L-lyxose degradation

MetaCyc:LYXMET-PWY

The source-defined four-event L-lyxose 5-phosphate route joins RhaA isomerization, LyxK phosphorylation and successive 3- and 4-epimerization to D-xylulose 5-phosphate. Whole-route genetic support concerns adapted K-12 derivatives such as JA134 with plaR/yiaJ derepression; it does not establish complete flux in ordinary wild-type MG1655. SgbU remains a tentative 3-epimerase assignment after two negative enzyme assays. Native beta-L-lyxopyranose initiating chemistry is distinct from generic RhaT lyxopyranose transport; no anomerization is invented. The separate 1991 mutant-rhaB L-xylulose 1-phosphate route is excluded. AraD and SgbE are alternatives; frozen PathBank UlaF conflicts with native enzymes-not-used. Regulatory, metal, construct and source-access limits are preserved beside their edges. PMID:10913096 additionally reports that pectinase-digested citrus or apple pectin increased the yiaJ/plaR-lacZ reporter 10-20-fold in ECL1, but not JA134. Structural-gene expression was unaffected even without the repressor, and the biological significance remained unresolved. Preparation: 0.14% pectin in sodium acetate, pH 4.0; overnight at 25 C with 400 U Aspergillus niger pectinase; tenfold dilution into medium. This undefined hydrolysate is retained as experimental context, without assigning an individual chemical or a PlaR-binding interaction.

Pathway type
carbohydrate degradation
Organism scope

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Pathway network

74 nodes · 111 asserted directed edges

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Pathway network: L-lyxose degradation 74 nodes · 111 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. MetaCyc:LYXISOM-RXN — part_of → MetaCyc:LYXMET-PWY; The exact native reaction-list includes LYXISOM-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.; Evidence: MetaCyc:LYXMET-PWYpart of RHEA:18870 — part_of → MetaCyc:LYXMET-PWY; The exact native reaction-list includes LYXK-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.; Evidence: MetaCyc:LYXMET-PWYpart of RHEA:18499 — part_of → MetaCyc:LYXMET-PWY; The exact native reaction-list includes LXULRU5P-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.; Evidence: MetaCyc:LYXMET-PWYpart of RHEA:22369 — part_of → MetaCyc:LYXMET-PWY; The exact native reaction-list includes RIBULPEPIM-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.; Evidence: MetaCyc:LYXMET-PWYpart of CHEBI:147210 — consumes → MetaCyc:LYXISOM-RXN; Native left side contains L-LYXOSE; this pathway selects left-to-right flux. Its L-LYXOSE structure is beta-L-lyxopyranose, unlike the anomer-unspecified Rhea 28059 substrate.; Evidence: MetaCyc:LYXISOM-RXN, EcoCyc:L-LYXOSEconsumes MetaCyc:LYXISOM-RXN — produces → CHEBI:17399; Native right side contains L-XYLULOSE; this pathway selects left-to-right flux. Its L-LYXOSE structure is beta-L-lyxopyranose, unlike the anomer-unspecified Rhea 28059 substrate.; Evidence: MetaCyc:LYXISOM-RXNproduces CHEBI:17399 — consumes → RHEA:18870; RHEA:18870 substrates contains CHEBI:17399, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:18870consumes CHEBI:30616 — consumes → RHEA:18870; RHEA:18870 substrates contains CHEBI:30616, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:18870consumes RHEA:18870 — produces → CHEBI:57829; RHEA:18870 products contains CHEBI:57829, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:18870produces RHEA:18870 — produces → CHEBI:456216; RHEA:18870 products contains CHEBI:456216, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:18870produces RHEA:18870 — produces → CHEBI:15378; RHEA:18870 products contains CHEBI:15378, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:18870produces CHEBI:57829 — consumes → RHEA:18499; RHEA:18499 substrates contains CHEBI:57829, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:18499consumes RHEA:18499 — produces → CHEBI:58226; RHEA:18499 products contains CHEBI:58226, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:18499produces CHEBI:58226 — consumes → RHEA:22369; RHEA:22369 substrates contains CHEBI:58226, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:22369consumes RHEA:22369 — produces → CHEBI:57737; RHEA:22369 products contains CHEBI:57737, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:22369produces CHEBI:62321 — consumes → RHEA:29993; RHEA:29993 substrates contains CHEBI:62321, coefficient 1; external input. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:29993consumes CHEBI:15378 — consumes → RHEA:29993; RHEA:29993 substrates contains CHEBI:15378, coefficient 1; external input. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:29993consumes RHEA:29993 — produces → CHEBI:62321; RHEA:29993 products contains CHEBI:62321, coefficient 1; internal output. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:29993produces RHEA:29993 — produces → CHEBI:15378; RHEA:29993 products contains CHEBI:15378, coefficient 1; internal output. This is the selected formal directional equation; metal cofactors are not added as chemical sides.; Evidence: RHEA:29993produces MetaCyc:LYXISOM-RXN — provides_input_for → RHEA:18870; Native reaction-layout carries the shared intermediate L-XYLULOSE between these successive core events, with LXULRU5P selected right-to-left.; Evidence: MetaCyc:LYXMET-PWYprovides input for RHEA:18870 — provides_input_for → RHEA:18499; Native reaction-layout carries the shared intermediate L-XYLULOSE-5-P between these successive core events, with LXULRU5P selected right-to-left.; Evidence: MetaCyc:LYXMET-PWYprovides input for RHEA:18499 — provides_input_for → RHEA:22369; Native reaction-layout carries the shared intermediate L-RIBULOSE-5-P between these successive core events, with LXULRU5P selected right-to-left.; Evidence: MetaCyc:LYXMET-PWYprovides input for RHEA:29993 — provides_input_for → MetaCyc:LYXISOM-RXN; The native narrative places RhaT uptake before RhaA isomerization. The formal transport substrate is generic L-lyxopyranose, while the core first reaction specifies beta-L-lyxopyranose; this source-level interface is not an anomerization reaction.; Evidence: MetaCyc:LYXMET-PWYprovides input for RHEA:22369 — provides_input_for → MetaCyc:NONOXIPENT-PWY; The endpoint D-xylulose 5-phosphate is linked to NONOXIPENT-PWY. This downstream pentose-phosphate pathway is an opaque interface; its reactions are not additional LYXMET core events.; Evidence: MetaCyc:LYXMET-PWYprovides input for MetaCyc:LYXMET-PWY — part_of → MetaCyc:PWY-5257; The native in-pathway slot places LYXMET-PWY in parent superpathway PWY-5257. This is a hierarchy relationship rather than another catalytic event.; Evidence: MetaCyc:LYXMET-PWYpart of MetaCyc:CPLX0-7652 — catalyzes → MetaCyc:LYXISOM-RXN; The native enzyme slot assigns CPLX0-7652 to this reaction. Assemblies are retained separately from their reference chains; membership alone is not individual-subunit catalysis.; Evidence: MetaCyc:LYXISOM-ENZRXNcatalyzes MetaCyc:LYXK-CPLX — catalyzes → RHEA:18870; The native enzyme slot assigns LYXK-CPLX to this reaction. Assemblies are retained separately from their reference chains; membership alone is not individual-subunit catalysis.; Evidence: MetaCyc:LYXK-ENZRXNcatalyzes MetaCyc:RIBULPEPIM-CPLX — catalyzes → RHEA:22369; The native enzyme slot assigns RIBULPEPIM-CPLX to this reaction. Assemblies are retained separately from their reference chains; membership alone is not individual-subunit catalysis.; Evidence: MetaCyc:RIBULPEPIM-ENZRXNcatalyzes UniProtKB:P37679 — enables → RHEA:18499; The source assigns SgbU/YiaR to this event with EV-COMP-HINF-FN-FROM-SEQ. This is a tentative functional assignment, not experimentally established catalysis.; Evidence: EcoCyc:ENZRXN0-6410, PMID:10913097, PMID:11741871enables UniProtKB:P37680 — catalyzes → RHEA:22369; Reviewed SgbE catalyzes L-ribulose 5-phosphate to D-xylulose 5-phosphate, supported by PMID10913097 and PMID11741871. It is an alternative to AraD, not an obligate AraD-SgbE complex.; Evidence: UniProtKB:P37680, PMID:10913097catalyzes UniProtKB:P27125 — catalyzes → RHEA:29993; The native enzymatic-reaction assigns RHAT-MONOMER to L-lyxose transport. Generic L-lyxopyranose and proton coupling are source annotations; the 1991 radiotracer experiment directly measured lyxose competition with rhamnose uptake.; Evidence: EcoCyc:ENZRXN0-6409, PMID:1650346catalyzes MetaCyc:CPLX0-7652 — has_part → UniProtKB:P32170; The native assembly has 4 copies of RHAMNISOM-MONOMER; the corresponding UniProt chain is a component rather than an independently asserted complete catalyst.; Evidence: MetaCyc:CPLX0-7652, EcoCyc:RHAMNISOM-MONOMERhas part MetaCyc:LYXK-CPLX — has_part → UniProtKB:P37677; The native assembly has 2 copies of LYXK-MONOMER; the corresponding UniProt chain is a component rather than an independently asserted complete catalyst.; Evidence: MetaCyc:LYXK-CPLX, EcoCyc:LYXK-MONOMERhas part MetaCyc:RIBULPEPIM-CPLX — has_part → UniProtKB:P08203; The native assembly has 4 copies of RIBULPEPIM-MONOMER; the corresponding UniProt chain is a component rather than an independently asserted complete catalyst.; Evidence: MetaCyc:RIBULPEPIM-CPLX, EcoCyc:RIBULPEPIM-MONOMERhas part UniProtKB:P32170 — catalyzes → MetaCyc:LYXISOM-RXN; subject experimental construct: JA121 (JA120 carrying pJB4.3) overexpressed RhaA preparation; reference P32170 is an identity anchor, not proof of exact assayed sequence. Mn2+/reducing purification conditions; native oligomer not independently established by this assay.; Evidence PMID:1650346: RhaA was purified from JA121, produced by transforming JA120 with pJB4.3. Purification buffers contained Mn2+ and reducing reagent; this overexpressed preparation is not a whole-culture MG1655 assay. (PDF printed pp. 5145-5146, strains and purification); Purified overexpressed RhaA converted L-lyxose to L-xylulose, with Km 5 mM and apparent Vmax 6.0 U/mg. The assay did not resolve substrate anomers; beta specificity here is native pathway structure, not an independent assay finding.; Evidence: PMID:1650346catalyzes UniProtKB:P37677 — catalyzes → RHEA:18870; subject experimental construct: MG1655-derived LyxK expressed in BL21(DE3) from modified pET15b with retained N-terminal 10His tag; current native reference chain is 498 residues. This tagged assay material is not asserted identical to unmodified LyxK.; Evidence PMID:11741871: The MG1655-derived genes were expressed in BL21(DE3) from modified pET15b with N-terminal 10His tags. Tags remained for LyxK; SgbE and SgbU tags were removed with thrombin. Residual cleavage sequences were not reported. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[3]; paragraph containing 'N-terminal His tags'); Evidence PMID:11741871: Enzyme genes were PCR-amplified from MG1655 genomic DNA and cloned into modified pET15b encoding an N-terminal 10His tag. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[1]; paragraph containing 'PCR amplified from genomic DNA'); Purified LyxK phosphorylated L-xylulose and also 3-keto-L-gulonate. The later alternate substrate result limits the older description of absolute specificity.; Evidence: PMID:11741871catalyzes UniProtKB:P37680 — catalyzes → RHEA:22369; subject experimental construct: MG1655-derived SgbE expressed with N-terminal 10His in BL21(DE3), then thrombin-cleaved; residual cleavage sequence unreported. Current reference is 231 residues; the article 232-codon wording does not establish a 232-residue assayed variant.; Evidence PMID:11741871: The MG1655-derived genes were expressed in BL21(DE3) from modified pET15b with N-terminal 10His tags. Tags remained for LyxK; SgbE and SgbU tags were removed with thrombin. Residual cleavage sequences were not reported. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[3]; paragraph containing 'N-terminal His tags'); Evidence PMID:11741871: Enzyme genes were PCR-amplified from MG1655 genomic DNA and cloned into modified pET15b encoding an N-terminal 10His tag. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[1]; paragraph containing 'PCR amplified from genomic DNA'); Purified SgbE catalyzed the L-ribulose 5-phosphate to D-xylulose 5-phosphate reaction in a coupled assay; The purified preparation independently extends the earlier cell-extract evidence.; Evidence: PMID:11741871catalyzes UniProtKB:P32170 — has_cofactor → CHEBI:29035; Reviewed RhaA binds one Mn2+ per subunit (HAMAP and cited experimental sources). This is source annotation; the 1991 use of Mn2+ in purification does not independently establish physiological metal occupancy.; Evidence: UniProtKB:P32170has cofactor MetaCyc:LYXK-CPLX — has_cofactor → CHEBI:18420; Native LyxK lists Mg2+ as cofactor, citing PMID7961955. Its original full body was unavailable here, so this remains an annotation-level cofactor assertion.; Evidence: EcoCyc:LYXK-ENZRXNhas cofactor UniProtKB:P37677 — has_cofactor → CHEBI:18420; subject experimental construct: MG1655-derived, BL21(DE3)-expressed LyxK retaining N-terminal 10His tag; assay used 10 mM MgCl2. Presence in a coupled assay is not a direct metal-binding measurement.; Evidence PMID:11741871: The MG1655-derived genes were expressed in BL21(DE3) from modified pET15b with N-terminal 10His tags. Tags remained for LyxK; SgbE and SgbU tags were removed with thrombin. Residual cleavage sequences were not reported. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[3]; paragraph containing 'N-terminal His tags'); Evidence PMID:11741871: Enzyme genes were PCR-amplified from MG1655 genomic DNA and cloned into modified pET15b encoding an N-terminal 10His tag. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[1]; paragraph containing 'PCR amplified from genomic DNA'); Table 2 note e describes the LyxK assay with 10 mM MgCl2, 1.5 mM ATP and coupled pyruvate kinase/lactate dehydrogenase. This is an assay condition, not measured intracellular occupancy.; Evidence: PMID:11741871has cofactor UniProtKB:P37680 — has_cofactor → CHEBI:29105; SgbE zinc binding and one-zinc-per-subunit stoichiometry are annotated by similarity to AraD P08203 (ECO:0000250), not a direct SgbE metal determination.; Evidence: UniProtKB:P37680has cofactor UniProtKB:P08203 — has_cofactor → CHEBI:29105; subject experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12 reference sequence; native commentary reports 98.7% deduced identity. No assertion that every cited preparation was unmodified MG1655 AraD.; Evidence EcoCyc:RIBULPEPIM-MONOMER: The native AraD commentary explicitly identifies B/r UP1000 and the K-12/B-r sequence difference for the cited biochemical/structural work. (XPath /ptools-xml/Protein/comment); Reviewed AraD can use zinc; zinc is the annotated cofactor and cobalt/manganese alternatives are less efficient. These are alternatives rather than jointly required metals.; Evidence: UniProtKB:P08203, EcoCyc:RIBULPEPIM-MONOMERhas cofactor UniProtKB:P08203 — has_cofactor → CHEBI:48828; subject experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12 reference sequence; native commentary reports 98.7% deduced identity. No assertion that every cited preparation was unmodified MG1655 AraD.; Evidence EcoCyc:RIBULPEPIM-MONOMER: The native AraD commentary explicitly identifies B/r UP1000 and the K-12/B-r sequence difference for the cited biochemical/structural work. (XPath /ptools-xml/Protein/comment); Reviewed AraD can use cobalt; zinc is the annotated cofactor and cobalt/manganese alternatives are less efficient. These are alternatives rather than jointly required metals.; Evidence: UniProtKB:P08203, EcoCyc:RIBULPEPIM-MONOMERhas cofactor UniProtKB:P08203 — has_cofactor → CHEBI:29035; subject experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12 reference sequence; native commentary reports 98.7% deduced identity. No assertion that every cited preparation was unmodified MG1655 AraD.; Evidence EcoCyc:RIBULPEPIM-MONOMER: The native AraD commentary explicitly identifies B/r UP1000 and the K-12/B-r sequence difference for the cited biochemical/structural work. (XPath /ptools-xml/Protein/comment); Reviewed AraD can use manganese; zinc is the annotated cofactor and cobalt/manganese alternatives are less efficient. These are alternatives rather than jointly required metals.; Evidence: UniProtKB:P08203, EcoCyc:RIBULPEPIM-MONOMERhas cofactor CHEBI:30616 — inhibits → RHEA:18870; The native negative regulation event identifies ATP inhibition of LyxK activity, citing the 1994 paper. ATP remains a reaction substrate; concentrations, allosteric mechanism and in-vivo flux effects are not inferred.; Evidence: EcoCyc:REG0-7578inhibits UniProtKB:P32170 — located_in → GO:0005829; The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.; Evidence: EcoCyc:RHAMNISOM-MONOMERlocated in UniProtKB:P37677 — located_in → GO:0005829; The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.; Evidence: EcoCyc:LYXK-MONOMERlocated in UniProtKB:P37679 — located_in → GO:0005829; The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.; Evidence: EcoCyc:EG12286-MONOMERlocated in UniProtKB:P37680 — located_in → GO:0005829; The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.; Evidence: EcoCyc:EG12287-MONOMERlocated in UniProtKB:P08203 — located_in → GO:0005829; The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.; Evidence: EcoCyc:RIBULPEPIM-MONOMERlocated in UniProtKB:P37671 — located_in → GO:0005829; The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.; Evidence: EcoCyc:EG12278-MONOMERlocated in UniProtKB:P27125 — located_in → GO:0005886; Reviewed RhaT is a multipass inner-membrane protein; membrane location belongs to the transporter rather than to all substrate molecules.; Evidence: UniProtKB:P27125located in MetaCyc:LYXISOM-RXN — occurs_in → GO:0005829; The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.; Evidence: MetaCyc:LYXMET-PWY, EcoCyc:RHAMNISOM-MONOMERoccurs in RHEA:18870 — occurs_in → GO:0005829; The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.; Evidence: MetaCyc:LYXMET-PWY, EcoCyc:LYXK-MONOMERoccurs in RHEA:18499 — occurs_in → GO:0005829; The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.; Evidence: MetaCyc:LYXMET-PWY, EcoCyc:EG12286-MONOMERoccurs in RHEA:22369 — occurs_in → GO:0005829; The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.; Evidence: MetaCyc:LYXMET-PWY, EcoCyc:EG12287-MONOMERoccurs in RHEA:29993 — occurs_in → GO:0005886; RhaT-mediated uptake crosses the bacterial inner membrane; the corresponding reviewed protein is a multipass inner-membrane transporter.; Evidence: UniProtKB:P27125occurs in EcoCyc:PC00004 — has_part → UniProtKB:P0ACJ8; Native PC00004 contains PD00257. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.; Evidence: EcoCyc:PC00004, UniProtKB:P0ACJ8has part EcoCyc:PC00086 — has_part → UniProtKB:P09377; Native PC00086 contains PD00221. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.; Evidence: EcoCyc:PC00086, UniProtKB:P09377has part EcoCyc:PC00027 — has_part → UniProtKB:P0A6X7; Native PC00027 contains PD00347. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.; Evidence: EcoCyc:PC00027, UniProtKB:P0A6X7, UniProtKB:P0A6X7has part EcoCyc:PC00027 — has_part → UniProtKB:P0A6Y1; Native PC00027 contains PD00348. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.; Evidence: EcoCyc:PC00027, UniProtKB:P0A6Y1, UniProtKB:P0A6Y1has part EcoCyc:CPLX0-226 — has_part → EcoCyc:PC00004; Native CPLX0-226 explicitly contains PC00004; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.; Evidence: EcoCyc:CPLX0-226has part EcoCyc:CPLX0-226 — has_part → CHEBI:58165; Native CPLX0-226 explicitly contains CAMP; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.; Evidence: EcoCyc:CPLX0-226has part EcoCyc:CPLX-124 — has_part → EcoCyc:PC00086; Native CPLX-124 explicitly contains PC00086; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.; Evidence: EcoCyc:CPLX-124has part EcoCyc:CPLX-124 — has_part → CHEBI:62345; Native CPLX-124 explicitly contains L-rhamnose; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.; Evidence: EcoCyc:CPLX-124has part UniProtKB:P37671 — inhibits → Entrez:948101; Native REG0-4907 assigns - regulation of yiaKp1 (PM692) by EG12278-MONOMER. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.; Evidence: EcoCyc:TU592, EcoCyc:TU592, Entrez:948101, PMID:10913096inhibits EcoCyc:CPLX0-226 — activates → Entrez:948101; Native REG0-4905 assigns + regulation of yiaKp1 (PM692) by CPLX0-226. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.; Evidence: EcoCyc:TU592, EcoCyc:TU592, Entrez:948101, PMID:10913096activates EcoCyc:PC00027 — activates → Entrez:948101; Native REG0-4906 assigns + regulation of yiaKp1 (PM692) by PC00027. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.; Evidence: EcoCyc:TU592, EcoCyc:TU592, Entrez:948101, PMID:10913096activates UniProtKB:P37671 — inhibits → Entrez:948100; Native REG0-4907 assigns - regulation of yiaKp1 (PM692) by EG12278-MONOMER. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.; Evidence: EcoCyc:TU592, EcoCyc:TU592, Entrez:948100, PMID:10913096inhibits EcoCyc:CPLX0-226 — activates → Entrez:948100; Native REG0-4905 assigns + regulation of yiaKp1 (PM692) by CPLX0-226. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.; Evidence: EcoCyc:TU592, EcoCyc:TU592, Entrez:948100, PMID:10913096activates EcoCyc:PC00027 — activates → Entrez:948100; Native REG0-4906 assigns + regulation of yiaKp1 (PM692) by PC00027. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.; Evidence: EcoCyc:TU592, EcoCyc:TU592, Entrez:948100, PMID:10913096activates UniProtKB:P37671 — inhibits → Entrez:948099; Native REG0-4907 assigns - regulation of yiaKp1 (PM692) by EG12278-MONOMER. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.; Evidence: EcoCyc:TU592, EcoCyc:TU592, Entrez:948099, PMID:10913096inhibits EcoCyc:CPLX0-226 — activates → Entrez:948099; Native REG0-4905 assigns + regulation of yiaKp1 (PM692) by CPLX0-226. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.; Evidence: EcoCyc:TU592, EcoCyc:TU592, Entrez:948099, PMID:10913096activates EcoCyc:PC00027 — activates → Entrez:948099; Native REG0-4906 assigns + regulation of yiaKp1 (PM692) by PC00027. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.; Evidence: EcoCyc:TU592, EcoCyc:TU592, Entrez:948099, PMID:10913096activates UniProtKB:P37671 — inhibits → Entrez:948084; Native REG0-10778 negatively regulates plaRp (PM449) by EG12278-MONOMER. This is gene expression control; IHF repression is retained at native annotation level.; Evidence: EcoCyc:TU368, Entrez:948084inhibits EcoCyc:CPLX0-226 — inhibits → Entrez:948084; Native REG0-4987 negatively regulates plaRp (PM449) by CPLX0-226. This is gene expression control; IHF repression is retained at native annotation level.; Evidence: EcoCyc:TU368, Entrez:948084inhibits EcoCyc:PC00027 — inhibits → Entrez:948084; Native REG0-4986 negatively regulates plaRp (PM449) by PC00027. This is gene expression control; IHF repression is retained at native annotation level.; Evidence: EcoCyc:TU368, Entrez:948084inhibits EcoCyc:CPLX-124 — activates → Entrez:948398; Native REG0-5372 positively regulates PM00293, the promoter of the rhaT-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.; Evidence: EcoCyc:TU00208, EcoCyc:TU00208, Entrez:948398activates EcoCyc:CPLX0-226 — activates → Entrez:948398; Native REG0-5374 positively regulates PM00293, the promoter of the rhaT-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.; Evidence: EcoCyc:TU00208, EcoCyc:TU00208, Entrez:948398activates EcoCyc:CPLX-124 — activates → Entrez:948400; Native REG0-5986 positively regulates PM00303, the promoter of the rhaA-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.; Evidence: EcoCyc:TU00219, EcoCyc:TU00219, Entrez:948400activates EcoCyc:CPLX0-226 — activates → Entrez:948400; Native REG0-5985 positively regulates PM00303, the promoter of the rhaA-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.; Evidence: EcoCyc:TU00219, EcoCyc:TU00219, Entrez:948400activates UniProtKB:P0A9Q1 — inhibits → Entrez:948398; subject molecular state: Phosphorylated ArcA corresponding to native PHOSPHO-ARCA, not the unmodified P0A9Q1 reference chain. Native Asp54 aspartylphosphate is annotated by similarity; promoter-binding-site inference is computational and expression effects may be indirect.; Evidence EcoCyc:PHOSPHO-ARCA: Native PHOSPHO-ARCA is a modified protein with unmodified-form ARCA-MONOMER and modified residue 54 aspartylphosphate annotated by similarity. (XPath /ptools-xml/Protein); Native negative rhaTp regulation is backed by gene-expression analysis; the associated promoter-binding-site evidence is similarity to consensus. Expression evidence does not exclude indirect regulation or prove direct rhaT binding.; Evidence: EcoCyc:REG0-5375, EcoCyc:REG0-5376, EcoCyc:REG0-5377, Entrez:948398inhibits CHEBI:62320 — activates → Entrez:948400; Reviewed rhaA is induced by L-lyxose. The original 1991 ECL1 assays measured enzyme/transport activities after growth with sugar; they do not establish direct lyxose binding to RhaS or RhaR.; Evidence: UniProtKB:P32170, Entrez:948400, PMID:1650346activates CHEBI:62320 — activates → Entrez:948398; Reviewed rhaT is induced by L-lyxose. The original 1991 ECL1 assays measured enzyme/transport activities after growth with sugar; they do not establish direct lyxose binding to RhaS or RhaR.; Evidence: UniProtKB:P27125, Entrez:948398, PMID:1650346activates CHEBI:62320 — activates → Entrez:945294; L-lyxose induced the ara operon even in the JA199 rhaA insertion mutant, supporting induction independent of RhaA conversion. This does not establish direct binding to AraC or identify an active lyxose anomer.; Evidence: PMID:10913097, Entrez:945294activates CHEBI:38290 — inhibits → UniProtKB:P37671; object experimental construct: His-tagged PlaR from pET21a(+) expressed in BL21(DE3), affinity-purified for promoter gel shifts; exact complete tag/construct sequence unreported. BW25113 supplied gel-shift probes; W3110 type-A supplied separate gSELEX genome fragments.; Evidence PMID:31892694: The assayed PlaR was His-tagged, expressed from pET21a(+) in BL21(DE3), and affinity-purified. The exact tag position/complete construct sequence is not specified in the inspected text. (XPath /article/body/sec[4]/sec[2]/p; paragraph containing 'Expression plasmid pPlaR'); Evidence PMID:31892694: Gel shifts used BW25113-derived promoter probes and buffer containing Tris pH 7.8, NaCl and magnesium acetate. These conditions support chosen solution species without measuring ligand protonation or anomer purity. (XPath /article/body/sec[4]/sec[4]/p; paragraph containing 'The gel shift assay was performed'); L-ascorbate reduced PlaR-yiaK promoter complexes in the 10 mM effector screen; dose-dependent dissociation was examined. The edge concerns PlaR DNA-binding activity, not inhibition of a metabolic enzyme or complete lyxose flux.; Evidence: PMID:31892694inhibits CHEBI:38290 — activates → Entrez:948101; L-ascorbate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.; Evidence: PMID:31892694, EcoCyc:TU592, Entrez:948101activates CHEBI:38290 — activates → Entrez:948100; L-ascorbate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.; Evidence: PMID:31892694, EcoCyc:TU592, Entrez:948100activates CHEBI:38290 — activates → Entrez:948099; L-ascorbate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.; Evidence: PMID:31892694, EcoCyc:TU592, Entrez:948099activates CHEBI:58658 — inhibits → UniProtKB:P37671; object experimental construct: His-tagged PlaR from pET21a(+) expressed in BL21(DE3), affinity-purified for promoter gel shifts; exact complete tag/construct sequence unreported. BW25113 supplied gel-shift probes; W3110 type-A supplied separate gSELEX genome fragments.; Evidence PMID:31892694: The assayed PlaR was His-tagged, expressed from pET21a(+) in BL21(DE3), and affinity-purified. The exact tag position/complete construct sequence is not specified in the inspected text. (XPath /article/body/sec[4]/sec[2]/p; paragraph containing 'Expression plasmid pPlaR'); Evidence PMID:31892694: Gel shifts used BW25113-derived promoter probes and buffer containing Tris pH 7.8, NaCl and magnesium acetate. These conditions support chosen solution species without measuring ligand protonation or anomer purity. (XPath /article/body/sec[4]/sec[4]/p; paragraph containing 'The gel shift assay was performed'); alpha-D-galacturonate reduced PlaR-yiaK promoter complexes in the 10 mM effector screen; dose-dependent dissociation was examined. The edge concerns PlaR DNA-binding activity, not inhibition of a metabolic enzyme or complete lyxose flux.; Evidence: PMID:31892694inhibits CHEBI:58658 — activates → Entrez:948101; alpha-D-galacturonate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.; Evidence: PMID:31892694, EcoCyc:TU592, Entrez:948101activates CHEBI:58658 — activates → Entrez:948100; alpha-D-galacturonate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.; Evidence: PMID:31892694, EcoCyc:TU592, Entrez:948100activates CHEBI:58658 — activates → Entrez:948099; alpha-D-galacturonate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.; Evidence: PMID:31892694, EcoCyc:TU592, Entrez:948099activates CHEBI:57925 — activates → RHEA:18870; The native positive regulation event assigns glutathione activation to LyxK activity, citing PMID7961955. Its original full body was unavailable; no concentration, allosteric mechanism or in-vivo flux effect is invented.; Evidence: EcoCyc:REG0-7579activates UniProtKB:P0A6X7 — located_in → GO:0009295; The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.; Evidence: UniProtKB:P0A6X7located in UniProtKB:P0A6Y1 — located_in → GO:0005737; The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.; Evidence: UniProtKB:P0A6Y1located in UniProtKB:P0A9Q1 — located_in → GO:0005737; The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.; Evidence: UniProtKB:P0A9Q1located in UniProtKB:P09377 — located_in → GO:0005737; The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.; Evidence: UniProtKB:P09377located in CHEBI:17634 — activates → Entrez:948084; Glucose enhanced the divergent yiaJ/plaR reporter while repressing yiaK-S. This is coordinated carbon-source-dependent expression in the examined reporter backgrounds, not direct glucose binding to PlaR.; Evidence: PMID:10913096, Entrez:948084activates CHEBI:17634 — inhibits → Entrez:948101; Glucose reduced yiaK-S reporter activity in JA134 under aerobic and anaerobic conditions. Exogenous cAMP partly restored activity; this is carbon-source-dependent expression, not direct inhibition of LyxK/SgbU/SgbE.; Evidence: PMID:10913096, EcoCyc:TU592, Entrez:948101inhibits CHEBI:17634 — inhibits → Entrez:948100; Glucose reduced yiaK-S reporter activity in JA134 under aerobic and anaerobic conditions. Exogenous cAMP partly restored activity; this is carbon-source-dependent expression, not direct inhibition of LyxK/SgbU/SgbE.; Evidence: PMID:10913096, EcoCyc:TU592, Entrez:948100inhibits CHEBI:17634 — inhibits → Entrez:948099; Glucose reduced yiaK-S reporter activity in JA134 under aerobic and anaerobic conditions. Exogenous cAMP partly restored activity; this is carbon-source-dependent expression, not direct inhibition of LyxK/SgbU/SgbE.; Evidence: PMID:10913096, EcoCyc:TU592, Entrez:948099inhibits CHEBI:30031 — activates → Entrez:948101; Growth on succinate increased yiaK-S reporter expression about threefold in the JA134 derepressed background. This bounded culture response is not evidence for direct succinate binding to any enzyme or regulator.; Evidence: PMID:10913096, EcoCyc:TU592, Entrez:948101activates CHEBI:30031 — activates → Entrez:948100; Growth on succinate increased yiaK-S reporter expression about threefold in the JA134 derepressed background. This bounded culture response is not evidence for direct succinate binding to any enzyme or regulator.; Evidence: PMID:10913096, EcoCyc:TU592, Entrez:948100activates CHEBI:30031 — activates → Entrez:948099; Growth on succinate increased yiaK-S reporter expression about threefold in the JA134 derepressed background. This bounded culture response is not evidence for direct succinate binding to any enzyme or regulator.; Evidence: PMID:10913096, EcoCyc:TU592, Entrez:948099activates CHEBI:18287 — activates → Entrez:948101; L-fucose modestly increased the yiaK-S reporter in ECL1 under the 2000 screening conditions, while JA134 was constitutively high. The physiological inducer was then unresolved; direct PlaR ligand binding was not shown.; Evidence: PMID:10913096, EcoCyc:TU592, Entrez:948101activates CHEBI:18287 — activates → Entrez:948100; L-fucose modestly increased the yiaK-S reporter in ECL1 under the 2000 screening conditions, while JA134 was constitutively high. The physiological inducer was then unresolved; direct PlaR ligand binding was not shown.; Evidence: PMID:10913096, EcoCyc:TU592, Entrez:948100activates CHEBI:18287 — activates → Entrez:948099; L-fucose modestly increased the yiaK-S reporter in ECL1 under the 2000 screening conditions, while JA134 was constitutively high. The physiological inducer was then unresolved; direct PlaR ligand binding was not shown.; Evidence: PMID:10913096, EcoCyc:TU592, Entrez:948099activates MetaCyc:LYXMET-PWY — has_part → PathBank:SMP0121065; Frozen SMP0002112 directly attaches Pentose Phosphate child SMP0121065. This is source-specific opaque child membership associated with the lyxose route; child chemistry is not expanded and frozen UlaF assignment is not adopted.; Evidence: PathBank:SMP0002112has part UniProtKB:P76268 — inhibits → Entrez:948084; Northern blots show increased plaR mRNA after deletion of KdgR, supporting a negative influence on plaR expression under these conditions. Regulation may be indirect; direct promoter binding is not established. Northern blots: BW25113 versus JW3546 (plaR deletion) or JW1816 (kdgR deletion); M9 + 0.5% casamino acids, 37 C, aerobic shaking, mid-exponential phase.; Evidence: PMID:31892694, PMID:31892694, PMID:31892694, UniProtKB:P76268, Entrez:946129, UniProtKB:P37671, Entrez:948084inhibits UniProtKB:P37671 — inhibits → Entrez:946129; Northern blots show increased kdgR mRNA after deletion of PlaR, supporting a negative influence on kdgR expression under these conditions. Regulation may be indirect; direct promoter binding is not established. Northern blots: BW25113 versus JW3546 (plaR deletion) or JW1816 (kdgR deletion); M9 + 0.5% casamino acids, 37 C, aerobic shaking, mid-exponential phase.; Evidence: PMID:31892694, PMID:31892694, PMID:31892694, UniProtKB:P76268, Entrez:946129, UniProtKB:P37671, Entrez:948084inhibits beta-L-lyxopyranose; CHEBI:147210; Declared type: small_molecule small molecule beta-L-lyxopyranose L-xylulose; CHEBI:17399; Declared type: small_molecule small molecule L-xylulose L-xylulose 5-phosphate(2-); CHEBI:57829; Declared type: small_molecule small molecule L-xylulose 5-phosphate(2-) L-ribulose 5-phosphate(2-); CHEBI:58226; Declared type: small_molecule small molecule L-ribulose 5-phosphate(2-) D-xylulose 5-phosphate(2-); CHEBI:57737; Declared type: small_molecule small molecule D-xylulose 5-phosphate(2-) ATP(4-); CHEBI:30616; Declared type: small_molecule small molecule ATP(4-) ADP(3-); CHEBI:456216; Declared type: small_molecule small molecule ADP(3-) hydron; CHEBI:15378; Declared type: small_molecule small molecule hydron L-lyxopyranose; CHEBI:62321; Declared type: small_molecule small molecule L-lyxopyranose L-lyxose; CHEBI:62320; Declared type: small_molecule small molecule L-lyxose 3',5'-cyclic AMP(1-); CHEBI:58165; Declared type: small_molecule small molecule 3',5'-cyclic AMP(1-) L-ascorbate; CHEBI:38290; Declared type: small_molecule small molecule L-ascorbate alpha-D-galacturonate; CHEBI:58658; Declared type: small_molecule small molecule alpha-D-galacturonate manganese(2+); CHEBI:29035; Declared type: cofactor cofactor manganese(2+) magnesium(2+); CHEBI:18420; Declared type: cofactor cofactor magnesium(2+) zinc(2+); CHEBI:29105; Declared type: cofactor cofactor zinc(2+) cobalt(2+); CHEBI:48828; Declared type: cofactor cofactor cobalt(2+) L-rhamnose isomerase; UniProtKB:P32170; Declared type: protein protein L-rhamnose isomerase L-xylulose/3-keto-L-gulonate kinase; UniProtKB:P37677; Declared type: protein protein L-xylulose/3-keto-L-gulonate kinase Putative L-ribulose-5-phosphate 3-epimerase SgbU; UniProtKB:P37679; Declared type: protein protein Putative L-ribulose-5-phosphate 3-epimerase SgbU L-ribulose-5-phosphate 4-epimerase SgbE; UniProtKB:P37680; Declared type: protein protein L-ribulose-5-phosphate 4-epimerase SgbE L-ribulose-5-phosphate 4-epimerase AraD; UniProtKB:P08203; Declared type: protein protein L-ribulose-5-phosphate 4-epimerase AraD L-rhamnose-proton symporter; UniProtKB:P27125; Declared type: protein protein L-rhamnose-proton symporter HTH-type transcriptional repressor PlaR; UniProtKB:P37671; Declared type: protein protein HTH-type transcriptional repressor PlaR L-rhamnose isomerase; MetaCyc:CPLX0-7652; Declared type: complex complex L-rhamnose isomerase L-xylulose kinase; MetaCyc:LYXK-CPLX; Declared type: complex complex L-xylulose kinase L-ribulose-5-phosphate 4-epimerase AraD; MetaCyc:RIBULPEPIM-CPLX; Declared type: complex complex L-ribulose-5-phosphate 4-epimerase AraD cytosol; GO:0005829; Declared type: cellular_component cellular component cytosol plasma membrane; GO:0005886; Declared type: cellular_component cellular component plasma membrane DNA-binding transcriptional dual regulator CRP; EcoCyc:PC00004; Declared type: complex complex DNA-binding transcriptional dual regulator CRP transcriptional activator RhaS; EcoCyc:PC00086; Declared type: complex complex transcriptional activator RhaS araD; Entrez:945294; Declared type: gene gene araD rhaT; Entrez:948398; Declared type: gene gene rhaT rhaA; Entrez:948400; Declared type: gene gene rhaA sgbE; Entrez:948099; Declared type: gene gene sgbE 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 Aerobic respiration control protein ArcA; UniProtKB:P0A9Q1; Declared type: protein protein Aerobic respiration control protein ArcA HTH-type transcriptional activator RhaS; UniProtKB:P09377; Declared type: protein protein HTH-type transcriptional activator RhaS plaR; Entrez:948084; Declared type: gene gene plaR lyxK; Entrez:948101; Declared type: gene gene lyxK DNA-binding transcriptional dual regulator CRP; UniProtKB:P0ACJ8; Declared type: protein protein DNA-binding transcriptional dual regulator CRP sgbU; Entrez:948100; Declared type: gene gene sgbU CRP-cyclic-AMP DNA-binding transcriptional dual regulator; EcoCyc:CPLX0-226; Declared type: complex complex CRP-cyclic-AMP DNA-binding transcriptional dual regulator DNA-binding transcriptional dual regulator IHF; EcoCyc:PC00027; Declared type: complex complex DNA-binding transcriptional dual regulator IHF RhaS-L-rhamnose DNA-binding transcriptional activator; EcoCyc:CPLX-124; Declared type: complex complex RhaS-L-rhamnose DNA-binding transcriptional activator glutathionate(1-); CHEBI:57925; Declared type: small_molecule small molecule glutathionate(1-) L-rhamnose; CHEBI:62345; Declared type: small_molecule small molecule L-rhamnose cytoplasm; GO:0005737; Declared type: cellular_component cellular component cytoplasm nucleoid; GO:0009295; Declared type: cellular_component cellular component nucleoid D-glucose; CHEBI:17634; Declared type: small_molecule small molecule D-glucose succinate(2-); CHEBI:30031; Declared type: small_molecule small molecule succinate(2-) L-fucose; CHEBI:18287; Declared type: small_molecule small molecule L-fucose HTH-type transcriptional regulator KdgR; UniProtKB:P76268; Declared type: protein protein HTH-type transcriptional regulator KdgR kdgR; Entrez:946129; Declared type: gene gene kdgR beta-L-lyxopyranose to L-xylulose isomerization; MetaCyc:LYXISOM-RXN; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity beta-L-lyxopyranose to L-xylulose isomerization L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+); RHEA:18870; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+) L-xylulose 5-phosphate => L-ribulose 5-phosphate; RHEA:18499; Declared type: molecular_activity; Source reaction direction: right_to_left molecular activity L-xylulose 5-phosphate => L-ribulose 5-phosphate L-ribulose 5-phosphate => D-xylulose 5-phosphate; RHEA:22369; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity L-ribulose 5-phosphate => D-xylulose 5-phosphate L-lyxopyranose(out) + H(+)(out) => L-lyxopyranose(in) + H(+)(in); RHEA:29993; Declared type: molecular_activity; Source reaction direction: right_to_left molecular activity L-lyxopyranose(out) + H(+)(out) => L-lyxopyranose(in) + H(+)(in) pentose phosphate pathway (non-oxidative branch); MetaCyc:NONOXIPENT-PWY; Declared type: pathway pathway pentose phosphate pathway (non-oxidative branch) superpathway of pentose and pentitol degradation; MetaCyc:PWY-5257; Declared type: pathway pathway superpathway of pentose and pentitol degradation Pentose Phosphate; PathBank:SMP0121065; Declared type: pathway pathway Pentose Phosphate L-lyxose degradation; MetaCyc:LYXMET-PWY; Declared type: pathway pathway L-lyxose degradation L-rhamnose isomerase; UniProtKB:P32170; Declared type: protein; experimental construct: JA121 (JA120 carrying pJB4.3) overexpressed RhaA preparation; reference P32170 is an identity anchor, not proof of exact assayed sequence. Mn2+/reducing purification conditions; native oligomer not independently established by this assay.; Evidence PMID:1650346: RhaA was purified from JA121, produced by transforming JA120 with pJB4.3. Purification buffers contained Mn2+ and reducing reagent; this overexpressed preparation is not a whole-culture MG1655 assay. (PDF printed pp. 5145-5146, strains and purification) experimental construct L-rhamnose isomerase [experimental construct: JA121 (JA120 carrying pJB4.3) overexpressed RhaA preparation; reference P32170 is an identity…] L-xylulose/3-keto-L-gulonate kinase; UniProtKB:P37677; Declared type: protein; experimental construct: MG1655-derived LyxK expressed in BL21(DE3) from modified pET15b with retained N-terminal 10His tag; current native reference chain is 498 residues. This tagged assay material is not asserted identical to unmodified LyxK.; Evidence PMID:11741871: The MG1655-derived genes were expressed in BL21(DE3) from modified pET15b with N-terminal 10His tags. Tags remained for LyxK; SgbE and SgbU tags were removed with thrombin. Residual cleavage sequences were not reported. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[3]; paragraph containing 'N-terminal His tags'); Evidence PMID:11741871: Enzyme genes were PCR-amplified from MG1655 genomic DNA and cloned into modified pET15b encoding an N-terminal 10His tag. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[1]; paragraph containing 'PCR amplified from genomic DNA') experimental construct L-xylulose/3-keto-L-gulonate kinase [experimental construct: MG1655-derived LyxK expressed in BL21(DE3) from modified pET15b with retained N-terminal 10His tag;…] L-ribulose-5-phosphate 4-epimerase SgbE; UniProtKB:P37680; Declared type: protein; experimental construct: MG1655-derived SgbE expressed with N-terminal 10His in BL21(DE3), then thrombin-cleaved; residual cleavage sequence unreported. Current reference is 231 residues; the article 232-codon wording does not establish a 232-residue assayed variant.; Evidence PMID:11741871: The MG1655-derived genes were expressed in BL21(DE3) from modified pET15b with N-terminal 10His tags. Tags remained for LyxK; SgbE and SgbU tags were removed with thrombin. Residual cleavage sequences were not reported. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[3]; paragraph containing 'N-terminal His tags'); Evidence PMID:11741871: Enzyme genes were PCR-amplified from MG1655 genomic DNA and cloned into modified pET15b encoding an N-terminal 10His tag. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[1]; paragraph containing 'PCR amplified from genomic DNA') experimental construct L-ribulose-5-phosphate 4-epimerase SgbE [experimental construct: MG1655-derived SgbE expressed with N-terminal 10His in BL21(DE3), then thrombin-cleaved; residual…] L-xylulose/3-keto-L-gulonate kinase; UniProtKB:P37677; Declared type: protein; experimental construct: MG1655-derived, BL21(DE3)-expressed LyxK retaining N-terminal 10His tag; assay used 10 mM MgCl2. Presence in a coupled assay is not a direct metal-binding measurement.; Evidence PMID:11741871: The MG1655-derived genes were expressed in BL21(DE3) from modified pET15b with N-terminal 10His tags. Tags remained for LyxK; SgbE and SgbU tags were removed with thrombin. Residual cleavage sequences were not reported. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[3]; paragraph containing 'N-terminal His tags'); Evidence PMID:11741871: Enzyme genes were PCR-amplified from MG1655 genomic DNA and cloned into modified pET15b encoding an N-terminal 10His tag. (XPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[1]; paragraph containing 'PCR amplified from genomic DNA') experimental construct L-xylulose/3-keto-L-gulonate kinase [experimental construct: MG1655-derived, BL21(DE3)-expressed LyxK retaining N-terminal 10His tag; assay used 10 mM MgCl2.…] L-ribulose-5-phosphate 4-epimerase AraD; UniProtKB:P08203; Declared type: protein; experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12 reference sequence; native commentary reports 98.7% deduced identity. No assertion that every cited preparation was unmodified MG1655 AraD.; Evidence EcoCyc:RIBULPEPIM-MONOMER: The native AraD commentary explicitly identifies B/r UP1000 and the K-12/B-r sequence difference for the cited biochemical/structural work. (XPath /ptools-xml/Protein/comment) experimental construct L-ribulose-5-phosphate 4-epimerase AraD [experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12…] L-ribulose-5-phosphate 4-epimerase AraD; UniProtKB:P08203; Declared type: protein; experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12 reference sequence; native commentary reports 98.7% deduced identity. No assertion that every cited preparation was unmodified MG1655 AraD.; Evidence EcoCyc:RIBULPEPIM-MONOMER: The native AraD commentary explicitly identifies B/r UP1000 and the K-12/B-r sequence difference for the cited biochemical/structural work. (XPath /ptools-xml/Protein/comment) experimental construct L-ribulose-5-phosphate 4-epimerase AraD [experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12…] L-ribulose-5-phosphate 4-epimerase AraD; UniProtKB:P08203; Declared type: protein; experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12 reference sequence; native commentary reports 98.7% deduced identity. No assertion that every cited preparation was unmodified MG1655 AraD.; Evidence EcoCyc:RIBULPEPIM-MONOMER: The native AraD commentary explicitly identifies B/r UP1000 and the K-12/B-r sequence difference for the cited biochemical/structural work. (XPath /ptools-xml/Protein/comment) experimental construct L-ribulose-5-phosphate 4-epimerase AraD [experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12…] Aerobic respiration control protein ArcA; UniProtKB:P0A9Q1; Declared type: protein; molecular state: Phosphorylated ArcA corresponding to native PHOSPHO-ARCA, not the unmodified P0A9Q1 reference chain. Native Asp54 aspartylphosphate is annotated by similarity; promoter-binding-site inference is computational and expression effects may be indirect.; Evidence EcoCyc:PHOSPHO-ARCA: Native PHOSPHO-ARCA is a modified protein with unmodified-form ARCA-MONOMER and modified residue 54 aspartylphosphate annotated by similarity. (XPath /ptools-xml/Protein) molecular state Aerobic respiration control protein ArcA [molecular state: Phosphorylated ArcA corresponding to native PHOSPHO-ARCA, not the unmodified P0A9Q1 reference…] HTH-type transcriptional repressor PlaR; UniProtKB:P37671; Declared type: protein; experimental construct: His-tagged PlaR from pET21a(+) expressed in BL21(DE3), affinity-purified for promoter gel shifts; exact complete tag/construct sequence unreported. BW25113 supplied gel-shift probes; W3110 type-A supplied separate gSELEX genome fragments.; Evidence PMID:31892694: The assayed PlaR was His-tagged, expressed from pET21a(+) in BL21(DE3), and affinity-purified. The exact tag position/complete construct sequence is not specified in the inspected text. (XPath /article/body/sec[4]/sec[2]/p; paragraph containing 'Expression plasmid pPlaR'); Evidence PMID:31892694: Gel shifts used BW25113-derived promoter probes and buffer containing Tris pH 7.8, NaCl and magnesium acetate. These conditions support chosen solution species without measuring ligand protonation or anomer purity. (XPath /article/body/sec[4]/sec[4]/p; paragraph containing 'The gel shift assay was performed') experimental construct HTH-type transcriptional repressor PlaR [experimental construct: His-tagged PlaR from pET21a(+) expressed in BL21(DE3), affinity-purified for promoter gel shifts;…] HTH-type transcriptional repressor PlaR; UniProtKB:P37671; Declared type: protein; experimental construct: His-tagged PlaR from pET21a(+) expressed in BL21(DE3), affinity-purified for promoter gel shifts; exact complete tag/construct sequence unreported. BW25113 supplied gel-shift probes; W3110 type-A supplied separate gSELEX genome fragments.; Evidence PMID:31892694: The assayed PlaR was His-tagged, expressed from pET21a(+) in BL21(DE3), and affinity-purified. The exact tag position/complete construct sequence is not specified in the inspected text. (XPath /article/body/sec[4]/sec[2]/p; paragraph containing 'Expression plasmid pPlaR'); Evidence PMID:31892694: Gel shifts used BW25113-derived promoter probes and buffer containing Tris pH 7.8, NaCl and magnesium acetate. These conditions support chosen solution species without measuring ligand protonation or anomer purity. (XPath /article/body/sec[4]/sec[4]/p; paragraph containing 'The gel shift assay was performed') experimental construct HTH-type transcriptional repressor PlaR [experimental construct: His-tagged PlaR from pET21a(+) expressed in BL21(DE3), affinity-purified for promoter gel shifts;…]

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Escherichia coli K-12
NCBITaxon:83333		taxon
Escherichia coli str. K-12 substr. MG1655
NCBITaxon:511145		taxon
beta-L-lyxopyranose
CHEBI:147210		small molecule
L-xylulose
CHEBI:17399		small molecule
L-xylulose 5-phosphate(2-)
CHEBI:57829		small molecule
L-ribulose 5-phosphate(2-)
CHEBI:58226		small molecule
D-xylulose 5-phosphate(2-)
CHEBI:57737		small molecule
ATP(4-)
CHEBI:30616		small molecule
ADP(3-)
CHEBI:456216		small molecule
hydron
CHEBI:15378		small molecule
L-lyxopyranose
CHEBI:62321		small molecule
L-lyxose
CHEBI:62320		small molecule
3',5'-cyclic AMP(1-)
CHEBI:58165		small molecule
L-ascorbate
CHEBI:38290		small molecule
alpha-D-galacturonate
CHEBI:58658		small molecule
manganese(2+)
CHEBI:29035		cofactor
magnesium(2+)
CHEBI:18420		cofactor
zinc(2+)
CHEBI:29105		cofactor
cobalt(2+)
CHEBI:48828		cofactor
L-rhamnose isomerase
UniProtKB:P32170		protein
L-xylulose/3-keto-L-gulonate kinase
UniProtKB:P37677		protein
Putative L-ribulose-5-phosphate 3-epimerase SgbU
UniProtKB:P37679		protein
L-ribulose-5-phosphate 4-epimerase SgbE
UniProtKB:P37680		protein
L-ribulose-5-phosphate 4-epimerase AraD
UniProtKB:P08203		protein
L-rhamnose-proton symporter
UniProtKB:P27125		protein
HTH-type transcriptional repressor PlaR
UniProtKB:P37671		protein
L-rhamnose isomerase
MetaCyc:CPLX0-7652		complex
L-xylulose kinase
MetaCyc:LYXK-CPLX		complex
L-ribulose-5-phosphate 4-epimerase AraD
MetaCyc:RIBULPEPIM-CPLX		complex
cytosol
GO:0005829		cellular component
plasma membrane
GO:0005886		cellular component
DNA-binding transcriptional dual regulator CRP
EcoCyc:PC00004		complex
transcriptional activator RhaS
EcoCyc:PC00086		complex
araD
Entrez:945294		gene
rhaT
Entrez:948398		gene
rhaA
Entrez:948400		gene
sgbE
Entrez:948099		gene
Integration host factor subunit alpha
UniProtKB:P0A6X7		protein
Integration host factor subunit beta
UniProtKB:P0A6Y1		protein
Aerobic respiration control protein ArcA
UniProtKB:P0A9Q1		protein
HTH-type transcriptional activator RhaS
UniProtKB:P09377		protein
plaR
Entrez:948084		gene
lyxK
Entrez:948101		gene
DNA-binding transcriptional dual regulator CRP
UniProtKB:P0ACJ8		protein
sgbU
Entrez:948100		gene
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		complex
DNA-binding transcriptional dual regulator IHF
EcoCyc:PC00027		complex
RhaS-L-rhamnose DNA-binding transcriptional activator
EcoCyc:CPLX-124		complex
glutathionate(1-)
CHEBI:57925		small molecule
L-rhamnose
CHEBI:62345		small molecule
cytoplasm
GO:0005737		cellular component
nucleoid
GO:0009295		cellular component
D-glucose
CHEBI:17634		small molecule
succinate(2-)
CHEBI:30031		small molecule
L-fucose
CHEBI:18287		small molecule
HTH-type transcriptional regulator KdgR
UniProtKB:P76268		protein
kdgR
Entrez:946129		gene
beta-L-lyxopyranose to L-xylulose isomerization
MetaCyc:LYXISOM-RXN		molecular activityleft to right
L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870		molecular activityleft to right
L-xylulose 5-phosphate => L-ribulose 5-phosphate
RHEA:18499		molecular activityright to left
L-ribulose 5-phosphate => D-xylulose 5-phosphate
RHEA:22369		molecular activityleft to right
L-lyxopyranose(out) + H(+)(out) => L-lyxopyranose(in) + H(+)(in)
RHEA:29993		molecular activityright to left
pentose phosphate pathway (non-oxidative branch)
MetaCyc:NONOXIPENT-PWY		pathway
superpathway of pentose and pentitol degradation
MetaCyc:PWY-5257		pathway
Pentose Phosphate
PathBank:SMP0121065		pathway

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
beta-L-lyxopyranose to L-xylulose isomerization
MetaCyc:LYXISOM-RXN		part_of

The exact native reaction-list includes LYXISOM-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.

MetaCyc:LYXMET-PWY
  • MetaCyc:LYXMET-PWY

    Source assertion: The exact native reaction-list includes LYXISOM-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.

    Source locationXPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="LYXISOM-RXN"]
L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870		part_of

The exact native reaction-list includes LYXK-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.

MetaCyc:LYXMET-PWY
  • MetaCyc:LYXMET-PWY

    Source assertion: The exact native reaction-list includes LYXK-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.

    Source locationXPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="LYXK-RXN"]
L-xylulose 5-phosphate => L-ribulose 5-phosphate
RHEA:18499		part_of

The exact native reaction-list includes LXULRU5P-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.

MetaCyc:LYXMET-PWY
  • MetaCyc:LYXMET-PWY

    Source assertion: The exact native reaction-list includes LXULRU5P-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.

    Source locationXPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="LXULRU5P-RXN"]
L-ribulose 5-phosphate => D-xylulose 5-phosphate
RHEA:22369		part_of

The exact native reaction-list includes RIBULPEPIM-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.

MetaCyc:LYXMET-PWY
  • MetaCyc:LYXMET-PWY

    Source assertion: The exact native reaction-list includes RIBULPEPIM-RXN in this four-event route. The L-xylulose 1-phosphate route described separately in the comment is not part of this definition.

    Source locationXPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="RIBULPEPIM-RXN"]
beta-L-lyxopyranose
CHEBI:147210		consumes

Native left side contains L-LYXOSE; this pathway selects left-to-right flux. Its L-LYXOSE structure is beta-L-lyxopyranose, unlike the anomer-unspecified Rhea 28059 substrate.

beta-L-lyxopyranose to L-xylulose isomerization
MetaCyc:LYXISOM-RXN
  • MetaCyc:LYXISOM-RXN

    Source assertion: Native left side contains L-LYXOSE; this pathway selects left-to-right flux. Its L-LYXOSE structure is beta-L-lyxopyranose, unlike the anomer-unspecified Rhea 28059 substrate.

    Source locationXPath /ptools-xml/Reaction/left/Compound[@frameid="L-LYXOSE"]
  • EcoCyc:L-LYXOSE

    Source assertion: The exact native L-LYXOSE InChI is identical to ChEBI 147210 beta-L-lyxopyranose. Native partial EC-5.1.3 metadata is not used as an identity or transformation claim.

    Source locationXPath /ptools-xml/Compound/inchi
beta-L-lyxopyranose to L-xylulose isomerization
MetaCyc:LYXISOM-RXN		produces

Native right side contains L-XYLULOSE; this pathway selects left-to-right flux. Its L-LYXOSE structure is beta-L-lyxopyranose, unlike the anomer-unspecified Rhea 28059 substrate.

L-xylulose
CHEBI:17399
  • MetaCyc:LYXISOM-RXN

    Source assertion: Native right side contains L-XYLULOSE; this pathway selects left-to-right flux. Its L-LYXOSE structure is beta-L-lyxopyranose, unlike the anomer-unspecified Rhea 28059 substrate.

    Source locationXPath /ptools-xml/Reaction/right/Compound[@frameid="L-XYLULOSE"]
L-xylulose
CHEBI:17399		consumes

RHEA:18870 substrates contains CHEBI:17399, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870
  • RHEA:18870

    Source assertion: RHEA:18870 substrates contains CHEBI:17399, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/18870"]/rh:substrates; http://rdf.rhea-db.org/Participant_18869_compound_1888/rh:compound; http://rdf.rhea-db.org/Compound_1888/rh:accession
ATP(4-)
CHEBI:30616		consumes

RHEA:18870 substrates contains CHEBI:30616, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870
  • RHEA:18870

    Source assertion: RHEA:18870 substrates contains CHEBI:30616, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/18870"]/rh:substrates; http://rdf.rhea-db.org/Participant_18869_compound_6372/rh:compound; http://rdf.rhea-db.org/Compound_6372/rh:accession
L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870		produces

RHEA:18870 products contains CHEBI:57829, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

L-xylulose 5-phosphate(2-)
CHEBI:57829
  • RHEA:18870

    Source assertion: RHEA:18870 products contains CHEBI:57829, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/18870"]/rh:products; http://rdf.rhea-db.org/Participant_18869_compound_2209/rh:compound; http://rdf.rhea-db.org/Compound_2209/rh:accession
L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870		produces

RHEA:18870 products contains CHEBI:456216, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

ADP(3-)
CHEBI:456216
  • RHEA:18870

    Source assertion: RHEA:18870 products contains CHEBI:456216, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/18870"]/rh:products; http://rdf.rhea-db.org/Participant_18869_compound_2710/rh:compound; http://rdf.rhea-db.org/Compound_2710/rh:accession
L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870		produces

RHEA:18870 products contains CHEBI:15378, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

hydron
CHEBI:15378
  • RHEA:18870

    Source assertion: RHEA:18870 products contains CHEBI:15378, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/18870"]/rh:products; http://rdf.rhea-db.org/Participant_18869_compound_3249/rh:compound; http://rdf.rhea-db.org/Compound_3249/rh:accession
L-xylulose 5-phosphate(2-)
CHEBI:57829		consumes

RHEA:18499 substrates contains CHEBI:57829, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

L-xylulose 5-phosphate => L-ribulose 5-phosphate
RHEA:18499
  • RHEA:18499

    Source assertion: RHEA:18499 substrates contains CHEBI:57829, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/18499"]/rh:substrates; http://rdf.rhea-db.org/Participant_18497_compound_2209/rh:compound; http://rdf.rhea-db.org/Compound_2209/rh:accession
L-xylulose 5-phosphate => L-ribulose 5-phosphate
RHEA:18499		produces

RHEA:18499 products contains CHEBI:58226, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

L-ribulose 5-phosphate(2-)
CHEBI:58226
  • RHEA:18499

    Source assertion: RHEA:18499 products contains CHEBI:58226, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/18499"]/rh:products; http://rdf.rhea-db.org/Participant_18497_compound_4065/rh:compound; http://rdf.rhea-db.org/Compound_4065/rh:accession
L-ribulose 5-phosphate(2-)
CHEBI:58226		consumes

RHEA:22369 substrates contains CHEBI:58226, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

L-ribulose 5-phosphate => D-xylulose 5-phosphate
RHEA:22369
  • RHEA:22369

    Source assertion: RHEA:22369 substrates contains CHEBI:58226, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/22369"]/rh:substrates; http://rdf.rhea-db.org/Participant_22368_compound_4065/rh:compound; http://rdf.rhea-db.org/Compound_4065/rh:accession
L-ribulose 5-phosphate => D-xylulose 5-phosphate
RHEA:22369		produces

RHEA:22369 products contains CHEBI:57737, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

D-xylulose 5-phosphate(2-)
CHEBI:57737
  • RHEA:22369

    Source assertion: RHEA:22369 products contains CHEBI:57737, coefficient 1. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/22369"]/rh:products; http://rdf.rhea-db.org/Participant_22368_compound_1624/rh:compound; http://rdf.rhea-db.org/Compound_1624/rh:accession
L-lyxopyranose
CHEBI:62321		consumes

RHEA:29993 substrates contains CHEBI:62321, coefficient 1; external input. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

L-lyxopyranose(out) + H(+)(out) => L-lyxopyranose(in) + H(+)(in)
RHEA:29993
  • RHEA:29993

    Source assertion: RHEA:29993 substrates contains CHEBI:62321, coefficient 1; external input. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/29993"]/rh:substrates; http://rdf.rhea-db.org/Participant_29991_compound_17978_out/rh:compound; http://rdf.rhea-db.org/Compound_17978/rh:accession
hydron
CHEBI:15378		consumes

RHEA:29993 substrates contains CHEBI:15378, coefficient 1; external input. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

L-lyxopyranose(out) + H(+)(out) => L-lyxopyranose(in) + H(+)(in)
RHEA:29993
  • RHEA:29993

    Source assertion: RHEA:29993 substrates contains CHEBI:15378, coefficient 1; external input. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/29993"]/rh:substrates; http://rdf.rhea-db.org/Participant_29991_compound_3249_out/rh:compound; http://rdf.rhea-db.org/Compound_3249/rh:accession
L-lyxopyranose(out) + H(+)(out) => L-lyxopyranose(in) + H(+)(in)
RHEA:29993		produces

RHEA:29993 products contains CHEBI:62321, coefficient 1; internal output. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

L-lyxopyranose
CHEBI:62321
  • RHEA:29993

    Source assertion: RHEA:29993 products contains CHEBI:62321, coefficient 1; internal output. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/29993"]/rh:products; http://rdf.rhea-db.org/Participant_29991_compound_17978_in/rh:compound; http://rdf.rhea-db.org/Compound_17978/rh:accession
L-lyxopyranose(out) + H(+)(out) => L-lyxopyranose(in) + H(+)(in)
RHEA:29993		produces

RHEA:29993 products contains CHEBI:15378, coefficient 1; internal output. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

hydron
CHEBI:15378
  • RHEA:29993

    Source assertion: RHEA:29993 products contains CHEBI:15378, coefficient 1; internal output. This is the selected formal directional equation; metal cofactors are not added as chemical sides.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/29993"]/rh:products; http://rdf.rhea-db.org/Participant_29991_compound_3249_in/rh:compound; http://rdf.rhea-db.org/Compound_3249/rh:accession
beta-L-lyxopyranose to L-xylulose isomerization
MetaCyc:LYXISOM-RXN		provides_input_for

Native reaction-layout carries the shared intermediate L-XYLULOSE between these successive core events, with LXULRU5P selected right-to-left.

L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870
  • MetaCyc:LYXMET-PWY

    Source assertion: Native reaction-layout carries the shared intermediate L-XYLULOSE between these successive core events, with LXULRU5P selected right-to-left.

    Source locationXPath /ptools-xml/Pathway/reaction-layout[Reaction[@frameid="LYXISOM-RXN"]]
L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870		provides_input_for

Native reaction-layout carries the shared intermediate L-XYLULOSE-5-P between these successive core events, with LXULRU5P selected right-to-left.

L-xylulose 5-phosphate => L-ribulose 5-phosphate
RHEA:18499
  • MetaCyc:LYXMET-PWY

    Source assertion: Native reaction-layout carries the shared intermediate L-XYLULOSE-5-P between these successive core events, with LXULRU5P selected right-to-left.

    Source locationXPath /ptools-xml/Pathway/reaction-layout[Reaction[@frameid="LYXK-RXN"]]
L-xylulose 5-phosphate => L-ribulose 5-phosphate
RHEA:18499		provides_input_for

Native reaction-layout carries the shared intermediate L-RIBULOSE-5-P between these successive core events, with LXULRU5P selected right-to-left.

L-ribulose 5-phosphate => D-xylulose 5-phosphate
RHEA:22369
  • MetaCyc:LYXMET-PWY

    Source assertion: Native reaction-layout carries the shared intermediate L-RIBULOSE-5-P between these successive core events, with LXULRU5P selected right-to-left.

    Source locationXPath /ptools-xml/Pathway/reaction-layout[Reaction[@frameid="LXULRU5P-RXN"]]
L-lyxopyranose(out) + H(+)(out) => L-lyxopyranose(in) + H(+)(in)
RHEA:29993		provides_input_for

The native narrative places RhaT uptake before RhaA isomerization. The formal transport substrate is generic L-lyxopyranose, while the core first reaction specifies beta-L-lyxopyranose; this source-level interface is not an anomerization reaction.

beta-L-lyxopyranose to L-xylulose isomerization
MetaCyc:LYXISOM-RXN
  • MetaCyc:LYXMET-PWY

    Source assertion: The native narrative places RhaT uptake before RhaA isomerization. The formal transport substrate is generic L-lyxopyranose, while the core first reaction specifies beta-L-lyxopyranose; this source-level interface is not an anomerization reaction.

    Source locationXPath /ptools-xml/Pathway/comment
L-ribulose 5-phosphate => D-xylulose 5-phosphate
RHEA:22369		provides_input_for

The endpoint D-xylulose 5-phosphate is linked to NONOXIPENT-PWY. This downstream pentose-phosphate pathway is an opaque interface; its reactions are not additional LYXMET core events.

pentose phosphate pathway (non-oxidative branch)
MetaCyc:NONOXIPENT-PWY
  • MetaCyc:LYXMET-PWY

    Source assertion: The endpoint D-xylulose 5-phosphate is linked to NONOXIPENT-PWY. This downstream pentose-phosphate pathway is an opaque interface; its reactions are not additional LYXMET core events.

    Source locationXPath /ptools-xml/Pathway/pathway-link[Compound[@frameid="XYLULOSE-5-PHOSPHATE"]]/link-target/Pathway[@frameid="NONOXIPENT-PWY"]
MetaCyc:LYXMET-PWYpart_of

The native in-pathway slot places LYXMET-PWY in parent superpathway PWY-5257. This is a hierarchy relationship rather than another catalytic event.

superpathway of pentose and pentitol degradation
MetaCyc:PWY-5257
  • MetaCyc:LYXMET-PWY

    Source assertion: The native in-pathway slot places LYXMET-PWY in parent superpathway PWY-5257. This is a hierarchy relationship rather than another catalytic event.

    Source locationXPath /ptools-xml/Pathway/in-pathway/Pathway[@frameid="PWY-5257"]
L-rhamnose isomerase
MetaCyc:CPLX0-7652		catalyzes

The native enzyme slot assigns CPLX0-7652 to this reaction. Assemblies are retained separately from their reference chains; membership alone is not individual-subunit catalysis.

beta-L-lyxopyranose to L-xylulose isomerization
MetaCyc:LYXISOM-RXN
  • MetaCyc:LYXISOM-ENZRXN

    Source assertion: The native enzyme slot assigns CPLX0-7652 to this reaction. Assemblies are retained separately from their reference chains; membership alone is not individual-subunit catalysis.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/enzyme
L-xylulose kinase
MetaCyc:LYXK-CPLX		catalyzes

The native enzyme slot assigns LYXK-CPLX to this reaction. Assemblies are retained separately from their reference chains; membership alone is not individual-subunit catalysis.

L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870
  • MetaCyc:LYXK-ENZRXN

    Source assertion: The native enzyme slot assigns LYXK-CPLX to this reaction. Assemblies are retained separately from their reference chains; membership alone is not individual-subunit catalysis.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/enzyme
L-ribulose-5-phosphate 4-epimerase AraD
MetaCyc:RIBULPEPIM-CPLX		catalyzes

The native enzyme slot assigns RIBULPEPIM-CPLX to this reaction. Assemblies are retained separately from their reference chains; membership alone is not individual-subunit catalysis.

L-ribulose 5-phosphate => D-xylulose 5-phosphate
RHEA:22369
  • MetaCyc:RIBULPEPIM-ENZRXN

    Source assertion: The native enzyme slot assigns RIBULPEPIM-CPLX to this reaction. Assemblies are retained separately from their reference chains; membership alone is not individual-subunit catalysis.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/enzyme
Putative L-ribulose-5-phosphate 3-epimerase SgbU
UniProtKB:P37679		enables

The source assigns SgbU/YiaR to this event with EV-COMP-HINF-FN-FROM-SEQ. This is a tentative functional assignment, not experimentally established catalysis.

L-xylulose 5-phosphate => L-ribulose 5-phosphate
RHEA:18499
  • EcoCyc:ENZRXN0-6410

    Source assertion: The source assigns SgbU/YiaR to this event with EV-COMP-HINF-FN-FROM-SEQ. This is a tentative functional assignment, not experimentally established catalysis.

    Source locationXPath /ptools-xml/Enzymatic-Reaction
  • PMID:10913097

    Source assertion: The 2000 study genetically implicated yiaR but failed to detect 3-epimerase activity, including a purified GST-based preparation. It retained the assignment as tentative, with possible instability or missing cofactor.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/p[8]; paragraph containing 'all attempts to obtain experimental evidence'
  • PMID:11741871

    Source assertion: The independent 2002 study also failed to detect SgbU 3-epimerase activity under conditions that detected UlaE. Inappropriate assay conditions or a sequence defect were hypotheses, not proof of universal SgbU inactivity.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[8]/p[3]; paragraph containing 'unable to demonstrate that SgbU'
L-ribulose-5-phosphate 4-epimerase SgbE
UniProtKB:P37680		catalyzes

Reviewed SgbE catalyzes L-ribulose 5-phosphate to D-xylulose 5-phosphate, supported by PMID10913097 and PMID11741871. It is an alternative to AraD, not an obligate AraD-SgbE complex.

L-ribulose 5-phosphate => D-xylulose 5-phosphate
RHEA:22369
  • UniProtKB:P37680

    Source assertion: Reviewed SgbE catalyzes L-ribulose 5-phosphate to D-xylulose 5-phosphate, supported by PMID10913097 and PMID11741871. It is an alternative to AraD, not an obligate AraD-SgbE complex.

    Source locationcomments[commentType=FUNCTION]
  • PMID:10913097

    Source assertion: Complementation of the JA198 araD yiaS double mutant by plasmids carrying either gene restored the examined metabolism, supporting alternative 4-epimerase functions.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/p[3]; paragraph containing 'A double mutant'
L-rhamnose-proton symporter
UniProtKB:P27125		catalyzes

The native enzymatic-reaction assigns RHAT-MONOMER to L-lyxose transport. Generic L-lyxopyranose and proton coupling are source annotations; the 1991 radiotracer experiment directly measured lyxose competition with rhamnose uptake.

L-lyxopyranose(out) + H(+)(out) => L-lyxopyranose(in) + H(+)(in)
RHEA:29993
  • EcoCyc:ENZRXN0-6409

    Source assertion: The native enzymatic-reaction assigns RHAT-MONOMER to L-lyxose transport. Generic L-lyxopyranose and proton coupling are source annotations; the 1991 radiotracer experiment directly measured lyxose competition with rhamnose uptake.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/enzyme
  • PMID:1650346

    Source assertion: L-lyxose reduced uptake of radiolabelled L-rhamnose in ECL1 cells. This competition supports recognition by RhaT but does not directly measure lyxose radiotracer flux or proton stoichiometry.

    Source locationPDF printed pp. 5146-5147, Results and Figure 3
L-rhamnose isomerase
MetaCyc:CPLX0-7652		has_part

The native assembly has 4 copies of RHAMNISOM-MONOMER; the corresponding UniProt chain is a component rather than an independently asserted complete catalyst.

L-rhamnose isomerase
UniProtKB:P32170
  • MetaCyc:CPLX0-7652

    Source assertion: The native assembly has 4 copies of RHAMNISOM-MONOMER; the corresponding UniProt chain is a component rather than an independently asserted complete catalyst.

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

    Source assertion: The native chain has an exact UNIPROT cross-reference to P32170.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P32170"]
L-xylulose kinase
MetaCyc:LYXK-CPLX		has_part

The native assembly has 2 copies of LYXK-MONOMER; the corresponding UniProt chain is a component rather than an independently asserted complete catalyst.

L-xylulose/3-keto-L-gulonate kinase
UniProtKB:P37677
  • MetaCyc:LYXK-CPLX

    Source assertion: The native assembly has 2 copies of LYXK-MONOMER; the corresponding UniProt chain is a component rather than an independently asserted complete catalyst.

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

    Source assertion: The native chain has an exact UNIPROT cross-reference to P37677.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P37677"]
L-ribulose-5-phosphate 4-epimerase AraD
MetaCyc:RIBULPEPIM-CPLX		has_part

The native assembly has 4 copies of RIBULPEPIM-MONOMER; the corresponding UniProt chain is a component rather than an independently asserted complete catalyst.

L-ribulose-5-phosphate 4-epimerase AraD
UniProtKB:P08203
  • MetaCyc:RIBULPEPIM-CPLX

    Source assertion: The native assembly has 4 copies of RIBULPEPIM-MONOMER; the corresponding UniProt chain is a component rather than an independently asserted complete catalyst.

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

    Source assertion: The native chain has an exact UNIPROT cross-reference to P08203.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P08203"]
L-rhamnose isomerase
UniProtKB:P32170

experimental construct: JA121 (JA120 carrying pJB4.3) overexpressed RhaA preparation; reference P32170 is an identity anchor, not proof of exact assayed sequence. Mn2+/reducing purification conditions; native oligomer not independently established by this assay.

Qualification evidence
  • PMID:1650346

    Source assertion: RhaA was purified from JA121, produced by transforming JA120 with pJB4.3. Purification buffers contained Mn2+ and reducing reagent; this overexpressed preparation is not a whole-culture MG1655 assay.

    Source locationPDF printed pp. 5145-5146, strains and purification
catalyzes

Purified overexpressed RhaA converted L-lyxose to L-xylulose, with Km 5 mM and apparent Vmax 6.0 U/mg. The assay did not resolve substrate anomers; beta specificity here is native pathway structure, not an independent assay finding.

beta-L-lyxopyranose to L-xylulose isomerization
MetaCyc:LYXISOM-RXN
  • PMID:1650346

    Source assertion: Purified overexpressed RhaA converted L-lyxose to L-xylulose, with Km 5 mM and apparent Vmax 6.0 U/mg. The assay did not resolve substrate anomers; beta specificity here is native pathway structure, not an independent assay finding.

    Source locationPDF printed p. 5147, L-Lyxose as a substrate of rhamnose isomerase
L-xylulose/3-keto-L-gulonate kinase
UniProtKB:P37677

experimental construct: MG1655-derived LyxK expressed in BL21(DE3) from modified pET15b with retained N-terminal 10His tag; current native reference chain is 498 residues. This tagged assay material is not asserted identical to unmodified LyxK.

Qualification evidence
  • PMID:11741871

    Source assertion: The MG1655-derived genes were expressed in BL21(DE3) from modified pET15b with N-terminal 10His tags. Tags remained for LyxK; SgbE and SgbU tags were removed with thrombin. Residual cleavage sequences were not reported.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[3]; paragraph containing 'N-terminal His tags'
  • PMID:11741871

    Source assertion: Enzyme genes were PCR-amplified from MG1655 genomic DNA and cloned into modified pET15b encoding an N-terminal 10His tag.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[1]; paragraph containing 'PCR amplified from genomic DNA'
catalyzes

Purified LyxK phosphorylated L-xylulose and also 3-keto-L-gulonate. The later alternate substrate result limits the older description of absolute specificity.

L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870
  • PMID:11741871

    Source assertion: Purified LyxK phosphorylated L-xylulose and also 3-keto-L-gulonate. The later alternate substrate result limits the older description of absolute specificity.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[7]/p[3]; paragraph containing 'We observed that the 3-keto'
L-ribulose-5-phosphate 4-epimerase SgbE
UniProtKB:P37680

experimental construct: MG1655-derived SgbE expressed with N-terminal 10His in BL21(DE3), then thrombin-cleaved; residual cleavage sequence unreported. Current reference is 231 residues; the article 232-codon wording does not establish a 232-residue assayed variant.

Qualification evidence
  • PMID:11741871

    Source assertion: The MG1655-derived genes were expressed in BL21(DE3) from modified pET15b with N-terminal 10His tags. Tags remained for LyxK; SgbE and SgbU tags were removed with thrombin. Residual cleavage sequences were not reported.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[3]; paragraph containing 'N-terminal His tags'
  • PMID:11741871

    Source assertion: Enzyme genes were PCR-amplified from MG1655 genomic DNA and cloned into modified pET15b encoding an N-terminal 10His tag.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[1]; paragraph containing 'PCR amplified from genomic DNA'
catalyzes

Purified SgbE catalyzed the L-ribulose 5-phosphate to D-xylulose 5-phosphate reaction in a coupled assay; The purified preparation independently extends the earlier cell-extract evidence.

L-ribulose 5-phosphate => D-xylulose 5-phosphate
RHEA:22369
  • PMID:11741871

    Source assertion: Purified SgbE catalyzed the L-ribulose 5-phosphate to D-xylulose 5-phosphate reaction in a coupled assay; The purified preparation independently extends the earlier cell-extract evidence.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[5]/p; paragraph containing 'Both SgaE and SgbE catalyzed'
L-rhamnose isomerase
UniProtKB:P32170		has_cofactor

Reviewed RhaA binds one Mn2+ per subunit (HAMAP and cited experimental sources). This is source annotation; the 1991 use of Mn2+ in purification does not independently establish physiological metal occupancy.

manganese(2+)
CHEBI:29035
  • UniProtKB:P32170

    Source assertion: Reviewed RhaA binds one Mn2+ per subunit (HAMAP and cited experimental sources). This is source annotation; the 1991 use of Mn2+ in purification does not independently establish physiological metal occupancy.

    Source locationcomments[commentType=COFACTOR]
L-xylulose kinase
MetaCyc:LYXK-CPLX		has_cofactor

Native LyxK lists Mg2+ as cofactor, citing PMID7961955. Its original full body was unavailable here, so this remains an annotation-level cofactor assertion.

magnesium(2+)
CHEBI:18420
  • EcoCyc:LYXK-ENZRXN

    Source assertion: Native LyxK lists Mg2+ as cofactor, citing PMID7961955. Its original full body was unavailable here, so this remains an annotation-level cofactor assertion.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/cofactor/Compound[@frameid="MG+2"]
L-xylulose/3-keto-L-gulonate kinase
UniProtKB:P37677

experimental construct: MG1655-derived, BL21(DE3)-expressed LyxK retaining N-terminal 10His tag; assay used 10 mM MgCl2. Presence in a coupled assay is not a direct metal-binding measurement.

Qualification evidence
  • PMID:11741871

    Source assertion: The MG1655-derived genes were expressed in BL21(DE3) from modified pET15b with N-terminal 10His tags. Tags remained for LyxK; SgbE and SgbU tags were removed with thrombin. Residual cleavage sequences were not reported.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[3]; paragraph containing 'N-terminal His tags'
  • PMID:11741871

    Source assertion: Enzyme genes were PCR-amplified from MG1655 genomic DNA and cloned into modified pET15b encoding an N-terminal 10His tag.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[1]; paragraph containing 'PCR amplified from genomic DNA'
has_cofactor

Table 2 note e describes the LyxK assay with 10 mM MgCl2, 1.5 mM ATP and coupled pyruvate kinase/lactate dehydrogenase. This is an assay condition, not measured intracellular occupancy.

magnesium(2+)
CHEBI:18420
  • PMID:11741871

    Source assertion: Table 2 note e describes the LyxK assay with 10 mM MgCl2, 1.5 mM ATP and coupled pyruvate kinase/lactate dehydrogenase. This is an assay condition, not measured intracellular occupancy.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[5]/section/div[4]/div[5]/p; paragraph containing 'phosphoenolpyruvate'
L-ribulose-5-phosphate 4-epimerase SgbE
UniProtKB:P37680		has_cofactor

SgbE zinc binding and one-zinc-per-subunit stoichiometry are annotated by similarity to AraD P08203 (ECO:0000250), not a direct SgbE metal determination.

zinc(2+)
CHEBI:29105
  • UniProtKB:P37680

    Source assertion: SgbE zinc binding and one-zinc-per-subunit stoichiometry are annotated by similarity to AraD P08203 (ECO:0000250), not a direct SgbE metal determination.

    Source locationcomments[commentType=COFACTOR]
L-ribulose-5-phosphate 4-epimerase AraD
UniProtKB:P08203

experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12 reference sequence; native commentary reports 98.7% deduced identity. No assertion that every cited preparation was unmodified MG1655 AraD.

Qualification evidence
  • EcoCyc:RIBULPEPIM-MONOMER

    Source assertion: The native AraD commentary explicitly identifies B/r UP1000 and the K-12/B-r sequence difference for the cited biochemical/structural work.

    Source locationXPath /ptools-xml/Protein/comment
has_cofactor

Reviewed AraD can use zinc; zinc is the annotated cofactor and cobalt/manganese alternatives are less efficient. These are alternatives rather than jointly required metals.

zinc(2+)
CHEBI:29105
  • UniProtKB:P08203

    Source assertion: Reviewed AraD can use zinc; zinc is the annotated cofactor and cobalt/manganese alternatives are less efficient. These are alternatives rather than jointly required metals.

    Source locationcomments[commentType=COFACTOR]
  • EcoCyc:RIBULPEPIM-MONOMER

    Source assertion: The native commentary distinguishes B/r UP1000 metal/structure preparations from K-12 AraD (98.7% deduced amino-acid identity), and a separate DH1 K-12 tetramer study. Reviewed metal evidence must retain this preparation scope.

    Source locationXPath /ptools-xml/Protein/comment
L-ribulose-5-phosphate 4-epimerase AraD
UniProtKB:P08203

experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12 reference sequence; native commentary reports 98.7% deduced identity. No assertion that every cited preparation was unmodified MG1655 AraD.

Qualification evidence
  • EcoCyc:RIBULPEPIM-MONOMER

    Source assertion: The native AraD commentary explicitly identifies B/r UP1000 and the K-12/B-r sequence difference for the cited biochemical/structural work.

    Source locationXPath /ptools-xml/Protein/comment
has_cofactor

Reviewed AraD can use cobalt; zinc is the annotated cofactor and cobalt/manganese alternatives are less efficient. These are alternatives rather than jointly required metals.

cobalt(2+)
CHEBI:48828
  • UniProtKB:P08203

    Source assertion: Reviewed AraD can use cobalt; zinc is the annotated cofactor and cobalt/manganese alternatives are less efficient. These are alternatives rather than jointly required metals.

    Source locationcomments[commentType=COFACTOR]
  • EcoCyc:RIBULPEPIM-MONOMER

    Source assertion: The native commentary distinguishes B/r UP1000 metal/structure preparations from K-12 AraD (98.7% deduced amino-acid identity), and a separate DH1 K-12 tetramer study. Reviewed metal evidence must retain this preparation scope.

    Source locationXPath /ptools-xml/Protein/comment
L-ribulose-5-phosphate 4-epimerase AraD
UniProtKB:P08203

experimental construct: AraD metal annotation includes B/r UP1000-derived preparations, distinct from the P08203 K-12 reference sequence; native commentary reports 98.7% deduced identity. No assertion that every cited preparation was unmodified MG1655 AraD.

Qualification evidence
  • EcoCyc:RIBULPEPIM-MONOMER

    Source assertion: The native AraD commentary explicitly identifies B/r UP1000 and the K-12/B-r sequence difference for the cited biochemical/structural work.

    Source locationXPath /ptools-xml/Protein/comment
has_cofactor

Reviewed AraD can use manganese; zinc is the annotated cofactor and cobalt/manganese alternatives are less efficient. These are alternatives rather than jointly required metals.

manganese(2+)
CHEBI:29035
  • UniProtKB:P08203

    Source assertion: Reviewed AraD can use manganese; zinc is the annotated cofactor and cobalt/manganese alternatives are less efficient. These are alternatives rather than jointly required metals.

    Source locationcomments[commentType=COFACTOR]
  • EcoCyc:RIBULPEPIM-MONOMER

    Source assertion: The native commentary distinguishes B/r UP1000 metal/structure preparations from K-12 AraD (98.7% deduced amino-acid identity), and a separate DH1 K-12 tetramer study. Reviewed metal evidence must retain this preparation scope.

    Source locationXPath /ptools-xml/Protein/comment
ATP(4-)
CHEBI:30616		inhibits

The native negative regulation event identifies ATP inhibition of LyxK activity, citing the 1994 paper. ATP remains a reaction substrate; concentrations, allosteric mechanism and in-vivo flux effects are not inferred.

L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870
  • EcoCyc:REG0-7578

    Source assertion: The native negative regulation event identifies ATP inhibition of LyxK activity, citing the 1994 paper. ATP remains a reaction substrate; concentrations, allosteric mechanism and in-vivo flux effects are not inferred.

    Source locationXPath /ptools-xml/Regulation[mode="-"]/regulator/Compound[@frameid="ATP"]
L-rhamnose isomerase
UniProtKB:P32170		located_in

The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

cytosol
GO:0005829
  • EcoCyc:RHAMNISOM-MONOMER

    Source assertion: The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
L-xylulose/3-keto-L-gulonate kinase
UniProtKB:P37677		located_in

The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

cytosol
GO:0005829
  • EcoCyc:LYXK-MONOMER

    Source assertion: The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
Putative L-ribulose-5-phosphate 3-epimerase SgbU
UniProtKB:P37679		located_in

The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

cytosol
GO:0005829
  • EcoCyc:EG12286-MONOMER

    Source assertion: The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
L-ribulose-5-phosphate 4-epimerase SgbE
UniProtKB:P37680		located_in

The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

cytosol
GO:0005829
  • EcoCyc:EG12287-MONOMER

    Source assertion: The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
L-ribulose-5-phosphate 4-epimerase AraD
UniProtKB:P08203		located_in

The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

cytosol
GO:0005829
  • EcoCyc:RIBULPEPIM-MONOMER

    Source assertion: The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
HTH-type transcriptional repressor PlaR
UniProtKB:P37671		located_in

The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

cytosol
GO:0005829
  • EcoCyc:EG12278-MONOMER

    Source assertion: The native location slot places the protein in Gram-negative cytosol; this annotation is not a new direct localization measurement.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
L-rhamnose-proton symporter
UniProtKB:P27125		located_in

Reviewed RhaT is a multipass inner-membrane protein; membrane location belongs to the transporter rather than to all substrate molecules.

plasma membrane
GO:0005886
  • UniProtKB:P27125

    Source assertion: Reviewed RhaT is a multipass inner-membrane protein; membrane location belongs to the transporter rather than to all substrate molecules.

    Source locationcomments[commentType=SUBCELLULAR LOCATION]
beta-L-lyxopyranose to L-xylulose isomerization
MetaCyc:LYXISOM-RXN		occurs_in

The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.

cytosol
GO:0005829
  • MetaCyc:LYXMET-PWY

    Source assertion: The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.

    Source locationXPath /ptools-xml/Pathway/comment
  • EcoCyc:RHAMNISOM-MONOMER

    Source assertion: The native protein location slot supplies cytosolic context for its associated activity; assigning process location from catalyst annotation is a qualified inference.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870		occurs_in

The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.

cytosol
GO:0005829
  • MetaCyc:LYXMET-PWY

    Source assertion: The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.

    Source locationXPath /ptools-xml/Pathway/comment
  • EcoCyc:LYXK-MONOMER

    Source assertion: The native protein location slot supplies cytosolic context for its associated activity; assigning process location from catalyst annotation is a qualified inference.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
L-xylulose 5-phosphate => L-ribulose 5-phosphate
RHEA:18499		occurs_in

The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.

cytosol
GO:0005829
  • MetaCyc:LYXMET-PWY

    Source assertion: The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.

    Source locationXPath /ptools-xml/Pathway/comment
  • EcoCyc:EG12286-MONOMER

    Source assertion: The native protein location slot supplies cytosolic context for its associated activity; assigning process location from catalyst annotation is a qualified inference.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
L-ribulose 5-phosphate => D-xylulose 5-phosphate
RHEA:22369		occurs_in

The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.

cytosol
GO:0005829
  • MetaCyc:LYXMET-PWY

    Source assertion: The source-defined intracellular route converts imported lyxose to cytosolic pentose-phosphate intermediates; native catalyst location slots support cytosolic context. Tentative SgbU catalysis remains tentative.

    Source locationXPath /ptools-xml/Pathway/comment
  • EcoCyc:EG12287-MONOMER

    Source assertion: The native protein location slot supplies cytosolic context for its associated activity; assigning process location from catalyst annotation is a qualified inference.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
L-lyxopyranose(out) + H(+)(out) => L-lyxopyranose(in) + H(+)(in)
RHEA:29993		occurs_in

RhaT-mediated uptake crosses the bacterial inner membrane; the corresponding reviewed protein is a multipass inner-membrane transporter.

plasma membrane
GO:0005886
  • UniProtKB:P27125

    Source assertion: RhaT-mediated uptake crosses the bacterial inner membrane; the corresponding reviewed protein is a multipass inner-membrane transporter.

    Source locationcomments[commentType=SUBCELLULAR LOCATION]
DNA-binding transcriptional dual regulator CRP
EcoCyc:PC00004		has_part

Native PC00004 contains PD00257. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.

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

    Source assertion: Native PC00004 contains PD00257. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PD00257"]]
  • UniProtKB:P0ACJ8

    Source assertion: The exact issuing UniProt entry cross-references EcoCyc PD00257, binding the native assembly component to this chain.

    Source locationuniProtKBCrossReferences[database=BioCyc,id=EcoCyc:PD00257]
transcriptional activator RhaS
EcoCyc:PC00086		has_part

Native PC00086 contains PD00221. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.

HTH-type transcriptional activator RhaS
UniProtKB:P09377
  • EcoCyc:PC00086

    Source assertion: Native PC00086 contains PD00221. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PD00221"]]
  • UniProtKB:P09377

    Source assertion: The exact issuing UniProt entry cross-references EcoCyc PD00221, binding the native assembly component to this chain.

    Source locationuniProtKBCrossReferences[database=BioCyc,id=EcoCyc:PD00221]
DNA-binding transcriptional dual regulator IHF
EcoCyc:PC00027		has_part

Native PC00027 contains PD00347. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.

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

    Source assertion: Native PC00027 contains PD00347. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PD00347"]]
  • UniProtKB:P0A6X7

    Source assertion: The exact issuing UniProt entry cross-references EcoCyc PD00347, binding the native assembly component to this chain.

    Source locationuniProtKBCrossReferences[database=BioCyc,id=EcoCyc:PD00347]
  • UniProtKB:P0A6X7

    Source assertion: Reviewed IHF consists of an alpha and a beta chain, supporting a 1:1 heterodimer. Native component slots supply membership but omit numerical coefficients; no additional subunits are inferred.

    Source locationcomments[commentType=SUBUNIT]
DNA-binding transcriptional dual regulator IHF
EcoCyc:PC00027		has_part

Native PC00027 contains PD00348. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.

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

    Source assertion: Native PC00027 contains PD00348. CRP and RhaS components have coefficient 2; IHF lists alpha/beta membership without numeric coefficients, with the heterodimer interpretation supplied by reviewed annotation.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="PD00348"]]
  • UniProtKB:P0A6Y1

    Source assertion: The exact issuing UniProt entry cross-references EcoCyc PD00348, binding the native assembly component to this chain.

    Source locationuniProtKBCrossReferences[database=BioCyc,id=EcoCyc:PD00348]
  • UniProtKB:P0A6Y1

    Source assertion: Reviewed IHF consists of an alpha and a beta chain, supporting a 1:1 heterodimer. Native component slots supply membership but omit numerical coefficients; no additional subunits are inferred.

    Source locationcomments[commentType=SUBUNIT]
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		has_part

Native CPLX0-226 explicitly contains PC00004; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.

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

    Source assertion: Native CPLX0-226 explicitly contains PC00004; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.

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

Native CPLX0-226 explicitly contains CAMP; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.

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

    Source assertion: Native CPLX0-226 explicitly contains CAMP; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.

    Source locationXPath /ptools-xml/Protein/component/Compound[@frameid="CAMP"]
RhaS-L-rhamnose DNA-binding transcriptional activator
EcoCyc:CPLX-124		has_part

Native CPLX-124 explicitly contains PC00086; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.

transcriptional activator RhaS
EcoCyc:PC00086
  • EcoCyc:CPLX-124

    Source assertion: Native CPLX-124 explicitly contains PC00086; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.

    Source locationXPath /ptools-xml/Protein/component/Protein[@frameid="PC00086"]
RhaS-L-rhamnose DNA-binding transcriptional activator
EcoCyc:CPLX-124		has_part

Native CPLX-124 explicitly contains L-rhamnose; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.

L-rhamnose
CHEBI:62345
  • EcoCyc:CPLX-124

    Source assertion: Native CPLX-124 explicitly contains L-rhamnose; this slot has no coefficient, so ligand occupancy and additional stoichiometry are not inferred. RhaS-rhamnose is not claimed to be a lyxose-bound complex.

    Source locationXPath /ptools-xml/Protein/component/Compound[@frameid="L-rhamnose"]
HTH-type transcriptional repressor PlaR
UniProtKB:P37671		inhibits

Native REG0-4907 assigns - regulation of yiaKp1 (PM692) by EG12278-MONOMER. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

lyxK
Entrez:948101
  • EcoCyc:TU592

    Source assertion: Native REG0-4907 assigns - regulation of yiaKp1 (PM692) by EG12278-MONOMER. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

    Source locationXPath //Regulation[@frameid="REG0-4907" and mode="-" and regulator/Protein[@frameid="EG12278-MONOMER"]]/regulated-entity/Promoter[@frameid="PM692"]
  • EcoCyc:TU592

    Source assertion: Native TU592 contains EG12284, the pathway-associated lyxK gene, linking promoter regulation to this exact target. Other operon genes are not assigned extra lyxose reactions.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12284"]
  • Entrez:948101

    Source assertion: Issuing MG1655 NCBI Gene identifies lyxK and its exact EcoCyc frame EG12284. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12284"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:10913096

    Source assertion: The yiaK reporter showed low activity in ECL1 and high constitutive activity in the yiaJ-defective JA134 background, supporting repression at the operon promoter rather than direct enzyme 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[2]; paragraph containing 'resulted in a β-galactosidase activity of 42'
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-4905 assigns + regulation of yiaKp1 (PM692) by CPLX0-226. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

lyxK
Entrez:948101
  • EcoCyc:TU592

    Source assertion: Native REG0-4905 assigns + regulation of yiaKp1 (PM692) by CPLX0-226. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

    Source locationXPath //Regulation[@frameid="REG0-4905" and mode="+" and regulator/Protein[@frameid="CPLX0-226"]]/regulated-entity/Promoter[@frameid="PM692"]
  • EcoCyc:TU592

    Source assertion: Native TU592 contains EG12284, the pathway-associated lyxK gene, linking promoter regulation to this exact target. Other operon genes are not assigned extra lyxose reactions.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12284"]
  • Entrez:948101

    Source assertion: Issuing MG1655 NCBI Gene identifies lyxK and its exact EcoCyc frame EG12284. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12284"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:10913096

    Source assertion: The study supports CRP-cAMP activation of yiaK-S through site 1 centered at -106. Binding at site 2 had unknown function and supplies no signed regulatory edge.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[2]; paragraph containing 'In spite of the binding observed to Crp site 2'
DNA-binding transcriptional dual regulator IHF
EcoCyc:PC00027		activates

Native REG0-4906 assigns + regulation of yiaKp1 (PM692) by PC00027. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

lyxK
Entrez:948101
  • EcoCyc:TU592

    Source assertion: Native REG0-4906 assigns + regulation of yiaKp1 (PM692) by PC00027. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

    Source locationXPath //Regulation[@frameid="REG0-4906" and mode="+" and regulator/Protein[@frameid="PC00027"]]/regulated-entity/Promoter[@frameid="PM692"]
  • EcoCyc:TU592

    Source assertion: Native TU592 contains EG12284, the pathway-associated lyxK gene, linking promoter regulation to this exact target. Other operon genes are not assigned extra lyxose reactions.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12284"]
  • Entrez:948101

    Source assertion: Issuing MG1655 NCBI Gene identifies lyxK and its exact EcoCyc frame EG12284. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12284"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:10913096

    Source assertion: himA and himD3 mutations in the JA134 background reduced yiaK-S reporter activity about fourfold. Gel shifts supported IHF binding; DNA looping was proposed, not directly demonstrated.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[3]/p[4]; paragraph containing 'Introduction of each of these IHF mutations'
HTH-type transcriptional repressor PlaR
UniProtKB:P37671		inhibits

Native REG0-4907 assigns - regulation of yiaKp1 (PM692) by EG12278-MONOMER. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

sgbU
Entrez:948100
  • EcoCyc:TU592

    Source assertion: Native REG0-4907 assigns - regulation of yiaKp1 (PM692) by EG12278-MONOMER. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

    Source locationXPath //Regulation[@frameid="REG0-4907" and mode="-" and regulator/Protein[@frameid="EG12278-MONOMER"]]/regulated-entity/Promoter[@frameid="PM692"]
  • EcoCyc:TU592

    Source assertion: Native TU592 contains EG12286, the pathway-associated sgbU gene, linking promoter regulation to this exact target. Other operon genes are not assigned extra lyxose reactions.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12286"]
  • Entrez:948100

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbU and its exact EcoCyc frame EG12286. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12286"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:10913096

    Source assertion: The yiaK reporter showed low activity in ECL1 and high constitutive activity in the yiaJ-defective JA134 background, supporting repression at the operon promoter rather than direct enzyme 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[2]; paragraph containing 'resulted in a β-galactosidase activity of 42'
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-4905 assigns + regulation of yiaKp1 (PM692) by CPLX0-226. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

sgbU
Entrez:948100
  • EcoCyc:TU592

    Source assertion: Native REG0-4905 assigns + regulation of yiaKp1 (PM692) by CPLX0-226. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

    Source locationXPath //Regulation[@frameid="REG0-4905" and mode="+" and regulator/Protein[@frameid="CPLX0-226"]]/regulated-entity/Promoter[@frameid="PM692"]
  • EcoCyc:TU592

    Source assertion: Native TU592 contains EG12286, the pathway-associated sgbU gene, linking promoter regulation to this exact target. Other operon genes are not assigned extra lyxose reactions.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12286"]
  • Entrez:948100

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbU and its exact EcoCyc frame EG12286. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12286"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:10913096

    Source assertion: The study supports CRP-cAMP activation of yiaK-S through site 1 centered at -106. Binding at site 2 had unknown function and supplies no signed regulatory edge.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[2]; paragraph containing 'In spite of the binding observed to Crp site 2'
DNA-binding transcriptional dual regulator IHF
EcoCyc:PC00027		activates

Native REG0-4906 assigns + regulation of yiaKp1 (PM692) by PC00027. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

sgbU
Entrez:948100
  • EcoCyc:TU592

    Source assertion: Native REG0-4906 assigns + regulation of yiaKp1 (PM692) by PC00027. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

    Source locationXPath //Regulation[@frameid="REG0-4906" and mode="+" and regulator/Protein[@frameid="PC00027"]]/regulated-entity/Promoter[@frameid="PM692"]
  • EcoCyc:TU592

    Source assertion: Native TU592 contains EG12286, the pathway-associated sgbU gene, linking promoter regulation to this exact target. Other operon genes are not assigned extra lyxose reactions.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12286"]
  • Entrez:948100

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbU and its exact EcoCyc frame EG12286. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12286"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:10913096

    Source assertion: himA and himD3 mutations in the JA134 background reduced yiaK-S reporter activity about fourfold. Gel shifts supported IHF binding; DNA looping was proposed, not directly demonstrated.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[3]/p[4]; paragraph containing 'Introduction of each of these IHF mutations'
HTH-type transcriptional repressor PlaR
UniProtKB:P37671		inhibits

Native REG0-4907 assigns - regulation of yiaKp1 (PM692) by EG12278-MONOMER. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

sgbE
Entrez:948099
  • EcoCyc:TU592

    Source assertion: Native REG0-4907 assigns - regulation of yiaKp1 (PM692) by EG12278-MONOMER. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

    Source locationXPath //Regulation[@frameid="REG0-4907" and mode="-" and regulator/Protein[@frameid="EG12278-MONOMER"]]/regulated-entity/Promoter[@frameid="PM692"]
  • EcoCyc:TU592

    Source assertion: Native TU592 contains EG12287, the pathway-associated sgbE gene, linking promoter regulation to this exact target. Other operon genes are not assigned extra lyxose reactions.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12287"]
  • Entrez:948099

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbE and its exact EcoCyc frame EG12287. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12287"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:10913096

    Source assertion: The yiaK reporter showed low activity in ECL1 and high constitutive activity in the yiaJ-defective JA134 background, supporting repression at the operon promoter rather than direct enzyme 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[2]; paragraph containing 'resulted in a β-galactosidase activity of 42'
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-4905 assigns + regulation of yiaKp1 (PM692) by CPLX0-226. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

sgbE
Entrez:948099
  • EcoCyc:TU592

    Source assertion: Native REG0-4905 assigns + regulation of yiaKp1 (PM692) by CPLX0-226. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

    Source locationXPath //Regulation[@frameid="REG0-4905" and mode="+" and regulator/Protein[@frameid="CPLX0-226"]]/regulated-entity/Promoter[@frameid="PM692"]
  • EcoCyc:TU592

    Source assertion: Native TU592 contains EG12287, the pathway-associated sgbE gene, linking promoter regulation to this exact target. Other operon genes are not assigned extra lyxose reactions.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12287"]
  • Entrez:948099

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbE and its exact EcoCyc frame EG12287. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12287"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:10913096

    Source assertion: The study supports CRP-cAMP activation of yiaK-S through site 1 centered at -106. Binding at site 2 had unknown function and supplies no signed regulatory edge.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[4]/p[2]; paragraph containing 'In spite of the binding observed to Crp site 2'
DNA-binding transcriptional dual regulator IHF
EcoCyc:PC00027		activates

Native REG0-4906 assigns + regulation of yiaKp1 (PM692) by PC00027. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

sgbE
Entrez:948099
  • EcoCyc:TU592

    Source assertion: Native REG0-4906 assigns + regulation of yiaKp1 (PM692) by PC00027. This concerns transcription of the yiaK-S unit, not direct enzyme control; JA134 has the native PlaR lesion.

    Source locationXPath //Regulation[@frameid="REG0-4906" and mode="+" and regulator/Protein[@frameid="PC00027"]]/regulated-entity/Promoter[@frameid="PM692"]
  • EcoCyc:TU592

    Source assertion: Native TU592 contains EG12287, the pathway-associated sgbE gene, linking promoter regulation to this exact target. Other operon genes are not assigned extra lyxose reactions.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12287"]
  • Entrez:948099

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbE and its exact EcoCyc frame EG12287. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12287"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:10913096

    Source assertion: himA and himD3 mutations in the JA134 background reduced yiaK-S reporter activity about fourfold. Gel shifts supported IHF binding; DNA looping was proposed, not directly demonstrated.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[3]/p[4]; paragraph containing 'Introduction of each of these IHF mutations'
HTH-type transcriptional repressor PlaR
UniProtKB:P37671		inhibits

Native REG0-10778 negatively regulates plaRp (PM449) by EG12278-MONOMER. This is gene expression control; IHF repression is retained at native annotation level.

plaR
Entrez:948084
  • EcoCyc:TU368

    Source assertion: Native REG0-10778 negatively regulates plaRp (PM449) by EG12278-MONOMER. This is gene expression control; IHF repression is retained at native annotation level.

    Source locationXPath //Regulation[@frameid="REG0-10778" and mode="-"]/regulated-entity/Promoter[@frameid="PM449"]
  • Entrez:948084

    Source assertion: Issuing MG1655 NCBI Gene identifies plaR and its exact EcoCyc frame EG12278. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12278"] | //Gene-ref_locus | //Gene-ref_locus-tag
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		inhibits

Native REG0-4987 negatively regulates plaRp (PM449) by CPLX0-226. This is gene expression control; IHF repression is retained at native annotation level.

plaR
Entrez:948084
  • EcoCyc:TU368

    Source assertion: Native REG0-4987 negatively regulates plaRp (PM449) by CPLX0-226. This is gene expression control; IHF repression is retained at native annotation level.

    Source locationXPath //Regulation[@frameid="REG0-4987" and mode="-"]/regulated-entity/Promoter[@frameid="PM449"]
  • Entrez:948084

    Source assertion: Issuing MG1655 NCBI Gene identifies plaR and its exact EcoCyc frame EG12278. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12278"] | //Gene-ref_locus | //Gene-ref_locus-tag
DNA-binding transcriptional dual regulator IHF
EcoCyc:PC00027		inhibits

Native REG0-4986 negatively regulates plaRp (PM449) by PC00027. This is gene expression control; IHF repression is retained at native annotation level.

plaR
Entrez:948084
  • EcoCyc:TU368

    Source assertion: Native REG0-4986 negatively regulates plaRp (PM449) by PC00027. This is gene expression control; IHF repression is retained at native annotation level.

    Source locationXPath //Regulation[@frameid="REG0-4986" and mode="-"]/regulated-entity/Promoter[@frameid="PM449"]
  • Entrez:948084

    Source assertion: Issuing MG1655 NCBI Gene identifies plaR and its exact EcoCyc frame EG12278. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12278"] | //Gene-ref_locus | //Gene-ref_locus-tag
RhaS-L-rhamnose DNA-binding transcriptional activator
EcoCyc:CPLX-124		activates

Native REG0-5372 positively regulates PM00293, the promoter of the rhaT-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.

rhaT
Entrez:948398
  • EcoCyc:TU00208

    Source assertion: Native REG0-5372 positively regulates PM00293, the promoter of the rhaT-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.

    Source locationXPath //Regulation[@frameid="REG0-5372" and mode="+"]/regulated-entity/Promoter[@frameid="PM00293"]
  • EcoCyc:TU00208

    Source assertion: The exact native transcription unit contains EG11313; nested neighboring promoters and their regulators are not transferred to this gene.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG11313"]
  • Entrez:948398

    Source assertion: Issuing MG1655 NCBI Gene identifies rhaT and its exact EcoCyc frame EG11313. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG11313"] | //Gene-ref_locus | //Gene-ref_locus-tag
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-5374 positively regulates PM00293, the promoter of the rhaT-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.

rhaT
Entrez:948398
  • EcoCyc:TU00208

    Source assertion: Native REG0-5374 positively regulates PM00293, the promoter of the rhaT-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.

    Source locationXPath //Regulation[@frameid="REG0-5374" and mode="+"]/regulated-entity/Promoter[@frameid="PM00293"]
  • EcoCyc:TU00208

    Source assertion: The exact native transcription unit contains EG11313; nested neighboring promoters and their regulators are not transferred to this gene.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG11313"]
  • Entrez:948398

    Source assertion: Issuing MG1655 NCBI Gene identifies rhaT and its exact EcoCyc frame EG11313. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG11313"] | //Gene-ref_locus | //Gene-ref_locus-tag
RhaS-L-rhamnose DNA-binding transcriptional activator
EcoCyc:CPLX-124		activates

Native REG0-5986 positively regulates PM00303, the promoter of the rhaA-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.

rhaA
Entrez:948400
  • EcoCyc:TU00219

    Source assertion: Native REG0-5986 positively regulates PM00303, the promoter of the rhaA-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.

    Source locationXPath //Regulation[@frameid="REG0-5986" and mode="+"]/regulated-entity/Promoter[@frameid="PM00303"]
  • EcoCyc:TU00219

    Source assertion: The exact native transcription unit contains EG11867; nested neighboring promoters and their regulators are not transferred to this gene.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG11867"]
  • Entrez:948400

    Source assertion: Issuing MG1655 NCBI Gene identifies rhaA and its exact EcoCyc frame EG11867. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG11867"] | //Gene-ref_locus | //Gene-ref_locus-tag
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-5985 positively regulates PM00303, the promoter of the rhaA-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.

rhaA
Entrez:948400
  • EcoCyc:TU00219

    Source assertion: Native REG0-5985 positively regulates PM00303, the promoter of the rhaA-containing unit. Rhamnose-bound RhaS and CRP-cAMP provide transcriptional context; no lyxose binding to RhaS is inferred.

    Source locationXPath //Regulation[@frameid="REG0-5985" and mode="+"]/regulated-entity/Promoter[@frameid="PM00303"]
  • EcoCyc:TU00219

    Source assertion: The exact native transcription unit contains EG11867; nested neighboring promoters and their regulators are not transferred to this gene.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG11867"]
  • Entrez:948400

    Source assertion: Issuing MG1655 NCBI Gene identifies rhaA and its exact EcoCyc frame EG11867. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG11867"] | //Gene-ref_locus | //Gene-ref_locus-tag
Aerobic respiration control protein ArcA
UniProtKB:P0A9Q1

molecular state: Phosphorylated ArcA corresponding to native PHOSPHO-ARCA, not the unmodified P0A9Q1 reference chain. Native Asp54 aspartylphosphate is annotated by similarity; promoter-binding-site inference is computational and expression effects may be indirect.

Qualification evidence
  • EcoCyc:PHOSPHO-ARCA

    Source assertion: Native PHOSPHO-ARCA is a modified protein with unmodified-form ARCA-MONOMER and modified residue 54 aspartylphosphate annotated by similarity.

    Source locationXPath /ptools-xml/Protein
inhibits

Native negative rhaTp regulation is backed by gene-expression analysis; the associated promoter-binding-site evidence is similarity to consensus. Expression evidence does not exclude indirect regulation or prove direct rhaT binding.

rhaT
Entrez:948398
  • EcoCyc:REG0-5375

    Source assertion: Native negative rhaTp regulation is backed by gene-expression analysis; the associated promoter-binding-site evidence is similarity to consensus. Expression evidence does not exclude indirect regulation or prove direct rhaT binding.

    Source locationXPath /ptools-xml/Regulation[mode="-" and regulator/Protein[@frameid="PHOSPHO-ARCA"]]/regulated-entity/Promoter[@frameid="PM00293"]
  • EcoCyc:REG0-5376

    Source assertion: Native negative rhaTp regulation is backed by gene-expression analysis; the associated promoter-binding-site evidence is similarity to consensus. Expression evidence does not exclude indirect regulation or prove direct rhaT binding.

    Source locationXPath /ptools-xml/Regulation[mode="-" and regulator/Protein[@frameid="PHOSPHO-ARCA"]]/regulated-entity/Promoter[@frameid="PM00293"]
  • EcoCyc:REG0-5377

    Source assertion: Native negative rhaTp regulation is backed by gene-expression analysis; the associated promoter-binding-site evidence is similarity to consensus. Expression evidence does not exclude indirect regulation or prove direct rhaT binding.

    Source locationXPath /ptools-xml/Regulation[mode="-" and regulator/Protein[@frameid="PHOSPHO-ARCA"]]/regulated-entity/Promoter[@frameid="PM00293"]
  • Entrez:948398

    Source assertion: Issuing MG1655 NCBI Gene identifies rhaT and its exact EcoCyc frame EG11313. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG11313"] | //Gene-ref_locus | //Gene-ref_locus-tag
L-lyxose
CHEBI:62320		activates

Reviewed rhaA is induced by L-lyxose. The original 1991 ECL1 assays measured enzyme/transport activities after growth with sugar; they do not establish direct lyxose binding to RhaS or RhaR.

rhaA
Entrez:948400
  • UniProtKB:P32170

    Source assertion: Reviewed rhaA is induced by L-lyxose. The original 1991 ECL1 assays measured enzyme/transport activities after growth with sugar; they do not establish direct lyxose binding to RhaS or RhaR.

    Source locationcomments[commentType=INDUCTION]
  • Entrez:948400

    Source assertion: Issuing MG1655 NCBI Gene identifies rhaA and its exact EcoCyc frame EG11867. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG11867"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:1650346

    Source assertion: ECL1 grown with casein acid hydrolysate plus 12 mM L-lyxose showed increased rhamnose-system activities. This is induction context at generic L-lyxose granularity, not evidence for a specific anomer-binding mechanism.

    Source locationPDF printed p. 5146, Table 1 and induction Results
L-lyxose
CHEBI:62320		activates

Reviewed rhaT is induced by L-lyxose. The original 1991 ECL1 assays measured enzyme/transport activities after growth with sugar; they do not establish direct lyxose binding to RhaS or RhaR.

rhaT
Entrez:948398
  • UniProtKB:P27125

    Source assertion: Reviewed rhaT is induced by L-lyxose. The original 1991 ECL1 assays measured enzyme/transport activities after growth with sugar; they do not establish direct lyxose binding to RhaS or RhaR.

    Source locationcomments[commentType=INDUCTION]
  • Entrez:948398

    Source assertion: Issuing MG1655 NCBI Gene identifies rhaT and its exact EcoCyc frame EG11313. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG11313"] | //Gene-ref_locus | //Gene-ref_locus-tag
  • PMID:1650346

    Source assertion: ECL1 grown with casein acid hydrolysate plus 12 mM L-lyxose showed increased rhamnose-system activities. This is induction context at generic L-lyxose granularity, not evidence for a specific anomer-binding mechanism.

    Source locationPDF printed p. 5146, Table 1 and induction Results
L-lyxose
CHEBI:62320		activates

L-lyxose induced the ara operon even in the JA199 rhaA insertion mutant, supporting induction independent of RhaA conversion. This does not establish direct binding to AraC or identify an active lyxose anomer.

araD
Entrez:945294
  • PMID:10913097

    Source assertion: L-lyxose induced the ara operon even in the JA199 rhaA insertion mutant, supporting induction independent of RhaA conversion. This does not establish direct binding to AraC or identify an active lyxose anomer.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/p[4]; paragraph containing 'Induction of the ara operon by'
  • Entrez:945294

    Source assertion: Issuing MG1655 NCBI Gene identifies araD and its exact EcoCyc frame EG10055. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10055"] | //Gene-ref_locus | //Gene-ref_locus-tag
L-ascorbate
CHEBI:38290		inhibits

L-ascorbate reduced PlaR-yiaK promoter complexes in the 10 mM effector screen; dose-dependent dissociation was examined. The edge concerns PlaR DNA-binding activity, not inhibition of a metabolic enzyme or complete lyxose flux.

HTH-type transcriptional repressor PlaR
UniProtKB:P37671

experimental construct: His-tagged PlaR from pET21a(+) expressed in BL21(DE3), affinity-purified for promoter gel shifts; exact complete tag/construct sequence unreported. BW25113 supplied gel-shift probes; W3110 type-A supplied separate gSELEX genome fragments.

Qualification evidence
  • PMID:31892694

    Source assertion: The assayed PlaR was His-tagged, expressed from pET21a(+) in BL21(DE3), and affinity-purified. The exact tag position/complete construct sequence is not specified in the inspected text.

    Source locationXPath /article/body/sec[4]/sec[2]/p; paragraph containing 'Expression plasmid pPlaR'
  • PMID:31892694

    Source assertion: Gel shifts used BW25113-derived promoter probes and buffer containing Tris pH 7.8, NaCl and magnesium acetate. These conditions support chosen solution species without measuring ligand protonation or anomer purity.

    Source locationXPath /article/body/sec[4]/sec[4]/p; paragraph containing 'The gel shift assay was performed'
  • PMID:31892694

    Source assertion: L-ascorbate reduced PlaR-yiaK promoter complexes in the 10 mM effector screen; dose-dependent dissociation was examined. The edge concerns PlaR DNA-binding activity, not inhibition of a metabolic enzyme or complete lyxose flux.

    Source locationXPath /article/body/sec[2]/sec[7]/p[1]; paragraph containing 'First we tested 10 mM concentrations'
L-ascorbate
CHEBI:38290		activates

L-ascorbate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

lyxK
Entrez:948101
  • PMID:31892694

    Source assertion: L-ascorbate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

    Source locationXPath /article/body/sec[2]/sec[7]/p[2]; paragraph containing 'We then examined the possible influence'
  • EcoCyc:TU592

    Source assertion: EG12284 belongs to native yiaK-S transcription unit TU592. Reporter evidence is at operon promoter level rather than an independent assay of each downstream gene.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12284"]
  • Entrez:948101

    Source assertion: Issuing MG1655 NCBI Gene identifies lyxK and its exact EcoCyc frame EG12284. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12284"] | //Gene-ref_locus | //Gene-ref_locus-tag
L-ascorbate
CHEBI:38290		activates

L-ascorbate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

sgbU
Entrez:948100
  • PMID:31892694

    Source assertion: L-ascorbate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

    Source locationXPath /article/body/sec[2]/sec[7]/p[2]; paragraph containing 'We then examined the possible influence'
  • EcoCyc:TU592

    Source assertion: EG12286 belongs to native yiaK-S transcription unit TU592. Reporter evidence is at operon promoter level rather than an independent assay of each downstream gene.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12286"]
  • Entrez:948100

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbU and its exact EcoCyc frame EG12286. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12286"] | //Gene-ref_locus | //Gene-ref_locus-tag
L-ascorbate
CHEBI:38290		activates

L-ascorbate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

sgbE
Entrez:948099
  • PMID:31892694

    Source assertion: L-ascorbate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

    Source locationXPath /article/body/sec[2]/sec[7]/p[2]; paragraph containing 'We then examined the possible influence'
  • EcoCyc:TU592

    Source assertion: EG12287 belongs to native yiaK-S transcription unit TU592. Reporter evidence is at operon promoter level rather than an independent assay of each downstream gene.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12287"]
  • Entrez:948099

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbE and its exact EcoCyc frame EG12287. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12287"] | //Gene-ref_locus | //Gene-ref_locus-tag
alpha-D-galacturonate
CHEBI:58658		inhibits

alpha-D-galacturonate reduced PlaR-yiaK promoter complexes in the 10 mM effector screen; dose-dependent dissociation was examined. The edge concerns PlaR DNA-binding activity, not inhibition of a metabolic enzyme or complete lyxose flux.

HTH-type transcriptional repressor PlaR
UniProtKB:P37671

experimental construct: His-tagged PlaR from pET21a(+) expressed in BL21(DE3), affinity-purified for promoter gel shifts; exact complete tag/construct sequence unreported. BW25113 supplied gel-shift probes; W3110 type-A supplied separate gSELEX genome fragments.

Qualification evidence
  • PMID:31892694

    Source assertion: The assayed PlaR was His-tagged, expressed from pET21a(+) in BL21(DE3), and affinity-purified. The exact tag position/complete construct sequence is not specified in the inspected text.

    Source locationXPath /article/body/sec[4]/sec[2]/p; paragraph containing 'Expression plasmid pPlaR'
  • PMID:31892694

    Source assertion: Gel shifts used BW25113-derived promoter probes and buffer containing Tris pH 7.8, NaCl and magnesium acetate. These conditions support chosen solution species without measuring ligand protonation or anomer purity.

    Source locationXPath /article/body/sec[4]/sec[4]/p; paragraph containing 'The gel shift assay was performed'
  • PMID:31892694

    Source assertion: alpha-D-galacturonate reduced PlaR-yiaK promoter complexes in the 10 mM effector screen; dose-dependent dissociation was examined. The edge concerns PlaR DNA-binding activity, not inhibition of a metabolic enzyme or complete lyxose flux.

    Source locationXPath /article/body/sec[2]/sec[7]/p[1]; paragraph containing 'First we tested 10 mM concentrations'
alpha-D-galacturonate
CHEBI:58658		activates

alpha-D-galacturonate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

lyxK
Entrez:948101
  • PMID:31892694

    Source assertion: alpha-D-galacturonate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

    Source locationXPath /article/body/sec[2]/sec[7]/p[2]; paragraph containing 'We then examined the possible influence'
  • EcoCyc:TU592

    Source assertion: EG12284 belongs to native yiaK-S transcription unit TU592. Reporter evidence is at operon promoter level rather than an independent assay of each downstream gene.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12284"]
  • Entrez:948101

    Source assertion: Issuing MG1655 NCBI Gene identifies lyxK and its exact EcoCyc frame EG12284. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12284"] | //Gene-ref_locus | //Gene-ref_locus-tag
alpha-D-galacturonate
CHEBI:58658		activates

alpha-D-galacturonate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

sgbU
Entrez:948100
  • PMID:31892694

    Source assertion: alpha-D-galacturonate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

    Source locationXPath /article/body/sec[2]/sec[7]/p[2]; paragraph containing 'We then examined the possible influence'
  • EcoCyc:TU592

    Source assertion: EG12286 belongs to native yiaK-S transcription unit TU592. Reporter evidence is at operon promoter level rather than an independent assay of each downstream gene.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12286"]
  • Entrez:948100

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbU and its exact EcoCyc frame EG12286. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12286"] | //Gene-ref_locus | //Gene-ref_locus-tag
alpha-D-galacturonate
CHEBI:58658		activates

alpha-D-galacturonate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

sgbE
Entrez:948099
  • PMID:31892694

    Source assertion: alpha-D-galacturonate increased the yiaK reporter in wild-type BW25113, with little additional activation in the plaR mutant. Conditions were 0.2% alpha-D-galacturonate or 30 mM L-ascorbate; this is operon-expression context, not complete L-lyxose flux.

    Source locationXPath /article/body/sec[2]/sec[7]/p[2]; paragraph containing 'We then examined the possible influence'
  • EcoCyc:TU592

    Source assertion: EG12287 belongs to native yiaK-S transcription unit TU592. Reporter evidence is at operon promoter level rather than an independent assay of each downstream gene.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12287"]
  • Entrez:948099

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbE and its exact EcoCyc frame EG12287. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12287"] | //Gene-ref_locus | //Gene-ref_locus-tag
glutathionate(1-)
CHEBI:57925		activates

The native positive regulation event assigns glutathione activation to LyxK activity, citing PMID7961955. Its original full body was unavailable; no concentration, allosteric mechanism or in-vivo flux effect is invented.

L-xylulose + ATP => L-xylulose 5-phosphate + ADP + H(+)
RHEA:18870
  • EcoCyc:REG0-7579

    Source assertion: The native positive regulation event assigns glutathione activation to LyxK activity, citing PMID7961955. Its original full body was unavailable; no concentration, allosteric mechanism or in-vivo flux effect is invented.

    Source locationXPath /ptools-xml/Regulation[mode="+"]/regulator/Compound[@frameid="GLUTATHIONE"]
Integration host factor subunit alpha
UniProtKB:P0A6X7		located_in

The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.

nucleoid
GO:0009295
  • UniProtKB:P0A6X7

    Source assertion: The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.

    Source locationcomments[commentType=SUBCELLULAR LOCATION]
Integration host factor subunit beta
UniProtKB:P0A6Y1		located_in

The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.

cytoplasm
GO:0005737
  • UniProtKB:P0A6Y1

    Source assertion: The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.

    Source locationcomments[commentType=SUBCELLULAR LOCATION]
Aerobic respiration control protein ArcA
UniProtKB:P0A9Q1		located_in

The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.

cytoplasm
GO:0005737
  • UniProtKB:P0A9Q1

    Source assertion: The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.

    Source locationcomments[commentType=SUBCELLULAR LOCATION]
HTH-type transcriptional activator RhaS
UniProtKB:P09377		located_in

The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.

cytoplasm
GO:0005737
  • UniProtKB:P09377

    Source assertion: The reviewed protein entry supplies this cellular location. IhfA nucleoid annotation includes experimental localization; ArcA is curator-inferred and RhaS is HAMAP-supported. Location does not establish pathway-specific regulator action.

    Source locationcomments[commentType=SUBCELLULAR LOCATION]
D-glucose
CHEBI:17634		activates

Glucose enhanced the divergent yiaJ/plaR reporter while repressing yiaK-S. This is coordinated carbon-source-dependent expression in the examined reporter backgrounds, not direct glucose binding to PlaR.

plaR
Entrez:948084
  • PMID:10913096

    Source assertion: Glucose enhanced the divergent yiaJ/plaR reporter while repressing yiaK-S. This is coordinated carbon-source-dependent expression in the examined reporter backgrounds, not direct glucose binding to PlaR.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[3]/p[2]; paragraph containing 'Cultures of strain JA134 carrying'
  • Entrez:948084

    Source assertion: Issuing MG1655 NCBI Gene identifies plaR and its exact EcoCyc frame EG12278. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12278"] | //Gene-ref_locus | //Gene-ref_locus-tag
D-glucose
CHEBI:17634		inhibits

Glucose reduced yiaK-S reporter activity in JA134 under aerobic and anaerobic conditions. Exogenous cAMP partly restored activity; this is carbon-source-dependent expression, not direct inhibition of LyxK/SgbU/SgbE.

lyxK
Entrez:948101
  • PMID:10913096

    Source assertion: Glucose reduced yiaK-S reporter activity in JA134 under aerobic and anaerobic conditions. Exogenous cAMP partly restored activity; this is carbon-source-dependent expression, not direct inhibition of LyxK/SgbU/SgbE.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[3]/p[2]; paragraph containing 'Cultures of strain JA134 carrying'
  • EcoCyc:TU592

    Source assertion: TU592 includes EG12284; culture reporter results describe this transcription unit, not a separate gene-specific enzyme assay.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12284"]
  • Entrez:948101

    Source assertion: Issuing MG1655 NCBI Gene identifies lyxK and its exact EcoCyc frame EG12284. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12284"] | //Gene-ref_locus | //Gene-ref_locus-tag
D-glucose
CHEBI:17634		inhibits

Glucose reduced yiaK-S reporter activity in JA134 under aerobic and anaerobic conditions. Exogenous cAMP partly restored activity; this is carbon-source-dependent expression, not direct inhibition of LyxK/SgbU/SgbE.

sgbU
Entrez:948100
  • PMID:10913096

    Source assertion: Glucose reduced yiaK-S reporter activity in JA134 under aerobic and anaerobic conditions. Exogenous cAMP partly restored activity; this is carbon-source-dependent expression, not direct inhibition of LyxK/SgbU/SgbE.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[3]/p[2]; paragraph containing 'Cultures of strain JA134 carrying'
  • EcoCyc:TU592

    Source assertion: TU592 includes EG12286; culture reporter results describe this transcription unit, not a separate gene-specific enzyme assay.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12286"]
  • Entrez:948100

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbU and its exact EcoCyc frame EG12286. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12286"] | //Gene-ref_locus | //Gene-ref_locus-tag
D-glucose
CHEBI:17634		inhibits

Glucose reduced yiaK-S reporter activity in JA134 under aerobic and anaerobic conditions. Exogenous cAMP partly restored activity; this is carbon-source-dependent expression, not direct inhibition of LyxK/SgbU/SgbE.

sgbE
Entrez:948099
  • PMID:10913096

    Source assertion: Glucose reduced yiaK-S reporter activity in JA134 under aerobic and anaerobic conditions. Exogenous cAMP partly restored activity; this is carbon-source-dependent expression, not direct inhibition of LyxK/SgbU/SgbE.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[3]/p[2]; paragraph containing 'Cultures of strain JA134 carrying'
  • EcoCyc:TU592

    Source assertion: TU592 includes EG12287; culture reporter results describe this transcription unit, not a separate gene-specific enzyme assay.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12287"]
  • Entrez:948099

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbE and its exact EcoCyc frame EG12287. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12287"] | //Gene-ref_locus | //Gene-ref_locus-tag
succinate(2-)
CHEBI:30031		activates

Growth on succinate increased yiaK-S reporter expression about threefold in the JA134 derepressed background. This bounded culture response is not evidence for direct succinate binding to any enzyme or regulator.

lyxK
Entrez:948101
  • PMID:10913096

    Source assertion: Growth on succinate increased yiaK-S reporter expression about threefold in the JA134 derepressed background. This bounded culture response is not evidence for direct succinate binding to any enzyme or regulator.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[3]/p[2]; paragraph containing 'Cultures of strain JA134 carrying'
  • EcoCyc:TU592

    Source assertion: TU592 includes EG12284; culture reporter results describe this transcription unit, not a separate gene-specific enzyme assay.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12284"]
  • Entrez:948101

    Source assertion: Issuing MG1655 NCBI Gene identifies lyxK and its exact EcoCyc frame EG12284. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12284"] | //Gene-ref_locus | //Gene-ref_locus-tag
succinate(2-)
CHEBI:30031		activates

Growth on succinate increased yiaK-S reporter expression about threefold in the JA134 derepressed background. This bounded culture response is not evidence for direct succinate binding to any enzyme or regulator.

sgbU
Entrez:948100
  • PMID:10913096

    Source assertion: Growth on succinate increased yiaK-S reporter expression about threefold in the JA134 derepressed background. This bounded culture response is not evidence for direct succinate binding to any enzyme or regulator.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[3]/p[2]; paragraph containing 'Cultures of strain JA134 carrying'
  • EcoCyc:TU592

    Source assertion: TU592 includes EG12286; culture reporter results describe this transcription unit, not a separate gene-specific enzyme assay.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12286"]
  • Entrez:948100

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbU and its exact EcoCyc frame EG12286. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12286"] | //Gene-ref_locus | //Gene-ref_locus-tag
succinate(2-)
CHEBI:30031		activates

Growth on succinate increased yiaK-S reporter expression about threefold in the JA134 derepressed background. This bounded culture response is not evidence for direct succinate binding to any enzyme or regulator.

sgbE
Entrez:948099
  • PMID:10913096

    Source assertion: Growth on succinate increased yiaK-S reporter expression about threefold in the JA134 derepressed background. This bounded culture response is not evidence for direct succinate binding to any enzyme or regulator.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[3]/p[2]; paragraph containing 'Cultures of strain JA134 carrying'
  • EcoCyc:TU592

    Source assertion: TU592 includes EG12287; culture reporter results describe this transcription unit, not a separate gene-specific enzyme assay.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12287"]
  • Entrez:948099

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbE and its exact EcoCyc frame EG12287. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12287"] | //Gene-ref_locus | //Gene-ref_locus-tag
L-fucose
CHEBI:18287		activates

L-fucose modestly increased the yiaK-S reporter in ECL1 under the 2000 screening conditions, while JA134 was constitutively high. The physiological inducer was then unresolved; direct PlaR ligand binding was not shown.

lyxK
Entrez:948101
  • PMID:10913096

    Source assertion: L-fucose modestly increased the yiaK-S reporter in ECL1 under the 2000 screening conditions, while JA134 was constitutively high. The physiological inducer was then unresolved; direct PlaR ligand binding was not shown.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[6]/p[2]; paragraph containing 'Among 80 different compounds'
  • EcoCyc:TU592

    Source assertion: TU592 includes EG12284; culture reporter results describe this transcription unit, not a separate gene-specific enzyme assay.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12284"]
  • Entrez:948101

    Source assertion: Issuing MG1655 NCBI Gene identifies lyxK and its exact EcoCyc frame EG12284. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12284"] | //Gene-ref_locus | //Gene-ref_locus-tag
L-fucose
CHEBI:18287		activates

L-fucose modestly increased the yiaK-S reporter in ECL1 under the 2000 screening conditions, while JA134 was constitutively high. The physiological inducer was then unresolved; direct PlaR ligand binding was not shown.

sgbU
Entrez:948100
  • PMID:10913096

    Source assertion: L-fucose modestly increased the yiaK-S reporter in ECL1 under the 2000 screening conditions, while JA134 was constitutively high. The physiological inducer was then unresolved; direct PlaR ligand binding was not shown.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[6]/p[2]; paragraph containing 'Among 80 different compounds'
  • EcoCyc:TU592

    Source assertion: TU592 includes EG12286; culture reporter results describe this transcription unit, not a separate gene-specific enzyme assay.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12286"]
  • Entrez:948100

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbU and its exact EcoCyc frame EG12286. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12286"] | //Gene-ref_locus | //Gene-ref_locus-tag
L-fucose
CHEBI:18287		activates

L-fucose modestly increased the yiaK-S reporter in ECL1 under the 2000 screening conditions, while JA134 was constitutively high. The physiological inducer was then unresolved; direct PlaR ligand binding was not shown.

sgbE
Entrez:948099
  • PMID:10913096

    Source assertion: L-fucose modestly increased the yiaK-S reporter in ECL1 under the 2000 screening conditions, while JA134 was constitutively high. The physiological inducer was then unresolved; direct PlaR ligand binding was not shown.

    Source locationXPath /html/body/div[2]/div[2]/div/div[1]/div/div[2]/main/article/section[2]/section/section[3]/section[6]/p[2]; paragraph containing 'Among 80 different compounds'
  • EcoCyc:TU592

    Source assertion: TU592 includes EG12287; culture reporter results describe this transcription unit, not a separate gene-specific enzyme assay.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG12287"]
  • Entrez:948099

    Source assertion: Issuing MG1655 NCBI Gene identifies sgbE and its exact EcoCyc frame EG12287. This binds the native transcription target to the Entrez gene, not directly to enzyme catalytic activity.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG12287"] | //Gene-ref_locus | //Gene-ref_locus-tag
MetaCyc:LYXMET-PWYhas_part

Frozen SMP0002112 directly attaches Pentose Phosphate child SMP0121065. This is source-specific opaque child membership associated with the lyxose route; child chemistry is not expanded and frozen UlaF assignment is not adopted.

Pentose Phosphate
PathBank:SMP0121065
  • PathBank:SMP0002112

    Source assertion: Frozen SMP0002112 directly attaches Pentose Phosphate child SMP0121065. This is source-specific opaque child membership associated with the lyxose route; child chemistry is not expanded and frozen UlaF assignment is not adopted.

    Source locationXPath //bp:Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002112"]/bp:pathwayComponent[@rdf:resource="http://identifiers.org/smpdb/SMP0121065"]
HTH-type transcriptional regulator KdgR
UniProtKB:P76268		inhibits

Northern blots show increased plaR mRNA after deletion of KdgR, supporting a negative influence on plaR expression under these conditions. Regulation may be indirect; direct promoter binding is not established. Northern blots: BW25113 versus JW3546 (plaR deletion) or JW1816 (kdgR deletion); M9 + 0.5% casamino acids, 37 C, aerobic shaking, mid-exponential phase.

plaR
Entrez:948084
  • PMID:31892694

    Source assertion: Northern blots show increased plaR mRNA after deletion of KdgR, supporting a negative influence on plaR expression under these conditions. Regulation may be indirect; direct promoter binding is not established.

    Source locationXPath /article/body/sec[2]/sec[5]/p[3]
  • PMID:31892694

    Source assertion: Figure 5 compares BW25113 with plaR- and kdgR-defective derivatives in M9 plus 0.5% casamino acids, 37 C, aerobic shaking; RNA was sampled at mid-exponential phase for Northern blots.

    Source locationXPath /article/body/sec[2]/sec[5]/p[1]/fig/caption
  • PMID:31892694

    Source assertion: Methods identify BW25113, JW3546 (plaR deletion) and JW1816 (kdgR deletion) for Northern blots. The K-12 protein and MG1655 gene accessions provide reference identities; the reported experiment used these BW25113 derivatives.

    Source locationXPath /article/body/sec[4]/sec[1]/p
  • UniProtKB:P76268

    Source assertion: The issuing K-12 protein record links kdgR protein P76268 to NCBI Gene 946129; the protein identity is distinct from the measured gene-expression target.

    Source locationJSON uniProtKBCrossReferences database=GeneID, id=946129
  • Entrez:946129

    Source assertion: The issuing MG1655 NCBI Gene record grounds kdgR/b1827 as the KdgR regulator subject's reference gene. The separately cited UniProt GeneID join identifies the protein subject; the expression target is plaR (Entrez:948084), and assay observations remain scoped to BW25113 derivatives.

    Source locationXPath //Gene-track_geneid | //Gene-ref_locus | //Gene-ref_locus-tag | //Org-ref_taxname
  • UniProtKB:P37671

    Source assertion: The issuing K-12 protein record links plaR protein P37671 to NCBI Gene 948084; the protein identity is distinct from the measured gene-expression target.

    Source locationJSON uniProtKBCrossReferences database=GeneID, id=948084
  • Entrez:948084

    Source assertion: The issuing MG1655 NCBI Gene record identifies plaR and its locus tag. This grounds the gene-expression endpoint while preserving the BW25113 assay-strain limitation.

    Source locationXPath //Gene-track_geneid | //Gene-ref_locus | //Gene-ref_locus-tag | //Org-ref_taxname
HTH-type transcriptional repressor PlaR
UniProtKB:P37671		inhibits

Northern blots show increased kdgR mRNA after deletion of PlaR, supporting a negative influence on kdgR expression under these conditions. Regulation may be indirect; direct promoter binding is not established. Northern blots: BW25113 versus JW3546 (plaR deletion) or JW1816 (kdgR deletion); M9 + 0.5% casamino acids, 37 C, aerobic shaking, mid-exponential phase.

kdgR
Entrez:946129
  • PMID:31892694

    Source assertion: Northern blots show increased kdgR mRNA after deletion of PlaR, supporting a negative influence on kdgR expression under these conditions. Regulation may be indirect; direct promoter binding is not established.

    Source locationXPath /article/body/sec[2]/sec[5]/p[3]
  • PMID:31892694

    Source assertion: Figure 5 compares BW25113 with plaR- and kdgR-defective derivatives in M9 plus 0.5% casamino acids, 37 C, aerobic shaking; RNA was sampled at mid-exponential phase for Northern blots.

    Source locationXPath /article/body/sec[2]/sec[5]/p[1]/fig/caption
  • PMID:31892694

    Source assertion: Methods identify BW25113, JW3546 (plaR deletion) and JW1816 (kdgR deletion) for Northern blots. The K-12 protein and MG1655 gene accessions provide reference identities; the reported experiment used these BW25113 derivatives.

    Source locationXPath /article/body/sec[4]/sec[1]/p
  • UniProtKB:P76268

    Source assertion: The issuing K-12 protein record links kdgR protein P76268 to NCBI Gene 946129; the protein identity is distinct from the measured gene-expression target.

    Source locationJSON uniProtKBCrossReferences database=GeneID, id=946129
  • Entrez:946129

    Source assertion: The issuing MG1655 NCBI Gene record identifies kdgR and its locus tag. This grounds the gene-expression endpoint while preserving the BW25113 assay-strain limitation.

    Source locationXPath //Gene-track_geneid | //Gene-ref_locus | //Gene-ref_locus-tag | //Org-ref_taxname
  • UniProtKB:P37671

    Source assertion: The issuing K-12 protein record links plaR protein P37671 to NCBI Gene 948084; the protein identity is distinct from the measured gene-expression target.

    Source locationJSON uniProtKBCrossReferences database=GeneID, id=948084
  • Entrez:948084

    Source assertion: The issuing MG1655 NCBI Gene record grounds plaR/b3574 as the PlaR regulator subject's reference gene. The separately cited UniProt GeneID join identifies the protein subject; the expression target is kdgR (Entrez:946129), and assay observations remain scoped to BW25113 derivatives.

    Source locationXPath //Gene-track_geneid | //Gene-ref_locus | //Gene-ref_locus-tag | //Org-ref_taxname

References

Curation history