trxC Resolved · high auto-curated
H37Rv Rv3914 · MTBC0 mtbc0_004148 ·
116 aa · 4426983–4427333 (+) ·
RefSeq NP_218431.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | thioredoxin TrxC |
|---|---|
| MTBC0 PGAP re-annotation | thioredoxin |
| Revised (this work) | Thioredoxin. Pfam: Thioredoxin (PF00085.27), Thioredoxin_2 (PF13098.14), Thioredoxin_9 (PF14595.13), KaiB (PF07689.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG67
SwissProt · reviewed
· 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 | trxC |
| eggNOG description | belongs to the thioredoxin family |
| Orthologous group | COG3118 |
| KEGG orthology |
K03671
|
| KEGG pathways |
map04621, map05418
|
| Gene Ontology (58) |
GO:0003674, GO:0003824, GO:0004791, GO:0005575, GO:0005576, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006091 +46 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 | 1.631 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Thioredoxin | PF00085.27 | 1.0e-33 | 9–108 | Thioredoxin |
Thioredoxin_2 | PF13098.14 | 2.4e-09 | 21–110 | Thioredoxin-like domain |
Thioredoxin_9 | PF14595.13 | 2.0e-05 | 28–88 | Thioredoxin |
KaiB | PF07689.19 | 2.4e-06 | 57–105 | KaiB domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trxB2 (thioredoxin reductase), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3913 trxB2 |
thioredoxin reductase | 999 | 998 ctx | neighborhood:882 fusion:890 experimental:770 textmining:951 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 781 | 781 ctx | neighborhood:776 |
Rv3915 cwlM |
peptidoglycan hydrolase | 794 | 754 ctx | neighborhood:719 |
Rv3911 sigM |
ECF RNA polymerase sigma factor SigM | 704 | 605 ctx | neighborhood:603 |
Rv3910 murJ |
peptidoglycan biosynthesis protein | 594 | 594 ctx | neighborhood:592 |
Rv2373c dnaJ2 |
chaperone protein DnaJ | 596 | 571 | |
Rv3908 mutT4 |
mutator protein MutT | 570 | 553 ctx | neighborhood:549 |
Rv3909 hyp |
hypothetical protein | 549 | 549 ctx | neighborhood:549 |
Rv2299c htpG |
chaperone protein HtpG | 571 | 537 | |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 647 | 529 | experimental:438 |
Rv0440 groEL2 |
molecular chaperone GroEL | 662 | 528 | |
Rv3417c groEL1 |
chaperonin GroEL | 661 | 526 | |
Rv0350 dnaK |
chaperone protein DnaK | 732 | 493 | textmining:494 |
Rv0351 grpE |
stress response protein GrpE | 551 | 493 | coexpression:422 |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 729 | 484 | experimental:413 textmining:497 |
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 TrxC
- MTBC0 PGAP product: thioredoxin
- Pfam (hmmscan --cut_ga): Thioredoxin PF00085.27 (E=1e-33), Thioredoxin_2 PF13098.14 (E=2e-09), Thioredoxin_9 PF14595.13 (E=2e-05), KaiB PF07689.19 (E=2e-06)
- (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_218431.1)
- Domains: Pfam-A via hmmscan --cut_ga — Thioredoxin (PF00085.27), Thioredoxin_2 (PF13098.14), Thioredoxin_9 (PF14595.13), KaiB (PF07689.19)
- 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 P9WG67 (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 —
75 functional partner(s); context anchor
trxB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004148|Rv3914|trxC MTDSEKSATIKVTDASFATDVLSSNKPVLVDFWATWCGPCKMVAPVLEEIATERATDLTVAKLDVDTNPETARNFQVVSIPTLILFKDGQPVKRIVGAKGKAALLRELSDVVPNLN