Rv1615 Family assigned · medium auto-curated
H37Rv Rv1615 · MTBC0 mtbc0_001722 ·
146 aa · 1827217–1827657 (+) ·
RefSeq NP_216131.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | TM2 domain-containing protein |
| Revised (this work) | TM2 domain-containing protein. Pfam: TM2 (PF05154.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06132
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | COG2314 |
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 | 0.368 · 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 |
|---|---|---|---|---|
TM2 | PF05154.22 | 9.0e-11 | 72–125 | TM2 domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pykA (pyruvate kinase), medium confidence from genomic context alone (score 597 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1616 hyp |
hypothetical protein | 882 | 882 ctx | neighborhood:882 |
Rv1617 pykA |
pyruvate kinase | 597 | 597 ctx | neighborhood:597 |
Rv1618 tesB1 |
acyl-CoA thioesterase II | 594 | 594 ctx | neighborhood:594 |
Rv2360c hyp |
hypothetical protein | 539 | 539 ctx | cooccurence:539 |
Rv2468c hyp |
hypothetical protein | 507 | 507 ctx | cooccurence:507 |
Rv2709 |
transmembrane protein | 460 | 460 ctx | cooccurence:460 |
Rv3415c hyp |
hypothetical protein | 437 | 437 ctx | cooccurence:437 |
Rv0312 hyp |
hypothetical protein | 434 | 434 ctx | cooccurence:434 |
Rv1619 hyp |
hypothetical protein | 430 | 430 ctx | neighborhood:430 |
Rv1638A hyp |
hypothetical protein | 414 | 414 ctx | cooccurence:414 |
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: TM2 domain-containing protein
- Pfam (hmmscan --cut_ga): TM2 PF05154.22 (E=9e-11)
- (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_216131.1)
- Domains: Pfam-A via hmmscan --cut_ga — TM2 (PF05154.22)
- 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
COG2314 - Curated reference: UniProt O06132 (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 —
10 functional partner(s); context anchor
pykA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001722|Rv1615| MGLRPARVVRPARSGMLKGVTDPLQHGAFEPGWQSAPPGYPPPYPQYPGPGSYFDPFAPYGRHPVTGQPFSDKSKTVAGLLQLLGLFGIAGIGRIYLGHTGLGIAQLLVGWVTCGLGAVIWGVIDALLILTDKVGDPWGRPLRDGS