ahpD Resolved · high auto-curated
H37Rv Rv2429 · MTBC0 mtbc0_002587 ·
177 aa · 2751054–2751587 (+) ·
RefSeq NP_216945.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | alkyl hydroperoxide reductase AphD |
|---|---|
| MTBC0 PGAP re-annotation | alkyl hydroperoxide reductase |
| Revised (this work) | Alkyl hydroperoxide reductase. Pfam: CMD (PF02627.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQB5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alkyl hydroperoxide reductase AhpD |
| EC (curated) |
EC 1.11.1.28
|
| Curated function | Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity.; FUNCTION: Together with AhpC, DlaT and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | ahpD |
| eggNOG description | Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity |
| Orthologous group | COG0599 |
| KEGG orthology |
K04756
|
| Gene Ontology (29) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0008152, GO:0009987, GO:0015036 +17 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 | 0.337 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
CMD | PF02627.26 | 1.3e-14 | 101–174 | Carboxymuconolactone decarboxylase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ahpC (alkyl hydroperoxide reductase subunit AhpC), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 999 | 994 ctx | neighborhood:844 cooccurence:766 coexpression:837 textmining:902 |
Rv2427A oxyR |
Rv2427A, Pseudogene oxyR', inactivated by multiple mutations; identical to sequence in u16243 (see Deretic et al., 1995). | 578 | 489 ctx | neighborhood:489 |
Rv1286 cysC |
adenylyl-sulfate kinase | 525 | 482 | coexpression:482 |
Rv1874 hyp |
hypothetical protein | 480 | 481 ctx | neighborhood:401 |
Rv0477 hyp |
hypothetical protein | 471 | 471 ctx | cooccurence:471 |
Rv2399c cysT |
sulfate ABC transporter permease CysT | 406 | 407 | coexpression:407 |
Rv0433 |
carboxylate-amine ligase | 403 | 404 | coexpression:404 |
Rv2391 sirA |
sulfite reductase | 451 | 310 | |
Rv3846 sodA |
superoxide dismutase | 731 | 71 | textmining:723 |
Rv2238c ahpE |
peroxiredoxin | 665 | 54 | textmining:661 |
Rv1649 pheS |
phenylalanine--tRNA ligase subunit alpha | 412 | 52 | textmining:406 |
Rv0432 sodC |
superoxide dismutase | 639 | 50 | textmining:636 |
Rv3600c coaX |
type III pantothenate kinase | 460 | 50 | textmining:456 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 880 | 47 | textmining:880 |
Rv2037c |
transmembrane protein | 451 | 47 | textmining:448 |
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: alkyl hydroperoxide reductase AphD
- MTBC0 PGAP product: alkyl hydroperoxide reductase
- Pfam (hmmscan --cut_ga): CMD PF02627.26 (E=1e-14)
- (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_216945.1)
- Domains: Pfam-A via hmmscan --cut_ga — CMD (PF02627.26)
- 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
COG0599 - Curated reference: UniProt P9WQB5 (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 —
17 functional partner(s); context anchor
ahpC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002587|Rv2429|ahpD MSIEKLKAALPEYAKDIKLNLSSITRSSVLDQEQLWGTLLASAAATRNPQVLADIGAEATDHLSAAARHAALGAAAIMGMNNVFYRGRGFLEGRYDDLRPGLRMNIIANPGIPKANFELWSFAVSAINGCSHCLVAHEHTLRTVGVDREAIFEALKAAAIVSGVAQALATIEALSPS