Rv0188 Resolved · high auto-curated
H37Rv Rv0188 · MTBC0 mtbc0_000202 ·
143 aa · 219834–220265 (+) ·
RefSeq NP_214702.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | SPW repeat protein |
| Revised (this work) | SPW repeat protein. Pfam: SPW (PF03779.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07432
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | SPW repeat |
| Orthologous group | 2DUIA |
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 | 0.354 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
SPW | PF03779.21 | 4.6e-19 | 35–129 | SPW repeat domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0048c (membrane protein), high confidence from genomic context alone (score 747 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0048c |
membrane protein | 746 | 747 ctx | cooccurence:746 |
Rv1171 hyp |
hypothetical protein | 693 | 694 ctx | cooccurence:691 |
Rv1635c |
mannosyltransferase | 600 | 600 ctx | cooccurence:596 |
Rv0187 |
O-methyltransferase | 543 | 544 ctx | neighborhood:541 |
Rv1885c |
chorismate mutase | 538 | 538 ctx | cooccurence:538 |
Rv3773c hyp |
hypothetical protein | 531 | 532 ctx | cooccurence:525 |
Rv3202c adnA |
ATP-dependent DNA helicase | 518 | 518 ctx | cooccurence:518 |
Rv0648 |
alpha-mannosidase | 505 | 506 ctx | cooccurence:499 |
Rv0875c hyp |
hypothetical protein | 490 | 490 ctx | cooccurence:487 |
Rv3830c |
TetR family transcriptional regulator | 486 | 487 ctx | cooccurence:472 |
Rv2079 hyp |
hypothetical protein | 483 | 484 ctx | cooccurence:477 |
Rv2423 hyp |
hypothetical protein | 468 | 468 ctx | cooccurence:466 |
Rv1226c |
transmembrane protein | 461 | 462 ctx | cooccurence:459 |
Rv1776c |
transcriptional regulator | 440 | 440 ctx | cooccurence:423 |
Rv3779 |
transmembrane protein | 434 | 434 ctx | cooccurence:434 |
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: transmembrane protein
- MTBC0 PGAP product: SPW repeat protein
- Pfam (hmmscan --cut_ga): SPW PF03779.21 (E=5e-19)
- (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_214702.1)
- Domains: Pfam-A via hmmscan --cut_ga — SPW (PF03779.21)
- 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
2DUIA - Curated reference: UniProt O07432 (TrEMBL, unreviewed; 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 —
35 functional partner(s); context anchor
Rv0048c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000202|Rv0188| MSTVHSSIDQHPDLLALRASFDRAAESTIAHFTFGLALLAGLYVAASPWIVGFSATRGLPTCDLIVGIAVAYLAYGFASALDRTHGMTWTLPVLGVWVIFSPWVLPGVAVTAGMMWSHIIAGAVVAVLGFYFGMRTRAAANQG