Rv2219A Family assigned · medium auto-curated
H37Rv Rv2219A · MTBC0 - ·
140 aa · 2486994–2487416 (-) ·
RefSeq YP_177661.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Membrane protein. Pfam: RDD (PF06271.19). |
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 |
Q79FG7
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | pfam rdd |
| Orthologous group | COG1714 |
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 | 0.431 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
RDD | PF06271.19 | 6.4e-08 | 24–120 | RDD family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glnA1 (glutamine synthetase), high confidence from genomic context alone (score 789 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2220 glnA1 |
glutamine synthetase | 806 | 789 ctx | neighborhood:759 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 661 | 661 ctx | cooccurence:660 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 654 | 655 ctx | cooccurence:640 |
Rv0102 |
integral membrane protein | 558 | 559 ctx | cooccurence:552 |
Rv2169c |
transmembrane protein | 534 | 535 ctx | cooccurence:532 |
Rv2242 hyp |
hypothetical protein | 528 | 528 ctx | cooccurence:526 |
Rv0528 |
transmembrane protein | 522 | 523 ctx | cooccurence:520 |
Rv0504c hyp |
hypothetical protein | 474 | 475 ctx | cooccurence:471 |
Rv1457c |
antibiotic ABC transporter permease | 449 | 450 ctx | cooccurence:443 |
Rv2146c |
transmembrane protein | 434 | 435 ctx | cooccurence:431 |
Rv0635 hadA |
(3R)-hydroxyacyl-ACP dehydratase subunit HadA | 428 | 429 ctx | cooccurence:425 |
Rv1342c hyp |
hypothetical protein | 427 | 427 ctx | cooccurence:418 |
Rv2206 |
transmembrane protein | 410 | 411 ctx | cooccurence:405 |
Rv3208A TB9.4 hyp |
hypothetical protein | 408 | 409 | |
Rv0360c hyp |
hypothetical protein | 408 | 408 ctx | cooccurence:408 |
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): membrane protein
- Pfam (hmmscan --cut_ga): RDD PF06271.19 (E=6e-08)
- (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 YP_177661.1)
- Domains: Pfam-A via hmmscan --cut_ga — RDD (PF06271.19)
- 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
COG1714 - Curated reference: UniProt Q79FG7 (TrEMBL, unreviewed; 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 —
23 functional partner(s); context anchor
glnA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2219A| MTAKSPPDYPGKTLGLPDTGPGSLAPMGRRLAALLIDWLIAYGLALLGVEFGVWSTPMLSTVVLVIWLLLGVAAVRLFGFTPGQLMLGLVVVAVGGRRPVGIGRLVVRGLLIGLVVPPLFTDSDGRGLHDRLTATAVVRR