Rv0090 Still unknown · low auto-curated
H37Rv Rv0090 · MTBC0 mtbc0_000100 ·
256 aa · 98643–99413 (+) ·
RefSeq NP_214604.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2127 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2127. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM71
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0090 |
UniProt still lists this protein as Uncharacterized protein Rv0090; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Predicted membrane protein (DUF2127) |
| Orthologous group | COG3305 |
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 | 0.903 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 0.67% of strains (977) · 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 |
|---|---|---|---|---|
DUF2127 | PF09900.15 | 2.0e-33 | 83–224 | Predicted membrane protein (DUF2127) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0180c (transmembrane protein), medium confidence from genomic context alone (score 687 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2577 hyp |
hypothetical protein | 728 | 728 ctx | cooccurence:713 |
Rv0180c |
transmembrane protein | 686 | 687 ctx | cooccurence:685 |
Rv2963 |
integral membrane protein | 668 | 668 ctx | cooccurence:665 |
Rv3310 sapM |
acid phosphatase | 649 | 649 ctx | cooccurence:649 |
Rv0089 |
methyltransferase | 622 | 623 ctx | neighborhood:581 |
Rv1619 hyp |
hypothetical protein | 565 | 565 ctx | cooccurence:565 |
Rv1006 hyp |
hypothetical protein | 550 | 550 ctx | cooccurence:550 |
Rv3434c |
transmembrane protein | 535 | 535 ctx | cooccurence:535 |
Rv2314c hyp |
hypothetical protein | 531 | 531 ctx | cooccurence:531 |
Rv3484 cpsA hyp |
hypothetical protein | 503 | 503 ctx | cooccurence:503 |
Rv1762c hyp |
hypothetical protein | 485 | 485 ctx | cooccurence:483 |
Rv1435c hyp |
hypothetical protein | 473 | 473 ctx | cooccurence:473 |
Rv0219 |
transmembrane protein | 447 | 447 ctx | cooccurence:430 |
Rv0088 |
polyketide cyclase/dehydrase | 429 | 429 | |
Rv1639c hyp |
hypothetical protein | 419 | 419 |
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: membrane protein
- MTBC0 PGAP product: DUF2127 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF2127 PF09900.15 (E=2e-33)
- (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_214604.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2127 (PF09900.15)
- 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
COG3305 - Curated reference: UniProt P9WM71 (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 —
19 functional partner(s); context anchor
Rv0180c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000100|Rv0090| MAKNQNRIRNRWELITCGLGGHVTYAPDDAALAARLRASTGLGEVWRCLRCGDFALGGPQGRGAPEDAPLIMRGKALRQAIIIRALGVERLVRALVLALAAWAVWEFRGARGAIQATLDRDLPVLRAAGFKVDQMTVIHALEKALAAKPSTLALITGMLAAYAVLQAVEGVGLWLLKRWGEYFAVVATSIFLPLEVHDLAKGITTTRVVTFSINVAAVVYLLISKRLFGVRGGRKAYDVERRGEQLLDLERAAMLT