Rv0227c Family assigned · medium auto-curated
H37Rv Rv0227c · MTBC0 - ·
421 aa · 271574–272839 (-) ·
RefSeq NP_214741.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Membrane protein. Pfam: PorA (PF11271.14). |
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 |
P96409
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | porA |
| eggNOG description | Protein of unknown function (DUF3068) |
| Orthologous group | 2B1K4 |
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 | 0.347 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 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 |
|---|---|---|---|---|
PorA | PF11271.14 | 6.2e-96 | 6–336 | Porin PorA |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0226c (transmembrane protein), high confidence from genomic context alone (score 973 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0226c |
transmembrane protein | 996 | 973 ctx | neighborhood:881 cooccurence:772 textmining:871 |
Rv0479c |
membrane protein | 771 | 772 ctx | cooccurence:760 |
Rv1476 |
membrane protein | 766 | 766 ctx | cooccurence:759 |
Rv3668c |
protease | 756 | 756 ctx | cooccurence:756 |
Rv1275 lprC |
lipoprotein LprC | 854 | 752 ctx | cooccurence:748 textmining:437 |
Rv0228 |
acyltransferase | 748 | 744 ctx | neighborhood:582 cooccurence:409 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 851 | 740 ctx | cooccurence:720 textmining:452 |
Rv3035 hyp |
hypothetical protein | 737 | 738 ctx | cooccurence:734 |
Rv0224c |
methyltransferase | 736 | 736 ctx | cooccurence:734 |
Rv3802c |
membrane protein | 752 | 734 ctx | cooccurence:732 |
Rv3224 |
iron-regulated short-chain dehydrogenase/reductase | 734 | 734 | coexpression:734 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 733 | 733 | coexpression:733 |
Rv3635 |
transmembrane protein | 731 | 732 ctx | cooccurence:715 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 729 | 729 ctx | cooccurence:716 |
Rv3244c lpqB |
lipoprotein LpqB | 723 | 724 ctx | cooccurence:721 |
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): PorA PF11271.14 (E=6e-96)
- (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_214741.1)
- Domains: Pfam-A via hmmscan --cut_ga — PorA (PF11271.14)
- 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
2B1K4 - Curated reference: UniProt P96409 (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 —
96 functional partner(s); context anchor
Rv0226c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0227c| MLRFAACGAIGLGAALLIAALLLSTYTTSRIAEIPLDIDATLISDGTGTALDSASLATEHIVVNQDVPLVSQQQVTVESPANADVVTLQVGSSLRRTDKQKDSGLLLAIVDTVTLNRKTAMAVSDDTHTGGAVQKPRGLNDENPPTAIPLRHDGLSYRFPFHTEKKTYPYFDPIAQKAFDANYEGEEDVNGLTTYRFTQNVGYTPEGKLVAPLKYPSLYAGDEDGKVTTSAAMWGLPGDPNEQITMTRYYAAQRTFWVDPVSGTIVKETERANHYFARDPLKPEVTFADYQVTSTEETVESQVNAARDERDRLALWSRVLPITFTAAGLVALVGGGLFASFSLRTEGALMAASGDRDDHDYRRGGFEEPVPGAEAETEKLPTQRPDFPREPSGSDPPRLGSAQPPPPPDAGHPDPGPPERR