Rv0097 Family assigned · medium auto-curated
H37Rv Rv0097 · MTBC0 mtbc0_000106 ·
289 aa · 106897–107766 (+) ·
RefSeq NP_214611.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | TauD/TfdA family dioxygenase |
| Revised (this work) | TauD/TfdA family dioxygenase. Pfam: TauD (PF02668.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG83
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase |
| EC (curated) |
EC 1.14.11.78
|
| 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 the conversion of (3R)-3-[(carboxymethyl)amino]fatty acids to (3R)-3-isocyanyl-fatty acids through an oxidative decarboxylation mechanism, thereby generating the isonitrile group of INLPs (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Taurine catabolism dioxygenase TauD, TfdA family |
| Orthologous group | COG2175 |
| KEGG orthology |
K22303
|
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 | 0.615 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
TauD | PF02668.23 | 4.6e-32 | 10–263 | Taurine catabolism dioxygenase TauD, TfdA family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD10 (fatty-acid--CoA ligase FadD10), high confidence from genomic context alone (score 985 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0099 fadD10 |
fatty-acid--CoA ligase FadD10 | 994 | 985 ctx | neighborhood:785 cooccurence:530 coexpression:866 textmining:661 |
Rv0098 fcoT |
fatty acyl CoA thioesterase FcoT | 996 | 983 ctx | neighborhood:881 coexpression:860 textmining:807 |
Rv0101 nrp |
peptide synthetase Nrp | 993 | 976 ctx | neighborhood:804 coexpression:864 textmining:724 |
Rv0100 hyp |
hypothetical protein | 993 | 969 ctx | neighborhood:785 coexpression:860 textmining:809 |
Rv0096 PPE1 |
PPE family protein PPE1 | 992 | 963 ctx | neighborhood:752 coexpression:857 textmining:801 |
Rv2687c |
antibiotic ABC transporter permease | 673 | 673 ctx | cooccurence:673 |
Rv2686c |
antibiotic ABC transporter permease | 670 | 670 ctx | cooccurence:670 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 625 | 625 ctx | cooccurence:623 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 624 | 624 ctx | cooccurence:624 |
Rv1978 hyp |
hypothetical protein | 603 | 603 ctx | cooccurence:603 |
Rv1288 hyp |
hypothetical protein | 603 | 603 ctx | cooccurence:601 |
Rv0701 rplC |
50S ribosomal protein L3 | 573 | 573 | database:571 |
Rv0640 rplK |
50S ribosomal protein L11 | 572 | 573 | database:571 |
Rv0095c hyp |
hypothetical protein | 526 | 526 ctx | neighborhood:521 |
Rv0102 |
integral membrane protein | 572 | 522 ctx | neighborhood:458 |
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: oxidoreductase
- MTBC0 PGAP product: TauD/TfdA family dioxygenase
- Pfam (hmmscan --cut_ga): TauD PF02668.23 (E=5e-32)
- (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_214611.1)
- Domains: Pfam-A via hmmscan --cut_ga — TauD (PF02668.23)
- 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
COG2175 - Curated reference: UniProt P9WG83 (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 —
58 functional partner(s); context anchor
fadD10 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000106|Rv0097| MTLKVKGEGLGAQVTGVDPKNLDDITTDEIRDIVYTNKLVVLKDVHPSPREFIKLGRIIGQIVPYYEPMYHHEDHPEIFVSSTEEGQGVPKTGAFWHIDYMFMPEPFAFSMVLPLAVPGHDRGTYFIDLARVWQSLPAAKRDPARGTVSTHDPRRHIKIRPSDVYRPIGEVWDEINRTTPPIKWPTVIRHPKTGQEILYICATGTTKIEDKDGNPVDPEVLQELMAATGQLDPEYQSPFIHTQHYQVGDIILWDNRVLMHRAKHGSAAGTLTTYRLTMLDGLKTPGYAA