sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature D280A to reconstruct the assayed variant sequence.

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row D280A; column Vmax (units/mg) = 195 +/- 10; column Km, HMG-CoA (uM) = 17 +/- 3; column kcat (s^-1) = 110.5; column kcat/Km (s^-1 uM^-1) = 6.39; the Ki, HG-CoA column is blank on this line. captured primary segment: D280A | Vmax 195 +/- 10 units/mg | Km, HMG-CoA 17 +/- 3 uM | kcat 110.5 s^-1 | kcat/Km 6.39 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 17 uM; 1 uM is 1/1000 mM, so 17 / 1000 = 0.017 mM. kcat: printed TABLE II kcat cell 110.5 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 6.39 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 6.39 x 1000 = 6390.0 s^-1 mM^-1. Quotient disclosure for this table line: 110.5 / 0.017 = 6499.999999999999 s^-1 mM^-1, against the printed catalytic-efficiency cell 6390.0 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line D280A: Km, HMG-CoA = 17 +/- 3 uM; kcat = 110.5 s^-1; printed kcat/Km = 6.39 s^-1 uM^-1; Vmax = 195 +/- 10 units/mg.

row_label: TABLE II, enzyme row D280A


enzyme_display_name: hydroxymethylglutaryl-CoA lyase

organism: Homo sapiens

source_db: oed

verification_status: verified

ki_display: Not reported

protein_accession_database: UniProt

kcat_over_km_origin: calculated

source_license: CC BY 4.0

km_unit: mM

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature D42E to reconstruct the assayed variant sequence.

mutation_type: substitution

assay_conditions_summary: pH 8.2; 303.15 K; cofactor CoA

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row D42E; column Vmax (units/mg) = 20 +/- 1; column Km, HMG-CoA (uM) = 32 +/- 6; column kcat (s^-1) = 11.3; column kcat/Km (s^-1 uM^-1) = 0.35; the Ki, HG-CoA column is blank on this line. captured primary segment: D42E | Vmax 20 +/- 1 units/mg | Km, HMG-CoA 32 +/- 6 uM | kcat 11.3 s^-1 | kcat/Km 0.35 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 32 uM; 1 uM is 1/1000 mM, so 32 / 1000 = 0.032 mM. kcat: printed TABLE II kcat cell 11.3 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 0.35 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 0.35 x 1000 = 350.0 s^-1 mM^-1. Quotient disclosure for this table line: 11.3 / 0.032 = 353.125 s^-1 mM^-1, against the printed catalytic-efficiency cell 350.0 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line D42E: Km, HMG-CoA = 32 +/- 6 uM; kcat = 11.3 s^-1; printed kcat/Km = 0.35 s^-1 uM^-1; Vmax = 20 +/- 1 units/mg.

row_label: TABLE II, enzyme row D42E

data_origin: experimental

enzyme: hydroxymethylglutaryl-CoA lyase

status: verified

source: oed


verification_status: corrected

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature D42N to reconstruct the assayed variant sequence.

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row D42N; column Vmax (units/mg) = 0.33 +/- 0.17; column Km, HMG-CoA (uM) = 43 +/- 7; column kcat (s^-1) = 0.187; column kcat/Km (s^-1 uM^-1) = 0.0044; the Ki, HG-CoA column is blank on this line. captured primary segment: D42N | Vmax 0.33 +/- 0.17 units/mg | Km, HMG-CoA 43 +/- 7 uM | kcat 0.187 s^-1 | kcat/Km 0.0044 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 43 uM; 1 uM is 1/1000 mM, so 43 / 1000 = 0.043 mM. kcat: printed TABLE II kcat cell 0.187 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 0.0044 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 0.0044 x 1000 = 4.4 s^-1 mM^-1. Quotient disclosure for this table line: 0.187 / 0.043 = 4.348837209302326 s^-1 mM^-1, against the printed catalytic-efficiency cell 4.4 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line D42N: Km, HMG-CoA = 43 +/- 7 uM; kcat = 0.187 s^-1; printed kcat/Km = 0.0044 s^-1 uM^-1; Vmax = 0.33 +/- 0.17 units/mg.

row_label: TABLE II, enzyme row D42N

status: corrected


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature E279A to reconstruct the assayed variant sequence.

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row E279A; column Vmax (units/mg) = 163 +/- 9; column Km, HMG-CoA (uM) = 27 +/- 5; column kcat (s^-1) = 92.4; column kcat/Km (s^-1 uM^-1) = 3.38; the Ki, HG-CoA column is blank on this line. captured primary segment: E279A | Vmax 163 +/- 9 units/mg | Km, HMG-CoA 27 +/- 5 uM | kcat 92.4 s^-1 | kcat/Km 3.38 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 27 uM; 1 uM is 1/1000 mM, so 27 / 1000 = 0.027 mM. kcat: printed TABLE II kcat cell 92.4 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 3.38 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 3.38 x 1000 = 3380.0 s^-1 mM^-1. Quotient disclosure for this table line: 92.4 / 0.027 = 3422.2222222222226 s^-1 mM^-1, against the printed catalytic-efficiency cell 3380.0 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line E279A: Km, HMG-CoA = 27 +/- 5 uM; kcat = 92.4 s^-1; printed kcat/Km = 3.38 s^-1 uM^-1; Vmax = 163 +/- 9 units/mg.

row_label: TABLE II, enzyme row E279A


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature E37D to reconstruct the assayed variant sequence.

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row E37D; column Vmax (units/mg) = 152 +/- 6; column Km, HMG-CoA (uM) = 36 +/- 6; column kcat (s^-1) = 86.2; column kcat/Km (s^-1 uM^-1) = 2.39; the Ki, HG-CoA column is blank on this line. captured primary segment: E37D | Vmax 152 +/- 6 units/mg | Km, HMG-CoA 36 +/- 6 uM | kcat 86.2 s^-1 | kcat/Km 2.39 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 36 uM; 1 uM is 1/1000 mM, so 36 / 1000 = 0.036 mM. kcat: printed TABLE II kcat cell 86.2 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 2.39 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 2.39 x 1000 = 2390.0 s^-1 mM^-1. Quotient disclosure for this table line: 86.2 / 0.036 = 2394.444444444445 s^-1 mM^-1, against the printed catalytic-efficiency cell 2390.0 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line E37D: Km, HMG-CoA = 36 +/- 6 uM; kcat = 86.2 s^-1; printed kcat/Km = 2.39 s^-1 uM^-1; Vmax = 152 +/- 6 units/mg.

row_label: TABLE II, enzyme row E37D


sequence_variant_note: Mutation signature E42A could not be applied safely because the resolved sequence does not match the expected reference residue(s).


verification_status: unverified

mutation_signature: Unknown

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

status: unverified


substrate_name: magnesium ion

source_db: uniprot

kcat_display: Not reported

kcat_over_km_display: Not reported

assay_conditions_summary: cofactor CoA

column_label: Official JBC full text Table III row/parameter Km Mg2+ (mM), wild-type column, gives 0.20 +/- 0.02.

raw_value_unit_evidence: Table III wild-type Km Mg2+ raw_value=0.20 +/- 0.02 raw_unit=mM

row_label: Wild-type human HMG-CoA lyase / Mg2+

table_label: Table III: Kinetic and cation binding parameters of wild-type and mutant HMG-CoA lyases

substrate: magnesium ion

source: uniprot


enzyme_display_name: N-acetylneuraminate lyase

organism: Clostridium perfringens (strain 13 / Type A)

substrate_name: Unknown

km_display: Not reported

enzyme: N-acetylneuraminate lyase

substrate: Unknown


organism: Escherichia coli

substrate_name: N-Acetyl-L-neuraminate

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

sequence_source: multiple

assay_conditions_summary: pH 7

proof_lines: kcat is 7.7 sec(-1) with N-acetylneuraminate as substrate (PubMed:12711733). kcat is 0.47 sec(-1) for the aldol condensation of L-aspartate beta-semialdehyde and pyruvate (at pH 7.0) (PubMed:12711733). kcat is 0.27 sec(-1) for the aldol con

substrate: N-Acetyl-L-neuraminate


organism: Staphylococcus aureus (strain NCTC 8325 / PS 47)

proof_lines: kcat is 250 min(-1) for the cleavage of Neu5Ac at pH 7.4, and is 260 min(-1) at pH 6.8 (PubMed:23418011). kcat is 22.1 sec(-1) with N-acetylneuraminate as substrate (PubMed:27943302). kcat is 510 min(-1) with N-acetylneuraminate as substrat


organism: Sus scrofa


sequence_variant_note: Resolved canonical sequence from uniprotkb:P35914 and applied mutation signature R41Q to reconstruct the assayed variant sequence.

column_label: Primary Results prose on PDF page 5, Kinetic Characterization of Arginine-41 Mutants: row context R41Q; metric Km Mg; raw value 88; raw unit uM; normalized value 0.088 mM; metric kcat; raw/normalized value 0.0004 s^-1; derived same-prose ratio 0.004545454545454546 s^-1 mM^-1. Table 1 identifies the R41Q kinetic row and standard assay context.

raw_value_unit_evidence: Results prose: wild-type Km Mg = 200 uM; R41Q Km Mg = 88 uM; R41Q kcat = 0.0004 s^-1. Same-prose pair gives kcat/Km Mg = 0.0004 s^-1 / 0.088 mM = 0.004545454545454546 s^-1 mM^-1.

row_label: R41Q human HMG-CoA lyase; Km Mg and kcat

table_label: Kinetic Characterization of Arginine-41 Mutants prose adjacent to Table 1


enzyme_display_name: isocitrate lyase

organism: Sulfolobus acidocaldarius

substrate_name: isocitrate

source_db: brenda

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

column_label: Table 1 lists KM (uM) = 720 +/- 150 for isocitrate under the Isocitrate lyase column.

raw_value_unit_evidence: Km raw_value=720 +/- 150 uM raw_unit=microM

row_label: KM (uM) row, Isocitrate lyase column, substrate isocitrate

table_label: ScienceDirect full text Table 1: Characterization of isocitrate lyase and malate synthase from S. acidocaldarius

enzyme: isocitrate lyase

substrate: isocitrate

source: brenda


substrate_name: N-acetylneuraminate

column_label: Abstract reports the lyase exhibits a Km of 3.2 mM for Neu5Ac and a Vmax of 27.5 U mg(-1).

raw_value_unit_evidence: Km raw_value=3.2 mM raw_unit=mM

row_label: Clostridium perfringens N-acetylneuraminate lyase / Neu5Ac

table_label: PubMed XML abstract PMID 11432751

substrate: N-acetylneuraminate


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

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

assay_conditions_summary: 310.15 K; cofactor CoA

proof_lines: Abstract-level context: mutant HMG-CoA lyases were kinetically characterized and Km values were reported as comparable to wild-type.

source_databases_merged: sabio_rk skid uniprot


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

substrate_name: HMG-CoA (at pH 6.7 and 37 degrees Celsius)


organism: Aspergillus nidulans

substrate_name: D-Isocitrate

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

substrate: D-Isocitrate


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


substrate_name: N-acetylneuraminic acid

substrate: N-acetylneuraminic acid


proof_lines:
E192S mutant protein, pH 7.5, 25°C
pH 7.5, 25°C, mutant enzyme E192S


proof_lines:
E192N mutant protein, pH 7.7.5, 25°C
pH 7.5, 25°C, mutant enzyme E192N
E192N mutant protein , pH 7.5, 25°C


substrate_name: N-acetyl-L-neuraminic acid

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

substrate: N-acetyl-L-neuraminic acid


proof_lines: pH 7.5, 25°C, mutant enzyme Y98H/F115L/V251I


proof_lines: pH 7.5, 25°C, mutant enzyme Y98H/F115L/V251I/V265I


substrate_name: L-3-deoxy-manno-2-octulosonic acid

proof_lines:
pH 7.5, 25°C, wild-type enzyme
wild type (E192), pH 7.5, 25°C

substrate: L-3-deoxy-manno-2-octulosonic acid


substrate_name: N-acetyl-D-neuraminic acid

substrate: N-acetyl-D-neuraminic acid


substrate_name: D-3-deoxy-manno-2-octulosonic acid

substrate: D-3-deoxy-manno-2-octulosonic acid


proof_lines:
pH 7.5, 25°C, Y98H/F115L
pH 7.5, 25°C, mutant enzyme Y98H/F115L


assay_conditions_summary: pH 7.6; 303.15 K; buffer sodium phosphate

proof_lines: mutant enzyme L199N/I229D, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L199N/I229N, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L171N/I229N, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme I229D, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L171R, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme I229N, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme I229R, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L199N, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L199N/I229R, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L199R/I229N, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


organism: Clostridium perfringens


proof_lines: pH 7.2, 50 mM phosphate buffer, wild-type

proof_lines: pH 7.2, 250 mM phosphate buffer, wild-type


proof_lines:
pH 7.5, 25°C, mutant enzyme E192V
E192V mutant protein, pH 7.5, 25°C


proof_lines:
pH 7.5, 25°C, mutant enzyme E192N
E192N mutant protein, pH 7.7.5, 25°C


assay_conditions_summary: pH 7.5; 298.15 K; buffer sodium phosphate

proof_lines: wild type enzyme, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


substrate_name: N-Formylneuraminic acid

substrate: N-Formylneuraminic acid


substrate_name: N-Succinylneuraminic acid

substrate: N-Succinylneuraminic acid


substrate_name: N-glycolylneuraminic acid

substrate: N-glycolylneuraminic acid


substrate_name: N-Acetyl-7-O-acetylneuraminic acid

substrate: N-Acetyl-7-O-acetylneuraminic acid


substrate_name: N-acetyl-4-O-acetylneuraminic acid

substrate: N-acetyl-4-O-acetylneuraminic acid


enzyme_display_name: citrate (pro-3S)-lyase

organism: Lacrimispora sphenoides

substrate_name: citrate

proof_lines:
citrate lyase
C. sphenoides
L-glutamate

enzyme: citrate (pro-3S)-lyase

substrate: citrate


organism: Mycobacterium tuberculosis

substrate_name: threo-DL-Isocitrate

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_ranked_match and applied mutation signature E423D/E424D to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme E423D/E424D, at pH 7.5 and 30°C

substrate: threo-DL-Isocitrate


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_ranked_match and applied mutation signature E423D to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_ranked_match and applied mutation signature E424D to reconstruct the assayed variant sequence.


organism: Escherichia coli K-12

substrate_name: pyruvate

substrate: pyruvate


substrate_name: N-acetyl-D-mannosamine

substrate: N-acetyl-D-mannosamine


substrate_name: N-acetylneuraminate


organism: Pseudomonas aeruginosa

substrate_name: isocitrate

proof_lines: recombinant His-tagged mutant N214D, pH 7.8, 30°C

substrate: isocitrate


proof_lines: recombinant His-tagged mutant Q221K, pH 7.8, 30°C


proof_lines: recombinant His-tagged mutant Q211H, pH 7.8, 30°C


proof_lines: recombinant His-tagged mutant E219A, pH 7.8, 30°C


proof_lines: recombinant His-tagged wild-type enzyme, pH 7.8, 30°C


organism: Pasteurella multocida


substrate: N-acetylneuraminate


substrate_name: glyoxylate

proof_lines: recombinant detagged enzyme, pH 7.0, 37°C

substrate: glyoxylate


substrate_name: succinate

substrate: succinate


organism: Colwellia psychrerythraea


organism: Pyricularia oryzae


organism: Staphylococcus aureus

proof_lines: purified recombinant mutant K165C, pH 7.4, 30°C


proof_lines: purified recombinant mutant K165-gamma-thialysine, pH 6.8, 30°C

proof_lines: purified recombinant mutant K165-gamma-thialysine, pH 7.4, 30°C


proof_lines: purified recombinant wild-type enzyme, pH 7.4, 30°C

proof_lines: purified recombinant wild-type enzyme, pH 6.8, 30°C


organism: Staphylococcus carnosus

proof_lines: recombinant His-taggged enzyme, pH 7.0, 37°C


substrate_name: N-acetylneuraminic acid

substrate: N-acetylneuraminic acid


organism: Mycoplasma sp.


organism: Escherichia coli


substrate_name: threo-Ds-isocitrate

substrate: threo-Ds-isocitrate


substrate_name: DL-isocitrate

assay_conditions_summary: pH 6.8; buffer 100 mM potassium phosphate

proof_lines: in 100 mM potassium phosphate buffer (pH 7.1), 10 mM MgCl2, 12 mM cysteine

substrate: DL-isocitrate


organism: Homo sapiens


substrate_name: Unknown

ki_unit: mM

substrate: Unknown


organism: Bos taurus


organism: Lactiplantibacillus plantarum


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

proof_lines: cross-linked enzyme aggregates, pH 7.5, 37°C


organism: Lupinus sp.


organism: Haemophilus influenzae


assay_conditions_summary: 303.15 K; cofactor CoA

proof_lines: K48Q mutant protein, pH not specified in the publication, 30°C


proof_lines: K48N mutant protein, pH not specified in the publication, 30°C


organism: Ricinus communis

proof_lines:
pH 6.5
phosphate, pH 7.0
phosphate, pH 6.8


substrate_name: hydroxymethylglutaryl-CoA

assay_conditions_summary: pH 8.2; 310.15 K; cofactor CoA

proof_lines: HMGCLL1 mutant G2A and wild-type HMGCL, pH 8.2, 37°C

substrate: hydroxymethylglutaryl-CoA


organism: Yarrowia lipolytica


organism: Anas sp.


organism: Candida tropicalis


organism: Pseudomonas sp. 'mevalonii'


organism: Bacillus sp. (in: firmicutes)

proof_lines: 0.4 M KCl, 25 mM imidazole buffer, pH 6.8


organism: Cucumis sativus


substrate_name: N-acetyl-neuraminic acid

assay_conditions_summary: pH 7; buffer 0.1 M phosphate

substrate: N-acetyl-neuraminic acid


organism: Clostridium perfringens


organism: Faecalispora sporosphaeroides


proof_lines:
Hepes, pH 7.4
Hepes, pH 7.4, 60 mM Cl-


organism: Glycine max


organism: Staphylococcus aureus

proof_lines: at 30°C, pH not specified in the publication


organism: Helianthus annuus

assay_conditions_summary: pH 6

proof_lines:
phosphate, pH 6.0
phosphate, pH 7.5


organism: Acinetobacter calcoaceticus


organism: Homo sapiens

mutation_signature: deletion mutant Mut15

mutation_type: deletion


organism: Escherichia coli

substrate_name: N-glycolylneuraminic acid

substrate: N-glycolylneuraminic acid


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


organism: Klebsiella pneumoniae


organism: Lactiplantibacillus plantarum


assay_conditions_summary: pH 7.5; 310.15 K; cofactor CoA


organism: Paecilomyces variotii


organism: Mycobacterium tuberculosis

proof_lines: AceA enzyme, Tricine buffer, 37°C, pH 7.5


organism: Rubrivivax gelatinosus

proof_lines:
with 2 mM Mg2+
with 5 mM Mg2+


organism: Vogesella indigofera


organism: Zea mays

substrate_name: Isocitrate

substrate: Isocitrate


organism: Lupinus sp.

assay_conditions_summary: pH 6.8; buffer conditions (imidazole

proof_lines: Tris, triethanolamine or imidazole buffer


organism: Anas platyrhynchos


organism: Raphanus sativus


organism: Pseudomonas indigofera


organism: Geobacillus stearothermophilus


organism: Sus scrofa


organism: Rhodopseudomonas sp.


enzyme_display_name: 4-Hydroxy-2-oxoglutarate aldolase

organism: Rattus norvegicus

enzyme: 4-Hydroxy-2-oxoglutarate aldolase


substrate_name: Pyruvic acid ethyl ester

smiles: CCOC(=O)C(=O)C

substrate: Pyruvic acid ethyl ester


substrate_name: pyruvic acid methyl ester

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

substrate: pyruvic acid methyl ester


substrate_name: Pyruvaldehyde

smiles: CC(=O)C=O

substrate: Pyruvaldehyde


substrate_name: acetaldehyde

smiles: CC=O

substrate: acetaldehyde


enzyme_display_name: L-erythro-3-hydroxyaspartate aldolase

organism: Paracoccus denitrificans

enzyme: L-erythro-3-hydroxyaspartate aldolase


enzyme_display_name: 4-hydroxy-2-oxoglutarate aldolase

organism: Homo sapiens

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature N78T to reconstruct the assayed variant sequence.

proof_lines: pH and temperature not specified in the publication, mutant enzyme N78T

enzyme: 4-hydroxy-2-oxoglutarate aldolase


proof_lines: pH and temperature not specified in the publication, wild-type enzyme


substrate_name: oxaloacetate

proof_lines:
condensation with glyoxylate
competitive

substrate: oxaloacetate


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature S77A to reconstruct the assayed variant sequence.

proof_lines: pH and temperature not specified in the publication, mutant enzyme S77A


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature S198A with inferred residue-numbering offset -11 to reconstruct the assayed variant sequence.

proof_lines: pH and temperature not specified in the publication, mutant enzyme S198A


organism: Bos taurus

assay_conditions_summary: pH 8.3; cofactor NADH

column_label: Table IV row DL-KHG; columns Km and Vmax.

raw_value_unit_evidence: Table IV row DL-KHG: Km 26 uM; Vmax 10.7 umol pyruvate/min/mg protein.

row_label: DL-KHG

table_label: Table IV Kinetic values for the aldolase and beta-decarboxylase activities of bovine kidney 2-keto-4-hydroxyglutarate aldolase


column_label: Table IV row L-KHG; columns Km and Vmax.

raw_value_unit_evidence: Table IV row L-KHG: Km 24 uM; Vmax 12.1 umol pyruvate/min/mg protein.

row_label: L-KHG


substrate_name: Oxaloacetate

column_label: Table IV row Oxalacetate; columns Km and Vmax.

raw_value_unit_evidence: Table IV row Oxalacetate: Km 164 uM; Vmax 1.27 umol pyruvate/min/mg protein.

row_label: Oxalacetate

substrate: Oxaloacetate


column_label: Abstract/Fig. 5 discussion; substrate glyoxylate; apparent Km = 0.43 mM.

raw_value_unit_evidence: Abstract reports apparent Km values at pH 7.5 for pyruvate, glyoxylate and gamma-hydroxy-alpha-ketoglutarate were 10 mM, 0.43 mM and 1.33 mM respectively.

row_label: Glyoxylate

table_label: Abstract and Fig. 5 discussion: apparent Km values for rat liver gamma-hydroxy-alpha-ketoglutarate synthase


substrate_name: pyruvate

column_label: Abstract/Fig. 5 discussion; substrate pyruvate; apparent Km = 10 mM.

row_label: Pyruvate

substrate: pyruvate


organism: Pseudomonas straminea

proof_lines: Cloning, sequencing, and expression of the gene encoding 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae NGJ1


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature S77T to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8.5; 310.15 K; cofactor NADH

column_label: Table 2 (Kinetic parameters.), body row 'S77T'; column 'k cat (sec-1)' = 0.8; column 'K M (uM)' = 58; column 'k cat /K M (M-1 sec-1) x 10^3' = 14; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 0.8 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 0.8 s^(-1). Km: printed Table 2 cell 58 in a column headed uM; 58 / 1000 = 0.058 mM. kcat/Km: printed Table 2 cell 14 in a column headed (M-1 sec-1) x 10^3, that is 14000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 14000 / 1000 = 14.0 s^-1 mM^-1, while the exported ratio is 13.793103448275863.

raw_value_unit_evidence: Table 2, body row 'S77T': k cat = 0.8 sec-1; K M = 58 uM; printed k cat /K M = 14 in a column headed (M-1 sec-1) x 10^3, that is 14 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row S77T

table_label: Table 2: Kinetic parameters. (PLoS ONE 2011, 6(10): e26021)


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature S77V to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'S77V'; column 'k cat (sec-1)' = 1.2; column 'K M (uM)' = 82; column 'k cat /K M (M-1 sec-1) x 10^3' = 15; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 1.2 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 1.2 s^(-1). Km: printed Table 2 cell 82 in a column headed uM; 82 / 1000 = 0.082 mM. kcat/Km: printed Table 2 cell 15 in a column headed (M-1 sec-1) x 10^3, that is 15000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 15000 / 1000 = 15.0 s^-1 mM^-1, while the exported ratio is 14.634146341463413.

raw_value_unit_evidence: Table 2, body row 'S77V': k cat = 1.2 sec-1; K M = 82 uM; printed k cat /K M = 15 in a column headed (M-1 sec-1) x 10^3, that is 15 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row S77V


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature Y140F to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature N78Q to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'N78Q'; column 'k cat (sec-1)' = 6.2; column 'K M (uM)' = 281; column 'k cat /K M (M-1 sec-1) x 10^3' = 22; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 6.2 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 6.2 s^(-1). Km: printed Table 2 cell 281 in a column headed uM; 281 / 1000 = 0.281 mM. kcat/Km: printed Table 2 cell 22 in a column headed (M-1 sec-1) x 10^3, that is 22000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 22000 / 1000 = 22.0 s^-1 mM^-1, while the exported ratio is 22.06405693950178.

raw_value_unit_evidence: Table 2, body row 'N78Q': k cat = 6.2 sec-1; K M = 281 uM; printed k cat /K M = 22 in a column headed (M-1 sec-1) x 10^3, that is 22 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row N78Q


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature N78A to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'N78A'; column 'k cat (sec-1)' = 7.6; column 'K M (uM)' = 66; column 'k cat /K M (M-1 sec-1) x 10^3' = 115; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 7.6 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 7.6 s^(-1). Km: printed Table 2 cell 66 in a column headed uM; 66 / 1000 = 0.066 mM. kcat/Km: printed Table 2 cell 115 in a column headed (M-1 sec-1) x 10^3, that is 115000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 115000 / 1000 = 115.0 s^-1 mM^-1, while the exported ratio is 115.15151515151514.

raw_value_unit_evidence: Table 2, body row 'N78A': k cat = 7.6 sec-1; K M = 66 uM; printed k cat /K M = 115 in a column headed (M-1 sec-1) x 10^3, that is 115 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row N78A


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature S198T to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'S198T'; column 'k cat (sec-1)' = 7.8; column 'K M (uM)' = 77; column 'k cat /K M (M-1 sec-1) x 10^3' = 101; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 7.8 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 7.8 s^(-1). Km: printed Table 2 cell 77 in a column headed uM; 77 / 1000 = 0.077 mM. kcat/Km: printed Table 2 cell 101 in a column headed (M-1 sec-1) x 10^3, that is 101000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 101000 / 1000 = 101.0 s^-1 mM^-1, while the exported ratio is 101.2987012987013.

raw_value_unit_evidence: Table 2, body row 'S198T': k cat = 7.8 sec-1; K M = 77 uM; printed k cat /K M = 101 in a column headed (M-1 sec-1) x 10^3, that is 101 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row S198T


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

column_label: Table IV row DL-KHG; Km column.


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

column_label: Abstract/Fig. 5 discussion; substrate gamma-hydroxy-alpha-ketoglutarate; apparent Km = 1.33 mM.

row_label: Gamma-hydroxy-alpha-ketoglutarate


enzyme_display_name: UniProt P9WFX2

substrate_name: chorismate

source_db: skid

source_license: CC BY-NC-ND 4.0

enzyme: UniProt P9WFX2

substrate: chorismate

source: skid


enzyme_display_name: UniProt P00900

organism: Serratia marcescens

enzyme: UniProt P00900


enzyme_display_name: 2-methylisocitrate lyase, mitochondrial

organism: Yarrowia lipolytica (strain CLIB 122 / E 150)

enzyme: 2-methylisocitrate lyase, mitochondrial


substrate_name: magnesium chloride (MgCl(2))

substrate: magnesium chloride (MgCl(2))


substrate_name: cysteine

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

substrate: cysteine


enzyme_display_name: UniProt Q2L887

organism: Aspergillus niger

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

enzyme: UniProt Q2L887


enzyme_display_name: anthranilate synthase

organism: Ailanthus altissimus

substrate_name: Gln

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

enzyme: anthranilate synthase

substrate: Gln


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


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature N78T to reconstruct the assayed variant sequence.

column_label: Table 2. Kinetic parameters; row N78T; columns kcat (sec^-1), KM (uM), kcat/KM (M^-1 sec^-1) x 10^3.

normalized_value_unit_evidence: kcat paper=4.0 s^-1; Km paper=0.016 mM; kcat/Km paper=250 s^-1 mM^-1

table_label: Table 2. Kinetic parameters


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature S198A to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'S198A'; column 'k cat (sec-1)' = 2.4; column 'K M (uM)' = 44; column 'k cat /K M (M-1 sec-1) x 10^3' = 55; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 2.4 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 2.4 s^(-1). Km: printed Table 2 cell 44 in a column headed uM; 44 / 1000 = 0.044 mM. kcat/Km: printed Table 2 cell 55 in a column headed (M-1 sec-1) x 10^3, that is 55000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 55000 / 1000 = 55.0 s^-1 mM^-1, while the exported ratio is 54.54545454545455.

raw_value_unit_evidence: Table 2, body row 'S198A': k cat = 2.4 sec-1; K M = 44 uM; printed k cat /K M = 55 in a column headed (M-1 sec-1) x 10^3, that is 55 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row S198A


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature S77A to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'S77A'; column 'k cat (sec-1)' = 2.5; column 'K M (uM)' = 84; column 'k cat /K M (M-1 sec-1) x 10^3' = 30; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 2.5 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 2.5 s^(-1). Km: printed Table 2 cell 84 in a column headed uM; 84 / 1000 = 0.084 mM. kcat/Km: printed Table 2 cell 30 in a column headed (M-1 sec-1) x 10^3, that is 30000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 30000 / 1000 = 30.0 s^-1 mM^-1, while the exported ratio is 29.76190476190476.

raw_value_unit_evidence: Table 2, body row 'S77A': k cat = 2.5 sec-1; K M = 84 uM; printed k cat /K M = 30 in a column headed (M-1 sec-1) x 10^3, that is 30 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row S77A


column_label: Table 2. Kinetic parameters; row WT; columns kcat (sec^-1), KM (uM), kcat/KM (M^-1 sec^-1) x 10^3.

normalized_value_unit_evidence: kcat paper=6.1 s^-1; Km paper=0.011 mM; kcat/Km paper=555 s^-1 mM^-1

row_label: WT


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature Y140F to reconstruct the assayed variant sequence.

column_label: Table 2. Kinetic parameters; row Y140F; columns kcat (sec^-1), KM (uM), kcat/KM (M^-1 sec^-1) x 10^3.

normalized_value_unit_evidence: kcat paper=5.2 s^-1; Km paper=0.008 mM; kcat/Km paper=650 s^-1 mM^-1


organism: Ogataea henricii

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

proof_lines: Gln-dependent enzyme that is composed of 2 NH4+-dependent subunits and of 2 amidotransferase subunits (I2II2)


enzyme_display_name: 2,3-dimethylmalate lyase

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

proof_lines:
mutant P240T
mutant enzyme P240T, at pH 7.5 and 25°C

enzyme: 2,3-dimethylmalate lyase


proof_lines:
mutant C124A
mutant enzyme C124A, at pH 7.5 and 25°C


proof_lines: wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines:
mutant P240S
mutant enzyme P240S, at pH 7.5 and 25°C


assay_conditions_summary: buffer direct optical method

proof_lines: direct optical method, K+-Hepes as buffer

proof_lines: pH and temperature not specified in the publication

proof_lines: direct optical method, imidazole as buffer


proof_lines:
wild type
wild type enzyme, at pH 7.5 and 25°C


proof_lines: mutant enzyme P240T, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines: mutant enzyme P240S, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines:
smaller than 0.00001 s-1
larger than 5 mM
Ki above 5 mM


substrate_name: (R)-malate

proof_lines: kcat less than 0.00001 sec-1, pH and temperature not specified in the publication

substrate: (R)-malate


substrate_name: Phosphonopyruvate

proof_lines:
smaller than 0.00001 s-1
in 50 mM K+-HEPES (pH 7.5 and 25°C)

substrate: Phosphonopyruvate


proof_lines: mutant enzyme Y44F, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines: mutant enzyme C124S, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines: mutant enzyme D59S, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines: mutant enzyme C124A, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines: mutant enzyme D59A, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines:
mutant C124S
mutant enzyme C124S, at pH 7.5 and 25°C


enzyme_display_name: (S)-citramalyl-CoA lyase

substrate_name: (3S)-citramalyl-CoA (for citramalyl-CoA lyase activity)

proof_lines: kcat is 0.12 sec(-1) for malate synthase reaction (PubMed:24334609). kcat is 0.09 sec(-1) for beta-methylmalate synthase reaction (PubMed:24334609). kcat is 0.135 sec(-1) for beta-methylmalate synthase reaction (PubMed:29056341). kcat is 0.

enzyme: (S)-citramalyl-CoA lyase


substrate_name: propionyl-CoA (for beta-methylmalate synthase)


substrate_name: acetyl-CoA (for malate synthase)

substrate: acetyl-CoA (for malate synthase)


organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)


substrate_name: anthranilate (with the dimeric form and for the phosphoribosyltransferase activity at pH 7.5)


substrate_name: phosphoribosylpyrophosphate (with the monomeric and dimeric forms and for the phosphoribosyltransferase activity at pH 7.5)


substrate_name: magnesium ion (with the monomeric and dimeric forms and for the phosphoribosyltransferase activity at pH 7.5)


substrate_name: glyoxylate (with acetyl-CoA as cosubstrate)


substrate_name: (S)-malyl-CoA (for malyl-CoA thioesterase activity)


enzyme_display_name: methylisocitrate lyase

organism: Escherichia coli (strain K12)

substrate_name: magnesium

smiles: [Mg]

proof_lines: kcat is 12 sec(-1) for methylisocitrate lyase with threo-2-methylisocitrate as substrate (mixture of (2R,3S)- and (2S,3R)-2-methylisocitrate at pH 7 and 30 degrees Celsius).

enzyme: methylisocitrate lyase

substrate: magnesium


organism: Oryza sativa

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature Y367A to reconstruct the assayed variant sequence.

proof_lines: pH 8.3, 32°C, Y367A mutant anthranilate synthase alpha-subunit OASA2


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature S126F to reconstruct the assayed variant sequence.

proof_lines: pH 8.3, 32°C, S126F mutant anthranilate synthase alpha-subunit OASA2


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature A369L to reconstruct the assayed variant sequence.

proof_lines: pH 8.3, 32°C, A369L mutant anthranilate synthase alpha-subunit OASA2


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature A369L/L530D to reconstruct the assayed variant sequence.

proof_lines: pH 8.3, 32°C, A369L/L530D mutant anthranilate synthase alpha-subunit OASA2


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature S126F/L530D to reconstruct the assayed variant sequence.

proof_lines: pH 8.3, 32°C, S126F/L530D mutant anthranilate synthase alpha-subunit OASA2


organism: Arabidopsis thaliana

substrate_name: L-Glutamine; Chorismate

substrate: L-Glutamine; Chorismate


organism: Escherichia coli

substrate_name: Chorismate; L-Glutamine

substrate: Chorismate; L-Glutamine


substrate_name: Chorismate

substrate: Chorismate


organism: Pseudomonas putida


organism: Saccharomyces cerevisiae


organism: Salmonella typhimurium


organism: [Bacillus] caldotenax

substrate_name: chorismate

assay_conditions_summary: pH 9

column_label: Primary-paper prose in the wild-type ASI kinetic-parameter segment: kcat was 2.3 x 10^4 min^-1; the same sentence identifies chorismate Km and the preceding sentence fixes pH 9 and 37 C.

normalized_value_unit_evidence: 23000 min^-1 / 60 = 383.3333333333333 s^-1; target 383.0 s^-1 is accepted as whole-s^-1 rounding while preserving the unrounded conversion.

raw_value_unit_evidence: The paper reports kcat = 2.3 x 10^4 min^-1.

row_label: Wild-type B. caldotenax anthranilate synthase I; chorismate assay

table_label: Results and Discussion: Enzymatic Properties of B. caldotenax ASI (prose kinetic-parameter statement)


column_label: Primary-paper prose in the wild-type ASI kinetic-parameter segment: the Km values for NH4Cl and chorismate were 46 mM and 38 micromolar, respectively; the preceding sentence fixes pH 9 and 37 C.

raw_value_unit_evidence: The paper reports chorismate Km = 38 micromolar.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R429H with inferred residue-numbering offset -13 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R358H/R416H to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R321H to reconstruct the assayed variant sequence.


organism: Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

substrate_name: DL-threo-2-methylisocitrate (MICA) (at pH 7.5)

proof_lines: kcat is 5.24 sec(-1) for isocitrate lyase activity with threo-DL-isocitrate as substrate (at pH 6). kcat is 1.25 sec(-1) for methylisocitrate lyase activity with DL-threo-2-methylisocitrate as substrate (at pH 7.5).


organism: Oryza sativa subsp. japonica

substrate_name: chorismate (for recombinant ASA1 and ASB1 proteins synthesized with the wheat germ cell-free system)

proof_lines: kcat is 34.7 sec(-1) with chorismate as substrate (for recombinant ASA1 and ASB1 proteins synthesized with the wheat germ cell-free system).


substrate_name: chorismate (for recombinant ASA2 and ASB1 proteins synthesized with the wheat germ cell-free system)

proof_lines: kcat is 14.6 sec(-1) with chorismate as substrate (for recombinant ASA2 and ASB1 proteins synthesized with the wheat germ cell-free system).


proof_lines: kcat is 34.7 sec(-1) with chorismate as substrate (for recombinant ASA1 and ASB1 proteins synthesized with the wheat germ cell-free system). kcat is 14.6 sec(-1) with chorismate as substrate (for recombinant ASA2 and ASB1 proteins synthesiz

substrate: chorismate (for recombinant ASA1 and ASB1 proteins synthesized with the wheat germ cell-free system)


organism: Homo sapiens

substrate_name: Unknown

substrate: Unknown


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


enzyme_display_name: UniProt P0A853

substrate_name: L-tryptophan

enzyme: UniProt P0A853

substrate: L-tryptophan


substrate_name: S-ethyl-L-cysteine

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

substrate: S-ethyl-L-cysteine


enzyme_display_name: tyrosine phenol-lyase

organism: Symbiobacterium sp.

substrate_name: L-tyrosine

enzyme: tyrosine phenol-lyase

substrate: L-tyrosine


substrate_name: S-(o-nitrophenyl)-L-cysteine

substrate: S-(o-nitrophenyl)-L-cysteine


organism: Symbiobacterium thermophilum

substrate_name: S-methyl-L-Cys

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

substrate: S-methyl-L-Cys


organism: Pantoea agglomerans


substrate_name: S-methyl-L-cysteine

substrate: S-methyl-L-cysteine


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


substrate_name: beta-chloro-L-alanine

substrate: beta-chloro-L-alanine


substrate_name: L-Ser

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

substrate: L-Ser


enzyme_display_name: UniProt P31013

organism: Citrobacter freundii

substrate_name: S-Benzyl-L-cysteine

enzyme: UniProt P31013

substrate: S-Benzyl-L-cysteine


substrate_name: L-Tyr

proof_lines:
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=25°C, pH=8
Raw SKiD Env: Temp=30°C, pH=8

substrate: L-Tyr


proof_lines:
Raw SKiD Env: Temp=25°C, pH=8
Raw SKiD Env: Temp=30°C, pH=8


proof_lines:
Raw SKiD Env: Temp=30°C, pH=8
Raw SKiD Env: Temp=25°C, pH=8


enzyme_display_name: UniProt Q8ZNC4

organism: Salmonella enterica subsp. enterica serovar Typhimurium

substrate_name: D-Lysine

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

proof_lines:
Raw SKiD Env: Temp=37°C, pH=7
Raw SKiD Env: Temp=25°C, pH=7

enzyme: UniProt Q8ZNC4

substrate: D-Lysine


substrate_name: D-ornithine

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

substrate: D-ornithine


substrate_name: NH3; Chorismate

substrate: NH3; Chorismate


organism: Catharanthus roseus

substrate_name: L-Glutamine; Chorismate

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

substrate: L-Glutamine; Chorismate


organism: Aspergillus niger

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


substrate_name: chorismate

substrate: chorismate


substrate_name: Gln

substrate: Gln


assay_conditions_summary: pH 7.5; 298.15 K; buffer imidazole or K+-Hepes

column_label: Table 1: Steady-state kinetic and competitive inhibition constants determined for A. niger DMML; 2R-Methylmalate row; 2R-Methylmalate row: kcat 2.64 +/- 0.09 s^-1; Km 2.2 +/- 0.2 mM; kcat/Km 1 × 10^3 M^-1 s^-1.

normalized_value_unit_evidence: Km already mM; kcat already s^-1; kcat/Km 1 × 10^3 M^-1 s^-1 normalized to 1 s^-1 mM^-1.

row_label: 2R-Methylmalate row


column_label: Table 1: Steady-state kinetic and competitive inhibition constants determined for A. niger DMML; 2R-Propyl-3S-methylmalate row; 2R-Propyl-3S-methylmalate row: kcat 0.79 +/- 0.01 s^-1; Km 2.7 +/- 0.1 mM; kcat/Km 3 × 10^2 M^-1 s^-1.

normalized_value_unit_evidence: Km already mM; kcat already s^-1; kcat/Km 3 × 10^2 M^-1 s^-1 normalized to 0.3 s^-1 mM^-1.

row_label: 2R-Propyl-3S-methylmalate row


organism: Chloroflexus aurantiacus

substrate_name: (S)-malyl-CoA (for L-malyl-CoA lyase activity)

assay_conditions_summary: pH 7.1; cofactor CoA

column_label: Table 2 properties table; Apparent Km values (mM); L-malyl-CoA entry 0.061 +/- 0.01.

normalized_value_unit_evidence: Paper reports L-malyl-CoA Km 0.061 mM; exported row is 0.01 mM.

raw_value_unit_evidence: Apparent Km values (mM): 0.061 +/- 0.01 (L-malyl-CoA)

row_label: Apparent Km values row for L-malyl-CoA

table_label: Table 2: Properties of recombinant L-malyl-CoA lyase/beta-methylmalyl-CoA lyase


substrate_name: (2R,3S)-beta-methylmalyl-CoA (for beta-methylmalyl-CoA lyase activity)

column_label: Table 2 properties table; Apparent Km values (mM); beta-methylmalyl-CoA entry 0.089 +/- 0.02.

normalized_value_unit_evidence: Paper reports beta-methylmalyl-CoA Km 0.089 mM.

raw_value_unit_evidence: Apparent Km values (mM): 0.089 +/- 0.02 (beta-methylmalyl-CoA)

row_label: Apparent Km values row for beta-methylmalyl-CoA


substrate_name: acetyl-CoA (for L-malyl-CoA lyase activity)

assay_conditions_summary: cofactor CoA

column_label: Table 2 properties table; Apparent Km values (mM); acetyl-CoA entry 0.36 +/- 0.15.

normalized_value_unit_evidence: Paper reports acetyl-CoA Km 0.36 mM.

raw_value_unit_evidence: Apparent Km values (mM): 0.36 +/- 0.15 (acetyl-CoA)

row_label: Apparent Km values row for acetyl-CoA


substrate_name: propionyl-CoA (for beta-methylmalyl-CoA lyase activity)

column_label: Table 2 properties table; Apparent Km values (mM); propionyl-CoA entry 1.2 +/- 0.6.

normalized_value_unit_evidence: Paper reports propionyl-CoA Km 1.2 mM.

raw_value_unit_evidence: Apparent Km values (mM): 1.2 +/- 0.6 (propionyl-CoA)

row_label: Apparent Km values row for propionyl-CoA


substrate_name: glyoxylate (for beta-methylmalyl-CoA and L-malyl-CoA lyase activities)

column_label: Table 2 properties table; Apparent Km values (mM); glyoxylate entry 2.0 +/- 0.5.

normalized_value_unit_evidence: Paper reports glyoxylate Km 2.0 mM.

raw_value_unit_evidence: Apparent Km values (mM): 2.0 +/- 0.5 (glyoxylate)

row_label: Apparent Km values row for glyoxylate


organism: Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)

substrate_name: glyoxylate (for L-malyl-CoA formation)

column_label: PMC HTML Table 1 Mcl1 column reports 3.1 mM for glyoxylate in the acetyl-CoA + glyoxylate condensation; the same table separately lists 4.1 mM glyoxylate for the propionyl-CoA condition.

raw_value_unit_evidence: Km raw_value=3.1 raw_unit=mM

row_label: 3.1 (glyoxylate), acetyl-CoA + glyoxylate condition

table_label: Table 1. Molecular and catalytic properties of recombinant Mcl1 and Mcl2 from R. sphaeroides

substrate: glyoxylate (for L-malyl-CoA formation)


substrate_name: acetyl-CoA (for L-malyl-CoA formation)

column_label: Primary Results prose adjacent to Table 1 gives an apparent Km of 0.07 mM for acetyl-CoA in the acetyl-CoA + glyoxylate condensation reaction.

raw_value_unit_evidence: Km raw_value=0.07 raw_unit=mM

row_label: acetyl-CoA in acetyl-CoA + glyoxylate condensation to (3S)-malyl-CoA

table_label: Results prose adjacent to Table 1, Heterologous production of Mcl1 from R. sphaeroides

substrate: acetyl-CoA (for L-malyl-CoA formation)


substrate_name: propionyl-CoA (for beta-methylmalyl-CoA formation)

column_label: PMC HTML Table 1 Mcl1 column reports apparent Km values including 0.2 mM for propionyl-CoA in the propionyl-CoA + glyoxylate to beta-methylmalyl-CoA reaction.

raw_value_unit_evidence: Km raw_value=0.2 raw_unit=mM

row_label: 0.2 (propionyl-CoA)


column_label: PMC HTML Table 1 Mcl1 column reports apparent Km values including 0.02 mM for (3S)-malyl-CoA.

raw_value_unit_evidence: Km raw_value=0.02 raw_unit=mM


substrate_name: beta-methylmalyl-CoA

column_label: PMC HTML Table 1 Mcl1 column reports apparent Km values including 0.01 mM for beta-methylmalyl-CoA.

raw_value_unit_evidence: Km raw_value=0.01 raw_unit=mM

row_label: 0.01 (beta-methylmalyl-CoA)

substrate: beta-methylmalyl-CoA


organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

substrate_name: Unknown

substrate: Unknown


organism: Escherichia coli (strain K12)

substrate_name: threo-2-methylisocitrate (a mixture of (2R,3S)- and (2S,3R)-2-methylisocitrate in presence of 2 mM magnesium at pH 7 and 30 degrees Celsius)

assay_conditions_summary: pH 7


substrate_name: threo-D-isocitrate (at pH 6.8 and 37 degrees Celsius)


organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

substrate_name: threo-D(S)-isocitrate (at pH 7.0)

proof_lines: The Vmax with threo-D(S)-isocitrate as substrate is 5-fold higher than with threo-D(S)-2-methylisocitrate as substrate.

substrate: threo-D(S)-isocitrate (at pH 7.0)


proof_lines: kcat is 74 sec(-1) for 2-methylisocitrate lyase with 2-methylisocitrate as substrate.


enzyme_display_name: UniProt Q54764

organism: Synechococcus elongatus

substrate_name: n-Heptanal

smiles: CCCCCCC=O

enzyme: UniProt Q54764

substrate: n-Heptanal


enzyme_display_name: UniProt Q55688

organism: Synechocystis sp. PCC 6803

substrate_name: n-hexadecanal

smiles: CCCCCCCCCCCCCCCC=O

enzyme: UniProt Q55688

substrate: n-hexadecanal


column_label: Table 1: Steady-state kinetic and competitive inhibition constants determined for A. niger DMML; 2R,3S- and 2S,3R-2-methylisocitrate row; 2R,3S- and 2S,3R-2-methylisocitrate row: kcat 0.13 +/- 0.01 s^-1; Km 12 +/- 3 mM; kcat/Km 1 × 10^1 M^-1 s^-1.

normalized_value_unit_evidence: Km already mM; kcat already s^-1; kcat/Km 1 × 10^1 M^-1 s^-1 normalized to 0.01 s^-1 mM^-1.

row_label: 2R,3S- and 2S,3R-2-methylisocitrate row


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature C124A to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row C124A under DMM: kcat=(1.78 +/- 0.05) x 10^-4 s^-1; Km=36 +/- 3 microM; kcat/Km=5 x 10^0 M^-1 s^-1. Table caption gives 50 mM K+-Hepes pH 7.5, 25 C, and 5 mM MgCl2.

normalized_value_unit_evidence: kcat=0.000178 s^-1; Km=0.036 mM; explicit paper kcat/Km=0.005 s^-1 mM^-1 after converting 5 M^-1 s^-1 by dividing by 1000.

row_label: C124A; DMM

table_label: Table 3: Steady-state kinetic constants determined for the A. niger DMML site-directed mutants


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature C124S to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row C124S under DMM: kcat=(1.21 +/- 0.05) x 10^-4 s^-1; Km=3600 +/- 300 microM; kcat/Km=3 x 10^-2 M^-1 s^-1. Table caption gives 50 mM K+-Hepes pH 7.5, 25 C, and 5 mM MgCl2.

normalized_value_unit_evidence: kcat=0.000121 s^-1; Km=3.6 mM; explicit paper kcat/Km=0.00003 s^-1 mM^-1 after converting 3 x 10^-2 M^-1 s^-1 by dividing by 1000.

row_label: C124S; DMM


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature D59A to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row D59A under DMM: kcat=(4.27 +/- 0.09) x 10^-4 s^-1; Km=7400 +/- 400 microM; kcat/Km=6 x 10^-2 M^-1 s^-1. Table caption gives 50 mM K+-Hepes pH 7.5, 25 C, and 5 mM MgCl2.

normalized_value_unit_evidence: kcat=0.000427 s^-1; Km=7.4 mM; explicit paper kcat/Km=0.00006 s^-1 mM^-1 after converting 6 x 10^-2 M^-1 s^-1 by dividing by 1000.

row_label: D59A; DMM


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature D59S to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row D59S under DMM: kcat=(1.4 +/- 0.1) x 10^-4 s^-1; Km=6000 +/- 1000 microM; kcat/Km=2 x 10^-2 M^-1 s^-1. Table caption gives 50 mM K+-Hepes pH 7.5, 25 C, and 5 mM MgCl2.

normalized_value_unit_evidence: kcat=0.00014 s^-1; Km=6.0 mM; explicit paper kcat/Km=0.00002 s^-1 mM^-1 after converting 2 x 10^-2 M^-1 s^-1 by dividing by 1000.

row_label: D59S; DMM


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature P240S to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row P240S footnote b under DMM: kcat=11.7 +/- 0.6 s^-1; Km=5900 +/- 700 microM; kcat/Km=2 x 10^3 M^-1 s^-1. Footnote b explains the soluble His6-tagged construct and matched His6-WT control.

normalized_value_unit_evidence: kcat=11.7 s^-1; Km=5.9 mM; explicit paper kcat/Km=2.0 s^-1 mM^-1 after converting 2 x 10^3 M^-1 s^-1 by dividing by 1000.

row_label: P240S footnote b; DMM


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature P240T to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row P240T under DMM: kcat=2.8 +/- 0.2 s^-1; Km=4100 +/- 800 microM; kcat/Km=7 x 10^2 M^-1 s^-1. Table caption gives 50 mM K+-Hepes pH 7.5, 25 C, and 5 mM MgCl2.

normalized_value_unit_evidence: kcat=2.8 s^-1; Km=4.1 mM; explicit paper kcat/Km=0.7 s^-1 mM^-1 after converting 7 x 10^2 M^-1 s^-1 by dividing by 1000.

row_label: P240T; DMM


column_label: Table 1: Steady-state kinetic and competitive inhibition constants determined for A. niger DMML; 2R,3S-Dimethylmalate row; 2R,3S-Dimethylmalate row: kcat 19.2 +/- 0.5 s^-1; Km 0.22 +/- 0.02 mM; kcat/Km 9 × 10^4 M^-1 s^-1.

normalized_value_unit_evidence: Km already mM; kcat already s^-1; kcat/Km 9 × 10^4 M^-1 s^-1 normalized to 90 s^-1 mM^-1.

row_label: 2R,3S-Dimethylmalate row


column_label: Table 1: Steady-state kinetic and competitive inhibition constants determined for A. niger DMML; 2R-Ethyl-3S-methylmalate row; 2R-Ethyl-3S-methylmalate row: kcat 63 +/- 2 s^-1; Km 1.17 +/- 0.09 mM; kcat/Km 5 × 10^4 M^-1 s^-1.

normalized_value_unit_evidence: Km already mM; kcat already s^-1; kcat/Km 5 × 10^4 M^-1 s^-1 normalized to 50 s^-1 mM^-1.

row_label: 2R-Ethyl-3S-methylmalate row


organism: Escherichia coli

substrate_name: L-Tyr

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


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


substrate_name: L-Asp

substrate: L-Asp


substrate_name: L-Glu

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

substrate: L-Glu


enzyme_display_name: tryptophanase

organism: Porphyromonas gingivalis

substrate_name: L-Trp

assay_conditions_summary: pH 7.5; 310.15 K; buffer 200 mM sodium phosphate

proof_lines: purified recombinant tryptophanase in 200 mM sodium phosphate buffer (pH 7.5), at 37°C

proof_lines: purified recombinant tryptophanase in 200 mM potassium phosphate buffer (pH 7.5), at 37°C

enzyme: tryptophanase

substrate: L-Trp


substrate_name: S-methyl-L-cysteine

assay_conditions_summary: pH 7.5; 310.15 K; buffer 200 mM potassium phosphate

substrate: S-methyl-L-cysteine


substrate_name: S-ethyl-L-cysteine

substrate: S-ethyl-L-cysteine


enzyme_display_name: 3-hydroxybenzoate synthase

organism: Lentzea aerocolonigenes

substrate_name: chorismate

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

enzyme: 3-hydroxybenzoate synthase


organism: Prevotella intermedia


substrate_name: L-tryptophan

substrate: L-tryptophan


enzyme_display_name: 4-hydroxy-2-oxohexanoate aldolase

organism: Burkholderia xenovorans

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

enzyme: 4-hydroxy-2-oxohexanoate aldolase


organism: Aeromonas phenologenes

substrate: L-Tyr


organism: Streptomyces conglobatus


enzyme_display_name: UniProt A0A0H2UN41

organism: Streptococcus pneumoniae

substrate_name: D-ribulose 5-phosphate

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

enzyme: UniProt A0A0H2UN41

substrate: D-ribulose 5-phosphate


organism: Xylella fastidiosa

substrate: chorismate


enzyme_display_name: (4S)-4-hydroxy-2-oxoglutarate aldolase

organism: Azotobacter vinelandii

enzyme: (4S)-4-hydroxy-2-oxoglutarate aldolase


organism: Paraburkholderia xenovorans

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L87W/Y290F to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8

proof_lines: L87W/Y290F variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: L87W/Y290F variant of BphI, app. Km-value, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: L87W/Y290F variant of BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C


substrate_name: oxaloacetate

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature L87N to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8; 298.15 K; buffer 100 mM HEPES

column_label: Table 2: Steady-State Kinetic Parameters of BphI and Its Variants for Oxaloacetate Decarboxylation (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87N'; column block 'oxaloacetate decarboxylation'; column 'Km,app (mM)' = 0.21; column 'kcat (10^-1 s^-1)' = 0.5; column 'kcat/Km,app (M^-1 s^-1)' = 254.

normalized_value_unit_evidence: Km: printed Table 2 cell 0.21 mM; already in mM, so the canonical value is 0.21 mM; the catalog value is 0.21 mM. kcat: printed Table 2 cell 0.5 x 10^-1 s^-1 under the column head kcat (10^-1 s^-1); already in s^-1 after the printed power of ten is applied, giving 0.05 s^(-1); the catalog value is 0.05 s^(-1). kcat/Km: printed Table 2 cell 254 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 254.0 / 1000 = 0.254 s^-1 mM^-1.

raw_value_unit_evidence: Table 2, enzyme row 'L87N', column block 'oxaloacetate decarboxylation': Km,app = 0.21 mM; kcat = 0.5 (column head kcat (10^-1 s^-1)); printed kcat/Km,app = 254 M^-1 s^-1.

substrate: oxaloacetate


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature L87N/Y290F to reconstruct the assayed variant sequence.

column_label: Table 2: Steady-State Kinetic Parameters of BphI and Its Variants for Oxaloacetate Decarboxylation (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87N;Y290F'; column block 'oxaloacetate decarboxylation'; column 'Km,app (mM)' = 0.84; column 'kcat (10^-1 s^-1)' = 0.8; column 'kcat/Km,app (M^-1 s^-1)' = 98.

normalized_value_unit_evidence: Km: printed Table 2 cell 0.84 mM; already in mM, so the canonical value is 0.84 mM; the catalog value is 0.84 mM. kcat: printed Table 2 cell 0.8 x 10^-1 s^-1 under the column head kcat (10^-1 s^-1); already in s^-1 after the printed power of ten is applied, giving 0.08 s^(-1); the catalog value is 0.08 s^(-1). kcat/Km: printed Table 2 cell 98 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 98.0 / 1000 = 0.098 s^-1 mM^-1.

raw_value_unit_evidence: Table 2, enzyme row 'L87N;Y290F', column block 'oxaloacetate decarboxylation': Km,app = 0.84 mM; kcat = 0.8 (column head kcat (10^-1 s^-1)); printed kcat/Km,app = 98 M^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L87N/Y290F to reconstruct the assayed variant sequence.

proof_lines: L87N/Y290F variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: L87N/Y290F variant of BphI, app. Km-value, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: L87N/Y290F variant of BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C


substrate_name: propionaldehyde

smiles: CCC=O

proof_lines: L87N/Y290F variant of BphI, app. kcat-value, steady-state kinetic parameter, pH 8.0, 25°C

substrate: propionaldehyde


substrate_name: pyruvate

substrate: pyruvate


proof_lines: L87W/Y290F variant of BphI, app. kcat-value, steady-state kinetic parameter, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature L87W/Y290F to reconstruct the assayed variant sequence.

column_label: Table 5: Steady-State Kinetic Parameters for the Utilization of Pyruvate in the Aldol Addition Reaction (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87W;Y290F'; column block 'pyruvate'; column 'Km,app (mM)' = 38.2; column 'kcat,app (s^-1)' = 0.16; column '(kcat/Km)app (M^-1 s^-1)' = 4.3.

normalized_value_unit_evidence: Km: printed Table 5 cell 38.2 mM; already in mM, so the canonical value is 38.2 mM; the catalog value is 38.2 mM. kcat: printed Table 5 cell 0.16 s^-1 under the column head kcat,app (s^-1); already in s^-1 after the printed power of ten is applied, giving 0.16 s^(-1); the catalog value is 0.16 s^(-1). kcat/Km: printed Table 5 cell 4.3 M^-1 s^-1 under the column head (kcat/Km)app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 4.3 / 1000 = 0.0043 s^-1 mM^-1.

raw_value_unit_evidence: Table 5, enzyme row 'L87W;Y290F', column block 'pyruvate': Km,app = 38.2 mM; kcat,app = 0.16 s^-1; printed (kcat/Km)app = 4.3 M^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature Y290F to reconstruct the assayed variant sequence.

proof_lines: Y290F variant of BphI, app. kcat-value, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: Y290F variant of BphI, app. Km-value, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: Y290F variant of BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C


substrate_name: Butyraldehyde

smiles: CCCC=O

substrate: Butyraldehyde


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature Y290F to reconstruct the assayed variant sequence.

column_label: Table 5: Steady-State Kinetic Parameters for the Utilization of Pyruvate in the Aldol Addition Reaction (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'Y290F'; column block 'pyruvate'; column 'Km,app (mM)' = 20.0; column 'kcat,app (s^-1)' = 0.19; column '(kcat/Km)app (M^-1 s^-1)' = 8.4.

normalized_value_unit_evidence: Km: printed Table 5 cell 20.0 mM; already in mM, so the canonical value is 20.0 mM; the catalog value is 20.0 mM. kcat: printed Table 5 cell 0.19 s^-1 under the column head kcat,app (s^-1); already in s^-1 after the printed power of ten is applied, giving 0.19 s^(-1); the catalog value is 0.19 s^(-1). kcat/Km: printed Table 5 cell 8.4 M^-1 s^-1 under the column head (kcat/Km)app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 8.4 / 1000 = 0.0084 s^-1 mM^-1.

raw_value_unit_evidence: Table 5, enzyme row 'Y290F', column block 'pyruvate': Km,app = 20.0 mM; kcat,app = 0.19 s^-1; printed (kcat/Km)app = 8.4 M^-1 s^-1.


substrate_name: acetaldehyde

smiles: CC=O

substrate: acetaldehyde


column_label: Table 2: Steady-State Kinetic Parameters of BphI and Its Variants for Oxaloacetate Decarboxylation (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'Y290F'; column block 'oxaloacetate decarboxylation'; column 'Km,app (mM)' = 0.92; column 'kcat (10^-1 s^-1)' = 2.7; column 'kcat/Km,app (M^-1 s^-1)' = 530.

normalized_value_unit_evidence: Km: printed Table 2 cell 0.92 mM; already in mM, so the canonical value is 0.92 mM; the catalog value is 0.92 mM. kcat: printed Table 2 cell 2.7 x 10^-1 s^-1 under the column head kcat (10^-1 s^-1); already in s^-1 after the printed power of ten is applied, giving 0.27 s^(-1); the catalog value is 0.27 s^(-1). kcat/Km: printed Table 2 cell 530 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 530.0 / 1000 = 0.53 s^-1 mM^-1.

raw_value_unit_evidence: Table 2, enzyme row 'Y290F', column block 'oxaloacetate decarboxylation': Km,app = 0.92 mM; kcat = 2.7 (column head kcat (10^-1 s^-1)); printed kcat/Km,app = 530 M^-1 s^-1.


column_label: Table 6: Steady-State Kinetic Parameters for the Utilization of Various Aldehydes of the BphI Wild Type and Variants in the Aldol Addition Reaction (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87N;Y290F'; column block 'acetaldehyde, two carbons'; column 'Km,app (mM)' = 70.7; column 'kcat,app (s^-1)' = 0.30; column 'kcat/Km,app (M^-1 s^-1)' = 4.3.

normalized_value_unit_evidence: Km: printed Table 6 cell 70.7 mM; already in mM, so the canonical value is 70.7 mM; the catalog value is 70.7 mM. kcat: printed Table 6 cell 0.30 s^-1 under the column head kcat,app (s^-1); already in s^-1 after the printed power of ten is applied, giving 0.3 s^(-1); the catalog value is 0.3 s^(-1). kcat/Km: printed Table 6 cell 4.3 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 4.3 / 1000 = 0.0043 s^-1 mM^-1.

raw_value_unit_evidence: Table 6, enzyme row 'L87N;Y290F', column block 'acetaldehyde, two carbons': Km,app = 70.7 mM; kcat,app = 0.30 s^-1; printed kcat/Km,app = 4.3 M^-1 s^-1.


column_label: Table 2: Steady-State Kinetic Parameters of BphI and Its Variants for Oxaloacetate Decarboxylation (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87W;Y290F'; column block 'oxaloacetate decarboxylation'; column 'Km,app (mM)' = 6.2; column 'kcat (10^-1 s^-1)' = 4; column 'kcat/Km,app (M^-1 s^-1)' = 64.

normalized_value_unit_evidence: Km: printed Table 2 cell 6.2 mM; already in mM, so the canonical value is 6.2 mM; the catalog value is 6.2 mM. kcat: printed Table 2 cell 4 x 10^-1 s^-1 under the column head kcat (10^-1 s^-1); already in s^-1 after the printed power of ten is applied, giving 0.4 s^(-1); the catalog value is 0.4 s^(-1). kcat/Km: printed Table 2 cell 64 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 64.0 / 1000 = 0.064 s^-1 mM^-1.

raw_value_unit_evidence: Table 2, enzyme row 'L87W;Y290F', column block 'oxaloacetate decarboxylation': Km,app = 6.2 mM; kcat = 4 (column head kcat (10^-1 s^-1)); printed kcat/Km,app = 64 M^-1 s^-1.


column_label: Table 6: Steady-State Kinetic Parameters for the Utilization of Various Aldehydes of the BphI Wild Type and Variants in the Aldol Addition Reaction (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87W;Y290F'; column block 'acetaldehyde, two carbons'; column 'Km,app (mM)' = 86.3; column 'kcat,app (s^-1)' = 0.59; column 'kcat/Km,app (M^-1 s^-1)' = 6.9.

normalized_value_unit_evidence: Km: printed Table 6 cell 86.3 mM; already in mM, so the canonical value is 86.3 mM; the catalog value is 86.3 mM. kcat: printed Table 6 cell 0.59 s^-1 under the column head kcat,app (s^-1); already in s^-1 after the printed power of ten is applied, giving 0.59 s^(-1); the catalog value is 0.59 s^(-1). kcat/Km: printed Table 6 cell 6.9 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 6.9 / 1000 = 0.0069 s^-1 mM^-1.

raw_value_unit_evidence: Table 6, enzyme row 'L87W;Y290F', column block 'acetaldehyde, two carbons': Km,app = 86.3 mM; kcat,app = 0.59 s^-1; printed kcat/Km,app = 6.9 M^-1 s^-1.


column_label: Table 2: Steady-State Kinetic Parameters of BphI and Its Variants for Oxaloacetate Decarboxylation (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'wild-type BphI'; column block 'oxaloacetate decarboxylation'; column 'Km,app (mM)' = 7.4; column 'kcat (10^-1 s^-1)' = 163; column 'kcat/Km,app (M^-1 s^-1)' = 2200.

normalized_value_unit_evidence: Km: printed Table 2 cell 7.4 mM; already in mM, so the canonical value is 7.4 mM; the catalog value is 7.4 mM. kcat: printed Table 2 cell 163 x 10^-1 s^-1 under the column head kcat (10^-1 s^-1); already in s^-1 after the printed power of ten is applied, giving 16.3 s^(-1); the catalog value is 16.3 s^(-1). kcat/Km: printed Table 2 cell 2200 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 2200.0 / 1000 = 2.2 s^-1 mM^-1.

raw_value_unit_evidence: Table 2, enzyme row 'wild-type BphI', column block 'oxaloacetate decarboxylation': Km,app = 7.4 mM; kcat = 163 (column head kcat (10^-1 s^-1)); printed kcat/Km,app = 2200 M^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature H20S to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8; 298.15 K; buffer 100 mM HEPES; cofactor NADH

column_label: Table 5 (Biochemistry 2011, 50, 3559-3569): steady-state kinetic parameters for the aldol cleavage of (4S)-HOPA; the transcribed cells come from the 'Km (uM)', 'kcat (x 10^-2 s^-1)' and 'kcat/Km (x 10^2 M^-1 s^-1)' of construct 'H20S' at column '(4S)-HOPA': Km = 228 uM, kcat = 8.9 x 10^-2 s^-1, kcat/Km = 3.4 x 10^2 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 5 cell 228 uM; 228 / 1000 = 0.228 mM; the exported value is 0.228 mM. kcat: printed Table 5 cell 8.9 under the column head kcat (x 10^-2 s^-1); 8.9 x 10^-2 = 0.08900000000000001 s^-1; the exported value is 0.089 s^(-1). kcat/Km: printed Table 5 cell 3.4 x 10^2 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 340.0 / 1000 = 0.34 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 5, construct 'H20S', (4S)-HOPA: Km = 228 uM; kcat = 8.9 x 10^-2 s^-1; printed kcat/Km = 3.4 x 10^2 M^-1 s^-1.

row_label: Table 5, row 'H20S', (4S)-HOPA block


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature H20A to reconstruct the assayed variant sequence.

proof_lines: H20A variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C


proof_lines: Y290F variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature Y290S to reconstruct the assayed variant sequence.

proof_lines: Y290S variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature L87A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8; 298.15 K; buffer varying concentrations of aldehydes in 100 mM HEPES

column_label: Table 2 (Biochemistry 2011, 50, 3559-3569): aldehyde specificities of BphI in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'L87A' at column 'butryaldehyde (four carbons)': Km = 323 mM, kcat = 0.260 s^-1, kcat/Km = 0.790 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 2 cell 323 mM; already in mM, so no unit conversion applies; the exported value is 323.0 mM. kcat: printed Table 2 cell 0.260 s^-1; already in s^-1, so no unit conversion applies; the exported value is 0.26 s^(-1). kcat/Km: printed Table 2 cell 0.790 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 0.79 / 1000 = 0.00079 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 2, construct 'L87A', butryaldehyde (four carbons): Km = 323 mM; kcat = 0.260 s^-1; printed kcat/Km = 0.790 M^-1 s^-1.

row_label: Table 2, kinetic-parameter cells of construct 'L87A', column 'butryaldehyde (four carbons)'


column_label: Table 2 (Biochemistry 2011, 50, 3559-3569): aldehyde specificities of BphI in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'L87A' at column 'propionaldehyde (three carbons)': Km = 16.8 mM, kcat = 0.290 s^-1, kcat/Km = 17.5 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 2 cell 16.8 mM; already in mM, so no unit conversion applies; the exported value is 16.8 mM. kcat: printed Table 2 cell 0.290 s^-1; already in s^-1, so no unit conversion applies; the exported value is 0.29 s^(-1). kcat/Km: printed Table 2 cell 17.5 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 17.5 / 1000 = 0.0175 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 2, construct 'L87A', propionaldehyde (three carbons): Km = 16.8 mM; kcat = 0.290 s^-1; printed kcat/Km = 17.5 M^-1 s^-1.

row_label: Table 2, kinetic-parameter cells of construct 'L87A', column 'propionaldehyde (three carbons)'


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L87A/L89A to reconstruct the assayed variant sequence.

proof_lines: L87A/L89A variant of BphI, app. kcat-value, pH 8.0, 25°C

proof_lines: L87A/L89A variant of BphI, app. Km-value, pH 8.0, 25°C

proof_lines: L87A/L89A variant of BphI, app. kcat/Km-value, pH 8.0, 25°C


assay_conditions_summary: pH 8; 298.15 K; buffer varying concentrations of pyruvate in 100 mM HEPES

column_label: Table 1 (Biochemistry 2011, 50, 3559-3569): steady-state kinetic parameters for the utilization of pyruvate in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'L87A' at column 'varied substrate pyruvate': Km = 20.2 mM, kcat = 0.32 s^-1, kcat/Km = 15.9 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 1 cell 20.2 mM; already in mM, so no unit conversion applies; the exported value is 20.2 mM. kcat: printed Table 1 cell 0.32 s^-1; already in s^-1, so no unit conversion applies; the exported value is 0.32 s^(-1). kcat/Km: printed Table 1 cell 15.9 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 15.9 / 1000 = 0.0159 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 1, construct 'L87A', varied substrate pyruvate: Km = 20.2 mM; kcat = 0.32 s^-1; printed kcat/Km = 15.9 M^-1 s^-1.

row_label: Table 1, kinetic-parameter cells of construct 'L87A', column 'varied substrate pyruvate'


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature L89A to reconstruct the assayed variant sequence.

column_label: Table 2 (Biochemistry 2011, 50, 3559-3569): aldehyde specificities of BphI in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'L89A' at column 'propionaldehyde (three carbons)': Km = 40.2 mM, kcat = 0.630 s^-1, kcat/Km = 15.6 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 2 cell 40.2 mM; already in mM, so no unit conversion applies; the exported value is 40.2 mM. kcat: printed Table 2 cell 0.630 s^-1; already in s^-1, so no unit conversion applies; the exported value is 0.63 s^(-1). kcat/Km: printed Table 2 cell 15.6 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 15.6 / 1000 = 0.0156 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 2, construct 'L89A', propionaldehyde (three carbons): Km = 40.2 mM; kcat = 0.630 s^-1; printed kcat/Km = 15.6 M^-1 s^-1.

row_label: Table 2, kinetic-parameter cells of construct 'L89A', column 'propionaldehyde (three carbons)'


column_label: Table 1 (Biochemistry 2011, 50, 3559-3569): steady-state kinetic parameters for the utilization of pyruvate in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'L89A' at column 'varied substrate pyruvate': Km = 11.0 mM, kcat = 0.64 s^-1, kcat/Km = 58.7 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 1 cell 11.0 mM; already in mM, so no unit conversion applies; the exported value is 11.0 mM. kcat: printed Table 1 cell 0.64 s^-1; already in s^-1, so no unit conversion applies; the exported value is 0.64 s^(-1). kcat/Km: printed Table 1 cell 58.7 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 58.7 / 1000 = 0.0587 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 1, construct 'L89A', varied substrate pyruvate: Km = 11.0 mM; kcat = 0.64 s^-1; printed kcat/Km = 58.7 M^-1 s^-1.

row_label: Table 1, kinetic-parameter cells of construct 'L89A', column 'varied substrate pyruvate'


column_label: Table 2 (Biochemistry 2011, 50, 3559-3569): aldehyde specificities of BphI in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'L89A' at column 'butryaldehyde (four carbons)': Km = 49.2 mM, kcat = 0.640 s^-1, kcat/Km = 12.9 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 2 cell 49.2 mM; already in mM, so no unit conversion applies; the exported value is 49.2 mM. kcat: printed Table 2 cell 0.640 s^-1; already in s^-1, so no unit conversion applies; the exported value is 0.64 s^(-1). kcat/Km: printed Table 2 cell 12.9 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 12.9 / 1000 = 0.0129 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 2, construct 'L89A', butryaldehyde (four carbons): Km = 49.2 mM; kcat = 0.640 s^-1; printed kcat/Km = 12.9 M^-1 s^-1.

row_label: Table 2, kinetic-parameter cells of construct 'L89A', column 'butryaldehyde (four carbons)'


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

column_label: Table 2 (Biochemistry 2011, 50, 3559-3569): aldehyde specificities of BphI in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'WT' at column 'acetaldehyde (two carbons)': Km = 64.2 mM, kcat = 0.860 s^-1, kcat/Km = 13.4 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 2 cell 64.2 mM; already in mM, so no unit conversion applies; the exported value is 64.2 mM. kcat: printed Table 2 cell 0.860 s^-1; already in s^-1, so no unit conversion applies; the exported value is 0.86 s^(-1). kcat/Km: printed Table 2 cell 13.4 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 13.4 / 1000 = 0.0134 s^-1 mM^-1, the printed cell rounded to the paper's own precision; the exported 0.013395638629283488 s^(-1)*mM^(-1) is the exact quotient of the two printed component cells and rounds to that same printed cell, so the exported catalytic efficiency stands.

raw_value_unit_evidence: Table 2, construct 'WT', acetaldehyde (two carbons): Km = 64.2 mM; kcat = 0.860 s^-1; printed kcat/Km = 13.4 M^-1 s^-1.

row_label: Table 2, kinetic-parameter cells of construct 'WT', column 'acetaldehyde (two carbons)'


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L89A to reconstruct the assayed variant sequence.

proof_lines: L89A variant of BphI, app. kcat-value, pH 8.0, 25°C

proof_lines: L89A variant of BphI, app. Km-value, pH 8.0, 25°C

proof_lines: L89A variant of BphI, app. kcat/Km-value, pH 8.0, 25°C


column_label: Table 1 (Biochemistry 2011, 50, 3559-3569): steady-state kinetic parameters for the utilization of pyruvate in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'WT' at column 'varied substrate pyruvate': Km = 13.0 mM, kcat = 1.20 s^-1, kcat/Km = 91.5 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 1 cell 13.0 mM; already in mM, so no unit conversion applies; the exported value is 13.0 mM. kcat: printed Table 1 cell 1.20 s^-1; already in s^-1, so no unit conversion applies; the exported value is 1.2 s^(-1). kcat/Km: printed Table 1 cell 91.5 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 91.5 / 1000 = 0.0915 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 1, construct 'WT', varied substrate pyruvate: Km = 13.0 mM; kcat = 1.20 s^-1; printed kcat/Km = 91.5 M^-1 s^-1.

row_label: Table 1, kinetic-parameter cells of construct 'WT', column 'varied substrate pyruvate'


column_label: Table 2 (Biochemistry 2011, 50, 3559-3569): aldehyde specificities of BphI in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'WT' at column 'propionaldehyde (three carbons)': Km = 136 mM, kcat = 1.79 s^-1, kcat/Km = 13.2 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 2 cell 136 mM; already in mM, so no unit conversion applies; the exported value is 136.0 mM. kcat: printed Table 2 cell 1.79 s^-1; already in s^-1, so no unit conversion applies; the exported value is 1.79 s^(-1). kcat/Km: printed Table 2 cell 13.2 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 13.2 / 1000 = 0.0132 s^-1 mM^-1, the printed cell rounded to the paper's own precision; the exported 0.013161764705882354 s^(-1)*mM^(-1) is the exact quotient of the two printed component cells and rounds to that same printed cell, so the exported catalytic efficiency stands.

raw_value_unit_evidence: Table 2, construct 'WT', propionaldehyde (three carbons): Km = 136 mM; kcat = 1.79 s^-1; printed kcat/Km = 13.2 M^-1 s^-1.

row_label: Table 2, kinetic-parameter cells of construct 'WT', column 'propionaldehyde (three carbons)'


organism: Citrobacter intermedius

substrate_name: Phe

substrate: Phe


substrate_name: Ser

proof_lines: transamination beta-elimination

substrate: Ser


substrate_name: Ala

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

substrate: Ala


substrate_name: L-m-Tyr

substrate: L-m-Tyr


substrate_name: Tyr

proof_lines: at 30°C, pH not specified in the publication

substrate: Tyr


substrate_name: KDPG

proof_lines: kcat is 83 sec(-1) with KDPG as substrate (PubMed:17962400). kcat is 80 sec(-1) with KDPG as substrate (PubMed:17981470). kcat is 11 sec(-1) with KHPB as substrate (PubMed:17962400). kcat is 0.0063 sec(-1) with KDPGal as substrate (PubMed:1

substrate: KDPG


substrate_name: KDG

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

substrate: KDG


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


organism: Streptomyces hygroscopicus

assay_conditions_summary: pH 7; buffer deuterated potassium phosphate

proof_lines: in deuterated potassium phosphate buffer (20 mM, pH 7.0), at 20°C

proof_lines: kcat is 22.4 sec(-1) for 3-hydroxybenzoate synthase activity with chorismate as substrate.

source_databases_merged: brenda uniprot


organism: Escherichia coli (strain K12)


enzyme_display_name: (R)-citramalyl-CoA lyase

organism: Chloroflexus aurantiacus

assay_conditions_summary: pH 7; cofactor CoA

column_label: PMID 17259315 Table 2, Molecular and catalytic properties of recombinant R-citramalyl-CoA lyase (Ccl); rows Apparent Km value and Catalytic no. for alpha2; values 70 +/- 20 uM for R-citramalyl-CoA and 1.7 s^-1. The strict kcat/Km value is the same-row central-value ratio 1.7/0.07.

normalized_value_unit_evidence: kcat normalized_value=1.7 normalized_unit=s^-1; km normalized_value=0.07 normalized_unit=mM; kcat_over_km normalized_value=24.28571428571428 normalized_unit=s^-1*mM^-1.

raw_value_unit_evidence: Table 2: Apparent Km value 70 +/- 20 uM (R-citramalyl-CoA); Catalytic no. for alpha2 1.7 s^-1.

row_label: R-citramalyl-CoA / purified recombinant Ccl

table_label: Table 2. Molecular and catalytic properties of recombinant R-citramalyl-CoA lyase (Ccl)

enzyme: (R)-citramalyl-CoA lyase


organism: Pantoea agglomerans

substrate_name: L-tyrosine

substrate: L-tyrosine


organism: Symbiobacterium thermophilum

substrate_name: L-Tyr

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

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


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature G323L to reconstruct the assayed variant sequence.

proof_lines: G323L mutant, steady state, absence of BphJ cofactors, pH 8.0, 25°C

proof_lines: G323L mutant, steady state, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature G322L to reconstruct the assayed variant sequence.

proof_lines: G322L mutant, steady state, absence of BphJ cofactors, pH 8.0, 25°C

proof_lines: G322L mutant, steady state, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature G323A to reconstruct the assayed variant sequence.

proof_lines: G323A mutant, steady state, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature G322F to reconstruct the assayed variant sequence.

proof_lines: G322F mutant, steady state, absence of BphJ cofactors, pH 8.0, 25°C

proof_lines: G322F mutant, steady state, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature G323F to reconstruct the assayed variant sequence.

proof_lines: G323F mutant, steady state, absence of BphJ cofactors, pH 8.0, 25°C

proof_lines: G323F mutant, steady state, pH 8.0, 25°C


proof_lines: wild-type protein, steady state, absence of BphJ cofactors, pH 8.0, 25°C

proof_lines: wild-type BphI, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: wild-type protein, steady state, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature G322A to reconstruct the assayed variant sequence.

proof_lines: G322A mutant, steady state, pH 8.0, 25°C


column_label: Table 1, enzyme row 'WT'; under the substrate heading HOHA: column 'Km (uM)' = 117; column 'kcat (s-1)' = 3.9; Table 1 carries no kcat/Km column.

normalized_value_unit_evidence: kcat: printed Table 1 cell 3.9 s-1; already in s^-1, no conversion applies (this paper prints no min^-1 kinetic cell); the paper value is 3.9 s^(-1). Km: printed Table 1 cell 117 uM; 117 / 1000 = 0.117 mM; the paper value is 0.117 mM. kcat/Km: Table 1 has no kcat/Km column, so the paper value 33.33333333333333 s^(-1)*mM^(-1) is not a printed cell; it is the quotient 3.9 / 0.117 of this row's own two printed cells, typed derived_same_measurement.

raw_value_unit_evidence: Table 1, enzyme row 'WT', HOHA substrate block: kcat = 3.9 s-1; Km = 117 uM; Table 1 prints no kcat/Km cell for this row.

table_label: Table 1: Steady-State Kinetic Constants of BphI and Variants for the Aldol Cleavage of HOPA and HOHA (Biochemistry 2011, 50(39):8407-8416)


organism: Thermus thermophilus

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

assay_conditions_summary: pH 8; cofactor NADH

proof_lines: TTHB246-TTHB247 complex, 1 mM MnCl2, pH 8.0, 25°C

proof_lines: single TTHB246, 1 mM MnCl2, pH 8.0, 25°C

proof_lines: BphI-TTHB247 complex, 1 mM MnCl2, pH 8.0, 25°C

source_databases_merged: sabio_rk brenda uniprot


proof_lines:
with Ca2+ chloride salt, pH 8.0, 25°C
with Mg2+ chloride salt, pH 8.0, 25°C
with Mn2+ chloride salt, pH 8.0, 25°C


organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

proof_lines: kcat is 0.38 sec(-1) with 4-hydroxy-2-oxohexanoate as substrate. kcat is 0.41 sec(-1) with 4-hydroxy-2-oxopentanoate as substrate.


organism: Citrobacter freundii

substrate_name: S-ethyl-L-Cys

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

substrate: S-ethyl-L-Cys


substrate_name: p-L-Tyr

substrate: p-L-Tyr


enzyme_display_name: 3-hydroxy-D-aspartate aldolase

organism: Paracoccus denitrificans

substrate_name: Unknown

enzyme: 3-hydroxy-D-aspartate aldolase

substrate: Unknown


substrate_name: KHPB

proof_lines: kcat is 83 sec(-1) with KDPG as substrate (PubMed:17962400). kcat is 80 sec(-1) with KDPG as substrate (PubMed:17981470). kcat is 11 sec(-1) with KHPB as substrate (PubMed:17962400). kcat is 0.0063 sec(-1) with KDPGal as substrate (PubMed:1

substrate: KHPB


assay_conditions_summary: pH 8; 298.15 K; cofactor NADH

proof_lines: kcat(app)/Km(app) with pyruvate as carbonyl donor, pH 8.0 and 25°C

proof_lines: The catalytic efficiency is similar when using 4-hydroxy-2-oxopentanoate or 4-hydroxy-2-oxohexanoate as substrate, but is 10-fold lower with 4-hydroxy-2-oxoheptanoate. It is also 25-fold higher when NADH is present than the value obtained w


substrate_name: Isobutyraldehyde

smiles: CC(C)C=O

substrate: Isobutyraldehyde


proof_lines: L87A/L89A variant of BphI, app. kcat/Km-value, pH 8.0, 25°C


substrate_name: hexaldehyde

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L87A to reconstruct the assayed variant sequence.

smiles: CCCCCC=O

proof_lines: L87A variant of BphI, app. kcat/Km-value, pH 8.0, 25°C

substrate: hexaldehyde


substrate_name: pentaldehyde

substrate: pentaldehyde


proof_lines: L87A/L89A variant of BphI, app. kcat-value, pH 8.0, 25°C

proof_lines: L87A/L89A variant of BphI, app. Km-value, pH 8.0, 25°C


substrate_name: propionaldehyde

substrate: propionaldehyde


proof_lines: wild-type BphI, app. kcat/Km-value, pH 8.0, 25°C

proof_lines: wild-type BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R16K with inferred residue-numbering offset +7 to reconstruct the assayed variant sequence.

proof_lines: R16K variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C


proof_lines: L89A variant of BphI, app. kcat-value, pH 8.0, 25°C

proof_lines: L89A variant of BphI, app. Km-value, pH 8.0, 25°C

proof_lines: L89A variant of BphI, app. kcat/Km-value, pH 8.0, 25°C


substrate_name: acetaldehyde

substrate: acetaldehyde


substrate_name: Butyraldehyde

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L87N/Y290F to reconstruct the assayed variant sequence.

proof_lines: L87N/Y290F variant of BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C

substrate: Butyraldehyde


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature Y290F to reconstruct the assayed variant sequence.

proof_lines: Y290F variant of BphI, app. kcat-value, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: Y290F variant of BphI, app. Km-value, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: Y290F variant of BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C


substrate_name: oxaloacetate

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L87W to reconstruct the assayed variant sequence.

proof_lines: L87W variant of BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C

substrate: oxaloacetate


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L87W/Y290F to reconstruct the assayed variant sequence.

proof_lines: L87W/Y290F variant of BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C


organism: Proteus vulgaris

substrate_name: L-Tryptophan; H2O

substrate: L-Tryptophan; H2O


substrate_name: L-Tryptophan

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y72F to reconstruct the assayed variant sequence.

substrate: L-Tryptophan


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature S51A 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.


substrate_name: beta-chloro-L-alanine

substrate: beta-chloro-L-alanine


substrate_name: S-Benzyl-L-cysteine

substrate: S-Benzyl-L-cysteine


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P28796 and applied mutation signature H458A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 7.8; 303.15 K; cofactor NADH

column_label: Table 1 prints, under each enzyme block, the three column heads Km, mM | kcat, s-1 | kcat/Km , M-1 s-1. The cited cells are the H458A enzyme block, substrate row L-Trp: column Km, mM = 1.15; column kcat, s-1 = 0.11; column kcat/Km , M-1 s-1 = 9.5 x 10^1. captured primary segment: Table 1, H458A enzyme block, substrate row L-Trp | construct H458A mutant Proteus vulgaris tryptophan indole-lyase | substrate L-Trp | condition 0.05 M potassium phosphate, pH 8, at 30 C | Km 1.15 mM | kcat 0.11 s-1 | kcat/Km 9.5 x 10^1 M-1 s-1

normalized_value_unit_evidence: Km: printed Table 1 cell 1.15 mM; the printed Km column head of this table is Km, mM, so no unit conversion applies and the paper value is 1.15 mM. kcat: printed Table 1 cell 0.11 s-1; the printed turnover column head is kcat, s-1, so no unit conversion applies and the paper value is 0.11 s^(-1). kcat/Km: printed Table 1 cell 9.5 x 10^1 M-1 s-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 95.0 / 1000 = 0.095 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 1, H458A enzyme block, substrate row L-Trp: Km = 1.15 mM; kcat = 0.11 s-1; printed kcat/Km = 9.5 x 10^1 M-1 s-1.

table_label: Table 1: Steady-State Kinetic Parameters, H458A enzyme block (Biochemistry 2003, 42(38):11161-11169)


substrate_name: S-Ethyl-L-cysteine

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D133A to reconstruct the assayed variant sequence.

proof_lines:
Proteus vulgaris
tryptophan indole-lyase
S-alkyl-L-cysteines

substrate: S-Ethyl-L-cysteine


assay_conditions_summary: pH 8; 303.15 K; cofactor NADH

column_label: Table 1 prints, under each enzyme block, the three column heads Km, mM | kcat, s-1 | kcat/Km , M-1 s-1. The cited cells are the H458A enzyme block, substrate row S-Et-L-Cys: column Km, mM = 0.42; column kcat, s-1 = 6.41; column kcat/Km , M-1 s-1 = 1.52 x 10^4. captured primary segment: Table 1, H458A enzyme block, substrate row S-Et-L-Cys | construct H458A mutant Proteus vulgaris tryptophan indole-lyase | substrate S-Et-L-Cys | condition 0.05 M potassium phosphate, pH 8, at 30 C | Km 0.42 mM | kcat 6.41 s-1 | kcat/Km 1.52 x 10^4 M-1 s-1

normalized_value_unit_evidence: Km: printed Table 1 cell 0.42 mM; the printed Km column head of this table is Km, mM, so no unit conversion applies and the paper value is 0.42 mM. kcat: printed Table 1 cell 6.41 s-1; the printed turnover column head is kcat, s-1, so no unit conversion applies and the paper value is 6.41 s^(-1). kcat/Km: printed Table 1 cell 1.52 x 10^4 M-1 s-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 15200.0 / 1000 = 15.200000000000001 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 1, H458A enzyme block, substrate row S-Et-L-Cys: Km = 0.42 mM; kcat = 6.41 s-1; printed kcat/Km = 1.52 x 10^4 M-1 s-1.


column_label: Table 1 prints, under each enzyme block, the three column heads Km, mM | kcat, s-1 | kcat/Km , M-1 s-1. The cited cells are the wild type enzyme block, substrate row S-Et-L-Cys: column Km, mM = 3.17; column kcat, s-1 = 3.59; column kcat/Km , M-1 s-1 = 1.13 x 10^3. captured primary segment: Table 1, wild type enzyme block, substrate row S-Et-L-Cys | construct wild-type Proteus vulgaris tryptophan indole-lyase | substrate S-Et-L-Cys | condition 0.05 M potassium phosphate, pH 8, at 30 C | Km 3.17 mM | kcat 3.59 s-1 | kcat/Km 1.13 x 10^3 M-1 s-1

normalized_value_unit_evidence: Km: printed Table 1 cell 3.17 mM; the printed Km column head of this table is Km, mM, so no unit conversion applies and the paper value is 3.17 mM. kcat: printed Table 1 cell 3.59 s-1; the printed turnover column head is kcat, s-1, so no unit conversion applies and the paper value is 3.59 s^(-1). kcat/Km: printed Table 1 cell 1.13 x 10^3 M-1 s-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 1130.0 / 1000 = 1.1300000000000001 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 1, wild type enzyme block, substrate row S-Et-L-Cys: Km = 3.17 mM; kcat = 3.59 s-1; printed kcat/Km = 1.13 x 10^3 M-1 s-1.

table_label: Table 1: Steady-State Kinetic Parameters, wild type enzyme block (Biochemistry 2003, 42(38):11161-11169)


substrate_name: S-Methyl-L-cysteine

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P28796 and applied mutation signature D133A to reconstruct the assayed variant sequence.

column_label: Table 1 prints, under each enzyme block, the three column heads Km, mM | kcat, s-1 | kcat/Km , M-1 s-1. The cited cells are the D133A enzyme block, substrate row S-Me-L-Cys: column Km, mM = 0.19; column kcat, s-1 = 0.35; column kcat/Km , M-1 s-1 = 1.84 x 10^3. captured primary segment: Table 1, D133A enzyme block, substrate row S-Me-L-Cys | construct D133A mutant Proteus vulgaris tryptophan indole-lyase | substrate S-Me-L-Cys | condition 0.05 M potassium phosphate, pH 8, at 30 C | Km 0.19 mM | kcat 0.35 s-1 | kcat/Km 1.84 x 10^3 M-1 s-1

normalized_value_unit_evidence: Km: printed Table 1 cell 0.19 mM; the printed Km column head of this table is Km, mM, so no unit conversion applies and the paper value is 0.19 mM. kcat: printed Table 1 cell 0.35 s-1; the printed turnover column head is kcat, s-1, so no unit conversion applies and the paper value is 0.35 s^(-1). kcat/Km: printed Table 1 cell 1.84 x 10^3 M-1 s-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 1840.0 / 1000 = 1.84 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 1, D133A enzyme block, substrate row S-Me-L-Cys: Km = 0.19 mM; kcat = 0.35 s-1; printed kcat/Km = 1.84 x 10^3 M-1 s-1.

table_label: Table 1: Steady-State Kinetic Parameters, D133A enzyme block (Biochemistry 2003, 42(38):11161-11169)

substrate: S-Methyl-L-cysteine