trxB1 Resolved · high auto-curated
H37Rv Rv1471 · MTBC0 - ·
123 aa · 1659370–1659741 (+) ·
RefSeq YP_177815.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | thioredoxin |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Thioredoxin. Pfam: Thioredoxin (PF00085.27), Thioredoxin_2 (PF13098.14). |
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 |
L7N664
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Thioredoxin |
| Curated function | Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | trxA |
| eggNOG description | belongs to the thioredoxin family |
| Orthologous group | COG0526 |
| EC number |
EC 1.8.1.9
|
| KEGG orthology |
K00384, K03671
|
| KEGG pathways |
map00450, map04621, map05418
|
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 | 1.233 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (209) · 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 |
|---|---|---|---|---|
Thioredoxin | PF00085.27 | 1.9e-25 | 5–101 | Thioredoxin |
Thioredoxin_2 | PF13098.14 | 3.5e-09 | 10–103 | Thioredoxin-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trxA (thioredoxin TrxA), high confidence from genomic context alone (score 815 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3913 trxB2 |
thioredoxin reductase | 998 | 983 | experimental:770 database:900 textmining:886 |
Rv1464 csd |
cysteine desulfurase | 902 | 902 | database:900 |
Rv1470 trxA |
thioredoxin TrxA | 819 | 815 ctx | neighborhood:803 |
Rv1472 echA12 |
enoyl-CoA hydratase EchA12 | 867 | 784 ctx | neighborhood:740 textmining:410 |
Rv3463 hyp |
hypothetical protein | 746 | 746 | coexpression:746 |
Rv1473 |
macrolide ABC transporter ATP-binding protein | 733 | 733 ctx | neighborhood:647 |
Rv1469 ctpD |
cobalt/nickel-exporting P-type ATPase | 754 | 657 ctx | neighborhood:648 |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 657 | 542 | experimental:438 |
Rv2299c htpG |
chaperone protein HtpG | 563 | 529 | |
Rv0440 groEL2 |
molecular chaperone GroEL | 555 | 528 | |
Rv3417c groEL1 |
chaperonin GroEL | 553 | 525 | |
Rv0794c |
oxidoreductase | 534 | 485 | |
Rv2373c dnaJ2 |
chaperone protein DnaJ | 515 | 485 | |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 559 | 478 | experimental:413 |
Rv2234 ptpA |
protein-tyrosine-phosphatase | 507 | 477 | experimental:438 |
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): thioredoxin
- Pfam (hmmscan --cut_ga): Thioredoxin PF00085.27 (E=2e-25), Thioredoxin_2 PF13098.14 (E=3e-09)
- (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_177815.1)
- Domains: Pfam-A via hmmscan --cut_ga — Thioredoxin (PF00085.27), Thioredoxin_2 (PF13098.14)
- 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
COG0526 - Curated reference: UniProt L7N664 (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 —
57 functional partner(s); context anchor
trxA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1471|trxB1 MTTRDLTAAQFNETIQSSDMVLVDYWASWCGPCRAFAPTFAESSEKHPDVVHAKVDTEAERELAAAAQIRSIPTIMAFKNGKLLFNQAGALPPAALESLVQQLKAYEVEAGEATTQNGRAQQA