Rv0094c Still unknown · low auto-curated
H37Rv Rv0094c · MTBC0 - ·
317 aa · 103710–104663 (-) ·
RefSeq NP_214608.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF222. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
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 |
Q50655
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | HNH nuclease domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | Domain of unknown function (DUF222) |
| Orthologous group | COG1403 |
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 | 2.349 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 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 |
|---|---|---|---|---|
DUF222 | PF02720.23 | 1.3e-71 | 2–223 | Domain of unknown function (DUF222) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0093c (membrane protein), medium confidence from genomic context alone (score 677 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) |
|---|---|---|---|---|
Rv3467 hyp |
hypothetical protein | 831 | 832 | coexpression:831 |
Rv1702c hyp |
hypothetical protein | 802 | 803 | coexpression:797 |
Rv3776 hyp |
hypothetical protein | 760 | 761 ctx | cooccurence:688 |
Rv0515 hyp |
hypothetical protein | 744 | 745 ctx | cooccurence:730 |
Rv0336 hyp |
hypothetical protein | 742 | 742 ctx | cooccurence:730 |
Rv0393 hyp |
hypothetical protein | 734 | 734 ctx | cooccurence:726 |
Rv2100 hyp |
hypothetical protein | 732 | 733 ctx | cooccurence:677 |
Rv0093c |
membrane protein | 677 | 677 ctx | neighborhood:630 |
Rv1765c hyp |
hypothetical protein | 667 | 668 ctx | cooccurence:657 |
Rv2015c hyp |
hypothetical protein | 630 | 630 ctx | cooccurence:626 |
Rv1587c hyp |
hypothetical protein | 587 | 587 | coexpression:580 |
Rv1378c hyp |
hypothetical protein | 548 | 549 ctx | cooccurence:542 |
Rv3074 hyp |
hypothetical protein | 546 | 546 ctx | cooccurence:532 |
Rv0095c hyp |
hypothetical protein | 500 | 501 ctx | neighborhood:485 |
Rv1303 hyp |
hypothetical protein | 456 | 457 ctx | cooccurence:455 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): DUF222 PF02720.23 (E=1e-71)
- (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_214608.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF222 (PF02720.23)
- 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
COG1403 - Curated reference: UniProt Q50655 (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 —
25 functional partner(s); context anchor
Rv0093c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0094c| MSTRQAAEADLAGKAAQYRPDELARYAQRVMDWLHPDGDLTDTERARKRGITLSNQQYDGMSRLSGYLTPQARATFEAVLAKLAAPGATNPDDHTPVIDTTPDAAAIDRDTRSQAQRNHDGLLAGLRALIASGKLGQHNGLPVSIVVTTTLTDLQTGAGKGFTGGGTLLPMADVIRMTSHAHHYSPASGRYPQAIFDHGTPLALYHTKRLASPAQRIMLFANDRGCTKPGCDAPAYHSQAHHVTAWTSTGRTDITELTLACGPDNRLAEKGWTTHNNTHGHTEWLPPPHLDHGQPRTNTFHHPERFLHNQDDDDKPD