Rv2426c Family assigned · medium auto-curated
H37Rv Rv2426c · MTBC0 mtbc0_002583 ·
291 aa · 2747576–2748451 (-) ·
RefSeq NP_216942.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | MoxR family ATPase |
| Revised (this work) | MoxR family ATPase. Pfam: AAA_5 (PF07728.21), AAA (PF00004.36), AAA_2 (PF07724.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71922
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | AAA+ ATPase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | clpL |
| eggNOG description | associated with various cellular activities |
| Orthologous group | COG0714 |
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) pseudogene candidate
| pN/pS | 0.942 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 14.10% of strains (20477) · clonal |
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 |
|---|---|---|---|---|
AAA_5 | PF07728.21 | 6.7e-11 | 46–194 | AAA domain (dynein-related subfamily) |
AAA | PF00004.36 | 7.7e-10 | 47–194 | ATPase family associated with various cellular activities (AAA) |
AAA_2 | PF07724.21 | 1.5e-07 | 47–190 | AAA domain (Cdc48 subfamily) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: proA (gamma-glutamyl phosphate reductase), high confidence from genomic context alone (score 826 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2425c hyp |
hypothetical protein | 976 | 976 ctx | neighborhood:882 cooccurence:771 |
Rv2427c proA |
gamma-glutamyl phosphate reductase | 826 | 826 ctx | neighborhood:817 |
Rv0368c hyp |
hypothetical protein | 783 | 780 ctx | cooccurence:752 |
Rv0373c |
carbon monoxyde dehydrogenase large subunit | 621 | 604 ctx | cooccurence:553 |
Rv2420c rsfS hyp |
hypothetical protein | 592 | 591 ctx | neighborhood:544 |
Rv2424c |
transposase | 566 | 566 ctx | neighborhood:561 |
Rv2417c |
DegV domain-containing protein | 553 | 554 ctx | neighborhood:544 |
Rv2418c octT hyp |
hypothetical protein | 546 | 547 ctx | neighborhood:544 |
Rv2421c nadD |
nicotinate-nucleotide adenylyltransferase | 544 | 544 ctx | neighborhood:544 |
Rv0369c |
membrane oxidoreductase | 495 | 496 ctx | cooccurence:434 |
Rv2435c |
cyclase | 482 | 482 ctx | neighborhood:482 |
Rv0375c |
carbon monoxyde dehydrogenase medium subunit | 492 | 469 ctx | cooccurence:403 |
Rv2427A oxyR |
Rv2427A, Pseudogene oxyR', inactivated by multiple mutations; identical to sequence in u16243 (see Deretic et al., 1995). | 445 | 445 ctx | neighborhood:445 |
Rv2332 mez |
malate oxidoreductase | 425 | 426 | coexpression:416 |
Rv2531c |
amino acid decarboxylase | 438 | 414 | experimental:405 |
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: hypothetical protein
- MTBC0 PGAP product: MoxR family ATPase
- Pfam (hmmscan --cut_ga): AAA_5 PF07728.21 (E=7e-11), AAA PF00004.36 (E=8e-10), AAA_2 PF07724.21 (E=1e-07)
- (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_216942.1)
- Domains: Pfam-A via hmmscan --cut_ga — AAA_5 (PF07728.21), AAA (PF00004.36), AAA_2 (PF07724.21)
- 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
COG0714 - Curated reference: UniProt P71922 (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 —
15 functional partner(s); context anchor
proA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002583|Rv2426c| MTVPARPTPLFADIADVSRRLAETGYLPDTATATAVFLADRLGKPLLVEGPAGVGKTELARAVAQATGSGLVRLQCYEGVDEARALYEWNHAKQILRIQAGSGDWEATKTDVFSEEFLLQRPLLTAIRRTEPTVLLIDETDKADIEIEGLLLEVLSDFAVTVPELGTLTATRAPFVLLTSNATRELSEALKRRCLYLHIDFPTPELERRILLSRVPELPEHFAEELVRIIGVLRGMQLKKVPSIAETIDWGRTVLALGLDTIDDAVVAATLGVVLKHQSDQQRATGELRLN