Rv1062 Family assigned · medium auto-curated
H37Rv Rv1062 · MTBC0 mtbc0_001142 ·
285 aa · 1192222–1193079 (+) ·
RefSeq NP_215578.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | patatin-like phospholipase family protein |
| Revised (this work) | Patatin-like phospholipase family protein. Pfam: Patatin (PF01734.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53410
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PNPLA domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | esterase of the alpha-beta hydrolase superfamily |
| Orthologous group | COG1752 |
| KEGG orthology |
K07001
|
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, 3 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 |
|---|---|---|---|---|
Patatin | PF01734.28 | 2.7e-23 | 7–203 | Patatin-like phospholipase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD14 (fatty-acid--CoA ligase FadD14), high confidence from genomic context alone (score 716 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) |
|---|---|---|---|---|
Rv1061 hyp |
hypothetical protein | 908 | 908 ctx | neighborhood:882 |
Rv1060 hyp |
hypothetical protein | 831 | 832 ctx | neighborhood:832 |
Rv1059 hyp |
hypothetical protein | 810 | 810 ctx | neighborhood:772 |
Rv1058 fadD14 |
fatty-acid--CoA ligase FadD14 | 716 | 716 ctx | neighborhood:712 |
Rv1057 hyp |
hypothetical protein | 706 | 706 ctx | neighborhood:662 |
Rv0941c hyp |
hypothetical protein | 441 | 441 ctx | cooccurence:432 |
Rv0332 hyp |
hypothetical protein | 429 | 430 ctx | cooccurence:428 |
Rv2558 hyp |
hypothetical protein | 410 | 411 ctx | cooccurence:407 |
Rv2557 hyp |
hypothetical protein | 402 | 402 |
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: patatin-like phospholipase family protein
- Pfam (hmmscan --cut_ga): Patatin PF01734.28 (E=3e-23)
- (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_215578.1)
- Domains: Pfam-A via hmmscan --cut_ga — Patatin (PF01734.28)
- 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
COG1752 - Curated reference: UniProt O53410 (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 —
9 functional partner(s); context anchor
fadD14 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001142|Rv1062| MTTRRALVLAGGGLAGIAWETGVLRGIADESPAAARLLLDSDVLVGTSAGATVAAQISSGCPLDTLYERQLAETSAEIDPGVDIDAITDLFLTAVTEPHISTRRRLQRIGAVALAVDTVPESVRRQVIAQRLPSHDWPDRVLRVTAIDIATGELVVFHRESNVALVDAVAASCSVPGAWPPVTIAGRRYMDGGVASSVNLGVADDCDAAVVLVPAGADAPSPFGGGAAAEIAAATGMVFAVFADDDSLAAFGPNPLDPLCRVNSAMAGRQQGRREAQAVARLLGV