mtr Resolved · high auto-curated
H37Rv Rv2855 · MTBC0 - ·
459 aa · 3165205–3166584 (+) ·
RefSeq YP_177910.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | mycothione reductase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Mycothione reductase. Pfam: Pyr_redox_2 (PF07992.21), Pyr_redox_3 (PF13738.13), Lys_Orn_oxgnase (PF13434.13), Pyr_redox (PF00070.34), Pyr_redox_dim (PF02852.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WHH3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Mycothione reductase |
| EC (curated) |
EC 1.8.1.15
|
| Curated function | Catalyzes the NAD(P)H-dependent reduction of mycothione (the oxidized disulfide form of mycothiol) to mycothiol. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | mtr |
| eggNOG description | Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family |
| Orthologous group | COG1249 |
| EC number |
EC 1.8.1.15
|
| KEGG orthology |
K17883
|
| Gene Ontology (41) |
GO:0000166, GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006790, GO:0008150, GO:0008152 +29 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) pseudogene candidate
| pN/pS | 0.334 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 4 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 1.05% of strains (1528) · 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 |
|---|---|---|---|---|
Pyr_redox_2 | PF07992.21 | 2.6e-47 | 4–316 | Pyridine nucleotide-disulphide oxidoreductase |
Pyr_redox_3 | PF13738.13 | 2.2e-08 | 119–304 | Pyridine nucleotide-disulphide oxidoreductase |
Lys_Orn_oxgnase | PF13434.13 | 2.9e-05 | 127–190 | L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase |
Pyr_redox | PF00070.34 | 2.8e-15 | 174–249 | Pyridine nucleotide-disulphide oxidoreductase |
Pyr_redox_dim | PF02852.29 | 5.0e-29 | 345–454 | Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: bkdC (branched-chain keto acid dehydrogenase E2 component), high confidence from genomic context alone (score 918 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 999 | 999 | coexpression:756 experimental:970 database:844 |
Rv2496c bkdB |
3-methyl-2-oxobutanoate dehydrogenase subunit beta | 950 | 946 | coexpression:645 experimental:465 database:617 |
Rv2495c bkdC |
branched-chain keto acid dehydrogenase E2 component | 922 | 918 ctx | cooccurence:442 coexpression:451 experimental:443 database:565 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 933 | 908 | coexpression:454 experimental:443 database:565 |
Rv2854 hyp |
hypothetical protein | 883 | 877 ctx | neighborhood:869 |
Rv1734c hyp |
hypothetical protein | 866 | 860 | coexpression:451 experimental:443 database:565 |
Rv0843 |
dehydrogenase | 864 | 852 | coexpression:500 database:580 |
Rv2497c bkdA |
3-methyl-2-oxobutanoate dehydrogenase subunit alpha | 860 | 848 | coexpression:497 database:580 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 793 | 777 | database:615 |
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 765 | 753 | experimental:410 database:550 |
Rv0526 |
thioredoxin | 758 | 748 | experimental:410 database:550 |
Rv1677 dsbF |
lipoprotein DsbF | 754 | 743 | experimental:410 database:550 |
Rv3673c |
membrane-anchored thioredoxin-like protein | 753 | 743 | experimental:410 database:550 |
Rv0816c thiX |
thioredoxin ThiX | 752 | 741 | experimental:410 database:550 |
Rv2878c mpt53 |
soluble secreted antigen Mpt53 | 752 | 741 | experimental:410 database:550 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): mycothione reductase
- Pfam (hmmscan --cut_ga): Pyr_redox_2 PF07992.21 (E=3e-47), Pyr_redox_3 PF13738.13 (E=2e-08), Lys_Orn_oxgnase PF13434.13 (E=3e-05), Pyr_redox PF00070.34 (E=3e-15), Pyr_redox_dim PF02852.29 (E=5e-29)
- (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 YP_177910.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pyr_redox_2 (PF07992.21), Pyr_redox_3 (PF13738.13), Lys_Orn_oxgnase (PF13434.13), Pyr_redox (PF00070.34), Pyr_redox_dim (PF02852.29)
- 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
COG1249 - Curated reference: UniProt P9WHH3 (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 —
114 functional partner(s); context anchor
bkdC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2855|mtr METYDIAIIGTGSGNSILDERYASKRAAICEQGTFGGTCLNVGCIPTKMFVYAAEVAKTIRGASRYGIDAHIDRVRWDDVVSRVFGRIDPIALSGEDYRRCAPNIDVYRTHTRFGPVQADGRYLLRTDAGEEFTAEQVVIAAGSRPVIPPAILASGVDYHTSDTVMRIAELPEHIVIVGSGFIAAEFAHVFSALGVRVTLVIRGSCLLRHCDDTICERFTRIASTKWELRTHRNVVDGQQRGSGVALRLDDGCTINADLLLVATGRVSNADLLDAEQAGVDVEDGRVIVDEYQRTSARGVFALGDVSSPYLLKHVANHEARVVQHNLLCDWEDTQSMIVTDHRYVPAAVFTDPQIAAVGLTENQAVAKGLDISVKIQDYGDVAYGWAMEDTSGIVKLITERGSGRLLGAHIMGYQASSLIQPLIQAMSFGLTAAEMARGQYWIHPALPEVVENALLGLR