trxA Family assigned · medium auto-curated
H37Rv Rv1470 · MTBC0 mtbc0_001572 ·
124 aa · 1668785–1669159 (+) ·
RefSeq NP_215986.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | thioredoxin TrxA |
|---|---|
| MTBC0 PGAP re-annotation | thioredoxin family protein |
| Revised (this work) | Thioredoxin family protein. Pfam: Thioredoxin (PF00085.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53161
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable thioredoxin TrxA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | trxA |
| eggNOG description | thioredoxin participates in various redox reactions through the reversible oxidation of its active center dithiol, to a disulfide, catalyzes dithiol-disulfide exchange reactions |
| Orthologous group | COG3118 |
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
Thioredoxin | PF00085.27 | 2.3e-17 | 5–92 | Thioredoxin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trxB1 (thioredoxin), high confidence from genomic context alone (score 815 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1471 trxB1 |
thioredoxin | 819 | 815 ctx | neighborhood:803 |
Rv3913 trxB2 |
thioredoxin reductase | 942 | 793 | experimental:770 textmining:736 |
Rv1472 echA12 |
enoyl-CoA hydratase EchA12 | 868 | 743 ctx | neighborhood:707 textmining:510 |
Rv1469 ctpD |
cobalt/nickel-exporting P-type ATPase | 848 | 690 ctx | neighborhood:677 textmining:530 |
Rv1473 |
macrolide ABC transporter ATP-binding protein | 664 | 664 ctx | neighborhood:620 |
Rv2299c htpG |
chaperone protein HtpG | 563 | 529 | |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 645 | 526 | experimental:438 |
Rv0440 groEL2 |
molecular chaperone GroEL | 552 | 525 | |
Rv3417c groEL1 |
chaperonin GroEL | 550 | 522 | |
Rv0794c |
oxidoreductase | 526 | 476 | |
Rv2234 ptpA |
protein-tyrosine-phosphatase | 506 | 475 | experimental:438 |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 732 | 473 | experimental:413 textmining:514 |
Rv2855 mtr |
mycothione reductase | 612 | 473 | |
Rv3859c gltB |
glutamate synthase large subunit | 532 | 469 | experimental:455 |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 514 | 468 | experimental:441 |
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 TrxA
- MTBC0 PGAP product: thioredoxin family protein
- Pfam (hmmscan --cut_ga): Thioredoxin PF00085.27 (E=2e-17)
- (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_215986.1)
- Domains: Pfam-A via hmmscan --cut_ga — Thioredoxin (PF00085.27)
- 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
COG3118 - Curated reference: UniProt O53161 (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 —
50 functional partner(s); context anchor
trxB1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001572|Rv1470|trxA MTTRDLTAAYFQQTISANSNVLVYFWAPLCAPCDLFTPTYEASSRKHFDVVHGKVNIETEKDLASIAGVKLLPTLMAFKKGKLVFKQAGIANPAIMDNLVQQLRAYTFKSPAGEGIGPGTKTSS