proX Family assigned · medium auto-curated
H37Rv Rv3759c · MTBC0 mtbc0_003983 ·
315 aa · 4228547–4229494 (-) ·
RefSeq NP_218276.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding lipoprotein ProX |
|---|---|
| MTBC0 PGAP re-annotation | glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding protein ProX |
| Revised (this work) | Glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding protein ProX. Pfam: OpuAC (PF04069.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O69725
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible osmoprotectant |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | proX |
| eggNOG description | Glycine betaine |
| Orthologous group | COG1732 |
| KEGG orthology |
K05845
|
| 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 | 0.605 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 10 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 |
|---|---|---|---|---|
OpuAC | PF04069.18 | 9.5e-52 | 41–305 | Substrate binding domain of ABC-type glycine betaine transport system |
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 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3756c proZ |
glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ | 999 | 999 ctx | neighborhood:881 fusion:511 cooccurence:774 coexpression:527 database:800 textmining:580 |
Rv3758c proV |
glycine betaine/carnitine/choline/L-proline ABC transporter ATP-binding protein ProV | 999 | 999 ctx | neighborhood:882 cooccurence:769 coexpression:775 database:800 textmining:692 |
Rv3757c proW |
glycine betaine/carnitine/choline/L-proline ABC transporter permease ProW | 999 | 998 ctx | neighborhood:882 cooccurence:774 coexpression:536 database:800 textmining:711 |
Rv3755c hyp |
hypothetical protein | 903 | 903 ctx | neighborhood:881 |
Rv1244 lpqZ |
lipoprotein LpqZ | 789 | 789 ctx | cooccurence:684 |
Rv3760 |
membrane protein | 771 | 771 ctx | neighborhood:768 |
Rv1234 |
transmembrane protein | 739 | 740 | coexpression:706 |
Rv2060 |
integral membrane protein | 434 | 435 | |
Rv3470c ilvB2 |
acetolactate synthase large subunit | 420 | 420 | coexpression:417 |
Rv0888 spmT hyp |
hypothetical protein | 409 | 409 | coexpression:409 |
Rv0932c pstS2 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 527 | 383 | |
Rv0928 pstS3 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 408 | 380 | |
Rv0934 pstS1 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 456 | 376 | |
Rv3666c dppA |
dipeptide ABC transporter substrate-binding lipoprotein DppA | 401 | 364 | |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 541 | 363 |
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 substrate-binding lipoprotein ProX
- MTBC0 PGAP product: glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding protein ProX
- Pfam (hmmscan --cut_ga): OpuAC PF04069.18 (E=1e-51)
- (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_218276.1)
- Domains: Pfam-A via hmmscan --cut_ga — OpuAC (PF04069.18)
- 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
COG1732 - Curated reference: UniProt O69725 (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 —
33 functional partner(s); context anchor
proZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003983|Rv3759c|proX MRMLRRLRRATVAAAVWLATVCLVASCANADPLGSATGSVKSIVVGSGDFPESQVIAEIYAQVLQANGFDVGRRLGIGSRETYIPALKDHSIDLVPEYIGNLLLYFQPDATVTMLDAVELELYKRLPGDLSILTPSPASDTDTVTVTAATAARWNLKTIADLAPHSADVKFAAPSAFQTRPSGLPGLRHKYSLDIAPGNFVTINDGGGAVTVRALVEGTATAANLFSTSAAIPQNHLVVLEDPEHNFLAGNIVPLVNSRKKSDHLKDVLDAVSAKLTTAGLAELNAAVSGNSGVDPDQAARKWVRDNGFDHPVRQ