PaperBLAST
PaperBLAST Hits for reanno::psRCH2:GFF2080 fusion of gluconokinase (EC 2.7.1.12) and the small permease component of the D-gluconate TRAP transporter (Pseudomonas stutzeri RCH2) (376 a.a., MPSVHTSKAS...)
Show query sequence
>reanno::psRCH2:GFF2080 fusion of gluconokinase (EC 2.7.1.12) and the small permease component of the D-gluconate TRAP transporter (Pseudomonas stutzeri RCH2)
MPSVHTSKASALPVLVVMGVSGSGKTETSHAVADALGLPHIEADNFHPAENVARMRAGTP
LSDADRMEWLHALIAEMQRTLAAGSGFVLACSALKRSYRELLRSAVPELRFAHLAIDYET
AVQRVGGRAGHFMPISLVDSQFATLESPEGEPGVLTVDASQPREGVLRQIVEWMQGSGLD
ELIETRVDLSSRPFDSATTAPPLTNEPIYSGRVAQHFDRLTDWLMAALMAFMVIVVFSSV
VLRYAFGTGWTGAEELSRLAFVWLVFVGVASSMRRGELMSFSMLRDRFPRLFRRVVDSLS
WLLVAAASCLAAWGGWNQMQFGWTINSPVVGYPLGLAMLPVAASMVALAVLALLQLVNVW
RRDQPSATAAANVTAD
Running BLASTp...
Found 81 similar proteins in the literature:
Psest_2123 fusion of gluconokinase (EC 2.7.1.12) and the small permease component of the D-gluconate TRAP transporter from Pseudomonas stutzeri RCH2
100% identity, 100% coverage
- mutant phenotype: This protein has pleiotropic phenotypes which are not explained, but it is most important for fitness with D-gluconate as the carbon source, consistent with its putative roles as part of the tripartite gluconate transport system and as gluconate kinase. Also, the N-terminal part is 49% identical to PP3416 or gnuK from P. putida, which is the catabolic gluconate kinase (PMC1951859). The SEED and KEGG annotations ignore the dctQ-like C-terminal portion.
PP_3416 gluconokinase from Pseudomonas putida KT2440
PP3416 gluconokinase from Pseudomonas putida KT2440
49% identity, 47% coverage
- Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system
Pause, Microbial biotechnology 2024 - “...), 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 protocols (Volke et al., 2021 ). In brief, homology...”
- Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol
Beckers, Microbial cell factories 2016 - “...6-P-gluconate dehydrogenase 0.65 0.42 1.15 0.77 gnd PP4043 6-P-gluconate dehydrogenase 0.08 0.15 0.1 0.23 gnuK PP3416 Carbohydrate kinase 0.06 0.52 0.10 0.7 kguK PP3378 Dehydroglucokinase 0.02 0.63 0.10 0.21 kguD PP3376 2-Ketogluconate 6-phosphate reductase 0.15 0.17 0.10 0.2 rpiA PP5150 Ribose-5-phosphate isomerase A 0.09 0.06 0.10...”
- Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida
Borrero-de, Microbial cell factories 2014 - “...0.2 0.4 pgl PP1023 6-phosphogluconate dehydrogenase 0.5 -0.9 gnd PP4043 6-phosphoglucolacto dehydrogenase -0.6 -0.1 gnuK PP3416 Carbohydrate kinase -1.1 -0.6 kguK PP3378 Dehydroglucokinase 0.45 -0.4 kguD PP3376 2-Ketogluconate 6-phosphate reductase -0.7 -0.5 rpiA PP5150 Ribose-5-phosphate isomerase A 0.3 0.0 rpe PP0415 Ribulose-phosphate 3-epimerase -0.5 -0.1 tktA...”
- “...-0.1 -0.3 pgl PP1023 6-phosphogluconate dehydrogenase 9.3 7.8 gnd PP4043 6-phosphoglucolacto dehydrogenase 0.2 -0.3 gnuK PP3416 Carbohydrate kinase -0.1 0.3 kguK PP3378 Dehydroglucokinase 0.6 0.5 kguD PP3376 2-Ketogluconate 6-phosphate reductase 0.1 -0.1 rpiA PP5150 Ribose-5-phosphate isomerase A 0.3 -0.4 rpe PP0415 Ribulose-phosphate 3-epimerase 0.2 -0.1 tktA...”
- A set of activators and repressors control peripheral glucose pathways in Pseudomonas putida to yield a common central intermediate
del, Journal of bacteriology 2008 - “...study This study PP1023 PP1516 PP2333 PP2741 PP3415 PP3416 PP3417 PP3418 PP3642 a Gene Function pgl 6-Phosphogluconolactonase RND efflux pump GntR family of...”
- Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis
del, Journal of bacteriology 2007 - “...PP1444), glucokinase (glk; PP1011), gluconokinase (gnuK; PP3416), and 2-ketogluconate-6-phosphate reductase (kguD; PP3376), we hypothesized that the inability...”
- “...5). Gluconokinase involved in the phosphorylation of gluconate (PP3416) was induced almost fourfold. The reactions from glucose to gluconate and from gluconate...”
PA2321 gluconokinase from Pseudomonas aeruginosa PAO1
48% identity, 43% coverage
- Genome-wide association study of signature genetic alterations among pseudomonas aeruginosa cystic fibrosis isolates
Hwang, PLoS pathogens 2021 - “...reason, we speculate that some CF isolates have evolved with mutations in glucose catabolism genes (PA2321 and PA3193) to avoid spending unnecessary energy in catabolizing a less optimal carbon source (glucose). Additionally, mannitol has been used as a therapeutic treatment to increase mucociliary clearance in the...”
- “...repressor Beta-Lactam resistance PA2320 K06145 LacI 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...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...+ Respiratory nitrate reductase beta chain PA3875 narG 2.2 + Respiratory nitrate reductase alpha chain PA2321 gntK 3.1 + GntK PA2516 xylZ 4.1 1.7 Toluate 1,2-dioxygenase electron transfer component PA3183 zwf 2.1 + Glucose-6-phosphate 1-dehydrogenase PA3194 edd 1.5 + Phosphogluconate dehydratase PA3195 gapA 2.5 + Glyceraldehyde...”
- Inhibition of Pseudomonas aeruginosa swarming motility by 1-naphthol and other bicyclic compounds bearing hydroxyl groups
Oura, Applied and environmental microbiology 2015 - “...PA2009 PA2014 PA2015 PA2016 PA2247 PA2248 PA2249 PA2250 PA2321 PA2554 PA2555 PA3183 PA3194 PA3195 PA3559 PA3584 PA3723 PA3924 PA4022 PA5056 PA5435 PA5436 Cell...”
- Transcriptional and proteomic responses of Pseudomonas aeruginosa PAO1 to spaceflight conditions involve Hfq regulation and reveal a role for oxygen
Crabbé, Applied and environmental microbiology 2011 - “...PA2007 PA2009 PA2021 PA2024 PA2225 PA2247 PA2248 PA2300 PA2321 PA2453 PA2570 PA2573 PA2612 PA2619 PA2620 PA2634 PA2639 PA2662 PA2743 PA2747 PA2753 PA2788 PA2851...”
- “...bdhA maiA hmgA PA2021 PA2024 PA2225 bkdA1 bkdA2 chiC PA2321 PA2453 palL PA2573 serS infA clpA PA2634 nuoD PA2662 infC PA2747 PA2753 PA2788 efp acpP rpmF PA2971...”
- Novel inner membrane retention signals in Pseudomonas aeruginosa lipoproteins
Lewenza, Journal of bacteriology 2008 - “...OmlA 2 variant PA4876, OsmE PA5310 PA3262 PA0425, MexA PA2321 Not present PA3677 PA5041, PilP PA5414 PA1723, PscJ PA1812, MltD PA4370, IcmP a b c Protein...”
- 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 - “...Negatively Mg2 regulated PA2260 PA2261 PA2262 PA2265 PA2266 PA2321 PA2322 PA2323 PA4236 PA4463 PA4761 PA4835 PA4836 Positively Mg2 and positively PhoP regulated...”
- “...utilization of 2-ketogluconate in P. aeruginosa (44). Additionally, PA2321 (gntK, a homologue of the gene encoding gluconokinase), PA2322 (gntT, a homologue of...”
- Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment
Wagner, Journal of bacteriology 2003 - “...PA0512 PA0714 PA1978 PA1983 PA1984 PA2259 PA2260 PA2261 PA2321 PA2539 PA2540 PA2711 Change in PAO-JP2 (induced to uninduced) (fold)b 2086 WAGNER ET AL. phase...”
DR_1910 thermoresistant gluconokinase from Deinococcus radiodurans R1
45% identity, 47% coverage
blr6762 gluconokinase from Bradyrhizobium japonicum USDA 110
42% identity, 44% coverage
SLIV_29345 gluconokinase from Streptomyces lividans TK24
SCO1679 gluconokinase from Streptomyces coelicolor A3(2)
45% identity, 43% coverage
- Coupling of the engineered DNA "mutator" to a biosensor as a new paradigm for activation of silent biosynthetic gene clusters in Streptomyces
Sekurova, Nucleic acids research 2021 - “...ribosomal protein L10 and SLIV_22980 encoding putative sugar hydrolase. One mutation within coding region of SLIV_29345 (glucokinase) was synonymous, and hence would not cause a functional defect. Two other mutations were located within intergenic regions, namely G to A transition upstream of SLIV_03310 encoding a putative...”
- Multi-level regulation of coelimycin synthesis in Streptomyces coelicolor A3(2)
Bednarz, Applied microbiology and biotechnology 2019 - “...cluster inhibitor. GntR GntR (SCO1678) is a FadR subfamily gluconate-binding repressor of the gluconate operon SCO1679 SCO1682 . ACT synthesis was shown to be decreased in gluconate-supplemented in comparison with the glucose-supplemented SMM medium in S. coelicolor A3(2). What is more, in gntR mutant, gluconate induced...”
- A Novel Two-Component System, Encoded by the sco5282/sco5283 Genes, Affects Streptomyces coelicolor Morphology in Liquid Culture
Arroyo-Pérez, Frontiers in microbiology 2019 - “...degradation F 2.17E-26 7.02E-20 0.00E+00 SCO6248 Allantoate amidinohydrolase 2.43 Purine degradation F 4.30E-19 2.53E-13 1.51E-11 SCO1679 Gluconokinase 2.54 Pentose phosphate G 5.38E-20 4.82E-02 6.66E-16 SCO6497 Transketolase 1.99 Pentose phosphate G 1.32E-12 3.37E-16 0.00E+00 SCO6658 6-phosphogluconate dehydrogenase 3.92 Pentose phosphate G 2.50E-44 1.07E-03 3.33E-16 SCO6661 glucose-6-phosphate 1-dehydrogenase...”
- Role of GntR Family Regulatory Gene SCO1678 in Gluconate Metabolism in Streptomyces coelicolor M145
Tsypik, BioMed research international 2017 - “...so via repression of its transcription from a single promoter located between genes SCO1678 and SCO1679 . The knockout also influenced, in a medium-dependent manner, the production of secondary metabolites by S. coelicolor . In comparison to the wild type, on gluconate-containing minimal medium, the SCO1678...”
- “...encodes a repressor of the gluconate operon and that the promoter of gluconate kinase gene SCO1679 is the main target of Sco1678 regulatory action. Interestingly, a knockout of SCO1678 also altered the secondary metabolite profile of S. coelicolor . Our work reveals one more regulatory checkpoint...”
- Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor
Romero-Rodríguez, BMC microbiology 2016 - “...proteomics [ 27 ] data was observed. Additionally, a putative gluconokinase (Glnk) coding gene ( SCO1679 ) was also stimulated by glucose in the Glc/Agar comparison, while no changes were detected in the Sco M145/ ScoZm comparison. The finding of up-regulation in the GlnK encoding gene...”
- Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures
Yagüe, PloS one 2014 - “...RNA helicase 1.1 0 SCO1522 Glutamine amidotransferase 1.8 0.6 SCO5059 Polyphosphate glucokinase, ppgK 2 0.4 SCO1679 Gluconokinase 2.8 0.5 SCO5657 Aldehyde dehydrogenase 1.4 0 SCO2470 Deoxyguanosinetriphosphate Triphosphohydrolase-like protein 1.7 0.2 SCO6211 Uricase 2.1 0.4 SCO2655 Putative nuclease 0.9 3.9 SCO6341 Exonuclease 2 0.3 SCO3023 S-adenosyl-L-homocysteine hydrolase...”
SMa0514 gluconate kinase IdnK from Sinorhizobium meliloti 1021
46% identity, 41% coverage
YPO2540 putative thermosensitive gluconokinase from Yersinia pestis CO92
44% identity, 42% coverage
Q10242 gluconokinase (EC 2.7.1.12) from Schizosaccharomyces pombe (see paper)
SPAC4G9.12 / GI|1204213 gluconokinase from Schizosaccharomyces pombe (see 2 papers)
SPAC4G9.12 gluconokinase from Schizosaccharomyces pombe
42% identity, 40% coverage
- CharProtDB Source (per GeneDB): GeneDB_Spombe
- Dataset describing the genome wide effects on transcription resulting from alterations in the relative levels of the bZIP transcription factors Atf1 and Pcr1 in Schizosaccharomyces pombe
Basu, Data in brief 2022 - “...subunit Git5 SPAC9E9.04 SPAC9E9.04 bcap family homolog, implicated in vesicle-mediated transport SPAC15A10.05c mug182 NADHX epimerase SPAC4G9.12 idn1 gluconokinase SPBC23G7.16 ctr6 vacuolar copper exporter Ctr6 SPBC21B10.04c nrf1 vacuolar transporter chaperone (VTC) complex, GTPase regulator subunit Nrf1 SPCC965.06 osr2 potassium channel, beta subunit, aldo-keto reductase SPNCRNA.906 snR30 non-coding...”
- Comparative transcriptome analysis reveals candidate genes related to cadmium accumulation and tolerance in two almond mushroom (Agaricus brasiliensis) strains with contrasting cadmium tolerance
Liu, PloS one 2020 - “...6-phosphofructokinase subunit beta PFK2 1.64 -1.20 -1.19 c23648.graph_c0 Glucose-6-phosphate isomerase gpi1 1.28 c27170.graph_c0 Probable gluconokinase SPAC4G9.12 1.12 c31657.graph_c1 Transketolase 1 TKL1 1.28 Glycolysis/gluconeogenesis c23648.graph_c0 Glucose-6-phosphate isomerase gpi1 1.28 c19366.graph_c0 Fructose-bisphosphate aldolase FBA1 1.33 1.02 c27792.graph_c0 Phosphoenolpyruvate carboxykinase [ATP] acuF 1.58 2.21 c28283.graph_c0 Glyceraldehyde-3-phosphate dehydrogenase 2 gpd2...”
- A metabolic strategy to enhance long-term survival by Phx1 through stationary phase-specific pyruvate decarboxylases in fission yeast
Kim, Aging 2014 - “...carbohydrate & energy metabolism 19 agl1, inv1, SPAC1039.11c, cyc1, cit1, aco1, SPAC3A11.07, SPAC26H5.09c, SPAC3C7.13c, zwf1, SPAC4G9.12, SPACUNK4.10, gut2, SPAC9E9.09c, psd2, tms1, erg25, SPCC191.05c, SPBC800.11 response to stress 12 rds1, tos4, SPBC660.05, SPBC1271.08c, SPCC1739.08c, hri1, SPACUNK4.15, SPAC27D7.11c, sod1, srx1, SPAC11D3.16c, alo1 conjugation / meiosis 13 ste7, mfm1,...”
- “...for the pentose phosphate pathway such as glucose-6-phosphate dehydrogenase ( zwf1 + , SPAC3C7.13c), glucokinase (SPAC4G9.12), and the gfo/idh family oxidoreductase (SPAC26H5.09c) were induced in phx1 mutants, possibly reflecting that the mutant cells are under oxidative stress. This finding coincides with the observation that several genes...”
- Comparative whole genome sequencing reveals phenotypic tRNA gene duplication in spontaneous Schizosaccharomyces pombe La mutants
Iben, Nucleic acids research 2011 - “...G T 51 SPAC1327.01c (txn fctr) L191I G T 1 2E+06 2277237 C A 63 SPAC4G9.12 (glco kinase) Y13stop C A 1 2E+06 2283617 T C 42 * T C 1 3E+06 2643596 C A 67 * C A 1 3E+06 2747078 A G 49 SPAC6F6.08c...”
Q8NMT0 gluconokinase (EC 2.7.1.12) from Corynebacterium glutamicum (see paper)
NCgl2399 gluconokinase from Corynebacterium glutamicum ATCC 13032
cg2732 putative gluconokinase from Corynebacterium glutamicum ATCC 13032
42% identity, 43% coverage
- Recent Advances of L-ornithine Biosynthesis in Metabolically Engineered Corynebacterium glutamicum
Wu, Frontiers in bioengineering and biotechnology 2019 - “...51.8%. L-Ornithine production yield in the engineered C. glutamicum SJC8399 strain with double deletion of NCgl2399 and NCgl2905 was 13.16 g/L, which is higher than that (8.78 g/L) in the parent C. glutamicum SJC8039 strain (Hwang and Cho, 2012 ). Furthermore, inactivation of NCgl0281, NCgl2582 ,...”
- Metabolic engineering of microorganisms for the production of L-arginine and its derivatives
Shin, Microbial cell factories 2014 - “...proB, kgd 4.78 [ 82 ] 2012 SJC8399 C. glutamicum ATCC argF , argR , Ncgl2399 , Ncgl2905 13.16 [ 83 ] 2013 APRE:: rocG C. glutamicum ATCC 13032 argF , proB , argR, speE:: P tac - M - rocG 14.84 [ 84 ] 2013...”
- “...], speE [ 84 ],[ 85 ], argR [ 81 ],[ 83 ]-[ 85 ], NCgl2399 [ 83 ] , NCgl2905 [ 83 ], and kgd [ 82 ] have been employed for developing strains for ORN overproduction (Table 1 ). Figure 2 Systems metabolic engineering...”
- Complex regulation of the phosphoenolpyruvate carboxykinase gene pck and characterization of its GntR-type regulator IolR as a repressor of myo-inositol utilization genes in Corynebacterium glutamicum
Klaffl, Journal of bacteriology 2013 - “...cg3096 cg3107 cg3169 cg3195 cg3216 NCgl2248 NCgl2399 NCgl2698 NCgl2709 NCgl2765 NCgl2787 NCgl2808 myo-Inositol catabolism, carbohydrate kinase Hypothetical...”
- Cytometry meets next-generation sequencing - RNA-Seq of sorted subpopulations reveals regional replication and iron-triggered prophage induction in Corynebacterium glutamicum
Freiherr, Scientific reports 2018 - “...manufacturers instructions. Successful removal of DNA was tested by standard PCR with the primers fw_PgntK_OL (cg2732) and rv_PgntK_OL (cg2732). rRNA depletion (Ribo-Zero) The Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) (Epicentre/Illumina, Munich, Germany) was used to remove rRNA of all samples. Samples received from large volumes were...”
- Impact of LytR-CpsA-Psr Proteins on Cell Wall Biosynthesis in Corynebacterium glutamicum
Baumgart, Journal of bacteriology 2016 - “...with (i) the promoter of the gluconate kinase gene (gntK; cg2732) (26), which is repressed in the absence of gluconate in the medium, and (ii) the promoter of...”
- Complex regulation of the phosphoenolpyruvate carboxykinase gene pck and characterization of its GntR-type regulator IolR as a repressor of myo-inositol utilization genes in Corynebacterium glutamicum
Klaffl, Journal of bacteriology 2013 - “...NCgl0167 NCgl0178 NCgl0900 NCgl1353 NCgl1650 iolC cg2560 cg2732 cg3096 cg3107 cg3169 cg3195 cg3216 NCgl2248 NCgl2399 NCgl2698 NCgl2709 NCgl2765 NCgl2787...”
- Co-ordinated regulation of gluconate catabolism and glucose uptake in Corynebacterium glutamicum by two functionally equivalent transcriptional regulators, GntR1 and GntR2
Frunzke, Molecular microbiology 2008 - “...1.01 0.95 1.05 11.53 cg0385 Periplasmic -glucosidase/-xylosidase, bglS 935.79 1.36 0.01 n.d. 1.27 1.77 21.08 cg2732 Gluconate kinase, gntK 2716.50 1.05 1.06 1.11 1.10 1.19 4.69 The mRNA ratios shown represent mean values from two or three independent microarray experiments starting from independent cultures (see Experimental...”
- Global gene expression during stringent response in Corynebacterium glutamicum in presence and absence of the rel gene encoding (p)ppGpp synthase
Brockmann-Gretza, BMC genomics 2006 - “...C oxidase chain II C cg2644 1.83 2.93 clpP2 ATP-dependent Clp protease, proteolytic subunit OU cg2732 1.68 2.41 gntV gluconokinase G cg3114 1.55 2.90 cysN sulfate adenyltransferase subunit 1 P cg3327 3.03 2.89 dps starvation-induced DNA protecting protein P a L ocus tag according to [50]...”
MSMEG_0453 shikimate kinase from Mycobacterium smegmatis str. MC2 155
41% identity, 44% coverage
KPHS_49540 gluconate kinase from Klebsiella pneumoniae subsp. pneumoniae HS11286
41% identity, 43% coverage
- Use of a combined antibacterial synergy approach and the ANNOgesic tool to identify novel targets within the gene networks of multidrug-resistant Klebsiella pneumoniae
Lee, mSystems 2024 - “...to the downregulation of KPHS_50720 (putative kinase) and KPHS_38680 (transaldolase kinase) and the upregulation of KPHS_49540 (gluconate kinase) and KPHS_31180 (pyruvate kinase). KPHS_38680 is an enzyme involved in the pentose phosphate pathway and forms an integrative network with KPHS_02470 (glucose-6-phosphate), KPHS_09830 (hypothetical protein), KPHS_09840 (hypothetical protein),...”
- “...pathways. According to the Database for Annotation, Visualization, and Integrated Discovery (DAVID), KPHS_31180 (pyruvate kinase), KPHS_49540 (gluconate kinase), and KPHS_31750 (6-phosphofructokinase) are functionally related ( 34 , 35 ). KPHS_31180 is associated with pyruvate conversion during glycolysis ( 36 ), and KPHS_51160 is involved in the...”
WP_051299846 gluconokinase from Methylobacter luteus IMV-B-3098
44% identity, 43% coverage
- Enzymes of an alternative pathway of glucose metabolism in obligate methanotrophs
Rozova, Scientific reports 2021 - “...from methanotrophs The genes encoding the gluconate kinase from Mtm. alcaliphilum (CE23379) and Mb. luteus (WP_051299846) were heterologously expressed in E. coli Rosetta (DE3). The recombinant proteins MtmGntK and MbGntK with 6 histidines at the C-terminus were purified by affinity Ni-NTA chromatography. SDS-PAGE of each enzyme...”
GntV / b4268 D-gluconate kinase, thermosensitive (EC 2.7.1.12) from Escherichia coli K-12 substr. MG1655 (see 11 papers)
idnK / P39208 D-gluconate kinase, thermosensitive (EC 2.7.1.12) from Escherichia coli (strain K12) (see 9 papers)
idnK / GB|AAC77225.1 gluconokinase; EC 2.7.1.12 from Escherichia coli K12 (see paper)
P39208 Thermosensitive gluconokinase from Escherichia coli (strain K12)
42% identity, 41% coverage
c5369 Thermosensitive gluconokinase from Escherichia coli CFT073
42% identity, 41% coverage
- Sequence validation of candidates for selectively important genes in sunflower
Chapman, PloS one 2013 - “...0.0162 0.7361 0.8933 0.3601 N c2307 Glyceraldehyde-3-phosphate dehydrogenase 0.0050 0.0055 0.0062 0.8146 0.7105 0.7910 N c5369 S-adenosylmethionine synthetase 0.0111 0.0097 0.0052 0.8648 0.8339 0.7842 N c5456 Vacuolar H+-ATPase subunit A 0.0185 0.0101 0.0054 0.2398 0.3041 0.8800 AVG 0.0160 0.0111 0.0086 D c1357 Pentatricopeptide repeat-containing protein 0.0107...”
t3980 putative gluconokinase from Salmonella enterica subsp. enterica serovar Typhi Ty2
STM3542 gluconate kinase 2 in GNT I system, thermoresistant from Salmonella typhimurium LT2
42% identity, 44% coverage
- Genome-wide Analysis of Salmonella enterica serovar Typhi in Humanized Mice Reveals Key Virulence Features
Karlinsey, Cell host & microbe 2019 - “...carboxylase catalytic subunit 5.45 purH t3455 phosphoribosylaminoimidazolecarboxamide formyltransferase 3.45 purD t3456 phosphoribosylglycineamide synthetase 4.47 gntK t3980 putative gluconokinase 4.24 purA t4417 adenylosuccinate synthetase 3.93 Vi antigen biosynthesis vexE t4344 Vi polysaccharide export protein 4.61 vexD t4345 Vi polysaccharide export inner-membrane protein 5.5 vexC t4346 Vi polysaccharide...”
- Stress response, amino acid biosynthesis and pathogenesis genes expressed in Salmonella enterica colonizing tomato shoot and root surfaces
Han, Heliyon 2020 - “...reflecting nutrient limitations on shoots. The highest increase in transcription (4.4-fold) was detected in gntK (STM3542), which encodes a gluconokinase, specifically an ATP:D-gluconate 6-phosphotransferase in the pentose phosphate pathway, but this value was not significant ( q = 0.02). Tomato colonization induced Se T gene expression...”
- High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach
Allard, BMC genomics 2012 - “...b,c,d,e,f shikimate kinase I yrfI STM3498 SEEM020_01145 C/T T/I 353 b,c,d,e,f heat shock protein gntK STM3542 SEEM020_01330 G/A H/Q 93 a1 1) gluconate transporter GntU, 2) shikimate kinase dppA STM3630 SEEM020_01925 C/T H 282 a1 dipeptide transport protein tolB STM0748 SEEM020_01960 G/T A/S 64 a1 tolB...”
AO090003001003 No description from Aspergillus oryzae RIB40
37% identity, 45% coverage
Entcl_3682 gluconokinase from [Enterobacter] lignolyticus SCF1
41% identity, 39% coverage
- Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
Orellana, PloS one 2017 - “...Phosphogluconate dehydrogenase, EC 1.1.1.44, encoded by Entcl_1664; (29) Gluconokinase, EC 2.7.1.12, encoded by Entcl_0304, and Entcl_3682; (30) Gluconolactonase, EC 3.1.1.17, encoded by Entcl_0174; and (31) 2-dehydro-3-deoxy-phosphogluconate aldolase, EC 4.1.2.14, encoded by Entcl_1940. (DOCX) Click here for additional data file. S2 Fig Optical density measured at 600...”
GCNK_GLUOX / Q5FQ97 Gluconokinase; Gluconate kinase; EC 2.7.1.12 from Gluconobacter oxydans (strain 621H) (Gluconobacter suboxydans) (see paper)
GOX1709 Gluconokinase from Gluconobacter oxydans 621H
43% identity, 43% coverage
- function: Phosphorylates gluconate to 6-phosphogluconate.
catalytic activity: D-gluconate + ATP = 6-phospho-D-gluconate + ADP + H(+) (RHEA:19433)
subunit: Monomer. - Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
Kranz, BMC genomics 2018 - “...glucokinase (GOX1182); gltA , citrate synthase (GOX1999); gnd , 6-phosphogluconate dehydrogenase (GOX1705); gnk , gluconokinase (GOX1709); gno , gluconate 5-dehydrogenase (GOX2187); gpm phosphoglyceromutase (GOX0330); icd , isocitrate dehydrogenase (GOX1336); lpd , dihydrolipoamide dehydrogenase (GOX2292); mqo , malate:quinone oxidoreductase (GOX2070); odhA , 2-oxoglutarate dehydrogenase E1 component (GOX0882);...”
- (13)C Tracers for Glucose Degrading Pathway Discrimination in Gluconobacter oxydans 621H
Ostermann, Metabolites 2015 - “...a gluconate-5-dehydrogenase ( gno , GOX2187), or phosphorylated by a gluconate kinase ( gnk , GOX1709) [ 2 , 16 ]. The metabolite 6-phosphogluconate (6-PG) exclusively serves as a precursor molecule for both intracellular glucose degradation pathways, i.e. , PPP and EDP, and ends up in...”
- Metabolic engineering of Gluconobacter oxydans for improved growth rate and growth yield on glucose by elimination of gluconate formation
Krajewski, Applied and environmental microbiology 2010 - “...completely phosphorylated by gluconate kinase (EC 2.7.1.12; GOX1709) and then metabolized in the pentose phosphate or Entner-Doudoroff pathway. In the strain...”
1ko5A / P46859 Crystal structure of gluconate kinase (see paper)
40% identity, 43% coverage
- Ligand: adenosine-5'-triphosphate (1ko5A)
Entcl_0304 gluconokinase from [Enterobacter] lignolyticus SCF1
42% identity, 41% coverage
- Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
Orellana, PloS one 2017 - “...Entcl_3966; (28) Phosphogluconate dehydrogenase, EC 1.1.1.44, encoded by Entcl_1664; (29) Gluconokinase, EC 2.7.1.12, encoded by Entcl_0304, and Entcl_3682; (30) Gluconolactonase, EC 3.1.1.17, encoded by Entcl_0174; and (31) 2-dehydro-3-deoxy-phosphogluconate aldolase, EC 4.1.2.14, encoded by Entcl_1940. (DOCX) Click here for additional data file. S2 Fig Optical density measured...”
GntK / b3437 D-gluconate kinase, thermostable (EC 2.7.1.12) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
gntK / P46859 D-gluconate kinase, thermostable (EC 2.7.1.12) from Escherichia coli (strain K12) (see 13 papers)
gntK gluconokinase; EC 2.7.1.12 from Escherichia coli K12 (see 2 papers)
P46859 Thermoresistant gluconokinase from Escherichia coli (strain K12)
NP_417894 D-gluconate kinase, thermostable from Escherichia coli str. K-12 substr. MG1655
b3437 gluconokinase 2, thermoresistant from Escherichia coli str. K-12 substr. MG1655
Z4805 gluconate kinase 1 from Escherichia coli O157:H7 EDL933
40% identity, 43% coverage
- Nicotinamide riboside kinase structures reveal new pathways to NAD+
Tempel, PLoS biology 2007 - “...S. cerevisiae Pnp1 (Q05788); S. cerevisiae Qns1 (P38795); S. cerevisiae Urh1 (Q04179); E. coli gntK (P46859); E. coli panK (P0A615); and B. stearothermophilus adk (P27142). The Protein Data Bank (PDB) ( http://www.rcsb.org/pdb ) accession numbers for human Nrk1 are 2QSY, 2QT1, 2QT0, 2QSZ, and 2P0E; for...”
- Functional versatility and molecular diversity of the metabolic map of Escherichia coli
Tsoka, Genome research 2001 - “...OCTAPRENYLTRANSFERASE P18404 PROTOHEME IX FARNESYLTRANSFERASE P46859 THERMORESISTANT GLUCONOKINASE (GLUCONATE KINASE 2) P39208 THERMOSENSITIVE GLUCONOKINASE...”
- 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 - “...c E. coli gluconate kinase encoded by gntK (P46859). d Sheep sorbitol dehydrogenase encoded by sorD (P07846). e G. oxydans gluconate:NADP 5-oxidoreductase...”
- Cloning and molecular genetic characterization of the Escherichia coli gntR, gntK, and gntU genes of GntI, the main system for gluconate metabolism.
Tong, Journal of bacteriology 1996 - GeneRIF: N-terminus verified by Edman degradation on mature peptide
- 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 - “...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 II secretion protein GspH 3.0 UTI89_C3381 gspL Hypothetical type II secretion protein GspL 3.3 UTI89_C3377 hpt Hypoxanthine phosphoribosyltransferase 2.1 b0125 ibaG Acid...”
- Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract
Roos, Infection and immunity 2006 - “...b4013 b2941 b2552 c4141 b1475 b0873 b3240 b3556 b2732 b3437 b3242 b0872 c3046 c3973 c1382 b1445 b0620 c2901 b3241 b1335 Z1954 b1430 b3238 b0849 b0151 fepE ydhC...”
- Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
Segura, BMC genomics 2018 - “...Z3498 glpT Glycerol 3-phosphate transporter 5.65 1.72E-09 3.47 5.41E-04 5.44 8.86E-09 3.71 1.57E-04 4.05 3.23E-05 Z4805 gntK Gluconokinase NDE 2.44 3.04E-04 NDE NDE NDE Z5919 gntP High-affinity gluconate transporter 5.85 5.74E-16 3.17 4.16E-05 NDE NDE NDE Z4770 gntT Gnt-I system high-affinity gluconate transporter NDE 2.52 1.95E-07...”
LKW31_01600 gluconokinase from Pantoea agglomerans
40% identity, 45% coverage
Npun_R5331 carbohydrate kinase from Nostoc punctiforme
39% identity, 42% coverage
YPO3953 putative gluconokinase from Yersinia pestis CO92
41% identity, 42% coverage
APA386B_1158 gluconokinase from Acetobacter pasteurianus 386B
44% identity, 38% coverage
NCU02702 glucokinase from Neurospora crassa OR74A
41% identity, 45% coverage
- Unravelling the molecular basis for light modulated cellulase gene expression - the role of photoreceptors in Neurospora crassa
Schmoll, BMC genomics 2012 - “...VVD40), wc-1 (WC1 28 or WC1 40) and wc-2 (WC2 28 or WC2 40). l6e (NCU02702), a gene encoding a ribosomal protein, was used as control. Analysis was done in triplicates and error bars show standard deviation of these triplicates. Analysis of transcriptional patterns of WT...”
- “...fluorescein (Bio-Rad, Hercules, USA) and the iCycler iQ5 Real-time PCR System (Bio-Rad). The l6e gene (NCU02702; primers: RT_NC_L6eF (5' CAGAAATGGTACCCTGCTGAGG 3') and RT_NC_L6eR (5' GCGGATGGTCTTGCGG 3')) was used as reference gene [ 29 , 92 ]. Primers used for analysis of cbh-1 (NCU07340) were RT_NC_cbh1F (5'...”
HS_0379 gluconokinase (gluconate kinase) from Haemophilus somnus 129PT
36% identity, 43% coverage
BKKJ1_0208 gluconokinase from Bifidobacterium catenulatum subsp. kashiwanohense
44% identity, 39% coverage
- Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal
James, Scientific reports 2019 - “...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 BKKJ1_0341 BKKJ1_0341 aldehyde-alcohol dehydrogenase 2...”
APPSER1_RS09135 gluconokinase from Actinobacillus pleuropneumoniae serovar 1 str. 4074
36% identity, 43% coverage
- The morphology and metabolic changes of Actinobacillus pleuropneumoniae during its growth as a biofilm
Zhang, Veterinary research 2023 - “...metabolism APPSER1_RS05460-APPSER1_RS05465 galT/K galactokinase APPSER1_RS07965-APPSER1_RS07970 mglAC galactose/methyl galactoside ABC transporter APPSER1_RS09115-APPSER1_RS09120 manYZ mannose PTS system APPSER1_RS09135 idnK gluconokinase APPSER1_RS06715-APPSER1_RS06725 malM- APPSER1_RS06720- malK maltose/maltodextrin ABC transporter APPSER1_RS06730, APPSER1_RS06740 malE-malG maltose/maltodextrin ABC transporter APPSER1_RS05415 APPSER1_RS05415 glycosyltransferase APPSER1_RS09220 fucRIKU L-fucose isomerase; L-fuculokinase; L-fucose mutarotase APPSER1_RS09580-APPSER1_RS09605 APPSER1_RS09580- nanEKA-nagBA N-acetylmannosamine kinase;...”
MAP1778c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
46% identity, 39% coverage
- Genomic variations associated with attenuation in Mycobacterium avium subsp. paratuberculosis vaccine strains
Bull, BMC microbiology 2013 - “...Steroid metabolism MAP1774c pncA Isochorismatase Nicotinamide metabolism MAP1775 doxX Unknown MAP1776c Nucleotide phosphokinase-like MAP1777c Unknown MAP1778c aroK Shikimate kinase MAP1779c Phosphotransferase MAP1780c lipT Esterase_lipase Fatty acid Metabolism MAP1781 lppI Lipoprotein MAP1782c p450 cytochrome MAP1783 Transcriptional regulator MAP1784c Lipoprotein MAP1785 IS 900 MAP1786c Dihydropicolinate reductase-like MAP1787c Short...”
ZMO1757 carbohydrate kinase, thermoresistant glucokinase family from Zymomonas mobilis subsp. mobilis ZM4
ZMO_RS07905 gluconokinase from Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
39% identity, 43% 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 - “...ZMO1258 , 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...”
- Transcriptome profiling of Zymomonas mobilis under ethanol stress
He, Biotechnology for biofuels 2012 - “...array experiment ZMO0366 glf 0.92 ZMO0369 glk (glucokinase) 0.86 ZMO0367 zwf 0.79 ZMO1649 gnl 0.34 ZMO1757 gntK 0.48 ZMO1478 pgl 0.67 ZMO0368 edd 0.89 ZMO0997 eda 0.88 ZMO0177 gap 0.97 ZMO0178 pgk 0.8 ZMO1240 gpm 0.91 ZMO1608 eno 0.87 ZMO0152 pyk 0.87 ZMO1496 Ppc 0.64 ZMO1237...”
- “...and coenzyme transport and metabolism showed a down-regulated expression pattern, such as gnl (ZMO1649), gntK (ZMO1757) and ZMO0899 (see Additional file 1 : Table S2). Induction of plasmid encoding genes under ethanol stress Interestingly, 30 genes from ZM4 plasmids were shown to be more abundant (1.0-2.7...”
- Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress
Shabbir, Microbial cell factories 2023 - “...Z. mobilis to acetic acid and furfural stressors. Up-regulated proteins, ZMO_RS00760 (Pgk), ZMO_RS05570 (gpmA), and ZMO_RS07905 (glucokinase) were found only in mutant strain ZM532 in both transcriptomics and proteomics data, while ZMO_RS06615 (pgl) was up-regulated in both strains (Additional file 1 : Tables S7, S8, S9,...”
- “...(EMP) in E. coli or S. cerevisiae [ 96 ]. Up-regulated proteins, Pgk, gpmA, and ZMO_RS07905 (glucokinase) were found only in mutant strain ZM532 in our omics data, while ZMO_RS06615 (pgl) was up-regulated in both strains (Additional file 1 : Tables S7, 8, S9, S10). ZMO_RS03395...”
PMI2673 thermoresistant gluconokinase from Proteus mirabilis HI4320
37% identity, 43% coverage
BAD_RS01050 gluconokinase from Bifidobacterium adolescentis ATCC 15703
42% identity, 42% 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 - “...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 transporter, solutebinding protein 486.74 51.88 BAD_RS08735 3.18 RNA polymerase sigma factor 18.24 2.01 BAD_RS00260 3.01...”
- “...RNAseq Gene no. Log 2 (Fc) Symbol Annotation Linear FMPK value KEGG pathway XOS Xylose BAD_RS01050 3.47 Idnk Shikimate kinase 173.6 15.68 ko01100 BAD_RS07400 2.44 BGAL16 Betagalactosidase 70.88 13.06 ko01100/ko00052/ko00600/ko00511 BAD_RS01040 2.42 gnd 6phosphogluconate dehydrogenase 240.52 45.07 ko01100/ko01110/ko01130/ko01120//ko01200/ko00030/ko00480 BAD_RS08195 2.20 malL Alphaamylase 3,359.55 733.05 ko01100/ko00500/ko00052 BAD_RS02270...”
RHA1_ro02362 probable gluconokinase from Rhodococcus sp. RHA1
42% identity, 42% coverage
- Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis
Gilmore, mBio 2020 - “...41 ). In R. jostii , the ED genes occur in an operon that includes RHA1_ro02362 (a putative gluconokinase) and colinear genes RHA1_ro02367 to -69 (respectively, eda , edd , and zwf , encoding a glucose-6-phosphate dehydrogenase that is part of the SoxR oxidative stress regulon...”
- Nutrient starvation leading to triglyceride accumulation activates the Entner Doudoroff pathway in Rhodococcus jostii RHA1
Juarez, Microbial cell factories 2017 - “...superfamily RHA1_ro06058 610 57,816 95 Possible ATP-dependent protease RHA1_ro06057 1465 128,281 88 Probable 1,3-propanediol dehydrogenase RHA1_ro02362 2544 203,714 80 Probable gluconokinase RHA1_ro02369 2036 105,557 52 Glucose-6-phosphate 1-dehydrogenase RHA1_ro04138 1740 89,076 51 Possible hydratase RHA1_ro02367 2703 133,001 49 KHG/KDPG aldolase RHA1_ro02368 2874 126,594 44 Phosphogluconate dehydratase RHA1_ro06059...”
BCAL3364 putative gluconokinase from Burkholderia cenocepacia J2315
41% identity, 36% coverage
- Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
O'Grady, Frontiers in cellular and infection microbiology 2011 - “...transporter, membrane permease 1.5 BCAL3040 ABC transporter, membrane permease 1.7 BCAL3041 MalE, maltose-binding protein 2.1 BCAL3364 Putative gluconokinase 1.7 BCAM0094 Xylulose kinase 1.7 BCAM1330 Cellulose polysaccharide export protein 1.7 BCAM1333 Cellulose exopolysaccharide acyltransferase 1.6 BCAM1390 Putative aldolase 3.0 BCAM2260 Major facilitator superfamily protein 1.6 BCAS0230 Putative...”
- “...1.74 BCAL3311 Putative exported protein 1.60 BCAL3314 Putative membrane protein 2.43 BCAL3362 Putative oxidoreductase 1.77 BCAL3364 Putative gluconokinase 1.66 BCAL3473 Putative outer membrane porin 1.87 BCAL3486 Putative RNA polymerase sigma factor, sigma-70 1.84 BCAL3490 Putative exported protein 1.96 BCAL3492 Putative exported protein 1.63 BCAM0027 PadR family...”
IDNK / Q5T6J7 gluconokinase monomer (EC 2.7.1.12) from Homo sapiens (see 5 papers)
Q5T6J7 gluconokinase (EC 2.7.1.12) from Homo sapiens (see 4 papers)
36% identity, 43% coverage
- The O-GlcNAc Modification on Kinases
Schwein, ACS chemical biology 2020 - “...Pdgfrb Pdgfr Pdgfr1 Mus musculus S308 P05622 91 Probable gluconokinase IDNK C9orf103 Homo sapiens S125 Q5T6J7 84 Protein kinase superfamily protein At1g73460 T9L24.35 T9L24_35 Arabidopsis thaliana S191/S193 F4HQ88 91 , 94 Putative 3-phosphoinositide-dependent protein kinase 2 PDPK2P PDPK2 Homo sapiens T182 Q6A1A2 84 Pyruvate kinase PKM...”
- No human protein is exempt from bacterial motifs, not even one
Trost, Self/nonself 2010 - “...126 GVDVLIA Q8WXI7 127 VDVLIAT 1 Q6ZND7 ABCB7; ABCBA; Q5T6J7; Q5T6J8 128 DVLIATP 1 Q6ZND7 K. pneumoniae ATP-binding protein: 41 VGTSGSG 1 Q6ZND7 44 SGSGKST 4 45...”
ZPR_2582 carbohydrate kinase, thermoresistant glucokinase family protein from Zunongwangia profunda SM-A87
40% identity, 40% coverage
AFUA_4G12050, Afu4g12050 thermoresistant gluconokinase family protein from Aspergillus fumigatus Af293
37% identity, 44% coverage
- Nitrate assimilation compensates for cell wall biosynthesis in the absence of <i>Aspergillus fumigatus</i> phosphoglucose isomerase
Gong, Applied and environmental microbiology 2024 (secret) - In-host microevolution of Aspergillus fumigatus: A phenotypic and genotypic analysis
Ballard, Fungal genetics and biology : FG & B 2018 - “...AFUA_4G08360 Mediator of RNA polymerase II transcription subunit 8 E188V AFUA_4G09560 ZIP Zinc transporter F125L AFUA_4G12050 Thermoresistant gluconokinase family protein L196V AFUA_5G12440 Cell cycle control protein (Cwf23) A242V AFUA_4G13000 Lysine-specific histone demethylase Aof2 E2D AFUA_4G13800 Exo-alpha-sialidase T214K T214K T214K T214K AFUA_4G14310 Uncharacterised protein A207I V209I A207I...”
- Regulation of Secondary Metabolism by the Velvet Complex Is Temperature-Responsive in Aspergillus
Lind, G3 (Bethesda, Md.) 2016 - “...known Afu4g11980 , Afu4g11990 , Afu4g12000 , Afu4g12010 , Afu4g12020 , Afu4g12030 , Afu4g12040 , Afu4g12050 , Afu4g12060 , Afu4g12070 Inglis et al. (2013) Cluster 20 Trypacidin Afu4g14460 , Afu4g14480 , Afu4g14470 , Afu4g14490 , Afu4g14500 , Afu4g14510 , Afu4g14520 , Afu4g14530 , Afu4g14540 , Afu4g14550...”
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...1.67 [2.27, 1.88] Afu1g06710 2.55 [2.08, 0.69] Afu2g10840 1.81 [1.29, 0.01] Afu6g11810 2.47 [1.61, 0.10] Afu4g12050 1.84 [2.22, 1.62] Afu1g00530 3.55 [1.99, 0.39] Afu4g09700 1.89 [2.21, 1.61] Afu6g07000 3.57 [1.84, 0.71] Afu8g04090 1.91 [2.22, 1.58] Afu1g00460 2.36 [2.16, 0.99] Afu8g04020 1.93 [1.85, 0.71] Afu1g00610 3.99 [1.95,...”
HMPREF0421_20297 gluconokinase from Gardnerella vaginalis ATCC 14019
43% identity, 39% coverage
- Transcriptomic and Proteomic Analysis of Gardnerella vaginalis Responding to Acidic pH and Hydrogen Peroxide Stress
Zhang, Microorganisms 2023 - “...10 118 Ribonuclease HII HMPREF0421_20331 2.40 4.83 10 258 7.35 10 57 Serine/threonine protein kinase HMPREF0421_20297 2.33 8.19 10 91 2.49 10 89 Shikimate kinase HMPREF0421_20303 2.23 5.91 10 212 6.60 10 210 Actinobacterial surface-anchored domain protein HMPREF0421_20209 2.11 5.75 10 224 8.56 10 222 Thiamine...”
- “...reductase HMPREF0421_21364 1.21 0.004129 Response regulator Downregulated HMPREF0421_20893 0.65 0.000724 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...”
VSAL_II0666 gluconokinase from Aliivibrio salmonicida LFI1238
VSAL_II0666 thermosensitive gluconokinase from Vibrio salmonicida LFI1238
34% identity, 42% coverage
FOIG_15767 shikimate kinase from Fusarium odoratissimum NRRL 54006
39% identity, 43% coverage
ABZJ_00529 gluconokinase from Acinetobacter baumannii MDR-ZJ06
32% identity, 43% coverage
- Colistin Resistance in Acinetobacter baumannii MDR-ZJ06 Revealed by a Multiomics Approach
Hua, Frontiers in cellular and infection microbiology 2017 - “...384144338 ABZJ_03092 Zn-dependent hydrolase, including glyoxylase 5 4 15.00 35333.86 8.91 0.62839 0.000407 780 384141775 ABZJ_00529 gluconate kinase 12 4 30.59 18924.48 4.88 0.6352 0.000353 1259 384142716 ABZJ_01470 hypothetical protein 1 1 2.52 36304.38 9.04 0.63588 0.000348 424 384142064 ABZJ_00818 3-oxoacyl-ACP reductase 42 8 45.90 26098.39...”
VP0063 thermoresistant gluconokinase from Vibrio parahaemolyticus RIMD 2210633
37% identity, 38% coverage
- Fis Connects Two Sensory Pathways, Quorum Sensing and Surface Sensing, to Control Motility in Vibrio parahaemolyticus
Tague, Frontiers in microbiology 2021 - “...and 545bp DNA regions upstream of flhA (VP2235-VP2231), lafB (VPA1550-VPA1557), araB (VPA1674), nagB (VPA0038), gntK (VP0063), and scrABC (VPA1513) respectively, were used as inputs for Fis binding. The regulatory regions of qrr1 (193-bp), qrr2 (338-bp), qrr3 (162-bp), qrr4 (287-bp), and qrr5 (177-bp) were also used as...”
- “...probes of P nagB (VPA0038, glucosamine-6-phosphate isomerase, D-glucosamine catabolism), and a138-bp probe of P gntK (VP0063, gluconokinase, D-gluconate catabolism) were used in EMSAs. The EMSA probes were PCR amplified using Phusion Hifidelity Polymerase in 50l reaction mixture using respective primers sets listed in Supplementary Table S2...”
- Loss of sigma factor RpoN increases intestinal colonization of Vibrio parahaemolyticus in an adult mouse model
Whitaker, Infection and immunity 2014 - “...represent the expression of the gluconokinase (VP0063), ribokinase (VPA1083), ribulokinase (VP1674), and mannose-6phosphate isomerase (VPA1425) normalized to...”
- “...the expression patterns of genes encoding gluconokinase (VP0063), ribokinase (VPA1083), Vibrio Colonization February 2014 Volume 82 Number 2 fliAP, and fliAP...”
VC0287 thermoresistant gluconokinase from Vibrio cholerae O1 biovar eltor str. N16961
36% identity, 38% coverage
Q32PY9 Probable gluconokinase from Rattus norvegicus
41% identity, 36% coverage
JHW33_RS05130 gluconokinase from Rahnella aceris
39% identity, 43% coverage
- Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium
Xu, Frontiers in microbiology 2022 - “...synthase JHW33_RS14905 WP_200223138.1 WP_119262163.1 99 WP_013577391.1 99 WP_013577391.1 99 WP_015699022.1 96 ED Pathway gntk gluconokinase JHW33_RS05130 WP_200225227.1 WP_015689980.1 99 WP_015689980.1 99 WP_015689980.1 98 WP_013573544.1 52 edd phosphogluconate dehydratase JHW33_RS05140 WP_200225228.1 WP_119261688.1 99 WP_015689978.1 99 WP_013575660.1 99 WP_015697147.1 95 eda bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase JHW33_RS05145 WP_037035690.1 WP_013575316.1...”
AT2G16790 shikimate kinase family protein from Arabidopsis thaliana
34% identity, 44% coverage
BPHYT_RS16720 Gluconokinase (EC 2.7.1.12) from Burkholderia phytofirmans PsJN
38% identity, 42% coverage
- mutant phenotype: Specifically important for utilizing D-Gluconic Acid sodium salt. Automated validation from mutant phenotype: the predicted function (GLUCONOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
Sde_0904 gluconokinase from Saccharophagus degradans 2-40
37% identity, 40% coverage
AFUA_1G00530, Afu1g00530 thermoresistant gluconokinase family protein from Aspergillus fumigatus Af293
38% identity, 37% coverage
- Transcript levels of the Aspergillus fumigatus Cdc42 module, polarisome, and septin genes show little change from dormancy to polarity establishment
Oda, Medical mycology 2017 - “...fumigatus annotation log2 Afu2g15440 Afu8g01710 Afu1g00530 Afu5g13020 Afu7g00920 Afu5g14210 Afu3g08990 Afu4g04270 Afu6g11130 Afu5g02520 Afu3g14010 Afu2g10020...”
- Transcriptome and biochemical analysis reveals that suppression of GPI-anchor synthesis leads to autophagy and possible necroptosis in Aspergillus fumigatus
Yan, PloS one 2013 - “...calcium/calmodulin dependent protein kinase 2.1 AFUA_1G04920 calmodulin-binding protein Sha1 1.5 AFUA_3G07050 WSC domain protein/Wsc2 1.5 AFUA_1G00530 thermoresistant gluconokinase family protein 7.4 AFUA_6G10240 sensor histidine kinase/response regulatorFos-1/TcsA 2.3 AFUA_8G06140 sensor histidine kinase/response regulator 2.0 AFUA_2G08470 GTP binding protein (Bud4) 1.6 AFUA_7G03720 serine/threonine protein kinase (Kin28) 1.9 AFUA_4G14740...”
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...2.55 [2.08, 0.69] Afu2g10840 1.81 [1.29, 0.01] Afu6g11810 2.47 [1.61, 0.10] Afu4g12050 1.84 [2.22, 1.62] Afu1g00530 3.55 [1.99, 0.39] Afu4g09700 1.89 [2.21, 1.61] Afu6g07000 3.57 [1.84, 0.71] Afu8g04090 1.91 [2.22, 1.58] Afu1g00460 2.36 [2.16, 0.99] Afu8g04020 1.93 [1.85, 0.71] Afu1g00610 3.99 [1.95, 0.88] Afu3g01560 1.93 [2.22,...”
NCU07626 thermoresistant gluconokinase from Neurospora crassa OR74A
40% identity, 39% coverage
- mus-52 disruption and metabolic regulation in Neurospora crassa: Transcriptional responses to extracellular phosphate availability
Martins, PloS one 2018 - “...fold change = 4.64). In high-Pi condition, the most down-regulated DEG was the thermoresistant gluconokinase (NCU07626; log2 fold change = 4.48), ( Fig 4 and S4 Table ). Another specific down-regulated kinase was CK-1a (NCU00685), which is part of the oscillator core of N . crassa...”
- Cellobionic acid utilization: from Neurospora crassa to Saccharomyces cerevisiae
Li, Biotechnology for biofuels 2015 - “...pathway to function. To test this hypothesis, gluconokinases from S. cerevisiae (YDR248C) and N. crassa (NCU07626) were purified and tested for activity in vitro. In comparison to YDR248C, N. crassa gluconokinase (GnK, hereafter) was capable of converting more gluconic acid to 6-phosphogluconate at all enzyme concentrations...”
- “...expressing CBT-1 and CAP. b In vitro assays of the purified gluconokinases from N. crassa (NCU07626, GnK) and S. cerevisiae (YDR248C). c Aerobic cellobionic acid consumption of S. cerevisiae expressing CBT-1, CAP and GnK. d Anaerobic cellobionic acid consumption of S. cerevisiae expressing CBT-1, CAP and...”
BPSL2929 putative thermoresistant gluconokinase from Burkholderia pseudomallei K96243
38% identity, 36% coverage
CNAG_03048 gluconokinase from Cryptococcus neoformans var. grubii H99
34% identity, 43% coverage
GNTK_YEAST / Q03786 Probable gluconokinase; Gluconate kinase; EC 2.7.1.12 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
YDR248C Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm from Saccharomyces cerevisiae
36% identity, 37% coverage
- catalytic activity: D-gluconate + ATP = 6-phospho-D-gluconate + ADP + H(+) (RHEA:19433)
- Development of a genome scale metabolic model for the lager hybrid yeastS. pastorianusto understand evolution of metabolic pathways in industrial settings
Timouma, 2023 - Saccharomyces cerevisiae employs complex regulation strategies to tolerate low pH stress during ethanol production
Wu, Microbial cell factories 2022 - “...metabolism were differentially expressed, including FBP1 , ERR1 // 2 // 3 , SOL4 , YDR248C , IDP2 , CIT3 , PDC5 , ADH2 , ALD3, and ALD4 . Fig. 7 DEGs involved in the central carbon metabolism. Green, blue, and red backgrounds indicated groups B3...”
- Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina
Čadež, PloS one 2019 - “...6-phosphogluconate dehydrogenase encoded by GND1 , and gluconokinase which might be encoded by the ORF YDR248C . We found that, even though it cannot consume the carbon source, H . gamundiae has homologs of all four genes that are thought to be essential for the growth...”
- Dosage Mutator Genes in Saccharomyces cerevisiae: A Novel Mutator Mode-of-Action of the Mph1 DNA Helicase
Ang, Genetics 2016 - “...SPT5 YHR041C SRB2 YGL097W SRM1 YLR005W SSL1 YCR042C TAF2 YOL006C TOP1 YJL197W UBP12 YIL017C VID28 YDR248C YDR248C YGR126W YGR126W YHR122W YHR122W YMR167W MLH1 Prior to this work, MLH1 was the only previously known dmutator gene ( Shcherbakova and Kunkel 1999 ). Since it was not in...”
- Cellobionic acid utilization: from Neurospora crassa to Saccharomyces cerevisiae
Li, Biotechnology for biofuels 2015 - “...Pgm1 in yeast), we hypothesized that the activity of the putative endogenous S. cerevisiae gluconokinase (YDR248C) responsible for converting gluconic acid to 6-phosphogluconate was limited, resulting in the failure of the cellobionic acid consumption pathway to function. To test this hypothesis, gluconokinases from S. cerevisiae (YDR248C)...”
- “...and N. crassa (NCU07626) were purified and tested for activity in vitro. In comparison to YDR248C, N. crassa gluconokinase (GnK, hereafter) was capable of converting more gluconic acid to 6-phosphogluconate at all enzyme concentrations tested (Fig. 5 b). When GnK was co-expressed along with CBT-1 and...”
- Deletion of PHO13, encoding haloacid dehalogenase type IIA phosphatase, results in upregulation of the pentose phosphate pathway in Saccharomyces cerevisiae
Kim, Applied and environmental microbiology 2015 - “...5.3 Glyoxylate reductase YEF1 2.6 13.8 ATP-NADH kinase YDR248C 4.3 YHR182C-A 6.0 YLR152C 4.4 4.9 16.6 6.0 Putative gluconokinase Transposable element gene...”
- ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion
Zhang, Nucleic acids research 2015 - “...in response to growth stimuli and environmental stresses ( 66 ). RAP1 also directly regulates YDR248C in the pentose phosphate pathway (Figure 7 ). The protein product of PUT3 , with rewired links to the proline metabolism pathway, activates PUT1 and PUT2 which encode enzymes of...”
- Molecular determinants and genetic modifiers of aggregation and toxicity for the ALS disease protein FUS/TLS
Sun, PLoS biology 2011 - “...putative transcription factor that may interact with proteins involved in histone acetylation or deacetylation Enhancer YDR248C C9orf103 Putative protein of unknown function Enhancer YER128W Putative protein of unknown function Enhancer YLR218C Protein that localizes to the mitochondrial intermembrane space Discussion We have established a pure protein...”
- More
Ac3H11_3228 gluconate TRAP transporter, small permease component from Acidovorax sp. GW101-3H11
40% identity, 38% coverage
- mutant phenotype: Specifically important for gluconate utilization
NMA0412 putative glucokinase from Neisseria meningitidis Z2491
40% identity, 34% coverage
RR42_RS06130 Gluconokinase (EC 2.7.1.12) from Cupriavidus basilensis FW507-4G11
37% identity, 43% coverage
- mutant phenotype: Specifically important for utilizing D-Gluconic Acid sodium salt. Automated validation from mutant phenotype: the predicted function (GLUCONOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
AO090009000033 No description from Aspergillus oryzae RIB40
35% identity, 17% coverage
PFICI_12508 uncharacterized protein from Pestalotiopsis fici W106-1
33% identity, 13% coverage
- Characterization of a NRPS-like Protein from Pestalotiopsis fici for Aldehyde Generation
Li, Journal of fungi (Basel, Switzerland) 2022 - “...in thirteen enzymes, including PFICI_01589, PFICI_00364, PFICI_05312, PFICI_05398, PFICI_06834, PFICI_08544, PFICI_08738, PFICI_10568, PFICI_11160, PFICI_11332, PFICI_11756, PFICI_12508 and PFICI_12763. However, neither biosynthetic nor biochemical investigation was reported for these thirteen CARs [ 23 , 28 ]. Hence, we carried out a sequence comparison among these 84 CARs...”
TC 2.A.56.1.9 / R4JRJ8 TRAP transporter DctQ subunit, component of The possible disulfide 3,3'-dithiodipropionic acid (DTDP) tripartite transporter, DctMPQ from Advenella mimigardefordensis DPN7
37% identity, 31% coverage
- substrates: D-fuconate, D-galactonate, D-glucoonate, D-xylonate, L-arabonate
tcdb comment: More probably takes up an array of oxidized sugar onic acids, D-gluconate, D-galactonate, L-arabonate, D-fuconate and D-xylonate. The sugars are oxidized by a broad-range, membrane bound sogar oxidase. The acids that have been studied kineticall have Kms between 8 and 15 μM (Meinert et al. 2017; )
P44994 Putative TRAP transporter small permease protein HI_1030 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI1030 conserved hypothetical transmembrane protein from Haemophilus influenzae Rd KW20
29% identity, 33% coverage
PM1254 unknown from Pasteurella multocida subsp. multocida str. Pm70
28% identity, 39% coverage
STM14_4428 2,3-diketo-L-gulonate TRAP transporter small permease YiaM from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM3671 putative transporter from Salmonella typhimurium LT2
28% identity, 39% coverage
- Integrative DNA methylome and transcriptome analysis reveals DNA adenine methylation is involved in Salmonella enterica Typhimurium response to oxidative stress
Zhang, Microbiology spectrum 2023 - “...Putative acetyltransferase STM14_4426 yiaL 0.87 0.0012 Putative cytoplasmic protein STM14_4427 0.93 0.0023 Putative chemotaxis protein STM14_4428 yiaM 0.80 0.029 2,3-Diketo- L -gulonate TRAP transporter small permease STM14_4429 yiaN 0.89 0.0078 Hypothetical protein STM14_4429 STM14_4430 yiaO 0.76 0.048 Putative periplasmic dicarboxylate-binding protein STM14_4431 lyxK 0.88 0.0084 L...”
- Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
Seif, Nature communications 2018 - “...allantoin STM0974 ( focA ) Formate transport via proton symport (C-O2+) Formate AND (C-O2-) formaldehyde STM3671 ( yiaM ) l -xylulose transport in via proton symport (C-O2+/) l -Xylulose STM2282 ( glpQ ) Glycerophosphodiester phosphodiesterase (C-O2+/, P-O2+/) Sn-Glycero-3-phosphocholine STM2037 ( pduF ) (R)-Propane-1,2-diol facilitated transport (C-O2+)...”
- Salmonella enterica serovar typhimurium colonizing the lumen of the chicken intestine grows slowly and upregulates a unique set of virulence and metabolism genes
Harvey, Infection and immunity 2011 - “...STM4298 STM3674 STM3675 STM0018 STM1560 STM3254 STM3671 otsA melA lyxK sgbH Trehalose-6-phosphate synthase -Galactosidase L-Xylulose kinase Putative...”
- Salmonella serovar identification using PCR-based detection of gene presence and absence
Arrach, Journal of clinical microbiology 2008 - “...STM3034, STM3125, STM3358, STM3546, STM3652, STM3653, STM3671, STM3771, STM3859, STM4066, STM4206, STM4215, STM4218, STM4447, STM4483, STM4498, STM4528,...”
SMa0249 conserved hypothetical protein from Sinorhizobium meliloti 1021
35% identity, 27% coverage
HI0051 conserved hypothetical transmembrane protein from Haemophilus influenzae Rd KW20
P44484 Putative TRAP transporter small permease protein HI_0051 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
22% identity, 40% coverage
NGR_b22590 TRAP transporter small permease from Sinorhizobium fredii NGR234
38% identity, 28% coverage
NGR_b22590 putative C4-dicarboxylate transport system, permease protein from Rhizobium sp. NGR234
38% identity, 28% coverage
YiaM / b3577 2,3-diketo-L-gulonate:Na+ symporter - membrane subunit from Escherichia coli K-12 substr. MG1655 (see 3 papers)
yiaM / P37674 2,3-diketo-L-gulonate:Na+ symporter - membrane subunit from Escherichia coli (strain K12) (see 2 papers)
YIAM_ECOLI / P37674 2,3-diketo-L-gulonate TRAP transporter small permease protein YiaM from Escherichia coli (strain K12) (see paper)
TC 2.A.56.1.2 / P37674 YiaM, component of The 2,3-diketo-L-gulonate (2,3-DKG) transporter, YiaMNO [2,3-KDG is a breakdown product of L-ascorbate] from Escherichia coli (see 7 papers)
b3577 predicted transporter from Escherichia coli str. K-12 substr. MG1655
NP_418034 2,3-diketo-L-gulonate:Na(+) symporter - membrane subunit from Escherichia coli str. K-12 substr. MG1655
27% identity, 38% coverage
- function: Part of the tripartite ATP-independent periplasmic (TRAP) transport system YiaMNO involved in the uptake of 2,3-diketo-L- gulonate.
subunit: The complex comprises the extracytoplasmic solute receptor protein YiaO, and the two transmembrane proteins YiaM and YiaN - substrates: 2,3-diketo-L-gulonate
- Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022)
González, Journal of bacteriology 2006 - “...aceA glpA b1137 b3926 b1145 b3927 b4014 b4015 b2241 yiaM b3577 ymfG ymfJ b1146 ymfL ppdD pyrL caiT intE ykfG arp yzgL yncH mcrA b1141 b1144 b1146 b1147 b0108...”
- Identification of genomic features using microsyntenies of domains: domain teams
Pasek, Genome research 2005 - “...3-isopropylmalate dehydratase large subunit* H. influenzae b3577 DctQ E=2.4 Hypothetical protein* E. coli b2678 (proW) BPD_transp_1 Glycine betaine/L-proline...”
- Deletion of the yiaMNO transporter genes affects the growth characteristics of Escherichia coli K-12.
Plantinga, Microbiology (Reading, England) 2005 (PubMed)- GeneRIF: Deletion of the yiaMNO genes in E. coli K-12 strain MC4100 resulted in remarkable changes in the transition from exponential growth to the stationary phase, high-salt survival and biofilm formation.
- Word-based GWAS harnesses the rich potential of genomic data for E. coli quinolone resistance
Malekian, Frontiers in microbiology 2023 - “...P00350), or an essential catalytic domain for the cheA (UniProt ID P07363), yiaM (UniProt ID P37674), and cheZ (UniProt ID P0A9H9) genes. For a full list of genes that contain joint mutations, refer to Table 1 . For further details on unitigs that contain such mutations,...”
- Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli
Jindal, BMC microbiology 2019 - “...affect the uptake of Sybr Green Gene Comments Uniprot ID Representative reference(s) yiaM 2,3-diketo-L-gulonate transporter P37674 (none) setC Putative sugar efflux system B7L779 [ 159 ] tsgA Uncharacterised transporter P60778 (none) yhjV Uncharacterised transporter P37660 [ 160 ] yggT Unknown transporter involved in osmotolerance P64564 [...”
BP1918 putative membrane protein from Bordetella pertussis Tohama I
29% identity, 32% coverage
Asuc_0270 Tripartite ATP-independent periplasmic transporter DctQ component from Actinobacillus succinogenes 130Z
24% identity, 36% coverage
- Transcriptome analysis and anaerobic C4 -dicarboxylate transport in Actinobacillus succinogenes
Rhie, MicrobiologyOpen 2018 - “...Asuc_0158 DctP (SBP) 19 5 21 11 1.572 .145 0.741 .463 0.027 .979 0.857 .414 Asuc_0270 DctQ 77 87 88 33 0.096 .921 1.331 .172 0.188 .846 1.252 .196 Asuc_0271 DctM 80 144 90 51 0.751 .425 0.818 .384 0.136 .885 1.447 .127 Asuc_0272 DctP (SBP)...”
- “...three potential C 4 dicarboxylate transporters, Asuc_0272 (TRAP family, clustered with three other subunit genes, Asuc_0270, Asuc_0271, and Asuc_0273), Asuc_0304 (divalent anionsodium symporter (DASS) family), and Asuc_1999 (C4dicarboxylate uptake (Dcu) family) were designated as CE transporters (Table 1 , Figure 4 ). Among the three, the...”
WP_060798477 TRAP transporter large permease subunit from Fusobacterium nucleatum
27% identity, 17% coverage
- Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter
Currie, eLife 2024 - “...( Hs , WP_249962964), Aggregatibacter actinomycetemcomitans ( Aa , WP_005592763), Fusobacterium nucleatum ( Fn , WP_060798477), Photobacterium profundum ( Pp , WP_011218955/WP_011218954), Vibrio vulnificus ( Vv , WP_001889698/WP_000233105), and Vibrio cholerae ( Vc , WP_011081661/BAC97226) were aligned with TRAP-QM protein sequences from Desulfovibrio alaskensis ( Da...”
Q5T6J8 gluconokinase from Homo sapiens
49% identity, 13% coverage
Q9KQS0 C4-dicarboxylate TRAP transporter small permease protein DctQ from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
VC1928 C4-dicarboxylate transport protein DctQ, putative from Vibrio cholerae O1 biovar eltor str. N16961
28% identity, 30% coverage
WP_033060252 TRAP transporter large permease subunit from Pseudomonas mandelii PD30
27% identity, 23% coverage
- Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter
Currie, eLife 2024 - “...( Bj , WP_248883330), Virgibacillus massiliensis ( Vm , WP_051739028), Pseudomonas mandelii ( Pm , WP_033060252), Bradyrhizobium sp. BTAi1 ( Bsp ., WP_011942649/WP_011942650), Xanthobacter autotrophicus ( Xa , ABS68596/ABS68595), Polaromonas sp. JS666 ( Psp ., WP_011482802/WP_011482801), Verminephrobacter eiseniae ( Ve , ABM59662/WP_011811650), Anaerococcus prevotii ( Ap...”
VC_1928 TRAP transporter small permease from Vibrio cholerae O1 biovar El Tor str. N16961
30% identity, 30% coverage
- Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae.
Mukherjee, Genomics discovery 2014 - “...transporter VC_1448 Q9KS14 Uncharacterized protein similar to VCA0109 VC_A0109 Q9KN56 C4-dicarboxylate transport protein DctQ, putative VC_1928 Q9KQS0 Trk system potassium uptake protein VC_0042 Q9KVU7 PTS system, cellobiose-specific IIC component VC_1282 Q9KSH4 Multidrug resistance protein VceB VC_1411 Q9KS49 Iron(III) compound receptor VC_0200 Q9KVE6 Sugar transporter family protein...”
Pden_1646 Tripartite ATP-independent periplasmic transporter, DctQ component from Paracoccus denitrificans PD1222
27% identity, 38% coverage
HF298_RS12835 TRAP transporter small permease from Vibrio parahaemolyticus
26% identity, 30% coverage
VP_RS04435, WU75_21765 TRAP transporter small permease from Vibrio parahaemolyticus RIMD 2210633
26% identity, 30% coverage
- Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn
Tang, Foods (Basel, Switzerland) 2023 - “...transporter WU75_01920 mcp 0.32 Chemotaxis protein WU75_21745 dctB 0.352 ATPase WU75_10200 phoA 0.353 Alkaline phosphatase WU75_21765 dctQ 0.368 C4-dicarboxylate ABC transporter permease WU75_00210 dctD 0.406 C4-dicarboxylate ABC transporter WU75_16210 qseC 0.423 Histidine kinase WU75_23015 fliC 0.435 Flagellin WU75_07100 mcp 0.453 Chemotaxis protein WU75_13380 crp 0.457 Transcriptional...”
- Comparative Transcriptome Analysis Reveals Regulatory Factors Involved in Vibrio Parahaemolyticus Biofilm Formation
Wang, Frontiers in cellular and infection microbiology 2022 - “...subunit I VP_RS22155 5.10 phosphate ABC transporter substrate-binding protein VP_RS04430 4.66 TRAP transporter substrate-binding protein VP_RS04435 4.13 TRAP transporter small permease VP_RS15995 3.98 response regulator transcription factor ompR 3.40 two-component system response regulator OmpR VP_RS20550 3.07 thiolase family protein VP_RS22100 2.93 methyl-accepting chemotaxis protein VP_RS10510 2.92...”
- “...is speculated that MCP interacts with flagellin to affect bacterial attachment and clustering. VP_RS04430 and VP_RS04435 were upregulated by about 4.66 and 4.13, and their encoded proteins are TRAP transporter protein substrate binding protein and TRAP transporter protein small permease, which use ion electrochemical gradients to...”
Asuc_0367 Tripartite ATP-independent periplasmic transporter DctQ component from Actinobacillus succinogenes 130Z
29% identity, 21% coverage
BTH_I1952 adenylylsulfate kinase from Burkholderia thailandensis E264
31% identity, 30% 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