Rv0401 Still unknown · low auto-curated
H37Rv Rv0401 · MTBC0 mtbc0_000421 ·
123 aa · 483153–483524 (+) ·
RefSeq NP_214915.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF3054 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3054. 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 |
P95210
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3054) |
| Orthologous group | 2E6D0 |
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 | 0.413 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
DUF3054 | PF11255.14 | 4.2e-31 | 10–112 | Protein of unknown function (DUF3054) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE7 (acyl-CoA dehydrogenase FadE7), high confidence from genomic context alone (score 789 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0400c fadE7 |
acyl-CoA dehydrogenase FadE7 | 789 | 789 ctx | neighborhood:789 |
Rv0399c lpqK |
lipoprotein LpqK | 649 | 649 ctx | neighborhood:649 |
Rv0398c hyp |
hypothetical protein | 616 | 616 ctx | neighborhood:616 |
Rv3399 |
S-adenosylmethionine-dependent methyltransferase | 461 | 462 ctx | neighborhood:462 |
Rv0360c hyp |
hypothetical protein | 445 | 446 ctx | cooccurence:444 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 440 | 440 ctx | cooccurence:440 |
Rv0204c |
transmembrane protein | 462 | 423 ctx | neighborhood:418 |
Rv2740 ephG |
epoxide hydrolase | 422 | 422 ctx | cooccurence:422 |
Rv0921 |
resolvase | 613 | 44 | textmining:612 |
Rv2886c |
resolvase | 586 | 44 | textmining:585 |
Rv3828c |
resolvase | 515 | 42 | textmining:515 |
Rv2566 hyp |
hypothetical protein | 870 | 41 | textmining:870 |
Rv1272c |
drug ABC transporter ATP-binding protein | 803 | 41 | textmining:803 |
Rv3341 metA |
homoserine O-acetyltransferase | 659 | 41 | textmining:659 |
Rv0605 |
IS1536 family serine type transposase | 616 | 41 | textmining:616 |
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: transmembrane protein
- MTBC0 PGAP product: DUF3054 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF3054 PF11255.14 (E=4e-31)
- (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_214915.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3054 (PF11255.14)
- 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
2E6D0 - Curated reference: UniProt P95210 (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 —
20 functional partner(s); context anchor
fadE7 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000421|Rv0401| MRPRRALAGLAADVVAVLVFCAVGRRSHAEGLSVTGLAATAWPFLTGTGIGWVLARGWRRPTALAPTGVIVWLCTIVVGMVLRKVSSAGVAASFVVVASAVTAVLLLGWRAAVALMAPHRADG