Rv3083 Resolved · high auto-curated
H37Rv Rv3083 · MTBC0 mtbc0_003277 ·
495 aa · 3469868–3471355 (+) ·
RefSeq NP_217599.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | FAD-containing monooxygenase MymA |
|---|---|
| MTBC0 PGAP re-annotation | NAD(P)/FAD-dependent oxidoreductase |
| Revised (this work) | NAD(P)/FAD-dependent oxidoreductase. Pfam: Pyr_redox_2 (PF07992.21), NAD_binding_8 (PF13450.13), FMO-like (PF00743.26), Lys_Orn_oxgnase (PF13434.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNF7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative FAD-containing monooxygenase MymA |
| EC (curated) |
EC 1.14.13.-
|
| Curated function | Required for maintaining the appropriate mycolic acid composition and permeability of the envelope on its exposure to acidic pH. |
UniProt still lists this protein as Putative FAD-containing monooxygenase MymA; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | ethA |
| eggNOG description | L-lysine 6-monooxygenase (NADPH-requiring) |
| Orthologous group | COG2072 |
| KEGG orthology |
K10215
|
| KEGG pathways |
map00627, map01120
|
| Gene Ontology (19) |
GO:0005575, GO:0005618, GO:0005623, GO:0008150, GO:0009268, GO:0009628, GO:0010447, GO:0030312, GO:0040007, GO:0044110, GO:0044116, GO:0044117 +7 more
|
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 | 0.535 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 15 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 |
|---|---|---|---|---|
Pyr_redox_2 | PF07992.21 | 9.9e-08 | 5–216 | Pyridine nucleotide-disulphide oxidoreductase |
NAD_binding_8 | PF13450.13 | 3.3e-07 | 9–62 | NAD(P)-binding Rossmann-like domain |
FMO-like | PF00743.26 | 1.9e-13 | 76–349 | Flavin-binding monooxygenase-like |
Lys_Orn_oxgnase | PF13434.13 | 4.0e-05 | 94–216 | L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sadH (oxidoreductase SadH), high confidence from genomic context alone (score 989 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3085 sadH |
oxidoreductase SadH | 997 | 989 ctx | neighborhood:882 coexpression:860 textmining:803 |
Rv3084 lipR |
acetyl-hydrolase LipR | 994 | 984 ctx | neighborhood:882 coexpression:869 textmining:660 |
Rv3086 adhD |
alcohol dehydrogenase D | 982 | 962 ctx | neighborhood:721 coexpression:869 textmining:561 |
Rv3088 tgs4 |
diacyglycerol O-acyltransferase | 990 | 951 ctx | neighborhood:616 coexpression:860 textmining:803 |
Rv3089 fadD13 |
long chain-fatty-acid--CoA ligase FadD13 | 989 | 945 ctx | neighborhood:616 coexpression:862 textmining:809 |
Rv3087 |
diacyglycerol O-acyltransferase | 987 | 940 ctx | neighborhood:590 coexpression:860 textmining:803 |
Rv3854c ethA |
monooxygenase EthA | 906 | 905 | database:900 |
Rv0233 nrdB |
ribonucleoside-diphosphate reductase subunit beta NrdB | 733 | 733 | coexpression:733 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 931 | 659 ctx | neighborhood:602 textmining:807 |
Rv0943c |
monooxygenase | 608 | 608 ctx | cooccurence:608 |
Rv1308 atpA |
ATP synthase subunit alpha | 437 | 437 | experimental:427 |
Rv1507c hyp |
hypothetical protein | 412 | 413 | |
Rv1309 atpG |
ATP synthase subunit gamma | 411 | 412 | |
Rv3456c rplQ |
50S ribosomal protein L17 | 408 | 409 | |
Rv1310 atpD |
ATP synthase subunit beta | 403 | 404 |
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: FAD-containing monooxygenase MymA
- MTBC0 PGAP product: NAD(P)/FAD-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): Pyr_redox_2 PF07992.21 (E=1e-07), NAD_binding_8 PF13450.13 (E=3e-07), FMO-like PF00743.26 (E=2e-13), Lys_Orn_oxgnase PF13434.13 (E=4e-05)
- (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_217599.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pyr_redox_2 (PF07992.21), NAD_binding_8 (PF13450.13), FMO-like (PF00743.26), Lys_Orn_oxgnase (PF13434.13)
- 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
COG2072 - Curated reference: UniProt P9WNF7 (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 —
27 functional partner(s); context anchor
sadH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003277|Rv3083| MNQHFDVLIIGAGLSGIGTACHVTAEFPDKTIALLERRERLGGTWDLFRYPGVRSDSDMFTFGYKFRPWRDVKVLADGASIRQYIADTATEFGVDEKIHYGLKVNTAEWSSRQCRWTVAGVHEATGETRTYTCDYLISCTGYYNYDAGYLPDFPGVHRFGGRCVHPQHWPEDLDYSGKKVVVIGSGATAVTLVPAMAGSNPGSAAHVTMLQRSPSYIFSLPAVDKISEVLGRFLPDRWVYEFGRRRNIAIQRKLYQACRRWPKLMRRLLLWEVRRRLGRSVDMSNFTPNYLPWDERLCAVPNGDLFKTLASGAASVVTDQIETFTEKGILCKSGREIEADIIVTATGLNIQMLGGMRLIVDGAEYQLPEKMTYKGVLLENAPNLAWIIGYTNASWTLKSDIAGAYLCRLLRHMADNGYTVATPRDAQDCALDVGMFDQLNSGYVKRGQDIMPRQGSKHPWRVLMHYEKDAKILLEDPIDDGVLHFAAAAQDHAAA