Rv1225c Family assigned · medium auto-curated
H37Rv Rv1225c · MTBC0 mtbc0_001313 ·
276 aa · 1376335–1377165 (-) ·
RefSeq NP_215741.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | HAD-IIA family hydrolase |
| Revised (this work) | HAD-IIA family hydrolase. Pfam: Hydrolase_6 (PF13344.13), Hydrolase (PF00702.33), HAD_2 (PF13419.13), Hydrolase_like (PF13242.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33221
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Haloacid dehalogenase-like hydrolase domain-containing protein 2 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Hydrolase |
| Orthologous group | COG0647 |
| KEGG orthology |
K02566
|
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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 25.67% of strains (37276) · 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 |
|---|---|---|---|---|
Hydrolase_6 | PF13344.13 | 4.5e-23 | 11–106 | Haloacid dehalogenase-like hydrolase |
Hydrolase | PF00702.33 | 2.6e-09 | 174–232 | haloacid dehalogenase-like hydrolase |
HAD_2 | PF13419.13 | 1.1e-05 | 182–237 | Haloacid dehalogenase-like hydrolase |
Hydrolase_like | PF13242.13 | 1.4e-20 | 192–269 | HAD-hyrolase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1226c (transmembrane protein), medium confidence from genomic context alone (score 642 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) |
|---|---|---|---|---|
Rv1226c |
transmembrane protein | 641 | 642 ctx | neighborhood:577 |
Rv1227c |
transmembrane protein | 573 | 574 ctx | neighborhood:571 |
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 455 | 432 | |
Rv1712 cmk |
cytidylate kinase | 419 | 419 | |
Rv3760 |
membrane protein | 418 | 419 | coexpression:419 |
Rv2966c rsmD |
methyltransferase | 412 | 413 | coexpression:402 |
Rv1539 lspA |
lipoprotein signal peptidase | 409 | 410 |
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: HAD-IIA family hydrolase
- Pfam (hmmscan --cut_ga): Hydrolase_6 PF13344.13 (E=4e-23), Hydrolase PF00702.33 (E=3e-09), HAD_2 PF13419.13 (E=1e-05), Hydrolase_like PF13242.13 (E=1e-20)
- (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_215741.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase_6 (PF13344.13), Hydrolase (PF00702.33), HAD_2 (PF13419.13), Hydrolase_like (PF13242.13)
- 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
COG0647 - Curated reference: UniProt O33221 (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 —
7 functional partner(s); context anchor
Rv1226c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001313|Rv1225c| MDVAHLMAAAVLFDIDGVLVLSWRAIPGAAETVRQLTHRGIACAYLTNTTTRTRRQIAEALGAAGIPVAADDVITAGVLTAEYLHGAYPGARCFLVNNGDITEDLPGIDVVLSTEIGPEDCPEAPDVVVLGSAGPQFDHRTLSRVYGWMLDGVPVVAMHRNMTWNTTDGLRIDTGMYLTGMEQACGKTATAIGKPAAEGFLAAADRVGVDPQQMVMIGDDLHNDVLAAQAVGMTGVLVRTGKFRQQTLDRWLAGASATRPHHVIDSVAGLPPLLGC