Rv0479c Family assigned · medium auto-curated
H37Rv Rv0479c · MTBC0 mtbc0_000504 ·
348 aa · 571286–572332 (-) ·
RefSeq NP_214993.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2993 domain-containing protein |
| Revised (this work) | DUF2993 domain-containing protein. Pfam: LmeA (PF11209.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKV7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0479c |
UniProt still lists this protein as Uncharacterized protein Rv0479c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF2993) |
| Orthologous group | 2E4QP |
| Gene Ontology (14) |
GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0008150, GO:0016020, GO:0016021, GO:0031224, GO:0031226, GO:0040007, GO:0044425, GO:0044459 +2 more
|
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 | 0.707 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
LmeA | PF11209.14 | 4.7e-19 | 133–326 | LmeA-like phospholipid-binding |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0480c (amidohydrolase), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0480c |
amidohydrolase | 882 | 882 ctx | neighborhood:881 |
Rv0481c hyp |
hypothetical protein | 876 | 877 ctx | neighborhood:741 cooccurence:544 |
Rv0227c |
membrane protein | 771 | 772 ctx | cooccurence:760 |
Rv3810 pirG |
cell surface protein | 767 | 767 ctx | cooccurence:759 |
Rv1476 |
membrane protein | 767 | 767 ctx | cooccurence:764 |
Rv0256c PPE2 |
PPE family protein PPE2 | 749 | 749 ctx | cooccurence:746 |
Rv2721c hyp |
hypothetical protein | 745 | 746 ctx | cooccurence:742 |
Rv1275 lprC |
lipoprotein LprC | 744 | 745 ctx | cooccurence:737 |
Rv3244c lpqB |
lipoprotein LpqB | 743 | 744 ctx | cooccurence:742 |
Rv0817c lmeA hyp |
hypothetical protein | 737 | 737 ctx | cooccurence:737 |
Rv2342 hyp |
hypothetical protein | 732 | 733 ctx | cooccurence:729 |
Rv2743c hyp |
hypothetical protein | 730 | 731 ctx | cooccurence:729 |
Rv3668c |
protease | 720 | 721 ctx | cooccurence:720 |
Rv2719c chiZ |
membrane protein | 719 | 719 ctx | cooccurence:718 |
Rv3446c hyp |
hypothetical protein | 718 | 718 ctx | cooccurence:717 |
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: DUF2993 domain-containing protein
- Pfam (hmmscan --cut_ga): LmeA PF11209.14 (E=5e-19)
- (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_214993.1)
- Domains: Pfam-A via hmmscan --cut_ga — LmeA (PF11209.14)
- 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
2E4QP - Curated reference: UniProt P9WKV7 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
142 functional partner(s); context anchor
Rv0480c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000504|Rv0479c| MTNPQGPPNDPSPWARPGDQGPLARPPASSEASTGRLRPGEPAGHIQEPVSPPTQPEQQPQTEHLAASHAHTRRSGRQAAHQAWDPTGLLAAQEEEPAAVKTKRRARRDPLTVFLVLIIVFSLVLAGLIGGELYARHVANSKVAQAVACVVKDQATASFGVAPLLLWQVATRHFTNISVETAGNQIRDAKGMQIKLTIQNVRLKNTPNSRGTIGALDATITWSSEGIKESVQNAIPILGAFVTSSVVTHPADGTVELKGLLNNITAKPIVAGKGLELQIINFNTLGFSLPKETVQSTLNEFTSSLTKNYPLGIHADSVQVTSTGVVSRFSTRDAAIPTGIQNPCFSHI