proV Family assigned · medium auto-curated
H37Rv Rv3758c · MTBC0 mtbc0_003982 ·
376 aa · 4227408–4228538 (-) ·
RefSeq NP_218275.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycine betaine/carnitine/choline/L-proline ABC transporter ATP-binding protein ProV |
|---|---|
| MTBC0 PGAP re-annotation | glycine betaine/L-proline ABC transporter ATP-binding protein ProV |
| Revised (this work) | Glycine betaine/L-proline ABC transporter ATP-binding protein ProV. Pfam: ABC_tran (PF00005.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O69724
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ABC-type quaternary amine transporter |
| EC (curated) |
EC 7.6.2.9
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | proV |
| eggNOG description | ABC transporter |
| Orthologous group | COG1125 |
| KEGG orthology |
K05847
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00209
|
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 | 0.898 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 |
|---|---|---|---|---|
ABC_tran | PF00005.34 | 1.9e-32 | 19–163 | ABC transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: proZ (glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3756c proZ |
glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ | 999 | 1000 ctx | neighborhood:881 cooccurence:772 coexpression:869 database:900 textmining:699 |
Rv3757c proW |
glycine betaine/carnitine/choline/L-proline ABC transporter permease ProW | 999 | 1000 ctx | neighborhood:882 cooccurence:773 coexpression:954 database:900 textmining:829 |
Rv3759c proX |
glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding lipoprotein ProX | 999 | 999 ctx | neighborhood:882 cooccurence:769 coexpression:775 database:800 textmining:692 |
Rv1244 lpqZ |
lipoprotein LpqZ | 902 | 889 ctx | cooccurence:500 coexpression:726 |
Rv3755c hyp |
hypothetical protein | 888 | 888 ctx | neighborhood:881 |
Rv3760 |
membrane protein | 775 | 775 ctx | neighborhood:768 |
Rv2936 drrA |
daunorubicin ABC transporter ATP-binding protein DrrA | 678 | 678 ctx | fusion:641 |
Rv3336c trpS |
tryptophan--tRNA ligase | 510 | 510 | coexpression:494 |
Rv2688c |
antibiotic ABC transporter ATP-binding protein | 408 | 408 | |
Rv0204c |
transmembrane protein | 431 | 406 | coexpression:406 |
Rv0585c |
integral membrane protein | 431 | 406 | coexpression:406 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 663 | 77 | textmining:650 |
Rv3534c hsaF |
4-hydroxy-2-oxovalerate aldolase | 529 | 76 | textmining:512 |
Rv2391 sirA |
sulfite reductase | 530 | 51 | textmining:526 |
Rv2072c cobL |
precorrin-6Y C(5,15)-methyltransferase | 658 | 44 | textmining:657 |
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: glycine betaine/carnitine/choline/L-proline ABC transporter ATP-binding protein ProV
- MTBC0 PGAP product: glycine betaine/L-proline ABC transporter ATP-binding protein ProV
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=2e-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_218275.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34)
- 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
COG1125 - Curated reference: UniProt O69724 (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 —
16 functional partner(s); context anchor
proZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003982|Rv3758c|proV MICFDDVSKVYAHGATAVDRLTLEVPNGMLTVFVGPSGCGKTTALRMINRMVDPTSGTITVDGTDVSTVNAVKLRLGIGYVIQNAGLMPHQRVIDNVATVPVLKGQPRRAARKAGYEVLERVGLDPKVATRYPAQLSGGEQQRVGVARALAADPPILLMDEPFSAVDPVVRHELQNEILRLQAELHKTIVFVTHDIDEALKLADLVAVFAPGGALAQYDETARLLSSPANDFVSKFIGLGRGYRWLQLFDAAGLPVRDIEQVSVNGLSDARDRQVRDGWVLVVDGAGAPLGWIDADGRRRHRGGAALSDAMTVGGSVFRPNGNLSQALDAALSSPSGVGVAVDGGGKVIGGILAADVLAEFQKGKKAGGGAKPCTT