Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | multidrug resistance protein |
|---|
| MTBC0 PGAP re-annotation | multidrug resistance protein Stp |
|---|
| Revised (this work) | Multidrug resistance protein Stp. Pfam: MFS_1 (PF07690.22), Sugar_tr (PF00083.31). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG91
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Multidrug resistance protein Stp |
|---|
| Curated function | Contributes to spectinomycin and tetracycline resistance. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
G Carbohydrate transport and metabolism
P Inorganic ion transport and metabolism
|
|---|
| eggNOG description | Major facilitator superfamily |
|---|
| Orthologous group | COG0477 |
|---|
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 |
2.168 · diversifying/relaxed
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
2 synonymous, 11 missense, 1 nonsense, 2 frameshift
|
|---|
| Disruption |
3 distinct premature-stop/frameshift site(s); most common in
29.81% of strains
(43284) · 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 |
1.6e-57 | 14–403 |
Major Facilitator Superfamily |
Sugar_tr | PF00083.31 |
1.4e-07 | 45–186 |
Sugar (and other) transporter |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv1410c |
aminoglycosides/tetracycline-transport integral membrane protein |
446 |
345 |
|
Rv1776c |
transcriptional regulator |
469 |
64 |
textmining:457 |
Rv0134 ephF |
epoxide hydrolase EphF |
425 |
49 |
textmining:421 |
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 resistance protein
- MTBC0 PGAP product: multidrug resistance protein Stp
- Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=2e-57), Sugar_tr PF00083.31 (E=1e-07)
- (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_216849.1)
- Domains: Pfam-A via hmmscan --cut_ga — MFS_1 (PF07690.22), Sugar_tr (PF00083.31)
- 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
P9WG91
(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 —
3 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002483|Rv2333c|stp
MNRTQLLTLIATGLGLFMIFLDALIVNVALPDIQRSFAVGEDGLQWVVASYSLGMAVFIMSAATLADLYGRRRWYLIGVSLFTLGSIACGLAPSIAVLTTARGAQGLGAAAVSVTSLALVSAAFPEAKEKARAIGIWTAIASIGTTTGPTLGGLLVDQWGWRSIFYVNLPMGALVLFLTLCYVEESCNERARRFDLSGQLLFIVAVGALVYAVIEGPQIGWTSVQTIVMLWTAAVGCALFVWLERRSSNPMMDLTLFRDTSYALAIATICTVFFAVYGMLLLTTQFLQNVRGYTPSVTGLMILPFSAAVAIVSPLVGHLVGRIGARVPILAGLCMLMLGLLMLIFSEHRSSALVLVGLGLCGSGVALCLTPITTVAMTAVPAERAGMASGIMSAQRAIGSTIGFAVLGSVLAAWLSATLEPHLERAVPDPVQRHVLAEIIIDSANPRAHVGGIVPRRHIEHRDPVAIAEEDFIEGIRVALLVATATLAVVFLAGWRWFPRDVHTAGSDAKREAAYSDDRRVRG
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