recG Resolved · high auto-curated
H37Rv Rv2973c · MTBC0 mtbc0_003158 ·
737 aa · 3348908–3351121 (-) ·
RefSeq NP_217489.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP-dependent DNA helicase RecG |
|---|---|
| MTBC0 PGAP re-annotation | ATP-dependent DNA helicase RecG |
| Revised (this work) | ATP-dependent DNA helicase RecG. Pfam: RecG_wedge (PF17191.11), ResIII (PF04851.22), DEAD (PF00270.36), Helicase_C (PF00271.38). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMQ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP-dependent DNA helicase RecG |
| EC (curated) |
EC 5.6.2.3, EC 5.6.2.4
|
| Curated function | Plays a critical role in recombination and DNA repair (Probable). Helps process Holliday junction (HJ) intermediates to mature products by catalyzing branch migration. Has replication fork regression activity, able to displace proteins bound to DNA. An ATP-dependent helicase with a preference for HJ DNA, followed by lagging strand replication forks (RF). Has DNA helicase activity in both directions in vitro. Unwinds branched DNA substrates such as HJs to flayed complexes, unwinds full RFs, R-loop and D-loops, has weak and strong unwinding activities on leading and lagging strand RFs respective. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | recG |
| eggNOG description | Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has a DNA unwinding activity characteristic of a DNA helicase with a 3'- to 5'- polarity. Unwinds branched duplex DNA (Y-DNA) |
| Orthologous group | COG1200 |
| EC number |
EC 3.6.4.12
|
| KEGG orthology |
K03655
|
| KEGG pathways |
map03440
|
| Gene Ontology (41) |
GO:0003674, GO:0003724, GO:0003824, GO:0004004, GO:0004386, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006139, GO:0006725 +29 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 | 0.275 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
RecG_wedge | PF17191.11 | 7.6e-07 | 20–136 | RecG wedge domain |
ResIII | PF04851.22 | 2.5e-09 | 287–459 | Type III restriction enzyme, res subunit |
DEAD | PF00270.36 | 2.8e-22 | 292–464 | DEAD/DEAH box helicase |
Helicase_C | PF00271.38 | 1.9e-17 | 548–628 | Helicase conserved C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: murB (UDP-N-acetylenolpyruvoylglucosamine reductase), medium confidence from genomic context alone (score 531 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2974c hyp |
hypothetical protein | 944 | 944 ctx | neighborhood:800 coexpression:732 |
Rv2972c hyp |
hypothetical protein | 929 | 929 ctx | neighborhood:881 coexpression:431 |
Rv2975c hyp |
hypothetical protein | 801 | 801 ctx | neighborhood:800 |
Rv0482 murB |
UDP-N-acetylenolpyruvoylglucosamine reductase | 531 | 531 ctx | cooccurence:430 |
Rv2896c dprA hyp |
hypothetical protein | 493 | 493 ctx | cooccurence:490 |
Rv0720 rplR |
50S ribosomal protein L18 | 490 | 490 ctx | cooccurence:488 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 462 | 463 ctx | cooccurence:445 |
Rv2154c ftsW |
lipid II flippase FtsW | 458 | 458 ctx | cooccurence:430 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 445 | 446 ctx | cooccurence:421 |
Rv3646c topA |
DNA topoisomerase I | 656 | 439 | textmining:413 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 437 | 437 ctx | cooccurence:415 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 445 | 425 | |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 425 | 425 | |
Rv2343c dnaG |
DNA primase | 496 | 420 | coexpression:420 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 438 | 408 |
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 DNA helicase RecG
- MTBC0 PGAP product: ATP-dependent DNA helicase RecG
- Pfam (hmmscan --cut_ga): RecG_wedge PF17191.11 (E=8e-07), ResIII PF04851.22 (E=3e-09), DEAD PF00270.36 (E=3e-22), Helicase_C PF00271.38 (E=2e-17)
- (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_217489.1)
- Domains: Pfam-A via hmmscan --cut_ga — RecG_wedge (PF17191.11), ResIII (PF04851.22), DEAD (PF00270.36), Helicase_C (PF00271.38)
- 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
COG1200 - Curated reference: UniProt P9WMQ7 (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 —
53 functional partner(s); context anchor
murB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003158|Rv2973c|recG MASLSDRLDRVLGATAADALDEQFGMRTVDDLLRHYPRSYVEGAARVGIGDARPEAGEHITIVDVITDTYSFPMKKKPNRKCLRITVGGGRNKVTATFFNADYIMRDLTKHTKVMLSGEVGYYKGAMQLTHPAFLILDSPDGKNHGTRSLKSIADASKAISGELVVEEFERRFFPIYPASTKVQSWDIFKCVRQVLDVLDRVDDPLPAELRAKHGLIPEDEALRAIHLAESQSLRERARERLTFDEAVGLQWALVARRHGELSESGPSAAWKSNGLAAELLRRLPFELTAGQREVLDVLSDGLAANRPLNRLLQGEVGSGKTIVAVLAMLQMVDAGYQCALLAPTEVLAAQHLRSIRDVLGPLAMGGQLGGAENATRVALLTGSMTAGQKKQVRAEIASGQVGIVIGTHALLQEAVDFHNLGMVVVDEQHRFGVEQRDQLRAKAPAGITPHLLVMTATPIPRTVALTVYGDLETSTLRELPLGRQPIATNVIFVKDKPAWLDRAWRRIIEEAAAGRQAYVVAPRIDESDDTDVQGGVRPSATAEGLFSRLRSAELAELRLALMHGRLSADDKDAAMAAFRAGEVDVLVCTTVIEVGVDVPNATVMLVMDADRFGISQLHQLRGRIGRGEHPSVCLLASWVPPDTPAGQRLRAVAGTMDGFALADLDLKERKEGDVLGRNQSGKAITLRLLSLAEHEEYIVAARDFCIEAYKNPTDPALALMAARFTSTDRIEYLDKS