caboxamycin

naturalproductmech:mibig-3a5e98b320 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	CRLJZJZGYIYVSO-UHFFFAOYSA-N
SMILES	OC(=O)C1=CC=CC2=C1N=C(O2)C1=C(O)C=CC=C1
Stereochemistry	fully defined
Cross-references	npatlas:NPA016764

Filing pathway

Unclassified — 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 other, 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 sp. NTK 937 NCBITaxon:1487711	SOURCE_ASSERTION	mibig:BGC0001444	PMID:28417606

Occurrences 2

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 NCBITaxon:1883	LOTUS	DOI:10.1038/JA.2008.24
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.1111/1751-7915.12716

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0001444	Streptomyces sp. NTK 937 NCBITaxon:1487711	CLUSTER_UNSTATED	genbank:JJOB01000001.1

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 9 nodes, 9 edges

Five versioned native protein references are linked by explicitly inferred CDS-to-insert mappings to the reported pSET-cbxABCDE construct. Separate primary experimental edges describe caboxamycin production in S. albus J1074 and B29. The five complete native CDSs do not establish one-to-one cbx aliases, individual enzyme reactions or a physical protein complex; 15 nt of the next CDS is not a sixth intact protein. The authors report PCR sequence checking, but the exact assayed insert sequence was not independently inspected. The product endpoint is acid caboxamycin (compound 1), not its methyl ester or other derivatives. Native producer/BGC evidence grades and the natural-origin classification are unchanged.

Subject	Predicate	Object	Notes	Evidence
DT87_23840 native reference (NTK937)	has a native CDS inferred within the reported insert interval of	pSET-cbxABCDE (reported expression construct)	This is an inferred native-reference-to-insert mapping, not direct sequencing of the assayed plasmid, a confirmed cbxA-E alias assignment, or a claim of individual expression, necessity, sufficiency or catalysis. No physical protein complex is asserted.	DOI:10.1186/s12934-017-0709-6 https://www.ncbi.nlm.nih.gov/nuccore/JJOB01000001.1 https://www.ncbi.nlm.nih.gov/protein/KDQ70105.1 https://rest.uniprot.org/uniparc/UPI0004A8E19B.json reference DOI:10.1186/s12934-017-0709-6 evidence type CURATOR_INFERENCE retrieved on 2026-10-11 notes Methods give SS/fw and AH/rv for the reported cbxABCDE insert. Removing their restriction-site extensions leaves GATCTGCGACGTGTCGCCGTC and GGTGTTGTCGGGCATGGTG. Their inward exact matches delimit native JJOB01000001.1:5312386..5318622 (6237 nt), which contains this complete CDS. The authors report sequence-checking the PCR fragment, but the actual assayed insert sequence was not independently inspected here. reference https://www.ncbi.nlm.nih.gov/nuccore/JJOB01000001.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-11 notes Each primer annealing sequence has one exact match in the expected orientation across this deposited 7003153-nt contig and none in the opposite orientation. The interval contains five complete CDSs, KDQ70105.1-KDQ70109.1, plus 15 nt of KDQ70110.1; the latter is not a sixth intact protein. Other contigs and mismatch-tolerant PCR are outside this check. reference https://www.ncbi.nlm.nih.gov/protein/KDQ70105.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-11 snippet hypothetical protein notes Native KDQ70105.1, locus DT87_23840, 456 aa, coded by JJOB01000001.1:5312522..5313892; Streptomyces sp. NTK 937, taxon 1487711. Native DNA/code-11 translation, CDS and separately retrieved GenPept sequence agree exactly. Product text is deposited annotation, not an adopted substrate-specific enzyme function. reference https://rest.uniprot.org/uniparc/UPI0004A8E19B.json evidence type DATABASE_ASSERTION notes UniParc UPI0004A8E19B (456 aa) links active EMBL KDQ70105.1 (Streptomyces sp. NTK 937, taxon 1487711, locus DT87_23840) and inactive UniProtKB/TrEMBL A0A069K1L6 and A0A1C4RVL3, with zero active UniProtKB cross-references. retrieved on 2026-10-30
DT87_23845 native reference (NTK937)	has a native CDS inferred within the reported insert interval of	pSET-cbxABCDE (reported expression construct)	This is an inferred native-reference-to-insert mapping, not direct sequencing of the assayed plasmid, a confirmed cbxA-E alias assignment, or a claim of individual expression, necessity, sufficiency or catalysis. No physical protein complex is asserted.	DOI:10.1186/s12934-017-0709-6 https://www.ncbi.nlm.nih.gov/nuccore/JJOB01000001.1 https://www.ncbi.nlm.nih.gov/protein/KDQ70106.1 https://rest.uniprot.org/uniparc/UPI00049149D2.json reference DOI:10.1186/s12934-017-0709-6 evidence type CURATOR_INFERENCE retrieved on 2026-10-11 notes Methods give SS/fw and AH/rv for the reported cbxABCDE insert. Removing their restriction-site extensions leaves GATCTGCGACGTGTCGCCGTC and GGTGTTGTCGGGCATGGTG. Their inward exact matches delimit native JJOB01000001.1:5312386..5318622 (6237 nt), which contains this complete CDS. The authors report sequence-checking the PCR fragment, but the actual assayed insert sequence was not independently inspected here. reference https://www.ncbi.nlm.nih.gov/nuccore/JJOB01000001.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-11 notes Each primer annealing sequence has one exact match in the expected orientation across this deposited 7003153-nt contig and none in the opposite orientation. The interval contains five complete CDSs, KDQ70105.1-KDQ70109.1, plus 15 nt of KDQ70110.1; the latter is not a sixth intact protein. Other contigs and mismatch-tolerant PCR are outside this check. reference https://www.ncbi.nlm.nih.gov/protein/KDQ70106.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-11 snippet 3-oxoacyl-ACP synthase notes Native KDQ70106.1, locus DT87_23845, 351 aa, coded by JJOB01000001.1:5313889..5314944; Streptomyces sp. NTK 937, taxon 1487711. Native DNA/code-11 translation, CDS and separately retrieved GenPept sequence agree exactly. Product text is deposited annotation, not an adopted substrate-specific enzyme function. reference https://rest.uniprot.org/uniparc/UPI00049149D2.json evidence type DATABASE_ASSERTION notes UniParc UPI00049149D2 (351 aa) links active EMBL KDQ70106.1 (Streptomyces sp. NTK 937, taxon 1487711, locus DT87_23845) and inactive UniProtKB/TrEMBL A0A069JZJ7, A0A1A9CU65 and A0A1C4L5A3, with zero active UniProtKB cross-references. retrieved on 2026-10-30
DT87_23850 native reference (NTK937)	has a native CDS inferred within the reported insert interval of	pSET-cbxABCDE (reported expression construct)	This is an inferred native-reference-to-insert mapping, not direct sequencing of the assayed plasmid, a confirmed cbxA-E alias assignment, or a claim of individual expression, necessity, sufficiency or catalysis. No physical protein complex is asserted.	DOI:10.1186/s12934-017-0709-6 https://www.ncbi.nlm.nih.gov/nuccore/JJOB01000001.1 https://www.ncbi.nlm.nih.gov/protein/KDQ70107.1 https://rest.uniprot.org/uniparc/UPI0004A9154B.json reference DOI:10.1186/s12934-017-0709-6 evidence type CURATOR_INFERENCE retrieved on 2026-10-11 notes Methods give SS/fw and AH/rv for the reported cbxABCDE insert. Removing their restriction-site extensions leaves GATCTGCGACGTGTCGCCGTC and GGTGTTGTCGGGCATGGTG. Their inward exact matches delimit native JJOB01000001.1:5312386..5318622 (6237 nt), which contains this complete CDS. The authors report sequence-checking the PCR fragment, but the actual assayed insert sequence was not independently inspected here. reference https://www.ncbi.nlm.nih.gov/nuccore/JJOB01000001.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-11 notes Each primer annealing sequence has one exact match in the expected orientation across this deposited 7003153-nt contig and none in the opposite orientation. The interval contains five complete CDSs, KDQ70105.1-KDQ70109.1, plus 15 nt of KDQ70110.1; the latter is not a sixth intact protein. Other contigs and mismatch-tolerant PCR are outside this check. reference https://www.ncbi.nlm.nih.gov/protein/KDQ70107.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-11 snippet Triostin synthetase I notes Native KDQ70107.1, locus DT87_23850, 557 aa, coded by JJOB01000001.1:5314937..5316610; Streptomyces sp. NTK 937, taxon 1487711. Native DNA/code-11 translation, CDS and separately retrieved GenPept sequence agree exactly. Product text is deposited annotation, not an adopted substrate-specific enzyme function. reference https://rest.uniprot.org/uniparc/UPI0004A9154B.json evidence type DATABASE_ASSERTION notes UniParc UPI0004A9154B (557 aa) links active EMBL KDQ70107.1 (Streptomyces sp. NTK 937, taxon 1487711, locus DT87_23850) and inactive UniProtKB/TrEMBL A0A069K883, with zero active UniProtKB cross-references. retrieved on 2026-10-30
DT87_23855 native reference (NTK937)	has a native CDS inferred within the reported insert interval of	pSET-cbxABCDE (reported expression construct)	This is an inferred native-reference-to-insert mapping, not direct sequencing of the assayed plasmid, a confirmed cbxA-E alias assignment, or a claim of individual expression, necessity, sufficiency or catalysis. No physical protein complex is asserted.	DOI:10.1186/s12934-017-0709-6 https://www.ncbi.nlm.nih.gov/nuccore/JJOB01000001.1 https://www.ncbi.nlm.nih.gov/protein/KDQ70108.1 https://rest.uniprot.org/uniparc/UPI0004A940A8.json reference DOI:10.1186/s12934-017-0709-6 evidence type CURATOR_INFERENCE retrieved on 2026-10-11 notes Methods give SS/fw and AH/rv for the reported cbxABCDE insert. Removing their restriction-site extensions leaves GATCTGCGACGTGTCGCCGTC and GGTGTTGTCGGGCATGGTG. Their inward exact matches delimit native JJOB01000001.1:5312386..5318622 (6237 nt), which contains this complete CDS. The authors report sequence-checking the PCR fragment, but the actual assayed insert sequence was not independently inspected here. reference https://www.ncbi.nlm.nih.gov/nuccore/JJOB01000001.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-11 notes Each primer annealing sequence has one exact match in the expected orientation across this deposited 7003153-nt contig and none in the opposite orientation. The interval contains five complete CDSs, KDQ70105.1-KDQ70109.1, plus 15 nt of KDQ70110.1; the latter is not a sixth intact protein. Other contigs and mismatch-tolerant PCR are outside this check. reference https://www.ncbi.nlm.nih.gov/protein/KDQ70108.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-11 snippet hypothetical protein notes Native KDQ70108.1, locus DT87_23855, 125 aa, coded by JJOB01000001.1:5316607..5316984; Streptomyces sp. NTK 937, taxon 1487711. Native DNA/code-11 translation, CDS and separately retrieved GenPept sequence agree exactly. Product text is deposited annotation, not an adopted substrate-specific enzyme function. reference https://rest.uniprot.org/uniparc/UPI0004A940A8.json evidence type DATABASE_ASSERTION notes UniParc UPI0004A940A8 (125 aa) links active EMBL KDQ70108.1 (Streptomyces sp. NTK 937, taxon 1487711, locus DT87_23855) and inactive UniProtKB/TrEMBL A0A069JZH0, with zero active UniProtKB cross-references. retrieved on 2026-10-30
DT87_23860 native reference (NTK937)	has a native CDS inferred within the reported insert interval of	pSET-cbxABCDE (reported expression construct)	This is an inferred native-reference-to-insert mapping, not direct sequencing of the assayed plasmid, a confirmed cbxA-E alias assignment, or a claim of individual expression, necessity, sufficiency or catalysis. No physical protein complex is asserted.	DOI:10.1186/s12934-017-0709-6 https://www.ncbi.nlm.nih.gov/nuccore/JJOB01000001.1 https://www.ncbi.nlm.nih.gov/protein/KDQ70109.1 https://rest.uniprot.org/uniparc/UPI0004A8E9B0.json reference DOI:10.1186/s12934-017-0709-6 evidence type CURATOR_INFERENCE retrieved on 2026-10-11 notes Methods give SS/fw and AH/rv for the reported cbxABCDE insert. Removing their restriction-site extensions leaves GATCTGCGACGTGTCGCCGTC and GGTGTTGTCGGGCATGGTG. Their inward exact matches delimit native JJOB01000001.1:5312386..5318622 (6237 nt), which contains this complete CDS. The authors report sequence-checking the PCR fragment, but the actual assayed insert sequence was not independently inspected here. reference https://www.ncbi.nlm.nih.gov/nuccore/JJOB01000001.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-11 notes Each primer annealing sequence has one exact match in the expected orientation across this deposited 7003153-nt contig and none in the opposite orientation. The interval contains five complete CDSs, KDQ70105.1-KDQ70109.1, plus 15 nt of KDQ70110.1; the latter is not a sixth intact protein. Other contigs and mismatch-tolerant PCR are outside this check. reference https://www.ncbi.nlm.nih.gov/protein/KDQ70109.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-11 snippet amidohydrolase notes Native KDQ70109.1, locus DT87_23860, 519 aa, coded by JJOB01000001.1:5316981..5318540; Streptomyces sp. NTK 937, taxon 1487711. Native DNA/code-11 translation, CDS and separately retrieved GenPept sequence agree exactly. Product text is deposited annotation, not an adopted substrate-specific enzyme function. reference https://rest.uniprot.org/uniparc/UPI0004A8E9B0.json evidence type DATABASE_ASSERTION notes UniParc UPI0004A8E9B0 (519 aa) links active EMBL KDQ70109.1 (Streptomyces sp. NTK 937, taxon 1487711, locus DT87_23860) and inactive UniProtKB/TrEMBL A0A069JYK6, A0A1A9CVR2 and A0A1C4L5I3, with zero active UniProtKB cross-references. retrieved on 2026-10-30
pSET-cbxABCDE (reported expression construct)	was the construct used in	pSET-cbxABCDE expression in S. albus J1074	J1074 is kept separate from the B29 replacement background. Host metabolic contributions are not assigned to specific proteins by this experiment.	DOI:10.1186/s12934-017-0709-6 reference DOI:10.1186/s12934-017-0709-6 evidence type PRIMARY_EXPERIMENT retrieved on 2026-10-11 notes Results and Methods report pSET-cbxABCDE in S. albus J1074, with the cbxABCDE cassette under ermE*p and pSETeTc vector controls. This is the reported experimental construct, not an independently sequenced copy of the mapped native reference interval.
pSET-cbxABCDE expression in S. albus J1074	yielded detectable production of	caboxamycin (acid; compound 1)	This supports production in the whole engineered host context, not production by any one mapped protein or a cell-free five-protein system. Products 2-19, proposed host compensation and bioactivity claims are outside this edge.	DOI:10.1186/s12934-017-0709-6 reference DOI:10.1186/s12934-017-0709-6 evidence type PRIMARY_EXPERIMENT retrieved on 2026-10-11 snippet afforded a substantial production of 1 in both strains notes Results and Figure 2 identify compound 1 after pSET-cbxABCDE expression in S. albus J1074; compare its pSETeTc control and the NTK937 reference chromatogram. The figure reports UPLC at 330 nm. Figure 1 distinguishes acid caboxamycin (1) from its methyl ester (2) and hydroxylated analog (3). No absolute yield is adopted.
pSET-cbxABCDE (reported expression construct)	was the construct used in	pSET-cbxABCDE expression in S. albus B29	B29 is the reported plm15-plm16 replacement background; it is not interchangeable with J1074. No particular host compensating protein is identified here.	DOI:10.1186/s12934-017-0709-6 reference DOI:10.1186/s12934-017-0709-6 evidence type PRIMARY_EXPERIMENT retrieved on 2026-10-11 notes Results and Methods report pSET-cbxABCDE in S. albus B29, with the cbxABCDE cassette under ermE*p and pSETeTc vector controls. This is the reported experimental construct, not an independently sequenced copy of the mapped native reference interval.
pSET-cbxABCDE expression in S. albus B29	yielded detectable production of	caboxamycin (acid; compound 1)	This supports production in the whole engineered host context, not production by any one mapped protein or a cell-free five-protein system. Products 2-19, proposed host compensation and bioactivity claims are outside this edge.	DOI:10.1186/s12934-017-0709-6 reference DOI:10.1186/s12934-017-0709-6 evidence type PRIMARY_EXPERIMENT retrieved on 2026-10-11 snippet afforded a substantial production of 1 in both strains notes Results and Figure 2 identify compound 1 after pSET-cbxABCDE expression in S. albus B29; compare its pSETeTc control and the NTK937 reference chromatogram. The figure reports UPLC at 330 nm. Figure 1 distinguishes acid caboxamycin (1) from its methyl ester (2) and hydroxylated analog (3). No absolute yield is adopted.

Every edge carries its own citation; an uncited edge is refused by the corpus tests.

Explore across X-Mech

AntibioticMech (caboxamycin) ↗ MediaIngredientMech (naturalproductmech:mibig-3a5e98b320) ↗ TaxonMech: Streptomyces sp. NTK 937 (NCBITaxon:1487711) ↗ PathwayMech (mibig:BGC0001444) ↗

Open questions 1

curator-caboxamycin-cassette-and-protein-scope — Can the cbxA-E aliases and assayed construct be tied directly to exact native protein versions, and which individual catalytic or genetic effects are established?

Provenance

Source concept	Source	Version
BGC0001444	MIBIG	5

This page is generated from data/natural_products/unclassified/caboxamycin.yaml, which is generated from the committed inventories. Neither is edited by hand.