PaperBLAST
PaperBLAST Hits for reanno::Btheta:352331 ribokinase (EC 2.7.1.15) (Bacteroides thetaiotaomicron VPI-5482) (311 a.a., MKVVVIGSSN...)
Show query sequence
>reanno::Btheta:352331 ribokinase (EC 2.7.1.15) (Bacteroides thetaiotaomicron VPI-5482)
MKVVVIGSSNIDMVAQVNHLPAPGETVGDASFMQSLGGKGANQAVAAARLGGSVTFITSL
GNDMYAEILKKHFKKEGITTDYIIDDVNQPTGTALIFVADSGENCIAVAPGANYSLLPGS
IIHFSKVIDEADIIVMQAEIPYETIKRIALLAKQKGKKVLFNPAPACLIDEELMKAIDIL
VVNELEAAFISGIEYTGNNLEEIALSLLQAGARNAVITLGSQGVYMKNDKEIIQLPGYKV
NAIDTIAAGDTFCGALAVICAQREIDRDALSFANAAAAIAVTRSGAQPSIPTLDEVKHFM
LEKELALSFNF
Running BLASTp...
Found 250 similar proteins in the literature:
BT2804 ribokinase (EC 2.7.1.15) from Bacteroides thetaiotaomicron VPI-5482
BT2804 ribokinase from Bacteroides thetaiotaomicron VPI-5482
BT_2804, BT_RS14220 ribokinase from Bacteroides thetaiotaomicron VPI-5482
100% identity, 100% coverage
- mutant phenotype: Specifically important in carbon source D-Ribose. An adjacent protein (BT2803) is also expected to be a ribokinase and is also required. It is not clear why both proteins are required.
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...transporters ExbD, MotA/TolQ/ExbB proton channel family protein 6.4 to 4.5 0 to 4E-08 rbsK, BT_RS14220 BT2804, BT_2804 Ribokinase, TonB-dependent receptor, RagB/SusD family nutrient uptake outer memb. protein, DUF4969 domain-containing protein, nucleoside hydrolase, multidrug DMT transporter permease 4.2 0.352 BT_RS14270 BT2814 Dihydrodipicolinate synthase family protein 11 0.107...”
- “...BT3344 to BT3347, BT3087 to BT3090, BT3045 to BT3047, BT3024 to BT3028, BT3012 to BT3016, BT2804 to BT2809, BT2614 to BT2632, BT2392 to BT2395, BT1280 to BT1285, BT1046 to BT1047, BT0438 to BT0440, BT0360 to BT0365, and BT0317 to BT0318) were downregulated ( Table6 ). Finally,...”
- Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments
Liu, Cell reports 2021 - “...on D-ribose, in particular a hypothetical protein (BT2802; fitness, 4.3), two predicted ribokinases (BT2803 and BT2804), and a sugar transporter (BT2809) ( Figure 3D ). The SusCD homologs in this cluster were also mildly important on D-ribose (BT2805 fitness, 1.3; BT2806 fitness, 1.4). Finally, a putative...”
- Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis
Wurster, Cell reports 2021 - “...BT42964298, BT3025, BT1761, and BT1762) and sugar import systems for fructose (BT17591763, and BT1759), ribose (BT2804), and fucose (BT3665) ( Figure 6D ; Table S5 ) only in HG mice ( Figure 6D ; Table S5 ; Lynch and Sonnenburg, 2012 ; Mardo et al., 2017...”
- A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner
Glowacki, Cell host & microbe 2020 - “...using the pETite N-His vector (Lucigen). PCR primers were designed to amplify products for BT2803, BT2804, BT2807 and BT2808 containing all amino acids for BT2804 residues 1-311, or all amino acids downstream of the predicted signal peptide sequences, residues 22-539 for BT2807 and residues 22-338 for...”
- “...according to manufactures protocol (Lucigen, Expresso T7 cloning and expression system). pETite plasmids containing BT2803, BT2804, or BT2807 were transformed into E. coli strains TUNER or for BT2808 into BL21-AI rihABC + pLysS. A single colony was grown in 5 mL of LB+Kan 50 for 16h....”
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...ExbD, MotA/TolQ/ExbB proton channel family protein 6.4 to 4.5 0 to 4E-08 rbsK, BT_RS14220 BT2804, BT_2804 Ribokinase, TonB-dependent receptor, RagB/SusD family nutrient uptake outer memb. protein, DUF4969 domain-containing protein, nucleoside hydrolase, multidrug DMT transporter permease 4.2 0.352 BT_RS14270 BT2814 Dihydrodipicolinate synthase family protein 11 0.107 BT_RS14485...”
- “...biopolymer transporters ExbD, MotA/TolQ/ExbB proton channel family protein 6.4 to 4.5 0 to 4E-08 rbsK, BT_RS14220 BT2804, BT_2804 Ribokinase, TonB-dependent receptor, RagB/SusD family nutrient uptake outer memb. protein, DUF4969 domain-containing protein, nucleoside hydrolase, multidrug DMT transporter permease 4.2 0.352 BT_RS14270 BT2814 Dihydrodipicolinate synthase family protein 11...”
BXY_19520 ribokinase from Bacteroides xylanisolvens XB1A
45% identity, 95% coverage
- Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis
Despres, BMC genomics 2016 - “...them belong to PUL 12 (BXY_14320 to BXY_14380) possibly targeting inulin-type fructans and PUL 18 (BXY_19520 to BXY_19610; unknown substrate). Among the 74 PULs predicted from genome analysis [ 24 ], 20 PULs were more or less up-regulated on citrus pectin (result based on the average...”
- “...repressed genes (Additional file 1 : Figure S1) and they mainly belonged to PUL 18 (BXY_19520 to BXY_19610) and 65 (BXY_42670 to BXY_42750) whose functions are unknown. From these RNA-seq data, contamination of apple pectin with starch was suspected and eventually confirmed by analyzing the composition...”
BT2803 ribokinase (EC 2.7.1.15) from Bacteroides thetaiotaomicron VPI-5482
BT2803 ribokinase from Bacteroides thetaiotaomicron VPI-5482
46% identity, 92% coverage
- mutant phenotype: Specifically important in carbon source D-Ribose. An adjacent protein (BT2804) is also expected to be a ribokinase and is also required. It is not clear why both proteins are required.
- Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments
Liu, Cell reports 2021 - “...for growth on D-ribose, in particular a hypothetical protein (BT2802; fitness, 4.3), two predicted ribokinases (BT2803 and BT2804), and a sugar transporter (BT2809) ( Figure 3D ). The SusCD homologs in this cluster were also mildly important on D-ribose (BT2805 fitness, 1.3; BT2806 fitness, 1.4). Finally,...”
- A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner
Glowacki, Cell host & microbe 2020 - “...accomplished using the pETite N-His vector (Lucigen). PCR primers were designed to amplify products for BT2803, BT2804, BT2807 and BT2808 containing all amino acids for BT2804 residues 1-311, or all amino acids downstream of the predicted signal peptide sequences, residues 22-539 for BT2807 and residues 22-338...”
- “...cells according to manufactures protocol (Lucigen, Expresso T7 cloning and expression system). pETite plasmids containing BT2803, BT2804, or BT2807 were transformed into E. coli strains TUNER or for BT2808 into BL21-AI rihABC + pLysS. A single colony was grown in 5 mL of LB+Kan 50 for...”
QT17_05185 ribokinase from Thermus sp. 2.9
42% identity, 97% coverage
- Multi-Enzymatic Cascades in the Synthesis of Modified Nucleosides: Comparison of the Thermophilic and Mesophilic Pathways
Fateev, Biomolecules 2021 - “...nucleosides, we previously obtained and described ribokinase from Thermus species 2.9 ( T spRK, gene QT17_05185) [ 23 ], purine nucleoside phosphorylases from Thermus thermophilus HB27 ( Tth PNPI, gene TT_RS05405, and Tth PNPII, gene TT_RS00985) [ 24 ]. The synthesis of natural nucleosides using various...”
- “...PNP, gene AAA24401) [ 29 ], ribokinase from Thermus species 2.9 ( T spRK, gene QT17_05185) [ 23 ], purine nucleoside phosphorylases from Thermus thermophilus HB27 ( Tth PNPI, gene TT_RS05405, and Tth PNPII, gene TT_RS00985) [ 24 ]. Using the protocols described in their respective...”
- A Cascade of Thermophilic Enzymes As an Approach to the Synthesis of Modified Nucleotides
Esipov, Acta naturae 2016 - “...the Thermus thermophilus HB27 strain by a polymerase chain reaction (PCR) using synthetic primers. The QT17_05185 gene encoding RK from Thermus sp. 2.9 was codon-optimized for expression in Escherichia coli and synthesized by a chemical and enzymatic method from overlapping oligonucleotides. All genes were cloned into...”
- “...PRPP-synthetases, and APR-transferase from T. thermophilus ) and an investigation of their substrate properties The QT17_05185 gene encoding RK from Thermus sp. 2.9 was generated by a chemical-enzymatic method. Genes TT_RS05985, TT_RS06430, and TT_RS06315 encoding Tth PRPPS1, Tth PRPPS2, and Tth APRT from T. thermophilus HB27,...”
8cqxA / A0A0B0SD75 Ribokinase from t.Sp mutant a92g
42% identity, 96% coverage
- Ligands: adenosine-5'-diphosphate; magnesium ion (8cqxA)
PMCN03_1092 ribokinase from Pasteurella multocida subsp. multocida str. HB03
42% identity, 96% coverage
Pf1N1B4_6031 Ribokinase (EC 2.7.1.15) from Pseudomonas fluorescens FW300-N1B4
43% identity, 96% coverage
- mutant phenotype: Specifically important for utilizing D-Ribose. Automated validation from mutant phenotype: the predicted function (RIBOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
AO353_20835 Ribokinase (EC 2.7.1.15) from Pseudomonas fluorescens FW300-N2E3
42% identity, 96% coverage
- mutant phenotype: Specifically important for utilizing D-Ribose. Automated validation from mutant phenotype: the predicted function (RIBOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
CPE1632 ribokinase from Clostridium perfringens str. 13
41% identity, 95% coverage
PFLU_4156 ribokinase from Pseudomonas [fluorescens] SBW25
42% identity, 96% coverage
VIBHAR_06142 ribokinase from Vibrio harveyi ATCC BAA-1116
42% identity, 97% coverage
HI0505 ribokinase (rbsK) from Haemophilus influenzae Rd KW20
P44331 Ribokinase from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
40% identity, 96% coverage
A0A0H2UL04 ribokinase (EC 2.7.1.15) from Vibrio cholerae (see paper)
43% identity, 97% coverage
4xckA / A0A0H2UL04 Vibrio cholerae o395 ribokinase complexed with adp, ribose and cesium ion. (see paper)
VCA0131 ribokinase from Vibrio cholerae O1 biovar eltor str. N16961
43% identity, 97% coverage
SA0258 probable ribokinase from Staphylococcus aureus subsp. aureus N315
41% identity, 95% coverage
- Deciphering the activation and recognition mechanisms of Staphylococcus aureus response regulator ArlR
Ouyang, Nucleic acids research 2019 - “...was ATAGCATATTTATATGCAAT, which is within 40 bp of hypothetical protein SA0257 and probable ribokinase rbsK SA0258, genes shown to be downregulated in biofilm formation and close to other genes shown to be downregulated by ArlR (SA0252 and SA0253) ( 40 , 42 ). Crystal structures of...”
- Exposure of clinical MRSA heterogeneous strains to β-lactams redirects metabolism to optimize energy production through the TCA cycle
Keaton, PloS one 2013 - “...strains SA13011-HoR vs . SA13011-HeR. ORF Gene Fold change Name Description Carbohydrate transport and metabolism SA0258 rbsK 3.7 ribokinase Catalyses the phosphorylation of ribose to ribose-5-P SA0259 rbsD 5.3 D-ribose pyranase Catalyzes the conversion between beta-pyran and beta-furan forms of D-ribose. SA0260 rbsU 4.2 hypothetical protein...”
- “...the utilization of ribose as a carbon source, namely rbsK, rbsD , and rbsU , (SA0258, SA0259 and SA0260, respectively) all of which were up-regulated during HoR selection. RbsD functions as an ABC-type ribose transporter which also catalyzes conversion between -pyran and -furan forms of D-ribose...”
- Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
Donat, Journal of bacteriology 2009 - “...indole-3-pyruvate decarboxylase SA0239 Sorbitol dehydrogenase SA0258 rbsK Ribokinase SA0304 nanA N-Acetylneuraminate lyase subunit SA0342 Acetyl-CoA...”
VPA1083 ribokinase from Vibrio parahaemolyticus RIMD 2210633
42% identity, 97% coverage
FTN_1767 ribokinase, pfkB family from Francisella tularensis subsp. novicida U112
42% identity, 97% coverage
- Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
Asare, Environmental microbiology 2010 - “...wbtH glutamine amidotransferase/asparagine synthase 3 tnfn1_pw060419p04q135 FTN_1415 thioredoxin 6 tnfn1_pw060510p04q185 FTN_1701 glutamate decarboxylase 3 tnfn1_pw060510p04q136 FTN_1767 rbsK ribokinase, pfkB family 3 tnfn1_pw060328p05q154 FTN_1777 trpG anthranilate synthase component II 2 # Transporter Proteins tnfn1_pw060420p04q158 FTN_0800 ArsB arsenite/antimonite exporter 2 tnfn1_pw060510p01q152 FTN_1711 tyrP tyrosine permease 6 DNA Modification...”
- “...bd-II terminal oxidase subunit I tnfn1_pw060328p02q105 FTN_1620 appB cytochrome bd-II terminal oxidase subunit II tnfn1_pw060510p04q136 FTN_1767 rbsK ribokinase, pfkB family Nucleotide metabolism tnfn1_pw060323p08q120 FTN_0020 carB carbamoyl-phosphate synthase large chain tnfn1_pw060510p02q160 FTN_0021 carA carbamoyl-phosphate synthase small chain tnfn1_pw060418p03q133 FTN_0199 cyoE heme O synthase tnfn1_pw060323p06q113 FTN_0420 SAICAR synthetase/phosphoribosylamine-glycine...”
- Exploitation of host cell biology and evasion of immunity by francisella tularensis
Asare, Frontiers in microbiology 2010 - “...FTN_1621 Predicted NAD/FAD-dependent oxidoreductase FTN_1655 rluC Ribosomal large subunit pseudouridine synthase C FTN_1701 Glutamate decarboxylase FTN_1767 rbsK Ribokinase, pfkB family FTN_1777 trpG Anthranilate synthase component II FTT0203c purH Bifunctional purine biosynthesis protein FTT0204 purA Adenylosuccinate synthetase FTT0435 Ctu Citrulline ureidase FTT0588 aroA 3-Phosphoshikimate 1-carboxyvinyl transferase FTT1234...”
- Molecular bases of proliferation of Francisella tularensis in arthropod vectors
Asare, Environmental microbiology 2010 - “...wbtH glutamine amidotransferase/asparagine synthase 3 tnfn1_pw060419p04q135 FTN_1415 thioredoxin 6 tnfn1_pw060510p04q185 FTN_1701 glutamate decarboxylase 3 tnfn1_pw060510p04q136 FTN_1767 rbsK ribokinase, pfkB family 3 tnfn1_pw060328p05q154 FTN_1777 trpG anthranilate synthase component II 2 # Transporter Proteins tnfn1_pw060420p04q158 FTN_0800 ArsB arsenite/antimonite exporter 2 tnfn1_pw060510p01q152 FTN_1711 tyrP tyrosine permease 6 DNA Modification...”
- “...bd-II terminal oxidase subunit I tnfn1_pw060328p02q105 FTN_1620 appB cytochrome bd-II terminal oxidase subunit II tnfn1_pw060510p04q136 FTN_1767 rbsK ribokinase, pfkB family Nucleotide metabolism tnfn1_pw060323p08q120 FTN_0020 carB carbamoyl-phosphate synthase large chain tnfn1_pw060510p02q160 FTN_0021 carA carbamoyl-phosphate synthase small chain tnfn1_pw060418p03q133 FTN_0199 cyoE heme O synthase tnfn1_pw060323p06q113 FTN_0420 SAICAR synthetase/phosphoribosylamine-glycine...”
RBSK_STAAC / A0A0H2WZY4 Ribokinase; RK; EC 2.7.1.15 from Staphylococcus aureus (strain COL) (see paper)
A0A0H2WZY4 ribokinase (EC 2.7.1.15) from Staphylococcus aureus (see paper)
SACOL0253 ribokinase from Staphylococcus aureus subsp. aureus COL
YP_498834 ribokinase from Staphylococcus aureus subsp. aureus NCTC 8325
41% identity, 95% coverage
- function: Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.
catalytic activity: D-ribose + ATP = D-ribose 5-phosphate + ADP + H(+) (RHEA:13697)
cofactor: Mg(2+) (Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate.)
subunit: Homodimer. - Staphylococcus aureus gene expression in a rat model of infective endocarditis
Hanses, Genome medicine 2014 - “...125.7 116.5 157.6 pyruvate formate-lyase-activating enzyme pflB SACOL0204 44.7 46.9 59.9 65.6 formate acetyltransferase rbsK SACOL0253 6.9 2.5 4.9 ns. ribokinase SACOL2396 19.0 14.3 7.4 6.1 uroporphyrin-III C-methyl transferase SACOL1476 24.8 22.4 18.7 18.6 amino acid permease Regulators agrA SACOL2026 ns ns 4.8 ns accessory gene...”
- Crystal structure of Sa239 reveals the structural basis for the activation of ribokinase by monovalent cations.
Li, Journal of structural biology 2012 (PubMed)- GeneRIF: the crystal structure of Sa239, a ribokinase from Staphylococcus aureus, in the absence of monovalent ions.
PA1950 ribokinase from Pseudomonas aeruginosa PAO1
39% identity, 96% coverage
TM0960 ribokinase from Thermotoga maritima MSB8
42% identity, 96% coverage
- Diversity and versatility of the Thermotoga maritima sugar kinome
Rodionova, Journal of bacteriology 2012 - “...Joint Center for Structural Genomics (20). In addition, the TM0960, TM0952, TM1430, and TM1190 genes were amplified using specific primer pairs (see Table S1 in...”
- “...kinases (TM0116, TM0284, TM0443, TM1073, TM1430, TM0067, TM0960, TM0296, and TM1190), the experimentally observed narrow substrate specificity matched precisely...”
- An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima
Conners, Journal of bacteriology 2005 - “...LacI family gene TM0949 and the predicted ribokinase TM0960 during growth on xylose (11). Computational analysis of LacI regulators has determined that TM0949...”
- “...are arrayed consecutively upstream of the ribokinase TM0960 (Table S2 in the supplemental material), and a predicted rho-independent terminator located...”
- The rfaE gene from Escherichia coli encodes a bifunctional protein involved in biosynthesis of the lipopolysaccharide core precursor ADP-L-glycero-D-manno-heptose
Valvano, Journal of bacteriology 2000 - “...WaaE, ADP-heptose synthase RfaE, ADP-heptose synthase TM0960, ribokinase RbsK, ribokinase F20D23.14, ribokinase RbsK, ribokinase RbsK, ribokinase YihV, sugar...”
PP2458 ribokinase from Pseudomonas putida KT2440
40% identity, 95% coverage
SERP2100 ribokinase from Staphylococcus epidermidis RP62A
39% identity, 95% coverage
RBSKI_FRUSL / P83534 Bifunctional ribokinase/ribose-5-phosphate isomerase A; EC 2.7.1.15; EC 5.3.1.6 from Fructilactobacillus sanfranciscensis (strain ATCC 27651 / DSM 20451 / JCM 5668 / CCUG 30143 / KCTC 3205 / NCIMB 702811 / NRRL B-3934 / L-12) (Lactobacillus sanfranciscensis) (see paper)
38% identity, 56% coverage
- function: Bifunctional enzyme that catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium, and the reversible conversion of ribose 5-phosphate to ribulose 5-phosphate.
catalytic activity: D-ribose + ATP = D-ribose 5-phosphate + ADP + H(+) (RHEA:13697)
catalytic activity: aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate (RHEA:14657)
cofactor: Mg(2+) (Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate.)
LGG_00373 ribokinase from Lacticaseibacillus rhamnosus GG
LGG_00373 sugar kinase, ribokinase family from Lactobacillus rhamnosus GG
39% identity, 94% coverage
BCAL1661 putative ribokinase from Burkholderia cenocepacia J2315
40% identity, 95% coverage
- The Small RNA ncS35 Regulates Growth in Burkholderia cenocepacia J2315
Kiekens, mSphere 2018 - “...transport system BCAL1549 2.4 3.0 Sugar ABC transport system BCAL1550 2.3 Sugar ABC transport system BCAL1661 2.0 Ribokinase BCAL3038 2.0 ABC-type glycerol-3-phosphate transport BCAL3039 2.0 ABC-type glycerol-3-phosphate transport Ornibactin biosynthesis BCAL1696 2.3 Ornibactin biosynthesis protein BCAL1697 2.8 Ornibactin biosynthesis protein BCAL1698 2.5 Ornibactin biosynthesis protein Respiration...”
- The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia
Sass, The ISME journal 2013 - “...ATP-binding protein 8.8 BCAL1659 Ribose transport system, permease protein 2.9 BCAL1660 Ribose operon repressor 3.1 BCAL1661 Ribokinase 8.9 BCAM0310 a Ribonucleotide reductase, class II 15 BCAM0311 a Ribokinase 89 Amino-acid turnover BCAL1796 Saccharopine dehydrogenase 152 BCAM0283 a Lysine decarboxylase 20 BCAM1111 Ornithine decarboxylase 30 BCAM1112 Biodegradative...”
AO356_00950 Ribokinase (EC 2.7.1.15) from Pseudomonas fluorescens FW300-N2C3
42% identity, 96% coverage
- mutant phenotype: Specifically important for utilizing D-Ribose. Automated validation from mutant phenotype: the predicted function (RIBOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
OEOE_RS07775 ribokinase from Oenococcus oeni PSU-1
38% identity, 95% coverage
HM1_2416 ribokinase from Heliobacterium modesticaldum Ice1
37% identity, 96% coverage
HSERO_RS11500 Ribokinase (EC 2.7.1.15) from Herbaspirillum seropedicae SmR1
42% identity, 95% coverage
- mutant phenotype: Specifically important for utilizing D-Ribose. Automated validation from mutant phenotype: the predicted function (RIBOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
6znxC / A0A0B0SD75 Ribokinase from thermus species
39% identity, 96% coverage
- Ligand: adenosine-5'-diphosphate (6znxC)
STM14_4682 ribokinase from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
40% identity, 97% coverage
1gqtB / P0A9J6 Activation of ribokinase by monovalent cations (see paper)
40% identity, 96% coverage
- Ligands: cesium ion; phosphomethylphosphonic acid adenylate ester; alpha-d-ribofuranose (1gqtB)
BWI76_RS00290 Ribokinase (EC 2.7.1.15) from Klebsiella michiganensis M5al
40% identity, 97% coverage
- mutant phenotype: Specifically important for utilizing D-Ribose. Automated validation from mutant phenotype: the predicted function (RIBOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
RbsK / b3752 ribokinase (EC 2.7.1.15) from Escherichia coli K-12 substr. MG1655 (see 20 papers)
rbsK / P0A9J6 ribokinase (EC 2.7.1.15) from Escherichia coli (strain K12) (see 19 papers)
RBSK_ECOLI / P0A9J6 Ribokinase; RK; EC 2.7.1.15 from Escherichia coli (strain K12) (see 5 papers)
rbsK / RF|NP_418208 ribokinase from Escherichia coli K12 (see 4 papers)
NP_418208 ribokinase from Escherichia coli str. K-12 substr. MG1655
P0A9J7 Ribokinase from Escherichia coli O157:H7
b3752 ribokinase from Escherichia coli str. K-12 substr. MG1655
Z5253 ribokinase from Escherichia coli O157:H7 EDL933
40% identity, 96% coverage
- function: Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.
catalytic activity: D-ribose + ATP = D-ribose 5-phosphate + ADP + H(+) (RHEA:13697)
cofactor: Mg(2+) Mn(2+) (Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate (Probable). Also active with manganase (PubMed:16784868).)
subunit: Homodimer. - Identification and characterization of human ribokinase and comparison of its properties with E. coli ribokinase and human adenosine kinase.
Park, FEBS letters 2007 (PubMed)- GeneRIF: Homologies between E. coli and human ribokinase.
- Ribokinase from Escherichia coli K12. Nucleotide sequence and overexpression of the rbsK gene and purification of ribokinase.
Hope, The Journal of biological chemistry 1986 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor
Imai, Nature communications 2023 - “...using inFusion reactions. The cloned enzymes were ribose-phosphate pyrophosphokinase (PRPPS, UniProt P0A717), ribokinase (RK, UniProt P0A9J6), adenine phosphoribosyltransferase (APRT, UniProt P69503), guanylate kinase (GMK, UniProt P60546), xanthine-guanine phosphoribosyl transferase (XGPRT, UniProt P0A9M5), uracil phosphoribosyltransferase (UPRT, UniProt P0A8F0), uridylate kinase (UMPK, UniProtP0A7E9), and CTP synthetase (CTPS, UniProt...”
- “...Protein sequences used in this study are available from Uniprot under accession codes P0A717 (PRPPS), P0A9J6 (RK), P69503 (APRT), P60546 (GMK), P0A9M5 (XGPRT), P0A8F0 (UPRT), P0A7E9 (UMPK), P0A7E5 (CTPS), Q04637 (eIF4G), and P60842 (eIF4A). Source data are provided with this paper. Code availability Custom codes used...”
- Rational Mutagenesis in the Lid Domain of Ribokinase from E. coli Results in an Order of Magnitude Increase in Activity towards D-arabinose
Zayats, International journal of molecular sciences 2022 - “...research (Chuvikovsky et al., 2006), containing the rbsK gene, encoding ribokinase from E. coli (Uniprot P0A9J6), [ 15 ]. Mutations in the rbsK gene were performed using the Phusion Site-Directed Mutagenesis Kit (Thermo Fisher Scientific, Waltham, MA, USA). The obtained expression vectors (along with the one...”
- Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
Sutter, Extremophiles : life under extreme conditions 2020 - “..., A1A6H3; Ferroplasma acidiphilum , A0A1V0N6I9; Sulfolobus solfataricus , SSO0004; Human, Q9H477; E. coli , P0A9J6; Staphylococcus aureus , A0A0H2WZY4; Nucleoside/adenosine kinase: Thermoplasma acidophilum , Ta0880; Methanocaldococcus jannaschii , MJ0406; Mycobacterium tuberculosis , P9WID5; Phosphofructokinase/ribose-1-phosphate kinase: Desulfurococcus amylolyticus , WP_042667458 (Hansen and Schnheit 2000 ); Aeropyrum...”
- Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12
Huddleston, Biochemistry 2019 - “...is annotated as part of the ribokinase/fructokinase family. This family of enzymes contains ribokinase (Uniprot: P0A9J6), fructokinase (Uniprot: Q6XZ78), 6-phosphofructokinase (Uniprot: P06999), inosine kinase (Uniprot: P0AEW6) 2-dehydro-3-deoxyglucokinase (Uniprot: P37647), and fructolysine kinase (Uniprot: P45543). In this paper, we describe the functional characterization of the substrates for...”
- “...and thus the SSN is probably isofunctional. Abbreviation for enzymes are as follows: rbks-ribokinase (Uniprot: P0A9J6); kdgk-2-dehydro-3-deoxygluconokinase (Uniprot: P37647); frk1/frk2-fructokinase1/2 (Uniprot: Q6XZ78/Q0JGZ6); psuK-pseudouridine kinase (Uniprot: P30235); adoK-adenosine kinase (Uniprot: P9WID5); TK2029-ADP-dependent ribose-1-phosphate kinase from Thermococcus kodakarensis (Uniprot: Q5JDG9); mik-inositol 3-kinase (Uniprot: Q5GA22); MJ0406-nucleoside kinase from Methanocaldococcus...”
- A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate
Aziz, Journal of bacteriology 2018 - “...pernix, BAA78921; D. amylolyticus, WP_042667458; and E. coli, P0A9J6. The NXXE motif involved in metal binding is indicated with the black box. The...”
- Structures of alternatively spliced isoforms of human ketohexokinase
Trinh, Acta crystallographica. Section D, Biological crystallography 2009 - “...KHK-A (Swiss-Prot P50053); KHK-C, H. sapiens ketohexokinase KHK-C (Swiss-Prot P50053-2); ecRK, E. coli ribokinase (Swiss-Prot P0A9J6; PDB code 1rkd ; Sigrell et al. , 1998 ); hsAK, H. sapiens adenosine kinase (Swiss-Prot P55263; PDB code 1bx4 ; Mathews et al. , 1998 ); tgAK, Toxoplasma gondii...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...4.5-6.5) 5.61/58,475 (DIGE 4.5-6.5) RbsK RecA P0A9J6 P0A7G6 Ribokinase Protein RecA 4.99/32,290.52 5.09/37,842.18 5.08/41,137 RelB P0C079 Antitoxin...”
- A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate
Aziz, Journal of bacteriology 2018 - “...(Lys43 and Glu143 in E. coli ribokinase; accession no. P0A9J7), are commonly found in ribokinases and interact with the C-1 hydroxy group of ribose, a group not...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...0.49* 0.41 0.73* 0.62 0.97 0.75 b3750 b3751 b3752 rbsC rbsB rbsK 2 2 2 high-affinity transport system ATP-binding component of D-ribose high-affinity transport...”
- Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
Segura, BMC genomics 2018 - “...3.27E-17 Z5249 rbsD D-ribose pyranase 6.17 2.40E-23 5.28 5.82E-17 3.40 1.91E-07 6.10 2.29E-22 4.81 3.25E-14 Z5253 rbsK Ribokinase 3.82 6.03E-12 2.13 3.67E-04 NDE 2.81 9.77E-07 NDE Z2857 sdaA L-serine dehydratase 2.18 2.59E-15 NDE 2.46 3.92E-19 2.47 4.52E-19 2.25 3.44E-16 Z4114 sdaB L-serine dehydratase (deaminase) 4.36 2.42E-18...”
Lreu_1285 ribokinase from Lactobacillus reuteri DSM 20016
LAR_RS06895, Lreu_1285 ribokinase from Limosilactobacillus reuteri subsp. reuteri
39% identity, 95% coverage
BC0660 Ribokinase from Bacillus cereus ATCC 14579
38% identity, 96% coverage
D0R362 Ribokinase from Lactobacillus johnsonii (strain FI9785)
35% identity, 97% coverage
WP_136687548 ribokinase from Halorhabdus amylolytica
40% identity, 94% coverage
- Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
Sutter, Extremophiles : life under extreme conditions 2020 - “...HTIA_p2910 WP_136689493 Ribulokinase Huta_1150 HTIA_1042 HTIA_p2892 WP_136689520 L-Ribulose-5-phosphate-4-epimerase Huta_1149 HTIA_1041 HTIA_p2891 WP_136689521 Ribokinase HTIA_0439 WP_135662271 WP_136687548 Ribose-5-phosphate isomerase Huta_0832 HTIA_0710 WP_135665987 WP_136689787 D-Ribulose-5-phosphate-3-epimerase Huta_0833 HTIA_0711 WP_135665983 WP_136689785 Transaldolase Huta_0859 HTIA_0717 WP_135665975 WP_136687890 Transketolase Huta_0861 Huta_0860 HTIA_0719 HTIA_0718 WP_135665971 WP_167880040 WP_135665973 WP_169051793 WP_136687892 WP_136687891 Sequence comparison and...”
- “...the ribokinase superfamily. Ribokinase: Halorhabdus tiamatea , HTIA_0439; Halorhabdus rudnickae , WP_135662271; Halorhabdus sp. H27, WP_136687548; Arabidopsis thaliana , A1A6H3; Ferroplasma acidiphilum , A0A1V0N6I9; Sulfolobus solfataricus , SSO0004; Human, Q9H477; E. coli , P0A9J6; Staphylococcus aureus , A0A0H2WZY4; Nucleoside/adenosine kinase: Thermoplasma acidophilum , Ta0880; Methanocaldococcus jannaschii...”
CDQ83_03295 ribokinase from Clostridium thermosuccinogenes
38% identity, 98% coverage
- Assessing Cofactor Usage in Pseudoclostridium thermosuccinogenes via Heterologous Expression of Central Metabolic Enzymes
Koendjbiharie, Frontiers in microbiology 2019 - “...the selected P. thermosuccinogenes genes into pET-28b(+). Locus tag Primers CDQ83_02810 TACTTCCAATCCAATGCAGATATTAATCAATTAAAGCAAAAAT TCATT TTATCCACTTCCAATGTTACTTAATCTCCCTGCCT CDQ83_03295 TACTTCCAATCCAATGCAATGGAGGGTCAAGTAAAAATAC TTATCCACTTCCAATGCTATCCTTCAAGCCCC CDQ83_03625 TACTTCCAATCCAATGCAGAAATTTACGAAAAGGTTAGC TTATCCACTTCCAATGCTATTTACATATGAGCTTTTGG CDQ83_04880 TACTTCCAATCCAATGCAAGTACGAAAGTTGGAATTAAC TTATCCACTTCCAATGTCATATGCTTGAAGATACATATG CDQ83_07070 TACTTCCAATCCAATGCAGTAAAGGTTGGAGTGGC TTATCCACTTCCAATGTTACTTCCATTTTCCCATCC CDQ83_07225 TACTTCCAATCCAATGCACCTGATATAAGAACTATAGGAGTC TTATCCACTTCCAATGTTATAAGGCCAGTATCCTG CDQ83_07295 TACTTCCAATCCAATGCAAAAGTTTTGGTTATCAATGC TTATCCACTTCCAATGTTATTTGCTCAATATAGCCACT CDQ83_07455 TACTTCCAATCCAATGCAACAAAGTATGTTTATCTTTTTAG TGAAG TTATCCACTTCCAATGTTATTTATTTTTAATGGCAGCTTGAG CDQ83_08625 TACTTCCAATCCAATGCAGAAAAAATCAAAATGCGAGTTC TTATCCACTTCCAATGTCAAAGGGTTTGCTCC CDQ83_09600 TACTTCCAATCCAATGCAAGAAAAACAAAAATAATCTGTACAT TTATCCACTTCCAATGTTAGTTCTCAGCGTCTG CDQ83_10590...”
- “...GTP, or PP i ). Assay Locus tag Annotation Activity ATP GTP PP i Ribokinase CDQ83_03295 ribokinase 36 3 54 2 Galactokinase CDQ83_02810 galactokinase 5.1 0.5 33 1 Acetate Kinase CDQ83_07295 acetate kinase 71 7 10 0 6-Phosphofructokinase CDQ83_07225 6-phosphofructokinase 13 1 13 5 ND CDQ83_10650...”
Lreu_0404 ribokinase from Lactobacillus reuteri DSM 20016
LAR_RS02150, LREU_RS02105, Lreu_0404 ribokinase from Limosilactobacillus reuteri subsp. reuteri
39% identity, 95% coverage
LS25_0208 ribokinase from Latilactobacillus sakei subsp. sakei LS25
38% identity, 93% coverage
AZOLI_p20643 ribokinase from Azospirillum lipoferum 4B
37% identity, 96% coverage
LSA0202 Ribokinase from Lactobacillus sakei subsp. sakei 23K
38% identity, 93% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...2.0 1.0 1.6 Specific carbohydrate metabolic pathway LSA0201 * rbsD D-ribose pyranase 2.5 2.5 3.4 LSA0202 * rbsK Ribokinase 3.0 3.9 4.3 LSA0289 * xpk Xylulose-5-phosphate phosphoketolase 3.2 2.3 2.6 LSA0297 gntZ 6-phosphogluconate dehydrogenase -1.2 -0.9 -1.7 LSA0298 gntK Gluconokinase -0.8 LSA0381 zwf Glucose-6-phosphate 1-dehydrogenase -0.6...”
BAB2_0004 Ribokinase:Carbohydrate kinase, PfkB from Brucella melitensis biovar Abortus 2308
38% identity, 96% coverage
Q8NQR0 ribokinase (EC 2.7.1.15) from Corynebacterium glutamicum (see paper)
cg1546 putative ribokinase protein from Corynebacterium glutamicum ATCC 13032
38% identity, 94% coverage
EF2961 ribokinase from Enterococcus faecalis V583
36% identity, 95% coverage
- Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis
Innocenti, RNA (New York, N.Y.) 2015 - “...and Fig. 5 ). For instance, operons celAB , ef1017 ef1020 , and ef2959 - ef2961 have a higher expression in S compared with R conditions, and are predicted to code for phosphor-sugar transfer systems (PTSs) of cellobiose and ribose uptake, and degrading enzymes, respectively. These...”
- Transcriptional regulator PerA influences biofilm-associated, platelet binding, and metabolic gene expression in Enterococcus faecalis
Maddox, PloS one 2012 - “...of genes involved in basic cellular metabolism were down-regulated in DBS01, including galK , rbsK (EF2961) and rbsD (EF2960) ( Fig. 1B ). galK encodes for galactokinase, while rbsK and rbsD encode for ribokinase and a ribose transporter, respectively, and are potentially required for transport and...”
- Survey of genomic diversity among Enterococcus faecalis strains by microarray-based comparative genomic hybridization
Aakra, Applied and environmental microbiology 2007 - “...(rhaD) EF1243 EF0197 (rpiA) EF1922 EF2959 EF2960 (rbsD) EF2961 (rbsK) EF1603 (scrB1) EF1746 (galU) EFA0069 (scrB2) EF0955 (galM) EF0956 (pgmB) EF1068 (galM)...”
- Transcriptional response of Enterococcus faecalis V583 to erythromycin
Aakra, Antimicrobial agents and chemotherapy 2005 - “...EF1349 EF1526 EF1612 EF1613 EF1826 EF2589 EF2646 EF2863 EF2961 EF3157 EF0169 EF0514 EF0913 EF0302 EF0685 EF0897 EF1111 EF1817 EF3027 EF3178 EF0045 EF0047 EF0633...”
F9ULK7 Ribokinase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
lp_3660 ribokinase from Lactobacillus plantarum WCFS1
36% identity, 95% coverage
- Phenotypic and proteomic differences in biofilm formation of two Lactiplantibacillus plantarum strains in static and dynamic flow environments
Huijboom, Biofilm 2024 - “...static biofilm were related to various (general) processes such as cysteine/methionine metabolism (F9URY4), sugar metabolism (F9ULK7, F9URE1 and F9UT00) and proteins related to magnesium (binding) (F9URJ9 and F9USN4), along with two transcription regulators of the TntR family (F9ULB4 and F9URB9). Of the lower expressed proteins in...”
- “...GntR family araR 1.6 3 F9URB9 lp _2615 Transcription regulator, GntR family - 1.5 4 F9ULK7 lp _3660 Ribokinase rsbK1 3.1 5 F9URE1 lp _2648 PTS system, N -acetylglucosamine-specific EIID component pts19D 2.5 6 F9UT00 lp _0189 Raffinose-6-phosphate hydrolase & stachyose-6-phosphate hydrolase - 4.2 7 F9URJ9...”
- Identification of key proteins and pathways in cadmium tolerance of Lactobacillus plantarum strains by proteomic analysis.
Zhai, Scientific reports 2017 - “...gluconokinase 1.99 F9URA8 tal1; Transaldolase 5.21 F9UN43 lp_1251;6-phosphogluconate dehydrogenase 7.13 Q88S87 xfp; xylulose-5-phosphate phosphoketolase 1.64 F9ULK7 rbsK1; ribokinase 1.72 Glycolysis Q88YY8 pgm2; phosphoglycerate mutase family protein 2.56 F9URP6 pbg4; 6-phospho-beta-glucosidase 1.94 F9URP7 pbg5; 6-phospho-beta-glucosidase 2.03 Other F9US84 pgmB2; Beta-phosphoglucomutase 2.71 F9USZ1 malS; Alpha-amylase, maltodextrins and cyclomaltodextrins...”
- Molecular adaptation of Lactobacillus plantarum WCFS1 to gallic acid revealed by genome-scale transcriptomic signature and physiological analysis
Reverón, Microbial cell factories 2015 - “...Genes coding for a ribose transport protein ( lp_3659 ) and a ribose kinase ( lp_3660 ) were downregulated and a gene coding for a phosphoketolase ( lp_2659 ), involved in boosting the carbon flow from the pentose phosphate pathway to glycolytic intermediates, was also underexpressed....”
- “...encoded by lp_2742 (GntR family, YtrA subfamily) and the RbsR regulon which encompass rbsK ( lp_3660 ) and rbsD ( lp_3659 ) genes. Discussion Here, we have explored the mechanisms of adaptation of L. plantarum to GA. Gene expression-wide analyses did not reveal stringent or general...”
- Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice
Marco, Applied and environmental microbiology 2007 - “...lp_1164 lp_1403 lp_1603 lp_2940 lp_3055 lp_3176 lp_3473 lp_3660 lp_3662 lp_0006 lp_0537 lp_0727 lp_1021 lp_1027 lp_1144 lp_1898 lp_2187 lp_2301 General Locus...”
FOXG_13522 ribokinase from Fusarium oxysporum f. sp. lycopersici 4287
39% identity, 90% coverage
BMEII0089 RIBOKINASE from Brucella melitensis 16M
38% identity, 96% coverage
- Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis
Boggiatto, BMC molecular biology 2018 - “...upregulated genes are known virulence genes: BMEI1766 ( cysI ), BMEII0527 ( xseA ), and BMEII0089 ( rbsK ). Other genes in Table 4 may be (a) upregulated in persistent infection but not essential for virulence, or (b) essential for persistence in the long-term goat model,...”
- “...GlcE 4.8 No BMEII1029 3-Deoxy- d -manno-octulosonic-acid transferase 4.3 No BMEI1927 Enoyl-CoA hydratase 4.1 No BMEII0089 Ribokinase ( rbsK ) 4.1 Yes BMEII0086 Galactoside transport system permease MglC 4.0 No BMEI1816 Sensory transduction protein kinase 4.0 No BMEII0524 Hypothetical protein 3.7 No BMEII0860 Oligopeptide transport system...”
- Comparative genomic analysis of Brucella melitensis vaccine strain M5 provides insights into virulence attenuation
Jiang, PloS one 2013 - “...For example, mutants of genes encoding sugar transport systems, such as pyruvate carboxylase (BMEI0266), ribokinase (BMEII0089), 6-phosphogluconate dehydrogenase (BMEII1124), inosamine methylase (BMEI1301), glycosyl transferase (BMEII1101), ribose transport (BMEII0300), and glucose/galactose transport (BMEII1053) limit carbon or energy supply and affect gene regulation. In addition, the production of...”
- Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics
He, Frontiers in cellular and infection microbiology 2012 - “...10678941 55 pgm BMEI1886 Mice 12525425 56 pmm BMEI1396 Mice, macrophages, HeLa 14979322 57 rbsK BMEII0089 Macrophages 14979322 58 ugpA BMEII0624 Mice 14638795 59 xfp BMEII0881 Mice, macrophages, HeLa 14979322 60 zwf BMEII0513 HeLa, macrophages 12761078 H: COENZYME TRANSPORT AND METABOLISM 61 BMEI1902 BMEI1902 Mice, macrophages,...”
AZL_b05870 ribokinase from Azospirillum sp. B510
37% identity, 96% coverage
NCU04339 ribokinase from Neurospora crassa OR74A
36% identity, 85% coverage
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...18702 weak lipoic acid synthetase LIA-1 E. coli CS Orth Catalytic Activity Cellular Process/Metabolic Process NCU04339 16454 weak ribokinase RIK-8 E. coli CS Orth Catalytic Activity Cellular Process/Metabolic Process NCU03894 11325 weak serine/threonine protein kinase-4 stk-4 Morph/Hyph Binding/signal transducer activity Biological Regulation/Cellular Process/Developmental Process/ Response to...”
RBSK_SCHPO / O60116 Ribokinase; RK; EC 2.7.1.15 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
SPBC16G5.02c ribokinase (predicted) from Schizosaccharomyces pombe
38% identity, 95% coverage
deoK / Q8XGW5 deoxyribokinase monomer (EC 2.7.1.229) from Salmonella typhi (see 4 papers)
DEOK_SALTI / P0DX97 Deoxyribokinase; dRK; ATP:2-deoxy-D-ribose 5-phosphotransferase; EC 2.7.1.229 from Salmonella typhi (see paper)
DEOK_SALTY / Q7CPF5 Deoxyribokinase; dRK; ATP:2-deoxy-D-ribose 5-phosphotransferase; EC 2.7.1.229 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
STY3989 putative carbohydrate kinase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
STM3793 putative sugar kinase, ribokinase family from Salmonella typhimurium LT2
34% identity, 96% coverage
- function: Catalyzes the ATP-dependent phosphorylation of 2-deoxy-D- ribose to 2-deoxy-D-ribose 5-phosphate (dRib-5P), allowing the use of deoxyribose as the sole carbon source (PubMed:10648508). Can also use D-ribose, with much lower efficiency (PubMed:10648508).
catalytic activity: 2-deoxy-D-ribose + ATP = 2-deoxy-D-ribose 5-phosphate + ADP + H(+) (RHEA:30871)
cofactor: Mg(2+)
subunit: Homodimer. - function: Catalyzes the ATP-dependent phosphorylation of 2-deoxy-D- ribose to 2-deoxy-D-ribose 5-phosphate (dRib-5P), allowing the use of deoxyribose as the sole carbon source (PubMed:4376665). Can also use D- ribose and 2-deoxy-D-ribitol, with lower efficiency (PubMed:4376665). Several ribo- and deoxyribonucleotides can replace ATP as phosphoryl donor (PubMed:4376665).
catalytic activity: 2-deoxy-D-ribose + ATP = 2-deoxy-D-ribose 5-phosphate + ADP + H(+) (RHEA:30871)
cofactor: Mg(2+) (Has an absolute requirement for divalent cations which is best satisfied by Mg(2+) (PubMed:4376665). Can also use Co(2+), Cd(2+), Mn(2+), Ni(2+), Zn(2+) and Cu(2+), with lower efficiency (PubMed:4376665).)
subunit: Homodimer. - Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray
Anjum, Infection and immunity 2005 - “...SF4384 to SF4379, respectively), uropathogenic E. coli CTF073 (STY3989 and STY3990 show 96% amino acid identity with c0331and c0332, respectively, and STY4804...”
- Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
Seif, Nature communications 2018 - “...STM3792 ( deoP ) Deoxy D ribose transport via proton symport (C-O2+/) Deoxy D Ribose STM3793 ( deoK ) Ribokinase and deoxyribokinase (C-O2+/) Deoxy D Ribose STM4467 Arginine deiminase (C-O2-) l -Arginine STM2793 ( gabP ) 4-aminobutyrate transport in via proton symport (C-O2+, N-O2+/) 4-Aminobutanoate STM1627...”
P36945 Ribokinase from Bacillus subtilis (strain 168)
37% identity, 96% coverage
AK34_5286 ribokinase from Burkholderia dolosa AU0158
35% identity, 97% coverage
WP_135662271 ribokinase from Halorhabdus rudnickae
37% identity, 96% coverage
- Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
Sutter, Extremophiles : life under extreme conditions 2020 - “...HTIA_1046 HTIA_p2910 WP_136689493 Ribulokinase Huta_1150 HTIA_1042 HTIA_p2892 WP_136689520 L-Ribulose-5-phosphate-4-epimerase Huta_1149 HTIA_1041 HTIA_p2891 WP_136689521 Ribokinase HTIA_0439 WP_135662271 WP_136687548 Ribose-5-phosphate isomerase Huta_0832 HTIA_0710 WP_135665987 WP_136689787 D-Ribulose-5-phosphate-3-epimerase Huta_0833 HTIA_0711 WP_135665983 WP_136689785 Transaldolase Huta_0859 HTIA_0717 WP_135665975 WP_136687890 Transketolase Huta_0861 Huta_0860 HTIA_0719 HTIA_0718 WP_135665971 WP_167880040 WP_135665973 WP_169051793 WP_136687892 WP_136687891 Sequence comparison...”
- “...and related members of the ribokinase superfamily. Ribokinase: Halorhabdus tiamatea , HTIA_0439; Halorhabdus rudnickae , WP_135662271; Halorhabdus sp. H27, WP_136687548; Arabidopsis thaliana , A1A6H3; Ferroplasma acidiphilum , A0A1V0N6I9; Sulfolobus solfataricus , SSO0004; Human, Q9H477; E. coli , P0A9J6; Staphylococcus aureus , A0A0H2WZY4; Nucleoside/adenosine kinase: Thermoplasma acidophilum...”
BCAS0100 putative ribokinase from Burkholderia cenocepacia J2315
41% identity, 96% coverage
BPHYT_RS25805 deoxyribose kinase (EC 2.7.1.15) from Burkholderia phytofirmans PsJN
36% identity, 91% coverage
- mutant phenotype: Specifically important in carbon source 2-Deoxy-D-Ribose
SMc01103 Ribokinase (EC 2.7.1.15) from Sinorhizobium meliloti 1021
SMc01103 PROBABLE RIBOKINASE PROTEIN from Sinorhizobium meliloti 1021
36% identity, 95% coverage
- mutant phenotype: Specifically important for utilizing D-Ribose. Automated validation from mutant phenotype: the predicted function (RIBOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
- Construction and expression of sugar kinase transcriptional gene fusions by using the Sinorhizobium meliloti ORFeome
Humann, Applied and environmental microbiology 2008 - “...SMb21648 SMb21217 SMb21373 SMb21374 SMc00473 SMc00881 SMc01103 SMc01165 SMc01531 SMc01618 SMc01623 SMc02164 SMc02335 SMc02341 SMc02846 SMc03138 SMc03164...”
- “...Raffinose Succinate SM1021 SMb21009 SMb21022 SMb21184 SMb21374 SMc00881 SMc01103 SMc03138 SMc03817 2.51 1.56 19.67 1.44 9.19 14.57 2.00 2.82 3.25 1.55 25.47...”
FOXG_08568 ribokinase from Fusarium oxysporum f. sp. lycopersici 4287
38% identity, 92% coverage
5c41A / Q9H477 Crystal structure of human ribokinase in complex with amppcp in p21 spacegroup and with 4 protomers
36% identity, 91% coverage
- Ligand: phosphomethylphosphonic acid adenylate ester (5c41A)
DR76_RS24705 ribokinase from Escherichia coli ATCC 25922
c0331 Putative ribokinase from Escherichia coli CFT073
34% identity, 98% coverage
KP1_RS12825 ribokinase from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
37% identity, 96% coverage
AZL_b03490 ribokinase from Azospirillum sp. B510
37% identity, 95% coverage
HTIA_0439 ribokinase from Halorhabdus tiamatea SARL4B
40% identity, 94% coverage
- Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
Sutter, Extremophiles : life under extreme conditions 2020 - “...Huta_1154 HTIA_1046 HTIA_p2910 WP_136689493 Ribulokinase Huta_1150 HTIA_1042 HTIA_p2892 WP_136689520 L-Ribulose-5-phosphate-4-epimerase Huta_1149 HTIA_1041 HTIA_p2891 WP_136689521 Ribokinase HTIA_0439 WP_135662271 WP_136687548 Ribose-5-phosphate isomerase Huta_0832 HTIA_0710 WP_135665987 WP_136689787 D-Ribulose-5-phosphate-3-epimerase Huta_0833 HTIA_0711 WP_135665983 WP_136689785 Transaldolase Huta_0859 HTIA_0717 WP_135665975 WP_136687890 Transketolase Huta_0861 Huta_0860 HTIA_0719 HTIA_0718 WP_135665971 WP_167880040 WP_135665973 WP_169051793 WP_136687892 WP_136687891 Sequence...”
- “...involved in D-ribose degradation in H. utahensis and H. tiamatea . A homologous gene of HTIA_0439 (black arrow) encoding ribokinase of H. tiamatea is absent in H. utahensis . HTIA_0710 and Huta_0832 encode ribose-5-phosphate isomerase and HTIA_0711 and Huta_0833 encode D-ribulose-5-phosphate-3-epimerase (grey arrows) HTIA_0439 encoding putative...”
CDR20291_0302 ribokinase from Clostridioides difficile R20291
CDR20291_0302 putative ribokinase from Clostridium difficile R20291
34% identity, 97% coverage
DIP0655 Putative ribokinase from Corynebacterium diphtheriae NCTC 13129
37% identity, 94% coverage
CD0299 putative ribokinase from Clostridium difficile 630
34% identity, 97% coverage
- Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
Antunes, Nucleic acids research 2012 - “...(CD2319), putative ribulose-phosphate 3-epimerase; rpiB1 (CD2320), ribose-5-phosphate isomerase B1; rpiB2 (CD3480), ribose-5-phosphate isomerase B2; rbsK (CD0299), ribokinase; tkt (CD2321), transketolase, central and C-terminal; tkt (CD2322), transketolase, N-terminal; CD0764CD0768, PTS sorbitol IIC, IIB, IIA; CD3089CD3088, PTS cellobiose IIBC; CD2327CD2325, PTS galactitol IIA, IIB, IIC; CD0208CD0206, PTS fructose-like...”
Bbr_1432 PfkB family carbohydrate kinase from Bifidobacterium breve UCC2003
34% identity, 46% coverage
RBSK_HUMAN / Q9H477 Ribokinase; RK; EC 2.7.1.15 from Homo sapiens (Human) (see paper)
Q9H477 ribokinase (EC 2.7.1.15) from Homo sapiens (see paper)
NP_071411 ribokinase isoform 1 from Homo sapiens
36% identity, 89% coverage
- function: Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.
catalytic activity: D-ribose + ATP = D-ribose 5-phosphate + ADP + H(+) (RHEA:13697)
cofactor: Mg(2+) (Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate.)
subunit: Homodimer. - Role of monovalent and divalent metal cations in human ribokinase catalysis and regulation.
Quiroga-Roger, Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 2015 (PubMed)- GeneRIF: Asn199 and Glu202 play an important role in the regulation of human ribokinase activity.
- Identification and characterization of human ribokinase and comparison of its properties with E. coli ribokinase and human adenosine kinase.
Park, FEBS letters 2007 (PubMed)- GeneRIF: Identification and characterization of human ribokinase.
- Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Rose, Molecular medicine (Cambridge, Mass.) - GeneRIF: Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
- Characterization of Circulating Protein Profiles in Individuals with Prader-Willi Syndrome and Individuals with Non-Syndromic Obesity.
Pascut, Journal of clinical medicine 2024 - “...0.74 0.03768 SRP14 Signal Recognition Particle 14 P37108 5.78 5.27 0.504 0.71 0.04092 RBKS Ribokinase Q9H477 7.84 7.44 0.403 0.76 0.04723 p -values were adjusted for multiple testing using the BenjaminHochberg method (adj. p -value). PWS: PraderWilli syndrome; OB: non-syndromic obesity, FC: linear fold of change...”
- The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - Protein Profiling of a Cellular Model of NAFLD by Advanced Bioanalytical Approaches.
Altomare, International journal of molecular sciences 2022 - “...J3KPX7 Prohibitin-2 PHB2 8 33,239 0.83 B2R4R9 40S ribosomal protein S28 RPS28 2 78,409 0.81 Q9H477 Ribokinase RBKS 2 34,143 0.76 A0A024RA32 Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 C1GALT1 2 42,202 0.76 Q53H37 Calmodulin-like protein 5 CALML5 4 15,876 0.73 Q5QNW6 Histone H2B type 2-F HIST2H2BF 5 13,920 0.70...”
- Screening and identification of endometrial proteins as novel potential biomarkers for repeated implantation failure.
Wang, PeerJ 2021 - “...P05230 FGF1 Fibroblast growth factor 1 2.56 Q8NFU3 TSTD1 Thiosulfate:glutathionesulfurtransferase 2.49 Q8NDA2 HMCN2 Hemicentin-2 2.49 Q9H477 RBSK Ribokinase 2.40 P15169 CBPN Carboxypeptidase N catalytic chain 2.37 P02763 A1AG1 Alpha-1-acid glycoprotein 1 2.15 Q86VY4 TSYL5 Testis-specific Y-encoded-like protein 5 2.03 Q9UKJ8 ADA21 Disintegrin and metalloproteinase domain-containing protein...”
- Proteome-Wide Characterizations of N6-Methyl-Adenosine Triphosphate- and N6-Furfuryl-Adenosine Triphosphate-Binding Capabilities of Kinases.
Dong, Analytical chemistry 2021 - “...CDK7 0.59 0.13 Q16513 PKN2 0.60 0.26 Q9P0L2 MARK1 0.63 0.03 Q14680 MELK 0.65 0.17 Q9H477 RBKS 0.68 0.08 O00418 EEF2K 0.69 0.19 Q96S44 TP53RK 0.70 0.13 P48729 CSNK1A1 0.70 0.12 Q9Y2K2 SIK3 0.71 0.09 Q15349 RPS6KA2 0.72 0.22 P53350 PLK1 0.72 0.48 O75676 RPS6KA4 0.73...”
- Identification of HO-1 as a novel biomarker for graft acute cellular rejection and prognosis prediction after liver transplantation
Jia, Annals of translational medicine 2020 - “...P450 1A2 CYP1A2 0.672 Q9H488 GDP-fucose protein O-fucosyltransferase 1 POFUT1 0.673 P09327 Villin-1 VIL1 0.674 Q9H477 Ribokinase RBKS 0.675 P02763 Alpha-1-acid glycoprotein 1 ORM1 0.676 P06331 immunoglobulin heavy variable 4-34 IGHV4-34 0.677 P51857 3-oxo-5-beta-steroid 4-dehydrogenase AKR1D1 0.678 P49419 Alpha-aminoadipic semialdehyde dehydrogenase ALDH7A1 0.679 Q14749 Glycine N-methyltransferase...”
- A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity.
Zhou, Genomics 2009 - “...E YCR036W RBK1 Ribokinase; member of a family of sugar kinases that includes Pfk2p 0.6283 Q9H477 Ribokinase YML121W GTR1 Cytoplasmic GTP binding protein and negative regulator of the Ran/Tc4 GTPase cycle; component of GSE complex, which is required for sorting of Gap1p; involved in phosphate transport...”
gbs0117 Unknown from Streptococcus agalactiae NEM316
34% identity, 95% coverage
SAG0118 ribokinase from Streptococcus agalactiae 2603V/R
34% identity, 95% coverage
- Adaptive response of neonatal sepsis-derived Group B Streptococcus to bilirubin
Hansen, Scientific reports 2018 - “...SAG1898 PTS system transporter subunit IID 1.87 1.06E-06 5.81E-04 SAG0547 Hypothetical protein 1.32 1.22E-06 5.81E-04 SAG0118 Ribokinase 1.12 2.96E-05 1.13E-02 SAG1902 PTS system transporter subunit IIA 1.34 4.07E-05 1.29E-02 SAG1899 PTS system transporter subunit IIC 1.83 5.82E-05 1.59E-02 SAG0169 Formate acetyltransferase 1.32 1.26E-04 2.46E-02 SAG1350 Surface...”
RBSK_LEIMA / E9AD19 Ribokinase; RK; EC 2.7.1.15 from Leishmania major (see paper)
35% identity, 89% coverage
- function: Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway. Specifically phosphorylates D-ribose. Fails to phosphorylate 4, 5 or 6 D-carbon sugars (erythrose, threose, xylulose, arabinose, fructose and glucose).
catalytic activity: D-ribose + ATP = D-ribose 5-phosphate + ADP + H(+) (RHEA:13697)
cofactor: Mg(2+) (Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate.)
subunit: Homodimer.
c2492 Putative carbohydrate kinase from Escherichia coli CFT073
35% identity, 74% coverage
SAK_0170 ribokinase from Streptococcus agalactiae A909
33% identity, 95% coverage
- The Role of Regulator Catabolite Control Protein A (CcpA) in Streptococcus agalactiae Physiology and Stress Response
Roux, Microbiology spectrum 2022 - “...from 0.25% to 1% in the A909WT strain: SAK_0087 and SAK_1651 coding two alcohol dehydrogenases, SAK_0170 and SAK_0171 belonging to a ribose operon, SAK_0528 and SAK_0529 belonging to a galactitol PTS operon, and SAK_0257 coding a trehalose PTS. In order to demonstrate a glucose effect in...”
- “...transporter; SAK_1475-1477 , cyclodextrin ABC transporter; rbsABC ( SAK_0166-0168 ), ribose ABC transporter; rbsK ( SAK_0170 ), ribokinase; rpiA ( SAK_1270 ), ribose 5-phosphate isomerase A; rpe ( SAK_1798 ), ribulose-phosphate 3-epimerase; tkt ( SAK_0350 ), transketolase; SAK_0262 , 0263 , putative transketolase, N- and C-terminal...”
F1N8A7 Ribokinase from Gallus gallus
37% identity, 88% coverage
A4HFG6 Ribokinase from Leishmania braziliensis
34% identity, 89% coverage
6a8aA / A0A3S7X0F5 Ribokinase from leishmania donovani with atp (see paper)
34% identity, 90% coverage
- Ligands: glycerol; adenosine-5'-triphosphate (6a8aA)
KPN_01699 ribokinase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
36% identity, 93% coverage
F9UQH2 Ribokinase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
36% identity, 95% coverage
LINJ_27_0430 putative ribokinase from Leishmania infantum JPCM5
34% identity, 89% coverage
SSO0004 Ribokinase (rbsK-1) from Sulfolobus solfataricus P2
Q981E2 Ribokinase from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
36% identity, 96% coverage
- Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
Sutter, Extremophiles : life under extreme conditions 2020 - “...Halorhabdus sp. H27, WP_136687548; Arabidopsis thaliana , A1A6H3; Ferroplasma acidiphilum , A0A1V0N6I9; Sulfolobus solfataricus , SSO0004; Human, Q9H477; E. coli , P0A9J6; Staphylococcus aureus , A0A0H2WZY4; Nucleoside/adenosine kinase: Thermoplasma acidophilum , Ta0880; Methanocaldococcus jannaschii , MJ0406; Mycobacterium tuberculosis , P9WID5; Phosphofructokinase/ribose-1-phosphate kinase: Desulfurococcus amylolyticus , WP_042667458...”
- Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways.
Sutter, Extremophiles : life under extreme conditions 2020 - “...6ILT; S. aureus , 3RY7. UniProt entry number: H. tiamatea ,HTIA_0439, C7NMH0; Sulfolobus solfataricus , Q981E2 Ribokinase from H. tiamatea and archaeal homologs from other Halorhabdus species and from S. solfataricus and F. acidiphilum are members of the ribokinase superfamily (PfkB family of carbohydrate kinases). A...”
STM1382 putative regulatory protein, deoR family from Salmonella typhimurium LT2
37% identity, 73% coverage
- High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach
Allard, BMC genomics 2012 - “...263 d,e,f hypothetical protein pduV STM2056 SEEM020_14356 G/A D/G 353 b,c,d,e,f propanediol utilization protein orf408 STM1382 SEEM020_15066 G/A T/A 1096 a1 putative regulatory protein, deoR family ydiA STM1348 SEEM020_15231 C/T F 126 b,c,d,e,f putative inner membrane protein envE STM1242 SEEM020_15746 T/C I/T 446 a1 EnvE ycfX...”
- Modulation of horizontally acquired genes by the Hha-YdgT proteins in Salmonella enterica serovar Typhimurium
Vivero, Journal of bacteriology 2008 - “...from http://jb.asm.org/ on April 16, 2019 by guest SPI2 STM1381 STM1382 STM1390 ssrB ssrA ssaE sseB sscA sseC sseD sseE sscB ssaH ssaI ssaJ ssaK ssaV ssaO ssaT...”
- Identification of Salmonella enterica serovar Typhimurium genes important for survival in the swine gastric environment
Bearson, Applied and environmental microbiology 2006 - “...Cell envelope Cell envelope SB 135/16H3 SB 104/2G3 dgt STM1382 STM0208 616/1,227 780/1,518 SB SB SB SB SB SB SB SB 117/8B6 162/18F6 157/18D2 115/8G3 114/6C6...”
t3974 putative ribokinase from Salmonella enterica subsp. enterica serovar Typhi Ty2
T_RS20210 PfkB family carbohydrate kinase from Salmonella enterica subsp. enterica serovar Typhi str. Ty2
34% identity, 73% coverage
SC1403 putative regulatory protein, deoR family from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
37% identity, 73% coverage
- Sarecycline: A Review of Preclinical and Clinical Evidence
Moore, Clinical, cosmetic and investigational dermatology 2020 - “...Treatment-Emergent Adverse Events Common to Tetracycline-Class Antibiotics Selected TEAE Safety Population n (%) SC1401 SC1402 SC1403 Placebo (n=483) Sarecycline (n=481) Placebo (n=513) Sarecycline (n=513) Sarecycline (n=483) Sunburn 2 (0.4) 3 (0.6) 1 (0.2) 4(0.8) 1(0.2) Urticaria 1 (0.2) 0 2 (0.4) 1(0.2) 2(0.4) Vulvovaginal mycotic infection...”
SEET0819_01325 PfkB family carbohydrate kinase from Salmonella enterica subsp. enterica serovar Tennessee str.
34% identity, 73% coverage
AOL_s00004g627 hypothetical protein from Orbilia oligospora ATCC 24927
36% identity, 91% coverage
H281DRAFT_01116 deoxyribose kinase (EC 2.7.1.15) from Paraburkholderia bryophila 376MFSha3.1
36% identity, 94% coverage
- mutant phenotype: Important for utilization of deoxyribose and deoxynucleosides. Deoxynucleosides might be hydrolyzed to deoxyribose.
Q8R1Q9 Ribokinase from Mus musculus
34% identity, 88% coverage
EF1922 transcriptional regulator, LacI family/carbohydrate kinase, PfkB family protein from Enterococcus faecalis V583
31% identity, 48% coverage
Bbr_1422 ribokinase from Bifidobacterium breve UCC2003
36% identity, 96% coverage
OG1RF_11586 PfkB family carbohydrate kinase from Enterococcus faecalis OG1RF
31% identity, 48% coverage
Bbr_1415 ribokinase from Bifidobacterium breve UCC2003
35% identity, 89% coverage
cg2554 ribokinase protein from Corynebacterium glutamicum ATCC 13032
35% identity, 93% coverage
BL105A_1456 ribokinase from Bifidobacterium longum
34% identity, 92% coverage
D3ZVU4 Ribokinase from Rattus norvegicus
34% identity, 88% coverage
6ilsB / A1A6H3 Structure of arabidopsis thaliana ribokinase complexed with ribose and atp (see paper)
31% identity, 95% coverage
- Ligands: adenosine-5'-triphosphate; alpha-d-ribofuranose (6ilsB)
RBSK / A1A6H3 ribokinase (EC 2.7.1.15) from Arabidopsis thaliana (see 2 papers)
RBSK_ARATH / A1A6H3 Ribokinase; AtRBSK; RK; EC 2.7.1.15 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
A1A6H3 ribokinase (EC 2.7.1.15) from Arabidopsis thaliana (see paper)
AT1G17160 pfkB-type carbohydrate kinase family protein from Arabidopsis thaliana
NP_173159 pfkB-like carbohydrate kinase family protein from Arabidopsis thaliana
31% identity, 79% coverage
- function: Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway (By similarity) (PubMed:27601466). Can also use xylose and fructose as carbohydrate substrates with a low efficiency (PubMed:27601466). Can use GTP, and, to a lower extent, CTP and UTP as alternative phosphoryl donors (PubMed:27601466).
catalytic activity: D-ribose + ATP = D-ribose 5-phosphate + ADP + H(+) (RHEA:13697)
cofactor: Mg(2+) (Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate.)
subunit: Homodimer.
disruption phenotype: Abnormal accumulation of D-ribose. D-ribose hypersensitivity; normal growth except in the presence of D-ribose, which leads to chlorosis and growth inhibition. - Development of a Target Enrichment Probe Set for Conifer (REMcon)
Khan, Biology 2024 - “...315 23 MA_10428134 AT2G04560 273 24 MA_10427767 AT1G21370 291 25 MA_10427729 AT5G67530 1224 26 MA_10427590 AT1G17160 480 27 MA_10427203 AT2G36740 543 28 MA_10426631 AT4G36390 1533 29 MA_10426581 AT2G33450 231 30 MA_10426376 AT2G38270 504 31 MA_9578808 AT4G18372 387 32 MA_9514062 AT5G20220 315 33 MA_9503281 AT1G48175 257 34...”
- Identification and biochemical characterization of the fructokinase gene family in Arabidopsis thaliana
Riggs, BMC plant biology 2017 - “...only biochemically characterized enzyme in the unresolved polytomy of proteins related to the FRK clade, At1g17160, specifically phosphorylates ribose [ 28 ], suggesting that the seven FRKs identified herein likely comprise the Arabidopsis FRK family. As such, we propose the nomenclature in Table 1 based on...”
- Identification of the Plant Ribokinase and Discovery of a Role for Arabidopsis Ribokinase in Nucleoside Metabolism
Riggs, The Journal of biological chemistry 2016 - “...of the protein encoded by the Arabidopsis gene At1g17160 as a ribokinase (AtRBSK) and demonstrate its in vivo role in nucleotide metabolism. The pro2...”
- “...Escherichia coli RBSK identified a single candidate RBSK, At1g17160 (AtRBSK). AtRBSK is more similar to predicted RBSKs from other plant species and known...”
- Arabidopsis thaliana resistance to fusarium oxysporum 2 implicates tyrosine-sulfated peptide signaling in susceptibility and resistance to root infection
Shen, PLoS genetics 2013 - “...AT1G17120, AT1G17130, AT1G17140, AT1G17145 and AT1G17147; Pac1.1 includes nucleotides 5866025 to 5878981 and genes AT1G17150, AT1G17160, AT1G17170, AT1G17180 and AT1G17190; Sal1.4 includes nucleotides 5867417 to 5882030 and genes AT1G17160, AT1G17170, AT1G17180, AT1G17190 and AT1G17200; Sal1.3 includes nucleotides 5882030 to 5891121 and genes AT1G17210 and AT1G17220; Xba1.1...”
- Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana.
Kang, Journal of structural biology 2019 (PubMed)- GeneRIF: The structural data combined with activity analyses of mutants ATP-dependent ribokinase (RBSK) allowed assignment of functional roles for the active site residues..
- Identification of the Plant Ribokinase and Discovery of a Role for Arabidopsis Ribokinase in Nucleoside Metabolism.
Riggs, The Journal of biological chemistry 2016 - GeneRIF: At1g17160 (AtRBSK). AtRBSK is more similar to predicted RBSKs from other plant species and known mammalian and prokaryotic RBSK than to all other PfkB proteins in Arabidopsis AtRBSK contains a predicted chloroplast transit peptide, and we confirmed plastid localization using AtRBSK fused to YFP.
AS87_03725 ribokinase from Riemerella anatipestifer Yb2
30% identity, 95% coverage
- Deletion of AS87_03730 gene changed the bacterial virulence and gene expression of Riemerella anatipestifer
Wang, Scientific reports 2016 - “...however, inactivation of the AS87_03730 gene had no effect on the transcription of chromosomally upstream AS87_03725 and downstream AS87_03735 genes ( Fig. 1B ). The AS87_03730 deletion mutant strain was designated as Yb2AS87_03730. Mutant strain Yb2AS87_03730 was viable when grown on TSB medium supplemented with kanamycin...”
- “...with the SpecR cassette. ( B ) Real-time PCR analysis. The transcription levels of upstream AS87_03725 gene and downstream AS87_03735 gene were measured. The changes of mRNAs were expressed as fold expression and calculated using the comparative CT (2 CT ) method. No transcription of AS87_03730...”
GL50803_15297 Ribokinase from Giardia intestinalis
34% identity, 86% coverage
PAS_chr3_0604 Putative ribokinase from Komagataella phaffii GS115
32% identity, 86% coverage
CG13369 uncharacterized protein from Drosophila melanogaster
34% identity, 93% coverage
- Kinome-Wide RNAi Screen Uncovers Role of Ballchen in Maintenance of Gene Activation by Trithorax Group in Drosophila
Khan, Frontiers in cell and developmental biology 2021 - “...Sphingosine kinase 1 (Sk1) 15.27 CG1747 Converts sphingosine to sphingosine 1-phosphate. SPHK1, SPHK2 Not checked CG13369 13.17 CG13369 Ribokinase RBKS Not checked Female sterile (1) homeotic [fs(1)h] 10.72 CG2252 Involved in pattern formation by regulating homeotic genes expression. BRD2, BRD3, BRD4, BRDT Not checked S6 Kinase...”
- Functional requirements of protein kinases and phosphatases in the development of the Drosophila melanogaster wing
Ostalé, G3 (Bethesda, Md.) 2021 - “...after gene knockdown Family CG number Name H. Ortholog Transformant f(x) Ref. GO Kinases CHK CG13369 CG13369 RBKS 100,747 EPL MET CG3400 Pfrx PFKFB3 25,959 S/V MET IPK CG45017 IP3K2 ITPKA-C 19,159 EPL/nec//S-P Inositol hexakisphosphate substrate Dean et al. (2015) SIG LK CG10260 PI4KIII PI4KA 105,614...”
- Genetic Basis of Increased Lifespan and Postponed Senescence in Drosophila melanogaster
Parker, G3 (Bethesda, Md.) 2020 - “...10 of these genes had sexually antagonistic effects on lifespan ( capu , Cdc7 , CG13369 , CG3326 , Dredd , egh , lama , MED22 , Nmd3 , Pgant1 ). The effects on lifespan were highly sex-specific: seven genes increased lifespan in both sexes and...”
- “...sov increased productivity at an early age and decreased productivity at later ages. RNAi of CG13369 , CG32809 , CG4281 , CG4554 , DAAM , and wds lowered productivity at an early age and increased productivity at later ages. Figure 4 Differences in lifetime productivity (number...”
- Cross-species genetic screens to identify kinase targets for APP reduction in Alzheimer's disease
Huichalaf, Human molecular genetics 2019 - “...NPR2 Egfr EGFR Nrk Sik2 CG11255 ADK Eip63E Pak CG13369 CG14721 RBKS TPK1 fh gskt CDK14, CDK15, CDK16, CDK17, CDK18 FXN GSK3B AATK, MUSK, PTK7 PAK1, PAK2,...”
- From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies
Benos, Genome research 2001 - “...CG18104 CG4262 CG4293 CG7727 CG6172 CG13366 CG17828 CG13369 CG18451 CG17829 CG7622 CG6189 CG7486 LD06838 GH16756 GH22310 LD03312 LD03188 GM02010 CG6222 CG13367...”
PFREUD_03250 ribokinase from Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1
33% identity, 91% coverage
PFCIRM129_01510 ribokinase from Propionibacterium freudenreichii subsp. freudenreichii
33% identity, 91% coverage
XP_001033476 pfkB family carbohydrate kinase from Tetrahymena thermophila SB210
33% identity, 88% coverage
F2CTM5 Ribokinase from Hordeum vulgare subsp. vulgare
31% identity, 83% coverage
KLMA_10157 probable ribokinase from Kluyveromyces marxianus DMKU3-1042
31% identity, 88% coverage
I1HQ58 Ribokinase from Brachypodium distachyon
30% identity, 83% coverage
- Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon
Barros, The Plant cell 2022 - “...I1GZH6; gamma-glutamylcyclotransferase, I1IY91; hexosyltransferase, I1GQZ2); BdHCT1i (magnesium chelatase, I1GRM4; 5-deoxynucleotidase, I1HPU1; 3-oxoacyl-ACP synthase, I1J2H0; ribokinase, I1HQ58; uncharacterized protein, A0A0Q3HY64; asparaginase, I1J2P3; glutathione transferase, I1HCG7; glutathione transferase, I1GZH6; glutathione transferase, I1I5M1; gamma-glutamylcyclotransferase, I1IY91; 3-methylcrotonyl-CoA carboxylase, I1I750). Full metabolic shifts by RNAi line are provided in Supplemental Figures...”
Pc12g02790 uncharacterized protein from Penicillium rubens
36% identity, 82% coverage
- Studying the Gene Expression of Penicillium rubens Under the Effect of Eight Essential Oils
Kisová, Antibiotics (Basel, Switzerland) 2020 - “...were achieved: at glycolysis (Pc18g01490, Pc12g10630, Pc20g01630, Pc12g13500, Pc20g04410 and Pc12g16040); the pentose phosphate pathway (Pc12g02790, Pc13g14570, Pc12g13500 and Pc20g04410); fructose and mannose metabolisms (Pc16g12970, Pc22g09390, Pc21g05470, Pc20g01550, Pc13g12020, Pc12g09190, Pc12g13500, Pc21g04410, Pc21g04400 and Pc16g10970) and galactose metabolism (Pc12g13500, Pc14g00310, Pc12g07810 and Pc20g04410). The dominant gene...”
XAC0818 ribokinase from Xanthomonas axonopodis pv. citri str. 306
35% identity, 92% coverage
BDP_2024 Ribokinase from Bifidobacterium dentium Bd1
30% identity, 92% coverage
RBSK_YEAST / P25332 Ribokinase; RK; EC 2.7.1.15 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
YCR036W Putative ribokinase from Saccharomyces cerevisiae
30% identity, 89% coverage
- function: Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.
catalytic activity: D-ribose + ATP = D-ribose 5-phosphate + ADP + H(+) (RHEA:13697)
cofactor: Mg(2+) (Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate.)
subunit: Homodimer. - Chemical genomic screening of a Saccharomyces cerevisiae genomewide mutant collection reveals genes required for defense against four antimicrobial peptides derived from proteins found in human saliva
Lis, Antimicrobial agents and chemotherapy 2013 - “...YKL143W YOR233W YPR133W-A YJL130C YBL097W YGR185C YDR310C YPR094W YCR036W YDL235C YER125W YIL051C Lis et al. TABLE 4 Functional groups of genes identified by...”
- Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?
Venkataram, Genome biology and evolution 2010 - “...based on concatenation of 13 genes (YMR009W, YLR147C, YJR034W, YLR029C, YIL074C, YHR142W, YGR284C, YCL055W, YJL072C, YCR036W, YOR250C, YBR196C, YBR282W) for which homologs were identified in all species. Branch lengths show the synonymous substitution rate calculated using HYPHY and model MG94xHKY85. ( B ) Syntenic intergenic regions...”
- Exploring the mode of action of antimicrobial peptide MUC7 12-mer by fitness profiling of Saccharomyces cerevisiae genomewide mutant collection
Lis, Antimicrobial agents and chemotherapy 2009 - “...YHR021C YGL250W YCR045C YCR087C-A YCR050C YNL025C YDR414C YCR036W YMR154C YHL009C YBR290W YCL001W-A YDR069C YML097C YMR063W YOL004W YDR323C YLR423C YDR443C...”
- A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity
Zhou, Genomics 2009 - “...PAC2 Putative tubulin-specific chaperone, involved in formation of alpha-beta-tubulin heterodimer 0.6177 Q15813 Tubulin-specific chaperone E YCR036W RBK1 Ribokinase; member of a family of sugar kinases that includes Pfk2p 0.6283 Q9H477 Ribokinase YML121W GTR1 Cytoplasmic GTP binding protein and negative regulator of the Ran/Tc4 GTPase cycle; component...”
- Identification of human intracellular targets of the medicinal Herb St. John's Wort by chemical-genetic profiling in yeast
McCue, Journal of agricultural and food chemistry 2008 - “...wall organization 72 YOR260W GCD1 regulation of translational initiation 73 YEL030W ECM10 protein refolding 74 YCR036W RBK1 ribose metabolism 75 YDR346C SVF1 response to oxidative stress 76 YPL254W HFI1 telomere maintenance 77 YPR189W SKI3 mRNA catabolism 78 YDR298C ATP5 ATP synthesis coupled proton transport Table 3...”
- Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization
Cheng, BMC bioinformatics 2008 - “...YAL059W, YAR015W, YBL016W, YBL024W, YBL054W, YBL093C, YBR034C, YBR066C, YBR090C, YBR112C, YBR160W, YBR173C, YCL011C, YCL031C, YCL054W, YCR036W, YCR051W, YCR059C, YCR060W, YCR090C, YDL002C, YDL006W, YDL047W, YDL051W, YDL070W, YDL076C, YDL153C, YDL166C, YDR006C, YDR091C, YDR098C, YDR143C, YDR155C, YDR162C, YDR165W, YDR260C, YDR296W, YDR305C, YDR361C, YDR365C, YDR390C, YDR432W, YDR465C, YDR477W, YEL007W, YER012W,...”
- Covert genetic selections to optimize phenotypes
Wu, PloS one 2007 - “...STO1/CBC1 YMR125W #3 control 1 0.6 NT GTT3 YEL017W #18 control 0.94 1.19 NT RBK1 YCR036W #19 control 0.78 0.29 NT OTHER TRANSFORMANTS ON THE PLATE ( FIGURE 3 ) VID22 YLR373C #4 1.15 3.6 NT YJR039W YJR039W #5 0.92 4.4 NT BNA1 YJR025C #6 0.9...”
- The thioredoxin system protects ribosomes against stress-induced aggregation
Rand, Molecular biology of the cell 2006 - “...YDR028C YBL058W YDR477W YBR126C YJR090C YCR036W 6-Phosphofructokinase Glycolytic genes transcriptional activator Alcohol dehydrogenase 6-Phosphogluconate...”
- More
Smp_044850 putative ribokinase from Schistosoma mansoni
30% identity, 83% coverage
- Daily rhythms in gene expression of the human parasite Schistosoma mansoni
Rawlinson, BMC biology 2021 - “...eggshell synthesis domain-containing protein 1.56 6.5 0.00191 Smp_004780 FKBP-type peptidylprolyl isomerase (PPIase) 1.41 16.5 0.00019 Smp_044850 Ribokinase 1.41 16.5 0.00770 Smp_342000 FMRFamide-activated amiloride-sensitive sodium channel 1.38 8.5 0.00191 Smp_069130 Heat shock protein 70 (Hsp70)-4 1.35 14.5 0.00029 Smp_319380 n/a 1.33 2.5 0.00362 Smp_244190 ZP domain-containing protein...”
I6G91_05165 PfkB family carbohydrate kinase from Fannyhessea vaginae
27% identity, 41% coverage
- Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia Strongly Influence Each Other's Transcriptome in Triple-Species Biofilms
Sousa, Microbial ecology 2024 - “...I6G91_05895 LytTR family transcriptional regulator 15.41 2.4110 18 I6G91_05900 DUF3021 domaincontaining protein 11.60 6.9610 8 I6G91_05165 LacI family DNAbinding transcriptional regulator 8.29 1.7310 4 I6G91_04355 Plasmid mobilization relaxosome protein MobC 5.13 1.6110 5 I6G91_04350 Relaxase/mobilization nuclease domaincontaining protein 4.80 3.9810 3 rbsK Ribokinase 4.65 2.7110 28...”
- “...upregulated on the triple-species biofilms while several associated with transcriptional regulation were downregulated (namely I6G91_05895, I6G91_05165, and I6G91_05185). Despite not having any enrichment detected for the DEGs of F. vaginae , the analysis on Cytoscape allowed the identification of the main clusters for the upregulated and...”
N186_RS07290 carbohydrate kinase family protein from Thermofilum adornatum
31% identity, 94% coverage
B7P0U8 Ribokinase from Ixodes scapularis
29% identity, 93% coverage
Pcal_0041 PfkB domain protein from Pyrobaculum calidifontis JCM 11548
30% identity, 96% coverage
- A non-carboxylating pentose bisphosphate pathway in halophilic archaea
Sato, Communications biology 2022 - “...archaeon T. kodakarensis (TK2029) and an ATP-dependent R1P kinase from the hyperthermophilic archaeon Pyrobaculum calidifontis (Pcal_0041). The ATP-dependent R1P kinase identified in this study (Halxa_1682) was 25% identical with the TK2029 protein and 36.8% identical to the Pcal_0041 protein. When comparing the properties of the three...”
- The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism
Hove-Jensen, Microbiology and molecular biology reviews : MMBR 2019 - “...ribosyl 1-phosphate 5-kinase of P. calidifontis (gene Pcal_0041) resembles that described above, with the replacement of ADP for ATP: ribosyl 1-phosphate...”
- “...the gene specifying ATP-dependent ribosyl 1-phosphate 5-kinase (Pcal_0041 of P. calidifontis) is restricted to species of the Crenarchaeota phylum (53). OUTLOOK...”
- A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate
Aziz, Journal of bacteriology 2018 - “...Pyrobaculum calidifontis contains an open reading frame, Pcal_0041, annotated as encoding a PfkB family ribokinase, consisting of phosphofructokinase and...”
- “...domains. Among the biochemically characterized enzymes, the Pcal_0041 protein was 37% identical to the phosphofructokinase (Ape_0012) from Aeropyrum pernix,...”
TTX_1882 carbohydrate kinase family protein from Thermoproteus tenax Kra 1
31% identity, 96% coverage
6xk2A / J9VQ51 Crystal structure of ribokinase from cryptococcus neoformans var. Grubii serotype a in complex with adp
31% identity, 93% coverage
- Ligand: adenosine-5'-diphosphate (6xk2A)
MT2511 ribokinase from Mycobacterium tuberculosis CDC1551
36% identity, 92% coverage
P71913 ribokinase (EC 2.7.1.15) from Mycobacterium tuberculosis (see paper)
Rv2436 RIBOKINASE RBSK from Mycobacterium tuberculosis H37Rv
NP_216952 ribokinase RbsK from Mycobacterium tuberculosis H37Rv
36% identity, 91% coverage
- Novel kinase platform for the validation of the anti-tubercular activities of Pelargonium sidoides (Geraniaceae)
Lukman, BMC biotechnology 2020 - “...Rv0409), glpK (glycerol kinase GK; Rv3696c), thiL (thiamine monophosphate kinase Thil; Rv2977c), rbks (ribokinase RBKS; Rv2436) and ask (aspartokinase AsK; Rv3709c). The aroK gene (encoding Shikimate Kinase) was obtained from the laboratory of Chris Abell, University of Cambridge. The genes were amplified from H37Rv genomic DNA...”
- “...pET-28a GGTA CATATG ACCACTAAAGATCACTC Nde I thil -Rev GAT CTCGAG TTACCCTAGCGAACCTTG Xho I RBKS rbks Rv2436 rbks -Fwd pET-28a GTA CATATG GCAAACGCCAGTGAG Nde I rbks -Rev GAT CTCGAG TTATGAACCGTTGTG Xho I AsK a ask Rv3709c ask alpha-Fwd pCDF- GATTA CATATG GCGCTCGTCGTGCAG Nde I Duet-1 ask alpha-Rev...”
- Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress
Lin, Infection and immunity 2016 - “...Rv1623c Rv1631 Rv1652 Rv1726 Rv1854c Rv1937 Rv2043c Rv2217 Rv2276 Rv2436 Rv2497c galE3 mmsA mog 1.80 2.24 1.81 1.84 1.83 1.79 1.91 1.89 1.88 1.82 1.89 1.77 1.77...”
- Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
Farhat, Nature genetics 2013 - “...34 rpoC Rv0668 12 11,12 13 dnaQ Rv3711c 35 15 opcA Rv1446c 35 36 rbsK Rv2436 37 35 rrs promoter (pre-Rvnr01) 38 39...”
- Targeting drug tolerance in mycobacteria: a perspective from mycobacterial biofilms
Islam, Expert review of anti-infective therapy 2012 - “...(imported), putative MSMEG_0422 Carboxyphosphonoenolpyruvatephosphonomutase-like protein Rv1998c MSMEG_0457 DNA gyrase subunit B, putative Rv0005 MSMEG_0504 Ribokinase Rv2436 MSMEG_0534 Multidrug-resistance protein, putative MSMEG_0550 ABC transporter, periplasmic substrate-binding protein MSMEG_0782 Aminotransferase, class III Rv2598 MSMEG_0790 MUTT3 Rv0413 MSMEG_0911 Isocitratelyase Rv0467 MSMEG_1123 Putativecobalamin synthesis protein MSMEG_1129 D-amino acid dehydrogenase, small...”
- Physical and functional interaction between D-ribokinase and topoisomerase I has opposite effects on their respective activity in Mycobacterium smegmatis and Mycobacterium tuberculosis
Yang, Archives of biochemistry and biophysics 2011 (PubMed)- “...characterized the activities of two putative ribokinases, Rv2436 and Ms4585, from M. tuberculosis and Mycobacterium smegmatis, respectively. The mycobacterial...”
- “...of the activity of ribokinase in M. tuberculosis (Rv2436) and M. smegmatis (Ms4585) M. smegmatis d -ribokinase interacts with its topoisomerase I (MsTopA) d...”
- Physical and functional interaction between D-ribokinase and topoisomerase I has opposite effects on their respective activity in Mycobacterium smegmatis and Mycobacterium tuberculosis.
Yang, Archives of biochemistry and biophysics 2011 (PubMed)- GeneRIF: uncovered an interplay between ribokinase and topoisomerase I, which implies the existence of a novel regulatory strategy for efficient utilization of D-ribose that may be useful in stressful environments with restricted access to nutrients
CNAG_02296 ATP-binding protein from Cryptococcus neoformans var. grubii H99
31% identity, 92% coverage
- Interplay between acetylation and ubiquitination of imitation switch chromatin remodeler Isw1 confers multidrug resistance in <i>Cryptococcus neoformans</i>
Meng, eLife 2024 - “...( Denning and Bromley, 2015 ), including seven genes encoding ATP-binding cassette (ABC) transporters ( CNAG_02296 , CNAG_02430 , CNAG_06338 , CNAG_00792 , CNAG_01575 , CNAG_03600 , and CNAG_02764 ), two genes encoding efflux proteins ( CNAG_03101 and CNAG_01960 ), and three genes encoding major facilitator...”
3go6A / P71913 Crystal structure of m. Tuberculosis ribokinase (rv2436) in complex with ribose and amp-pnp
36% identity, 91% coverage
- Ligands: alpha-d-ribofuranose; magnesium ion (3go6A)
Q42645 fructokinase (EC 2.7.1.4) from Beta vulgaris (see paper)
31% identity, 88% coverage
LOC106356810 probable fructokinase-4 from Brassica napus
29% identity, 91% coverage
- Comparative Cytological and Transcriptome Analyses of Anther Development in Nsa Cytoplasmic Male Sterile (1258A) and Maintainer Lines in Brassica napus Produced by Distant Hybridization
Xing, International journal of molecular sciences 2022 - “...period, namely LOC106421218 , LOC106399638 , LOC106346734 , LOC106440633 , LOC106439029 , LOC106413118 , and LOC106356810 ( Figure 9 C). Seven genes in Class V had abnormally low expression levels, namely LOC106422956 , LOC106454372 , LOC106350934 , LOC106428191 , LOC106382995 , LOC106419470 , and LOC106361841 (...”
LOC110718125 probable fructokinase-1 from Chenopodium quinoa
29% identity, 85% coverage
- Molecular mechanisms regulating glucose metabolism in quinoa (Chenopodium quinoa Willd.) seeds under drought stress
Wang, BMC plant biology 2024 - “...KEGG pathway. UDP-glucose, D-glucose, D-fructose-6-phosphate, D-glucose-6-phosphate, and D-glucose-1-phosphate were positively correlated with CqINV (LOC110717458), CqFK4 (LOC110718125), CqCELB (LOC29490), Cqbg1x (LOC110695967, LOC110685748), CqSUS (LOC110689796, LOC110727927), and CqHK2 (LOC110729879), respectively (PCC0.6). Fructose-6-phosphate, D-glucose-6-phosphate, and D-glucose-1-phosphate were highly positively correlated with CqINV (LOC110717458), and PCCs were 0.98, 0.91, 0.93,...”
Q9M1B9 fructokinase (EC 2.7.1.4) from Arabidopsis thaliana (see paper)
NP_191507 pfkB-type carbohydrate kinase family protein from Arabidopsis thaliana
AT3G59480 pfkB-like carbohydrate kinase family protein from Arabidopsis thaliana
28% identity, 91% coverage
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of five of the AtFRK genes ( AtFRK1,3,4,6,7 )...”
- Transcriptomics of different tissues of blueberry and diversity analysis of rhizosphere fungi under cadmium stress
Chen, BMC plant biology 2021 - “...other glycan degradation (map00511), and galactose metabolism (map00052). It was found that bgal3, os03g0165400, at5g34940, at3g59480, chitinase, bxl2, xyl2 and chil3 were up-regulated, but only JKD was down-regulated. All of these results indicated that the cell wall and cell membrane of blueberry root are important sites...”
- Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis
Zhang, Nature communications 2020 - “...selected. As shown in Supplementary Fig. 10bd , nuclear run-on assay showed that AT2G43570 , AT3G59480 , and AT3G53650 genes were transcriptionally upregulated compared to wild type, indicating that these three genes are subjected to BPC complex-mediated transcriptional repression. Interestingly, ChIP-qPCR results indicated that H3K27me3 levels...”
- Codon usage pattern and predicted gene expression in Arabidopsis thaliana
Sahoo, Gene: X 2019 - “...Synthase AT4G23710 Transmembrane Protein AT2G04621 CML42 AT3G01390 AT2G01870 CML11 AT2G33040 AT2G13965 Acyltransferase AT5G11670 Carbohydrate kinase AT3G59480 AT5G19875 Basic helix-loop-helix transcription factor AT4G10480 AT1G50390 AT5G03120 AT3G12390 AT1G79550 AT2G29180 Basic leucine zipper transcription factor AT4G35900 AT3G18800 AT2G17770 Extracellular matrix structural protein AT4G08410 AT2G25297 Homeodomain transcription factor AT5G53980 AT3G54580...”
- Effects of Simulated Space Radiations on the Tomato Root Proteome
Desiderio, Frontiers in plant science 2019 - “...Oxidation/reduction 2347: 1.0; 1.5; 1.6 2347: 5.40/5.43 2347: 38.528/32.009 2347: 5.6/2 2475 2482 Fructokinase-2 AT3G59480.1 AT3G59480 Carbon metabolism 2475: 1.2; 1.3; 1.6 2482: 1.0; 1.7; 1.8 2475: 5.76/5.72 2482: 5.76/5.82 2475: 34.969/29.769 2482: 34.969/29.207 2475: 54.9/15 2482: 66.5/20 2475 Malate dehydrogenase AT3G47520.1 MDH Oxidation/reduction 2475: 8.34/5.72...”
- “...different tissues under challenge conditions ( Granot et al., 2014 ). The increase in fructokinase-2 (AT3G59480) representation levels obtained after -rays exposure should likely refer to the need of the plant to metabolize hexose sugars through phosphorylation, thus providing energy necessary to sustain the corresponding stress...”
- Proteomic and metabolomic analyses provide insight into the off-flavour of fruits from citrus trees infected with 'Candidatus Liberibacter asiaticus'
Yao, Horticulture research 2019 - “...0.55 9.42E03 gi|568845013 AT4G10960 UGE5 UDP- d -glucose 4-epimerase 5 EC 5.1.3.2 0.51 2.93E02 gi|568849997 AT3G59480 FRK3 Fructokinase 3 EC 2.7.1.4 0.55 1.02E04 gi|568855816 AT5G03290 IDH-V NAD + -dependent isocitric dehydrogenase V EC 1.1.1.41 0.55 1.28E03 gi|568856679 AT2G36530 ENO2 Enolase 2 EC 4.2.1.11 0.62 1.85E10 gi|568864726...”
- Plant Fructokinases: Evolutionary, Developmental, and Metabolic Aspects in Sink Tissues
Stein, Frontiers in plant science 2018 - “...(AAB57733), SlFRK2 (AAB57734), SlFRK3 (NP_001234396), SlFRK4 (AAM44084), At1g06020 (AAF80125), At1g06030 (AAF80126), At1g66430 (AAG51160), At2g31390 (AAM14251), At3g59480 (CAB75445), At4g10260 (CAB78149), At5g51830 (AAL34211), Os01g0894300(AAL26574), Os08g0113100 (AAL26573), Zm00001d035037 (AAP42806), Zm00001d042536 (AAP42805), BvFRK (AAA80675), StFRK (CAA78283), AtFLN1 (AEE79187), AtFLN2 (NP_177080), SlFLN1 (XP_004246362), SlFLN2 (XP_004239035), ZmFLN1 (ONM36391),and ZmFLN2 (ONM06924). The structure...”
- “...al., 2013 ). In Arabidopsis, seven FRK genes (At5g51830, At2g31390, At1g66430, At4g10260, At1g06020, At1g06030, and At3g59480) were identified and named AtFRK17 , respectively ( Riggs et al., 2017 ). The identities of the Arabidopsis FRKs were verified following protein expression in E. coli , purification and...”
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...that were used in the mega4 software for creating the phylogenetic tree were incorrect. AtFRK3 (At3g59480) should read AtFRK3 (At1g06020) and AtFRK4 (At4g06030) should read AtFRK4 (At3g59480) as in the text, Table S1 and uniprot annotation for arabidopsis probable fructokinases. The corrected Figure 1 appears below....”
- “...sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that...”
- Identification and biochemical characterization of the fructokinase gene family in Arabidopsis thaliana
Riggs, BMC plant biology 2017 - “...divided into two branches. One branch within this clade comprised the two fructokinase-like proteins FLN1 (At3g59480) and FLN2 (At1g69200), for which no kinase activity has been detected [ 23 ]. The other branch comprised seven proteins including FRK3. An eighth putative pfkB family member was excluded...”
- “...et al.) FRK3 At4g10260 FRK3 (Pego and Smeekens) FRK4 At1g06020 na FRK5 At1g06030 na FRK6 At3g59480 na FRK7 Another predicted pfkB protein, At1g50390, claded with the FRK branch, but the predicted protein is only 16kDa, while other FRKs range from ~3441kDa. The 16kDa protein is missing...”
- More
- Protein Changes in Response to Lead Stress of Lead-Tolerant and Lead-Sensitive Industrial Hemp Using SWATH Technology.
Xia, Genes 2019 - “...diphosphate; the key enzyme in the sugar degradation pathway, fructose bisphosphate aldolase 6(Q9SJQ9), probablyfructokinase-4 (FRK) (Q9M1B9) for the decomposition of sucrose and fructose in glycometabolism and the respiratory electron transporters cytochrome C oxidase subunit 6b-1 (Q9S7L9) and cytochrome C oxidase subunit 5b-1 (Q9LW15). APE regulates ATP...”
- Proteomic analysis on roots of Oenothera glazioviana under copper-stress conditions
Wang, Scientific reports 2017 - “...9, plasma membrane-type Arabidopsis thaliana Q9LU41 ACA9 2 3.38 0.02257 32 P37829 Fructokinase Solanum tuberosum Q9M1B9 N/A 3 3.73 1.3E-08 33 B9T118 NADH-ubiquinone oxidoreductase, putative Ricinus communis Q9FGI6 RCOM_0458390 3 0.60 0.00043 Signal Transduction 34 P40392 Ras-related protein RIC1 Oryza sativa P28188 RIC1 1 0.35 6E-07...”
CRIB_152 carbohydrate kinase from Romboutsia ilealis
28% identity, 95% coverage
- Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
Gerritsen, PeerJ 2017 - “...sucrose-specific EIIBC component (CRIB_1461); 3, -fructofuranosidase with RDD family protein (CRIB_1459 and CRIB_1460); 4, fructokinase (CRIB_152 and CRIB_1458); 5; ABC-type transporter (CRIB_148-CRIB_150); 6, -fructofuranosidase (CRIB_151); 7, glucokinase (CRIB_1849); 8, glucose 6-phosphate isomerase (CRIB_140); 9, fructose 1,6-bisphosphatase (CRIB_45 and CRIB_2020); 10, 6-phosphofructokinase ; (CRIB_104); 11, fructose-bisphosphate aldolase...”
XP_002268097 probable fructokinase-4 from Vitis vinifera
A5B8T3 fructokinase from Vitis vinifera
30% identity, 88% coverage
D2D2Z5 fructokinase from Gossypium hirsutum
30% identity, 88% coverage
SERP1494 fructokinase, putative from Staphylococcus epidermidis RP62A
28% identity, 93% coverage
PAE0835 sugar kinase, possible phosphofructokinase from Pyrobaculum aerophilum str. IM2
29% identity, 96% coverage
SCRK1_ORYSJ / Q0JGZ6 Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 from Oryza sativa subsp. japonica (Rice) (see paper)
27% identity, 92% coverage
- function: Fructokinase that may play an important role in maintaining the flux of carbon towards starch formation. May also be involved in a sugar-sensing pathway.
catalytic activity: D-fructose + ATP = D-fructose 6-phosphate + ADP + H(+) (RHEA:16125) - iTRAQ-based proteome profile analysis of superior and inferior Spikelets at early grain filling stage in japonica Rice
You, BMC plant biology 2017 - “...Putative alpha-glucosidase 0.480.04 ns ns 44 Os01g0633100 Q7G065 ADP-glucose pyrophosphorylase/AGPase 3.360.44 ns ns 45 Os01g0894300 Q0JGZ6 Fructokinase-1 0.530.04 ns ns 46 Os01g0841600 Q8LR75 Triosephosphate isomerase ns 0.330.05 ns 49 Os06g0675700 Q0DA62 Probable alpha-glucosidase Os06g0675700 4.711.86 2.510.76 ns 84 Os09g0553200 Q93X08 Os09g0553200 protein 3.230.63 ns ns 86...”
AZOLI_p20179 ribokinase from Azospirillum lipoferum 4B
33% identity, 97% coverage
SCRK1_ORYSI / A2WXV8 Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 from Oryza sativa subsp. indica (Rice) (see paper)
27% identity, 92% coverage
- function: May play an important role in maintaining the flux of carbon towards starch formation. May also be involved in a sugar-sensing pathway
catalytic activity: D-fructose + ATP = D-fructose 6-phosphate + ADP + H(+) (RHEA:16125) - Comparative study of the protein profiles of Sunki mandarin and Rangpur lime plants in response to water deficit
Oliveira, BMC plant biology 2015 - “...-4.18 113 2-dehydro-3-deoxyphosphooctonate aldolase Medicago truncatula ABN05924 427/2e-13 31.9/28 6.61/4.91 np 116 Fructokinase Oryza sativa A2WXV8 70/1e-34 30.3/87 5.50/6.19 np 154 Heat shock protein-70 cognate protein Arabidopsis thaliana NP_176036 73/0.0 71.4/65 5.10/5.27 np 194 F-box family protein Vitis vinifera XP_002279122 414/4e-139 47.2/55 9.4/6.39 1.57 np 196...”
- Proteomic analysis of salt-responsive proteins in the leaves of mangrove Kandelia candel during short-term stress
Wang, PloS one 2014 - “...communis XP_002519975 FGHVTFFWNGNR(1481.7295) LPSHYLVSPPEIER(1636.8873) 61.15/5.52 59.96/5.81 217/163 2/15 18% 32 Fructokinase-1 Oryza sativa Indica Group A2WXV8 TALAFVTLR(991.6175) APGGAPANVAIAVAR(1334.7853) 34.71/5.14 36.98/5.31 186/142 2/9 32% 34 Malate dehydrogenase, cytoplasmic Mesembryantheum crystallinum O24047 NVIIWGNHSSTQYPDVNHATVK (2480.1733) 35.48/6.00 37.02/6.41 77/38 1/3 15% 39 triosephosphate isomerase Gossypium hirsutum ACJ11723 FFVGGNWK(954.5039) 27.19/6.00 25.33/6.04...”
- Comparative proteomics analysis of proteins expressed in the I-1 and I-2 internodes of strawberry stolons
Fang, Proteome science 2011 - “...phosphoglycerate mutase P30792 manganese ion binding Zea mays 60.7/5.2 41.3/4.9 59 24 8/27 133 Fructokinase-1 A2WXV8 ATP binding Oryza sativa 34878/5.1 36.1/3.8 76 23 6/15 142 S-adenosylmethionine synthase 4 A9PHC5 metal ion binding Populus trichocarpa 42999/5.7 46.5/6.3 74 18 5/2 162 Phosphoglucomutase P93804 magnesium ion binding...”
- “...d Experimental kDa/pI e Score f SC g (%) Matched/Unmatched queries h Metabolism 91 Fructokinase-1 A2WXV8 ATP binding Oryza sativa 34.9/5.1 35.8/3.4 76 20 6/59 95 Caffeic acid 3-O-methyltransferase Q8GU25 caffeate O-methyltransferase activity Rosa chinensis 40.1/5.6 43.7/4.4 110 35 12/30 129 Malate dehydrogenase, mitochondrial P83373 Oxidoreductase...”
Q9SID0 fructokinase (EC 2.7.1.4) from Arabidopsis thaliana (see paper)
NP_180697 pfkB-like carbohydrate kinase family protein from Arabidopsis thaliana
AT2G31390 pfkB-type carbohydrate kinase family protein from Arabidopsis thaliana
29% identity, 93% coverage
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...(NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...(NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of five of the AtFRK genes ( AtFRK1,3,4,6,7 ) were identified and obtained from ABRC stocks...”
- Comparative proteome analyses of rhizomania resistant transgenic sugar beets based on RNA silencing mechanism.
Hejri, GM crops & food 2021 - “...Magnesium ion binding and inorganic diphosphatase activity Phosphate-containing compound metabolism Cytoplasm S6 26 Probable fructokinase-1 Q9SID0 (SCRK1_ARATH) 71 40 35,424 5.31 ATP binding and fructokinase activity Carbohydrate metabolism Plasma Membrane, Peroxisome, Cytosol S3 *, S6 27 Eukaryotic translation initiation factor 3 subunit B Q9C5Z1 (EIF3B_ARATH) 47...”
- Identification of MAMP-Responsive Plasma Membrane-Associated Proteins in Arabidopsis thaliana Following Challenge with Different LPS Chemotypes from Xanthomonas campestris
Hussan, Pathogens (Basel, Switzerland) 2020 - “...1 P32961 Adenine nucleotide alpha hydrolases-like superfamily protein Q9M328 Cytochrome P450 71B28 Q9SAE3 Probable fructokinase-1 Q9SID0 Phosphoglucomutase/phosphomannomutase family protein F4I6W4 Common proteins bound to LPS Xcc 8530 functionalized MagReSyn TM and EndoTrap Aldolase-type TIM barrel family protein A8MS37 a the protein identified by LC/MS/MS. b the...”
- Integrated physiologic, proteomic, and metabolomic analyses of Malus halliana adaptation to saline-alkali stress
Jia, Horticulture research 2019 - “...4-epimerase 3 Q8LDN8 3.498 1.806 XYL2 Putative alpha-xylosidase 2 F4J6T7 3.845 1.943 At2g31390 Probable fructokinase-1 Q9SID0 2.408 1.268 AMY1 Alpha-amylase 1 Q8VZ56 4.100 2.036 BGLU13 Beta-glucosidase 13 Q9LU02 13.965 3.804 BGLU44 Beta-glucosidase 44 Q9LV33 2.814 1.493 PMM Phosphomannomutase O80840 0.418 1.260 At5g28840 GDP-mannose 3,5-epimerase Q93VR3 0.379...”
- Comparative Proteomics Reveals Cold Acclimation Machinery Through Enhanced Carbohydrate and Amino Acid Metabolism in Wucai (Brassica Campestris L.)
Yuan, Plants (Basel, Switzerland) 2019 - “...and the abundance of three uncharacterized proteins mapped to the corresponding genes PDX13 (Q8L940), At2g31390 (Q9SID0), and CP12-2 (Q9LZP9)also increased under low temperatures ( Figure 4 A). 2.3.2. DEPs Involved in Photosynthesis and Energy Metabolism Several critical proteins related to photosynthesis and energy metabolism were found...”
- Arabidopsis Response to Inhibitor of Cytokinin Degradation INCYDE: Modulations of Cytokinin Signaling and Plant Proteome
Berková, Plants (Basel, Switzerland) 2020 - “...cation-binding protein 1 0.66 1.5 10 3 AT3G55800 Carbohydrate metabolism Sedoheptulose-1,7-bisphosphatase 0.72 3.4 10 4 AT2G31390 Carbohydrate metabolism Fructokinase-1 0.73 2.7 10 4 AT1G65960 GABA biosynthesis Glutamate decarboxylase 2 0.66 1.5 10 3 AT5G26000 Glucosinolate degradation Myrosinase 1 0.65 1.7 10 3 AT5G56010 Chaperon, defense response...”
- Investigation of the effects of P1 on HC-pro-mediated gene silencing suppression through genetics and omics approaches
Hu, Botanical studies 2020 - “...Glucose-6-phosphate 1-dehydrogenase, cytoplasmic isoform 1 + + AT2G23930 Probable small nuclear ribonucleoprotein G + + AT2G31390 Probable fructokinase-1 + + AT3G62830 UDP-glucuronic acid decarboxylase 2 + + AT5G03630 Monodehydroascorbate reductase 2 + + AT3G52560 Ubiquitin-conjugating enzyme E2 variant 1D + + AT1G64520 26S proteasome non-ATPase regulatory...”
- Integrated physiologic, proteomic, and metabolomic analyses of Malus halliana adaptation to saline-alkali stress
Jia, Horticulture research 2019 - “...31 proteins and 13 metabolites were mapped to the diagram. The expression of UGE3, XYL2, At2g31390, AMY1, BGLU13, BGLU44, and sucrose, which are involved in starch and sucrose metabolism, was upregulated. Notably, the upregulation of UGE3 catalyzes the interconversion of UDP-glucose and UDP-galactose, which is the...”
- “...4-epimerase and UDP-xylose 4-epimerase 3 Q8LDN8 3.498 1.806 XYL2 Putative alpha-xylosidase 2 F4J6T7 3.845 1.943 At2g31390 Probable fructokinase-1 Q9SID0 2.408 1.268 AMY1 Alpha-amylase 1 Q8VZ56 4.100 2.036 BGLU13 Beta-glucosidase 13 Q9LU02 13.965 3.804 BGLU44 Beta-glucosidase 44 Q9LV33 2.814 1.493 PMM Phosphomannomutase O80840 0.418 1.260 At5g28840 GDP-mannose...”
- Comparative Proteomics Reveals Cold Acclimation Machinery Through Enhanced Carbohydrate and Amino Acid Metabolism in Wucai (Brassica Campestris L.)
Yuan, Plants (Basel, Switzerland) 2019 - “...up-regulated, and the abundance of three uncharacterized proteins mapped to the corresponding genes PDX13 (Q8L940), At2g31390 (Q9SID0), and CP12-2 (Q9LZP9)also increased under low temperatures ( Figure 4 A). 2.3.2. DEPs Involved in Photosynthesis and Energy Metabolism Several critical proteins related to photosynthesis and energy metabolism were...”
- Plant Fructokinases: Evolutionary, Developmental, and Metabolic Aspects in Sink Tissues
Stein, Frontiers in plant science 2018 - “...alignment: SlFRK1 (AAB57733), SlFRK2 (AAB57734), SlFRK3 (NP_001234396), SlFRK4 (AAM44084), At1g06020 (AAF80125), At1g06030 (AAF80126), At1g66430 (AAG51160), At2g31390 (AAM14251), At3g59480 (CAB75445), At4g10260 (CAB78149), At5g51830 (AAL34211), Os01g0894300(AAL26574), Os08g0113100 (AAL26573), Zm00001d035037 (AAP42806), Zm00001d042536 (AAP42805), BvFRK (AAA80675), StFRK (CAA78283), AtFLN1 (AEE79187), AtFLN2 (NP_177080), SlFLN1 (XP_004246362), SlFLN2 (XP_004239035), ZmFLN1 (ONM36391),and ZmFLN2 (ONM06924)....”
- “...et al., 2012 ; Koenig et al., 2013 ). In Arabidopsis, seven FRK genes (At5g51830, At2g31390, At1g66430, At4g10260, At1g06020, At1g06030, and At3g59480) were identified and named AtFRK17 , respectively ( Riggs et al., 2017 ). The identities of the Arabidopsis FRKs were verified following protein expression...”
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict...”
- Identification and biochemical characterization of the fructokinase gene family in Arabidopsis thaliana
Riggs, BMC plant biology 2017 - “...[ 18 ]. At4g10260 is designated FRK4 here [ 25 ]. FRK1 (At5g51830) and FRK2 (At2g31390) were previously annotated due to their similarity to the tomato isozymes [ 25 ]. To visualize specific regions of highest identity we aligned the peptide sequences of the seven putative...”
- “...AGI number Previous designation (citation) Designation in this manuscript At5g51830 FRK1 (Pego and Smeekens) FRK1 At2g31390 FRK2 (Pego and Smeekens) FRK2 At1g66430 FRK3 (Arsova et al.) FRK3 At4g10260 FRK3 (Pego and Smeekens) FRK4 At1g06020 na FRK5 At1g06030 na FRK6 At3g59480 na FRK7 Another predicted pfkB protein,...”
- TWIN SISTER OF FT (TSF) Interacts with FRUCTOKINASE6 and Inhibits Its Kinase Activity in Arabidopsis
Jin, Frontiers in plant science 2017 - “...The Arabidopsis genome contains seven FRK genes encoding proteins with fructose phosphorylating activity: FRK1 ( At2g31390 ), FRK2 ( At1g06030 ), FRK3 ( At1g06020 ), FRK4 ( At3g59480 ), FRK5 ( At4g10260 ), FRK6 ( At1g66430 ), and FRK7 ( At5g51830 ) ( Stein et al.,...”
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LOC110113984 fructokinase-1 from Dendrobium catenatum
27% identity, 92% coverage
- The varying responses of leaves and roots and the link between sugar metabolic genes and the SWEET family in Dendrobium officinale under salt stress
Hao, BMC genomics 2024 - “...A and Additional file 1: Table S7 ). At the single gene level, scrK ( LOC110113984 and LOC110116405 ), INV ( LOC110096666 ), and SUS ( LOC110110417 ) exhibited positive correlations with most DoSWEETs (Fig. 6 A and Additional file 1: Table S8 ). RT-qPCR analysis...”
- “...DoSWEET2a , DoSWEET13 , and DoSWEET16 exhibited high positive correlations (correlation coefficient>0.82) with scrK ( LOC110113984 ), INV ( LOC110096666 ), and SUS ( LOC110110417 ). In roots, the up-regulated DoSWEET2a , DoSWEET6a , DoSWEET12a , DoSWEET14 , and DoSWEET16 showed positive correlations with INV (...”
XAC1557 fructokinase from Xanthomonas axonopodis pv. citri str. 306
27% identity, 86% coverage
LOC18046804 probable fructokinase-4 from Citrus x clementina
29% identity, 91% coverage
- Transcriptome analysis of Harumi tangor fruits: Insights into interstock-mediated fruit quality
Liao, Frontiers in plant science 2022 - “...(SUS6, LOC18038613), serine carboxypeptidase-like (LOC18043305, LOC18039558, LOC18043732), pyruvate kinase (LOC18045215, LOC18050485), fructokinase-4 ( FRK4 , LOC18046804), and isocitrate dehydrogenase ( NAD-IDH , LOC18037111) were >1.2-fold higher in the HP4 group than in the HPP4 group. In contrast, the expression levels of genes encoding pyruvate kinase (...”
- “...the HPP group at 180 DAF. The isocitrate dehydrogenase gene IDH-III (LOC18037111), fructokinase gene FRK4 (LOC18046804), alkaline/neutral invertase gene CINV2 (CICLE_v10003734mg, LOC18042730), hexokinase gene HXK1 (LOC18035909), and sucrase/ferredoxin-like gene (LOC18051223) were downregulated in the HPP group at 45, 90, and 180 DAF and upregulated in the...”
Q9LNE3 Probable fructokinase-2 from Arabidopsis thaliana
AT1G06030 pfkB-like carbohydrate kinase family protein from Arabidopsis thaliana
NP_172093 pfkB-type carbohydrate kinase family protein from Arabidopsis thaliana
29% identity, 91% coverage
- iTRAQ-Based Proteomic Analysis Reveals Potential Regulation Networks of IBA-Induced Adventitious Root Formation in Apple
Lei, International journal of molecular sciences 2018 - “...P46283 83.72 5.8 3 1.57 MDP0000277811 Fructose-1,6-bisphosphatase P46283 80.67 5 1 1.95 MDP0000275261 Probable fructokinase-2 Q9LNE3 65.8 8.5 1 1.57 MDP0000178814 Pyruvate dehydrogenase complex Q54M22 53.72 6.3 1 1.59 MDP0000325085 Isocitrate dehydrogenase P50217 89.78 21.1 3 1.54 MDP0000214399 2-oxoglutarate and Fe(II)-dependent oxygenase superfamily protein Q39110 26.8...”
- Identification of differentially accumulated proteins associated with embryogenic and non-embryogenic calli in saffron (Crocus sativus L.)
Sharifi, Proteome science 2012 - “...Ricinus communis B9RWU6 12/86 2/1 -9.1** -7.7** 1.2 1443 35/43 4.9/4.91 Probable fructokinase-2/ Arabidopsis thaliana Q9LNE3 22/182 7/3 1.2 1199 51/50 5.8/5.61 Elongation factor Tu, chloroplastic/ Arabidopsis thaliana P17745 16/360 5/5 1.8** 1.4 ns 1.3 1868 92/31 5.8/5.14 Initiation factor eIF-4 gamma, middle; Up-frameshift suppressor2/ Medicago...”
- Arabidopsis thaliana MYC2 and MYC3 Are Involved in Ethylene-Regulated Hypocotyl Growth as Negative Regulators
Li, International journal of molecular sciences 2024 - “...hydrolases AT4G25150 Acid phosphatase-like protein AT1G06520 GPAT1 Glycerol-3-phosphate acyltransferase 1 AT1G66040 ORTH4 E3 ubiquitin-protein ligase AT1G06030 Fructokinase-2 AT5G05270 CHI3 Chalconeflavonone isomerase 3, involved in response to karrikin AT1G65060 4CL3 4-coumarate-CoA ligase 3, involved in phenylpropanoid synthesis AT1G72520 LOX4 Lipoxygenase 4, involved in growth and defense response...”
- Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening
Nilo-Poyanco, BMC genomics 2021 - “...1 3 Qualit_O1 Triose-phosphate isomerase / Triosephosphate mutase AT3G55440 Prupe.1G196700 1 5 Qualit_O1 Probable fructokinase-2 AT1G06030 Prupe.1G354000 1 2 Qualit_O1 1,4-alpha-glucan-branching enzyme 1, chloroplastic/amyloplastic AT5G03650 Prupe.1G376200 1 6 Up_O1 GLUCOSE-1-PHOSPHATE ADENYLYLTRANSFERASE LARGE SUBUNIT 2, CHLOROPLASTIC AT1G27680 Prupe.1G378500 0.998 2 Up_O1 SUGAR TRANSPORTER ERD6-LIKE 4-RELATED AT1G75220 Carbohydrates/Energy...”
- Plant Fructokinases: Evolutionary, Developmental, and Metabolic Aspects in Sink Tissues
Stein, Frontiers in plant science 2018 - “...used for the sequence alignment: SlFRK1 (AAB57733), SlFRK2 (AAB57734), SlFRK3 (NP_001234396), SlFRK4 (AAM44084), At1g06020 (AAF80125), At1g06030 (AAF80126), At1g66430 (AAG51160), At2g31390 (AAM14251), At3g59480 (CAB75445), At4g10260 (CAB78149), At5g51830 (AAL34211), Os01g0894300(AAL26574), Os08g0113100 (AAL26573), Zm00001d035037 (AAP42806), Zm00001d042536 (AAP42805), BvFRK (AAA80675), StFRK (CAA78283), AtFLN1 (AEE79187), AtFLN2 (NP_177080), SlFLN1 (XP_004246362), SlFLN2 (XP_004239035),...”
- “...Koenig et al., 2013 ). In Arabidopsis, seven FRK genes (At5g51830, At2g31390, At1g66430, At4g10260, At1g06020, At1g06030, and At3g59480) were identified and named AtFRK17 , respectively ( Riggs et al., 2017 ). The identities of the Arabidopsis FRKs were verified following protein expression in E. coli ,...”
- The Role of Programmed Cell Death Regulator LSD1 in Nematode-Induced Syncytium Formation
Matuszkiewicz, Frontiers in plant science 2018 - “...2.28E-32 AT4G37160 SKS15 -3.17 2.19E-13 LSD1 independent AT1G68460 IPT1 5.05 1.73E-46 AT1G08440 ALMT2 4.50 6.90E-39 AT1G06030 TPS7 4.19 6.27E-17 AT1G71890 SUC5 4.09 5.56E-21 AT4G15210 BAM5 3.59 1.66E-10 AT5G01740 NTF2 -4.32 8.68E-30 AT4G15370 BARS1 -4.17 4.76E-16 AT1G80340 YUC9 -3.84 2.93E-17 AT1G65570 RNA HELICASE -3.77 2.54E-15 AT3G29430 GGPS11...”
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...(NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be...”
- Identification and biochemical characterization of the fructokinase gene family in Arabidopsis thaliana
Riggs, BMC plant biology 2017 - “...At1g66430 FRK3 (Arsova et al.) FRK3 At4g10260 FRK3 (Pego and Smeekens) FRK4 At1g06020 na FRK5 At1g06030 na FRK6 At3g59480 na FRK7 Another predicted pfkB protein, At1g50390, claded with the FRK branch, but the predicted protein is only 16kDa, while other FRKs range from ~3441kDa. The 16kDa...”
- “...bacterial expression GGGGACCACTTTGTACAAGAAAGCTGGGTCTTAAACGACGGCTTTGAG At4g10260 forward FRK4 bacterial/plant expression GGGGACAAGTTTGTACAAAAAAGCAGGCTTGATGGCTAATACTCCATTG At4g10260 reverse FRK4 bacterial expression GGGGACCACTTTGTACAAGAAAGCTGGGTCCTATTTAGACTTAGATTTC At1g06030 forward FRK6 bacterial/plant expression GGGGACAAGTTTGTACAAAAAAGCAGGCTTGATGACGTCATCCAACGGCG At1g06030 reverse FRK6 bacterial expression GGGGACCACTTTGTACAAGAAAGCTGGGTCCTATTCTACTTGTATCTTAAG At3g59480 forward FRK7 bacterial/plant expression GGGGACAAGTTTGTACAAAAAAGCAGGCTTGATGGCTGCATCTAACGGCGAG At3g59480 reverse FRK7 bacterial expression GGGGACCACTTTGTACAAGAAAGCTGGGTCTTAGTTTCCTTTCAGGAGGC At5g51830 forward FRK1 plant expression GGGGACAAGTTTGTACAAAAAAGCAGGCTTGATGGGTGAGGATGCAATCTC At5g51830...”
- TWIN SISTER OF FT (TSF) Interacts with FRUCTOKINASE6 and Inhibits Its Kinase Activity in Arabidopsis
Jin, Frontiers in plant science 2017 - “...seven FRK genes encoding proteins with fructose phosphorylating activity: FRK1 ( At2g31390 ), FRK2 ( At1g06030 ), FRK3 ( At1g06020 ), FRK4 ( At3g59480 ), FRK5 ( At4g10260 ), FRK6 ( At1g66430 ), and FRK7 ( At5g51830 ) ( Stein et al., 2017 ). FRK17 contain...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...FRK (At5g51830, assigned FRK7), is closely related to SlFRK1 , while five other proteins (At2g31390, At1g06030, At1g06020, At3g59480, At4g10260 assigned FRK1-5, respectively) are closely related to SlFRK2 , the main cytosolic FRK in tomato. Although a comparison of their respective sequences does not suggest any relation,...”
- “...(NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of five of the AtFRK genes ( AtFRK1,3,4,6,7 ) were...”
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- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of five of the AtFRK genes ( AtFRK1,3,4,6,7 ) were identified...”
O82616 fructokinase (EC 2.7.1.4) from Arabidopsis thaliana (see paper)
NP_192764 pfkB-type carbohydrate kinase family protein from Arabidopsis thaliana
AT4G10260 pfkB-like carbohydrate kinase family protein from Arabidopsis thaliana
28% identity, 93% coverage
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of five of the AtFRK genes (...”
- Barley Root Proteome and Metabolome in Response to Cytokinin and Abiotic Stimuli
Berka, Frontiers in plant science 2020 - “...Energy metabolism HORVU6Hr1G088420 2-Oxoglutarate (2OG) and Fe(II)-dependent oxygenase AT1G49390 NR NR NR NR HORVU1Hr1G083470 5-Dehydro-2-deoxygluconokinase AT4G10260 NR NR NR NR HORVU1Hr1G090720 Malate dehydrogenase AT1G53240 NR NR NR HORVU5Hr1G111620 Methylenetetrahydrofolate reductase 2 AT2G44160 NR NR NR Histone HORVU1Hr1G074340 Histone superfamily protein AT1G09200 NR NR NR NR HORVU6Hr1G031580...”
- Plant Fructokinases: Evolutionary, Developmental, and Metabolic Aspects in Sink Tissues
Stein, Frontiers in plant science 2018 - “...(AAB57734), SlFRK3 (NP_001234396), SlFRK4 (AAM44084), At1g06020 (AAF80125), At1g06030 (AAF80126), At1g66430 (AAG51160), At2g31390 (AAM14251), At3g59480 (CAB75445), At4g10260 (CAB78149), At5g51830 (AAL34211), Os01g0894300(AAL26574), Os08g0113100 (AAL26573), Zm00001d035037 (AAP42806), Zm00001d042536 (AAP42805), BvFRK (AAA80675), StFRK (CAA78283), AtFLN1 (AEE79187), AtFLN2 (NP_177080), SlFLN1 (XP_004246362), SlFLN2 (XP_004239035), ZmFLN1 (ONM36391),and ZmFLN2 (ONM06924). The structure of a...”
- “...2012 ; Koenig et al., 2013 ). In Arabidopsis, seven FRK genes (At5g51830, At2g31390, At1g66430, At4g10260, At1g06020, At1g06030, and At3g59480) were identified and named AtFRK17 , respectively ( Riggs et al., 2017 ). The identities of the Arabidopsis FRKs were verified following protein expression in E....”
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial...”
- Identification and biochemical characterization of the fructokinase gene family in Arabidopsis thaliana
Riggs, BMC plant biology 2017 - “...following paragraph). Two peptide sequences that were present in the FRK3 inclusive branch, At1g66430 and At4g10260, were both designated FRK3 in different publications [ 23 , 25 ]. We have chosen to denote At1g66430 as FRK3 because of its similarity to the tomato FRK3 (Table 1...”
- “...and Smeekens) FRK1 At2g31390 FRK2 (Pego and Smeekens) FRK2 At1g66430 FRK3 (Arsova et al.) FRK3 At4g10260 FRK3 (Pego and Smeekens) FRK4 At1g06020 na FRK5 At1g06030 na FRK6 At3g59480 na FRK7 Another predicted pfkB protein, At1g50390, claded with the FRK branch, but the predicted protein is only...”
- TWIN SISTER OF FT (TSF) Interacts with FRUCTOKINASE6 and Inhibits Its Kinase Activity in Arabidopsis
Jin, Frontiers in plant science 2017 - “...), FRK2 ( At1g06030 ), FRK3 ( At1g06020 ), FRK4 ( At3g59480 ), FRK5 ( At4g10260 ), FRK6 ( At1g66430 ), and FRK7 ( At5g51830 ) ( Stein et al., 2017 ). FRK17 contain 325, 329, 345, 326, 324, 384, and 343 amino acids. Notably, FRK6...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...FRK7), is closely related to SlFRK1 , while five other proteins (At2g31390, At1g06030, At1g06020, At3g59480, At4g10260 assigned FRK1-5, respectively) are closely related to SlFRK2 , the main cytosolic FRK in tomato. Although a comparison of their respective sequences does not suggest any relation, it appears that...”
- “...following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of five of the AtFRK genes...”
- Hexose kinases and their role in sugar-sensing and plant development
Granot, Frontiers in plant science 2013 - “...development and during pollen germination (German et al., 2002 ). Interestingly, the Arabidopsis FRK ortholog (At4g10260) displays a similar restricted expression pattern. It is likely that other species possess pollen-specific FRK isozymes as well (David-Schwartz et al., 2013 ). In a study that aimed to elucidate...”
- Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development
Deluc, BMC genomics 2007 - “...2 13.54 1616642_at BQ800221 TC64250 Q9FEP9 Glycerol-3-phosphate acyltransferase Carbohydrate metabolism 16 11.07 1616255_at CF516475 TC57339 O82616 Fructokinase Carbohydrate metabolism 12 10.13 1612918_at CB972844 TC52651 Q9MBD7 NAD-dependent sorbitol dehydrogenase Carbohydrate metabolism 2 9.14 1608393_at CF403620 TC64860 O22658 ADP-glucose pyrophosphorylase Carbohydrate metabolism 7 8.79 1621067_at CF511425 TC51908 Q8W3C8...”
3ikhA / A6T989 Crystal structure of ribokinase in complex with atp and glycerol in the active site from klebsiella pneumoniae
28% identity, 96% coverage
- Ligand: adenosine-5'-triphosphate (3ikhA)
FD720_04180 aminoimidazole riboside kinase from Photobacterium damselae subsp. damselae
26% identity, 93% coverage
K3XK17 fructokinase from Setaria italica
27% identity, 92% coverage
- Comparative proteomic investigation of drought responses in foxtail millet
Pan, BMC plant biology 2018 - “...translocator 2, chloroplastic-like 0.6 K3ZXS7 thylakoid membrane phosphoprotein 14 kDa, chloroplastic-like 0.6 C Carbon metabolism K3XK17 fructokinase-1-like 1.6 K3YH95 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) 2.4 K3YS38 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) 1.6 K3ZIS7 fructose-bisphosphate aldolase (FBA) 1.6 K3XT03 fructose-bisphosphate aldolase (FBA) cytoplasmic isozyme-like 1.5 K3XXC5 Phosphoglycerate kinase 2.4 K3Z681 enolase...”
Smar_0007 PfkB domain protein from Staphylothermus marinus F1
27% identity, 98% coverage
BC0773 Fructokinase from Bacillus cereus ATCC 14579
28% identity, 95% coverage
I1M561 fructokinase from Glycine max
30% identity, 87% coverage
Q7XJ81 Fructokinase-2 from Solanum habrochaites
29% identity, 89% coverage
N646_3834 aminoimidazole riboside kinase from Vibrio alginolyticus NBRC 15630 = ATCC 17749
27% identity, 96% coverage
LOC104605215 probable fructokinase-1 from Nelumbo nucifera
28% identity, 92% coverage
FD719_10825, FD722_11580, H3N34_00960, HU831_00540, HU985_14395, HVV26_09230 aminoimidazole riboside kinase from Photobacterium damselae subsp. damselae
27% identity, 96% coverage
- Diverse Horizontally-Acquired Gene Clusters Confer Sucrose Utilization to Different Lineages of the Marine Pathogen Photobacterium damselae subsp. damselae
Abushattal, Genes 2020 - “...FD722_11585 HU831_00535 HWA77_17195 scrB HU985_14390 HVV26_09225 FD719_10820 H3N34_00955 FD720_04175 FD722_11575 HU831_00545 HWA77_17185 scrK HU985_14395 HVV26_09230 FD719_10825 H3N34_00960 FD720_04180 FD722_11580 HU831_00540 HWA77_17190 scrR HU985_14405 HVV26_09240 FD719_10835 H3N34_00970 FD720_04190 FD722_11590 HU831_00530 HWA77_17200...”
- “...scrB HU985_14390 HVV26_09225 FD719_10820 H3N34_00955 FD720_04175 FD722_11575 HU831_00545 HWA77_17185 scrK HU985_14395 HVV26_09230 FD719_10825 H3N34_00960 FD720_04180 FD722_11580 HU831_00540 HWA77_17190 scrR HU985_14405 HVV26_09240 FD719_10835 H3N34_00970 FD720_04190 FD722_11590 HU831_00530 HWA77_17200...”
- “...HU831_00535 HWA77_17195 scrB HU985_14390 HVV26_09225 FD719_10820 H3N34_00955 FD720_04175 FD722_11575 HU831_00545 HWA77_17185 scrK HU985_14395 HVV26_09230 FD719_10825 H3N34_00960 FD720_04180 FD722_11580 HU831_00540 HWA77_17190 scrR HU985_14405 HVV26_09240 FD719_10835 H3N34_00970 FD720_04190 FD722_11590 HU831_00530 HWA77_17200...”
- “...HU985_14390 HVV26_09225 FD719_10820 H3N34_00955 FD720_04175 FD722_11575 HU831_00545 HWA77_17185 scrK HU985_14395 HVV26_09230 FD719_10825 H3N34_00960 FD720_04180 FD722_11580 HU831_00540 HWA77_17190 scrR HU985_14405 HVV26_09240 FD719_10835 H3N34_00970 FD720_04190 FD722_11590 HU831_00530 HWA77_17200...”
- “...H3N34_00965 FD720_04185 FD722_11585 HU831_00535 HWA77_17195 scrB HU985_14390 HVV26_09225 FD719_10820 H3N34_00955 FD720_04175 FD722_11575 HU831_00545 HWA77_17185 scrK HU985_14395 HVV26_09230 FD719_10825 H3N34_00960 FD720_04180 FD722_11580 HU831_00540 HWA77_17190 scrR HU985_14405 HVV26_09240 FD719_10835 H3N34_00970 FD720_04190 FD722_11590 HU831_00530 HWA77_17200...”
- “...FD720_04185 FD722_11585 HU831_00535 HWA77_17195 scrB HU985_14390 HVV26_09225 FD719_10820 H3N34_00955 FD720_04175 FD722_11575 HU831_00545 HWA77_17185 scrK HU985_14395 HVV26_09230 FD719_10825 H3N34_00960 FD720_04180 FD722_11580 HU831_00540 HWA77_17190 scrR HU985_14405 HVV26_09240 FD719_10835 H3N34_00970 FD720_04190 FD722_11590 HU831_00530 HWA77_17200...”
LOC108992456 probable fructokinase-4 from Juglans regia
29% identity, 89% coverage
- Combined transcriptomic and metabolomic analysis of the mechanism by which <i>Bacillus velezensis</i> induces resistance to anthracnose in walnut
Wang, Frontiers in microbiology 2024 - “...LOC109007785; LOC109010220; LOC109003634; LOC108998278; LOC108996646; LOC108985317; LOC108979963; LOC109004987; LOC108996947; LOC108988942; LOC108999180; LOC108988131; LOC108984074; LOC108981179; LOC108998652; LOC108992456; LOC108980812 LOC108989738; LOC109018267; LOC108987596; LOC108984851; LOC109019460; LOC108988131; LOC108984074; LOC108995469; LOC109009357; LOC108982978; LOC109011808; LOC108981208; LOC108983086; LOC109010098; LOC109002259; LOC109017388; LOC109003474; LOC109002260 DEM up D-xylulose 5-phosphate; 5-O-caffeoylquinic acid; Palmitic acid; UDP-N-acetyl--D-glucosamine; UDP-N-acetylglucosamine; -ketoglutaric...”
AO090038000092 No description from Aspergillus oryzae RIB40
33% identity, 85% coverage
Q7XAE2 fructokinase from Petunia integrifolia subsp. inflata
29% identity, 89% coverage
- Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development.
Deluc, BMC genomics 2007 - “...metabolism 11 15.38 1620347_at CA814065 TC66065 Q5QPZ6 Glycosyltransferase Carbohydrate metabolism 10 15.36 1622282_at CD712313 TC54393 Q7XAE2 Fructokinase Carbohydrate metabolism 2 13.54 1616642_at BQ800221 TC64250 Q9FEP9 Glycerol-3-phosphate acyltransferase Carbohydrate metabolism 16 11.07 1616255_at CF516475 TC57339 O82616 Fructokinase Carbohydrate metabolism 12 10.13 1612918_at CB972844 TC52651 Q9MBD7 NAD-dependent sorbitol...”
CAC0395 2-keto-3-deoxygluconate kinase (gene kdgK) from Clostridium acetobutylicum ATCC 824
CA_C0395 sugar kinase from Clostridium acetobutylicum ATCC 824
29% identity, 93% coverage
- Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostridium acetobutylicum
Borden, Applied and environmental microbiology 2007 - “...subunit with a role in antibiotic resistance (35). CAC0395 is annotated as kdgK, coding for 2-keto3-deoxygluconate kinase, a carbohydrate metabolism enzyme that...”
- “...exponential phase, while CAC0003, CAC3143, CAC0854, and CAC0395 were all downregulated at the onset of the transitional phase (3). Interestingly, transcription...”
- Fermentation of oxidized hexose derivatives by Clostridium acetobutylicum
Servinsky, Microbial cell factories 2014 - “...CA_C0694; 23) galacturonate isomerase, CA_C0692 24) altronate oxidoreductase, CA_C0695; 25) altronate dehydratase, CA_C0696; 26) 2-keto-3-deoxygluconokinase, CA_C0395; 27) 2-keto-3-deoxygluconate 6-phosphate aldolase, CA_C0394, CA_C2973; 28) gluconate symporter, CA_C3605; 29) gluconate dehydratase, CA_C3604. The pathway for gluconate metabolism in MetaCyc proceeded via the ED pathway, where phosphorylation of gluconate...”
P37829 fructokinase (EC 2.7.1.4) from Solanum tuberosum (see 2 papers)
29% identity, 92% coverage
- Comparative Proteomics of Potato Cultivars with a Variable Dormancy Period
Mouzo, Molecules (Basel, Switzerland) 2022 - “...14.25 1 P25083 ADP, ATP carrier protein, mitochondrial 9.8/5.3 42.1/33.6 8 4.51 >99 14.42 2 P37829 Fructokinase 5.5/5.2 33.8/39.3 9 6.00 >99 9.07 3 P25083 ADP, ATP carrier protein, mitochondrial 9.8/5.8 42.1/31.2 10 2.00 99 3.10 1 Q3YJT5 Patatin-05 5.4/6.0 42.5/42.0 11 18.26 >99 19.16 9...”
- Allergen false-detection using official bioinformatic algorithms.
Herman, GM crops & food 2020 - “...Q00782 B4FFK9 2 P12353 M1BPE5 E9JVD4 Q41385 Q9AWA5 P29518 P11402 1 Q3HRY7 1 B6SL97 P13788 P37829 Q01526 O20252 1 Q9M4G5 25 B4FUH2 P17353 Q9M4G4 B4FPL1 P22418 C6F3B7 2 B6UGJ4 A1XIR6 P33191 7 1 5 P55240 Q8RU73 P37830 Q84J79 P09559 K7WJT8 K7UNW7 P05435 Q948Z8 B6T7B2 P06508 P23509...”
- Proteomic analysis on roots of Oenothera glazioviana under copper-stress conditions
Wang, Scientific reports 2017 - “...31 Q9LU41 Calcium-transporting ATPase 9, plasma membrane-type Arabidopsis thaliana Q9LU41 ACA9 2 3.38 0.02257 32 P37829 Fructokinase Solanum tuberosum Q9M1B9 N/A 3 3.73 1.3E-08 33 B9T118 NADH-ubiquinone oxidoreductase, putative Ricinus communis Q9FGI6 RCOM_0458390 3 0.60 0.00043 Signal Transduction 34 P40392 Ras-related protein RIC1 Oryza sativa P28188...”
- Comparative proteomics reveals the physiological differences between winter tender shoots and spring tender shoots of a novel tea (Camellia sinensis L.) cultivar evergrowing in winter
Liu, BMC plant biology 2017 - “...score MS coverage% Theoretical Mr.(kDa)/pI Expressed Mr.(kDa)/pI Metabolism /Sugars and polysaccharides 25 Fructokinase Actinidia eriantha P37829 0.45 45 3 33.97/5.4 32.18/5.16 26 Phosphomannomutase Nicotiana tabacum Q1W375 0.05 37 7 28.79/5.7 26.47/7.17 27 Eukaryotic galactinol synthase Camellia sinensis AFR79417 0.19 59 6 33.78/6.0 30.87/6.27 Secondary metabolism 28...”
Q9LNE4 fructokinase (EC 2.7.1.4) from Arabidopsis thaliana (see paper)
AT1G06020 pfkB-like carbohydrate kinase family protein from Arabidopsis thaliana
NP_172092 pfkB-type carbohydrate kinase family protein from Arabidopsis thaliana
27% identity, 88% coverage
- Early Low-Fluence Red Light or Darkness Modulates the Shoot Regeneration Capacity of Excised Arabidopsis Roots
Wei, Plants (Basel, Switzerland) 2020 - “...ko04141 3.76 10 3 2.37 AT1G17420 LOX3 alpha-Linolenic acid metabolism ko00592 5.59 10 3 4.89 AT1G06020 FRK3 Starch and sucrose metabolism ko00500 1.94 10 2 2.23 AT1G72450 JAZ6 Plant hormone signal transduction ko04075 0.10 1.89 AT4G28720 YUC8 Tryptophan metabolism ko00380 0.16 3.49 AT1G02920 GST11 Glutathione metabolism...”
- Plant Fructokinases: Evolutionary, Developmental, and Metabolic Aspects in Sink Tissues
Stein, Frontiers in plant science 2018 - “...the proteins used for the sequence alignment: SlFRK1 (AAB57733), SlFRK2 (AAB57734), SlFRK3 (NP_001234396), SlFRK4 (AAM44084), At1g06020 (AAF80125), At1g06030 (AAF80126), At1g66430 (AAG51160), At2g31390 (AAM14251), At3g59480 (CAB75445), At4g10260 (CAB78149), At5g51830 (AAL34211), Os01g0894300(AAL26574), Os08g0113100 (AAL26573), Zm00001d035037 (AAP42806), Zm00001d042536 (AAP42805), BvFRK (AAA80675), StFRK (CAA78283), AtFLN1 (AEE79187), AtFLN2 (NP_177080), SlFLN1 (XP_004246362),...”
- “...; Koenig et al., 2013 ). In Arabidopsis, seven FRK genes (At5g51830, At2g31390, At1g66430, At4g10260, At1g06020, At1g06030, and At3g59480) were identified and named AtFRK17 , respectively ( Riggs et al., 2017 ). The identities of the Arabidopsis FRKs were verified following protein expression in E. coli...”
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...the mega4 software for creating the phylogenetic tree were incorrect. AtFRK3 (At3g59480) should read AtFRK3 (At1g06020) and AtFRK4 (At4g06030) should read AtFRK4 (At3g59480) as in the text, Table S1 and uniprot annotation for arabidopsis probable fructokinases. The corrected Figure 1 appears below. The authors apologize for...”
- “...(NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as...”
- Identification and biochemical characterization of the fructokinase gene family in Arabidopsis thaliana
Riggs, BMC plant biology 2017 - “...and Smeekens) FRK2 At1g66430 FRK3 (Arsova et al.) FRK3 At4g10260 FRK3 (Pego and Smeekens) FRK4 At1g06020 na FRK5 At1g06030 na FRK6 At3g59480 na FRK7 Another predicted pfkB protein, At1g50390, claded with the FRK branch, but the predicted protein is only 16kDa, while other FRKs range from...”
- “...plant expression stop codon mutation GGGGACCACTTTGTACAAGAAAGCTGGGTCTGAAACGACGGCTTTGAG At4g10260 reverse FRK4 plant expression stop codon mutation GGGGACCACTTTGTACAAGAAAGCTGGGTCCGATTTAGACTTAGATTTC At1g06020 forward FRK5 plant expression GGGGACAAGTTTGTACAAAAAAGCAGGCTTGATGGCATCATCCACCGGCG At1g06020 reverse FRK5 plant expression stop codon mutation GGGGACCACTTTGTACAAGAAAGCTGGGTCTGAACAAGGgctAGCCGTACAACACC At1g06030 reverse FRK6 plant expression stop codon mutation GGGGACCACTTTGTACAAGAAAGCTGGGTCCGATTCTACTTGTATCTTAAG At3g59480 reverse FRK7 plant expression stop codon...”
- TWIN SISTER OF FT (TSF) Interacts with FRUCTOKINASE6 and Inhibits Its Kinase Activity in Arabidopsis
Jin, Frontiers in plant science 2017 - “...proteins with fructose phosphorylating activity: FRK1 ( At2g31390 ), FRK2 ( At1g06030 ), FRK3 ( At1g06020 ), FRK4 ( At3g59480 ), FRK5 ( At4g10260 ), FRK6 ( At1g66430 ), and FRK7 ( At5g51830 ) ( Stein et al., 2017 ). FRK17 contain 325, 329, 345, 326,...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...(At5g51830, assigned FRK7), is closely related to SlFRK1 , while five other proteins (At2g31390, At1g06030, At1g06020, At3g59480, At4g10260 assigned FRK1-5, respectively) are closely related to SlFRK2 , the main cytosolic FRK in tomato. Although a comparison of their respective sequences does not suggest any relation, it...”
- “...(NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of five of the AtFRK genes ( AtFRK1,3,4,6,7 ) were identified and...”
- Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization
Albertin, BMC genomics 2007 - “...#1352 and #1353 were HDEM- and Z1-specific respectively, and were both identified as putative fructokinases (At1g06020). These probable homeoallelic gene products displayed ''opposite'' patterns of regulation in synthetic Brassica napus in comparison to the mid-parent pattern: spot #1352 was up-regulated while spot #1353 was down-regulated. Figure...”
- Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte
Johnston, Genome biology 2007 - “...17 Protein 2 1 1 1 1 At1g56530 Hydroxyproline-Rich Glycoprotein 1 0 0 0 0 At1g06020 Pfkb-Type Carbohydrate Kinase 2 1 0 1 1 At2g43860 Polygalacturonase 2 0 0 0 1 At1g78400 Glycoside Hydrolase Family 28 Protein 1 0 0 0 1 At5g22960 Serine Carboxypeptidase A10...”
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of five of the AtFRK genes ( AtFRK1,3,4,6,7 ) were identified and obtained...”
CRIB_1458 carbohydrate kinase from Romboutsia ilealis
26% identity, 93% coverage
- Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
Gerritsen, PeerJ 2017 - “...component (CRIB_1461); 3, -fructofuranosidase with RDD family protein (CRIB_1459 and CRIB_1460); 4, fructokinase (CRIB_152 and CRIB_1458); 5; ABC-type transporter (CRIB_148-CRIB_150); 6, -fructofuranosidase (CRIB_151); 7, glucokinase (CRIB_1849); 8, glucose 6-phosphate isomerase (CRIB_140); 9, fructose 1,6-bisphosphatase (CRIB_45 and CRIB_2020); 10, 6-phosphofructokinase ; (CRIB_104); 11, fructose-bisphosphate aldolase (CRIB_2223); 12,...”
Q42896 fructokinase (EC 2.7.1.4) from Solanum lycopersicum (see paper)
NP_001233888 fructokinase-2 from Solanum lycopersicum
28% identity, 89% coverage
- Physiological and Transcriptional Responses of Apocynum venetum to Salt Stress at the Seed Germination Stage.
Li, International journal of molecular sciences 2023 - “...3.29 Fructose (9) FKFBP Q9MB58 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3.50 RHVI2 H2DF88 Acid beta-fructofuranosidase 2, vacuolar 1.32 FRK2 Q42896 Fructokinase-2 5.37 FBP P46275 Fructose-1,6-bisphosphatase, chloroplastic 3.26 F16P2 P46276 Fructose-1,6-bisphosphatase, cytosolic 4.07 FBA2 Q944G9 Fructose-bisphosphate aldolase 2, chloroplastic 3.49 FBA3 Q9ZU52 Fructose-bisphosphate aldolase 3, chloroplastic 1.93 FBA6 Q9SJQ9 Fructose-bisphosphate aldolase...”
- Effects of Fe and Mn Deficiencies on the Root Protein Profiles of Tomato (Solanum lycopersicum) Using Two-Dimensional Electrophoresis and Label-Free Shotgun Analyses
Ceballos-Laita, International journal of molecular sciences 2022 - “...A0A3Q7HT77 bifunctional dTDP-4-dehydrorhamnose 3,5-epimerase/reductase 0.81 - 9 Solyc07g052350.3.1 A0A3Q7HBK4 aconitate hydratase 1.17 3.00 10 Solyc06g073190.3.1 Q42896 fructokinase-like 2.30 Polysaccharide Metabolism (3) 11 Solyc12g098540.2.1 A0A3Q7JEE6 * apyrase 1.91 12 Solyc01g104950.4.1 A0A3Q7EQN7 beta-D-xylosidase 2 precursor 0.90 1.14 - 13 Solyc01g107590.3.1 A0A3Q7ESC5 cinnamyl alcohol dehydrogenase 1.54 - Protein Metabolism...”
- Analysis of cell wall proteins regulated in stem of susceptible and resistant tomato species after inoculation with Ralstonia solanacearum: a proteomic approach
Dahal, Plant molecular biology 2010 - “...0.61 8* Luminal-binding protein P49118 Solanum lycopersicum 219 73.23/5.10 7 9.9 1.72 Y 9* Fructokinase-2 Q42896 Solanum lycopersicum 510 34.76/5.76 9 33 1.91 0.68 10 Vacuolar proton ATPase subunit E Q9LKG0 Solanum lycopersicum 46 27.13/6.63 1 4.2 0.51 0.27 11 Oxygen-evolving complex protein 2 P29795 Solanum...”
- “...0.73 7 Hypothetical protein O04428 Citrus paradisi 92.8 32.64/5.46 1 4.1 0.38 0.50 8 Fructokinase-2 Q42896 Solanum lycopersicum 208 34.76/5.76 3 11 0.36 0.68 9* Enolase P26300 Solanum lycopersicum 291 47.79/5.68 5 14 0.50 0.52 10* Oxygen-evolving enhancer protein 1 P23322 Solanum lycopersicum 423 34.98/5.91 12...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...2007 ). This phylogenetic tree is based on the following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta...”
- LeFRK2 is required for phloem and xylem differentiation and the transport of both sugar and water.
Damari-Weissler, Planta 2009 (PubMed)- GeneRIF: Antisense interstock restricted the downward movement of sucrose, suggesting that LeFRK2 is required for both phloem and xylem development and the transport of both sugar and water. [LeFRK2]
A9PEZ9 fructokinase from Populus trichocarpa
29% identity, 88% coverage
- The proteome of Populus nigra woody root: response to bending
Trupiano, Annals of botany 2012 - “...37.6 97* 98 Putative fructokinase 2 Major storage protein A9PEZ9 A9PFD1 Populus trichocarpa Populus trichocarpa TMS TMS 2 7 7 25 81 390 4.93/35 6.90/36 38.6...”
- “...dehydrogenase, putative Bark storage protein A B9HH42 A9PEZ9 A9P841 Q07469 Populus trichocarpa Populus trichocarpa Populus trichocarpa Populus deltoides PMF PMF...”
B9HH42 fructokinase from Populus trichocarpa
29% identity, 91% coverage
- The proteome of Populus nigra woody root: response to bending
Trupiano, Annals of botany 2012 - “...trichocarpa TMS 8 23 406 4.92/37 40.9 Fructokinase, putative B9HH42 Populus trichocarpa TMS 6 21 282 5.01/36 40.9 85 86 Disease/ defence Disease/ defence Energy...”
- “...40.9 99 Fructokinase, putative Late embryogenesis abundant, putative B9HH42 B9HXA8 Populus trichocarpa Populus trichocarpa TMS TMS 5 8 24 20 213 369 5.01/36...”
LOC8056099 fructokinase-1 from Sorghum bicolor
27% identity, 93% coverage
- Transcriptome analysis of the impact of exogenous methyl jasmonate on the opening of sorghum florets
Liu, PloS one 2021 - “...in several significant pathways by blast analysis in NCBI database. Among of which, LOC8075740 , LOC8056099 , LOC8064482 , LOC8058060 , LOC110437037 and LOC8069151 were involved in starch and sucrose metabolism, and LOC8084355 was involved in hormone signal transduction pathways and LOC110429834 was involved in the...”
- “...AGTGGGGCACCGACTACTTCAT CTGCCAGCAGTAGTGGTCCGT 12 LOC8072504 ACTCTGTTAGCTTTCTACCTTTGC AGATTCCAGTCAAGGCACAGC 13 LOC8064482 GTACCCTCCTGGTCACTGCTC AACCACCTTGTTTCCCCTGAT 14 LOC110429834 TTACCTCTCGTTGACACCATC CACACCACATCCTTGCTTTAG 15 LOC8056099 ATTTGGGACCAGGCAGACATT GAGCACCAACAAACGCATCAC 16 LOC8083790 TAGCAAAAGATGTCAGTTTCAAGG GTAATCCCATCGTATTCTTCCAAAA 17 LOC8155361 CCACTTCAAGTTCGGCCTCTT AACCAGTGGGACTTCCAGACG Functional pathway analysis of DEGs Based on the results of DEGs detection, biological pathway classification and enrichment analysis was performed...”
3lkiB / Q87CC0 Crystal structure of fructokinase with bound atp from xylella fastidiosa
30% identity, 93% coverage
- Ligand: adenosine-5'-triphosphate (3lkiB)
SCRK1_MAIZE / Q6XZ79 Fructokinase-1; ZmFRK1; EC 2.7.1.4 from Zea mays (Maize)
27% identity, 93% coverage
- function: May play an important role in maintaining the flux of carbon towards starch formation in endosperm. May also be involved in a sugar- sensing pathway
catalytic activity: D-fructose + ATP = D-fructose 6-phosphate + ADP + H(+) (RHEA:16125) - Genetic Engineering of Starch Biosynthesis in Maize Seeds for Efficient Enzymatic Digestion of Starch during Bioethanol Production
Niu, International journal of molecular sciences 2023 - “...synthesis AGPase large subunit 2 (EC:2.7.7.27) P55234 AGP2 Amyloplast Involvement of ADP-glucose synthesis Fructokinase-1 (EC:2.7.1.4) Q6XZ79 FRK1 Cytosol Fructokinase activity Phosphoglucomutase (EC:5.4.2.2) P93805 N/A Cytosol Interconverting glucose-6-P and glucose-1-P -1,4-glucan phosphorylase (EC:2.4.1.1) B5AMJ8 100285259 Amyloplast * Glycogen phosphorylase activity Granule-bound starch synthase Q93WP1, Q94FZ6 waxy Amyloplast...”
- Proteomic Changes in Paspalum fasciculatum Leaves Exposed to Cd Stress
Salas-Moreno, Plants (Basel, Switzerland) 2022 - “...1.0 9.8 Mitochondrion 42 P42895 Enolase 2 48.132 45.0672646 Zea mays 6.4 6.4 Cytoplasm 43 Q6XZ79 Fructokinase-1 34.669 26.0061919 Zea mays 2.1 0.2 Cytosol 44 P26518 Glyceraldehyde-3-phosphate dehydrogenase 36.959 20.5278592 Magnolia liliiflora 1.4 8.5 Cytoplasm 45 P26517 Glyceraldehyde-3-phosphate dehydrogenase 1 36.491 44.2136499 Hordeum vulgare 10.7 10.7...”
- Leaf proteome modulation and cytological features of seagrass Cymodocea nodosa in response to long-term high CO2 exposure in volcanic vents.
Piro, Scientific reports 2020 - “...D 57,389.9 ko04146 Oxidativ stress P02582 K06759 Actin-1 2.058 4.164 D 41,902.1 ko04514 Citoskeleton metabolism Q6XZ79 K00847 Fructokinase-1 2.028 4.078 D 34,861.4 ko00500 Starch and sucrose metabolism Q9SP22 K08057 Calreticulin 1.854 3.616 SLD 48,052.8 ko04141 Protein folding and sorting O22424 K02987 40S ribosomal protein S4 1.832...”
STM4066 / Q8ZKR2 aminoimidazole riboside kinase (EC 2.7.1.223) from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
AIRSK_SALTY / Q8ZKR2 Aminoimidazole riboside kinase; AIRs kinase; EC 2.7.1.223 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
Q8ZKR2 aminoimidazole riboside kinase (EC 2.7.1.223) from Salmonella enterica subsp. enterica serovar Typhimurium (see 2 papers)
STM4066 putative sugar kinase, ribokinase family from Salmonella typhimurium LT2
25% identity, 96% coverage
- function: Phosphorylates 5-amino-1-(beta-D-ribosyl)imidazole (AIRs) to form 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole (AIR), an important intermediate in the purine and thiamine biosynthetic pathways (PubMed:12486071). It allows the use of exogenous aminoimidazole riboside (AIRs) to satisfy the cellular requirement for purines and thiamine (PubMed:12486071).
catalytic activity: 5-amino-1-(beta-D-ribosyl)imidazole + ATP = 5-amino-1-(5- phospho-beta-D-ribosyl)imidazole + ADP + H(+) (RHEA:44748)
subunit: Homodimer.
disruption phenotype: Disruption of the gene prevents the efficient use of AIRs as a source of thiamine. - Tissue-specific Salmonella Typhimurium gene expression during persistence in pigs
Van, PloS one 2011 - “...yet unknown function In Salmonella Typhimurium. STM4067 is part of the STM4065-4066-4067 operon of which STM4066 has aminoimidazole riboside (AIR) kinase activity, phosphorylating AIRs and satisfying the thiamine requirement of pur mutant strains [56] . Because our IVET library was constructed in a purA Salmonella Typhimurium,...”
- “...(LTTR) family proteins. Microbiology 154 3609 3623 19047729 56 Dougherty M Downs DM 2003 The stm4066 gene product of Salmonella enterica serovar Typhimurium has aminoimidazole riboside (AIRs) kinase activity and allows AIRS to satisfy the thiamine requirement of pur mutant strains. J Bacteriol 185 332 339...”
- Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes
Soyer, BMC evolutionary biology 2009 - “...flavoprotein alpha-component - Central intermediary metabolism STM3174 DNA topoisomerase IV, A subunit parC DNA metabolism STM4066 Fructokinase cscK Energy metabolism a These genes showed evidence for recombination ( Q < 0.1) in four tests (i.e., GENECONV, Maximum 2 [Max- 2 ], pairwise homoplasy index [PHI], and...”
- Salmonella serovar identification using PCR-based detection of gene presence and absence
Arrach, Journal of clinical microbiology 2008 - “...STM3546, STM3652, STM3653, STM3671, STM3771, STM3859, STM4066, STM4206, STM4215, STM4218, STM4447, STM4483, STM4498, STM4528, PSLT040, PSLT060, PSLT107,...”
- Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily
Zhang, Structure (London, England : 1993) 2004 (PubMed)- “... , respectively. The product of the Salmonella-specific gene stm4066, AIRs kinase, is a homodimer with one active site per monomer. The core structure,...”
- “... , respectively. The product of the Salmonella -specific gene stm4066 , AIRs kinase, is a homodimer with one active site per monomer. The core structure,...”
- A mutant allele of rpoD results in increased conversion of aminoimidazole ribotide to hydroxymethyl pyrimidine in Salmonella enterica
Dougherty, Journal of bacteriology 2004 - “...phosphorylation of AIRs to AIR by STM4066 (8) is represented. Abbreviations: THZ-P, 4-methyl-5(-hydroxyethyl) thiazole phosphate; TMP, thiamine phosphate;...”
- “...in an 100-fold increase in expression of stm4066 (8). Representative growth for strain DM7256 [purG3111 purE3043 stm4068-6::Tn10d(Tc) zxx-9149::MudJ rpoD1181]...”
- The stm4066 gene product of Salmonella enterica serovar Typhimurium has aminoimidazole riboside (AIRs) kinase activity and allows AIRs to satisfy the thiamine requirement of pur mutant strains
Dougherty, Journal of bacteriology 2003 - “...operon (stm4065-4067) that encoded a predicted kinase. The stm4066 gene product was purified and shown to have AIRs kinase activity in vitro. This activity...”
- “...overproduction of a single gene in this operon (stm4066) that encoded a kinase able to phosphorylate AIRs. Characterization of biochemical pathways in vivo is...”
- Metabolic flux in both the purine mononucleotide and histidine biosynthetic pathways can influence synthesis of the hydroxymethyl pyrimidine moiety of thiamine in Salmonella enterica
Allen, Journal of bacteriology 2002 - “...shown to be caused by derepression of a kinase (STM4066) that is able to phosphorylate AIR riboside (AIRs). The causative mutation (stm4068-1) is a null allele...”
SCRK2_ORYSI / A2YQL4 Fructokinase-2; Fructokinase II; OsFKII; EC 2.7.1.4 from Oryza sativa subsp. indica (Rice) (see paper)
SCRK2_ORYSJ / Q0J8G4 Fructokinase-2; Fructokinase II; OsFKII; EC 2.7.1.4 from Oryza sativa subsp. japonica (Rice) (see 2 papers)
A2YQL4 fructokinase (EC 2.7.1.4) from Oryza sativa (see paper)
28% identity, 87% coverage
- function: May play an important role in maintaining the flux of carbon towards starch formation in endosperm. May also be involved in a sugar- sensing pathway
catalytic activity: D-fructose + ATP = D-fructose 6-phosphate + ADP + H(+) (RHEA:16125) - function: May play an important role in maintaining the flux of carbon towards starch formation in endosperm. May also be involved in a sugar- sensing pathway
catalytic activity: D-fructose + ATP = D-fructose 6-phosphate + ADP + H(+) (RHEA:16125) - CRISPR/Cas9-Induced Mutagenesis of TMS5 Confers Thermosensitive Genic Male Sterility by Influencing Protein Expression in Rice (Oryza sativa L.)
Fang, International journal of molecular sciences 2022 - “...mutant line. A0A0E0IIY5 (sugar transporter), A0A0E0GNW4 (sucrose synthase), A0A0E0GAC4 (sugar transporter), B8AIG0 (starch synthase), and A2YQL4 (fructokinase-2) were related to the synthesis and transport of starchy carbohydrates. All of them were downregulated in the mutant line. 2.7. GO and KEGG Pathway Enrichment Analysis Results of DEPs...”
- “...sugar transporter Down A0A0E0GNW4 sucrose synthase Down A0A0E0GAC4 sugar transporter Down B8AIG0 starch synthase Down A2YQL4 fructokinase-2 Down ijms-23-08354-t003_Table 3 Table 3 Quality traits of hybrids and their parents. Line Grain Length (mm) Grain Width (mm) Grain LengthWidth Ratio Gel Consistency (mm) Amylose Content (%) Content...”
- Comparative protein profiles of the Ambrosia plants.
Barton, Biochimica et biophysica acta. Proteins and proteomics 2017 - “...O. sativa.jap P35683 47088 2 100 13 36 1 1 Translation Fructokinase-2 O. sativa. ind A2YQL4 35518 2 100 5 12 1 1 1 Starch Biosynthesis GTP-binding protein SAR1A A. thaliana O04834 22032 5 100 12 54 1 1 1 Vesicle-mediated Transport Glutamate decarboxylase P. hybrida...”
- Proteomic Analysis Revealed the Antagonistic Effect of Decapitation and Strigolactones on the Tillering Control in Rice
Zhao, Plants (Basel, Switzerland) 2023 - “...NS 0.486 Triosephosphate isomerase (TPI), cytosolic LOC_Os03g28330 P31924 NS 0.425 Sucrose synthase 1 (SUS1) LOC_Os08g02120 Q0J8G4 NS 0.497 Fructokinase-2 (FRK2) LOC_Os10g33800 Q7XDC8 NS 0.451 Malate dehydrogenase (MDH), cytoplasmic NS not significant....”
- Lipid and Protein Oxidation of Brown Rice and Selenium-Rich Brown Rice during Storage.
Zhang, Foods (Basel, Switzerland) 2022 - “...branching enzyme - 0.5445 - - Q0D9D0 9 1,4-alpha-glucan branching enzyme - 2.7542 - 0.4207 Q0J8G4 448 Fructokinase-2 - - 1.5276 - B9FUP9 737 Amylomaltase - - 1.5417 - Q653V7 33 Probable alpha-glucosidase Os06g0675700 - - 1.7539 1.9055 Q93 08 26 UTP--glucose-1-phosphate uridylyltransferase - - 1.6444...”
- Identification of proteins of altered abundance in oil palm infected with Ganoderma boninense
Al-Obaidi, International journal of molecular sciences 2014 - “...activity 36 M0YUL2 Uncharacterized protein 2.60 0.00011 38,971 8.47 105 4 13 Hordeum vulgare 48 Q0J8G4 Fructokinase-2 4.15 0.0072 35,893 5.02 86 3 9 Oryza sativa starch biosynthestic process ATP binding; fructokinase activity 49 G1FCF5 Fructokinase 6.04 0.013 36,460 5.61 72 2 7 Dimocarpus longan D-ribose...”
- A proteomic study on molecular mechanism of poor grain-filling of rice (Oryza sativa L.) inferior spikelets
Zhang, PloS one 2014 - “...51.7/5.59 15 DR 293 h Q93X08 UDP-glucose pyrophosphorylase 143 51.7/5.59 10 DR 8 69 g Q0J8G4 Similar to Fructokinase 430 35.9/5.02 4 DR 9 13 g Q8H8T0 UDP-L-arabinose mutase 1 324 40.1/8.21 3 DR 1.2-Starch synthesis 10 14 g B8XED2 ADP-glucose pyrophosphorylase large subunit 556 58.2/5.55...”
lpg1651 IolC/IolB transferase kinase protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
24% identity, 43% coverage
- Migration of Acanthamoeba through Legionella biofilms is regulated by the bacterial Lqs-LvbR network, effector proteins and the flagellum
Hochstrasser, Environmental microbiology 2022 - “...S1 ). In contrast, enzymes implicated in myo inositol catabolism, such as IolG (Lpg1652), IolCB (Lpg1651), IolD (Lpg1650) and IolE (Lpg1649) (Manske et al ., 2016 ) were more abundant in biofilms formed by the lvbR or lqsR mutant strains (Fig. S1 , box 4), indicating...”
- Metabolism of myo-Inositol by Legionella pneumophila Promotes Infection of Amoebae and Macrophages
Manske, Applied and environmental microbiology 2016 - “...(Lpg1652), a myo-inositol-2-dehydrogenase; IolCB (Lpg1651), a combined 5-dehydro-2-deoxygluconokinase-5-deoxy-glucuronate isomerase protein; IolD (Lpg1650), an...”
Tagg_0553 carbohydrate kinase family protein from Thermosphaera aggregans DSM 11486
27% identity, 98% coverage
- Complete genome sequence of Thermosphaera aggregans type strain (M11TL)
Spring, Standards in genomic sciences 2010 - “...phosphorylation of glucose (ADP-GLK) and fructose-6-phosphate (ADP-PFK), in T. aggregans corresponding ATP-dependent kinases (Tagg_0486 and Tagg_0553, respectively) are involved in the first steps of glycolysis. The key enzyme of the modified Embden-Meyerhof-Parnas pathway in Archaea is glyceraldehyde-3-phosphate-ferredoxin oxidoreductase [ 43 ] (Tagg_0452), which oxidizes glyceraldehyde-3-phosphate directly...”
WP_042667458 carbohydrate kinase family protein from Desulfurococcus amylolyticus Z-533
27% identity, 97% coverage
- Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
Sutter, Extremophiles : life under extreme conditions 2020 - “..., Ta0880; Methanocaldococcus jannaschii , MJ0406; Mycobacterium tuberculosis , P9WID5; Phosphofructokinase/ribose-1-phosphate kinase: Desulfurococcus amylolyticus , WP_042667458 (Hansen and Schnheit 2000 ); Aeropyrum pernix , Ape0012 (Hansen and Schnheit 2001 ); Thermoproteus tenax , TTX_1882; Pyrobaculum calidifontis , Pcal 0041 (Aziz et al. 2018 ); Haloterrigena hispanica...”
- A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate
Aziz, Journal of bacteriology 2018 - “...identical to a 6-phosphofructokinase from D. amylolyticus (WP_042667458) (22). A sequence alignment among biochemically characterized proteins with PfkB domains...”
- “...M. jannaschii, AAB98396; A. pernix, BAA78921; D. amylolyticus, WP_042667458; and E. coli, P0A9J6. The NXXE motif involved in metal binding is indicated with the...”
TM0296 fructokinase from Thermotoga maritima MSB8
28% identity, 97% coverage
- Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima
Rodionov, Frontiers in microbiology 2013 - “...sole carbon source (Figure 5 ). This observation correlates with the presence of functional fructokinase TM0296 (Rodionova et al., 2012b ), however, the fructose uptake transporter remains unknown in T. maritima . In summary, the comparative genomics-based regulon and pathway reconstruction combined with some experimental data...”
- Diversity and versatility of the Thermotoga maritima sugar kinome
Rodionova, Journal of bacteriology 2012 - “...maritima gene TM1469, TM0067, TM0443, TM1073, TM0828, TM0209, or TM0296 and E. coli HK100 strains that harbor the gene TM0116, TM0284, TM0415, or TM1280 in the...”
- “...(TM0116, TM0284, TM0443, TM1073, TM1430, TM0067, TM0960, TM0296, and TM1190), the experimentally observed narrow substrate specificity matched precisely the...”
LOC110116405 fructokinase-1 from Dendrobium catenatum
28% identity, 82% coverage
HNY42_RS00620 carbohydrate kinase from Exiguobacterium sp. Helios
27% identity, 96% coverage
- Xerotolerance: A New Property in Exiguobacterium Genus
López, Microorganisms 2021 - “...use several sugars and polymeric carbohydrates as carbon sources. For instance, among them, HNY42_RS05125 and HNY42_RS00620 genes encode a putative sucrose-6-phosphate hydrolase and a putative fructokinase, respectively, most probably involved in sucrose catabolism. Table 1 shows the sugars that can be used as carbon and energy...”
Amuc_0075 PfkB domain protein from Akkermansia muciniphila ATCC BAA-835
27% identity, 75% coverage
Desfe_0717 carbohydrate kinase family protein from Desulfurococcus amylolyticus DSM 16532
27% identity, 98% coverage
LOC105035371 fructokinase-1 from Elaeis guineensis
28% identity, 91% coverage
- Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield
Apriyanto, Frontiers in plant science 2023 - “...positively correlated with oil yield are shown. These genes are EgSUT1 (LOC105041710), EgPGI (LOC105060694), EgFRK1.2 (LOC105035371), EgHK2.2 (LOC105040520), EgAPL1.1 (LOC105047182), EgAPS1.1 (LOC105060488), EgSS1 (LOC105040918), EgAMY3 (LOC105047709), EgBAM3 (LOC105043800), and EgAGL (LOC105059813). The (A) total starch, (B) sucrose, (C) maltotriose, and (D) maltose contents during fruit development...”
- “...Only genes that were positively correlated with oil yield are shown. These genes are EgFRK1.2 (LOC105035371), EgHK2.2 (LOC105040520), EgPGI (LOC105060694), EgPFK3.1 (LOC105040103), EgFBA1.1 (LOC105052993), EgFBA1.2 (LOC105059022), EgTPI1.1 (LOC105045658), EgG3PDH1.1 (LOC105034336), EgPGK3 (LOC105059872), EgPGAM1.1 (LOC105052340), EgENO2 (LOC105053561), and EgPK1.1 (LOC105038179). The abundances of (A) fructose and (B)...”
RBAM_RS03320 carbohydrate kinase from Bacillus velezensis FZB42
27% identity, 83% coverage
cscK / GB|CAA57218.2 fructokinase; EC 2.7.1.4 from Escherichia coli (see paper)
27% identity, 95% coverage
RO3G_01375 uncharacterized protein from Rhizopus delemar RA 99-880
34% identity, 62% coverage
ECW_m2595 aminoimidazole riboside kinase from Escherichia coli W
27% identity, 95% coverage
- Engineering consortia by polymeric microbial swarmbots
Wang, Nature communications 2022 - “...transformed with a circuit that constitutively expressing the sucrose metabolism genes ( cscB (ECW_m2594), cscK (ECW_m2595) and cscA (ECW_m2596)) were used to generate (Fig. 7) 52 . Circuit and plasmids ePop (ColE1 origin) was published previously 53 . Briefly, it was constructed using the luxbox region...”
- Construction and analysis of an artificial consortium based on the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 to produce the platform chemical 3-hydroxypropionic acid from CO2
Zhang, Biotechnology for biofuels 2020 - “...and expressed the essential genes for sucrose metabolism, namely, cscB ( ECW_m2594 ), cscK ( ECW_m2595 ) and cscA ( ECW_m2596 ), into E. coli BL21 to generate an engineered strain, E. coli cscN. In addition, to synthesize 3-HP, the malonyl-CoA reductase-coding gene mcr ( Caur_2614...”
PF1886 sugar kinase from Pyrococcus furiosus DSM 3638
27% identity, 100% coverage
B6TPJ8 Fructokinase-2 from Zea mays
28% identity, 87% coverage
SCRK2_MAIZE / Q6XZ78 Fructokinase-2; ZmFRK2; EC 2.7.1.4 from Zea mays (Maize)
27% identity, 87% coverage
- function: May play an important role in maintaining the flux of carbon towards starch formation. May also be involved in a sugar-sensing pathway
catalytic activity: D-fructose + ATP = D-fructose 6-phosphate + ADP + H(+) (RHEA:16125) - Identification of cross-reactive IgE-binding proteins from Philippine allergenic grass pollen extracts
Castor, Asia Pacific allergy 2024 - “...protein spots Spot Protein Accession number MW/pI * (theoretical) UP/PSM/SC Mascot Protein Score 4 Fructokinase-2 Q6XZ78 35.5/5.58 4/16/23 582 9 Triosephosphate isomerase, cytosolic P12863 27/5.68 3/12/26 503 11 PMEI domain-containing protein A0A0P0XZJ5 19.3/7.93 1/70/61 2598 14 FAD-binding PCMH-type domain-containing protein (glycoprotein) A0A0E0HS70 58.3/9.2 16/31/34 1044 17...”
- Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12.
Huddleston, Biochemistry 2019 - “...part of the ribokinase/fructokinase family. This family of enzymes contains ribokinase (Uniprot: P0A9J6), fructokinase (Uniprot: Q6XZ78), 6-phosphofructokinase (Uniprot: P06999), inosine kinase (Uniprot: P0AEW6) 2-dehydro-3-deoxyglucokinase (Uniprot: P37647), and fructolysine kinase (Uniprot: P45543). In this paper, we describe the functional characterization of the substrates for YdjH and provide...”
WP_225760329 sugar kinase from Citrobacter sp. Marseille-Q3906
28% identity, 96% coverage
A5BUI9 fructokinase from Vitis vinifera
29% identity, 79% coverage
- Mass Spectrometry-Based Proteomic Profiling of a Silvaner White Wine
Albuquerque, Biomolecules 2023 - “...15 Uncharacterized protein Vitis vinifera 24.9 37 A5BEX7 15 Uncharacterized protein Vitis vinifera 118.5 38 A5BUI9 15 Uncharacterized protein Vitis vinifera 40.2 39 A5CAU1 15 Uncharacterized protein Vitis vinifera 84.7 40 A5AT89 16 Uncharacterized protein Vitis vinifera 65.6 IN-SOLUTION (exclusively identified by in-solution digestion) Accession SEC...”
JV35_16100 sugar kinase from Pectobacterium betavasculorum
27% identity, 96% coverage
Cthe_0389 PfkB from Clostridium thermocellum ATCC 27405
Clo1313_1832, Cthe_0389 carbohydrate kinase from Acetivibrio thermocellus DSM 1313
26% identity, 93% coverage
- Kinetic characterization of annotated glycolytic enzymes present in cellulose-fermenting Clostridium thermocellum suggests different metabolic roles
Daley, Biotechnology for biofuels and bioproducts 2023 - “...an ATP-dependent PFK (Cthe_1261), a pyrophosphate (PP i )-dependent PFK (Cthe_0347) and another ATP-dependent PFK (Cthe_0389); as well as two FBAs (Cthe_0349 & Cthe_0319). All three PFKs were detected in the proteome, with the PP i -PFK being the prevalent isozyme translated in comparison to its...”
- “...thermocellum ATCC 27405 retrieved from Integrated Microbial Genomics [ 71 ] for pfkA (Cthe_1261), pfkB (Cthe_0389) and FBA ( aldoa ) (Cthe_0349), which were codon optimized for expression in E. coli . The plasmids were synthesized by Geneart (Life Technology Inc. Burlington, Ontario) using a pRSET-A...”
- Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression
Rydzak, BMC microbiology 2012 - “...i )-dependent 6-P-fructokinase (RAI=5.64), which was detected at higher levels than ATP-dependent 6-P-fructokinases Cthe_1261 and Cthe_0389 (RAI=1.47 and 1.06, respectively). Of the two encoded fructose-1,6-P aldolases (Cthe_0349 and Cthe_2938), only Cthe_0349 was detected. While seven copies of putative phosphoglycerate mutase are encoded, Cthe_0140, which is encoded...”
- “...observed a decrease in mRNA expression of ATP-dependent phosphofuctokinase Cthe_1261 and PP i -dependent phosphofructokinase Cthe_0389 during transition to stationary phase, we did not observe any changes in protein levels. However, we did observe a decrease in phosphoglycerate mutase Cthe_0946 and an increase in Cthe_1292, consistent...”
- Functional Analysis of H+-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum
Kuil, Applied and environmental microbiology 2022 - “...candidate genes, and whole-genome sequencing. As a secondary outcome, enzymatic assays confirmed functional annotation of clo1313_1832 as ATP- and GTP-dependent fructokinase. These results indicate that the four investigated PP i sources individually and combined play no significant PP i -supplying role, and the true source(s) of...”
- “...and translational level ( 6 , 35 , 36 ). Furthermore, two other candidate genes, clo1313_1832 and clo1313_2627 , are both annotated as members of the carbohydrate kinase PfkB family ( 48 ) in the Pfam database, whereas the KEGG database annotated these genes as a...”
CAC0424 Fructokinase from Clostridium acetobutylicum ATCC 824
CA_C0424 carbohydrate kinase from Clostridium acetobutylicum ATCC 824
26% identity, 93% coverage
- Large number of phosphotransferase genes in the Clostridium beijerinckii NCIMB 8052 genome and the study on their evolution
Shi, BMC bioinformatics 2010 - “...model strains. In both genomes, there are two copies of fructokinase genes, Cbei3497 and Cbei5009 ;CAC0424 and CAC1523. It remains an unsolved question why these three sugars, fructose, mannose and sorbose, can form such a distinctive phosphotransferase family. In terms of their chemical structures, all three...”
- Metabolic engineering of Thermoanaerobacterium aotearoense strain SCUT27 for biofuels production from sucrose and molasses
Dai, Biotechnology for biofuels and bioproducts 2023 - “...PTS-dependent transporter ScrA (CA_C0423, Fig. 1 ), sucrose-6-phosphate hydrolase or ScrB (CA_C0425) and fructokinase ScrK (CA_C0424) are responsible for sucrose transport and metabolism [ 26 28 ]. First, scrBAK from C. acetobutylicum was introduced into T. aotearoense SCUT27 and resultant mutant P8S01, unfortunately, could not grow...”
B6TB29 Fructokinase-2 from Zea mays
28% identity, 87% coverage
F502_15435 carbohydrate kinase from Clostridium pasteurianum DSM 525 = ATCC 6013
25% identity, 93% coverage
Q9FLH8 fructokinase (EC 2.7.1.4) from Arabidopsis thaliana (see 2 papers)
NP_199996 pfkB-like carbohydrate kinase family protein from Arabidopsis thaliana
AT5G51830 pfkB-type carbohydrate kinase family protein from Arabidopsis thaliana
27% identity, 87% coverage
- Proteomic and Metabolic Analysis of Pinus halepensis Mill. Embryonal Masses Induced under Heat Stress
Pereira, International journal of molecular sciences 2023 - “...0.015 1.45 Aconitate hydratase, cytoplasmic P49608 Cucurbita maxima 0.39 0.26 0.51 0.006 2.30 Probable fructokinase-7 Q9FLH8 Arabidopsis thaliana 0.30 0.20 0.23 0.024 2.74 Agglutinin P06750 Ricinus communis 0.23 0.22 0.18 0.011 2.80 25.3 kDa vesicle transport protein Q94AU2 Arabidopsis thaliana 0.44 0.20 0.20 0.036 2.59 Protein...”
- iTRAQ-based proteomic and physiological analyses of mustard sprouts in response to heat stress
Cheng, RSC advances 2020 - “...phosphorylase (Q9LIB2) and alpha-1,4 glucan phosphorylase (W8PUS4) related to sucrose metabolism were increased. Probable fructokinase-7 (Q9FLH8) catalyzes the synthesis of d -fructose 6-phosphate from d -fructose, it is part of the glycolytic/gluconeogenic pathway and plays an important role in maintaining the flux of carbon towards starch...”
- Identification of the Candidate Proteins Related to Oleic Acid Accumulation during Peanut (Arachis hypogaea L.) Seed Development through Comparative Proteome Analysis
Liu, International journal of molecular sciences 2018 - “...1.27 Q9LD43 CAC3 fatty acid biosynthetic process Araip.10008554.1 1.27 Q9M8L4 GLPK lipid oxidation Araip.10034912.1 1.27 Q9FLH8 At5g51830 lipid biosynthetic process Araip.10032969.1 1.23 Q9ZVQ3 GSTZ1 lipid oxidation Araip.10039882.1 1.17 Q8L9C4 KCR1 fatty acid biosynthetic process Araip.10034519.1 1.08 O04983 CAC2 fatty acid derivative biosynthetic process Araip.10005278.1 1.03 O04420...”
- “...fatty acid biosynthetic process Araip.10004625.1 1.26 Q9FVS9 CYP96A15 fatty acid derivative metabolic process Araip.10034912.1 1.25 Q9FLH8 At5g51830 lipid metabolic process Araip.10032969.1 1.23 Q9ZVQ3 GSTZ1 lipid oxidation Araip.10034519.1 1.13 O04983 CAC2 lipid biosynthetic process Araip.10000107.1 1.02 P56765 accD lipid biosynthetic process Araip.10036992.1 1 Q9CAP8 LACS9 fatty acid...”
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...based on the following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...based on the following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of five of...”
- Nucleotide Imbalance, Provoked by Downregulation of Aspartate Transcarbamoylase Impairs Cold Acclimation in Arabidopsis
Bellin, Molecules (Basel, Switzerland) 2023 - “...2.22 1.14 1.59 Mt dehydrogenase AT3G03250 UGP2 0.57 1.19 0.95 0.40 0.52 Ct, PM pyrophosphorylase AT5G51830 FRK1 0.53 2.46 3.27 1.22 1.93 Ct kinase AT5G56630 PFK7 0.35 2.15 1.87 1.26 1.44 Ct kinase AT5G56350 PK 0.46 1.59 2.04 0.76 Ct kinase AT4G26520 FBA7 0.40 1.85 1.62...”
- Genome-wide identification of FRK genes in Populus trichocarpa and their expression under different nitrogen treatments
Zuo, Physiology and molecular biology of plants : an international journal of functional plant biology 2021 - “...al. 2017). Using the protein sequence of Arabidopsis FRK1 (At5g51830) as a probe (Riggs et al. 2017), a BLASTP search was performed in the P. trichocarpa genome...”
- Comparative Analysis of the Transcriptomes of Persisting and Abscised Fruitlets: Insights into Plant Hormone and Carbohydrate Metabolism Regulated Self-Thinning of Pecan Fruitlets during the Early Stage
Zhang, Current issues in molecular biology 2021 - “...HXK1 1.958 1.53 10 12 CIL1518S0008 Hexokinase-2 2.7.1.1 HXK2 2.598 0.005 CIL1568S0010 Probable fructokinase-7 2.7.1.4 At5g51830 2.623 2.65 10 36 CIL0508S0004 Beta-glucosidase 12-like isoform X3 3.2.1.21 BGLU12 3.745 0.003 CIL1537S0001 Beta-glucosidase 12-like 3.2.1.21 BGLU12 8.471 5.16 10 51 CIL0493S0002 Beta-glucosidase 12-like 3.2.1.21 BGLU13 11.919 2.12 10...”
- Proteomic and metabolomic analyses provide insight into the off-flavour of fruits from citrus trees infected with 'Candidatus Liberibacter asiaticus'
Yao, Horticulture research 2019 - “...1 EC 1.1.1.37 0.64 1.10E04 gi|641839211 AT5G13420 TRA2 Transaldolase 2 EC 2.2.1.2 0.55 8.15E04 gi|641841250 AT5G51830 FRK7 Fructokinase 7 EC 2.7.1.4 0.60 3.11E03 gi|641841327 AT1G08110 GLYI2 Glyoxalase I2 EC 4.4.1.5 0.66 3.00E02 gi|641842093 AT3G52990 AT3G52990 Pyruvate kinase EC 2.7.1.40 0.60 1.30E02 gi|641847603 AT1G67280 GLYI6 Glyoxalase I6...”
- Plant Fructokinases: Evolutionary, Developmental, and Metabolic Aspects in Sink Tissues
Stein, Frontiers in plant science 2018 - “...(NP_001234396), SlFRK4 (AAM44084), At1g06020 (AAF80125), At1g06030 (AAF80126), At1g66430 (AAG51160), At2g31390 (AAM14251), At3g59480 (CAB75445), At4g10260 (CAB78149), At5g51830 (AAL34211), Os01g0894300(AAL26574), Os08g0113100 (AAL26573), Zm00001d035037 (AAP42806), Zm00001d042536 (AAP42805), BvFRK (AAA80675), StFRK (CAA78283), AtFLN1 (AEE79187), AtFLN2 (NP_177080), SlFLN1 (XP_004246362), SlFLN2 (XP_004239035), ZmFLN1 (ONM36391),and ZmFLN2 (ONM06924). The structure of a ribokinase from...”
- “...Sato et al., 2012 ; Koenig et al., 2013 ). In Arabidopsis, seven FRK genes (At5g51830, At2g31390, At1g66430, At4g10260, At1g06020, At1g06030, and At3g59480) were identified and named AtFRK17 , respectively ( Riggs et al., 2017 ). The identities of the Arabidopsis FRKs were verified following protein...”
- Identification of the Candidate Proteins Related to Oleic Acid Accumulation during Peanut (Arachis hypogaea L.) Seed Development through Comparative Proteome Analysis
Liu, International journal of molecular sciences 2018 - “...Q9LD43 CAC3 fatty acid biosynthetic process Araip.10008554.1 1.27 Q9M8L4 GLPK lipid oxidation Araip.10034912.1 1.27 Q9FLH8 At5g51830 lipid biosynthetic process Araip.10032969.1 1.23 Q9ZVQ3 GSTZ1 lipid oxidation Araip.10039882.1 1.17 Q8L9C4 KCR1 fatty acid biosynthetic process Araip.10034519.1 1.08 O04983 CAC2 fatty acid derivative biosynthetic process Araip.10005278.1 1.03 O04420 At2g26230...”
- “...acid biosynthetic process Araip.10004625.1 1.26 Q9FVS9 CYP96A15 fatty acid derivative metabolic process Araip.10034912.1 1.25 Q9FLH8 At5g51830 lipid metabolic process Araip.10032969.1 1.23 Q9ZVQ3 GSTZ1 lipid oxidation Araip.10034519.1 1.13 O04983 CAC2 lipid biosynthetic process Araip.10000107.1 1.02 P56765 accD lipid biosynthetic process Araip.10036992.1 1 Q9CAP8 LACS9 fatty acid metabolic...”
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...is based on the following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of...”
- Identification and biochemical characterization of the fructokinase gene family in Arabidopsis thaliana
Riggs, BMC plant biology 2017 - “...as previously noted [ 18 ]. At4g10260 is designated FRK4 here [ 25 ]. FRK1 (At5g51830) and FRK2 (At2g31390) were previously annotated due to their similarity to the tomato isozymes [ 25 ]. To visualize specific regions of highest identity we aligned the peptide sequences of...”
- “...respectively Table 1 Arabidopsis FRK nomenclature AGI number Previous designation (citation) Designation in this manuscript At5g51830 FRK1 (Pego and Smeekens) FRK1 At2g31390 FRK2 (Pego and Smeekens) FRK2 At1g66430 FRK3 (Arsova et al.) FRK3 At4g10260 FRK3 (Pego and Smeekens) FRK4 At1g06020 na FRK5 At1g06030 na FRK6 At3g59480...”
- More
O34768 Uncharacterized sugar kinase YdjE from Bacillus subtilis (strain 168)
26% identity, 83% coverage
7ag6A / P32143 Crystal structure of sf kinase yihv from e. Coli in complex with sulfofructose (sf), adp-mg (see paper)
29% identity, 96% coverage
- Ligands: adenosine-5'-diphosphate; 6-deoxy-6-sulfo-d-fructose (7ag6A)
SquV / b3883 6-deoxy-6-sulfofructose kinase (EC 2.7.1.184) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
yihV / P32143 6-deoxy-6-sulfofructose kinase (EC 2.7.1.184) from Escherichia coli (strain K12) (see 2 papers)
SQUV_ECOLI / P32143 Sulfofructose kinase; SF kinase; EC 2.7.1.184 from Escherichia coli (strain K12) (see 2 papers)
b3883 putative kinase from Escherichia coli str. K-12 substr. MG1655
29% identity, 96% coverage
- function: Phosphorylates 6-deoxy-6-sulfo-D-fructose (SF) to 6-deoxy-6- sulfo-D-fructose 1-phosphate (SFP) (PubMed:24463506, PubMed:33791429). Cannot phosphorylate fructose 6-phosphate (PubMed:33791429).
catalytic activity: 6-deoxy-6-sulfo-D-fructose + ATP = 6-deoxy-6-sulfo-D-fructose 1-phosphate + ADP + H(+) (RHEA:40443)
subunit: Homodimer.
disruption phenotype: Mutant fails to grow on sulfoquinovose as a sole carbon source. - Genome sequences of Arthrobacter spp. that use a modified sulfoglycolytic Embden-Meyerhof-Parnas pathway
Kaur, Archives of microbiology 2022 - “...(NP_418315.3, locus tag b3879), SQ isomerase (NP_418316.4, locus tag b3880), SF kinase (NP_418319.2, locus tag b3883), SFP aldolase (NP_418317.1, locus tag b3881), SLA reductase (NP_418318.1, locus tag b3882) and sulfo-EMP regulator (NP_418320.2, locus tag b3884) were submitted separately as queries to the NCBI BLASTp tool. The...”
- The rfaE gene from Escherichia coli encodes a bifunctional protein involved in biosynthesis of the lipopolysaccharide core precursor ADP-L-glycero-D-manno-heptose
Valvano, Journal of bacteriology 2000 - “...AAD43345 AC06797 AAD36039 P36945 AAD50017 P44331 P05054 P32143 BAA17561 O60116 AAD00536 O34768 AAC99323 AAD34338 P06999 Domain II only TagD1,...”
OCC_03567 carbohydrate kinase from Thermococcus litoralis DSM 5473
H3ZP68 Sugar kinase from Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C)
Q7LYW8 Sugar kinase from Thermococcus litoralis
PF1738 sugar kinase from Pyrococcus furiosus DSM 3638
27% identity, 95% coverage
- Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...- yes 37% - P26984 [ 312 ] 1809835 9b halTADL_1913 (cont.) - yes 31% OCC_03567 Q7LYW8 H3ZP68 [ 313 ] 15138858 9c HVO_1711 - probably 33% - P29761 [ 314 ] 1633799 P29761 matches to C-term half of HVO_1711 9c HVO_1711 (cont.) - probably 51%...”
- Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...37% - P26984 [ 312 ] 1809835 9b halTADL_1913 (cont.) - yes 31% OCC_03567 Q7LYW8 H3ZP68 [ 313 ] 15138858 9c HVO_1711 - probably 33% - P29761 [ 314 ] 1633799 P29761 matches to C-term half of HVO_1711 9c HVO_1711 (cont.) - probably 51% SAMN 04487937_...”
- Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
Pfeiffer, Genes 2021 - “...yes 37% - P26984 [ 312 ] 1809835 9b halTADL_1913 (cont.) - yes 31% OCC_03567 Q7LYW8 H3ZP68 [ 313 ] 15138858 9c HVO_1711 - probably 33% - P29761 [ 314 ] 1633799 P29761 matches to C-term half of HVO_1711 9c HVO_1711 (cont.) - probably 51% SAMN...”
- Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation
Bräsen, Microbiology and molecular biology reviews : MMBR 2014 - “...ABC transporter components, genes encoding fructokinase (PF1738) (divergently oriented), trehalose synthase (TreT; PF1742 involved in trehalose utilization),...”
- Genome sequencing of a genetically tractable Pyrococcus furiosus strain reveals a highly dynamic genome
Bridger, Journal of bacteriology 2012 - “...1 of 2 PF0189 PF0190 PF0271 PF0272 PF0401 PF1738 PF1739 PF_t006 PF0497 PF1239 PF1240 Dihydroorotase [Cold-induced protein A, CipA (57)] Hypothetical protein...”
- “...(CelB; PF0073), 4--glucanotransferase (PF0272), sugar kinase (PF1738), trehalose/maltose binding protein (PF1739), and GAPN (PF0755). However, the growth rates...”
- Metabolic and evolutionary relationships among Pyrococcus Species: genetic exchange within a hydrothermal vent environment
Hamilton-Brehm, Journal of bacteriology 2005 - “...PF0795 PF0796 PF0797 PF0798 PF1337 PF1339 PF1340 PF1737 PF1738 PF1339 PF1740 PF1741 PF1742 PF1743 PF1744 PF1745 PF1746 PF1747 PF1748 PF1749 PF1750 PF1751 * *...”
Saci_0553 carbohydrate kinase from Sulfolobus acidocaldarius DSM 639
28% identity, 94% coverage
1tz3A / Q8ZKR2 Crystal structure of aminoimidazole riboside kinase complexed with aminoimidazole riboside (see paper)
25% identity, 96% coverage
- Ligand: 5-aminoimidazole ribonucleoside (1tz3A)
TK2029 / Q5JDG9 α-D-ribose-1-phosphate 5-kinase (ADP) (EC 2.7.1.212) from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (see paper)
R1PKD_THEKO / Q5JDG9 ADP-dependent ribose-1-phosphate kinase; ADP-R1P kinase; ADP:alpha-D-ribose-1-phosphate 5-phosphotransferase; Alpha-D-ribose-1-phosphate 5-kinase (ADP); EC 2.7.1.212 from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)) (see paper)
TK2029 carbohydrate/pyrimidine kinase, PfkB family from Thermococcus kodakaraensis KOD1
27% identity, 100% coverage
- function: Involved in nucleoside degradation (PubMed:25822915). Catalyzes the ADP-dependent phosphorylation of ribose 1-phosphate (R1P) to ribose 1,5-bisphosphate (R15P) (PubMed:25822915). Can also act on deoxyribose 1-phosphate (dR1P), but is most active with R1P (PubMed:25822915). ADP is the most preferred phosphate donor, followed by GDP and UDP (PubMed:25822915).
catalytic activity: alpha-D-ribose 1-phosphate + ADP = alpha-D-ribose 1,5- bisphosphate + AMP + H(+) (RHEA:49416)
cofactor: Mg(2+) Ca(2+) (Can use Mg(2+) and Ca(2+) with equal efficiency in vitro, and to a lesser extent, Co(2+).)
disruption phenotype: Disruption of the gene abolishes the generation of ribose 1,5-bisphosphate. - Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12
Huddleston, Biochemistry 2019 - “...psuK-pseudouridine kinase (Uniprot: P30235); adoK-adenosine kinase (Uniprot: P9WID5); TK2029-ADP-dependent ribose-1-phosphate kinase from Thermococcus kodakarensis (Uniprot: Q5JDG9); mik-inositol 3-kinase (Uniprot: Q5GA22); MJ0406-nucleoside kinase from Methanocaldococcus jannaschii (Uniprot: Q57849); gsk-inosine-guanosine kinase (Uniprot: P0AEW6); pfkb-ATP-dependent 6-phosphofructokinase (Uniprot: D9TT10); and frld-fructoselysine 6-kinase (Uniprot: P45543). Figure 3. Genomic neighborhood of YdjH...”
- A non-carboxylating pentose bisphosphate pathway in halophilic archaea
Sato, Communications biology 2022 - “...R5P in the pentose phosphate pathway, R1P is phosphorylated by an ADP-dependent ribose-1-phosphate kinase (ADP-R1PK; TK2029) in T. kodakarensis , generating ribose-1,5-bisphosphate (R15P). R15P isomerase (TK0185) then converts R15P to ribulose-1,5-bisphosphate (RuBP), which is subsequently converted to 3-phosphoglycerate (3-PGA) by the carboxylase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase...”
- “...been identified in previous studies; an ADP-dependent R1P kinase from the hyperthermophilic archaeon T. kodakarensis (TK2029) and an ATP-dependent R1P kinase from the hyperthermophilic archaeon Pyrobaculum calidifontis (Pcal_0041). The ATP-dependent R1P kinase identified in this study (Halxa_1682) was 25% identical with the TK2029 protein and 36.8%...”
- Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways
Sutter, Extremophiles : life under extreme conditions 2020 - “..., Pcal 0041 (Aziz et al. 2018 ); Haloterrigena hispanica , A0A1G6RMF8; Thermococcus kodakarensis , TK2029 (Aono et al. 2015 ); Glucokinase/phosphofructokinase: T. tenax , TTX0060 (Drr et al. 2003 ); A. pernix , Ape2091; Zymomonas mobilis , Q03417 (King et al. 1996 ); E. coli...”
- The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism
Hove-Jensen, Microbiology and molecular biology reviews : MMBR 2019 - “...(gene TK0353) or ADP-dependent ribosyl 1-phosphate 5-kinase (gene TK2029). In cell extracts, the ribose moiety of ribonucleosides is converted to PRibP via...”
- A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate
Aziz, Journal of bacteriology 2018 - “...the TK2285 protein is a myo-inositol kinase (34), the TK2029 protein is an ADP-dependent R1P kinase, and the protein encoded by TK1843 is an ATP-dependent...”
- “...activity with R1P. However, with the exception of the TK2029 protein from T. kodakarensis, which is an ADP-dependent R1P kinase, none of the ribokinases from...”
- An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism
Makino, Nature communications 2016 - “...glucokinase (TK1110), 20.7% identical to ADP-dependent phosphofructokinase (TK0376) and 18.6% identical to ADP-dependent ribose-1-phosphate kinase (TK2029) from T. kodakarensis . These results suggest that TK0378 homologs form a group of kinases distinct to previously recognized kinase families, including ADP-dependent sugar kinases. The protein also displays only...”
- An uncharacterized member of the ribokinase family in Thermococcus kodakarensis exhibits myo-inositol kinase activity
Sato, The Journal of biological chemistry 2013 - “...as sugar kinases of the ribokinase family, TK1843, TK2029, and TK2285. The substrate specificities and physiological roles of these gene products are currently...”
- “...phosphofructokinase (19) and glucokinase (20), respectively. TK1843 and TK2029 are distantly related to the MJ0406 protein and the APE0012 protein from the...”
Hore_18220 Fructokinase from Halothermothrix orenii H 168
25% identity, 92% coverage
B6TP93 Fructokinase-2 from Zea mays
27% identity, 87% coverage
- Transient alkalinization of the leaf apoplast stiffens the cell wall during onset of chloride salinity in corn leaves
Geilfus, The Journal of biological chemistry 2017 - “...B6SPX4 B6SS31 B6SX33 B6T681 B6T7J7 B6T8K2 B6TB29 B6TDJ0 B6TP93 B6TPJ8 B6TSG5 B6U7D8 B7ZYP5 B7ZYX8 B8A046 B8A068 C0PCV2 C4J722 K7UNP2 K7V5Z8 K7VQR1 Q41785 Q43706...”
- “...SUS1, Q43706; and Shrunken1, K7V5Z8) and fructokinases (B6TB29, B6TP93, and B6TPJ8) (Table 3), which is indicative for a role in the production of UDP-glucose...”
- A comparative glycoproteome study of developing endosperm in the hexose-deficient miniature1 (mn1) seed mutant and its wild type Mn1 in maize
Silva-Sanchez, Frontiers in plant science 2014 - “...P0 5.27 5.19 26.68 34.49 0.77 1.58 12 11 1 0.52 Zhou et al., 2007 B6TP93 Fructokinase-2 5.34 35.53 18 22 0 0.41 478 B4FW31 Protein phosphatase 2C isoform epsilon 4.9 4.76 23.85 31.21 0.78 1.39 8 12 3 0.13 Lu, 2008 319 B6TR84 Glycine-rich RNA-binding...”
- Proteomic comparison of basal endosperm in maize miniature1 mutant and its wild-type Mn1
Silva-Sanchez, Frontiers in plant science 2013 - “...ND B6TYM9 f Vignain 1.61 0.04 ND ND C5JA67 BETL-9 protein ND ND 0.45 0.01 B6TP93 Fructokinase-2 ND ND 1.20 0.02 B4FBF4 Serine hydroxymethyltransferase ND ND 1.24 0.01 B6TJM5 26S protease regulatory subunit 6A ND ND 1.26 0.02 B4FZV6 Similar to 26S protease regulatory subunit 7...”
- Abscisic acid refines the synthesis of chloroplast proteins in maize (Zea mays) in response to drought and light
Hu, PloS one 2012 - “...P00874 4.9/32 6.33/52.70 221 39% (23) Chloroplast Chloroplast Chloroplast Cytosol Ribulose-bisphosphate carboxylase activity 19 Fructokinase-2 B6TP93 5.3/33 5.34/35.53 425 68% (25) Chloroplast Chloroplast ChloroplastCytosol Kinase activity 20 ARF-related protein B6TF60 5.8/30 6.56/22.78 64 15% (2) Intracellular Chloroplast Cytosol Mitochondrial GTP binding 21 Fructose-bisphosphate aldolase C0PD30 5.9/30...”
DR1525 carbohydrate kinase, PfkB family from Deinococcus radiodurans R1
DR_1525 carbohydrate kinase family protein from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
27% identity, 83% coverage
- Identification of new genes contributing to the extreme radioresistance of Deinococcus radiodurans using a Tn5-based transposon mutant library
Dulermo, PloS one 2015 - “...enzyme ( o ) DRA0276 39.4 4.2 R R R Carbohydrate metabolism Fructokinase RbsK ortholog DR1525 48.7 3.4 SS S s Amino acid transport and metabolism Glycine/serine hydroxymethyltransferase (GlyA) DR0038 41 2.1 s s R Metabolism of coenzymes , cofactors and vitamins Pantothenate synthetase, PanC DR1164...”
- Proteomic Response of Deinococcus radiodurans to Short-Term Real Microgravity during Parabolic Flight Reveals Altered Abundance of Proteins Involved in Stress Response and Cell Envelope Functions
Moors, Life (Basel, Switzerland) 2021 - “...Fold Change Pentose Phosphate Pathway (PPP) phosphopentomutase DR_2135 1.28 glucose-6-phosphate 1-dehydrogenase DR_1596 0.80 carbohydrate kinase DR_1525 0.61 glucose-6-phosphate isomerase pgi 0.52 2-deoxyribose-5-phosphate aldolase DR_1205 0.49 DNA Damage and Repair, DNA Processing DNA ligase DR_2069 1.04 DNA-directed DNA polymerase DR_1707 1.01 hypothetical protein DR_0428 0.83 exconuclease ABC...”
- Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species
Lim, FEMS microbiology reviews 2019 - “...of DR_0199 (encoding nucleoid-associated protein, YbaB/EbfC family), DR_0382 (YgjD/TsaD), DR_0756 (YeaZ/TsaB), DR_1321 (signal peptidase I), DR_1525 (fructokinase RbsK), DR_1972 (ClpP, ATP-dependent Clp protease proteolytic subunit), DR_1973 (ClpX, ATP-dependent Clp protease ATP-binding subunit), DR_2417 (DncA/RNase J), DR_2462 (RNase Y). Homologues of DR_0342 (Rieske-like Fe-S protein) and DR_1471...”
3ih0A / O59128 Crystal structure of an uncharacterized sugar kinase ph1459 from pyrococcus horikoshii in complex with amp-pnp
26% identity, 88% coverage
- Ligand: phosphoaminophosphonic acid-adenylate ester (3ih0A)
G1FCF5 fructokinase from Dimocarpus longan
28% identity, 88% coverage
STM4024.S putative sugar kinase from Salmonella typhimurium LT2
27% identity, 96% coverage
BMQ_1157 carbohydrate kinase family protein from Bacillus megaterium QM B1551
26% identity, 83% coverage
- Flux Connections Between Gluconate Pathway, Glycolysis, and Pentose-Phosphate Pathway During Carbohydrate Metabolism in Bacillus megaterium QM B1551
Wushensky, Frontiers in microbiology 2018 - “...system transporter I; gdh , glucose 1-dehydrogenase; pgi , glucose-6-phosphate isomerase; gntK , gluconate kinase; BMQ_1157 , fructokinase; xylT , xylose permease; xylA , D -xylose isomerase; xylB , xylokinase; BMQ_0309 , 6-phosphogluconolactonase; BMQ_3633 , 2-dehydro-3-deoxyphosphogluconate aldolase; fruA , PTS system fructose-specific II subunit IIA; fruB...”
O04897 fructokinase (EC 2.7.1.4) from Solanum lycopersicum (see paper)
NP_001233893 fructokinase from Solanum lycopersicum
26% identity, 86% coverage
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...et al., 2007 ). This phylogenetic tree is based on the following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s...”
A0A0H3AER7 fructokinase (EC 2.7.1.4) from Vibrio cholerae (see paper)
28% identity, 82% coverage
ABZR86_RS11105 Fructokinase (EC 2.7.1.4) from Dyella japonica UNC79MFTsu3.2
29% identity, 83% coverage
- mutant phenotype: Specifically important for utilizing D-Fructose. Automated validation from mutant phenotype: the predicted function (2.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
ZMO1895 PfkB domain protein from Zymomonas mobilis subsp. mobilis ZM4
28% identity, 82% coverage
ECs2481 putative kinase from Escherichia coli O157:H7 str. Sakai
27% identity, 87% coverage
OA04_04060 aminoimidazole riboside kinase from Pectobacterium versatile
24% identity, 93% coverage
NP_001234206 fructokinase from Solanum lycopersicum
28% identity, 78% coverage
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...tree is based on the following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of...”
- The SlFRK4 promoter is active only during late stages of pollen and anther development.
David-Schwartz, Plant science : an international journal of experimental plant biology 2013 (PubMed)- GeneRIF: SlFRK4 promoter is gradually activated in pollen grains throughout the later stages of anther development and upon pollen germination. SlFRK4 may play an important role in pollen and anther development.
VCA0656 fructokinase from Vibrio cholerae O1 biovar eltor str. N16961
28% identity, 82% coverage
MS1233 RbsK protein from Mannheimia succiniciproducens MBEL55E
25% identity, 96% coverage
- Mannheimia succiniciproducens phosphotransferase system for sucrose utilization
Lee, Applied and environmental microbiology 2010 - “...in M. succiniciproducens. The genes, MS0784, MS0807, MS0909, MS1233, and MS1237, were knocked out from the chromosome of the wild-type M. succiniciproducens...”
- “...sucrose PTS, MS0909 for sucrose 6-phosphate hydrolase, and MS1233 for fructokinase (Fig. 1D). It has been shown that the genes encoding proteins responsible for...”
LOC108998652 probable fructokinase-7 from Juglans regia
28% identity, 86% coverage
- Combined transcriptomic and metabolomic analysis of the mechanism by which <i>Bacillus velezensis</i> induces resistance to anthracnose in walnut
Wang, Frontiers in microbiology 2024 - “...LOC109005150; LOC109007785; LOC109010220; LOC109003634; LOC108998278; LOC108996646; LOC108985317; LOC108979963; LOC109004987; LOC108996947; LOC108988942; LOC108999180; LOC108988131; LOC108984074; LOC108981179; LOC108998652; LOC108992456; LOC108980812 LOC108989738; LOC109018267; LOC108987596; LOC108984851; LOC109019460; LOC108988131; LOC108984074; LOC108995469; LOC109009357; LOC108982978; LOC109011808; LOC108981208; LOC108983086; LOC109010098; LOC109002259; LOC109017388; LOC109003474; LOC109002260 DEM up D-xylulose 5-phosphate; 5-O-caffeoylquinic acid; Palmitic acid; UDP-N-acetyl--D-glucosamine; UDP-N-acetylglucosamine;...”
Htur_0569 PfkB domain protein from Haloterrigena turkmenica DSM 5511
29% identity, 97% coverage
- A non-carboxylating pentose bisphosphate pathway in halophilic archaea
Sato, Communications biology 2022 - “...and H. xanaduensi s ( Hs -RbsK, Ht -RbsK, and Hx -RbsK encoded by VNG_1851G, Htur_0569, and Halxa_1682, respectively) were produced in E. coli . Hs -RbsK formed inclusion bodies and expression levels of the Ht -RbsK gene were low. Sufficient amounts of soluble Hx -RbsK...”
SVXHr_1094 carbohydrate kinase family protein from Halorhabdus sp. SVX81
26% identity, 93% coverage
- Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea
La, Microbial biotechnology 2023 - “...isomerase, Dmannonate oxidoreductase and Dmannonate hydrolase (SVXHr_075759). KDG is likely then phosphorylated by KDG kinase (SVXHr_1094) to form 6phosphoKGP (KDGP), which can finally be cleaved by KDGP aldolase (SVXHr_0294) to yield pyruvate and glyceraldehyde3phosphate, which may be involved in the EmbdenMeyerhofParnas pathway (Figure 5A ). This...”
3in1A / P77493 Crystal structure of a putative ribokinase in complex with adp from e.Coli
26% identity, 87% coverage
- Ligand: adenosine-5'-diphosphate (3in1A)
YdjH / b1772 L-glycero-L-galacto-octuluronate kinase from Escherichia coli K-12 substr. MG1655 (see 2 papers)
ydjH / P77493 L-glycero-L-galacto-octuluronate kinase from Escherichia coli (strain K12) (see 2 papers)
b1772 putative kinase from Escherichia coli str. K-12 substr. MG1655
26% identity, 86% coverage
scrK / P26420 fructokinase (EC 2.7.1.4) from Klebsiella pneumoniae (see paper)
SCRK_KLEPN / P26420 Fructokinase; EC 2.7.1.4 from Klebsiella pneumoniae (see paper)
scrK / GB|CAA43322.1 fructokinase; EC 2.7.1.4 from Klebsiella pneumoniae (see paper)
scrK / CAA43322.1 fructokinase from Klebsiella pneumoniae (see paper)
27% identity, 95% coverage
- function: Involved in sucrose metabolism.
catalytic activity: D-fructose + ATP = D-fructose 6-phosphate + ADP + H(+) (RHEA:16125)
CD1806 putative fructokinase from Clostridium difficile 630
25% identity, 93% coverage
- Transcriptional analysis of temporal gene expression in germinating Clostridium difficile 630 endospores
Dembek, PloS one 2013 - “...up-regulated in germinating spores. These included fruABC (fructose-specific phosphotransferase; 75.2-fold), CD2270 (putative 1-phosphofructokinase; 79.8-fold) and CD1806 (putative fructokinase; 2.8-fold) ( Figure 4D ). While this could simply reflect the composition of the culture medium, it could also indicate the preference for fructose as the main carbon...”
- Genetic organisation, mobility and predicted functions of genes on integrated, mobile genetic elements in sequenced strains of Clostridium difficile
Brouwer, PloS one 2011 - “...second CTn 1 -like element in strain QCD-63Q42 is inserted between homologues of CD1807 and CD1806. Two insertions in the conjugation module include genes encoding a putative alpha/beta hydrolase, a lactoylglutathione lyase, a group II intron reverse transcriptase, as well as several hypothetical proteins. The accessory...”
- Integration of metabolism and virulence by Clostridium difficile CodY
Dineen, Journal of bacteriology 2010 - “...Amino acid transport 3/3 CD1779* Unknown 1.27 3/3 CD1806 Fructokinase 0.77 2 3 3 3 CD1988 CD2007 CD2010* CD2029* Tryptophan transport Erythromycin resistance...”
5yggA / A0A0H3AER7 Crystal structure of fructokinase double-mutant (t261c-h108c) from vibrio cholerae o395 in fructose, adp and potassium ion bound form (see paper)
27% identity, 85% coverage
- Ligands: adenosine-5'-diphosphate; beta-d-fructofuranose (5yggA)
LOC110703632 probable fructokinase-6, chloroplastic from Chenopodium quinoa
26% identity, 77% coverage
Sb01g046230 No description from Sorghum bicolor
26% identity, 63% coverage
- Evolution and expression of the fructokinase gene family in Saccharum
Chen, BMC genomics 2017 - “...SsFRK2 Sb10g008280 XM_002436715.1 XP_002436760.1 NC_012879.1|:84224808426810 chromosome 10 SsFRK3 Sb01g015030 XM_002466795.1 XP_002466840.1 NC_012870.1|:c1444119714437165 chromosome 1 SsFRK4 Sb01g046230 XM_002468410.1 XP_002468455.1 NC_012870.1|:c6927478369271917 chromosome 1 SsFRK5 Sb03g040010 XM_002456599.1 XP_002456644.1 NC_012872.1|:6762653867628943 chromosome 3 SsFRK6 Sb09g018040 XM_002440925.1 XP_002440970.1 NC_012878.1|:c4512527845122178 chromosome 9 SsFRK7 Sb07g027900 XM_002445866.1 XP_002445911.1 NC_012876.1|:c6287318262869987 chromosome 7 The coding sequences of...”
scrK / Q9ZHJ6 fructokinase (EC 2.7.1.4) from Clostridium beijerinckii (see paper)
27% identity, 94% coverage
Q9C524 fructokinase (EC 2.7.1.4) from Arabidopsis thaliana (see 2 papers)
NP_564875 pfkB-like carbohydrate kinase family protein from Arabidopsis thaliana
AT1G66430 pfkB-type carbohydrate kinase family protein from Arabidopsis thaliana
27% identity, 78% coverage
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...the following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...the following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA mutants of five of the AtFRK...”
- Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles
Fernández, Frontiers in plant science 2021 - “...62 O65258 0 2.81 6 4 pfkB-like carbohydrate kinase family protein 621 222710-119_2_ORF2 [5] 45 Q9C524 2.947E-180 1.66 19 9 Phosphoglucan, water dikinases 1,089 316777-59_1_ORF2 135 Q6ZY51 0 2.08 18 17 Probable sucrose-phosphate synthase 3 1,081 165303-173_5_ORF1 [19] 123 Q8RY24 0 2.81 7.3 9 Glucose-1-phosphate adenylyltransferase...”
- Proteome-Wide Analysis of Heat-Stress in Pinus radiata Somatic Embryos Reveals a Combined Response of Sugar Metabolism and Translational Regulation Mechanisms.
Castander-Olarieta, Frontiers in plant science 2021 - “...0.71 0.58 0.82 0.018 2.42 Actin-2 P0C539 1.3 0.4 0.31 0.018 1.51 Probable fructokinase-6, chloroplastic Q9C524 0.7 0.65 0.93 0.018 2.08 Ferredoxinnitrite reductase, chloroplastic Q39161 0.59 0.64 1.09 0.018 1.51 60S ribosomal protein L23 Q9XEK8 0.98 1.37 1.4 0.018 2.11 Adenosylhomocysteinase P68173 0.93 0.22 0.24 0.018...”
- Subgroup 4 R2R3-MYBs in conifer trees: gene family expansion and contribution to the isoprenoid- and flavonoid-oriented responses
Bedon, Journal of experimental botany 2010 - “...2.0E-03 GQ03230_I01 BT102565 Cystathionine -synthase P55217 9E-69 1.3 5.8E-04 1.4 9.7E-04 GQ02802_I24 BT103811 Fructokinase, putative Q9C524 4E-41 1.5 1.1E-05 1.4 1.0E-03 GO:0006810 Transport GQ03810_L15 BT101863 ABC transporter, PRD-like Q8GU87 1E-35 FV 2.2 1.2E-05 1.9 1.0E-03 GQ03810_L15 BT101863 ABC transporter, PDR-like Q0IRX8 1E-30 FV 2.3 3.4E-06 1.8...”
- Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions
Nose, PloS one 2023 - “...three sites. Probe Sequence ID Arabidopsis ID e-value Symbol Description Parameter Pearson r CUST_8654_PI429951308 reCj23286:MSWR:isotig23138 AT1G66430 1.1E-179 - pfkB-like carbohydrate kinase family protein temp-30d -0.88 CUST_6435_PI429951308 reCj21042:MSWR:isotig20894 AT1G70730 0.0 PGM2 phosphoglucomutase/phosphomannomutase family protein temp-7d -0.85 CUST_5677_PI429951308 reCj20278:MSWR:isotig20130 AT3G01510 0.0 LSF1 like sex four 1 temp-0h -0.84...”
- “...9B1 temp-0h 0.88 CUST_4959_PI429951308 reCj19556:MSWR:isotig19408 AT5G49720 0.0 GH9A1 glycosyl hydrolase 9A1 temp-0h 0.89 CUST_7451_PI429951308 reCj22073:MSWR:isotig21925 AT1G66430 2.4E-164 - pfkB-like carbohydrate kinase family protein temp-0h 0.89 CUST_5821_PI429951308 reCj20424:-SWR:isotig20276 AT4G24040 0.0 TRE1 trehalase 1 temp-30d 0.91 CUST_7431_PI429951308 reCj22053:-SW-:isotig21905 AT1G27680 0.0 APL2 AGPase large subunit 2 temp-0h 0.93 CUST_4967_PI429951308...”
- Deciphering Pleiotropic Signatures of Regulatory SNPs in Zea mays L. Using Multi-Omics Data and Machine Learning Algorithms
Haleem, International journal of molecular sciences 2022 - “...the developing maize kernels and the flag leaf for translocation of proteins. The arabidopsis homologue, AT1G66430, of the oil content related gene, Zm00001eb372200 is associated with ear row number and ear leaf height in this cluster and is also known for its role in carbohydrate biosynthetic,...”
- An expanded role for the transcription factor WRINKLED1 in the biosynthesis of triacylglycerols during seed development
Kuczynski, Frontiers in plant science 2022 - “...0.96 ** ENO 2 (Enolase, AT2G36530) (c) +33(+) 13.43.7 0.92 0.89 ** FRK 3 (Fructokinase, AT1G66430) (p) 37(+) 85.232.8 0.83 0.96 ** GPDHC 1 (glycerol-3-phosphate dehydrogenase, AT2G41540) (c) +178() 81.715.5 0.92 0.98 ** GPDH (glycerol-3-phosphate dehydrogenase, AT3G07690) (c) +34(+) 105.230.8 0.83 0.94 ** LEC 1 (Leafy...”
- An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging "Golden Delicious" Apple
Yuan, International journal of molecular sciences 2019 - “...peptidase 2 [EC:3.4.21.108] K08669 MD09G1252100 20.72 0.58 -, ribulose-bisphosphate carboxylase [EC:4.1.1.39] K01602 MD09G1262800 41.17 0.65 At1g66430, fructokinase [EC:2.7.1.4] K00847 MD10G1011900 19.93 0.59 At4g03520, thioredoxin 1 K03671 MD10G1195700 52.49 0.55 At3g14420, (S)-2-hydroxy-acid oxidase [EC:1.1.3.15] K11517 MD14G1219000 41.45 0.69 -, chitinase domain-containing protein 1 K17525 MD15G1006300 16.86 0.72...”
- Plant Fructokinases: Evolutionary, Developmental, and Metabolic Aspects in Sink Tissues
Stein, Frontiers in plant science 2018 - “...the sequence alignment: SlFRK1 (AAB57733), SlFRK2 (AAB57734), SlFRK3 (NP_001234396), SlFRK4 (AAM44084), At1g06020 (AAF80125), At1g06030 (AAF80126), At1g66430 (AAG51160), At2g31390 (AAM14251), At3g59480 (CAB75445), At4g10260 (CAB78149), At5g51830 (AAL34211), Os01g0894300(AAL26574), Os08g0113100 (AAL26573), Zm00001d035037 (AAP42806), Zm00001d042536 (AAP42805), BvFRK (AAA80675), StFRK (CAA78283), AtFLN1 (AEE79187), AtFLN2 (NP_177080), SlFLN1 (XP_004246362), SlFLN2 (XP_004239035), ZmFLN1 (ONM36391),and...”
- “...al., 2012 ; Koenig et al., 2013 ). In Arabidopsis, seven FRK genes (At5g51830, At2g31390, At1g66430, At4g10260, At1g06020, At1g06030, and At3g59480) were identified and named AtFRK17 , respectively ( Riggs et al., 2017 ). The identities of the Arabidopsis FRKs were verified following protein expression in...”
- Proteomic Analysis of the Function of a Novel Cold-Regulated Multispanning Transmembrane Protein COR413-PM1 in Arabidopsis
Su, International journal of molecular sciences 2018 - “...(VTC1)/cytokinesis defective 1 (CYT1)/GDP-mannose pyrophosphorylase (GMP1) (AT2G39770), trehalose-6-phosphatase synthase S7 (TPSA/TPS7) (AT1G06410), fructokinase 3 (FRK3/FRK6) (AT1G66430), sucrose phosphate synthase A1 (SPSA1) (AT5G20280), and pyrimidine 1 (PYD1) (AT3G17810). Expression levels of most of the eight proteins were downregulated in cor413-pm1 when compared to those of WT, whether...”
- “...11 ). Among pathways, we found that, confirmed using qRT-PCR, four DAPs, including FAB1/KAS2, FRK3/FRK6 (AT1G66430), SPSA1/SPS1, and ASE2, were involved in metabolic processes of fatty acids, sugars, and purine, which suggests that COR413-PM1 mainly regulated freezing tolerance through affecting these metabolism processes in plants. 3....”
- Corrigendum: Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2017 - “...on the following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial...”
- Identification and biochemical characterization of the fructokinase gene family in Arabidopsis thaliana
Riggs, BMC plant biology 2017 - “...related to FRKs, Arsova et al. demonstrated FRK activity for a plastidic Arabidopsis pfkB protein, At1g66430, and denoted it as FRK3 due to sequence similarity to tomato FRK3 [ 23 ]. To explore the diversity of FRKs within a single species, we report here the identification...”
- “...one member of the pfkB family of proteins in Arabidopsis thaliana ecotype Col-0, encoded in At1g66430, therein named FRK3, was an active FRK after expression of the recombinant protein in E. coli . To determine whether other pfkB enzymes in Arabidopsis are active FRKs, we first...”
- More
EC958_3041 aminoimidazole riboside kinase from Escherichia coli O25b:H4-ST131
25% identity, 93% coverage
orf13 PfkB family carbohydrate kinase from Gramella forsetii KT0803
25% identity, 83% coverage
Q6VWJ5 fructokinase from Solanum lycopersicum
28% identity, 78% coverage
- Hexose kinases and their role in sugar-sensing and plant development
Granot, Frontiers in plant science 2013 - “...Dai et al. ( 2002a ), German et al. ( 2003 ) SlFRK3/ FKIII AY323226/AAR24912, Q6VWJ5 Yes P Petreikov et al. ( 2001 ), German et al. ( 2004 ) SlFRK4 AY099454/AAM44084 No C * Involved in pollen development German et al. ( 2002 ), David-Schwartz...”
- Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development.
Deluc, BMC genomics 2007 - “...metabolism 20 2.49 1608995_at BQ796616 TC54941 Q84NI6 a-galactosidase Carbohydrate metabolism 11 2.48 1622806_at CB009073 TC63769 Q6VWJ5 Fructokinase Carbohydrate metabolism 1 2.48 1609510_at CF513342 TC69905 Q0WV85 O-linked GlcNAc transferase Carbohydrate metabolism 16 2.47 1609232_at CA811215 TC56883 Q9ZVJ5 Phosphoglucomutase Carbohydrate metabolism 15 2.45 1613514_s_at CF202452 TC54941 Q9M442 a-galactosidase...”
- “...metabolism 2 2.25 1621432_s_at CD005042 TC52007 Q8VXZ7 a-galactosidase Carbohydrate metabolism 10 2.18 1621053_at CF414284 TC63955 Q6VWJ5 Fructokinase Carbohydrate metabolism 3 2.16 1621719_at CF404994 TC65554 Q8LGH6 Dihydrolipoamide S-acetyltransferase Carbohydrate metabolism 3 2.14 1619373_at CB920390 TC69024 P80572 Alcohol dehydrogenase Carbohydrate metabolism 3 2.13 1614612_at CF513589 TC63370 Q9LSG3 Glucose...”
Sde_3280 diguanylate cyclase/phosphodiesterase (GGDEF & EAL domains) from Saccharophagus degradans 2-40
25% identity, 80% coverage
CH51_RS11580 carbohydrate kinase from Staphylococcus aureus
SA1845 hypothetical protein from Staphylococcus aureus subsp. aureus N315
27% identity, 84% coverage
- Staphylococcus aureus PhoU Homologs Regulate Persister Formation and Virulence
Shang, Frontiers in microbiology 2020 - “...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 hydrolase 2.17 ND CH51_RS06555 Ribulose-phosphate 3-epimerase 2.16 ND CH51_RS08720 Glycine dehydrogenase 2.94 ND CH51_RS02915 Serine acetyltransferase 2.52 ND CH51_RS00820 Formate dehydrogenase 2.06 ND CH51_RS09725...”
- Exposure of clinical MRSA heterogeneous strains to β-lactams redirects metabolism to optimize energy production through the TCA cycle
Keaton, PloS one 2013 - “...aspartate metabolism, pyruvate metabolism. SA1510 gapB 4.8 glyceraldehyde 3-phosphate dehydrogenase Involved in glycolysis and glyconeogenesis. SA1845 2.2 hypothetical protein similar to fructokinase Catalyzes conversion of fructose to fructose-6-P Energy metabolism SA1927 fbaA 2.3 fructose-bisphosphate aldolase Involved in gluconeogenesis SA2204 gpmA 4 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase Involved in...”
MSMEG_4661 sugar kinase, ribokinase family protein from Mycobacterium smegmatis str. MC2 155
26% identity, 82% coverage
- Azido Inositol Probes Enable Metabolic Labeling of Inositol-Containing Glycans and Reveal an Inositol Importer in Mycobacteria
Hodges, ACS chemical biology 2023 - “...immediately downstream of MSMEG_4659 ( Figure 4B ) revealed a cluster of 6 genes ( MSMEG_4661 MSMEG_4666 ) with sequence similarity to genes reported to catabolize inositol to acetyl-CoA and dihydroxyacetone in various soil bacteria. 43 Reports investigating genes under control of IolR in Corynebacterium glutamicum...”
- RNase E and HupB dynamics foster mycobacterial cell homeostasis and fitness
Griego, iScience 2022 - “...3B). We identified 14 proteins implicated in RNA turnover, including a ribonucleoprotein (MSMEG_1193), a ribokinase (MSMEG_4661), and MutT2, belonging to the nudix family and responsible for generating 5-monophosphorylated transcripts, which are more susceptible to RNase E( Deana etal., 2008 ). As expected, we measured enrichment of...”
- A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
McKenzie, Journal of bacteriology 2012 - “...MSMEG_4656 MSMEG_4657 MSMEG_4658 MSMEG_4659 MSMEG_4660 MSMEG_4661 MSMEG_4662 MSMEG_4663 MSMEG_4664 MSMEG_4665 MSMEG_4666 MSMEG_5057 MSMEG_5058 MSMEG_5059...”
NP_001234396 fructokinase 3 from Solanum lycopersicum
28% identity, 77% coverage
- A new insight into the evolution and functional divergence of FRK genes in Pyrus bretschneideri
Cao, Royal Society open science 2018 - “...is CAA78283) and 389 aa long ( Solanum lycopersicum FRK3, whose GenBank accession number is NP_001234396 and includes a chloroplast transit peptide), whereas SlFRK2 (GenBank accession number: XP_004239035) is greater than 600 aa long[ 16 , 26 ]. Common characteristics might be shared by these proteins...”
- Plant Fructokinases: Evolutionary, Developmental, and Metabolic Aspects in Sink Tissues
Stein, Frontiers in plant science 2018 - “...Accession IDs of the proteins used for the sequence alignment: SlFRK1 (AAB57733), SlFRK2 (AAB57734), SlFRK3 (NP_001234396), SlFRK4 (AAM44084), At1g06020 (AAF80125), At1g06030 (AAF80126), At1g66430 (AAG51160), At2g31390 (AAM14251), At3g59480 (CAB75445), At4g10260 (CAB78149), At5g51830 (AAL34211), Os01g0894300(AAL26574), Os08g0113100 (AAL26573), Zm00001d035037 (AAP42806), Zm00001d042536 (AAP42805), BvFRK (AAA80675), StFRK (CAA78283), AtFLN1 (AEE79187), AtFLN2...”
- Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development
Stein, Frontiers in plant science 2016 - “...This phylogenetic tree is based on the following protein sequences: SlFRK1 (NP_001233893), SlFRK2 (NP_001233888), SlFRK3 (NP_001234396), SlFRK4 (NP_001234206), At5g51830 (NP_199996), At1g66430 (NP_564875), At4g10260 (NP_192764), At3g59480 (NP_191507), At1g06030 (NP_172093), At1g06020 (NP_172092), and At2g31390 (NP_180697). In order to characterize the function of AtFRK s in planta , T-DNA...”
- The tomato plastidic fructokinase SlFRK3 plays a role in xylem development.
Stein, The New phytologist 2016 (PubMed)- GeneRIF: Data demonstrate a role of the plastidic SlFRK3 in xylem development and hydraulic conductance. [SlFRK3]
Z3624 aminoimidazole riboside kinase from Escherichia coli O157:H7 EDL933
24% identity, 95% coverage
- Global effect of RpoS on gene expression in pathogenic Escherichia coli O157:H7 strain EDL933
Dong, BMC genomics 2009 - “...protein Z1924 137 Prophage CP-933X protein Z2296 57 Unknown Z2297 254 Unknown Z2298 55 Unknown Z3624 64 D-fructokinase Z3625 139 Sucrose hydrolase Z4874 60 Unknown Z5000 48 Putative regulatory protein Z5352 125 Unknown * Indicates that some genes in the known operon are not listed because...”
- “...13 O-Island 95 Putative transporter Z3623 9.4 0.3 4.8 0.1 24 O-Island 102 Sucrose permease Z3624 8.5 0.2 2.5 0.0 64 O-Island 102 D-fructokinase Z3625 9.4 0.1 2.2 0.0 139 O-Island 102 Sucrose hydrolase Z3947 8.3 0.4 4.0 0.5 19 O-Island 108 Unknown (Phage or Prophage...”
G7K1Y1 fructokinase from Medicago truncatula
27% identity, 78% coverage
- Label-free quantitative proteomic analysis of alfalfa in response to microRNA156 under high temperature
Arshad, BMC genomics 2020 - “...G7JCT4 MTR_4g095360 1.76 0.0130 Putative tripeptidyl-peptidase II G7L4Q1 MTR_7g077880 1.76 0.0258 Putative HAD-like domain-containing protein G7K1Y1 MTR_5g079460 1.80 0.0173 PfkB family carbohydrate kinase G7KG86 MTR_5g011990 1.82 0.0155 Uncharacterized protein G7KET9 MTR_5g011220 1.84 0.0080 PGR5-like protein 1A G7I2N9 MTR_1g073130 1.85 0.0479 Carboxy-terminal processing peptidase-like protein G7K4T4 MTR_5g096670...”
TEU_01625 ADP-dependent ribose-1-phosphate kinase from Thermococcus eurythermalis
26% identity, 99% coverage
- Cross-Stress Adaptation in a Piezophilic and Hyperthermophilic Archaeon From Deep Sea Hydrothermal Vent
Zhao, Frontiers in microbiology 2020 - “...well as the other seven kinases using substrates as nucleoside diphosphate (TEU_09080), uridylate (TEU_04165), ribose (TEU_01625 and TEU_02660), and cofactors, i.e., NAD (TEU_02205), riboflavin (TEU_09890), and pantoate (TEU_01430). Among the total 12 kinases, only carbamate kinase (TEU_01535) was up-expressed, which is involved in the arginine biosynthesis...”
SERP2216 ribokinase, putative from Staphylococcus epidermidis RP62A
24% identity, 91% coverage
- Characterization of a complex context containing mecA but lacking genes encoding cassette chromosome recombinases in Staphylococcus haemolyticus
Zong, BMC microbiology 2013 - “...99%, S. epidermidis RP62a (locus SERP2217) rbk d 2781-3719 Ribokinase 99%, S. epidermidis RP62a (locus SERP2216) IS 431 3701-4401 IS 431 merR 4888-5235 Transcriptional regulator of the merR family 100%, type IX SCC mec of S. aureus JCSC6943 and S. haemolyticus JCSC1435 (locus SH0094) thiJ 5313-5996...”
- “...contained genes encoding ADP-ribosylglycohydrolase, permease and ribokinase. R1 was almost identical to the counterpart (loci SERP2216 to SERP2218) of the integrative plasmid v Se1 on the chromosome of S. epidermidis RP62a (GenBank accession no. CP000029) but was absent from S. haemolyticus JCSC1435, suggesting a foreign origin....”
lmo0385 similar to B. subtilis IolC protein and to fructokinase from Listeria monocytogenes EGD-e
24% identity, 93% coverage
- Comparative genomics analysis to explore the biodiversity and mining novel target genes of Listeria monocytogenes strains from different regions
Zhang, Frontiers in microbiology 2024 - “...This study dapX lmo1006 1,146 343 (100%) 0 Putative N-acetyl-LL-diaminopimelate aminotransferase 381 This study iolC lmo0385 978 343 (100%) 0 5-dehydro-2-deoxygluconokinase 325 This study gshAB lmo2770 2,331 343 (100%) 0 Glutathione biosynthesis bifunctional protein GshAB 776 This study cysG lmo1201 1,481 343 (100%) 0 Siroheme synthase...”
- Glycerol metabolism and PrfA activity in Listeria monocytogenes
Joseph, Journal of bacteriology 2008 - “...lmo0345 lmo0346 lmo0347 lmo0348 lmo0358 lmo0384a,b lmo0385 lmo0386b lmo0400 lmo0405 lmo0415 lmo0426a,b lmo0427a,b lmo0428a,b lmo0429a,b lmo0431 inlAb,d inlBb,d...”
GAH_01843 carbohydrate kinase family protein from Geoglobus ahangari
26% identity, 91% coverage
LSA0254 Putative carbohydrate kinase from Lactobacillus sakei subsp. sakei 23K
25% identity, 94% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...lsa0123 Putative sugar kinase, ROK family 1.2 LSA0198 ack1 Acetate kinase (acetokinase) 1.7 1.3 LSA0254* lsa0254 Putative carbohydrate kinase 2.4 0.8 1.8 LSA0292* budC Acetoin reductase (acetoin dehydrogenase) (meso-2,3-butanediol dehydrogenase) 3.4 2.3 3.4 LSA0444 lsa0444 Putative malate dehydrogenase 3.4 D 2.1 LSA0516 hprK Hpr kinase/phosphorylase 2.0...”
- “...galP GA ACAT CG TTATCA -46 LSA0200 rbsU GT AAAC CG TTTTCA -113 rbsUDK LSA0200-0202 LSA0254 lsa0254 TGTAAG CG TTTT AT -56 lsa0254-lsa0255-lsa0256_a LSA0254-0256_a LSA0289 xpk CT ATTA CG ATGACA -8 LSA0292 budC TGTAAC CG TTTT A A -51 LSA0353 lsa0353 A GAAAG CG CTTA T...”
C_RS12810 pseudouridine kinase from Escherichia coli CFT073
25% identity, 89% coverage
yeiC / Q1R9Q6 pseudouridine kinase (EC 2.7.1.83) from Escherichia coli (strain UTI89 / UPEC) (see 2 papers)
c2701 Hypothetical sugar kinase yeiC from Escherichia coli CFT073
25% identity, 79% coverage
Q9YG89 6-phosphofructokinase (EC 2.7.1.11) from Aeropyrum pernix (see 2 papers)
APE_0012 ATP-dependent 6-phosphofructokinase from Aeropyrum pernix K1
27% identity, 95% coverage
- A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate
Aziz, Journal of bacteriology 2018 - “...protein was 37% identical to the phosphofructokinase (Ape_0012) from Aeropyrum pernix, which displayed kinase activity toward a broad spectrum of substrates,...”
- “...37% identical to the PfkB from A. pernix (Ape_0012) (19) and 36% identical to a 6-phosphofructokinase from D. amylolyticus (WP_042667458) (22). A sequence...”
- Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System
Takami, PloS one 2015 - “...sequence similarities. In the KEGG database, the orthologous group containing ATP-PFK from A . pernix (APE_0012) belonging to the PFK-B family is defined as ribokinase (EC: 2.7.1.15) and the different K number of K00852 is assigned to this orthologous group. At present, K00852 has not yet...”
- “...the Ca . C. subterraneum genome, there are two K00852-assigned genes, CSUB_C0883 and CSUB_C1035, and APE_0012 and CSUB_C1035 share 74.4% similarity (ca. 30% identity). Thus, the gene product of CSUB_C1035 presumably acts as ATP-PFK, responsible for reaction step 3. Similar to the enzymes involve in the...”
- A broad specificity nucleoside kinase from Thermoplasma acidophilum
Elkin, Proteins 2013 - “...GI: 83654474, UniProt: Q2SZE4) , and Aeropyrum pernix 2 , 4 (ApPFK; GI: 118430835, UniProt: Q9YG89) have been identified and functionally characterized. Both MjNK and BtNK are classified as NKs because they catalyze the phosphorylation of both purine and pyrimidine nucleosides but do not phosphorylate sugar...”
scrK / GB|AAA08602.1 fructokinase; EC 2.7.1.4 from Salmonella enterica subsp. enterica serovar Typhimurium (see paper)
scrK / CAA43323.1 fructokinase from Salmonella enterica subsp. enterica serovar Typhimurium (see paper)
P26984 Fructokinase from Salmonella typhimurium
25% identity, 93% coverage
ECs3058 putative kinase from Escherichia coli O157:H7 str. Sakai
27% identity, 89% coverage
- Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
Bergholz, Applied and environmental microbiology 2009 - “...ECs2445 ECs2706 ECs2783 ECs2784 ECs2988 ECs2993 ECs3014 ECs3058 ECs3136 ECs3260 ECs3427 ECs3668 ECs3911 ECs4310 ECs4697 ECs4867 ECs4890 ECs5004 ECs5044 ECs5313...”
- “...Viral functions ECs0278 ECs0507 ECs0902 ECs0967 ECs1110 ECs1758 ECs3058 ECs3503 ECs3911 ECs4588 ECs4968 ECs4969 ECs4970 ECs4977 ECs4982 O157 ybaY ybiY yljA O157...”
F8D4I6 α-D-ribose-1-phosphate 5-kinase (ATP) (EC 2.7.1.239) from Halopiger xanaduensis (strain DSM 18323 / JCM 14033 / SH-6) (see 2 papers)
R1PKT_HALXS / F8D4I6 ATP-dependent ribose-1-phosphate kinase; ATP-R1P kinase; Alpha-D-ribose-1-phosphate 5-kinase (ATP); Hx-RbsK; EC 2.7.1.239 from Halopiger xanaduensis (strain DSM 18323 / JCM 14033 / SH-6) (see paper)
Halxa_1682 carbohydrate kinase family protein from Halopiger xanaduensis SH-6
29% identity, 97% coverage
- function: Kinase involved in the non-carboxylating pentose bisphosphate pathway, a nucleoside degradation pathway present in some halophilic archaea (PubMed:36434094). Catalyzes the ATP-dependent phosphorylation of ribose 1-phosphate (R1P) to ribose 1,5-bisphosphate (R15P) (PubMed:36434094). Shows weak activity towards various other phosphate acceptors, such as xylulose, 2'-deoxyguanosine and D-ribulose (PubMed:36434094). ATP is the most preferred phosphate donor, followed by CTP and GTP (PubMed:36434094).
catalytic activity: alpha-D-ribose 1-phosphate + ATP = alpha-D-ribose 1,5- bisphosphate + ADP + H(+) (RHEA:29775)
cofactor: Mg(2+) - A non-carboxylating pentose bisphosphate pathway in halophilic archaea
Sato, Communications biology 2022 - “...xanaduensi s ( Hs -RbsK, Ht -RbsK, and Hx -RbsK encoded by VNG_1851G, Htur_0569, and Halxa_1682, respectively) were produced in E. coli . Hs -RbsK formed inclusion bodies and expression levels of the Ht -RbsK gene were low. Sufficient amounts of soluble Hx -RbsK protein were...”
- “...we observed a specific activity of 30.1molmin 1 mg 1 . The analyses on the Halxa_1682 protein indicated that the protein Hx -RbsK is an ATP-dependent ribose-1-phosphate kinase (ATP-R1PK) generating the substrate for R15P isomerase. Identification of a guanosine phosphorylase Almost all genomes of halophilic archaea...”
NCgl0155 5-dehydro-2-deoxygluconokinase from Corynebacterium glutamicum ATCC 13032
26% identity, 86% coverage
cg0197 ribokinase family sugar kinase from Corynebacterium glutamicum ATCC 13032
26% identity, 79% coverage
- Physiological, Biochemical, and Structural Bioinformatic Analysis of the Multiple Inositol Dehydrogenases from Corynebacterium glutamicum
Ramp, Microbiology spectrum 2022 - “...iol1 ( Fig.1 ) contains 16 genes, which include a putative operon comprising 10 genes (cg0197 to cg0207), including those for the seven enzymes assumed to be responsible for MI conversion to dihydroxyacetone, acetyl-CoA, and CO 2 . Whereas many genes of cluster iol1 , such...”
- Single-Domain Peptidyl-Prolyl cis/trans Isomerase FkpA from Corynebacterium glutamicum Improves the Biomass Yield at Increased Growth Temperatures
Kallscheuer, Applied and environmental microbiology 2015 - “...cg1853 cg2181 cg1606 cg3186 cg1053 cg0848 cg1108 cg0172 cg0197 cg1169 cg0835 cg2870 cg3323 cg1345 cg1076 cg1697 cg3431 cg0149 cg3096 cg0444 cg0760 cg0759 cg0950...”
- 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 - “...or predicted function of the gene product Gene cg0197 cg0198 cg0199 cg0201 cg0202 cg0203 cg0204 cg0205 cg0206 cg0207 cg0210 cg0223 cg1069 cg1595 cg1935 NCgl0155...”
- “...iol cluster of B. subtilis (62). The iolC gene (cg0197) was annotated as 2-deoxy-5-keto-gluconokinase and is the first of 10 genes that are most likely...”
- Phosphotransferase system-independent glucose utilization in corynebacterium glutamicum by inositol permeases and glucokinases
Lindner, Applied and environmental microbiology 2011 - “...0.45 0.48 0.39 0.37 0.45 0.41 0.49 0.35 cg0197 cg0199 cg0202 cg0203 cg0204 cg0205 cg0223 cg3385 cg3386 cg3387 iolC, inositol catabolism, carbohydrate kinase...”
AZL_b01060 5-dehydro-2-deoxygluconokinase from Azospirillum sp. B510
24% identity, 47% coverage
A0A140N873 PfkB domain protein from Escherichia coli (strain B / BL21-DE3)
26% identity, 89% coverage
- Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK
Li, Frontiers in microbiology 2022 - “...question. Materials and Methods Protein Expression and Purification Plasmids encoding E. coli PsuK (Uniprot ID: A0A140N873) were PCR amplified from E. coli BL21 (DE3) genome. The PCR product was double-digested with restriction endonuclease BamH I and Xho I and then ligated into a modified pET-28a plasmid...”
Echvi_2804 Fructokinase (EC 2.7.1.4) from Echinicola vietnamensis KMM 6221, DSM 17526
26% identity, 86% coverage
- mutant phenotype: Specifically important for utilizing D-Fructose. Automated validation from mutant phenotype: the predicted function (2.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 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