Rv2209 Resolved · medium auto-curated
H37Rv Rv2209 · MTBC0 mtbc0_002345 ·
512 aa · 2499557–2501095 (+) ·
RefSeq NP_216725.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | MFS transporter |
| Revised (this work) | MFS transporter. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLI3
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2209 |
UniProt still lists this protein as Uncharacterized protein Rv2209; 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
|
|---|---|
| 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 | 1.176 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 12 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 2.51% of strains (3645) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1004c (membrane protein), high confidence from genomic context alone (score 777 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1004c |
membrane protein | 785 | 777 ctx | cooccurence:774 |
Rv0341 iniB |
isoniazid inducible protein IniB | 784 | 777 ctx | cooccurence:774 |
Rv3347c PPE55 |
PPE family protein PPE55 | 777 | 777 ctx | cooccurence:774 |
Rv3343c PPE54 |
PPE family protein PPE54 | 777 | 777 ctx | cooccurence:774 |
Rv1917c PPE34 |
PPE family protein PPE34 | 776 | 776 ctx | cooccurence:774 |
Rv0355c PPE8 |
PPE family protein PPE8 | 775 | 776 ctx | cooccurence:774 |
Rv0304c PPE5 |
PPE family protein PPE5 | 775 | 775 ctx | cooccurence:774 |
Rv2082 hyp |
hypothetical protein | 775 | 775 ctx | cooccurence:773 |
Rv3350c PPE56 |
PPE family protein PPE56 | 775 | 775 ctx | cooccurence:774 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 774 | 774 ctx | cooccurence:774 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 774 | 774 ctx | cooccurence:774 |
Rv0305c PPE6 |
PPE family protein PPE6 | 774 | 774 ctx | cooccurence:773 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 774 | 774 ctx | cooccurence:774 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 774 | 774 ctx | cooccurence:774 |
Rv2954c hyp |
hypothetical protein | 774 | 774 ctx | cooccurence:773 |
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: integral membrane protein
- MTBC0 PGAP product: MFS transporter
- (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_216725.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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 P9WLI3 (SwissProt, reviewed; Predicted)
- 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 —
150 functional partner(s); context anchor
Rv1004c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002345|Rv2209| MPASRLVRQVSAPRNLFGRLVAQGGFYTAGLQLGSGAVVLPVICAHQGLTWAAGLLYPAFCIGAILGNSLSPLILQRAGQLRHLLMAAISATAAALVVCNAAVPWTGVGVAAVFLATTGAGGVVTGVSSVAYTDMISSMLPAVRRGELLLTQGAAGSVLATGVTLVIVPMLAHGNEMARYHDLLWLGAAGLVCSGIAALFVGPMRSVSVTTATRMPLREIYWMGFAIARSQPWFRRYMTTYLLFVPISLGTTFFSLRAAQSNGSLHVLVILSSIGLVVGSMLWRQINRLFGVRGLLLGSALLNAAAALLCMVAESCGQWVHAWAYGTAFLLATVAAQTVVAASISWISVLAPERYRATLICVGSTLAAVEATVLGVALGGIAQKHATIWPVVVVLTLAVIAAVASLRAPTRIGVTADTSPQAATLQAYRPATPNPIHSDERSTPPDHLSVRRGQLRHVWDSRRPAPPLNRPSCRRAARRPAPGKPAAALPQPRHPAVGVREGAPLDAGQRIA