PaperBLAST
PaperBLAST Hits for SwissProt::A0A0H2VAP9 D-serine transporter DsdX; D-serine-specific permease (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) (445 a.a., MHSQIWVVST...)
Show query sequence
>SwissProt::A0A0H2VAP9 D-serine transporter DsdX; D-serine-specific permease (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
MHSQIWVVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIG
GTLGFLAAVIGLGTILGKMMEVSGAAERIGLTLQRCRWLSADVIMVLVGLICGITLFVEV
GVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIV
YGLLVGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVRDEKTLPSLGATLFTVLLPIA
LMLVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTMLTHTEN
GFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSA
TVAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETF
KYYTTATFIASVIALAGTFLLSFII
Running BLASTp...
Found 77 similar proteins in the literature:
DSDX_ECOL6 / A0A0H2VAP9 D-serine transporter DsdX; D-serine-specific permease from Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (see paper)
c2900 DsdX permease from Escherichia coli CFT073
100% identity, 100% coverage
- function: Protein that allows transport of D-serine across the inner membrane, does not transport D-alanine nor probably glycine. Is probably a H(+) symporter, as CCCP inhibits transport. Transports D- serine more efficiently than CycA.
disruption phenotype: Single deletion, grows on D-serine, D-serine plus glycerol and D-alanine. A double dsdX-cycA deletion grows in D-serine plus glycerol, but not D-serine or D-alanine alone, growth on D-serine (but not D-alanine) is restored by dsdX, while growth on both D-alanine and D-serine is restored by cycA. Double dsdX-cycA deletion cannot take up D-serine. - In vivo gene expression analysis identifies genes required for enhanced colonization of the mouse urinary tract by uropathogenic Escherichia coli strain CFT073 dsdA
Haugen, Infection and immunity 2007 - “...2017 by University of California, Berkeley c2486 c2490 c0468 c2900 c2489 c3568 c3592 c2487 c0704 c3566 c2488 c1239 c0459 c3569 c3570 c2541 c1244 c2398 c0728...”
UTI89_C4956 hypothetical protein from Escherichia coli UTI89
99% identity, 100% coverage
- Glycosuria Alters Uropathogenic Escherichia coli Global Gene Expression and Virulence
Islam, mSphere 2022 - “...and UTI89-fUG showed upregulation of genes encoding transporters of amino acids serine ( dsdX , UTI89_C4956; cycA , UTI89_C4817; sstT , UTI89_C3527), arginine ( artJMQJP , UTI89_C0863-67), histidine ( hisQJ , UTI89_C2592/93), and branched-chain amino acids ( livFGMHKJ , UTI89_C3961-65, C3969) and dipeptides ( dppBA ,...”
DsdC / b2365 D-serine transporter from Escherichia coli K-12 substr. MG1655 (see 4 papers)
DSDX_ECOLI / P08555 D-serine transporter DsdX from Escherichia coli (strain K12) (see 2 papers)
TC 2.A.8.1.5 / P08555 The D-serine transporter, DsdX (KM=60µM) (may also transport D-threonine which inhibits D-serine uptake) (Anfora and Welch, 2006). Eliminating the dsdX gene renders the cell more sensitive to chloramphenicol from Escherichia coli (strain K12) (see 9 papers)
b2365 predicted transporter from Escherichia coli str. K-12 substr. MG1655
BW25113_2365 D-serine transporter DsdX from Escherichia coli BW25113
99% identity, 100% coverage
- function: A D-serine-specific transporter, may function as a H(+) symporter.
- substrates: Serine
- Bridging the gap: a GFP-based strategy for overexpression and purification of membrane proteins with intra and extracellular C-termini
Hsieh, Protein science : a publication of the Protein Society 2010 - “...This Study Target Accession # ArsB DsdX GntP P0AB93 P08555 P0AC94 GntU P0AC96 LldP Mtr SdaC TdcC P33231 P0AAD2 P0AAD6 P0AAD8 TyrP ChaA YrbG P0AAD4 P31801 P45394...”
- The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model
Frick-Cheng, mBio 2020 - “...component 2.6 b0605 cspA Cold shock protein CspA 4.3 b3556 dsdX d -Serine transporter 2.7 b2365 fis DNA-binding transcriptional dual regulator Fis 2.4 b3261 ftsB Cell division protein FtsB 2.3 b2748 gntK d -Gluconate kinase, thermostable 2.7 b3437 gpt Xanthine-guanine phsophoribosyltransferase 2.4 b0238 gspH Hypothetical type...”
- Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022)
González, Journal of bacteriology 2006 - “...b2092 dsdX ygdI b3254 yiaG tra5_3 yhjS rbsC b2365 b2809 b3254 b3555 b0372 b3536 b3750 Hypothetical protein Transcriptional regulator of cryptic csgA gene for...”
- Stationary-phase quorum-sensing signals affect autoinducer-2 and gene expression in Escherichia coli
Ren, Applied and environmental microbiology 2004 - “...b0400 b2310 5.6 5 nlpC dsdX gltB ompF guaC phoE bcr b1708 b2365 b3212 b0929 b0104 b0241 b2182 4.5 4.4 3.4 3.3 3.2 3.2 3.1 nupG carA b2964 b0032 3 2.7 gltD carB...”
- Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
Wei, Infection and immunity 2003 - “...b2479 b2090 b3763 b1384 b1892 b1074 b1942 b2365 b1899 b3907 Putative replicase Putative enzyme Putative transaldolase Putative acyl coenzyme A dehydrogenase...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...0.76* b2364 dsdC 1 D-Serine 0.40* 0.60* 1.01 b2365 b2366 dsdX dsdA 2 2 Transport system permease (serine?) D-Serine dehydratase (deaminase) 1.00 0.21* 0.85...”
- DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide
Zheng, Journal of bacteriology 2001 - “...soxS sbp sufC phoH hemH yljA ycgZ b0006 b3708 b3924 b2414 b1683 b2365 b0848 b2012 b2366 b4062 b3917 b1682 b1020 b0475 b0881 b1164 18 18 17 16 16 15 15 14 13 13...”
- “...yeeD ygaQ yaiA yceP glgS ydcH tnaL b3708 b4326 b2414 b4322 b2365 b4217 b2616 b4062 b2366 b3924 b1166 b2012 b2654 b0389 b1060 b3049 b1426 b3707 30 29 25 23 22 20...”
- Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate
Wytock, PLoS genetics 2018 - “...BW25113_3988 Fast_6b 4,178,881 G > A rpoC (E1202K) BW25113_3988 2,471,573 C > T dsdX (S83F) BW25113_2365 Strains evolved from mutant parents z w f s u p 1 * b 4,178,209 C > A rpoC (R978S) BW25113_3988 1,301,660 IS 5 (+) clsA( L414::IS 5) BW25113_1249 zwf...”
STM3801 putative Gnt family transport protein from Salmonella typhimurium LT2
SEEHRA37_02334 D-serine transporter DsdX from Salmonella enterica subsp. enterica serovar Heidelberg str. SARA37
94% identity, 100% coverage
PAU_02599 dsdx permease from Photorhabdus asymbiotica
81% identity, 100% coverage
PMI0186 DsdX permease from Proteus mirabilis HI4320
79% identity, 100% coverage
HWQ47_08850 D-serine transporter DsdX from Shewanella sp. MTB7
75% identity, 100% coverage
PfGW456L13_3649 D-serine permease from Pseudomonas fluorescens GW456-L13
49% identity, 97% coverage
- mutant phenotype: Specific phenotype: utilization of D-Serine
RR42_RS28835 gluconate:H+ symporter (gntT) from Cupriavidus basilensis FW507-4G11
40% identity, 93% coverage
- mutant phenotype: 67% identical to the gluconate permease (gntT, ACIAD0544) of A. baylayi ADP1 (PMCid:PMC4254613).
BCAL3365 putative gluconate permease from Burkholderia cenocepacia J2315
43% identity, 96% coverage
- Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism
Sass, Scientific reports 2017 - “...into categories metabolism and transport of amino acids, carbohydrates and aromatic compounds, e.g. gluconate permease (BCAL3365), galactonate transporter (BCAL0184, BCAM2500), glycerol kinase (BCAL0925), glycerol-phosphate transporter (BCAL3041), 6-phosphogluconolactonase (BCAL3043) and salicylate hydroxylase(BCAM1274). Predicted targets of ncS16 include a higher percentage of outer membrane and cell envelope components,...”
- Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
Fang, BMC systems biology 2011 - “...protein in this pathway; BLAST search against UNIPROT database gave an E value of 3E-46 BCAL3365 Putative gluconate permease D-gluconate: H+ symporter GntP TC-2.A.8.1.3 BIOLOG assays indicated growth on D-Gluconic acid; modelling revealed a lack of transporter; BLAST E values of 4E-68 BCAM0469 Putative aldehyde dehydrogenase...”
AbA118F_1623 gluconate:H+ symporter from Acinetobacter baumannii
42% identity, 96% coverage
ACIAD0544 high-affinity gluconate permease (GntP family) from Acinetobacter sp. ADP1
41% identity, 98% coverage
- Rationally engineered synthetic coculture for improved biomass and product formation
Santala, PloS one 2014 - “...knock-out strain of A. baylyi ADP1 (DSM 24193) (gene deletion high-affinity gluconate permease, gntT , ACIAD0544) was employed in the study (kindly provided by Dr. Veronique de Berardinis, Genoscope, France). In the single gene knock-out mutant, the target gene is replaced with a gene cassette containing...”
- “...the metabolic model of ADP1, the disruption of a high-affinity gluconate permease ( gntT , ACIAD0544) blocks the glucose pathway. Due to the exceptional glucose utilization pathway of ADP1, a glucose molecule is oxidized to gluconate on the outer surface of the inner membrane by an...”
PA14_34630 gluconate permease from Pseudomonas aeruginosa UCBPP-PA14
PA2322 gluconate permease from Pseudomonas aeruginosa PAO1
39% identity, 99% coverage
- Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation
Dahal, Communications biology 2023 - “...wild-type. The simulations provided insights into other mutants such as deletion of gluconate symporter gene (PA14_34630) leading to increased flux through glucose transport reaction (GLCabcpp, from periplasm to cytosol; Fig. 4 a). Fig. 4 Our model can accurately predict gluconate production in the mutants of the...”
- Genome-wide association study of signature genetic alterations among pseudomonas aeruginosa cystic fibrosis isolates
Hwang, PLoS pathogens 2021 - “...family transcriptional regulator, gluconate utilization system Gnt-I transcriptional repressor PA2321 K00851 gluconokinase Pentose phosphate pathway PA2322 K03299 gluconate:H+ symporter, GntP family PA2323 K00131 glyceraldehyde-3-phosphate dehydrogenase (NADP+) Glycolysis / Gluconeogenesis, Pentose phosphate pathway PA2327 K02050 NitT/TauT family transport system permease protein PA2328 K02051 NitT/TauT family transport system...”
- Transcriptome Analysis of Pseudomonas aeruginosa Cultured in Human Burn Wound Exudates
Gonzalez, Frontiers in cellular and infection microbiology 2018 - “...expression of glucose porin oprB (PA3186), both glucose dehydrogenase gcd (PA2290) and gluconate permase gnuT (PA2322) showed induction in BWE compared to LB control conditions (Supplementary Table 3 ). These data suggest that P. aeruginosa stimulates the pathway involved in gluconate production, whereas glucose catabolism, via...”
- Pseudomonas aeruginosa mutants defective in glucose uptake have pleiotropic phenotype and altered virulence in non-mammal infection models
Raneri, Scientific reports 2018 - “...for glucose IM transporters deleted in this work PA2262 kguT 1.3 0.3 0.4 2-ketogluconate transporter PA2322 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...”
- Comparative systems biology analysis to study the mode of action of the isothiocyanate compound Iberin on Pseudomonas aeruginosa
Tan, Antimicrobial agents and chemotherapy 2014 - “...PA2170 PA2177 PA2193 PA2194 PA2195 PA2261 PA2300 PA2305 PA2322 PA2345 PA2363 PA2371 PA2377 PA2384 PA2414 PA2415 PA2416 PA2427 PA2448 PA2566 PA2570 PA2573 PA2587...”
- Gene expression in Pseudomonas aeruginosa swarming motility
Tremblay, BMC genomics 2010 - “...pyrQ dihydroorotase 2.5 Transcriptional regulators PA4878 1 probable transcriptional regulator 3.7 Transport of small 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...”
- Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum
Palmer, Journal of bacteriology 2007 - “...synthase component I Anthranilate synthase component II PA2322 PA2323 PA3181 Flagellar synthesis and chemotaxis Pseudomonas quinolone signaling SCFM versus...”
- Contribution of the PhoP-PhoQ and PmrA-PmrB two-component regulatory systems to Mg2+-induced gene regulation in Pseudomonas aeruginosa
McPhee, Journal of bacteriology 2006 - “...Mg2 regulated PA2260 PA2261 PA2262 PA2265 PA2266 PA2321 PA2322 PA2323 PA4236 PA4463 PA4761 PA4835 PA4836 Positively Mg2 and positively PhoP regulated PA0265...”
- “...(gntK, a homologue of the gene encoding gluconokinase), PA2322 (gntT, a homologue of the gene encoding high-affinity gluconate permease), and PA2323 (encoding a...”
- Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology
Palmer, Journal of bacteriology 2005 - “...PA4470 PA5302 PA5304 Glucose transport and metabolism PA2322 PA2323 PA3181 PA3186 PA3195 Flagellar synthesis and chemotaxis PA1092 PA2867 PA4307 PA4310...”
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YPO3954 putative gluconate permease from Yersinia pestis CO92
37% identity, 97% coverage
PP3417, PP_3417 gluconate transporter from Pseudomonas putida KT2440
39% identity, 96% coverage
- Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system
Pause, Microbial biotechnology 2024 - “..., PP_1015 PP_1018 ), glucokinase ( glk , PP_1011 ), gluconate transporters ( gntT , PP_3417 and PP_0652 ) and gluconokinase ( gnuK , PP_3416 ); streamlined for crossmembrane transportation pathway via 2ketogluconate This study Genetic deletions in P. putida were carried out following previously published...”
- Metabolic bottlenecks of Pseudomonas taiwanensis VLB120 during growth on d-xylose via the Weimberg pathway
Nerke, Metabolic engineering communications 2024 - “...date, no xylonate transporter has been verified for P. taiwanensis VLB120. The gluconate transporter GntP (PP_3417) was hypothesized in earlier studies as a transporter in Pseudomonas putida strains ( Bator et al., 2019 ; Meijnen et al., 2009 ). Recently, the 2-ketogluconate transporter KguT (PP_3377) was...”
- Comparison of Three Xylose Pathways in Pseudomonas putida KT2440 for the Synthesis of Valuable Products
Bator, Frontiers in bioengineering and biotechnology 2019 - “...of xylonate from the periplasm to the cytoplasm. P. putida KT2440 harbors the transporter GntT (PP_3417), enabling the transport of gluconate from the periplasm into the cytoplasm (Porco et al., 1997 ). Such a transporter is characterized for E. coli . A conceivable possibility would be,...”
- A set of activators and repressors control peripheral glucose pathways in Pseudomonas putida to yield a common central intermediate
del, Journal of bacteriology 2008 - “...This study PP1023 PP1516 PP2333 PP2741 PP3415 PP3416 PP3417 PP3418 PP3642 a Gene Function pgl 6-Phosphogluconolactonase RND efflux pump GntR family of...”
- “...expression. Reverse transcription-PCR confirmed that the ORFs encoding PP3417 and PP3418 formed an operon. In agreement with this observation was the fact that...”
- Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis
del, Journal of bacteriology 2007 - “...to a gene involved in the transport of gluconate (PP3417). Divergent with respect to gnuK is a gene encoding a transcriptional repressor that belongs to the...”
- “...oxidation products requires a gluconate-specific transport system (PP3417), as well as a 2-ketogluconate transporter (PP3377). These two transporters were also...”
ZMO1756 gluconate transporter from Zymomonas mobilis subsp. mobilis ZM4
36% identity, 95% coverage
- Investigation of the impact of a broad range of temperatures on the physiological and transcriptional profiles of Zymomonas mobilis ZM4 for high-temperature-tolerant recombinant strain development
Li, Biotechnology for biofuels 2021 - “...ZMO1255 , ZMO1253 , ZMO1572 , and ZMO0806 ), glucose metabolism-related genes ( ZMO1757 , ZMO1756 , ZMO1649 , ZMO0366 , ZMO1981 , and ZMO0689 ), glutamate, histidine, and cysteine synthesis-related genes ( ZMO1117 , ZMO0457 , ZMO1964 , ZMO0783 , ZMO0782 , ZMO0784 ; ZMO0480...”
SA2293 gluconate permease from Staphylococcus aureus subsp. aureus N315
SAUSA300_2442 gluconate permease from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL2514 gluconate transporter, permease protein from Staphylococcus aureus subsp. aureus COL
SA_RS13150 gluconate:H+ symporter from Staphylococcus aureus subsp. aureus N315
36% identity, 98% coverage
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...NifU domain-containing protein sa_c2220s1920_a_at * 4.7 2.5 30 SA1514 glycerol-3-phosphate dehydrogenase sa_c5074s4372_a_at 7.1 2.5 2.5 SA2293 NAD/NADP octopine/nopaline dehydrogenase family protein Transport sa_c6427s5598_a_at 3.8 2.5 15 cudT SA2632 osmoprotectant transporter sa_c10649s11102cv_s_at 5.9 2.5 2.5 opuD1 SA1384 osmoprotectant transporter sa_c3118s2672_a_at * 2.1 2.5 2.5 SA0159 ABC transporter...”
- Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus
Seidl, BMC microbiology 2009 - “...0.4 SA2007 NWNM_2110 alsD alpha-acetolactate decarboxylase 9.1 2.7 SA2008 NWNM_2111 alsS alpha-acetolactate synthase 9.1 3.1 SA2293 NWNM_2401 gntP gluconate permease 0.7 2.5 SA2294 NWNM_2402 gntK gluconate kinase 1.6 3.7 *SA2295 NWNM_2403 gntR gluconate operon transcriptional repressor 1.5 3.2 SA2321 NWMN_2432 hypothetical protein 0.1 2.5 SA2434 NWNM_2540...”
- Global regulation of Staphylococcus aureus genes by Rot
Saïd-Salim, Journal of bacteriology 2003 - “...1815 1816 1994 SA1267 SA1268 SA1091 SA0309 SA2294 SA2293 SA2209 SA2208 SA1881 SA1879 SA1090 SA0549 SA2334 SA2185 SA2435 SA1659 SA2326 SA1589 SA1631 SA1630...”
- Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci
Dunman, Journal of bacteriology 2001 - “...SA2240 SA0253 SA0923 SA1517 SA1961 SA2424 SA0187 SA1140 SA2293 SA0186 SA0021 SA0212 SA0271 SA0363 SA0412 SA1618 SA1937 SA2378 SA2448 SA2430 SA2431 SA2463 SA0746...”
- Impact of the pentose phosphate pathway on metabolism and pathogenesis of Staphylococcus aureus
Kim, PLoS pathogens 2023 (no snippet) - Metabolic reprogramming and altered cell envelope characteristics in a pentose phosphate pathway mutant increases MRSA resistance to β-lactam antibiotics
Zeden, PLoS pathogens 2023 (no snippet) - Response of Staphylococcus aureus to salicylate challenge
Riordan, Journal of bacteriology 2007 - “...in gene expression Microarray SCOTS SACOL2515 SACOL2514 SACOL2300 SACOL2176 SACOL1062 SACOL0856 SACOL1913 SACOL2301 SACOL0589 SACOL2462 SACOL1329 SACOL2229...”
- Development of a Single-nucleotide Polymorphism Genotyping Assay for the Rapid Detection of Vancomycin-intermediate Resistance in Staphylococcus aureus Epidemic Lineage ST5
Kim, Annals of laboratory medicine 2023 - “...Sodium ABC transporter ATP-binding protein 85.7 SA_RS12550 2,458,970 GC G478A Nitrite reductase 85.7 SA_RS13145 / SA_RS13150 2,575,425 CA Intergenic (85/+49) Hypothetical protein/gluconate permease 78.6 SA_RS13485 / SA_RS13490 2,646,865 AT Intergenic (16/+497) O-acetyltransferase OatA/GNAT family acetyltransferase 78.6 SA_RS13735 2,689,707 CT P294L Malate:quinone oxidoreductase 78.6 SA_RS13995 2,748,292 GT...”
SERP2057 gluconate transporter, permease protein from Staphylococcus epidermidis RP62A
SE2044 gluconate permease from Staphylococcus epidermidis ATCC 12228
36% identity, 98% coverage
CH51_RS14180 gluconate:H+ symporter from Staphylococcus aureus
36% identity, 98% coverage
- Staphylococcus aureus PhoU Homologs Regulate Persister Formation and Virulence
Shang, Frontiers in microbiology 2020 - “...USA500 2395. Gene Description Fold change RNA-seq qRT-PCR Carbon metabolism CH51_RS01175 Sorbitol dehydrogenase 2.04 ND CH51_RS14180 Gluconate permease 2.17 ND CH51_RS14185 Gluconokinase 2.52 ND CH51_RS14680 Acyl esterase 2.26 ND CH51_RS14690 Pantoate-beta-alanine ligase 2.14 ND CH51_RS14700 2-Dehydropantoate 2-reductase 2.63 ND CH51_RS11580 Carbohydrate kinase 2.33 ND CH51_RS11585 Sucrose-6-phosphate...”
BPHYT_RS16725 gluconate:H+ symporter (gntT) from Burkholderia phytofirmans PsJN
39% identity, 91% coverage
- mutant phenotype: Specific phenotype on gluconate and 72% identical to the gluconate permease (gntT, ACIAD0544) of A. baylayi ADP1 (PMCid:PMC4254613).
YhgC / b3415 high-affinity gluconate transporter from Escherichia coli K-12 substr. MG1655 (see 5 papers)
gntT / P39835 high-affinity gluconate transporter from Escherichia coli (strain K12) (see 4 papers)
GNTT_ECOLI / P39835 High-affinity gluconate transporter; Gluconate permease; Gnt-I system from Escherichia coli (strain K12) (see paper)
TC 2.A.8.1.4 / P39835 D-Gluconate:H+ symporter, GntT from Escherichia coli (see 9 papers)
A0A140N385 Gluconate transporter from Escherichia coli (strain B / BL21-DE3)
b3415 gluconate transporter, high-affinity GNT I system from Escherichia coli str. K-12 substr. MG1655
37% identity, 97% coverage
- function: Part of the gluconate utilization system Gnt-I; high-affinity intake of gluconate
- substrates: D-gluconate
- Omics analysis coupled with gene editing revealed potential transporters and regulators related to levoglucosan metabolism efficiency of the engineered Escherichia coli
Chang, Biotechnology for biofuels and bioproducts 2022 - “...A0A140NGD0 treC 2.06 3.50 sn-glycerol-3-phosphate import ATP-binding protein UgpC A0A140N2F0 ugpC 1.47 1.22 Gluconate transporter A0A140N385 gntT 1.44 1.03 Metabolite/H + symporter, major facilitator superfamily (MFS) A0A140N8T9 kgtP 2.47 2.74 Glyoxylate carboligase A0A140NEP9 gcl 3.83 3.61 Levoglucosan kinase lgk 2.87 3.39 Lipid transport and metabolismrelated proteins...”
- “...4.6, and 2.3-fold at the mid-log phase, respectively. The MFS proteins like KgtP (A0A140N8T9), GntT (A0A140N385), and ActP (A0A140SS45) were also upregulated at both phases. During levoglucosan consumption at the early- and mid-log phases, the proton-driven -ketoglutarate transporter KgtP consisting of many transmembrane spanning segments and...”
- Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli
Bausch, Journal of bacteriology 1998 - “...f E. coli gluconate transporter encoded by gntT (P39835). g E. coli gluconate regulator encoded by gntR (P46860). b Spectronic 601 spectrometer (Milton Roy...”
- Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism
Porco, Journal of bacteriology 1997 - “...deduced amino acid sequence of GntT (Swiss-Prot accession number, P39835) is 50% identical to GntP of Bacillus subtilis (30), 40% identical to GntP of E. coli...”
- Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains
Lennen, Applied and environmental microbiology 2014 - “...Strain Gene Description Fold change b0463 b0121 b2095 b4240 b3415 b2664 b2943 ECD_01942 b2028 b4114 b2845 b2663 acrA speE gatZ treB gntT csiR galP vioA ugd eptA...”
- Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding
Myers, PLoS genetics 2013 - “...Isomerase A + + [58] , [149] , (Park and Kiley, Personal Communication) 3544500 gntT b3415 Gluconate Transporter + + [19] , [150] , (Park and Kiley, Personal Communication) 4366425 aspA b4139 Aspartate Ammonia-Lyase + + [19] , [136] , (Park and Kiley, Personal Communication) a...”
Z4770 high-affinity transport of gluconate / gluconate permease from Escherichia coli O157:H7 EDL933
37% identity, 97% coverage
TC 2.A.8.1.1 / P12012 D-Gluconate:H+ symporter of 448 aas and 11 TMSs from Bacillus subtilis (see 3 papers)
37% identity, 97% coverage
- substrates: Gluconate
tcdb comment: It is encoded in an operon with gluconate kinase (Fujita et al. 1986) - Characterization of Shigella flexneri in northern Vietnam in 2012-2016.
Nguyen, Access microbiology 2023 - “...Table 1. List of isolates used in this study Isolate Year Province Serotype Incident Accession P12012 2012 Lao Cai 2a A BSBP01000000 P12048 2012 Son La 1a B BSBQ01000000 P12049 2012 Son La 1a B BSBR01000000 P14013 2014 Dien Bien 1a C BSBS01000000 P14014 2014 Dien...”
- “...the GyrAS83L mutation and bla TEM-1B . In Sub-2, only one isolate in this study, P12012, had the GyrAS83L mutation. No other types of gyrA mutation were found in this study. A recent study identified two sub-lineages in PG3, Lin-3.1 and Lin-3.2 [ 8 ]. The...”
- Autoinducer 2 affects biofilm formation by Bacillus cereus
Auger, Applied and environmental microbiology 2006 - “...wildtype strain TT01 and to the luxS mutant P12012 was used to define the reference levels of luminescence. Cell-free supernatants (CFS) were collected from...”
BWI76_RS26615 gluconate:H+ symporter from Klebsiella michiganensis M5al
37% identity, 97% coverage
- mutant phenotype: Specific phenotype: utilization of D-Gluconic Acid
STM3512 GntP family, high-affinity gluconate permease in GNT I system from Salmonella typhimurium LT2
37% identity, 97% coverage
SXYL_00159 gluconate:H+ symporter from Staphylococcus xylosus
38% identity, 98% coverage
- Insight into the Genome of Staphylococcus xylosus, a Ubiquitous Species Well Adapted to Meat Products
Leroy, Microorganisms 2017 - “...Glycerol, transport, catabolism, regulation SXYL_02455-57 Trehalose, regulation, catabolism, EIIBC SXYL_00438-40 gntRKP Gluconate, transport, catabolism, regulation SXYL_00159, SXYL_02351 Gluconate, transport SXYL_01518-22 rbsBCADR Ribose, transport, catabolism, regulation SXYL_00132-35 xylEBAR Xylulose, transport, catabolism, regulation In red, genes overexpressed in a meat model. microorganisms-05-00052-t002_Table 2 Table 2 Peptide transport, peptidases...”
CA_C3605 gluconate:H+ symporter from Clostridium acetobutylicum ATCC 824
35% identity, 98% coverage
SAR2582 putative gluconate permease from Staphylococcus aureus subsp. aureus MRSA252
36% identity, 98% coverage
GOX2188 Gluconate permease from Gluconobacter oxydans 621H
37% identity, 95% coverage
GBAA3429 gluconate permease from Bacillus anthracis str. 'Ames Ancestor'
37% identity, 98% coverage
BAS0165 gluconate permease from Bacillus anthracis str. Sterne
BA0163 gluconate permease from Bacillus anthracis str. Ames
AW20_2625 gluconate permease GntP from Bacillus anthracis str. Sterne
36% identity, 94% coverage
- Beyond the spore, the exosporium sugar anthrose impacts vegetative Bacillus anthracis gene regulation in cis and trans
Norris, Scientific reports 2023 - “...Magnesium and cobalt transport protein CorA 1.33 AW20_3236 BAS4922 Nucleoside transporter, NupC family 1.45 AW20_2625 BAS0165 GntP; Gluconate permease, Bsu4004 homolog 1.45 AW20_2115 BAS0599 TreC; Trehalose-6-phosphate hydrolase 1.46 AW20_453 BAS2203 Oxalate/formate antiporter 1.57 AW20_2626 BAS0164 FGGY family of carbohydrate kinase; gluconokinase 1.60 AW20_2866 BAS5293 LrgA-associated membrane...”
- Carbohydrate metabolism differences between subgroup A1 and B2 strains of Bacillus anthracis as assessed by comparative genomics and functional genetics
Sylvestre, Applied and environmental microbiology 2009 - “...organization. The gntR (BA0161), gntK (BA0162), gntP (BA0163), and yqjI (BA0164) genes encode a potential gluconate operon transcriptional regulator, a...”
- Beyond the spore, the exosporium sugar anthrose impacts vegetative Bacillus anthracis gene regulation in cis and trans
Norris, Scientific reports 2023 - “...BAS2949 Magnesium and cobalt transport protein CorA 1.33 AW20_3236 BAS4922 Nucleoside transporter, NupC family 1.45 AW20_2625 BAS0165 GntP; Gluconate permease, Bsu4004 homolog 1.45 AW20_2115 BAS0599 TreC; Trehalose-6-phosphate hydrolase 1.46 AW20_453 BAS2203 Oxalate/formate antiporter 1.57 AW20_2626 BAS0164 FGGY family of carbohydrate kinase; gluconokinase 1.60 AW20_2866 BAS5293 LrgA-associated...”
RHA1_ro02363 gluconate permease family protein from Rhodococcus sp. RHA1
37% identity, 94% coverage
PVLB_13665 GntP family permease from Pseudomonas sp. VLB120
39% identity, 96% coverage
STM4482 GntP family, L-idonate transport protein from Salmonella typhimurium LT2
33% identity, 97% coverage
- Pseudomonas stutzeri as an alternative host for membrane proteins
Sommer, Microbial cell factories 2017 - “...enterica STM3541 GntP 16422100 + + S. enterica STM3801 GntP 16422374 + ++ S. enterica STM4482 GntP 16423047 NT P. aeruginosa PA3553 GTT 9949705 + + NT P. furiosus PF0520 MFS 18976892 + S. enterica STM1360 MFS 16764711 ++ NT P. aeruginosa PA1236 MFS 9947166 +...”
YjgT / b4265 L-idonate/5-ketogluconate/gluconate transporter from Escherichia coli K-12 substr. MG1655 (see paper)
idnT / P39344 L-idonate/5-ketogluconate/gluconate transporter from Escherichia coli (strain K12) (see 5 papers)
IDNT_ECOLI / P39344 Gnt-II system L-idonate transporter; L-Ido transporter; L-idonate transporter; 5-keto-D-gluconate transporter; L-idonate/5-ketogluconate/gluconate transporter from Escherichia coli (strain K12) (see 5 papers)
TC 2.A.8.1.2 / P39344 L-Idonate/D-Gluconate:H+ symporter, IdnT, GntW, YjgT from Escherichia coli (see 5 papers)
b4265 L-idonate and D-gluconate transporter from Escherichia coli str. K-12 substr. MG1655
33% identity, 95% coverage
- function: Transporter which is probably involved in L-idonate metabolism (PubMed:9658018). Transports L-idonate from the periplasm across the inner membrane (PubMed:9658018). Can also transport D- gluconate and 5-keto-D-gluconate (PubMed:17088549, PubMed:9119199). It has been reported that gluconate uptake probably occurs via a proton- symport mechanism in E.coli (PubMed:4585187).
catalytic activity: L-idonate(in) + H(+)(in) = L-idonate(out) + H(+)(out) (RHEA:29571)
catalytic activity: D-gluconate(in) + H(+)(in) = D-gluconate(out) + H(+)(out) (RHEA:28831)
catalytic activity: 5-dehydro-D-gluconate(in) + H(+)(in) = 5-dehydro-D- gluconate(out) + H(+)(out) (RHEA:28819)
disruption phenotype: Reduced growth rate when grown on 5-keto-D- gluconate as sole carbon source. - substrates: D-gluconate, H+, l-idonate
- 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 - “...3.6 ytfR b4228 putative ATP-binding component of a transport system 5.2 idnT f , g b4265 L-idonate transporter -3.3 * -3.0 sgcX b4305 putative PTS transport system 4.4 Carbon & Energy metabolism acnB b , f b0118 aconitate hydrase B -3.0 ** prpB b , f...”
- Systematizing the generation of missing metabolic knowledge
Orth, Biotechnology and bioengineering 2010 - “...substrates. The putP (b1015) strain had a reduced growth rate on propionate and the idnT (b4265) strain had a reduced growth rate on 5-keto-D-gluconate. It was also determined by RT-PCR that expression of both of these genes in wild type E. coli increased during growth on...”
- Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing.
Bhattacharya, ACS nano 2024 - “...primers complementary to the mRNA generated from transcription of the E. coli idnT gene (UniProt P39344, used to probe the level of host cell RNA nonspecifically incorporated within the engineered encapsulin variants) showed that the level of packaged idnT mRNA followed a very similar trend to...”
- Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing.
Bhattacharya, bioRxiv : the preprint server for biology 2024 - “...primers complementary to the mRNA generated from transcription of the E. coli idnT gene (UniProt P39344, used to probe the level of host cell RNA non-specifically incorporated within the engineered encapsulin variants) showed that the level of packaged idnT mRNA followed a very similar trend to...”
- Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.
Paparoditis, Biochimica et biophysica acta 2014 - “...4 2.A.7.23.1 P42243 10 amino acids tryptophan Q7UGZ9 10 2.A.8 Gluconate:H+ Symporter (GntP) Family 2.A.8.1.2 P39344 10 monocarboxyl L-idonate/D- gluconate:H + symporter Q7UNE5 13 2.A.8.1.7 Q46892 14 monocarboxyl gluconate:H + Symporter Q7UET7 12 2.A.9 Cytochrome Oxidase Biogenesis (Oxal) Family 2.A.9.3.1 P25714 3 protein proteins Q7UFZ2 6...”
- Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli
Bausch, Journal of bacteriology 1998 - “...(P39346) yjgU idnO (P39345) gntW yjgS idnT (P39344) idnR (P39343) Gene product D-Gluconate L-Idonate kinase 5-dehydrog- enase 5-Keto-D-gluconate 5-reductase...”
- Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism
Porco, Journal of bacteriology 1997 - “...number, U14003; Swiss-Prot accession numbers, P39208 and P39344, respectively). Possible catabolite gene activator protein (CAP) binding sites (34) are...”
SR35_21910 gnt-II system L-idonate transporter from Escherichia coli
33% identity, 95% coverage
SCO1680 gluconate permease from Streptomyces coelicolor A3(2)
36% identity, 95% coverage
- Role of GntR Family Regulatory Gene SCO1678 in Gluconate Metabolism in Streptomyces coelicolor M145
Tsypik, BioMed research international 2017 - “...that phosphorylates gluconate to glucono-5-phosphate which is then metabolized in the pentose phosphate pathway. Gene SCO1680 (gntP) encodes gluconate permease that transports the molecule into a cell. The next two genes, SCO1681 - SCO1682 (gntZ - gntZ2) , overlap by 4 nucleotides and encode gluconate dehydrogenase...”
- “...39% identity to GntP permease of Bacillus subtilis and 38% to S. coelicolor gluconate permease Sco1680. The former, therefore, might be involved in gluconate uptake as well. This agrees with recent global analysis of the entire array of transport proteins in S. coelicolor , where Sco1680...”
- Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor
Romero-Rodríguez, BMC microbiology 2016 - “...GlnK encoding gene SCO1679 (log 2 =1.98), correlated well with a glucose positive regulation of SCO1680 (log 2 =1.99), encoding a gluconate transporter (Fig. 3a ). In Streptomyces lividans , the consumption of gluconate as a sole carbon source has been reported by [ 29 ]....”
SXYL_02351 gluconate:H+ symporter from Staphylococcus xylosus
36% identity, 92% coverage
- Insight into the Genome of Staphylococcus xylosus, a Ubiquitous Species Well Adapted to Meat Products
Leroy, Microorganisms 2017 - “...transport, catabolism, regulation SXYL_02455-57 Trehalose, regulation, catabolism, EIIBC SXYL_00438-40 gntRKP Gluconate, transport, catabolism, regulation SXYL_00159, SXYL_02351 Gluconate, transport SXYL_01518-22 rbsBCADR Ribose, transport, catabolism, regulation SXYL_00132-35 xylEBAR Xylulose, transport, catabolism, regulation In red, genes overexpressed in a meat model. microorganisms-05-00052-t002_Table 2 Table 2 Peptide transport, peptidases and...”
U876_22450 gluconate transporter from Aeromonas hydrophila NJ-35
36% identity, 95% coverage
llmg_2467 gluconate transport protein from Lactococcus lactis subsp. cremoris MG1363
33% identity, 90% coverage
BKKJ1_0207 GntP family permease from Bifidobacterium catenulatum subsp. kashiwanohense
35% identity, 94% coverage
- Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal
James, Scientific reports 2019 - “...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 BKKJ1_0339 BKKJ1_0339 xylitol (sorbitol) dehydrogenase 34.61 BKKJ1_0340 BKKJ1_0340 transcriptional regulator 36.34...”
YPTB3287 putative GntP family gluconate transporter from Yersinia pseudotuberculosis IP 32953
32% identity, 99% coverage
YjiB / b4321 fructuronate transporter from Escherichia coli K-12 substr. MG1655 (see 6 papers)
gntP / P0AC94 fructuronate transporter from Escherichia coli (strain K12) (see 6 papers)
TC 2.A.8.1.3 / P0AC94 D-Fructuronate/D-gluconate:H+ symporter, GntP from Escherichia coli (see 5 papers)
b4321 fructuronate transporter from Escherichia coli str. K-12 substr. MG1655
NP_418741 fructuronate transporter from Escherichia coli str. K-12 substr. MG1655
Z5919 gluconate transport system permease 3 from Escherichia coli O157:H7 EDL933
ETEC_4633 gluconate permease GntP from Escherichia coli ETEC H10407
31% identity, 98% coverage
PP0652, PP_0652 gluconate transporter from Pseudomonas putida KT2440
31% identity, 91% coverage
- A versatile microbial platform as a tunable whole-cell chemical sensor
Hernández-Sancho, Nature communications 2024 - “...was blocked by eliminating genes encoding sugar transporters ( gtsABCD , glucose transporter; gntT and PP_0652 , gluconate transporters; and kguT , 2KG transporter), sugar kinases ( glk , glucose kinase; gnuK , gluconate kinase; and kguK , 2KG kinase), and specific dehydrogenases ( gcd ,...”
- “...glucose uptake and processing ( gcd , gad , gtsABCD , glk , gntT , PP_0652 , gnuK , kguT , and kguK ) and aceA . The corresponding suicide plasmid to eliminate each of these functions, derived from pGNW2 (Supplementary Table 1 ), was delivered...”
- Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system
Pause, Microbial biotechnology 2024 - “...crossmembrane transportation pathway via gluconate This study KTKG P. putida KT2440 glk gtsABCD gnuK gntT PP_0652 Inframe gene deletion mutant of glucose ABC transporter ( gtsABCD , PP_1015 PP_1018 ), glucokinase ( glk , PP_1011 ), gluconate transporters ( gntT , PP_3417 and PP_0652 ) and...”
- UEG Week 2024 Poster Presentations
, United European gastroenterology journal 2024 - UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023
YjhF / b4296 KpLE2 phage-like element; putative transporter YjhF from Escherichia coli K-12 substr. MG1655 (see 4 papers)
33% identity, 93% coverage
PPUBIRD1_0697 GntP family permease from Pseudomonas putida BIRD-1
32% identity, 88% coverage
SCO4991 sugar transport integral membrane protein from Streptomyces coelicolor A3(2)
35% identity, 84% coverage
- Role of GntR Family Regulatory Gene SCO1678 in Gluconate Metabolism in Streptomyces coelicolor M145
Tsypik, BioMed research international 2017 - “...confirmed transcriptional coupling of genes SCO1679-1680-1681 ( Figure 1(b) ). Another carbohydrate transport membrane protein Sco4991 shows 39% identity to GntP permease of Bacillus subtilis and 38% to S. coelicolor gluconate permease Sco1680. The former, therefore, might be involved in gluconate uptake as well. This agrees...”
- “...analysis of the entire array of transport proteins in S. coelicolor , where Sco1680 and Sco4991 were annotated as high-affinity gluconate permease and gluconate permease, respectively [ 20 ]. 3.2. Expression and Knockout of SCO1678 Organization and regulation of gnt operons in Escherichia coli and Bacillus...”
LKW31_01605 gluconate transporter from Pantoea agglomerans
37% identity, 95% coverage
GntU / b4476 low-affinity gluconate transporter from Escherichia coli K-12 substr. MG1655 (see 4 papers)
gntU / P0AC96 low-affinity gluconate transporter from Escherichia coli (strain K12) (see 4 papers)
TC 2.A.8.1.8 / P0AC96 Low-affinity (212 from Escherichia coli (strain K12) (see 7 papers)
Z4804 low affinity gluconate permease from Escherichia coli O157:H7 EDL933
35% identity, 95% coverage
STM3541 low affinity gluconate permease from Salmonella typhimurium LT2
35% identity, 98% coverage
- Pseudomonas stutzeri as an alternative host for membrane proteins
Sommer, Microbial cell factories 2017 - “...enterica STM2913 GntP 16421462 ++ NT S. enterica STM3512 GntP 16422071 + ++ S. enterica STM3541 GntP 16422100 + + S. enterica STM3801 GntP 16422374 + ++ S. enterica STM4482 GntP 16423047 NT P. aeruginosa PA3553 GTT 9949705 + + NT P. furiosus PF0520 MFS 18976892...”
PFREUD_22850 gluconate:H+ symporter from Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1
33% identity, 94% coverage
- A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment
Saraoui, BMC genomics 2013 - “...iolB (Myo-inositol catabolism IolB protein) 2.1.1 Specific carbohydrate metabolic pathway 2,4 3,2E-07 1,9 4,3E-01 CUST_1808_PI426428742 PFREUD_22850 gntP Gluconate transporter (transmembrane) 2.1.1 Specific carbohydrate metabolic pathway 3,8 3,1E-06 24,1 5,0E-03 CUST_2167_PI426428742 PFREUD_04270 eda, hga, kdgA 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase 2.1.1 Specific carbohydrate metabolic pathway 2,1 2,6E-05 2,8 2,0E-01...”
STM2913 putative permease from Salmonella typhimurium LT2
33% identity, 87% coverage
- Pseudomonas stutzeri as an alternative host for membrane proteins
Sommer, Microbial cell factories 2017 - “...yields. Upscaling of protein production and purification of a Gluconate:H + Symporter (GntP) family transporter (STM2913) from Salmonella enterica to high purity was demonstrated. Conclusions Pseudomonas stutzeri is an alternative production host for membrane proteins with success rates comparable to E. coli . However, some proteins...”
- “...DMT 16422334 + + + S. enterica STM3746 ESS 16767031 + + + S. enterica STM2913 GntP 16421462 ++ NT S. enterica STM3512 GntP 16422071 + ++ S. enterica STM3541 GntP 16422100 + + S. enterica STM3801 GntP 16422374 + ++ S. enterica STM4482 GntP 16423047...”
- Modulation of horizontally acquired genes by the Hha-YdgT proteins in Salmonella enterica serovar Typhimurium
Vivero, Journal of bacteriology 2008 - “...2.45 13.18 13.18 6.04 3.47 3.39 4.03 STM2913 0.37 Secreted effector protein Transcriptional regulator Invasion regulatory protein Putative cytoplasmic protein...”
STM14_3515 GntP family permease from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
33% identity, 87% coverage
- L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation
Vasicek, Frontiers in cellular and infection microbiology 2021 - “...kinase hycH 5.38 hydrogenase 3 large subunit processing protein hycD 5.15 Hydrogenase 3, membrane subunit STM14_3515 5.03 putative permease hycG 4.82 hydrogenase argH 4.75 argininosuccinate lyase hycI 4.46 Protease involved in processing C-terminal end of HycE hycF 4.43 formate hydrogenlyase complex iron-sulfur subunit glpB 4.27 anaerobic...”
SEEHRA37_18800 GntP family permease from Salmonella enterica subsp. enterica serovar Heidelberg str. SARA37
33% identity, 87% coverage
MSMEG_3789 inner membrane permease YgbN from Mycobacterium smegmatis str. MC2 155
31% identity, 94% coverage
- Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis
Goethe, mSystems 2020 - “...4.18 Molecular chaperone GroEL MSMEG_3787 <0.0001 4.00 d -Aminoacylase eda MSMEG_3788 <0.0001 4.00 2-Dehydro-3-deoxyphosphogluconate aldolase MSMEG_3789 <0.0001 5.63 Inner membrane permease YgbN thpD MSMEG_3898 <0.0001 4.94 4.44 Ectoine hydroxylase ectC MSMEG_3899 <0.0001 6.47 4.55 l -Ectoine synthase ectB MSMEG_3900 <0.0001 5.74 (3.86) Diaminobutyrate-2-oxoglutarate aminotransferase ectA MSMEG_3901...”
HI1015 gluconate permease (gntP) from Haemophilus influenzae Rd KW20
33% identity, 84% coverage
- There is a specific response to pH by isolates of Haemophilus influenzae and this has a direct influence on biofilm formation
Ishak, BMC microbiology 2014 - “...Additional file 1 : Figure S4) revealed predominantly an up-regulation of two gluconate:H + symporters (HI1015 and HI0092) and the associated gluconate (or sugar acid) metabolic genes (HI1010-1015, see Figure 3 ) and a potential glycerate kinase (HI0091) that links into glycolysis. It is worth noting...”
- “...1.88 3.0410 -7 2.8610 -5 Hydroxypyruvate isomerase HI1014 1.52 2.3310 -5 1.5410 -3 Sugar epimerase HI1015 1.12 1.1810 -3 4.7010 -2 GntP family, gluconate:H + symporter HI0091 1.74 5.9810 -7 5.3310 -5 Hypothetical protein; homologous to GlxK, glycerate kinase HI0092 2.14 1.4910 -9 2.4110 -7 GntP...”
- What's for dinner?: Entner-Doudoroff metabolism in Escherichia coli
Peekhaus, Journal of bacteriology 1998 - “...databasesa Organism GntT d x 482; GntP x 671; HI1015 x x 194; contig269 250; contig1173 x 89; Ch XIV, SCR14 Streptococcus pneumoniae Streptococcus pyogenes...”
PMI2672 low-affinity gluconate transporter from Proteus mirabilis HI4320
31% identity, 99% coverage
SO1771 permease, GntP family from Shewanella oneidensis MR-1
33% identity, 95% coverage
- SO2426 is a positive regulator of siderophore expression in Shewanella oneidensis MR-1
Henne, BMC microbiology 2011 - “...( ftn ) CAAAAGCAACAAAA - -63 2.08E-06 SO1580 TonB-dependent heme receptor AAAAAGCAGAAAAA - -112 3.68E-06 SO1771 permease, GntP family CTACAACAGCCAAA + -41 2.81E-06 SO2045 cation efflux family protein CACCCTCAACAGAA + +11 5.98E-05 SO3030 siderophore biosynthesis protein ( alcA ) CTGTAACAGCAAAT + -133 2.86E-05 SO3032 siderophore biosynthesis...”
- Genomic encyclopedia of sugar utilization pathways in the Shewanella genus
Rodionov, BMC genomics 2010 - “...in additional files 7 and 8 . In-frame deletion mutagenesis In-frame deletion mutagenesis of glyT (SO1771) or nagP (SO3503) was performed using previously published method [ 42 ] with minor modifications. Upstream and downstream fragments flanking the target locus were PCR amplified using S. oneidensis MR-1...”
- “...in N- acetylglucosamine (Nag) utilization in Shewanella oneidensis MR-1; C. Phenotypic characterization of grtP ( SO1771 ) for its involvement in D-glycerate; D. Complementation of the E. coli cellobiose utilization by the bglA-bglT ( Sbal_1133-1132 ) genes from S. baltica OS155; E. Substrate specificity of Shewanella...”
- Transcriptome analysis reveals response regulator SO2426-mediated gene expression in Shewanella oneidensis MR-1 under chromate challenge
Chourey, BMC genomics 2008 - “...0.22 0.11 0.08 0.05 0.19 SO1580 TonB-dependent heme receptor 0.32 0.39 0.37 0.19 0.23 0.92* SO1771 Permease, GntP family 0.88* 0.23 0.43 0.37 0.14 0.2 SO2045 Cation efflux family protein 0.57 0.24 0.3 0.22 0.13 1.19* SO3030 Siderophore biosynthesis protein AlcA ( alcA ) 0.67 0.27...”
- “...transport and binding, in particular Fe acquisition and homeostasis: ftn (ferritin), so1580 (TonB-dependent heme receptor), so1771 (GntP family permease), so2045 (cation efflux family protein), alcA (siderophore biosynthesis protein), so3031 and so3032 (both putative siderophore biosynthesis proteins encoded immediately downstream of alcA ), so3033 (ferric alcaligin siderophore...”
FN0554 D-serine permease from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
32% identity, 94% coverage
APL_1665 gluconate permease from Actinobacillus pleuropneumoniae L20
31% identity, 96% coverage
cg3216 gluconate permease from Corynebacterium glutamicum ATCC 13032
31% identity, 89% coverage
VCA0904 permease from Vibrio cholerae O1 biovar eltor str. N16961
34% identity, 95% coverage
- The Type II Secretory System Mediates Phage Infection in Vibrio cholerae
Sun, Frontiers in cellular and infection microbiology 2021 - “...of six different insertion sites were identified, including in the coding sequences of the genes VCA0904 (H+/gluconate symporter and related permease), VC1936 (phosphatidate cytidylyltransferase), VC0718 (DNA recombination-dependent growth factor C), VC0420 (conserved hypothetical protein CHP02099), VCA0863 (lipase, Pla-1/cef, extracellular), and VC2724 (EpsM). Among these genes, VC2724...”
YgbN / b2740 putative transporter YgbN from Escherichia coli K-12 substr. MG1655 (see 4 papers)
b2740 predicted transporter from Escherichia coli str. K-12 substr. MG1655
Q46892 Inner membrane permease YgbN from Escherichia coli (strain K12)
30% identity, 92% coverage
- Correlation between the genomic o454-nlpD region polymorphisms, virulence gene equipment and phylogenetic group of extraintestinal Escherichia coli (ExPEC) enables pathotyping irrespective of host, disease and source of isolation
Ewers, Gut pathogens 2014 - “...by the absence of a PCR product due to a lack of o454 gene (synonyms b2740 and ygbN ), which codes for a putative Zn ++ -dependent hydrolase and a permease; pattern II showed an amplicon of 1.319bp in length consisting of the full sequence of...”
- “...(syn. kpdC ), 4-hydroxybenzoate decarboxylase determinant; f265 (syn. ygbL ), hypothetical transcriptional regulator; o454 (syn. b2740 and ygbN ), putative zinc-dependent hydrolase; o347 (syn. c3302 ), limited level of similarity to enzymes implicated in antibiotic hydrolysis and synthesis; slyA (syn. kpdR ), 4-hydroxybenzoate decarboxylase determinant, in...”
- Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements
Ge, Journal of biosciences 2011 - “...378338 1.72 frmB b0355 18 4175399 4175544 3.08 secE b3981 19 2862792 2863225 1.72 ygbN b2740 19 366289 366434 3.03 lacl b0345 20 898140 898525 1.67 ybjS b0859 20 1167862 1167983 3.03 ycfQ b1111 21 2050859 2051100 1.67 shiA b1981 21 1958737 1959026 3.03 argS b1876...”
- Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts
Lorenz, Nucleic acids research 2010 - “...737 yfaA b2230 Antisense Predicted protein 1237 170 2 863 240 2 863 409 ygbN b2740 Antisense Predicted transporter 998 165 1 241 194 1 241 315 cvrA b1191 Sense Predicted cation/proton antiporter 1044 157 1 439 032 1 439 135 ydbJ b4529 Antisense Predicted protein...”
- Identification of the CRP regulon using in vitro and in vivo transcriptional profiling
Zheng, Nucleic acids research 2004 - “...b2463 b2611_ypjE_yfjD b2710_ygbD b2736_b2737 b2740 b2876_b2875 b2997_hybABCDEF b3001 b3836_b3837_b3838_yigU_yigW_1 cchB_eutEJG celABCDF_ydjC csgDEFG cyoABCDE...”
- Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics
van, Proceedings of the National Academy of Sciences of the United States of America 2002 - “...85 thiCEFGH tpbAyabKJ thiMD thiL idnK,idnDOTR gntKU gntT b2740 eddeda tufB nrdAB nrdDG nrdHIEF coaA tgtyajCDsecDF yegQ b3975 tpr yeeO yhbcnusAinfB mutM arsRBC...”
- “...as the idnK protein, and a low-affinity gluconate permease. b2740 is a gene of unknown function that belongs to the family of gluconate transporters. Finally,...”
- Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.
Paparoditis, Biochimica et biophysica acta 2014 - “...Gluconate:H+ Symporter (GntP) Family 2.A.8.1.2 P39344 10 monocarboxyl L-idonate/D- gluconate:H + symporter Q7UNE5 13 2.A.8.1.7 Q46892 14 monocarboxyl gluconate:H + Symporter Q7UET7 12 2.A.9 Cytochrome Oxidase Biogenesis (Oxal) Family 2.A.9.3.1 P25714 3 protein proteins Q7UFZ2 6 2.A.12 ATP:ADP Antiporter (AAA) Family 2.A.12.4.1 Q6MDZ0 12 nucleotides NAD...”
PA1051 probable transporter from Pseudomonas aeruginosa PAO1
PA14_50770 probable transporter from Pseudomonas aeruginosa UCBPP-PA14
32% identity, 95% coverage
- Transcriptional profiling of Pseudomonas aeruginosa mature single- and dual-species biofilms in response to meropenem
Alam, Microbiology (Reading, England) 2023 - “...six involved in efflux or membrane transport (PA0603, PA0604, mexE , mexF , PA0860 and PA1051). This suggests that the presence of C. albicans may result in reduced production of the MexEF-OprN efflux pump in P. aeruginosa biofilm cells. Discussion Biofilms are medically important, as they...”
- 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 - “...TolQ protein 0,41 1,03 2,52 Transport tolR PA0970 TolR protein 0,33 0,62 1,43 Transport gntP PA1051 Probable transporter 2,46 0,33 3,4 Transport braG PA1070 Branched-chain amino acid transport protein BraG 0,94 0,79 1,32 Transport braF PA1071 Branched-chain amino acid transport protein BraF 1,06 1,07 2 Transport...”
- Uracil influences quorum sensing and biofilm formation in Pseudomonas aeruginosa and fluorouracil is an antagonist
Ueda, Microbial biotechnology 2009 - “...8.6 Cis aconitate porin OpdH PA14_54170 PA0782 putA 6.5 1.1 8.6 Proline dehydrogenase PutA PA14_50770 PA1051 4.9 1.2 6.5 Probable transporter PA14_46080 PA1420 5.3 1.7 4 Hypothetical protein PA14_46070 PA1421 speB2 9.8 1.1 9.8 Agmatinase PA14_38170 PA2038 4.9 1.3 5.7 Hypothetical protein PA14_35460 PA2252 7 1.2...”
- Uracil influences quorum sensing and biofilm formation in Pseudomonas aeruginosa and fluorouracil is an antagonist
Ueda, Microbial biotechnology 2009 - “...1.4 8.6 Cis aconitate porin OpdH PA14_54170 PA0782 putA 6.5 1.1 8.6 Proline dehydrogenase PutA PA14_50770 PA1051 4.9 1.2 6.5 Probable transporter PA14_46080 PA1420 5.3 1.7 4 Hypothetical protein PA14_46070 PA1421 speB2 9.8 1.1 9.8 Agmatinase PA14_38170 PA2038 4.9 1.3 5.7 Hypothetical protein PA14_35460 PA2252 7...”
ESA_02715 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
33% identity, 89% coverage
ESA_02715 GntP family permease from Cronobacter sakazakii ATCC BAA-894
33% identity, 90% coverage
NMV_2230, NMY220_1858 GntP family permease from Neisseria meningitidis 8013
30% identity, 92% coverage
VC0286 gluconate permease, putative from Vibrio cholerae O1 biovar eltor str. N16961
30% identity, 92% coverage
- Suppressor Mutations in Type II Secretion Mutants of Vibrio cholerae: Inactivation of the VesC Protease
Rule, mSphere 2020 - “...(%) that contain an SNP a epsL epsG1 epsG2 epsM PU3 PU5 VC0259 RfbV 72 VC0286 Gluconate permease 100 VC0613 - N -acetylhexosaminidase 100 VC1133 HisD 100 VC1649 VesC 100 SV VC1718 Hypothetical 100 VC2252 BamA 100 VCA0254 Hypothetical 98 VC2701 DsbD SV VC2506 HepA SV...”
- “...VC2252 Outer membrane protein assembly factor BamA Nonsynonymous 100 c. 1502T>C p. I501T 85 epsM VC0286 Gluconate permease Nonsynonymous 100 c. 298A>T p. I100F 139 VC0613 - N -acetylhexosaminidase Nonsynonymous 100 c. 1012G>A p. G338S 116 VC1718 Hypothetical Nonsynonymous 100 c. 568G>A p. V190M 67 PU3...”
- IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in Vibrio cholerae
Sachman-Ruiz, Genes 2020 - “...Probable thiol oxidoreductase with 2 cytochrome c hemebinding sites VC0364 bfd 2.22671 <5.00E05 Bacterioferritinassociated ferredoxin VC0286 gntU 2.22969 <5.00E05 Lowaffinity gluconate/H+ symporter GntU VCA0976 2.23539 <5.00E05 Hypotetical protein VCA0984 ildD 2.27194 <5.00E05 Llactate dehydrogenase | lldD VC1332 2.34818 <5.00E05 Tripartite tricarboxylate transporter TctA family VCA0983 2.43475...”
Q7UET7 Gluconate permease gntP from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
26% identity, 86% coverage
NJ7G_3288 GntP family permease from Natrinema sp. J7-2
27% identity, 92% coverage
Q7UNE5 Probable Gnt-II system L-idonate transporter from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
31% identity, 37% coverage
VSAL_I2593 gluconate permease from Vibrio salmonicida LFI1238
VSAL_I2593 GntP family permease from Aliivibrio salmonicida LFI1238
26% identity, 56% coverage
VV1_1655 H+/gluconate symporter from Vibrio vulnificus CMCP6
26% identity, 51% coverage
MA0021 high-affinity gluconate transporter (gluconate permease) from Methanosarcina acetivorans C2A
28% identity, 36% coverage
CPE0860 probable gluconate permease from Clostridium perfringens str. 13
21% identity, 80% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory