uvrC Family assigned · medium auto-curated
H37Rv Rv1420 · MTBC0 mtbc0_001520 ·
646 aa · 1603386–1605326 (+) ·
RefSeq NP_215936.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | excinuclease ABC subunit UvrC |
|---|---|
| MTBC0 PGAP re-annotation | excinuclease ABC subunit UvrC |
| Revised (this work) | Excinuclease ABC subunit UvrC. Pfam: GIY-YIG (PF01541.31), UvrC_M (PF27096.1), UVR (PF02151.26), UvrC_RNaseH (PF22920.3), UvrC_RNaseH_dom (PF08459.18), HHH_5 (PF14520.13), HHH_2 (PF12826.14), HHH (PF00633.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFC5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UvrABC system protein C |
| Curated function | The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | uvrC |
| eggNOG description | The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision |
| Orthologous group | COG0322 |
| KEGG orthology |
K03703
|
| KEGG pathways |
map03420
|
| Gene Ontology (24) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005886, GO:0006950, GO:0006974, GO:0008150, GO:0009380, GO:0009987, GO:0016020, GO:0030312 +12 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 | 0.272 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (160) · 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 |
|---|---|---|---|---|
GIY-YIG | PF01541.31 | 1.7e-09 | 18–91 | GIY-YIG catalytic domain |
UvrC_M | PF27096.1 | 1.1e-17 | 103–201 | UvrC/Cho excinuclease, middle domain |
UVR | PF02151.26 | 7.7e-09 | 210–242 | UvrB/uvrC motif |
UvrC_RNaseH | PF22920.3 | 1.7e-35 | 256–384 | UvrC Ribonuclease H-like domain |
UvrC_RNaseH_dom | PF08459.18 | 1.3e-51 | 403–571 | UvrC RNAse H endonuclease domain |
HHH_5 | PF14520.13 | 8.5e-11 | 586–638 | Helix-hairpin-helix domain |
HHH_2 | PF12826.14 | 1.1e-07 | 589–635 | Helix-hairpin-helix motif |
HHH | PF00633.30 | 3.1e-06 | 609–635 | Helix-hairpin-helix motif |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uvrB (excinuclease ABC subunit UvrB), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1633 uvrB |
excinuclease ABC subunit UvrB | 999 | 988 ctx | cooccurence:750 coexpression:654 experimental:772 textmining:965 |
Rv1421 rapZ hyp |
hypothetical protein | 893 | 888 ctx | neighborhood:882 |
Rv1422 cuvA hyp |
hypothetical protein | 890 | 885 ctx | neighborhood:882 |
Rv1423 whiA |
transcriptional regulator WhiA | 883 | 883 ctx | neighborhood:882 |
Rv1638 uvrA |
excinuclease ABC subunit UvrA | 995 | 876 ctx | cooccurence:697 textmining:962 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 802 | 687 ctx | neighborhood:682 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 685 | 685 ctx | neighborhood:682 |
Rv1417 |
membrane protein | 685 | 685 ctx | neighborhood:682 |
Rv1419 hyp |
hypothetical protein | 615 | 616 ctx | neighborhood:607 |
Rv2191 hyp |
hypothetical protein | 687 | 546 | database:540 |
Rv1711 |
RNA pseudouridine synthase | 481 | 481 ctx | cooccurence:442 |
Rv1402 priA |
primosomal protein N' | 479 | 479 | |
Rv1418 lprH |
lipoprotein LprH | 437 | 437 ctx | neighborhood:435 |
Rv1629 polA |
DNA polymerase I | 679 | 431 | textmining:460 |
Rv1406 fmt |
methionyl-tRNA formyltransferase | 425 | 405 |
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: excinuclease ABC subunit UvrC
- MTBC0 PGAP product: excinuclease ABC subunit UvrC
- Pfam (hmmscan --cut_ga): GIY-YIG PF01541.31 (E=2e-09), UvrC_M PF27096.1 (E=1e-17), UVR PF02151.26 (E=8e-09), UvrC_RNaseH PF22920.3 (E=2e-35), UvrC_RNaseH_dom PF08459.18 (E=1e-51), HHH_5 PF14520.13 (E=9e-11), HHH_2 PF12826.14 (E=1e-07), HHH PF00633.30 (E=3e-06)
- (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_215936.1)
- Domains: Pfam-A via hmmscan --cut_ga — GIY-YIG (PF01541.31), UvrC_M (PF27096.1), UVR (PF02151.26), UvrC_RNaseH (PF22920.3), UvrC_RNaseH_dom (PF08459.18), HHH_5 (PF14520.13), HHH_2 (PF12826.14), HHH (PF00633.30)
- 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
COG0322 - Curated reference: UniProt P9WFC5 (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 —
57 functional partner(s); context anchor
uvrB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001520|Rv1420|uvrC MPDPATYRPAPGSIPVEPGVYRFRDQHGRVIYVGKAKSLRSRLTSYFADVASLAPRTRQLVTTAAKVEWTVVGTEVEALQLEYTWIKEFDPRFNVRYRDDKSYPVLAVTLGEEFPRLMVYRGPRRKGVRYFGPYSHAWAIRETLDLLTRVFPARTCSAGVFKRHRQIDRPCLLGYIDKCSAPCIGRVDAAQHRQIVADFCDFLSGKTDRFARALEQQMNAAAEQLDFERAARLRDDLSALKRAMEKQAVVLGDGTDADVVAFADDELEAAVQVFHVRGGRVRGQRGWIVEKPGEPGDSGIQLVEQFLTQFYGDQAALDDAADESANPVPREVLVPCLPSNAEELASWLSGLRGSRVVLRVPRRGDKRALAETVHRNAEDALQQHKLKRASDFNARSAALQSIQDSLGLADAPLRIECVDVSHVQGTDVVGSLVVFEDGLPRKSDYRHFGIREAAGQGRSDDVACIAEVTRRRFLRHLRDQSDPDLLSPERKSRRFAYPPNLYVVDGGAPQVNAASAVIDELGVTDVAVIGLAKRLEEVWVPSEPDPIIMPRNSEGLYLLQRVRDEAHRFAITYHRSKRSTRMTASALDSVPGLGEHRRKALVTHFGSIARLKEATVDEITAVPGIGVATATAVHDALRPDSSGAAR