Rv0887c Family assigned · medium auto-curated
H37Rv Rv0887c · MTBC0 mtbc0_000942 ·
152 aa · 988727–989185 (-) ·
RefSeq NP_215402.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | VOC family protein |
| Revised (this work) | VOC family protein. Pfam: Glyoxalase (PF00903.32), Glyoxalase_6 (PF18029.8). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKQ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0887c |
UniProt still lists this protein as Uncharacterized protein Rv0887c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Glyoxalase bleomycin resistance protein dioxygenase |
| Orthologous group | COG2764 |
| KEGG orthology |
K04750
|
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 | 0.325 · 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 |
|---|---|---|---|---|
Glyoxalase | PF00903.32 | 4.8e-16 | 13–129 | Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily |
Glyoxalase_6 | PF18029.8 | 2.3e-08 | 14–129 | Glyoxalase-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sigI (ECF RNA polymerase sigma factor SigI), high confidence from genomic context alone (score 831 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) |
|---|---|---|---|---|
Rv1931c |
transcriptional regulator | 858 | 858 | coexpression:801 |
Rv1190 hyp |
hypothetical protein | 835 | 836 | coexpression:799 |
Rv1725c hyp |
hypothetical protein | 834 | 835 | coexpression:797 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 831 | 831 ctx | cooccurence:431 coexpression:716 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 829 | 830 | coexpression:796 |
Rv2488c |
LuxR family transcriptional regulator | 816 | 817 | coexpression:817 |
Rv1674c |
transcriptional regulator | 810 | 811 | coexpression:800 |
Rv0494 |
HTH-type transcriptional regulator | 798 | 798 | coexpression:798 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 797 | 797 | coexpression:797 |
Rv1027c kdpE |
transcriptional regulator KdpE | 797 | 797 | coexpression:797 |
Rv1267c embR |
transcriptional regulator EmbR | 797 | 797 | coexpression:797 |
Rv3736 |
AraC/XylS family transcriptional regulator | 786 | 787 | coexpression:749 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 761 | 761 | coexpression:761 |
Rv1151c cobB |
NAD-dependent protein deacylase | 741 | 742 | coexpression:733 |
Rv3167c |
TetR family transcriptional regulator | 738 | 738 | coexpression:734 |
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: VOC family protein
- Pfam (hmmscan --cut_ga): Glyoxalase PF00903.32 (E=5e-16), Glyoxalase_6 PF18029.8 (E=2e-08)
- (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_215402.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyoxalase (PF00903.32), Glyoxalase_6 (PF18029.8)
- 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
COG2764 - Curated reference: UniProt P9WKQ3 (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 —
56 functional partner(s); context anchor
sigI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000942|Rv0887c| MAINVEPALSPHLVVDDAASAIDFYVKAFDAVELGRVPGPDGKLIHAALRINGFTVMLNDDVPQMCGGKSMTPTSLGGTPVTIHLTVTDVDAKFQRALNAGATVVTALEDQLWGDRYGVVADPFGHHWSLGQPVREVNMDEIQAAMSSQGDG