proZ Family assigned · medium auto-curated
H37Rv Rv3756c · MTBC0 mtbc0_003980 ·
239 aa · 4226015–4226734 (-) ·
RefSeq NP_218273.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ |
|---|---|
| MTBC0 PGAP re-annotation | glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ |
| Revised (this work) | Glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ. 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 |
O69722
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 | proZ |
| eggNOG description | 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 | 0.136 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
BPD_transp_1 | PF00528.28 | 3.5e-16 | 45–207 | 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:881 cooccurence:772 coexpression:869 database:900 textmining:699 |
Rv3759c proX |
glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding lipoprotein ProX | 999 | 999 ctx | neighborhood:881 fusion:511 cooccurence:774 coexpression:527 database:800 textmining:580 |
Rv3757c proW |
glycine betaine/carnitine/choline/L-proline ABC transporter permease ProW | 998 | 998 ctx | neighborhood:881 coexpression:805 database:900 |
Rv3755c hyp |
hypothetical protein | 883 | 883 ctx | neighborhood:881 |
Rv3760 |
membrane protein | 769 | 769 ctx | neighborhood:768 |
Rv1244 lpqZ |
lipoprotein LpqZ | 783 | 762 ctx | cooccurence:469 coexpression:516 |
Rv2502c accD1 |
acetyl-/propionyl-CoA carboxylase subunit beta | 448 | 73 | textmining:430 |
Rv0191 |
MFS-type transporter | 661 | 64 | textmining:653 |
Rv0404 fadD30 |
long-chain-fatty-acid--AMP ligase FadD30 | 439 | 53 | textmining:432 |
Rv1667c |
Rv1667c, (MTV047.03c), len: 217 aa. Probable second part of macrolide-transport ATP-binding protein ABC transporter (see citation below), wi | 659 | 51 | textmining:656 |
Rv3008 hyp |
hypothetical protein | 809 | 44 | textmining:809 |
Rv0323c hyp |
hypothetical protein | 631 | 44 | textmining:630 |
Rv2080 lppJ |
lipoprotein LppJ | 517 | 44 | textmining:516 |
Rv0565c |
monooxygenase | 512 | 44 | textmining:511 |
Rv3601c panD |
aspartate 1-decarboxylase | 438 | 44 | textmining:437 |
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 ProZ
- MTBC0 PGAP product: glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=4e-16)
- (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_218273.1)
- 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 O69722 (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
proV - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003980|Rv3756c|proZ MNFLQQALSYLLTASNWTGPVGLAVRTCEHLEYTAVAVAASALIAVPVGLLIGHTGRGTLLVVGAVNGLRALPTLGVLLLGVLLFGLGLGPPLVALMLLGIPSLLASTYAGIASVDPLVVDAARAMGMTESQVLLRVEVPNALPLMLGGLRSATLQVVATATVAAYASLGGLGGYLIDGIKERRFHIALVGAMMVAALALTLDGLLALAGWVSVPGTGRMRKLAAVVDKPAAGGGHALR