Rv0794c Resolved · high auto-curated
H37Rv Rv0794c · MTBC0 - ·
499 aa · 887137–888636 (-) ·
RefSeq YP_177756.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Oxidoreductase. Pfam: Pyr_redox_2 (PF07992.21), 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 |
I6Y4U4
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | lpdB |
| eggNOG description | Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain |
| Orthologous group | COG1249 |
| EC number |
EC 1.8.1.4
|
| KEGG orthology |
K00382
|
| KEGG pathways |
map00010, map00020, map00260, map00280, map00620, map00630, map00640, map01100, map01110, map01120, map01130, map01200
|
| KEGG modules |
M00009, M00011, M00036, M00307, M00532
|
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 | 0.555 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.10% of strains (14670) · 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 | 4.8e-46 | 22–338 | Pyridine nucleotide-disulphide oxidoreductase |
Pyr_redox | PF00070.34 | 4.4e-11 | 193–258 | Pyridine nucleotide-disulphide oxidoreductase |
Pyr_redox_dim | PF02852.29 | 1.2e-19 | 377–483 | Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain |
Functional interaction network (STRING v12, guilt-by-association)
| 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 textmining:705 |
Rv2496c bkdB |
3-methyl-2-oxobutanoate dehydrogenase subunit beta | 943 | 939 | coexpression:648 experimental:465 database:617 |
Rv2495c bkdC |
branched-chain keto acid dehydrogenase E2 component | 915 | 911 | coexpression:454 experimental:443 database:565 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 923 | 894 | coexpression:457 experimental:443 database:565 |
Rv1734c hyp |
hypothetical protein | 867 | 861 | coexpression:454 experimental:443 database:565 |
Rv0843 |
dehydrogenase | 857 | 844 | coexpression:502 database:580 |
Rv2497c bkdA |
3-methyl-2-oxobutanoate dehydrogenase subunit alpha | 841 | 827 | coexpression:503 database:580 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 793 | 777 | database:615 |
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 766 | 755 | experimental:410 database:550 |
Rv0526 |
thioredoxin | 758 | 747 | experimental:410 database:550 |
Rv3673c |
membrane-anchored thioredoxin-like protein | 755 | 744 | experimental:410 database:550 |
Rv0816c thiX |
thioredoxin ThiX | 755 | 744 | experimental:410 database:550 |
Rv1677 dsbF |
lipoprotein DsbF | 754 | 743 | experimental:410 database:550 |
Rv2878c mpt53 |
soluble secreted antigen Mpt53 | 754 | 743 | experimental:410 database:550 |
Rv1826 gcvH |
glycine cleavage system protein H | 760 | 741 | database:622 |
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): oxidoreductase
- Pfam (hmmscan --cut_ga): Pyr_redox_2 PF07992.21 (E=5e-46), Pyr_redox PF00070.34 (E=4e-11), Pyr_redox_dim PF02852.29 (E=1e-19)
- (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_177756.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pyr_redox_2 (PF07992.21), 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 I6Y4U4 (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 — 80 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0794c| MTAAQQDQAPMATPGCREGETYDVVVLGAGPVGQNVADRARAGGLRVAVVERELVGGECSYWACVPSKALLRPVIAISDARRVDGAREAVDGSINTAGVFGRRNRYVAHWDDTGQADWVSGIGATLIRGDGRLDGPRRVVVTKSSGESVALTARHAVVICTGSRPALPDLPGITEARPWTNRQATDNSTVPDRLAIVGAGGVGVEMATAWQGLGASVTLLARGSGLLPRMEPFVGELIGRGLADAGVDVRVGVSVRALGRPNPTGPVVLELDDGTELRVDEVLFATGRAPRTDDIGLETIGLTPGSWLDVDDTCRVRAVDDGWLYAAGDVNHRALLTHQGKYQARIAGTAIGARAAGRPLDTTSWGMHATTADHHAVPQAFFTDPEAAAVGLTADQAAQAGHRIKAIDVEIGDVVMGAKLFADGYTGRARMVVDVDRGHLLGVTMVGPGAAELLHSATVAVAGQVPIDRLWHAVPCFPTISELWLRLLESYRDSFYLLV