fcoT Resolved · high auto-curated
H37Rv Rv0098 · MTBC0 mtbc0_000107 ·
183 aa · 107763–108314 (+) ·
RefSeq NP_214612.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fatty acyl CoA thioesterase FcoT |
|---|---|
| MTBC0 PGAP re-annotation | fatty acyl CoA thioesterase FcoT |
| Revised (this work) | Fatty acyl CoA thioesterase FcoT. Pfam: FcoT (PF10862.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM67
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | (2E)-enoyl-[ACP] glycyltransferase |
| EC (curated) |
EC 3.1.2.-, EC 3.1.2.2, EC 4.3.2.11
|
| Curated function | Involved in the biosynthesis of a unique class of isonitrile lipopeptides (INLPs) that seem to function as virulence factors in M.tuberculosis and to play a role in metal acquisition. Catalyzes a Michael addition of glycine to the beta-position of an alpha,beta-unsaturated fatty acyl-[ACP], producing a (3R)-3-[(carboxymethyl)amino]fatty acid. Acts on the (2E)-decenoyl moiety loaded on the acyl-carrier protein (ACP) Rv0100, forming the product (3R)-3-[(carboxymethyl)amino]decanoate released from the ACP (By similarity). Displays thioesterase activity with a preference for long chain fatty acyl . |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | fcoT |
| eggNOG description | FcoT-like thioesterase domain |
| Orthologous group | 2CJNX |
| Gene Ontology (36) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006082, GO:0006629, GO:0006631, GO:0006633, GO:0008150, GO:0008152, GO:0008610 +24 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.127 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 2 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
FcoT | PF10862.15 | 2.5e-64 | 28–178 | FcoT-like thioesterase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0097 (oxidoreductase), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0097 |
oxidoreductase | 996 | 983 ctx | neighborhood:881 coexpression:860 textmining:807 |
Rv0101 nrp |
peptide synthetase Nrp | 994 | 971 ctx | neighborhood:800 coexpression:860 textmining:807 |
Rv0099 fadD10 |
fatty-acid--CoA ligase FadD10 | 988 | 967 ctx | neighborhood:776 coexpression:860 textmining:656 |
Rv0100 hyp |
hypothetical protein | 995 | 964 ctx | neighborhood:776 coexpression:848 textmining:870 |
Rv0096 PPE1 |
PPE family protein PPE1 | 988 | 964 ctx | neighborhood:787 coexpression:839 textmining:696 |
Rv0095c hyp |
hypothetical protein | 541 | 527 ctx | neighborhood:522 |
Rv0102 |
integral membrane protein | 539 | 458 ctx | neighborhood:458 |
Rv2214c ephD |
oxidoreductase EphD | 514 | 47 | textmining:511 |
Rv1640c lysX |
bifunctional lysine--tRNA ligase/phosphatidylglycerol lysyltransferase | 440 | 44 | textmining:439 |
Rv0052 hyp |
hypothetical protein | 656 | 42 | textmining:656 |
Rv0109 PE_PGRS1 |
PE-PGRS family protein PE_PGRS1 | 435 | 41 | textmining:435 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: fatty acyl CoA thioesterase FcoT
- MTBC0 PGAP product: fatty acyl CoA thioesterase FcoT
- Pfam (hmmscan --cut_ga): FcoT PF10862.15 (E=3e-64)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_214612.1)
- Domains: Pfam-A via hmmscan --cut_ga — FcoT (PF10862.15)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
2CJNX - Curated reference: UniProt P9WM67 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
11 functional partner(s); context anchor
Rv0097 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000107|Rv0098|fcoT MSHTDLTPCTRVLASSGTVPIAEELLARVLEPYSCKGCRYLIDAQYSATEDSVLAYGNFTIGESAYIRSTGHFNAVELILCFNQLAYSAFAPAVLNEEIRVLRGWSIDDYCQHQLSSMLIRKASSRFRKPLNPQKFSARLLCRDLQVIERTWRYLKVPCVIEFWDENGGAASGEIELAALNIP