Rv3618 Resolved · high auto-curated
H37Rv Rv3618 · MTBC0 mtbc0_003835 ·
395 aa · 4082402–4083589 (+) ·
RefSeq NP_218135.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | monooxygenase |
|---|---|
| MTBC0 PGAP re-annotation | LLM class flavin-dependent oxidoreductase |
| Revised (this work) | LLM class flavin-dependent oxidoreductase. Pfam: Bac_luciferase (PF00296.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X7W8
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible monooxygenase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | limB |
| eggNOG description | COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases |
| Orthologous group | COG2141 |
| EC number |
EC 1.14.13.107
|
| KEGG orthology |
K14733
|
| KEGG pathways |
map00903
|
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 | 0.893 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (175) · 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 |
|---|---|---|---|---|
Bac_luciferase | PF00296.27 | 2.9e-42 | 6–317 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ephA (epoxide hydrolase EphA), high confidence from genomic context alone (score 964 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3617 ephA |
epoxide hydrolase EphA | 964 | 964 ctx | neighborhood:789 coexpression:803 |
Rv2740 ephG |
epoxide hydrolase | 926 | 901 | database:900 |
Rv0517 |
acyltransferase | 484 | 485 ctx | cooccurence:483 |
Rv3779 |
transmembrane protein | 476 | 476 ctx | cooccurence:476 |
Rv3007c |
oxidoreductase | 411 | 388 |
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: monooxygenase
- MTBC0 PGAP product: LLM class flavin-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=3e-42)
- (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_218135.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bac_luciferase (PF00296.27)
- 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
COG2141 - Curated reference: UniProt I6X7W8 (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 —
5 functional partner(s); context anchor
ephA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003835|Rv3618| MKAPLRFGVFITPFHPTGQSPTVALQYDMERVVALDRLGYDEAWFGEHHSGGYELIACPEVFIAAAAERTTHIRLGTGVVSLPYHHPLMVADRWVLLDHLTRGRVMFGTGPGALPSDAYMMGIDPVEQRRMMQESLEAILALFRAAPDERIDRHSDWFTLREAQLHIRPYTWPYPEIATAAMISPSGPRLAGALGTSLLSLSMSVPGGYAALETAWGVVREQAAKAGRGEPDRADWRVLSIMHLSDSRDQAIDDCTYGLPDFSRYFGAAGFVPLANTVEGTQSSREFVEQYAAKGNCCIGTPDDAIAHIEDLLHRSGGFGTLLLLGHDWAPPPATFHSYELFARAVIPYFKGQLAAPRASHEWARGKRDQLIGRAGEAVVKAITEHVAEQGEAGS