Adenine and Adenosine Salvage II

PathBank:SMP0002083

This complete current PathBank definition couples AdeP-mediated adenine uptake to DeoD-dependent adenosine synthesis, Add deamination and Gsk-dependent inosine phosphorylation to IMP. It contains four elementary events and the native, non-elementary Aspartate Metabolism input interface; the latter does not import the entire connected pathway. E. coli K-12 protein evidence, MG1655 regulatory experiments and specific transport-assay strains remain distinct. PathBank labels its protein BioSource K-12 but links BW25113; that conflicting annotation is not adopted as universal strain identity. The native 1:1 proton/adenine transport ratio is a database assertion, not a measured coupling ratio in the inspected papers. Rhea gives the balanced charged chemistry; native neutral IMP_Cytosol and IMP_Cytoplasm remain separate source-view instances, with no invented transport or protonation reaction between them. DeoD is a hexamer and Gsk an active dimer; GDP/ppGpp promote concentration-dependent tetramerization, with ppGpp-bound tetramers less active than bound dimers. No issuing identifier was established for that conditional tetramer, so its state is retained in evidence. A crystallographic octamer is not assigned physiological status. PurR represses adeP transcription; adenine increases add transcription without direct PurR regulation of add. Older GTP-inhibition annotation conflicts with the 2020 GDP-not-GTP result. Native MetaCyc PWY-6611 is the related three-reaction core, not an exact alias for this transport/interface-inclusive record.

Pathway type

purine nucleotide salvage

Organism scope

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Pathway network

45 nodes · 57 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Reaction / activity
Chemical / cofactor
Protein / complex
Other participant
Cell / process context
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 K-12 `NCBITaxon:83333`	taxon
Escherichia coli str. K-12 substr. MG1655 `NCBITaxon:511145`	taxon
alpha-D-ribose 1-phosphate(2-) `CHEBI:57720`	small molecule
adenine `CHEBI:16708`	small molecule
adenosine `CHEBI:16335`	small molecule
hydrogenphosphate `CHEBI:43474`	small molecule
water `CHEBI:15377`	small molecule
hydron `CHEBI:15378`	small molecule
inosine `CHEBI:17596`	small molecule
ammonium `CHEBI:28938`	small molecule
ATP(4-) `CHEBI:30616`	small molecule
IMP(2-) `CHEBI:58053`	small molecule
ADP(3-) `CHEBI:456216`	small molecule
GDP(3-) `CHEBI:58189`	small molecule
guanosine 3',5'-bis(diphosphate)(5-) `CHEBI:77828`	small molecule
hypoxanthine `CHEBI:17368`	small molecule
guanine `CHEBI:16235`	small molecule
potassium(1+) `CHEBI:29103`	small molecule
copper(2+) `CHEBI:29036`	small molecule
magnesium(2+) `CHEBI:18420`	cofactor
zinc(2+) `CHEBI:29105`	cofactor
Purine nucleoside phosphorylase DeoD-type `UniProtKB:P0ABP8`	protein
Adenosine deaminase `UniProtKB:P22333`	protein
Guanosine-inosine kinase `UniProtKB:P0AEW6`	protein
Adenine permease AdeP `UniProtKB:P31466`	protein
HTH-type transcriptional repressor PurR `UniProtKB:P0ACP7`	protein
purine nucleoside phosphorylase `MetaCyc:DEOD-CPLX`	complex
inosine/guanosine kinase `MetaCyc:CPLX0-322`	complex
DNA-binding transcriptional repressor PurR `MetaCyc:PC00033`	complex
adeP `Entrez:948224`	gene
add `Entrez:945851`	gene
Adenine `PathBank:SMP0002083/Compound/PW_C000024_Periplasmic_Space`	small molecule
Adenine `PathBank:SMP0002083/Compound/PW_C000024_Cytosol`	small molecule
Hydrogen Ion `PathBank:SMP0002083/Compound/PW_C040034_Periplasmic_Space`	small molecule
Hydrogen Ion `PathBank:SMP0002083/Compound/PW_C040034_Cytosol`	small molecule
Inosinic acid `PathBank:SMP0002083/Compound/PW_C000114_Cytosol`	small molecule
Inosinic acid `PathBank:SMP0002083/Compound/PW_C000114_Cytoplasm`	small molecule
cytosol `GO:0005829`	cellular component
periplasmic space `GO:0042597`	cellular component
cytoplasm `GO:0005737`	cellular component
plasma membrane `GO:0005886`	cellular component
alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate `RHEA:27644`	reaction	right to left
adenosine + H2O + H(+) => inosine + NH4(+) `RHEA:24409`	reaction	left to right
inosine + ATP => IMP + ADP + H(+) `RHEA:21141`	reaction	left to right
Transport505 `PathBank:SMP0002083/Transports/505`	molecular activity	left to right
Aspartate Metabolism `PathBank:SMP0000809`	biological process

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
alpha-D-ribose 1-phosphate(2-) `CHEBI:57720`	consumes Stoichiometric coefficient 1.	alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate `RHEA:27644`	RHEA:27644 Source assertion: The original directional Rhea reaction places CHEBI:57720 on its substrates side with coefficient 1; its master-relative orientation is right_to_left. Source location `rhea.rdf.gz; rh:27644 rh:substrates rh:27642_R; rh:27642_R rh:contains1 <http://rdf.rhea-db.org/Participant_27642_compound_2276>; rh:compound <http://rdf.rhea-db.org/Compound_2276> / rh:chebi`
adenine `CHEBI:16708`	consumes Stoichiometric coefficient 1.	alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate `RHEA:27644`	RHEA:27644 Source assertion: The original directional Rhea reaction places CHEBI:16708 on its substrates side with coefficient 1; its master-relative orientation is right_to_left. Source location `rhea.rdf.gz; rh:27644 rh:substrates rh:27642_R; rh:27642_R rh:contains1 <http://rdf.rhea-db.org/Participant_27642_compound_4174>; rh:compound <http://rdf.rhea-db.org/Compound_4174> / rh:chebi`
alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate `RHEA:27644`	produces Stoichiometric coefficient 1.	adenosine `CHEBI:16335`	RHEA:27644 Source assertion: The original directional Rhea reaction places CHEBI:16335 on its products side with coefficient 1; its master-relative orientation is right_to_left. Source location `rhea.rdf.gz; rh:27644 rh:products rh:27642_L; rh:27642_L rh:contains1 <http://rdf.rhea-db.org/Participant_27642_compound_2547>; rh:compound <http://rdf.rhea-db.org/Compound_2547> / rh:chebi`
alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate `RHEA:27644`	produces Stoichiometric coefficient 1.	hydrogenphosphate `CHEBI:43474`	RHEA:27644 Source assertion: The original directional Rhea reaction places CHEBI:43474 on its products side with coefficient 1; its master-relative orientation is right_to_left. Source location `rhea.rdf.gz; rh:27644 rh:products rh:27642_L; rh:27642_L rh:contains1 <http://rdf.rhea-db.org/Participant_27642_compound_5518>; rh:compound <http://rdf.rhea-db.org/Compound_5518> / rh:chebi`
adenosine `CHEBI:16335`	consumes Stoichiometric coefficient 1.	adenosine + H2O + H(+) => inosine + NH4(+) `RHEA:24409`	RHEA:24409 Source assertion: The original directional Rhea reaction places CHEBI:16335 on its substrates side with coefficient 1; its master-relative orientation is left_to_right. Source location `rhea.rdf.gz; rh:24409 rh:substrates rh:24408_L; rh:24408_L rh:contains1 <http://rdf.rhea-db.org/Participant_24408_compound_2547>; rh:compound <http://rdf.rhea-db.org/Compound_2547> / rh:chebi`
water `CHEBI:15377`	consumes Stoichiometric coefficient 1.	adenosine + H2O + H(+) => inosine + NH4(+) `RHEA:24409`	RHEA:24409 Source assertion: The original directional Rhea reaction places CHEBI:15377 on its substrates side with coefficient 1; its master-relative orientation is left_to_right. Source location `rhea.rdf.gz; rh:24409 rh:substrates rh:24408_L; rh:24408_L rh:contains1 <http://rdf.rhea-db.org/Participant_24408_compound_1283>; rh:compound <http://rdf.rhea-db.org/Compound_1283> / rh:chebi`
hydron `CHEBI:15378`	consumes Stoichiometric coefficient 1.	adenosine + H2O + H(+) => inosine + NH4(+) `RHEA:24409`	RHEA:24409 Source assertion: The original directional Rhea reaction places CHEBI:15378 on its substrates side with coefficient 1; its master-relative orientation is left_to_right. Source location `rhea.rdf.gz; rh:24409 rh:substrates rh:24408_L; rh:24408_L rh:contains1 <http://rdf.rhea-db.org/Participant_24408_compound_3249>; rh:compound <http://rdf.rhea-db.org/Compound_3249> / rh:chebi`
adenosine + H2O + H(+) => inosine + NH4(+) `RHEA:24409`	produces Stoichiometric coefficient 1.	inosine `CHEBI:17596`	RHEA:24409 Source assertion: The original directional Rhea reaction places CHEBI:17596 on its products side with coefficient 1; its master-relative orientation is left_to_right. Source location `rhea.rdf.gz; rh:24409 rh:products rh:24408_R; rh:24408_R rh:contains1 <http://rdf.rhea-db.org/Participant_24408_compound_1231>; rh:compound <http://rdf.rhea-db.org/Compound_1231> / rh:chebi`
adenosine + H2O + H(+) => inosine + NH4(+) `RHEA:24409`	produces Stoichiometric coefficient 1.	ammonium `CHEBI:28938`	RHEA:24409 Source assertion: The original directional Rhea reaction places CHEBI:28938 on its products side with coefficient 1; its master-relative orientation is left_to_right. Source location `rhea.rdf.gz; rh:24409 rh:products rh:24408_R; rh:24408_R rh:contains1 <http://rdf.rhea-db.org/Participant_24408_compound_1012>; rh:compound <http://rdf.rhea-db.org/Compound_1012> / rh:chebi`
inosine `CHEBI:17596`	consumes Stoichiometric coefficient 1.	inosine + ATP => IMP + ADP + H(+) `RHEA:21141`	RHEA:21141 Source assertion: The original directional Rhea reaction places CHEBI:17596 on its substrates side with coefficient 1; its master-relative orientation is left_to_right. Source location `rhea.rdf.gz; rh:21141 rh:substrates rh:21140_L; rh:21140_L rh:contains1 <http://rdf.rhea-db.org/Participant_21140_compound_1231>; rh:compound <http://rdf.rhea-db.org/Compound_1231> / rh:chebi`
ATP(4-) `CHEBI:30616`	consumes Stoichiometric coefficient 1.	inosine + ATP => IMP + ADP + H(+) `RHEA:21141`	RHEA:21141 Source assertion: The original directional Rhea reaction places CHEBI:30616 on its substrates side with coefficient 1; its master-relative orientation is left_to_right. Source location `rhea.rdf.gz; rh:21141 rh:substrates rh:21140_L; rh:21140_L rh:contains1 <http://rdf.rhea-db.org/Participant_21140_compound_6372>; rh:compound <http://rdf.rhea-db.org/Compound_6372> / rh:chebi`
inosine + ATP => IMP + ADP + H(+) `RHEA:21141`	produces Stoichiometric coefficient 1.	IMP(2-) `CHEBI:58053`	RHEA:21141 Source assertion: The original directional Rhea reaction places CHEBI:58053 on its products side with coefficient 1; its master-relative orientation is left_to_right. Source location `rhea.rdf.gz; rh:21141 rh:products rh:21140_R; rh:21140_R rh:contains1 <http://rdf.rhea-db.org/Participant_21140_compound_1663>; rh:compound <http://rdf.rhea-db.org/Compound_1663> / rh:chebi`
inosine + ATP => IMP + ADP + H(+) `RHEA:21141`	produces Stoichiometric coefficient 1.	ADP(3-) `CHEBI:456216`	RHEA:21141 Source assertion: The original directional Rhea reaction places CHEBI:456216 on its products side with coefficient 1; its master-relative orientation is left_to_right. Source location `rhea.rdf.gz; rh:21141 rh:products rh:21140_R; rh:21140_R rh:contains1 <http://rdf.rhea-db.org/Participant_21140_compound_2710>; rh:compound <http://rdf.rhea-db.org/Compound_2710> / rh:chebi`
inosine + ATP => IMP + ADP + H(+) `RHEA:21141`	produces Stoichiometric coefficient 1.	hydron `CHEBI:15378`	RHEA:21141 Source assertion: The original directional Rhea reaction places CHEBI:15378 on its products side with coefficient 1; its master-relative orientation is left_to_right. Source location `rhea.rdf.gz; rh:21141 rh:products rh:21140_R; rh:21140_R rh:contains1 <http://rdf.rhea-db.org/Participant_21140_compound_3249>; rh:compound <http://rdf.rhea-db.org/Compound_3249> / rh:chebi`
`PathBank:SMP0002083`	has_part	alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate `RHEA:27644`	PathBank:SMP0002083 Source assertion: The primary Pathway's pathwayComponent explicitly contains Reactions/6047; the complete local biochemical event is represented by its independently grounded directional Rhea chemistry. Source location `bp:Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0002083']/bp:pathwayComponent[@rdf:resource='#Reactions/6047']; bp:BiochemicalReaction[@rdf:ID='Reactions/6047']`
`PathBank:SMP0002083`	has_part	adenosine + H2O + H(+) => inosine + NH4(+) `RHEA:24409`	PathBank:SMP0002083 Source assertion: The primary Pathway's pathwayComponent explicitly contains Reactions/6049; the complete local biochemical event is represented by its independently grounded directional Rhea chemistry. Source location `bp:Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0002083']/bp:pathwayComponent[@rdf:resource='#Reactions/6049']; bp:BiochemicalReaction[@rdf:ID='Reactions/6049']`
`PathBank:SMP0002083`	has_part	inosine + ATP => IMP + ADP + H(+) `RHEA:21141`	PathBank:SMP0002083 Source assertion: The primary Pathway's pathwayComponent explicitly contains Reactions/6053; the complete local biochemical event is represented by its independently grounded directional Rhea chemistry. Source location `bp:Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0002083']/bp:pathwayComponent[@rdf:resource='#Reactions/6053']; bp:BiochemicalReaction[@rdf:ID='Reactions/6053']`
`PathBank:SMP0002083`	has_part	Transport505 `PathBank:SMP0002083/Transports/505`	PathBank:SMP0002083 Source assertion: The native primary Pathway explicitly includes Transport505, separate from its three biochemical reactions. Source location `bp:Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0002083']/bp:pathwayComponent[@rdf:resource='#Transports/505']`
`PathBank:SMP0002083`	has_part Native non-elementary downstream interface; whole Aspartate Metabolism is not expanded into this record.	Aspartate Metabolism `PathBank:SMP0000809`	PathBank:SMP0002083 Source assertion: The primary Pathway includes SMP0000809 as a Pathway component; its local SubPathway instance contains only the IMP interface interaction, not a reaction list. Source location `bp:Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0002083']/bp:pathwayComponent; bp:Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0000809']/bp:pathwayComponent`
Transport505 `PathBank:SMP0002083/Transports/505`	has_input	Hydrogen Ion `PathBank:SMP0002083/Compound/PW_C040034_Periplasmic_Space`	PathBank:SMP0002083 Source assertion: Transport505 lists Compound/PW_C040034_Periplasmic_Space on bp:left, with native coefficient 1.0 and LEFT_TO_RIGHT conversionDirection. The exact proton ratio is a source assertion, not a primary coupling measurement. Source location `bp:Transport[@rdf:ID='Transports/505']/bp:left[@rdf:resource='#Compound/PW_C040034_Periplasmic_Space']; bp:Stoichiometry[@rdf:ID='Compound/PW_C040034_Periplasmic_Space/Stoichiometry/1.0']`
Transport505 `PathBank:SMP0002083/Transports/505`	has_input	Adenine `PathBank:SMP0002083/Compound/PW_C000024_Periplasmic_Space`	PathBank:SMP0002083 Source assertion: Transport505 lists Compound/PW_C000024_Periplasmic_Space on bp:left, with native coefficient 1.0 and LEFT_TO_RIGHT conversionDirection. The exact proton ratio is a source assertion, not a primary coupling measurement. Source location `bp:Transport[@rdf:ID='Transports/505']/bp:left[@rdf:resource='#Compound/PW_C000024_Periplasmic_Space']; bp:Stoichiometry[@rdf:ID='Compound/PW_C000024_Periplasmic_Space/Stoichiometry/1.0']`
Transport505 `PathBank:SMP0002083/Transports/505`	has_output	Adenine `PathBank:SMP0002083/Compound/PW_C000024_Cytosol`	PathBank:SMP0002083 Source assertion: Transport505 lists Compound/PW_C000024_Cytosol on bp:right, with native coefficient 1.0 and LEFT_TO_RIGHT conversionDirection. The exact proton ratio is a source assertion, not a primary coupling measurement. Source location `bp:Transport[@rdf:ID='Transports/505']/bp:right[@rdf:resource='#Compound/PW_C000024_Cytosol']; bp:Stoichiometry[@rdf:ID='Compound/PW_C000024_Cytosol/Stoichiometry/1.0']`
Transport505 `PathBank:SMP0002083/Transports/505`	has_output	Hydrogen Ion `PathBank:SMP0002083/Compound/PW_C040034_Cytosol`	PathBank:SMP0002083 Source assertion: Transport505 lists Compound/PW_C040034_Cytosol on bp:right, with native coefficient 1.0 and LEFT_TO_RIGHT conversionDirection. The exact proton ratio is a source assertion, not a primary coupling measurement. Source location `bp:Transport[@rdf:ID='Transports/505']/bp:right[@rdf:resource='#Compound/PW_C040034_Cytosol']; bp:Stoichiometry[@rdf:ID='Compound/PW_C040034_Cytosol/Stoichiometry/1.0']`
Adenine `PathBank:SMP0002083/Compound/PW_C000024_Periplasmic_Space`	located_in	periplasmic space `GO:0042597`	PathBank:SMP0002083 Source assertion: The native compartment-specific molecule points to #CellularLocation/Periplasmic_Space; its location is preserved separately from the unlocalized Rhea chemical form. Source location `bp:SmallMolecule[@rdf:ID='Compound/PW_C000024_Periplasmic_Space']/bp:cellularLocation; bp:CellularLocationVocabulary[@rdf:ID='CellularLocation/Periplasmic_Space']`
Hydrogen Ion `PathBank:SMP0002083/Compound/PW_C040034_Periplasmic_Space`	located_in	periplasmic space `GO:0042597`	PathBank:SMP0002083 Source assertion: The native compartment-specific molecule points to #CellularLocation/Periplasmic_Space; its location is preserved separately from the unlocalized Rhea chemical form. Source location `bp:SmallMolecule[@rdf:ID='Compound/PW_C040034_Periplasmic_Space']/bp:cellularLocation; bp:CellularLocationVocabulary[@rdf:ID='CellularLocation/Periplasmic_Space']`
Adenine `PathBank:SMP0002083/Compound/PW_C000024_Cytosol`	located_in	cytosol `GO:0005829`	PathBank:SMP0002083 Source assertion: The native compartment-specific molecule points to #CellularLocation/Cytosol; its location is preserved separately from the unlocalized Rhea chemical form. Source location `bp:SmallMolecule[@rdf:ID='Compound/PW_C000024_Cytosol']/bp:cellularLocation; bp:CellularLocationVocabulary[@rdf:ID='CellularLocation/Cytosol']`
Hydrogen Ion `PathBank:SMP0002083/Compound/PW_C040034_Cytosol`	located_in	cytosol `GO:0005829`	PathBank:SMP0002083 Source assertion: The native compartment-specific molecule points to #CellularLocation/Cytosol; its location is preserved separately from the unlocalized Rhea chemical form. Source location `bp:SmallMolecule[@rdf:ID='Compound/PW_C040034_Cytosol']/bp:cellularLocation; bp:CellularLocationVocabulary[@rdf:ID='CellularLocation/Cytosol']`
Inosinic acid `PathBank:SMP0002083/Compound/PW_C000114_Cytosol`	located_in	cytosol `GO:0005829`	PathBank:SMP0002083 Source assertion: The native compartment-specific molecule points to #CellularLocation/Cytosol; its location is preserved separately from the unlocalized Rhea chemical form. Source location `bp:SmallMolecule[@rdf:ID='Compound/PW_C000114_Cytosol']/bp:cellularLocation; bp:CellularLocationVocabulary[@rdf:ID='CellularLocation/Cytosol']`
Inosinic acid `PathBank:SMP0002083/Compound/PW_C000114_Cytoplasm`	located_in	cytoplasm `GO:0005737`	PathBank:SMP0002083 Source assertion: The native compartment-specific molecule points to #CellularLocation/Cytoplasm; its location is preserved separately from the unlocalized Rhea chemical form. Source location `bp:SmallMolecule[@rdf:ID='Compound/PW_C000114_Cytoplasm']/bp:cellularLocation; bp:CellularLocationVocabulary[@rdf:ID='CellularLocation/Cytoplasm']`
alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate `RHEA:27644`	has_input Native compartment view of adenine; not an additional stoichiometric substrate.	Adenine `PathBank:SMP0002083/Compound/PW_C000024_Cytosol`	PathBank:SMP0002083 Source assertion: Native Reactions/6047 uses Compound/PW_C000024_Cytosol (adenine). This is its compartment-specific source view, corresponding to the separately balanced adenine substrate. Source location `bp:BiochemicalReaction[@rdf:ID='Reactions/6047']/bp:left[@rdf:resource='#Compound/PW_C000024_Cytosol']; bp:SmallMoleculeReference[@rdf:ID='CompoundReference/PW_C000024']/bp:xref`
inosine + ATP => IMP + ADP + H(+) `RHEA:21141`	has_output Native generic output view; no extra product coefficient or protonation reaction is asserted.	Inosinic acid `PathBank:SMP0002083/Compound/PW_C000114_Cytosol`	PathBank:SMP0002083 Source assertion: Native Reactions/6053 outputs Compound/PW_C000114_Cytosol, whose reference is neutral inosinic acid CHEBI:17202. This source-view output is distinct from balanced Rhea IMP(2-). Source location `bp:BiochemicalReaction[@rdf:ID='Reactions/6053']/bp:right[@rdf:resource='#Compound/PW_C000114_Cytosol']; bp:SmallMoleculeReference[@rdf:ID='CompoundReference/PW_C000114']`
Aspartate Metabolism `PathBank:SMP0000809`	has_input Opaque native input interface, without an elementary equation or invented Cytosol-to-Cytoplasm transfer.	Inosinic acid `PathBank:SMP0002083/Compound/PW_C000114_Cytoplasm`	PathBank:SMP0002083 Source assertion: The SMP0000809 SubPathway contains Interaction581268 with participant Compound/PW_C000114_Cytoplasm, named SubPathwayInput. Source location `bp:Pathway[@rdf:about='http://identifiers.org/smpdb/SMP0000809']/bp:pathwayComponent; bp:Interaction[@rdf:ID='SubPathwayInteractions/581268']/bp:participant; bp:SmallMolecule[@rdf:ID='Compound/PW_C000114_Cytoplasm']/bp:name` PathBank:SMP0002083/PWML Source assertion: Native sub-pathway581268 references pathway551 and declares Compound114 as a sub-pathway-input. Sub-pathway-visualization595297 refers to581268 and contains a compound visualization with side Left. Source location `Original PWML lines24-38: sub-pathways/sub-pathway[id=581268]/reference-pathway-id=551 and sub-pathway-inputs/sub-pathway-input/element-id=114, element-type=Compound; lines8627-8645: sub-pathway-visualizations/sub-pathway-visualization[id=595297, sub-pathway-id=581268]/sub_pathway_compound_visualizations/sub-pathway-compound-visualization/side=Left`
Transport505 `PathBank:SMP0002083/Transports/505`	provides_input_for	alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate `RHEA:27644`	PathBank:SMP0002083 Source assertion: Transport505 has cytosolic adenine as its output, and Reactions/6047 has the exact same native molecule instance as input. Source location `bp:Transport[@rdf:ID='Transports/505']/bp:right; bp:BiochemicalReaction[@rdf:ID='Reactions/6047']/bp:left: #Compound/PW_C000024_Cytosol` RHEA:27644 Source assertion: The directional reaction consumes adenine CHEBI:16708. Source location `rhea.rdf.gz; rh:27644 rh:substrates rh:27642_R; Compound_4174 rh:chebi CHEBI:16708`
alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate `RHEA:27644`	provides_input_for	adenosine + H2O + H(+) => inosine + NH4(+) `RHEA:24409`	PathBank:SMP0002083 Source assertion: Native Reactions/6047 supplies the nucleoside used by Reactions/6049; both reference the same compartment-specific molecule. Source location `bp:BiochemicalReaction[@rdf:ID='Reactions/6047']/bp:right; bp:BiochemicalReaction[@rdf:ID='Reactions/6049']/bp:left` RHEA:27644 Source assertion: The directional upstream reaction produces CHEBI:16335. Source location `rhea.rdf.gz; rh:27644 rh:products / rh:contains / rh:compound / rh:chebi CHEBI:16335` RHEA:24409 Source assertion: The directional downstream reaction consumes CHEBI:16335. Source location `rhea.rdf.gz; rh:24409 rh:substrates / rh:contains / rh:compound / rh:chebi CHEBI:16335`
adenosine + H2O + H(+) => inosine + NH4(+) `RHEA:24409`	provides_input_for	inosine + ATP => IMP + ADP + H(+) `RHEA:21141`	PathBank:SMP0002083 Source assertion: Native Reactions/6049 supplies the nucleoside used by Reactions/6053; both reference the same compartment-specific molecule. Source location `bp:BiochemicalReaction[@rdf:ID='Reactions/6049']/bp:right; bp:BiochemicalReaction[@rdf:ID='Reactions/6053']/bp:left` RHEA:24409 Source assertion: The directional upstream reaction produces CHEBI:17596. Source location `rhea.rdf.gz; rh:24409 rh:products / rh:contains / rh:compound / rh:chebi CHEBI:17596` RHEA:21141 Source assertion: The directional downstream reaction consumes CHEBI:17596. Source location `rhea.rdf.gz; rh:21141 rh:substrates / rh:contains / rh:compound / rh:chebi CHEBI:17596`
purine nucleoside phosphorylase `MetaCyc:DEOD-CPLX`	has_part Native 6-copy assembly; has_part does not encode stoichiometry in a separate scalar field.	Purine nucleoside phosphorylase DeoD-type `UniProtKB:P0ABP8`	MetaCyc:DEOD-CPLX Source assertion: The META27 complex has 6 copies of DEOD-MONOMER; its component identity is independently grounded to P0ABP8. Source location `/ptools-xml/Protein[@frameid='DEOD-CPLX']/component[Protein/@frameid='DEOD-MONOMER']/coefficient` UniProtKB:P0ABP8 Source assertion: The reviewed record specifies a homohexamer, a trimer of homodimers (ECO:0000269 and HAMAP inference). Source location `/primaryAccession; /comments/10` PMID:30337572 Source assertion: The crystallographic structures are homohexamers of six identical 238-residue chains. The current reviewed sequence is 239 residues; processing is not inferred. Source location `BioC document/passages, passage40 Results assembly; passage63 Methods preparation` PathBank:SMP0002083 Source assertion: The native DeoD complex has six copies of Protein6182; its protein reference contains the UniProt P0ABP8 unification xref. Source location `bp:Complex[@rdf:ID='ProteinComplex/4056_Cytosol']/bp:componentStoichiometry; bp:ProteinReference[@rdf:ID='ProteinReference/6182']/bp:xref`
inosine/guanosine kinase `MetaCyc:CPLX0-322`	has_part Native 2-copy assembly; has_part does not encode stoichiometry in a separate scalar field.	Guanosine-inosine kinase `UniProtKB:P0AEW6`	MetaCyc:CPLX0-322 Source assertion: The META27 complex has 2 copies of GSK-MONOMER; its component identity is independently grounded to P0AEW6. Source location `/ptools-xml/Protein[@frameid='CPLX0-322']/component[Protein/@frameid='GSK-MONOMER']/coefficient` UniProtKB:P0AEW6 Source assertion: The reviewed record specifies a homodimer (ECO:0000269, PMID10879466). Source location `/primaryAccession; /comments/8` PMID:32857952 Source assertion: Gsk is dimeric without ppGpp in SEC-MALS; ppGpp shifts it toward a tetramer in a concentration-dependent manner. Dimer-interface mutants lose activity. Source location `section#S3; section#S4; figure#F1; figure#F2` MetaCyc:GSK-MONOMER Source assertion: The native GSK-MONOMER has a UniProt unification link to P0AEW6, bridging the complex subunit to the reviewed protein. Source location `/ptools-xml/Protein[@frameid="GSK-MONOMER"]/dblink[dblink-db="UNIPROT"]; /ptools-xml/Protein/component-of`
DNA-binding transcriptional repressor PurR `MetaCyc:PC00033`	has_part Native 2-copy assembly; has_part does not encode stoichiometry in a separate scalar field.	HTH-type transcriptional repressor PurR `UniProtKB:P0ACP7`	MetaCyc:PC00033 Source assertion: The META27 complex has 2 copies of PD00219; its component identity is independently grounded to P0ACP7. Source location `/ptools-xml/Protein[@frameid='PC00033']/component[Protein/@frameid='PD00219']/coefficient` UniProtKB:P0ACP7 Source assertion: The reviewed record specifies a homodimer supported by experimental literature (ECO:0000269). Source location `/primaryAccession; /comments/2` MetaCyc:PD00219 Source assertion: Native PurR monomer PD00219 has UniProt unification link P0ACP7 and component-of PC00033. Source location `/ptools-xml/Protein[@frameid="PD00219"]/dblink[dblink-db="UNIPROT"]; /ptools-xml/Protein/component-of`
purine nucleoside phosphorylase `MetaCyc:DEOD-CPLX`	catalyzes	alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate `RHEA:27644`	PathBank:SMP0002083 Source assertion: ReactionCatalysis6011 controls adenine-to-adenosine Reactions/6047 through Complex4056, which explicitly contains six Protein6182 (P0ABP8) copies. Source location `bp:Catalysis[@rdf:ID='ReactionCatalysis/6011']; bp:Complex[@rdf:ID='ProteinComplex/4056_Cytosol']; bp:ProteinReference[@rdf:ID='ProteinReference/6182']` UniProtKB:P0ABP8 Source assertion: Reviewed DeoD catalyzes reversible adenosine phosphorolysis; the selected synthesis direction is the native pathway orientation (experimental ECO:0000269). Source location `/comments/0; /comments/4; /comments/10`
Adenosine deaminase `UniProtKB:P22333`	catalyzes	adenosine + H2O + H(+) => inosine + NH4(+) `RHEA:24409`	UniProtKB:P22333 Source assertion: The reviewed adenosine deaminase explicitly lists physiological RHEA:24409, converting adenosine to inosine and ammonium; ECO:0000269 and HAMAP ECO:0000255 are preserved. Source location `/comments/1/physiologicalReactions; /primaryAccession` PathBank:SMP0002083 Source assertion: ReactionCatalysis6013 connects Add Protein6409 to Reactions/6049. Source location `bp:Catalysis[@rdf:ID='ReactionCatalysis/6013']; bp:ProteinReference[@rdf:ID='ProteinReference/6409']`
inosine/guanosine kinase `MetaCyc:CPLX0-322`	catalyzes	inosine + ATP => IMP + ADP + H(+) `RHEA:21141`	UniProtKB:P0AEW6 Source assertion: The reviewed protein lists physiological RHEA:21141 and a homodimer assembly, with experimental ECO:0000269 evidence. Source location `/comments/2/physiologicalReactions; /comments/8` PMID:32857952 Source assertion: Purified Gsk was assayed with inosine and ATP-Mg; IMP formation was coupled to IMP dehydrogenase and NADH readout. The dimer interface is required for activity. Source location `section#S3; section#S4; section#S48` PMID:765747 Source assertion: In the specified K-12 mutant comparison, adding the gsk lesion reduced guanosine kinase activity and also lowered measured inosine kinase activity; adenosine kinase activity was unchanged. No complete-route flux is inferred. Source location `Original seven-page PDF, printed p89 Table4; strain definitions p87 Table1`
Adenine permease AdeP `UniProtKB:P31466`	catalyzes	Transport505 `PathBank:SMP0002083/Transports/505`	PathBank:SMP0002083 Source assertion: TransportCatalysis436 controls Transport505 through Protein7110, whose reference identifies UniProt P31466. Source location `bp:Catalysis[@rdf:ID='TransportCatalysis/436']; bp:ProteinReference[@rdf:ID='ProteinReference/7110']` PMID:24214977 Source assertion: PurP was directly identified as a high-affinity adenine transporter (Km about 1 micromolar). Constructs came from T184; uptake hosts were specified mutant strains. This does not measure proton stoichiometry. Source location `section#sec2; section#sec12; section#T1` PMID:6198438 Source assertion: The indexed abstract reports proton-motive-force dependence and metabolic trapping of adenine uptake. Only the abstract was inspected. Source location `Europe PMC core resultList/result[id=6198438]/abstractText`
Adenine permease AdeP `UniProtKB:P31466`	located_in	plasma membrane `GO:0005886`	UniProtKB:P31466 Source assertion: Reviewed AdeP is a multipass cell-inner-membrane protein (ECO:0000269). Source location `/comments/3/subcellularLocations`
Adenosine deaminase `UniProtKB:P22333`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P22333 Source assertion: One Zn(2+) per Add subunit is annotated from HAMAP MF_00540 with ECO:0000255; this is an inference, not a directly inspected metal-occupancy experiment. Source location `/comments/3/cofactors; /comments/3/note`
inosine/guanosine kinase `MetaCyc:CPLX0-322`	has_cofactor	magnesium(2+) `CHEBI:18420`	UniProtKB:P0AEW6 Source assertion: Mg(2+) is the annotated cofactor. Free Mg(2+) in addition to Mg-ATP is described as probable; experimental ECO:0000269 and HAMAP ECO:0000255 are retained. Source location `/comments/3` PMID:32857952 Source assertion: The inosine kinase assay used 5 mM ATP-Mg and 5 mM MgCl2; these are measured assay conditions, not resolved microscopic occupancy. Source location `section#S48`
GDP(3-) `CHEBI:58189`	inhibits Condition-dependent Gsk population; this edge does not assert an isolated monomer or an obligate tetramer.	Guanosine-inosine kinase `UniProtKB:P0AEW6`	PMID:32857952 Source assertion: GDP binds and inhibits Gsk; ligands shift the dimer/tetramer equilibrium. ppGpp-bound tetramers are less active than ppGpp-bound dimers. Charged ChEBI forms identify the ligand, not measured assay protonation. Source location `section#S3; section#S5; figure#F1; figure#F3`
guanosine 3',5'-bis(diphosphate)(5-) `CHEBI:77828`	inhibits Condition-dependent Gsk population; this edge does not assert an isolated monomer or an obligate tetramer.	Guanosine-inosine kinase `UniProtKB:P0AEW6`	PMID:32857952 Source assertion: ppGpp binds and inhibits Gsk; ligands shift the dimer/tetramer equilibrium. ppGpp-bound tetramers are less active than ppGpp-bound dimers. Charged ChEBI forms identify the ligand, not measured assay protonation. Source location `section#S3; section#S5; figure#F1; figure#F3`
potassium(1+) `CHEBI:29103`	activates Database-reported assay regulation; no physiological ion concentration or cofactor role is inferred.	Guanosine-inosine kinase `UniProtKB:P0AEW6`	UniProtKB:P0AEW6 Source assertion: K(+) stimulates kinase activity in the reviewed activity-regulation comment (ECO:0000269, PMID7665468). The cited original was accessible only as an abstract; quantitative conditions are not asserted. Source location `/comments/4`
copper(2+) `CHEBI:29036`	inhibits Database-reported assay regulation; no physiological ion concentration or cofactor role is inferred.	Guanosine-inosine kinase `UniProtKB:P0AEW6`	UniProtKB:P0AEW6 Source assertion: Cu(2+) inhibits both guanosine and inosine kinase activities in the reviewed activity-regulation comment (ECO:0000269, PMID7665468). The cited original was accessible only as an abstract; quantitative conditions are not asserted. Source location `/comments/4`
zinc(2+) `CHEBI:29105`	inhibits Database-reported assay regulation; no physiological ion concentration or cofactor role is inferred.	Guanosine-inosine kinase `UniProtKB:P0AEW6`	UniProtKB:P0AEW6 Source assertion: Zn(2+) inhibits both guanosine and inosine kinase activities in the reviewed activity-regulation comment (ECO:0000269, PMID7665468). The cited original was accessible only as an abstract; quantitative conditions are not asserted. Source location `/comments/4`
hypoxanthine `CHEBI:17368`	activates Activation of repressor DNA binding, which enables transcriptional repression.	DNA-binding transcriptional repressor PurR `MetaCyc:PC00033`	UniProtKB:P0ACP7 Source assertion: hypoxanthine is an alternative purine corepressor that allosterically activates homodimeric PurR DNA binding (ECO:0000269). Hypoxanthine and guanine are alternatives, not both obligatorily present. Source location `/comments/0; /comments/2`
guanine `CHEBI:16235`	activates Activation of repressor DNA binding, which enables transcriptional repression.	DNA-binding transcriptional repressor PurR `MetaCyc:PC00033`	UniProtKB:P0ACP7 Source assertion: guanine is an alternative purine corepressor that allosterically activates homodimeric PurR DNA binding (ECO:0000269). Hypoxanthine and guanine are alternatives, not both obligatorily present. Source location `/comments/0; /comments/2`
DNA-binding transcriptional repressor PurR `MetaCyc:PC00033`	inhibits PurR represses adeP/yieG gene expression; no encoding edge is fabricated in the current predicate vocabulary.	adeP `Entrez:948224`	PMID:21572102 Source assertion: Combined ChIP-chip and transcription analysis identifies yieG among directly PurR-repressed genes in MG1655. Direct repression is assigned to adeP transcription, not transport-protein catalytic activity. Source location `section#sec12` UniProtKB:P31466 Source assertion: The reviewed AdeP protein lists adeP, purP and yieG as gene names/synonyms, grounding the primary paper gene name. Source location `/genes/0` Entrez:948224 Source assertion: NCBI Gene948224 is adeP, locus b3714, MG1655 taxon511145, with Swiss-Prot P31466 cross-reference. Source location `/Entrezgene-Set/Entrezgene/Entrezgene_gene/Gene-ref; //Dbtag[Dbtag_db="UniProtKB/Swiss-Prot"]; //Org-ref_db/Dbtag[Dbtag_db="taxon"]`
adenine `CHEBI:16708`	activates Adenine-induced add transcription under the measured culture conditions; no direct Add enzyme activation is asserted.	add `Entrez:945851`	PMID:21572102 Source assertion: Adenine supplementation increased add transcript abundance 17.61-fold in the measured MG1655 comparison. The study explicitly finds add not directly regulated by PurR; this is an expression response, not direct ligand binding. Source location `section#sec9; section#sec13` Entrez:945851 Source assertion: NCBI Gene945851 is add, locus b1623, MG1655 taxon511145, with Swiss-Prot P22333 cross-reference. Source location `/Entrezgene-Set/Entrezgene/Entrezgene_gene/Gene-ref; //Dbtag[Dbtag_db="UniProtKB/Swiss-Prot"]; //Org-ref_db/Dbtag[Dbtag_db="taxon"]`
Purine nucleoside phosphorylase DeoD-type `UniProtKB:P0ABP8`	located_in	cytosol `GO:0005829`	PathBank:SMP0002083 Source assertion: Native Protein/6182_Cytosol has cellularLocation Cytosol; its entityReference identifies P0ABP8. Source location `bp:Protein[@rdf:ID='Protein/6182_Cytosol']/bp:cellularLocation; bp:Protein[@rdf:ID='Protein/6182_Cytosol']/bp:entityReference`
Adenosine deaminase `UniProtKB:P22333`	located_in	cytosol `GO:0005829`	PathBank:SMP0002083 Source assertion: Native Protein/6409_Cytosol has cellularLocation Cytosol; its entityReference identifies P22333. Source location `bp:Protein[@rdf:ID='Protein/6409_Cytosol']/bp:cellularLocation; bp:Protein[@rdf:ID='Protein/6409_Cytosol']/bp:entityReference`
Guanosine-inosine kinase `UniProtKB:P0AEW6`	located_in	cytosol `GO:0005829`	PathBank:SMP0002083 Source assertion: Native Protein/6254_Cytosol has cellularLocation Cytosol; its entityReference identifies P0AEW6. Source location `bp:Protein[@rdf:ID='Protein/6254_Cytosol']/bp:cellularLocation; bp:Protein[@rdf:ID='Protein/6254_Cytosol']/bp:entityReference`

References

UniProtKB:P0ABP8 Purine nucleoside phosphorylase DeoD-type (source version: Reviewed entry 149; sequence 2; annotation 2026-09-02)
UniProtKB:P22333 Adenosine deaminase (source version: Reviewed entry 183; sequence 2; annotation 2026-09-02)
UniProtKB:P0AEW6 Guanosine-inosine kinase (source version: Reviewed entry 135; sequence 1; annotation 2026-09-02)
UniProtKB:P31466 Adenine permease AdeP (source version: Reviewed entry 161; sequence 2; annotation 2026-01-28)
UniProtKB:P0ACP7 HTH-type transcriptional repressor PurR (source version: Reviewed entry 145; sequence 2; annotation 2026-09-02)
MetaCyc:DEOD-CPLX purine nucleoside phosphorylase (source version: META PGDB 27.0; acquired 2026-10-11)
MetaCyc:CPLX0-322 inosine/guanosine kinase (source version: META PGDB 27.0; acquired 2026-10-11)
MetaCyc:PC00033 DNA-binding transcriptional repressor PurR (source version: META PGDB 27.0; acquired 2026-10-11)
Entrez:948224 adeP (source version: NCBI Gene original fetched 2026-10-11; update 2026-09-03)
Entrez:945851 add (source version: NCBI Gene original fetched 2026-10-11; update 2026-09-03)
PathBank:SMP0002083 Adenine and Adenosine Salvage II (source version: Current original acquired 2026-10-11; source page updated 2026-08-11 (not a global release))
RHEA:27644 alpha-D-ribose 1-phosphate + adenine => adenosine + phosphate (source version: Rhea 142 / 2026-09-02; retained original rehashed; hash covers complete original gzip)
RHEA:24409 adenosine + H2O + H(+) => inosine + NH4(+) (source version: Rhea 142 / 2026-09-02; retained original rehashed; hash covers complete original gzip)
RHEA:21141 inosine + ATP => IMP + ADP + H(+) (source version: Rhea 142 / 2026-09-02; retained original rehashed; hash covers complete original gzip)
PathBank:SMP0002083/PWML Current native pathway diagram markup (source version: Original fetched 2026-10-11; strict XML fails at unbound option prefix line 8275; bounded raw-text interface inspected)
PMID:32857952 ppGpp Coordinates Nucleotide and Amino-Acid Synthesis in E. coli During Starvation. (source version: Relevant primary Results S3-S5, F1-F3 and methods S45/S48 inspected; complete original retained; original hash)
PMID:24214977 Functional Identification of the Hypoxanthine/Guanine Transporters YjcD and YgfQ and the Adenine Transporters PurP and YicO of Escherichia coli K-12 (source version: Relevant primary introduction, methods, transport results and discussion inspected; complete original retained; original hash)
PMID:21572102 The PurR regulon in Escherichia coli K-12 MG1655 (source version: Relevant primary Results sec9-sec13 and Discussion sec14 inspected; complete original retained; original hash)
PMID:30337572 Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis (source version: Retained complete BioC XML; relevant passages 40-52 and 63 inspected; original hash)
PMID:765747 Location on the chromosome of Escherichia coli of genes governing purine metabolism. Adenosine deaminase (add), guanosine kinase (gsk) and hypoxanthine phosphoribosyltransferase (hpt). (source version: Retained 7-page primary PDF; all pages extracted; pp85,87,89,90 figures/tables visually inspected; original hash)
PMID:6198438 Transport of nucleic acid bases into Escherichia coli. (source version: Indexed primary abstract only; requested full PDF access failed; original hash)
MetaCyc:GSK-MONOMER inosine/guanosine kinase (source version: META PGDB 27.0; original fetched 2026-10-11)
MetaCyc:PD00219 DNA-binding transcriptional repressor PurR (source version: META PGDB 27.0; original fetched 2026-10-11)

Curation history

2026-10-11T22:21:42Z codex
- CREATE — Add complete Adenine and Adenosine Salvage II with scoped microbial evidence
  Added PathBank:SMP0002083 with 47 named IDs, 39 participants, 5 reaction/process nodes, 57 edges, 81 evidence items, and 23 references. The fifth node is the opaque Aspartate Metabolism input interface, not an invented elementary reaction. Exact target SHA256 8b8eb42ace01b8d663ecff30a85e47d6de7b25e7cde785b268655ab281153157. Original full independent review found the PWML interface evidence locator defect #422; the accepted successor changes exactly two evidence fields and preserves all biology. External original-RDF replay, correction controls, and independent exact-delta reassessment passed with strain, compartment/protonation, regulatory, conditional-assembly, and abstract-only evidence limits retained. The current 222-record duplicate audit included ignored/hidden files and followed symlinks, with actual merged tree 929b9b0578a280aed04e20cf33d412b13ba0d822 independently bridged. The dossier research/pathway_additions/2026-10-11-next-222 archives the original and resolved finding separately. Maintained rendering, full corpus gates, graph/KGX preservation, and canonical review follow adoption and are not claimed complete by this event. Data licensing is deferred for public release; no source-exhaustion claim.
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