Rv0966c Still unknown · low
H37Rv Rv0966c · MTBC0 mtbc0_001032 ·
200 aa · 1084448–1085050 (-) ·
RefSeq NP_215481.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF1707 domain-containing protein |
| Revised (this work) | DUF1707; Foldseek hits non-conclusive (moderate TM). Function unknown. |
Curated reference (UniProt)
| UniProt |
P9WKM1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0966c |
UniProt still lists this protein as Uncharacterized protein Rv0966c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF1707) |
| Orthologous group | COG4758 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.359 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 17.56% of strains (25502) · 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 |
|---|---|---|---|---|
DUF1707 | PF08044.17 | 9.1e-16 | 18–69 | DUF1707 SHOCT-like domain |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 87.3 (confident). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
4qrk-assembly1_A |
1.00 | 0.57 | 9.5e-03 sig | 4qrk-assembly1_A Crystal structure of a putative cell adhesion protein (CLOSPO_03726) from Clostridium sporogenes ATCC 15579 at 1.95 A resolution |
3tv2-assembly1_A |
0.07 | 0.39 | 6.7e+00 | 3tv2-assembly1_A Structure of a class II fumarate hydratase from Burkholderia pseudomallei |
3rrp-assembly1_A |
0.05 | 0.38 | 9.2e+00 | 3rrp-assembly1_A Crystal structure of fumarate hydratase Fum from Mycobacterium abscessus with malate bound |
3uyu-assembly1_A |
0.03 | 0.20 | 2.3e+00 | 3uyu-assembly1_A Structural basis for the antifreeze activity of an ice-binding protein (LeIBP) from Arctic yeast |
7dc5-assembly2_B |
0.00 | 0.12 | 7.9e+00 | 7dc5-assembly2_B Crystal structure of fungal antifreeze protein with intermediate activity |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: csoR (copper-sensing transcriptional repressor CsoR), medium confidence from genomic context alone (score 578 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) |
|---|---|---|---|---|
Rv0965c hyp |
hypothetical protein | 718 | 718 ctx | neighborhood:711 |
Rv0967 csoR |
copper-sensing transcriptional repressor CsoR | 578 | 578 ctx | neighborhood:574 |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 569 | 569 | coexpression:426 |
Rv2027c dosT |
two component sensor histidine kinase DosT | 520 | 500 | coexpression:483 |
Rv0845 narS |
sensor histidine kinase NarS | 519 | 499 | coexpression:482 |
Rv3132c devS |
two component sensor histidine kinase DevS | 517 | 497 | coexpression:480 |
Rv0964c hyp |
hypothetical protein | 490 | 490 ctx | neighborhood:488 |
Rv0412c glnX |
membrane protein | 479 | 479 ctx | cooccurence:466 |
Rv0971c echA7 |
enoyl-CoA hydratase EchA7 | 457 | 458 ctx | neighborhood:455 |
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha | 455 | 456 ctx | neighborhood:454 |
Rv1638A hyp |
hypothetical protein | 484 | 455 | coexpression:436 |
Rv0974c accD2 |
acetyl-/propionyl-CoA carboxylase subunit beta | 453 | 453 ctx | neighborhood:453 |
Rv2744c 35kd_ag hyp |
hypothetical protein | 478 | 449 | coexpression:430 |
Rv0968 hyp |
hypothetical protein | 448 | 448 ctx | neighborhood:448 |
Rv1337 |
integral membrane protein | 443 | 443 ctx | cooccurence:436 |
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
- MTBC0 PGAP product: DUF1707 domain-containing protein
- Pfam: DUF1707 PF08044.17
- Foldseek best: 4qrk-assembly1_A Crystal structure of a putative cell adhesion protein (CLOSPO_0 (prob 1.00, E=1e-02, TM=0.57)
- (structure-only promotion reviewed by hand, 2026-06-01)
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_215481.2)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1707 (PF08044.17)
- 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
COG4758 - Curated reference: UniProt P9WKM1 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 87.3, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
33 functional partner(s); context anchor
csoR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001032|Rv0966c| MSNSAQRDARNSRDESARASDTDRIQIAQLLAYAAEQGRLQLTDYEDRLARAYAATTYQELDRLRADLPGAAIGPRRGGECNPAPSTLLLALLGGFERRGRWNVPKKLTTFTLWGSGVLDLRYADFTSTEVDIRAYSIMGAQTILLPPEVNVEIHGHRVMGGFDRKVVGEGTRGAPTVRIRGFSLWGDVGIKRKPRKPRK