Rv1648 Family assigned · medium auto-curated
H37Rv Rv1648 · MTBC0 mtbc0_001757 ·
268 aa · 1869752–1870558 (+) ·
RefSeq NP_216164.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | rhomboid-like protein |
| Revised (this work) | Rhomboid-like protein. Pfam: Rhomboid_2 (PF20401.4). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P94983
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2CJZS |
|---|
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 | 0.375 · 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 |
|---|---|---|---|---|
Rhomboid_2 | PF20401.4 | 1.4e-19 | 24–189 | Rhomboid-like protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1647 (adenylate cyclase), high confidence from genomic context alone (score 885 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1647 |
adenylate cyclase | 885 | 885 ctx | neighborhood:882 |
Rv0538 |
membrane protein | 744 | 745 ctx | cooccurence:744 |
Rv0493c hyp |
hypothetical protein | 716 | 716 ctx | cooccurence:716 |
Rv3835 hyp |
hypothetical protein | 706 | 707 ctx | cooccurence:705 |
Rv3903c cpnT hyp |
hypothetical protein | 698 | 698 ctx | cooccurence:698 |
Rv3909 hyp |
hypothetical protein | 696 | 697 ctx | cooccurence:696 |
Rv2843 hyp |
hypothetical protein | 676 | 676 ctx | cooccurence:675 |
Rv1024 |
membrane protein | 665 | 665 ctx | cooccurence:664 |
Rv1853 ureD |
urease accessory protein UreD | 626 | 627 ctx | cooccurence:625 |
Rv1646 PE17 |
PE family protein PE17 | 610 | 611 ctx | neighborhood:611 |
Rv0312 hyp |
hypothetical protein | 601 | 602 ctx | cooccurence:599 |
Rv3413c rsdA |
anti-sigma-D factor RsdA | 571 | 571 ctx | cooccurence:571 |
Rv0262c aac |
aminoglycoside 2'-N-acetyltransferase | 550 | 550 ctx | cooccurence:549 |
Rv0007 |
membrane protein | 548 | 549 ctx | cooccurence:542 |
Rv1906c hyp |
hypothetical protein | 546 | 546 ctx | cooccurence:546 |
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: rhomboid-like protein
- Pfam (hmmscan --cut_ga): Rhomboid_2 PF20401.4 (E=1e-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_216164.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rhomboid_2 (PF20401.4)
- 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
2CJZS - Curated reference: UniProt P94983 (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 —
44 functional partner(s); context anchor
Rv1647 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001757|Rv1648| MIYRVACLLARIRFTVGYVAALASVSTTILMHGPQVHAQVIRHASTNLHNLAHGHLGTLWNSAFVIDEGPLYFWLPCLACLLAVAELQLRSLRLTVAFVVGHIGATLLVAAVLAGAIEIGWLPWSISRVSDVGMSYGALAALGALTAAIPGRWRPAWIGWWVSLGLATATIGGGFTDAGHTVALLLGMLVTACFTRPARWTLGRCALLAVASGFCLVLLAHSWWSLVSGSALGLLGALGAAGFARWTRARATSLPPGALAIPQPALSR