ahpC Resolved · high auto-curated
H37Rv Rv2428 · MTBC0 mtbc0_002586 ·
195 aa · 2750441–2751028 (+) ·
RefSeq NP_216944.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | alkyl hydroperoxide reductase subunit AhpC |
|---|---|
| MTBC0 PGAP re-annotation | peroxiredoxin AhpC |
| Revised (this work) | Peroxiredoxin AhpC. Pfam: AhpC-TSA (PF00578.28), Redoxin (PF08534.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQB7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alkyl hydroperoxide reductase C |
| EC (curated) |
EC 1.11.1.28
|
| 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. Together with AhpD, 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. Does not however seem to play a role in detoxification of isoniazid. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | ahpC |
| eggNOG description | Alkyl hydroperoxide reductase |
| Orthologous group | COG0450 |
| EC number |
EC 1.11.1.15
|
| KEGG orthology |
K03386
|
| KEGG pathways |
map04214
|
| Gene Ontology (77) |
GO:0003674, GO:0003824, GO:0004601, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006950, GO:0008150 +65 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 | 0.401 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
AhpC-TSA | PF00578.28 | 5.7e-34 | 27–146 | AhpC/TSA family |
Redoxin | PF08534.17 | 6.4e-13 | 32–155 | Redoxin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ahpD (alkyl hydroperoxide reductase AphD), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2429 ahpD |
alkyl hydroperoxide reductase AphD | 999 | 994 ctx | neighborhood:844 cooccurence:766 coexpression:837 textmining:902 |
Rv3913 trxB2 |
thioredoxin reductase | 955 | 896 | coexpression:437 experimental:808 textmining:588 |
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 873 | 834 | experimental:468 database:611 |
Rv1677 dsbF |
lipoprotein DsbF | 882 | 831 | experimental:468 database:611 |
Rv0816c thiX |
thioredoxin ThiX | 868 | 831 | experimental:468 database:611 |
Rv3673c |
membrane-anchored thioredoxin-like protein | 841 | 831 | experimental:468 database:611 |
Rv2878c mpt53 |
soluble secreted antigen Mpt53 | 843 | 830 | experimental:468 database:611 |
Rv0526 |
thioredoxin | 840 | 830 | experimental:468 database:611 |
Rv2359 zur |
zinc uptake regulation protein | 645 | 598 | coexpression:575 |
Rv1909c furA |
ferric uptake regulation protein FurA | 870 | 596 | coexpression:573 textmining:692 |
Rv3841 bfrB |
bacterioferritin BfrB | 664 | 595 | coexpression:562 |
Rv1875 hyp |
hypothetical protein | 588 | 589 ctx | neighborhood:521 |
Rv0440 groEL2 |
molecular chaperone GroEL | 661 | 576 | |
Rv3417c groEL1 |
chaperonin GroEL | 626 | 576 | |
Rv2521 bcp |
peroxiredoxin | 590 | 557 ctx | cooccurence:467 |
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 subunit AhpC
- MTBC0 PGAP product: peroxiredoxin AhpC
- Pfam (hmmscan --cut_ga): AhpC-TSA PF00578.28 (E=6e-34), Redoxin PF08534.17 (E=6e-13)
- (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_216944.1)
- Domains: Pfam-A via hmmscan --cut_ga — AhpC-TSA (PF00578.28), Redoxin (PF08534.17)
- 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
COG0450 - Curated reference: UniProt P9WQB7 (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 —
128 functional partner(s); context anchor
ahpD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002586|Rv2428|ahpC MPLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPMLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQSDELCACNWRKGDPTLDAGELLKASA