betP Family assigned · medium auto-curated
H37Rv Rv0917 · MTBC0 mtbc0_000973 ·
593 aa · 1025302–1027083 (+) ·
RefSeq NP_215432.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycine betaine transport integral membrane protein BetP |
|---|---|
| MTBC0 PGAP re-annotation | BCCT family transporter |
| Revised (this work) | BCCT family transporter. Pfam: BCCT (PF02028.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPR7
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized transporter Rv0917 |
UniProt still lists this protein as Uncharacterized transporter Rv0917; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| Preferred name | betP |
| eggNOG description | Belongs to the BCCT transporter (TC 2.A.15) family |
| Orthologous group | COG1292 |
| KEGG orthology |
K02168
|
| Gene Ontology (12) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0006810, GO:0008150, GO:0016020, GO:0044464, GO:0051179, GO:0051234, GO:0071705, GO:0071944
|
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 | 0.594 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
BCCT | PF02028.25 | 1.1e-184 | 23–509 | BCCT, betaine/carnitine/choline family transporter |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0919 |
GCN5-like N-acetyltransferase | 419 | 397 | |
Rv0985c mscL |
large-conductance ion mechanosensitive channel | 491 | 93 | textmining:462 |
Rv1731 gabD2 |
succinate-semialdehyde dehydrogenase | 706 | 78 | textmining:695 |
Rv0001 dnaA |
chromosomal replication initiator protein DnaA | 527 | 67 | textmining:514 |
Rv3772 hisC2 |
histidinol-phosphate aminotransferase | 872 | 63 | textmining:870 |
Rv1435c hyp |
hypothetical protein | 872 | 61 | textmining:870 |
Rv1726 |
oxidoreductase | 872 | 58 | textmining:870 |
Rv1683 |
bifunctional long-chain acyl-CoA synthase/lipase | 779 | 53 | textmining:777 |
Rv2749 hyp |
hypothetical protein | 871 | 49 | textmining:870 |
Rv1403c |
methyltransferase | 809 | 46 | textmining:809 |
Rv0059 darT hyp |
hypothetical protein | 653 | 46 | textmining:652 |
Rv1704c cycA |
D-serine/alanine/glycine transporter protein CycA | 513 | 46 | textmining:511 |
Rv3331 sugI |
sugar-transport integral membrane protein SugI | 812 | 44 | textmining:812 |
Rv3859c gltB |
glutamate synthase large subunit | 423 | 44 | textmining:422 |
Rv0759c hyp |
hypothetical protein | 806 | 42 | textmining:806 |
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 transport integral membrane protein BetP
- MTBC0 PGAP product: BCCT family transporter
- Pfam (hmmscan --cut_ga): BCCT PF02028.25 (E=1e-184)
- (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_215432.1)
- Domains: Pfam-A via hmmscan --cut_ga — BCCT (PF02028.25)
- 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
COG1292 - Curated reference: UniProt P9WPR7 (SwissProt, reviewed; Inferred from homology)
- 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 — 18 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000973|Rv0917|betP MSAKERGDQNAVVDALRSIQPAVFIPASVVIVAMIVVSVVYSSVAENAFVRLNSAITGGVGWWYILVATGFVVFALYCGISRIGTIRLGRDDELPEFSFWAWLAMLFSAGMGIGLVFYGVAEPLSHYLRPPRSRGVPALTDAAANQAMALTVFHWGLHAWAIYVVVGLGMAYMTYRRGRPLSVRWLLEPVVGRGRVEGALGHAVDVIAIVGTLFGVATSLGFGITQIASGLEYLGWIRVDNWWMVGMIAAITATATASVVSGVSKGLKWLSNINMALAAALALFVLLLGPTLFLLQSWVQNLGGYVQSLPQFMLRTAPFSHDGWLGDWTIFYWGWWISWAPFVGMFIARISRGRTIREFIGAVLLVPTVIASLWFTIFGDSALLRQRNNGDMLVNGAVDTNTSLFRLLDGLPIGAITSVLAVLVIVFFFVTSSDSGSLVIDILSAGGELDPPKLTRVYWAVLEGVAAAVLLLIGGAGSLTALRTAAIATALPFSIVMVVACYAMTKAFHFDLAATPRLLHVTVPDVVAAGNRRRHDISATLSGLIAVRDVDSGTYIVHPDTGALTVTAPPDPLDDHVFESDRHVTRRNTTSSR