Rv1250 Resolved · high auto-curated
H37Rv Rv1250 · MTBC0 mtbc0_001339 ·
579 aa · 1402623–1404362 (+) ·
RefSeq NP_215766.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | MFS-type drug transporter |
|---|---|
| MTBC0 PGAP re-annotation | MFS transporter |
| Revised (this work) | MFS transporter. Pfam: MFS_1 (PF07690.22), TRI12 (PF06609.19), Sugar_tr (PF00083.31), PUCC (PF03209.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG87
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized MFS-type transporter Rv1250 |
UniProt still lists this protein as Uncharacterized MFS-type transporter Rv1250; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismG Carbohydrate transport and metabolismP Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | emrB |
| eggNOG description | Major facilitator superfamily |
| Orthologous group | COG0477 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, 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 | 0.478 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
MFS_1 | PF07690.22 | 5.8e-53 | 25–415 | Major Facilitator Superfamily |
TRI12 | PF06609.19 | 1.2e-05 | 39–300 | Fungal trichothecene efflux pump (TRI12) |
Sugar_tr | PF00083.31 | 6.6e-09 | 55–190 | Sugar (and other) transporter |
PUCC | PF03209.22 | 1.8e-06 | 100–170 | PUCC protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1249c (membrane protein), medium confidence from genomic context alone (score 518 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1249c |
membrane protein | 518 | 518 ctx | neighborhood:513 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 412 | 412 | |
Rv3239c |
transmembrane transport protein | 406 | 362 | |
Rv3728 |
membrane protein | 457 | 355 | |
Rv2459 jefA |
MFS-type transporter | 432 | 335 | |
Rv1877 |
MFS-type transporter | 455 | 328 | |
Rv0783c emrB |
multidrug resistance protein EmrB | 472 | 325 | |
Rv1634 |
multidrug-efflux transporter | 543 | 314 | |
Rv2209 |
integral membrane protein | 650 | 73 | textmining:638 |
Rv2042c hyp |
hypothetical protein | 663 | 53 | textmining:659 |
Rv1819c bacA |
vitamin B12 transport ATP-binding protein BacA | 553 | 50 | textmining:549 |
Rv0507 mmpL2 |
transmembrane transport protein MmpL2 | 513 | 46 | textmining:511 |
Rv1273c |
drug ABC transporter ATP-binding protein | 455 | 46 | textmining:453 |
Rv3823c mmpL8 |
integral membrane transport protein MmpL8 | 433 | 44 | textmining:432 |
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: MFS-type drug transporter
- MTBC0 PGAP product: MFS transporter
- Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=6e-53), TRI12 PF06609.19 (E=1e-05), Sugar_tr PF00083.31 (E=7e-09), PUCC PF03209.22 (E=2e-06)
- (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_215766.1)
- Domains: Pfam-A via hmmscan --cut_ga — MFS_1 (PF07690.22), TRI12 (PF06609.19), Sugar_tr (PF00083.31), PUCC (PF03209.22)
- 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
COG0477 - Curated reference: UniProt P9WG87 (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 —
14 functional partner(s); context anchor
Rv1249c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001339|Rv1250| MTTAIRRAAGSSYFRNPWPALWAMMVGFFMIMLDSTVVAIANPTIMAQLRIGYATVVWVTSAYLLAYAVPMLVAGRLGDRFGPKNLYLIGLGVFTVASLGCGLSSGAGMLIAARVVQGVGAGLLTPQTLSTITRIFPAHRRGVALGAWGTVASVASLVGPLAGGALVDSMGWEWIFFVNVPVGVIGLILAAYLIPALPHHPHRFDWFGVGLSGAGMFLIVFGLQQGQSANWQPWIWAVIVGGIGFMSLFVYWQARNAREPLIPLEVFNDRNFSLSNLGIAIIAFAGTGMMLPVTFYAQAVCGLSPTHTAVLFAPTAIVGGVLAPFVGMIIDRSHPLCVLGFGFSVLAIAMTWLLCEMAPGTPIWRLVLPFIALGVAGAFVWSPLTVTATRNLRPHLAGASSGVFNAVRQLGAVLGSASMAAFMTSRIAAEMPGGVDALTGPAGQDATVLQLPEFVREPFAAAMSQSMLLPAFVALFGIVAALFLVDFTGAAVAKEPLPESDGDADDDDYVEYILRREPEEDCDTQPLRASRPAAAAASRSGAGGPLAVSWSTSAQGMPPGPPGRRAWQADTESTAPSAL