Rv1262c Family assigned · medium auto-curated
H37Rv Rv1262c · MTBC0 mtbc0_001351 ·
144 aa · 1418382–1418816 (-) ·
RefSeq NP_215778.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | HIT family protein |
| Revised (this work) | HIT family protein. Pfam: DcpS_C (PF11969.14), HIT (PF01230.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WML1
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized HIT-like protein Rv1262c |
UniProt still lists this protein as Uncharacterized HIT-like protein Rv1262c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolismG Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Hit family |
| Orthologous group | COG0537 |
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, 1 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 |
|---|---|---|---|---|
DcpS_C | PF11969.14 | 4.0e-12 | 3–103 | Scavenger mRNA decapping enzyme C-term binding |
HIT | PF01230.30 | 3.0e-30 | 11–106 | HIT domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: amiB2 (amidase AmiB), medium confidence from genomic context alone (score 660 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) |
|---|---|---|---|---|
Rv1261c hyp |
hypothetical protein | 886 | 886 ctx | neighborhood:882 |
Rv1263 amiB2 |
amidase AmiB | 660 | 660 ctx | neighborhood:614 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 655 | 642 | database:592 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 618 | 618 | database:585 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 610 | 602 | database:538 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 609 | 601 | database:538 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 599 | 600 | database:595 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 604 | 599 | database:586 |
Rv1329c dinG |
ATP-dependent helicase DinG | 568 | 568 | database:563 |
Rv2101 helZ |
helicase HelZ | 567 | 567 | database:563 |
Rv0861c ercc3 |
DNA helicase Ercc3 | 565 | 566 | database:543 |
Rv1179c hyp |
hypothetical protein | 565 | 566 | database:543 |
Rv2917 hyp |
hypothetical protein | 562 | 563 | database:543 |
Rv1961 hyp |
hypothetical protein | 561 | 562 | database:543 |
Rv1947 hyp |
hypothetical protein | 561 | 562 | database:543 |
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: HIT family protein
- Pfam (hmmscan --cut_ga): DcpS_C PF11969.14 (E=4e-12), HIT PF01230.30 (E=3e-30)
- (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_215778.1)
- Domains: Pfam-A via hmmscan --cut_ga — DcpS_C (PF11969.14), HIT (PF01230.30)
- 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
COG0537 - Curated reference: UniProt P9WML1 (SwissProt, reviewed; Predicted)
- 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 —
21 functional partner(s); context anchor
amiB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001351|Rv1262c| MPCVFCAIIAGEAPAIRIYEDGGYLAILDIRPFTRGHTLVLPKRHTVDLTDTPPEALADMVAIGQRIARAARATKLADATHIAINDGRAAFQTVFHVHLHVLPRRNGDKLSVAKGMMLRRDPDREATGRILREALAQQDAAAQD