pyrimidine deoxyribonucleotide salvage

GO:0010139

This complete five-reaction Escherichia coli implementation converts 2'-deoxycytidine through 2'-deoxyuridine to dUMP, or uses deoxyuridine-derived 2-deoxy-alpha-D-ribose 1-phosphate to salvage thymine through thymidine to dTMP. Cdd deaminates deoxycytidine, the reversible DeoA phosphorolyses supply or consume the sugar phosphate, and Tdk phosphorylates deoxyuridine or thymidine. The selected biochemical boundary matches the five-reaction native EcoCyc pathway; NupC/NupG uptake is incoming context and subsequent nucleotide phosphorylation is outside it. MG1655 is the native protein-annotation scope; primary K-12 mutant studies and E. coli B enzyme studies do not establish constitutive wild-type MG1655 flux. Tdk is represented by its source-defined multimeric assembly without fixing its stoichiometry across conditions. This GO process implementation is not asserted equivalent to the differently composed MetaCyc PWY-7199 pathway.

Pathway type

Organism scope

Escherichia coli str. K-12 substr. MG1655 NCBITaxon:511145

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Pathway network

27 nodes · 41 asserted directed edges

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Reaction / activity
Chemical / cofactor
Protein / complex
Pathway
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Escherichia coli str. K-12 substr. MG1655 `NCBITaxon:511145`	taxon
2'-deoxycytidine `CHEBI:15698`	small molecule
water `CHEBI:15377`	small molecule
hydron `CHEBI:15378`	small molecule
2'-deoxyuridine `CHEBI:16450`	small molecule
ammonium `CHEBI:28938`	small molecule
hydrogenphosphate `CHEBI:43474`	small molecule
2-deoxy-alpha-D-ribose 1-phosphate(2-) `CHEBI:57259`	small molecule
uracil `CHEBI:17568`	small molecule
thymine `CHEBI:17821`	small molecule
thymidine `CHEBI:17748`	small molecule
ATP(4-) `CHEBI:30616`	small molecule
dUMP(2-) `CHEBI:246422`	small molecule
ADP(3-) `CHEBI:456216`	small molecule
dTMP(2-) `CHEBI:63528`	small molecule
zinc(2+) `CHEBI:29105`	cofactor
Cytidine deaminase `UniProtKB:P0ABF6`	protein
Thymidine phosphorylase `UniProtKB:P07650`	protein
Thymidine kinase `UniProtKB:P23331`	protein
cytidine/deoxycytidine deaminase `MetaCyc:CYTIDEAM-CPLX`	complex
thymidine phosphorylase / uracil phosphorylase `MetaCyc:DEOA-CPLX`	complex
thymidine kinase / deoxyuridine kinase `MetaCyc:CPLX0-8261`	complex
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	molecular activity	left to right
2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	molecular activity	left to right
2-deoxy-alpha-D-ribose 1-phosphate + thymine => thymidine + phosphate `RHEA:16039`	molecular activity	right to left
2'-deoxyuridine + ATP => dUMP + ADP + H(+) `RHEA:28207`	molecular activity	left to right
thymidine + ATP => dTMP + ADP + H(+) `RHEA:19130`	molecular activity	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
2'-deoxycytidine `CHEBI:15698`	consumes	2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	RHEA:13434 Source assertion: Rhea 13434 assigns CHEBI:15698 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_5580']; http://rdf.rhea-db.org/Participant_13433_compound_5580/rh:compound; http://rdf.rhea-db.org/Compound_5580/rh:chebi`
water `CHEBI:15377`	consumes	2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	RHEA:13434 Source assertion: Rhea 13434 assigns CHEBI:15377 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_1283']; http://rdf.rhea-db.org/Participant_13433_compound_1283/rh:compound; http://rdf.rhea-db.org/Compound_1283/rh:chebi`
hydron `CHEBI:15378`	consumes	2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	RHEA:13434 Source assertion: Rhea 13434 assigns CHEBI:15378 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_3249']; http://rdf.rhea-db.org/Participant_13433_compound_3249/rh:compound; http://rdf.rhea-db.org/Compound_3249/rh:chebi`
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	produces	2'-deoxyuridine `CHEBI:16450`	RHEA:13434 Source assertion: Rhea 13434 assigns CHEBI:16450 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_5154']; http://rdf.rhea-db.org/Participant_13433_compound_5154/rh:compound; http://rdf.rhea-db.org/Compound_5154/rh:chebi`
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	produces	ammonium `CHEBI:28938`	RHEA:13434 Source assertion: Rhea 13434 assigns CHEBI:28938 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_1012']; http://rdf.rhea-db.org/Participant_13433_compound_1012/rh:compound; http://rdf.rhea-db.org/Compound_1012/rh:chebi`
2'-deoxyuridine `CHEBI:16450`	consumes	2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	RHEA:22825 Source assertion: Rhea 22825 assigns CHEBI:16450 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_22824_compound_5154']; http://rdf.rhea-db.org/Participant_22824_compound_5154/rh:compound; http://rdf.rhea-db.org/Compound_5154/rh:chebi`
hydrogenphosphate `CHEBI:43474`	consumes	2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	RHEA:22825 Source assertion: Rhea 22825 assigns CHEBI:43474 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_22824_compound_5518']; http://rdf.rhea-db.org/Participant_22824_compound_5518/rh:compound; http://rdf.rhea-db.org/Compound_5518/rh:chebi`
2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	produces	2-deoxy-alpha-D-ribose 1-phosphate(2-) `CHEBI:57259`	RHEA:22825 Source assertion: Rhea 22825 assigns CHEBI:57259 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_22824_compound_3098']; http://rdf.rhea-db.org/Participant_22824_compound_3098/rh:compound; http://rdf.rhea-db.org/Compound_3098/rh:chebi`
2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	produces	uracil `CHEBI:17568`	RHEA:22825 Source assertion: Rhea 22825 assigns CHEBI:17568 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_22824_compound_4063']; http://rdf.rhea-db.org/Participant_22824_compound_4063/rh:compound; http://rdf.rhea-db.org/Compound_4063/rh:chebi`
2-deoxy-alpha-D-ribose 1-phosphate(2-) `CHEBI:57259`	consumes	2-deoxy-alpha-D-ribose 1-phosphate + thymine => thymidine + phosphate `RHEA:16039`	RHEA:16039 Source assertion: Rhea 16039 assigns CHEBI:57259 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16039']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16037_compound_3098']; http://rdf.rhea-db.org/Participant_16037_compound_3098/rh:compound; http://rdf.rhea-db.org/Compound_3098/rh:chebi`
thymine `CHEBI:17821`	consumes	2-deoxy-alpha-D-ribose 1-phosphate + thymine => thymidine + phosphate `RHEA:16039`	RHEA:16039 Source assertion: Rhea 16039 assigns CHEBI:17821 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16039']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16037_compound_2794']; http://rdf.rhea-db.org/Participant_16037_compound_2794/rh:compound; http://rdf.rhea-db.org/Compound_2794/rh:chebi`
2-deoxy-alpha-D-ribose 1-phosphate + thymine => thymidine + phosphate `RHEA:16039`	produces	thymidine `CHEBI:17748`	RHEA:16039 Source assertion: Rhea 16039 assigns CHEBI:17748 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16039']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16037_compound_4636']; http://rdf.rhea-db.org/Participant_16037_compound_4636/rh:compound; http://rdf.rhea-db.org/Compound_4636/rh:chebi`
2-deoxy-alpha-D-ribose 1-phosphate + thymine => thymidine + phosphate `RHEA:16039`	produces	hydrogenphosphate `CHEBI:43474`	RHEA:16039 Source assertion: Rhea 16039 assigns CHEBI:43474 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16039']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16037_compound_5518']; http://rdf.rhea-db.org/Participant_16037_compound_5518/rh:compound; http://rdf.rhea-db.org/Compound_5518/rh:chebi`
2'-deoxyuridine `CHEBI:16450`	consumes	2'-deoxyuridine + ATP => dUMP + ADP + H(+) `RHEA:28207`	RHEA:28207 Source assertion: Rhea 28207 assigns CHEBI:16450 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/28207']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/28206_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_28206_compound_5154']; http://rdf.rhea-db.org/Participant_28206_compound_5154/rh:compound; http://rdf.rhea-db.org/Compound_5154/rh:chebi`
ATP(4-) `CHEBI:30616`	consumes	2'-deoxyuridine + ATP => dUMP + ADP + H(+) `RHEA:28207`	RHEA:28207 Source assertion: Rhea 28207 assigns CHEBI:30616 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/28207']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/28206_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_28206_compound_6372']; http://rdf.rhea-db.org/Participant_28206_compound_6372/rh:compound; http://rdf.rhea-db.org/Compound_6372/rh:chebi`
2'-deoxyuridine + ATP => dUMP + ADP + H(+) `RHEA:28207`	produces	dUMP(2-) `CHEBI:246422`	RHEA:28207 Source assertion: Rhea 28207 assigns CHEBI:246422 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/28207']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/28206_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_28206_compound_4655']; http://rdf.rhea-db.org/Participant_28206_compound_4655/rh:compound; http://rdf.rhea-db.org/Compound_4655/rh:chebi`
2'-deoxyuridine + ATP => dUMP + ADP + H(+) `RHEA:28207`	produces	ADP(3-) `CHEBI:456216`	RHEA:28207 Source assertion: Rhea 28207 assigns CHEBI:456216 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/28207']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/28206_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_28206_compound_2710']; http://rdf.rhea-db.org/Participant_28206_compound_2710/rh:compound; http://rdf.rhea-db.org/Compound_2710/rh:chebi`
2'-deoxyuridine + ATP => dUMP + ADP + H(+) `RHEA:28207`	produces	hydron `CHEBI:15378`	RHEA:28207 Source assertion: Rhea 28207 assigns CHEBI:15378 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/28207']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/28206_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_28206_compound_3249']; http://rdf.rhea-db.org/Participant_28206_compound_3249/rh:compound; http://rdf.rhea-db.org/Compound_3249/rh:chebi`
thymidine `CHEBI:17748`	consumes	thymidine + ATP => dTMP + ADP + H(+) `RHEA:19130`	RHEA:19130 Source assertion: Rhea 19130 assigns CHEBI:17748 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19130']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/19129_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_19129_compound_4636']; http://rdf.rhea-db.org/Participant_19129_compound_4636/rh:compound; http://rdf.rhea-db.org/Compound_4636/rh:chebi`
ATP(4-) `CHEBI:30616`	consumes	thymidine + ATP => dTMP + ADP + H(+) `RHEA:19130`	RHEA:19130 Source assertion: Rhea 19130 assigns CHEBI:30616 to substrates with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19130']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/19129_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_19129_compound_6372']; http://rdf.rhea-db.org/Participant_19129_compound_6372/rh:compound; http://rdf.rhea-db.org/Compound_6372/rh:chebi`
thymidine + ATP => dTMP + ADP + H(+) `RHEA:19130`	produces	dTMP(2-) `CHEBI:63528`	RHEA:19130 Source assertion: Rhea 19130 assigns CHEBI:63528 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19130']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/19129_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_19129_compound_5064']; http://rdf.rhea-db.org/Participant_19129_compound_5064/rh:compound; http://rdf.rhea-db.org/Compound_5064/rh:chebi`
thymidine + ATP => dTMP + ADP + H(+) `RHEA:19130`	produces	ADP(3-) `CHEBI:456216`	RHEA:19130 Source assertion: Rhea 19130 assigns CHEBI:456216 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19130']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/19129_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_19129_compound_2710']; http://rdf.rhea-db.org/Participant_19129_compound_2710/rh:compound; http://rdf.rhea-db.org/Compound_2710/rh:chebi`
thymidine + ATP => dTMP + ADP + H(+) `RHEA:19130`	produces	hydron `CHEBI:15378`	RHEA:19130 Source assertion: Rhea 19130 assigns CHEBI:15378 to products with coefficient 1; this is the exact charge and stereochemical species in the native RDF. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19130']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/19129_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_19129_compound_3249']; http://rdf.rhea-db.org/Participant_19129_compound_3249/rh:compound; http://rdf.rhea-db.org/Compound_3249/rh:chebi`
Cytidine deaminase `UniProtKB:P0ABF6`	part_of Homodimer membership; catalysis is assigned to the assembly.	cytidine/deoxycytidine deaminase `MetaCyc:CYTIDEAM-CPLX`	MetaCyc:CYTIDEAM-CPLX Source assertion: The native complex contains two copies of CYTIDEAM-MONOMER. Source location `Protein[@frameid='CYTIDEAM-CPLX']/component/Protein; component/coefficient` MetaCyc:CYTIDEAM-MONOMER Source assertion: The native component has a UNIPROT unification cross-reference to P0ABF6. Source location `Protein[@frameid='CYTIDEAM-MONOMER']/dblink[dblink-db='UNIPROT'][dblink-relationship='unification']/dblink-oid` PMID:8289286 Source assertion: The primary abstract reports an E. coli cytidine deaminase alpha2 dimer with active sites formed across its subunit interface. Source location `Europe PMC /resultList/result/0/abstractText; primary abstract only`
Thymidine phosphorylase `UniProtKB:P07650`	part_of Homodimer membership; catalysis is assigned to the assembly.	thymidine phosphorylase / uracil phosphorylase `MetaCyc:DEOA-CPLX`	MetaCyc:DEOA-CPLX Source assertion: The native complex contains two copies of DEOA-MONOMER. Source location `Protein[@frameid='DEOA-CPLX']/component/Protein; component/coefficient` MetaCyc:DEOA-MONOMER Source assertion: The native component has a UNIPROT unification cross-reference to P07650. Source location `Protein[@frameid='DEOA-MONOMER']/dblink[dblink-db='UNIPROT'][dblink-relationship='unification']/dblink-oid` PMID:2199449 Source assertion: The primary abstract reports an E. coli thymidine phosphorylase crystal dimer and the deoA-derived sequence. Source location `Europe PMC /resultList/result/0/abstractText; primary abstract only`
Thymidine kinase `UniProtKB:P23331`	part_of Component membership only. The graph does not fix a tetramer or transfer E. coli B ligand-dependent dimerization to all K-12 conditions.	thymidine kinase / deoxyuridine kinase `MetaCyc:CPLX0-8261`	MetaCyc:CPLX0-8261 Source assertion: The native assembly contains TDK-MONOMER and reports an 82 kDa K-12 enzyme from crude-extract gel filtration; its comment distinguishes ligand-dependent dimerization studies of the E. coli B enzyme. Source location `Protein[@frameid='CPLX0-8261']/component/Protein; molecular-weight-exp; comment paragraphs 2-3` MetaCyc:TDK-MONOMER Source assertion: The native component has a UNIPROT unification cross-reference to P23331. Source location `Protein[@frameid='TDK-MONOMER']/dblink[dblink-db='UNIPROT'][dblink-relationship='unification']/dblink-oid` UniProtKB:P23331 Source assertion: Reviewed UniProt annotates a homotetramer by HAMAP MF_00124 (ECO:0000255); this is an inference rather than a condition-resolved native assembly measurement. Source location `/comments/3/texts/0/value; /comments/3/texts/0/evidences` PMID:2041474 Source assertion: The primary abstract reports W3110 tdk complementation of TK-deficient KY895 and gel-filtration evidence for a multimeric active enzyme; the abstract does not specify a subunit count. Source location `Europe PMC /resultList/result/0/abstractText; truncated primary abstract only`
cytidine/deoxycytidine deaminase `MetaCyc:CYTIDEAM-CPLX`	catalyzes Native enzyme annotation is distinguished from the strain and access limits of inspected primary evidence.	2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	MetaCyc:CYTIDEAM-CPLX Source assertion: The native CYTIDEAM-CPLX catalyzes annotation links CYTIDEAM-ENZRXN to CYTIDEAM-RXN. Source location `Protein[@frameid='CYTIDEAM-CPLX']/catalyzes/Enzymatic-Reaction[@frameid='CYTIDEAM-ENZRXN']/reaction/Reaction[@frameid='CYTIDEAM-RXN']` MetaCyc:CYTIDEAM-RXN Source assertion: The native reaction has an explicit RHEA:13434 unification cross-reference; its own left/right compounds are retained separately from the selected Rhea direction. Source location `Reaction[@frameid='CYTIDEAM-RXN']/dblink[dblink-db='RHEA']/dblink-oid; left; right` RHEA:13434 Source assertion: Rhea master 13433 explicitly lists directional member 13434; its substrates, products and equation specify the selected left-to-right transformation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/13434']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:substrates; rh:products; rh:equation` PMID:4202859 Source assertion: Partially purified cytidine deaminase from E. coli Y-70-272 deaminates deoxycytidine; this strain-specific enzyme assay supports the activity, not MG1655 wild-type salvage flux. Source location `Full primary PDF pp.797-798 Materials and Methods/Strains of bacteria and Enzyme assay; p.802 Substrate specificity and Table VI`
thymidine phosphorylase / uracil phosphorylase `MetaCyc:DEOA-CPLX`	catalyzes Selected salvage direction; reversible DeoA chemistry does not imply constitutive net flux.	2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	MetaCyc:DEOA-CPLX Source assertion: The native DEOA-CPLX catalyzes annotation links URA-PHOSPH-ENZRXN to URA-PHOSPH-RXN. Source location `Protein[@frameid='DEOA-CPLX']/catalyzes/Enzymatic-Reaction[@frameid='URA-PHOSPH-ENZRXN']/reaction/Reaction[@frameid='URA-PHOSPH-RXN']` MetaCyc:URA-PHOSPH-RXN Source assertion: The native reaction has an explicit RHEA:22827 unification cross-reference; its own left/right compounds are retained separately from the selected Rhea direction. Source location `Reaction[@frameid='URA-PHOSPH-RXN']/dblink[dblink-db='RHEA']/dblink-oid; left; right` RHEA:22825 Source assertion: Rhea master 22824 explicitly lists directional member 22825; its substrates, products and equation specify the selected left-to-right transformation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/22825']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:substrates; rh:products; rh:equation` UniProtKB:P07650 Source assertion: Reviewed DeoA catalyzes reversible pyrimidine nucleoside phosphorolysis for degradation or rescue of pyrimidine bases; the graph selects deoxyuridine cleavage and thymidine synthesis in this salvage route. Source location `/comments/0/texts/0/value; /comments/1/reaction; /comments/2/texts`
thymidine phosphorylase / uracil phosphorylase `MetaCyc:DEOA-CPLX`	catalyzes Selected salvage direction; reversible DeoA chemistry does not imply constitutive net flux.	2-deoxy-alpha-D-ribose 1-phosphate + thymine => thymidine + phosphate `RHEA:16039`	MetaCyc:DEOA-CPLX Source assertion: The native DEOA-CPLX catalyzes annotation links THYM-PHOSPH-ENZRXN to THYM-PHOSPH-RXN. Source location `Protein[@frameid='DEOA-CPLX']/catalyzes/Enzymatic-Reaction[@frameid='THYM-PHOSPH-ENZRXN']/reaction/Reaction[@frameid='THYM-PHOSPH-RXN']` MetaCyc:THYM-PHOSPH-RXN Source assertion: The native reaction has an explicit RHEA:16040 unification cross-reference; its own left/right compounds are retained separately from the selected Rhea direction. Source location `Reaction[@frameid='THYM-PHOSPH-RXN']/dblink[dblink-db='RHEA']/dblink-oid; left; right` RHEA:16039 Source assertion: Rhea master 16037 explicitly lists directional member 16039; its substrates, products and equation specify the selected right-to-left transformation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/16039']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16039']/rh:substrates; rh:products; rh:equation` UniProtKB:P07650 Source assertion: Reviewed DeoA catalyzes reversible pyrimidine nucleoside phosphorolysis for degradation or rescue of pyrimidine bases; the graph selects deoxyuridine cleavage and thymidine synthesis in this salvage route. Source location `/comments/0/texts/0/value; /comments/1/reaction; /comments/2/texts`
thymidine kinase / deoxyuridine kinase `MetaCyc:CPLX0-8261`	catalyzes Native enzyme annotation is distinguished from the strain and access limits of inspected primary evidence.	2'-deoxyuridine + ATP => dUMP + ADP + H(+) `RHEA:28207`	MetaCyc:CPLX0-8261 Source assertion: The native CPLX0-8261 catalyzes annotation links DURIDKI-ENZRXN to DURIDKI-RXN. Source location `Protein[@frameid='CPLX0-8261']/catalyzes/Enzymatic-Reaction[@frameid='DURIDKI-ENZRXN']/reaction/Reaction[@frameid='DURIDKI-RXN']` MetaCyc:DURIDKI-RXN Source assertion: The native reaction has an explicit RHEA:28207 unification cross-reference; its own left/right compounds are retained separately from the selected Rhea direction. Source location `Reaction[@frameid='DURIDKI-RXN']/dblink[dblink-db='RHEA']/dblink-oid; left; right` RHEA:28207 Source assertion: Rhea master 28206 explicitly lists directional member 28207; its substrates, products and equation specify the selected left-to-right transformation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/28206']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/28207']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/28207']/rh:substrates; rh:products; rh:equation` MetaCyc:DURIDKI-ENZRXN Source assertion: The native deoxyuridine kinase assignment is physiologically left-to-right and carries an unpurified-protein assay evidence code linked to Hiraga 1967. This is inspected database annotation, not direct inspection of that paper. Source location `Enzymatic-Reaction[@frameid='DURIDKI-ENZRXN']/enzyme; reaction; reaction-direction; evidence` UniProtKB:P23331 Source assertion: Reviewed UniProt states that Tdk phosphorylates both thymidine and deoxyuridine. Source location `/comments/0/texts/0/value` PMID:17827303 Source assertion: The introduction describes deoxycytidine deamination followed by thymidine-kinase conversion of deoxyuridine to dUMP; Table 1 identifies the studied strains as K-12 derivatives. Source location `Full PMC2168750 HTML Introduction paragraph beginning "Escherichia coli has three known routes"; Table 1 footnote a`
thymidine kinase / deoxyuridine kinase `MetaCyc:CPLX0-8261`	catalyzes Native enzyme annotation is distinguished from the strain and access limits of inspected primary evidence.	thymidine + ATP => dTMP + ADP + H(+) `RHEA:19130`	MetaCyc:CPLX0-8261 Source assertion: The native CPLX0-8261 catalyzes annotation links THYKI-ENZRXN to THYKI-RXN. Source location `Protein[@frameid='CPLX0-8261']/catalyzes/Enzymatic-Reaction[@frameid='THYKI-ENZRXN']/reaction/Reaction[@frameid='THYKI-RXN']` MetaCyc:THYKI-RXN Source assertion: The native reaction has an explicit RHEA:19130 unification cross-reference; its own left/right compounds are retained separately from the selected Rhea direction. Source location `Reaction[@frameid='THYKI-RXN']/dblink[dblink-db='RHEA']/dblink-oid; left; right` RHEA:19130 Source assertion: Rhea master 19129 explicitly lists directional member 19130; its substrates, products and equation specify the selected left-to-right transformation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19129']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/19130']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/19130']/rh:substrates; rh:products; rh:equation` PMID:2041474 Source assertion: W3110 DNA carrying tdk confers thymidine kinase activity on TK-deficient KY895 in the reported genetic complementation assay. Source location `Europe PMC /resultList/result/0/abstractText; primary abstract only`
cytidine/deoxycytidine deaminase `MetaCyc:CYTIDEAM-CPLX`	has_cofactor Bound catalytic zinc is distinct from inhibition by excess externally supplied zinc in older assays.	zinc(2+) `CHEBI:29105`	UniProtKB:P0ABF6 Source assertion: Cdd has Zn(2+) cofactor CHEBI:29105 with experimental ECO:0000269 evidence; the note states one zinc per subunit. Source location `/comments/3/cofactors; /comments/3/note/texts` PMID:8289286 Source assertion: The primary abstract identifies zinc-binding pockets in the cytidine deaminase dimer and the metal-ligand coordination at its active sites. Source location `Europe PMC /resultList/result/0/abstractText; primary abstract only`
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	part_of The source map also includes four incoming NupC/NupG transport objects, dispositioned separately. No equivalence to the differently composed MetaCyc PWY-7199 is asserted.	`GO:0010139`	PathBank:SMP0002073 Source assertion: The named native salvage map explicitly contains biochemical reaction 6014, whose written conversion is retained in this five-reaction biochemical implementation. Source location `Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0002073']/bp:pathwayComponent[@rdf:resource='#Reactions/6014']; BiochemicalReaction[@rdf:ID='Reactions/6014']/bp:left; bp:right; bp:conversionDirection` GO:0010139 Source assertion: GO defines recovery of pyrimidine bases or deoxyribonucleotides from nucleotide breakdown back to pyrimidine deoxyribonucleotides; this graph represents one complete E. coli biochemical implementation. Source location `QuickGO /results/0/id; /results/0/name; /results/0/definition/text` RHEA:13434 Source assertion: Rhea master 13433 explicitly lists directional member 13434; its substrates, products and equation specify the selected left-to-right transformation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/13434']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:substrates; rh:products; rh:equation`
2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	part_of The source map also includes four incoming NupC/NupG transport objects, dispositioned separately. No equivalence to the differently composed MetaCyc PWY-7199 is asserted.	`GO:0010139`	PathBank:SMP0002073 Source assertion: The named native salvage map explicitly contains biochemical reaction 6018, whose written conversion is retained in this five-reaction biochemical implementation. Source location `Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0002073']/bp:pathwayComponent[@rdf:resource='#Reactions/6018']; BiochemicalReaction[@rdf:ID='Reactions/6018']/bp:left; bp:right; bp:conversionDirection` GO:0010139 Source assertion: GO defines recovery of pyrimidine bases or deoxyribonucleotides from nucleotide breakdown back to pyrimidine deoxyribonucleotides; this graph represents one complete E. coli biochemical implementation. Source location `QuickGO /results/0/id; /results/0/name; /results/0/definition/text` RHEA:22825 Source assertion: Rhea master 22824 explicitly lists directional member 22825; its substrates, products and equation specify the selected left-to-right transformation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/22825']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:substrates; rh:products; rh:equation`
2-deoxy-alpha-D-ribose 1-phosphate + thymine => thymidine + phosphate `RHEA:16039`	part_of The source map also includes four incoming NupC/NupG transport objects, dispositioned separately. No equivalence to the differently composed MetaCyc PWY-7199 is asserted.	`GO:0010139`	PathBank:SMP0002073 Source assertion: The named native salvage map explicitly contains biochemical reaction 6019, whose written conversion is retained in this five-reaction biochemical implementation. Source location `Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0002073']/bp:pathwayComponent[@rdf:resource='#Reactions/6019']; BiochemicalReaction[@rdf:ID='Reactions/6019']/bp:left; bp:right; bp:conversionDirection` GO:0010139 Source assertion: GO defines recovery of pyrimidine bases or deoxyribonucleotides from nucleotide breakdown back to pyrimidine deoxyribonucleotides; this graph represents one complete E. coli biochemical implementation. Source location `QuickGO /results/0/id; /results/0/name; /results/0/definition/text` RHEA:16039 Source assertion: Rhea master 16037 explicitly lists directional member 16039; its substrates, products and equation specify the selected right-to-left transformation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/16039']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16039']/rh:substrates; rh:products; rh:equation`
2'-deoxyuridine + ATP => dUMP + ADP + H(+) `RHEA:28207`	part_of The source map also includes four incoming NupC/NupG transport objects, dispositioned separately. No equivalence to the differently composed MetaCyc PWY-7199 is asserted.	`GO:0010139`	PathBank:SMP0002073 Source assertion: The named native salvage map explicitly contains biochemical reaction 6015, whose written conversion is retained in this five-reaction biochemical implementation. Source location `Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0002073']/bp:pathwayComponent[@rdf:resource='#Reactions/6015']; BiochemicalReaction[@rdf:ID='Reactions/6015']/bp:left; bp:right; bp:conversionDirection` GO:0010139 Source assertion: GO defines recovery of pyrimidine bases or deoxyribonucleotides from nucleotide breakdown back to pyrimidine deoxyribonucleotides; this graph represents one complete E. coli biochemical implementation. Source location `QuickGO /results/0/id; /results/0/name; /results/0/definition/text` RHEA:28207 Source assertion: Rhea master 28206 explicitly lists directional member 28207; its substrates, products and equation specify the selected left-to-right transformation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/28206']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/28207']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/28207']/rh:substrates; rh:products; rh:equation`
thymidine + ATP => dTMP + ADP + H(+) `RHEA:19130`	part_of The source map also includes four incoming NupC/NupG transport objects, dispositioned separately. No equivalence to the differently composed MetaCyc PWY-7199 is asserted.	`GO:0010139`	PathBank:SMP0002073 Source assertion: The named native salvage map explicitly contains biochemical reaction 6021, whose written conversion is retained in this five-reaction biochemical implementation. Source location `Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0002073']/bp:pathwayComponent[@rdf:resource='#Reactions/6021']; BiochemicalReaction[@rdf:ID='Reactions/6021']/bp:left; bp:right; bp:conversionDirection` GO:0010139 Source assertion: GO defines recovery of pyrimidine bases or deoxyribonucleotides from nucleotide breakdown back to pyrimidine deoxyribonucleotides; this graph represents one complete E. coli biochemical implementation. Source location `QuickGO /results/0/id; /results/0/name; /results/0/definition/text` RHEA:19130 Source assertion: Rhea master 19129 explicitly lists directional member 19130; its substrates, products and equation specify the selected left-to-right transformation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19129']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/19130']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/19130']/rh:substrates; rh:products; rh:equation`
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	provides_input_for Inferred material continuity from separately inspected product and substrate identities, consistent with native EcoCyc ordering; no channeling or obligatory wild-type flux claim.	2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	RHEA:13434 Source assertion: The exact directed reaction 13434 produces CHEBI:16450, the shared intermediate linking these two selected transformations. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_5154']; http://rdf.rhea-db.org/Participant_13433_compound_5154/rh:compound; http://rdf.rhea-db.org/Compound_5154/rh:chebi` RHEA:22825 Source assertion: The exact directed reaction 22825 consumes CHEBI:16450, the shared intermediate linking these two selected transformations. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_22824_compound_5154']; http://rdf.rhea-db.org/Participant_22824_compound_5154/rh:compound; http://rdf.rhea-db.org/Compound_5154/rh:chebi`
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	provides_input_for Inferred material continuity from separately inspected product and substrate identities, consistent with native EcoCyc ordering; no channeling or obligatory wild-type flux claim.	2'-deoxyuridine + ATP => dUMP + ADP + H(+) `RHEA:28207`	RHEA:13434 Source assertion: The exact directed reaction 13434 produces CHEBI:16450, the shared intermediate linking these two selected transformations. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_5154']; http://rdf.rhea-db.org/Participant_13433_compound_5154/rh:compound; http://rdf.rhea-db.org/Compound_5154/rh:chebi` RHEA:28207 Source assertion: The exact directed reaction 28207 consumes CHEBI:16450, the shared intermediate linking these two selected transformations. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/28207']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/28206_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_28206_compound_5154']; http://rdf.rhea-db.org/Participant_28206_compound_5154/rh:compound; http://rdf.rhea-db.org/Compound_5154/rh:chebi`
2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	provides_input_for Inferred material continuity from separately inspected product and substrate identities, consistent with native EcoCyc ordering; no channeling or obligatory wild-type flux claim.	2-deoxy-alpha-D-ribose 1-phosphate + thymine => thymidine + phosphate `RHEA:16039`	RHEA:22825 Source assertion: The exact directed reaction 22825 produces CHEBI:57259, the shared intermediate linking these two selected transformations. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_22824_compound_3098']; http://rdf.rhea-db.org/Participant_22824_compound_3098/rh:compound; http://rdf.rhea-db.org/Compound_3098/rh:chebi` RHEA:16039 Source assertion: The exact directed reaction 16039 consumes CHEBI:57259, the shared intermediate linking these two selected transformations. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16039']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16037_compound_3098']; http://rdf.rhea-db.org/Participant_16037_compound_3098/rh:compound; http://rdf.rhea-db.org/Compound_3098/rh:chebi`
2-deoxy-alpha-D-ribose 1-phosphate + thymine => thymidine + phosphate `RHEA:16039`	provides_input_for Inferred material continuity from separately inspected product and substrate identities, consistent with native EcoCyc ordering; no channeling or obligatory wild-type flux claim.	thymidine + ATP => dTMP + ADP + H(+) `RHEA:19130`	RHEA:16039 Source assertion: The exact directed reaction 16039 produces CHEBI:17748, the shared intermediate linking these two selected transformations. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16039']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16037_compound_4636']; http://rdf.rhea-db.org/Participant_16037_compound_4636/rh:compound; http://rdf.rhea-db.org/Compound_4636/rh:chebi` RHEA:19130 Source assertion: The exact directed reaction 19130 consumes CHEBI:17748, the shared intermediate linking these two selected transformations. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19130']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/19129_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_19129_compound_4636']; http://rdf.rhea-db.org/Participant_19129_compound_4636/rh:compound; http://rdf.rhea-db.org/Compound_4636/rh:chebi`

References

RHEA:13434 Rhea exact directed reaction 13434 (source version: Rhea release 142; complete native RDF gzip)
RHEA:22825 Rhea exact directed reaction 22825 (source version: Rhea release 142; complete native RDF gzip)
RHEA:16039 Rhea exact directed reaction 16039 (source version: Rhea release 142; complete native RDF gzip)
RHEA:28207 Rhea exact directed reaction 28207 (source version: Rhea release 142; complete native RDF gzip)
RHEA:19130 Rhea exact directed reaction 19130 (source version: Rhea release 142; complete native RDF gzip)
MetaCyc:CYTIDEAM-CPLX MetaCyc native CYTIDEAM-CPLX (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:CYTIDEAM-MONOMER MetaCyc native CYTIDEAM-MONOMER (source version: MetaCyc 22.5 public SGD-hosted native XML)
PMID:8289286 Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex. (source version: Primary abstract inspected; no full-text claim)
MetaCyc:DEOA-CPLX MetaCyc native DEOA-CPLX (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:DEOA-MONOMER MetaCyc native DEOA-MONOMER (source version: MetaCyc 22.5 public SGD-hosted native XML)
PMID:2199449 Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution. (source version: Primary abstract inspected; no full-text claim)
MetaCyc:CPLX0-8261 MetaCyc native CPLX0-8261 (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:TDK-MONOMER MetaCyc native TDK-MONOMER (source version: MetaCyc 22.5 public SGD-hosted native XML)
UniProtKB:P23331 Reviewed UniProtKB P23331 (source version: UniProt 2026_03; original response release header and entry audit retained)
PMID:2041474 Nucleotide sequence of the Escherichia coli thymidine kinase gene provides evidence for conservation of functional domains and quaternary structure. (source version: Primary abstract inspected; no full-text claim)
MetaCyc:CYTIDEAM-RXN MetaCyc native CYTIDEAM-RXN (source version: MetaCyc 22.5 public SGD-hosted native XML)
PMID:4202859 The purification and properties of cytidine deaminase from Escherichia coli. (source version: 1973 primary full text, pp.797-803)
MetaCyc:URA-PHOSPH-RXN MetaCyc native URA-PHOSPH-RXN (source version: MetaCyc 22.5 public SGD-hosted native XML)
UniProtKB:P07650 Reviewed UniProtKB P07650 (source version: UniProt 2026_03; original response release header and entry audit retained)
MetaCyc:THYM-PHOSPH-RXN MetaCyc native THYM-PHOSPH-RXN (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:DURIDKI-RXN MetaCyc native DURIDKI-RXN (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:DURIDKI-ENZRXN MetaCyc native DURIDKI-ENZRXN (source version: MetaCyc 22.5 public SGD-hosted native XML)
PMID:17827303 The Deoxycytidine Pathway for Thymidylate Synthesis in Escherichia coli (source version: 2007 primary full text; mutant and K-12 strain scope retained)
MetaCyc:THYKI-RXN MetaCyc native THYKI-RXN (source version: MetaCyc 22.5 public SGD-hosted native XML)
UniProtKB:P0ABF6 Reviewed UniProtKB P0ABF6 (source version: UniProt 2026_03; original response release header and entry audit retained)
PathBank:SMP0002073 Salvage Pathways of Pyrimidine Deoxyribonucleotides (source version: Frozen PathBank BioPAX member PW002061.owl; member SHA scope)
GO:0010139 Gene Ontology pyrimidine deoxyribonucleotide salvage (source version: QuickGO original GO term response retrieved 2026-10-11)

Curation history

2026-10-11T07:08:03Z Codex; add-pathway; Curated the complete five-reaction E. coli salvage implementation after hidden/ignored-inclusive semantic deduplication; retained native pathway identity mismatch, four uptake-context dispositions, exact Rhea direction families and Tdk assembly/primary-strain limits.
2026-10-11T07:08:44Z claude-code
- CREATE — Add the complete source-defined pathway and generated network page
  Original native pathway, Rhea reaction sides, independent identifiers and protein evidence are captured in research/pathway_additions/2026-10-11-next-198. Preserve taxon, assembly and source conflicts explicitly. Independent scientific review and full repository checks are recorded separately for this cohort.
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