Rv1393c Resolved · high auto-curated
H37Rv Rv1393c · MTBC0 mtbc0_001494 ·
492 aa · 1577453–1578931 (-) ·
RefSeq NP_215909.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | monoxygenase |
|---|---|
| MTBC0 PGAP re-annotation | NAD(P)/FAD-dependent oxidoreductase |
| Revised (this work) | NAD(P)/FAD-dependent oxidoreductase. Pfam: Pyr_redox_2 (PF07992.21), Pyr_redox_3 (PF13738.13), NAD_binding_8 (PF13450.13), FMO-like (PF00743.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71662
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable monoxygenase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | flavoprotein involved in K transport |
| Orthologous group | COG2072 |
| EC number |
EC 1.14.13.22
|
| KEGG orthology |
K03379
|
| KEGG pathways |
map00930, map01120, map01220
|
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 | 0.215 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 4 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 | 5.8e-09 | 6–214 | Pyridine nucleotide-disulphide oxidoreductase |
Pyr_redox_3 | PF13738.13 | 2.1e-18 | 8–205 | Pyridine nucleotide-disulphide oxidoreductase |
NAD_binding_8 | PF13450.13 | 4.8e-09 | 9–75 | NAD(P)-binding Rossmann-like domain |
FMO-like | PF00743.26 | 7.3e-06 | 79–224 | Flavin-binding monooxygenase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cyp132 (cytochrome P450 Cyp132), high confidence from genomic context alone (score 985 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1394c cyp132 |
cytochrome P450 Cyp132 | 985 | 985 ctx | neighborhood:882 coexpression:860 |
Rv1395 |
HTH-type transcriptional regulator | 829 | 829 ctx | neighborhood:784 |
Rv1399c nlhH |
carboxylesterase NlhH | 624 | 622 ctx | neighborhood:544 |
Rv1401 |
membrane protein | 534 | 534 ctx | neighborhood:462 |
Rv3741c |
oxidoreductase | 522 | 522 ctx | cooccurence:519 |
Rv3742c |
oxidoreductase | 516 | 517 ctx | cooccurence:514 |
Rv1402 priA |
primosomal protein N' | 496 | 495 ctx | neighborhood:492 |
Rv1834 lipZ |
hydrolase | 441 | 441 | |
Rv1308 atpA |
ATP synthase subunit alpha | 437 | 437 | experimental:427 |
Rv1245c |
short-chain type dehydrogenase/reductase | 424 | 424 ctx | cooccurence:418 |
Rv2913c |
D-amino acid aminohydrolase | 423 | 424 ctx | cooccurence:419 |
Rv1507c hyp |
hypothetical protein | 412 | 413 | |
Rv1309 atpG |
ATP synthase subunit gamma | 409 | 410 | |
Rv3456c rplQ |
50S ribosomal protein L17 | 407 | 407 | |
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: monoxygenase
- MTBC0 PGAP product: NAD(P)/FAD-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): Pyr_redox_2 PF07992.21 (E=6e-09), Pyr_redox_3 PF13738.13 (E=2e-18), NAD_binding_8 PF13450.13 (E=5e-09), FMO-like PF00743.26 (E=7e-06)
- (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_215909.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pyr_redox_2 (PF07992.21), Pyr_redox_3 (PF13738.13), NAD_binding_8 (PF13450.13), FMO-like (PF00743.26)
- 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
COG2072 - Curated reference: UniProt P71662 (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 —
37 functional partner(s); context anchor
cyp132 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001494|Rv1393c| MMPDYHALIVGAGFSGIGAAIKLDRAGFSDYLVVEAGDGVGGTWHWNTYPGIAVDIPSFSYQFSFEQSRHWSRTYAPGHELKAYAEHCVDKYGIRSRIRLNTKVLAAEFDDEHSLWRVQTDPGGEITARFLISACGILTVPKLPDIDGVDSFEGVTMHTARWDHTQDLTGKRVGIIGTGASAVQVIPEMAPIVSHLTVFQRTPIWCFPKFDVPLPTAVRWAMRIPGGKAVHRLLSQAFVEATFPIAAHYFAVFPLAKHMESAGRRYLRQQVHDPVVREQLTPRYAVGCKRPGFHNTYLSTFNRDNVRLVTEPIDKITPTAVATTDGASHEIDVLVLATGFKVLDTDSIPTYAVTGTGGASLSRFWDEHRLQAYEGVSVPGYPNFFTVFGPYGYVGSSYFALIETQAHHIIRCLKRARRTGATRIEVTEEANARYFAEVMRRRHRQVFWQDSCRLANSYYFDKNGDVPLRPTTTVEAYWRSRRFDLGDYRISS