Rv3161c Family assigned · medium auto-curated
H37Rv Rv3161c · MTBC0 mtbc0_003360 ·
382 aa · 3554838–3555986 (-) ·
RefSeq NP_217677.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dioxygenase |
|---|---|
| MTBC0 PGAP re-annotation | aromatic ring-hydroxylating dioxygenase subunit alpha |
| Revised (this work) | Aromatic ring-hydroxylating dioxygenase subunit alpha. Pfam: Rieske (PF00355.33), Ring_hydroxyl_A (PF00848.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53311
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible dioxygenase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | Rieske 2Fe-2S |
| Orthologous group | COG4638 |
| KEGG orthology |
K00479
|
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 | 0.517 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 8 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.46% of strains (664) · 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 |
|---|---|---|---|---|
Rieske | PF00355.33 | 1.2e-19 | 52–136 | Rieske [2Fe-2S] domain |
Ring_hydroxyl_A | PF00848.26 | 1.5e-18 | 188–372 | Ring hydroxylating alpha subunit (catalytic domain) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3160c (TetR family transcriptional regulator), high confidence from genomic context alone (score 797 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3160c |
TetR family transcriptional regulator | 923 | 797 ctx | neighborhood:797 textmining:637 |
Rv2776c |
oxidoreductase | 732 | 650 ctx | cooccurence:519 |
Rv3163c hyp |
hypothetical protein | 580 | 580 ctx | neighborhood:580 |
Rv3162c |
integral membrane protein | 580 | 580 ctx | neighborhood:580 |
Rv3166c hyp |
hypothetical protein | 513 | 513 ctx | neighborhood:513 |
Rv3165c hyp |
hypothetical protein | 513 | 513 ctx | neighborhood:513 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 513 | 513 ctx | neighborhood:513 |
Rv1937 |
oxygenase | 686 | 484 | coexpression:404 textmining:417 |
Rv3159c PPE53 |
PPE family protein PPE53 | 672 | 475 ctx | neighborhood:475 textmining:401 |
Rv1215c hyp |
hypothetical protein | 421 | 421 ctx | cooccurence:415 |
Rv0316 |
muconolactone isomerase | 463 | 409 | |
Rv3554 fdxB |
electron transfer protein FdxB | 541 | 400 | |
Rv2964 purU |
formyltetrahydrofolate deformylase | 427 | 400 | |
Rv3377c |
type B diterpene cyclase | 402 | 391 | |
Rv3230c |
stearoyl-CoA 9-desaturase electron transfer protein | 471 | 307 |
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: dioxygenase
- MTBC0 PGAP product: aromatic ring-hydroxylating dioxygenase subunit alpha
- Pfam (hmmscan --cut_ga): Rieske PF00355.33 (E=1e-19), Ring_hydroxyl_A PF00848.26 (E=1e-18)
- (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_217677.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rieske (PF00355.33), Ring_hydroxyl_A (PF00848.26)
- 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
COG4638 - Curated reference: UniProt O53311 (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 —
32 functional partner(s); context anchor
Rv3160c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003360|Rv3161c| MLSTDNRAELGDILTDIGDYLDDNPPALSLPPAAYTSSELWQLERERIFNRSWMLVAHVDQLAKTGDYVTVSVAGEPVMVVRDVDGQLHALSPICRHRLMLMVEPGAGRIDTLTCQYHLWRYGLDGRLRGAPHMAANLDFNRRECRLPQFAVATWNGLVWINLDADAEPIAAHLDLTDDEFAGYRLGEMVQVESWSHEWRANWKVAAENGHENYHVLGLHRQTLEPFVPGGGDLDVRQYSRWALRLRVPFTVPVEAKSLQLNEVQKSNLVVLWTFPNSALAIAGERVVWFGFIPQSIDRVQVLGGVLTTPELAADAAATAQTSQFVMAMINDEDRLGLEAVQVGAGSRFAERGHLSSKEWPGMLAFYRNLAMALVGDHPGAS