Rv2024c Family assigned · medium auto-curated
H37Rv Rv2024c · MTBC0 - ·
515 aa · 2268693–2270240 (-) ·
RefSeq NP_216540.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Mrr_cat (PF04471.19), Mrr_cat_2 (PF13156.13), ResIII (PF04851.22), DEAD (PF00270.36) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O53470
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Helicase ATP-binding domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | helicase |
| Orthologous group | COG4889 |
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 | 0.862 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 16 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 |
|---|---|---|---|---|
Mrr_cat | PF04471.19 | 8.2e-06 | 23–135 | Restriction endonuclease |
Mrr_cat_2 | PF13156.13 | 1.7e-51 | 34–154 | Restriction endonuclease |
ResIII | PF04851.22 | 1.8e-27 | 166–363 | Type III restriction enzyme, res subunit |
DEAD | PF00270.36 | 4.1e-11 | 169–363 | DEAD/DEAH box helicase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2020c (Rv2020c, (MTV018.07c), len: 99 aa. Conserved hypothetical protein, nearly identical to C-terminal part of hypothetical protein RvD1-Rv2024c'), high confidence from genomic context alone (score 924 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) |
|---|---|---|---|---|
Rv2020c |
Rv2020c, (MTV018.07c), len: 99 aa. Conserved hypothetical protein, nearly identical to C-terminal part of hypothetical protein RvD1-Rv2024c' | 924 | 924 ctx | fusion:677 cooccurence:774 |
Rv2756c hsdM |
type I restriction/modification system DNA methylase HsdM | 872 | 62 | textmining:870 |
Rv3263 |
DNA methylase | 871 | 54 | textmining:870 |
Rv2119 hyp |
hypothetical protein | 754 | 54 | textmining:751 |
Rv2761c hsdS |
type I restriction/modification system specificity determinant HsdS | 657 | 50 | textmining:654 |
Rv0126 treS |
trehalose synthase/amylase TreS | 521 | 46 | textmining:519 |
Rv2755c hsdS.1 |
Rv2755c, (MTV002.20c), len: 91 aa. Possible hsdS.1,fragment of type I restriction/modification system specificity determinant (S protein), s | 803 | 44 | textmining:803 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): Mrr_cat PF04471.19 (E=8e-06), Mrr_cat_2 PF13156.13 (E=2e-51), ResIII PF04851.22 (E=2e-27), DEAD PF00270.36 (E=4e-11)
- (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_216540.1)
- Domains: Pfam-A via hmmscan --cut_ga — Mrr_cat (PF04471.19), Mrr_cat_2 (PF13156.13), ResIII (PF04851.22), DEAD (PF00270.36)
- 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
COG4889 - Curated reference: UniProt O53470 (TrEMBL, unreviewed; Predicted)
- 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 —
7 functional partner(s); context anchor
Rv2020c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2024c| MGSVHDVIEAFRKAPSNAERGTKFEQLMVRYFELDPTMAQQYDAVWWWIDWPERRGRTDTGIDLVARERDTGNYTAIQCKFYEPTHTLAKGDIDSFFTASGKTGFTNRVIISTTDRWGRNAEDALADQLVPVQRIGMAEIAESPIDWDIAWPADDLQVNLTPAKRHELRPHQQQAIDAVFRGFAVGNDRGKLIMACGTGKTFTALKIAERIAADNGGSARILLLVPSISLLSQTLREWTAQSELDVRAFAVCSDTKVSRSAEDYHVHDVPIPVTTDARVLLHEMAHRRRAQGLTVVFCTYQSLPTVAKAQRLGVDEFDLVMCDEAHRTTGVTLAGDDESNFVRVHDGQYLKAARRLYMTATPRIFTESIKDRADQHSAELVSMDDELTFGPEFHRLSFGEAVERGLLTDYKVMVLTVDQGVIAPRLQQELSGVSGELMLDDASKIVGCWNGLAKRSGTGIVAGEPPMRRAVAFAKDIKTSKQVAELFPKVVEAYRELVDDGPGLACLNSSRRIQA