trxB2 Resolved · high auto-curated
H37Rv Rv3913 · MTBC0 mtbc0_004147 ·
335 aa · 4425979–4426986 (+) ·
RefSeq NP_218430.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | thioredoxin reductase |
|---|---|
| MTBC0 PGAP re-annotation | thioredoxin-disulfide reductase |
| Revised (this work) | Thioredoxin-disulfide reductase. Pfam: Pyr_redox_2 (PF07992.21), FAD_binding_2 (PF00890.31), Pyr_redox_3 (PF13738.13), Pyr_redox (PF00070.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHH1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Thioredoxin reductase |
| EC (curated) |
EC 1.8.1.9
|
| Curated function | Essential thiol-reducing enzyme that protects the cell from thiol-specific oxidizing stress. Plays a minor role in defense against oxidative and nitrosative stress. Is essential to establish and maintain infection in mice. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | trxB |
| eggNOG description | Belongs to the class-II pyridine nucleotide-disulfide oxidoreductase family |
| Orthologous group | COG0492 |
| EC number |
EC 1.8.1.9
|
| KEGG orthology |
K00384, K03671
|
| KEGG pathways |
map00450, map04621, map05418
|
| Gene Ontology (57) |
GO:0000166, GO:0001666, GO:0003674, GO:0003824, GO:0004791, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006950 +45 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 | 0.295 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 5 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 | 1.2e-49 | 16–304 | Pyridine nucleotide-disulphide oxidoreductase |
FAD_binding_2 | PF00890.31 | 8.9e-05 | 16–51 | FAD binding domain |
Pyr_redox_3 | PF13738.13 | 1.8e-18 | 91–287 | Pyridine nucleotide-disulphide oxidoreductase |
Pyr_redox | PF00070.34 | 3.1e-18 | 158–230 | Pyridine nucleotide-disulphide oxidoreductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trxC (thioredoxin TrxC), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3914 trxC |
thioredoxin TrxC | 999 | 998 ctx | neighborhood:882 fusion:890 experimental:770 textmining:951 |
Rv1471 trxB1 |
thioredoxin | 998 | 983 | experimental:770 database:900 textmining:886 |
Rv1464 csd |
cysteine desulfurase | 923 | 920 | database:900 |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 955 | 896 | coexpression:437 experimental:808 textmining:588 |
Rv1324 |
thioredoxin | 911 | 795 | experimental:770 textmining:589 |
Rv1470 trxA |
thioredoxin TrxA | 942 | 793 | experimental:770 textmining:736 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 776 | 777 ctx | neighborhood:776 |
Rv3910 murJ |
peptidoglycan biosynthesis protein | 717 | 657 ctx | neighborhood:653 |
Rv3915 cwlM |
peptidoglycan hydrolase | 708 | 653 ctx | neighborhood:632 |
Rv3911 sigM |
ECF RNA polymerase sigma factor SigM | 722 | 612 ctx | neighborhood:603 |
Rv3908 mutT4 |
mutator protein MutT | 625 | 607 ctx | neighborhood:549 |
Rv3909 hyp |
hypothetical protein | 549 | 549 ctx | neighborhood:549 |
Rv1937 |
oxygenase | 714 | 529 | experimental:456 textmining:420 |
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 661 | 529 | experimental:440 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 570 | 509 |
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: thioredoxin reductase
- MTBC0 PGAP product: thioredoxin-disulfide reductase
- Pfam (hmmscan --cut_ga): Pyr_redox_2 PF07992.21 (E=1e-49), FAD_binding_2 PF00890.31 (E=9e-05), Pyr_redox_3 PF13738.13 (E=2e-18), Pyr_redox PF00070.34 (E=3e-18)
- (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_218430.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pyr_redox_2 (PF07992.21), FAD_binding_2 (PF00890.31), Pyr_redox_3 (PF13738.13), Pyr_redox (PF00070.34)
- 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
COG0492 - Curated reference: UniProt P9WHH1 (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 —
116 functional partner(s); context anchor
trxC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004147|Rv3913|trxB2 MTAPPVHDRAHHPVRDVIVIGSGPAGYTAALYAARAQLAPLVFEGTSFGGALMTTTDVENYPGFRNGITGPELMDEMREQALRFGADLRMEDVESVSLHGPLKSVVTADGQTHRARAVILAMGAAARYLQVPGEQELLGRGVSSCATCDGFFFRDQDIAVIGGGDSAMEEATFLTRFARSVTLVHRRDEFRASKIMLDRARNNDKIRFLTNHTVVAVDGDTTVTGLRVRDTNTGAETTLPVTGVFVAIGHEPRSGLVREAIDVDPDGYVLVQGRTTSTSLPGVFAAGDLVDRTYRQAVTAAGSGCAAAIDAERWLAEHAATGEADSTDALIGAQR