Rv0052 Family assigned · medium auto-curated
H37Rv Rv0052 · MTBC0 - ·
187 aa · 57410–57973 (+) ·
RefSeq NP_214566.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains DJ-1_PfpI (PF01965.31) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
I6Y6S3
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 | DJ-1 PfpI family |
| Orthologous group | COG0693 |
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 | 0.362 · 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 |
|---|---|---|---|---|
DJ-1_PfpI | PF01965.31 | 2.5e-20 | 4–140 | DJ-1/PfpI family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0051 (transmembrane protein), high confidence from genomic context alone (score 938 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) |
|---|---|---|---|---|
Rv0051 |
transmembrane protein | 937 | 938 ctx | neighborhood:722 coexpression:785 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 734 | 735 ctx | neighborhood:722 |
Rv1931c |
transcriptional regulator | 656 | 656 ctx | cooccurence:644 |
Rv0053 rpsF |
30S ribosomal protein S6 | 465 | 466 ctx | neighborhood:466 |
Rv2720 lexA |
repressor LexA | 452 | 450 | |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 463 | 435 | |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 463 | 434 | |
Rv2043c pncA |
pyrazinamidase/nicotinamidase PncA | 426 | 427 | coexpression:405 |
Rv2074 |
pyridoxamine 5'-phosphate oxidase | 406 | 407 | |
Rv2025c |
cation efflux system protein | 447 | 155 | |
Rv2704 hyp |
hypothetical protein | 527 | 61 | textmining:517 |
Rv3256c hyp |
hypothetical protein | 522 | 55 | textmining:516 |
Rv3916c hyp |
hypothetical protein | 444 | 55 | textmining:436 |
Rv3192 hyp |
hypothetical protein | 871 | 51 | textmining:870 |
Rv1775 hyp |
hypothetical protein | 403 | 46 | textmining:400 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): DJ-1_PfpI PF01965.31 (E=2e-20)
- (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_214566.3)
- Domains: Pfam-A via hmmscan --cut_ga — DJ-1_PfpI (PF01965.31)
- 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
COG0693 - Curated reference: UniProt I6Y6S3 (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 —
21 functional partner(s); context anchor
Rv0051 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0052| MPSFDVVFVGHRRGEVRSDNAMLGLLCDAAFDELTRPDVVIFPGGIGTRTLIHDQTVLDWVREAHRHTLLTTSVCTGGLVLAAAGLLNGLTATTHWRVQDLFNSLGARYVPQRVVEHLPERVITAAGVSSGIDMGLRLVELLVSREAAEASQLMIEYDPQPPVDAGSLAKASPATHRLALEFYQHRL