Rv2994 Resolved · high auto-curated
H37Rv Rv2994 · MTBC0 - ·
445 aa · 3351269–3352606 (+) ·
RefSeq NP_217510.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | MFS-type transporter |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | MFS-type transporter. Pfam: MFS_1 (PF07690.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WJW7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized MFS-type transporter Rv2994 |
UniProt still lists this protein as Uncharacterized MFS-type transporter Rv2994; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Major facilitator superfamily |
| Orthologous group | COG2271 |
| KEGG orthology |
K02445
|
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | 0.528 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 6 missense, 1 nonsense, 3 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 17.35% of strains (25190) · convergent |
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 | 5.7e-49 | 21–356 | Major Facilitator Superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2993c (2-hydroxyhepta-2,4-diene-1,7-dioate isomerase), high confidence from genomic context alone (score 763 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2993c |
2-hydroxyhepta-2,4-diene-1,7-dioate isomerase | 763 | 763 ctx | neighborhood:728 |
Rv2992c gltS |
glutamate--tRNA ligase | 741 | 731 ctx | neighborhood:728 |
Rv1773c |
transcriptional regulator | 403 | 372 | |
Rv0220 lipC |
esterase LipC | 811 | 81 | textmining:803 |
Rv0230c php |
phosphotriesterase | 635 | 55 | textmining:630 |
Rv2957 |
PGL/p-HBAD biosynthesis glycosyltransferase | 806 | 49 | textmining:805 |
Rv3347c PPE55 |
PPE family protein PPE55 | 657 | 47 | textmining:655 |
Rv2958c |
PGL/p-HBAD biosynthesis glycosyltransferase | 803 | 44 | textmining:803 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): MFS-type transporter
- Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=6e-49)
- (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_217510.1)
- Domains: Pfam-A via hmmscan --cut_ga — MFS_1 (PF07690.22)
- 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
COG2271 - Curated reference: UniProt P9WJW7 (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 —
8 functional partner(s); context anchor
Rv2993c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2994| MSRDPTGVGARWAIMIVSLGVTASSFLFINGVAFLIPRLENARGTPLSHAGLLASMPSWGLVVTMFAWGYLLDHVGERMVMAVGSALTAAAAYAAASVHSLLWIGVFLFLGGMAAGGCNSAGGRLVSGWFPPQQRGLAMGIRQTAQPLGIASGALVIPELAERGVHAGLMFPAVVCTLAAVASVLGIVDPPRKSRTKASEQELASPYRGSSILWRIHAASALLMMPQTVTVTFMLVWLINHHGWSVAQAGVLVTISQLLGALGRVAVGRWSDHVGSRMRPVRLIAAAAAATLFLLAAVDNEGSRYDVLLMIAISVIAVLDNGLEATAITEYAGPYWSGRALGIQNTTQRLMAAAGPPLFGSLITTAAYPTAWALCGVFPLAAVPLVPVRLLPPGLETRARRQSVRRHRWWQAVRCHAWPNGPRRPGPPGQPRRVRQGGTAITPPT