Rv0293c Resolved · high auto-curated
H37Rv Rv0293c · MTBC0 mtbc0_000312 ·
400 aa · 360156–361358 (-) ·
RefSeq NP_214807.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | alpha/beta fold hydrolase |
| Revised (this work) | Alpha/beta fold hydrolase. Pfam: Abhydrolase_1 (PF00561.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53697
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 | alpha beta |
| Orthologous group | COG1073 |
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 | 0.518 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.20% of strains (287) · 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 |
|---|---|---|---|---|
Abhydrolase_1 | PF00561.27 | 1.4e-07 | 170–307 | alpha/beta hydrolase fold |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tam (trans-aconitate methyltransferase), high confidence from genomic context alone (score 778 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) |
|---|---|---|---|---|
Rv0294 tam |
trans-aconitate methyltransferase | 778 | 778 ctx | neighborhood:777 |
Rv1874 hyp |
hypothetical protein | 697 | 698 ctx | cooccurence:696 |
Rv3810 pirG |
cell surface protein | 637 | 638 ctx | cooccurence:618 |
Rv3775 lipE |
lipase LipE | 617 | 617 ctx | cooccurence:613 |
Rv2913c |
D-amino acid aminohydrolase | 560 | 560 ctx | cooccurence:558 |
Rv0982 mprB |
two component histidine-protein kinase/phosphatase MprB | 559 | 560 | coexpression:558 |
Rv3446c hyp |
hypothetical protein | 533 | 534 ctx | cooccurence:530 |
Rv2910c hyp |
hypothetical protein | 531 | 532 ctx | cooccurence:524 |
Rv2484c |
diacyglycerol O-acyltransferase | 527 | 527 ctx | cooccurence:522 |
Rv1275 lprC |
lipoprotein LprC | 500 | 500 ctx | cooccurence:481 |
Rv0518 hyp |
hypothetical protein | 523 | 495 ctx | cooccurence:483 |
Rv0383c ttfA hyp |
hypothetical protein | 490 | 490 ctx | cooccurence:465 |
Rv0221 |
diacyglycerol O-acyltransferase | 498 | 478 ctx | cooccurence:474 |
Rv2015c hyp |
hypothetical protein | 468 | 468 ctx | cooccurence:446 |
Rv3707c hyp |
hypothetical protein | 466 | 466 ctx | cooccurence:463 |
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: alpha/beta fold hydrolase
- Pfam (hmmscan --cut_ga): Abhydrolase_1 PF00561.27 (E=1e-07)
- (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_214807.1)
- Domains: Pfam-A via hmmscan --cut_ga — Abhydrolase_1 (PF00561.27)
- 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
COG1073 - Curated reference: UniProt O53697 (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 —
35 functional partner(s); context anchor
tam - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000312|Rv0293c| MSGTFTADAIGPPVPIPDVPGADAGAEGLPSRSVLSARQRILVESSAIADVALRTAVASVLSATVTPAVVANALRHVNEGSERSNLNFYAELAAAHDPAKSFPAPTELPKVTSRPASPLTEWVARGTVDNIAFASGFRAINPTMRQRWSALTANNIVHAQHWRHRDGPRPTLCVIHGFMGSSYLLNGLFFSLPWYYRSGYDVLLYTLPFHGQRAEKFSPFSGFGYFTSGLSGFAEAMAQAVYDFRSIVDYLRHIGVDRIALTGISLGGYTSALLASVESRLEAVIPNCPVVMPAKLFDEWFPANKLVKLGLRLTNISRDELIAGLAYHGPLNYRPLLPKDRRMIITGLGDRMAPPEHAVTLWKQWDRCALHWFPGSHLLHVSQLDYLRRMTVFLQGLMFD