Rv1052 Family assigned · medium
H37Rv Rv1052 · MTBC0 - ·
129 aa · 1175723–1176112 (+) ·
RefSeq NP_215568.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Nucleotidyltransferase (eggNOG COG2184, COG category D): a polymerase-beta-like nucleotidyltransferase, often associated with DNA repair / cell-division functions. RefSeq leaves it 'hypothetical protein'. The acceptor/substrate is undetermined. |
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O53400
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| eggNOG description | nucleotidyltransferase activity |
| Orthologous group | COG2184 |
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 | 0.312 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 412 | 413 | coexpression:413 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 412 | 413 | coexpression:413 |
Rv0887c hyp |
hypothetical protein | 437 | 412 | coexpression:412 |
Rv2450c rpfE |
resuscitation-promoting factor RpfE | 410 | 410 | coexpression:410 |
Rv1884c rpfC |
resuscitation-promoting factor RpfC | 410 | 410 | coexpression:410 |
Rv2970A hyp |
hypothetical protein | 405 | 406 | coexpression:405 |
Rv2971 |
oxidoreductase | 404 | 404 | coexpression:403 |
Rv2389c rpfD |
resuscitation-promoting factor RpfD | 401 | 402 | coexpression:402 |
Rv0867c rpfA |
resuscitation-promoting factor RpfA | 400 | 401 | coexpression:401 |
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
- eggNOG COG2184 = nucleotidyltransferase activity (COG category D)
- eggNOG-mapper orthology (COG functional assignment, under-propagated by the auto-curation). A family/activity-level assignment from orthology, not a substrate demonstrated in M. tuberculosis.
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_215568.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG2184 - Curated reference: UniProt O53400 (TrEMBL, unreviewed; 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 — 9 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1052| MDCCEERGVARHKGLSQVGTPGCPRWSQAVSCRCSAYREAAVTAVQMPLTPGYGETPLPHDELAALLPEVVEVLDKPITRADVYDLEQGLQDQVFDLLMPTAVEGSLSLDELLSDHFVRDLHARMFGPV