Rv0546c Family assigned · medium auto-curated
H37Rv Rv0546c · MTBC0 mtbc0_000575 ·
128 aa · 641134–641520 (-) ·
RefSeq NP_215060.1
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). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06412
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 |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | gloA |
| eggNOG description | Glyoxalase bleomycin resistance protein dioxygenase |
| Orthologous group | COG0346 |
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 | 0.236 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 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 | 1.2e-20 | 8–111 | Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0547c (oxidoreductase), medium confidence from genomic context alone (score 597 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) |
|---|---|---|---|---|
Rv0547c |
oxidoreductase | 597 | 597 ctx | neighborhood:590 |
Rv0545c pitA |
low-affinity inorganic phosphate transporter | 526 | 526 ctx | neighborhood:519 |
Rv0544c |
transmembrane protein | 519 | 519 ctx | neighborhood:513 |
Rv1473A |
transcriptional regulator | 467 | 467 ctx | cooccurence:467 |
Rv0548c menB |
1,4-dihydroxy-2-naphthoyl-CoA synthase | 425 | 426 ctx | neighborhood:419 |
Rv0543c hyp |
hypothetical protein | 410 | 410 ctx | neighborhood:406 |
Rv0863 hyp |
hypothetical protein | 560 | 167 | textmining:494 |
Rv1159 pimE |
polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase | 457 | 75 | textmining:438 |
Rv2564 glnQ |
glutamine ABC transporter ATP-binding protein | 808 | 69 | textmining:803 |
Rv1080c greA |
transcription elongation factor GreA | 522 | 56 | textmining:515 |
Rv2224c caeA |
carboxylesterase A | 439 | 49 | textmining:435 |
Rv3274c fadE25 |
acyl-CoA dehydrogenase | 549 | 47 | textmining:547 |
Rv0108c hyp |
hypothetical protein | 497 | 47 | textmining:494 |
Rv0180c |
transmembrane protein | 674 | 44 | textmining:673 |
Rv1086 |
(2Z,6E)-farnesyl diphosphate synthase | 618 | 42 | textmining:618 |
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=1e-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_215060.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyoxalase (PF00903.32)
- 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
COG0346 - Curated reference: UniProt O06412 (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 —
18 functional partner(s); context anchor
Rv0547c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000575|Rv0546c| MEILASRMLLRPADYQRSLSFYRDQIGLAIAREYGAGTVFFAGQSLLELAGYGEPDHSRGPFPGALWLQVRDLEATQTELVSRGVSIAREPRREPWGLHEMHVTDPDGITLIFVEVPEGHPLRTDTRA