Rv0012 Family assigned · low auto-curated
H37Rv Rv0012 · MTBC0 - ·
262 aa · 14089–14877 (+) ·
RefSeq NP_214526.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Membrane protein. |
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 |
L0T243
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Bacterial protein of unknown function (DUF881) |
| Orthologous group | COG3879 |
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 | 0.819 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
DUF881 | PF05949.18 | 7.8e-42 | 104–255 | Bacterial protein of unknown function (DUF881) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trpG (anthranilate synthase component II), high confidence from genomic context alone (score 829 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1824 hyp |
hypothetical protein | 840 | 834 ctx | cooccurence:774 |
Rv0013 trpG |
anthranilate synthase component II | 829 | 829 ctx | neighborhood:827 |
Rv0011c crgA |
cell division protein CrgA | 784 | 785 ctx | neighborhood:782 |
Rv1825 hyp |
hypothetical protein | 774 | 775 ctx | cooccurence:774 |
Rv0010c |
membrane protein | 648 | 649 ctx | neighborhood:646 |
Rv1009 rpfB |
resuscitation-promoting factor RpfB | 430 | 431 ctx | cooccurence:424 |
Rv2375 hyp |
hypothetical protein | 423 | 424 ctx | cooccurence:420 |
Rv3586 disA |
DNA integrity scanning protein DisA | 405 | 406 ctx | cooccurence:402 |
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): membrane protein
- Pfam (hmmscan --cut_ga): DUF881 PF05949.18 (E=8e-42)
- (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_214526.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF881 (PF05949.18)
- 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
COG3879 - Curated reference: UniProt L0T243 (TrEMBL, unreviewed; 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 —
8 functional partner(s); context anchor
trpG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0012| MRLTHPTPCPENGETMIDRRRSAWRFSVPLVCLLAGLLLAATHGVSGGTEIRRSDAPRLVDLVRRAQASVNRLATEREALTTRIDSVHGRSVDTALAAMQRRSAKLAGVAAMNPVHGPGLVVTLQDAQRDANGRFPRDASPDDLVVHQQDIEAVLNALWNAGAEAIQMQDQRIIAMSIARCVGNTLLLNGRTYSPPYTIAAIGDAAAMQAALAAAPLVTLYKQYVVRFGLGYCEEVHPDLQIVGYADPVRMHFAQPAGPLDY