Rv2915c Family assigned · medium auto-curated
H37Rv Rv2915c · MTBC0 mtbc0_003097 ·
370 aa · 3244397–3245509 (-) ·
RefSeq NP_217431.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | amidohydrolase family protein |
| Revised (this work) | Amidohydrolase family protein. Pfam: Amidohydro_1 (PF01979.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL23
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2915c |
UniProt still lists this protein as Uncharacterized protein Rv2915c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | amidohydrolase |
| Orthologous group | COG1228 |
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 | 0.463 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.27% of strains (397) · clonal |
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 |
|---|---|---|---|---|
Amidohydro_1 | PF01979.27 | 2.0e-15 | 54–330 | Amidohydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ffh (signal recognition particle protein), high confidence from genomic context alone (score 846 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) |
|---|---|---|---|---|
Rv2916c ffh |
signal recognition particle protein | 846 | 846 ctx | neighborhood:844 |
Rv2914c pknI |
serine/threonine-protein kinase PknI | 799 | 659 ctx | neighborhood:648 textmining:434 |
Rv2912c |
TetR family HTH-type transcriptional regulator | 925 | 624 ctx | neighborhood:624 textmining:810 |
Rv2052c hyp |
hypothetical protein | 595 | 596 ctx | cooccurence:589 |
Rv2913c |
D-amino acid aminohydrolase | 831 | 537 ctx | neighborhood:537 textmining:650 |
Rv2917 hyp |
hypothetical protein | 506 | 506 ctx | neighborhood:506 |
Rv3268 hyp |
hypothetical protein | 478 | 478 ctx | cooccurence:475 |
Rv3143 |
response regulator | 476 | 476 ctx | cooccurence:476 |
Rv2216 |
epimerase family protein | 436 | 436 | coexpression:404 |
Rv0862c hyp |
hypothetical protein | 417 | 417 ctx | cooccurence:406 |
Rv1101c hyp |
hypothetical protein | 445 | 66 | textmining:431 |
Rv2911 dacB2 |
penicillin-binding protein DacB2 | 658 | 46 | textmining:657 |
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: amidohydrolase family protein
- Pfam (hmmscan --cut_ga): Amidohydro_1 PF01979.27 (E=2e-15)
- (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_217431.1)
- Domains: Pfam-A via hmmscan --cut_ga — Amidohydro_1 (PF01979.27)
- 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
COG1228 - Curated reference: UniProt P9WL23 (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 —
12 functional partner(s); context anchor
ffh - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003097|Rv2915c| MKRVDTIRPRSRAVRLHVRGLGLPDETAIQLWIVDGRISTEPVAGADTVFDGGWILPGLVDAHCHVGLGKHGNVELDEAIAQAETERDVGALLLRDCGSPTDTRGLDDHEDLPRIIRAGRHLARPKRYIAGFAVELEDESQLPAAVAEQARRGDGWVKLVGDWIDRQIGDLAPLWSDDVLKAAIDTAHAQGARVTAHVFSEDALPGLINAGIDCIEHGTGLTDDTIALMLEHGTALVPTLINLENFPGIADAAGRYPTYAAHMRDLYARGYGRVAAAREAGVPVYAGTDAGSTIEHGRIADEVAALQRIGMTAHEALGAACWDARRWLGRPGLDDRASADLLCYAQDPRQGPGVLQHPDLVILRGRTFGP