tpx Resolved · high auto-curated
H37Rv Rv1932 · MTBC0 mtbc0_002046 ·
165 aa · 2202488–2202985 (+) ·
RefSeq NP_216448.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 2-Cys peroxiredoxin |
|---|---|
| MTBC0 PGAP re-annotation | thiol peroxidase |
| Revised (this work) | Thiol peroxidase. Pfam: Redoxin (PF08534.17), AhpC-TSA (PF00578.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG35
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Thiol peroxidase |
| EC (curated) |
EC 1.11.1.24
|
| Curated function | Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | tpx |
| eggNOG description | Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides |
| Orthologous group | COG2077 |
| EC number |
EC 1.11.1.15
|
| KEGG orthology |
K11065
|
| Gene Ontology (70) |
GO:0003674, GO:0003824, GO:0004601, GO:0005575, GO:0005576, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006950, GO:0006979 +58 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 | 1.772 · 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 |
|---|---|---|---|---|
Redoxin | PF08534.17 | 2.8e-31 | 20–160 | Redoxin |
AhpC-TSA | PF00578.28 | 1.8e-16 | 20–143 | AhpC/TSA family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1931c (transcriptional regulator), medium confidence from genomic context alone (score 636 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1930c hyp |
hypothetical protein | 763 | 764 ctx | neighborhood:764 |
Rv3846 sodA |
superoxide dismutase | 885 | 728 | coexpression:712 textmining:595 |
Rv1931c |
transcriptional regulator | 636 | 636 ctx | neighborhood:636 |
Rv1929c hyp |
hypothetical protein | 513 | 513 ctx | neighborhood:511 |
Rv1928c |
short-chain type dehydrogenase/reductase | 465 | 465 ctx | neighborhood:438 |
Rv3025c iscS |
cysteine desulfurase | 459 | 460 | coexpression:417 |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 766 | 456 | coexpression:426 textmining:589 |
Rv2711 ideR |
iron-dependent repressor and activator IdeR | 476 | 448 | coexpression:416 |
Rv2788 sirR |
transcriptional repressor SirR | 475 | 446 | coexpression:414 |
Rv2216 |
epimerase family protein | 443 | 444 | coexpression:444 |
Rv2903c lepB |
signal peptidase | 439 | 440 | coexpression:440 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 437 | 438 | coexpression:425 |
Rv2359 zur |
zinc uptake regulation protein | 457 | 425 | coexpression:423 |
Rv2457c clpX |
ATP-dependent CLP protease ATP-binding subunit ClpX | 491 | 424 | coexpression:404 |
Rv1909c furA |
ferric uptake regulation protein FurA | 456 | 424 | coexpression:422 |
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: 2-Cys peroxiredoxin
- MTBC0 PGAP product: thiol peroxidase
- Pfam (hmmscan --cut_ga): Redoxin PF08534.17 (E=3e-31), AhpC-TSA PF00578.28 (E=2e-16)
- (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_216448.1)
- Domains: Pfam-A via hmmscan --cut_ga — Redoxin (PF08534.17), AhpC-TSA (PF00578.28)
- 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
COG2077 - Curated reference: UniProt P9WG35 (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 —
44 functional partner(s); context anchor
Rv1931c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002046|Rv1932|tpx MAQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA