uvrA Family assigned · medium auto-curated
H37Rv Rv1638 · MTBC0 mtbc0_001746 ·
972 aa · 1855762–1858680 (+) ·
RefSeq NP_216154.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | excinuclease ABC subunit UvrA |
|---|---|
| MTBC0 PGAP re-annotation | excinuclease ABC subunit UvrA |
| Revised (this work) | Excinuclease ABC subunit UvrA. Pfam: UvrA_inter (PF17760.7), UvrA_DNA-bind (PF17755.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQK7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UvrABC system protein A |
| Curated function | The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate. Alone it slightly inhibits RecA-mediated DNA strand exchange, in concert with UvrD1 greatly inhibits RecA-mediated DNA strand exchange. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | uvrA |
| eggNOG description | The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate |
| Orthologous group | COG0178 |
| KEGG orthology |
K03701
|
| KEGG pathways |
map03420
|
| Gene Ontology (42) |
GO:0000018, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006950, GO:0006974, GO:0008150, GO:0009892 +30 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 | 0.392 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 10 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 |
|---|---|---|---|---|
UvrA_inter | PF17760.7 | 5.5e-40 | 131–238 | UvrA interaction domain |
UvrA_DNA-bind | PF17755.7 | 4.9e-35 | 295–404 | UvrA DNA-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uvrB (excinuclease ABC subunit UvrB), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1633 uvrB |
excinuclease ABC subunit UvrB | 999 | 998 ctx | cooccurence:773 coexpression:836 experimental:928 textmining:979 |
Rv1020 mfd |
transcription-repair coupling factor | 975 | 918 | experimental:912 textmining:716 |
Rv1420 uvrC |
excinuclease ABC subunit UvrC | 995 | 876 ctx | cooccurence:697 textmining:962 |
Rv1637c hyp |
hypothetical protein | 796 | 789 ctx | neighborhood:788 |
Rv2191 hyp |
hypothetical protein | 746 | 662 | |
Rv0949 uvrD1 |
ATP-dependent DNA helicase UvrD | 969 | 639 ctx | cooccurence:413 textmining:920 |
Rv2737c recA |
recombinase A | 915 | 584 | coexpression:442 textmining:806 |
Rv3198c uvrD2 |
ATP-dependent DNA helicase UvrD | 876 | 580 | textmining:717 |
Rv2373c dnaJ2 |
chaperone protein DnaJ | 622 | 572 | |
Rv3859c gltB |
glutamate synthase large subunit | 770 | 547 ctx | neighborhood:544 textmining:515 |
Rv2592c ruvB |
Holliday junction ATP-dependent DNA helicase RuvB | 887 | 502 ctx | cooccurence:457 textmining:783 |
Rv1297 rho |
transcription termination factor Rho | 533 | 457 | coexpression:426 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 480 | 447 | coexpression:429 |
Rv3014c ligA |
DNA ligase A | 673 | 446 | textmining:434 |
Rv0352 dnaJ1 |
chaperone protein DnaJ | 510 | 444 |
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 UvrA
- MTBC0 PGAP product: excinuclease ABC subunit UvrA
- Pfam (hmmscan --cut_ga): UvrA_inter PF17760.7 (E=6e-40), UvrA_DNA-bind PF17755.7 (E=5e-35)
- (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_216154.1)
- Domains: Pfam-A via hmmscan --cut_ga — UvrA_inter (PF17760.7), UvrA_DNA-bind (PF17755.7)
- 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
COG0178 - Curated reference: UniProt P9WQK7 (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 —
73 functional partner(s); context anchor
uvrB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001746|Rv1638|uvrA MADRLIVKGAREHNLRSVDLDLPRDALIVFTGLSGSGKSSLAFDTIFAEGQRRYVESLSAYARQFLGQMDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEVYDYLRLLYARAGTPHCPTCGERVARQTPQQIVDQVLAMPEGTRFLVLAPVVRTRKGEFADLFDKLNAQGYSRVRVDGVVHPLTDPPKLKKQEKHDIEVVVDRLTVKAAAKRRLTDSVETALNLADGIVVLEFVDHELGAPHREQRFSEKLACPNGHALAVDDLEPRSFSFNSPYGACPECSGLGIRKEVDPELVVPDPDRTLAQGAVAPWSNGHTAEYFTRMMAGLGEALGFDVDTPWRKLPAKARKAILEGADEQVHVRYRNRYGRTRSYYADFEGVLAFLQRKMSQTESEQMKERYEGFMRDVPCPVCAGTRLKPEILAVTLAGESKGEHGAKSIAEVCELSIADCADFLNALTLGPREQAIAGQVLKEIRSRLGFLLDVGLEYLSLSRAAATLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLTRLRDLGNTLIVVEHDEDTIEHADWIVDIGPGAGEHGGRIVHSGPYDELLRNKDSITGAYLSGRESIEIPAIRRSVDPRRQLTVVGAREHNLRGIDVSFPLGVLTSVTGVSGSGKSTLVNDILAAVLANRLNGARQVPGRHTRVTGLDYLDKLVRVDQSPIGRTPRSNPATYTGVFDKIRTLFAATTEAKVRGYQPGRFSFNVKGGRCEACTGDGTIKIEMNFLPDVYVPCEVCQGARYNRETLEVHYKGKTVSEVLDMSIEEAAEFFEPIAGVHRYLRTLVDVGLGYVRLGQPAPTLSGGEAQRVKLASELQKRSTGRTVYILDEPTTGLHFDDIRKLLNVINGLVDKGNTVIVIEHNLDVIKTSDWIIDLGPEGGAGGGTVVAQGTPEDVAAVPASYTGKFLAEVVGGGASAATSRSNRRRNVSA