Rv3649 Resolved · high auto-curated
H37Rv Rv3649 · MTBC0 mtbc0_000791 ·
81 aa · 839409–839653 (+) ·
RefSeq NP_218166.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | helicase |
|---|---|
| MTBC0 PGAP re-annotation | Zn-binding domain-containing protein |
| Revised (this work) | DEAD/DEAH box helicase. Pfam: DEAD (PF00270.36), Helicase_C (PF00271.38), WHD_HRQ1 (PF22982.4), MZB (PF09369.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06359
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable helicase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | ATP-dependent DNA helicase (RecQ) |
| Orthologous group | COG0514 |
| EC number |
EC 3.6.4.12
|
| KEGG orthology |
K03654, K03657, K06877
|
| KEGG pathways |
map03018, map03420, map03430
|
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 | 0.306 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 9 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (243) · 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 |
|---|---|---|---|---|
DEAD | PF00270.36 | 6.8e-26 | 61–232 | DEAD/DEAH box helicase |
Helicase_C | PF00271.38 | 8.4e-11 | 294–402 | Helicase conserved C-terminal domain |
WHD_HRQ1 | PF22982.4 | 3.4e-08 | 437–504 | ATP-dependent helicase HRQ1, winged helix domain |
MZB | PF09369.16 | 3.4e-22 | 660–738 | MrfA Zn-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cspA (cold shock protein A), medium confidence from genomic context alone (score 519 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3648c cspA |
cold shock protein A | 825 | 519 ctx | neighborhood:518 textmining:653 |
Rv3650 PE33 |
PE family protein PE33 | 503 | 503 ctx | neighborhood:503 |
Rv2908c hyp |
hypothetical protein | 897 | 242 | textmining:870 |
Rv3920c hyp |
hypothetical protein | 891 | 201 | textmining:870 |
Rv0871 cspB |
cold shock-like protein CspB | 812 | 74 | textmining:806 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 874 | 73 | textmining:871 |
Rv1340 rphA |
ribonuclease PH | 808 | 44 | textmining:808 |
Rv2752c rnj |
ribonuclease J | 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
- Legacy H37Rv annotation: helicase
- MTBC0 PGAP product: DEAD/DEAH box helicase
- Pfam (hmmscan --cut_ga): DEAD PF00270.36 (E=7e-26), Helicase_C PF00271.38 (E=8e-11), WHD_HRQ1 PF22982.4 (E=3e-08), MZB PF09369.16 (E=3e-22)
- (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_218166.1)
- Domains: Pfam-A via hmmscan --cut_ga — DEAD (PF00270.36), Helicase_C (PF00271.38), WHD_HRQ1 (PF22982.4), MZB (PF09369.16)
- 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
COG0514 - Curated reference: UniProt O06359 (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 —
8 functional partner(s); context anchor
cspA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000791|Rv3649| MPTTAVIHTVTAEALGRIGIDAPRIPGSLDVAAHAAIGLLPLVAGCDRRHRRPVRGARAGRAAQVSLCMTAIRVEPVSSNA