proW Family assigned · medium auto-curated
H37Rv Rv3757c · MTBC0 mtbc0_003981 ·
229 aa · 4226731–4227420 (-) ·
RefSeq NP_218274.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycine betaine/carnitine/choline/L-proline ABC transporter permease ProW |
|---|---|
| MTBC0 PGAP re-annotation | glycine betaine/carnitine/choline/L-proline ABC transporter permease ProW |
| Revised (this work) | Glycine betaine/carnitine/choline/L-proline ABC transporter permease ProW. Pfam: BPD_transp_1 (PF00528.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O69723
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible osmoprotectant |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | proW |
| eggNOG description | PFAM binding-protein-dependent transport systems inner membrane component |
| Orthologous group | COG1174 |
| KEGG orthology |
K05846
|
| 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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 |
|---|---|---|---|---|
BPD_transp_1 | PF00528.28 | 9.3e-18 | 33–203 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: proV (glycine betaine/carnitine/choline/L-proline ABC transporter ATP-binding protein ProV), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3758c proV |
glycine betaine/carnitine/choline/L-proline ABC transporter ATP-binding protein ProV | 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 | 998 ctx | neighborhood:882 cooccurence:774 coexpression:536 database:800 textmining:711 |
Rv3756c proZ |
glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ | 998 | 998 ctx | neighborhood:881 coexpression:805 database:900 |
Rv3755c hyp |
hypothetical protein | 884 | 885 ctx | neighborhood:881 |
Rv1244 lpqZ |
lipoprotein LpqZ | 802 | 781 ctx | cooccurence:511 coexpression:516 |
Rv3760 |
membrane protein | 769 | 769 ctx | neighborhood:768 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 559 | 75 | textmining:543 |
Rv3534c hsaF |
4-hydroxy-2-oxovalerate aldolase | 459 | 75 | textmining:440 |
Rv2391 sirA |
sulfite reductase | 445 | 50 | textmining:440 |
Rv1304 atpB |
ATP synthase subunit A | 457 | 44 | textmining:456 |
Rv2072c cobL |
precorrin-6Y C(5,15)-methyltransferase | 630 | 41 | textmining:630 |
Rv2571c |
transmembrane protein | 546 | 41 | textmining:546 |
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 permease ProW
- MTBC0 PGAP product: glycine betaine/carnitine/choline/L-proline ABC transporter permease ProW
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=9e-18)
- (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_218274.1)
- Domains: Pfam-A via hmmscan --cut_ga — BPD_transp_1 (PF00528.28)
- 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
COG1174 - Curated reference: UniProt O69723 (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 —
12 functional partner(s); context anchor
proV - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003981|Rv3757c|proW MHYLMTHPGAAWALTVVHLRLSLLPVLIGLMSAVPLGLLVQRAPLLRRLTTATASVIFTIPSLALFVVLPLIIGTRILDEANVIVALAAYTTALLVRAVLEALDAVPAQVHDAATAIGYSRIAQMLKVELPLSIPVLVAGLRVVAVTNIAMVSVGSVIGIGGLGTWFTAGYQTNKSDQIVAGVVAMFLLAIVVDVVINLAGRLATPWERAPRAARRRRQVAAPITGGAR