ribose phosphorylation

MetaCyc:RIBOKIN-PWY

This complete native ribose-phosphorylation route contains three chemical events: beta-D-ribopyranose/beta-D-ribofuranose interconversion, spontaneous alpha/beta furanose interconversion, and ATP-dependent phosphorylation to alpha-D-ribofuranose 5-phosphate. Both enzymatic members of the native reaction-list are retained, together with the spontaneous event explicitly described by its narrative. RXN-14904 is the exact reversible native spontaneous reaction; its selected route direction is right-to-left. Its source also marks physiologically-relevant=true and orphan=YES-PUTATIVE; no catalyst is assigned. RbsD and FucU are separate alternative pyranases, not obligate partners. The META narrative specifies alpha-furanose kinase chemistry while its formal reaction-layout and Rhea 13697/13698 use generic furanose classes. This graph explicitly refines the generic RIBOKIN-RXN sugar sides to that narrative's alpha forms; it does not claim an exact Rhea synonym, consume both generic and alpha sugars, or equate cyclic and aldehydo forms. Ryu 2004 NMR suggests alpha preference rather than proving exclusivity; the stronger specificity statement is the inspected native annotation citing Sigrell 1998. The generic and anomer-specific definitions remain separately preserved in the evidence audit. Incoming ABC-28-RXN transports the native D-ribopyranose class from outside to inside with ATP/water consumption and ADP/phosphate/hydron output. Rhea 29903/29904 instead uses D-ribofuranose and is not treated as an exact alias of this pyranose transport event. RbsB beta-pyranose binding is established in the native summary, while beta-selective transport is explicitly presumed. Current EcoCyc/UniProt specify RbsA1-RbsC2-RbsB1; the frozen 2019 PathBank rendering uses A2-C2-B1. RbsA has two ATP-binding domains in one chain. Cofactor-dependent RbsAC2B, RbsAC and RbsBC cycle states are not simultaneously permanent assemblies. The transport step is an incoming interface, not a third enzymatic member of the native pathway reaction-list. Native RbsD and FucU homodecamers and the RbsK homodimer remain source-defined complexes. They are not equated to Ryu 2004 gel-filtration preparations: C-His RbsD had estimated 7.1/15.3 oligomers, N-His FucU was monomeric and inactive, C-His FucU about 5, and untagged FucU about 6.2/18.9. RbsK(C-His) was about 1.9. Those are construct- and method-specific estimates, not exact alternative native stoichiometries. The full Ryu scientific body and Table I were inspected via an author-uploaded web rendering; a complete original publisher PDF and supplement were not obtained. RbsC ten-helix topology likewise derives from His-tagged cysteineless templates with single-cysteine replacements (PMID12923096), not an unmodified-chain assay. Ribokinase uses a divalent cation, with Mg2+ considered likely in vivo and Mn2+ an active alternative; probable metal-nucleotide substrate assignment is retained as inference. Potassium and ammonium are alternative monovalent activators. Phosphate activation is condition dependent; native kinetic commentary also names arsenate and vanadate without resolving their exact chemical forms here. No cofactor independence is inferred for either pyranase. Native localization and curator-inferred localization are distinguished. RbsR represses and CRP-cAMP positively regulates the rbsDACBKR transcription unit; D-ribose lowers RbsR DNA-binding affinity. These edges target exact MG1655 genes and do not imply direct enzyme inhibition. YidZ deletion/RNA-seq supports negative control of rbsD under the assayed M9-glucose conditions; associated ChIP-exo used a C-terminal 8-myc construct, not unmodified purified YidZ. CRP expression-based evidence may include indirect effects. The iModulon observations remain external computational context and do not add causal edges. Historical K-12 experiments and engineered derivatives are not all relabelled as MG1655. The non-oxidative pentose phosphate pathway and PRPP biosynthesis are opaque downstream source links, not expanded core chemistry. No unobserved cyclic/open-chain isomerization or exact endpoint identity is invented to connect them. This is a full source-defined microbial route with preserved anomer, assembly, experimental and access limits, not proof that every annotated alternative and regulatory condition operates simultaneously.

Pathway type
ribose phosphorylation
Organism scope

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Pathway network

49 nodes · 66 asserted directed edges

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Pathway network: ribose phosphorylation 49 nodes · 66 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. RHEA:25433 — part_of → MetaCyc:RIBOKIN-PWY; The native pathway reaction-list includes RXN0-5304; this enzymatic event is retained in the complete pathway boundary.; Evidence: MetaCyc:RIBOKIN-PWYpart of MetaCyc:RIBOKIN-RXN — part_of → MetaCyc:RIBOKIN-PWY; The native pathway reaction-list includes RIBOKIN-RXN; this enzymatic event is retained in the complete pathway boundary.; Evidence: MetaCyc:RIBOKIN-PWYpart of MetaCyc:RXN-14904 — part_of → MetaCyc:RIBOKIN-PWY; The pathway narrative explicitly places fast spontaneous alpha/beta D-ribofuranose interconversion between pyranase and alpha-specific ribokinase; this chemically necessary event is retained although omitted from reaction-list.; Evidence: MetaCyc:RIBOKIN-PWY, MetaCyc:RXN-14904part of CHEBI:27476 — consumes → RHEA:25433; The native reversible pyranase reaction has CPD0-1110 on its left side; the source pathway selects left-to-right beta-pyranose to beta-furanose flux.; Evidence: EcoCyc:RXN0-5304, RHEA:25433consumes RHEA:25433 — produces → CHEBI:47002; The native reversible pyranase reaction has CPD0-1108 on its right side; the source pathway selects left-to-right beta-pyranose to beta-furanose flux.; Evidence: EcoCyc:RXN0-5304, RHEA:25433produces CHEBI:47002 — consumes → MetaCyc:RXN-14904; Native right participant CPD0-1108 is retained. The selected right-to-left route converts beta-D-ribofuranose to alpha-D-ribofuranose without an enzyme; native chemistry is reversible.; Evidence: MetaCyc:RXN-14904consumes MetaCyc:RXN-14904 — produces → CHEBI:45506; Native left participant CPD-10330 is retained. The selected right-to-left route converts beta-D-ribofuranose to alpha-D-ribofuranose without an enzyme; native chemistry is reversible.; Evidence: MetaCyc:RXN-14904produces CHEBI:45506 — consumes → MetaCyc:RIBOKIN-RXN; Native RIBOKIN-RXN includes D-Ribofuranose on its left side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.; Evidence: MetaCyc:RIBOKIN-RXN, MetaCyc:RIBOKIN-PWYconsumes CHEBI:30616 — consumes → MetaCyc:RIBOKIN-RXN; Native RIBOKIN-RXN includes ATP on its left side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.; Evidence: MetaCyc:RIBOKIN-RXNconsumes MetaCyc:RIBOKIN-RXN — produces → CHEBI:140679; Native RIBOKIN-RXN includes CPD-15317 on its right side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.; Evidence: MetaCyc:RIBOKIN-RXN, MetaCyc:RIBOKIN-PWYproduces MetaCyc:RIBOKIN-RXN — produces → CHEBI:456216; Native RIBOKIN-RXN includes ADP on its right side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.; Evidence: MetaCyc:RIBOKIN-RXNproduces MetaCyc:RIBOKIN-RXN — produces → CHEBI:15378; Native RIBOKIN-RXN includes PROTON on its right side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.; Evidence: MetaCyc:RIBOKIN-RXNproduces CHEBI:30616 — consumes → MetaCyc:ABC-28-RXN; Native transport left participant ATP occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.; Evidence: EcoCyc:ABC-28-RXNconsumes CHEBI:47006 — consumes → MetaCyc:ABC-28-RXN; Native transport left participant D-Ribopyranose occupies CCO-OUT; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.; Evidence: EcoCyc:ABC-28-RXNconsumes CHEBI:15377 — consumes → MetaCyc:ABC-28-RXN; Native transport left participant WATER occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.; Evidence: EcoCyc:ABC-28-RXNconsumes MetaCyc:ABC-28-RXN — produces → CHEBI:456216; Native transport right participant ADP occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.; Evidence: EcoCyc:ABC-28-RXNproduces MetaCyc:ABC-28-RXN — produces → CHEBI:43474; Native transport right participant Pi occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.; Evidence: EcoCyc:ABC-28-RXNproduces MetaCyc:ABC-28-RXN — produces → CHEBI:47006; Native transport right participant D-Ribopyranose occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.; Evidence: EcoCyc:ABC-28-RXNproduces MetaCyc:ABC-28-RXN — produces → CHEBI:15378; Native transport right participant PROTON occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.; Evidence: EcoCyc:ABC-28-RXNproduces RHEA:25433 — provides_input_for → MetaCyc:RXN-14904; The narrative places beta-pyranose/furanose conversion before spontaneous alpha/beta furanose interconversion; beta-D-ribofuranose is the shared chemical intermediate.; Evidence: MetaCyc:RIBOKIN-PWYprovides input for MetaCyc:RXN-14904 — provides_input_for → MetaCyc:RIBOKIN-RXN; Spontaneous anomer interconversion supplies the alpha-furanose substrate assigned to ribokinase by the META narrative.; Evidence: MetaCyc:RIBOKIN-PWYprovides input for MetaCyc:ABC-28-RXN — provides_input_for → RHEA:25433; The source places ABC uptake before pyranase and reports RbsB binding of beta-D-ribopyranose, with facilitation of its transport explicitly presumed. The formal transporter substrate remains the broader D-ribopyranose class.; Evidence: MetaCyc:RIBOKIN-PWYprovides input for MetaCyc:RIBOKIN-RXN — provides_input_for → MetaCyc:NONOXIPENT-PWY; Native pathway-links connect the generic ribose-furanose 5-phosphate output to NONOXIPENT-PWY. This opaque pathway interface preserves that source link without asserting an exact alpha/cyclic/open-chain identity or expanding downstream reactions.; Evidence: MetaCyc:RIBOKIN-PWYprovides input for MetaCyc:RIBOKIN-RXN — provides_input_for → MetaCyc:PWY0-662; Native pathway-links connect the generic ribose-furanose 5-phosphate output to PWY0-662. This opaque pathway interface preserves that source link without asserting an exact alpha/cyclic/open-chain identity or expanding downstream reactions.; Evidence: MetaCyc:RIBOKIN-PWYprovides input for EcoCyc:CPLX0-7646 — catalyzes → RHEA:25433; The native enzymatic-reaction assigns CPLX0-7646 as enzyme; the two pyranase complexes are alternatives, not obligate partners. The kinase edge uses the explicitly declared pathway-specific alpha refinement.; Evidence: EcoCyc:ENZRXN0-6479catalyzes EcoCyc:CPLX0-7645 — catalyzes → RHEA:25433; The native enzymatic-reaction assigns CPLX0-7645 as enzyme; the two pyranase complexes are alternatives, not obligate partners. The kinase edge uses the explicitly declared pathway-specific alpha refinement.; Evidence: EcoCyc:ENZRXN0-8627catalyzes EcoCyc:CPLX0-7647 — catalyzes → MetaCyc:RIBOKIN-RXN; The native enzymatic-reaction assigns CPLX0-7647 as enzyme; the two pyranase complexes are alternatives, not obligate partners. The kinase edge uses the explicitly declared pathway-specific alpha refinement.; Evidence: EcoCyc:RIBOKIN-ENZRXNcatalyzes EcoCyc:ABC-28-CPLX — catalyzes → MetaCyc:ABC-28-RXN; The source describes a high-affinity ATP-dependent ribose uptake system and active RbsAC2B reconstituted in liposomes; it proposes a cofactor-dependent association/dissociation cycle.; Evidence: EcoCyc:ABC-28-CPLXcatalyzes EcoCyc:CPLX0-7646 — has_part → UniProtKB:P04982; The current native complex lists 10 copy/copies of EG10817-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.; Evidence: EcoCyc:CPLX0-7646, EcoCyc:EG10817-MONOMERhas part EcoCyc:CPLX0-7645 — has_part → UniProtKB:P0AEN8; The current native complex lists 10 copy/copies of EG10355-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.; Evidence: EcoCyc:CPLX0-7645, EcoCyc:EG10355-MONOMERhas part EcoCyc:CPLX0-7647 — has_part → UniProtKB:P0A9J6; The current native complex lists 2 copy/copies of RIBOKIN-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.; Evidence: EcoCyc:CPLX0-7647, EcoCyc:RIBOKIN-MONOMERhas part EcoCyc:ABC-28-CPLX — has_part → UniProtKB:P04983; Native RbsAC2B contains one RbsA chain. Its two ATP-binding domains are within that chain and do not imply two RbsA subunits; frozen 2019 PathBank instead specifies two RbsA chains.; Evidence: EcoCyc:ABC-28-CPLX, EcoCyc:RBSA-MONOMER, EcoCyc:RBSA-MONOMER, PathBank:SMP0002114has part EcoCyc:ABC-28-CPLX — has_part → UniProtKB:P0AGI1; The current native complex lists 2 copy/copies of RBSC-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.; Evidence: EcoCyc:ABC-28-CPLX, EcoCyc:RBSC-MONOMERhas part EcoCyc:ABC-28-CPLX — has_part → UniProtKB:P02925; The current native complex lists 1 copy/copies of RBSB-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.; Evidence: EcoCyc:ABC-28-CPLX, EcoCyc:RBSB-MONOMERhas part EcoCyc:ABC-28-CPLX — has_cofactor → CHEBI:18420; The source proposes RbsA-ATP-Mg2+ association with ribose-loaded RbsBC. This is a cofactor-dependent transport-cycle state, not permanent simultaneous occupancy of every cycle intermediate.; Evidence: EcoCyc:ABC-28-CPLXhas cofactor EcoCyc:CPLX0-7647 — has_cofactor → CHEBI:29103; Native ribokinase lists K+ as a cofactor; this direct slot does not specify intracellular occupancy or simultaneous use of alternative monovalent ions.; Evidence: EcoCyc:RIBOKIN-ENZRXNhas cofactor EcoCyc:CPLX0-7647 — has_cofactor → CHEBI:18420; Native ribokinase lists Mg2+ as a cofactor; this direct slot does not itself establish intracellular occupancy.; Evidence: EcoCyc:RIBOKIN-ENZRXN, UniProtKB:P0A9J6has cofactor EcoCyc:CPLX0-7647 — has_cofactor → CHEBI:29035; Reviewed ribokinase is also active with Mn2+; this is an alternative divalent cofactor, not evidence that magnesium and manganese are jointly required. The actual metal-nucleotide substrate assignment is marked probable.; Evidence: UniProtKB:P0A9J6has cofactor CHEBI:28938 — activates → EcoCyc:CPLX0-7647; Ammonium can also activate ribokinase as an alternative monovalent ion; potassium is considered the most likely occupant in vivo. Ion-induced affinity change is marked probable.; Evidence: UniProtKB:P0A9J6activates CHEBI:43474 — activates → MetaCyc:RIBOKIN-RXN; The native positive regulation event assigns inorganic phosphate activation to ribokinase activity; this is regulation rather than phosphate incorporation into ribose.; Evidence: EcoCyc:REG0-9220, EcoCyc:RIBOKIN-ENZRXNactivates UniProtKB:P04982 — located_in → GO:0005829; The native protein location slot places this protein in the Gram-negative cytosol; this is a source annotation, not a newly measured localization.; Evidence: EcoCyc:EG10817-MONOMERlocated in UniProtKB:P0A9J6 — located_in → GO:0005829; The native protein location slot places this protein in the Gram-negative cytosol; this is a source annotation, not a newly measured localization.; Evidence: EcoCyc:RIBOKIN-MONOMERlocated in UniProtKB:P0ACQ0 — located_in → GO:0005829; The native protein location slot places this protein in the Gram-negative cytosol; this is a source annotation, not a newly measured localization.; Evidence: EcoCyc:PD03867located in UniProtKB:P0AEN8 — located_in → GO:0005737; Reviewed FucU is annotated to cytoplasm with curator-inferred evidence (ECO:0000305), not a direct localization measurement.; Evidence: UniProtKB:P0AEN8located in UniProtKB:P04983 — located_in → GO:0005886; RbsA is annotated to the bacterial cell inner membrane as a peripheral membrane protein, using HAMAP and curator inference.; Evidence: UniProtKB:P04983located in UniProtKB:P0AGI1 — located_in → GO:0005886; Reviewed RbsC is annotated as an inner-membrane multipass permease. This edge reports the reviewed localization annotation, not the construct-specific topology of a newly assayed preparation.; Evidence: UniProtKB:P0AGI1located in UniProtKB:P02925 — located_in → GO:0042597; Reviewed RbsB is periplasmic; this binding component is not the transmembrane permease.; Evidence: UniProtKB:P02925located in UniProtKB:P0ACQ0 — inhibits → Entrez:948267; Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5371, EcoCyc:TU00206, Entrez:948267inhibits EcoCyc:CPLX0-226 — activates → Entrez:948267; Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5370, EcoCyc:TU00206, Entrez:948267activates UniProtKB:P0ACQ0 — inhibits → Entrez:948264; Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5371, EcoCyc:TU00206, Entrez:948264inhibits EcoCyc:CPLX0-226 — activates → Entrez:948264; Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5370, EcoCyc:TU00206, Entrez:948264activates UniProtKB:P0ACQ0 — inhibits → Entrez:948262; Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5371, EcoCyc:TU00206, Entrez:948262inhibits EcoCyc:CPLX0-226 — activates → Entrez:948262; Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5370, EcoCyc:TU00206, Entrez:948262activates UniProtKB:P0ACQ0 — inhibits → Entrez:948261; Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5371, EcoCyc:TU00206, Entrez:948261inhibits EcoCyc:CPLX0-226 — activates → Entrez:948261; Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5370, EcoCyc:TU00206, Entrez:948261activates UniProtKB:P0ACQ0 — inhibits → Entrez:948260; Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5371, EcoCyc:TU00206, Entrez:948260inhibits EcoCyc:CPLX0-226 — activates → Entrez:948260; Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5370, EcoCyc:TU00206, Entrez:948260activates UniProtKB:P0ACQ0 — inhibits → Entrez:948266; Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5371, EcoCyc:TU00206, Entrez:948266inhibits EcoCyc:CPLX0-226 — activates → Entrez:948266; Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.; Evidence: EcoCyc:REG0-5370, EcoCyc:TU00206, Entrez:948266activates UniProtKB:P31463 — inhibits → Entrez:948267; The native RNA-seq-backed regulation event assigns YidZ negative control of EG10817 (rbsD) transcription; this event is not a direct enzyme inhibition or purified protein-binding assay.; Evidence: EcoCyc:REG0-15980, PMID:34428301inhibits EcoCyc:MONOMER-60 — has_part → UniProtKB:P0ACQ0; The native RbsR-D-ribose complex lists component PD03867; no coefficient is supplied, so no oligomer or ligand copy number is inferred.; Evidence: EcoCyc:MONOMER-60has part EcoCyc:MONOMER-60 — has_part → CHEBI:16988; The native RbsR-D-ribose complex lists component RIBOSE; no coefficient is supplied, so no oligomer or ligand copy number is inferred.; Evidence: EcoCyc:MONOMER-60has part CHEBI:16988 — inhibits → UniProtKB:P0ACQ0; D-ribose binding reduces RbsR DNA-binding affinity and relieves repression of the ribose operon. This inhibition concerns the repressor DNA-binding function, not destruction of RbsR or direct inhibition of pathway chemistry.; Evidence: EcoCyc:PD03867inhibits EcoCyc:CPLX0-226 — has_part → EcoCyc:PC00004; The native CRP-cAMP assembly lists PC00004; the component slot supplies no coefficient and is not evidence for a specific number of cAMP ligands.; Evidence: EcoCyc:CPLX0-226has part EcoCyc:CPLX0-226 — has_part → CHEBI:58165; The native CRP-cAMP assembly lists CAMP; the component slot supplies no coefficient and is not evidence for a specific number of cAMP ligands.; Evidence: EcoCyc:CPLX0-226has part EcoCyc:PC00004 — has_part → UniProtKB:P0ACJ8; The native CRP complex contains two PD00257 chains; this component slot supplies the homodimer stoichiometry.; Evidence: EcoCyc:PC00004, UniProtKB:P0ACJ8has part beta-D-ribopyranose; CHEBI:27476; Declared type: small_molecule small molecule beta-D-ribopyranose beta-D-ribose; CHEBI:47002; Declared type: small_molecule small molecule beta-D-ribose alpha-D-ribose; CHEBI:45506; Declared type: small_molecule small molecule alpha-D-ribose alpha-D-Ribose 5-phosphate(2-); CHEBI:140679; Declared type: small_molecule small molecule alpha-D-Ribose 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 D-ribopyranose; CHEBI:47006; Declared type: small_molecule small molecule D-ribopyranose water; CHEBI:15377; Declared type: small_molecule small molecule water hydrogenphosphate; CHEBI:43474; Declared type: small_molecule small molecule hydrogenphosphate D-ribose; CHEBI:16988; Declared type: small_molecule small molecule D-ribose 3',5'-cyclic AMP(1-); CHEBI:58165; Declared type: small_molecule small molecule 3',5'-cyclic AMP(1-) magnesium(2+); CHEBI:18420; Declared type: cofactor cofactor magnesium(2+) manganese(2+); CHEBI:29035; Declared type: cofactor cofactor manganese(2+) potassium(1+); CHEBI:29103; Declared type: cofactor cofactor potassium(1+) ammonium; CHEBI:28938; Declared type: cofactor cofactor ammonium D-ribose pyranase; UniProtKB:P04982; Declared type: protein protein D-ribose pyranase L-fucose mutarotase; UniProtKB:P0AEN8; Declared type: protein protein L-fucose mutarotase Ribokinase; UniProtKB:P0A9J6; Declared type: protein protein Ribokinase Ribose import ATP-binding protein RbsA; UniProtKB:P04983; Declared type: protein protein Ribose import ATP-binding protein RbsA Ribose import permease protein RbsC; UniProtKB:P0AGI1; Declared type: protein protein Ribose import permease protein RbsC Ribose import binding protein RbsB; UniProtKB:P02925; Declared type: protein protein Ribose import binding protein RbsB Ribose operon repressor; UniProtKB:P0ACQ0; Declared type: protein protein Ribose operon repressor DNA-binding transcriptional dual regulator CRP; UniProtKB:P0ACJ8; Declared type: protein protein DNA-binding transcriptional dual regulator CRP HTH-type transcriptional regulator YidZ; UniProtKB:P31463; Declared type: protein protein HTH-type transcriptional regulator YidZ D-ribose pyranase; EcoCyc:CPLX0-7646; Declared type: complex complex D-ribose pyranase L-fucose mutarotase; EcoCyc:CPLX0-7645; Declared type: complex complex L-fucose mutarotase ribokinase; EcoCyc:CPLX0-7647; Declared type: complex complex ribokinase ribose ABC transporter; EcoCyc:ABC-28-CPLX; Declared type: complex complex ribose ABC transporter RbsR-D-ribose; EcoCyc:MONOMER-60; Declared type: complex complex RbsR-D-ribose 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 CRP; EcoCyc:PC00004; Declared type: complex complex DNA-binding transcriptional dual regulator CRP cytosol; GO:0005829; Declared type: cellular_component cellular component cytosol cytoplasm; GO:0005737; Declared type: cellular_component cellular component cytoplasm plasma membrane; GO:0005886; Declared type: cellular_component cellular component plasma membrane periplasmic space; GO:0042597; Declared type: cellular_component cellular component periplasmic space rbsD; Entrez:948267; Declared type: gene gene rbsD rbsA; Entrez:948264; Declared type: gene gene rbsA rbsC; Entrez:948262; Declared type: gene gene rbsC rbsB; Entrez:948261; Declared type: gene gene rbsB rbsK; Entrez:948260; Declared type: gene gene rbsK rbsR; Entrez:948266; Declared type: gene gene rbsR beta-D-ribopyranose => beta-D-ribofuranose; RHEA:25433; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity beta-D-ribopyranose => beta- D-ribofuranose spontaneous beta-D-ribofuranose to alpha-D-ribofuranose interconversion; MetaCyc:RXN-14904; Declared type: molecular_activity; Source reaction direction: right_to_left molecular activity spontaneous beta-D- ribofuranose to alpha-D- ribofuranose interconversion alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate; MetaCyc:RIBOKIN-RXN; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity alpha-D-ribofuranose phosphorylation to alpha-D- ribofuranose 5-phosphate ATP-dependent D-ribopyranose uptake; MetaCyc:ABC-28-RXN; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity ATP-dependent D-ribopyranose uptake pentose phosphate pathway (non-oxidative branch); MetaCyc:NONOXIPENT-PWY; Declared type: pathway pathway pentose phosphate pathway (non-oxidative branch) PRPP biosynthesis; MetaCyc:PWY0-662; Declared type: pathway pathway PRPP biosynthesis ribose phosphorylation; MetaCyc:RIBOKIN-PWY; Declared type: pathway pathway ribose phosphorylation

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-D-ribopyranose
CHEBI:27476		small molecule
beta-D-ribose
CHEBI:47002		small molecule
alpha-D-ribose
CHEBI:45506		small molecule
alpha-D-Ribose 5-phosphate(2-)
CHEBI:140679		small molecule
ATP(4-)
CHEBI:30616		small molecule
ADP(3-)
CHEBI:456216		small molecule
hydron
CHEBI:15378		small molecule
D-ribopyranose
CHEBI:47006		small molecule
water
CHEBI:15377		small molecule
hydrogenphosphate
CHEBI:43474		small molecule
D-ribose
CHEBI:16988		small molecule
3',5'-cyclic AMP(1-)
CHEBI:58165		small molecule
magnesium(2+)
CHEBI:18420		cofactor
manganese(2+)
CHEBI:29035		cofactor
potassium(1+)
CHEBI:29103		cofactor
ammonium
CHEBI:28938		cofactor
D-ribose pyranase
UniProtKB:P04982		protein
L-fucose mutarotase
UniProtKB:P0AEN8		protein
Ribokinase
UniProtKB:P0A9J6		protein
Ribose import ATP-binding protein RbsA
UniProtKB:P04983		protein
Ribose import permease protein RbsC
UniProtKB:P0AGI1		protein
Ribose import binding protein RbsB
UniProtKB:P02925		protein
Ribose operon repressor
UniProtKB:P0ACQ0		protein
DNA-binding transcriptional dual regulator CRP
UniProtKB:P0ACJ8		protein
HTH-type transcriptional regulator YidZ
UniProtKB:P31463		protein
D-ribose pyranase
EcoCyc:CPLX0-7646		complex
L-fucose mutarotase
EcoCyc:CPLX0-7645		complex
ribokinase
EcoCyc:CPLX0-7647		complex
ribose ABC transporter
EcoCyc:ABC-28-CPLX		complex
RbsR-D-ribose
EcoCyc:MONOMER-60		complex
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		complex
DNA-binding transcriptional dual regulator CRP
EcoCyc:PC00004		complex
cytosol
GO:0005829		cellular component
cytoplasm
GO:0005737		cellular component
plasma membrane
GO:0005886		cellular component
periplasmic space
GO:0042597		cellular component
rbsD
Entrez:948267		gene
rbsA
Entrez:948264		gene
rbsC
Entrez:948262		gene
rbsB
Entrez:948261		gene
rbsK
Entrez:948260		gene
rbsR
Entrez:948266		gene
beta-D-ribopyranose => beta-D-ribofuranose
RHEA:25433		molecular activityleft to right
spontaneous beta-D-ribofuranose to alpha-D-ribofuranose interconversion
MetaCyc:RXN-14904		molecular activityright to left
alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN		molecular activityleft to right
ATP-dependent D-ribopyranose uptake
MetaCyc:ABC-28-RXN		molecular activityleft to right
pentose phosphate pathway (non-oxidative branch)
MetaCyc:NONOXIPENT-PWY		pathway
PRPP biosynthesis
MetaCyc:PWY0-662		pathway

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
beta-D-ribopyranose => beta-D-ribofuranose
RHEA:25433		part_of

The native pathway reaction-list includes RXN0-5304; this enzymatic event is retained in the complete pathway boundary.

MetaCyc:RIBOKIN-PWY
  • MetaCyc:RIBOKIN-PWY

    Source assertion: The native pathway reaction-list includes RXN0-5304; this enzymatic event is retained in the complete pathway boundary.

    Source locationXPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="RXN0-5304"]
alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN		part_of

The native pathway reaction-list includes RIBOKIN-RXN; this enzymatic event is retained in the complete pathway boundary.

MetaCyc:RIBOKIN-PWY
  • MetaCyc:RIBOKIN-PWY

    Source assertion: The native pathway reaction-list includes RIBOKIN-RXN; this enzymatic event is retained in the complete pathway boundary.

    Source locationXPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="RIBOKIN-RXN"]
spontaneous beta-D-ribofuranose to alpha-D-ribofuranose interconversion
MetaCyc:RXN-14904		part_of

The pathway narrative explicitly places fast spontaneous alpha/beta D-ribofuranose interconversion between pyranase and alpha-specific ribokinase; this chemically necessary event is retained although omitted from reaction-list.

MetaCyc:RIBOKIN-PWY
  • MetaCyc:RIBOKIN-PWY

    Source assertion: The pathway narrative explicitly places fast spontaneous alpha/beta D-ribofuranose interconversion between pyranase and alpha-specific ribokinase; this chemically necessary event is retained although omitted from reaction-list.

    Source locationXPath /ptools-xml/Pathway/comment
  • MetaCyc:RXN-14904

    Source assertion: The exact native reaction is reversible alpha-D-ribofuranose/beta-D-ribofuranose interconversion, marked spontaneous and physiologically relevant; the route selects its right-to-left sense.

    Source locationXPath /ptools-xml/Reaction[left/Compound[@frameid="CPD-10330"] and right/Compound[@frameid="CPD0-1108"]]/spontaneous
beta-D-ribopyranose
CHEBI:27476		consumes

The native reversible pyranase reaction has CPD0-1110 on its left side; the source pathway selects left-to-right beta-pyranose to beta-furanose flux.

beta-D-ribopyranose => beta-D-ribofuranose
RHEA:25433
  • EcoCyc:RXN0-5304

    Source assertion: The native reversible pyranase reaction has CPD0-1110 on its left side; the source pathway selects left-to-right beta-pyranose to beta-furanose flux.

    Source locationXPath /ptools-xml/Reaction/left/Compound[@frameid="CPD0-1110"]
  • RHEA:25433

    Source assertion: Rhea 25433 explicitly selects substrates CHEBI:27476, coefficient one, in the left-to-right beta-pyranose to beta-furanose reaction.

    Source locationRDF http://rdf.rhea-db.org/25433; master 25432; substrates participant CHEBI CHEBI:27476
beta-D-ribopyranose => beta-D-ribofuranose
RHEA:25433		produces

The native reversible pyranase reaction has CPD0-1108 on its right side; the source pathway selects left-to-right beta-pyranose to beta-furanose flux.

beta-D-ribose
CHEBI:47002
  • EcoCyc:RXN0-5304

    Source assertion: The native reversible pyranase reaction has CPD0-1108 on its right side; the source pathway selects left-to-right beta-pyranose to beta-furanose flux.

    Source locationXPath /ptools-xml/Reaction/right/Compound[@frameid="CPD0-1108"]
  • RHEA:25433

    Source assertion: Rhea 25433 explicitly selects products CHEBI:47002, coefficient one, in the left-to-right beta-pyranose to beta-furanose reaction.

    Source locationRDF http://rdf.rhea-db.org/25433; master 25432; products participant CHEBI CHEBI:47002
beta-D-ribose
CHEBI:47002		consumes

Native right participant CPD0-1108 is retained. The selected right-to-left route converts beta-D-ribofuranose to alpha-D-ribofuranose without an enzyme; native chemistry is reversible.

spontaneous beta-D-ribofuranose to alpha-D-ribofuranose interconversion
MetaCyc:RXN-14904
  • MetaCyc:RXN-14904

    Source assertion: Native right participant CPD0-1108 is retained. The selected right-to-left route converts beta-D-ribofuranose to alpha-D-ribofuranose without an enzyme; native chemistry is reversible.

    Source locationXPath /ptools-xml/Reaction/right/Compound[@frameid="CPD0-1108"]
spontaneous beta-D-ribofuranose to alpha-D-ribofuranose interconversion
MetaCyc:RXN-14904		produces

Native left participant CPD-10330 is retained. The selected right-to-left route converts beta-D-ribofuranose to alpha-D-ribofuranose without an enzyme; native chemistry is reversible.

alpha-D-ribose
CHEBI:45506
  • MetaCyc:RXN-14904

    Source assertion: Native left participant CPD-10330 is retained. The selected right-to-left route converts beta-D-ribofuranose to alpha-D-ribofuranose without an enzyme; native chemistry is reversible.

    Source locationXPath /ptools-xml/Reaction/left/Compound[@frameid="CPD-10330"]
alpha-D-ribose
CHEBI:45506		consumes

Native RIBOKIN-RXN includes D-Ribofuranose on its left side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.

alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN
  • MetaCyc:RIBOKIN-RXN

    Source assertion: Native RIBOKIN-RXN includes D-Ribofuranose on its left side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.

    Source locationXPath /ptools-xml/Reaction/left/Compound[@frameid="D-Ribofuranose"]
  • MetaCyc:RIBOKIN-PWY

    Source assertion: The META narrative specifies alpha-D-ribofuranose (CPD-10330) phosphorylation to alpha-D-ribose 5-phosphate (CPD-15318); formal reaction-layout remains a broader furanose class. This edge is that declared refinement, not an exact generic Rhea alias.

    Source locationXPath /ptools-xml/Pathway/comment
ATP(4-)
CHEBI:30616		consumes

Native RIBOKIN-RXN includes ATP on its left side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.

alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN
  • MetaCyc:RIBOKIN-RXN

    Source assertion: Native RIBOKIN-RXN includes ATP on its left side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.

    Source locationXPath /ptools-xml/Reaction/left/Compound[@frameid="ATP"]
alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN		produces

Native RIBOKIN-RXN includes CPD-15317 on its right side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.

alpha-D-Ribose 5-phosphate(2-)
CHEBI:140679
  • MetaCyc:RIBOKIN-RXN

    Source assertion: Native RIBOKIN-RXN includes CPD-15317 on its right side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.

    Source locationXPath /ptools-xml/Reaction/right/Compound[@frameid="CPD-15317"]
  • MetaCyc:RIBOKIN-PWY

    Source assertion: The META narrative specifies alpha-D-ribofuranose (CPD-10330) phosphorylation to alpha-D-ribose 5-phosphate (CPD-15318); formal reaction-layout remains a broader furanose class. This edge is that declared refinement, not an exact generic Rhea alias.

    Source locationXPath /ptools-xml/Pathway/comment
alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN		produces

Native RIBOKIN-RXN includes ADP on its right side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.

ADP(3-)
CHEBI:456216
  • MetaCyc:RIBOKIN-RXN

    Source assertion: Native RIBOKIN-RXN includes ADP on its right side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.

    Source locationXPath /ptools-xml/Reaction/right/Compound[@frameid="ADP"]
alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN		produces

Native RIBOKIN-RXN includes PROTON on its right side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.

hydron
CHEBI:15378
  • MetaCyc:RIBOKIN-RXN

    Source assertion: Native RIBOKIN-RXN includes PROTON on its right side. The pathway-specific equation refines only its generic sugar classes to the alpha forms specified by the META pathway narrative.

    Source locationXPath /ptools-xml/Reaction/right/Compound[@frameid="PROTON"]
ATP(4-)
CHEBI:30616		consumes

Native transport left participant ATP occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

ATP-dependent D-ribopyranose uptake
MetaCyc:ABC-28-RXN
  • EcoCyc:ABC-28-RXN

    Source assertion: Native transport left participant ATP occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

    Source locationXPath /ptools-xml/Reaction/left[Compound[@frameid="ATP"] and compartment/cco[@frameid="CCO-IN"]]
D-ribopyranose
CHEBI:47006		consumes

Native transport left participant D-Ribopyranose occupies CCO-OUT; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

ATP-dependent D-ribopyranose uptake
MetaCyc:ABC-28-RXN
  • EcoCyc:ABC-28-RXN

    Source assertion: Native transport left participant D-Ribopyranose occupies CCO-OUT; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

    Source locationXPath /ptools-xml/Reaction/left[Compound[@frameid="D-Ribopyranose"] and compartment/cco[@frameid="CCO-OUT"]]
water
CHEBI:15377		consumes

Native transport left participant WATER occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

ATP-dependent D-ribopyranose uptake
MetaCyc:ABC-28-RXN
  • EcoCyc:ABC-28-RXN

    Source assertion: Native transport left participant WATER occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

    Source locationXPath /ptools-xml/Reaction/left[Compound[@frameid="WATER"] and compartment/cco[@frameid="CCO-IN"]]
ATP-dependent D-ribopyranose uptake
MetaCyc:ABC-28-RXN		produces

Native transport right participant ADP occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

ADP(3-)
CHEBI:456216
  • EcoCyc:ABC-28-RXN

    Source assertion: Native transport right participant ADP occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

    Source locationXPath /ptools-xml/Reaction/right[Compound[@frameid="ADP"] and compartment/cco[@frameid="CCO-IN"]]
ATP-dependent D-ribopyranose uptake
MetaCyc:ABC-28-RXN		produces

Native transport right participant Pi occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

hydrogenphosphate
CHEBI:43474
  • EcoCyc:ABC-28-RXN

    Source assertion: Native transport right participant Pi occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

    Source locationXPath /ptools-xml/Reaction/right[Compound[@frameid="Pi"] and compartment/cco[@frameid="CCO-IN"]]
ATP-dependent D-ribopyranose uptake
MetaCyc:ABC-28-RXN		produces

Native transport right participant D-Ribopyranose occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

D-ribopyranose
CHEBI:47006
  • EcoCyc:ABC-28-RXN

    Source assertion: Native transport right participant D-Ribopyranose occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

    Source locationXPath /ptools-xml/Reaction/right[Compound[@frameid="D-Ribopyranose"] and compartment/cco[@frameid="CCO-IN"]]
ATP-dependent D-ribopyranose uptake
MetaCyc:ABC-28-RXN		produces

Native transport right participant PROTON occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

hydron
CHEBI:15378
  • EcoCyc:ABC-28-RXN

    Source assertion: Native transport right participant PROTON occupies CCO-IN; coefficient is one. D-ribopyranose is a class with distinct external-input/internal-output roles, not a furanose or an exact beta-only transport claim.

    Source locationXPath /ptools-xml/Reaction/right[Compound[@frameid="PROTON"] and compartment/cco[@frameid="CCO-IN"]]
beta-D-ribopyranose => beta-D-ribofuranose
RHEA:25433		provides_input_for

The narrative places beta-pyranose/furanose conversion before spontaneous alpha/beta furanose interconversion; beta-D-ribofuranose is the shared chemical intermediate.

spontaneous beta-D-ribofuranose to alpha-D-ribofuranose interconversion
MetaCyc:RXN-14904
  • MetaCyc:RIBOKIN-PWY

    Source assertion: The narrative places beta-pyranose/furanose conversion before spontaneous alpha/beta furanose interconversion; beta-D-ribofuranose is the shared chemical intermediate.

    Source locationXPath /ptools-xml/Pathway/comment
spontaneous beta-D-ribofuranose to alpha-D-ribofuranose interconversion
MetaCyc:RXN-14904		provides_input_for

Spontaneous anomer interconversion supplies the alpha-furanose substrate assigned to ribokinase by the META narrative.

alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN
  • MetaCyc:RIBOKIN-PWY

    Source assertion: Spontaneous anomer interconversion supplies the alpha-furanose substrate assigned to ribokinase by the META narrative.

    Source locationXPath /ptools-xml/Pathway/comment
ATP-dependent D-ribopyranose uptake
MetaCyc:ABC-28-RXN		provides_input_for

The source places ABC uptake before pyranase and reports RbsB binding of beta-D-ribopyranose, with facilitation of its transport explicitly presumed. The formal transporter substrate remains the broader D-ribopyranose class.

beta-D-ribopyranose => beta-D-ribofuranose
RHEA:25433
  • MetaCyc:RIBOKIN-PWY

    Source assertion: The source places ABC uptake before pyranase and reports RbsB binding of beta-D-ribopyranose, with facilitation of its transport explicitly presumed. The formal transporter substrate remains the broader D-ribopyranose class.

    Source locationXPath /ptools-xml/Pathway/comment
alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN		provides_input_for

Native pathway-links connect the generic ribose-furanose 5-phosphate output to NONOXIPENT-PWY. This opaque pathway interface preserves that source link without asserting an exact alpha/cyclic/open-chain identity or expanding downstream reactions.

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

    Source assertion: Native pathway-links connect the generic ribose-furanose 5-phosphate output to NONOXIPENT-PWY. This opaque pathway interface preserves that source link without asserting an exact alpha/cyclic/open-chain identity or expanding downstream reactions.

    Source locationXPath /ptools-xml/Pathway/pathway-link[link-target/Pathway[@frameid="NONOXIPENT-PWY"]]
alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN		provides_input_for

Native pathway-links connect the generic ribose-furanose 5-phosphate output to PWY0-662. This opaque pathway interface preserves that source link without asserting an exact alpha/cyclic/open-chain identity or expanding downstream reactions.

PRPP biosynthesis
MetaCyc:PWY0-662
  • MetaCyc:RIBOKIN-PWY

    Source assertion: Native pathway-links connect the generic ribose-furanose 5-phosphate output to PWY0-662. This opaque pathway interface preserves that source link without asserting an exact alpha/cyclic/open-chain identity or expanding downstream reactions.

    Source locationXPath /ptools-xml/Pathway/pathway-link[link-target/Pathway[@frameid="PWY0-662"]]
D-ribose pyranase
EcoCyc:CPLX0-7646		catalyzes

The native enzymatic-reaction assigns CPLX0-7646 as enzyme; the two pyranase complexes are alternatives, not obligate partners. The kinase edge uses the explicitly declared pathway-specific alpha refinement.

beta-D-ribopyranose => beta-D-ribofuranose
RHEA:25433
  • EcoCyc:ENZRXN0-6479

    Source assertion: The native enzymatic-reaction assigns CPLX0-7646 as enzyme; the two pyranase complexes are alternatives, not obligate partners. The kinase edge uses the explicitly declared pathway-specific alpha refinement.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/enzyme
L-fucose mutarotase
EcoCyc:CPLX0-7645		catalyzes

The native enzymatic-reaction assigns CPLX0-7645 as enzyme; the two pyranase complexes are alternatives, not obligate partners. The kinase edge uses the explicitly declared pathway-specific alpha refinement.

beta-D-ribopyranose => beta-D-ribofuranose
RHEA:25433
  • EcoCyc:ENZRXN0-8627

    Source assertion: The native enzymatic-reaction assigns CPLX0-7645 as enzyme; the two pyranase complexes are alternatives, not obligate partners. The kinase edge uses the explicitly declared pathway-specific alpha refinement.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/enzyme
ribokinase
EcoCyc:CPLX0-7647		catalyzes

The native enzymatic-reaction assigns CPLX0-7647 as enzyme; the two pyranase complexes are alternatives, not obligate partners. The kinase edge uses the explicitly declared pathway-specific alpha refinement.

alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN
  • EcoCyc:RIBOKIN-ENZRXN

    Source assertion: The native enzymatic-reaction assigns CPLX0-7647 as enzyme; the two pyranase complexes are alternatives, not obligate partners. The kinase edge uses the explicitly declared pathway-specific alpha refinement.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/enzyme
ribose ABC transporter
EcoCyc:ABC-28-CPLX		catalyzes

The source describes a high-affinity ATP-dependent ribose uptake system and active RbsAC2B reconstituted in liposomes; it proposes a cofactor-dependent association/dissociation cycle.

ATP-dependent D-ribopyranose uptake
MetaCyc:ABC-28-RXN
  • EcoCyc:ABC-28-CPLX

    Source assertion: The source describes a high-affinity ATP-dependent ribose uptake system and active RbsAC2B reconstituted in liposomes; it proposes a cofactor-dependent association/dissociation cycle.

    Source locationXPath /ptools-xml/Protein/comment
D-ribose pyranase
EcoCyc:CPLX0-7646		has_part

The current native complex lists 10 copy/copies of EG10817-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

D-ribose pyranase
UniProtKB:P04982
  • EcoCyc:CPLX0-7646

    Source assertion: The current native complex lists 10 copy/copies of EG10817-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="EG10817-MONOMER"]]/coefficient
  • EcoCyc:EG10817-MONOMER

    Source assertion: The exact native protein frame EG10817-MONOMER carries the UNIPROT unification link P04982.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P04982"]
L-fucose mutarotase
EcoCyc:CPLX0-7645		has_part

The current native complex lists 10 copy/copies of EG10355-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

L-fucose mutarotase
UniProtKB:P0AEN8
  • EcoCyc:CPLX0-7645

    Source assertion: The current native complex lists 10 copy/copies of EG10355-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

    Source locationXPath /ptools-xml/Protein/component[Protein[@frameid="EG10355-MONOMER"]]/coefficient
  • EcoCyc:EG10355-MONOMER

    Source assertion: The exact native protein frame EG10355-MONOMER carries the UNIPROT unification link P0AEN8.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0AEN8"]
ribokinase
EcoCyc:CPLX0-7647		has_part

The current native complex lists 2 copy/copies of RIBOKIN-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

Ribokinase
UniProtKB:P0A9J6
  • EcoCyc:CPLX0-7647

    Source assertion: The current native complex lists 2 copy/copies of RIBOKIN-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

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

    Source assertion: The exact native protein frame RIBOKIN-MONOMER carries the UNIPROT unification link P0A9J6.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0A9J6"]
ribose ABC transporter
EcoCyc:ABC-28-CPLX		has_part

Native RbsAC2B contains one RbsA chain. Its two ATP-binding domains are within that chain and do not imply two RbsA subunits; frozen 2019 PathBank instead specifies two RbsA chains.

Ribose import ATP-binding protein RbsA
UniProtKB:P04983
  • EcoCyc:ABC-28-CPLX

    Source assertion: The current native complex lists 1 copy/copies of RBSA-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

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

    Source assertion: The exact native protein frame RBSA-MONOMER carries the UNIPROT unification link P04983.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P04983"]
  • EcoCyc:RBSA-MONOMER

    Source assertion: The RbsA monomer is annotated with an ABC-ABC domain architecture. Its two ATP-binding domains belong to the same polypeptide rather than establishing a two-chain assembly.

    Source locationXPath /ptools-xml/Protein/comment
  • PathBank:SMP0002114

    Source assertion: The frozen 2019 transporter Complex4095 assigns coefficient 2 to Protein5876, whose reference identifies UniProt P04983. This historical two-RbsA-chain assertion conflicts with current native A1C2B1 and is retained as a conflict, not adopted as current stoichiometry.

    Source locationBioPAX Complex4095, Protein5876 stoichiometry, ProteinReference5876 and UniProt_P04983 xref; XPath //*[@*[local-name()="ID"]="ProteinComplex/4095_Inner_Membrane" or @*[local-name()="ID"]="Protein/5876_Inner_Membrane/Stoichiometry/2.0" or @*[local-name()="ID"]="ProteinReference/5876" or @*[local-name()="ID"]="Reference/UniProt_P04983"]
ribose ABC transporter
EcoCyc:ABC-28-CPLX		has_part

The current native complex lists 2 copy/copies of RBSC-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

Ribose import permease protein RbsC
UniProtKB:P0AGI1
  • EcoCyc:ABC-28-CPLX

    Source assertion: The current native complex lists 2 copy/copies of RBSC-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

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

    Source assertion: The exact native protein frame RBSC-MONOMER carries the UNIPROT unification link P0AGI1.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P0AGI1"]
ribose ABC transporter
EcoCyc:ABC-28-CPLX		has_part

The current native complex lists 1 copy/copies of RBSB-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

Ribose import binding protein RbsB
UniProtKB:P02925
  • EcoCyc:ABC-28-CPLX

    Source assertion: The current native complex lists 1 copy/copies of RBSB-MONOMER. This source-defined assembly is not equated to differently tagged, chromatographically estimated, or historical PathBank assemblies.

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

    Source assertion: The exact native protein frame RBSB-MONOMER carries the UNIPROT unification link P02925.

    Source locationXPath /ptools-xml/Protein/dblink[dblink-db="UNIPROT" and dblink-oid="P02925"]
ribose ABC transporter
EcoCyc:ABC-28-CPLX		has_cofactor

The source proposes RbsA-ATP-Mg2+ association with ribose-loaded RbsBC. This is a cofactor-dependent transport-cycle state, not permanent simultaneous occupancy of every cycle intermediate.

magnesium(2+)
CHEBI:18420
  • EcoCyc:ABC-28-CPLX

    Source assertion: The source proposes RbsA-ATP-Mg2+ association with ribose-loaded RbsBC. This is a cofactor-dependent transport-cycle state, not permanent simultaneous occupancy of every cycle intermediate.

    Source locationXPath /ptools-xml/Protein/comment
ribokinase
EcoCyc:CPLX0-7647		has_cofactor

Native ribokinase lists K+ as a cofactor; this direct slot does not specify intracellular occupancy or simultaneous use of alternative monovalent ions.

potassium(1+)
CHEBI:29103
  • EcoCyc:RIBOKIN-ENZRXN

    Source assertion: Native ribokinase lists K+ as a cofactor; this direct slot does not specify intracellular occupancy or simultaneous use of alternative monovalent ions.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/cofactor[Compound[@frameid="K+"]]
ribokinase
EcoCyc:CPLX0-7647		has_cofactor

Native ribokinase lists Mg2+ as a cofactor; this direct slot does not itself establish intracellular occupancy.

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

    Source assertion: Native ribokinase lists Mg2+ as a cofactor; this direct slot does not itself establish intracellular occupancy.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/cofactor[Compound[@frameid="MG+2"]]
  • UniProtKB:P0A9J6

    Source assertion: Reviewed ribokinase requires a divalent cation, with magnesium considered most likely in vivo; metal-nucleotide chelation as the actual substrate is explicitly probable rather than directly established intracellular occupancy.

    Source locationcomments[commentType=COFACTOR]
ribokinase
EcoCyc:CPLX0-7647		has_cofactor

Reviewed ribokinase is also active with Mn2+; this is an alternative divalent cofactor, not evidence that magnesium and manganese are jointly required. The actual metal-nucleotide substrate assignment is marked probable.

manganese(2+)
CHEBI:29035
  • UniProtKB:P0A9J6

    Source assertion: Reviewed ribokinase is also active with Mn2+; this is an alternative divalent cofactor, not evidence that magnesium and manganese are jointly required. The actual metal-nucleotide substrate assignment is marked probable.

    Source locationcomments[commentType=COFACTOR]
ammonium
CHEBI:28938		activates

Ammonium can also activate ribokinase as an alternative monovalent ion; potassium is considered the most likely occupant in vivo. Ion-induced affinity change is marked probable.

ribokinase
EcoCyc:CPLX0-7647
  • UniProtKB:P0A9J6

    Source assertion: Ammonium can also activate ribokinase as an alternative monovalent ion; potassium is considered the most likely occupant in vivo. Ion-induced affinity change is marked probable.

    Source locationcomments[commentType=ACTIVITY REGULATION]
hydrogenphosphate
CHEBI:43474		activates

The native positive regulation event assigns inorganic phosphate activation to ribokinase activity; this is regulation rather than phosphate incorporation into ribose.

alpha-D-ribofuranose phosphorylation to alpha-D-ribofuranose 5-phosphate
MetaCyc:RIBOKIN-RXN
  • EcoCyc:REG0-9220

    Source assertion: The native positive regulation event assigns inorganic phosphate activation to ribokinase activity; this is regulation rather than phosphate incorporation into ribose.

    Source locationXPath /ptools-xml/Regulation[mode="+"]/regulator/Compound[@frameid="Pi"]
  • EcoCyc:RIBOKIN-ENZRXN

    Source assertion: The kinetic commentary describes ribose Km measurements across pH values with or without phosphate, arsenate and vanadate activators. Exact arsenate/vanadate chemical forms are not resolved here.

    Source locationXPath /ptools-xml/Enzymatic-Reaction/comment
D-ribose pyranase
UniProtKB:P04982		located_in

The native protein location slot places this protein in the Gram-negative cytosol; this is a source annotation, not a newly measured localization.

cytosol
GO:0005829
  • EcoCyc:EG10817-MONOMER

    Source assertion: The native protein location slot places this protein in the Gram-negative cytosol; this is a source annotation, not a newly measured localization.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
Ribokinase
UniProtKB:P0A9J6		located_in

The native protein location slot places this protein in the Gram-negative cytosol; this is a source annotation, not a newly measured localization.

cytosol
GO:0005829
  • EcoCyc:RIBOKIN-MONOMER

    Source assertion: The native protein location slot places this protein in the Gram-negative cytosol; this is a source annotation, not a newly measured localization.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
Ribose operon repressor
UniProtKB:P0ACQ0		located_in

The native protein location slot places this protein in the Gram-negative cytosol; this is a source annotation, not a newly measured localization.

cytosol
GO:0005829
  • EcoCyc:PD03867

    Source assertion: The native protein location slot places this protein in the Gram-negative cytosol; this is a source annotation, not a newly measured localization.

    Source locationXPath /ptools-xml/Protein/location/cco[@frameid="CCI-CYTOSOL-GN"]
L-fucose mutarotase
UniProtKB:P0AEN8		located_in

Reviewed FucU is annotated to cytoplasm with curator-inferred evidence (ECO:0000305), not a direct localization measurement.

cytoplasm
GO:0005737
  • UniProtKB:P0AEN8

    Source assertion: Reviewed FucU is annotated to cytoplasm with curator-inferred evidence (ECO:0000305), not a direct localization measurement.

    Source locationcomments[commentType=SUBCELLULAR LOCATION]
Ribose import ATP-binding protein RbsA
UniProtKB:P04983		located_in

RbsA is annotated to the bacterial cell inner membrane as a peripheral membrane protein, using HAMAP and curator inference.

plasma membrane
GO:0005886
  • UniProtKB:P04983

    Source assertion: RbsA is annotated to the bacterial cell inner membrane as a peripheral membrane protein, using HAMAP and curator inference.

    Source locationcomments[commentType=SUBCELLULAR LOCATION]
Ribose import permease protein RbsC
UniProtKB:P0AGI1		located_in

Reviewed RbsC is annotated as an inner-membrane multipass permease. This edge reports the reviewed localization annotation, not the construct-specific topology of a newly assayed preparation.

plasma membrane
GO:0005886
  • UniProtKB:P0AGI1

    Source assertion: Reviewed RbsC is annotated as an inner-membrane multipass permease. This edge reports the reviewed localization annotation, not the construct-specific topology of a newly assayed preparation.

    Source locationcomments[commentType=SUBCELLULAR LOCATION]
Ribose import binding protein RbsB
UniProtKB:P02925		located_in

Reviewed RbsB is periplasmic; this binding component is not the transmembrane permease.

periplasmic space
GO:0042597
  • UniProtKB:P02925

    Source assertion: Reviewed RbsB is periplasmic; this binding component is not the transmembrane permease.

    Source locationcomments[commentType=SUBCELLULAR LOCATION]
Ribose operon repressor
UniProtKB:P0ACQ0		inhibits

Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsD
Entrez:948267
  • EcoCyc:REG0-5371

    Source assertion: Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="-"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10817.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10817"]
  • Entrez:948267

    Source assertion: The exact MG1655 NCBI Gene 948267 original identifies rbsD/b3748 and explicitly cross-references EcoCyc EG10817. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10817"] | //Gene-ref_locus | //Gene-ref_locus-tag
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsD
Entrez:948267
  • EcoCyc:REG0-5370

    Source assertion: Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="+"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10817.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10817"]
  • Entrez:948267

    Source assertion: The exact MG1655 NCBI Gene 948267 original identifies rbsD/b3748 and explicitly cross-references EcoCyc EG10817. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10817"] | //Gene-ref_locus | //Gene-ref_locus-tag
Ribose operon repressor
UniProtKB:P0ACQ0		inhibits

Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsA
Entrez:948264
  • EcoCyc:REG0-5371

    Source assertion: Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="-"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10814.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10814"]
  • Entrez:948264

    Source assertion: The exact MG1655 NCBI Gene 948264 original identifies rbsA/b3749 and explicitly cross-references EcoCyc EG10814. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10814"] | //Gene-ref_locus | //Gene-ref_locus-tag
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsA
Entrez:948264
  • EcoCyc:REG0-5370

    Source assertion: Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="+"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10814.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10814"]
  • Entrez:948264

    Source assertion: The exact MG1655 NCBI Gene 948264 original identifies rbsA/b3749 and explicitly cross-references EcoCyc EG10814. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10814"] | //Gene-ref_locus | //Gene-ref_locus-tag
Ribose operon repressor
UniProtKB:P0ACQ0		inhibits

Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsC
Entrez:948262
  • EcoCyc:REG0-5371

    Source assertion: Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="-"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10816.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10816"]
  • Entrez:948262

    Source assertion: The exact MG1655 NCBI Gene 948262 original identifies rbsC/b3750 and explicitly cross-references EcoCyc EG10816. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10816"] | //Gene-ref_locus | //Gene-ref_locus-tag
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsC
Entrez:948262
  • EcoCyc:REG0-5370

    Source assertion: Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="+"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10816.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10816"]
  • Entrez:948262

    Source assertion: The exact MG1655 NCBI Gene 948262 original identifies rbsC/b3750 and explicitly cross-references EcoCyc EG10816. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10816"] | //Gene-ref_locus | //Gene-ref_locus-tag
Ribose operon repressor
UniProtKB:P0ACQ0		inhibits

Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsB
Entrez:948261
  • EcoCyc:REG0-5371

    Source assertion: Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="-"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10815.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10815"]
  • Entrez:948261

    Source assertion: The exact MG1655 NCBI Gene 948261 original identifies rbsB/b3751 and explicitly cross-references EcoCyc EG10815. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10815"] | //Gene-ref_locus | //Gene-ref_locus-tag
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsB
Entrez:948261
  • EcoCyc:REG0-5370

    Source assertion: Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="+"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10815.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10815"]
  • Entrez:948261

    Source assertion: The exact MG1655 NCBI Gene 948261 original identifies rbsB/b3751 and explicitly cross-references EcoCyc EG10815. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10815"] | //Gene-ref_locus | //Gene-ref_locus-tag
Ribose operon repressor
UniProtKB:P0ACQ0		inhibits

Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsK
Entrez:948260
  • EcoCyc:REG0-5371

    Source assertion: Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="-"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10818.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10818"]
  • Entrez:948260

    Source assertion: The exact MG1655 NCBI Gene 948260 original identifies rbsK/b3752 and explicitly cross-references EcoCyc EG10818. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10818"] | //Gene-ref_locus | //Gene-ref_locus-tag
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsK
Entrez:948260
  • EcoCyc:REG0-5370

    Source assertion: Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="+"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10818.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10818"]
  • Entrez:948260

    Source assertion: The exact MG1655 NCBI Gene 948260 original identifies rbsK/b3752 and explicitly cross-references EcoCyc EG10818. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10818"] | //Gene-ref_locus | //Gene-ref_locus-tag
Ribose operon repressor
UniProtKB:P0ACQ0		inhibits

Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsR
Entrez:948266
  • EcoCyc:REG0-5371

    Source assertion: Native REG0-5371 assigns - regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="-"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10819.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10819"]
  • Entrez:948266

    Source assertion: The exact MG1655 NCBI Gene 948266 original identifies rbsR/b3753 and explicitly cross-references EcoCyc EG10819. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10819"] | //Gene-ref_locus | //Gene-ref_locus-tag
CRP-cyclic-AMP DNA-binding transcriptional dual regulator
EcoCyc:CPLX0-226		activates

Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

rbsR
Entrez:948266
  • EcoCyc:REG0-5370

    Source assertion: Native REG0-5370 assigns + regulation of rbsDp (PM00290). The edge concerns transcription from this promoter, not direct control of the encoded protein activity.

    Source locationXPath /ptools-xml/Regulation[mode="+"]/regulated-entity/Promoter[@frameid="PM00290"]
  • EcoCyc:TU00206

    Source assertion: The native rbsDACBKR transcription unit includes exact gene frame EG10819.

    Source locationXPath /ptools-xml/Transcription-Unit/component/Gene[@frameid="EG10819"]
  • Entrez:948266

    Source assertion: The exact MG1655 NCBI Gene 948266 original identifies rbsR/b3753 and explicitly cross-references EcoCyc EG10819. This binds the native transcription-unit component to the Entrez target.

    Source locationXPath //Dbtag[Dbtag_db="ECOCYC" and Dbtag_tag/Object-id/Object-id_str="EG10819"] | //Gene-ref_locus | //Gene-ref_locus-tag
HTH-type transcriptional regulator YidZ
UniProtKB:P31463		inhibits

The native RNA-seq-backed regulation event assigns YidZ negative control of EG10817 (rbsD) transcription; this event is not a direct enzyme inhibition or purified protein-binding assay.

rbsD
Entrez:948267
  • EcoCyc:REG0-15980

    Source assertion: The native RNA-seq-backed regulation event assigns YidZ negative control of EG10817 (rbsD) transcription; this event is not a direct enzyme inhibition or purified protein-binding assay.

    Source locationXPath /ptools-xml/Regulation[mode="-"]/regulated-entity/Gene[@frameid="EG10817"]
  • PMID:34428301

    Source assertion: The YidZ results identify rbsD upregulation in the deletion strain. RNA-seq used MG1655 derivatives in M9 glucose; the associated binding experiment used C-terminal 8-myc constructs. No exact rbsD fold change is claimed without the supplement.

    Source locationBioC passages: YidZ results containing rbsD; Materials and methods, RNA sequencing and ChIP-exo
RbsR-D-ribose
EcoCyc:MONOMER-60		has_part

The native RbsR-D-ribose complex lists component PD03867; no coefficient is supplied, so no oligomer or ligand copy number is inferred.

Ribose operon repressor
UniProtKB:P0ACQ0
  • EcoCyc:MONOMER-60

    Source assertion: The native RbsR-D-ribose complex lists component PD03867; no coefficient is supplied, so no oligomer or ligand copy number is inferred.

    Source locationXPath /ptools-xml/Protein/component/Protein[@frameid="PD03867"]
RbsR-D-ribose
EcoCyc:MONOMER-60		has_part

The native RbsR-D-ribose complex lists component RIBOSE; no coefficient is supplied, so no oligomer or ligand copy number is inferred.

D-ribose
CHEBI:16988
  • EcoCyc:MONOMER-60

    Source assertion: The native RbsR-D-ribose complex lists component RIBOSE; no coefficient is supplied, so no oligomer or ligand copy number is inferred.

    Source locationXPath /ptools-xml/Protein/component/Compound[@frameid="RIBOSE"]
D-ribose
CHEBI:16988		inhibits

D-ribose binding reduces RbsR DNA-binding affinity and relieves repression of the ribose operon. This inhibition concerns the repressor DNA-binding function, not destruction of RbsR or direct inhibition of pathway chemistry.

Ribose operon repressor
UniProtKB:P0ACQ0
  • EcoCyc:PD03867

    Source assertion: D-ribose binding reduces RbsR DNA-binding affinity and relieves repression of the ribose operon. This inhibition concerns the repressor DNA-binding function, not destruction of RbsR or direct inhibition of pathway chemistry.

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

The native CRP-cAMP assembly lists PC00004; the component slot supplies no coefficient and is not evidence for a specific number of cAMP ligands.

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

    Source assertion: The native CRP-cAMP assembly lists PC00004; the component slot supplies no coefficient and is not evidence for a specific number of cAMP ligands.

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

The native CRP-cAMP assembly lists CAMP; the component slot supplies no coefficient and is not evidence for a specific number of cAMP ligands.

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

    Source assertion: The native CRP-cAMP assembly lists CAMP; the component slot supplies no coefficient and is not evidence for a specific number of cAMP ligands.

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

The native CRP complex contains two PD00257 chains; this component slot supplies the homodimer stoichiometry.

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

    Source assertion: The native CRP complex contains two PD00257 chains; this component slot supplies the homodimer stoichiometry.

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

    Source assertion: The reviewed P0ACJ8 entry explicitly cross-references EcoCyc:PD00257, binding the native CRP component to its UniProt identity.

    Source locationresults[primaryAccession=P0ACJ8].uniProtKBCrossReferences[database=BioCyc,id=EcoCyc:PD00257]

References

Curation history