Rv0356c Family assigned · medium auto-curated
H37Rv Rv0356c · MTBC0 mtbc0_000376 ·
214 aa · 438192–438836 (-) ·
RefSeq NP_214870.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | PaaI family thioesterase |
| Revised (this work) | PaaI family thioesterase. Pfam: 4HBT (PF03061.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06307
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Acyl-coenzyme A thioesterase THEM4 |
| EC (curated) |
EC 3.1.2.2
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | thioesterase |
| Orthologous group | COG2050 |
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 | 0.19 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 6 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 |
|---|---|---|---|---|
4HBT | PF03061.29 | 3.2e-10 | 126–199 | Thioesterase superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purA (adenylosuccinate synthetase), high confidence from genomic context alone (score 945 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0357c purA |
adenylosuccinate synthetase | 944 | 945 ctx | neighborhood:801 coexpression:733 |
Rv2383c mbtB |
phenyloxazoline synthase | 707 | 664 | coexpression:431 experimental:402 |
Rv1125 hyp |
hypothetical protein | 647 | 641 ctx | cooccurence:542 |
Rv2042c hyp |
hypothetical protein | 638 | 638 ctx | cooccurence:637 |
Rv3035 hyp |
hypothetical protein | 624 | 624 ctx | cooccurence:609 |
Rv0358 hyp |
hypothetical protein | 623 | 623 ctx | neighborhood:563 |
Rv2524c fas |
fatty acid synthase | 731 | 620 | coexpression:412 |
Rv3531c hyp |
hypothetical protein | 599 | 599 ctx | cooccurence:599 |
Rv1780 hyp |
hypothetical protein | 589 | 589 ctx | cooccurence:589 |
Rv3529c hyp |
hypothetical protein | 588 | 588 ctx | cooccurence:544 |
Rv2876 |
transmembrane protein | 563 | 563 ctx | cooccurence:559 |
Rv0359 rip2 |
zinc metalloprotease | 561 | 560 ctx | neighborhood:551 |
Rv2342 hyp |
hypothetical protein | 557 | 557 ctx | cooccurence:557 |
Rv0310c hyp |
hypothetical protein | 562 | 536 ctx | cooccurence:499 |
Rv3792 aftA |
arabinofuranosyltransferase | 534 | 535 ctx | cooccurence:529 |
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: hypothetical protein
- MTBC0 PGAP product: PaaI family thioesterase
- Pfam (hmmscan --cut_ga): 4HBT PF03061.29 (E=3e-10)
- (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_214870.1)
- Domains: Pfam-A via hmmscan --cut_ga — 4HBT (PF03061.29)
- 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
COG2050 - Curated reference: UniProt O06307 (TrEMBL, unreviewed; 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 —
32 functional partner(s); context anchor
purA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000376|Rv0356c| MTDASVHPDELDPEYHHHGGFPEYGPASPGAGFGQFVATMRRLQDLAVAADPGDAVWDEAAERAAALVELLSPFEADEGKAPAGRTPGLPGMGSLLLPPWTVTRYGTDGVEMRGSFSRFHVGGNSAVHGGVLPLLFDHMFGMISHAAGRPISRTAFLHVDYRRITPIDVPLIVRGRVTNTEGRKAFVCAELFDSDETLLAEGNGLMVRLLPGQP