avilamycin A
naturalproductmech:mibig-69e644c0de MINTED SEEDED
Grounding review: No 3-star ChEBI entry shares this structure, so the record keeps a content-hashed identifier.
What these status tags mean
Curation status describes a workflow state. SEEDED means the record entered through the source-seeding workflow; it does not imply that no later curation occurred. PROPOSED marks an addition awaiting review; REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record. These are workflow decisions, not independently verified human review. Agent-assisted contributions may appear in the record history.
Grounding describes the identifier mapping: EXACT uses an ontology identity asserted by the source; MINTED keeps a local identifier when no defensible ontology identity is available; REVIEW_NEEDED flags an exact structure whose ontology identity needs adjudication. The grounding note retains any unresolved alternatives. These tags do not establish the strength of producer or activity evidence.
Structure
| Standard InChIKey | XIRGHRXBGGPPKY-RTWAPUGOSA-N |
|---|---|
| SMILES | C[C@@H]1[C@H]([C@@H](C[C@@H](O1)O[C@@H]2[C@H](OC3(C[C@@H]2O)O[C@@H]4[C@H](O[C@H](C[C@]4(O3)C)O[C@@H]5[C@H]([C@@H](O[C@@H]([C@@H]5OC)C)O[C@@H]6[C@H](O[C@H]([C@H]([C@H]6O)OC)O[C@H]7[C@@H]([C@H]8[C@H](CO7)O[C@@]9(O8)C1C([C@@]([C@H](O9)C)(C(=O)C)O)OCO1)OC(=O)C(C)C)COC)O)C)C)O)OC(=O)C1=C(C(=C(C(=C1OC)Cl)O)Cl)C |
| Stereochemistry | undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers |
| Cross-references | pubchem:122779 |
Filing pathway
Carbohydrates — computed by NPClassifier npclassifier.gnps2.org@2026-09-07, which is why it is pinned rather than recomputed. The gene cluster's asserted class is saccharide, from MIBiG.
Producer organisms 1
A claim that this taxon makes the compound. The basis says what the evidence addressed — a knockout and a database assertion are not the same claim.
| Taxon | Basis | Cluster | Evidence |
|---|---|---|---|
| Streptomyces viridochromogenes Tue57 NCBITaxon:1160705 |
BGC_CHARACTERIZED | mibig:BGC0000026 | PMID:11410376 |
Occurrences 1
Somebody found the compound in this organism and cited it. That is not a claim that the organism makes it, and nothing here promotes one to the other.
| Taxon | Source | Reference |
|---|---|---|
| Streptomyces viridochromogenes NCBITaxon:1938 |
LOTUS | DOI:10.1016/S1074-5521(01)00040-0 |
Biosynthetic gene clusters 1
| Accession | Host | Locus evidence | Genome |
|---|---|---|---|
| mibig:BGC0000026 | Streptomyces viridochromogenes Tue57 NCBITaxon:1160705 |
CLUSTER_DEMONSTRATED | genbank:AF333038.2 |
A locus claim and a taxon claim are different questions. Heterologous expression settles the first and leaves the second where the isolation report left it.
Mechanism & Biosynthesis Overview
Causal graph — biosynthesis 4 nodes, 3 edges
Streptomyces viridochromogenes Tue57 AviG2-catalyzed SAM-dependent 6-O-methylation of the D-mannose moiety forms avilamycin A.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| 6-O-demethylavilamycin A intermediate | is 6-O-methylated by | AviG2 O-methyltransferase | MITE represents AviG2 as the O-methyltransferase that methylates the C6 hydroxyl of the D-mannose moiety in the avilamycin A scaffold. | DOI:10.1016/j.chembiol.2004.08.016 |
| S-adenosyl-L-methionine | supplies a methyl group to | AviG2 O-methyltransferase | MITE lists SAM as AviG2's organic cofactor for this D-mannose 6-O-methylation reaction. | https://mite.bioinformatics.nl/repository/MITE0000001 |
| AviG2 O-methyltransferase | forms | avilamycin A | Open Babel assigned the same Standard InChIKey, XIRGHRXBGGPPKY-RTWAPUGOSA-N, to the MITE reaction product SMILES and the avilamycin A record SMILES. | DOI:10.1016/j.chembiol.2004.08.016 |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 4 nodes, 3 edges
Streptomyces viridochromogenes Tue57 AviG6-catalyzed SAM-dependent 2-O-methylation of the D-mannose moiety forms avilamycin A.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| 2-O-demethylavilamycin A intermediate | is 2-O-methylated by | AviG6 O-methyltransferase | MITE represents AviG6 as the O-methyltransferase that methylates the C2 hydroxyl of the D-mannose moiety in the avilamycin A scaffold. | DOI:10.1016/j.chembiol.2004.08.016 |
| S-adenosyl-L-methionine | supplies a methyl group to | AviG6 O-methyltransferase | MITE lists SAM as AviG6's organic cofactor for this D-mannose 2-O-methylation reaction. | https://mite.bioinformatics.nl/repository/MITE0000003 |
| AviG6 O-methyltransferase | forms | avilamycin A | Open Babel assigned the same Standard InChIKey, XIRGHRXBGGPPKY-RTWAPUGOSA-N, to the MITE reaction product SMILES and the avilamycin A record SMILES. | DOI:10.1016/j.chembiol.2004.08.016 |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 4 nodes, 3 edges
Streptomyces viridochromogenes Tue57 AviG5-catalyzed SAM-dependent 4-O-methylation of the D-fucose moiety forms avilamycin A.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| 4-O-demethylavilamycin A intermediate | is 4-O-methylated by | AviG5 O-methyltransferase | MITE represents AviG5 as the O-methyltransferase that methylates the C4 hydroxyl of the D-fucose moiety in the avilamycin A scaffold. | DOI:10.1016/j.chembiol.2004.08.016 |
| S-adenosyl-L-methionine | supplies a methyl group to | AviG5 O-methyltransferase | MITE lists SAM as AviG5's organic cofactor for this D-fucose 4-O-methylation reaction. | https://mite.bioinformatics.nl/repository/MITE0000004 |
| AviG5 O-methyltransferase | forms | avilamycin A | Open Babel assigned the same Standard InChIKey, XIRGHRXBGGPPKY-RTWAPUGOSA-N, to the MITE reaction product SMILES and the avilamycin A record SMILES. | DOI:10.1016/j.chembiol.2004.08.016 |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 7 nodes, 8 edges
AviO1/AviO3 genetic requirements in Streptomyces viridochromogenes Tue57. Frameshift alleles and complementation are separate from protein nodes. These results do not assign specific ring closures or purified-enzyme reactions.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| aviO1 frameshift in ITO1 | inactivates_encoding_gene_of | Native AviO1 parent | NcoI fill-in frameshift, not whole-gene deletion. The native 223-aa parent exactly matches AAK83181.1 and independently translated AF333038.2:25761..26432; UniProt names the same Tue57 strain. | DOI:10.1128/AEM.71.1.400-406.2005 |
| aviO1 frameshift in ITO1 | abolishes_detectable | Detectable avilamycin A/C production | Culture-supernatant TLC/HPLC-UV/HPLC-ESI-MS found no avilamycin derivatives. This is a production phenotype, not direct enzyme catalysis. | DOI:10.1128/AEM.71.1.400-406.2005
|
| O1pSET complementation of ITO1 | expresses | Native AviO1 parent | The corresponding native gene was supplied behind ermE in a pSET152 derivative to its matching frameshift mutant. | DOI:10.1128/AEM.71.1.400-406.2005 |
| O1pSET complementation of ITO1 | restores_detectable | Detectable avilamycin A/C production | HPLC-ESI-MS confirmed restored avilamycin A and C production. | DOI:10.1128/AEM.71.1.400-406.2005
|
| aviO3 frameshift in ITO3 | inactivates_encoding_gene_of | Native AviO3 parent | NcoI fill-in frameshift, not whole-gene deletion. The native 314-aa parent exactly matches AAK83187.1 and independently translated AF333038.2:31230..32174; UniProt names the same Tue57 strain. | DOI:10.1128/AEM.71.1.400-406.2005 |
| aviO3 frameshift in ITO3 | abolishes_detectable | Detectable avilamycin A/C production | Culture-supernatant TLC/HPLC-UV/HPLC-ESI-MS found no avilamycin derivatives. This is a production phenotype, not direct enzyme catalysis. | DOI:10.1128/AEM.71.1.400-406.2005
|
| O3pSET complementation of ITO3 | expresses | Native AviO3 parent | The corresponding native gene was supplied behind ermE in a pSET152 derivative to its matching frameshift mutant. | DOI:10.1128/AEM.71.1.400-406.2005 |
| O3pSET complementation of ITO3 | restores_detectable | Detectable avilamycin A/C production | HPLC-ESI-MS confirmed restored avilamycin A and C production. | DOI:10.1128/AEM.71.1.400-406.2005
|
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 2 nodes, 1 edge
Structural evidence for recombinant AviO1, not an oxygenation assay.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Crystallized AviO1 | contains_observed_bound_metal | Substituting nickel(II) | 4XAA is a monomeric 2.30 A structure containing NI and water, not modeled AKG or carbohydrate. Its deposited 223-aa polymer equals Q93KW4 and native AAK83181.1 exactly; this does not verify tag-processing details in the inaccessible supplement. The paper used inactive Ni-substituted preparations, not native iron turnover. Docking does not establish substrate binding or a particular ring-closure assignment. | DOI:10.1073/pnas.1500964112 |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 6 nodes, 5 edges
AviX12 evidence from the aviG4-defective GW4 background. Gavibamycins are distinct congeners, not this avilamycin A structure.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| aviX12 frameshift in GW4-X12 | inactivates_encoding_gene_of | Native AviX12 parent | A 2-bp SacII frameshift, not complete gene deletion. Q93KV6 equals the paper's AAK83189.1 and independently translated AF333038.2:33001..34191 (396 aa, Tue57). | DOI:10.1074/jbc.M601508200 |
| aviX12 frameshift in GW4-X12 | causes_accumulation_of | Gavibamycin N1 accumulation in GW4-X12 | MS/NMR identified N1 with glucose instead of mannose at ring F and absent ring-F 2-O-methylation. The parent GW4 already lacks orsellinic O-methylation. N1 is not avilamycin A. | DOI:10.1074/jbc.M601508200
|
| pSETerm-aviX12 complementation | expresses | Native AviX12 parent | Native aviX12 under ermE* in the matching GW4-X12 mutant. | DOI:10.1074/jbc.M601508200 |
| pSETerm-aviX12 complementation | restores_detectable | Restored GW4 gavibamycin production | Rescue restored gavibamycins, not wild-type avilamycin A. | DOI:10.1074/jbc.M601508200
|
| Native AviX12 parent | is_proposed_to_catalyze | Proposed scaffold ring-F C2 epimerization | Inferred from genetics and NMR, not demonstrated turnover. Neither direct N1-to-avilamycin A conversion nor SAM cleavage was established. | DOI:10.1074/jbc.M601508200
|
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Causal graph — biosynthesis 2 nodes, 1 edge
Iron-sulfur spectroscopy on recombinant AviX12; no active reconstitution.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| N-terminal His6-AviX12 preparation | contains_spectroscopically_observed | Observed [3Fe-4S] cluster | pRSETb/BL21(DE3)pLysS expression; UniProt denotes the native parent, not the full tagged construct. UV-visible/EPR supported approximately one [3Fe-4S] cluster per protein. Functional [4Fe-4S] reconstitution failed and the preparation lacked enzymatic activity. No native cofactor-state or catalytic-assembly claim is made. | DOI:10.1074/jbc.M601508200 |
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Causal graph — biosynthesis 4 nodes, 3 edges
Purified recombinant AviE2 converts UDP-glucuronic acid to UDP-D-xylose, a proposed precursor of avilamycin's L-lyxose. This assay does not demonstrate the subsequent epimerizations or full avilamycin A synthesis.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Assayed N-terminal His6-AviE2 preparation | is_recombinant_preparation_of | Native AviE2 parent | Ni-NTA-purified E. coli N-terminal His6 preparation. The native 337-aa parent matches AAK83183.1 and AF333038.2:27779..28792. Thesis Table 51 agrees at residues 2-337 but prints V1 instead of the accession's M1; the native CDS begins GTG. The accession identifies the parent, not a verified complete fusion sequence. | https://freidok.uni-freiburg.de/data/1891 |
| UDP-alpha-D-glucuronic acid | is_decarboxylated_by | Assayed N-terminal His6-AviE2 preparation | The 60-minute room-temperature assay included NAD+. Vector-only Ni-NTA and no-protein controls lacked the product peak. Substitution with NADP+ or UDP-glucose gave no detected conversion under the reported conditions. Conflicting protein-concentration units in the thesis are not adopted. ChEBI denotes the acid-normalized substrate, not a measured solution protonation state. | https://freidok.uni-freiburg.de/data/1891 |
| Assayed N-terminal His6-AviE2 preparation | forms_in_vitro | UDP-alpha-D-xylose | HPLC/negative-ion MS showed a 44-Da mass difference; NMR and coupling analysis assigned UDP-alpha-D-xylose, not UDP-L-lyxose. The node uses the acid-normalized chemical identity. No direct AviE2-to-avilamycin A conversion or measured CO2 release is asserted. | https://freidok.uni-freiburg.de/data/1891 |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 6 nodes, 6 edges
AviGT4 evidence in the aviG4-defective GW4 background, not wild-type avilamycin A production. Gavibamycins A1 and P1 are distinct congeners.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| aviGT4 NotI-fill-in frameshift in GW4 | inactivates_encoding_gene_of | Native AviGT4 parent | NotI fill-in frameshift confirmed through double-crossover PCR and restriction analysis, not a whole-gene deletion despite the source's delta notation. Q93KV2 exactly matches AAK83193.1 and AF333038.2:38971..39999. The thesis used Tue57 genomic DNA; the screening primers map inside this CDS. | https://freidok.uni-freiburg.de/data/2280 |
| aviGT4 NotI-fill-in frameshift in GW4 | abolishes_detectable | Detectable gavibamycin A1 production | HPLC/ESI-MS of GW4 mutant culture extracts lacked the parental gavibamycin A1 signal. This is a genetic production phenotype, not a purified-protein assay. | https://freidok.uni-freiburg.de/data/2280
|
| aviGT4 NotI-fill-in frameshift in GW4 | causes_accumulation_of | Gavibamycin P1 accumulation | P1 gave m/z 1189 [M-H]- versus 1387 for A1. Comparative APCI-MS fragments support proposed loss of the terminal eurekanate unit; this thesis does not establish P1's complete structure by NMR. Neither metabolite is avilamycin A. | https://freidok.uni-freiburg.de/data/2280
|
| pSET-aviGT4 genomic-fragment complementation | supplies_wild_type_encoding_gene_for | Native AviGT4 parent | The pSET complementation insert contains aviGT4 plus flanking aviGT3/aviO2-region DNA, not an isolated single-gene construct. The source describes a 2.8-kb amplicon behind ermE*; its cloning primer changes are outside the aviGT4 CDS. | https://freidok.uni-freiburg.de/data/2280 |
| pSET-aviGT4 genomic-fragment complementation | restores_detectable | Detectable gavibamycin A1 production | Complemented GW4 mutant extracts recovered the m/z 1387 A1 signal. This is not restoration of wild-type avilamycin A or evidence that AviGT4 alone is sufficient for turnover. | https://freidok.uni-freiburg.de/data/2280
|
| Native AviGT4 parent | is_proposed_to_catalyze | Proposed eurekanate-precursor transfer to L-lyxose | Genetic/metabolite evidence plus glycosyltransferase homology supports the assignment. The exact sugar donor and AviGT4's ability to form the second orthoester linkage were unresolved; no direct P1-to-avilamycin A conversion is demonstrated. | https://freidok.uni-freiburg.de/data/2280
|
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Causal graph — biosynthesis 3 nodes, 2 edges
AviGT4 UDP binding and deposited assembly, distinct from catalytic evidence.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Deposited AviGT4 polymer (2IV3) | contains_observed_bound | Observed bound UDP | The 2.30 A 2IV3 model contains UDP, glycerol and water, not a modeled donor sugar or avilamycin acceptor. Its 342-aa polymer equals Q93KV2 and native AAK83193.1 exactly. DSMZ identifies the deposited producer DSM 40721 as Tue57. Sequence agreement does not verify expression-tag processing in the inaccessible paper. | https://www.rcsb.org/structure/2IV3 |
| Deposited AviGT4 polymer (2IV3) | is_subunit_of_deposited_assembly | Author/PQS-assigned AviGT4 dimer | 2IV3 has four protein chains in its asymmetric unit and two author/PQS-assigned biological dimers (A/B and C/D), not a tetrameric functional complex. This database assembly assignment does not by itself demonstrate native solution oligomerization or a catalytically required dimer. | https://www.rcsb.org/structure/2IV3
|
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Causal graph — biosynthesis 5 nodes, 5 edges
AviB1 genetic evidence in aviG4-defective GW4. Gavibamycin A1/A3 and the GW4-ITB1 product are distinct from wild-type avilamycin A.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| aviB1 NcoI-fill-in frameshift in GW4-ITB1 | inactivates_encoding_gene_of | Native AviB1 parent | NcoI fill-in frameshift, not whole-gene deletion; confirmed by PCR/restriction and Southern analysis. Q93KV5 matches thesis AAK83190 and AF333038.2:35950..36954 (334 aa). The printed S3B primer does not map exactly and is not exact sequence evidence. | DOI:10.1128/AEM.71.1.400-406.2005 |
| aviB1 NcoI-fill-in frameshift in GW4-ITB1 | abolishes_detectable | Detectable gavibamycin A1/A3 production | Mutant NMR spectra showed only nonacetylated congeners, not parental A1/A3. This is not loss of all natural-product production. | DOI:10.1128/AEM.71.1.400-406.2005
|
| aviB1 NcoI-fill-in frameshift in GW4-ITB1 | causes_accumulation_of | Nonacetylated GW4-ITB1 congener accumulation | Negative-ion HPLC-ESI-MS: m/z 1345 versus A1/A3 1387/1389. NMR: ring-H C4 branch loss (whole-molecule C56), retaining GW4 orsellinic demethylation; distinct from ITO2 product and avilamycin A. Reference extracts also contained minor nonacetylated congeners. | DOI:10.1128/AEM.71.1.400-406.2005 |
| B1pKC genomic-fragment complementation | supplies_wild_type_encoding_gene_for | Native AviB1 parent | B1pKC/B1pKCerm supplies an H4S112 fragment behind ermE in pKC1218. H4S112 includes partial aviB2 DNA: not a verified isolated-CDS construct. PvuI/PvuII source wording differs; precise rescue endpoints and AviB1-alone sufficiency are not asserted. | DOI:10.1128/AEM.71.1.400-406.2005 |
| B1pKC genomic-fragment complementation | restores_detectable | Detectable gavibamycin A1/A3 production | HPLC-ESI-MS confirmed restored A1/A3 in GW4-ITB1, not wild-type avilamycin A. Genetic rescue is not purified-protein turnover. | DOI:10.1128/AEM.71.1.400-406.2005
|
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Causal graph — biosynthesis 5 nodes, 5 edges
AviO2 genetics in Tue57-derived ITO2. The experimental protein remains ungrounded because an exact public protein accession has not been verified.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| aviO2 NdeI-fill-in frameshift in ITO2 | inactivates_encoding_gene_of | Native experimental AviO2 parent | NdeI fill-in frameshift in Tue57, not GW4 or whole-gene deletion. PCR/restriction/sequencing, not Southern, confirmed ITO2. Candidate AF333038.2 complement(40047..40823) encodes 258 aa, matching thesis length and flanking primers. ELS56119.1 (244 aa) lacks 14 N-terminal residues and differs at its initial residue and C145W. Locus mapping is inferred; no exact protein accession is verified. | DOI:10.1128/AEM.71.1.400-406.2005 |
| aviO2 NdeI-fill-in frameshift in ITO2 | abolishes_detectable | Detectable avilamycin A/C production | Mutant NMR spectra showed only nonacetylated products, not parental A/C. Avilamycin-family metabolite production persisted. | DOI:10.1128/AEM.71.1.400-406.2005
|
| aviO2 NdeI-fill-in frameshift in ITO2 | causes_accumulation_of | Nonacetylated ITO2 congener accumulation | Negative-ion HPLC-ESI-MS: m/z 1359 versus A/C 1401/1403. NMR: ring-H C4 branch loss (whole-molecule C56), retaining orsellinic methylation unlike GW4-ITB1. Reference extracts also contained minor nonacetylated congeners. This is not an enzyme-turnover assay. | DOI:10.1128/AEM.71.1.400-406.2005 |
| O2pSET complementation | supplies_wild_type_encoding_gene_for | Native experimental AviO2 parent | Genomic aviO2 behind ermE in O2pSET (pSET152 derivative). Cloning primers flank the candidate ORF; introduced changes are outside it. The amplicon includes flanking DNA, not a verified isolated-CDS or GST construct. | DOI:10.1128/AEM.71.1.400-406.2005 |
| O2pSET complementation | restores_detectable | Detectable avilamycin A/C production | HPLC-ESI-MS confirmed restored A/C in ITO2. Rescue does not identify AviO2's individual catalytic reaction. | DOI:10.1128/AEM.71.1.400-406.2005
|
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Causal graph — biosynthesis 6 nodes, 5 edges
Proposed AviB1/AviB2 assembly and two-carbon branch chemistry. Every edge is an inference, not a demonstrated assembly or turnover assay.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Native AviB1 parent | is_proposed_subunit_of | Proposed AviB1/AviB2 alpha2beta2 complex | Alpha assignment and alpha2beta2 stoichiometry are sequence inferences, not observed assembly or a complete PDH complex. | DOI:10.1128/AEM.71.1.400-406.2005 |
| Native AviB2 parent | is_proposed_subunit_of | Proposed AviB1/AviB2 alpha2beta2 complex | Beta assignment is inferred. Q93KV4 matches AAK83191.1 and AF333038.2:36954..37916 (320 aa). No aviB2 disruption, measured stoichiometry, physical interaction or turnover in this study. | DOI:10.1128/AEM.71.1.400-406.2005 |
| Proposed AviB1/AviB2 alpha2beta2 complex | is_proposed_to_catalyze | Proposed ThDP-dependent pyruvate activation | Genetics/homology motivate ThDP-dependent pyruvate activation to a bound two-carbon nucleophile. No measured intermediate, cofactor requirement, CO2 release or reconstituted reaction. Thesis expression experiments are not activity assays. | DOI:10.1128/AEM.71.1.400-406.2005 |
| Native experimental AviO2 parent | is_proposed_to_participate_in | Proposed ring-H two-carbon branch formation | Unresolved alternatives: branch attachment or C4-OH oxidation before AviB1/AviB2-mediated condensation. No demonstrated ITO2-product-to-avilamycin A conversion, metal dependence, reaction order or ring-closure assignment. | DOI:10.1128/AEM.71.1.400-406.2005 |
| Proposed ThDP-dependent pyruvate activation | is_proposed_to_supply_two_carbon_unit_for | Proposed ring-H two-carbon branch formation | The model links pyruvate activation to branch formation through a ThDP-bound two-carbon unit. This is not measured flux or turnover and does not distinguish AviO2-mediated condensation from prior sugar oxidation. | DOI:10.1128/AEM.71.1.400-406.2005 |
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Causal graph — biosynthesis 4 nodes, 3 edges
MITE-reported AviG4 phenolic O-methylation yielding the encoded avilamycin A model. AviG4 identity remains REVIEW_NEEDED without an accepted protein accession; the linked sequence is a candidate, not a verified assayed protein. Both database product and owner retain unresolved stereocentres. This is a separate database context, not primary biochemical turnover or a reinterpretation of existing GW4 genetics.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| MITE-named AviG4, sequence identity unresolved | is_database_reported_catalyst_of | Database-reported dichloroisoeverninic-moiety O-methylation | Functional attribution is solely the named MITE database assertion. Candidate sequence agreement does not settle the AviG4/mmcR mapping, so no protein identifier is assigned. No direct turnover, mutant allele, rescue, cofactor occupancy, FeS-dependent mechanism, dimer, rates or assay conditions are inferred. | https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000002.json |
| MITE-encoded phenolic O-demethylated precursor | is_database_example_substrate_of | Database-reported dichloroisoeverninic-moiety O-methylation | The source's reaction0/example0 supplies this O-demethylated substrate model. It is not assigned an external identity or equated to every GW4 gavibamycin congener. No experiment-specific metabolite, reaction order or complete pathway is inferred. | https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000002.json
|
| Database-reported dichloroisoeverninic-moiety O-methylation | has_database_example_product | avilamycin A | The pinned source product has the owner's full InChI and key XIRGHRXBGGPPKY-RTWAPUGOSA-N. Both are stereo-incomplete: matching encodings do not resolve the unassigned centres or establish exact assay-congener stereochemistry. No primary turnover, native locus-grade upgrade or producer transfer follows. All13 existing graphs, including GW4 contexts, stay unchanged. | https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000002.json
|
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Explore across X-Mech
AntibioticMech (avilamycin A) ↗
MediaIngredientMech (naturalproductmech:mibig-69e644c0de) ↗
TaxonMech: Streptomyces viridochromogenes Tue57 (NCBITaxon:1160705) ↗
PathwayMech (mibig:BGC0000026) ↗
Provenance
| Source concept | Source | Version |
|---|---|---|
| BGC0000026 | MIBIG | 5 |
This page is generated from data/natural_products/carbohydrates/avilamycin-a.yaml, which is generated from the committed inventories. Neither is edited by hand.