substrate_name: arbekacin

substrate: arbekacin


enzyme_display_name: aminoglycoside 2''-phosphotransferase

organism: Campylobacter jejuni

substrate_name: ATP

source_db: oed

verification_status: verified

ki_display: Not reported

mutation_signature: Unknown

protein_accession_database: UniProt

source_license: CC BY 4.0

km_unit: mM

sequence_variant_note: Sequence is treated as wild-type because the source explicitly marked the record as wild-type.

assay_conditions_summary: pH 7; 295.15 K; cofactor ATP

column_label: Table label: Table 2. Substrate profiles for phosphotransferase activity of APH(2″)-Ia and APH(2″)-If. Row: ATP. Enzyme column group: APH(2″)-If. Columns read: k cat (s^-1) cell 0.38, K m (uM) cell 2000, k cat / K m (M^-1 s^-1) cell 1.9 x 10^2. metric: kcat; raw value: 0.38; raw unit: s^-1; normalized value: 0.38 s^(-1); metric: Km; raw value: 2000; raw unit: uM; normalized value: 2.0 mM; metric: kcat/Km; raw value: 1.9 x 10^2; raw unit: M^-1 s^-1; normalized value: 0.19 s^-1 mM^-1; assay condition: APH(2″)-If, the Campylobacter jejuni aminoglycoside 2″-phosphotransferase; nucleotide steady-state kinetic parameters were measured at 20 uM tobramycin in 100 mM HEPES pH 7.0, 10 mM MgCl2, 20 mM KCl with phosphoenolpyruvate/NADH/PK/LDH coupling at room temperature. Export row conditions: pH 7; 295.15 K; cofactor ATP.

normalized_value_unit_evidence: APH(2″)-If columns of Table 2 row ATP: kcat 0.38 s^-1 = 0.38 s^(-1); K m 2000 uM = 2.0 mM (1 uM = 0.001 mM); k cat / K m 1.9 x 10^2 M^-1 s^-1 = 190 M^-1 s^-1 = 0.19 s^-1 mM^-1 (1 M^-1 s^-1 = 0.001 s^-1 mM^-1). In the saved PMC HTML the multiplication sign renders as ×, the superscript minus one as −1, the micro sign as μ, the double-prime of APH(2″) as ″, and superscript exponents are flattened onto the baseline, so the printed cell `(1.9 ± 0.5) × 10 2` is the paper's (1.9 +/- 0.5) x 10^2 M^-1 s^-1 and the ± tokens are the reported fit standard errors, not part of the central values.

raw_value_unit_evidence: Table 2. Substrate profiles for phosphotransferase activity of APH(2″)-Ia and APH(2″)-If | column group header row of Table 2: Substrate a APH(2″)-Ia APH(2″)-If; metric header row: k cat (s −1 ) K m (μM) k cat / K m (M −1 s −1 ) k cat (s −1 ) K m (μM) k cat / K m (M −1 s −1 ) | row: ATP 0.25 ± 0.01 1100 ± 100 (2.3 ± 0.2) × 10 2 0.38 ± 0.05 2000 ± 400 (1.9 ± 0.5) × 10 2 | APH(2″)-If cells read: k cat = 0.38 s^-1 (printed 0.38 ± 0.05); K m = 2000 uM (printed 2000 ± 400); k cat / K m = 1.9 x 10^2 M^-1 s^-1 (printed (1.9 ± 0.5) × 10 2). The first three numeric cells of the row belong to the APH(2″)-Ia column group and are not used.

row_label: APH(2″)-If | ATP

data_origin: experimental

enzyme: aminoglycoside 2''-phosphotransferase

substrate: ATP

status: verified

source: oed


substrate_name: dibekacin

verification_status: corrected

assay_conditions_summary: pH 7; 295.15 K; cofactor NADH

column_label: Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row dibekacin / APH(2"-If), column APH(2"-If); kcat s^-1, raw cell 0.79 +/- 0.01, normalized 0.79 s^-1; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row dibekacin / APH(2"-If), column APH(2"-If); Km uM, raw cell 1.2 +/- 0.1, normalized 0.0012 mM; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row dibekacin / APH(2"-If), column APH(2"-If); kcat/Km M^-1 s^-1, raw cell (6.6 +/- 0.5) x 10^5, normalized 660 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=0.79 normalized_unit=s^-1; Km normalized_value=0.0012 normalized_unit=mM; kcat/Km normalized_value=660 normalized_unit=s^-1*mM^-1

row_label: dibekacin / APH(2"-If)

substrate: dibekacin

status: corrected


substrate_name: gentamicin C

column_label: Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row gentamicin C / APH(2"-If), column APH(2"-If); kcat s^-1, raw cell 8.3 +/- 0.3, normalized 8.3 s^-1; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row gentamicin C / APH(2"-If), column APH(2"-If); Km uM, raw cell 0.7 +/- 0.2, normalized 0.0007 mM; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row gentamicin C / APH(2"-If), column APH(2"-If); kcat/Km M^-1 s^-1, raw cell (1.2 +/- 0.3) x 10^7, normalized 12000 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=8.3 normalized_unit=s^-1; Km normalized_value=0.0007 normalized_unit=mM; kcat/Km normalized_value=12000 normalized_unit=s^-1*mM^-1

row_label: gentamicin C / APH(2"-If)

substrate: gentamicin C


substrate_name: GTP

column_label: Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row GTP / APH(2"-If), column APH(2"-If); kcat s^-1, raw cell 0.40 +/- 0.01, normalized 0.4 s^-1; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row GTP / APH(2"-If), column APH(2"-If); Km uM, raw cell 0.80 +/- 0.06, normalized 0.0008 mM; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row GTP / APH(2"-If), column APH(2"-If); kcat/Km M^-1 s^-1, raw cell (5.1 +/- 0.4) x 10^5, normalized 510 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=0.4 normalized_unit=s^-1; Km normalized_value=0.0008 normalized_unit=mM; kcat/Km normalized_value=510 normalized_unit=s^-1*mM^-1

row_label: GTP / APH(2"-If)

substrate: GTP


substrate_name: isepamicin

column_label: Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row isepamicin / APH(2"-If), column APH(2"-If); kcat s^-1, raw cell 0.25 +/- 0.01, normalized 0.25 s^-1; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row isepamicin / APH(2"-If), column APH(2"-If); Km uM, raw cell 560 +/- 60, normalized 0.56 mM; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row isepamicin / APH(2"-If), column APH(2"-If); kcat/Km M^-1 s^-1, raw cell (4.5 +/- 0.5) x 10^2, normalized 0.45 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=0.25 normalized_unit=s^-1; Km normalized_value=0.56 normalized_unit=mM; kcat/Km normalized_value=0.45 normalized_unit=s^-1*mM^-1

row_label: isepamicin / APH(2"-If)

substrate: isepamicin


substrate_name: kanamycin A

column_label: Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row kanamycin A / APH(2"-If), column APH(2"-If); kcat s^-1, raw cell 1.7 +/- 0.1, normalized 1.7 s^-1; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row kanamycin A / APH(2"-If), column APH(2"-If); Km uM, raw cell 1.1 +/- 0.2, normalized 0.0011 mM; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row kanamycin A / APH(2"-If), column APH(2"-If); kcat/Km M^-1 s^-1, raw cell (1.5 +/- 0.3) x 10^6, normalized 1500 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=1.7 normalized_unit=s^-1; Km normalized_value=0.0011 normalized_unit=mM; kcat/Km normalized_value=1500 normalized_unit=s^-1*mM^-1

row_label: kanamycin A / APH(2"-If)

substrate: kanamycin A


substrate_name: kanamycin B

column_label: Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row kanamycin B / APH(2"-If), column APH(2"-If); kcat s^-1, raw cell 0.38 +/- 0.01, normalized 0.38 s^-1; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row kanamycin B / APH(2"-If), column APH(2"-If); Km uM, raw cell 0.55 +/- 0.05, normalized 0.00055 mM; Table 2. Steady-state kinetic parameters for aminoglycosides and nucleotides row kanamycin B / APH(2"-If), column APH(2"-If); kcat/Km M^-1 s^-1, raw cell (6.9 +/- 0.7) x 10^5, normalized 690 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=0.38 normalized_unit=s^-1; Km normalized_value=0.00055 normalized_unit=mM; kcat/Km normalized_value=690 normalized_unit=s^-1*mM^-1

row_label: kanamycin B / APH(2"-If)

substrate: kanamycin B


enzyme_display_name: Nucleoside kinase

organism: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

source_db: uniprot

kcat_display: Not reported

kcat_over_km_display: Not reported

enzyme: Nucleoside kinase

source: uniprot


enzyme_display_name: C7-cyclitol 7-kinase

organism: Streptomyces hygroscopicus subsp. jinggangensis

substrate_name: validone

verification_status: unverified

kcat_over_km_origin: calculated

enzyme: C7-cyclitol 7-kinase

substrate: validone

status: unverified


substrate_name: valienone

substrate: valienone


organism: Enterococcus casseliflavus

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:O68183 and applied mutation signature F95M to reconstruct the assayed variant sequence.

mutation_type: substitution

assay_conditions_summary: pH 7.5; 310.15 K; cofactor ATP

column_label: Table 2 (Steady state kinetic parameters for APH(2'')-IVa), Protein row 'F95M', NTP row 'ATP'; column 'kcat (s^-1)' = 3.06; column 'Km (uM)' = 55; column 'kcat/Km (M^-1 s^-1)' = 5.5 x 10^4.

normalized_value_unit_evidence: kcat: printed Table 2 cell 3.06 s^-1; already in s^-1, no unit conversion applies; the paper value is 3.06 s^(-1). Km: printed Table 2 cell 55 uM; 55 / 1000 = 0.055 mM. kcat/Km: printed Table 2 cell 5.5 x 10^4 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 55000 / 1000 = 55.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, Protein row 'F95M', NTP row 'ATP': kcat = 3.06 s^-1; Km = 55 uM; printed kcat/Km = 5.5 x 10^4 M^-1 s^-1.

table_label: Table 2: Steady state kinetic parameters for APH(2'')-IVa (J. Biol. Chem. 2012, 287(16):13094-13102)


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:O68183 and applied mutation signature F95Y to reconstruct the assayed variant sequence.

column_label: Table 2 (Steady state kinetic parameters for APH(2'')-IVa), Protein row 'F95Y', NTP row 'ATP'; column 'kcat (s^-1)' = 1.06; column 'Km (uM)' = 72; column 'kcat/Km (M^-1 s^-1)' = 1.5 x 10^4.

normalized_value_unit_evidence: kcat: printed Table 2 cell 1.06 s^-1; already in s^-1, no unit conversion applies; the paper value is 1.06 s^(-1). Km: printed Table 2 cell 72 uM; 72 / 1000 = 0.072 mM. kcat/Km: printed Table 2 cell 1.5 x 10^4 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 15000 / 1000 = 15.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, Protein row 'F95Y', NTP row 'ATP': kcat = 1.06 s^-1; Km = 72 uM; printed kcat/Km = 1.5 x 10^4 M^-1 s^-1.


column_label: Table 2 (Steady state kinetic parameters for APH(2'')-IVa), Protein row 'Wild type', NTP row 'ATP'; column 'kcat (s^-1)' = 4.37; column 'Km (uM)' = 69; column 'kcat/Km (M^-1 s^-1)' = 6.3 x 10^4.

normalized_value_unit_evidence: kcat: printed Table 2 cell 4.37 s^-1; already in s^-1, no unit conversion applies; the paper value is 4.37 s^(-1). Km: printed Table 2 cell 69 uM; 69 / 1000 = 0.069 mM. kcat/Km: printed Table 2 cell 6.3 x 10^4 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 63000 / 1000 = 63.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, Protein row 'Wild type', NTP row 'ATP': kcat = 4.37 s^-1; Km = 69 uM; printed kcat/Km = 6.3 x 10^4 M^-1 s^-1.


column_label: Table 2 (Steady state kinetic parameters for APH(2'')-IVa), Protein row 'F95M', NTP row 'GTP'; column 'kcat (s^-1)' = 4.35; column 'Km (uM)' = 156; column 'kcat/Km (M^-1 s^-1)' = 2.8 x 10^4.

normalized_value_unit_evidence: kcat: printed Table 2 cell 4.35 s^-1; already in s^-1, no unit conversion applies; the paper value is 4.35 s^(-1). Km: printed Table 2 cell 156 uM; 156 / 1000 = 0.156 mM. kcat/Km: printed Table 2 cell 2.8 x 10^4 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 28000 / 1000 = 28.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, Protein row 'F95M', NTP row 'GTP': kcat = 4.35 s^-1; Km = 156 uM; printed kcat/Km = 2.8 x 10^4 M^-1 s^-1.


column_label: Table 2 (Steady state kinetic parameters for APH(2'')-IVa), Protein row 'F95Y', NTP row 'GTP'; column 'kcat (s^-1)' = 1.15; column 'Km (uM)' = 49; column 'kcat/Km (M^-1 s^-1)' = 2.3 x 10^4.

normalized_value_unit_evidence: kcat: printed Table 2 cell 1.15 s^-1; already in s^-1, no unit conversion applies; the paper value is 1.15 s^(-1). Km: printed Table 2 cell 49 uM; 49 / 1000 = 0.049 mM. kcat/Km: printed Table 2 cell 2.3 x 10^4 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 23000 / 1000 = 23.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, Protein row 'F95Y', NTP row 'GTP': kcat = 1.15 s^-1; Km = 49 uM; printed kcat/Km = 2.3 x 10^4 M^-1 s^-1.


column_label: Table 2 (Steady state kinetic parameters for APH(2'')-IVa), Protein row 'Wild type', NTP row 'GTP'; column 'kcat (s^-1)' = 5.03; column 'Km (uM)' = 168; column 'kcat/Km (M^-1 s^-1)' = 3.0 x 10^4.

normalized_value_unit_evidence: kcat: printed Table 2 cell 5.03 s^-1; already in s^-1, no unit conversion applies; the paper value is 5.03 s^(-1). Km: printed Table 2 cell 168 uM; 168 / 1000 = 0.168 mM. kcat/Km: printed Table 2 cell 3.0 x 10^4 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 30000 / 1000 = 30.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, Protein row 'Wild type', NTP row 'GTP': kcat = 5.03 s^-1; Km = 168 uM; printed kcat/Km = 3.0 x 10^4 M^-1 s^-1.


enzyme_display_name: cytidine diphosphoramidate kinase

organism: Campylobacter jejuni subsp. jejuni serotype O:2

substrate_name: 2'-deoxycytidine 5'-diphosphoramidate

assay_conditions_summary: pH 8; 298.15 K; cofactor ATP

column_label: Table 1. Kinetic Constants of Cj1415 at 25 C, pH 8.0; row dCDP-NH2 (2); kcat column (s^-1) = 2.2 +/- 0.2 s^-1; kcat/Km column (M^-1 s^-1), normalized to s^-1 mM^-1 by dividing by 1000 = 5600 +/- 1100 M^-1 s^-1; Km column (mM) = 0.39 +/- 0.07 mM

row_label: dCDP-NH2 (2)

enzyme: cytidine diphosphoramidate kinase

substrate: 2'-deoxycytidine 5'-diphosphoramidate


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature S85A to reconstruct the assayed variant sequence.


column_label: Table 1. Kinetic Constants of Cj1415 at 25 C, pH 8.0; row ATP; kcat column (s^-1) = 2.2 +/- 0.3 s^-1; kcat/Km column (M^-1 s^-1), normalized to s^-1 mM^-1 by dividing by 1000 = 1500 +/- 200 M^-1 s^-1; Km column (mM) = 1.5 +/- 0.1 mM

normalized_value_unit_evidence: kcat 2.2 s^-1; kcat_over_km 1.5 s^-1 mM^-1; km 1.5 mM

row_label: ATP


substrate_name: CDP-methyl phosphonate

column_label: Table 1. Kinetic Constants of Cj1415 at 25 C, pH 8.0; row CDP-Me (5); kcat column (s^-1) = 1.4 +/- 0.1 s^-1; kcat/Km column (M^-1 s^-1), normalized to s^-1 mM^-1 by dividing by 1000 = 1700 +/- 400 M^-1 s^-1; Km column (mM) = 0.8 +/- 0.2 mM

normalized_value_unit_evidence: kcat 1.4 s^-1; kcat_over_km 1.7 s^-1 mM^-1; km 0.8 mM

row_label: CDP-Me (5)

substrate: CDP-methyl phosphonate


substrate_name: cytidine 5'-diphosphoramidate

substrate: cytidine 5'-diphosphoramidate


column_label: Table 1. Kinetic Constants of Cj1415 at 25 C, pH 8.0; row CDP-NH2 (1); kcat column (s^-1) = 2.2 +/- 0.3 s^-1; kcat/Km column (M^-1 s^-1), normalized to s^-1 mM^-1 by dividing by 1000 = 20000 +/- 3300 M^-1 s^-1; Km column (mM) = 0.11 +/- 0.01 mM

normalized_value_unit_evidence: kcat 2.2 s^-1; kcat_over_km 20 s^-1 mM^-1; km 0.11 mM

row_label: CDP-NH2 (1)


enzyme_display_name: 4-hydroxytryptamine kinase

organism: Psilocybe cubensis

source_db: brenda

km_display: Not reported

sequence_source: multiple

sequence_variant_note: Sequence identity was resolved, but no explicit wild-type or mutant call was captured.

assay_conditions_summary: pH 7; 313.15 K; buffer pH 7; cofactor ATP

column_label: Optimum turnover was found at 40 °C and at pH 7.0. Furthermore, PsiK activity depended on Mg2+. PsiK followed a sigmoid kinetic response to increasing 2 and 4-hydroxytryptamine concentrations, with K0.5 values of 72 μM and 67 μM, and a kcat of 16.1 s^-1 and 4.5 s^-1 for these substrates (Figure S2). This translates into catalytic efficiencies (kcat/K0.5) of 2.24×10^5 and 6.67×10^4 M^-1 s^-1, respectively, with 2 and 4-hydroxytryptamine as acceptor substrates. The K0.5 value for ATP was 89 μM.

normalized_value_unit_evidence: kcat paper=4.5 s^-1; export kcat=4.5 s^-1.

raw_value_unit_evidence: kcat 4.5 s^-1 for 4-hydroxytryptamine.

table_label: PMC article kinetic paragraph; Figure S2 referenced

source_databases_merged: brenda uniprot

enzyme: 4-hydroxytryptamine kinase

source: brenda


assay_conditions_summary: pH 7; 313.15 K; cofactor ATP


substrate_name: psilocin

normalized_value_unit_evidence: kcat paper=16.1 s^-1; export kcat=16.1 s^-1.

raw_value_unit_evidence: kcat 16.1 s^-1 for substrate 2 (psilocin).

row_label: substrate 2 (psilocin)

substrate: psilocin


assay_conditions_summary: cofactor ATP


enzyme_display_name: Fructoselysine 6-kinase

organism: Escherichia coli (strain K12)

substrate_name: fructoselysine

smiles: C(CCNCC(=O)C(C(C(CO)O)O)O)CC(C(=O)O)N

enzyme: Fructoselysine 6-kinase

substrate: fructoselysine


enzyme_display_name: UniProt P9WJH7

organism: Mycobacterium tuberculosis

source_db: skid

source_license: CC BY-NC-ND 4.0

enzyme: UniProt P9WJH7

source: skid


enzyme_display_name: UniProt P61136

organism: Halobacterium salinarum

substrate_name: ADP

enzyme: UniProt P61136

substrate: ADP


substrate_name: UTP

substrate: UTP


enzyme_display_name: UniProt Q4E256

organism: Trypanosoma cruzi strain CL Brener

substrate_name: dTDP

enzyme: UniProt Q4E256

substrate: dTDP


enzyme_display_name: UniProt Q9SP13

organism: Pisum sativum

enzyme: UniProt Q9SP13


substrate_name: dCDP

substrate: dCDP


enzyme_display_name: UMP-CMP kinase 2, mitochondrial

organism: Homo sapiens

substrate_name: CMP

enzyme: UMP-CMP kinase 2, mitochondrial

substrate: CMP


substrate_name: UMP

substrate: UMP


substrate_name: dCMP

substrate: dCMP


substrate_name: dUMP

substrate: dUMP


enzyme_display_name: Nucleoside diphosphate kinase 4, chloroplastic

organism: Spinacia oleracea

substrate_name: GDP

substrate: GDP


enzyme: Nucleoside diphosphate kinase 4, chloroplastic


enzyme_display_name: Nucleoside diphosphate kinase 3

enzyme: Nucleoside diphosphate kinase 3


enzyme_display_name: UniProt P23919

proof_lines:
Raw SKiD Env: Temp=25°C, pH=7.5
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=-----, pH=7.4

enzyme: UniProt P23919


substrate_name: ddTMP

substrate: ddTMP


substrate_name: ATP

substrate: ATP


enzyme_display_name: GTP-dependent dephospho-CoA kinase

organism: Thermococcus kodakarensis

assay_conditions_summary: pH 8; 353.15 K; cofactor CoA

column_label: Table 1 columns Substrate, Km (mM), kcat (s^-1), kcat/Km (s^-1 mM^-1); row Dephospho-CoA under T. kodakarensis

normalized_value_unit_evidence: Km 0.14 mM; kcat 5.57 s^-1; kcat/Km paper cell 40.4 s^-1 mM^-1 (sheet ratio 39.785714285714285 comes from rounded kcat/Km)

raw_value_unit_evidence: Dephospho-CoA row: Km 0.14 +/- 0.02 mM; kcat 5.57 s^-1; kcat/Km 40.4 s^-1 mM^-1

row_label: T. kodakarensis / Dephospho-CoA

table_label: PMC6650551 Table 1 - Kinetic parameters of DPCK toward dephospho-CoA and GTP

enzyme: GTP-dependent dephospho-CoA kinase


substrate_name: GTP

column_label: Table 1 columns Substrate, Km (mM), kcat (s^-1), kcat/Km (s^-1 mM^-1); row GTP under T. kodakarensis

normalized_value_unit_evidence: Km 0.26 mM; kcat 6.68 s^-1; kcat/Km 25.7 s^-1 mM^-1 (sheet ratio 25.69230769230769 is the same to paper precision)

row_label: T. kodakarensis / GTP

substrate: GTP


enzyme_display_name: L-serine kinase (ADP)

assay_conditions_summary: pH 7.5; 358.15 K; cofactor ADP

normalized_value_unit_evidence: kcat 204 s^-1; Km 2.4 mM; paper kcat/Km 86.4 s^-1*mM^-1, while expected row has 85.0 s^-1*mM^-1.

raw_value_unit_evidence: Main text reports kcat: 204+/-12 s^-1, Km: 2.4+/-0.5 mM, and kcat/Km: 86.4 mM^-1 s^-1 towards ADP.

row_label: TK0378 SerK; ADP varied with 50 mM L-serine

table_label: Main text Results / Supplementary Fig. 11 kinetic analysis of TK0378 protein

enzyme: L-serine kinase (ADP)


substrate_name: L-serine

raw_value_unit_evidence: Main text reports kcat: 218+/-5 s^-1, Km: 5.1+/-0.5 mM, and kcat/Km: 42.4 mM^-1 s^-1 towards Ser.

row_label: TK0378 SerK; L-serine varied with 20 mM ADP

substrate: L-serine


enzyme_display_name: erythritol kinase (D-erythritol 1-phosphate-forming)

organism: Brucella abortus

substrate_name: meso-erythritol

smiles: C(C(C(CO)O)O)O

assay_conditions_summary: pH 8; cofactor ATP

substrate: meso-erythritol


enzyme: erythritol kinase (D-erythritol 1-phosphate-forming)


enzyme_display_name: PTS system maltose-specific EIICB component

organism: Bacillus subtilis (strain 168)

substrate_name: maltose

column_label: Official PMC article abstract/prose; substrate maltose; enzyme/transporter MalP/GlvC; apparent Km = 5 uM.

normalized_value_unit_evidence: Km 0.005 mM from 5 uM.

raw_value_unit_evidence: Official PMC article abstract/prose reports maltose uptake by MalP/GlvC with apparent Km 5 uM and Vmax 91 nmol min-1 per 10^10 CFU.

row_label: Maltose-specific enzyme IICB MalP (GlvC)

table_label: Abstract/prose: maltose uptake by MalP/GlvC enzyme IICB

substrate: maltose


enzyme_display_name: Bifunctional AAC/APH

organism: Enterococcus faecalis (strain ATCC 700802 / V583)

column_label: Results and Discussion / GTP as the Phosphate Donor; row/segment bifunctional AAC(6')-Ie/APH(2'')-Ia / GTP; Km column (uM), normalized to mM by dividing by 1000 = Km = 3 uM for GTP

raw_value_unit_evidence: km Km = 3 uM for GTP

enzyme: Bifunctional AAC/APH


enzyme_display_name: PTS system lactose-specific EIICB component

organism: Staphylococcus aureus


enzyme_display_name: PTS system sorbose-specific EIIB component

organism: Klebsiella pneumoniae

substrate_name: L-sorbose

proof_lines:
L-sorbose
Klebsiella pneumoniae
enzyme IIsor

substrate: L-sorbose


enzyme_display_name: Ascorbate-specific PTS system EIIB component

substrate_name: L-ascorbate

substrate: L-ascorbate


enzyme_display_name: D-threonate 4-kinase

organism: Cupriavidus necator

column_label: Table 1; row Q0K4F6 (ReDtnK) / 4-Hydroxy-l-threonine; columns kcat (s^-1), KM (mM), kcat/KM (M^-1 s^-1); cells 27, 86, 3.1 x 10^2; normalized kcat/Km 0.31 s^-1 mM^-1

normalized_value_unit_evidence: kcat=27 s^-1; Km=86 mM; kcat/Km=0.31 s^-1 mM^-1 (explicit table value converted from M^-1 s^-1)

raw_value_unit_evidence: Q0K4F6 (ReDtnK) / 4-Hydroxy-l-threonine: kcat=27 s^-1; KM=86 mM; kcat/KM=3.1 x 10^2 M^-1 s^-1

row_label: Q0K4F6 (ReDtnK) / 4-Hydroxy-l-threonine

table_label: Table 1. Selected kinetic parameters for DtnK, PdxA2, LtnD, and DenD

enzyme: D-threonate 4-kinase


substrate_name: D-threonate

column_label: Table 1; row Q0K4F6 (ReDtnK) / d-Threonate; columns kcat (s^-1), KM (mM), kcat/KM (M^-1 s^-1); cells 45, 0.12, 3.8 x 10^5; normalized kcat/Km 380 s^-1 mM^-1

normalized_value_unit_evidence: kcat=45 s^-1; Km=0.12 mM; kcat/Km=380 s^-1 mM^-1 (explicit table value converted from M^-1 s^-1)

raw_value_unit_evidence: Q0K4F6 (ReDtnK) / d-Threonate: kcat=45 s^-1; KM=0.12 mM; kcat/KM=3.8 x 10^5 M^-1 s^-1

row_label: Q0K4F6 (ReDtnK) / d-Threonate

substrate: D-threonate


enzyme_display_name: UniProt P0A7E9

organism: Escherichia coli

enzyme: UniProt P0A7E9


enzyme_display_name: UniProt P56106

organism: Helicobacter pylori

enzyme: UniProt P56106


enzyme_display_name: UniProt P9WHK5

enzyme: UniProt P9WHK5


enzyme_display_name: UniProt O26153

organism: Methanothermobacter thermautotrophicus

substrate_name: dimethylallyl phosphate

smiles: CC(=CCOP(=O)(O)O)C

enzyme: UniProt O26153

substrate: dimethylallyl phosphate


substrate_name: isopentenyl diphosphate

smiles: CC(=C)CCOP(=O)(O)OP(=O)(O)O

substrate: isopentenyl diphosphate


substrate_name: butyl phosphate

substrate: butyl phosphate


substrate_name: geranyl phosphate

smiles: CC(=CCCC(=CCOP(=O)(O)O)C)C

substrate: geranyl phosphate


enzyme_display_name: UniProt Q9HLX1

organism: Thermoplasma acidophilum

substrate_name: fosfomycin

enzyme: UniProt Q9HLX1

substrate: fosfomycin


substrate_name: ADP

substrate: ADP


enzyme_display_name: PTS system sucrose-specific EIIBCA component

organism: Streptococcus mutans serotype c (strain ATCC 700610 / UA159)

substrate_name: sucrose

column_label: Abstract states sucrose phosphotransferase activity was inducible by sucrose and had an apparent Km for sucrose of 70 microM.

raw_value_unit_evidence: Km raw_value=70 raw_unit=microM

row_label: Streptococcus mutans sucrose phosphotransferase system with sucrose

table_label: PubMed/PMC abstract PMID 468378

substrate: sucrose


enzyme_display_name: autoinducer-2 kinase

organism: Salmonella enterica

sequence_variant_note: No sequence was resolved for this record, so variant-aware sequence handling could not be applied.

smiles: CCCCC(=O)C(=O)C(CO)O

proof_lines: pH and temperature not specified in the publication

enzyme: autoinducer-2 kinase


smiles: CCC(=O)C(=O)C(CO)O


smiles: CCCC(=O)C(=O)C(CO)O


smiles: CC(=O)C(=O)C(CO)O


enzyme_display_name: UniProt Q9HYF1

organism: Pseudomonas aeruginosa

substrate_name: AMP

assay_conditions_summary: pH 8

enzyme: UniProt Q9HYF1

substrate: AMP


substrate_name: GMP

substrate: GMP


enzyme_display_name: fructoselysine 6-kinase

enzyme: fructoselysine 6-kinase


substrate_name: ATP

assay_conditions_summary: pH 7.1; 303.15 K; cofactor ATP

substrate: ATP


substrate_name: fructosylglycine

smiles: C(C(C(C(C(=O)CNCC(=O)O)O)O)O)O

substrate: fructosylglycine


organism: Salmonella enterica subsp. enterica serovar Typhimurium

column_label: Table S2: Kinetic parameters for PdxA2-DUF1537 proteins (PNAS 2016, 113(29):E4161-9); Table S2, UniProt Q8ZRS5 (StDtnK) row, substrate 4-Hydroxy-L-threonine; column 'kcat [s-1]' = 4.0 ± 0.1; column 'KM [mM]' = 3.8 ± 0.5; column 'kcat/KM [M-1s-1]' = 1.1 x 10^3. captured primary segment: Table S2 row: Q8ZRS5 (StDtnK) | 4-Hydroxy-L-threonine | kcat 4.0 ± 0.1 s^-1 | KM 3.8 ± 0.5 mM | kcat/KM 1.1 x 10^3 M^-1 s^-1

normalized_value_unit_evidence: kcat: printed Table S2 cell 4.0 s^-1; already in s^-1, so no unit conversion applies and the normalized value is 4.0 s^(-1). Km: printed Table S2 cell 3.8 mM; already in mM, so no unit conversion applies and the normalized value is 3.8 mM. kcat/Km: the exact quotient of this row's own two printed cells is 4.0 / 3.8 = 1.0526315789473684 s^-1 mM^-1; the printed kcat/KM cell 1.1 x 10^3 M^-1 s^-1 converts (1 M^-1 s^-1 is 0.001 s^-1 mM^-1) to 1.1 s^-1 mM^-1, which is that same quotient written to the table's two-significant-figure precision, so the printed cell is a rounded corroboration of the exact quotient, not an independent value.

raw_value_unit_evidence: Table S2, UniProt Q8ZRS5 (StDtnK) row, substrate '4-Hydroxy-L-threonine': kcat = 4.0 ± 0.1 s^-1; KM = 3.8 ± 0.5 mM; printed kcat/KM = 1.1 x 10^3 M^-1 s^-1.


column_label: Table 1; row Q8ZRS5 (SeDtnK) / d-Threonate; columns kcat (s^-1), KM (mM), kcat/KM (M^-1 s^-1); cells 22, 0.29, 7.5 x 10^4; normalized kcat/Km 75 s^-1 mM^-1

normalized_value_unit_evidence: kcat=22 s^-1; Km=0.29 mM; kcat/Km=75 s^-1 mM^-1 (explicit table value converted from M^-1 s^-1)

raw_value_unit_evidence: Q8ZRS5 (SeDtnK) / d-Threonate: kcat=22 s^-1; KM=0.29 mM; kcat/KM=7.5 x 10^4 M^-1 s^-1

row_label: Q8ZRS5 (SeDtnK) / d-Threonate


enzyme_display_name: aminoglycoside 2''-phosphotransferase

organism: Enterococcus sp.

assay_conditions_summary: pH 7.5; 298.15 K; cofactor ATP

enzyme: aminoglycoside 2''-phosphotransferase


substrate_name: UTP

substrate: UTP


substrate_name: gentamicin C

substrate: gentamicin C


substrate_name: dibekacin

substrate: dibekacin


substrate_name: tobramycin

substrate: tobramycin


substrate_name: netilmicin

substrate: netilmicin


substrate_name: GTP

substrate: GTP


substrate_name: kanamycin A

substrate: kanamycin A


substrate_name: ITP

substrate: ITP


enzyme_display_name: N-acetylmuramate 1-kinase

organism: Pseudomonas putida

proof_lines: pH not specified in the publication, temperature not specified in the publication

enzyme: N-acetylmuramate 1-kinase


substrate_name: N-acetyl-D-muramate

substrate: N-acetyl-D-muramate


substrate_name: N-acetyl-D-glucosamine

substrate: N-acetyl-D-glucosamine


enzyme_display_name: UniProt Q58761

organism: Methanocaldococcus jannaschii

substrate_name: D-ribose 5-phosphate

enzyme: UniProt Q58761

substrate: D-ribose 5-phosphate


enzyme_display_name: UniProt Q9H3S4

organism: Homo sapiens

enzyme: UniProt Q9H3S4


substrate_name: thiamine

substrate: thiamine


enzyme_display_name: D-erythronate 4-kinase

organism: Heliomicrobium modesticaldum

column_label: Table S2: Kinetic parameters for PdxA2-DUF1537 proteins (PNAS 2016, 113(29):E4161-9); Table S2, UniProt B0TBI9 (HmDenK) row, substrate 4-Hydroxy-L-threonine; column 'kcat [s-1]' = 41 ± 4; column 'KM [mM]' = 44 ± 9; column 'kcat/KM [M-1s-1]' = 9.4 × 10^2. captured primary segment: Table S2 row: B0TBI9 (HmDenK) | 4-Hydroxy-L-threonine | kcat 41 ± 4 s^-1 | KM 44 ± 9 mM | kcat/KM 9.4 x 10^2 M^-1 s^-1

normalized_value_unit_evidence: kcat: printed Table S2 cell 41 s^-1; already in s^-1, so no unit conversion applies and the normalized value is 41.0 s^(-1). Km: printed Table S2 cell 44 mM; already in mM, so no unit conversion applies and the normalized value is 44.0 mM. kcat/Km: printed Table S2 kcat/KM cell 9.4 x 10^2 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 940.0 x 0.001 = 0.94 s^(-1)*mM^(-1). The exact quotient of this row's own printed kcat and Km cells is 41 / 44 = 0.9318181818181818 s^-1 mM^-1, which is not the printed efficiency cell 0.94 s^-1 mM^-1 even after rounding to the table's own two-significant-figure precision (0.9318... rounds to 0.93, not 0.94), so the printed cell is the paper's own independently fitted value for this row, not a rounded rendering of the quotient.

raw_value_unit_evidence: Table S2, UniProt B0TBI9 (HmDenK) row, substrate '4-Hydroxy-L-threonine': kcat = 41 ± 4 s^-1; KM = 44 ± 9 mM; printed kcat/KM = 9.4 x 10^2 M^-1 s^-1.

enzyme: D-erythronate 4-kinase


substrate_name: D-erythronate

column_label: Table S2; row B0TBI9 (HmDenK) / D-Erythronate; columns kcat (s^-1), KM (mM), kcat/KM (M^-1 s^-1); cells 16, 0.081, 1.9 x 10^5; normalized kcat/Km 190 s^-1 mM^-1

normalized_value_unit_evidence: kcat=16 s^-1; Km=0.081 mM; kcat/Km=190 s^-1 mM^-1 (explicit table value converted from M^-1 s^-1)

raw_value_unit_evidence: B0TBI9 (HmDenK) / D-Erythronate: kcat=16 s^-1; KM=0.081 mM; kcat/KM=1.9 x 10^5 M^-1 s^-1

row_label: B0TBI9 (HmDenK) / D-Erythronate

table_label: Table S2. Kinetic parameters for PdxA2-DUF1537 proteins

substrate: D-erythronate


proof_lines: The PdxA2–DUF1537 enzymes (DtnK, d-threonate kinase and DenK, d-erythronate kinase) catalyze the ATP-dependent phosphorylation of d-threonate or d-erythronate to generate d-threonate 4-phosphate or d-erythronate 4-phosphate.


substrate_name: kanamycin B

substrate: kanamycin B


substrate_name: arbekacin

substrate: arbekacin


substrate_name: amikacin

substrate: amikacin


substrate_name: sisomicin

substrate: sisomicin


substrate_name: neomycin B

ki_unit: mM

substrate: neomycin B


substrate_name: Unknown

substrate: Unknown


enzyme_display_name: GDP-polyphosphate phosphotransferase

organism: Delftia tsuruhatensis

substrate_name: GMP

enzyme: GDP-polyphosphate phosphotransferase

substrate: GMP


enzyme_display_name: AMP-polyphosphate phosphotransferase

organism: Acinetobacter johnsonii

enzyme: AMP-polyphosphate phosphotransferase


substrate_name: AMP

assay_conditions_summary: pH 8; cofactor ADP

proof_lines: recombinant PAP, pH 8.0, 37°C, in presence of 50 mM (NH4)2SO4

substrate: AMP


organism: Francisella tularensis subsp. tularensis


substrate_name: GDP

substrate: GDP


enzyme_display_name: ribose-phosphate diphosphokinase

organism: Rattus norvegicus

proof_lines:
pH 8.0, 37°C, isoenzyme II
pH 8.0, 37°C, isoenzyme I

enzyme: ribose-phosphate diphosphokinase


proof_lines:
pH 8.0, 37°C, isoenzyme I
pH 8.0, 37°C, isoenzyme II


organism: Spinacia oleracea

substrate_name: CTP

substrate: CTP


substrate_name: UTP

substrate: UTP


substrate_name: dATP

substrate: dATP


substrate_name: GTP

substrate: GTP


substrate_name: D-Ribose 5-phosphate; ATP

source_license: SABIO-RK terms (free for academic use; see sabiork.h-its.org)

substrate: D-Ribose 5-phosphate; ATP


substrate_name: ATP; D-Ribose 5-phosphate

substrate: ATP; D-Ribose 5-phosphate


organism: Thermus thermophilus

substrate_name: ATP

assay_conditions_summary: pH 8; 348.15 K; cofactor ATP

substrate: ATP


substrate_name: D-ribose 5-phosphate

proof_lines:
pH conditions not mentioned, 37°C
pH 7.6, 37°C, isoenzyme 3

substrate: D-ribose 5-phosphate


assay_conditions_summary: pH 7.6; 310.15 K; cofactor ATP


proof_lines: pH conditions not mentioned, 37°C, ATP as substrate, Kis value

proof_lines: pH conditions not mentioned, 37°C, D-ribose 5-phosphate as substrate, Kis value

proof_lines: pH 7.6, 37°C, 5-phospho-alpha-D-ribose 1-diphosphate as substrate, isoenzyme 3


assay_conditions_summary: pH 7


proof_lines: pH and temperature conditions not mentioned, rPRSI isoenzyme


substrate_name: phosphate

proof_lines:
pH 7.5, 37°C, isoenzyme PRSI
pH 7.5, 37°C, isoenzyme PRSII

substrate: phosphate


proof_lines:
pH 7.4, 37°C
pH 7.5, 37°C, isoenzyme PRSI
pH 7.5, 37°C, isoenzyme PRSII


assay_conditions_summary: pH 8; 310.15 K; cofactor ATP

proof_lines: pH and temperature conditions not mentioned


substrate_name: 5-phospho-alpha-D-ribose 1-diphosphate

proof_lines:
pH 7.4, 37°C, native enzyme from liver
pH 7.4, 37°C, isoenzyme rPRSII
pH 7.4, 37°C, isoenzyme rPRSI

substrate: 5-phospho-alpha-D-ribose 1-diphosphate


proof_lines:
pH 8.0, 37°C, isoenzyme I
pH 7.4, 37°C, isoenzyme PRSI
pH 7.4, 37°C, isoenzyme rPRSI


proof_lines:
pH 7.4, 37°C, isoenzyme PRSI
pH 7.4, 37°C, isoenzyme rPRSI
pH 7.4, 37°C, native enzyme from liver


enzyme_display_name: UniProt Q5NGA7

organism: Francisella tularensis

enzyme: UniProt Q5NGA7


enzyme_display_name: UniProt O31611

organism: Bacillus subtilis

enzyme: UniProt O31611


substrate_name: guanosine 3'-diphosphate 5'-diphosphate

substrate: guanosine 3'-diphosphate 5'-diphosphate


organism: Pyrococcus horikoshii


substrate_name: nicotinamide ribonucleotide

substrate: nicotinamide ribonucleotide


enzyme_display_name: UniProt Q8IE38

organism: Plasmodium falciparum

enzyme: UniProt Q8IE38


enzyme_display_name: UniProt P0A752

organism: Escherichia coli

enzyme: UniProt P0A752


substrate_name: nicotinamide mononucleotide

substrate: nicotinamide mononucleotide


enzyme_display_name: UniProt Q96T66

substrate_name: nicotinic acid mononucleotide

proof_lines:
Raw SKiD Env: Temp=37°C, pH=7.5
Raw SKiD Env: Temp=-----, pH=-----

enzyme: UniProt Q96T66

substrate: nicotinic acid mononucleotide


substrate_name: diphosphate

substrate: diphosphate


enzyme_display_name: UniProt Q99JR6

organism: Mus musculus

enzyme: UniProt Q99JR6


enzyme_display_name: UniProt Q9HAN9

enzyme: UniProt Q9HAN9


enzyme_display_name: UniProt P9WPA5

organism: Mycobacterium tuberculosis

enzyme: UniProt P9WPA5


substrate_name: pantetheine 4'-phosphate

smiles: CC(C)(COP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O

substrate: pantetheine 4'-phosphate


enzyme_display_name: sulfate adenylyltransferase

organism: Pyropia yezoensis

enzyme: sulfate adenylyltransferase


enzyme_display_name: UniProt Q12650

organism: Penicillium chrysogenum

enzyme: UniProt Q12650


enzyme_display_name: UniProt Q8SAG1

organism: Glycine max

proof_lines:
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=25°C, pH=8

enzyme: UniProt Q8SAG1


substrate_name: sulfate

substrate: sulfate


substrate_name: adenylyl sulfate

substrate: adenylyl sulfate


substrate_name: adenylylsulfate

substrate: adenylylsulfate


enzyme_display_name: UniProt O67174

organism: Aquifex aeolicus

enzyme: UniProt O67174


substrate_name: adenosine 5'-phosphosulfate

substrate: adenosine 5'-phosphosulfate


proof_lines:
Raw SKiD Env: Temp=30°C, pH=8
Raw SKiD Env: Temp=-----, pH=-----


substrate_name: 5-phospho-D-ribose diphosphate

substrate: 5-phospho-D-ribose diphosphate


enzyme_display_name: thiamine diphosphokinase

organism: Arabidopsis thaliana

substrate_name: thiamine

enzyme: thiamine diphosphokinase

substrate: thiamine


substrate_name: D-Ribose 5-phosphate

substrate: D-Ribose 5-phosphate


organism: Petroselinum crispum


substrate_name: ATP

substrate: ATP


substrate_name: Unknown

substrate: Unknown


organism: Salmonella enterica subsp. enterica serovar Typhimurium

substrate_name: D-ribose 5-phosphate

substrate: D-ribose 5-phosphate


substrate_name: AMP

substrate: AMP


substrate_name: phosphate

proof_lines:
pH 7.5, 37°C, high affinity site
pH 7.5, 37°C, low affinity site

substrate: phosphate


organism: Homo sapiens

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:A0A090N8Y0 and applied mutation signature D100N to reconstruct the assayed variant sequence.

column_label: Table 3; row D100N / thiamin; columns kcat [s^-1], Km thiamin [uM], kcat/Km thiamin [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

raw_value_unit_evidence: kcat raw_value=0.0002 raw_unit=s^-1

row_label: D100N / thiamin

table_label: Table 3. Kinetic parameters for wild-type and mutant hTPK1 proteins


column_label: Table 3; row D100N / ATP; columns kcat [s^-1], Km ATP [mM], kcat/Km ATP [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

row_label: D100N / ATP


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:A0A090N8Y0 and applied mutation signature D73N to reconstruct the assayed variant sequence.

column_label: Table 3; row D73N / thiamin; columns kcat [s^-1], Km thiamin [uM], kcat/Km thiamin [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

raw_value_unit_evidence: kcat raw_value=0.0003 raw_unit=s^-1

row_label: D73N / thiamin


column_label: Table 3; row D73N / ATP; columns kcat [s^-1], Km ATP [mM], kcat/Km ATP [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

row_label: D73N / ATP


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:A0A090N8Y0 and applied mutation signature D71N to reconstruct the assayed variant sequence.

column_label: Table 3; row D71N / thiamin; columns kcat [s^-1], Km thiamin [uM], kcat/Km thiamin [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

raw_value_unit_evidence: kcat raw_value=0.0005 raw_unit=s^-1

row_label: D71N / thiamin


column_label: Table 3; row D71N / ATP; columns kcat [s^-1], Km ATP [mM], kcat/Km ATP [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

row_label: D71N / ATP


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature T99A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:A0A090N8Y0 and applied mutation signature T99A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 7.5; cofactor ATP

column_label: Table 3; row T99A / ATP; columns kcat [s^-1], Km ATP [mM], kcat/Km ATP [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

normalized_value_unit_evidence: kcat normalized_value=0.026 normalized_unit=s^-1; Km normalized_value=3.5 normalized_unit=mM; kcat/Km normalized_value=0.0074285714285714285 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.026 raw_unit=s^-1; Km ATP raw_value=3.5 raw_unit=mM; kcat/Km ATP raw_value=7.4 raw_unit=s^-1 M^-1

row_label: T99A / ATP


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R131G to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:A0A090N8Y0 and applied mutation signature R131G to reconstruct the assayed variant sequence.

column_label: Table 3; row R131G / ATP; columns kcat [s^-1], Km ATP [mM], kcat/Km ATP [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

normalized_value_unit_evidence: kcat normalized_value=0.028 normalized_unit=s^-1; Km normalized_value=2.0 normalized_unit=mM; kcat/Km normalized_value=0.014 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.028 raw_unit=s^-1; Km ATP raw_value=2.0 raw_unit=mM; kcat/Km ATP raw_value=1.4 x 10^1 raw_unit=s^-1 M^-1

row_label: R131G / ATP


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature D133N with inferred residue-numbering offset -13 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:A0A090N8Y0 and applied mutation signature D133N to reconstruct the assayed variant sequence.

column_label: Table 3; row D133N / ATP; columns kcat [s^-1], Km ATP [mM], kcat/Km ATP [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

normalized_value_unit_evidence: kcat normalized_value=0.034 normalized_unit=s^-1; Km normalized_value=0.65 normalized_unit=mM; kcat/Km normalized_value=0.05230769230769231 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.034 raw_unit=s^-1; Km ATP raw_value=0.65 raw_unit=mM; kcat/Km ATP raw_value=5.2 x 10^1 raw_unit=s^-1 M^-1

row_label: D133N / ATP


substrate_name: thiamin

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:A0A090N8Y0 and applied mutation signature Q96E to reconstruct the assayed variant sequence.

column_label: Table 3; row Q96E / thiamin; columns kcat [s^-1], Km thiamin [uM], kcat/Km thiamin [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

raw_value_unit_evidence: kcat raw_value=0.045 raw_unit=s^-1; Km thiamin raw_value=0.039 raw_unit=uM; kcat/Km thiamin raw_value=1.2 x 10^6 raw_unit=s^-1 M^-1

row_label: Q96E / thiamin

substrate: thiamin


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature Q96E with inferred residue-numbering offset +13 to reconstruct the assayed variant sequence.


column_label: Table 3; row Q96E / ATP; columns kcat [s^-1], Km ATP [mM], kcat/Km ATP [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

normalized_value_unit_evidence: kcat normalized_value=0.045 normalized_unit=s^-1; Km normalized_value=1.0 normalized_unit=mM; kcat/Km normalized_value=0.045 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.045 raw_unit=s^-1; Km ATP raw_value=1.0 raw_unit=mM; kcat/Km ATP raw_value=4.4 x 10^1 raw_unit=s^-1 M^-1

row_label: Q96E / ATP


sequence_variant_note: Sequence is treated as wild-type because the source explicitly marked the record as wild-type.

column_label: Table 3; row Wild-type / thiamin; columns kcat [s^-1], Km thiamin [uM], kcat/Km thiamin [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

normalized_value_unit_evidence: kcat normalized_value=0.069 normalized_unit=s^-1; Km normalized_value=0.00021 normalized_unit=mM; kcat/Km normalized_value=328.57142857142856 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.069 raw_unit=s^-1; Km thiamin raw_value=0.21 raw_unit=uM; kcat/Km thiamin raw_value=3.3 x 10^5 raw_unit=s^-1 M^-1

row_label: Wild-type / thiamin


column_label: Table 3; row Wild-type / ATP; columns kcat [s^-1], Km ATP [mM], kcat/Km ATP [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

normalized_value_unit_evidence: kcat normalized_value=0.069 normalized_unit=s^-1; Km normalized_value=1.2 normalized_unit=mM; kcat/Km normalized_value=0.05750000000000001 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.069 raw_unit=s^-1; Km ATP raw_value=1.2 raw_unit=mM; kcat/Km ATP raw_value=5.9 x 10^1 raw_unit=s^-1 M^-1

row_label: Wild-type / ATP


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature S74A with inferred residue-numbering offset -12 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:A0A090N8Y0 and applied mutation signature S74A to reconstruct the assayed variant sequence.

column_label: Table 3; row S74A / ATP; columns kcat [s^-1], Km ATP [mM], kcat/Km ATP [s^-1 M^-1]; footnote: kinetic parameters are best-fit values by fitting Eq. (1), mean from two experiments; ND means Km values could not be defined for very low activity mutants.

normalized_value_unit_evidence: kcat normalized_value=0.094 normalized_unit=s^-1; Km normalized_value=2.4 normalized_unit=mM; kcat/Km normalized_value=0.03916666666666667 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.094 raw_unit=s^-1; Km ATP raw_value=2.4 raw_unit=mM; kcat/Km ATP raw_value=4.0 x 10^1 raw_unit=s^-1 M^-1

row_label: S74A / ATP


enzyme_display_name: Thiamine pyrophosphokinase

organism: Bacillus subtilis (strain 168)

enzyme: Thiamine pyrophosphokinase


organism: Pseudomonas aeruginosa

substrate_name: (Phosphate)n

smiles: N#N

proof_lines: wild type enzyme, with GMP as cosubstrate, at pH 8.0 temperature not specified in the publication

proof_lines: wild type enzyme, with AMP as cosubstrate, at pH 8.0 temperature not specified in the publication

substrate: (Phosphate)n


substrate_name: GMP

column_label: PMC HTML Table 1 row PA3455 wt / GMP / Poly-P reports Km 1,550 +/- 120 uM and kcat 13.4 +/- 0.4 s^-1; kcat_over_km is exact arithmetic from those same row cells.

normalized_value_unit_evidence: kcat normalized_value=13.4 normalized_unit=s^-1; Km normalized_value=1.55 normalized_unit=mM; kcat_over_km normalized_value=8.64516129032258 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=13.4 +/- 0.4 raw_unit=s^-1; Km raw_value=1550 +/- 120 raw_unit=uM; table kcat/Km raw_value=0.9 x 10^4 raw_unit=M^-1*s^-1 rounded

row_label: PA3455 wt; variable substrate GMP; constant substrate Poly-P

table_label: Table 1. Kinetic parameters of PA3455 and SMc02148 with various substrates

substrate: GMP


column_label: PMC HTML Table 1 row PA3455 wt / AMP / Poly-P reports Km 820 +/- 40 uM and kcat 44.6 +/- 0.8 s^-1; kcat_over_km is exact arithmetic from those same row cells.

normalized_value_unit_evidence: kcat normalized_value=44.6 normalized_unit=s^-1; Km normalized_value=0.82 normalized_unit=mM; kcat_over_km normalized_value=54.39024390243903 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=44.6 +/- 0.8 raw_unit=s^-1; Km raw_value=820 +/- 40 raw_unit=uM; table kcat/Km raw_value=0.5 x 10^5 raw_unit=M^-1*s^-1 rounded

row_label: PA3455 wt; variable substrate AMP; constant substrate Poly-P


organism: Pyrobaculum calidifontis


assay_conditions_summary: pH 10.5; cofactor ATP


organism: Acinetobacter johnsonii

substrate_name: ADP

assay_conditions_summary: pH 8; 310.15 K; cofactor ADP

proof_lines: reverse reaction of polyphosphate synthesis, pH 8.0, 37°C

substrate: ADP


proof_lines: in the presence of 5 mM Mg2+, in 50 mM potassium phosphate pH 8.0, at 37°C

proof_lines: in the absence of Mg2+ or Mn2+, in 50 mM potassium phosphate pH 8.0, at 37°C

proof_lines: in the presence of 5 mM Mn2+, in 50 mM potassium phosphate pH 8.0, at 37°C


proof_lines: kcat is 37 sec(-1) with Rib-5-P as substrate (PubMed:21085589). kcat is 0.83 sec(-1) with Rib-5-P as substrate (PubMed:22745722). kcat is 0.66 sec(-1) with ATP as substrate (PubMed:22745722). kcat is 0.155 sec(-1) with UTP as substrate (Pub


column_label: Biochemical characterization prose, AtTPK1 sentence, thiamin Km; assay conditions in Experimental procedures.

raw_value_unit_evidence: Results prose: AtTPK1 thiamin Km 0.96 uM.

row_label: AtTPK1; free thiamin substrate

table_label: Biochemical characterization prose


organism: Mycolicibacterium smegmatis

source_license: CC BY 4.0; CC BY-NC-ND 4.0

proof_lines: S0.5 value, Hill coefficient 1.7, pH 7.5, 25°C

source_databases_merged: brenda skid


enzyme_display_name: Ribose-phosphate pyrophosphokinase

organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

substrate_name: CTP

column_label: Table 2 row CTP/R5P; columns KM (uM), kcat (s^-1), and kcat/KM (M^-1 s^-1) as applicable.

raw_value_unit_evidence: Table 2 row CTP/R5P reports KM 26 (+/-1) uM.

table_label: Table 2. Apparent kinetic parameters for Mt PRS reaction

enzyme: Ribose-phosphate pyrophosphokinase

substrate: CTP


substrate_name: GTP

column_label: Table 2 row GTP/R5P; columns KM (uM), kcat (s^-1), and kcat/KM (M^-1 s^-1) as applicable.

raw_value_unit_evidence: Table 2 row GTP/R5P reports KM 37 (+/-9) uM.

substrate: GTP


substrate_name: UTP

column_label: Table 2 row UTP/R5P; columns KM (uM), kcat (s^-1), and kcat/KM (M^-1 s^-1) as applicable.

raw_value_unit_evidence: Table 2 row UTP/R5P reports KM 52 (+/-7) uM.

substrate: UTP


organism: Bacillus subtilis

substrate_name: ATP; D-Ribose 5-phosphate

source_license: CC BY 4.0; SABIO-RK terms (free for academic use; see sabiork.h-its.org)

substrate: ATP; D-Ribose 5-phosphate


organism: Escherichia coli


organism: Methanocaldococcus jannaschii


organism: Rattus norvegicus


substrate_name: D-Ribose 5-phosphate; ATP

sequence_variant_note: Source notes indicate a mutant or variant enzyme, but no machine-applicable substitution signature was available.

substrate: D-Ribose 5-phosphate; ATP


organism: Spinacia oleracea


substrate_name: ATP; Thiamin

column_label: Biochemical characterization prose, AtTPK2 sentence, thiamin Km and Vmax; assay conditions in Experimental procedures.

raw_value_unit_evidence: Results prose: AtTPK2 thiamin Km 1.28 uM; Vmax 9.6 pmol/min.

row_label: AtTPK2; free thiamin substrate

substrate: ATP; Thiamin


column_label: Biochemical characterization prose, AtTPK1 sentence, thiamin Km and Vmax; assay conditions in Experimental procedures.

raw_value_unit_evidence: Results prose: AtTPK1 thiamin Km 0.96 uM; Vmax 8.4 pmol/min.


organism: Schizosaccharomyces pombe

substrate_name: Thiamin; ATP

sequence_variant_note: Resolved sequence already matches the mutant residue(s) after applying an inferred residue-numbering offset +11, so it is treated as a source-provided variant sequence.

substrate: Thiamin; ATP


organism: Plasmodium falciparum

substrate_name: thiamine

sequence_variant_note: Sequence identity was resolved, but no explicit wild-type or mutant call was captured.

column_label: PMID 17132104 abstract and Table 1, PfTPK row/column Km for thiamine.

normalized_value_unit_evidence: Abstract Km 73 uM = 0.073 mM; Table 1 mean 72 uM = 0.072 mM.

raw_value_unit_evidence: Abstract reports Km for thiamine = 73 uM; Table 1 reports Km for thiamine = 72 +/- 6 uM for PfTPK.

row_label: PfTPK / thiamine

table_label: Abstract plus Table 1

substrate: thiamine


enzyme_display_name: DNA-directed DNA polymerase

organism: [Bacillus] caldotenax

substrate_name: dNTP

enzyme: DNA-directed DNA polymerase

substrate: dNTP


enzyme_display_name: UniProt P19821

organism: Thermus aquaticus

substrate_name: dADP

enzyme: UniProt P19821

substrate: dADP


enzyme_display_name: UniProt Q97W02

organism: Saccharolobus solfataricus

substrate_name: dCTP

proof_lines:
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=37°C, pH=7.5
Raw SKiD Env: Temp=37°C, pH=7.4

enzyme: UniProt Q97W02

substrate: dCTP


substrate_name: dATP

proof_lines:
Raw SKiD Env: Temp=60°C, pH=-----
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=37°C, pH=-----

substrate: dATP


substrate_name: dGTP

proof_lines:
Raw SKiD Env: Temp=37°C, pH=7.5
Raw SKiD Env: Temp=37°C, pH=-----
Raw SKiD Env: Temp=-----, pH=-----

substrate: dGTP


substrate_name: dTTP

proof_lines:
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=37°C, pH=7.5
Raw SKiD Env: Temp=37°C, pH=-----

substrate: dTTP


enzyme_display_name: UniProt P96022

enzyme: UniProt P96022


enzyme_display_name: UniProt Q16851

organism: Homo sapiens

substrate_name: alpha-D-glucose 1-phosphate

enzyme: UniProt Q16851

substrate: alpha-D-glucose 1-phosphate


enzyme_display_name: UniProt Q9M9P3

organism: Arabidopsis thaliana

enzyme: UniProt Q9M9P3


substrate_name: diphosphate

substrate: diphosphate


substrate_name: UDP-glucose

substrate: UDP-glucose


organism: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

substrate_name: Unknown

substrate: Unknown


enzyme_display_name: AMP-polyphosphate phosphotransferase

substrate_name: [phosphate]n

proof_lines: polyphosphate with an average chain length of 35 phosphate groups, pH 8.5, 30°C

enzyme: AMP-polyphosphate phosphotransferase

substrate: [phosphate]n


organism: Pseudomonas aeruginosa


enzyme_display_name: ribose-phosphate diphosphokinase

organism: Mycobacterium tuberculosis

proof_lines: in the absence of free Mg2+ or Mn2+, in 50 mM potassium phosphate pH 8.0, at 37°C

source_databases_merged: sabio_rk brenda uniprot

enzyme: ribose-phosphate diphosphokinase


organism: Salmonella typhimurium

proof_lines: pH and temperature conditions not mentioned


substrate_name: ATP

substrate: ATP


substrate_name: AMP

substrate: AMP


organism: Salmonella enterica subsp. enterica serovar Typhimurium


organism: Mycolicibacterium smegmatis

substrate_name: D-ribose 5-phosphate

proof_lines:
pH 7.5, 25°C
Raw SKiD Env: Temp=25°C, pH=7.5

substrate: D-ribose 5-phosphate


column_label: Table 4 ATP row under kcat (s^-1), Km/S0.5 (mM), and Kcat/(Km/S0.5) (s^-1 mM^-1); the exact same-row kcat and Km cells yield the current catalytic-efficiency value.

row_label: ATP

table_label: Table 4. Kinetics parameters of MsPrsA in presence of Pi 50mM


substrate_name: D-Ribose 5-phosphate

assay_conditions_summary: pH 7.5; 298.15 K; cofactor NADH

column_label: Table 4 R5P row under kcat (s^-1), Km/S0.5 (mM), and Kcat/(Km/S0.5) (s^-1 mM^-1); the exact same-row kcat and Km cells yield the current catalytic-efficiency value.

substrate: D-Ribose 5-phosphate


enzyme_display_name: GDP-polyphosphate phosphotransferase

substrate_name: GDP

assay_conditions_summary: pH 7.2; cofactor ADP

enzyme: GDP-polyphosphate phosphotransferase

substrate: GDP


substrate_name: GTP

assay_conditions_summary: pH 7.2; cofactor ATP

substrate: GTP


enzyme_display_name: UniProt Q8IEE9

substrate_name: CTP

enzyme: UniProt Q8IEE9

substrate: CTP


enzyme_display_name: UniProt P19836

substrate_name: choline phosphate

enzyme: UniProt P19836

substrate: choline phosphate


enzyme_display_name: UniProt P9WJJ5

substrate_name: nicotinate beta-D-ribonucleotide

enzyme: UniProt P9WJJ5

substrate: nicotinate beta-D-ribonucleotide


enzyme_display_name: UniProt P29468

organism: Saccharomyces cerevisiae

enzyme: UniProt P29468


proof_lines:
Raw SKiD Env: Temp=30°C, pH=7
Raw SKiD Env: Temp=-----, pH=-----


substrate_name: pyrithiamine

proof_lines:
Plasmodium falciparum
thiamine pyrophosphokinase
thiamine specificity

substrate: pyrithiamine


assay_conditions_summary: cofactor ATP


organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

proof_lines:
Pseudomonas aeruginosa
polyphosphate kinase (PPK2)
ATP


substrate_name: ADP

assay_conditions_summary: cofactor ADP

substrate: ADP


substrate_name: thiamine

proof_lines:
Schizosaccharomyces pombe
thiamine pyrophosphokinase
thiamine

substrate: thiamine


assay_conditions_summary: pH 8.6; cofactor ATP

proof_lines:
Schizosaccharomyces pombe
thiamine pyrophosphokinase
ATP


organism: Acinetobacter johnsonii


substrate_name: GMP

substrate: GMP


organism: Bacillus subtilis (strain 168)

proof_lines: Bacillus subtilis phosphoribosyl diphosphate synthetase


enzyme_display_name: UniProt Q58761

organism: Methanocaldococcus jannaschii

source_databases_merged: skid uniprot

enzyme: UniProt Q58761


substrate_name: ribose 5-phosphate (at pH 9 and 85 degrees Celsius)

smiles: C(C(C(C(C=O)O)O)O)OP(=O)(O)O


enzyme_display_name: UDP-N-acetylglucosamine diphosphorylase

organism: Sulfurisphaera tokodaii

substrate_name: diphosphate

enzyme: UDP-N-acetylglucosamine diphosphorylase

substrate: diphosphate


substrate_name: UDP-N-acetyl-alpha-D-glucosamine

substrate: UDP-N-acetyl-alpha-D-glucosamine


substrate_name: UTP

substrate: UTP


enzyme_display_name: UniProt P23509

organism: Solanum tuberosum

substrate_name: ATP

proof_lines:
Raw SKiD Env: Temp=37°C, pH=7.4
Raw SKiD Env: Temp=37°C, pH=-----
Raw SKiD Env: Temp=-----, pH=-----

enzyme: UniProt P23509


substrate_name: alpha-D-glucose 1-phosphate

proof_lines:
Raw SKiD Env: Temp=37°C, pH=-----
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=37°C, pH=7.4

substrate: alpha-D-glucose 1-phosphate


enzyme_display_name: Ribose-phosphate pyrophosphokinase 1

enzyme: Ribose-phosphate pyrophosphokinase 1

substrate: ATP


substrate_name: D-ribose 5-phosphate


enzyme_display_name: Ribose-phosphate pyrophosphokinase

organism: Escherichia coli (strain K12)

substrate_name: ATP (at pH 8 and 37 degrees Celsius)

enzyme: Ribose-phosphate pyrophosphokinase

substrate: ATP (at pH 8 and 37 degrees Celsius)


organism: Bacillus subtilis

sequence_variant_note: Mutation context is present, but no sequence was resolved for this record.


substrate: D-ribose 5-phosphate


sequence_variant_note: No sequence was resolved for this record, so variant-aware sequence handling could not be applied.


organism: Bacillus amyloliquefaciens

assay_conditions_summary: pH 7.5; 310.15 K; cofactor ATP

proof_lines: wild type enzyme, in 50 mM potassium phosphate at pH 7.5, 5 mM MgCl2, at 37°C


proof_lines: mutant enzyme N120S, in 50 mM potassium phosphate at pH 7.5, 5 mM MgCl2, at 37°C


proof_lines: mutant enzyme D58H, in 50 mM potassium phosphate at pH 7.5, 5 mM MgCl2, at 37°C


proof_lines: mutant enzyme L135I, in 50 mM potassium phosphate at pH 7.5, 5 mM MgCl2, at 37°C


enzyme_display_name: fucose-1-phosphate guanylyltransferase

organism: Mortierella alpina

substrate_name: beta-L-fucose 1-phosphate

enzyme: fucose-1-phosphate guanylyltransferase

substrate: beta-L-fucose 1-phosphate


organism: Francisella tularensis subsp. tularensis

substrate_name: GDP

column_label: Table 1 row GDP, columns kcat/s^-1, KM/microM, and kcat/KM/s^-1.M^-1 match exported GDP metrics after unit conversion.

row_label: GDP substrate; measured product GTP

table_label: PMC4748334 Table 1. Steady state kinetic parameters for FtPPK2 from activity measurements using IP-HPLC

substrate: GDP


substrate_name: GTP

column_label: Table 1 row GTP, columns kcat/s^-1, KM/microM, and kcat/KM/s^-1.M^-1 match exported GTP metrics after unit conversion.

row_label: GTP substrate; measured product GDP

substrate: GTP


enzyme_display_name: Thiamine pyrophosphokinase 1

organism: Arabidopsis thaliana

proof_lines:
Arabidopsis thaliana
thiamin pyrophosphokinase
TPK

enzyme: Thiamine pyrophosphokinase 1


organism: Pyrobaculum calidifontis

substrate_name: D-Ribose 5-phosphate

substrate: D-Ribose 5-phosphate


organism: Hevea brasiliensis


substrate_name: Unknown

substrate: Unknown


organism: Escherichia coli


substrate_name: AMP

substrate: AMP


enzyme_display_name: UniProt O66914

organism: Aquifex aeolicus

smiles: C(C(C(C(C(CO)O)O)O)O)C(=O)C(=O)O

enzyme: UniProt O66914


enzyme_display_name: UniProt P04951

enzyme: UniProt P04951


substrate_name: CTP

substrate: CTP


enzyme_display_name: phosphatidate cytidylyltransferase

organism: Catharanthus roseus

substrate_name: phosphatidic acid

enzyme: phosphatidate cytidylyltransferase

substrate: phosphatidic acid


enzyme_display_name: UniProt P0A0Z8

organism: Neisseria meningitidis

substrate_name: N-glycolylneuraminate

enzyme: UniProt P0A0Z8

substrate: N-glycolylneuraminate


substrate_name: N-acetylneuraminate

proof_lines:
Raw SKiD Env: Temp=37°C, pH=8.5
Raw SKiD Env: Temp=22°C, pH=7.5

substrate: N-acetylneuraminate


enzyme_display_name: UniProt Q99KK2

organism: Mus musculus

enzyme: UniProt Q99KK2


substrate_name: N-acetylneuraminic acid

proof_lines:
Raw SKiD Env: Temp=25°C, pH=9
Raw SKiD Env: Temp=37°C, pH=9

substrate: N-acetylneuraminic acid


smiles: C(C(C(C(C(C(CO)O)O)O)O)O)C(=O)C(=O)O


enzyme_display_name: ribose-phosphate diphosphokinase

organism: Homo sapiens

assay_conditions_summary: 310.15 K; cofactor ATP

proof_lines: pH conditions not mentioned, 37°C, wild type and mutant enzyme

enzyme: ribose-phosphate diphosphokinase


proof_lines: pH conditions not mentioned, 37°C, mutant enzyme


proof_lines: pH conditions not mentioned, 37°C, wild type enzyme


proof_lines:
pH 8.0, 37°C, phosphate 50 mM
pH 8.0, 37°C, phosphate 5 mM


proof_lines:
pH 8.0, 37°C, phosphate 50 mM
pH 8.0, 37°C, Kii value
pH 8.0, 37°C, Kis value


proof_lines: pH 8.0, 37°C, D-ribose 5-phosphate 5 mM, Kis value

proof_lines: pH 8.0, 37°C, D-ribose 5-phosphate 5 mM, Kii value


substrate_name: ribose 5-phosphate

proof_lines: pH and temperature conditions not mentioned

substrate: ribose 5-phosphate


proof_lines:
pH 8.0, 37°C
pH 7.4, 37°C, with D-ribose-5-phosphate
pH 7.4, 37°C, with MgATP2-


substrate_name: 5-phospho-alpha-D-ribose 1-diphosphate

substrate: 5-phospho-alpha-D-ribose 1-diphosphate


organism: Rattus norvegicus

substrate_name: phosphate

substrate: phosphate


enzyme_display_name: UniProt P29991

organism: Dengue virus

enzyme: UniProt P29991


enzyme_display_name: UniProt P28887

organism: Human respiratory syncytial virus A

substrate_name: remdesivir triphosphate

enzyme: UniProt P28887

substrate: remdesivir triphosphate


substrate_name: ATP

substrate: ATP


enzyme_display_name: Genome polyprotein

organism: Hepatitis GB virus B

substrate_name: ATP for NS3 NTPase

enzyme: Genome polyprotein

substrate: ATP for NS3 NTPase


substrate_name: CTP for NS3 NTPase

substrate: CTP for NS3 NTPase


substrate_name: UTP for NS3 NTPase

substrate: UTP for NS3 NTPase


substrate_name: dATP for NS3 NTPase

substrate: dATP for NS3 NTPase


substrate_name: dCTP for NS3 NTPase

substrate: dCTP for NS3 NTPase


substrate_name: dTTP for NS3 NTPase

substrate: dTTP for NS3 NTPase


enzyme_display_name: UniProt Q06755

organism: Bacillus subtilis

substrate_name: 2-C-methyl-D-erythritol 4-phosphate

smiles: CC(CO)(C(COP(=O)(O)O)O)O

enzyme: UniProt Q06755

substrate: 2-C-methyl-D-erythritol 4-phosphate


substrate_name: CTP

substrate: CTP


enzyme_display_name: UniProt Q46893

proof_lines:
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=23°C, pH=6.5
Raw SKiD Env: Temp=30°C, pH=8

enzyme: UniProt Q46893


proof_lines:
Raw SKiD Env: Temp=23°C, pH=6.5
Raw SKiD Env: Temp=30°C, pH=8


organism: Bos taurus

substrate_name: D-ribose 5-phosphate

substrate: D-ribose 5-phosphate


assay_conditions_summary: pH 8.2; 310.15 K; cofactor ATP


organism: Clostridioides difficile

substrate_name: GDP-D-mannose

substrate: GDP-D-mannose


enzyme_display_name: UniProt D3G6S4

organism: Leishmania major

substrate_name: D-galactose 1-phosphate

enzyme: UniProt D3G6S4

substrate: D-galactose 1-phosphate


substrate_name: UDP-D-galacturonate

substrate: UDP-D-galacturonate


substrate_name: UDP-L-arabinopyranose

substrate: UDP-L-arabinopyranose


substrate_name: UDP-D-glucose

substrate: UDP-D-glucose


substrate_name: UTP

substrate: UTP


substrate_name: diphosphate

substrate: diphosphate


enzyme_display_name: UniProt Q72MQ6

organism: Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130

substrate_name: GTP

enzyme: UniProt Q72MQ6

substrate: GTP


enzyme_display_name: UniProt Q9X2A8

organism: Thermotoga maritima

enzyme: UniProt Q9X2A8


enzyme_display_name: UniProt P0AA89

enzyme: UniProt P0AA89


enzyme_display_name: UniProt Q9YF05

organism: Aeropyrum pernix

enzyme: UniProt Q9YF05


enzyme_display_name: autoinducer-2 kinase

organism: Escherichia coli

proof_lines: recombinant enzyme, pH and temperature not specified in the publication

enzyme: autoinducer-2 kinase


substrate_name: Unknown

proof_lines: inhibition of recombinant enzyme, pH and temperature not specified in the publication

substrate: Unknown


organism: Bifidobacterium longum

substrate_name: L-glutamine

smiles: C(CC(=O)N)C(C(=O)O)N

substrate: L-glutamine


enzyme_display_name: UniProt A0A1C7DQ98

organism: Planococcus halocryophilus

substrate_name: ATP

proof_lines:
Raw SKiD Env: Temp=25°C, pH=7.6
Raw SKiD Env: Temp=4°C, pH=7.6

enzyme: UniProt A0A1C7DQ98

substrate: ATP


enzyme_display_name: UniProt O28126

organism: Archaeoglobus fulgidus

proof_lines:
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=50°C, pH=8.5

enzyme: UniProt O28126


enzyme_display_name: UniProt Q7SIB1

organism: Geobacillus stearothermophilus

proof_lines:
Raw SKiD Env: Temp=25°C, pH=7.6
Raw SKiD Env: Temp=55°C, pH=7.6
Raw SKiD Env: Temp=4°C, pH=7.6

enzyme: UniProt Q7SIB1


enzyme_display_name: fructoselysine 6-kinase

substrate_name: fructosyl-L-epsilon-lysine

enzyme: fructoselysine 6-kinase

substrate: fructosyl-L-epsilon-lysine


enzyme_display_name: UniProt Q16222

organism: Homo sapiens

substrate_name: UDP-N-acetylglucosamine

enzyme: UniProt Q16222

substrate: UDP-N-acetylglucosamine


substrate_name: N-acetylglucosamine 1-phosphate

substrate: N-acetylglucosamine 1-phosphate


enzyme_display_name: hexokinase

assay_conditions_summary: pH 7.2; 310.15 K; cofactor ATP

proof_lines: pH 7.2, 37°C, recombinant full length enzyme

proof_lines: pH 7.2, 37°C, recombinant catalytic C-terminal domain

enzyme: hexokinase


enzyme_display_name: ribose-phosphate diphosphokinase

organism: Thermus thermophilus

assay_conditions_summary: pH 8; 348.15 K; cofactor ATP

enzyme: ribose-phosphate diphosphokinase


smiles: C(C(C(C(C(C=O)O)O)O)S)O

proof_lines: inhibition of fructose phosphorylation, at 37°C, pH 7.4


enzyme_display_name: Protein adenylyltransferase VopS

organism: Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

enzyme: Protein adenylyltransferase VopS


enzyme_display_name: tRNAHis guanylyltransferase

organism: Acanthamoeba castellanii

enzyme: tRNAHis guanylyltransferase


organism: Campylobacter jejuni


enzyme_display_name: UniProt P24224

substrate_name: malonyl-CoA

enzyme: UniProt P24224

substrate: malonyl-CoA


substrate_name: acetoacetyl-CoA

substrate: acetoacetyl-CoA


substrate_name: butyryl-CoA

substrate: butyryl-CoA


substrate_name: acetyl-CoA

substrate: acetyl-CoA


substrate_name: CoA

substrate: CoA


enzyme_display_name: Transferred entry: 2.7.7.108

organism: Legionella pneumophila

substrate_name: O-Phosphocholine-Rab1b-GppNHp; ATP

enzyme: Transferred entry: 2.7.7.108

substrate: O-Phosphocholine-Rab1b-GppNHp; ATP


substrate_name: Rab1b-GppNHp; ATP

substrate: Rab1b-GppNHp; ATP


substrate_name: CDP-choline

proof_lines: hCEPT1 CDP-choline CDP-ethanolamine

substrate: CDP-choline


substrate_name: CDP-ethanolamine

substrate: CDP-ethanolamine


enzyme_display_name: guanylylpyridinol adenylase

organism: Methanothermobacter marburgensis

assay_conditions_summary: pH 7; cofactor ATP

proof_lines: kcat is 7.2 min(-1) with ATP as substrate.

enzyme: guanylylpyridinol adenylase


enzyme_display_name: ethanolaminephosphotransferase

organism: Saccharomyces cerevisiae

proof_lines:
choline/ethanolaminephosphotransferases
Saccharomyces cerevisiae
CDP-ethanolamine

enzyme: ethanolaminephosphotransferase


enzyme_display_name: Ethanolaminephosphotransferase 1

column_label: Full text reports apparent Km and Vmax values for CDP-ethanolamine were 1.8 microM and 76.3 pmol/min/mg.

raw_value_unit_evidence: Km raw_value=1.8 microM raw_unit=microM

row_label: hEPT1 / CDP-ethanolamine substrate saturation

table_label: Journal of Lipid Research full-text kinetics prose / Fig. 3C

enzyme: Ethanolaminephosphotransferase 1


organism: Chlamydomonas reinhardtii


organism: Rattus norvegicus


organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)


organism: Bos taurus

substrate_name: CDPethanolamine; 1,2-Diacyl-sn-glycerol

substrate: CDPethanolamine; 1,2-Diacyl-sn-glycerol


substrate_name: 1,2-Diacyl-sn-glycerol; CDPethanolamine

substrate: 1,2-Diacyl-sn-glycerol; CDPethanolamine


proof_lines:
37°C, pH 8.2
cosubstrate CDP-choline, 37°C, pH 8.2


organism: Escherichia coli

substrate_name: L-ascorbate[side 1]

substrate: L-ascorbate[side 1]


substrate_name: Unknown

substrate: Unknown


substrate_name: S-adenosyl-L-methionine

proof_lines:
recombinant enzyme
native enzyme
pH 8.5, 37°C

substrate: S-adenosyl-L-methionine


substrate_name: D-glucose 6-phosphate

smiles: C(C(C(C(C(C=O)O)O)O)O)OP(=O)(O)O

proof_lines: pH 7.2, 37°C, isomerization catalyzed by C-terminal domain

substrate: D-glucose 6-phosphate


substrate_name: 2-O-alpha-mannosyl-D-glycerate [side 1]

proof_lines: apparent value, at pH 7.6, temperature not specified in the publication

substrate: 2-O-alpha-mannosyl-D-glycerate [side 1]


enzyme_display_name: pyruvate, phosphate dikinase

organism: Arundinaria sp.

substrate_name: AMP

enzyme: pyruvate, phosphate dikinase

substrate: AMP


substrate_name: diphosphate

substrate: diphosphate


substrate_name: pyruvate

substrate: pyruvate


organism: Flaveria brownii


substrate_name: ATP

substrate: ATP


substrate_name: phosphate

substrate: phosphate


enzyme_display_name: Rifampicin phosphotransferase

organism: Streptomyces sviceus (strain ATCC 29083 / DSM 924 / JCM 4929 / NBRC 13980 / NCIMB 11184 / NRRL 5439 / UC 5370)

substrate_name: RIF

enzyme: Rifampicin phosphotransferase

substrate: RIF


organism: Entamoeba histolytica

assay_conditions_summary: pH 6

proof_lines: with diphosphate as varied substrate, Ki(intercept)


substrate_name: phosphoenolpyruvate

substrate: phosphoenolpyruvate


proof_lines:
pH 6.0, 37°C
less than 0.005 mM ,pH 6.3, 25°C
pH 5.8-6.4 (optimal pH), 37°C


assay_conditions_summary: pH 6; cofactor ATP

proof_lines: with phosphoenolpyruvate as varied substrate, Ki(slope)


organism: Listeria monocytogenes serotype 4b (strain F2365)

proof_lines: kcat is 1.03 sec(-1) (PubMed:24778229). kcat is 2.87 sec(-1) with ATP as substrate. kcat is 2.25 sec(-1) with RIF as substrate (PubMed:27103605).


organism: Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)


enzyme_display_name: pyruvate, water dikinase

organism: Pyrococcus furiosus

assay_conditions_summary: pH 8.4; 353.15 K; cofactor ATP

proof_lines: 50°C, pH not specified in the publication

enzyme: pyruvate, water dikinase


organism: Flaveria bidentis


organism: Arabidopsis thaliana

substrate_name: ATP; Phosphate; Pyruvate

substrate: ATP; Phosphate; Pyruvate


organism: Clostridium symbiosum

substrate_name: Phosphoenolpyruvate; AMP; Diphosphate

substrate: Phosphoenolpyruvate; AMP; Diphosphate


substrate_name: ATP; Pyruvate; Phosphate

assay_conditions_summary: pH 6.3; 298.15 K; cofactor ATP

substrate: ATP; Pyruvate; Phosphate


substrate_name: Phosphate; Pyruvate; ATP

substrate: Phosphate; Pyruvate; ATP


organism: Saccharum hybrid


organism: Thermoproteus tenax

assay_conditions_summary: 343.15 K; cofactor ATP

proof_lines: 55°C, AMP saturation kinetics with ATP concentration of 50-200 micromol


organism: Triticum aestivum


organism: Zea mays

substrate_name: AMP; Diphosphate; Phosphoenolpyruvate

substrate: AMP; Diphosphate; Phosphoenolpyruvate


substrate_name: Pyruvate; ATP; H2O

substrate: Pyruvate; ATP; H2O


substrate_name: H2O; Pyruvate; ATP

substrate: H2O; Pyruvate; ATP


enzyme_display_name: alpha-glucan, water dikinase

organism: Solanum tuberosum

substrate_name: ATP; Amylopectin; H2O

enzyme: alpha-glucan, water dikinase

substrate: ATP; Amylopectin; H2O


proof_lines: with phosphoenolpyruvate as varied substrate

proof_lines: with diphosphate as varied substrate, Ki(slope)


organism: Giardia duodenalis

substrate_name: Unknown

proof_lines:
pH 7, 30°C, less than 0.001 mM
pH 7, 30°C

substrate: Unknown


organism: Miscanthus x giganteus

substrate_name: Phosphate; ATP; Pyruvate

substrate: Phosphate; ATP; Pyruvate


assay_conditions_summary: pH 7; 343.15 K; cofactor ATP

proof_lines: in 100 mM Tris/HCl, pH 7.0, in the presence of 20 mM beta-mercaptoethanol, 6 mM pyruvate, 10 mM ATP and 10 mM MgCl2, at 70°C


assay_conditions_summary: pH 7

proof_lines:
pyruvate phosphate dikinase
abstract-only retrieval
kinetics unverified


organism: Propionibacterium freudenreichii subsp. shermanii

substrate_name: AMP

proof_lines:
pyruvate, orthophosphate dikinase
Propionibacterium shermanii

substrate: AMP


assay_conditions_summary: pH 6.8; cofactor ATP


enzyme_display_name: rifampicin phosphotransferase

organism: Listeria monocytogenes

sequence_variant_note: Mutation signature E297A could not be applied safely because the resolved sequence does not match the expected reference residue(s).

assay_conditions_summary: pH 7.5; 298.15 K; cofactor ATP

enzyme: rifampicin phosphotransferase


sequence_variant_note: Mutation signature E667A could not be applied safely because the resolved sequence does not match the expected reference residue(s).


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Q337A with inferred residue-numbering offset +11 to reconstruct the assayed variant sequence.


sequence_variant_note: Mutation signature R117A could not be applied safely because the resolved sequence does not match the expected reference residue(s).


sequence_variant_note: Mutation signature R666A could not be applied safely because the resolved sequence does not match the expected reference residue(s).


sequence_variant_note: Resolved sequence already matches the mutant residue(s), so it is treated as a source-provided variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature V368E with inferred residue-numbering offset +6 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature V368T with inferred residue-numbering offset +6 to reconstruct the assayed variant sequence.


column_label: Table 2; row Wild-type RPH-Lm / ATP; columns for ATP; normalized values Km=0.00838 mM, kcat=2.87 s^-1, kcat/Km=342.0 s^-1*mM^-1.

raw_value_unit_evidence: Table 2 row Wild-type RPH-Lm / ATP; Km=0.00838 mM normalized from uM, kcat=2.87 s^-1, kcat/Km=342.0 s^-1*mM^-1 normalized from s^-1*M^-1.

row_label: Wild-type RPH-Lm / ATP

table_label: Table 2. RPH-Lm wild-type/mutant steady-state kinetics and RIF susceptibility in Escherichia coli


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y351F with inferred residue-numbering offset +2 to reconstruct the assayed variant sequence.


sequence_variant_note: Sequence is treated as wild-type because the source explicitly marked the record as wild-type.

assay_conditions_summary: pH 8.4; cofactor ATP

column_label: Table 2, Pyruvate formation row AMP, columns Apparent Km (mM)=1.0, Apparent kcat (s^-1)=8.7, Apparent kcat/Km (mM^-1 s^-1)=8.7.

raw_value_unit_evidence: Pyruvate formation AMP: Km=1.0 mM; kcat=8.7 s^-1; kcat/Km=8.7 mM^-1 s^-1

row_label: Pyruvate formation / AMP

table_label: Table 2. Kinetic parameters for P. furiosus PpsA


column_label: Table 2, Pyruvate formation row Phosphate, columns Apparent Km (mM)=38.4, Apparent kcat (s^-1)=11.9, Apparent kcat/Km (mM^-1 s^-1)=0.315.

raw_value_unit_evidence: Pyruvate formation Phosphate: Km=38.4 mM; kcat=11.9 s^-1; kcat/Km=0.315 mM^-1 s^-1

row_label: Pyruvate formation / Phosphate


column_label: Table 2, Pyruvate formation row PEP, columns Apparent Km (mM)=0.4, Apparent kcat (s^-1)=12.6, Apparent kcat/Km (mM^-1 s^-1)=31.5.

raw_value_unit_evidence: Pyruvate formation PEP: Km=0.4 mM; kcat=12.6 s^-1; kcat/Km=31.5 mM^-1 s^-1

row_label: Pyruvate formation / PEP


column_label: Table 2, PEP formation row Pyruvate, columns Apparent Km (mM)=0.11, Apparent kcat (s^-1)=1573.0, Apparent kcat/Km (mM^-1 s^-1)=1.43 x 10^4.

raw_value_unit_evidence: PEP formation Pyruvate: Km=0.11 mM; kcat=1573.0 s^-1; kcat/Km=1.43 x 10^4 mM^-1 s^-1

row_label: PEP formation / Pyruvate


column_label: Table 2, PEP formation row ATP, columns Apparent Km (mM)=0.39, Apparent kcat (s^-1)=1326.0, Apparent kcat/Km (mM^-1 s^-1)=3.40 x 10^3.

raw_value_unit_evidence: PEP formation ATP: Km=0.39 mM; kcat=1326.0 s^-1; kcat/Km=3.40 x 10^3 mM^-1 s^-1

row_label: PEP formation / ATP


substrate_name: Phosphate

smiles: O=P(O)(O)O

substrate: Phosphate


substrate_name: Phosphoenolpyruvate

substrate: Phosphoenolpyruvate


substrate_name: pyruvate

smiles: CC(=O)C(=O)O

substrate: pyruvate


substrate_name: ATP

assay_conditions_summary: pH 7.5; 295.15 K; cofactor ATP

column_label: Table III substrate row ATP gives the raw Km cell and the same direction block gives the molecular activity used for kcat normalization.

raw_value_unit_evidence: Km(ATP) = 15 microM; molecular activity = 2620 mol/min per mol enzyme.

row_label: Direction of P-enolpyruvate formation / Km(ATP) and molecular activity

table_label: Table III: Kinetic Data for the Dikinase from Maize Leaf

substrate: ATP


column_label: Table III substrate row Pi/phosphate gives the raw Km cell and the same direction block gives the molecular activity used for kcat normalization.

raw_value_unit_evidence: Km(Pi) = 1500 microM; molecular activity = 2620 mol/min per mol enzyme.

row_label: Direction of P-enolpyruvate formation / Km(Pi) and molecular activity


column_label: Table III substrate row P-enolpyruvate/phosphoenolpyruvate gives the raw Km cell and the same direction block gives the molecular activity used for kcat normalization.

raw_value_unit_evidence: Km(P-enolpyruvate) = 140 microM; molecular activity = 2420 mol/min per mol enzyme.

row_label: Direction of pyruvate formation / Km(P-enolpyruvate) and molecular activity


substrate_name: diphosphate

column_label: Table III substrate row PPi/diphosphate gives the raw Km cell and the same direction block gives the molecular activity used for kcat normalization.

raw_value_unit_evidence: Km(PPi) = 40 microM; molecular activity = 2420 mol/min per mol enzyme.

row_label: Direction of pyruvate formation / Km(PPi) and molecular activity

substrate: diphosphate


column_label: Table III substrate row pyruvate gives the raw Km cell and the same direction block gives the molecular activity used for kcat normalization.

raw_value_unit_evidence: Km(pyruvate) = 250 microM; molecular activity = 2620 mol/min per mol enzyme.

row_label: Direction of P-enolpyruvate formation / Km(pyruvate) and molecular activity


enzyme_display_name: UniProt P00523

organism: Gallus gallus

enzyme: UniProt P00523


enzyme_display_name: UniProt P49137

organism: Homo sapiens

substrate_name: Lys-Lys-Phe-Asn-Arg-Thr-Leu-Ser-Val-Ala

enzyme: UniProt P49137

substrate: Lys-Lys-Phe-Asn-Arg-Thr-Leu-Ser-Val-Ala


enzyme_display_name: Pyruvate, phosphate dikinase 1, chloroplastic

assay_conditions_summary: cofactor ATP

proof_lines: Km values for pyruvate, phosphate and ATP were slightly lower


enzyme: Pyruvate, phosphate dikinase 1, chloroplastic


substrate_name: phosphate

substrate: phosphate


substrate_name: rifampicin

substrate: rifampicin


column_label: Table 2; row Wild-type RPH-Lm / RIF; columns for RIF/rifampin; normalized values Km=0.00057 mM, kcat=2.25 s^-1, kcat/Km=3940.0 s^-1*mM^-1.

raw_value_unit_evidence: Table 2 row Wild-type RPH-Lm / RIF; Km=0.00057 mM normalized from uM, kcat=2.25 s^-1, kcat/Km=3940.0 s^-1*mM^-1 normalized from s^-1*M^-1.

row_label: Wild-type RPH-Lm / RIF


column_label: Table 2 reports C3 PPDK Km Pyr = 17 uM; the row requires only Km

normalized_value_unit_evidence: Km normalized_value=0.017 normalized_unit=mM; current_export_km=0.017 mM

raw_value_unit_evidence: Km raw_value=17 raw_unit=uM for Pyr with C3 PPDK

row_label: Km Pyr / C3 PPDK column

table_label: PMID 21414960 Oxford Academic HTML Table 2


substrate_name: phosphoenolpyruvate

column_label: Table 2 reports C3 PPDK Km PEP = 292 uM; the row requires only Km

normalized_value_unit_evidence: Km normalized_value=0.292 normalized_unit=mM; current_export_km=0.292 mM

raw_value_unit_evidence: Km raw_value=292 raw_unit=uM for PEP with C3 PPDK

row_label: Km PEP / C3 PPDK column

substrate: phosphoenolpyruvate


enzyme_display_name: UniProt P11071

organism: Escherichia coli

enzyme: UniProt P11071


enzyme_display_name: UniProt P17612

substrate_name: Kemptide

enzyme: UniProt P17612

substrate: Kemptide


column_label: PDF p.3087 states the maize enzyme has PEP Km=194 uM, compared with C3 enzyme Km=294 uM.

normalized_value_unit_evidence: 194 uM converts to 0.194 mM.

raw_value_unit_evidence: Results text states maize enzyme had PEP Km=194 uM.

row_label: Maize C4 PPDK / PEP substrate

table_label: JXB PDF p.3087 Results prose


enzyme_display_name: selenide, water dikinase

organism: Salmonella enterica subsp. enterica serovar Typhimurium

substrate_name: selenide

assay_conditions_summary: pH 7.2; cofactor ATP

column_label: Abstract reports dependence on selenide concentration obeys Michaelis-Menten kinetics with Km value 46 microM.

raw_value_unit_evidence: Km raw_value=46 microM raw_unit=microM

row_label: SELD protein / selenide

table_label: PubMed XML abstract PMID 1557403

enzyme: selenide, water dikinase

substrate: selenide


enzyme_display_name: Alpha-glucan water dikinase, chloroplastic


organism: [Clostridium] symbiosum

proof_lines: pH 6.8, 25°C, pyruvate-producing reaction, values for 7 mutant PPDK


assay_conditions_summary: pH 7; 298.15 K; cofactor ATP

proof_lines: pH 7, 25°C, E279A mutant, phosphoenolpyruvate-producing reaction


proof_lines: pH 7, 25°C, wild type and D280 mutant, phosphoenolpyruvate-producing reaction


substrate_name: 2',3'-dideoxyadenosine 5'-triphosphate

substrate: 2',3'-dideoxyadenosine 5'-triphosphate


proof_lines: pH 7, 25°C, R135A mutant, phosphoenolpyruvate-producing reaction


enzyme_display_name: Phosphoenolpyruvate synthase

organism: Escherichia coli (strain K12)

enzyme: Phosphoenolpyruvate synthase


proof_lines: mutant enzyme, Y351F, at pH 7.5 and 25°C


enzyme_display_name: UniProt P17252

proof_lines:
Raw SKiD Env: Temp=30Â°C, pH=7.5
Raw SKiD Env: Temp=30°C, pH=7.5

enzyme: UniProt P17252


enzyme_display_name: UniProt P34947

substrate_name: rhodopsin

enzyme: UniProt P34947

substrate: rhodopsin


enzyme_display_name: UniProt Q13554

enzyme: UniProt Q13554


enzyme_display_name: UniProt Q13555

enzyme: UniProt Q13555


enzyme_display_name: UniProt Q13557

enzyme: UniProt Q13557


enzyme_display_name: UniProt Q9UQM7

enzyme: UniProt Q9UQM7


enzyme_display_name: UniProt P00518

organism: Oryctolagus cuniculus

enzyme: UniProt P00518


enzyme_display_name: pyruvate, water dikinase

enzyme: pyruvate, water dikinase


column_label: Table 2. Structural and catalytic properties of recombinant PEPS and PPDK of T. tenax.; row Catalysis / pyruvate -> PEP; column PEPS; metric Km/S0.5 (ATP) (70 C); raw 1 mM; accompanying Wiley prose explicitly resolves the PEPS ATP value as a Michaelis-Menten Km of 1 mM.

normalized_value_unit_evidence: Km=1 mM

raw_value_unit_evidence: PEPS ATP value = 1 mM in the hybrid Km/S0.5 row; source prose identifies it as Km

row_label: Catalysis / pyruvate -> PEP


enzyme_display_name: pyruvate, phosphate dikinase

assay_conditions_summary: pH 6.7; 298.15 K; cofactor ATP

proof_lines:
pH 6.7, 25°C
pH 6.8, 25°C, pyruvate formation

enzyme: pyruvate, phosphate dikinase


assay_conditions_summary: pH 8; 298.15 K; cofactor ATP


proof_lines:
wild type enzyme
Mn-ATP, wild-type enzyme


enzyme_display_name: UniProt Q9H4B4

enzyme: UniProt Q9H4B4


enzyme_display_name: UniProt P53350

enzyme: UniProt P53350


enzyme_display_name: UniProt Q6DRK7

organism: Danio rerio

enzyme: UniProt Q6DRK7


proof_lines:
pH 6.8, 25°C, pyruvate formation
pH 6.7, 25°C


column_label: Table 2. Structural and catalytic properties of recombinant PEPS and PPDK of T. tenax.; row Catalysis / PEP -> pyruvate; column PPDK; metric Km (AMP) (55 C); raw 20 uM; normalized Km 0.02 mM.

row_label: Catalysis / PEP -> pyruvate


column_label: Table 2. Structural and catalytic properties of recombinant PEPS and PPDK of T. tenax.; row Catalysis / PEP -> pyruvate; column PPDK; metric Km (PPi) (55 C); raw 80 uM; normalized Km 0.08 mM; PPi is diphosphate/pyrophosphate.


column_label: Table 2. Structural and catalytic properties of recombinant PEPS and PPDK of T. tenax.; row Catalysis / PEP -> pyruvate; column PPDK; metric Km (PEP) (55 C); raw 0.5 mM; normalized Km 0.5 mM.

normalized_value_unit_evidence: Km=0.5 mM


column_label: Table 2. Structural and catalytic properties of recombinant PEPS and PPDK of T. tenax.; row Catalysis / pyruvate -> PEP; column PPDK; metric Km (pyruvate) (70 C); raw 0.8 mM; normalized Km 0.8 mM.

normalized_value_unit_evidence: Km=0.8 mM

raw_value_unit_evidence: Km (pyruvate) (70 C) = 0.8 mM


organism: Trypanosoma cruzi

proof_lines: recombinant enzyme, pH 8.3, temperature not specified in the publication


enzyme_display_name: UniProt Q13627

enzyme: UniProt Q13627


enzyme_display_name: UniProt Q02750

enzyme: UniProt Q02750


enzyme_display_name: selenide, water dikinase

assay_conditions_summary: pH 7.8; 310.15 K; cofactor ATP


organism: Saccharolobus solfataricus

assay_conditions_summary: 338.15 K; cofactor ATP

proof_lines: 65°C, pH not specified in the publication

proof_lines: 70°C, pH not specified in the publication


organism: Triticum aestivum


assay_conditions_summary: pH 8; 295.15 K; cofactor ATP


organism: Haemophilus influenzae


proof_lines: pH and temperature not specified in the publication


organism: Zea mays

assay_conditions_summary: pH 8.3; 303.15 K; cofactor ATP

proof_lines: pH 7.5, 22°C, phosphoenolpyruvate formation


proof_lines: pH 8.1, 25°C, phosphoenolpyruvate formation


proof_lines: pH 7.4, 25°C, phosphoenolpyruvate formation


proof_lines: pH 6.8, 25°C, phosphoenolpyruvate formation


enzyme_display_name: GDP-perosamine synthase

enzyme: GDP-perosamine synthase


enzyme_display_name: UniProt P12996

enzyme: UniProt P12996


enzyme_display_name: UniProt P77444

substrate_name: L-cysteine

smiles: C(C(C(=O)O)N)S

assay_conditions_summary: pH 8

enzyme: UniProt P77444

substrate: L-cysteine


substrate_name: L-glutamate

smiles: C(CC(=O)O)C(C(=O)O)N

substrate: L-glutamate


substrate_name: dimethylallyl diphosphate

smiles: CC(=CCOP(=O)(O)OP(=O)(O)O)C

substrate: dimethylallyl diphosphate


substrate_name: Unknown

proof_lines:
pH 7.5, 37°C
pH 7.5, room temperature
pH 7.5, 25°C

substrate: Unknown


proof_lines:
Mn-ATP, mutant SPS332
Mn-ATP, mutant SPS262
Mn-ATP, mutant SPS238

enzyme: selenide, water dikinase


substrate_name: L-glutamine

proof_lines:
hemisynthase activity, pH 7.2, 37°C
synthase activity, pH 7.2, 37°C
pH 7.5, 37°C

substrate: L-glutamine


substrate_name: sedoheptulose 7-phosphate

smiles: C(C(C(C(C(C(=O)CO)O)O)O)O)OP(=O)(O)O

substrate: sedoheptulose 7-phosphate


proof_lines:
pH 8.5, 37°C
native enzyme


proof_lines:
pH 7.4, 25°C, pyruvate formation
pH 7.5, 22°C, pyruvate formation
at pH 7.0 and 30°C


substrate_name: AMP

substrate: AMP


enzyme_display_name: UniProt P50225

enzyme: UniProt P50225


enzyme_display_name: UniProt O43704

substrate_name: dopamine

enzyme: UniProt O43704

substrate: dopamine


enzyme_display_name: UniProt O75897

substrate_name: rotigotine

enzyme: UniProt O75897

substrate: rotigotine


enzyme_display_name: UniProt P0DMM9

substrate_name: morphine

enzyme: UniProt P0DMM9

substrate: morphine


substrate_name: tapentadol

substrate: tapentadol


substrate_name: O-desmethyl tramadol

substrate: O-desmethyl tramadol


substrate_name: acetaminophen

substrate: acetaminophen


enzyme_display_name: fructokinase

organism: Glycine max

substrate_name: D-fructose

enzyme: fructokinase

substrate: D-fructose


substrate_name: beta-Alanine

smiles: C(CN)C(=O)O

substrate: beta-Alanine


enzyme_display_name: ribose-phosphate diphosphokinase

proof_lines: pH conditions and temperature conditions not mentioned

enzyme: ribose-phosphate diphosphokinase


enzyme_display_name: ethanolaminephosphotransferase

substrate_name: CDP-choline

proof_lines: cosubstrate di-18:0 diacylglycerol, 20°C, pH 8.0

enzyme: ethanolaminephosphotransferase

substrate: CDP-choline


enzyme_display_name: hexokinase

substrate_name: ATP

assay_conditions_summary: pH 7.2; 310.15 K; cofactor ATP

proof_lines: recombinant hexokinase I expressed in Escherichia coli

proof_lines: MgATP2-, hexokinases Ia, Ib and Ic, at 37°C, pH 7.2

enzyme: hexokinase

substrate: ATP


substrate_name: CDP-ethanolamine

substrate: CDP-ethanolamine


proof_lines: mutant enzyme V182L, glutathione S-transferase glucokinase B fusion protein


mutation_signature: N-terminal truncation mutant

mutation_type: truncation

assay_conditions_summary: pH 7.1; 298.15 K; cofactor ATP

proof_lines: N-terminal truncation mutant, pH 7.1, 25°C

proof_lines: N-terminal truncation mutant, presence of 5 mM AMP, pH 7.1, 25°C


assay_conditions_summary: pH 7.1; cofactor ATP

proof_lines: wild-type, 37°C, pH not specified in the puclication. Kinetic constants at high and low concentrations of the fixed substrate: 0.5 mM D-glucose


proof_lines: wild type enzyme, at pH 7.0 in 50 mM HEPES, 100 mM KCl, 5 mM MgCl2 and 25°C

proof_lines: wild type enzyme, without effectors, in 50 mM HEPES, 100 mM KCl, 5 mM MgCl2, pH 7.0, at 25°C


enzyme_display_name: UniProt Q8BGL3

organism: Mus musculus

substrate_name: cholic acid

enzyme: UniProt Q8BGL3

substrate: cholic acid


proof_lines: mutant enzyme D543A, without effectors, in 50 mM HEPES, 100 mM KCl, 5 mM MgCl2, pH 7.0, at 25°C

proof_lines: mutant enzyme D543A, in the presence of 1 mM ADP, in 50 mM HEPES, 100 mM KCl, 5 mM MgCl2, pH 7.0, at 25°C

proof_lines: mutant enzyme D543A, in the presence of 1 mM AMP, in 50 mM HEPES, 100 mM KCl, 5 mM MgCl2, pH 7.0, at 25°C


substrate_name: D-fructose 6-phosphate

proof_lines: pH 7.2, 25°C, red blood cell lysate as source of enzyme

substrate: D-fructose 6-phosphate


assay_conditions_summary: pH 7; cofactor ATP

proof_lines: pH 7.0, temperature not specified in the publication, recombinant His6-tagged enzyme mutant Sephs2-U60C


smiles: C(CC(=O)O)CN


enzyme_display_name: UniProt Q8FDI4

substrate_name: 4-Methylumbelliferyl sulfate

enzyme: UniProt Q8FDI4

substrate: 4-Methylumbelliferyl sulfate


assay_conditions_summary: pH 7.2; 298.15 K; cofactor ATP

proof_lines: pH 7.2, 25°C, red blood cell lysate from diabetic subjects as source of enzyme


organism: Hordeum vulgare

proof_lines:
fructokinase Ib, pH 7.6, 25°C
fructokinase II, pH 7.6, 25°C
fructokinase Ia, pH 7.6, 25°C


substrate_name: D-Glucose; ATP

proof_lines:
steady-state Ki value, pH 7.1, 25°C
initial Ki value, pH 7.1, 25°C
pH 8.5, 37°C

substrate: D-Glucose; ATP


enzyme_display_name: UniProt Q9C9C9

organism: Arabidopsis thaliana

substrate_name: desulfobenzylglucosinolate

enzyme: UniProt Q9C9C9

substrate: desulfobenzylglucosinolate


enzyme_display_name: galactokinase

substrate_name: D-galactose

enzyme: galactokinase

substrate: D-galactose


organism: Lathyrus oleraceus

proof_lines:
30°C, pH 8
Km below 1 mM, pH 7.5, 30°C


organism: Homo sapiens

proof_lines:
mutant enzyme A198V
pH 8, 37°C, mutant enzyme A198V


organism: Malus domestica

proof_lines: pH 8.0, temperature not specified in the publication, MdFRK2

proof_lines: pH 8.0, temperature not specified in the publication, MdFRK1


substrate_name: Unknown

substrate: Unknown


enzyme_display_name: 5-hydroxypentanoate CoA-transferase

organism: Anaerocolumna aminovalerica

assay_conditions_summary: pH 8; 298.15 K; cofactor CoA

proof_lines: pH 8.0, 25°C, cosubstrate (Z)-5-hydroxy-2-pentenoate

enzyme: 5-hydroxypentanoate CoA-transferase


substrate_name: propionyl-CoA

substrate: propionyl-CoA


substrate_name: acetyl-CoA

substrate: acetyl-CoA


substrate_name: butyryl-CoA

substrate: butyryl-CoA


proof_lines: pH 8.0, 25°C substrate acetate, non-competitive inhibition


substrate_name: pentanoyl-CoA

substrate: pentanoyl-CoA


substrate_name: acetate

substrate: acetate


enzyme_display_name: steroid sulfotransferase

organism: Cavia porcellus

enzyme: steroid sulfotransferase


substrate_name: allopregnanolone

substrate: allopregnanolone


substrate_name: testosterone

substrate: testosterone


substrate_name: pregnenolone

substrate: pregnenolone


substrate_name: androsterone

substrate: androsterone


substrate_name: dehydroepiandrosterone

substrate: dehydroepiandrosterone


substrate_name: 3'-phosphoadenylyl sulfate

substrate: 3'-phosphoadenylyl sulfate


enzyme_display_name: formyl-CoA transferase

organism: Oxalobacter formigenes

substrate_name: formyl-CoA

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature G259A to reconstruct the assayed variant sequence.

assay_conditions_summary: cofactor CoA

enzyme: formyl-CoA transferase

substrate: formyl-CoA


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature G260A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature Q17A with inferred residue-numbering offset +7 to reconstruct the assayed variant sequence.


substrate_name: oxalate

substrate: oxalate


organism: Mycobacterium tuberculosis

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R243A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 9

proof_lines: mutant enzyme R243A, with thiosulfate as cosubstrate, at pH 9.0 and 22°C


substrate_name: thiosulfate

substrate: thiosulfate


proof_lines: wild type enzyme, with thiosulfate as cosubstrate, at pH 9.0 and 22°C


enzyme_display_name: glutaconate CoA-transferase

organism: Acidaminococcus fermentans

substrate_name: Propanoyl-CoA; Acetate

enzyme: glutaconate CoA-transferase

substrate: Propanoyl-CoA; Acetate


substrate_name: (E)-Glutaconate; Acetyl-CoA

substrate: (E)-Glutaconate; Acetyl-CoA


organism: Thauera aromatica

substrate_name: Succinyl-CoA; (R)-2-Benzylsuccinate

substrate: Succinyl-CoA; (R)-2-Benzylsuccinate


enzyme_display_name: Formyl-CoA:oxalate CoA-transferase

organism: Escherichia coli (strain K12)

substrate_name: formyl-CoA (with succinate as acceptor at pH 6.7 and 30 degrees Celsius)

assay_conditions_summary: pH 6.7; cofactor CoA

proof_lines: kcat is 130 sec(-1) for CoA-transferase activity with formyl-CoA as substrate (with oxalate as acceptor at pH 6.7 and 30 degrees Celsius). kcat is 5.3 sec(-1) for CoA-transferase activity with formyl-CoA as substrate (with succinate as acce

enzyme: Formyl-CoA:oxalate CoA-transferase


substrate_name: oxalate (with formyl-CoA as donor at pH 6.7 and 30 degrees Celsius)


substrate_name: succinate (with formyl-CoA as donor at pH 6.7 and 30 degrees Celsius)


organism: Rhodospirillum rubrum

substrate_name: glutathione

smiles: C(CC(=O)NC(CS)C(=O)NCC(=O)O)C(C(=O)O)N

proof_lines: pH not specified in the publication, temperature not specified in the publication

substrate: glutathione


substrate_name: dihydrolipoate

smiles: C(CCC(=O)[O-])CC(CCS)S

substrate: dihydrolipoate


substrate_name: L-dithiothreitol

smiles: C(C(C(CS)O)O)S

substrate: L-dithiothreitol


proof_lines:
wild-type FRC
wild-type formyl-CoA transferase


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature W48Q to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature W48F to reconstruct the assayed variant sequence.


enzyme_display_name: 3-oxoacid CoA-transferase

organism: Unknown

substrate_name: Unknown

source_db: unknown

source_license: see source

sequence_variant_note: Mutation signature C196S could not be applied safely because the resolved sequence does not match the expected reference residue(s).

assay_conditions_summary: pH 8.1; cofactor CoA

enzyme: 3-oxoacid CoA-transferase

substrate: Unknown

source: unknown


organism: Acetobacter aceti

assay_conditions_summary: pH 6.7; 298.15 K; cofactor CoA

proof_lines: in 50 mM potassium phosphate, pH 6.7, at 25°C


substrate_name: succinate

proof_lines: kcat is 5.3 sec(-1) for CoA-transferase activity with formyl-CoA as substrate (with oxalate as acceptor at pH 6.7 and 30 degrees Celsius). kcat is 149 sec(-1) for CoA-transferase activity with formyl-CoA as substrate (with succinate as acce

substrate: succinate


enzyme_display_name: S-sulfocysteine synthase

organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

substrate_name: O-phospho-L-serine (in the presence of sulfide as cosubstrate)

proof_lines: kcat is 12.1 min(-1) with O-phospho-L-serine and sulfide as substrates. kcat is 54.8 min(-1) with O-phospho-L-serine and thiosulfate as substrates.

enzyme: S-sulfocysteine synthase


substrate_name: sulfide

substrate: sulfide


organism: Rattus norvegicus

substrate_name: glutaryl-CoA

assay_conditions_summary: pH 7.8; cofactor CoA

proof_lines:
pH 7.8, 30°C, cosubstrate adipate
pH 7.8, 30°C, cosubstrate succinate
pH 7.8, 30°C, cosubstrate malonate

substrate: glutaryl-CoA


substrate_name: adipyl-CoA

proof_lines: pH 7.8, 30°C, cosubstrate 3-hydroxy-3-methylglutarate

substrate: adipyl-CoA


substrate_name: malonyl-CoA

proof_lines: pH 8.5, 30°C, cosubstrate 3-hydroxy-3-methylglutarate

substrate: malonyl-CoA


substrate_name: succinyl-CoA

substrate: succinyl-CoA


proof_lines: pH 7.8, 30°C, cosubstrate adipate, reverse reaction

proof_lines: pH 7.8, 30°C, cosubstrate succinate or malonate, reverse reaction

proof_lines: pH 7.8, 30°C, cosubstrate succinate or glutarate, reverse reaction


substrate_name: Glutarate

smiles: C(CC(=O)O)CC(=O)O

proof_lines:
pH 7.8, 30°C, cosubstrate adipylCoA
pH 7.8, 30°C, cosubstrate malonylCoA
pH 7.8, 30°C, cosubstrate succinylCoA

substrate: Glutarate


substrate_name: adipate

proof_lines: pH 7.8, 30°C, cosubstrate 3-hydroxy-3-methylglutaryl-CoA , reverse reaction

substrate: adipate


proof_lines: pH 7.8, 30°C, cosubstrate 3-hydroxy-3-methylglutaryl-CoA, reverse reaction


substrate_name: methylmalonyl-CoA

proof_lines: pH 7.8, 30°C, cosubstrate glutarate or adipate

substrate: methylmalonyl-CoA