Rv1919c Family assigned · medium auto-curated
H37Rv Rv1919c · MTBC0 mtbc0_002033 ·
154 aa · 2190177–2190641 (-) ·
RefSeq NP_216435.1
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 |
O53961
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; 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 | COG3832 |
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 | 0.341 · 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 |
|---|---|---|---|---|
Polyketide_cyc2 | PF10604.16 | 3.2e-26 | 6–148 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1920 (membrane protein), high confidence from genomic context alone (score 775 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) |
|---|---|---|---|---|
Rv1920 |
membrane protein | 775 | 775 ctx | neighborhood:773 |
Rv1871c hyp |
hypothetical protein | 721 | 721 ctx | cooccurence:718 |
Rv0826 hyp |
hypothetical protein | 653 | 653 ctx | cooccurence:653 |
Rv1006 hyp |
hypothetical protein | 614 | 614 ctx | cooccurence:602 |
Rv1645c hyp |
hypothetical protein | 608 | 608 ctx | cooccurence:606 |
Rv1868 hyp |
hypothetical protein | 556 | 556 ctx | cooccurence:556 |
Rv3584 lpqE |
lipoprotein LpqE | 534 | 535 ctx | cooccurence:506 |
Rv3446c hyp |
hypothetical protein | 517 | 517 ctx | cooccurence:513 |
Rv1546 hyp |
hypothetical protein | 498 | 498 ctx | cooccurence:489 |
Rv2047c hyp |
hypothetical protein | 487 | 488 ctx | cooccurence:486 |
Rv0210 hyp |
hypothetical protein | 486 | 487 ctx | cooccurence:485 |
Rv0250c hyp |
hypothetical protein | 454 | 454 ctx | cooccurence:451 |
Rv2877c |
integral membrane protein | 452 | 452 ctx | cooccurence:449 |
Rv1435c hyp |
hypothetical protein | 449 | 449 ctx | cooccurence:446 |
Rv3509c ilvX |
acetohydroxyacid synthase large subunit | 438 | 439 ctx | cooccurence:429 |
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-26)
- (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_216435.1)
- 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
COG3832 - Curated reference: UniProt O53961 (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 —
23 functional partner(s); context anchor
Rv1920 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002033|Rv1919c| MSGRKFSFEVTKTSSAPAATLFRLVTDGGNWATWAKPIVAQSSWARRGDPAPGGIGAIRKLGMWPVFVQEETVEYEQDRRHVYKLVGARTPVQDYFGEVVLTPNASGGTDLRWSGSFTEKVRGTGPVMRAALGGAVRFFAGQLVKAAEREAVRR