uvrD1 Resolved · high auto-curated
H37Rv Rv0949 · MTBC0 - ·
771 aa · 1058260–1060575 (+) ·
RefSeq YP_177772.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP-dependent DNA helicase UvrD |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | ATP-dependent DNA helicase UvrD. Pfam: UvrD-helicase (PF00580.28), AAA_19 (PF13245.13), UvrD_C (PF13361.13), UvrD_C_2 (PF13538.13), PcrA_UvrD_tudor (PF21196.4). |
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 |
P9WMQ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP-dependent DNA helicase UvrD1 |
| EC (curated) |
EC 5.6.2.4
|
| Curated function | DNA-dependent ATPase, acting on dsDNA with a 3'-ssDNA tail, unwinding with 3'-to 5'-polarity. A minimal tail of 18 nt is required for activity. Also highly efficient on nicked DNA. Involved in the post-incision events of nucleotide excision repair, as well as in nitrosative and oxidative stress response and possibly in persistence in the host. Inhibits RecA-mediated DNA strand exchange; this does not require ATPase activity. When combined with UvrA greatly inhibits RecA-mediated DNA strand exchange. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | pcrA |
| eggNOG description | ATP-dependent DNA helicase |
| Orthologous group | COG0210 |
| EC number |
EC 3.6.4.12
|
| KEGG orthology |
K03657
|
| KEGG pathways |
map03420, map03430
|
| Gene Ontology (107) |
GO:0000018, GO:0000166, GO:0000287, GO:0003674, GO:0003678, GO:0003824, GO:0004003, GO:0004386, GO:0005488, GO:0005575, GO:0005618, GO:0005622 +95 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 | 0.77 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 9 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 |
|---|---|---|---|---|
UvrD-helicase | PF00580.28 | 2.2e-92 | 23–297 | UvrD/REP helicase N-terminal domain |
AAA_19 | PF13245.13 | 1.1e-21 | 27–282 | AAA domain |
UvrD_C | PF13361.13 | 2.9e-73 | 302–653 | UvrD-like helicase C-terminal domain |
UvrD_C_2 | PF13538.13 | 6.1e-08 | 594–651 | UvrD-like helicase C-terminal domain |
PcrA_UvrD_tudor | PF21196.4 | 2.2e-07 | 723–770 | PcrA/UvrD tudor domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0948c (chorismate mutase), high confidence from genomic context alone (score 719 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3201c adnB |
ATP-dependent DNA helicase | 951 | 952 | database:900 |
Rv3198c uvrD2 |
ATP-dependent DNA helicase UvrD | 950 | 926 | database:900 |
Rv3202c adnA |
ATP-dependent DNA helicase | 763 | 764 | database:540 |
Rv0937c mku |
non-homologous end joining protein Ku | 876 | 722 | database:720 textmining:575 |
Rv1633 uvrB |
excinuclease ABC subunit UvrB | 984 | 719 | experimental:564 textmining:948 |
Rv0948c |
chorismate mutase | 719 | 719 ctx | neighborhood:718 |
Rv2737c recA |
recombinase A | 946 | 716 | experimental:632 textmining:820 |
Rv3715c recR |
recombination protein RecR | 761 | 661 ctx | cooccurence:650 |
Rv1638 uvrA |
excinuclease ABC subunit UvrA | 969 | 639 ctx | cooccurence:413 textmining:920 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 655 | 634 | experimental:456 |
Rv3014c ligA |
DNA ligase A | 711 | 588 | coexpression:484 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 592 | 554 | experimental:431 |
Rv2090 |
5'-3' exonuclease | 574 | 547 | |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 544 | 544 | |
Rv3646c topA |
DNA topoisomerase I | 657 | 533 | experimental:407 |
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): ATP-dependent DNA helicase UvrD
- Pfam (hmmscan --cut_ga): UvrD-helicase PF00580.28 (E=2e-92), AAA_19 PF13245.13 (E=1e-21), UvrD_C PF13361.13 (E=3e-73), UvrD_C_2 PF13538.13 (E=6e-08), PcrA_UvrD_tudor PF21196.4 (E=2e-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 YP_177772.1)
- Domains: Pfam-A via hmmscan --cut_ga — UvrD-helicase (PF00580.28), AAA_19 (PF13245.13), UvrD_C (PF13361.13), UvrD_C_2 (PF13538.13), PcrA_UvrD_tudor (PF21196.4)
- 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
COG0210 - Curated reference: UniProt P9WMQ1 (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 —
62 functional partner(s); context anchor
Rv0948c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0949|uvrD1 MSVHATDAKPPGPSPADQLLDGLNPQQRQAVVHEGSPLLIVAGAGSGKTAVLTRRIAYLMAARGVGVGQILAITFTNKAAAEMRERVVGLVGEKARYMWVSTFHSTCVRILRNQAALIEGLNSNFSIYDADDSRRLLQMVGRDLGLDIKRYSPRLLANAISNLKNELIDPHQALAGLTEDSDDLARAVASVYDEYQRRLRAANALDFDDLIGETVAVLQAFPQIAQYYRRRFRHVLVDEYQDTNHAQYVLVRELVGRDSNDGIPPGELCVVGDADQSIYAFRGATIRNIEDFERDYPDTRTILLEQNYRSTQNILSAANSVIARNAGRREKRLWTDAGAGELIVGYVADNEHDEARFVAEEIDALAEGSEITYNDVAVFYRTNNSSRSLEEVLIRAGIPYKVVGGVRFYERKEIRDIVAYLRVLDNPGDAVSLRRILNTPRRGIGDRAEACVAVYAENTGVGFGDALVAAAQGKVPMLNTRAEKAIAGFVEMFDELRGRLDDDLGELVEAVLERTGYRRELEASTDPQELARLDNLNELVSVAHEFSTDRENAAALGPDDEDVPDTGVLADFLERVSLVADADEIPEHGAGVVTLMTLHTAKGLEFPVVFVTGWEDGMFPHMRALDNPTELSEERRLAYVGITRARQRLYVSRAIVRSSWGQPMLNPESRFLREIPQELIDWRRTAPKPSFSAPVSGAGRFGSARPSPTRSGASRRPLLVLQVGDRVTHDKYGLGRVEEVSGVGESAMSLIDFGSSGRVKLMHNHAPVTKL