Rv1231c Still unknown · low auto-curated
H37Rv Rv1231c · MTBC0 mtbc0_001320 ·
180 aa · 1382766–1383308 (-) ·
RefSeq NP_215747.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF1003 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF1003. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86314
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | COG4420 |
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 | 0.495 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
DUF1003 | PF06210.17 | 1.2e-32 | 39–139 | Protein of unknown function (DUF1003) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1230c (membrane protein), high confidence from genomic context alone (score 762 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1232c hyp |
hypothetical protein | 965 | 965 ctx | neighborhood:882 cooccurence:713 |
Rv1233c hyp |
hypothetical protein | 802 | 802 ctx | neighborhood:801 |
Rv1230c |
membrane protein | 913 | 762 ctx | neighborhood:761 textmining:653 |
Rv1234 |
transmembrane protein | 640 | 640 ctx | neighborhood:527 |
Rv1229c mrp |
multiple resistance/pH adaptation protein | 566 | 566 ctx | neighborhood:561 |
Rv1236 sugA |
sugar ABC transporter permease SugA | 429 | 429 ctx | neighborhood:425 |
Rv1235 lpqY |
trehalose ABC transporter substrate-binding lipoprotein LpqY | 427 | 427 ctx | neighborhood:423 |
Rv1237 sugB |
sugar ABC transporter permease SugB | 426 | 425 ctx | neighborhood:420 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 423 | 423 ctx | neighborhood:419 |
Rv0103c ctpB |
cation-transporter P-type ATPase B | 535 | 77 | textmining:518 |
Rv0950c hyp |
hypothetical protein | 658 | 47 | textmining:656 |
Rv0104 hyp |
hypothetical protein | 804 | 46 | textmining:803 |
Rv0951 sucC |
succinyl-CoA ligase subunit beta | 513 | 45 | textmining:511 |
Rv1159 pimE |
polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase | 438 | 45 | textmining:436 |
Rv3857c |
membrane protein | 804 | 44 | textmining:804 |
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: membrane protein
- MTBC0 PGAP product: DUF1003 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF1003 PF06210.17 (E=1e-32)
- (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_215747.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1003 (PF06210.17)
- 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
COG4420 - Curated reference: UniProt O86314 (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 —
18 functional partner(s); context anchor
Rv1230c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001320|Rv1231c| MSKPFAPRRLYTPRTSRTLAPRLDPEAVGRTTESIARFFGTGRYLLVQTLLVLTWIVLNLFAVGLRWDPYPFILLNLAFSTQASYAAPLILLAQNRQEKRDRAVFEEDRRRAAQTKADTEYNARELAALRLAIGEVPTRDYLRHELDSLRALLAELQPTDPDVAQPRVADEAEQHAKKSG