Rv2475c Family assigned · medium auto-curated
H37Rv Rv2475c · MTBC0 mtbc0_002637 ·
138 aa · 2801223–2801639 (-) ·
RefSeq NP_216991.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | thioesterase family protein |
| Revised (this work) | Thioesterase family protein. Pfam: Acyl-ACP_TE_C (PF20791.4), 4HBT_2 (PF13279.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y9E8
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | thioesterase |
| Orthologous group | COG0824 |
| KEGG orthology |
K07107
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
Acyl-ACP_TE_C | PF20791.4 | 1.0e-04 | 7–34 | Acyl-ACP thioesterase C-terminal domain |
4HBT_2 | PF13279.13 | 3.0e-13 | 11–129 | Thioesterase-like superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gdh (NAD-dependent glutamate dehydrogenase), high confidence from genomic context alone (score 968 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) |
|---|---|---|---|---|
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 968 | 968 ctx | neighborhood:881 coexpression:744 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 932 | 913 | coexpression:483 experimental:816 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 931 | 912 | coexpression:477 experimental:816 |
Rv2048c pks12 |
polyketide synthase | 931 | 912 | coexpression:474 experimental:816 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 931 | 911 | coexpression:473 experimental:816 |
Rv1527c pks5 |
polyketide synthase | 931 | 911 | coexpression:470 experimental:816 |
Rv2474c hyp |
hypothetical protein | 904 | 904 ctx | neighborhood:882 |
Rv2946c pks1 |
polyketide synthase | 844 | 826 | coexpression:652 experimental:454 |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 834 | 820 | coexpression:651 experimental:454 |
Rv2477c ettA |
macrolide ABC transporter ATP-binding protein | 778 | 778 ctx | neighborhood:771 |
Rv1661 pks7 |
polyketide synthase | 748 | 722 | coexpression:468 experimental:454 |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 748 | 721 | coexpression:467 experimental:454 |
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 743 | 721 | coexpression:406 |
Rv3800c pks13 |
polyketide synthase | 740 | 704 | coexpression:462 experimental:454 |
Rv2931 ppsA |
phthiocerol synthesis polyketide synthase type I PpsA | 724 | 704 | coexpression:463 experimental:454 |
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: thioesterase family protein
- Pfam (hmmscan --cut_ga): Acyl-ACP_TE_C PF20791.4 (E=1e-04), 4HBT_2 PF13279.13 (E=3e-13)
- (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_216991.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acyl-ACP_TE_C (PF20791.4), 4HBT_2 (PF13279.13)
- 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
COG0824 - Curated reference: UniProt I6Y9E8 (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 —
55 functional partner(s); context anchor
gdh - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002637|Rv2475c| MSVGFVTPVGVRWSDIDMYQHVNHATMVTILEEARVPFLKDAFGADITSTGLLIADVRVTYKGQLRLSDSPLQVTIWTKRLRAVDFTLGYEVRSVNAEPDSRPAVIAESQLAAFHIEEQRLVRLSPHHREYLQRWFRG