ethylene glycol degradation

MetaCyc:PWY0-1280

Two oxidative events convert ethylene glycol (EG) through glycolaldehyde to glycolate. The exact Rhea species give EG + 2 NAD(+) + water -> glycolate + 2 NADH + 3 H(+); the second event releases two protons. NAD regeneration, oxygen handling and glycolate assimilation are cellular context, not additional core reaction sides. Native FucO dimer and AldA tetramer catalysis are separated from qualified historical, tagged and mutant experiments. The record combines E. coli evidence without claiming that every taxon or ordinary wild-type MG1655 grows on EG alone. Historical physiological support comes from E15 strain 1, EMS-derived strain 3, glycolate-positive G1/G3 and EG-selected EG3, not a sequenced MG1655 isolate. Initial selection used 30 mM EG with 1 mM glucose; subsequent purification used EG-only plates. The primary 1983 Discussion leaves one versus two causal mutations unresolved, despite the native summary specifying two. In CAA extracts G1/G3/EG3 FucO activities were 0.005/0.130/0.415 and AldA 0.145/0.165/0.560 U/mg. Chromatography and labelled intermediates support glycolaldehyde/glycolate formation; P1 association does not identify a sequenced causal allele. EG oxidation used 250 mM EG and 0.33 mM NAD, glycine pH 9.5, 25 C. AldA used 1 mM glycolaldehyde and 2.5 mM NAD; NADP activity in that preparation was about tenfold lower. Later preparations and assay pH/substrates differ. The complete 1983 EG3 uptake comparison at 25 mM co-substrate is retained: relative uptake control 100, glucose 105, acetate 72, malate 54, glyoxylate 48, glycolate 39, glycolaldehyde 18; control 125 nmol/h/mg dry weight. Isotope dilution and mass action were discussed. No named EG transporter, transport stoichiometry or obligatory proton coupling was established. Passive diffusion is an early proposal and a later flux-model assumption; proton symport is a discussed alternative. These observations do not establish direct transporter inhibition. Current FucO P0A9S1 is 382 residues, whereas the 2005/2023 papers use historical 383-residue numbering and older P11549 context. Their Asp196/His200/His263/His277 Fe ligands, G17D/G97E/D39G, N-terminal deletion and I7L/L8V engineering labels are not silently renumbered onto the current reference. The pQE32/pCM1 N-terminal His6 preparation in M15(pREP4) supports the one-Fe-site crystal observation. Separately, solution metal analysis compared D196L/H200A/H200F mutants with WT containing 0.53 Fe atom/subunit. Methods assign WT/mutant site-directed-mutagenesis preparations to pGEX3X/pCM2 in BL21(DE3), with GST removed by factor Xa; this Methods/Results join supports the cleaved-WT comparator attribution, not a measured occupancy for the His6 crystal preparation. His267 is not the Fe ligand formerly proposed. N-terminal strand exchange supports the dimer; historical deltaN10 loses assembly/activity. Two NAD sites per dimer and D39G cofactor expansion do not create a wild-type NADPH core. Older partially purified mutant enzyme also used added manganese; that preparation-specific alternative is retained. The 2005 paper reports earlier Cu(II)/Cd(II) inhibition of FucO, citing PMID4306747. Its retained older-source evidence is abstract/landing material, not an inspected full experimental body; no Cu/Cd dose or direct assay is inferred. The 2005 Figure 4 experiment separately tests Zn/Fe. The 2023 L-lactaldehyde reduction work reports positive cooperativity, K0.5 rather than Km, preliminary ordered Bi-Bi behavior and isotope effects implicating chemistry. H267Q/D360N retain activity, so a unique obligatory base is not established. Reduction used pH 8, 30 C and 0.4 mM NADH; EG is achiral. N151G/L259V 7QNF has cryoprotectant EG and ADPR with unresolved nicotinamide; 7QNI apo L259V lacks Fe/coenzyme and 7R5T F254I is a closed holo state. Neither that mutant structure nor the unsuccessful 2005 glycolaldehyde complex demonstrates a productive wild-type EG ternary intermediate. Earlier expression methods and the 2023 supplement were not fully acquired. AldA P25553 is 479 residues. Later ultracentrifugation/crystals support a tetramer over older dimer estimates. The unavailable 1987 PDF is represented by a limited indexed primary excerpt: strain 3 preparation, JA102=EG3, tetramer/four NAD sites, glycolaldehyde Km0.38 mM, NAD Km0.28 mM and NADP Km6.25 mM. The latter is not Kd despite later wording; ambiguous Zn/Cu OCR values are not promoted. Direct glycolaldehyde assays in 1983, 2006 and 2019 remain separate. The 2019 Vmax/kcat unit inconsistency is disclosed without silently correcting a value. The 2006 NADH and Mg propionaldehyde-dehydrogenase inhibition is distinct from NADH activation of p-nitrophenyl-acetate esterase; neither sign is transferred between functions. The 2008 His-tag F180T BL21(DE3)pLysS cofactor expansion, Ki differences and Mg response are engineered context. In 2007 AldA was endogenous untagged BL21(DE3) protein contaminating a pBSET taxadiene-synthase preparation. C285/E251 mechanism, partial ligand occupancies and NADPH crystal binding do not prove native NADPH turnover or a measured EG-derived covalent intermediate. Heavy-atom/crystallization metals are not physiological cofactors. The annotation's p-hydroxy mercuribenzoate inhibitor lacks an exact supported charge/salt mapping here. Regulatory arrows distinguish activity from expression. CRP-cAMP has proximal aldA binding near-60 (overlap of strand-specific footprints -47 to -74) in the 1997 study; the distal-134 consensus failed the test. Purified binding used 20 micromolar cAMP; external5 mM cAMP partly relieved glucose repression but not glycerol repression. The reporter uses RYC1000 single-copy lambda fusions; MC1061 is a cloning host. An unknown ECL1 crude-extract factor binds-59 to-6 more strongly with glycolaldehyde or2-oxoglutarate; no named TF, direct purified effector binding or resolved multimer is invented. Purified IHF binds aldA fragments, but himA HN1491 and himD K2704 mutants showed no significant expression effect. IHF alpha/beta assembly is retained without a signed aldA edge. Phosphorylated ArcA endpoints retain the source modified state: 1997 ECL547/ECL968 reporter, later native promoter sites with distinct evidence classes, and 2014 native genomics context are separate. Specific 2014 aldA supplemental data were not inspected. DnaA-ATP negative control is native-state support plus an abstract reporting DnaA binding; the full paper was unavailable. FNR's aldA motif is computational expression-context support, not purified promoter binding. MarA/SoxS/Rob expression annotations explicitly allow indirect effects. Native fucAO CRP-cAMP/FucR-fuculose1-phosphate control is joined through the exact TU and fucO gene; fucPIK/IS5/crp201 mechanisms are not transplanted. The separately mapped internal fucO transcript remains distinct. SrsR/YgfI fucO RNA effects use BW25113/JW5476 and ASKA controls after 24 h LB, while purified C-terminal His-SrsR from W3110/pET21a in BL21(DE3) binds the shared fucA/fucP spacer; yfdP/yfdO supplied footprint sites. Its coinducer is unknown. Sugar-dependent expression is condition-specific. The 1988 ECL1/ECL3, JA104 temperature-sensitive, JA105 fucO::Tn5, ET6016 rhamnose-aldolase and ECL493 ald-1 comparisons suggest lactaldehyde induction, but direct addition arrested growth. Carbon-fed anaerobic shifts retain AldA; starvation causes activity loss without immediate protein loss. Broad native claims of exclusively aerobic AldA or exclusively anaerobic FucO are consequently bounded. Glutamate induction is retained as native prose without a forced ionic/stereochemical effector identity. Glycerol-associated AldA protein reduction in the 2002 MC4100/TB comparison does not establish every malT/EIIA intermediary for aldA. Engineering provides qualified full-route context. The 2021 MG1655-derived LMSE11/12 pTrc99a FucO/AldA variants used 2 g/L yeast extract and controlled aeration; those results are not sole-organic-carbon reference growth. The 2024 UV EG01 and DnaB-AID/evolved EG02 study separates modules I FucO/AldA, II GlcDEF, III glycerate Gcl/Hyi/GlxR/GlxK, IV GlcB. Inspected Fig. 4 supports module III and resolves contradictory III/IV Results wording; module I alone was insufficient in that assay. Defined M9 EG differs from PET digest containing glycine/TPA/MHET and EG-versus-LB RNA comparisons. Another 2024 study compares FucO I7L/L8V, heterologous Gox0313 or PedE/PQQ with fucO/yqhD/glcDEF deletions; it inconsistently names MG1655 and MG1655(DE3) and uses2 g/L yeast extract. Glycolate toxicity and metabolite pools are not direct AldA inhibition or measured flux. PMID39079834 and 41308929 remain abstract-only engineering leads, not completed native mechanisms. Native glycolate links to three opaque downstream pathways and the glycol superpathway are retained. Frozen PathBank root SMP0002105/PW002093 has the same two-event outline, FucO (two chains)/AldA (four chains) assemblies and two attached children. Their generic Interactions provide unsigned structural participant context. PathBank neutral glycolic acid17497 is distinct from Rhea glycolate 29805; its NAD species differ, its first reaction is reversible, and its glycolaldehyde BioCyc DIHYDROXYPHENYLGLYCOLALDEHYDE cross-reference conflicts with CHEBI17071. These conflicts are preserved rather than harmonized away. Native archaeal Q9HHR2 and yeast Q12177 first-reaction contexts describe reverse glycolaldehyde reduction, not complete EG degradation in those taxa. Native comments also cover FucO propanediol/isobutanol, reverse beta oxidation, mouse colonization and slow-codon effects, and AldA folate-derived glycolaldehyde removal, other sugar routes, glucose limitation, oleate and environmental expression. Those are bounded adjacent contexts; prpC synthetic lethality does not establish PrpC catalysis, and sequence-based succinate-semialdehyde predictions do not change this core.

Pathway type
alcohol degradation
Organism scope

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Pathway network

79 nodes · 82 asserted directed edges

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Pathway network: ethylene glycol degradation 79 nodes · 82 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. RHEA:27631 — part_of → MetaCyc:PWY0-1280; The exact native reaction-list includes GLYCOLALDREDUCT-RXN. The two-event pathway terminates at glycolate; downstream assimilation remains an interface.; Evidence: MetaCyc:PWY0-1280part of RHEA:20002 — part_of → MetaCyc:PWY0-1280; The exact native reaction-list includes GLYCOLALD-DEHYDROG-RXN. The two-event pathway terminates at glycolate; downstream assimilation remains an interface.; Evidence: MetaCyc:PWY0-1280part of CHEBI:30742 — consumes → RHEA:27631; RHEA:27631 substrates contains CHEBI:30742, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:27631consumes CHEBI:57540 — consumes → RHEA:27631; RHEA:27631 substrates contains CHEBI:57540, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:27631consumes RHEA:27631 — produces → CHEBI:17071; RHEA:27631 products contains CHEBI:17071, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:27631produces RHEA:27631 — produces → CHEBI:57945; RHEA:27631 products contains CHEBI:57945, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:27631produces RHEA:27631 — produces → CHEBI:15378; RHEA:27631 products contains CHEBI:15378, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:27631produces CHEBI:17071 — consumes → RHEA:20002; RHEA:20002 substrates contains CHEBI:17071, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:20002consumes CHEBI:57540 — consumes → RHEA:20002; RHEA:20002 substrates contains CHEBI:57540, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:20002consumes CHEBI:15377 — consumes → RHEA:20002; RHEA:20002 substrates contains CHEBI:15377, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:20002consumes RHEA:20002 — produces → CHEBI:29805; RHEA:20002 products contains CHEBI:29805, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:20002produces RHEA:20002 — produces → CHEBI:57945; RHEA:20002 products contains CHEBI:57945, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:20002produces RHEA:20002 — produces → CHEBI:15378; RHEA:20002 products contains CHEBI:15378, coefficient 2. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.; Evidence: RHEA:20002produces RHEA:27631 — provides_input_for → RHEA:20002; The ordered oxidative events share glycolaldehyde: GLYCOLALDREDUCT-RXN precedes GLYCOLALD-DEHYDROG-RXN. No additional transport or energy-coupling event is supplied by this relation.; Evidence: MetaCyc:PWY0-1280provides input for EcoCyc:LACTALDREDUCT-CPLX — catalyzes → RHEA:27631; The native enzyme slot identifies LACTALDREDUCT-CPLX as the catalytic assembly and assigns physiological left-to-right chemistry. Reference assembly identity does not establish ordinary wild-type EG growth.; Evidence: EcoCyc:GLYCOLALDREDUCT-ENZRXNcatalyzes EcoCyc:ALD-CPLX — catalyzes → RHEA:20002; The native enzyme slot identifies ALD-CPLX as the catalytic assembly and assigns physiological left-to-right chemistry. Reference assembly identity does not establish ordinary wild-type EG growth.; Evidence: EcoCyc:GLYCOLALD-DEHYDROG-ENZRXNcatalyzes EcoCyc:LACTALDREDUCT-CPLX — has_part → UniProtKB:P0A9S1; The native component slot specifies 2 copies of LACTALDREDUCT-MONOMER. This is assembly stoichiometry, not independent catalysis by each chain.; Evidence: EcoCyc:LACTALDREDUCT-CPLX, EcoCyc:LACTALDREDUCT-MONOMER, UniProtKB:P0A9S1has part UniProtKB:P0A9S1 — located_in → GO:0005829; The native cytosol GO annotation grounds this location. Its attached evidence class is retained; no fresh localization experiment or universal condition-independent distribution is claimed.; Evidence: EcoCyc:LACTALDREDUCT-MONOMERlocated in EcoCyc:ALD-CPLX — has_part → UniProtKB:P25553; The native component slot specifies 4 copies of LACTALDDEHYDROG-MONOMER. This is assembly stoichiometry, not independent catalysis by each chain.; Evidence: EcoCyc:ALD-CPLX, EcoCyc:LACTALDDEHYDROG-MONOMER, UniProtKB:P25553has part UniProtKB:P25553 — located_in → GO:0005829; The native cytosol GO annotation grounds this location. Its attached evidence class is retained; no fresh localization experiment or universal condition-independent distribution is claimed.; Evidence: EcoCyc:LACTALDDEHYDROG-MONOMERlocated in EcoCyc:LACTALDREDUCT-CPLX — catalyzes → RHEA:27631; subject experimental construct: 1983 E15-derived selected G1/G3/EG3 crude extracts; EG3 selected from G3. Historical proteins were not sequenced as current MG1655 accessions. EG oxidation: 250 mM EG, 0.33 mM NAD, 100 mM glycine pH 9.5, 25 C.; Evidence PMID:6336729: The study assayed EG oxidation in extracts of selected E15 derivatives, with 250 mM EG and NAD at alkaline pH. The selected strain history is distinct from the current reference strain. (PDF pp. 134-136, Materials and Methods and Table 1); Selected EG3 extracts oxidized EG with NAD. Constitutive oxidoreductase levels increased across G1/G3/EG3; the pathway selection did not identify a sequenced causal allele.; Evidence: PMID:6336729catalyzes EcoCyc:ALD-CPLX — catalyzes → RHEA:20002; subject experimental construct: 1983 E15-derived G1/G3/EG3 crude extracts: AldA assay 1 mM glycolaldehyde, 2.5 mM NAD, glycine pH 9.5, 25 C. Product chromatography separately used 3.5 mM glycolaldehyde and 5 mM NAD, 30 min at 37 C. Historical preparation is distinct from current MG1655.; Evidence PMID:6336729: The primary methods distinguish the spectrophotometric aldehyde-dehydrogenase assay from the separate glycolate product-identification incubation. (PDF pp. 134-137, Enzyme assays and product-identification experiment); Historical extract assays oxidized glycolaldehyde with NAD; paper chromatography identified glycolate after incubation. This directly supports the second event without assigning a sequenced genotype to E15 derivatives.; Evidence: PMID:6336729catalyzes EcoCyc:ALD-CPLX — catalyzes → RHEA:20002; subject experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography; vector construction refers to earlier work. Phosphate 100 mM pH 7.5, NaCl 100 mM, beta-mercaptoethanol 20 mM, NAD 2 mM; substrate specified per assay.; Evidence PMID:16731973: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p); Direct glycolaldehyde kinetics in the 2006 His6 preparation: Table 1 Km 0.14 mM and kcat 1100 min-1. These are not pooled with 1983 pH 9.5 extract values or 2019 Tris/Mg/37 C values.; Evidence: PMID:16731973, PMID:16731973catalyzes EcoCyc:ALD-CPLX — catalyzes → RHEA:20002; subject experimental construct: 2019 MG1655 aldA DNA cloned in pET28a/pVT-ALDA, produced in BL21(DE3) as N-terminal His-tagged protein and purified on cobalt resin; 1 mM IPTG, 16 C. Assay: 5 mM glycolaldehyde, 3 mM NAD, Tris pH 7.5, 10 mM MgCl2, 37 C.; Evidence PMID:31850327: The aldA gene was amplified from MG1655 genomic DNA for the engineered expression constructs. (XPath /article/body/sec[2]/sec[2]/p[2]); Evidence PMID:31850327: Methods describe pET28a expression in BL21(DE3), 1 mM IPTG at 16 C and cobalt-resin purification of His-tagged protein. (XPath /article/body/sec[2]/sec[5]/p[1]); Evidence PMID:31850327: Table 4 explicitly describes purified proteins carrying an N-terminal His tag. (XPath /article/body/sec[3]/sec[2]/table-wrap/caption/p); Independent direct glycolaldehyde oxidation assay. Table 4 reports Km 0.21 mM, Vmax 1.66 micromol/min/mg and kcat 52 s-1; its Vmax/kcat unit conversion is not internally consistent, so no corrected kinetic constant is silently substituted. This preparation also serves a separate engineered glycoptimus pathway.; Evidence: PMID:31850327, PMID:31850327catalyzes EcoCyc:LACTALDREDUCT-CPLX — has_cofactor → CHEBI:29033; subject experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in M15(pREP4). This qualifier applies to the crystal-site evidence; the separate cleaved-WT solution comparison is contextualized in the record description. Current P0A9S1 is 382 residues.; Evidence PMID:15995211: The FucO crystallographic preparation used ECL1-derived pCM1 in pQE32, N-terminal His6 expression in M15(pREP4) and Ni-NTA purification. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[2]/section[3]/p[1]); The native EG enzyme-reaction entry identifies iron as cofactor. It is catalytic context, not a consumed chemical side.; Evidence: EcoCyc:GLYCOLALDREDUCT-ENZRXN, PMID:15995211has cofactor EcoCyc:LACTALDREDUCT-CPLX — has_cofactor → CHEBI:29035; subject experimental construct: Older partially purified oxidoreductase from an E. coli K-12 mutant selected for growth on L-1,2-propanediol; abstract-only preparation information. Ferrous and manganous support are alternatives, not simultaneous obligatory cofactors.; Evidence PMID:4306747: The inspected abstract identifies a partially purified mutant K-12 enzyme and alternative added ferrous or manganous ions. Full experimental details were not acquired. (XPath //PubmedArticle[MedlineCitation/PMID="4306747"]/MedlineCitation/Article/Abstract); The abstract reports that partially purified oxidoreductase from a selected K-12 propanediol-growing mutant requires added ferrous or manganous ions; kinetics vary by metal. This is alternative preparation-specific support, not an obligatory Mn requirement for EG oxidation.; Evidence: PMID:4306747has cofactor EcoCyc:LACTALDREDUCT-CPLX — has_cofactor → CHEBI:57540; NAD coenzyme dependence accompanies the exact Rhea cosubstrate sides. AldA NADP activity in the 1983 alkaline preparation was about tenfold lower; later 2006 assays found no NADP activity under different conditions. The mutant F180T and FucO D39G cofactor expansions do not change the native core stoichiometry.; Evidence: EcoCyc:GLYCOLALDREDUCT-ENZRXNhas cofactor EcoCyc:ALD-CPLX — has_cofactor → CHEBI:57540; NAD coenzyme dependence accompanies the exact Rhea cosubstrate sides. AldA NADP activity in the 1983 alkaline preparation was about tenfold lower; later 2006 assays found no NADP activity under different conditions. The mutant F180T and FucO D39G cofactor expansions do not change the native core stoichiometry.; Evidence: EcoCyc:GLYCOLALD-DEHYDROG-ENZRXNhas cofactor CHEBI:29105 — inhibits → EcoCyc:LACTALDREDUCT-CPLX; object experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in M15(pREP4). The crystal site count is distinct from solution Fe occupancy. Paper residue numbers are retained; current P0A9S1 is 382 residues.; Evidence PMID:15995211: The FucO crystallographic preparation used ECL1-derived pCM1 in pQE32, N-terminal His6 expression in M15(pREP4) and Ni-NTA purification. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[2]/section[3]/p[1]); Direct Zn inhibition was measured in glycolaldehyde reduction with NADH, not as an EG-oxidation IC50. Figure 4 used 0.1 mM ZnCl2 and tested protective FeSO4 at 0.1 and 1 mM; no physiological zinc-regulation threshold is asserted.; Evidence: EcoCyc:REG0-9194, PMID:15995211inhibits CHEBI:29033 — activates → EcoCyc:LACTALDREDUCT-CPLX; object experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in M15(pREP4). The crystal site count is distinct from solution Fe occupancy. Paper residue numbers are retained; current P0A9S1 is 382 residues. Protection assay includes 0.1 mM ZnCl2.; Evidence PMID:15995211: The FucO crystallographic preparation used ECL1-derived pCM1 in pQE32, N-terminal His6 expression in M15(pREP4) and Ni-NTA purification. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[2]/section[3]/p[1]); Protection against Zn-mediated activity loss, measured with glycolaldehyde/NADH. This conditional rescue is not an additional EG-reactant requirement or a direct in vivo iron-activation dose response.; Evidence: PMID:15995211activates CHEBI:17071 — inhibits → EcoCyc:ALD-CPLX; The native regulation assigns glycolaldehyde substrate inhibition to AldA. This is a curated annotation citing PMID3308886, not a quotation from an acquired original PDF.; Evidence: EcoCyc:REG0-9207, UniProtKB:P25553inhibits CHEBI:29105 — inhibits → EcoCyc:ALD-CPLX; The native regulation explicitly assigns Zn(II) inhibition to AldA, citing the older biochemical characterization.; Evidence: EcoCyc:REG0-9208, UniProtKB:P25553inhibits CHEBI:29035 — inhibits → EcoCyc:ALD-CPLX; The issuing AldA ACTIVITY REGULATION annotation reports inhibition by Mn(2+), citing PMID3308886. The original paper PDF was not acquired; this is annotation-level biochemical support without a physiological threshold.; Evidence: UniProtKB:P25553inhibits CHEBI:29108 — inhibits → EcoCyc:ALD-CPLX; The issuing AldA ACTIVITY REGULATION annotation reports inhibition by Ca(2+), citing PMID3308886. The original paper PDF was not acquired; this is annotation-level biochemical support without a physiological threshold.; Evidence: UniProtKB:P25553inhibits CHEBI:29036 — inhibits → EcoCyc:ALD-CPLX; The issuing AldA ACTIVITY REGULATION annotation reports inhibition by Cu(2+), citing PMID3308886. The original paper PDF was not acquired; this is annotation-level biochemical support without a physiological threshold.; Evidence: UniProtKB:P25553inhibits CHEBI:57945 — inhibits → EcoCyc:ALD-CPLX; object experimental construct: 1988 purified ECL3 AldA from the constitutive fucA/fucO, noninducible fucPIK background. Fig. 5 uses glycolaldehyde 1 mM, NAD 2.5 mM, glycine 100 mM pH 9.5 at 25 C. This historical preparation is not an unqualified MG1655 measurement.; Evidence PMID:3275622: The study uses purified ECL3 lactaldehyde dehydrogenase; its standard assay substitutes glycolaldehyde for lactaldehyde and follows NADH formation. (PDF pp. 417-418, strain Table 1 and Enzyme assays; p. 420 Fig. 5); Figure 5 directly measures NADH inhibition of purified AldA in the glycolaldehyde oxidation assay, with approximately half inhibition near 0.45 mM and nearly complete inhibition at 1 mM NADH.; Evidence: PMID:3275622inhibits CHEBI:57945 — inhibits → EcoCyc:ALD-CPLX; object experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography; vector construction refers to earlier work. Phosphate 100 mM pH 7.5, NaCl 100 mM, beta-mercaptoethanol 20 mM, NAD 2 mM; substrate specified per assay.; Evidence PMID:16731973: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p); Propionaldehyde dehydrogenase assay, not an independently measured EG-specific inhibition constant. NADH has the opposite sign in the separately retained esterase assay.; Evidence: PMID:16731973inhibits CHEBI:18420 — inhibits → EcoCyc:ALD-CPLX; object experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography; vector construction refers to earlier work. Phosphate 100 mM pH 7.5, NaCl 100 mM, beta-mercaptoethanol 20 mM, NAD 2 mM; substrate specified per assay.; Evidence PMID:16731973: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p); Measured propionaldehyde dehydrogenase inhibition in the N-terminal His6 preparation. Mg is not an obligatory AldA cofactor; crystallization Mg or 2019 assay-buffer Mg does not reverse this measured sign.; Evidence: PMID:16731973inhibits CHEBI:57945 — activates → EcoCyc:ALD-CPLX; object experimental construct: 2006 N-terminal His6 AldA produced in BL21; this endpoint is restricted to p-nitrophenyl-acetate esterase activity at pH 7.4, not glycolaldehyde dehydrogenase or pathway flux.; Evidence PMID:16731973: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p); Activity sign applies only to the separate p-nitrophenyl-acetate esterase assay (0.1 mM substrate, pH 7.4). NADH raised activity from 135 to 326 nmol/min/mg; NAD did not. This is not activation of EG oxidation or of its aldehyde-dehydrogenase step.; Evidence: PMID:16731973, PMID:16731973activates CHEBI:57540 — activates → EcoCyc:LACTALDREDUCT-CPLX; object molecular state: Aerobically inactivated FucO preparation in the native annotation; reactivation by high NAD is source-limited. Concentration, binding mechanism and an EG-specific activity assay are not established by the inspected abstract.; Evidence EcoCyc:LACTALDREDUCT-MONOMER: The native comment distinguishes aerobic inactivation from subsequent in-vitro NAD-dependent reactivation. (XPath /ptools-xml/Protein/comment); The native comment reports in-vitro reactivation of aerobically inactivated FucO by high NAD concentrations, citing PMID2203757. The inspected abstract does not provide this reactivation assay or a concentration.; Evidence: EcoCyc:LACTALDREDUCT-MONOMERactivates CHEBI:15379 — inhibits → EcoCyc:LACTALDREDUCT-CPLX; Condition-dependent oxidative inactivation of reference-family FucO preparations. This is not stoichiometric oxygen consumption in RHEA27631, universal direct oxygen binding, or an assertion that every oxygen-resistant engineered variant is inactive.; Evidence: PMID:2203757, PMID:1730033inhibits CHEBI:16240 — inhibits → EcoCyc:LACTALDREDUCT-CPLX; Abstract-level anaerobic H2O2 inactivation and native metal-catalyzed oxidation context. No dose, rate, EG-specific assay, or direct regulatory binding is inferred.; Evidence: PMID:1730033, EcoCyc:LACTALDREDUCT-MONOMERinhibits EcoCyc:PC00004 — has_part → UniProtKB:P0ACJ8; The native complex specifies two copies of PD00257; unspecified component coefficients are not invented.; Evidence: EcoCyc:PC00004, EcoCyc:PD00257has part EcoCyc:CPLX0-7650 — has_part → UniProtKB:P0ACK8; The native complex specifies component membership without a numeric coefficient of PD00444; unspecified component coefficients are not invented.; Evidence: EcoCyc:CPLX0-7650, EcoCyc:PD00444has part EcoCyc:CPLX0-7797 — has_part → UniProtKB:P0A9E5; The native complex specifies two copies of PD00197; unspecified component coefficients are not invented.; Evidence: EcoCyc:CPLX0-7797, EcoCyc:PD00197has part EcoCyc:MONOMER0-160 — has_part → UniProtKB:P03004; The native complex specifies component membership without a numeric coefficient of PD03831; unspecified component coefficients are not invented.; Evidence: EcoCyc:MONOMER0-160, EcoCyc:PD03831has part EcoCyc:PC00027 — has_part → UniProtKB:P0A6X7; IHF assembly context. Purified IHF supplied by H. Nash bound aldA fragments 1/2/3; HN1491 himA and K2704 himD mutants showed no significant expression effect. Binding alone therefore supplies no signed IHF-to-aldA edge. No aldA-specific IHF stoichiometry is inferred.; Evidence: EcoCyc:PC00027, EcoCyc:PD00347, PMID:9202484has part EcoCyc:PC00027 — has_part → UniProtKB:P0A6Y1; IHF assembly context. Purified IHF supplied by H. Nash bound aldA fragments 1/2/3; HN1491 himA and K2704 himD mutants showed no significant expression effect. Binding alone therefore supplies no signed IHF-to-aldA edge. No aldA-specific IHF stoichiometry is inferred.; Evidence: EcoCyc:PC00027, EcoCyc:PD00348, PMID:9202484has part EcoCyc:CPLX0-226 — has_part → EcoCyc:PC00004; The native active CRP-cAMP object explicitly contains the CRP dimer PC00004; its component slot has no further numeric coefficient.; Evidence: EcoCyc:CPLX0-226has part EcoCyc:CPLX0-226 — has_part → CHEBI:58165; The exact source-defined ligand-bound regulatory assembly is retained. Native CAMP and FUCULOSE-1P ChEBI joins and ATP species are independently checked against their originals and the pinned ontology; missing ligand multiplicities remain unspecified.; Evidence: EcoCyc:CPLX0-226, EcoCyc:CAMPhas part EcoCyc:CPLX0-7650 — has_part → CHEBI:57846; The exact source-defined ligand-bound regulatory assembly is retained. Native CAMP and FUCULOSE-1P ChEBI joins and ATP species are independently checked against their originals and the pinned ontology; missing ligand multiplicities remain unspecified.; Evidence: EcoCyc:CPLX0-7650, EcoCyc:FUCULOSE-1Phas part EcoCyc:MONOMER0-160 — has_part → CHEBI:30616; The exact source-defined ligand-bound regulatory assembly is retained. Native CAMP and FUCULOSE-1P ChEBI joins and ATP species are independently checked against their originals and the pinned ontology; missing ligand multiplicities remain unspecified.; Evidence: EcoCyc:MONOMER0-160, EcoCyc:ATPhas part EcoCyc:CPLX0-7797 — has_cofactor → CHEBI:49883; The exact FNR result assigns one [4Fe-4S] cluster per chain. The native active assembly is a dimer; apo and oxygen-converted cluster forms are different states.; Evidence: UniProtKB:P0A9E5, EcoCyc:CPLX0-7797has cofactor CHEBI:15379 — inhibits → EcoCyc:CPLX0-7797; object molecular state: Active dimeric FNR with [4Fe-4S] clusters; the native annotation distinguishes this state from inactive monomeric apo-FNR and oxygen-converted [2Fe-2S] forms.; Evidence EcoCyc:CPLX0-7797: The native comment explicitly distinguishes active anaerobic Fe-S dimer from oxygen-inactivated and apo forms. (XPath /ptools-xml/Protein/comment); Oxygen inactivates FNR through [4Fe-4S] to [2Fe-2S] conversion and dimer dissociation; prolonged exposure yields apo-FNR.; Evidence: EcoCyc:CPLX0-7797inhibits CHEBI:16480 — inhibits → EcoCyc:CPLX0-7797; object molecular state: Active dimeric FNR with [4Fe-4S] clusters; the native annotation distinguishes this state from inactive monomeric apo-FNR and oxygen-converted [2Fe-2S] forms.; Evidence EcoCyc:CPLX0-7797: The native comment explicitly distinguishes active anaerobic Fe-S dimer from oxygen-inactivated and apo forms. (XPath /ptools-xml/Protein/comment); Nitric oxide can inactivate FNR through nitrosylation of its [4Fe-4S] cluster; this is general proximal regulator-state context, not an aldA-specific binding experiment.; Evidence: EcoCyc:CPLX0-7797inhibits EcoCyc:CPLX0-226 — activates → Entrez:945672; subject experimental construct: Native CRP-cAMP reference assembly; direct 1997 binding used purified CRP supplied by S. Adhya, with 20 micromolar cAMP. Production strain/tag details were not reported in the inspected methods. Reporter assays used RYC1000 single-copy aldA-lacZ fusions.; Evidence PMID:9202484: The methods identify purified CRP supplied by S. Adhya and describe the binding incubation. (XPath /html/body/div/div[1]/div[7]/div[7]/p[1]); Evidence PMID:9202484: The promoter fusions were constructed in pRS550 and transferred by lambdaRS45 to single-copy reporter backgrounds. (XPath /html/body/div/div[1]/div[7]/div[5]/p[3]); Positive aldA transcriptional control and proximal physical binding. The RYC1000 single-copy pRS550/lambdaRS45 reporters were studied in defined carbon-source conditions. CRP supplied by S. Adhya was used for binding with 20 micromolar cAMP; its tag/production strain was not established by the inspected methods. Five mM exogenous cAMP partially relieved glucose repression, whereas glycerol repression was cAMP-independent.; Evidence: EcoCyc:REG0-5996, EcoCyc:TU102, Entrez:945672, PMID:9202484, PMID:9202484activates UniProtKB:P0A9Q1 — inhibits → Entrez:945672; subject molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native PHOSPHO-ARCA. This qualifier preserves the modified regulator; a loss-of-arcA expression experiment alone does not measure its phosphorylation state.; Evidence EcoCyc:PHOSPHO-ARCA: The native phosphorylated regulator has unmodified-form ARCA-MONOMER. Its modified identity is retained as source evidence rather than silently flattened to the reference chain. (XPath /ptools-xml/Protein/unmodified-form | /ptools-xml/Protein/common-name); Evidence EcoCyc:ARCA-MONOMER: This native reference chain has an explicit UniProt unification cross-reference to P0A9Q1. It grounds identity only, not the assay construct or regulatory sign. (XPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9Q1"]); 1997 expression experiment: ECL547/ECL968 carrying the -287 aldA fusion, rhamnose minimal medium, anaerobiosis. ArcA mutant reporter activity was 18,700 versus aerobic parental/mutant values 19,375/20,750. This is gene-expression evidence; the 1997 consensus motif alone does not prove direct binding.; Evidence: PMID:9202484, EcoCyc:TU102, Entrez:945672inhibits UniProtKB:P0A9Q1 — inhibits → Entrez:945672; subject molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native PHOSPHO-ARCA. This qualifier preserves the modified regulator; a loss-of-arcA expression experiment alone does not measure its phosphorylation state.; Evidence EcoCyc:PHOSPHO-ARCA: The native phosphorylated regulator has unmodified-form ARCA-MONOMER. Its modified identity is retained as source evidence rather than silently flattened to the reference chain. (XPath /ptools-xml/Protein/unmodified-form | /ptools-xml/Protein/common-name); Evidence EcoCyc:ARCA-MONOMER: This native reference chain has an explicit UniProt unification cross-reference to P0A9Q1. It grounds identity only, not the assay construct or regulatory sign. (XPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9Q1"]); Native site-resolved ArcA-P repression: REG0-5998/5999/6000/6002/6003 and BS0-4943/4942/4941, BS43, BS42 are preserved together. Some source evidence is computational or expression-based; the PMID10071223 abstract supports direct promoter recognition without supplying full-body methods. No uninspected supplement is claimed.; Evidence: EcoCyc:REG0-5998, EcoCyc:REG0-5999, EcoCyc:REG0-6000, EcoCyc:REG0-6002, EcoCyc:REG0-6003, EcoCyc:TU102, Entrez:945672, PMID:10071223inhibits UniProtKB:P0A9Q1 — inhibits → Entrez:945672; subject molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native PHOSPHO-ARCA. This qualifier preserves the modified regulator; a loss-of-arcA expression experiment alone does not measure its phosphorylation state.; Evidence EcoCyc:PHOSPHO-ARCA: The native phosphorylated regulator has unmodified-form ARCA-MONOMER. Its modified identity is retained as source evidence rather than silently flattened to the reference chain. (XPath /ptools-xml/Protein/unmodified-form | /ptools-xml/Protein/common-name); Evidence EcoCyc:ARCA-MONOMER: This native reference chain has an explicit UniProt unification cross-reference to P0A9Q1. It grounds identity only, not the assay construct or regulatory sign. (XPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9Q1"]); 2014 study context: MG1655 and deletions, M9 0.2% glucose/0.1% ammonium chloride, 37 C, anaerobic exponential growth with or without 20 mM nitrate. Exact aldA-specific support is the native curated regulation; primary gene-specific supplemental rows were not inspected. Tagged ChIP context is not substituted for a fresh aldA-specific binding result, and modelled flux is not measured flux.; Evidence: EcoCyc:REG0-14027, Entrez:945672inhibits EcoCyc:MONOMER0-160 — inhibits → Entrez:945672; Native DnaA-ATP regulatory state plus abstract-level direct DnaA binding and expression evidence. The full publisher body was unavailable (403); no uninspected construct details or ATP-specific biochemical result are inferred from the abstract.; Evidence: EcoCyc:REG0-6001, EcoCyc:TU102, Entrez:945672, PMID:11160809inhibits EcoCyc:CPLX0-7797 — inhibits → Entrez:945672; subject molecular state: Native active FNR dimer with [4Fe-4S] clusters. The aldA regulatory link is expression evidence with a computational binding-site assignment, not a purified aldA-promoter binding measurement.; Evidence EcoCyc:CPLX0-7797: The native annotation links the active Fe-S-containing dimer to anaerobic transcriptional control. (XPath /ptools-xml/Protein/comment); The native regulation assigns negative FNR influence to PM324 using gene-expression evidence; its BS0-7160 motif annotation is computational, not direct binding proof.; Evidence: EcoCyc:REG0-5997, EcoCyc:TU102, Entrez:945672, PMID:16377617inhibits UniProtKB:P0ACH5 — activates → Entrez:945672; Curated potentially indirect MarA-dependent aldA expression, citing PMID12067348. Only its abstract was inspected; gene-level supplemental results were unavailable. General statements about directly activated promoters in that article cannot establish that aldA belongs to that subset.; Evidence: EcoCyc:REG0-12708, EcoCyc:PD00365, EcoCyc:TU102, Entrez:945672activates UniProtKB:P0ACI0 — activates → Entrez:945672; Curated potentially indirect Rob-dependent aldA expression, citing PMID12067348. Only its abstract was inspected; gene-level supplemental results were unavailable. General statements about directly activated promoters in that article cannot establish that aldA belongs to that subset.; Evidence: EcoCyc:REG0-12709, EcoCyc:PD04418, EcoCyc:TU102, Entrez:945672activates UniProtKB:P0A9E2 — activates → Entrez:945672; Curated potentially indirect SoxS-dependent aldA expression, citing PMID12067348. Only its abstract was inspected; gene-level supplemental results were unavailable. General statements about directly activated promoters in that article cannot establish that aldA belongs to that subset.; Evidence: EcoCyc:REG0-12710, EcoCyc:PD00406, EcoCyc:TU102, Entrez:945672activates EcoCyc:CPLX0-226 — activates → Entrez:947273; Native fucAO expression context, not a transplant of every fucPIK promoter experiment. The CRP BS00333 motif is computational; PMID10601201 examines a K52N CRP suppressor and fucPIK after IS5 insertion. Those selected backgrounds are not unqualified wild type. A separate mapped fucO transcript TU0-42697 remains distinct.; Evidence: EcoCyc:REG0-5579, EcoCyc:TU00135, Entrez:947273activates EcoCyc:CPLX0-7650 — activates → Entrez:947273; Native fucAO expression context, not a transplant of every fucPIK promoter experiment. The CRP BS00333 motif is computational; PMID10601201 examines a K52N CRP suppressor and fucPIK after IS5 insertion. Those selected backgrounds are not unqualified wild type. A separate mapped fucO transcript TU0-42697 remains distinct.; Evidence: EcoCyc:REG0-5580, EcoCyc:TU00135, Entrez:947273activates UniProtKB:P52044 — activates → Entrez:947273; subject experimental construct: 2022 BW25113, srsR deletion JW5476, and pCA24N-derived ASKA SrsR overexpression versus empty-vector controls; LB 37 C, 150 rpm, 24 h, 0.5 mM IPTG. Reference P52044/YgfI is named SrsR by the study; this is an expression construct context.; Evidence PMID:35682733: Methods distinguish W3110 genomic donor and BL21(DE3) protein production from BW25113/JW5476 and ASKA overexpression strains used for the expression comparison. (XPath /article/body/sec[4]/sec[1]/p); Evidence PMID:35682733: RT-qPCR used 24-hour LB cultures and 16S normalization, with three independent experiments. (XPath /article/body/sec[4]/sec[7]/p); SrsR (current issuing P52044 label still YgfI) positively influences fucO transcript abundance in the exact BW25113 deletion/overexpression assay. Figure 5 negative fold notation means reduced abundance, not negative RNA. Separate purified C-terminal His-SrsR from W3110/pET21a in BL21(DE3) bound the shared fucA/fucP spacer; this is not an independently mapped fucO internal promoter. The footprint experiment used yfdP/yfdO, not fucO. The SrsR coinducer remains unknown.; Evidence: PMID:35682733, EcoCyc:REG0-16133, EcoCyc:G7518-MONOMER, EcoCyc:TU00135, Entrez:947273, PMID:35682733, PMID:35682733activates CHEBI:17234 — inhibits → Entrez:945672; Condition-dependent aldA expression repression by glucose in the 1997 single-copy reporter experiments, not direct binding to AldA or inhibition of its catalytic activity. Glucose and glycerol effects differ in cAMP dependence. The 2002 MC4100/TB proteomic comparison separately identifies less AldA protein with 0.4% glycerol; its malT/EIIA experiments do not establish every intervening aldA-specific arrow.; Evidence: PMID:9202484, PMID:9202484, PMID:9202484, EcoCyc:TU102, Entrez:945672inhibits CHEBI:17754 — inhibits → Entrez:945672; Condition-dependent aldA expression repression by glycerol in the 1997 single-copy reporter experiments, not direct binding to AldA or inhibition of its catalytic activity. Glucose and glycerol effects differ in cAMP dependence. The 2002 MC4100/TB proteomic comparison separately identifies less AldA protein with 0.4% glycerol; its malT/EIIA experiments do not establish every intervening aldA-specific arrow.; Evidence: PMID:9202484, PMID:9202484, PMID:9202484, EcoCyc:TU102, Entrez:945672, PMID:12003946, PMID:12003946inhibits CHEBI:18287 — activates → Entrez:947273; Sugar-dependent fucO expression/activity context with respiratory conditions retained. Absolute source wording that FucO is only active anaerobically is limited by condition-dependent and oxygen-resistant-mutant evidence. The generic sugar identity does not select a particular pyranose anomer.; Evidence: EcoCyc:LACTALDREDUCT-MONOMER, Entrez:947273activates CHEBI:62345 — activates → Entrez:947273; Sugar-dependent fucO expression/activity context with respiratory conditions retained. Absolute source wording that FucO is only active anaerobically is limited by condition-dependent and oxygen-resistant-mutant evidence. The generic sugar identity does not select a particular pyranose anomer.; Evidence: EcoCyc:LACTALDREDUCT-MONOMER, Entrez:947273activates CHEBI:18287 — activates → Entrez:945672; Source-defined aerobic AldA induction in the historical studies; strain and metabolic backgrounds differ. The 1988 mutant comparisons suggest lactaldehyde as an indirect inducing intermediate, but direct lactaldehyde addition arrested growth and the regulatory factor was unidentified. Native glutamate induction is retained in prose without inventing a precise ionic/stereochemical effector identity.; Evidence: UniProtKB:P25553, Entrez:945672activates CHEBI:62345 — activates → Entrez:945672; Source-defined aerobic AldA induction in the historical studies; strain and metabolic backgrounds differ. The 1988 mutant comparisons suggest lactaldehyde as an indirect inducing intermediate, but direct lactaldehyde addition arrested growth and the regulatory factor was unidentified. Native glutamate induction is retained in prose without inventing a precise ionic/stereochemical effector identity.; Evidence: UniProtKB:P25553, Entrez:945672activates CHEBI:30742 — activates → Entrez:945672; Source-defined aerobic AldA induction in the historical studies; strain and metabolic backgrounds differ. The 1988 mutant comparisons suggest lactaldehyde as an indirect inducing intermediate, but direct lactaldehyde addition arrested growth and the regulatory factor was unidentified. Native glutamate induction is retained in prose without inventing a precise ionic/stereochemical effector identity.; Evidence: UniProtKB:P25553, Entrez:945672activates RHEA:20002 — provides_input_for → MetaCyc:PWY-6649; The glycolate product can enter this source-defined downstream context. The exact native opaque pathway is retained without importing its enzymes or changing the PWY0-1280 boundary.; Evidence: MetaCyc:PWY0-1280provides input for RHEA:20002 — provides_input_for → MetaCyc:GLYOXDEG-PWY; The glycolate product can enter this source-defined downstream context. The exact native opaque pathway is retained without importing its enzymes or changing the PWY0-1280 boundary.; Evidence: MetaCyc:PWY0-1280provides input for RHEA:20002 — provides_input_for → MetaCyc:GLYCOLATEMET-PWY; The glycolate product can enter this source-defined downstream context. The exact native opaque pathway is retained without importing its enzymes or changing the PWY0-1280 boundary.; Evidence: MetaCyc:PWY0-1280provides input for MetaCyc:PWY0-1280 — part_of → MetaCyc:GLYCOL-GLYOXDEG-PWY; The META original explicitly places the EG pathway in the glycol metabolism and degradation superpathway. The ECOLI original independently carries this parent; the META parent is not absent.; Evidence: MetaCyc:PWY0-1280, EcoCyc:PWY0-1280part of MetaCyc:PWY0-1280 — has_part → PathBank:SMP0002052; Frozen PathBank root SMP0002105/PW002093 describes the same two-event EG conversion and attaches this opaque child. The graph preserves the attachment without treating the child as part of the Rhea core or independently proving its biochemical mechanism.; Evidence: PathBank:SMP0002105has part PathBank:SMP0002052 — has_part → CHEBI:17071; Unsigned structural participant context only. The D-arabinose child includes glycolaldehyde; the glycolate/glyoxylate child includes neutral glycolic acid CHEBI17497. Neutral acid is not silently merged with Rhea glycolate CHEBI29805, and neither Interaction is converted to transport, inhibition or an extra core reaction.; Evidence: PathBank:SMP0002105has part MetaCyc:PWY0-1280 — has_part → PathBank:SMP0000847; Frozen PathBank root SMP0002105/PW002093 describes the same two-event EG conversion and attaches this opaque child. The graph preserves the attachment without treating the child as part of the Rhea core or independently proving its biochemical mechanism.; Evidence: PathBank:SMP0002105has part PathBank:SMP0000847 — has_part → CHEBI:17497; Unsigned structural participant context only. The D-arabinose child includes glycolaldehyde; the glycolate/glyoxylate child includes neutral glycolic acid CHEBI17497. Neutral acid is not silently merged with Rhea glycolate CHEBI29805, and neither Interaction is converted to transport, inhibition or an extra core reaction.; Evidence: PathBank:SMP0002105has part ethylene glycol; CHEBI:30742; Declared type: small_molecule small molecule ethylene glycol NAD(1-); CHEBI:57540; Declared type: cofactor cofactor NAD(1-) glycolaldehyde; CHEBI:17071; Declared type: small_molecule small molecule glycolaldehyde NADH(2-); CHEBI:57945; Declared type: small_molecule small molecule NADH(2-) hydron; CHEBI:15378; Declared type: small_molecule small molecule hydron water; CHEBI:15377; Declared type: small_molecule small molecule water glycolate; CHEBI:29805; Declared type: small_molecule small molecule glycolate glycolic acid; CHEBI:17497; Declared type: small_molecule small molecule glycolic acid 3',5'-cyclic AMP(1-); CHEBI:58165; Declared type: small_molecule small molecule 3',5'-cyclic AMP(1-) L-fuculose 1-phosphate(2-); CHEBI:57846; Declared type: small_molecule small molecule L-fuculose 1-phosphate(2-) ATP(4-); CHEBI:30616; Declared type: small_molecule small molecule ATP(4-) dioxygen; CHEBI:15379; Declared type: small_molecule small molecule dioxygen hydrogen peroxide; CHEBI:16240; Declared type: small_molecule small molecule hydrogen peroxide glycerol; CHEBI:17754; Declared type: small_molecule small molecule glycerol glucose; CHEBI:17234; Declared type: small_molecule small molecule glucose iron(2+); CHEBI:29033; Declared type: cofactor cofactor iron(2+) manganese(2+); CHEBI:29035; Declared type: cofactor cofactor manganese(2+) zinc(2+); CHEBI:29105; Declared type: small_molecule small molecule zinc(2+) magnesium(2+); CHEBI:18420; Declared type: small_molecule small molecule magnesium(2+) copper(2+); CHEBI:29036; Declared type: small_molecule small molecule copper(2+) calcium(2+); CHEBI:29108; Declared type: small_molecule small molecule calcium(2+) Lactaldehyde reductase; UniProtKB:P0A9S1; Declared type: protein protein Lactaldehyde reductase Lactaldehyde dehydrogenase; UniProtKB:P25553; Declared type: protein protein Lactaldehyde dehydrogenase DNA-binding transcriptional dual regulator CRP; UniProtKB:P0ACJ8; Declared type: protein protein DNA-binding transcriptional dual regulator CRP L-fucose operon activator; UniProtKB:P0ACK8; Declared type: protein protein L-fucose operon activator Fumarate and nitrate reduction regulatory protein; UniProtKB:P0A9E5; Declared type: protein protein Fumarate and nitrate reduction regulatory protein Chromosomal replication initiator protein DnaA; UniProtKB:P03004; Declared type: protein protein Chromosomal replication initiator protein DnaA Aerobic respiration control protein ArcA; UniProtKB:P0A9Q1; Declared type: protein protein Aerobic respiration control protein ArcA Uncharacterized HTH-type transcriptional regulator YgfI; UniProtKB:P52044; Declared type: protein protein Uncharacterized HTH-type transcriptional regulator YgfI Multiple antibiotic resistance protein MarA; UniProtKB:P0ACH5; Declared type: protein protein Multiple antibiotic resistance protein MarA Regulatory protein SoxS; UniProtKB:P0A9E2; Declared type: protein protein Regulatory protein SoxS Right origin-binding protein; UniProtKB:P0ACI0; Declared type: protein protein Right origin-binding protein Integration host factor subunit alpha; UniProtKB:P0A6X7; Declared type: protein protein Integration host factor subunit alpha Integration host factor subunit beta; UniProtKB:P0A6Y1; Declared type: protein protein Integration host factor subunit beta L-1,2-propanediol oxidoreductase; EcoCyc:LACTALDREDUCT-CPLX; Declared type: complex complex L-1,2-propanediol oxidoreductase aldehyde dehydrogenase A, NAD-linked; EcoCyc:ALD-CPLX; Declared type: complex complex aldehyde dehydrogenase A, NAD-linked DNA-binding transcriptional dual regulator CRP; EcoCyc:PC00004; Declared type: complex complex DNA-binding transcriptional dual regulator CRP CRP-cyclic-AMP DNA-binding transcriptional dual regulator; EcoCyc:CPLX0-226; Declared type: complex complex CRP-cyclic-AMP DNA-binding transcriptional dual regulator FucR-L-fuculose-1-phosphate DNA-binding transcriptional activator; EcoCyc:CPLX0-7650; Declared type: complex complex FucR-L-fuculose-1-phosphate DNA-binding transcriptional activator DNA-binding transcriptional dual regulator FNR; EcoCyc:CPLX0-7797; Declared type: complex complex DNA-binding transcriptional dual regulator FNR DnaA-ATP DNA-binding transcriptional dual regulator; EcoCyc:MONOMER0-160; Declared type: complex complex DnaA-ATP DNA-binding transcriptional dual regulator DNA-binding transcriptional dual regulator IHF; EcoCyc:PC00027; Declared type: complex complex DNA-binding transcriptional dual regulator IHF cytosol; GO:0005829; Declared type: cellular_component cellular component cytosol fucO; Entrez:947273; Declared type: gene gene fucO aldA; Entrez:945672; Declared type: gene gene aldA tetra-mu3-sulfido-tetrairon; CHEBI:49883; Declared type: cofactor cofactor tetra-mu3-sulfido-tetrairon nitric oxide; CHEBI:16480; Declared type: small_molecule small molecule nitric oxide L-fucose; CHEBI:18287; Declared type: small_molecule small molecule L-fucose L-rhamnose; CHEBI:62345; Declared type: small_molecule small molecule L-rhamnose ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+); RHEA:27631; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+) glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+); RHEA:20002; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+) glycolate and glyoxylate degradation III; MetaCyc:PWY-6649; Declared type: pathway pathway glycolate and glyoxylate degradation III glycolate and glyoxylate degradation II; MetaCyc:GLYOXDEG-PWY; Declared type: pathway pathway glycolate and glyoxylate degradation II glycolate and glyoxylate degradation I; MetaCyc:GLYCOLATEMET-PWY; Declared type: pathway pathway glycolate and glyoxylate degradation I superpathway of glycol metabolism and degradation; MetaCyc:GLYCOL-GLYOXDEG-PWY; Declared type: pathway pathway superpathway of glycol metabolism and degradation D-Arabinose Degradation I; PathBank:SMP0002052; Declared type: pathway pathway D-Arabinose Degradation I Glycolate and Glyoxylate Degradation; PathBank:SMP0000847; Declared type: pathway pathway Glycolate and Glyoxylate Degradation ethylene glycol degradation; MetaCyc:PWY0-1280; Declared type: pathway pathway ethylene glycol degradation L-1,2-propanediol oxidoreductase; EcoCyc:LACTALDREDUCT-CPLX; Declared type: complex; experimental construct: 1983 E15-derived selected G1/G3/EG3 crude extracts; EG3 selected from G3. Historical proteins were not sequenced as current MG1655 accessions. EG oxidation: 250 mM EG, 0.33 mM NAD, 100 mM glycine pH 9.5, 25 C.; Evidence PMID:6336729: The study assayed EG oxidation in extracts of selected E15 derivatives, with 250 mM EG and NAD at alkaline pH. The selected strain history is distinct from the current reference strain. (PDF pp. 134-136, Materials and Methods and Table 1) experimental construct L-1,2-propanediol oxidoreductase [experimental construct: 1983 E15-derived selected G1/G3/EG3 crude extracts; EG3 selected from G3. Historical proteins were…] aldehyde dehydrogenase A, NAD-linked; EcoCyc:ALD-CPLX; Declared type: complex; experimental construct: 1983 E15-derived G1/G3/EG3 crude extracts: AldA assay 1 mM glycolaldehyde, 2.5 mM NAD, glycine pH 9.5, 25 C. Product chromatography separately used 3.5 mM glycolaldehyde and 5 mM NAD, 30 min at 37 C. Historical preparation is distinct from current MG1655.; Evidence PMID:6336729: The primary methods distinguish the spectrophotometric aldehyde-dehydrogenase assay from the separate glycolate product-identification incubation. (PDF pp. 134-137, Enzyme assays and product-identification experiment) experimental construct aldehyde dehydrogenase A, NAD-linked [experimental construct: 1983 E15-derived G1/G3/EG3 crude extracts: AldA assay 1 mM glycolaldehyde, 2.5 mM NAD, glycine pH…] aldehyde dehydrogenase A, NAD-linked; EcoCyc:ALD-CPLX; Declared type: complex; experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography; vector construction refers to earlier work. Phosphate 100 mM pH 7.5, NaCl 100 mM, beta-mercaptoethanol 20 mM, NAD 2 mM; substrate specified per assay.; Evidence PMID:16731973: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p) experimental construct aldehyde dehydrogenase A, NAD-linked [experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography;…] aldehyde dehydrogenase A, NAD-linked; EcoCyc:ALD-CPLX; Declared type: complex; experimental construct: 2019 MG1655 aldA DNA cloned in pET28a/pVT-ALDA, produced in BL21(DE3) as N-terminal His-tagged protein and purified on cobalt resin; 1 mM IPTG, 16 C. Assay: 5 mM glycolaldehyde, 3 mM NAD, Tris pH 7.5, 10 mM MgCl2, 37 C.; Evidence PMID:31850327: The aldA gene was amplified from MG1655 genomic DNA for the engineered expression constructs. (XPath /article/body/sec[2]/sec[2]/p[2]); Evidence PMID:31850327: Methods describe pET28a expression in BL21(DE3), 1 mM IPTG at 16 C and cobalt-resin purification of His-tagged protein. (XPath /article/body/sec[2]/sec[5]/p[1]); Evidence PMID:31850327: Table 4 explicitly describes purified proteins carrying an N-terminal His tag. (XPath /article/body/sec[3]/sec[2]/table-wrap/caption/p) experimental construct aldehyde dehydrogenase A, NAD-linked [experimental construct: 2019 MG1655 aldA DNA cloned in pET28a/pVT- ALDA, produced in BL21(DE3) as N-terminal His-tagged…] L-1,2-propanediol oxidoreductase; EcoCyc:LACTALDREDUCT-CPLX; Declared type: complex; experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in M15(pREP4). This qualifier applies to the crystal-site evidence; the separate cleaved-WT solution comparison is contextualized in the record description. Current P0A9S1 is 382 residues.; Evidence PMID:15995211: The FucO crystallographic preparation used ECL1-derived pCM1 in pQE32, N-terminal His6 expression in M15(pREP4) and Ni-NTA purification. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[2]/section[3]/p[1]) experimental construct L-1,2-propanediol oxidoreductase [experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in…] L-1,2-propanediol oxidoreductase; EcoCyc:LACTALDREDUCT-CPLX; Declared type: complex; experimental construct: Older partially purified oxidoreductase from an E. coli K-12 mutant selected for growth on L-1,2-propanediol; abstract-only preparation information. Ferrous and manganous support are alternatives, not simultaneous obligatory cofactors.; Evidence PMID:4306747: The inspected abstract identifies a partially purified mutant K-12 enzyme and alternative added ferrous or manganous ions. Full experimental details were not acquired. (XPath //PubmedArticle[MedlineCitation/PMID="4306747"]/MedlineCitation/Article/Abstract) experimental construct L-1,2-propanediol oxidoreductase [experimental construct: Older partially purified oxidoreductase from an E. coli K-12 mutant selected for growth on…] L-1,2-propanediol oxidoreductase; EcoCyc:LACTALDREDUCT-CPLX; Declared type: complex; experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in M15(pREP4). The crystal site count is distinct from solution Fe occupancy. Paper residue numbers are retained; current P0A9S1 is 382 residues.; Evidence PMID:15995211: The FucO crystallographic preparation used ECL1-derived pCM1 in pQE32, N-terminal His6 expression in M15(pREP4) and Ni-NTA purification. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[2]/section[3]/p[1]) experimental construct L-1,2-propanediol oxidoreductase [experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in…] L-1,2-propanediol oxidoreductase; EcoCyc:LACTALDREDUCT-CPLX; Declared type: complex; experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in M15(pREP4). The crystal site count is distinct from solution Fe occupancy. Paper residue numbers are retained; current P0A9S1 is 382 residues. Protection assay includes 0.1 mM ZnCl2.; Evidence PMID:15995211: The FucO crystallographic preparation used ECL1-derived pCM1 in pQE32, N-terminal His6 expression in M15(pREP4) and Ni-NTA purification. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[2]/section[3]/p[1]) experimental construct L-1,2-propanediol oxidoreductase [experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in…] aldehyde dehydrogenase A, NAD-linked; EcoCyc:ALD-CPLX; Declared type: complex; experimental construct: 1988 purified ECL3 AldA from the constitutive fucA/fucO, noninducible fucPIK background. Fig. 5 uses glycolaldehyde 1 mM, NAD 2.5 mM, glycine 100 mM pH 9.5 at 25 C. This historical preparation is not an unqualified MG1655 measurement.; Evidence PMID:3275622: The study uses purified ECL3 lactaldehyde dehydrogenase; its standard assay substitutes glycolaldehyde for lactaldehyde and follows NADH formation. (PDF pp. 417-418, strain Table 1 and Enzyme assays; p. 420 Fig. 5) experimental construct aldehyde dehydrogenase A, NAD-linked [experimental construct: 1988 purified ECL3 AldA from the constitutive fucA/fucO, noninducible fucPIK background. Fig. 5…] aldehyde dehydrogenase A, NAD-linked; EcoCyc:ALD-CPLX; Declared type: complex; experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography; vector construction refers to earlier work. Phosphate 100 mM pH 7.5, NaCl 100 mM, beta-mercaptoethanol 20 mM, NAD 2 mM; substrate specified per assay.; Evidence PMID:16731973: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p) experimental construct aldehyde dehydrogenase A, NAD-linked [experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography;…] aldehyde dehydrogenase A, NAD-linked; EcoCyc:ALD-CPLX; Declared type: complex; experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography; vector construction refers to earlier work. Phosphate 100 mM pH 7.5, NaCl 100 mM, beta-mercaptoethanol 20 mM, NAD 2 mM; substrate specified per assay.; Evidence PMID:16731973: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p) experimental construct aldehyde dehydrogenase A, NAD-linked [experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography;…] aldehyde dehydrogenase A, NAD-linked; EcoCyc:ALD-CPLX; Declared type: complex; experimental construct: 2006 N-terminal His6 AldA produced in BL21; this endpoint is restricted to p-nitrophenyl-acetate esterase activity at pH 7.4, not glycolaldehyde dehydrogenase or pathway flux.; Evidence PMID:16731973: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p) experimental construct aldehyde dehydrogenase A, NAD-linked [experimental construct: 2006 N-terminal His6 AldA produced in BL21; this endpoint is restricted to p-nitrophenyl-acetate…] L-1,2-propanediol oxidoreductase; EcoCyc:LACTALDREDUCT-CPLX; Declared type: complex; molecular state: Aerobically inactivated FucO preparation in the native annotation; reactivation by high NAD is source-limited. Concentration, binding mechanism and an EG-specific activity assay are not established by the inspected abstract.; Evidence EcoCyc:LACTALDREDUCT-MONOMER: The native comment distinguishes aerobic inactivation from subsequent in-vitro NAD-dependent reactivation. (XPath /ptools-xml/Protein/comment) molecular state L-1,2-propanediol oxidoreductase [molecular state: Aerobically inactivated FucO preparation in the native annotation; reactivation by high NAD is…] DNA-binding transcriptional dual regulator FNR; EcoCyc:CPLX0-7797; Declared type: complex; molecular state: Active dimeric FNR with [4Fe-4S] clusters; the native annotation distinguishes this state from inactive monomeric apo-FNR and oxygen-converted [2Fe-2S] forms.; Evidence EcoCyc:CPLX0-7797: The native comment explicitly distinguishes active anaerobic Fe-S dimer from oxygen-inactivated and apo forms. (XPath /ptools-xml/Protein/comment) molecular state DNA-binding transcriptional dual regulator FNR [molecular state: Active dimeric FNR with [4Fe-4S] clusters; the native annotation distinguishes this state from…] DNA-binding transcriptional dual regulator FNR; EcoCyc:CPLX0-7797; Declared type: complex; molecular state: Active dimeric FNR with [4Fe-4S] clusters; the native annotation distinguishes this state from inactive monomeric apo-FNR and oxygen-converted [2Fe-2S] forms.; Evidence EcoCyc:CPLX0-7797: The native comment explicitly distinguishes active anaerobic Fe-S dimer from oxygen-inactivated and apo forms. (XPath /ptools-xml/Protein/comment) molecular state DNA-binding transcriptional dual regulator FNR [molecular state: Active dimeric FNR with [4Fe-4S] clusters; the native annotation distinguishes this state from…] CRP-cyclic-AMP DNA-binding transcriptional dual regulator; EcoCyc:CPLX0-226; Declared type: complex; experimental construct: Native CRP-cAMP reference assembly; direct 1997 binding used purified CRP supplied by S. Adhya, with 20 micromolar cAMP. Production strain/tag details were not reported in the inspected methods. Reporter assays used RYC1000 single-copy aldA-lacZ fusions.; Evidence PMID:9202484: The methods identify purified CRP supplied by S. Adhya and describe the binding incubation. (XPath /html/body/div/div[1]/div[7]/div[7]/p[1]); Evidence PMID:9202484: The promoter fusions were constructed in pRS550 and transferred by lambdaRS45 to single-copy reporter backgrounds. (XPath /html/body/div/div[1]/div[7]/div[5]/p[3]) experimental construct CRP-cyclic-AMP DNA-binding transcriptional dual regulator [experimental construct: Native CRP-cAMP reference assembly; direct 1997 binding used purified CRP supplied by S. Adhya,…] Aerobic respiration control protein ArcA; UniProtKB:P0A9Q1; Declared type: protein; molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native PHOSPHO-ARCA. This qualifier preserves the modified regulator; a loss-of-arcA expression experiment alone does not measure its phosphorylation state.; Evidence EcoCyc:PHOSPHO-ARCA: The native phosphorylated regulator has unmodified-form ARCA-MONOMER. Its modified identity is retained as source evidence rather than silently flattened to the reference chain. (XPath /ptools-xml/Protein/unmodified-form | /ptools-xml/Protein/common-name); Evidence EcoCyc:ARCA-MONOMER: This native reference chain has an explicit UniProt unification cross-reference to P0A9Q1. It grounds identity only, not the assay construct or regulatory sign. (XPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9Q1"]) molecular state Aerobic respiration control protein ArcA [molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native…] Aerobic respiration control protein ArcA; UniProtKB:P0A9Q1; Declared type: protein; molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native PHOSPHO-ARCA. This qualifier preserves the modified regulator; a loss-of-arcA expression experiment alone does not measure its phosphorylation state.; Evidence EcoCyc:PHOSPHO-ARCA: The native phosphorylated regulator has unmodified-form ARCA-MONOMER. Its modified identity is retained as source evidence rather than silently flattened to the reference chain. (XPath /ptools-xml/Protein/unmodified-form | /ptools-xml/Protein/common-name); Evidence EcoCyc:ARCA-MONOMER: This native reference chain has an explicit UniProt unification cross-reference to P0A9Q1. It grounds identity only, not the assay construct or regulatory sign. (XPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9Q1"]) molecular state Aerobic respiration control protein ArcA [molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native…] Aerobic respiration control protein ArcA; UniProtKB:P0A9Q1; Declared type: protein; molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native PHOSPHO-ARCA. This qualifier preserves the modified regulator; a loss-of-arcA expression experiment alone does not measure its phosphorylation state.; Evidence EcoCyc:PHOSPHO-ARCA: The native phosphorylated regulator has unmodified-form ARCA-MONOMER. Its modified identity is retained as source evidence rather than silently flattened to the reference chain. (XPath /ptools-xml/Protein/unmodified-form | /ptools-xml/Protein/common-name); Evidence EcoCyc:ARCA-MONOMER: This native reference chain has an explicit UniProt unification cross-reference to P0A9Q1. It grounds identity only, not the assay construct or regulatory sign. (XPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9Q1"]) molecular state Aerobic respiration control protein ArcA [molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native…] DNA-binding transcriptional dual regulator FNR; EcoCyc:CPLX0-7797; Declared type: complex; molecular state: Native active FNR dimer with [4Fe-4S] clusters. The aldA regulatory link is expression evidence with a computational binding-site assignment, not a purified aldA-promoter binding measurement.; Evidence EcoCyc:CPLX0-7797: The native annotation links the active Fe-S-containing dimer to anaerobic transcriptional control. (XPath /ptools-xml/Protein/comment) molecular state DNA-binding transcriptional dual regulator FNR [molecular state: Native active FNR dimer with [4Fe-4S] clusters. The aldA regulatory link is expression evidence…] Uncharacterized HTH-type transcriptional regulator YgfI; UniProtKB:P52044; Declared type: protein; experimental construct: 2022 BW25113, srsR deletion JW5476, and pCA24N-derived ASKA SrsR overexpression versus empty-vector controls; LB 37 C, 150 rpm, 24 h, 0.5 mM IPTG. Reference P52044/YgfI is named SrsR by the study; this is an expression construct context.; Evidence PMID:35682733: Methods distinguish W3110 genomic donor and BL21(DE3) protein production from BW25113/JW5476 and ASKA overexpression strains used for the expression comparison. (XPath /article/body/sec[4]/sec[1]/p); Evidence PMID:35682733: RT-qPCR used 24-hour LB cultures and 16S normalization, with three independent experiments. (XPath /article/body/sec[4]/sec[7]/p) experimental construct Uncharacterized HTH-type transcriptional regulator YgfI [experimental construct: 2022 BW25113, srsR deletion JW5476, and pCA24N-derived ASKA SrsR overexpression versus empty- vector…]

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Escherichia coli
NCBITaxon:562		taxon
Escherichia coli K-12
NCBITaxon:83333		taxon
Escherichia coli str. K-12 substr. MG1655
NCBITaxon:511145		taxon
ethylene glycol
CHEBI:30742		small molecule
NAD(1-)
CHEBI:57540		cofactor
glycolaldehyde
CHEBI:17071		small molecule
NADH(2-)
CHEBI:57945		small molecule
hydron
CHEBI:15378		small molecule
water
CHEBI:15377		small molecule
glycolate
CHEBI:29805		small molecule
glycolic acid
CHEBI:17497		small molecule
3',5'-cyclic AMP(1-)
CHEBI:58165		small molecule
L-fuculose 1-phosphate(2-)
CHEBI:57846		small molecule
ATP(4-)
CHEBI:30616		small molecule
dioxygen
CHEBI:15379		small molecule
hydrogen peroxide
CHEBI:16240		small molecule
glycerol
CHEBI:17754		small molecule
glucose
CHEBI:17234		small molecule
iron(2+)
CHEBI:29033		cofactor
manganese(2+)
CHEBI:29035		cofactor
zinc(2+)
CHEBI:29105		small molecule
magnesium(2+)
CHEBI:18420		small molecule
copper(2+)
CHEBI:29036		small molecule
calcium(2+)
CHEBI:29108		small molecule
Lactaldehyde reductase
UniProtKB:P0A9S1		protein
Lactaldehyde dehydrogenase
UniProtKB:P25553		protein
DNA-binding transcriptional dual regulator CRP
UniProtKB:P0ACJ8		protein
L-fucose operon activator
UniProtKB:P0ACK8		protein
Fumarate and nitrate reduction regulatory protein
UniProtKB:P0A9E5		protein
Chromosomal replication initiator protein DnaA
UniProtKB:P03004		protein
Aerobic respiration control protein ArcA
UniProtKB:P0A9Q1		protein
Uncharacterized HTH-type transcriptional regulator YgfI
UniProtKB:P52044		protein
Multiple antibiotic resistance protein MarA
UniProtKB:P0ACH5		protein
Regulatory protein SoxS
UniProtKB:P0A9E2		protein
Right origin-binding protein
UniProtKB:P0ACI0		protein
Integration host factor subunit alpha
UniProtKB:P0A6X7		protein
Integration host factor subunit beta
UniProtKB:P0A6Y1		protein
L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX		complex
aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX		complex
DNA-binding transcriptional dual regulator CRP
EcoCyc:PC00004		complex
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		complex
FucR-L-fuculose-1-phosphate DNA-binding transcriptional activator
EcoCyc:CPLX0-7650		complex
DNA-binding transcriptional dual regulator FNR
EcoCyc:CPLX0-7797		complex
DnaA-ATP DNA-binding transcriptional dual regulator
EcoCyc:MONOMER0-160		complex
DNA-binding transcriptional dual regulator IHF
EcoCyc:PC00027		complex
cytosol
GO:0005829		cellular component
fucO
Entrez:947273		gene
aldA
Entrez:945672		gene
tetra-mu3-sulfido-tetrairon
CHEBI:49883		cofactor
nitric oxide
CHEBI:16480		small molecule
L-fucose
CHEBI:18287		small molecule
L-rhamnose
CHEBI:62345		small molecule
ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+)
RHEA:27631		molecular activityleft to right
glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002		molecular activityleft to right
glycolate and glyoxylate degradation III
MetaCyc:PWY-6649		pathway
glycolate and glyoxylate degradation II
MetaCyc:GLYOXDEG-PWY		pathway
glycolate and glyoxylate degradation I
MetaCyc:GLYCOLATEMET-PWY		pathway
superpathway of glycol metabolism and degradation
MetaCyc:GLYCOL-GLYOXDEG-PWY		pathway
D-Arabinose Degradation I
PathBank:SMP0002052		pathway
Glycolate and Glyoxylate Degradation
PathBank:SMP0000847		pathway

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+)
RHEA:27631		part_of

The exact native reaction-list includes GLYCOLALDREDUCT-RXN. The two-event pathway terminates at glycolate; downstream assimilation remains an interface.

MetaCyc:PWY0-1280
  • MetaCyc:PWY0-1280

    Source assertion: The exact native reaction-list includes GLYCOLALDREDUCT-RXN. The two-event pathway terminates at glycolate; downstream assimilation remains an interface.

    Source locationXPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="GLYCOLALDREDUCT-RXN"]
glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002		part_of

The exact native reaction-list includes GLYCOLALD-DEHYDROG-RXN. The two-event pathway terminates at glycolate; downstream assimilation remains an interface.

MetaCyc:PWY0-1280
  • MetaCyc:PWY0-1280

    Source assertion: The exact native reaction-list includes GLYCOLALD-DEHYDROG-RXN. The two-event pathway terminates at glycolate; downstream assimilation remains an interface.

    Source locationXPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="GLYCOLALD-DEHYDROG-RXN"]
ethylene glycol
CHEBI:30742		consumes

RHEA:27631 substrates contains CHEBI:30742, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+)
RHEA:27631
  • RHEA:27631

    Source assertion: RHEA:27631 substrates contains CHEBI:30742, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:27631 rh:substrates; http://rdf.rhea-db.org/Participant_27630_compound_6252 rh:compound http://rdf.rhea-db.org/Compound_6252; rh:contains1
NAD(1-)
CHEBI:57540		consumes

RHEA:27631 substrates contains CHEBI:57540, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+)
RHEA:27631
  • RHEA:27631

    Source assertion: RHEA:27631 substrates contains CHEBI:57540, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:27631 rh:substrates; http://rdf.rhea-db.org/Participant_27630_compound_3484 rh:compound http://rdf.rhea-db.org/Compound_3484; rh:contains1
ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+)
RHEA:27631		produces

RHEA:27631 products contains CHEBI:17071, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

glycolaldehyde
CHEBI:17071
  • RHEA:27631

    Source assertion: RHEA:27631 products contains CHEBI:17071, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:27631 rh:products; http://rdf.rhea-db.org/Participant_27630_compound_3867 rh:compound http://rdf.rhea-db.org/Compound_3867; rh:contains1
ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+)
RHEA:27631		produces

RHEA:27631 products contains CHEBI:57945, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

NADH(2-)
CHEBI:57945
  • RHEA:27631

    Source assertion: RHEA:27631 products contains CHEBI:57945, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:27631 rh:products; http://rdf.rhea-db.org/Participant_27630_compound_1650 rh:compound http://rdf.rhea-db.org/Compound_1650; rh:contains1
ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+)
RHEA:27631		produces

RHEA:27631 products contains CHEBI:15378, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

hydron
CHEBI:15378
  • RHEA:27631

    Source assertion: RHEA:27631 products contains CHEBI:15378, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:27631 rh:products; http://rdf.rhea-db.org/Participant_27630_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249; rh:contains1
glycolaldehyde
CHEBI:17071		consumes

RHEA:20002 substrates contains CHEBI:17071, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002
  • RHEA:20002

    Source assertion: RHEA:20002 substrates contains CHEBI:17071, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:20002 rh:substrates; http://rdf.rhea-db.org/Participant_20001_compound_3867 rh:compound http://rdf.rhea-db.org/Compound_3867; rh:contains1
NAD(1-)
CHEBI:57540		consumes

RHEA:20002 substrates contains CHEBI:57540, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002
  • RHEA:20002

    Source assertion: RHEA:20002 substrates contains CHEBI:57540, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:20002 rh:substrates; http://rdf.rhea-db.org/Participant_20001_compound_3484 rh:compound http://rdf.rhea-db.org/Compound_3484; rh:contains1
water
CHEBI:15377		consumes

RHEA:20002 substrates contains CHEBI:15377, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002
  • RHEA:20002

    Source assertion: RHEA:20002 substrates contains CHEBI:15377, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:20002 rh:substrates; http://rdf.rhea-db.org/Participant_20001_compound_1283 rh:compound http://rdf.rhea-db.org/Compound_1283; rh:contains1
glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002		produces

RHEA:20002 products contains CHEBI:29805, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

glycolate
CHEBI:29805
  • RHEA:20002

    Source assertion: RHEA:20002 products contains CHEBI:29805, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:20002 rh:products; http://rdf.rhea-db.org/Participant_20001_compound_3455 rh:compound http://rdf.rhea-db.org/Compound_3455; rh:contains1
glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002		produces

RHEA:20002 products contains CHEBI:57945, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

NADH(2-)
CHEBI:57945
  • RHEA:20002

    Source assertion: RHEA:20002 products contains CHEBI:57945, coefficient 1. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:20002 rh:products; http://rdf.rhea-db.org/Participant_20001_compound_1650 rh:compound http://rdf.rhea-db.org/Compound_1650; rh:contains1
glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002		produces

RHEA:20002 products contains CHEBI:15378, coefficient 2. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

hydron
CHEBI:15378
  • RHEA:20002

    Source assertion: RHEA:20002 products contains CHEBI:15378, coefficient 2. The exact directional RDF species and containsN multiplicity define this balanced oxidative side.

    Source locationRHEA:20002 rh:products; http://rdf.rhea-db.org/Participant_20001_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249; rh:contains2
ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+)
RHEA:27631		provides_input_for

The ordered oxidative events share glycolaldehyde: GLYCOLALDREDUCT-RXN precedes GLYCOLALD-DEHYDROG-RXN. No additional transport or energy-coupling event is supplied by this relation.

glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002
  • MetaCyc:PWY0-1280

    Source assertion: The ordered oxidative events share glycolaldehyde: GLYCOLALDREDUCT-RXN precedes GLYCOLALD-DEHYDROG-RXN. No additional transport or energy-coupling event is supplied by this relation.

    Source locationXPath /ptools-xml/Pathway/reaction-ordering
L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX		catalyzes

The native enzyme slot identifies LACTALDREDUCT-CPLX as the catalytic assembly and assigns physiological left-to-right chemistry. Reference assembly identity does not establish ordinary wild-type EG growth.

ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+)
RHEA:27631
  • EcoCyc:GLYCOLALDREDUCT-ENZRXN

    Source assertion: The native enzyme slot identifies LACTALDREDUCT-CPLX as the catalytic assembly and assigns physiological left-to-right chemistry. Reference assembly identity does not establish ordinary wild-type EG growth.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/enzyme | /ptools-xml/Enzymatic-Reaction/reaction-direction
aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX		catalyzes

The native enzyme slot identifies ALD-CPLX as the catalytic assembly and assigns physiological left-to-right chemistry. Reference assembly identity does not establish ordinary wild-type EG growth.

glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002
  • EcoCyc:GLYCOLALD-DEHYDROG-ENZRXN

    Source assertion: The native enzyme slot identifies ALD-CPLX as the catalytic assembly and assigns physiological left-to-right chemistry. Reference assembly identity does not establish ordinary wild-type EG growth.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/enzyme | /ptools-xml/Enzymatic-Reaction/reaction-direction
L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX		has_part

The native component slot specifies 2 copies of LACTALDREDUCT-MONOMER. This is assembly stoichiometry, not independent catalysis by each chain.

Lactaldehyde reductase
UniProtKB:P0A9S1
  • EcoCyc:LACTALDREDUCT-CPLX

    Source assertion: The native component slot specifies 2 copies of LACTALDREDUCT-MONOMER. This is assembly stoichiometry, not independent catalysis by each chain.

    Source locationXPath /ptools-xml/Protein/component
  • EcoCyc:LACTALDREDUCT-MONOMER

    Source assertion: The exact native monomer unification cross-reference identifies UniProtKB:P0A9S1. The current reference chain is distinct from historical or tagged assay preparations.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9S1"]
  • UniProtKB:P0A9S1

    Source assertion: The issuing reviewed annotation independently identifies a homodimer.

    Source locationcomments[commentType=SUBUNIT]
Lactaldehyde reductase
UniProtKB:P0A9S1		located_in

The native cytosol GO annotation grounds this location. Its attached evidence class is retained; no fresh localization experiment or universal condition-independent distribution is claimed.

cytosol
GO:0005829
  • EcoCyc:LACTALDREDUCT-MONOMER

    Source assertion: The native cytosol GO annotation grounds this location. Its attached evidence class is retained; no fresh localization experiment or universal condition-independent distribution is claimed.

    Source locationXPath /ptools-xml/Protein/has-go-term[GO-Term[@frameid="GO:0005829"]]
aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX		has_part

The native component slot specifies 4 copies of LACTALDDEHYDROG-MONOMER. This is assembly stoichiometry, not independent catalysis by each chain.

Lactaldehyde dehydrogenase
UniProtKB:P25553
  • EcoCyc:ALD-CPLX

    Source assertion: The native component slot specifies 4 copies of LACTALDDEHYDROG-MONOMER. This is assembly stoichiometry, not independent catalysis by each chain.

    Source locationXPath /ptools-xml/Protein/component
  • EcoCyc:LACTALDDEHYDROG-MONOMER

    Source assertion: The exact native monomer unification cross-reference identifies UniProtKB:P25553. The current reference chain is distinct from historical or tagged assay preparations.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P25553"]
  • UniProtKB:P25553

    Source assertion: The issuing reviewed annotation independently identifies a homotetramer; earlier dimer estimates are superseded by later tetramer evidence.

    Source locationcomments[commentType=SUBUNIT]
Lactaldehyde dehydrogenase
UniProtKB:P25553		located_in

The native cytosol GO annotation grounds this location. Its attached evidence class is retained; no fresh localization experiment or universal condition-independent distribution is claimed.

cytosol
GO:0005829
  • EcoCyc:LACTALDDEHYDROG-MONOMER

    Source assertion: The native cytosol GO annotation grounds this location. Its attached evidence class is retained; no fresh localization experiment or universal condition-independent distribution is claimed.

    Source locationXPath /ptools-xml/Protein/has-go-term[GO-Term[@frameid="GO:0005829"]]
L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX

experimental construct: 1983 E15-derived selected G1/G3/EG3 crude extracts; EG3 selected from G3. Historical proteins were not sequenced as current MG1655 accessions. EG oxidation: 250 mM EG, 0.33 mM NAD, 100 mM glycine pH 9.5, 25 C.

Qualification evidence
  • PMID:6336729

    Source assertion: The study assayed EG oxidation in extracts of selected E15 derivatives, with 250 mM EG and NAD at alkaline pH. The selected strain history is distinct from the current reference strain.

    Source locationPDF pp. 134-136, Materials and Methods and Table 1
catalyzes

Selected EG3 extracts oxidized EG with NAD. Constitutive oxidoreductase levels increased across G1/G3/EG3; the pathway selection did not identify a sequenced causal allele.

ethylene glycol + NAD(+) => glycolaldehyde + NADH + H(+)
RHEA:27631
  • PMID:6336729

    Source assertion: Selected EG3 extracts oxidized EG with NAD. Constitutive oxidoreductase levels increased across G1/G3/EG3; the pathway selection did not identify a sequenced causal allele.

    Source locationPDF pp. 134-138, strain selection, Table 1 and enzymatic activities
aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX

experimental construct: 1983 E15-derived G1/G3/EG3 crude extracts: AldA assay 1 mM glycolaldehyde, 2.5 mM NAD, glycine pH 9.5, 25 C. Product chromatography separately used 3.5 mM glycolaldehyde and 5 mM NAD, 30 min at 37 C. Historical preparation is distinct from current MG1655.

Qualification evidence
  • PMID:6336729

    Source assertion: The primary methods distinguish the spectrophotometric aldehyde-dehydrogenase assay from the separate glycolate product-identification incubation.

    Source locationPDF pp. 134-137, Enzyme assays and product-identification experiment
catalyzes

Historical extract assays oxidized glycolaldehyde with NAD; paper chromatography identified glycolate after incubation. This directly supports the second event without assigning a sequenced genotype to E15 derivatives.

glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002
  • PMID:6336729

    Source assertion: Historical extract assays oxidized glycolaldehyde with NAD; paper chromatography identified glycolate after incubation. This directly supports the second event without assigning a sequenced genotype to E15 derivatives.

    Source locationPDF pp. 134-137, Enzyme assays and Identification of metabolic intermediates
aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX

experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography; vector construction refers to earlier work. Phosphate 100 mM pH 7.5, NaCl 100 mM, beta-mercaptoethanol 20 mM, NAD 2 mM; substrate specified per assay.

Qualification evidence
  • PMID:16731973

    Source assertion: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p
catalyzes

Direct glycolaldehyde kinetics in the 2006 His6 preparation: Table 1 Km 0.14 mM and kcat 1100 min-1. These are not pooled with 1983 pH 9.5 extract values or 2019 Tris/Mg/37 C values.

glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002
  • PMID:16731973

    Source assertion: The substrate comparison directly measures glycolaldehyde oxidation by purified AldA. Table 1 reports Km 0.14 mM and kcat 1100 min-1 for this preparation.

    Source locationXPath //img[contains(@src,"1387tbl1.jpg")]/ancestor::section[1]
  • PMID:16731973

    Source assertion: The activity assay measures NADH formation at 340 nm in phosphate pH 7.5, NaCl and beta-mercaptoethanol with 2 mM NAD; substrate varies by experiment.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[3]/p
aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX

experimental construct: 2019 MG1655 aldA DNA cloned in pET28a/pVT-ALDA, produced in BL21(DE3) as N-terminal His-tagged protein and purified on cobalt resin; 1 mM IPTG, 16 C. Assay: 5 mM glycolaldehyde, 3 mM NAD, Tris pH 7.5, 10 mM MgCl2, 37 C.

Qualification evidence
  • PMID:31850327

    Source assertion: The aldA gene was amplified from MG1655 genomic DNA for the engineered expression constructs.

    Source locationXPath /article/body/sec[2]/sec[2]/p[2]
  • PMID:31850327

    Source assertion: Methods describe pET28a expression in BL21(DE3), 1 mM IPTG at 16 C and cobalt-resin purification of His-tagged protein.

    Source locationXPath /article/body/sec[2]/sec[5]/p[1]
  • PMID:31850327

    Source assertion: Table 4 explicitly describes purified proteins carrying an N-terminal His tag.

    Source locationXPath /article/body/sec[3]/sec[2]/table-wrap/caption/p
catalyzes

Independent direct glycolaldehyde oxidation assay. Table 4 reports Km 0.21 mM, Vmax 1.66 micromol/min/mg and kcat 52 s-1; its Vmax/kcat unit conversion is not internally consistent, so no corrected kinetic constant is silently substituted. This preparation also serves a separate engineered glycoptimus pathway.

glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002
  • PMID:31850327

    Source assertion: The AldA assay directly follows NAD reduction with 5 mM glycolaldehyde and 3 mM NAD in 100 mM Tris pH 7.5 containing 10 mM MgCl2 at 37 C.

    Source locationXPath /article/body/sec[2]/sec[5]/p[2]
  • PMID:31850327

    Source assertion: Table 4 reports AldA Km 0.21 +/- 0.05 mM, Vmax 1.66 +/- 0.31 micromol/min/mg and kcat 52 s-1. The reported Vmax/kcat conversion is inconsistent; these numbers remain separate from other preparations.

    Source locationXPath /article/body/sec[3]/sec[2]/table-wrap/table
L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX

experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in M15(pREP4). This qualifier applies to the crystal-site evidence; the separate cleaved-WT solution comparison is contextualized in the record description. Current P0A9S1 is 382 residues.

Qualification evidence
  • PMID:15995211

    Source assertion: The FucO crystallographic preparation used ECL1-derived pCM1 in pQE32, N-terminal His6 expression in M15(pREP4) and Ni-NTA purification.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[2]/section[3]/p[1]
has_cofactor

The native EG enzyme-reaction entry identifies iron as cofactor. It is catalytic context, not a consumed chemical side.

iron(2+)
CHEBI:29033
  • EcoCyc:GLYCOLALDREDUCT-ENZRXN

    Source assertion: The native EG enzyme-reaction entry identifies iron as cofactor. It is catalytic context, not a consumed chemical side.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/cofactor
  • PMID:15995211

    Source assertion: The His6 pCM1 crystal identifies one Fe site per chain, coordinated by Asp196, His200, His263 and His277 in historical numbering; His267 is not a ligand. The separate WT/mutant solution metal comparison is retained in construct-qualified context.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[2]/p[1]
L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX

experimental construct: Older partially purified oxidoreductase from an E. coli K-12 mutant selected for growth on L-1,2-propanediol; abstract-only preparation information. Ferrous and manganous support are alternatives, not simultaneous obligatory cofactors.

Qualification evidence
  • PMID:4306747

    Source assertion: The inspected abstract identifies a partially purified mutant K-12 enzyme and alternative added ferrous or manganous ions. Full experimental details were not acquired.

    Source locationXPath //PubmedArticle[MedlineCitation/PMID="4306747"]/MedlineCitation/Article/Abstract
has_cofactor

The abstract reports that partially purified oxidoreductase from a selected K-12 propanediol-growing mutant requires added ferrous or manganous ions; kinetics vary by metal. This is alternative preparation-specific support, not an obligatory Mn requirement for EG oxidation.

manganese(2+)
CHEBI:29035
  • PMID:4306747

    Source assertion: The abstract reports that partially purified oxidoreductase from a selected K-12 propanediol-growing mutant requires added ferrous or manganous ions; kinetics vary by metal. This is alternative preparation-specific support, not an obligatory Mn requirement for EG oxidation.

    Source locationXPath //PubmedArticle[MedlineCitation/PMID="4306747"]/MedlineCitation/Article/Abstract
L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX		has_cofactor

NAD coenzyme dependence accompanies the exact Rhea cosubstrate sides. AldA NADP activity in the 1983 alkaline preparation was about tenfold lower; later 2006 assays found no NADP activity under different conditions. The mutant F180T and FucO D39G cofactor expansions do not change the native core stoichiometry.

NAD(1-)
CHEBI:57540
  • EcoCyc:GLYCOLALDREDUCT-ENZRXN

    Source assertion: The native enzyme-reaction annotation supports NAD-dependent catalysis. NAD is also the consumed redox cosubstrate of the formal reaction; this coenzyme relation does not add another chemical equivalent.

    Source locationXPath /ptools-xml/Enzymatic-Reaction
aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX		has_cofactor

NAD coenzyme dependence accompanies the exact Rhea cosubstrate sides. AldA NADP activity in the 1983 alkaline preparation was about tenfold lower; later 2006 assays found no NADP activity under different conditions. The mutant F180T and FucO D39G cofactor expansions do not change the native core stoichiometry.

NAD(1-)
CHEBI:57540
  • EcoCyc:GLYCOLALD-DEHYDROG-ENZRXN

    Source assertion: The native enzyme-reaction annotation supports NAD-dependent catalysis. NAD is also the consumed redox cosubstrate of the formal reaction; this coenzyme relation does not add another chemical equivalent.

    Source locationXPath /ptools-xml/Enzymatic-Reaction
zinc(2+)
CHEBI:29105		inhibits

Direct Zn inhibition was measured in glycolaldehyde reduction with NADH, not as an EG-oxidation IC50. Figure 4 used 0.1 mM ZnCl2 and tested protective FeSO4 at 0.1 and 1 mM; no physiological zinc-regulation threshold is asserted.

L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX

experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in M15(pREP4). The crystal site count is distinct from solution Fe occupancy. Paper residue numbers are retained; current P0A9S1 is 382 residues.

Qualification evidence
  • PMID:15995211

    Source assertion: The FucO crystallographic preparation used ECL1-derived pCM1 in pQE32, N-terminal His6 expression in M15(pREP4) and Ni-NTA purification.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[2]/section[3]/p[1]
  • EcoCyc:REG0-9194

    Source assertion: The exact native regulation assigns Zn(II) inhibition to the FucO enzyme activity; its source evidence is preserved separately from the direct reduction assay.

    Source locationXPath /ptools-xml/Regulation
  • PMID:15995211

    Source assertion: Figure 4 measures His6-FucO glycolaldehyde reduction after treatment with 0.1 mM ZnCl2; additional FeSO4 at 0.1 or 1 mM protects activity.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[2]/figure[2]/figcaption/p
iron(2+)
CHEBI:29033		activates

Protection against Zn-mediated activity loss, measured with glycolaldehyde/NADH. This conditional rescue is not an additional EG-reactant requirement or a direct in vivo iron-activation dose response.

L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX

experimental construct: 2005 ECL1-derived historical 383-residue FucO in pQE32/pCM1, N-terminal His6, produced in M15(pREP4). The crystal site count is distinct from solution Fe occupancy. Paper residue numbers are retained; current P0A9S1 is 382 residues. Protection assay includes 0.1 mM ZnCl2.

Qualification evidence
  • PMID:15995211

    Source assertion: The FucO crystallographic preparation used ECL1-derived pCM1 in pQE32, N-terminal His6 expression in M15(pREP4) and Ni-NTA purification.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[2]/section[3]/p[1]
  • PMID:15995211

    Source assertion: In Figure 4, added iron protects His6-FucO activity against zinc inhibition in the glycolaldehyde-reduction assay.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[2]/figure[2]/figcaption/p
glycolaldehyde
CHEBI:17071		inhibits

The native regulation assigns glycolaldehyde substrate inhibition to AldA. This is a curated annotation citing PMID3308886, not a quotation from an acquired original PDF.

aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX
  • EcoCyc:REG0-9207

    Source assertion: The native regulation assigns glycolaldehyde substrate inhibition to AldA. This is a curated annotation citing PMID3308886, not a quotation from an acquired original PDF.

    Source locationXPath /ptools-xml/Regulation
  • UniProtKB:P25553

    Source assertion: Reviewed AldA annotation reports substrate inhibition, with weaker inhibition by glycolaldehyde than lactaldehyde. This does not preclude activity at the tested lower concentrations.

    Source locationcomments[commentType=ACTIVITY REGULATION]
zinc(2+)
CHEBI:29105		inhibits

The native regulation explicitly assigns Zn(II) inhibition to AldA, citing the older biochemical characterization.

aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX
  • EcoCyc:REG0-9208

    Source assertion: The native regulation explicitly assigns Zn(II) inhibition to AldA, citing the older biochemical characterization.

    Source locationXPath /ptools-xml/Regulation
  • UniProtKB:P25553

    Source assertion: The issuing AldA ACTIVITY REGULATION annotation reports inhibition by Zn(2+), citing PMID3308886. The original paper PDF was not acquired; this is annotation-level biochemical support without a physiological threshold.

    Source locationcomments[commentType=ACTIVITY REGULATION]
manganese(2+)
CHEBI:29035		inhibits

The issuing AldA ACTIVITY REGULATION annotation reports inhibition by Mn(2+), citing PMID3308886. The original paper PDF was not acquired; this is annotation-level biochemical support without a physiological threshold.

aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX
  • UniProtKB:P25553

    Source assertion: The issuing AldA ACTIVITY REGULATION annotation reports inhibition by Mn(2+), citing PMID3308886. The original paper PDF was not acquired; this is annotation-level biochemical support without a physiological threshold.

    Source locationcomments[commentType=ACTIVITY REGULATION]
calcium(2+)
CHEBI:29108		inhibits

The issuing AldA ACTIVITY REGULATION annotation reports inhibition by Ca(2+), citing PMID3308886. The original paper PDF was not acquired; this is annotation-level biochemical support without a physiological threshold.

aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX
  • UniProtKB:P25553

    Source assertion: The issuing AldA ACTIVITY REGULATION annotation reports inhibition by Ca(2+), citing PMID3308886. The original paper PDF was not acquired; this is annotation-level biochemical support without a physiological threshold.

    Source locationcomments[commentType=ACTIVITY REGULATION]
copper(2+)
CHEBI:29036		inhibits

The issuing AldA ACTIVITY REGULATION annotation reports inhibition by Cu(2+), citing PMID3308886. The original paper PDF was not acquired; this is annotation-level biochemical support without a physiological threshold.

aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX
  • UniProtKB:P25553

    Source assertion: The issuing AldA ACTIVITY REGULATION annotation reports inhibition by Cu(2+), citing PMID3308886. The original paper PDF was not acquired; this is annotation-level biochemical support without a physiological threshold.

    Source locationcomments[commentType=ACTIVITY REGULATION]
NADH(2-)
CHEBI:57945		inhibits

Figure 5 directly measures NADH inhibition of purified AldA in the glycolaldehyde oxidation assay, with approximately half inhibition near 0.45 mM and nearly complete inhibition at 1 mM NADH.

aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX

experimental construct: 1988 purified ECL3 AldA from the constitutive fucA/fucO, noninducible fucPIK background. Fig. 5 uses glycolaldehyde 1 mM, NAD 2.5 mM, glycine 100 mM pH 9.5 at 25 C. This historical preparation is not an unqualified MG1655 measurement.

Qualification evidence
  • PMID:3275622

    Source assertion: The study uses purified ECL3 lactaldehyde dehydrogenase; its standard assay substitutes glycolaldehyde for lactaldehyde and follows NADH formation.

    Source locationPDF pp. 417-418, strain Table 1 and Enzyme assays; p. 420 Fig. 5
  • PMID:3275622

    Source assertion: Figure 5 directly measures NADH inhibition of purified AldA in the glycolaldehyde oxidation assay, with approximately half inhibition near 0.45 mM and nearly complete inhibition at 1 mM NADH.

    Source locationPDF p. 420, Fig. 5; standard assay p. 417
NADH(2-)
CHEBI:57945		inhibits

Propionaldehyde dehydrogenase assay, not an independently measured EG-specific inhibition constant. NADH has the opposite sign in the separately retained esterase assay.

aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX

experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography; vector construction refers to earlier work. Phosphate 100 mM pH 7.5, NaCl 100 mM, beta-mercaptoethanol 20 mM, NAD 2 mM; substrate specified per assay.

Qualification evidence
  • PMID:16731973

    Source assertion: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p
  • PMID:16731973

    Source assertion: The 2006 NADH product-inhibition experiment uses propionaldehyde; Table 4 reports an AldA NADH inhibition constant of 157 +/- 40 micromolar.

    Source locationXPath //img[contains(@src,"1387tbl4.jpg")]/ancestor::section[1]
magnesium(2+)
CHEBI:18420		inhibits

Measured propionaldehyde dehydrogenase inhibition in the N-terminal His6 preparation. Mg is not an obligatory AldA cofactor; crystallization Mg or 2019 assay-buffer Mg does not reverse this measured sign.

aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX

experimental construct: 2006 N-terminal His6 AldA expressed in E. coli BL21 and purified by Ni-chelate chromatography; vector construction refers to earlier work. Phosphate 100 mM pH 7.5, NaCl 100 mM, beta-mercaptoethanol 20 mM, NAD 2 mM; substrate specified per assay.

Qualification evidence
  • PMID:16731973

    Source assertion: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p
  • PMID:16731973

    Source assertion: Mg ions inhibit AldA dehydrogenase activity. Table 6 reports about 55% and 44% remaining activity at 2 and 10 mM Mg, respectively, under the propionaldehyde assay conditions.

    Source locationXPath //img[contains(@src,"1387tbl6.jpg")]/ancestor::section[1]
NADH(2-)
CHEBI:57945		activates

Activity sign applies only to the separate p-nitrophenyl-acetate esterase assay (0.1 mM substrate, pH 7.4). NADH raised activity from 135 to 326 nmol/min/mg; NAD did not. This is not activation of EG oxidation or of its aldehyde-dehydrogenase step.

aldehyde dehydrogenase A, NAD-linked
EcoCyc:ALD-CPLX

experimental construct: 2006 N-terminal His6 AldA produced in BL21; this endpoint is restricted to p-nitrophenyl-acetate esterase activity at pH 7.4, not glycolaldehyde dehydrogenase or pathway flux.

Qualification evidence
  • PMID:16731973

    Source assertion: Methods describe BL21 expression of an N-terminal His-tagged recombinant AldA and nickel-chelate purification; the construct differs from the reference untagged protein.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[1]/p
  • PMID:16731973

    Source assertion: NADH activates the separate AldA esterase assay, whereas NAD does not; Table 5 reports about 2.4-fold activation.

    Source locationXPath //img[contains(@src,"1387tbl5.jpg")]/ancestor::section[1]
  • PMID:16731973

    Source assertion: Esterase activity is measured using p-nitrophenyl acetate, a distinct substrate and function from aldehyde oxidation.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/section[6]/p
NAD(1-)
CHEBI:57540		activates

The native comment reports in-vitro reactivation of aerobically inactivated FucO by high NAD concentrations, citing PMID2203757. The inspected abstract does not provide this reactivation assay or a concentration.

L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX

molecular state: Aerobically inactivated FucO preparation in the native annotation; reactivation by high NAD is source-limited. Concentration, binding mechanism and an EG-specific activity assay are not established by the inspected abstract.

Qualification evidence
  • EcoCyc:LACTALDREDUCT-MONOMER

    Source assertion: The native comment distinguishes aerobic inactivation from subsequent in-vitro NAD-dependent reactivation.

    Source locationXPath /ptools-xml/Protein/comment
  • EcoCyc:LACTALDREDUCT-MONOMER

    Source assertion: The native comment reports in-vitro reactivation of aerobically inactivated FucO by high NAD concentrations, citing PMID2203757. The inspected abstract does not provide this reactivation assay or a concentration.

    Source locationXPath /ptools-xml/Protein/comment
dioxygen
CHEBI:15379		inhibits

Condition-dependent oxidative inactivation of reference-family FucO preparations. This is not stoichiometric oxygen consumption in RHEA27631, universal direct oxygen binding, or an assertion that every oxygen-resistant engineered variant is inactive.

L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX
  • PMID:2203757

    Source assertion: The abstract reports oxygen-associated inactivation despite synthesis of active oxidoreductase under both respiratory conditions; no protein-synthesis or carbon-source requirement was found for inactivation.

    Source locationXPath //PubmedArticle[MedlineCitation/PMID="2203757"]/MedlineCitation/Article/Abstract
  • PMID:1730033

    Source assertion: The abstract reports oxygen-dependent inactivation by an extract component, and in-vitro inactivation with Fe3+ plus ascorbate. Catalase protected against that oxidation system.

    Source locationXPath //PubmedArticle[MedlineCitation/PMID="1730033"]/MedlineCitation/Article/Abstract
hydrogen peroxide
CHEBI:16240		inhibits

Abstract-level anaerobic H2O2 inactivation and native metal-catalyzed oxidation context. No dose, rate, EG-specific assay, or direct regulatory binding is inferred.

L-1,2-propanediol oxidoreductase
EcoCyc:LACTALDREDUCT-CPLX
  • PMID:1730033

    Source assertion: Under anaerobic conditions, hydrogen peroxide strongly inactivated the oxidoreductase in the inspected abstract. The native annotation additionally names an Fe2+/H2O2 oxidation system.

    Source locationXPath //PubmedArticle[MedlineCitation/PMID="1730033"]/MedlineCitation/Article/Abstract
  • EcoCyc:LACTALDREDUCT-MONOMER

    Source assertion: The native comment reports Fe2+ plus H2O2-mediated FucO inactivation. Historical His277 oxidation is proposed, not a verified unique mechanism for every preparation.

    Source locationXPath /ptools-xml/Protein/comment
DNA-binding transcriptional dual regulator CRP
EcoCyc:PC00004		has_part

The native complex specifies two copies of PD00257; unspecified component coefficients are not invented.

DNA-binding transcriptional dual regulator CRP
UniProtKB:P0ACJ8
  • EcoCyc:PC00004

    Source assertion: The native complex specifies two copies of PD00257; unspecified component coefficients are not invented.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PD00257"]]
  • EcoCyc:PD00257

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0ACJ8. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0ACJ8"]
FucR-L-fuculose-1-phosphate DNA-binding transcriptional activator
EcoCyc:CPLX0-7650		has_part

The native complex specifies component membership without a numeric coefficient of PD00444; unspecified component coefficients are not invented.

L-fucose operon activator
UniProtKB:P0ACK8
  • EcoCyc:CPLX0-7650

    Source assertion: The native complex specifies component membership without a numeric coefficient of PD00444; unspecified component coefficients are not invented.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PD00444"]]
  • EcoCyc:PD00444

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0ACK8. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0ACK8"]
DNA-binding transcriptional dual regulator FNR
EcoCyc:CPLX0-7797		has_part

The native complex specifies two copies of PD00197; unspecified component coefficients are not invented.

Fumarate and nitrate reduction regulatory protein
UniProtKB:P0A9E5
  • EcoCyc:CPLX0-7797

    Source assertion: The native complex specifies two copies of PD00197; unspecified component coefficients are not invented.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PD00197"]]
  • EcoCyc:PD00197

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0A9E5. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9E5"]
DnaA-ATP DNA-binding transcriptional dual regulator
EcoCyc:MONOMER0-160		has_part

The native complex specifies component membership without a numeric coefficient of PD03831; unspecified component coefficients are not invented.

Chromosomal replication initiator protein DnaA
UniProtKB:P03004
  • EcoCyc:MONOMER0-160

    Source assertion: The native complex specifies component membership without a numeric coefficient of PD03831; unspecified component coefficients are not invented.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PD03831"]]
  • EcoCyc:PD03831

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P03004. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P03004"]
DNA-binding transcriptional dual regulator IHF
EcoCyc:PC00027		has_part

IHF assembly context. Purified IHF supplied by H. Nash bound aldA fragments 1/2/3; HN1491 himA and K2704 himD mutants showed no significant expression effect. Binding alone therefore supplies no signed IHF-to-aldA edge. No aldA-specific IHF stoichiometry is inferred.

Integration host factor subunit alpha
UniProtKB:P0A6X7
  • EcoCyc:PC00027

    Source assertion: The native complex specifies alpha-subunit membership without a numeric coefficient of PD00347; unspecified component coefficients are not invented.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PD00347"]]
  • EcoCyc:PD00347

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0A6X7. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A6X7"]
  • PMID:9202484

    Source assertion: Purified IHF bound aldA promoter-containing fragments, but himA and himD mutants did not significantly change aldA expression under the tested conditions.

    Source locationXPath /html/body/div/div[1]/div[8]/div[7]/p[1]
DNA-binding transcriptional dual regulator IHF
EcoCyc:PC00027		has_part

IHF assembly context. Purified IHF supplied by H. Nash bound aldA fragments 1/2/3; HN1491 himA and K2704 himD mutants showed no significant expression effect. Binding alone therefore supplies no signed IHF-to-aldA edge. No aldA-specific IHF stoichiometry is inferred.

Integration host factor subunit beta
UniProtKB:P0A6Y1
  • EcoCyc:PC00027

    Source assertion: The native complex specifies beta-subunit membership without a numeric coefficient of PD00348; unspecified component coefficients are not invented.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PD00348"]]
  • EcoCyc:PD00348

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0A6Y1. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A6Y1"]
  • PMID:9202484

    Source assertion: Purified IHF bound aldA promoter-containing fragments, but himA and himD mutants did not significantly change aldA expression under the tested conditions.

    Source locationXPath /html/body/div/div[1]/div[8]/div[7]/p[1]
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		has_part

The native active CRP-cAMP object explicitly contains the CRP dimer PC00004; its component slot has no further numeric coefficient.

DNA-binding transcriptional dual regulator CRP
EcoCyc:PC00004
  • EcoCyc:CPLX0-226

    Source assertion: The native active CRP-cAMP object explicitly contains the CRP dimer PC00004; its component slot has no further numeric coefficient.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PC00004"]]
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		has_part

The exact source-defined ligand-bound regulatory assembly is retained. Native CAMP and FUCULOSE-1P ChEBI joins and ATP species are independently checked against their originals and the pinned ontology; missing ligand multiplicities remain unspecified.

3',5'-cyclic AMP(1-)
CHEBI:58165
  • EcoCyc:CPLX0-226

    Source assertion: The native regulatory assembly contains CAMP; no ligand coefficient is stated. This assembly membership is not an extra EG-core substrate or proof of direct binding in each gene-expression experiment.

    Source locationXPath /ptools-xml/Protein/component/Compound[@frameid="CAMP"]
  • EcoCyc:CAMP

    Source assertion: The independently acquired native compound original supplies the exact ChEBI unification cross-reference for this regulatory ligand; no ligand coefficient is inferred.

    Source locationXPath /ptools-xml/Compound/dblink[dblink-db="CHEBI"]
FucR-L-fuculose-1-phosphate DNA-binding transcriptional activator
EcoCyc:CPLX0-7650		has_part

The exact source-defined ligand-bound regulatory assembly is retained. Native CAMP and FUCULOSE-1P ChEBI joins and ATP species are independently checked against their originals and the pinned ontology; missing ligand multiplicities remain unspecified.

L-fuculose 1-phosphate(2-)
CHEBI:57846
  • EcoCyc:CPLX0-7650

    Source assertion: The native regulatory assembly contains FUCULOSE-1P; no ligand coefficient is stated. This assembly membership is not an extra EG-core substrate or proof of direct binding in each gene-expression experiment.

    Source locationXPath /ptools-xml/Protein/component/Compound[@frameid="FUCULOSE-1P"]
  • EcoCyc:FUCULOSE-1P

    Source assertion: The independently acquired native compound original supplies the exact ChEBI unification cross-reference for this regulatory ligand; no ligand coefficient is inferred.

    Source locationXPath /ptools-xml/Compound/dblink[dblink-db="CHEBI"]
DnaA-ATP DNA-binding transcriptional dual regulator
EcoCyc:MONOMER0-160		has_part

The exact source-defined ligand-bound regulatory assembly is retained. Native CAMP and FUCULOSE-1P ChEBI joins and ATP species are independently checked against their originals and the pinned ontology; missing ligand multiplicities remain unspecified.

ATP(4-)
CHEBI:30616
  • EcoCyc:MONOMER0-160

    Source assertion: The native regulatory assembly contains ATP; no ligand coefficient is stated. This assembly membership is not an extra EG-core substrate or proof of direct binding in each gene-expression experiment.

    Source locationXPath /ptools-xml/Protein/component/Compound[@frameid="ATP"]
  • EcoCyc:ATP

    Source assertion: The independently acquired native compound original supplies the exact ChEBI unification cross-reference for this regulatory ligand; no ligand coefficient is inferred.

    Source locationXPath /ptools-xml/Compound/dblink[dblink-db="CHEBI"]
DNA-binding transcriptional dual regulator FNR
EcoCyc:CPLX0-7797		has_cofactor

The exact FNR result assigns one [4Fe-4S] cluster per chain. The native active assembly is a dimer; apo and oxygen-converted cluster forms are different states.

tetra-mu3-sulfido-tetrairon
CHEBI:49883
  • UniProtKB:P0A9E5

    Source assertion: The exact FNR result assigns one [4Fe-4S] cluster per chain. The native active assembly is a dimer; apo and oxygen-converted cluster forms are different states.

    Source locationresults[primaryAccession=P0A9E5].comments[commentType=COFACTOR]
  • EcoCyc:CPLX0-7797

    Source assertion: The native comment links acquisition of the [4Fe-4S] cluster under anaerobiosis to FNR dimerization and activation.

    Source locationXPath /ptools-xml/Protein/comment
dioxygen
CHEBI:15379		inhibits

Oxygen inactivates FNR through [4Fe-4S] to [2Fe-2S] conversion and dimer dissociation; prolonged exposure yields apo-FNR.

DNA-binding transcriptional dual regulator FNR
EcoCyc:CPLX0-7797

molecular state: Active dimeric FNR with [4Fe-4S] clusters; the native annotation distinguishes this state from inactive monomeric apo-FNR and oxygen-converted [2Fe-2S] forms.

Qualification evidence
  • EcoCyc:CPLX0-7797

    Source assertion: The native comment explicitly distinguishes active anaerobic Fe-S dimer from oxygen-inactivated and apo forms.

    Source locationXPath /ptools-xml/Protein/comment
  • EcoCyc:CPLX0-7797

    Source assertion: Oxygen inactivates FNR through [4Fe-4S] to [2Fe-2S] conversion and dimer dissociation; prolonged exposure yields apo-FNR.

    Source locationXPath /ptools-xml/Protein/comment
nitric oxide
CHEBI:16480		inhibits

Nitric oxide can inactivate FNR through nitrosylation of its [4Fe-4S] cluster; this is general proximal regulator-state context, not an aldA-specific binding experiment.

DNA-binding transcriptional dual regulator FNR
EcoCyc:CPLX0-7797

molecular state: Active dimeric FNR with [4Fe-4S] clusters; the native annotation distinguishes this state from inactive monomeric apo-FNR and oxygen-converted [2Fe-2S] forms.

Qualification evidence
  • EcoCyc:CPLX0-7797

    Source assertion: The native comment explicitly distinguishes active anaerobic Fe-S dimer from oxygen-inactivated and apo forms.

    Source locationXPath /ptools-xml/Protein/comment
  • EcoCyc:CPLX0-7797

    Source assertion: Nitric oxide can inactivate FNR through nitrosylation of its [4Fe-4S] cluster; this is general proximal regulator-state context, not an aldA-specific binding experiment.

    Source locationXPath /ptools-xml/Protein/comment
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226

experimental construct: Native CRP-cAMP reference assembly; direct 1997 binding used purified CRP supplied by S. Adhya, with 20 micromolar cAMP. Production strain/tag details were not reported in the inspected methods. Reporter assays used RYC1000 single-copy aldA-lacZ fusions.

Qualification evidence
  • PMID:9202484

    Source assertion: The methods identify purified CRP supplied by S. Adhya and describe the binding incubation.

    Source locationXPath /html/body/div/div[1]/div[7]/div[7]/p[1]
  • PMID:9202484

    Source assertion: The promoter fusions were constructed in pRS550 and transferred by lambdaRS45 to single-copy reporter backgrounds.

    Source locationXPath /html/body/div/div[1]/div[7]/div[5]/p[3]
activates

Positive aldA transcriptional control and proximal physical binding. The RYC1000 single-copy pRS550/lambdaRS45 reporters were studied in defined carbon-source conditions. CRP supplied by S. Adhya was used for binding with 20 micromolar cAMP; its tag/production strain was not established by the inspected methods. Five mM exogenous cAMP partially relieved glucose repression, whereas glycerol repression was cAMP-independent.

aldA
Entrez:945672
  • EcoCyc:REG0-5996

    Source assertion: The exact native regulation assigns positive CRP-cAMP influence to aldAp PM324. Its expression evidence does not by itself rule out indirect effects.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity
  • EcoCyc:TU102

    Source assertion: The exact native transcription unit includes gene EG10035; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10035"]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
  • PMID:9202484

    Source assertion: Purified CRP with 20 micromolar cAMP bound the proximal aldA fragment; the distal -134 consensus did not bind in this test.

    Source locationXPath /html/body/div/div[1]/div[8]/div[5]/p[4]
  • PMID:9202484

    Source assertion: DNase protection places the proximal CRP-cAMP region around -47 to -74; consensus similarity at the distal site is not physical binding evidence.

    Source locationXPath /html/body/div/div[1]/div[8]/div[5]/p[6]
Aerobic respiration control protein ArcA
UniProtKB:P0A9Q1

molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native PHOSPHO-ARCA. This qualifier preserves the modified regulator; a loss-of-arcA expression experiment alone does not measure its phosphorylation state.

Qualification evidence
  • EcoCyc:PHOSPHO-ARCA

    Source assertion: The native phosphorylated regulator has unmodified-form ARCA-MONOMER. Its modified identity is retained as source evidence rather than silently flattened to the reference chain.

    Source locationXPath /ptools-xml/Protein/unmodified-form | /ptools-xml/Protein/common-name
  • EcoCyc:ARCA-MONOMER

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0A9Q1. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9Q1"]
inhibits

1997 expression experiment: ECL547/ECL968 carrying the -287 aldA fusion, rhamnose minimal medium, anaerobiosis. ArcA mutant reporter activity was 18,700 versus aerobic parental/mutant values 19,375/20,750. This is gene-expression evidence; the 1997 consensus motif alone does not prove direct binding.

aldA
Entrez:945672
  • PMID:9202484

    Source assertion: In the rhamnose-grown anaerobic reporter comparison, loss of arcA in ECL968 relative to parental ECL547 abolished strong aldA repression. The aerobic activities were similar.

    Source locationXPath /html/body/div/div[1]/div[8]/div[6]/p[1]
  • EcoCyc:TU102

    Source assertion: The exact native transcription unit includes gene EG10035; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10035"]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
Aerobic respiration control protein ArcA
UniProtKB:P0A9Q1

molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native PHOSPHO-ARCA. This qualifier preserves the modified regulator; a loss-of-arcA expression experiment alone does not measure its phosphorylation state.

Qualification evidence
  • EcoCyc:PHOSPHO-ARCA

    Source assertion: The native phosphorylated regulator has unmodified-form ARCA-MONOMER. Its modified identity is retained as source evidence rather than silently flattened to the reference chain.

    Source locationXPath /ptools-xml/Protein/unmodified-form | /ptools-xml/Protein/common-name
  • EcoCyc:ARCA-MONOMER

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0A9Q1. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9Q1"]
inhibits

Native site-resolved ArcA-P repression: REG0-5998/5999/6000/6002/6003 and BS0-4943/4942/4941, BS43, BS42 are preserved together. Some source evidence is computational or expression-based; the PMID10071223 abstract supports direct promoter recognition without supplying full-body methods. No uninspected supplement is claimed.

aldA
Entrez:945672
  • EcoCyc:REG0-5998

    Source assertion: The native regulation assigns negative PHOSPHO-ARCA influence to PM324 and retains site BS0-4943 (absolute center 1488053). Attached binding, computational or expression evidence remains source-specific; not every site is a fresh physical-binding result.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity | /ptools-xml/Regulation/associated-binding-site
  • EcoCyc:REG0-5999

    Source assertion: The native regulation assigns negative PHOSPHO-ARCA influence to PM324 and retains site BS0-4942 (absolute center 1488202). Attached binding, computational or expression evidence remains source-specific; not every site is a fresh physical-binding result.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity | /ptools-xml/Regulation/associated-binding-site
  • EcoCyc:REG0-6000

    Source assertion: The native regulation assigns negative PHOSPHO-ARCA influence to PM324 and retains site BS0-4941 (absolute center 1488191). Attached binding, computational or expression evidence remains source-specific; not every site is a fresh physical-binding result.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity | /ptools-xml/Regulation/associated-binding-site
  • EcoCyc:REG0-6002

    Source assertion: The native regulation assigns negative PHOSPHO-ARCA influence to PM324 and retains site BS43 (absolute center 1488185). Attached binding, computational or expression evidence remains source-specific; not every site is a fresh physical-binding result.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity | /ptools-xml/Regulation/associated-binding-site
  • EcoCyc:REG0-6003

    Source assertion: The native regulation assigns negative PHOSPHO-ARCA influence to PM324 and retains site BS42 (absolute center 1488033). Attached binding, computational or expression evidence remains source-specific; not every site is a fresh physical-binding result.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity | /ptools-xml/Regulation/associated-binding-site
  • EcoCyc:TU102

    Source assertion: The exact native transcription unit includes gene EG10035; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10035"]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
  • PMID:10071223

    Source assertion: The abstract reports ArcA-P DNase protection at the aldA promoter; two altered sequence constructs reduced binding and abolished anaerobic reporter repression. This is abstract-only access to the later binding study.

    Source locationXPath //PubmedArticle[MedlineCitation/PMID="10071223"]/MedlineCitation/Article/Abstract
Aerobic respiration control protein ArcA
UniProtKB:P0A9Q1

molecular state: Phosphorylated ArcA reference chain P0A9Q1, the active state explicitly identified as native PHOSPHO-ARCA. This qualifier preserves the modified regulator; a loss-of-arcA expression experiment alone does not measure its phosphorylation state.

Qualification evidence
  • EcoCyc:PHOSPHO-ARCA

    Source assertion: The native phosphorylated regulator has unmodified-form ARCA-MONOMER. Its modified identity is retained as source evidence rather than silently flattened to the reference chain.

    Source locationXPath /ptools-xml/Protein/unmodified-form | /ptools-xml/Protein/common-name
  • EcoCyc:ARCA-MONOMER

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0A9Q1. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9Q1"]
inhibits

2014 study context: MG1655 and deletions, M9 0.2% glucose/0.1% ammonium chloride, 37 C, anaerobic exponential growth with or without 20 mM nitrate. Exact aldA-specific support is the native curated regulation; primary gene-specific supplemental rows were not inspected. Tagged ChIP context is not substituted for a fresh aldA-specific binding result, and modelled flux is not measured flux.

aldA
Entrez:945672
  • EcoCyc:REG0-14027

    Source assertion: The native gene-level microarray regulation assigns negative ArcA-P influence to EG10035 in MG1655 versus an arcA knockout under anaerobic M9 glucose conditions, including nitrate/no-nitrate comparisons.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity | /ptools-xml/Regulation/comment | /ptools-xml/Regulation/evidence
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
DnaA-ATP DNA-binding transcriptional dual regulator
EcoCyc:MONOMER0-160		inhibits

Native DnaA-ATP regulatory state plus abstract-level direct DnaA binding and expression evidence. The full publisher body was unavailable (403); no uninspected construct details or ATP-specific biochemical result are inferred from the abstract.

aldA
Entrez:945672
  • EcoCyc:REG0-6001

    Source assertion: The exact native regulation assigns negative DnaA-ATP influence to aldAp PM324. The ATP-bound assembly is the source-defined regulator state.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity
  • EcoCyc:TU102

    Source assertion: The exact native transcription unit includes gene EG10035; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10035"]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
  • PMID:11160809

    Source assertion: The abstract reports DnaA binding to the aldA regulatory region and repression/enhancement of the glucose-minimal-medium reporter on DnaA excess/depletion. It does not independently establish ATP-state specificity.

    Source locationXPath //PubmedArticle[MedlineCitation/PMID="11160809"]/MedlineCitation/Article/Abstract
DNA-binding transcriptional dual regulator FNR
EcoCyc:CPLX0-7797

molecular state: Native active FNR dimer with [4Fe-4S] clusters. The aldA regulatory link is expression evidence with a computational binding-site assignment, not a purified aldA-promoter binding measurement.

Qualification evidence
  • EcoCyc:CPLX0-7797

    Source assertion: The native annotation links the active Fe-S-containing dimer to anaerobic transcriptional control.

    Source locationXPath /ptools-xml/Protein/comment
inhibits

The native regulation assigns negative FNR influence to PM324 using gene-expression evidence; its BS0-7160 motif annotation is computational, not direct binding proof.

aldA
Entrez:945672
  • EcoCyc:REG0-5997

    Source assertion: The native regulation assigns negative FNR influence to PM324 using gene-expression evidence; its BS0-7160 motif annotation is computational, not direct binding proof.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity | /ptools-xml/Regulation/associated-binding-site | /ptools-xml/Regulation/evidence
  • EcoCyc:TU102

    Source assertion: The exact native transcription unit includes gene EG10035; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10035"]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
  • PMID:16377617

    Source assertion: The abstract describes MG1655/fnr-mutant transcript comparisons in anaerobic glycerol/TMAO/fumarate medium and predicted FNR motifs. The aldA-specific result here comes from the native regulation.

    Source locationXPath //PubmedArticle[MedlineCitation/PMID="16377617"]/MedlineCitation/Article/Abstract
Multiple antibiotic resistance protein MarA
UniProtKB:P0ACH5		activates

Curated potentially indirect MarA-dependent aldA expression, citing PMID12067348. Only its abstract was inspected; gene-level supplemental results were unavailable. General statements about directly activated promoters in that article cannot establish that aldA belongs to that subset.

aldA
Entrez:945672
  • EcoCyc:REG0-12708

    Source assertion: The exact native regulation assigns positive MarA influence to PM324. The attached expression-evidence definition explicitly allows an indirect effect; direct aldA binding is not established here.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity | /ptools-xml/Regulation/evidence
  • EcoCyc:PD00365

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0ACH5. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0ACH5"]
  • EcoCyc:TU102

    Source assertion: The exact native transcription unit includes gene EG10035; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10035"]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
Right origin-binding protein
UniProtKB:P0ACI0		activates

Curated potentially indirect Rob-dependent aldA expression, citing PMID12067348. Only its abstract was inspected; gene-level supplemental results were unavailable. General statements about directly activated promoters in that article cannot establish that aldA belongs to that subset.

aldA
Entrez:945672
  • EcoCyc:REG0-12709

    Source assertion: The exact native regulation assigns positive Rob influence to PM324. The attached expression-evidence definition explicitly allows an indirect effect; direct aldA binding is not established here.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity | /ptools-xml/Regulation/evidence
  • EcoCyc:PD04418

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0ACI0. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0ACI0"]
  • EcoCyc:TU102

    Source assertion: The exact native transcription unit includes gene EG10035; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10035"]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
Regulatory protein SoxS
UniProtKB:P0A9E2		activates

Curated potentially indirect SoxS-dependent aldA expression, citing PMID12067348. Only its abstract was inspected; gene-level supplemental results were unavailable. General statements about directly activated promoters in that article cannot establish that aldA belongs to that subset.

aldA
Entrez:945672
  • EcoCyc:REG0-12710

    Source assertion: The exact native regulation assigns positive SoxS influence to PM324. The attached expression-evidence definition explicitly allows an indirect effect; direct aldA binding is not established here.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity | /ptools-xml/Regulation/evidence
  • EcoCyc:PD00406

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P0A9E2. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9E2"]
  • EcoCyc:TU102

    Source assertion: The exact native transcription unit includes gene EG10035; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10035"]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native fucAO expression context, not a transplant of every fucPIK promoter experiment. The CRP BS00333 motif is computational; PMID10601201 examines a K52N CRP suppressor and fucPIK after IS5 insertion. Those selected backgrounds are not unqualified wild type. A separate mapped fucO transcript TU0-42697 remains distinct.

fucO
Entrez:947273
  • EcoCyc:REG0-5579

    Source assertion: The exact native regulation positively controls fucAOp PM00180 through this source-defined ligand-bound regulator. The transcription unit includes fucO.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity
  • EcoCyc:TU00135

    Source assertion: The exact native transcription unit includes gene EG10351; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10351"]
  • Entrez:947273

    Source assertion: Issuing NCBI Gene 947273 identifies fucO in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="947273"]
FucR-L-fuculose-1-phosphate DNA-binding transcriptional activator
EcoCyc:CPLX0-7650		activates

Native fucAO expression context, not a transplant of every fucPIK promoter experiment. The CRP BS00333 motif is computational; PMID10601201 examines a K52N CRP suppressor and fucPIK after IS5 insertion. Those selected backgrounds are not unqualified wild type. A separate mapped fucO transcript TU0-42697 remains distinct.

fucO
Entrez:947273
  • EcoCyc:REG0-5580

    Source assertion: The exact native regulation positively controls fucAOp PM00180 through this source-defined ligand-bound regulator. The transcription unit includes fucO.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity
  • EcoCyc:TU00135

    Source assertion: The exact native transcription unit includes gene EG10351; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10351"]
  • Entrez:947273

    Source assertion: Issuing NCBI Gene 947273 identifies fucO in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="947273"]
Uncharacterized HTH-type transcriptional regulator YgfI
UniProtKB:P52044

experimental construct: 2022 BW25113, srsR deletion JW5476, and pCA24N-derived ASKA SrsR overexpression versus empty-vector controls; LB 37 C, 150 rpm, 24 h, 0.5 mM IPTG. Reference P52044/YgfI is named SrsR by the study; this is an expression construct context.

Qualification evidence
  • PMID:35682733

    Source assertion: Methods distinguish W3110 genomic donor and BL21(DE3) protein production from BW25113/JW5476 and ASKA overexpression strains used for the expression comparison.

    Source locationXPath /article/body/sec[4]/sec[1]/p
  • PMID:35682733

    Source assertion: RT-qPCR used 24-hour LB cultures and 16S normalization, with three independent experiments.

    Source locationXPath /article/body/sec[4]/sec[7]/p
activates

SrsR (current issuing P52044 label still YgfI) positively influences fucO transcript abundance in the exact BW25113 deletion/overexpression assay. Figure 5 negative fold notation means reduced abundance, not negative RNA. Separate purified C-terminal His-SrsR from W3110/pET21a in BL21(DE3) bound the shared fucA/fucP spacer; this is not an independently mapped fucO internal promoter. The footprint experiment used yfdP/yfdO, not fucO. The SrsR coinducer remains unknown.

fucO
Entrez:947273
  • PMID:35682733

    Source assertion: Stationary-phase RT-qPCR compares deletion and SrsR overexpression to wild type. Figure 5 includes fucO: deletion lowers abundance 8.3-fold and overexpression raises it 23.9-fold.

    Source locationXPath /article/body/sec[2]/sec[4]/p
  • EcoCyc:REG0-16133

    Source assertion: The native regulation positively links SrsR/G7518-MONOMER to fucAO TU00135, using expression evidence that does not eliminate indirect effects.

    Source locationXPath /ptools-xml/Regulation/mode | /ptools-xml/Regulation/regulator | /ptools-xml/Regulation/regulated-entity
  • EcoCyc:G7518-MONOMER

    Source assertion: This native reference chain has an explicit UniProt unification cross-reference to P52044. It grounds identity only, not the assay construct or regulatory sign.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P52044"]
  • EcoCyc:TU00135

    Source assertion: The exact native transcription unit includes gene EG10351; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10351"]
  • Entrez:947273

    Source assertion: Issuing NCBI Gene 947273 identifies fucO in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="947273"]
  • PMID:35682733

    Source assertion: Purified His-SrsR shifted the tested fucA/fucP spacer, with lacUV5 as a negative control. This physical evidence is regional and does not map a separate internal fucO promoter.

    Source locationXPath /article/body/sec[2]/sec[2]/p[1]
  • PMID:35682733

    Source assertion: The purified SrsR preparation used W3110 genomic DNA, pET21a and BL21(DE3), with a C-terminal His tag; it is distinct from the BW25113 expression-assay preparation.

    Source locationXPath /article/body/sec[4]/sec[2]/p
glucose
CHEBI:17234		inhibits

Condition-dependent aldA expression repression by glucose in the 1997 single-copy reporter experiments, not direct binding to AldA or inhibition of its catalytic activity. Glucose and glycerol effects differ in cAMP dependence. The 2002 MC4100/TB proteomic comparison separately identifies less AldA protein with 0.4% glycerol; its malT/EIIA experiments do not establish every intervening aldA-specific arrow.

aldA
Entrez:945672
  • PMID:9202484

    Source assertion: The source reports low aldA reporter activity when glucose or glycerol is added to rhamnose cultures; these are expression effects, not enzyme inhibition.

    Source locationXPath /html/body/div/div[1]/div[8]/div[3]/p[2]
  • PMID:9202484

    Source assertion: Exogenous 5 mM cAMP partly restored the glucose-repressed reporter. Residual repression remains, and the source discusses a cAMP-independent glycerol mechanism.

    Source locationXPath /html/body/div/div[1]/div[8]/div[5]/p[3]
  • PMID:9202484

    Source assertion: The Discussion interprets glycerol repression as cAMP-independent; it is not a directly identified glycerol-binding regulator.

    Source locationXPath /html/body/div/div[1]/div[9]/p[5]
  • EcoCyc:TU102

    Source assertion: The exact native transcription unit includes gene EG10035; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10035"]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
glycerol
CHEBI:17754		inhibits

Condition-dependent aldA expression repression by glycerol in the 1997 single-copy reporter experiments, not direct binding to AldA or inhibition of its catalytic activity. Glucose and glycerol effects differ in cAMP dependence. The 2002 MC4100/TB proteomic comparison separately identifies less AldA protein with 0.4% glycerol; its malT/EIIA experiments do not establish every intervening aldA-specific arrow.

aldA
Entrez:945672
  • PMID:9202484

    Source assertion: The source reports low aldA reporter activity when glucose or glycerol is added to rhamnose cultures; these are expression effects, not enzyme inhibition.

    Source locationXPath /html/body/div/div[1]/div[8]/div[3]/p[2]
  • PMID:9202484

    Source assertion: Exogenous 5 mM cAMP partly restored the glucose-repressed reporter. Residual repression remains, and the source discusses a cAMP-independent glycerol mechanism.

    Source locationXPath /html/body/div/div[1]/div[8]/div[5]/p[3]
  • PMID:9202484

    Source assertion: The Discussion interprets glycerol repression as cAMP-independent; it is not a directly identified glycerol-binding regulator.

    Source locationXPath /html/body/div/div[1]/div[9]/p[5]
  • EcoCyc:TU102

    Source assertion: The exact native transcription unit includes gene EG10035; this joins the cited promoter/unit effect to this gene, without borrowing neighboring regulatory objects.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10035"]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
  • PMID:12003946

    Source assertion: MC4100 grown in TB with 0.4% glycerol showed a less abundant AldA spot in the two-dimensional proteomic comparison. This measures protein abundance, not direct AldA inhibition.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[1]/p
  • PMID:12003946

    Source assertion: Table 2 identifies the glycerol-repressed AldA spot as P25553 by peptide mass fingerprint. This grounds protein identity separately from the malT reporter experiments.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[1]/section[3]/div[2]/table
L-fucose
CHEBI:18287		activates

Sugar-dependent fucO expression/activity context with respiratory conditions retained. Absolute source wording that FucO is only active anaerobically is limited by condition-dependent and oxygen-resistant-mutant evidence. The generic sugar identity does not select a particular pyranose anomer.

fucO
Entrez:947273
  • EcoCyc:LACTALDREDUCT-MONOMER

    Source assertion: The native comment reports FucO induction associated with L-fucose. Fucose induction occurs under both respiratory conditions; rhamnose-dependent activity is emphasized under anaerobiosis. This is expression context, not direct ligand binding to FucO.

    Source locationXPath /ptools-xml/Protein/comment
  • Entrez:947273

    Source assertion: Issuing NCBI Gene 947273 identifies fucO in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="947273"]
L-rhamnose
CHEBI:62345		activates

Sugar-dependent fucO expression/activity context with respiratory conditions retained. Absolute source wording that FucO is only active anaerobically is limited by condition-dependent and oxygen-resistant-mutant evidence. The generic sugar identity does not select a particular pyranose anomer.

fucO
Entrez:947273
  • EcoCyc:LACTALDREDUCT-MONOMER

    Source assertion: The native comment reports FucO induction associated with L-rhamnose. Fucose induction occurs under both respiratory conditions; rhamnose-dependent activity is emphasized under anaerobiosis. This is expression context, not direct ligand binding to FucO.

    Source locationXPath /ptools-xml/Protein/comment
  • Entrez:947273

    Source assertion: Issuing NCBI Gene 947273 identifies fucO in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="947273"]
L-fucose
CHEBI:18287		activates

Source-defined aerobic AldA induction in the historical studies; strain and metabolic backgrounds differ. The 1988 mutant comparisons suggest lactaldehyde as an indirect inducing intermediate, but direct lactaldehyde addition arrested growth and the regulatory factor was unidentified. Native glutamate induction is retained in prose without inventing a precise ionic/stereochemical effector identity.

aldA
Entrez:945672
  • UniProtKB:P25553

    Source assertion: The issuing AldA annotation reports aerobic induction associated with L-fucose. This is source-defined expression context; direct purified-effector binding and ordinary wild-type EG-supported growth do not follow.

    Source locationcomments[commentType=INDUCTION]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
L-rhamnose
CHEBI:62345		activates

Source-defined aerobic AldA induction in the historical studies; strain and metabolic backgrounds differ. The 1988 mutant comparisons suggest lactaldehyde as an indirect inducing intermediate, but direct lactaldehyde addition arrested growth and the regulatory factor was unidentified. Native glutamate induction is retained in prose without inventing a precise ionic/stereochemical effector identity.

aldA
Entrez:945672
  • UniProtKB:P25553

    Source assertion: The issuing AldA annotation reports aerobic induction associated with L-rhamnose. This is source-defined expression context; direct purified-effector binding and ordinary wild-type EG-supported growth do not follow.

    Source locationcomments[commentType=INDUCTION]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
ethylene glycol
CHEBI:30742		activates

Source-defined aerobic AldA induction in the historical studies; strain and metabolic backgrounds differ. The 1988 mutant comparisons suggest lactaldehyde as an indirect inducing intermediate, but direct lactaldehyde addition arrested growth and the regulatory factor was unidentified. Native glutamate induction is retained in prose without inventing a precise ionic/stereochemical effector identity.

aldA
Entrez:945672
  • UniProtKB:P25553

    Source assertion: The issuing AldA annotation reports aerobic induction associated with ethylene glycol. This is source-defined expression context; direct purified-effector binding and ordinary wild-type EG-supported growth do not follow.

    Source locationcomments[commentType=INDUCTION]
  • Entrez:945672

    Source assertion: Issuing NCBI Gene 945672 identifies aldA in MG1655 taxon 511145. This grounds the expression endpoint and reference locus, not a claim that historical E15 or assay strains are MG1655.

    Source locationXPath //Entrezgene[Entrezgene_track-info/Gene-track/Gene-track_geneid="945672"]
glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002		provides_input_for

The glycolate product can enter this source-defined downstream context. The exact native opaque pathway is retained without importing its enzymes or changing the PWY0-1280 boundary.

glycolate and glyoxylate degradation III
MetaCyc:PWY-6649
  • MetaCyc:PWY0-1280

    Source assertion: The native glycolate pathway-link attaches this downstream pathway. It supports an interface, not the full downstream reaction sequence, flux magnitude, or another member of the two-event core.

    Source locationXPath /ptools-xml/Pathway/pathway-link[link-target/Pathway[@frameid="PWY-6649"]]
glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002		provides_input_for

The glycolate product can enter this source-defined downstream context. The exact native opaque pathway is retained without importing its enzymes or changing the PWY0-1280 boundary.

glycolate and glyoxylate degradation II
MetaCyc:GLYOXDEG-PWY
  • MetaCyc:PWY0-1280

    Source assertion: The native glycolate pathway-link attaches this downstream pathway. It supports an interface, not the full downstream reaction sequence, flux magnitude, or another member of the two-event core.

    Source locationXPath /ptools-xml/Pathway/pathway-link[link-target/Pathway[@frameid="GLYOXDEG-PWY"]]
glycolaldehyde + NAD(+) + H2O => glycolate + NADH + 2 H(+)
RHEA:20002		provides_input_for

The glycolate product can enter this source-defined downstream context. The exact native opaque pathway is retained without importing its enzymes or changing the PWY0-1280 boundary.

glycolate and glyoxylate degradation I
MetaCyc:GLYCOLATEMET-PWY
  • MetaCyc:PWY0-1280

    Source assertion: The native glycolate pathway-link attaches this downstream pathway. It supports an interface, not the full downstream reaction sequence, flux magnitude, or another member of the two-event core.

    Source locationXPath /ptools-xml/Pathway/pathway-link[link-target/Pathway[@frameid="GLYCOLATEMET-PWY"]]
MetaCyc:PWY0-1280part_of

The META original explicitly places the EG pathway in the glycol metabolism and degradation superpathway. The ECOLI original independently carries this parent; the META parent is not absent.

superpathway of glycol metabolism and degradation
MetaCyc:GLYCOL-GLYOXDEG-PWY
  • MetaCyc:PWY0-1280

    Source assertion: The META original explicitly places the EG pathway in the glycol metabolism and degradation superpathway. The ECOLI original independently carries this parent; the META parent is not absent.

    Source locationXPath /ptools-xml/Pathway/in-pathway
  • EcoCyc:PWY0-1280

    Source assertion: The ECOLI original independently identifies the glycol superpathway parent. Its outgoing glycolate link is narrower than the META collection.

    Source locationXPath /ptools-xml/Pathway/in-pathway
MetaCyc:PWY0-1280has_part

Frozen PathBank root SMP0002105/PW002093 describes the same two-event EG conversion and attaches this opaque child. The graph preserves the attachment without treating the child as part of the Rhea core or independently proving its biochemical mechanism.

D-Arabinose Degradation I
PathBank:SMP0002052
  • PathBank:SMP0002105

    Source assertion: The matching native EG root explicitly attaches this named child pathway. This is source structural membership, not a third core reaction or proof of causal direction between the pathways.

    Source locationXPath //*[local-name()="Pathway"][@*[local-name()="about"]="http://identifiers.org/smpdb/SMP0002105"]/*[local-name()="pathwayComponent"][@*[local-name()="resource"]="http://identifiers.org/smpdb/SMP0002052"]
D-Arabinose Degradation I
PathBank:SMP0002052		has_part

Unsigned structural participant context only. The D-arabinose child includes glycolaldehyde; the glycolate/glyoxylate child includes neutral glycolic acid CHEBI17497. Neutral acid is not silently merged with Rhea glycolate CHEBI29805, and neither Interaction is converted to transport, inhibition or an extra core reaction.

glycolaldehyde
CHEBI:17071
  • PathBank:SMP0002105

    Source assertion: The child contains a generic Interaction whose sole participant is this source-mapped chemical. BioPAX provides no left/right biochemical sides or regulatory sign for that Interaction.

    Source locationXPath //*[local-name()="Pathway"][@*[local-name()="about"]="http://identifiers.org/smpdb/SMP0002052"] | //*[local-name()="Interaction"][@*[local-name()="ID"]="SubPathwayInteractions/109875"] | //*[local-name()="SmallMolecule"][@*[local-name()="ID"]="Compound/PW_C001850"] | //*[local-name()="SmallMoleculeReference"][@*[local-name()="ID"]="CompoundReference/PW_C001850"]
MetaCyc:PWY0-1280has_part

Frozen PathBank root SMP0002105/PW002093 describes the same two-event EG conversion and attaches this opaque child. The graph preserves the attachment without treating the child as part of the Rhea core or independently proving its biochemical mechanism.

Glycolate and Glyoxylate Degradation
PathBank:SMP0000847
  • PathBank:SMP0002105

    Source assertion: The matching native EG root explicitly attaches this named child pathway. This is source structural membership, not a third core reaction or proof of causal direction between the pathways.

    Source locationXPath //*[local-name()="Pathway"][@*[local-name()="about"]="http://identifiers.org/smpdb/SMP0002105"]/*[local-name()="pathwayComponent"][@*[local-name()="resource"]="http://identifiers.org/smpdb/SMP0000847"]
Glycolate and Glyoxylate Degradation
PathBank:SMP0000847		has_part

Unsigned structural participant context only. The D-arabinose child includes glycolaldehyde; the glycolate/glyoxylate child includes neutral glycolic acid CHEBI17497. Neutral acid is not silently merged with Rhea glycolate CHEBI29805, and neither Interaction is converted to transport, inhibition or an extra core reaction.

glycolic acid
CHEBI:17497
  • PathBank:SMP0002105

    Source assertion: The child contains a generic Interaction whose sole participant is this source-mapped chemical. BioPAX provides no left/right biochemical sides or regulatory sign for that Interaction.

    Source locationXPath //*[local-name()="Pathway"][@*[local-name()="about"]="http://identifiers.org/smpdb/SMP0000847"] | //*[local-name()="Interaction"][@*[local-name()="ID"]="SubPathwayInteractions/109876"] | //*[local-name()="SmallMolecule"][@*[local-name()="ID"]="Compound/PW_C000073"] | //*[local-name()="SmallMoleculeReference"][@*[local-name()="ID"]="CompoundReference/PW_C000073"]

References

Curation history