desferrioxamine B biosynthesis

MetaCyc:PWY-6376

Complete five-transformation desferrioxamine B biosynthesis in Streptomyces coelicolor A3(2)/M145. Lysine decarboxylation and cadaverine N-hydroxylation supply both the succinylated HSC and acetylated HAC branches; DesD combines two HSC and one HAC in two successive ligations represented by one complete net reaction. RXN-11001 retains the source-issued complete organic transformation. Primary-supported successive adenylations imply two ATP, two AMP, two diphosphate and two H+ with no net water in the selected ionic forms. Native MetaCyc and KEGG instead encode one ATP and water. This is an explicit curated coefficient correction, not exact native-equation equivalence or a measured ATP/product coupling ratio. Native ionic compound identities preserve hydroxycadaverine(+1), HAC(+1), zwitterionic HSC and B(+1); old neutral ChEBI cross-references are not treated as exact. The native reaction retains generic reduced/oxidized electron-acceptor classes. It does not identify a specific physiological coelicolor donor. The S. sviceus NADPH/NADH experiments and the sequence-unmatched 2023 DesABC preparation do not establish donor specificity for this exact coelicolor protein. The coelicolor DesB activity remains a proposed native assignment. Current automatic UniProt MbtG/MbtK function names conflict with native/experimental DesB/DesC roles and are not adopted. PLP and FAD cofactor edges preserve current automatic inference rather than direct binding measurements on the selected proteins. Direct DesA evidence is abstract-limited; the M145-derived DesC preparation supports both acylations and monomeric behavior, but the complete construct sequence is not verified. The 2023 DesABC construct sequences differ from current coelicolor entries and are not transferred. In contrast, the coelicolor DesD native core is sequence-verified against the 2022 construct reused in 2023; the source-defined dimer is retained. Primary model details, physiological precursor-pool control, exact donor specificity and assembly outside the measured preparations remain limited. E synthesis/cyclization, ferric loading, uptake, longer-chain congeners and hypothetical DesG/DesH tailoring lie outside the complete B boundary.

Pathway type

desferrioxamine b biosynthesis

Organism scope

Streptomyces coelicolor A3(2) NCBITaxon:100226

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Pathway network

32 nodes · 50 asserted directed edges

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Streptomyces coelicolor A3(2) `NCBITaxon:100226`	taxon
water `CHEBI:15377`	small molecule
hydron `CHEBI:15378`	small molecule
dioxygen `CHEBI:15379`	small molecule
carbon dioxide `CHEBI:16526`	small molecule
ATP(4-) `CHEBI:30616`	small molecule
L-lysinium(1+) `CHEBI:32551`	small molecule
diphosphate(3-) `CHEBI:33019`	small molecule
adenosine 5'-monophosphate(2-) `CHEBI:456215`	small molecule
coenzyme A(4-) `CHEBI:57287`	small molecule
acetyl-CoA(4-) `CHEBI:57288`	small molecule
succinyl-CoA(5-) `CHEBI:57292`	small molecule
FAD(3-) `CHEBI:57692`	cofactor
cadaverine(2+) `CHEBI:58384`	small molecule
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
an oxidized electron acceptor `MetaCyc:Acceptor`	chemical entity
N-hydroxycadaverine `MetaCyc:CPD-11953`	small molecule
N-hydroxy-N-succinylcadaverine `MetaCyc:CPD-11955`	small molecule
N-hydroxy-N-acetylcadaverine `MetaCyc:CPD-11959`	small molecule
desferrioxamine B `MetaCyc:CPD-3764`	small molecule
a reduced electron acceptor `MetaCyc:Donor-H2`	chemical entity
lysine decarboxylase `MetaCyc:SCO2782-MONOMER`	protein
cadaverine hydroxylase `MetaCyc:SCO2783-MONOMER`	protein
hydroxycadaverine acyl transferase `MetaCyc:SCO2784-MONOMER`	protein
desferrioxamine E synthetase monomer `MetaCyc:SCO2785-MONOMER`	protein
desferrioxamine E synthetase `MetaCyc:CPLX-7949`	complex
L-lysine decarboxylation `MetaCyc:LYSDECARBOX-RXN`	molecular activity	left to right
Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	molecular activity	left to right
N-Hydroxycadaverine succinylation `MetaCyc:RXN-10996`	molecular activity	left to right
N-Hydroxycadaverine acetylation `MetaCyc:RXN-10999`	molecular activity	left to right
DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	molecular activity	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
hydron `CHEBI:15378`	consumes	L-lysine decarboxylation `MetaCyc:LYSDECARBOX-RXN`	MetaCyc:LYSDECARBOX-RXN Source assertion: The native left side assigns PROTON with coefficient 1. Source location `Reaction[@frameid="LYSDECARBOX-RXN"]/left[Compound/@frameid="PROTON"]; coefficient (absent means 1)` MetaCyc:PROTON Source assertion: The source PROTON CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="PROTON"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:15378 independently has the same full InChI as native PROTON, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:15378",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
L-lysinium(1+) `CHEBI:32551`	consumes	L-lysine decarboxylation `MetaCyc:LYSDECARBOX-RXN`	MetaCyc:LYSDECARBOX-RXN Source assertion: The native left side assigns LYS with coefficient 1. Source location `Reaction[@frameid="LYSDECARBOX-RXN"]/left[Compound/@frameid="LYS"]; coefficient (absent means 1)` MetaCyc:LYS Source assertion: The source LYS CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="LYS"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:32551 independently has the same full InChI as native LYS, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:32551",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
L-lysine decarboxylation `MetaCyc:LYSDECARBOX-RXN`	produces	carbon dioxide `CHEBI:16526`	MetaCyc:LYSDECARBOX-RXN Source assertion: The native right side assigns CARBON-DIOXIDE with coefficient 1. Source location `Reaction[@frameid="LYSDECARBOX-RXN"]/right[Compound/@frameid="CARBON-DIOXIDE"]; coefficient (absent means 1)` MetaCyc:CARBON-DIOXIDE Source assertion: The source CARBON-DIOXIDE CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="CARBON-DIOXIDE"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:16526 independently has the same full InChI as native CARBON-DIOXIDE, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:16526",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
L-lysine decarboxylation `MetaCyc:LYSDECARBOX-RXN`	produces	cadaverine(2+) `CHEBI:58384`	MetaCyc:LYSDECARBOX-RXN Source assertion: The native right side assigns CADAVERINE with coefficient 1. Source location `Reaction[@frameid="LYSDECARBOX-RXN"]/right[Compound/@frameid="CADAVERINE"]; coefficient (absent means 1)` MetaCyc:CADAVERINE Source assertion: The source CADAVERINE CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="CADAVERINE"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:58384 independently has the same full InChI as native CADAVERINE, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:58384",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
cadaverine(2+) `CHEBI:58384`	consumes	Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	MetaCyc:RXN-10995 Source assertion: The native left side assigns CADAVERINE with coefficient 1. Source location `Reaction[@frameid="RXN-10995"]/left[Compound/@frameid="CADAVERINE"]; coefficient (absent means 1)` MetaCyc:CADAVERINE Source assertion: The source CADAVERINE CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="CADAVERINE"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:58384 independently has the same full InChI as native CADAVERINE, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:58384",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
dioxygen `CHEBI:15379`	consumes	Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	MetaCyc:RXN-10995 Source assertion: The native left side assigns OXYGEN-MOLECULE with coefficient 1. Source location `Reaction[@frameid="RXN-10995"]/left[Compound/@frameid="OXYGEN-MOLECULE"]; coefficient (absent means 1)` MetaCyc:OXYGEN-MOLECULE Source assertion: The source OXYGEN-MOLECULE CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="OXYGEN-MOLECULE"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:15379 independently has the same full InChI as native OXYGEN-MOLECULE, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:15379",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
a reduced electron acceptor `MetaCyc:Donor-H2`	consumes The native reaction retains generic reduced/oxidized electron-acceptor classes. It does not identify a specific physiological coelicolor donor. The S. sviceus NADPH/NADH experiments and the sequence-unmatched 2023 DesABC preparation do not establish donor specificity for this exact coelicolor protein.	Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	MetaCyc:RXN-10995 Source assertion: The native left side assigns Donor-H2 with coefficient 1. Source location `Reaction[@frameid="RXN-10995"]/left[Compound/@frameid="Donor-H2"]; coefficient (absent means 1)` MetaCyc:Donor-H2 Source assertion: This native object denotes a generic electron-acceptor redox class rather than a specific flavin, nicotinamide donor or physiological partner. Source location `Compound/common-name; parent; comment; dblink`
Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	produces	N-hydroxycadaverine `MetaCyc:CPD-11953`	MetaCyc:RXN-10995 Source assertion: The native right side assigns CPD-11953 with coefficient 1. Source location `Reaction[@frameid="RXN-10995"]/right[Compound/@frameid="CPD-11953"]; coefficient (absent means 1)` MetaCyc:CPD-11953 Source assertion: The independently issued native compound preserves its CML structure and ionic form; stale external chemical cross-references are not treated as exact equivalence. Source location `Compound[@frameid="CPD-11953"]/cml/molecule; inchi; dblink`
Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	produces	water `CHEBI:15377`	MetaCyc:RXN-10995 Source assertion: The native right side assigns WATER with coefficient 1. Source location `Reaction[@frameid="RXN-10995"]/right[Compound/@frameid="WATER"]; coefficient (absent means 1)` MetaCyc:WATER Source assertion: The source WATER CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="WATER"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:15377 independently has the same full InChI as native WATER, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:15377",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	produces The native reaction retains generic reduced/oxidized electron-acceptor classes. It does not identify a specific physiological coelicolor donor. The S. sviceus NADPH/NADH experiments and the sequence-unmatched 2023 DesABC preparation do not establish donor specificity for this exact coelicolor protein.	an oxidized electron acceptor `MetaCyc:Acceptor`	MetaCyc:RXN-10995 Source assertion: The native right side assigns Acceptor with coefficient 1. Source location `Reaction[@frameid="RXN-10995"]/right[Compound/@frameid="Acceptor"]; coefficient (absent means 1)` MetaCyc:Acceptor Source assertion: This native object denotes a generic electron-acceptor redox class rather than a specific flavin, nicotinamide donor or physiological partner. Source location `Compound/common-name; parent; comment; dblink`
Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	produces	hydron `CHEBI:15378`	MetaCyc:RXN-10995 Source assertion: The native right side assigns PROTON with coefficient 1. Source location `Reaction[@frameid="RXN-10995"]/right[Compound/@frameid="PROTON"]; coefficient (absent means 1)` MetaCyc:PROTON Source assertion: The source PROTON CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="PROTON"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:15378 independently has the same full InChI as native PROTON, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:15378",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
N-hydroxycadaverine `MetaCyc:CPD-11953`	consumes	N-Hydroxycadaverine succinylation `MetaCyc:RXN-10996`	MetaCyc:RXN-10996 Source assertion: The native left side assigns CPD-11953 with coefficient 1. Source location `Reaction[@frameid="RXN-10996"]/left[Compound/@frameid="CPD-11953"]; coefficient (absent means 1)` MetaCyc:CPD-11953 Source assertion: The independently issued native compound preserves its CML structure and ionic form; stale external chemical cross-references are not treated as exact equivalence. Source location `Compound[@frameid="CPD-11953"]/cml/molecule; inchi; dblink`
succinyl-CoA(5-) `CHEBI:57292`	consumes	N-Hydroxycadaverine succinylation `MetaCyc:RXN-10996`	MetaCyc:RXN-10996 Source assertion: The native left side assigns SUC-COA with coefficient 1. Source location `Reaction[@frameid="RXN-10996"]/left[Compound/@frameid="SUC-COA"]; coefficient (absent means 1)` MetaCyc:SUC-COA Source assertion: The source SUC-COA CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="SUC-COA"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:57292 independently has the same full InChI as native SUC-COA, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:57292",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
N-Hydroxycadaverine succinylation `MetaCyc:RXN-10996`	produces	N-hydroxy-N-succinylcadaverine `MetaCyc:CPD-11955`	MetaCyc:RXN-10996 Source assertion: The native right side assigns CPD-11955 with coefficient 1. Source location `Reaction[@frameid="RXN-10996"]/right[Compound/@frameid="CPD-11955"]; coefficient (absent means 1)` MetaCyc:CPD-11955 Source assertion: The independently issued native compound preserves its CML structure and ionic form; stale external chemical cross-references are not treated as exact equivalence. Source location `Compound[@frameid="CPD-11955"]/cml/molecule; inchi; dblink`
N-Hydroxycadaverine succinylation `MetaCyc:RXN-10996`	produces	coenzyme A(4-) `CHEBI:57287`	MetaCyc:RXN-10996 Source assertion: The native right side assigns CO-A with coefficient 1. Source location `Reaction[@frameid="RXN-10996"]/right[Compound/@frameid="CO-A"]; coefficient (absent means 1)` MetaCyc:CO-A Source assertion: The source CO-A CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="CO-A"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:57287 independently has the same full InChI as native CO-A, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:57287",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
N-hydroxycadaverine `MetaCyc:CPD-11953`	consumes	N-Hydroxycadaverine acetylation `MetaCyc:RXN-10999`	MetaCyc:RXN-10999 Source assertion: The native left side assigns CPD-11953 with coefficient 1. Source location `Reaction[@frameid="RXN-10999"]/left[Compound/@frameid="CPD-11953"]; coefficient (absent means 1)` MetaCyc:CPD-11953 Source assertion: The independently issued native compound preserves its CML structure and ionic form; stale external chemical cross-references are not treated as exact equivalence. Source location `Compound[@frameid="CPD-11953"]/cml/molecule; inchi; dblink`
acetyl-CoA(4-) `CHEBI:57288`	consumes	N-Hydroxycadaverine acetylation `MetaCyc:RXN-10999`	MetaCyc:RXN-10999 Source assertion: The native left side assigns ACETYL-COA with coefficient 1. Source location `Reaction[@frameid="RXN-10999"]/left[Compound/@frameid="ACETYL-COA"]; coefficient (absent means 1)` MetaCyc:ACETYL-COA Source assertion: The source ACETYL-COA CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="ACETYL-COA"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:57288 independently has the same full InChI as native ACETYL-COA, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:57288",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
N-Hydroxycadaverine acetylation `MetaCyc:RXN-10999`	produces	N-hydroxy-N-acetylcadaverine `MetaCyc:CPD-11959`	MetaCyc:RXN-10999 Source assertion: The native right side assigns CPD-11959 with coefficient 1. Source location `Reaction[@frameid="RXN-10999"]/right[Compound/@frameid="CPD-11959"]; coefficient (absent means 1)` MetaCyc:CPD-11959 Source assertion: The independently issued native compound preserves its CML structure and ionic form; stale external chemical cross-references are not treated as exact equivalence. Source location `Compound[@frameid="CPD-11959"]/cml/molecule; inchi; dblink`
N-Hydroxycadaverine acetylation `MetaCyc:RXN-10999`	produces	coenzyme A(4-) `CHEBI:57287`	MetaCyc:RXN-10999 Source assertion: The native right side assigns CO-A with coefficient 1. Source location `Reaction[@frameid="RXN-10999"]/right[Compound/@frameid="CO-A"]; coefficient (absent means 1)` MetaCyc:CO-A Source assertion: The source CO-A CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="CO-A"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:57287 independently has the same full InChI as native CO-A, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:57287",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
N-hydroxy-N-succinylcadaverine `MetaCyc:CPD-11955`	consumes RXN-11001 retains the source-issued complete organic transformation. Primary-supported successive adenylations imply two ATP, two AMP, two diphosphate and two H+ with no net water in the selected ionic forms. Native MetaCyc and KEGG instead encode one ATP and water. This is an explicit curated coefficient correction, not exact native-equation equivalence or a measured ATP/product coupling ratio.	DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	MetaCyc:RXN-11001 Source assertion: The native left side assigns CPD-11955 with coefficient 2. Source location `Reaction[@frameid="RXN-11001"]/left[Compound/@frameid="CPD-11955"]; coefficient (absent means 1)` PMID:37207292 Source assertion: The complete organic assembly combines two HSC and one HAC. Figure 4 uses two successive ATP-dependent adenylation/condensation cycles; the curated net left coefficient for CPD-11955 is 2. Source location `Original author manuscript Figure 3 p.11; Figure 4 p.12; Results/discussion pp.3–5` PMID:42630954 Source assertion: The updated model describes formation of HSC-HSC-AMP after the first condensation, followed by HAC capping to form B; the co-substrate coefficients are derived from two cycles, not a measured coupling ratio. Source location `PMC13495013 body/sec[@id="sec1"]/p[3]; body/sec[@id="sec3"]/p[5]` MetaCyc:CPD-11955 Source assertion: The independently issued native compound preserves its CML structure and ionic form; stale external chemical cross-references are not treated as exact equivalence. Source location `Compound[@frameid="CPD-11955"]/cml/molecule; inchi; dblink`
N-hydroxy-N-acetylcadaverine `MetaCyc:CPD-11959`	consumes RXN-11001 retains the source-issued complete organic transformation. Primary-supported successive adenylations imply two ATP, two AMP, two diphosphate and two H+ with no net water in the selected ionic forms. Native MetaCyc and KEGG instead encode one ATP and water. This is an explicit curated coefficient correction, not exact native-equation equivalence or a measured ATP/product coupling ratio.	DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	MetaCyc:RXN-11001 Source assertion: The native left side assigns CPD-11959 with coefficient 1. Source location `Reaction[@frameid="RXN-11001"]/left[Compound/@frameid="CPD-11959"]; coefficient (absent means 1)` PMID:37207292 Source assertion: The complete organic assembly combines two HSC and one HAC. Figure 4 uses two successive ATP-dependent adenylation/condensation cycles; the curated net left coefficient for CPD-11959 is 1. Source location `Original author manuscript Figure 3 p.11; Figure 4 p.12; Results/discussion pp.3–5` PMID:42630954 Source assertion: The updated model describes formation of HSC-HSC-AMP after the first condensation, followed by HAC capping to form B; the co-substrate coefficients are derived from two cycles, not a measured coupling ratio. Source location `PMC13495013 body/sec[@id="sec1"]/p[3]; body/sec[@id="sec3"]/p[5]` MetaCyc:CPD-11959 Source assertion: The independently issued native compound preserves its CML structure and ionic form; stale external chemical cross-references are not treated as exact equivalence. Source location `Compound[@frameid="CPD-11959"]/cml/molecule; inchi; dblink`
ATP(4-) `CHEBI:30616`	consumes RXN-11001 retains the source-issued complete organic transformation. Primary-supported successive adenylations imply two ATP, two AMP, two diphosphate and two H+ with no net water in the selected ionic forms. Native MetaCyc and KEGG instead encode one ATP and water. This is an explicit curated coefficient correction, not exact native-equation equivalence or a measured ATP/product coupling ratio.	DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	MetaCyc:RXN-11001 Source assertion: The native left side assigns ATP with coefficient 1. Source location `Reaction[@frameid="RXN-11001"]/left[Compound/@frameid="ATP"]; coefficient (absent means 1)` PMID:37207292 Source assertion: The complete organic assembly combines two HSC and one HAC. Figure 4 uses two successive ATP-dependent adenylation/condensation cycles; the curated net left coefficient for ATP is 2. Source location `Original author manuscript Figure 3 p.11; Figure 4 p.12; Results/discussion pp.3–5` PMID:42630954 Source assertion: The updated model describes formation of HSC-HSC-AMP after the first condensation, followed by HAC capping to form B; the co-substrate coefficients are derived from two cycles, not a measured coupling ratio. Source location `PMC13495013 body/sec[@id="sec1"]/p[3]; body/sec[@id="sec3"]/p[5]` MetaCyc:ATP Source assertion: The source ATP CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="ATP"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:30616 independently has the same full InChI as native ATP, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:30616",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	produces RXN-11001 retains the source-issued complete organic transformation. Primary-supported successive adenylations imply two ATP, two AMP, two diphosphate and two H+ with no net water in the selected ionic forms. Native MetaCyc and KEGG instead encode one ATP and water. This is an explicit curated coefficient correction, not exact native-equation equivalence or a measured ATP/product coupling ratio.	desferrioxamine B `MetaCyc:CPD-3764`	MetaCyc:RXN-11001 Source assertion: The native right side assigns CPD-3764 with coefficient 1. Source location `Reaction[@frameid="RXN-11001"]/right[Compound/@frameid="CPD-3764"]; coefficient (absent means 1)` PMID:37207292 Source assertion: The complete organic assembly combines two HSC and one HAC. Figure 4 uses two successive ATP-dependent adenylation/condensation cycles; the curated net right coefficient for CPD-3764 is 1. Source location `Original author manuscript Figure 3 p.11; Figure 4 p.12; Results/discussion pp.3–5` PMID:42630954 Source assertion: The updated model describes formation of HSC-HSC-AMP after the first condensation, followed by HAC capping to form B; the co-substrate coefficients are derived from two cycles, not a measured coupling ratio. Source location `PMC13495013 body/sec[@id="sec1"]/p[3]; body/sec[@id="sec3"]/p[5]` MetaCyc:CPD-3764 Source assertion: The independently issued native compound preserves its CML structure and ionic form; stale external chemical cross-references are not treated as exact equivalence. Source location `Compound[@frameid="CPD-3764"]/cml/molecule; inchi; dblink`
DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	produces RXN-11001 retains the source-issued complete organic transformation. Primary-supported successive adenylations imply two ATP, two AMP, two diphosphate and two H+ with no net water in the selected ionic forms. Native MetaCyc and KEGG instead encode one ATP and water. This is an explicit curated coefficient correction, not exact native-equation equivalence or a measured ATP/product coupling ratio.	adenosine 5'-monophosphate(2-) `CHEBI:456215`	MetaCyc:RXN-11001 Source assertion: The native right side assigns AMP with coefficient 1. Source location `Reaction[@frameid="RXN-11001"]/right[Compound/@frameid="AMP"]; coefficient (absent means 1)` PMID:37207292 Source assertion: The complete organic assembly combines two HSC and one HAC. Figure 4 uses two successive ATP-dependent adenylation/condensation cycles; the curated net right coefficient for AMP is 2. Source location `Original author manuscript Figure 3 p.11; Figure 4 p.12; Results/discussion pp.3–5` PMID:42630954 Source assertion: The updated model describes formation of HSC-HSC-AMP after the first condensation, followed by HAC capping to form B; the co-substrate coefficients are derived from two cycles, not a measured coupling ratio. Source location `PMC13495013 body/sec[@id="sec1"]/p[3]; body/sec[@id="sec3"]/p[5]` MetaCyc:AMP Source assertion: The source AMP CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="AMP"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:456215 independently has the same full InChI as native AMP, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:456215",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	produces RXN-11001 retains the source-issued complete organic transformation. Primary-supported successive adenylations imply two ATP, two AMP, two diphosphate and two H+ with no net water in the selected ionic forms. Native MetaCyc and KEGG instead encode one ATP and water. This is an explicit curated coefficient correction, not exact native-equation equivalence or a measured ATP/product coupling ratio.	diphosphate(3-) `CHEBI:33019`	MetaCyc:RXN-11001 Source assertion: The native right side assigns PPI with coefficient 1. Source location `Reaction[@frameid="RXN-11001"]/right[Compound/@frameid="PPI"]; coefficient (absent means 1)` PMID:37207292 Source assertion: The complete organic assembly combines two HSC and one HAC. Figure 4 uses two successive ATP-dependent adenylation/condensation cycles; the curated net right coefficient for PPI is 2. Source location `Original author manuscript Figure 3 p.11; Figure 4 p.12; Results/discussion pp.3–5` PMID:42630954 Source assertion: The updated model describes formation of HSC-HSC-AMP after the first condensation, followed by HAC capping to form B; the co-substrate coefficients are derived from two cycles, not a measured coupling ratio. Source location `PMC13495013 body/sec[@id="sec1"]/p[3]; body/sec[@id="sec3"]/p[5]` MetaCyc:PPI Source assertion: The source PPI CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="PPI"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:33019 independently has the same full InChI as native PPI, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:33019",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	produces RXN-11001 retains the source-issued complete organic transformation. Primary-supported successive adenylations imply two ATP, two AMP, two diphosphate and two H+ with no net water in the selected ionic forms. Native MetaCyc and KEGG instead encode one ATP and water. This is an explicit curated coefficient correction, not exact native-equation equivalence or a measured ATP/product coupling ratio.	hydron `CHEBI:15378`	MetaCyc:RXN-11001 Source assertion: The native right side assigns PROTON with coefficient 1. Source location `Reaction[@frameid="RXN-11001"]/right[Compound/@frameid="PROTON"]; coefficient (absent means 1)` PMID:37207292 Source assertion: The complete organic assembly combines two HSC and one HAC. Figure 4 uses two successive ATP-dependent adenylation/condensation cycles; the curated net right coefficient for PROTON is 2. Source location `Original author manuscript Figure 3 p.11; Figure 4 p.12; Results/discussion pp.3–5` PMID:42630954 Source assertion: The updated model describes formation of HSC-HSC-AMP after the first condensation, followed by HAC capping to form B; the co-substrate coefficients are derived from two cycles, not a measured coupling ratio. Source location `PMC13495013 body/sec[@id="sec1"]/p[3]; body/sec[@id="sec3"]/p[5]` MetaCyc:PROTON Source assertion: The source PROTON CML structure and InChI specify the selected chemical charge and stereochemical form. Source location `Compound[@frameid="PROTON"]/cml/molecule/@formalCharge; cml/molecule/formula; inchi` CHEBI:30616 Source assertion: CHEBI:15378 independently has the same full InChI as native PROTON, including charge and any specified stereochemistry. Source location `statements[subject="CHEBI:15378",predicate="chemrof:inchi_string"]; chemrof:generalized_empirical_formula; chemrof:charge`
lysine decarboxylase `MetaCyc:SCO2782-MONOMER`	enables DesA gene-product activity is supported by the original coelicolor biochemical abstract and native annotation. Whole-cluster complementation is not proof of isolated monomer sufficiency; the original 2012 full methods were not inspected.	L-lysine decarboxylation `MetaCyc:LYSDECARBOX-RXN`	MetaCyc:SCO2782-MONOMER Source assertion: The native SCO2782/desA object identifies lysine decarboxylase in coelicolor A3(2); deletion and whole-cluster complementation support pathway involvement. Source location `Protein/catalyzes/Enzymatic-Reaction[@frameid="ENZRXN-17211"]; gene; comment` PMID:22906379 Source assertion: The original abstract directly reports that S. coelicolor desA encodes a lysine decarboxylase, distinct from the formerly predicted diaminobutyrate activity. Source location `PubmedArticle/MedlineCitation/Article/Abstract`
cadaverine hydroxylase `MetaCyc:SCO2783-MONOMER`	enables This enables relation preserves a proposed native coelicolor gene-product assignment, not an experimentally established isolated activity. The native reaction retains generic reduced/oxidized electron-acceptor classes. It does not identify a specific physiological coelicolor donor. The S. sviceus NADPH/NADH experiments and the sequence-unmatched 2023 DesABC preparation do not establish donor specificity for this exact coelicolor protein.	Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	MetaCyc:SCO2783-MONOMER Source assertion: SCO2783/desB is natively assigned the proposed cadaverine-hydroxylase step; the comment explicitly states that this coelicolor protein had not been purified or biochemically characterized. Source location `Protein/catalyzes/Enzymatic-Reaction[@frameid="ENZRXN-17212"]; gene; comment` PMID:33784308 Source assertion: The directly characterized enzyme is S. sviceus SSEG_08523, expressed with a His tag. Its NADPH/NADH kinetics, FAD and tetramer observations are cross-species context, not direct coelicolor evidence. Source location `PMC8009421 Methods/sec[@id="sec003"]/p[1]; cloning sec[@id="sec011"]/p[1]; Results and Discussion` UniProtKB:Q9L071 Source assertion: The current entry explicitly cross-identifies SCO2783/desB but automatically assigns MbtG lysine-hydroxylase function. That substrate/function transfer is not adopted for this native cadaverine pathway. Source location `results[primaryAccession="Q9L071"]/genes; proteinDescription; comments[commentType="CATALYTIC ACTIVITY"]; evidence ECO:0000256`
hydroxycadaverine acyl transferase `MetaCyc:SCO2784-MONOMER`	enables Directly tested in a M145-derived N-terminal His6 preparation. Gel filtration supports a monomer for that preparation, not all conditions. The published primers and locus bridge are preserved; the supplement’s 517-bp gene length differs from the current full entry, so exact complete construct equality is not asserted.	N-Hydroxycadaverine succinylation `MetaCyc:RXN-10996`	MetaCyc:SCO2784-MONOMER Source assertion: The native object identifies SCO2784/desC and UniProt Q9L070; its old uncharacterized annotation predates the direct 2018 DesC experiments. Source location `Protein/gene; dblink[dblink-db="UNIPROT"]; comment` PMID:29685972 Source assertion: Purified tagged DesC from coelicolor catalyzed N-hydroxycadaverine acylation with succinyl-CoA, giving the corresponding authentic-standard-matched product and CoA. Source location `PMC5915712 section[@id="s2a"] (Results and discussion §2(a)); figure[@id="RSTB20170068F4"] panel a; separately cited original supplement §1.6.1 and §1.7` DOI:10.6084/m9.figshare.5965882.v2 Source assertion: The gene was cloned from S. coelicolor M145 genomic DNA. Section 1.6.1 reports the succinyl-CoA assay and authentic-standard LC-MS/MS comparison; section1.7 supports CoA formation. Source location `Original DOC §1.3; §1.6.1; §1.7` UniProtKB:Q9L070 Source assertion: Q9L070 cross-identifies SCO2784/desC but its automatic MbtK/mycobactin assignment conflicts with the directly measured cadaverine acylation and is not used as pathway evidence. Source location `results[primaryAccession="Q9L070"]/genes; proteinDescription; comments[commentType="FUNCTION"]`
hydroxycadaverine acyl transferase `MetaCyc:SCO2784-MONOMER`	enables Directly tested in a M145-derived N-terminal His6 preparation. Gel filtration supports a monomer for that preparation, not all conditions. The published primers and locus bridge are preserved; the supplement’s 517-bp gene length differs from the current full entry, so exact complete construct equality is not asserted.	N-Hydroxycadaverine acetylation `MetaCyc:RXN-10999`	MetaCyc:SCO2784-MONOMER Source assertion: The native object identifies SCO2784/desC and UniProt Q9L070; its old uncharacterized annotation predates the direct 2018 DesC experiments. Source location `Protein/gene; dblink[dblink-db="UNIPROT"]; comment` PMID:29685972 Source assertion: Purified tagged DesC from coelicolor catalyzed N-hydroxycadaverine acylation with acetyl-CoA, giving the corresponding authentic-standard-matched product and CoA. Source location `PMC5915712 section[@id="s2a"] (Results and discussion §2(a)); figure[@id="RSTB20170068F4"] panel b; separately cited original supplement §1.6.2 and §1.7` DOI:10.6084/m9.figshare.5965882.v2 Source assertion: The gene was cloned from S. coelicolor M145 genomic DNA. Section 1.6.2 reports the acetyl-CoA assay and authentic-standard LC-MS/MS comparison; section1.7 supports CoA formation. Source location `Original DOC §1.3; §1.6.2; §1.7` UniProtKB:Q9L070 Source assertion: Q9L070 cross-identifies SCO2784/desC but its automatic MbtK/mycobactin assignment conflicts with the directly measured cadaverine acylation and is not used as pathway evidence. Source location `results[primaryAccession="Q9L070"]/genes; proteinDescription; comments[commentType="FUNCTION"]`
desferrioxamine E synthetase `MetaCyc:CPLX-7949`	catalyzes Native coelicolor DesD homodimer with B-forming activity supported by the sequence-grounded ScDesD preparation. Native assignment of dimeric assembly is separate from primary B-product measurement. Assay MgATP does not alone justify an obligatory free-Mg cofactor edge. The cellular control favoring B over G/E remains unresolved. RXN-11001 retains the source-issued complete organic transformation. Primary-supported successive adenylations imply two ATP, two AMP, two diphosphate and two H+ with no net water in the selected ionic forms. Native MetaCyc and KEGG instead encode one ATP and water. This is an explicit curated coefficient correction, not exact native-equation equivalence or a measured ATP/product coupling ratio.	DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	MetaCyc:CPLX-7949 Source assertion: The native coelicolor DesD complex contains two SCO2785-MONOMER subunits and reports dimeric recombinant enzyme; its canonical E-synthetase name does not limit the experimentally observed substrate range. Source location `Protein/component[Protein/@frameid="SCO2785-MONOMER"]/coefficient; species; comment` PMID:37207292 Source assertion: ScDesD catalyzed formation of B from HSC-HSC plus HAC. The tested HSC plus HSC-HAC combination did not yield detectable B; the proposed cycle requires successive adenylations. Source location `Original author manuscript Figure 3 p.11; Figure 4 p.12; Results pp.2–4` DOI:10.1016/j.jbc.2022.102166 Source assertion: The coelicolor native DesD sequence in Table S7 and the native core of the His6 construct in Table S9 both exactly match current Q9L069 after removal of the explicitly supplied tag. Source location `Original mmc1.pdf Table S7 p.S52; Table S9 p.S56; full native/construct sequence comparison` DOI:10.1021/acschembio.3c00167.s001 Source assertion: The DesD ortholog constructs were prepared as reported in the 2022 study; the B-product assay used HSC-HSC plus HAC and ATP/Mg-containing buffer. Source location `Original supplement p.S7 Protein expression and purification; p.S8 Product formation assay; Table S1 p.S10`
L-lysine decarboxylation `MetaCyc:LYSDECARBOX-RXN`	part_of	`MetaCyc:PWY-6376`	MetaCyc:PWY-6376 Source assertion: The native full B pathway includes LYSDECARBOX-RXN and selects its L2R pathway layout. Source location `Pathway[@frameid="PWY-6376"]/reaction-list; reaction-layout[Reaction/@frameid="LYSDECARBOX-RXN"]/direction`
Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	part_of	`MetaCyc:PWY-6376`	MetaCyc:PWY-6376 Source assertion: The native full B pathway includes RXN-10995 and selects its L2R pathway layout. Source location `Pathway[@frameid="PWY-6376"]/reaction-list; reaction-layout[Reaction/@frameid="RXN-10995"]/direction`
N-Hydroxycadaverine succinylation `MetaCyc:RXN-10996`	part_of	`MetaCyc:PWY-6376`	MetaCyc:PWY-6376 Source assertion: The native full B pathway includes RXN-10996 and selects its L2R pathway layout. Source location `Pathway[@frameid="PWY-6376"]/reaction-list; reaction-layout[Reaction/@frameid="RXN-10996"]/direction`
N-Hydroxycadaverine acetylation `MetaCyc:RXN-10999`	part_of	`MetaCyc:PWY-6376`	MetaCyc:PWY-6376 Source assertion: The native full B pathway includes RXN-10999 and selects its L2R pathway layout. Source location `Pathway[@frameid="PWY-6376"]/reaction-list; reaction-layout[Reaction/@frameid="RXN-10999"]/direction`
DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	part_of RXN-11001 retains the source-issued complete organic transformation. Primary-supported successive adenylations imply two ATP, two AMP, two diphosphate and two H+ with no net water in the selected ionic forms. Native MetaCyc and KEGG instead encode one ATP and water. This is an explicit curated coefficient correction, not exact native-equation equivalence or a measured ATP/product coupling ratio.	`MetaCyc:PWY-6376`	MetaCyc:PWY-6376 Source assertion: The native full B pathway includes RXN-11001 and selects its L2R pathway layout. Source location `Pathway[@frameid="PWY-6376"]/reaction-list; reaction-layout[Reaction/@frameid="RXN-11001"]/direction`
L-lysine decarboxylation `MetaCyc:LYSDECARBOX-RXN`	provides_input_for	Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	MetaCyc:LYSDECARBOX-RXN Source assertion: LYSDECARBOX-RXN produces native CADAVERINE, which supplies the connected transformation. Source location `Reaction/right[Compound/@frameid="CADAVERINE"]` MetaCyc:RXN-10995 Source assertion: RXN-10995 consumes the same native CADAVERINE. Source location `Reaction/left[Compound/@frameid="CADAVERINE"]; coefficient`
Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	provides_input_for	N-Hydroxycadaverine succinylation `MetaCyc:RXN-10996`	MetaCyc:RXN-10995 Source assertion: RXN-10995 produces native CPD-11953, which supplies the connected transformation. Source location `Reaction/right[Compound/@frameid="CPD-11953"]` MetaCyc:RXN-10996 Source assertion: RXN-10996 consumes the same native CPD-11953. Source location `Reaction/left[Compound/@frameid="CPD-11953"]; coefficient`
Cadaverine N-hydroxylation with native generic redox partners `MetaCyc:RXN-10995`	provides_input_for	N-Hydroxycadaverine acetylation `MetaCyc:RXN-10999`	MetaCyc:RXN-10995 Source assertion: RXN-10995 produces native CPD-11953, which supplies the connected transformation. Source location `Reaction/right[Compound/@frameid="CPD-11953"]` MetaCyc:RXN-10999 Source assertion: RXN-10999 consumes the same native CPD-11953. Source location `Reaction/left[Compound/@frameid="CPD-11953"]; coefficient`
N-Hydroxycadaverine succinylation `MetaCyc:RXN-10996`	provides_input_for The upstream decarboxylation and hydroxylation operate three times, the succinyl branch twice and the acetyl branch once per B product.	DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	MetaCyc:RXN-10996 Source assertion: RXN-10996 produces native CPD-11955, which supplies the connected transformation. Source location `Reaction/right[Compound/@frameid="CPD-11955"]` MetaCyc:RXN-11001 Source assertion: RXN-11001 consumes the same native CPD-11955; two HSC and one HAC are required per B product. Source location `Reaction/left[Compound/@frameid="CPD-11955"]; coefficient`
N-Hydroxycadaverine acetylation `MetaCyc:RXN-10999`	provides_input_for The upstream decarboxylation and hydroxylation operate three times, the succinyl branch twice and the acetyl branch once per B product.	DesD iterative B assembly: primary-supported two-ATP net `MetaCyc:RXN-11001`	MetaCyc:RXN-10999 Source assertion: RXN-10999 produces native CPD-11959, which supplies the connected transformation. Source location `Reaction/right[Compound/@frameid="CPD-11959"]` MetaCyc:RXN-11001 Source assertion: RXN-11001 consumes the same native CPD-11959; two HSC and one HAC are required per B product. Source location `Reaction/left[Compound/@frameid="CPD-11959"]; coefficient`
desferrioxamine E synthetase monomer `MetaCyc:SCO2785-MONOMER`	part_of Two-subunit source stoichiometry; membership does not make each monomer an independent catalyst.	desferrioxamine E synthetase `MetaCyc:CPLX-7949`	MetaCyc:CPLX-7949 Source assertion: The native physical DesD complex explicitly contains two copies of SCO2785-MONOMER. Source location `Protein/component[Protein/@frameid="SCO2785-MONOMER"]/coefficient`
lysine decarboxylase `MetaCyc:SCO2782-MONOMER`	part_of	Streptomyces coelicolor A3(2) `NCBITaxon:100226`	MetaCyc:SCO2782-MONOMER Source assertion: The native protein species object identifies coelicolor A3(2), taxon100226, and its own gene locus. Source location `Protein/species/Organism[@frameid="TAX-100226"]; gene` UniProtKB:Q9L072 Source assertion: The current entry cross-identifies desA/SCO2782 and taxon100226; automatic activity annotations are separately adjudicated. Source location `results[primaryAccession="Q9L072"]/organism/taxonId; genes`
cadaverine hydroxylase `MetaCyc:SCO2783-MONOMER`	part_of	Streptomyces coelicolor A3(2) `NCBITaxon:100226`	MetaCyc:SCO2783-MONOMER Source assertion: The native protein species object identifies coelicolor A3(2), taxon100226, and its own gene locus. Source location `Protein/species/Organism[@frameid="TAX-100226"]; gene` UniProtKB:Q9L071 Source assertion: The current entry cross-identifies desB/SCO2783 and taxon100226; automatic activity annotations are separately adjudicated. Source location `results[primaryAccession="Q9L071"]/organism/taxonId; genes`
hydroxycadaverine acyl transferase `MetaCyc:SCO2784-MONOMER`	part_of	Streptomyces coelicolor A3(2) `NCBITaxon:100226`	MetaCyc:SCO2784-MONOMER Source assertion: The native protein species object identifies coelicolor A3(2), taxon100226, and its own gene locus. Source location `Protein/species/Organism[@frameid="TAX-100226"]; gene` UniProtKB:Q9L070 Source assertion: The current entry cross-identifies desC/SCO2784 and taxon100226; automatic activity annotations are separately adjudicated. Source location `results[primaryAccession="Q9L070"]/organism/taxonId; genes`
desferrioxamine E synthetase monomer `MetaCyc:SCO2785-MONOMER`	part_of	Streptomyces coelicolor A3(2) `NCBITaxon:100226`	MetaCyc:SCO2785-MONOMER Source assertion: The native protein species object identifies coelicolor A3(2), taxon100226, and its own gene locus. Source location `Protein/species/Organism[@frameid="TAX-100226"]; gene` UniProtKB:Q9L069 Source assertion: The current entry cross-identifies desD/SCO2785 and taxon100226; automatic activity annotations are separately adjudicated. Source location `results[primaryAccession="Q9L069"]/organism/taxonId; genes`
desferrioxamine E synthetase `MetaCyc:CPLX-7949`	part_of	Streptomyces coelicolor A3(2) `NCBITaxon:100226`	MetaCyc:CPLX-7949 Source assertion: The native complex belongs to coelicolor A3(2), with an explicit taxon100226 cross-reference. Source location `Protein/species/Organism/dblink[dblink-db="NCBI-TAXONOMY-DB"]/dblink-oid`
`MetaCyc:PWY-6376`	part_of	Streptomyces coelicolor A3(2) `NCBITaxon:100226`	PMID:29685972 Source assertion: The introduction identifies coelicolor A3(2) as producing B and E; experiments and supplement establish the M145 DesC precursor branches. Source location `PMC5915712 Introduction §1; Results §2(a); Figure 3` PMID:37207292 Source assertion: ScDesD forms the B product from HSC-HSC and HAC in the purified-enzyme assay. The coelicolor implementation retains a proposed native DesB assignment. Source location `Original manuscript Figure 3 p.11; coelicolor ortholog scope pp.2–3` NCBITaxon:100226 Source assertion: NCBI Taxonomy identifies the scoped organism as Streptomyces coelicolor A3(2). Source location `TaxaSet/Taxon/TaxId; ScientificName`
lysine decarboxylase `MetaCyc:SCO2782-MONOMER`	has_cofactor Source-scoped automatic cofactor assignment; the complete original 2012 biochemical methods were not inspected.	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:Q9L072 Source assertion: The current unreviewed DesA entry explicitly assigns pyridoxal phosphate (CHEBI:597326) by automatic annotation; this is not direct cofactor binding measured on the selected native protein. Source location `results[primaryAccession="Q9L072"]/comments[commentType="COFACTOR"]/cofactors; evidences`
cadaverine hydroxylase `MetaCyc:SCO2783-MONOMER`	has_cofactor Explicitly inferred FAD cofactor assignment; direct FAD experiments concern S. sviceus. Bound flavin is not substituted for the generic exchanged redox classes.	FAD(3-) `CHEBI:57692`	UniProtKB:Q9L071 Source assertion: The current unreviewed entry separately assigns FAD (CHEBI:57692) as cofactor by ECO:0000256/ARBA00001974. This inferred binding assignment does not validate its conflicting MbtG substrate annotation or identify the physiological reductant. Source location `results[primaryAccession="Q9L071"]/comments[commentType="COFACTOR"]/cofactors; evidences` MetaCyc:SCO2783-MONOMER Source assertion: The native DesB comment identifies similarity to FAD-dependent amine monooxygenases but states that this coelicolor protein was not purified or biochemically characterized. Source location `Protein/comment`

References

MetaCyc:PWY-6376 MetaCyc 22.5 native PWY-6376 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:LYSDECARBOX-RXN MetaCyc 22.5 native LYSDECARBOX-RXN (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:RXN-10995 MetaCyc 22.5 native RXN-10995 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:RXN-10996 MetaCyc 22.5 native RXN-10996 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:RXN-10999 MetaCyc 22.5 native RXN-10999 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:RXN-11001 MetaCyc 22.5 native RXN-11001 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:LYS MetaCyc 22.5 native LYS (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:CADAVERINE MetaCyc 22.5 native CADAVERINE (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:CARBON-DIOXIDE MetaCyc 22.5 native CARBON-DIOXIDE (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:PROTON MetaCyc 22.5 native PROTON (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:OXYGEN-MOLECULE MetaCyc 22.5 native OXYGEN-MOLECULE (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:WATER MetaCyc 22.5 native WATER (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:ACETYL-COA MetaCyc 22.5 native ACETYL-COA (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:SUC-COA MetaCyc 22.5 native SUC-COA (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:CO-A MetaCyc 22.5 native CO-A (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:ATP MetaCyc 22.5 native ATP (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:AMP MetaCyc 22.5 native AMP (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:PPI MetaCyc 22.5 native PPI (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:CPD-11953 MetaCyc 22.5 native CPD-11953 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:CPD-11955 MetaCyc 22.5 native CPD-11955 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:CPD-11959 MetaCyc 22.5 native CPD-11959 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:CPD-3764 MetaCyc 22.5 native CPD-3764 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:Donor-H2 MetaCyc 22.5 native Donor-H2 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:Acceptor MetaCyc 22.5 native Acceptor (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:SCO2782-MONOMER MetaCyc 22.5 native SCO2782-MONOMER (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:SCO2783-MONOMER MetaCyc 22.5 native SCO2783-MONOMER (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:SCO2784-MONOMER MetaCyc 22.5 native SCO2784-MONOMER (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:SCO2785-MONOMER MetaCyc 22.5 native SCO2785-MONOMER (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
MetaCyc:CPLX-7949 MetaCyc 22.5 native CPLX-7949 (source version: MetaCyc 22.5 original XML; retrieved 2026-10-11)
UniProtKB:Q9L072 UniProtKB Q9L072 complete current native entry (source version: UniProtKB 2026_03; complete original four-entry search batch retrieved 2026-10-11; unreviewed entries)
UniProtKB:Q9L071 UniProtKB Q9L071 complete current native entry (source version: UniProtKB 2026_03; complete original four-entry search batch retrieved 2026-10-11; unreviewed entries)
UniProtKB:Q9L070 UniProtKB Q9L070 complete current native entry (source version: UniProtKB 2026_03; complete original four-entry search batch retrieved 2026-10-11; unreviewed entries)
UniProtKB:Q9L069 UniProtKB Q9L069 complete current native entry (source version: UniProtKB 2026_03; complete original four-entry search batch retrieved 2026-10-11; unreviewed entries)
NCBITaxon:100226 NCBI Taxonomy Streptomyces coelicolor A3(2) (source version: NCBI Taxonomy original XML retrieved 2026-10-11)
CHEBI:30616 ChEBI exact chemical structures and ionic forms (source version: ChEBI 255; hash covers the complete original uncompressed Semantic SQL database; selected term locators identify each cited chemical)
PMID:22906379 Evolution of a novel lysine decarboxylase in siderophore biosynthesis. (source version: Original PubMed indexed abstract only; retrieved 2026-10-11)
PMID:29685972 Desferrioxamine biosynthesis: diverse hydroxamate assembly by substrate-tolerant acyl transferase DesC (source version: Original full primary HTML retrieved 2026-10-11)
DOI:10.6084/m9.figshare.5965882.v2 Supplementary Material: Desferrioxamine biosynthesis: Diverse hydroxamate assembly by substrate-tolerant acyl transferase DesC (source version: Original Royal Society Figshare version2 CDFV2 DOC; collection4027009/article5965882/file10912295; retrieved 2026-10-11)
PMID:37207292 Siderophore Synthetase DesD Catalyzes N-to-C Condensation in Desferrioxamine Biosynthesis (source version: Original NSF-hosted author manuscript PDF; retrieved 2026-10-11)
DOI:10.1021/acschembio.3c00167.s001 Supporting Information: Siderophore Synthetase DesD Catalyzes N-to-C Condensation in Desferrioxamine Biosynthesis (source version: Original ACS Figshare supplement PDF; article22970446/file40713082; retrieved 2026-10-11)
PMID:35750210 An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD (source version: Original complete primary JATS XML retrieved 2026-10-11)
PMID:42630954 Modular Inhibitor Approach to Map the Catalytic Trajectory of an Iterative Siderophore Synthetase, DesD (source version: Original complete primary JATS XML retrieved 2026-10-11)
PMID:33784308 Characterization of a broadly specific cadaverine N-hydroxylase involved in desferrioxamine B biosynthesis in Streptomyces sviceus (source version: Original complete primary JATS XML retrieved 2026-10-11)
DOI:10.1016/j.jbc.2022.102166 Supporting Information mmc1.pdf to An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD (source version: Original archive member mmc1.pdf; reference digest covers extracted unchanged PDF; archive digest and extraction receipt in source manifest)

Curation history

2026-10-11T12:14:54Z codex
- CREATE — Prepared complete five-transformation Desferrioxamine B pathway for review
  Copied frozen full MetaCyc:PWY-6376 draft f9bb35866f883f0e47f5f5e98ba6ae2caf1d2d8ea967793b96f67d91e8fa1690 and preserved all original author/source observations. Independent external review confirms complete five-reaction scope with explicitly qualified DesB donor/cofactor inference, native versus experimental construct scopes, and primary-supported two-ATP terminal mechanism distinct from original one-ATP database equations. One grouped minor finding remains open: DesC assay evidence locators on edges029/030 should reference original Figure4a/4b. Source authorities were independently rebuilt with all baseline entries preserved; full integration gates, initial finding correction, final independent review, and actual merged-baseline transition remain pending.
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2026-10-11T12:18:07Z codex
- EDIT — Corrected two DesC assay locators to the original Figure4 panels
  Preserved initial review20261011T121520Z-desferrioxamine-b-initial-independent-review and exact original draft f9bb35866f883f0e47f5f5e98ba6ae2caf1d2d8ea967793b96f67d91e8fa1690. Corrected only evidence[1].source_locator on dfoB-edge-029 and dfoB-edge-030 to PMID:29685972 Figure4 panelsa/b and specific Results/supplement selectors. Currentrecord SHA-256 fc82621bf3a7b47ece33ab621b0412e98fe7d27aa5f72e5bc293a84a85b2145d. Original-body guard and parsed full-record comparison confirm that all other nodes, reactions, edge predicates, assertions, descriptions and references are unchanged; old locators fail the bounded acceptance comparison. Replay receipt bff14d4ca660a4d07d02e35077f11fbfecdfa8d51c7d6c13c3619779d85489e6. Full-corpus gates, merged baseline and final independent successor remain pending.
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