Rv1322 Family assigned · medium auto-curated
H37Rv Rv1322 · MTBC0 mtbc0_001418 ·
98 aa · 1495684–1495980 (+) ·
RefSeq NP_215838.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains Rv1322 (PF27609.1) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM27
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1322 |
UniProt still lists this protein as Uncharacterized protein Rv1322; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | ATP- GTP-binding protein |
| Orthologous group | 2E3EP |
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, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (189) · 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 |
|---|---|---|---|---|
Rv1322 | PF27609.1 | 9.6e-27 | 22–86 | Rv1322 family protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nucS (endonuclease NucS), high confidence from genomic context alone (score 888 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) |
|---|---|---|---|---|
Rv1321 nucS |
endonuclease NucS | 959 | 888 ctx | neighborhood:849 textmining:649 |
Rv1318c |
adenylate cyclase | 708 | 709 ctx | neighborhood:709 |
Rv1317c alkA |
bifunctional regulatory protein/DNA repair enzyme AlkA | 648 | 649 ctx | neighborhood:588 |
Rv1320c |
adenylate cyclase | 580 | 563 ctx | neighborhood:563 |
Rv1319c |
adenylate cyclase | 527 | 528 ctx | neighborhood:528 |
Rv3909 hyp |
hypothetical protein | 492 | 492 | |
Rv1316c ogt |
methylated-DNA--protein-cysteine methyltransferase | 492 | 491 ctx | neighborhood:478 |
Rv3221A rshA |
anti-sigma factor RshA | 510 | 487 | |
Rv0736 rslA |
anti-sigma-L factor RslA | 506 | 483 | |
Rv1222 rseA |
anti-sigma E factor RseA | 499 | 478 | |
Rv3258c hyp |
hypothetical protein | 465 | 465 ctx | cooccurence:462 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 487 | 459 | experimental:456 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 484 | 456 | experimental:451 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 466 | 436 | experimental:431 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 464 | 435 | experimental:431 |
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: hypothetical protein
- Pfam (hmmscan --cut_ga): Rv1322 PF27609.1 (E=1e-26)
- (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_215838.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv1322 (PF27609.1)
- 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
2E3EP - Curated reference: UniProt P9WM27 (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 —
22 functional partner(s); context anchor
nucS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001418|Rv1322| MARRRKPLHRQRPEPPSWALRRVEAGPDGHEYEVRPVAAARAVKTYRCPGCDHEIRSGTAHVVVWPTDLPQAGVDDRRHWHTPCWANRATRGPTRKWT