Rv0625c Family assigned · medium auto-curated
H37Rv Rv0625c · MTBC0 mtbc0_000658 ·
246 aa · 720706–721446 (-) ·
RefSeq NP_215139.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | TVP38/TMEM64 family protein |
| Revised (this work) | TVP38/TMEM64 family protein. Pfam: VTT_dom (PF09335.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFS5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | TVP38/TMEM64 family membrane protein Rv0625c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PFAM SNARE associated Golgi protein |
| Orthologous group | COG0398 |
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 | 0.079 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.63% of strains (915) · clonal |
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 |
|---|---|---|---|---|
VTT_dom | PF09335.17 | 1.1e-17 | 71–188 | VTT domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB5 (antitoxin VapB5), medium confidence from genomic context alone (score 582 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0626 vapB5 |
antitoxin VapB5 | 582 | 582 ctx | neighborhood:579 |
Rv0627 vapC5 |
ribonuclease VapC5 | 581 | 580 ctx | neighborhood:579 |
Rv1978 hyp |
hypothetical protein | 551 | 552 ctx | cooccurence:543 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 519 | 520 ctx | cooccurence:519 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 487 | 488 ctx | cooccurence:486 |
Rv2633c hyp |
hypothetical protein | 474 | 474 ctx | cooccurence:464 |
Rv3875 esxA |
ESAT-6 protein EsxA | 419 | 420 ctx | cooccurence:418 |
Rv2687c |
antibiotic ABC transporter permease | 433 | 412 ctx | cooccurence:411 |
Rv1355c moeY |
molybdopterin biosynthesis protein MoeY | 401 | 401 ctx | cooccurence:401 |
Rv2181 |
alpha-(1-2)-phosphatidylinositol mannoside mannosyltransferase | 603 | 397 | |
Rv0204c |
transmembrane protein | 620 | 333 | textmining:455 |
Rv3483c hyp |
hypothetical protein | 670 | 147 | textmining:630 |
Rv2182c |
1-acylglycerol-3-phosphate O-acyltransferase | 506 | 142 | textmining:448 |
Rv1337 |
integral membrane protein | 668 | 140 | textmining:630 |
Rv1275 lprC |
lipoprotein LprC | 625 | 78 | textmining:611 |
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: TVP38/TMEM64 family protein
- Pfam (hmmscan --cut_ga): VTT_dom PF09335.17 (E=1e-17)
- (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_215139.1)
- Domains: Pfam-A via hmmscan --cut_ga — VTT_dom (PF09335.17)
- 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
COG0398 - Curated reference: UniProt P9WFS5 (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 —
25 functional partner(s); context anchor
vapB5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000658|Rv0625c| MSTHNDSAPTSRRRHIVRLVVFAGFLVGMFYLVAATDVIDVAAVRGAVSATGPAAPLTYVVVSAVLGALFVPGPILAASSGLLFGPLVGVFVTLGATVGTAVVASLVGRRAGRASARALLGGERADRTDALIERCGLWAVVGQRFVPGISDAFASYAFGTFGVPLWQMAVGAFIGSAPRAFAYTALGAAIGDRSPLLASCAIAVWCVTAIIGAFAARHGYRQWRAHARGDGADGGVEDPDREVGAR