thiomarinol
naturalproductmech:mibig-6fc5164982 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 | JIEMCPGFAXNCQW-BFHPBESDSA-N |
|---|---|
| SMILES | CC(O)C(C)\C=C\CC1COC(C(O)C(\C)=C\C(=O)OCCCCCCCC(=O)NC2=C3SSC=C3NC2=O)C(O)C1O |
| Stereochemistry | undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers |
| Cross-references | npatlas:NPA011004, pubchem:5825095 |
Filing pathway
Polyketides — 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 nrps, pks, 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 |
|---|---|---|---|
| Pseudoalteromonas sp. SANK 73390 NCBITaxon:747457 |
SOURCE_ASSERTION | mibig:BGC0001115 | PMID:21483852 |
Occurrences 0
None cited.
Biosynthetic gene clusters 1
| Accession | Host | Locus evidence | Genome |
|---|---|---|---|
| mibig:BGC0001115 | Pseudoalteromonas sp. SANK 73390 NCBITaxon:747457 |
CLUSTER_UNSTATED | genbank:FN689524.1 |
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 8 nodes, 8 edges
Native tmlU genetics with source-assigned products and bounded loss of detection. Partial biosynthesis curation, not full-record sign-off. The owner retains unspecified stereochemistry and SEEDED status; source-assigned products remain ungrounded. Native sequence references do not identify complete engineered preparations or deletion alleles.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited TmlU sequence reference | FN689524.1 CDS 76680..78644(-), 1-based inclusive; CBK62739.1, 654 aa. CDS-aware table-11 translation exactly matches the deposited protein and selected UniProt sequence. Deposit source is Pseudoalteromonas sp. SANK 73390, taxon 747457, plasmid pTML1. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| Reported tmlU in-frame deletion allele | affects_coding_locus_of | Native deposited TmlU sequence reference | Native accession anchors the affected gene, not a full protein present in the deletion strain. Exact deletion endpoints and residual protein sequence are not established here. | DOI:10.1371/journal.pone.0018031
|
| Reported tmlU in-frame deletion allele | was_introduced_in | SANK 73390 tmlU deletion culture | PCR flanks joined through PstI were cloned into pAKE604; transfer used E. coli S17-1. Figure 3 calls the producer P. rava SANK 73390, while the text and current deposit use Pseudoalteromonas sp.; no taxonomic rename or stock-sequence equivalence is inferred. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 tmlU deletion culture | retained_reported_production_of | Source-assigned marinolic acid | Figure 3 shows culture-medium HPLC traces at 233 nm with source LCMS assignments. No replicate count, uncertainty or detection limit is given there; absence of a reported peak is not a universal or numerical zero-production assertion. Growth methods specify marine medium at 23 C. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 tmlU deletion culture | retained_reported_production_of | Source-assigned acylpyrrothine products | Figure 3 shows culture-medium HPLC traces at 233 nm with source LCMS assignments. No replicate count, uncertainty or detection limit is given there; absence of a reported peak is not a universal or numerical zero-production assertion. Growth methods specify marine medium at 23 C. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 tmlU deletion culture | lacked_detected_production_of | Source-assigned thiomarinol product | Figure 3 shows culture-medium HPLC traces at 233 nm with source LCMS assignments. No replicate count, uncertainty or detection limit is given there; absence of a reported peak is not a universal or numerical zero-production assertion. Growth methods specify marine medium at 23 C. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 tmlU deletion culture | supports_genetic_interpretation | TmlU contribution to pathway convergence | The deletion phenotype supports a contribution to joining the pathways, not direct amide catalysis by isolated TmlU. No complementation result or full exclusion of polarity is asserted for this experiment. | DOI:10.1371/journal.pone.0018031
|
| Native deposited TmlU sequence reference | has_genetically_supported_role | TmlU contribution to pathway convergence | The 2011 direct-amide-synthetase proposal is narrowed by the later TmlU CoA-ligase/HolE acyltransferase evidence. A genetic requirement alone does not establish a catalytic step. | DOI:10.1371/journal.pone.0018031 |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 11 nodes, 11 edges
Primary-abstract-supported TmlU activation followed by HolE amidation, not a physical complex. Detailed kinetic values and native-substrate reconstitution remain unasserted. Partial biosynthesis curation, not full-record sign-off. The owner retains unspecified stereochemistry and SEEDED status; source-assigned products remain ungrounded. Native sequence references do not identify complete engineered preparations or deletion alleles.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited TmlU sequence reference | FN689524.1 CDS 76680..78644(-), 1-based inclusive; CBK62739.1, 654 aa. CDS-aware table-11 translation exactly matches the deposited protein and selected UniProt sequence. Deposit source is Pseudoalteromonas sp. SANK 73390, taxon 747457, plasmid pTML1. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited HolE sequence reference | FN689524.1 CDS 92330..93214(+), 1-based inclusive; CBK62750.1, 294 aa. CDS-aware table-11 translation exactly matches the deposited protein and selected UniProt sequence. Deposit source is Pseudoalteromonas sp. SANK 73390, taxon 747457, plasmid pTML1. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| Native deposited TmlU sequence reference | is_native_sequence_reference_for | Study TmlU preparation | Gene-matched native reference only. Tags, insert sequence, host, culture, purity and complete fusion identity were not verified from the inaccessible 2015 methods. | https://www.uniprot.org/uniprotkb/F8J3D9 |
| Native deposited HolE sequence reference | is_native_sequence_reference_for | Study HolE preparation | Gene-matched native reference only. Tags, insert sequence, host, culture, purity and complete fusion identity were not verified from the inaccessible 2015 methods. | https://www.uniprot.org/uniprotkb/F8J3H2 |
| Assayed pseudomonic acid substrate | is_substrate_in | Pseudomonic acid CoA activation | The abstract identifies pseudomonic acid, not the native marinolic acid substrate. No exact congener-specific structure identifier is selected. | DOI:10.1002/anie.201411667
|
| Study TmlU preparation | catalyzes | Pseudomonic acid CoA activation | TmlU is supported as a CoA ligase, not a stand-alone amide synthetase. | DOI:10.1002/anie.201411667
|
| Pseudomonic acid CoA activation | forms | Activated pseudomonic-acid thioester | Reported activation product; ATP/CoA stoichiometry and detailed kinetic values are not supplied here. | DOI:10.1002/anie.201411667
|
| Activated pseudomonic-acid thioester | is_acyl_donor_in | HolE-dependent amidation | Sequential activation and amidation do not establish physical enzyme association or substrate channeling. | DOI:10.1002/anie.201411667
|
| Assayed holothin acceptor | is_acceptor_in | HolE-dependent amidation | Holothin is the amine partner of the reported hybrid product, not a native-producer abundance measurement. | DOI:10.1002/anie.201411667
|
| Study HolE preparation | catalyzes | HolE-dependent amidation | Abstract-supported acyltransferase activity. Qualitative substrate breadth is not a measured kinetic panel here. | DOI:10.1002/anie.201411667
|
| HolE-dependent amidation | forms_assayed_hybrid | Pseudomonic-acid holothin hybrid analogue | A pseudomonic-acid-derived hybrid is not exact-identity native thiomarinol. No complete native marinolic-acid turnover experiment or mature-owner synthesis is asserted. | DOI:10.1002/anie.201411667
|
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 15 nodes, 19 edges
Separate TmpD/HolA genetic disruptions, cofermentation and culture feeding. Predicted module intermediates and HolA dimerization are not asserted as measured results. Native proteins use original GenPept accessions; deleted UniProt entries are not selected as live examples. Partial biosynthesis curation, not full-record sign-off. The owner retains unspecified stereochemistry and SEEDED status; source-assigned products remain ungrounded. Native sequence references do not identify complete engineered preparations or deletion alleles.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited TmpD sequence reference | FN689524.1 CDS 50878..70959(+), 1-based inclusive; 6693 aa. CDS-aware table-11 translation exactly matches CBK62733.1, WP_013933285.1 and archive UPI000211AE5B. SANK 73390, taxon 747457, pTML1. RefSeq's generic SDR-family label is not a complete functional description of this multidomain protein. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited HolA sequence reference | FN689524.1 CDS 85410..88778(+), 1-based inclusive; 1122 aa. CDS-aware table-11 translation exactly matches CBK62746.1, WP_013933298.1 and archive UPI00021172A6. SANK 73390, taxon 747457, pTML1. HolA has an annotated possible non-Met start at 85542..85544; the deposited 1122-aa reference is not a verified mature proteoform. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| tmpD internal-fragment suicide construct | targets_coding_locus_of | Native deposited TmpD sequence reference | An approximately 1-kb internal segment, reported tmpD positions 5182..6158 in KS-D2. This is internal-fragment suicide mutagenesis, not a reconstructed complete coding deletion. | DOI:10.1371/journal.pone.0018031
|
| holA internal-fragment suicide construct | targets_coding_locus_of | Native deposited HolA sequence reference | The methods call the fragment 480 bp but give positions 1509..1990, whose inclusive span is 482 bp. Preserve the source discrepancy; exact vector junction and allele sequence remain unverified. | DOI:10.1371/journal.pone.0018031
|
| tmpD internal-fragment suicide construct | was_introduced_in | SANK 73390 tmpD-disrupted culture | pAKE604 suicide vector mobilized via E. coli S17-1 into SANK 73390; native reference does not identify an intact protein in the mutant. Possible polar effects remain unexcluded. | DOI:10.1371/journal.pone.0018031
|
| holA internal-fragment suicide construct | was_introduced_in | SANK 73390 holA-disrupted culture | pAKE604 suicide vector mobilized via E. coli S17-1 into SANK 73390; distinct from the tmlU in-frame deletion. The resulting mutants lacked yellow pigment; no mature HolA sequence inferred. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 tmpD-disrupted culture | retained_reported_production_of | Source-assigned pyrrothine-containing products | Figure 3 culture-medium HPLC traces at 233 nm, with source LCMS assignments; no numerical zero, detection limit, titers or replicate statistics inferred. No direct purified-protein catalysis follows from this genetic phenotype. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 tmpD-disrupted culture | lacked_detected_production_of | Source-assigned thiomarinol product | Figure 3 culture-medium HPLC traces at 233 nm, with source LCMS assignments; no numerical zero, detection limit, titers or replicate statistics inferred. No direct purified-protein catalysis follows from this genetic phenotype. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 holA-disrupted culture | retained_reported_production_of | Source-assigned marinolic acid | Figure 3 culture-medium HPLC traces at 233 nm, with source LCMS assignments; no numerical zero, detection limit, titers or replicate statistics inferred. No direct purified-protein catalysis follows from this genetic phenotype. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 holA-disrupted culture | lacked_detected_production_of | Source-assigned thiomarinol product | Figure 3 culture-medium HPLC traces at 233 nm, with source LCMS assignments; no numerical zero, detection limit, titers or replicate statistics inferred. No direct purified-protein catalysis follows from this genetic phenotype. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 tmpD-disrupted culture | participated_in | Paired-mutant cofermentation | The source uses delta-tmpD shorthand; methods describe the internal-fragment suicide mutant. Co-culture is not a protein complex or a claim that both lesions occur in one strain. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 holA-disrupted culture | participated_in | Paired-mutant cofermentation | The complementary holA-disrupted culture participates separately. No cell-to-cell transfer kinetics or transport protein identity is established. | DOI:10.1371/journal.pone.0018031
|
| Paired-mutant cofermentation | restored_reported_production_of | Source-assigned thiomarinol product | Source LCMS confirmation of restored production; not a reported quantitative wild-type titer or an exact owner-stereochemistry determination. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 tmpD-disrupted culture | was_recipient_in | Marinolic-acid feeding of tmpD-disrupted culture | Culture feeding, not purified TmpD or TmlU turnover. | DOI:10.1371/journal.pone.0018031
|
| Source-assigned marinolic acid | was_added_in | Marinolic-acid feeding of tmpD-disrupted culture | Source-assigned precursor supplied exogenously; no dose or time inferred from the inspected paragraph. | DOI:10.1371/journal.pone.0018031
|
| Marinolic-acid feeding of tmpD-disrupted culture | restored_reported_production_of | Source-assigned thiomarinol product | Qualitative biosynthetic rescue supports precursor use by the remaining culture machinery; it does not identify a sole amide-forming enzyme. | DOI:10.1371/journal.pone.0018031
|
| SANK 73390 tmpD-disrupted culture | was_recipient_in | Pseudomonic-acid-A feeding of tmpD-disrupted culture | Separate mutasynthesis condition, not native precursor feeding. | DOI:10.1371/journal.pone.0018031
|
| Fed pseudomonic acid A | was_added_in | Pseudomonic-acid-A feeding of tmpD-disrupted culture | Pseudomonic acid A is chemically distinct from the native marinolic-acid moiety. | DOI:10.1371/journal.pone.0018031
|
| Pseudomonic-acid-A feeding of tmpD-disrupted culture | yielded_reported_hybrids | Source-assigned novel pseudomonic-acid pyrrothine amides | Two novel pyrrothine amides are reported. Do not label these native thiomarinol or assign the stereochemically incomplete owner's exact identifier to them. | DOI:10.1371/journal.pone.0018031
|
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 17 nodes, 17 edges
Native TmlF deletion genetics and source-assigned metabolites, with a separately inferred 7-ketoreductase role. No isolated-enzyme turnover or complete pathway reconstitution is asserted. Exact congener/tautomer/stereochemical identities remain ungrounded; the owner retains SEEDED status.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited TmlF sequence reference | FN689524.1 CDS 73267..74319(+), 1-based inclusive; CBK62736.1, 350 aa. Table-11 CDS translation, original GenPept and UPI000211729C archive sequences match exactly. Native source is Pseudoalteromonas sp. SANK 73390, taxon 747457, pTML1. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| Reported tmlF in-frame deletion allele | affects_coding_locus_of | Native deposited TmlF sequence reference | The source reports removal from aa 10 to aa 327 using approximately 500-bp arms. These are reported native numbering boundaries, not a reconstructed junction or complete residual-protein sequence. | DOI:10.1002/anie.201611590
|
| Reported tmlF in-frame deletion allele | was_introduced_in | SANK 73390 tmlF deletion culture | Native SANK 73390 genetic intervention, distinct from heterologous mupirocin-host deletions. No complementation result, whole mutant-genome identity or full polarity exclusion is asserted. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | lacked_detected_production_of | Source-assigned thiomarinol A | Source extract analysis reports loss of thiomarinol A. Bounded detection claim; no detection-limit, numerical zero, replicate count or titer estimate is inferred. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | lacked_detected_production_of | Source-assigned thiomarinol C | The same mutant also loses detected thiomarinol C. The congener remains separate from thiomarinol A and from the stereochemically incomplete owner identity. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | retained_reported_production_of | Source-assigned xenorhabdin acylpyrrothines | The paper reports continued acylpyrrothine production; Figure 4 labels this chromatographic region. No equality of quantitative wild-type and mutant titers is asserted. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | yielded_source_assigned_metabolite | Source-assigned 8-hydroxythiomarinol C (22) | Figure 4/source text assign a minor metabolite from the mutant extract using reported NMR/HR-ESI-MS. Detailed spectra and replicate-level data were not inspected. This is not proof of a sole direct TmlF substrate. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | yielded_source_assigned_metabolite | Source-assigned 6,7-diketothiomarinol C (23) | Figure 4/source text assign a minor metabolite from the mutant extract using reported NMR/HR-ESI-MS. Detailed spectra and replicate-level data were not inspected. This is not proof of a sole direct TmlF substrate. The source represents this group as enol-ketone tautomers; no exact tautomer identifier is chosen. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | yielded_source_assigned_metabolite | Source-assigned 6,7-diketothiomarinol A (24) | Figure 4/source text assign a minor metabolite from the mutant extract using reported NMR/HR-ESI-MS. Detailed spectra and replicate-level data were not inspected. This is not proof of a sole direct TmlF substrate. The source represents this group as enol-ketone tautomers; no exact tautomer identifier is chosen. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | yielded_source_assigned_metabolite | Source-assigned 6,7-diketomarinolic acid C6 (25) | Figure 4/source text assign a minor metabolite from the mutant extract using reported NMR/HR-ESI-MS. Detailed spectra and replicate-level data were not inspected. This is not proof of a sole direct TmlF substrate. The source represents this group as enol-ketone tautomers; no exact tautomer identifier is chosen. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | yielded_source_assigned_metabolite | Source-assigned 7-ketothiomarinol C (26) | Figure 4/source text assign a minor metabolite from the mutant extract using reported NMR/HR-ESI-MS. Detailed spectra and replicate-level data were not inspected. This is not proof of a sole direct TmlF substrate. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | yielded_source_assigned_metabolite | Source-assigned 7-ketothiomarinol A (27) | Figure 4/source text assign a minor metabolite from the mutant extract using reported NMR/HR-ESI-MS. Detailed spectra and replicate-level data were not inspected. This is not proof of a sole direct TmlF substrate. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | yielded_source_assigned_metabolite | Source-assigned 8-epi-7-ketothiomarinol C (28) | Figure 4/source text assign a minor metabolite from the mutant extract using reported NMR/HR-ESI-MS. Detailed spectra and replicate-level data were not inspected. This is not proof of a sole direct TmlF substrate. Keto-enol tautomerism/epimerization may generate this product; do not force a linear biosynthetic step. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | yielded_source_assigned_metabolite | Source-assigned 8-epi-7-ketothiomarinol A (29) | Figure 4/source text assign a minor metabolite from the mutant extract using reported NMR/HR-ESI-MS. Detailed spectra and replicate-level data were not inspected. This is not proof of a sole direct TmlF substrate. Keto-enol tautomerism/epimerization may generate this product; do not force a linear biosynthetic step. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | yielded_source_assigned_metabolite | Source-assigned 8-epi-7-epi-6-ketothiomarinol A (30) | Figure 4/source text assign a minor metabolite from the mutant extract using reported NMR/HR-ESI-MS. Detailed spectra and replicate-level data were not inspected. This is not proof of a sole direct TmlF substrate. Keto-enol tautomerism/epimerization may generate this product; do not force a linear biosynthetic step. | DOI:10.1002/anie.201611590
|
| SANK 73390 tmlF deletion culture | supports_genetic_interpretation | Inferred TmlF 7-ketoreductase role | Accumulated oxidation-state variants are consistent with a late reductive role. They do not establish isolated TmlF catalysis, cofactor specificity, kinetics or a fixed order for all shunt products. | DOI:10.1002/anie.201611590
|
| Native deposited TmlF sequence reference | has_inferred_role | Inferred TmlF 7-ketoreductase role | The authors combine the deletion phenotype with 33% amino-acid identity to mupirocin MupF to propose a 7-ketoreductase role. MupF is an analogy, not a substitute protein identifier or direct TmlF assay. | DOI:10.1002/anie.201611590
|
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 6 nodes, 6 edges
Native TmuB I109N genetics and source-assigned thiomarinol C, without claiming an exact mutant proteoform or universal loss of product. Native references do not establish complete engineered proteoforms. Source-assigned congeners remain ungrounded; owner identity, incomplete stereochemistry and SEEDED status are unchanged.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited TmuB sequence reference | FN689524.1 CDS 82295..83089(+), 1-based inclusive; CBK62743.1,264 aa. CDS-aware table-11 translation matches original GenPept, WP_013933295.1 and UPI00021172A3. Native source is Pseudoalteromonas sp. SANK 73390,taxon747457,pTML1. The generic RefSeq family name is not itself experimental substrate evidence. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| Reported tmuB I109N allele | affects_coding_locus_of | Native deposited TmuB sequence reference | Native reference position109 is Ile; the reported substitution is I109N. This is a point-mutant allele, not a complete deletion or a claim that the mutant sequence is identical to the native accession. | DOI:10.1002/cbic.201800036
|
| Reported tmuB I109N allele | was_introduced_in | SANK 73390 tmuB I109N culture | The source describes pAKE604-mediated allelic replacement, E. coli S17-1 mobilization, kanamycin selection for integrants, followed by sucrose-resistant colonies screened for kanamycin sensitivity and PCR/sequencing checks. The target native locus is on pTML1; the methods' generic chromosome wording does not relocate it. No whole mutant-stock sequence is established. | DOI:10.1002/cbic.201800036
|
| SANK 73390 tmuB I109N culture | yielded_source_assigned_metabolite | Source-assigned thiomarinol C | The source prepared thiomarinol C after recombining I109N into the producer. This does not supply a quantitative native yield or prove complete absence of thiomarinol A in every condition. | DOI:10.1002/cbic.201800036
|
| SANK 73390 tmuB I109N culture | supports_genetic_interpretation | TmuB contribution to native 4-hydroxylation | Native point-mutant/product evidence supports a biosynthetic contribution; full complementation and exclusion of all secondary effects are not established here. | DOI:10.1002/cbic.201800036
|
| Native deposited TmuB sequence reference | has_genetically_supported_role | TmuB contribution to native 4-hydroxylation | Keep this genetic interpretation separate from the purified preparation's conversion of thiomarinol C to A. No antimicrobial target mechanism or MIC claim is copied into this biosynthesis graph. | DOI:10.1002/cbic.201800036
|
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 14 nodes, 15 edges
Purified TmuB tailoring with separate native and surrogate substrates, I109N negative control and delayed PA-B activity. Homology-model templates are not presented as TmuB crystal structures; unaudited kinetic values remain unasserted. Purified conversion does not establish native reaction order. Native references do not establish complete engineered proteoforms. Source-assigned congeners remain ungrounded; owner identity, incomplete stereochemistry and SEEDED status are unchanged.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited TmuB sequence reference | FN689524.1 CDS 82295..83089(+), 1-based inclusive; CBK62743.1,264 aa. CDS-aware table-11 translation matches original GenPept, WP_013933295.1 and UPI00021172A3. Native source is Pseudoalteromonas sp. SANK 73390,taxon747457,pTML1. The generic RefSeq family name is not itself experimental substrate evidence. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| Native deposited TmuB sequence reference | is_native_sequence_reference_for | Study N-terminal His-tagged WT TmuB preparation | Gene-matched reference for the WT preparation, not complete fusion-sequence equality. The source specifies pET28a,N-terminal His-tag,E. coli BL21(DE3),Ni-NTA and gel filtration. SI uses both SANK73390 and SANK73309 in strain/cloning text; retain that apparent typo rather than inventing a second strain or verified stock identity. | DOI:10.1002/cbic.201800036
|
| Native deposited TmuB sequence reference | is_native_sequence_reference_for | Study N-terminal His-tagged TmuB I109N preparation | Gene-matched reference for the I109N preparation, not complete fusion-sequence equality. The source specifies pET28a,N-terminal His-tag,E. coli BL21(DE3),Ni-NTA and gel filtration. SI uses both SANK73390 and SANK73309 in strain/cloning text; retain that apparent typo rather than inventing a second strain or verified stock identity. | DOI:10.1002/cbic.201800036
|
| Assayed pseudomonic acid A | was_substrate_in | Purified WT TmuB pseudomonic-acid-A hydroxylation | Purified WT activity requires the reported iron cofactor and alpha-ketoglutarate co-substrate in the pseudomonic-acid-A assay. This control is not silently transferred to every other experiment. | DOI:10.1002/cbic.201800036
|
| Study N-terminal His-tagged WT TmuB preparation | catalyzed | Purified WT TmuB pseudomonic-acid-A hydroxylation | Source enzymatic experiment; no numerical turnover/efficiency, replicate count or complete tagged-proteoform identity is inferred. | DOI:10.1002/cbic.201800036
|
| Purified WT TmuB pseudomonic-acid-A hydroxylation | yielded_source_assigned_product | Source-assigned 4-hydroxypseudomonic acid A | Retain the source chemical assignment and its congener boundary; no exact structure CURIE is selected. | DOI:10.1002/cbic.201800036
|
| Assayed thiomarinol C | was_substrate_in | Purified WT TmuB thiomarinol-C hydroxylation | Source-assigned thiomarinol C is converted to thiomarinol A by purified WT TmuB. This demonstrates capacity for late tailoring, but native pathway timing remains inferred. It is not de novo reconstitution or independent verification of the owner's exact stereochemistry. | DOI:10.1002/cbic.201800036
|
| Study N-terminal His-tagged WT TmuB preparation | catalyzed | Purified WT TmuB thiomarinol-C hydroxylation | Source enzymatic experiment; no numerical turnover/efficiency, replicate count or complete tagged-proteoform identity is inferred. | DOI:10.1002/cbic.201800036
|
| Purified WT TmuB thiomarinol-C hydroxylation | yielded_source_assigned_product | Source-assigned thiomarinol A | Retain the source chemical assignment and its congener boundary; no exact structure CURIE is selected. | DOI:10.1002/cbic.201800036
|
| Assayed pseudomonic acid B | was_substrate_in | Delayed pseudomonic-acid-B hydroxylation in vitro | Detectable conversion follows prolonged in vitro incubation. The abstract's blocked-action wording must not become an absolute zero; lack of detectable conversion in culture is a different observation. | DOI:10.1002/cbic.201800036
|
| Study N-terminal His-tagged WT TmuB preparation | catalyzed | Delayed pseudomonic-acid-B hydroxylation in vitro | Source enzymatic experiment; no numerical turnover/efficiency, replicate count or complete tagged-proteoform identity is inferred. | DOI:10.1002/cbic.201800036
|
| Delayed pseudomonic-acid-B hydroxylation in vitro | yielded_source_assigned_product | Source-assigned 4-hydroxypseudomonic acid B | Retain the source chemical assignment and its congener boundary; no exact structure CURIE is selected. | DOI:10.1002/cbic.201800036
|
| Study N-terminal His-tagged TmuB I109N preparation | was_tested_in | Purified I109N preparation with pseudomonic acid A | I109N was expressed and purified in parallel; this control pertains to pseudomonic acid A, not all possible substrates or proof of an experimentally determined binding pose. | DOI:10.1002/cbic.201800036
|
| Assayed pseudomonic acid A | was_substrate_in | Purified I109N preparation with pseudomonic acid A | Same named substrate as the WT comparison; no unsupported concentration matching or statistical replicate design asserted. | DOI:10.1002/cbic.201800036
|
| Purified I109N preparation with pseudomonic acid A | lacked_detected_formation_of | Source-assigned 4-hydroxypseudomonic acid A | Reported negative preparation control, not a universal absence of catalytic potential or a measured binding-affinity change. | DOI:10.1002/cbic.201800036
|
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Causal graph — biosynthesis 7 nodes, 6 edges
TmlW whole-cell activity on a mupirocin surrogate, with cellular redox context retained. Source-assigned surrogate products remain ungrounded. Native sequence references do not establish complete engineered proteoforms, native pathway timing or full thiomarinol reconstitution. Main-text-bounded curation, not full-method or full-record sign-off.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited TmlW sequence reference | FN689524.1 CDS 83143..84546(+),1-based inclusive; CBK62744.1,467 aa. CDS-aware table-11 translation matches original GenPept,WP_013933296.1 and UPI00021172A4. Native source is Pseudoalteromonas sp. SANK 73390,taxon747457,pTML1. This identifies the native reference, not a complete engineered construct. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| Native deposited TmlW sequence reference | is_native_sequence_reference_for | Study heterologously expressed TmlW | Gene-matched reference only; complete insert, fusion and mature sequence remain unverified. | DOI:10.1039/C9SC06192D
|
| Study heterologously expressed TmlW | was_heterologously_expressed_in | Study TmlW-overexpressing resting E. coli cells | Main-text expression context; no exact host-strain identifier, vector or tag is selected here. | DOI:10.1039/C9SC06192D
|
| Study TmlW-overexpressing resting E. coli cells | were_used_in | TmlW whole-cell biotransformation | Whole-cell experiment with glucose and endogenous redox support, not isolated TmlW catalysis. | DOI:10.1039/C9SC06192D
|
| Supplied mupirocin W5 | was_supplied_in | TmlW whole-cell biotransformation | Surrogate substrate; no native marinolic-acid identity or quantitative input measurement adopted. | DOI:10.1039/C9SC06192D
|
| TmlW whole-cell biotransformation | yielded_source_assigned_product | Source-assigned mupirocin Z2 | Main text reports LC-MS followed by product isolation/NMR assignment. No kinetic rate, replicate count, isolated epoxide intermediate or purified-enzyme sufficiency inferred. | DOI:10.1039/C9SC06192D
|
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Causal graph — biosynthesis 9 nodes, 8 edges
Mixed MupW/TmlZ whole-cell activity. Do not turn this experiment into a TmlW/TmlZ purified pair. Source-assigned surrogate products remain ungrounded. Native sequence references do not establish complete engineered proteoforms, native pathway timing or full thiomarinol reconstitution. Main-text-bounded curation, not full-method or full-record sign-off.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited TmlZ sequence reference | FN689524.1 CDS 84558..84941(+),1-based inclusive; CBK62745.1,127 aa. CDS-aware table-11 translation matches original GenPept,WP_013933297.1 and UPI00021172A5. Native source is Pseudoalteromonas sp. SANK 73390,taxon747457,pTML1. This identifies the native reference, not a complete engineered construct. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| Native deposited TmlZ sequence reference | is_native_sequence_reference_for | Study heterologously expressed TmlZ | Gene-matched native reference; complete fusion identity is not established. | DOI:10.1039/C9SC06192D
|
| Study heterologously expressed TmlZ | was_heterologously_expressed_in | Study MupW-and-TmlZ-coexpressing E. coli cells | TmlZ is the thiomarinol-derived partner; this is not a purified preparation assay. | DOI:10.1039/C9SC06192D
|
| Study coexpressed MupW | was_coexpressed_in | Study MupW-and-TmlZ-coexpressing E. coli cells | Keep the named mupirocin MupW partner, not TmlW. No convenient ortholog or exact MupW accession is substituted for an unverified study construct. | DOI:10.1039/C9SC06192D
|
| Study MupW-and-TmlZ-coexpressing E. coli cells | were_used_in | Mixed-origin whole-cell biotransformation | Coexpression does not establish a physical complex, substrate channeling or TmlZ-alone sufficiency. | DOI:10.1039/C9SC06192D
|
| Supplied mupirocin W4 | was_supplied_in | Mixed-origin whole-cell biotransformation | Distinct surrogate experiment from the TmlW/W5 condition; no cross-condition rate comparison. | DOI:10.1039/C9SC06192D
|
| Mixed-origin whole-cell biotransformation | yielded_source_assigned_product | Source-assigned desepoxy-pseudomonic acid B | Main-text product assignment; not exact native thiomarinol identity or direct observation of the proposed epoxide intermediate. | DOI:10.1039/C9SC06192D
|
| Native MupW sequence reference | is_native_reference_for | Study coexpressed MupW | UniProtKB:Q8RL46 is the deposited native sequence reference for Study coexpressed MupW (node 'mupw'); the experimental preparation node remains ungrounded because recombinant tags, host-specific processing, or undeposited construct sequences are not equated with the native entry. | https://www.uniprot.org/uniprotkb/Q8RL46 |
Every edge carries its own citation; an uncited edge is refused by the corpus tests.
Causal graph — biosynthesis 9 nodes, 10 edges
TmlW knockin rescue in two separate mupirocin-host backgrounds, without converting culture endpoints into enzyme kinetics. Source-assigned surrogate products remain ungrounded. Native sequence references do not establish complete engineered proteoforms, native pathway timing or full thiomarinol reconstitution. Main-text-bounded curation, not full-method or full-record sign-off.
| Subject | Predicate | Object | Notes | Evidence |
|---|---|---|---|---|
| Thiomarinol locus on native pTML1 | encodes_native_reference | Native deposited TmlW sequence reference | FN689524.1 CDS 83143..84546(+),1-based inclusive; CBK62744.1,467 aa. CDS-aware table-11 translation matches original GenPept,WP_013933296.1 and UPI00021172A4. Native source is Pseudoalteromonas sp. SANK 73390,taxon747457,pTML1. This identifies the native reference, not a complete engineered construct. | https://www.ncbi.nlm.nih.gov/nuccore/FN689524.1 |
| Reported tmlW knockin coding insert | encodes_a_study_counterpart_of | Native deposited TmlW sequence reference | Native protein reference anchors the introduced gene, not the complete promoter/junction sequence or a fully verified engineered proteoform. | DOI:10.1039/C9SC06192D
|
| Reported tmlW knockin coding insert | was_introduced_in | Study mupW-deleted tmlW-knockin culture | Main text reports tmlW replacement at the removed mupW locus by two-step allelic exchange. Native thiomarinol locus ownership is not transferred to this heterologous host. | DOI:10.1039/C9SC06192D
|
| P. fluorescens NCIMB 10586 mupW-deleted culture | was_genetic_background_for | Study mupW-deleted tmlW-knockin culture | This is the mupW-only deletion background, without the reported mmpE-OR mutation used in the other experiment. Full edited-stock sequence is not established. | DOI:10.1039/C9SC06192D
|
| P. fluorescens NCIMB 10586 mupW-deleted culture | lacked_detected_production_of | Source-assigned pseudomonic acid A | Bounded reported culture phenotype; no universal or numerical zero, detection limit or replicate-level estimate adopted. | DOI:10.1039/C9SC06192D
|
| Study mupW-deleted tmlW-knockin culture | restored_reported_production_of | Source-assigned pseudomonic acid A | Heterologous culture rescue, not native thiomarinol synthesis or isolated TmlW turnover. No equality of quantitative titres, substrate preference or rate-limiting assignment inferred. | DOI:10.1039/C9SC06192D
|
| Reported tmlW knockin coding insert | was_introduced_in | Study mmpE-OR-domain/mupW mutant with tmlW knockin | Main text reports tmlW replacement at the removed mupW locus by two-step allelic exchange. Native thiomarinol locus ownership is not transferred to this heterologous host. | DOI:10.1039/C9SC06192D
|
| Study mmpE-OR-domain and mupW double-mutant culture | was_genetic_background_for | Study mmpE-OR-domain/mupW mutant with tmlW knockin | This is the double-mutant background. mmpE-OR denotes the epoxidase domain, not deletion of the entire mmpE gene. Full edited-stock sequence is not established. | DOI:10.1039/C9SC06192D
|
| Study mmpE-OR-domain and mupW double-mutant culture | lacked_detected_production_of | Source-assigned pseudomonic acid C | Bounded reported culture phenotype; no universal or numerical zero, detection limit or replicate-level estimate adopted. | DOI:10.1039/C9SC06192D
|
| Study mmpE-OR-domain/mupW mutant with tmlW knockin | restored_reported_production_of | Source-assigned pseudomonic acid C | Heterologous culture rescue, not native thiomarinol synthesis or isolated TmlW turnover. No equality of quantitative titres, substrate preference or rate-limiting assignment inferred. | DOI:10.1039/C9SC06192D
|
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Explore across X-Mech
AntibioticMech (thiomarinol) ↗
MediaIngredientMech (naturalproductmech:mibig-6fc5164982) ↗
TaxonMech: Pseudoalteromonas sp. SANK 73390 (NCBITaxon:747457) ↗
PathwayMech (mibig:BGC0001115) ↗
Provenance
| Source concept | Source | Version |
|---|---|---|
| BGC0001115 | MIBIG | 5 |
This page is generated from data/natural_products/polyketides/thiomarinol.yaml, which is generated from the committed inventories. Neither is edited by hand.