dinG Resolved · high auto-curated
H37Rv Rv1329c · MTBC0 mtbc0_001426 ·
664 aa · 1507897–1509891 (-) ·
RefSeq NP_215845.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP-dependent helicase DinG |
|---|---|
| MTBC0 PGAP re-annotation | ATP-dependent helicase DinG |
| Revised (this work) | ATP-dependent helicase DinG. Pfam: DEAD (PF00270.36), Helicase_C_2 (PF13307.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMR5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP-dependent helicase DinG |
| EC (curated) |
EC 5.6.2.3
|
| Curated function | A structure-dependent 5'-3' DNA helicase that unwinds a number of substrates that resemble intermediates in DNA repair, recombination and replication. Translocates on ssDNA with 5'-3' polarity..; FUNCTION: Unwinds G4 DNA (planar arrays of 4 guanine bases stabilized by hydrogen bonds) with both 5'- and 3'- ss-tails. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K TranscriptionL Replication, recombination and repair
|
|---|---|
| Preferred name | dinG |
| eggNOG description | helicase |
| Orthologous group | COG1199 |
| EC number |
EC 3.6.4.12
|
| KEGG orthology |
K03722
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 1.539 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 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 |
|---|---|---|---|---|
DEAD | PF00270.36 | 4.9e-07 | 34–89 | DEAD/DEAH box helicase |
Helicase_C_2 | PF13307.13 | 3.7e-33 | 479–639 | Helicase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mec ([CysO), high confidence from genomic context alone (score 948 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 977 | 976 | experimental:854 database:844 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 973 | 971 | experimental:824 database:844 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 971 | 968 | experimental:801 database:844 |
Rv1334 mec |
[CysO | 950 | 948 ctx | neighborhood:750 database:774 |
Rv1277 hyp |
hypothetical protein | 930 | 919 | experimental:771 database:639 |
Rv1629 polA |
DNA polymerase I | 955 | 897 | experimental:721 database:621 textmining:580 |
Rv1179c hyp |
hypothetical protein | 892 | 884 | experimental:685 database:622 |
Rv0861c ercc3 |
DNA helicase Ercc3 | 948 | 882 | experimental:685 database:622 textmining:580 |
Rv1947 hyp |
hypothetical protein | 890 | 881 | experimental:685 database:622 |
Rv1961 hyp |
hypothetical protein | 888 | 879 | experimental:685 database:622 |
Rv2917 hyp |
hypothetical protein | 887 | 879 | experimental:685 database:622 |
Rv2101 helZ |
helicase HelZ | 942 | 869 | database:812 textmining:578 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 859 | 845 | database:844 |
Rv1330c pncB1 |
nicotinic acid phosphoribosyltransferase PncB1 | 830 | 830 ctx | neighborhood:817 |
Rv2090 |
5'-3' exonuclease | 819 | 796 | experimental:469 database:621 |
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: ATP-dependent helicase DinG
- MTBC0 PGAP product: ATP-dependent helicase DinG
- Pfam (hmmscan --cut_ga): DEAD PF00270.36 (E=5e-07), Helicase_C_2 PF13307.13 (E=4e-33)
- (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_215845.1)
- Domains: Pfam-A via hmmscan --cut_ga — DEAD (PF00270.36), Helicase_C_2 (PF13307.13)
- 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
COG1199 - Curated reference: UniProt P9WMR5 (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 —
140 functional partner(s); context anchor
mec - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001426|Rv1329c|dinG MSESVSMSVPELLAIAVAALGGTRRRGQQEMAAAVAHAFETGEHLVVQAGTGTGKSLAYLVPAIIRALCDDAPVVVSTATIALQRQLVDRDLPQLVDSLTNALPRRPKFALLKGRRNYLCLNKIHNSVTASDHDDERPQEELFDPVAVTALGRDVQRLTAWASTTVSGDRDDLKPGVGDRSWSQVSVSARECLGVARCPFGSECFSERARGAAGLADVVVTNHALLAIDAVAESAVLPEHRLLVVDEAHELADRVTSVAAAELTSATLGMAARRITRLVDPKVTQRLQAASATFSSAIHDARPGRIDCLDDEMATYLSALRDAASAARSAIDTGSDTTTASVRAEAGAVLTEISDTASRILASFAPAIPDRSDVVWLEHEDNHESARAVLRVAPLSVAELLATQVFARATTVLTSATLTIGGSFDAMATAWGLTADTPWRGLDVGSPFQHAKSGILYVAAHLPPPGRDGSGSAEQLTEIAELITAAGGRTLGLFSSMRAARAATEAMRERLSTPVLCQGDDSTSTLVEKFTADAATSLFGTLSLWQGVDVPGPSLSLVLIDRIPFPRPDDPLLSARQRAVAARGGNGFMTVAASHAALLLAQGSGRLLRRVTDRGVVAVLDSRMATARYGEFLRASLPPFWQTTNATQVRAALRRLARADAKAH