Rv1258c Resolved · high auto-curated
H37Rv Rv1258c · MTBC0 mtbc0_001347 ·
419 aa · 1414525–1415784 (-) ·
RefSeq NP_215774.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | multidrug-efflux transporter |
|---|---|
| MTBC0 PGAP re-annotation | MFS transporter |
| Revised (this work) | MFS transporter. Pfam: MFS_1 (PF07690.22), MFS_3 (PF05977.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJX9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Multidrug efflux pump Tap |
| Curated function | Efflux pump that contributes to intrinsic antibiotic resistance. The pump uses the electrochemical gradient as a source of energy (By similarity). Confers resistance to rifampicin. Confers low-level resistance to tetracycline and to several aminoglycosides, including streptomycin, gentamicin, 2'-N-ethylnetilmicin and 6'-N-ethylnetilmicin. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Major facilitator superfamily |
| Orthologous group | COG2271 |
| Gene Ontology (12) |
GO:0003674, GO:0005215, GO:0006810, GO:0008150, GO:0015562, GO:0022857, GO:0042221, GO:0046677, GO:0050896, GO:0051179, GO:0051234, GO:0055085
|
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) pseudogene candidate
| pN/pS | 0.968 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 24.23% of strains (35184) · clonal |
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 | 2.5e-31 | 12–363 | Major Facilitator Superfamily |
MFS_3 | PF05977.20 | 1.3e-18 | 12–414 | Transmembrane secretion effector |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1257c (oxidoreductase), high confidence from genomic context alone (score 912 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1257c |
oxidoreductase | 911 | 912 ctx | neighborhood:881 |
Rv2416c eis |
enhanced intracellular survival protein | 898 | 845 | coexpression:845 |
Rv1260 |
oxidoreductase | 774 | 766 ctx | neighborhood:760 |
Rv0339c iniR |
transcriptional regulator | 691 | 690 ctx | cooccurence:688 |
Rv0538 |
membrane protein | 639 | 626 ctx | cooccurence:624 |
Rv1259 udgB |
uracil DNA glycosylase | 595 | 595 ctx | neighborhood:585 |
Rv0343 iniC |
iIsoniazid inductible protein IniC | 595 | 595 ctx | cooccurence:586 |
Rv1255c |
HTH-type transcriptional regulator | 572 | 573 ctx | neighborhood:570 |
Rv0342 iniA |
isoniazid inductible protein IniA | 569 | 569 ctx | cooccurence:568 |
Rv2164c hyp |
hypothetical protein | 548 | 548 ctx | cooccurence:547 |
Rv1256c cyp130 |
cytochrome P450 Cyp130 | 535 | 535 ctx | neighborhood:527 |
Rv3835 hyp |
hypothetical protein | 533 | 532 ctx | cooccurence:532 |
Rv2843 hyp |
hypothetical protein | 499 | 500 ctx | cooccurence:495 |
Rv0097 |
oxidoreductase | 487 | 488 ctx | cooccurence:486 |
Rv1648 |
transmembrane protein | 487 | 488 ctx | cooccurence:486 |
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: multidrug-efflux transporter
- MTBC0 PGAP product: MFS transporter
- Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=3e-31), MFS_3 PF05977.20 (E=1e-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_215774.1)
- Domains: Pfam-A via hmmscan --cut_ga — MFS_1 (PF07690.22), MFS_3 (PF05977.20)
- 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
COG2271 - Curated reference: UniProt P9WJX9 (SwissProt, reviewed; 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 —
49 functional partner(s); context anchor
Rv1257c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001347|Rv1258c| MRNSNRGPAFLILFATLMAAAGDGVSIVAFPWLVLQREGSAGQASIVASATMLPLLFATLVAGTAVDYFGRRRVSMVADALSGAAVAGVPLVAWGYGGDAVNVLVLAVLAALAAAFGPAGMTARDSMLPEAAARAGWSLDRINGAYEAILNLAFIVGPAIGGLMIATVGGITTMWITATAFGLSILAIAALQLEGAGKPHHTSRPQGLVSGIAEGLRFVWNLRVLRTLGMIDLTVTALYLPMESVLFPKYFTDHQQPVQLGWALMAIAGGGLVGALGYAVLAIRVPRRVTMSTAVLTLGLASMVIAFLPPLPVIMVLCAVVGLVYGPIQPIYNYVIQTRAAQHLRGRVVGVMTSLAYAAGPLGLLLAGPLTDAAGLHATFLALALPIVCTGLVAIRLPALRELDLAPQADIDRPVGSAQ