Rv1063c Family assigned · medium auto-curated
H37Rv Rv1063c · MTBC0 mtbc0_001143 ·
360 aa · 1193080–1194162 (-) ·
RefSeq NP_215579.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | NTE family protein |
|---|---|
| MTBC0 PGAP re-annotation | patatin family protein |
| Revised (this work) | Patatin 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 |
P9WIY9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized NTE family protein Rv1063c |
UniProt still lists this protein as Uncharacterized NTE family protein Rv1063c; the revised annotation above is ahead of the current UniProt record.
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
|
| Gene Ontology (3) |
GO:0003674, GO:0003824, GO:0016787
|
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 | 0.75 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Patatin | PF01734.28 | 4.4e-23 | 19–176 | Patatin-like phospholipase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqV (lipoprotein LpqV), high confidence from genomic context alone (score 787 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1064c lpqV |
lipoprotein LpqV | 786 | 787 ctx | neighborhood:786 |
Rv1066 hyp |
hypothetical protein | 474 | 474 ctx | neighborhood:472 |
Rv2037c |
transmembrane protein | 426 | 427 ctx | cooccurence:425 |
Rv1065 hyp |
hypothetical protein | 423 | 423 ctx | neighborhood:421 |
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: NTE family protein
- MTBC0 PGAP product: patatin family protein
- Pfam (hmmscan --cut_ga): Patatin PF01734.28 (E=4e-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_215579.1)
- 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 P9WIY9 (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 —
4 functional partner(s); context anchor
lpqV - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001143|Rv1063c| MPAPAALRVRGSSSPRVALALGSGGARGYAHIGVIQALRERGYDIVGIAGSSMGAVVGGVHAAGRLDEFAHWAKSLTQRTILRLLDPSISAAGILRAEKILDAVRDIVGPVAIEQLPIPYTAVATDLLAGKSVWFQRGPLDAAIRASIAIPGVIAPHEVDGRLLADGGILDPLPMAPIAGVNADLTIAVSLNGSEAGPARDAEPNVTAEWLNRMVRSTSALFDVSAARSLLDRPTARAVLSRFGAAAAESDSWSQAPEIEQRPAGPPADREEAADTPGLPKMGSFEVMNRTIDIAQSALARHTLAGYPADLLIEVPRSTCRSLEFHRAVEVIAVGRALATQALEAFEIDDDESAAATIEG