Rv1546 Family assigned · medium auto-curated
H37Rv Rv1546 · MTBC0 mtbc0_001653 ·
143 aa · 1757004–1757435 (+) ·
RefSeq NP_216062.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | SRPBCC family protein |
| Revised (this work) | SRPBCC family protein. Pfam: Polyketide_cyc2 (PF10604.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLU7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1546 |
UniProt still lists this protein as Uncharacterized protein Rv1546; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Polyketide cyclase / dehydrase and lipid transport |
| Orthologous group | COG3427 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.044 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (192) · 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 |
|---|---|---|---|---|
Polyketide_cyc2 | PF10604.16 | 2.8e-27 | 1–141 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dnaE1 (DNA polymerase III subunit alpha), high confidence from genomic context alone (score 796 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 796 | 796 ctx | neighborhood:794 |
Rv1543 |
oxidoreductase | 792 | 792 ctx | neighborhood:685 |
Rv1544 |
ketoacyl reductase | 791 | 791 ctx | neighborhood:790 |
Rv3584 lpqE |
lipoprotein LpqE | 731 | 731 ctx | cooccurence:730 |
Rv0513 |
transmembrane protein | 683 | 684 ctx | cooccurence:679 |
Rv1545 hyp |
hypothetical protein | 860 | 655 ctx | neighborhood:641 textmining:613 |
Rv3217c |
integral membrane protein | 585 | 585 ctx | cooccurence:584 |
Rv3346c |
transmembrane protein | 577 | 577 ctx | cooccurence:571 |
Rv3527 hyp |
hypothetical protein | 570 | 570 ctx | cooccurence:569 |
Rv3415c hyp |
hypothetical protein | 554 | 554 ctx | cooccurence:553 |
Rv1368 lprF |
lipoprotein LprF | 541 | 542 ctx | cooccurence:536 |
Rv2418c octT hyp |
hypothetical protein | 535 | 536 ctx | cooccurence:530 |
Rv1871c hyp |
hypothetical protein | 530 | 530 ctx | cooccurence:526 |
Rv0826 hyp |
hypothetical protein | 530 | 530 ctx | cooccurence:530 |
Rv2001 hyp |
hypothetical protein | 512 | 513 ctx | cooccurence:511 |
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: hypothetical protein
- MTBC0 PGAP product: SRPBCC family protein
- Pfam (hmmscan --cut_ga): Polyketide_cyc2 PF10604.16 (E=3e-27)
- (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_216062.1)
- Domains: Pfam-A via hmmscan --cut_ga — Polyketide_cyc2 (PF10604.16)
- 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
COG3427 - Curated reference: UniProt P9WLU7 (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 —
44 functional partner(s); context anchor
dnaE1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001653|Rv1546| MASVELSADVPISPQDTWDHVSELSELGEWLVIHEGWRSELPDQLGEGVQIVGVARAMGMRNRVTWRVTKWDPPHEVAMTGSGKGGTKYGVTLTVRPTKGGSALGLRLELGGRALFGPLGSAAARAVKGDVEKSLKQFAELYG