Rv2762c Family assigned · low auto-curated
H37Rv Rv2762c · MTBC0 mtbc0_002939 ·
139 aa · 3095052–3095471 (-) ·
RefSeq NP_217278.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | winged helix-turn-helix domain-containing protein |
| Revised (this work) | Winged helix-turn-helix domain-containing protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X5B0
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Winged helix-turn-helix domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Winged helix DNA-binding domain |
| Orthologous group | COG3214 |
| KEGG orthology |
K09927
|
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 | 0.394 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 10.12% of strains (14697) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hsdS (type I restriction/modification system specificity determinant HsdS), high confidence from genomic context alone (score 947 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) |
|---|---|---|---|---|
Rv2761c hsdS |
type I restriction/modification system specificity determinant HsdS | 947 | 947 ctx | neighborhood:800 coexpression:746 |
Rv2763c dfrA |
dihydrofolate reductase | 937 | 827 ctx | neighborhood:791 textmining:651 |
Rv2759c vapC42 |
ribonuclease VapC42 | 802 | 803 ctx | neighborhood:800 |
Rv2760c vapB42 |
antitoxin VapB42 | 802 | 803 ctx | neighborhood:800 |
Rv2756c hsdM |
type I restriction/modification system DNA methylase HsdM | 745 | 745 ctx | neighborhood:741 |
Rv2764c thyA |
thymidylate synthase ThyA | 874 | 733 ctx | neighborhood:730 textmining:548 |
Rv2757c vapC21 |
ribonuclease VapC21 | 960 | 711 ctx | neighborhood:707 textmining:870 |
Rv2758c vapB21 |
antitoxin VapB21 | 710 | 710 ctx | neighborhood:707 |
Rv2765 |
hydrolase | 673 | 673 ctx | neighborhood:673 |
Rv2754c thyX |
thymidylate synthase ThyX | 755 | 669 ctx | neighborhood:667 |
Rv2753c dapA |
4-hydroxy-tetrahydrodipicolinate synthase | 755 | 655 ctx | neighborhood:643 |
Rv2752c rnj |
ribonuclease J | 788 | 640 ctx | neighborhood:635 textmining:436 |
Rv2755c hsdS.1 |
Rv2755c, (MTV002.20c), len: 91 aa. Possible hsdS.1,fragment of type I restriction/modification system specificity determinant (S protein), s | 560 | 560 ctx | neighborhood:557 |
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: winged helix-turn-helix domain-containing protein
- (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_217278.1)
- 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
COG3214 - Curated reference: UniProt I6X5B0 (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 —
13 functional partner(s); context anchor
hsdS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002939|Rv2762c| MSAATAAWDRRAAVVVGGVAEPGSAGPIAGADRKRLISRIQVRQLDSAAVAAKRRHLYYVRPLDGHPVARVDRKTDRAADSLPVAGVLGELDIPPVTVAEGLAGELASMASWLGLGGIAVSTRGDLAGELCAATKRTNG