Biomolecules 2022
  • “...atu4786 and others), maltose ( atu0391 , atu4559 , atu4450 ), oligogalacturonide ( atu3130 , atu3132 ), glucose ( atu3351 , atu3352 ), rhamnose ( atu34873490 ), sn-glycerol 3-phosphate ( ugpC = atu3099 / atu3188 ), branched-chain amino acid ( livH = atu4518 , livG =...”

HVO_0562 ABC-type transport system permease protein (probable substrate maltose) from Haloferax volcanii DS2
29% identity, 66% coverage

• A sweet new set of inducible and constitutive promoters in Haloferax volcanii
  Rados, Frontiers in microbiology 2023
  • “...inducer ( Figure 1C ). Above this threshold, we assigned 1 promoter for maltose ( HVO_0562 64 ); 4 for xylose ( HVO_B0027 - 29 , HVO_B0030 - 32 , HVO_B0035 , and HVO_B0036 - 38 ); 3 for arabinose ( HVO_B0027 - 29 , HVO_B0030...”

TC 3.A.1.1.24 / Q72KX4 Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) from Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (see paper)
TTHA0685 sugar ABC transporter, permease protein from Thermus thermophilus HB8
27% identity, 96% coverage

• substrates: Mannose, glucose
• Co-utilization of glucose and xylose by evolved Thermus thermophilus LC113 strain elucidated by (13)C metabolic flux analysis and whole genome sequencing
  Cordova, Metabolic engineering 2016
  • “...for details). Several mutations occurred in genes related to glucose and xylose metabolism, for example: TTHA0685 (ABC sugar transporter), TTHA0687 (ABC sugar transporter), TTHV084 (xylulokinase), and TTHV087 (ABC sugar transporter). In addition, three large structural changes were identified that can also help to explain the physiology...”

PMT0692 ABC transporter component, likely for sugar transport from Prochlorococcus marinus str. MIT 9313
32% identity, 89% coverage

• A suppression subtractive hybridization approach reveals niche-specific genes that may be involved in predator avoidance in marine Synechococcus isolates
  Jones, Applied and environmental microbiology 2006
  • “...4e-07 43/56 53/102 NP_894524 ZP_00264217 Rhizobium sp. strain NGR234 PMT0692 Pseudomonas fluorescens PfO-1 1 1 1 3 1 1 1 B096 B097 B102e B103e B108 B110 B112...”

Csac_0694 binding-protein-dependent transport systems inner membrane component from Caldicellulosiruptor saccharolyticus DSM 8903
29% identity, 100% coverage

• Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences
  Vanfossen, Applied and environmental microbiology 2009
  • “...monosaccharides and polysaccharides, the genes Csac_0692 to Csac_0694 were upregulated only in the monosaccharide mixture. The results presented here affirm the...”

BRA0519 sugar ABC transporter, permease protein from Brucella suis 1330
BMEII0752 MALTOSE TRANSPORT SYSTEM PERMEASE PROTEIN MALG from Brucella melitensis 16M
BCAN_B0518 hypothetical protein from Brucella canis ATCC 23365
28% identity, 91% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...import ABC BMEII0750 BruAb20702 BRA0521 BOV_A0454 BCAN_B0520 OSP Oligosaccharide or polyol import IM BMEII0752 BruAb20704 BRA0519 BOV_A0452 BCAN_B0518 OSP Oligosaccharide or polyol import IM BMEII0753 BruAb20705 BRA0518 BOV_A0451 BCAN_B0517 OSP Oligosaccharide or polyol import BP BMEII0754 BruAb20706 BRA0516 BOV_A0449 BCAN_B0516 OSP Oligosaccharide or polyol import BP...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...or polyol import ABC BMEII0750 BruAb20702 BRA0521 BOV_A0454 BCAN_B0520 OSP Oligosaccharide or polyol import IM BMEII0752 BruAb20704 BRA0519 BOV_A0452 BCAN_B0518 OSP Oligosaccharide or polyol import IM BMEII0753 BruAb20705 BRA0518 BOV_A0451 BCAN_B0517 OSP Oligosaccharide or polyol import BP BMEII0754 BruAb20706 BRA0516 BOV_A0449 BCAN_B0516 OSP Oligosaccharide or polyol...”
• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...BMEII0750 BruAb20702 BRA0521 BOV_A0454 BCAN_B0520 OSP Oligosaccharide or polyol import IM BMEII0752 BruAb20704 BRA0519 BOV_A0452 BCAN_B0518 OSP Oligosaccharide or polyol import IM BMEII0753 BruAb20705 BRA0518 BOV_A0451 BCAN_B0517 OSP Oligosaccharide or polyol import BP BMEII0754 BruAb20706 BRA0516 BOV_A0449 BCAN_B0516 OSP Oligosaccharide or polyol import BP BMEII0755 81...”

BC4011 Cyclodextrin transport system permease protein from Bacillus cereus ATCC 14579
27% identity, 99% coverage

• Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection
  Woo, Cell host & microbe 2021
  • “...elegans : Strain BC4011: srl-1(s2500) II; dpy-18(e364) III; unc-46(e177)rol-3(s1040) V. Caenorhabditis Genetics Center WB Strain: BC4011; WormBase: WBVar00241916 D. melanogaster : RNAi of Sxl. y[1] sc[*] v[1]; P{TRiP.HMS00609}attP2 Bloomington Drosophila Stock Center BDSC:34393; FlyBase: FBtp0064874 S. cerevisiae : Strain background: W303 ATCC ATTC: 208353 Mouse: R6/2:...”
• Cas4 Nucleases Define the PAM, Length, and Orientation of DNA Fragments Integrated at CRISPR Loci
  Shiimori, Molecular cell 2018
  • “...elegans : Strain BC4011: srl-1(s2500) II; dpy-18(e364) III; unc-46(e177)rol-3(s1040) V. Caenorhabditis Genetics Center WB Strain: BC4011; WormBase: WBVar00241916 D. melanogaster : RNAi of Sxl: y[1] sc[*] v[1]; P{TRiP.HMS00609}attP2 Bloomington Drosophila Stock Center BDSC:34393; FlyBase: FBtp0064874 S. cerevisiae : Strain background: W303 ATCC ATTC: 208353 Mouse: R6/2:...”
• Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring
  Jiang, Cell 2018
  • “...Organisms/Strains C. elegans : Strain BC4011: srl-1(s2500) II;dpy-18(e364) III;unc-46(e177)rol-3(s1040) V. Caenorhabditis Genetics Center WB Strain: BC4011; WormBase: WBVar00241916 D. melanogaster : RNAi of Sxl: y[1] sc[*] v[1]; P{TRiP.HMS00609}attP2 Bloomington Drosophila Stock Center BDSC:34393; FlyBase: FBtp0064874 S. cerevisiae : Strain background: W303 ATCC ATTC: 208353 Mouse: R6/2:...”

BOV_A0452 sugar ABC transporter, permease protein from Brucella ovis ATCC 25840
28% identity, 91% coverage

• ATP-Binding Cassette Systems of Brucella
  Jenner, Comparative and functional genomics 2009
  • “...ABC BMEII0750 BruAb20702 BRA0521 BOV_A0454 BCAN_B0520 OSP Oligosaccharide or polyol import IM BMEII0752 BruAb20704 BRA0519 BOV_A0452 BCAN_B0518 OSP Oligosaccharide or polyol import IM BMEII0753 BruAb20705 BRA0518 BOV_A0451 BCAN_B0517 OSP Oligosaccharide or polyol import BP BMEII0754 BruAb20706 BRA0516 BOV_A0449 BCAN_B0516 OSP Oligosaccharide or polyol import BP BMEII0755...”

Hlac_2864 binding-protein-dependent transport systems inner membrane component from Halorubrum lacusprofundi ATCC 49239
27% identity, 90% coverage

• Cloning, overexpression, purification, and characterization of a polyextremophilic β-galactosidase from the Antarctic haloarchaeon Halorubrum lacusprofundi
  Karan, BMC biotechnology 2013
  • “...IclR family transcriptional regulator; Hlac_2862, sugar-binding periplasmid protein; Hlac_2863, ABC-type sugar transport system permease component; Hlac_2864, sugar permease; Hlac_2865, ABC-type sugar transport system; ATPase component; Hlac_2866, L-alanine-DL-glutamate epimerase and related enzymes of enolase; Hlac_2867, short-chain dehydrogenase/reductase SDR; Hlac_2868, -galactosidase; Hlac_2869, -galactosidase; Hlac_2870, sugar kinase, and Hlac_2871...”

ARAQ_BACSU / P94530 Arabinooligosaccharides transport system permease protein AraQ from Bacillus subtilis (strain 168) (see 3 papers)
TC 3.A.1.1.34 / P94530 L-arabinose transport system permease protein AraQ, component of The arabinosaccharide transporter AraNPQMsmX. Transports α-1,5-arabinooligosaccharides, at least up to four L-arabinosyl units; the key transporter for α-1,5-arabinotriose and α-1,5-arabinotetraose, but not for α-1,5-arabinobiose which is transported by AraE. MsmX is also used by the MdxEFG-MsmX system (3.A.1.1.36) (Ferreira and Sá-Nogueira, 2010). Involved in the uptake of pectin oligosaccharides with either MsmX or YurJ as the ATPase from Bacillus subtilis (see 5 papers)
28% identity, 91% coverage

• function: Part of the ABC transporter complex AraNPQ involved in the uptake of arabinooligosaccharides. Transports alpha-1,5- arabinooligosaccharides, at least up to four L-arabinosyl units (PubMed:20693325). Responsible for the translocation of the substrate across the membrane (Probable).
  subunit: The complex is composed of two ATP-binding proteins (MsmX), two transmembrane proteins (AraP and AraQ) and a solute-binding protein (AraN).
• substrates: Arabinosides
• The MsmX ATPase plays a crucial role in pectin mobilization by Bacillus subtilis
  Ferreira, PloS one 2017
  • “...for deletion in the C-terminal end of AraQ are boxed. Accession numbers: AraP (P94529), AraQ (P94530), MdxF (O06990), MdxG (O06991), GanP (O32261), GanQ (O07011), OpuAB (P46921), MalF (P02916), and MalG (P68183). 10.1371/journal.pone.0189483.t008 Table 8 Effect of mutations in AraP and AraQ in the uptake of -1,5-arabinotriose....”

LMOf2365_1756 ABC transporter, permease protein from Listeria monocytogenes str. 4b F2365
lin1843 similar to sugar ABC transporter, permease protein from Listeria innocua Clip11262
28% identity, 99% coverage

• Catabolite control protein C contributes to virulence and hydrogen peroxide-induced oxidative stress responses in <i>Listeria monocytogenes</i>
  Ogunleye, Frontiers in microbiology 2024
  • “...Cobalt transport protein 2.8 2.2E-02 LMOf2365_1754 Putative binding protein (Bacterial extracellular solute-binding protein) 1.6 1.6E-02 LMOf2365_1756 L-arabinose transport system permease protein 1.6 1.3E-02 LMOf2365_2032 Probable ABC transporter permease protein 2.7 3.7E-03 LMOf2365_2157 Maltodextrin transport system permease protein 2.2 2.3E-03 LMOf2365_2318 L-cystine transport system permease protein 2.7...”
• 1,2-β-Oligoglucan phosphorylase from Listeria innocua
  Nakajima, PloS one 2014
  • “...is formed around the lin1839 gene. A putative ATP-binding protein ABC-type transporter gene ( lin1841 lin1843 ) may be involved in intake of Sop n s and/or 1,2--glucan. A putative GH3 -glucosidase gene ( lin1840 ) is thought to degrade the substrates with concerted action of...”

C289_0467 sugar ABC transporter permease from Anoxybacillus ayderensis
27% identity, 99% coverage

• A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization
  Kahar, International journal of molecular sciences 2013
  • “...(C289_2260), glycosidase (C289_2139), and oligo-1,6-glucosidase (C289_0857, C289_1909, and C289_2139). Several putative sugar transporters (C289_0465, C289_0466, C289_0467, C289_0603, C289_0763, C289_0764, C289_0765, C289_0778, C289_0779, C289_0780, C289_1015, C289_1174, C289_1392, C289_1394, C289_1910, C289_1911, and C289_1912) were also found in the Blast2GO annotation. The draft genome was submitted to the National...”

SPO_RS09345 carbohydrate ABC transporter permease from Ruegeria pomeroyi DSS-3
25% identity, 94% coverage

• Effects of iron concentration and DFB (Desferrioxamine-B) on transcriptional profiles of an ecologically relevant marine bacterium
  LeCleir, PloS one 2023
  • “...other metals, but were involved in other cellular processes ( i . e ., carbohydrate (SPO_RS09345 and SPO_RS09350) and amino acid metabolism (SPO_RS05130 and SPO_RS05135) (see Fig 4 and S6 and S7 Tables). These impacts may be due to secondary/ downstream effects of iron stress. For...”

BAD_RS07405 carbohydrate ABC transporter permease from Bifidobacterium adolescentis ATCC 15703
25% identity, 100% coverage

• Combining of transcriptome and metabolome analyses for understanding the utilization and metabolic pathways of Xylo-oligosaccharide in Bifidobacterium adolescentis ATCC 15703
  Yang, Food science & nutrition 2019
  • “...4,6dehydratase F:GTTCACGGAGCATACCCCATA 59.9 147 R:TGCTGGAAGGGACCGTAGTT 59.5 BAD_RS08125 Molecular chaperone DnaK F:ACCGACTGGACCGTTGAGAT 59.0 156 R:CTGGGCGTCGTTGAAGTATG 59.0 BAD_RS07405 Multiple sugarbinding transport system permease F:CAACGCCTTCAAGAACACC 56.1 200 R:GACCCACCTGTGCCTCCAT 59.9 BAD_RS01610 Xylanase F:ATGACGGAAAGCCGCATGT 57.6 163 R:CGGTCGTGGGTCAGGAAGA 59.6 BAD_RS03215 ABC transporter permease F:CTCATCTCGCTCGTCTCCG 58.8 200 R:GGTACTTTGACCGCTCTGC 55.4 BAD_RS06375 MFS transporter F:GAACATGATGATCGCACCG...”
  • “...Gene no. a Log 2 (Fc) b Annotation c Linear FMPK value d XOS Xylose BAD_RS07405 3.63 Multiple sugarbinding transport system permease 160.73 12.98 BAD_RS05940 3.51 MFS transporter 6.71 0.59 BAD_RS01050 3.47 Shikimate kinase 173.6 15.68 BAD_RS07410 3.27 ABC transporter permease 159.79 16.53 BAD_RS07415 3.23 ABC...”

all5282 ABC transporter sugar permease from Nostoc sp. PCC 7120
28% identity, 90% coverage

• Chemoheterotrophic growth of the Cyanobacterium Anabaena sp. strain PCC 7120 dependent on a functional cytochrome c oxidase
  Stebegg, Journal of bacteriology 2012
  • “...16 genes (all0261, all1027, all1823, all1916, all4824, all5282, alr0738, alr0789, alr2532, alr2722, alr3705, alr4277, alr4781, alr5362, alr5367, and alr5368)...”

cg1569 sn-glycerol-3-phosphate transport system permease protein from Corynebacterium glutamicum ATCC 13032
26% identity, 99% coverage

• Regulation of the pstSCAB operon in Corynebacterium glutamicum by the regulator of acetate metabolism RamB
  Sorger-Herrmann, BMC microbiology 2015
  • “...phoS , phosphate sensor kinase 0.47 cg2843 pstB , P i ABC transporter, ATPase 2.0 cg1569 ugpE , glycerol 3-phosphate ABC transporter, permease 2.1 cg1224 phnB1 , PhnB-like protein 2.3 cg0397 ushA , UDP sugar hydrolase/5-nucleotidase 2.4 cg0444 ramB , regulator of acetate metabolism B 3.5...”

MELC_BACSU / O34518 Melibiose/raffinose/stachyose import permease protein MelC from Bacillus subtilis (strain 168) (see paper)
BSU30290 maltose and multiple sugars ABC transporter (permease) from Bacillus subtilis subsp. subtilis str. 168
26% identity, 99% coverage

• function: Part of the ABC transporter complex MelEDC-MsmX involved in melibiose, raffinose and stachyose import. Probably responsible for the translocation of the substrate across the membrane.
  subunit: The complex is composed of two ATP-binding proteins (MsmX), two transmembrane proteins (MelC and MelD) and a solute-binding protein (MelE).
  disruption phenotype: Deletion of the gene abolishes induction in the presence of melibiose and raffinose.
• rocF affects the production of tetramethylpyrazine in fermented soybeans with Bacillus subtilis BJ3-2
  Liu, BMC biotechnology 2022
  • “...Up BSU19050 7.277 27.08 1.88 1.08E-03 3.68E-02 Up BSU30280 10.263 35.571 1.78 4.72E-04 1.96E-02 Up BSU30290 8.444 28.629 1.75 9.44E-04 3.34E-02 Up BSU38080 223.922 747.383 1.74 1.76E-04 9.59E-03 Up BSU31060 17.602 58.817 1.73 2.31E-04 1.16E-02 Up BSU25150 9.698 32.51 1.73 1.03E-03 3.53E-02 Up BSU16740 18.631 61.488...”

VCA0943 maltose ABC transporter, permease protein from Vibrio cholerae O1 biovar eltor str. N16961
31% identity, 93% coverage

• Small regulatory RNAs in Vibrio cholerae
  Ghandour, microLife 2023
  • “...the first reported 3UTR-derived sRNA and carries its own promoter, which is located in the vca0943 ( malG ) gene (Davis and Waldor 2007 , Papenfort et al. 2015 ). Nevertheless, MicX is also processed by RNase E giving rise to at least three sRNA isoforms...”
• Bacterial 3'UTRs: A Useful Resource in Post-transcriptional Regulation
  Menendez-Gil, Frontiers in molecular biosciences 2020
  • “...dapB DapZ oppA dppA HilD-dependent, represses two ABC transporters Chao et al., 2012 Vibrio cholerae vca0943 MicX vc0972 vc0620 Processed by RNase E in a Hfq-dependent manner, regulates an outer membrane protein, and an ABC transporter Davis and Waldor, 2007 Type II 3 UTR-derived sRNAs Escherichia...”
• The LonA Protease Regulates Biofilm Formation, Motility, Virulence, and the Type VI Secretion System in Vibrio cholerae
  Rogers, Journal of bacteriology 2016
  • “...Transport and binding proteins VC1927 VC2081 VCA0943 VCA0945 VCA1028 C4-dicarboxylate transport protein, dctM Zinc ABC transporter, periplasmic zinc-binding...”
• Mannitol and the mannitol-specific enzyme IIB subunit activate Vibrio cholerae biofilm formation
  Ymele-Leki, Applied and environmental microbiology 2013
  • “...and binding proteins VC1826a VC1820a VCA1045a VC1821a VCA0943 Mannitol Activates Vibrio cholerae Biofilms mental implications for V. cholerae, we investigated...”
• RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA
  Davis, Molecular microbiology 2007
  • “...for MicX's interactions with and regulation of these targets. The sequence encoding MicX overlaps with vca0943 ; however, primary transcripts of MicX are processed in an RNase E- and Hfq-dependent fashion to a shorter, still active and much more stable form consisting largely of the vca0943...”
  • “...we have renamed it MicX. The primary transcript for MicX overlaps the 3 end of vca0943 ; however, expression of MicX is controlled by a gene-specific promoter. MicX is processed by RNase E to a shorter form consisting largely of the vca0943 3 untranslated region (UTR)....”
• The transcriptional regulator VqmA increases expression of the quorum-sensing activator HapR in Vibrio cholerae
  Liu, Journal of bacteriology 2006
  • “...ABC transporter permease protein VC0018 VC0170 VC0171 VC0389 VC2013 VCA0137 VCA0943 VCA0944 4.3 2.7 2.7 2.8 3.6 63.9 2.7 3.7 0.3 0.0 0.0 0.2 0.1 0.0 0.5 0.8 P...”
• sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes
  Livny, Nucleic acids research 2005
  • “...A7 172 >>> VCA0526 <<< 176 VCA0527 >>> 117 A9 154 >>> VCA0942 >>> 131 VCA0943 <<< 37 A10 153 <<< VCA0942 >>> 170 VCA0943 <<< 0 a Distance between 3 boundary of upstream ORF and 5 boundary of predicted sRNA. b Distance between 3 boundary...”

HVO_RS17705 carbohydrate ABC transporter permease from Haloferax volcanii DS2
25% identity, 69% 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
  • “...110 family transposase/pseudoregion (HVO_RS07375), protein translocase TatA (HVO_RS09630), deoxyhypusine synthase (HVO_RS00895), sugar ABC transporter permease (HVO_RS17705), hydrolase (HVO_RS12225), peptidase (HVO_RS08770), RND transporter (HVO_RS14695), and IS 110 family transposase (HVO_RS02445). We do not report putative targets for intergenic sRNAs because of the inherent difficulty in reliably predicting...”

SCO2980 integral membrane transport protein from Streptomyces coelicolor A3(2)
27% identity, 84% coverage

• Genetic analysis of SCO2997, encoding a TagF homologue, indicates a role for wall teichoic acids in sporulation of Streptomyces coelicolor A3(2)
  Kleinschnitz, Journal of bacteriology 2011
  • “...(SCO2987 and SCO2994), and another ABC transporter (SCO2979/ SCO2980), whereas the tagO homologue (SCO5365) is encoded somewhere else in the genome. A second...”
  • “...PBP2, FtsI, SCO3580, and SCO3901 were found (19). Also, SCO2980, an integral membrane transport protein that is encoded by the putative WTA cluster I, showed...”

BWI75_01850 carbohydrate ABC transporter permease from Gloeocapsopsis dulcis AAB1 = 1H9
25% identity, 92% coverage

• Genomic Features for Desiccation Tolerance and Sugar Biosynthesis in the Extremophile Gloeocapsopsis sp. UTEX B3054
  Urrejola, Frontiers in microbiology 2019
  • “...BWI75_01845) was located upstream a gene cluster likely associated to sugar metabolism (gene locus IDs: BWI75_01850 to BWI75_01856) containing three glycosyltransferase genes in tandem. Its predicted amino acid sequence contains a sucrose phosphatase domain (InterProScan entry: IPR006380) and a haloacid dehydrogenase HAD-like domain (InterProScan entry: IPR023214)....”

MSMEG_5059 ABC transporter, permease protein SugB from Mycobacterium smegmatis str. MC2 155
30% identity, 80% coverage

• Structural basis of trehalose recycling by the ABC transporter LpqY-SugABC
  Liu, Science advances 2020
  • “...2 155 genomic DNA and overexpressed in M. smegmatis mc 2 155 . MSMEG_5058 , MSMEG_5059 , and MSMEG_5060 were amplified by polymerase chain reaction (PCR) and inserted into a pM261 vector, with a C-terminal 6 His-tag attached to SugC. The recombinant plasmid was transformed into...”
  • “...(SugC)] was mutated to glutamine. A coexpression vector was constructed by amplification of MSMEG_5058 (E164Q), MSMEG_5059 , MSMEG_5060 , and MSMEG_5061 from M. smegmatis strain mc 2 155 genomic DNA by PCR and insertion into a pM261 expression vector with a C-terminal 6 His-tag. LpqY-SugABC was...”
• The growth and survival of Mycobacterium smegmatis is enhanced by co-metabolism of atmospheric H2
  Greening, PloS one 2014
  • “...RNA samples. Genes were chosen that were downregulated (MSMEG_1203, MSMEG_3706), upregulated (MSMEG_3194, MSMEG_3249, MSMEG_3962, MSMEG_3769, MSMEG_5059), or unchanged (MSMEG_4640) in the microarray. All bars show the expression ratio of genes in hyd 2 vs. wild-type strains. Yellow bars show microarray data. Green bars show qRT-PCR data....”
• A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
  McKenzie, Journal of bacteriology 2012
  • “...MSMEG_4663 MSMEG_4664 MSMEG_4665 MSMEG_4666 MSMEG_5057 MSMEG_5058 MSMEG_5059 MSMEG_5060 MSMEG_5061 MSMEG_5062 iolB iolD iolE sugK sugG sugF sugE Succinate...”

LMOf2365_0191 sugar ABC transporter, permease protein from Listeria monocytogenes str. 4b F2365
29% identity, 95% coverage

• Contributions of a LysR Transcriptional Regulator to Listeria monocytogenes Virulence and Identification of Its Regulons
  Abdelhamed, Journal of bacteriology 2020 (secret)

TC 3.A.1.1.6 / Q48397 CymG, component of Cyclodextrin porter from Klebsiella oxytoca (see paper)
28% identity, 92% coverage

• substrates: Cyclodextrin
• Presynaptic calcium channel localization and calcium-dependent synaptic vesicle exocytosis regulated by the Fuseless protein
  Long, The Journal of neuroscience : the official journal of the Society for Neuroscience 2008
  • “...and plotted as a function cyclodextrin transport (Q48397); Wzx, Escherichia coli, transbilayer movement of a trisaccharide-lipid intermediate (P27834); Shi of...”

TC 3.A.1.1.4 / P29824 LacG, component of Lactose porter from Agrobacterium radiobacter (see paper)
27% identity, 100% coverage

• substrates: Lactose

SMc04257 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 from Sinorhizobium meliloti 1021
26% identity, 90% coverage

• mutant phenotype: Specific phenotypes on D-Cellobiose; D-Salicin.

all4824 permease protein of sugar ABC transporter from Nostoc sp. PCC 7120
25% identity, 95% coverage

• Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease
  Chouhan, Journal, genetic engineering & biotechnology 2023
  • “...Nostoc sp. PCC 7120 all5344 468 Nostoc sp. PCC 7120 all1863 864 Trichormus variabilis NIES-23 all4824 798 Trichormus variabilis ATCC 29413 all0781 1590 Trichormus variabilis ATCC 29413 all4426 1254 Pathway analysis Pathway analysis is a powerful tool to understand the biological significance of gene lists generated...”
• Chemoheterotrophic growth of the Cyanobacterium Anabaena sp. strain PCC 7120 dependent on a functional cytochrome c oxidase
  Stebegg, Journal of bacteriology 2012
  • “...7120, 16 genes (all0261, all1027, all1823, all1916, all4824, all5282, alr0738, alr0789, alr2532, alr2722, alr3705, alr4277, alr4781, alr5362, alr5367, and...”

BAS0537 glycerol-3-phosphate ABC transporter, permease protein, putative from Bacillus anthracis str. Sterne
AW20_2179 carbohydrate ABC transporter permease from Bacillus anthracis str. Sterne
26% identity, 100% coverage

• Beyond the spore, the exosporium sugar anthrose impacts vegetative Bacillus anthracis gene regulation in cis and trans
  Norris, Scientific reports 2023
  • “...regulatory YrvL family protein 3.00 AW20_3164 BAS4995 Stage V sporulation protein AC (SpoVAC) 2.80 AW20_2179 BAS0537 Glycerol-3-phosphate ABC transporter, permease protein UgpE 2.35 AW20_1941 BAS0749 Uncharacterized MFS-type transporter 2.26 AW20_1364 BAS1310 Ketol-acid reductoisomerase (NADP(+)) 2.11 AW20_981 BAS1681 MutT/Nudix family protein 2.00 AW20_170 BAS2472 EDD, DegV family...”
• Beyond the spore, the exosporium sugar anthrose impacts vegetative Bacillus anthracis gene regulation in cis and trans
  Norris, Scientific reports 2023
  • “...protein, regulatory YrvL family protein 3.00 AW20_3164 BAS4995 Stage V sporulation protein AC (SpoVAC) 2.80 AW20_2179 BAS0537 Glycerol-3-phosphate ABC transporter, permease protein UgpE 2.35 AW20_1941 BAS0749 Uncharacterized MFS-type transporter 2.26 AW20_1364 BAS1310 Ketol-acid reductoisomerase (NADP(+)) 2.11 AW20_981 BAS1681 MutT/Nudix family protein 2.00 AW20_170 BAS2472 EDD, DegV...”

ERH_1244 carbohydrate ABC transporter permease from Erysipelothrix rhusiopathiae str. Fujisawa
29% identity, 94% coverage

• Proteomic and Transcriptomic Analyses of Swine Pathogen Erysipelothrix rhusiopathiae Reveal Virulence Repertoire
  Li, PloS one 2016
  • “...systems, permease components gi|509078903 ABC transporter, permease protein 6.6 2 1.617 Predicted transcriptional regulators down ERH_1244 gi|336066105 ACT domain-containing protein 30.3 3 1.705 ABC-type sugar transport system, permease component up ERH_0867 gi|322464145 putative endoribonuclease L-PSP 27.1 3 1.806 ACT domain-containing protein gi|336065349 DNA binding helix-turn helix...”
• The genome of Erysipelothrix rhusiopathiae, the causative agent of swine erysipelas, reveals new insights into the evolution of firmicutes and the organism's intracellular adaptations
  Ogawa, Journal of bacteriology 2011
  • “...ERH_0414, ERH_0417, ERH_1083, ERH_1084, ERH_1085, ERH_1244, ERH_1245, ERH_1246, ERH_1523 ERH_0895, ERH_0896, ERH_1350, ERH_1351, ERH_1352, ERH_1517. ERH_1518,...”

PH1216 hypothetical protein from Pyrococcus horikoshii OT3
29% identity, 90% coverage

• Glucose transport in the extremely thermoacidophilic Sulfolobus solfataricus involves a high-affinity membrane-integrated binding protein
  Albers, Journal of bacteriology 1999
  • “...same transcription direction, PH1215 (accession no. G3915506) and PH1216 (accession no. G3915506) (Fig. 6). These two ORFs code for integral membrane proteins...”
  • “...PH1215 (28% identity, 51% similarity), and ORF35 and PH1216 (24% identity, 54% similarity) are homologous (Fig. 6). This genetic organization suggests that the...”

SCO2660 sugar transport membrane protein from Streptomyces coelicolor A3(2)
27% identity, 91% coverage

• Properties of CsnR, the transcriptional repressor of the chitosanase gene, csnA, of Streptomyces lividans
  Dubeau, Journal of bacteriology 2011
  • “...in the S. coelicolor A3(2) genome (SCO2658 to SCO2660; localized on the SC6D10.01 cosmid) found by in silico analysis of carbohydrate uptake systems. Trehalose,...”

TC 3.A.1.1.26 / O06991 MalG aka yvdI, component of The maltose porter, MdxEFG and MsmX from Bacillus subtilis (see 2 papers)
30% identity, 80% coverage

• substrates: Maltose
• The MsmX ATPase plays a crucial role in pectin mobilization by Bacillus subtilis
  Ferreira, PloS one 2017
  • “...C-terminal end of AraQ are boxed. Accession numbers: AraP (P94529), AraQ (P94530), MdxF (O06990), MdxG (O06991), GanP (O32261), GanQ (O07011), OpuAB (P46921), MalF (P02916), and MalG (P68183). 10.1371/journal.pone.0189483.t008 Table 8 Effect of mutations in AraP and AraQ in the uptake of -1,5-arabinotriose. Doubling time (min) of...”

GRD61_RS02145 carbohydrate ABC transporter permease from Clavibacter michiganensis subsp. michiganensis
26% identity, 87% coverage

• Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
  Méndez, Microorganisms 2020
  • “...strain VL527, genes encoding a peptidase (GRD61_RS13055), three carbohydrate ABC transporter permeases (GRD61_RS02135, GRD61_RS02140 and GRD61_RS02145), two LacI family transcriptional regulator (GRD61_RS00220 and GRD61_RS02125), and 21 hypothetical proteins were detected and identified. MSF322 possesses exclusively genes encoding two hydrolases (GRD74_RS03640 and GRD74_RS08035), two peptidases (GRD74_RS12885 and...”

PFREUD_23410 carbohydrate ABC transporter permease from Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1
28% identity, 65% coverage

• A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment
  Saraoui, BMC genomics 2013
  • “...(induced in colon) pvalue microarray FC RT-qPCR (induced in colon) pvalue RT- qPCR Probe name PFREUD_23410 Permease of glycerol 3 P ABC transporter 1.2 Transport/binding proteins and lipoproteins 4,8 5,0E-08 34,0 1,4E-01 CUST_2220_PI426428742 PFREUD_23760 Xanthine/uracil permease 1.2 Transport/binding proteins and lipoproteins 4,5 6,0E-08 3,7 9,0E-02 CUST_2250_PI426428742...”
  • “...substrate for P. freudenreichii in the gut environment. Similarly, the glycerol and glycerol 3P transporter PFREUD_23410 was induced +4.7 (confirmed with a fold change of +34 by RT-qPCR), whereas the degradation pathway of glycerol was not induced. Glycerol is another substrate available in the gut as...”

RPPS3_01230 carbohydrate ABC transporter permease from Rhodopseudomonas palustris
25% identity, 92% coverage

• Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3)
  Lo, Scientific reports 2018
  • “...fructose and glucose. In addition, there are genes encoding multiple sugar ABC transport systems (RPPS3_01220, RPPS3_01230, RPPS3_033890, RPPS3_35020, RPPS3_35050, RPPS3_35450, RPPS3_43670, RPPS3_45360, RPYSC3_01220, RPYSC3_01230, RPYSC3_35200, RPYSC3_35230, RPYSC3_35650, RPYSC3_44090 and RPYSC3_45830) and TonB-dependent transporters in the R. palustris genomes (Supplementary Tables S5 and S6 ). TonB-dependent transporters...”

pRL120558 putative transmembrane transporter permease component from Rhizobium leguminosarum bv. viciae 3841
26% identity, 92% coverage

• Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis
  Wheatley, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret)

Tsac_1464 carbohydrate ABC transporter permease from Thermoanaerobacterium saccharolyticum JW/SL-YS485
24% identity, 95% coverage

• Profile of secreted hydrolases, associated proteins, and SlpA in Thermoanaerobacterium saccharolyticum during the degradation of hemicellulose
  Currie, Applied and environmental microbiology 2014
  • “...and existed in two clusters (Tsac_1445 through Tsac_1464 for xylan/xylose and Tsac_1344 through Tsac_1349 for starch). A phosphotransferase system subunit,...”
  • “...in two major gene clusters (Tsac_1445 through Tsac_1464 for xylan/xylose and Tsac_1344 aem.asm.org 5007 Downloaded from http://aem.asm.org/ on February 11, 2017...”

RPYSC3_01230 carbohydrate ABC transporter permease from Rhodopseudomonas palustris
25% identity, 92% coverage

• Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3)
  Lo, Scientific reports 2018
  • “...encoding multiple sugar ABC transport systems (RPPS3_01220, RPPS3_01230, RPPS3_033890, RPPS3_35020, RPPS3_35050, RPPS3_35450, RPPS3_43670, RPPS3_45360, RPYSC3_01220, RPYSC3_01230, RPYSC3_35200, RPYSC3_35230, RPYSC3_35650, RPYSC3_44090 and RPYSC3_45830) and TonB-dependent transporters in the R. palustris genomes (Supplementary Tables S5 and S6 ). TonB-dependent transporters have been considered to be involved in dietary...”

Psest_0865 maltose ABC transporter, permease component 2 (MalG) from Pseudomonas stutzeri RCH2
30% identity, 93% coverage

• mutant phenotype: Specifically important for utilizing D-Maltose monohydrate.

TC 3.A.1.1.27 / Q8DT26 MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) from Streptococcus mutans (see paper)
SMU_1570, SMU_RS07120 sugar ABC transporter permease from Streptococcus mutans UA159
28% identity, 99% coverage

• substrates: Maltose, Maltotetraose, Maltotriose, Trehalose
• Identification of the antibacterial action mechanism of diterpenoids through transcriptome profiling
  Moon, Frontiers in microbiology 2022
  • “...protein UgpC msmK 1.95 0.66 0.59 SMU_RS07115 Sugar ABC transporter permease malF 1.99 0.69 0.62 SMU_RS07120 Sugar ABC transporter permease malG 1.36 0.11 0.03 SMU_RS02605 ROK family glucokinase glk 0.61 3.08 1.60 1.62 SMU_RS01525 Glucose-6-phosphate isomerase pgi 1.43 1.09 1.23 SMU_RS05480 6-Phosphofructokinase pfkA 0.78 1.77 1.82...”
• Genomic and phenotypic characterization of Streptococcus mutans isolates suggests key gene clusters in regulating its interaction with Streptococcus gordonii
  Liu, Frontiers in microbiology 2022
  • “...SMU_184 ABC transporter metal binding lipoprotein 412 658 <0.001 SMU_48 phosphoribosylamineglycine ligase 477 973 <0.001 SMU_1570 maltose ABC transporter permease 456 966 <0.001 SMU_1232c hypothetical protein 479 1,483 <0.001 SMU_270 PTS system ascorbate-specific transporter subunit IIC 417 680 <0.001 SMU_148 bifunctional acetaldehyde-CoA/alcohol dehydrogenase 3,287 8,200 <0.001...”
• Cnm of Streptococcus mutans is important for cell surface structure and membrane permeability
  Naka, Frontiers in cellular and infection microbiology 2022
  • “...4.614 SMU_1094 ABC transporter ATP-binding protein 1028415 SMU_1094 3.998 malG Maltose ABC transporter permease 1028808 SMU_1570 3.837 mtlA1 PTS system mannitol-specific transporter subunit IIBC 1028492 SMU_1185 3.792 SMU_241c Amino acid ABC transporter ATP-binding protein 1027838 SMU_241c 3.676 SMU_1899 ABC transporter ATP-binding protein/permease (fragment) 1029097 SMU_1899 3.498...”
• RNA-Seq Reveals Enhanced Sugar Metabolism in Streptococcus mutans Co-cultured with Candida albicans within Mixed-Species Biofilms
  He, Frontiers in microbiology 2017
  • “...S. mutans , albeit not nearly as effectively as the sucrose PTS. Still, both malG (SMU_1570) and malF (SMU_1569) encoding maltose/maltodextrin ABC transport permease, as well as malX (SMU_1568) encoding maltose/maltodextrin-binding protein were up-regulated in the presence of C. albicans (Supplementary Table S1 ). FIGURE 4...”

D805_1601 carbohydrate ABC transporter permease from Bifidobacterium thermophilum RBL67
26% identity, 93% coverage

• Bifidobacterium thermophilum RBL67 impacts on growth and virulence gene expression of Salmonella enterica subsp. enterica serovar Typhimurium
  Tanner, BMC microbiology 2016
  • “...3.6E-12 D805_1594 ClpB protein 1.06 8.68 2.1E-06 D805_1600 Maltodextrin glucosidase (EC 3.2.1.20) 1.17 6.23 5.6E-08 D805_1601 ABC-type sugar transport system, permease component 1.85 4.02 3.9E-09 D805_1602 MSM (multiple sugar metabolism) operon regulatory protein 1.68 3.28 1.1E-05 D805_1621 Sortase A, LPXTG specific 1.09 3.52 0.00557 D805_1622 hypothetical...”

LMOf2365_0269 sugar ABC transporter, permease protein from Listeria monocytogenes str. 4b F2365
27% identity, 90% coverage

• Contributions of a LysR Transcriptional Regulator to Listeria monocytogenes Virulence and Identification of Its Regulons
  Abdelhamed, Journal of bacteriology 2020 (secret)

RHS_1908 carbohydrate ABC transporter permease from Robinsoniella sp. RHS
25% identity, 100% coverage

• Bacteria from diverse habitats colonize and compete in the mouse gut
  Seedorf, Cell 2014
  • “...tract in soil; Table S7F ). The assembled genome also contained two genes (RHS_0676 and RHS_1908) encoding protein products with significant similarity to nine predicted bile salt hydrolyases from the class Clostridia (which contains the genus Robinsoniella ), and five genes (RHS_0652, RHS_1165, RHS_1257, RHS_2187 and...”

AOT13_07020 sugar ABC transporter permease from Parageobacillus thermoglucosidasius
27% identity, 97% coverage

• Functional characterization of the phosphotransferase system in Parageobacillus thermoglucosidasius
  Bidart, Scientific reports 2023
  • “...part of the MalEFGK ABC transporter complex 32 , is also found in P. thermoglucosidasius (AOT13_07020). The results presented in our work, the presence of a MalA homologue, and the presence of a putative maltodextrin phosphorylase in the genome of P. thermoglucosidasius DSM 2542 (AOT13_18705), suggesta...”

X276_22865 carbohydrate ABC transporter permease from Clostridium beijerinckii NRRL B-598
27% identity, 100% coverage

• Phenotypic and Genomic Analysis of Clostridium beijerinckii NRRL B-598 Mutants With Increased Butanol Tolerance
  Vasylkivska, Frontiers in bioengineering and biotechnology 2020
  • “...four strains. EB mutants strain A, B and C included SNPs in the same genes, X276_22865 and X276_03000 encoding a carbohydrate ABC transporter permease and an AAA family ATPase, respectively ( Figure 4 and Table 3 ), and no mutations were observed in these gene when...”
  • “...Locus Product Start End Strand Feature Aa_ref Aa_alt Mutant strain A* 1 863781 T G X276_22865 Carbohydrate ABC transporter permease 863698 864525 + I M 2 1661343 C T X276_19395 Peptidase S8 and S53 subtilisin kexin sedolisin 1661151 1662989 + L F 3 2775912 T C...”

G9MB86 ABC-type glycerol 3-phosphate transporter (subunit 1/3) (EC 7.6.2.10) from Thermus thermophilus (see paper)
30% identity, 87% coverage

SAK_1477 cyclodextrin ABC transporter, permease protein from Streptococcus agalactiae A909
SAG1443 maltose ABC transporter, permease protein from Streptococcus agalactiae 2603V/R
gbs1512 Unknown from Streptococcus agalactiae NEM316
26% identity, 99% coverage

• The Role of Regulator Catabolite Control Protein A (CcpA) in Streptococcus agalactiae Physiology and Stress Response
  Roux, Microbiology spectrum 2022
  • “...carbon metabolism were downregulated by CcpA: SAK_0532-0539 , SAK_0166 - SAK_0171 , and SAK_1475 - SAK_1477 coding the transporters of N -acetylglucosamine, ribose, and cyclodextrin, respectively, for which a cre site was present. Several genes involved in glycolysis and gluconeogenesis were regulated by CcpA, as already...”
• 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_1074 sak_1103 sak_1104 sak_1105 sak_1426 sak_1427 sak_1476 sak_1477 sak_1538 sak_1539 sak_1540 sak_1541 sak_1542 sak_1554 sak_1555 sak_1556 Gene name rbsB...”
• Adaptive response of Group B streptococcus to high glucose conditions: new insights on the CovRS regulation network
  Di, PloS one 2013
  • “...in the transport of complex carbohydrates were down-regulated, including: the region spanning from sag1441 to sag1443 ORFs, encoding for the maltose-maltodextrin transport system ( malE-F-G) ; sag0955 and sag1925 ( msmK ) genes, encoding a sugar-ABC transporter and a sugar transport ATP-binding protein, respectively; the ribose...”
• Transcriptome adaptation of group B Streptococcus to growth in human amniotic fluid
  Sitkiewicz, PloS one 2009
  • “...gbs1510 malE 3.8 Maltose maltodextrin-binding protein gbs1511 malF 4.6 Maltodextrin transport system permease protein malC gbs1512 malG 3.5 Maltose transport system permease protein malG gbs1692 2.7 Dihydroxyacetone kinase gbs1694 2.5 5.1 5.9 Dihydroxyacetone kinase gbs1695 3.9 8.4 Dihydroxyacetone kinase gbs1696 2.6 14.5 Dihydroxyacetone kinase phosphotransfer protein...”
• Relevance of peptide uptake systems to the physiology and virulence of Streptococcus agalactiae
  Samen, Journal of bacteriology 2004
  • “...obtained by RT-PCR with primers specific to the regions gbs1512 to dpsA and dpsA to gbs1514, indicating a monocistronic organization of the dpsA gene in S....”

RLO149_c015770 carbohydrate ABC transporter permease from Roseobacter litoralis Och 149
25% identity, 78% coverage

• Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis
  Kalhoefer, BMC genomics 2011
  • “...4.1.2.21) RLO149_c015740 DgoK: 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58) RLO149_c015750 short chain dehydrogenase RLO149_c015760 RafA: alpha-galactosidase (EC 3.2.1.22) RLO149_c015770 putative galactoside ABC transporter inner membrane component RLO149_c015780 putative galactoside ABC transporter inner membrane component RLO149_c015790 putative extracellular galactoside-binding protein RLO149_c015800 HTH-type transcriptional regulator, IclR family RLO149_c015810 putative galactoside ABC...”

LBA1864 maltose ABC transporter permease protein from Lactobacillus acidophilus NCFM
28% identity, 97% coverage

• Extracellular Vesicles of Probiotics: Shedding Light on the Biological Activity and Future Applications
  Krzyżek, Pharmaceutics 2023
  • “...12% - Surface proteins: FmtB, SlpX - Mucus binding protein Mub - Transporters of maltose (LBA1864) and glutamine (GlnP) - Bacteriocin LBA1805 [ 38 ] Lactobacillus gasseri BC12 Ultracentrifugation (vesicles) Electrophoresis + LC-ESI-MS/MS (proteome) 15 Membrane ~ 44% Cytoplasm ~ 44% Secretory ~ 11% - Foldase...”
• An 1,4-α-Glucosyltransferase Defines a New Maltodextrin Catabolism Scheme in Lactobacillus acidophilus
  Andersen, Applied and environmental microbiology 2020 (secret)
• An Extracellular Cell-Attached Pullulanase Confers Branched α-Glucan Utilization in Human Gut Lactobacillus acidophilus
  Møller, Applied and environmental microbiology 2017
  • “...through a maltodextrin-specific ATP-binding cassette (ABC) system (LBA1864 to LBA1867), which is conserved in acidophilus group lactobacilli (24). The...”

GK0706 maltose/maltodextrin transport system (permease) from Geobacillus kaustophilus HTA426
29% identity, 79% coverage

• Polysaccharide-degrading thermophiles generated by heterologous gene expression in Geobacillus kaustophilus HTA426
  Suzuki, Applied and environmental microbiology 2013
  • “...GK0708) and the Pgk704 region. The GK0704, GK0705, and GK0706 genes encode components of a sugar ABC transporter. The GK0707 and GK0708 genes encode -amylase...”

MSMEG_5147 sugar ABC-transporter integral membrane protein from Mycobacterium smegmatis str. MC2 155
26% identity, 86% coverage

• A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis
  Titgemeyer, Journal of bacteriology 2007
  • “...Xylose and -xylosides (msmeg_1704 to msmeg_1706, msmeg_5142 to msmeg_5147, and msmeg_6018 to msmeg_6022). Xylose is usually taken up by an ABC permease and...”
  • “...predicted -xyloside permease is encoded by msmeg_5142 to msmeg_5147. We have designated the genes bxlRAEFG according to their close relationship to the bxlEFG2...”

PA14_23000 putative permease of ABC sugar transporter from Pseudomonas aeruginosa UCBPP-PA14
27% identity, 98% coverage

• Convergent phenotypic evolution towards fosfomycin collateral sensitivity of Pseudomonas aeruginosa antibiotic-resistant mutants
  Laborda, Microbial biotechnology 2022
  • “...( glcB and PA14_30050 ), as well as of the glucose transporters PA14_22980, PA14_22990 and PA14_23000, yet a decreased expression of lactate dehydrogenase encoding genes ( lldA and lldD ). Moreover, we also found increased expression of some genes that encode amino acid and fatty acid...”
• Transcriptional profiling of Pseudomonas aeruginosa and Staphylococcus aureus during in vitro co-culture
  Tognon, BMC genomics 2019
  • “...virulence pchF 9.56 pyochelin synthesis virulence PA14_23010 9.47 GltK, ATP-binding component of ABC transporter transport PA14_23000 9.37 permease of ABC sugar transporter transport PA14_22990 9.19 permease of ABC sugar transporter transport PA14_23030 8.63 OprB, Glucose/carbohydrate porin transport bkdA2 8.05 2-oxoisovalerate dehydrogenase subunit beta aa metabolism bdhA...”
  • “...operon containing genes for the glucose/carbohydrate specific OprB porin and the adjacent ABC-transporters (PA14_22990 and PA14_23000) (10-fold decrease), the operon containing the OpdO porin and the co-transcribed ABC-transporter PA14_37250 (15 to 20-fold decrease), involved in pyroglutamate/lactam uptake as well as the gluconate permease gene gnuT ....”

BL1332 probable sugar permease of ABC transporter system from Bifidobacterium longum NCC2705
27% identity, 86% coverage

• The Pleiotropic Effects of Carbohydrate-Mediated Growth Rate Modifications in Bifidobacterium longum NCC 2705
  Duboux, Microorganisms 2023
  • “...conditions studied. During glucose growth, a gene involved in the transport of mannosylated oligosaccharides ( BL1332 ) was slightly but significatively upregulated. In contrast, in galactose growing cells several genes predicted to be involved in the import of various carbohydrates were induced, including the transporters for...”
• Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host
  Sonnenburg, PLoS biology 2006
  • “...in the gene cluster referred to above that contains two linked permease genes (BL1331 and BL1332; down-regulated 7.4- and 10.1-fold, respectively) and two other glycoside hydrolase activities (BL1333 [substrate specificity unknown]; BL1335 [endo--N-acetylglucosaminidase]; down-regulated 8.8- and 14.1-fold, respectively; Figure 1 B and 1 D). Expression of...”

PA3188 probable permease of ABC sugar transporter from Pseudomonas aeruginosa PAO1
27% identity, 98% coverage

• Commensal colonization reduces Pseudomonas aeruginosa burden and subsequent airway damage
  Stoner, Frontiers in cellular and infection microbiology 2023
  • “...the presence of S. salivarius . Genes PA3186 ( oprB ), PA3187 ( gltK ), PA3188 ( gltG ), PA3189 ( gltF ), and PA3190 are involved in glucose uptake. PA3181 ( edaA ), PA3182 ( pgl ), and PA3183 ( zwf ) are involved in...”
  • “...PA3186 (glucose outer membrane porin OprB), PA3187 (ATP binding component of ABC sugar transporter GltK), PA3188 (permease of ABC sugar transporter GltG), PA3189 (permease of ABC sugar transporter GltF), PA3190 (binding protein component of ABC sugar transporter), PA3191 (glucose transport sensor GtrS), and PA3192 (two-component response...”
• Catabolite repression control protein antagonist, a novel player in Pseudomonas aeruginosa carbon catabolite repression control
  Sonnleitner, Frontiers in microbiology 2023
  • “...membrane porin OprB precursor PA3187 9.26 7.80E-18 PA 3187 Probable ATP-binding component of ABC transporter PA3188 14.32 2.74E-8 PA 3188 Probable permease of ABC sugar transporter PA3189 12.67 4.63E-12 PA 3189 Probable permease of ABC sugar transporter PA3190 41.81 2.51E-71 PA 3190 Probable binding protein component...”
• Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics
  Salvà-Serra, Frontiers in microbiology 2022
  • “...transport protein AroP1 2 4 1.00 0.90 1.34 0.02 2.11 0.00 Up 1.27 0.04 WP_003091470.1 PA3188 GltG Probable permease of ABC sugar transporter 2 7 1.20 0.03 1.23 0.04 3.84 0.01 Down 1.26 0.01 WP_003091471.1 PA3189 GltF Probable permease of ABC sugar transporter 4 11 1.09...”
• Pseudomonas aeruginosa mutants defective in glucose uptake have pleiotropic phenotype and altered virulence in non-mammal infection models
  Raneri, Scientific reports 2018
  • “...gntP 35.5 0.0 0.6 gluconate permease PA3187 gltK 52.0 0.1 6.7 ABC transporter ATP-binding protein PA3188 gltG 31.6 0.0 0.4 sugar ABC transporter permease PA3189 gltF 3.5 0.3 0.9 probable permease of ABC sugar transporter a Boldface characters, genes analysed by RT-qPCR. b Genes up- and...”
• 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
  • “...5,5 Transport gltK PA3187 Probable ATP-binding component of ABC transporter 0,22 2,29 6,75 Transport gltG PA3188 Probable permease of ABC sugar transporter 0,46 3,56 10,6 Transport gltB PA3190 Probable binding protein component of ABC sugar transporter 0,2 2,92 8,1 CCM/catabolism glk PA3193 Glucokinase 0,02 1,11 3,15...”
• Gene expression in Pseudomonas aeruginosa swarming motility
  Tremblay, BMC genomics 2010
  • “...PA4616 1 probable c4-dicarboxylate-binding protein 2.2 PA3187 gltK probable ATP-binding component of ABC transporter 1.5 PA3188 gltG probable permease of ABC sugar transporter 2.0 PA4628 lysP lysine-specific permease 1.7 PA5479 gltP proton-glutamate symporter 1.6 PA0782 3 putA proline dehydrogenase 1.8 PA0783 1 putP sodium/proline symporter PutP...”
  • “...molecules PA2322 gntT gluconate permease 2.0 PA3187 2 gltK ATP-binding component of ABC transporter 2.6 PA3188 2 gltG permease of ABC sugar transporter 3.1 PA3189 gltF permease of ABC sugar transporter 2.5 PA3523 1 mexP probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor 4.2 PA3920...”
• Effect of anaerobiosis and nitrate on gene expression in Pseudomonas aeruginosa
  Filiatrault, Infection and immunity 2005
  • “...PA2629 PA2663 PA2691 PA2763 PA2798 PA2968 PA2969 PA3019 PA3188 PA3221 PA3222 PA3232 PA3234 PA3235 PA3294 PA3327 PA3328 PA3329 PA3330 PA3331 PA3333 PA3334 PA3335...”
• A cystic fibrosis epidemic strain of Pseudomonas aeruginosa displays enhanced virulence and antimicrobial resistance
  Salunkhe, Journal of bacteriology 2005
  • “...PA1404 PA1431 PA1432 PA2365 PA2445 PA2446 PA3181 PA3182 PA3183 PA3188 PA3190 Gene name GENE EXPRESSION IN A P. AERUGINOSA CF EPIDEMIC STRAIN VOL. 187, 2005 4915...”
• More

BBMN68_219 carbohydrate ABC transporter permease from Bifidobacterium longum subsp. longum BBMN68
25% identity, 89% coverage

• Transcriptomic analysis of Bifidobacterium longum subsp. longum BBMN68 in response to oxidative shock
  Zuo, Scientific reports 2018
  • “...systems permease component 2.66 1.62 BBMN68_218 MalG-type ABC sugar transport system permease component 1.74 1.49 BBMN68_219 Transmembrane transport protein 2.06 2.07 BBMN68_1264 Transmembrane transporter activity; MFS transporter (putative metabolite:H + symporter) 1.63 1.52 BBMN68_157 Peptide transport Peptide/nickel transport system substrate-binding protein ddpA1 1.16 NS BBMN68_236 Peptide/nickel...”
• Mechanism analysis of acid tolerance response of bifidobacterium longum subsp. longum BBMN 68 by gene expression profile using RNA-sequencing
  Jin, PloS one 2012
  • “...substrate-binding protein BBMN68_218 141.02 73.47 1.92 G COG1175 K02025, multiple sugar transport system permease protein BBMN68_219 147.02 72.27 2.03 * G COG0395 K02026, multiple sugar transport system permease protein BBMN68_1724 54.21 114.46 2.11 * G COG1129 MglA2, K02056, simple sugar transport system ATP-binding protein [EC:3.6.3.17] BBMN68_74...”

AT5A_24045 carbohydrate ABC transporter permease from Agrobacterium tumefaciens 5A
26% identity, 92% coverage

• Introducing the ArsR-Regulated Arsenic Stimulon
  Rawle, Frontiers in microbiology 2021
  • “...transporter substrate-binding protein 2.3 2.6 2.2 AT5A_24035 Sugar ABC transporter nucleotide ATPase 2.0 2.6 2.2 AT5A_24045 Sugar ABC transporter permease 2.0 2.9 2.1 AT5A_24050 Sugar ABC transporter permease 2.40 Gray highlighted data identifies genes uniquely affected in the respective arsR mutant and presumed to be controlled...”

HVO_B0230 ABC-type transport system permease protein (probable substrate sugar) from Haloferax volcanii DS2
28% identity, 92% coverage

• D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii
  Johnsen, The Journal of biological chemistry 2009
  • “...integral membrane-binding protein-dependent transport protein HVO_B0230, sugar ABC transporter permease HVO_B0231, hypothetical protein HVO_B0232,...”

Blon_0885 binding-protein-dependent transport systems inner membrane component from Bifidobacterium longum subsp. infantis ATCC 15697
23% identity, 83% coverage

• Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria Is Governed by Global Transcriptional Regulator NagR
  Arzamasov, mSystems 2022
  • “...substrate-binding protein TC 3.A.1.1 39 Blon_0884 gltG LNB/GNB ABC transporter permease protein 1 TC 3.A.1.1 Blon_0885 gltH LNB/GNB ABC transporter permease protein 2 TC 3.A.1.1 Blon_2171 lnpD UDP-hexose 4-epimerase EC 5.1.3.2 59 Blon_2172 lnpC UTP-hexose-1-phosphate uridylyltransferase EC 2.7.7.10 59 Blon_2173 lnpB N -Acetylhexosamine 1-kinase EC 2.7.1.162...”
• Inefficient Metabolism of the Human Milk Oligosaccharides Lacto-N-tetraose and Lacto-N-neotetraose Shifts Bifidobacterium longum subsp. infantis Physiology
  Özcan, Frontiers in nutrition 2018
  • “...both LNT and LNnT induced the F1SBP Blon_0883, although its adjacent permease proteins Blon_0884 and Blon_0885 were not induced ( p > 0.05). Main effect analysis via two-way ANOVA indicates that Blon_2347 exhibits the strongest induction among the four F1SBP genes regardless of substrate ( p...”
• Exposure of Bifidobacterium longum subsp. infantis to Milk Oligosaccharides Increases Adhesion to Epithelial Cells and Induces a Substantial Transcriptional Response
  Kavanaugh, PloS one 2013
  • “...1.28 0.0300 1.46 0.0040 Blon_0884 Extracellular solute binding protein 1.31 0.0200 1.29 0.0300 1.47 0.0500 Blon_0885 Binding protein dependent sugar transport inner membrane protein 1.25 0.0200 1.40 0.0020 1.50 0.0000 Blon_2174 Hypothetical protein 1.40 0.0200 1.55 0.0060 1.75 0.0020 Blon_2175 Solute transport 1.35 0.0300 1.56 0.0030...”

BAD_RS00815 carbohydrate ABC transporter permease from Bifidobacterium adolescentis ATCC 15703
27% identity, 86% coverage

• Combining of transcriptome and metabolome analyses for understanding the utilization and metabolic pathways of Xylo-oligosaccharide in Bifidobacterium adolescentis ATCC 15703
  Yang, Food science & nutrition 2019
  • “...1.58 lipO ABC transporter 10,020.43 3,361.71 BAD_RS08285 1.52 ugpB ABC transporter, solutebinding protein 1,971.94 686.94 BAD_RS00815 1.48 araQ Sugar ABC transporter permease 911.12 326.41 BAD_RS08280 1.46 msmF Sugar ABC transporter permease 1,353.65 491.14 BAD_RS00810 1.45 yurN Sugar ABC transporter permease 762.04 278.86 BAD_RS03705 1.35 ABC transporter...”
  • “...for bifidobacteria. Compared to xylose treatment, genes including the sugar transporter permease protein (encoded by BAD_RS00815, BAD_RS08280, BAD_RS00810, BAD_RS08205, BAD_RS03705, BAD_RS02260, BAD_RS07410) and transporter ATPbinding protein (encoded by BAD_RS02265, BAD_RS00495, BAD_RS04090, BAD_RS08375) were upregulated (Table 3 ), the same situation occurs in metabolites, including Lthreonine (meta_58),...”

FXV78_RS11800 carbohydrate ABC transporter permease from Mediterraneibacter gnavus ATCC 29149
27% identity, 90% coverage

• Agarooligosaccharides as a novel concept in prebiotics: selective inhibition of <i>Ruminococcus gnavus</i> and <i>Fusobacterium nucleatum</i> while preserving Bifidobacteria, Lactobacillales <i>in vitro</i>, and inhibiting Lachnospiraceae <i>in vivo</i>
  Fujii, Microbiology (Reading, England) 2024
  • “...process FXV78_RS11790 3.111310165 0.007294465 extracellular solute-binding protein - - - 0.55 GO:0055085 trans membrane transport FXV78_RS11800 3.109170332 0.00719394 ABC transporter ATP-binding protein/permease irtA - - 0.55 GO:0055085 trans membrane transport FXV78_RS11060 3.038357162 0.033489332 hypothetical protein - 0.73 Hemolysin XhlA - - - Gene_id Log 2 FC...”

SeseC_01625 sugar ABC transporter permease from Streptococcus equi subsp. zooepidemicus ATCC 35246
26% identity, 99% coverage

• Insight into the specific virulence related genes and toxin-antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp. zooepidemicus strain ATCC35246
  Ma, BMC genomics 2013
  • “...A (SeseC_01626), mal D (SeseC_01627), mal E (SeseC_01633, SeseC_01622), mal F (SeseC_01624, SeseC_01630), mal G (SeseC_01625) and mal Q (SeseC_01617) were upregulated when Sz35246 infected mice. These genes are related to maltose transport and metabolism and utilization of carbohydrates, which is essential for the ability of...”

VPA1399 maltose ABC transporter, permease protein from Vibrio parahaemolyticus RIMD 2210633
31% identity, 80% coverage

• Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis
  Sun, International journal of molecular sciences 2014
  • “...Ribose ABC transporter permease protein VPA1084 Chn25A_0596 7.7049 d -ribose transporter subunit RbsB Maltose transport VPA1399 ( malG ) Chn25A_1076 2.0352 Maltose transporter permease VPA1400 ( malF ) Chn25A_1077 2.8009 Maltose transporter membrane protein VPA1401( malE ) Chn25A_1078 3.0226 Maltose ABC transporter periplasmic protein VPA1402 Chn25A_1079...”

RL0093 putative transmembrane component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
27% identity, 92% coverage

• Identification and characterization of the TetR family transcriptional regulator NffT in Rhizobium johnstonii
  Li, Applied and environmental microbiology 2024 (secret)

lmo0861 similar to sugar ABC transporter, permease protein - from Listeria monocytogenes EGD-e
27% identity, 90% coverage

• The σ^B-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in Listeria monocytogenes through a direct interaction with the ilvA transcript
  Marinho, RNA biology 2019 (secret)
• Glycerol metabolism and PrfA activity in Listeria monocytogenes
  Joseph, Journal of bacteriology 2008
  • “...lmo0783 lmo0784b lmo0810 lmo0813 uhpTb,d lmo0859 lmo0860 lmo0861 lmo0862 lmo0865 lmo0875 lmo0876 lmo0877 lmo0878 lmo0880 lmo0913b lmo0914 lmo0915b lmo0916...”

C289_0778 carbohydrate ABC transporter permease from Anoxybacillus ayderensis
26% identity, 95% coverage

• A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization
  Kahar, International journal of molecular sciences 2013
  • “...(C289_0857, C289_1909, and C289_2139). Several putative sugar transporters (C289_0465, C289_0466, C289_0467, C289_0603, C289_0763, C289_0764, C289_0765, C289_0778, C289_0779, C289_0780, C289_1015, C289_1174, C289_1392, C289_1394, C289_1910, C289_1911, and C289_1912) were also found in the Blast2GO annotation. The draft genome was submitted to the National Center for Biotechnology Information (NCBI)...”

B8809_1751 carbohydrate ABC transporter permease from Bifidobacterium longum subsp. longum
BL0190 sugar permease of ABC transporter system from Bifidobacterium longum NCC2705
26% identity, 89% coverage

• Characterisation of a Hydroxycinnamic Acid Esterase From the Bifidobacterium longum subsp. longum Taxon
  Kelly, Frontiers in microbiology 2018
  • “...members of the B. longum subsp. longum taxon using Blastn revealed a highly conserved locus (B8809_1751 B8809_1762 in B. longum subsp. longum NCIMB8809), predicted to be involved in plant-derived oligosaccharide degradation within the B. longum subsp. longum taxon ( Schell et al., 2002 ; Arboleya et...”
• Characterization of a novel β-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member
  Fujita, The Journal of biological chemistry 2014
  • “...with five GH43 members and one -galactosidase (BL0176 -BL0190), whereas BLLJ_1826 is flanked by a small gene cluster without GH43 members (BLLJ_1824-BLLJ_1820)....”

YPO1721 putative sugar ABC transporter (permease) from Yersinia pestis CO92
YPTB2360 putative sugar ABC transporter (permease) from Yersinia pseudotuberculosis IP 32953
23% identity, 84% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB2318 (ppsA) YPO2409 phosphoenolpyruvate synthase 0.463 (0.008) YPTB2356 (kduI) YPO1725 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1.444 (0.047) YPTB2360 YPO1721 putative sugar ABC transporter (permease) 1.901 (0.032) YPTB2463 (ptsG) YPO1608 PTS system. glucose-specific IIBC component 4.033 (< 0.001) 1.607 (0.002) YPTB2515 YPO2474 conserved hypothetical protein 0.593 (0.036) YPTB2518 YPO2477 putative...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...0.001) YPTB2318 (ppsA) YPO2409 phosphoenolpyruvate synthase 0.463 (0.008) YPTB2356 (kduI) YPO1725 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1.444 (0.047) YPTB2360 YPO1721 putative sugar ABC transporter (permease) 1.901 (0.032) YPTB2463 (ptsG) YPO1608 PTS system. glucose-specific IIBC component 4.033 (< 0.001) 1.607 (0.002) YPTB2515 YPO2474 conserved hypothetical protein 0.593 (0.036) YPTB2518 YPO2477...”

SpyM3_0985 putative maltose/maltodextrin ABC transport system (permease) from Streptococcus pyogenes MGAS315
SPy1296 putative maltose/maltodextrin ABC transport system (permease) from Streptococcus pyogenes M1 GAS
M5005_Spy_1060 maltose transport system permease protein from Streptococcus pyogenes MGAS5005
M28_Spy1041 maltose transport system permease protein from Streptococcus pyogenes MGAS6180
SPy_1296 sugar ABC transporter permease from Streptococcus pyogenes M1 GAS
25% identity, 99% coverage

• A Single Amino Acid Replacement in the Sensor Kinase LiaS Contributes to a Carrier Phenotype in Group A Streptococcus
  Flores, Infection and immunity 2015
  • “...2.5 1.0E23 1.0E23 5.8E09 1.0E11 5.6E11 Downregulated SpyM3_1799 SpyM3_0985 SpyM3_0014 SpyM3_0984 SpyM3_0375 spxA2 malG malF rnc 3.8 2.4 2.4 2.3 2.3 1.0E38...”
• Adaptation of group A Streptococcus to human amniotic fluid
  Sitkiewicz, PloS one 2010
  • “...Maltodextrin phosphorylase M28_Spy1037 SPy1292 malM 14.96 4-alpha-glucanotransferase M28_Spy1039 SPy1294 malE 4.94 Maltose maltodextrin-binding protein M28_Spy1041 SPy1296 malG 2.19 Maltose transport system permease protein M28_Spy1044 SPy1299 malD 34.73 Maltodextrin transport system permease protein M28_Spy1045 SPy1301 malC 38.81 Maltodextrin transport system permease protein M28_Spy1046 SPy1302 amyA 82.63 Cyclodextrin...”
• Regulation of polysaccharide utilization contributes to the persistence of group a streptococcus in the oropharynx
  Shelburne, Infection and immunity 2007
  • “...located in the gene region from M5005_Spy_1055 to M5005_Spy_1060 (Fig. 1). This region includes M5005_Spy_ 1058 (malE), a gene encoding a maltodextrin binding...”
  • “...to the region comprising the genes M5005_Spy_1055 to M5005_Spy_1060 as the maltodextrin gene region and the region comprising the genes M5005_Spy_1680 to...”
• Adaptation of group A Streptococcus to human amniotic fluid
  Sitkiewicz, PloS one 2010
  • “...2.16 Maltodextrin phosphorylase M28_Spy1037 SPy1292 malM 14.96 4-alpha-glucanotransferase M28_Spy1039 SPy1294 malE 4.94 Maltose maltodextrin-binding protein M28_Spy1041 SPy1296 malG 2.19 Maltose transport system permease protein M28_Spy1044 SPy1299 malD 34.73 Maltodextrin transport system permease protein M28_Spy1045 SPy1301 malC 38.81 Maltodextrin transport system permease protein M28_Spy1046 SPy1302 amyA 82.63...”
• The role of CopA in Streptococcus pyogenes copper homeostasis and virulence
  Dao, Journal of inorganic biochemistry 2023
  • “...3-fold), belonged to the PTS family of transporters, while the maltose import pathway genes, SPy_1294, SPy_1296, and SPy_1297, were also upregulated (11.3-fold) ( Table S5 ). The putative PTS genes are predicted to encode a carbohydrate-uptake system with specificity for mannose, maltose, fructose, or N -acetylgalactosamine....”

Rv2317 PROBABLE SUGAR-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER USPB from Mycobacterium tuberculosis H37Rv
28% identity, 93% coverage

• ATP-binding cassette (ABC) import systems of Mycobacterium tuberculosis: target for drug and vaccine development
  Soni, Emerging microbes & infections 2020
  • “...formation [ 43 ] Amino-sugar importer (UspABC/Rv2316-Rv2318) SBP: UspC (Rv2318) TMD: UspA (Rv2316) and UspB (Rv2317) NBD: Remains to be identify Essential for in vitro growth [ 50 ] UspC have a substrate preference for sugars containing an amino group at the C2 or C3 position...”
• A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance
  Sheen, BMC genomics 2017
  • “...strains with critical mutations in pncA , were Rv2505c, Rv2777c, Rv0735, Rv0787A, Rv0994, Rv1327c, Rv1742, Rv2317, Rv2557, Rv2857c, Rv3362c, Rv3393, Rv3410c, Rv3767c, Rv2646, Rv0668 , and Rv0667 . Analysis of mutations in the special set of genes For each of the mutations identified as significantly associated...”

BKKJ1_0069 carbohydrate ABC transporter permease from Bifidobacterium catenulatum subsp. kashiwanohense
30% identity, 87% coverage

• Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal
  James, Scientific reports 2019
  • “...vs Lactose BKKJ1_0067 BKKJ1_0067 ABC transporter substrate-binding protein 8.12 BKKJ1_0068 BKKJ1_0068 ABC transporter permease 5.91 BKKJ1_0069 BKKJ1_0069 ABC transporter permease 5.71 BKKJ1_0206 BKKJ1_0206 6-phosphogluconate dehydrogenase 13.31 BKKJ1_0207 BKKJ1_0207 hypothetical protein 17.67 BKKJ1_0208 BKKJ1_0208 putative gluconokinase 17.21 BKKJ1_0336 BKKJ1_0336 hypothetical protein 16.99 BKKJ1_0338 BKKJ1_0338 hypothetical protein 27.69...”

SM_b21654 ABC transporter for Lactose, permease component 2 from Sinorhizobium meliloti 1021
27% identity, 92% coverage

• mutant phenotype: Specific phenotypes on Beta-Lactose. Not important for arabinose utilization but there is no other clear arabinose tranpsorter so who knows

Bbr_1656 carbohydrate ABC transporter permease from Bifidobacterium breve UCC2003
26% identity, 85% coverage

• Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation
  Lanigan, Frontiers in microbiology 2017
  • “...Bbr_0427 mntH , Mn 2+ /Fe 2+ transporter, NRAMP family +++ + +++ ++ No Bbr_1656 Sugar ABC transporter, permease protein +++ ++ ++ ++ ++ No Bbr_1657 Binding-protein-dependent transport system +++ ++ ++ ++ ++ No Bbr_1669 Hypothetical membrane spanning protein ++ + ++ No...”
• A two-component regulatory system controls autoregulated serpin expression in Bifidobacterium breve UCC2003
  Alvarez-Martin, Applied and environmental microbiology 2012
  • “...SerR overexpressiona Increased expression Bbr_1318 Bbr_1319 Bbr_1656 Bbr_1657 Bbr_1658 Bbr_1655 Bbr_0249 Bbr_0107 Bbr_1464 Bbr_0106 Bbr_1320 Bbr_0108 Bbr_1293...”
  • “...reverse Bbr_1319; conserved hypothetical membrane-spanning protein Bbr_1656; sugar ABC transporter, permease protein Bbr_1657; sugar-binding protein of ABC...”

B1745_06745 sugar ABC transporter permease from Lactobacillus amylolyticus
27% identity, 97% coverage

• Adaptive mechanism of Lactobacillus amylolyticus L6 in soymilk environment based on metabolism of nutrients and related gene-expression profiles
  Fei, Food science & nutrition 2022
  • “...(Table 2 ). However, several genes involved in sucrose transportation, especially sugar ABC transporters (B1745_06760, B1745_06745 and B1745_06745), and galactose metabolism (B1745_05485 and B1745_05490) were significantly downregulated in logarithmic phase. Microbes intend to utilize easily metabolizable carbohydrate and inhibit the metabolism of the other carbohydrate by...”
  • “...protein 1.36 B1745_02355 acyP acylphosphatase 1.50 B1745_06765 pgmB betaphosphoglucomutase 1.61 B1745_06730 gpmB hypothetical protein 2.38 B1745_06745 ganQ sugar ABC transporter permease 2.58 B1745_06750 ganP sugar ABC transporter permease 2.79 Amino acids transport and metabolism B1745_01435 rpoA DNAdirected RNA polymerase subunit alpha 1.02 B1745_02350 yidC insertase 1.07...”

MAP1767c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
28% identity, 96% coverage

• Genomic variations associated with attenuation in Mycobacterium avium subsp. paratuberculosis vaccine strains
  Bull, BMC microbiology 2013
  • “...Unknown MAP1764 Unknown MAP1765c rssA Patatin like esterase Fatty acid Metabolism MAP1766c Cellobiose ABC transporter MAP1767c ABC transporter MAP1768c ABC transporter MAP1769c Transcriptional regulator MAP1770c Sigma-70 factor MAP1771c IS 900 MAP1772 Unknown MAP1773c Nuclear transport factor 2 Steroid metabolism MAP1774c pncA Isochorismatase Nicotinamide metabolism MAP1775 doxX...”

Rv2039c Probable sugar-transport integral membrane protein ABC transporter from Mycobacterium tuberculosis H37Rv
28% identity, 94% coverage

• Comparison of carbohydrate ABC importers from Mycobacterium tuberculosis
  De, BMC genomics 2021
  • “...the building of a rooted tree (Fig. 3 A). Group 1 was formed by SugB, Rv2039c, UspB, and UgpE and group 2 by SugA, Rv2040c, UspA, and UgpA. Putative orthologs of SugAB permeases formed a separated group from the three other systems, as shown in SugC...”
  • “...TMDs in two groups, each one with one member of each transporter. Group 1: SugB, Rv2039c, UspB, and UgpE, and Group 2: SugA, Rv2040c, UspA, and UgpA. Dark gray: M. tuberculosis complex group (MTBC), light gray: other pathogenic mycobacteria, and white: environmental species, represented by M....”
• ATP-binding cassette (ABC) import systems of Mycobacterium tuberculosis: target for drug and vaccine development
  Soni, Emerging microbes & infections 2020
  • “...amino group at the C2 or C3 position [ 36 ] Rv2038c-Rv2041c SBP: Rv2041c TMD: Rv2039c and Rv2040c NBD: Rv2038c (two copies) Rv2041c treatment with macrophages and lymphocytes shows elevated expression of pro-inflammatory cytokines and raised up secretion of IFN- and TNF-, respectively [ 52 ]...”
• Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage
  Malinga, Genome announcements 2016
  • “...overexpress EPs ( 16 ). In RSA114, we identified mutations within the EP-encoding genes Rv0987, Rv2039c, and Rv0402c that are predicted by PROVEAN ( http://provean.jcvi.org/index.php ), to impact efflux activity. ESX export enzymes are involved in the synthesis of PDIM proteins, which have a role in...”
• Anti-mycobacterial activity of marine fungus-derived 4-deoxybostrycin and nigrosporin
  Wang, Molecules (Basel, Switzerland) 2013
  • “...processing: Translation, ribosomal structure and biogenesis gnd2 Rv1122 0.44 0.03 Metabolism: Carbohydrate transport and metabolism Rv2039c - 0.46 0.02 Metabolism: Carbohydrate transport and metabolism Rv1200 - 1.63 0.04 Metabolism: Carbohydrate transport and metabolism pgk Rv1437 1.65 0.07 Metabolism: Carbohydrate transport and metabolism Rv2471 - 1.83 0.12...”

MID13_22490 carbohydrate ABC transporter permease from Vibrio gigantis
28% identity, 80% coverage

• Contact-mediated algicidal mechanism of <i>Vibrio coralliirubri</i> ACE001 against the harmful alga Karenia mikimotoi
  Yu, iScience 2024
  • “...thecell part. Among the 483 upregulated genes, the gene with the most significant change was MID13_22490 (log 2 FC= 11.76), predicted to be a permease component of the bacterial ABC transporter system. The permease component refers to substances such as peptides, proteins, and other macromolecules that...”
  • “...bind to ABC transporter proteins and are then transported into or out of the cell. MID13_22490 showed a significant upregulation during the algicidal process, suggesting it may play an important role in the bacterium-algae interaction. MID13_03740, annotated as a protein containing the DUF3149 domain, showed a...”

BF29_RS09835 sugar ABC transporter permease from Heyndrickxia coagulans DSM 1 = ATCC 7050
28% identity, 78% coverage

• Time-resolved transcriptomic and proteomic profiling of <i>Heyndrickxia coagulans</i> during NaOH-buffered L-lactic acid production
  Huang, Frontiers in microbiology 2023
  • “...high concentration of sodium lactate in the fermentation broth. MdxE (BF29_RS09825), MdxF (BF29_RS09830), and MdxG (BF29_RS09835) collectively encode a maltodextrin transport system known as MdxEFG, where MdxE functions as the substrate-binding protein and the latter two act as permease proteins ( Schnert et al., 2006 )....”

lmo0767 similar to ABC transporter, permease protein from Listeria monocytogenes EGD-e
23% identity, 95% coverage

• The PAMP c-di-AMP Is Essential for Listeria monocytogenes Growth in Rich but Not Minimal Media due to a Toxic Increase in (p)ppGpp. [corrected]
  Whiteley, Cell host & microbe 2015
  • “...RNA binding domain protein similar to yabR LMRG 02640::121 43 1.2 72 2.6 102 2.7 lmo0767 Sugar ABC transporter permease LMRG 00455::222 42 1.4 80 0.9 100 1.3 lmo1884 Xanthine uptake transporter similar to pbuX LMRG 01031::319 41 0.7 77 1.5 107 2.9 P lmo0974 Promoter...”
• Stress response and adaptation of Listeria monocytogenes 08-5923 exposed to a sublethal dose of carnocyclin A
  Liu, Applied and environmental microbiology 2014
  • “...abc mfs ywzB mptAB mptC celA celB celC lmo0767 lmo1250 lmo2527 lmo0096 lmo0097 lmo2765 lmo2762 lmo2763 ABC transporter, permease protein Major facilitator...”
• Listeria monocytogenes differential transcriptome analysis reveals temperature-dependent Agr regulation and suggests overlaps with other regulons
  Garmyn, PloS one 2012
  • “..., lmo2000 , bvrB ) [35] and putative sugar ABC transporters (for example lmo0768 , lmo0767 and lmo0766 ) had higher transcript levels in DG125A compared to EGD-e. Two genes with higher transcript level ( lmo1884 and pyrP ) encode permeases for xanthine and uracil. Both...”
• Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
  Deng, BMC genomics 2010
  • “...IIIA + 119 lmo0766 Similar to putative sugar ABC transporter, permease protein IIIA + - lmo0767 Similar to ABC transporter, permease protein IIIA + - lmo1031 Hypothetical protein IIIA - 166 lmo1032 Similar to transketolase IIIA - 166 lmo1033 Similar to transketolase IIIA - 166 lmo1035...”

lmo2123 similar to maltodextrin ABC-transport system (permease) from Listeria monocytogenes EGD-e
LMOf2365_2157 maltose/maltodextrin ABC transporter, permease protein from Listeria monocytogenes str. 4b F2365
26% identity, 78% coverage

• Synergistic Antibacterial Mechanism of Mannosylerythritol Lipid-A and Lactic Acid on Listeria monocytogenes Based on Transcriptomic Analysis
  Liu, Foods (Basel, Switzerland) 2022
  • “..., we analyzed the transcription level of lmo0248 , lmo0249 , lmo2623 , lmo2628 , lmo2123 , lmo2124 , lmo2347, and lmo2348 by real-time quantitative PCR to verify the accuracy of the transcriptome data. It was highly consistent between the RNA-Seq and qPCR results (R 2...”
• Genomic characteristics of listeria that caused invasive listeriosis during the COVID-19 pandemic
  Voronina, 2022
• Antibacterial Efficacy and Mechanism of Mannosylerythritol Lipids-A on Listeria monocytogenes
  Liu, Molecules (Basel, Switzerland) 2020
  • “...[ 31 ]. The expression of genes involved in localization (lmo2124, lmo1740, etc.), transport (lmo2124, lmo2123, lmo2347, etc.) and the establishment of localization were downregulated ( Figure 6 B). These genes are mainly predicted to be related to the transport of sugar and amino acids, indicating...”
  • “...S2 ) were differentially regulated during cultivation in MEL-A, in which the ABC transporters-associated genes (lmo2123, lmo2123, opuCD, etc.) were significantly regulated. ABC transporters belong to a large and diverse protein family that are mainly responsible for transporting various substrates (including ions and macromolecules) and are...”
• Survival of Listeria monocytogenes in Soil Requires AgrA-Mediated Regulation
  Vivant, Applied and environmental microbiology 2015
  • “...of proteins, such as the ABC transporter (lmo2123 to lmo2125, lmo1739) and the phosphotransferase (PTS) system (lmo2782, lmo2665, lmo2666, lmo2780). Fourteen...”
• Maltose and maltodextrin utilization by Listeria monocytogenes depend on an inducible ABC transporter which is repressed by glucose
  Gopal, PloS one 2010
  • “...L. monoyctogenes cluster symbolize the position of insertion mutations and of the deletion generated in lmo2123 . T = putative transcriptional terminator. The GenBank accession nos. for the respective genome sequences are AL591824 ( L.m .) and AL009126 ( B.s .). A homology search for orthologues...”
  • “...as similar to a maltodextrin ABC transporter. ListiList also showed that in L. monocytogenes EGD-e, lmo2123 lmo2125 are part of a cluster of eight genes which, according to annotated gene product function and protein length, is almost identical to the major part of the maltodextrin utilization...”
• Transcriptome analysis of alkali shock and alkali adaptation in Listeria monocytogenes 10403S
  Giotis, Foodborne pathogens and disease 2010
  • “...induction of genes such as maltodextrin transporter (lmo2122, lmo2123, lmo2124, and lmo2126) suggests that initial uptake and processing of certain sugars, such...”
• Glycerol metabolism and PrfA activity in Listeria monocytogenes
  Joseph, Journal of bacteriology 2008
  • “...lmo2085b lmo2098 lmo2108 lmo2109 lmo2115 lmo2121a,b lmo2122 lmo2123 lmo2124 lmo2125b lmo2134 lmo2135 lmo2136 lmo2143 lmo2159b lmo2175 fruA lmo2341 lmo2389...”
• Catabolite control protein C contributes to virulence and hydrogen peroxide-induced oxidative stress responses in <i>Listeria monocytogenes</i>
  Ogunleye, Frontiers in microbiology 2024
  • “...L-arabinose transport system permease protein 1.6 1.3E-02 LMOf2365_2032 Probable ABC transporter permease protein 2.7 3.7E-03 LMOf2365_2157 Maltodextrin transport system permease protein 2.2 2.3E-03 LMOf2365_2318 L-cystine transport system permease protein 2.7 1.1E-05 LMOf2365_2553 Putative hemin transport system permease protein: FtsX-like permease family 1.7 4.3E-03 LMOf2365_2828 Inner membrane...”

SCO3482 sugar-permease from Streptomyces coelicolor A3(2)
25% identity, 76% coverage

• LacI-Family Transcriptional Regulator DagR Acts as a Repressor of the Agarolytic Pathway Genes in Streptomyces coelicolor A3(2)
  Tsevelkhoroloo, Frontiers in microbiology 2021
  • “...the genes assumed to be related to AHG metabolism, and the sugar transporter-associated gene ( sco3482 - 3484 ), which exists in the central region of the agarolytic pathway gene cluster, were all significantly increased. Thus, same expression pattern for all of genes in this cluster...”
• Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor
  Romero-Rodríguez, BMC microbiology 2016
  • “...maltose transporter malG and malF genes ( SCO2229 - SCO2230 ) and the putative operon SCO3482 - SCO3484 (coding for a sugar permease, an integral membrane transport protein and a sugar-binding protein) were repressed (Fig. 4b ). It is noteworthy mentioning that only a limited number...”
  • “...are described. Interestingly, in this study, a possible transporter associated with neoagarobiose incorporation (encoded by SCO3482 - 84 ), was found (Fig. 6c ). Since this chromosomal region is implicated in agar metabolism, genes SCO3482 - 84 showed the same expression pattern observed for agarases and...”
• Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2)
  Lewis, BMC research notes 2011
  • “...with the co-expressed SCO3472 (a transposase remnant). A glycosyltransferase homologue SCO3481 and a sugar permease (SCO3482) are also presumably expressed as an operon. The down regulation of these carbohydrate metabolism genes in the carbon limited culture may be a response to lack of substrate, however, we...”

TTHA0976 sugar ABC transporter, permease protein from Thermus thermophilus HB8
TTH_RS04960 carbohydrate ABC transporter permease from Thermus thermophilus HB8
28% identity, 70% coverage

• The role of ribonucleases in regulating global mRNA levels in the model organism Thermus thermophilus HB8
  Ohyama, BMC genomics 2014
  • “...the down-regulation of this operon. This observation suggests action of another regulatory mechanism. The genes TTHA0976 to TTHA0996 were down-regulated. In particular, TTHA0994 and TTHA0995 were dramatically down-regulated (86- and 1,166-fold, respectively) during both growth phases. TTHA0995 is a novel cyclic di-GMP-degrading protein which comprised a...”
  • “...RNase HI and Argonaute gene disruptants, particularly during the stationary phase. Furthermore, the region from TTHA0976 to TTHA0996 was markedly down-regulated in the Argonaute and RNase HI gene disruptants. It should be noted that the mRNA level of RNase R was increased (2.3-fold) by disruption of...”
• Comparison of carbohydrate ABC importers from Mycobacterium tuberculosis
  De, BMC genomics 2021
  • “...pathogenic mycobacteria, and white: environmental species, represented by M. smegmatis. The amino acid sequences of TTH_RS04960 and TTH_RS04965 from Thermus thermophilus , encoding putative carbohydrate TMDs, were used as outgroup. B Structural models of SugB, Rv2039c, UspB, UgpE and SugA, Rv2040c, UspA, and UgpA highlighting the...”

SACTE_2287 carbohydrate ABC transporter permease from Streptomyces sp. SirexAA-E
25% identity, 85% coverage

• Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces
  Takasuka, Scientific reports 2013
  • “...SACTE_6428 CBM33 Chitin-binding, domain 3 GGGAGCGCTCCCA 9 7.9 SACTE_2347 GH5 CBM2 Beta-mannosidase TGGGAGCGCTCCCA 11 5.0 SACTE_2287 Transport systems inner membrane component TGGGAGCGCTCCCA 15 4.3 SACTE_2289 Family 1 extracellular solute-binding protein TGGGAGCGCTCCCA 19 3.9 SACTE_0352 GCN5-related N-acetyltransferase TGGGAGCGCTCCCA 22 3.6 SACTE_2286 GH1 Glycoside hydrolase 1 GGGAGCGCTCCCA 27...”

llmg_0490 sugar transport system permease protein from Lactococcus lactis subsp. cremoris MG1363
30% identity, 88% coverage

• Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363
  Wegmann, Journal of bacteriology 2007
  • “...llmg_0330 llmg_0423 llmg_0487 llmg_0488 llmg_0489 llmg_0490 llmg_0666 llmg_0737 llmg_0738 llmg_0957 llmg_0958 llmg_0959 llmg_0960 llmg_0961 llmg_0963 llmg_1009...”

N186_RS07245 carbohydrate ABC transporter permease from Thermofilum adornatum
27% identity, 99% coverage

• Novel Hyperthermophilic Crenarchaeon Thermofilum adornatum sp. nov. Uses GH1, GH3, and Two Novel Glycosidases for Cellulose Hydrolysis
  Zayulina, Frontiers in microbiology 2019
  • “...). The close location of the carbohydrate ABC transporter and sugar permease ( N186_RS07240 , N186_RS07245 and N186_RS07250 ) genes suggest the co-action of all these proteins in alpha-mannan degradation. The following proteins were predicted to participate in beta-linked sugar hydrolysis including cellulose and its derivatives:...”

APY09_06055 sugar ABC transporter permease from Schaalia odontolytica
27% identity, 74% coverage

• Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence
  Zhong, Proceedings of the National Academy of Sciences of the United States of America 2024
  • “...encoding Uridine diphosphate (UDP)-phosphate galactose phosphotransferase (APY09_00485), TetR family transcriptional regulator (APY09_06000), ABC transporter (APY09_06050, APY09_06055), peptidase (APY09_09670), and cell wallbinding protein (APY09_09665). Fig. 3. Transcriptomic analysis of surface-growth XH001 and TM7x/XH001. ( A ) The transcriptomic data were subjected to PCA. The abscissa is the...”

EF1343 sugar ABC transporter, permease protein from Enterococcus faecalis V583
IUJ47_RS09695 sugar ABC transporter permease from Enterococcus faecalis
27% identity, 95% coverage

• Enterococcus faecalis Maltodextrin Gene Regulation by Combined Action of Maltose Gene Regulator MalR and Pleiotropic Regulator CcpA
  Grand, Applied and environmental microbiology 2020 (secret)
• Transcriptome, proteome, and metabolite analyses of a lactate dehydrogenase-negative mutant of Enterococcus faecalis V583
  Mehmeti, Applied and environmental microbiology 2011
  • “...EF0806 EF0900 EF0949 EF1017 EF1018 EF1019 EF1213 EF1214 EF1343 EF1353 EF1354 EF1355 EF1356 EF1612 EF1613 EF1712 ldh-1 Putative function pdhA pdhB aceF lpdA pflA...”
• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...family protein IUJ47_RS12720 3.049 Thiol reductant ABC exporter subunit CydD IUJ47_RS04405 3.21 BMP family protein IUJ47_RS09695 3.237 Sugar ABC transporter permease IUJ47_RS04420 3.248 ABC transporter permease IUJ47_RS12715 3.422 Thiol reductant ABC exporter subunit CydC IUJ47_RS02110 8.113 D-ribose pyranase IUJ47_RS03260 40.433 ZinT/AdcA family metal-binding protein...”

SSA_1300 Maltose ABC transporter, permease protein, putative from Streptococcus sanguinis SK36
26% identity, 99% coverage

• Glucose Phosphotransferase System Modulates Pyruvate Metabolism, Bacterial Fitness, and Microbial Ecology in Oral Streptococci
  Zeng, Journal of bacteriology 2023 (secret)

BBMN68_1168, BLLJ_0210 carbohydrate ABC transporter permease from Bifidobacterium longum subsp. longum BBMN68
26% identity, 92% coverage

• Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121
  Saito, PloS one 2020
  • “...that consists of a substrate-binding protein (SBP, BLLJ_0208) and two transmembrane domain proteins (BLLJ_0209 and BLLJ_0210). Hydroxyproline (Hyp) residues in HRGPs, such as extensin and solanaceous lectins, are usually O -glycosylated with 3 or 4 L-Ara f residues that are linked with three -bonds and one...”
• Characterization of a novel β-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member
  Fujita, The Journal of biological chemistry 2014
  • “...(BLLJ_0208) and two transmembrane subunits (BLLJ_0209 and BLLJ_0210). BLLJ_0208 exhibits 28% identity with the GNB/LNB-binding protein, and BLLJ_0209 and...”
• Mechanism analysis of acid tolerance response of bifidobacterium longum subsp. longum BBMN 68 by gene expression profile using RNA-sequencing
  Jin, PloS one 2012
  • “...the components of sugar ABC-transporter. Gene ID RPKM-control RPKM-acid-adapted Fold change COG Code Gene description BBMN68_1168 145.91 61.94 2.36 * G COG0395 K02026, multiple sugar transport system permease protein BBMN68_1169 98.62 30.32 3.25 * G COG1175 K02025, multiple sugar transport system permease protein BBMN68_1170 2153.69 298.91...”
• Characterization of a novel β-L-Arabinofuranosidase in Bifidobacterium longum: functional elucidation of A DUF1680 family member
  Fujita, The Journal of biological chemistry 2011
  • “...(BLLJ_0208) and 2 transmembrane subunits (BLLJ_0209 and BLLJ_0210). BLLJ_0208 exhibits 28% identity with the GNB/LNB-binding protein, and BLLJ_0209 and...”

HVO_A0146 ABC-type transport system permease protein (probable substrate sugar) from Haloferax volcanii DS2
24% identity, 68% coverage

• Assigning a function to a conserved archaeal metallo-β-lactamase from Haloferax volcanii
  Fischer, Extremophiles : life under extreme conditions 2012
  • “...prime kit ReadiprimeII (GE Healthcare). For detection of the ABC-type sugar transport protein (permease) mRNA (HVO_A0146) and the glucan 1,4--glucosidase (HVO_A0149) mRNA DNA probes were generated using PCR with oligos ABC#1 and ABC#2 and Glucan#1 and Glucan#2, respectively. The resulting PCR products were labelled with a-...”
  • “...in expression is well supported. A similar decrease in expression was found for the genes HVO_A0146 to HVO_A0148 annotated as an ABC-type sugar transport system (Table 1 ). To confirm the downregulation of those genes, we performed northern analyses for the ABC-type sugar transport protein (permease)...”

SYNW1284 ABC transporter, likely for trehalose/maltose, membrane component from Synechococcus sp. WH 8102
31% identity, 81% coverage

• Computational prediction of the osmoregulation network in Synechococcus sp. WH8102
  Mao, BMC genomics 2010
  • “...PCC6803 slr0747 GgtA SYNW1285 SYNW1279-1286 0.99 PCC6803 slr0530 GgtC SYNW1283 SYNW1279-1286 0.99 PCC6803 slr0531 GgtD SYNW1284 SYNW1279-1286 0.99 PCC6803 ABX75857 GpgS SYNW2436 P.marina ABX75858 GpgP SYNW2434 P.marina slr0662 SpeA SYNW2359 0.99 PCC6803 sll0045 Sps SYNW2520 0.69 PCC6803 b0855 PotG SYNW1544 0.99 E. coli YP_225044 MtrA SYNW2246...”

Balac_1569 MalG-type ABC sugar transport system permease component from Bifidobacterium animalis subsp. lactis Bl-04
29% identity, 94% coverage

• Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04
  Andersen, BMC genomics 2013
  • “...kinase xyloside A,C Xylobiose D 18.2 19.0 Balac_1567 4--glucanotransferase glucoside B,D Maltriose E 9.7 14.5 Balac_1569 ABC transporter, permease component glucoside B,D Cellobiose E 5.2 13.7 Balac_1570 ABC transporter, permease component glucoside B,D Cellobiose E 3.7 15.1 Balac_1571 Transcriptional regulator ( lacI type) glucoside B,D Cellobiose...”
  • “...all harbored the additional two -helical domain, suggesting the divergence of the maltotriose ABC transporter (Balac_1569, 1570 and 1572) from known maltose ABC transporters. Table 3 Prediction of -helical topology within oligosaccharide transporters identified in B. lactis Bl-04 ORF Predicted substrates Class Predicted TMH 1 Sequence...”
• Genetic and physiological responses of Bifidobacterium animalis subsp. lactis to hydrogen peroxide stress
  Oberg, Journal of bacteriology 2013
  • “...Balac_1598 Balac_1599 Balac_1601 Balac_1567 Balac_1568 Balac_1569 Balac_1570 Balac_1572 Balac_1573 Bifidobacterium lactis H2O2 Stress Response with no...”

llmg_0737 Maltose ABC transporter permease protein malG from Lactococcus lactis subsp. cremoris MG1363
LLNZ_03840 sugar ABC transporter permease from Lactococcus cremoris subsp. cremoris NZ9000
27% identity, 96% coverage

• Further Elucidation of Galactose Utilization in Lactococcus lactis MG1363
  Solopova, Frontiers in microbiology 2018
  • “...16.5 13.1 Maltose ABC transporter substrate binding protein llmg_0738 malF 11.0 9.6 Maltose ABC transporter llmg_0737 malG 4.6 5.5 Maltose ABC transporter permease llmg_0746 malR 2.1 2.3 Maltose operon transcriptional repressor llmg_0446 msmK 22.3 16.1 Multiple sugar-binding transport ATP-binding protein llmg_1569 fruC 4.5 1.1 Tagatose-6-phosphate kinase...”
• Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363
  Wegmann, Journal of bacteriology 2007
  • “...llmg_0487 llmg_0488 llmg_0489 llmg_0490 llmg_0666 llmg_0737 llmg_0738 llmg_0957 llmg_0958 llmg_0959 llmg_0960 llmg_0961 llmg_0963 llmg_1009 llmg_1010 llmg_1011...”
• High efficiency recombineering in lactic acid bacteria
  van, Nucleic acids research 2012
  • “...undergone a double recombineering event in which rpoB (locus tag LLNZ_10235) and malG (locus tag LLNZ_03840) were mutated (RPRB4004) simultaneously. Compared to the control strain (RPRB4000) no point mutations or other genome alterations were identified other than the mutations introduced by the oligonucleotides. Taken together these...”

BAA6_1555 carbohydrate ABC transporter permease from Bifidobacterium animalis
29% identity, 94% coverage

• Transcriptome analysis revealed growth phase-associated changes of a centenarian-originated probiotic Bifidobacterium animalis subsp. lactis A6
  Wang, BMC microbiology 2022
  • “...and raffinose transport were up-regulated over 2.0-fold during the stationary phase, however, genes BAA6_0488-0491 , BAA6_1555 , and BAA6_1548-1549 encoding three ABC-type transporters for galactooligosaccharides (GOS), maltotriose, and pullulan transport were down-regulated over 1.8-fold. Interestingly, BAA6_1415 encoding a putative cellobiose ABC transporter permease protein CebG and...”

SUB0164 ABC transporter permease subunit from Streptococcus uberis 0140J
27% identity, 38% coverage

• Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis
  Ward, BMC genomics 2009
  • “...two other CDSs that make a putative operon: SUB0163, binding-protein-dependent transport system membrane protein; and SUB0164, a fusion protein pseudogene. This latter CDS consists of an N-terminus similar to ABC transporter permease proteins and a C-terminus similar to fibronectin binding protein, containing an LPXTG motif. It...”
  • “...up an operon, however it is not apparent what effect, if any, the mutation in SUB0164 will have upon resistance to QACs. A distinct feature of the S. uberis genome that has emerged from the comparative genomic analysis with other streptococcal species is that there is...”

EF2232 ABC transporter, permease protein from Enterococcus faecalis V583
26% identity, 85% coverage

• Influence of the Alternative Sigma Factor RpoN on Global Gene Expression and Carbon Catabolism in Enterococcus faecalis V583
  Keffeler, mBio 2021
  • “...ABC transporter, permease protein 257.25 38 24 AT G AAAA CG CTATTA 0.986 6 EF2237-32 EF2232 ABC transporter, permease protein 4.20 35 21 ATTAAAG CG CTTTCT 0.997 6 EF2233 ABC transporter, permease protein 8.46 35 21 ATTAAAG CG CTTTCT 0.972 5 EF2234 Sugar ABC transporter, sugar...”

Csac_0428 binding-protein-dependent transport systems inner membrane component from Caldicellulosiruptor saccharolyticus DSM 8903
28% identity, 89% coverage

• Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus
  van, Applied and environmental microbiology 2008
  • “...carbohydrate-specific maltodextrin ABC transport system (Csac_0427, Csac_0428, and Csac_0431) and the maltose ABC transport system (Csac_2491 to Csac_2493)....”

XF2446 ABC transporter sugar permease from Xylella fastidiosa 9a5c
26% identity, 92% coverage

• Xylella fastidiosa gene expression analysis by DNA microarrays
  Travensolo, Genetics and molecular biology 2009
  • “...Mg 2+ / citrate complex transporter -1.39 XF2455 ccmA Heme ABC transporter ATP-binding protein -1.32 XF2446 malG ABC transporter sugar permease -1.30 XF0874 yecS ABC transporter permease -1.14 XF0933 feoB Ferrous iron transporter protein B -1.13 XF0324 afuA Periplasmic iron-binding protein -0.99 XF2685 sppA Protease IV...”
• Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa
  Meidanis, Microbiology and molecular biology reviews : MMBR 2002
  • “...XF1346 XF1345 XF1475 XF1409 XF0421 XF0419 XF0418 XF0420 XF0874 XF2695 XF0875 XF2448 XF2447 XF2446 XF1067 ORF 0 5 6 0 0 0 0 0 3 4 0 0 0 4 5 0 No. of TMSs Sulfate...”

OEOE_RS07040 carbohydrate ABC transporter permease from Oenococcus oeni PSU-1
27% identity, 82% coverage

• Transcriptomic and Proteomic Analysis of Oenococcus oeni Adaptation to Wine Stress Conditions
  Margalef-Català, Frontiers in microbiology 2016
  • “...II: OEOE_RS03595 (amino acid ABC transporter substrate-binding protein); Profile III: OEOE_RS05245 (oligoendopeptidase F); Profile IV: OEOE_RS07040 (glycerol-3-phosphate ABC transporter permease); Profile V: OEOE_RS03155 (F0F1 ATP synthase subunit A); Profile VI: OEOE_RS01045 (PTS sugar transporter subunit IIA). Proteomic analysis of O. oeni PSU-1 adaptation to WLM conditions...”
  • “...Glycerol-3-phosphate ABC transporter permease OEOE_RS07035 0.90 1.36 1.53 1.65 1.72 1.76 Glycerol-3-phosphate ABC transporter permease OEOE_RS07040 1.03 1.54 1.64 1.81 2.01 1.93 Glycerol-3-phosphate ABC transporter substrate-binding protein OEOE_RS07045 1.16 1.47 1.86 2.13 2.20 2.22 UDP-phosphate galactose phosphotransferase OEOE_RS07255 1.98 1.96 1.96 2.01 1.94 1.96 Ribokinase OEOE_RS07775...”

Ccel_2110 carbohydrate ABC transporter permease from Ruminiclostridium cellulolyticum H10
Ccel_2110 binding-protein-dependent transport systems inner membrane component from Clostridium cellulolyticum H10
25% identity, 99% coverage

• Internal Transcription Terminators Control Stoichiometry of ABC Transporters in Cellulolytic Clostridia
  Wu, Microbiology spectrum 2022
  • “...an SBP gene (Ccel_2112) at the 5 end, followed by two TMD genes (Ccel_2111 and Ccel_2110), and has a 106-bp long intergenic region between Ccel_2112 and Ccel_2111. Ccel_2112, encoding SBPs, was transcribed at significantly higher levels than its downstream genes ( Fig.3A ). Northern blotting with...”
  • “...and the transcripts of Ccel_2112-2110 were terminated at the 3 ends of Ccel_2112, Ccel_2111, and Ccel_2110. Subsequently, three stem-loop structures were predicted at the 3 ends of Ccel_2112, Ccel_2111, and Ccel_2110 ( Fig.3D ), suggesting that they potentially terminate the transcription of the cluster of Ccel_2112-2110...”

BL105A_1894 carbohydrate ABC transporter permease from Bifidobacterium longum
28% identity, 89% coverage

• Application of Recombinase-Based In Vivo Expression Technology to Bifidobacterium longum subsp. longum for Identification of Genes Induced in the Gastrointestinal Tract of Mice
  Koguchi, Microorganisms 2020
  • “...inhibitor), BL105A_1293 (galactoside transport protein), BL105A_1294 (glycoside hydrolase family 32 -fructofuranosidase), BL105A_1798 (putative glycosyltransferase), and BL105A_1894 (raffinose transport system permease protein). Among them, BL105A_1294 was not identified in the R-IVET analysis, but this gene was used as an expected positive control gene for in vivo-specific expression...”
  • “...showed significantly increased expression in the cecum, but the other three genes (BL105A_0547, BL105A_1798, and BL105A_1894) did not ( Figure 4 ). Although this inconsistency might be attributed to that different mice were used between these two assays, there are some other possible reasons. The first...”

Balac_0516 putative binding protein-dependent transporter from Bifidobacterium animalis subsp. lactis Bl-04
24% identity, 86% coverage

• Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04
  Andersen, BMC genomics 2013
  • “...XOS D 9.0 16.0 Balac_0515 ABC transporter, permease component xyloside A,C XOS D 16.8 16.5 Balac_0516 ABC transporter, permease component xyloside A,C XOS D 18.3 17.5 Balac_0517 -xylosidase, GH43 xyloside A,C XOS D 17.9 16.1 Balac_0518 Putative carbohydrate esterase xyloside A,C XOS D 14.2 11.3 Balac_0519...”

Blon_2456 binding-protein-dependent transport systems inner membrane component from Bifidobacterium longum subsp. infantis ATCC 15697
27% identity, 89% coverage

• Proteomic analysis of Bifidobacterium longum subsp. infantis reveals the metabolic insight on consumption of prebiotics and host glycans
  Kim, PloS one 2013
  • “...a similar or lower NSAF in the insoluble fraction. Finally, the expression of Family 13 (Blon_2456) and Family 36 (Blon_2460) GHs were found in GOS proteome however their amounts were relatively low compare to other GHs. 10.1371/journal.pone.0057535.g005 Figure 5 The expression of glycosyl hydrolases and glycosyltransferases...”

ABC1215 sugar ABC transporter permease from Bacillus clausii KSM-K16
25% identity, 86% coverage

• Widespread occurrence and genomic context of unusually small polyketide synthase genes in microbial consortia associated with marine sponges
  Fieseler, Applied and environmental microbiology 2007
  • “...halodurans BH1866 (BAB05585), B. halodurans ABC1215 (BAD63753), Bacillus clausii SAV6951 (BAC74662), Streptomyces avermitilis BC5091 (AAP11960), Bacillus...”

BL1523 sugar permease of ABC transporter system from Bifidobacterium longum NCC2705
27% identity, 89% coverage

• Differential transcriptional response of Bifidobacterium longum to human milk, formula milk, and galactooligosaccharide
  González, Applied and environmental microbiology 2008
  • “...BL0949-BL0950 BL0260-BL0261 BL0950-BL0951 BL0259 BL0951-BL0953 BL1638 BL1523 DVU1515 BL0157 BL1639 BL1674 BL0978 b BL0699 BL0454-BL0455 BL1211 BL1411...”
  • “...kind gift of purified GOS. REFERENCES mease transport system (BL1523) was also specifically induced by GOS; the latter was previously shown to be induced by...”

TM0598 sugar ABC transporter, permease protein from Thermotoga maritima MSB8
25% identity, 80% coverage

• An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
  Conners, Journal of bacteriology 2005
  • “...ugpBAEe TM0418-TM0421 TM0430-TM0432 TM0595, TM0596, TM0598 TM0810-TM0812 TM1202-TM1204 TM1232-TM1235 TM1276 TM1836, TM1839 TM1853-TM1855 Unknown This study...”

BAD_RS02265 carbohydrate ABC transporter permease from Bifidobacterium adolescentis ATCC 15703
25% identity, 84% coverage

• Combining of transcriptome and metabolome analyses for understanding the utilization and metabolic pathways of Xylo-oligosaccharide in Bifidobacterium adolescentis ATCC 15703
  Yang, Food science & nutrition 2019
  • “...protein 2,060.19 319.83 BAD_RS00390 2.33 BR1785 Branchedchain amino acid ABC transporter substratebinding protein 30.52 6.05 BAD_RS02265 2.38 yurM Thiamine ABC transporter ATPbinding protein 2,679.25 514.59 BAD_RS02260 2.34 malF Sugar ABC transporter permease 2,356.22 466 BAD_RS00385 2.28 livF ABCtype branchedchain amino acid transport systems ATPase component 25.2...”
  • “...(encoded by BAD_RS00815, BAD_RS08280, BAD_RS00810, BAD_RS08205, BAD_RS03705, BAD_RS02260, BAD_RS07410) and transporter ATPbinding protein (encoded by BAD_RS02265, BAD_RS00495, BAD_RS04090, BAD_RS08375) were upregulated (Table 3 ), the same situation occurs in metabolites, including Lthreonine (meta_58), cellobiose (meta_991), Dmannose (meta_166), Lisoleucine (meta_82), maltotriose (meta_1695), Dbiotin (meta_651), and glycerol (meta_15)...”

Atu3023 ABC transporter, membrane spanning protein (sugar) from Agrobacterium tumefaciens str. C58 (Cereon)
25% identity, 69% coverage

• A biosystem for alginate metabolism in Agrobacterium tumefaciens strain C58: molecular identification of Atu3025 as an exotype family PL-15 alginate lyase
  Ochiai, Research in microbiology 2006 (PubMed)
  • “...C58 (strain C58). These ORFs are Atu3021, Atu3022, Atu3023, and Atu3024, encoding a putative sugar ABC transporter system and Atu3025, which encodes a putative...”

MalG / b4032 maltose ABC transporter membrane subunit MalG (EC 7.5.2.1) from Escherichia coli K-12 substr. MG1655 (see 9 papers)
MalG / P68183 maltose ABC transporter membrane subunit MalG (EC 7.5.2.1) from Escherichia coli (strain K12) (see 6 papers)
MALG_ECOLI / P68183 Maltose/maltodextrin transport system permease protein MalG from Escherichia coli (strain K12) (see 5 papers)
P68183 ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) from Escherichia coli (see paper)
TC 3.A.1.1.1 / P68183 Maltose transport system permease protein MalG aka B4032, component of Maltooligosaccharide porter. The 3-D structure has been reported by Oldham et al. (2007). An altering access mechanism has been suggested for the maltose transporter resulting from rigid-body rotations (Khare et al., 2009). Bordignon et al. (2010) and Schneider et al. (2012) have reviewed the extensive knowledge available on MalEFGK2, its mode of action and its regulatory interactions from Escherichia coli (see 13 papers)
malG / RF|NP_418456 maltose transport system permease protein malG from Escherichia coli K12 (see 15 papers)
B21_RS20540 maltose ABC transporter permease MalG from Escherichia coli BL21(DE3)
NP_418456 maltose ABC transporter membrane subunit MalG from Escherichia coli str. K-12 substr. MG1655
b4032 maltose transporter subunit from Escherichia coli str. K-12 substr. MG1655
EcolC_3997 binding-protein-dependent transport systems inner membrane component from Escherichia coli C str. ATCC 8739
Z5630 part of maltose permease, inner membrane from Escherichia coli O157:H7 EDL933
32% identity, 69% coverage

• function: Part of the ABC transporter complex MalEFGK involved in maltose/maltodextrin import. Probably responsible for the translocation of the substrate across the membrane.
  subunit: The complex is composed of two ATP-binding proteins (MalK), two transmembrane proteins (MalG and MalF) and a solute-binding protein (MalE). Protein stability and stable complex formation require YidC.
• substrates: Maltooligosaccharides, Maltose
  tcdb comment: The transporter sequesters the MalT transcriptional activator at the cytoplasmic surface of the membrane in the absence of the transport substrate (Richet et al. 2012). The crystal structures of the transporter complex MBP-MalFGK2 bound with large malto-oligosaccharide in two different conformational states have also been determined. In the pretranslocation structure,Oldham et al. 2013 found that the transmembrane subunit MalG forms two hydrogen bonds with malto-oligosaccharide at the reducing end. In the outward-facing conformation, the transmrembrane subunit MalF binds three glucosyl units from the nonreducing end. These structural features explain why large modified malto-oligosaccharides are not transported by MalFGK2 despite their high binding affinity to MBP. In the transport cycle, substrate is channeled from MBP into the transmembrane pathway with a polarity such that both MBP and MalFGK2 contribute to the overall substrate selectivity of the system (Oldham et al. 2013). Stabilization of the semi-open MalK2 conformation by maltose-bound MBP is key to the coupling of maltose transport to ATP hydrolysis in vivo, because it facilitates the progression of the MalK dimer from the open to the semi-open conformation, from which it can proceed to hydrolyze ATP (Alvarez et al. 2015). Both the binding of MalE to the periplasmic side of the transmembrane complex and binding of ATP to MalK2 are necessary to facilitate the conformational change from the inward-facing state to the occluded state, in which MalK2 is completely dimerized (Hsu et al. 2017). An integrated transport mechanism of the maltose ABC importer has been proposed (Mächtel et al. 2019)
• Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress
  Chen, mSystems 2021
  • “...and B21_RS22395), sulfur metabolism (B21_RS17320, B21_RS13610, B21_RS13605, B21_RS13600, and B21_RS07750), stress response (B21_RS19915), sugar import (B21_RS20540, B21_RS20565, and B21_RS21625), cell wall remodeling (B21_RS05900), and energy production and conversion (B21_RS21615) ( Fig.2A ). In S. cerevisiae AH109, 11 selected DEGs (YLR303W, YIR017C, YKL001C, YLL061W, YDR502C, YLR180W, YPL274W,...”
• Conformational Dynamics in the Binding-Protein-Independent Mutant of the Escherichia coli Maltose Transporter, MalG511, and Its Interaction with Maltose Binding Protein.
  Bajaj, Biochemistry 2018
  • GeneRIF: the equilibrium of this mutant is shifted toward the semi-open state in its resting state and interacts with MBP with high affinity, providing an explanation for the inhibition of MalG511 by MBP at higher concentrations. In contrast, the mutant binding protein, MBPG13D, interacts with lower affinity and could restore MalG511 to a normal catalytic cycle
• Formation of a Chloride-conducting State in the Maltose ATP-binding Cassette (ABC) Transporter.
  Carlson, The Journal of biological chemistry 2016
  • GeneRIF: Data indicate that MalFGK2 transporter is comprised of two membrane proteins, MalF and MalG, and the nucleotide-binding domain, which controls the conformation of MalFG, is composed of the homodimeric MalK subunit.
• Allosteric transitions of the maltose transporter studied by an elastic network model.
  Li, Biopolymers 2014 (PubMed)
  • GeneRIF: Data suggest that the binding and conformational change of maltose transporter (MalFGK2) may provide some insights into the understanding of the mechanism of ABC transporters.
• Crystal structure of the maltose transporter in a pretranslocation intermediate state.
  Oldham, Science (New York, N.Y.) 2011 (PubMed)
  • GeneRIF: using x-ray crystallography, study captured the maltose transporter in an intermediate step between the inward- and outward-facing states
• Studies of the maltose transport system reveal a mechanism for coupling ATP hydrolysis to substrate translocation without direct recognition of substrate.
  Gould, The Journal of biological chemistry 2010
  • GeneRIF: analysis of the MalFGK2 mechanism for coupling ATP hydrolysis to substrate translocation without direct recognition of substrate
• ATP-driven MalK dimer closure and reopening and conformational changes of the "EAA" motifs are crucial for function of the maltose ATP-binding cassette transporter (MalFGK2).
  Daus, The Journal of biological chemistry 2007 (PubMed)
  • GeneRIF: ATP-driven MalK dimer closure and reopening are crucial steps in the translocation cycle of the intact maltose transporter MalFGK2
• Maltose binding protein (MalE) interacts with periplasmic loops P2 and P1 respectively of the MalFG subunits of the maltose ATP binding cassette transporter (MalFGK(2)) from Escherichia coli/Salmonella during the transport cycle.
  Daus, Molecular microbiology 2007 (PubMed)
  • GeneRIF: substrate availability is communicated from MalE to the MalK dimer via extracytoplasmic loops of MalFG
• Crystal structure of a catalytic intermediate of the maltose transporter.
  Oldham, Nature 2007 (PubMed)
  • GeneRIF: 2.8-A crystal structure of the intact maltose transporter in complex with the maltose-binding protein, maltose and ATP
• Biodistribution of ⁸⁹Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
  Li, Poultry science 2023
  • “...inner membrane 477 P64606 MLAE Secondary metabolites biosynthesis, transport and catabolism Cell inner membrane 478 P68183 MALG Carbohydrate transport and metabolism Cell inner membrane 479 P69425 TATB Intracellular trafficking, secretion, and vesicular transport Cell inner membrane 480 P75830 MACA Cell wall/membrane/envelope biogenesis Cell inner membrane 481...”
• The MsmX ATPase plays a crucial role in pectin mobilization by Bacillus subtilis
  Ferreira, PloS one 2017
  • “...(P94530), MdxF (O06990), MdxG (O06991), GanP (O32261), GanQ (O07011), OpuAB (P46921), MalF (P02916), and MalG (P68183). 10.1371/journal.pone.0189483.t008 Table 8 Effect of mutations in AraP and AraQ in the uptake of -1,5-arabinotriose. Doubling time (min) of different strains in liquid minimal medium (CSK) using glucose or arabinotriose...”
• Evolutionary relationships of ATP-Binding Cassette (ABC) uptake porters.
  Zheng, BMC microbiology 2013
  • “..., 22 , 23 ]. The bacterial maltose transport system proteins, MalF (P02916) and MalG (P68183) are two distinct membrane proteins that together comprise the channel of an ABC superfamily member. High resolution structural information is available for this system (TC# 3.A.1.1.1). Consequently, it is known...”
  • “...Protocol 1 on MalG in preparation for running ANCIENT REP [ 16 ]. We took P68183 from http://www.tcdb.org/search/result.php?tc=3.A.1.1.1 , not counting TMSs, using test as the output path, and 0.8 as the CD-HIT threshold. We then used ancient -i results.faa -r 3 -o test2 method=3 threads=4....”
• Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth
  Franchini, PloS one 2015
  • “...9.6 yjbB i b4020 putative alpha helix protein -3.6 malG f , g , i b4032 part of maltose permease, inner membrane 5.9 malF f , g , i b4033 part of maltose permease, periplasmic 6.9 malE c , f , g , i b4034 periplasmic...”
• Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
  Kim, Environmental microbiology 2010
  • “...1.8 1.5 2.1 Serine/threonine:H + symport permease malP b3417 1.7 1.1 2.6 Maltodextrin phosphorylase malG b4032 1.6 1.5 2.0 Maltose transport complex, inner membrane-spanning subunit malF b4033 1.3 1.0 2.0 Maltose transport complex, inner membrane-spanning subunit malE b4034 1.5 1.1 3.5 Maltose-binding protein, periplasmic, substrate recognition...”
• Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
  Stepanova, Journal of bacteriology 2007
  • “...Isocitrate lyase (glyoxylate cycle) malG malF malE malK lamB malM b4032 b4033 b4034 b4035 b4036 b4037 2.1 3.2 1.9 4.2 3.1 4.5 2.8 3.7 5.8 7.5 7.1 6.5 Part...”
• Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system
  Nishino, Journal of bacteriology 2005
  • “...aroF b2601 flgL malG fliD glpF fliT phnJ ycaC cheA b1083 b4032 b1924 b3927 b1926 b4098 b0897 b1888 icdA phoR flxA fliS motB b1141 motA agaZ cheW cheZ ybiC tsx...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...b2579 b2557 b2709 b2578 b4013 b0687 b4194 b0557 b1322 b4192 b1129 b4032 b1628 b1285 b1445 b1045 b4201 b0601 b3301 b4202 b2607 b2553 b0022 85 16 16 14 13 13 12...”
• Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression
  Soupene, Journal of bacteriology 2003
  • “...b4037 malK lamB malM 4.1 4.6 1.4 0.8 0.6 1.0 b4034 b4033 b4032 malE malF malG 5.2 1.6 1.5 0.7 0.7 1.0 b3417 b3416 malP malQ 3.9 2.9 0.3 0.6 b0679 nagE 0.9 3.3...”
• DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
  Polen, Applied and environmental microbiology 2003
  • “...1.59 1.57* 1.50* 3.31* 2.67* 2.39 1.35* 1.46* 1.45 b4032 b4033 b4034 malG malF malE 1 1 1 Part of maltose permease, inner membrane Part of maltose...”
• A novel point mutation in RpoB improves osmotolerance and succinic acid production in Escherichia coli
  Xiao, BMC biotechnology 2017
  • “...maintained stable under osmotic stress. For example, transcript levels of malE (EcolC_3995), malF (EcolC_3996), malG (EcolC_3997) malK (EcolC_3994), and lamB (EcolC_3993), which encode individual subunits of the maltose ABC (ATP-binding cassette) transporter, decreased 10- to 14- fold in Suc-T110 compared to the corresponding levels in RpoBD645Y...”
• Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
  Segura, BMC genomics 2018
  • “...3.70E-03 NDE Z5631 malF Maltose/maltodextrin transport system (permease protein) NDE 2.71 9.82E-06 NDE NDE NDE Z5630 malG Maltose/maltodextrin transport system (permease protein) NDE 2.79 3.81E-05 NDE NDE NDE Z5633 malK Multiple sugar transport system (ATP-binding protein) NDE 3.99 7.37E-08 NDE 2.36 3.38E-03 NDE Z2860 manX PTS...”

NP_463092 maltose transport protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
31% identity, 83% coverage

• Mapping putative contact sites between subunits in a bacterial ATP-binding cassette (ABC) transporter by synthetic peptide libraries.
  Blüschke, Journal of molecular biology 2007 (PubMed)
  • GeneRIF: Results identify specific molecular contacts made between MalK and MalFG that extend beyond the well-characterized EAA motif.
• Topography of the surface of the signal-transducing protein EIIA(Glc) that interacts with the MalK subunits of the maltose ATP-binding cassette transporter (MalFGK2) of Salmonella typhimurium.
  Blüschke, The Journal of biological chemistry 2006 (PubMed)
  • GeneRIF: the surface of the signal-transducing protein EIIA(Glc) interacts with the MalK subunits of the maltose ATP-binding cassette transporter (MalFGK2) of Salmonella typhimurium

Atu0593 ABC transporter, membrane spanning protein from Agrobacterium tumefaciens str. C58 (Cereon)
27% identity, 60% coverage

• Comparative Transcriptome Analysis of Agrobacterium tumefaciens Reveals the Molecular Basis for the Recalcitrant Genetic Transformation of Camellia sinensis L
  Jin, Biomolecules 2022
  • “...), mannopine ( attC = atu5129 ), alpha-glucoside ( aglF = atu0592 , aglG = atu0593 , aglK = atu0595 ), and dipeptide ( dppA = atu4113 ) were all down-regulated during the whole process of co-cultivation in the tea groups ( Figure 3 B). Meanwhile,...”

ML1769 sugar transport integral membrane protein from Mycobacterium leprae TN
27% identity, 92% coverage

• Mycobacterium leprae Transcriptome During In Vivo Growth and Ex Vivo Stationary Phases
  Ojo, Frontiers in cellular and infection microbiology 2021
  • “...sugA (ML1087), sugB (ML1088) and sugC (ML1089) were down regulated in ML96 along with uspE (ML1769), uspC (ML1770) and mmpL10 (ML1231). ML0283, a possible cation-efflux transporter was significantly upregulated at 96 hr in axenic medium along with multiple ATP-binding cassette (ABC) transporters like rfbE (ML0114c), ML0595,...”

TM1233 sugar ABC transporter, permease protein, putative from Thermotoga maritima MSB8
27% identity, 87% coverage

• In silico method for modelling metabolism and gene product expression at genome scale
  Lerman, Nature communications 2012
  • “...annotated as a LacI family transcription regulator. However, the promoter region of the TU for TM1233, which is directly upstream of TM1222, contains the CelR motif. TM1233 encodes for the cellobiose-binding protein that facilitates cellobiose transport. In the TU architecture of our model, there was a...”

WP_008726773 carbohydrate ABC transporter permease from Brachyspira hampsonii
25% identity, 100% coverage

• Confirmation that "Brachyspira hampsonii" clade I (Canadian strain 30599) causes mucohemorrhagic diarrhea and colitis in experimentally infected pigs
  Costa, BMC veterinary research 2014
  • “...reading frame in the B. hampsonii strain 30599 genome encoding a hypothetical protein (Genbank accession WP_008726773). The target region lies within an approximately 15.8kb region of the genome identified as being unique to strain 30599 in a comparison of the whole genome sequences of clade I...”

DR0563 maltose ABC transporter, permease protein from Deinococcus radiodurans R1
30% identity, 44% coverage

• A Novel Glycoside Hydrolase DogH Utilizing Soluble Starch to Maltose Improve Osmotic Tolerance in Deinococcus radiodurans
  Gui, International journal of molecular sciences 2023
  • “...into the intracellular domain by the maltose transport system osmotic enzyme MalF/MalG ( dr0562 / dr0563 ), thus mediating the TreS pathway. 3.3. Mechanisms of Osmoregulation in D. radiodurans Osmotic stress, caused by abiotic stresses such as desiccation, salt stress, high temperatures and freezing, is one...”

BBMN68_1424 carbohydrate ABC transporter permease from Bifidobacterium longum subsp. longum BBMN68
26% identity, 89% coverage

• Mechanism analysis of acid tolerance response of bifidobacterium longum subsp. longum BBMN 68 by gene expression profile using RNA-sequencing
  Jin, PloS one 2012
  • “...protein BBMN68_1423 340.04 96.16 3.54 * G COG1175 K10118, multiple sugar transport system permease protein BBMN68_1424 284.17 79.61 3.57 * G COG0395 K10119, multiple sugar transport system permease protein BBMN68_1726 1387.95 83.55 16.61 * G COG1879 K10546, putative multiple sugar transport system substrate-binding protein BBMN68_1727 322.43...”

PfGW456L13_1896 ABC transporter for D-Galactose and D-Glucose, permease component 2 from Pseudomonas fluorescens GW456-L13
25% identity, 91% coverage

• mutant phenotype: Specific phenotypes on D-Galactose; N L-Lysine. glucose is the C source for the N source experiments with a phenotype (i.e. lysine); may also transport fructose.

SAUSA300_0211 maltose ABC transporter, permease protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
SA0209 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV0216 maltose/maltodextrin transport permease homolog from Staphylococcus aureus subsp. aureus Mu50
SAR0208 putative sugar transport system permease from Staphylococcus aureus subsp. aureus MRSA252
SACOL0195 maltose ABC transporter, permease protein from Staphylococcus aureus subsp. aureus COL
28% identity, 80% coverage

• Human Urine Alters Methicillin-Resistant Staphylococcus aureus Virulence and Transcriptome
  Paudel, Applied and environmental microbiology 2021 (secret)
• Isothermal titration calorimetry analysis of the binding between the maltodextrin binding protein malE of Staphylococcus aureus with maltodextrins of various lengths
  Takemiya, Biochemical and biophysical research communications 2024 (secret)
• Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
  Chung, PloS one 2013
  • “...transduction mechanisms SA1883 kdpE KDP operon transcriptional regulatory protein 2.7 Signal transduction mechanisms Aminoacyl-tRNA biosynthesis SA0209 serS Seryl-tRNA synthetase 2.7 Translation SA0475 lysS Lysyl-tRNA synthetase 3.3 Translation SA1106 proS Propyl-tRNA synthase 2.3 Translation SA1287 asnC Asparaginyl-tRNA synthase 2.3 Translation SA1506 thrS Threonyl-tRNA synthase I 2.6 Translation...”
• Exposure of clinical MRSA heterogeneous strains to β-lactams redirects metabolism to optimize energy production through the TCA cycle
  Keaton, PloS one 2013
  • “...permease ( lctP , SA0106), probable homolog of lactate permease (SA2156), hypothetical maltose/maltodextrin permease homolog (SA0209) and glycerol-3-phosphate transporter ( glpT , SA0325). Amino Acid Transport and Metabolism and Cell Wall Precursors The second group of genes displaying differential expression between SA13011-HeR/HoR strains included up-regulation of...”
• walK and clpP mutations confer reduced vancomycin susceptibility in Staphylococcus aureus
  Shoji, Antimicrobial agents and chemotherapy 2011
  • “...1.86 2.28 2.22 2.16 2.54 2.52 2.24 SA0110 SA0111 SA0209 SA0229 SA0639 SA0640 SA0677 SA0891 SA1213 SA1214 SA1979 SA2234 SA2235 SA2236 SA2237 clpP gene SA0723...”
• Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
  Donat, Journal of bacteriology 2009
  • “...2.3 2.8 ABC transporter or transporter proteins SA0209 SA0599 SA1243 SA1744 SA1745 SA2227 Maltose/maltodextrin transport permease homolog ATP-binding cassette...”
• Characterization of a strain of community-associated methicillin-resistant Staphylococcus aureus widely disseminated in the United States
  Tenover, Journal of clinical microbiology 2006
  • “...Cell wall protein Cell wall protein SA2659 SA0209 SA1869 SA1868 SA1867 SA1866 SA1865 Aureolysin Coagulase Serine protease Serine protease Serine protease...”
• 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
  • “...ET AL. J. BACTERIOL. TABLE 2--Continued Fold changeb SA0432 SA0209 SA0206 SA0640 0.00 0.00 0.00 0.00 2.52 0.20 0.20 2.01 SA0172 SA0186 SA0639 0.00 0.00 0.01...”
• Comparative genomics of Staphylococcus aureus musculoskeletal isolates
  Cassat, Journal of bacteriology 2005
  • “...ORF in strain: ORF description a b SA0024 SA0078 SA0209 SA0317 SA0712 SA0857 SA0860 SA1028 SA1056 SA1057 SA1357 SA1864 SA1865 SA1866 SA1867 SA1868 SA1869 SA1970...”
• More
• Transcriptional Analysis of the Effects of Gambogic Acid and Neogambogic Acid on Methicillin-Resistant Staphylococcus aureus
  Hua, Frontiers in pharmacology 2019
  • “...None PTS system EIIBC component 2.5 2.82 SAV0193 None RpiR family transcriptional regulator 2.25 2.56 SAV0216 None arabinogalactan ABC transporter permease 1.91 2.17 SAV0217 None oxidoreductase 1.86 2.39 SAV0218 None NADH-dependent dehydrogenase 1.86 2.34 SAV0219 None xylose isomerase 1.58 2.16 SAV0222 uhpT antiporter [Staphylococcus sugar phosphate...”
• The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
  Kenny, PloS one 2009
  • “...SAR2117 groES 10 kDa chaperonin 2.78 1.92E-04 Metabolism SAR0189 putative thiamine pyrophosphate enzyme 2.94 1.51E-04 SAR0208 putative sugar transport system permease 2.94 2.68E-02 SAR0209 putative oxidoreductase 4.75 1.21E-02 SAR0210 putative oxidoreductase 9.09 3.75E-03 SAR0527 putative phosphotransferase 4.55 7.03E-08 SAR0752 putative phosphofructokinase 2.44 3.20E-02 SAR0753 fruA fructose-specific...”
• In vitro and in vivo models of Staphylococcus aureus endophthalmitis implicate specific nutrients in ocular infection
  Sadaka, PloS one 2014
  • “...(1.2) 4.2 (1.4) SACOL0194 Maltose ABC transporter permease protein 11.1 (1.5) 3.3 (1.4) 3.7 (1.4) SACOL0195 Maltose ABC transporter permease protein 13.9 (1.5) 3.7 (1.4) 3.4 (1.5) SACOL0196 Oxidoreductase, Gfo/Idh/MocA family 12.6 (1.5) 3.3 (1.3) 3.9 (1.5) SACOL0197 Oxidoreductase, Gfo/Idh/MocA family 10.2 (1.4) 3.2 (1.1) 3.2...”

NWMN_0154 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
28% identity, 73% coverage

• Staphylococcus aureus Preferentially Liberates Inorganic Phosphate from Organophosphates in Environments where This Nutrient Is Limiting
  Kelliher, Journal of bacteriology 2020 (secret)
• Sulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in Staphylococcus aureus
  Peng, mSphere 2017
  • “...aldehyde dehydrogenase, and hypothetical operons beginning with NWMN_0134 (NWMN_0134 to NWMN_0137) and NWMN_0151 (NWMN_0151 to NWMN_0154), the latter of which is associated with changes in carbohydrate metabolism and uptake in other Staphylococcus strains. Although some of these sulfide-inducible genes are also induced in the cstR strain,...”
• Inactivation of the Ecs ABC transporter of Staphylococcus aureus attenuates virulence by altering composition and function of bacterial wall
  Jonsson, PloS one 2010
  • “...drug transporter 2.0 NWMN_0136 PTS system component 2.7 NWMN_0153 maltose ABC transporter permease protein 2.7 NWMN_0154 maltose ABC transporter permease protein 2.5 NWMN_0199 PTS system IIA component 0.5 NWMN_0211 ABC transporter ATP-binding protein 1.9 NWMN_0343 ABC transporter ATP-binding protein 0.5 NWMN_0601 ABC transporter substrate-binding protein 1.8...”

HMPREF0421_20235 carbohydrate ABC transporter permease from Gardnerella vaginalis ATCC 14019
25% identity, 98% coverage

• Transcriptomic and Proteomic Analysis of Gardnerella vaginalis Responding to Acidic pH and Hydrogen Peroxide Stress
  Zhang, Microorganisms 2023
  • “...PTS system transporter subunit IIC HMPREF0421_20297 0.73 0.032017 Shikimate kinase HMPREF0421_20633 0.74 0.000496 Formate acetyltransferase HMPREF0421_20235 0.76 0.009039 Sugar ABC transporter membrane protein HMPREF0421_20979 0.76 0.001612 TM2 domain-containing protein HMPREF0421_20098 0.78 0.001898 Sugar ABC transporter membrane protein HMPREF0421_20232 0.81 0.003311 Maltose-binding protein HMPREF0421_20422 0.81 0.025688 Exopolyphosphatase...”

BWI76_RS01820 maltose ABC transporter, permease component 2 (MalG) from Klebsiella michiganensis M5al
30% identity, 83% coverage

• mutant phenotype: Specifically important for utilizing D-Maltose monohydrate.

EAE_08380 maltose ABC transporter permease MalG from Klebsiella aerogenes KCTC 2190
30% identity, 83% coverage

• Transcriptional effects of melatonin on the gut commensal bacterium Klebsiella aerogenes
  Graniczkowska, Genomics 2022
  • “...change EAE_08405 MalM maltose regulon periplasmic protein exponential 3.324 EAE_08400 LamB maltoporin lamB exponential 2.870 EAE_08380 MalG maltose permease exponential 2.491 EAE 22035 PflB pyruvate formate lyase 1 exponential 2.663 EAE_08405 MalM maltose regulon periplasmic protein stationary 1.986 EAE_00580 BglA 6-phospho-beta-glucosidase stationary 1.348 EAE_17965 BglC Aryl-phospho-beta-D-glucosidase...”

PSPTO_1294 glucose ABC transporter, permease protein, putative from Pseudomonas syringae pv. tomato str. DC3000
25% identity, 97% coverage

• Data-Independent Acquisition Proteomics Unravels the Effects of Iron Ions on Coronatine Synthesis in Pseudomonas syringae pv. tomato DC3000
  He, Frontiers in microbiology 2020
  • “...responsible for amino acid uptake (PSPTO_4887, PSPTO_4173, PSPTO_4919, PSPTO_1258, PSPTO_1256, and PSPTO_1255), glucose ABC transporter (PSPTO_1294, PSPTO_1293, and gltK), ribose ABC transporters (rbsA-1), iron ABC transporters (PSPTO_5562 and PSPTO_5561), peptide transporters (PSPTO_4562, PSPTO_4559, dppC, PSPTO_4558, and PSPTO_4564), a mannitol ABC transporter (PSPTO_2705), dipeptide ABC transporters (PSPTO_4562,...”

B9H01_RS10265 sugar ABC transporter permease from Streptococcus suis
24% identity, 99% coverage

• Orphan response regulator CovR plays positive regulative functions in the survivability and pathogenicity of Streptococcus suis serotype 2 isolated from a pig
  Zhang, BMC veterinary research 2023
  • “...B9H01_RS09195 B9H01_RS09195 K17320 lplC 0.694722357 B9H01_RS09190 B9H01_RS09190 K17318 lplA 0.747241755 B9H01_RS10010 B9H01_RS10010 K11710 troB 0.799013897 B9H01_RS10265 B9H01_RS10265 K15772 ganQ 0.843427031 B9H01_RS10260 B9H01_RS10260 K15771 ganP 0.8343401 B9H01_RS10025 B9H01_RS10025 K11707 troA 0.76620194 B9H01_RS10000 B9H01_RS10000 K11709 troD 0.863698938 B9H01_RS10255 B9H01_RS10255 K15770 cycB 0.830055652 B9H01_RS10005 B9H01_RS10005 K11708 troC 0.802254795 Amino...”

RVY76_RS12735 carbohydrate ABC transporter permease from Palleronia sp. LCG004
27% identity, 92% coverage

• The metabolic characteristics and environmental adaptations of the intertidal bacterium Palleronia sp. LCG004
  Wang, Frontiers in microbiology 2024
  • “...the genome of strain LCG004, the genes encoding the pectin ABC transporter subunits (RVY76_RS12725 to RVY76_RS12735) are organized within an operon, along with two Gfo/Idh/MocA family oxidoreductases (RVY76_RS12740 and RVY76_RS12745). These oxidoreductases have the potential to be involved in the oxidation of certain carbohydrate compounds to...”

BUE60_02790 carbohydrate ABC transporter permease from Pseudomonas syringae pv. actinidiae
25% identity, 97% coverage

• Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions
  Hirose, PeerJ 2020
  • “...0.092485 0.629163 BUE60_06270 efflux transporter periplasmic adaptor subunit 1.16271 0.59189 6.46943 7.196219 0.00117 0.092932 0.674268 BUE60_02790 sugar ABC transporter permease 1.60463 1.04277 1.66657 10.4278 0.001167 0.092932 0.729736 BUE60_11475 Cd(II)/Pb(II)-responsive transcriptional regulator 1.789462 1.420796 4.80667 7.242217 0.001252 0.098092 0.730896 BUE60_08690 flagellar biosynthetic protein FliO 1.326382 5.15132 5.15132...”

BSU06990 rhamnogalacturonan permease from Bacillus subtilis subsp. subtilis str. 168
25% identity, 91% coverage

• Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization
  Ochiai, Applied and environmental microbiology 2007
  • “...(fold)a Pb Functional class BSU06970 BSU06980c BSU06990 BSU07000c BSU07010 BSU07020c BSU07030c BSU07040c BSU07050 BSU07060 BSU07070 BSU07080 BSU30100 BSU30110...”

TC 3.A.1.1.11 / Q93KB9 TogN, component of Saturated and unsaturated oligogalacturonide transporter, TogMNAB (transports di- to tetrasaccharide pectin degradation products which consist of D-galacuronate, sometimes with 4-deoxy-L-threo-5-hexosulose uronate at the reducing end of the oligosaccharide) (Hugouvieux-Cotte-Pattat et al. 2001). Regulated by pectin utilization regulator KdgR from Erwinia chrysanthemi (see paper)
23% identity, 85% coverage

• substrates: Oligogalacturonides

TC 3.A.1.1.16 / Q8TZQ0 MalG, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) from Pyrococcus furiosus
PF1936 putative sugar transport inner membrane protein (malg-like) from Pyrococcus furiosus DSM 3638
28% identity, 51% coverage

• substrates: Maltooligosaccharides
• Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation
  Bräsen, Microbiology and molecular biology reviews : MMBR 2014
  • “...and PF1744]) and maltodextrins (MD system [PF1933 and PF1936 to PF1938]), were found in Pyr. furiosus. The charac- Microbiology and Molecular Biology Reviews...”
• Experimental and computational analysis of the secretome of the hyperthermophilic archaeon Pyrococcus furiosus
  Schmid, Extremophiles : life under extreme conditions 2013
  • “...69 5 8 No Transport PF1933 18894131 Putative sugar transport ATP-hydrolyzing 41 5 13 No PF1936 18894134 Putative sugar transport inner membrane protein (malg-like) 45 4 12 6 Translation and transcription PF1375 18893486 Translation elongation factor eF-1, subunit alpha 48 8 24 No PF1803 18893984 LSU...”
• 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
  • “...permease Putative sulfate transport, permease Mal II operon PF1933 PF1934 PF1935 PF1936 PF1937 PF1938 PF1939 3.9 8.3 8.4 8.1 NC 9.1 NC NC NC NC NC 2.1 NC NC NC...”
• Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus
  Lee, Journal of bacteriology 2006
  • “...PF1741 PF1742 PF1743 PF1744 PF1933 PF1935*d PF1936 PF1937 PF1938 Maltose/trehalose transport (Mal-I) Maltose/trehalose transport (Mal-I) Trehalose synthetase...”
  • “...maltooligosaccharides (29). The second transporter (Mal-II; PF1933, PF1936 to PF1938) is specific for maltooligosaccharides, but it does not transport maltose...”
• Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides
  Schut, Journal of bacteriology 2003
  • “...PF1741 PF1742 PF1784 PF1852 PF1870 [Maltose transport] PF1935 PF1936 PF1937 PF1938 PF1951 PF1975 Mean intensity ratio (log SD)b Descriptiona 3940 SCHUT ET AL....”
• Biochemical evidence for the presence of two alpha-glucoside ABC-transport systems in the hyperthermophilic archaeon Pyrococcus furiosus
  Koning, Archaea (Vancouver, B.C.) 2002
  • “...clusters. Pyrococcus furiosus Escherichia coli MalE PF1938 PF1937 PF1936 PF1933 PF1739 PF1740 PF1741 PF1744 1 2 Identity. Similarity. 1 MalF MalG MalK 2 28...”

BLGT_09095 carbohydrate ABC transporter permease from Bifidobacterium longum subsp. longum GT15
27% identity, 90% coverage

• The Gene Expression Profile Differs in Growth Phases of the Bifidobacterium Longum Culture
  Veselovsky, Microorganisms 2022
  • “...galactose metabolism. Enzymes (BLGT_03060, BLGT_09090, BLGT_03845), Messenger RNA biogenesis and Exosome (BLGT_03845, BLGT_07730), Transporters (BLGT_09100, BLGT_09095). 3.2. KEGG Pathway and Functional Annotation of DEGs The biologically significant DEGs were further analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. As predicted by KEGG, 50...”

Balac_1597 MalG-type ABC sugar transport system permease component from Bifidobacterium animalis subsp. lactis Bl-04
26% identity, 91% coverage

• An ATP Binding Cassette Transporter Mediates the Uptake of α-(1,6)-Linked Dietary Oligosaccharides in Bifidobacterium and Correlates with Competitive Growth on These Substrates
  Ejby, The Journal of biological chemistry 2016
  • “...cytoplasm by the ABC transport system (Balac_1598, Balac_1597, and Balac_1610). The -galactosidase (Balac_1601) and the -(1,6)-glucosidase are responsible for...”
• Genetic and physiological responses of Bifidobacterium animalis subsp. lactis to hydrogen peroxide stress
  Oberg, Journal of bacteriology 2013
  • “...Balac_1501 Balac_1502 Balac_1503 Balat_0464 Balac_1081 Balac_1597 Balac_1598 Balac_1599 Balac_1601 Balac_1567 Balac_1568 Balac_1569 Balac_1570 Balac_1572...”
  • “...different (P 0.05). included those involved in raffinose (Balac_1597 to Balac_1601) and maltose transport and metabolism (Balac_1567 to Balac_ 1573) (see Table...”
• Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04
  Andersen, BMC genomics 2013
  • “...B,D Cellobiose E 3.2 12.1 Balac_1593 oligo-1,6--glucosidase, GH13 Galactoside, Glucoside B,D,E Isomaltose F 4.5 14.0 Balac_1597 ABC transporter, permease component Galactoside, Glucoside B,D,E Raffinose F 14.1 13.9 Balac_1598 ABC transporter, permease component Galactoside, Glucoside B,D,E Isomaltose F 20.1 18.6 Balac_1599 ABC transporter, oligosaccharide-binding protein Galactoside, Glucoside...”

P73854 Lactose transport system permease protein LacG from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)
slr1723 lactose transport system permease protein; LacG from Synechocystis sp. PCC 6803
25% identity, 70% coverage

• Characterization of the binding protein-dependent cellobiose and cellotriose transport system of the cellulose degrader Streptomyces reticuli
  Schlösser, Applied and environmental microbiology 1999 (secret)
• A global transcriptional activator involved in the iron homeostasis in cyanobacteria
  Liu, Science advances 2024
  • “...MntC Others Sugar transport slr1202 , Slr1202, permease protein of sugar ABC transporter Motif-2, -3 slr1723 , Slr1723, permease protein of sugar ABC transporter Motif-1, -2 slr0044 , CmpD, bicarbonate transport system ATP-binding protein Motif-1, -2 slr0043 , CmpC, bicarbonate transport system ATP-binding protein Others slr0531...”
• Design and characterization of molecular tools for a Synthetic Biology approach towards developing cyanobacterial biotechnology
  Huang, Nucleic acids research 2010
  • “...transport lactose, and hence IPTG, into the cells, but there are candidate genes such as slr1723 and slr1202 (permeases) ( 68 ) and sll1374 (putative sugar transporter) ( 69 ). The low induction problem caused by limited diffusion of IPTG has been previously recognized ( 70...”

RSP_2871 ABC alpha-glucoside transporter, inner membrane subunit AglG from Rhodobacter sphaeroides 2.4.1
27% identity, 63% coverage

• A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions
  Billenkamp, Journal of bacteriology 2015
  • “...RSP_2749 21.5 RSP_2872 (aglF) 21.4 20.17 2 RSP_2870, 4 RSP_2871, 3 RSP_2873, 1 RSP_0573 (phoB) 21.2 19.86 5 RSP_0572, 6 RSP_0574, 4 RSP_0575, 3 RSP_0576, 2...”

BL0144 permease of ABC transporter possibly for oligosaccharides from Bifidobacterium longum NCC2705
26% identity, 92% coverage

• The Pleiotropic Effects of Carbohydrate-Mediated Growth Rate Modifications in Bifidobacterium longum NCC 2705
  Duboux, Microorganisms 2023
  • “...utilization, LacI family BL0529 aglA 0.925 0.063 Alpha-glucosidase BL0143 malF 0.713 0.222 Maltose/maltodextrin ABC transporter BL0144 malG 0.699 0.263 Maltose/maltodextrin ABC transporter...”
• Maltose uptake by the novel ABC transport system MusEFGK2I causes increased expression of ptsG in Corynebacterium glutamicum
  Henrich, Journal of bacteriology 2013
  • “...B. longum, the ORF bl0145 is directly following bl0143 and bl0144, which encode TMDs of the maltose ABC importer (77). In S. agalactiae 2603, the ORF sag0038 is...”

TC 3.A.1.1.13 / Q97UY9 GlcU, component of Glucose, mannose, galactose porter from Sulfolobus solfataricus (see paper)
SSO2849 ABC transporter, permease (glucose) from Sulfolobus solfataricus P2
25% identity, 85% coverage

• substrates: Galactose, Mannose, glucose
• Versatile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius
  Wagner, Frontiers in microbiology 2012
  • “...(sso2847) without signal sequence was amplified using the primers 987 and 988. glcT (sso2848), glcU (sso2849), and glcV (sso2850) were amplified in a single PCR with the primers 989 and 2259. The pyrEF marker cassette of S. solfataricus was amplified with the primers 2260 and 2261...”
• Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus
  Tachdjian, Journal of bacteriology 2006
  • “...SSO1281 SSO1282 oppD SSO1283 SSO3066 SSO3067 SSO3069 SSO2848 SSO2849 SSO2850 SSO1000 SSO1170 SSO3053 SSO2035 SSO2135 SSO2137 SSO2228 SSO2704 SSO3012 4.3 4.6 4.0...”

BAD_RS08275 carbohydrate ABC transporter permease from Bifidobacterium adolescentis ATCC 15703
26% identity, 93% coverage

• Combining of transcriptome and metabolome analyses for understanding the utilization and metabolic pathways of Xylo-oligosaccharide in Bifidobacterium adolescentis ATCC 15703
  Yang, Food science & nutrition 2019
  • “...ABC transporter substratebinding protein 34.99 13.91 BAD_RS03325 1.29 MJ1508 ABC transporter ATPbinding protein 209.24 85.46 BAD_RS08275 1.27 amyC ABC transporter permease 1,000.47 413.73 BAD_RS04090 1.14 TM_0352 Macrolide ABC transporter ATPbinding protein 33.93 15.42 BAD_RS00340 1.05 Pip ABC transporter 228.58 109.76 BAD_RS06680 1.27 yxeM Amino acid ABC...”

ACPL_5386 carbohydrate ABC transporter permease from Actinoplanes sp. SE50/110
27% identity, 91% coverage

• Reconstruction and in silico analysis of an Actinoplanes sp. SE50/110 genome-scale metabolic model for acarbose production
  Wang, Frontiers in microbiology 2015
  • “...The genes mal EFG in the pathway were ACPL_6402, ACPL_3200, ACPL_4618, ACPL_5585, ACPL_6401, ACPL_6726, ACPL_3782, ACPL_5386, and ACPL_6400. Figure 6 Chemical structure for acarbose . The essential genes for acarbose production were studied in acarbose synthesis medium. One hundred and thirty three genes were essential for...”

PS417_22135 glucose/xylose ABC transporter, permease component 1 from Pseudomonas simiae WCS417
25% identity, 86% coverage

• mutant phenotype: Specifically important for utilization of D-glucose 6-phosphate and D-xylose. Glucokinase (PS417_22685) is important for glucose-6-phosphate utilization, which implies that it is hydrolyzed to glucose before uptake.

TC 3.A.1.1.50 / Q5SLB5 Sugar ABC transporter, permease protein, component of Probable glycerophosphocholine (GPC) uptake porter (Chandravanshi et al. 2016). The system may include a receptor and three membrane proteins (of 378 aas and 6 TMSs, 299 aas and 7 TMSs, and 113 aas and 3 TMSs (?). The ATPase has not been identified from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
29% identity, 44% coverage

• substrates: glycerophosphocholine

SeseC_01627 sugar ABC transporter permease from Streptococcus equi subsp. zooepidemicus ATCC 35246
23% identity, 96% coverage

• Insight into the specific virulence related genes and toxin-antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp. zooepidemicus strain ATCC35246
  Ma, BMC genomics 2013
  • “...and purple, respectively. Additionally, we found that some genes, including mal A (SeseC_01626), mal D (SeseC_01627), mal E (SeseC_01633, SeseC_01622), mal F (SeseC_01624, SeseC_01630), mal G (SeseC_01625) and mal Q (SeseC_01617) were upregulated when Sz35246 infected mice. These genes are related to maltose transport and metabolism...”

SGO_0102 Maltodextrin transport system permease protein malD from Streptococcus gordonii str. Challis substr. CH1
23% identity, 98% coverage

• Dynamics of the Streptococcus gordonii Transcriptome in Response to Medium, Salivary α-Amylase, and Starch
  Haase, Applied and environmental microbiology 2015
  • “...upregulated in KS1abpA. Four genes (SGO_0099 to SGO_0102) encoding proteins involved in maltodextrin utilization and transport were upregulated 5- to 7-fold,...”
  • “...Gene locus RQa Log2 (ratio) P SGO_0100 SGO_0101 SGO_0102 SGO_0103 SGO_0104 2.6634 2.6666 2.9261 2.8531 2.3722 1.4133 1.415 1.549 1.5126 1.2462 0.0003 0.0011...”
• Effect of starch and amylase on the expression of amylase-binding protein A in Streptococcus gordonii
  Nikitkova, Molecular oral microbiology 2012
  • “...mutans . Potential Mal-like ABC transporters in S. gordonii are represented by annotated genes malD SGO_0102, malC SGO_0103, maltose/maltodextrin-binding protein precursor SGO_0104, and ATP-binding protein SGO_0352. A potential transcriptional regulator for this operon is the upstream positioned transcriptional repressor SGO_0100, which is a LacI/GalR family protein...”

SYNPCC7002_A2036 ABC transporter, ATPase subunit from Synechococcus sp. PCC 7002
23% identity, 97% coverage

• Synechococcus sp. Strain PCC 7002 Transcriptome: Acclimation to Temperature, Salinity, Oxidative Stress, and Mixotrophic Growth Conditions
  Ludwig, Frontiers in microbiology 2012
  • “...increases in transcripts (up to twofold) were also observed for genes encoding an osmolyte ABC-transporter (SYNPCC7002_A2036 to SYNPCC7002_A2039); these Synechococcus 7002 genes have highest similarity to ggtABC from Synechocystis sp. PCC 6803 (Marin et al., 2004 ). Interestingly, transcripts for genes encoding subunits of Na +...”

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How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.