uvrB Family assigned · medium auto-curated
H37Rv Rv1633 · MTBC0 - ·
698 aa · 1837075–1839171 (+) ·
RefSeq NP_216149.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | excinuclease ABC subunit UvrB |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Excinuclease ABC subunit UvrB. Pfam: ResIII (PF04851.22), DEAD (PF00270.36), UvrB_inter (PF17757.7), UvrB_3rd (PF27431.1), Helicase_C (PF00271.38), UvrB (PF12344.15), UVR (PF02151.26). |
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 |
P9WFC7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UvrABC system protein B |
| Curated function | The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | uvrB |
| eggNOG description | damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage |
| Orthologous group | COG0556 |
| KEGG orthology |
K03702
|
| KEGG pathways |
map03420
|
| Gene Ontology (41) |
GO:0002682, GO:0002684, GO:0005575, GO:0005623, GO:0005886, GO:0006950, GO:0008150, GO:0009605, GO:0009607, GO:0016020, GO:0035821, GO:0043207 +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 | 0.314 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 12 synonymous, 11 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 |
|---|---|---|---|---|
ResIII | PF04851.22 | 3.2e-09 | 18–89 | Type III restriction enzyme, res subunit |
DEAD | PF00270.36 | 2.3e-06 | 19–92 | DEAD/DEAH box helicase |
UvrB_inter | PF17757.7 | 6.9e-33 | 161–250 | UvrB interaction domain |
UvrB_3rd | PF27431.1 | 6.8e-30 | 255–316 | UvrB third helical domain |
Helicase_C | PF00271.38 | 1.4e-18 | 435–546 | Helicase conserved C-terminal domain |
UvrB | PF12344.15 | 4.5e-22 | 553–594 | Ultra-violet resistance protein B |
UVR | PF02151.26 | 7.5e-07 | 655–687 | UvrB/uvrC motif |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uvrA (excinuclease ABC subunit UvrA), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1638 uvrA |
excinuclease ABC subunit UvrA | 999 | 998 ctx | cooccurence:773 coexpression:836 experimental:928 textmining:979 |
Rv1420 uvrC |
excinuclease ABC subunit UvrC | 999 | 988 ctx | cooccurence:750 coexpression:654 experimental:772 textmining:965 |
Rv2191 hyp |
hypothetical protein | 977 | 967 | coexpression:670 experimental:772 |
Rv1634 |
multidrug-efflux transporter | 889 | 889 ctx | neighborhood:882 |
Rv0949 uvrD1 |
ATP-dependent DNA helicase UvrD | 984 | 719 | experimental:564 textmining:948 |
Rv3198c uvrD2 |
ATP-dependent DNA helicase UvrD | 931 | 690 | experimental:564 textmining:788 |
Rv3202c adnA |
ATP-dependent DNA helicase | 634 | 600 | experimental:564 |
Rv3201c adnB |
ATP-dependent DNA helicase | 625 | 590 | experimental:564 |
Rv1632c hyp |
hypothetical protein | 566 | 566 ctx | neighborhood:563 |
Rv2737c recA |
recombinase A | 933 | 557 | coexpression:443 textmining:856 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 767 | 503 ctx | neighborhood:409 textmining:552 |
Rv3585 radA |
DNA repair protein RadA | 666 | 482 | coexpression:407 |
Rv2756c hsdM |
type I restriction/modification system DNA methylase HsdM | 502 | 473 | experimental:464 |
Rv1629 polA |
DNA polymerase I | 802 | 472 | textmining:641 |
Rv3056 dinP |
DNA polymerase IV 2 | 743 | 471 | textmining:535 |
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): excinuclease ABC subunit UvrB
- Pfam (hmmscan --cut_ga): ResIII PF04851.22 (E=3e-09), DEAD PF00270.36 (E=2e-06), UvrB_inter PF17757.7 (E=7e-33), UvrB_3rd PF27431.1 (E=7e-30), Helicase_C PF00271.38 (E=1e-18), UvrB PF12344.15 (E=4e-22), UVR PF02151.26 (E=8e-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 NP_216149.3)
- Domains: Pfam-A via hmmscan --cut_ga — ResIII (PF04851.22), DEAD (PF00270.36), UvrB_inter (PF17757.7), UvrB_3rd (PF27431.1), Helicase_C (PF00271.38), UvrB (PF12344.15), UVR (PF02151.26)
- 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
COG0556 - Curated reference: UniProt P9WFC7 (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 —
72 functional partner(s); context anchor
uvrA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1633|uvrB MRAGGHFEVVSPHAPAGDQPAAIDELERRINAGERDVVLLGATGTGKSATTAWLIERLQRPTLVMAPNKTLAAQLANELREMLPHNAVEYFVSYYDYYQPEAYIAQTDTYIEKDSSINDDVERLRHSATSALLSRRDVVVVASVSCIYGLGTPQSYLDRSVELKVGEEVPRDGLLRLLVDVQYTRNDMSFTRGSFRVRGDTVEIIPSYEELAVRIEFFGDEIEALYYLHPLTGEVIRQVDSLRIFPATHYVAGPERMAHAVSAIEEELAERLAELESQGKLLEAQRLRMRTNYDIEMMRQVGFCSGIENYSRHIDGRGPGTPPATLLDYFPEDFLLVIDESHVTVPQIGGMYEGDISRKRNLVEYGFRLPSACDNRPLTWEEFADRIGQTVYLSATPGPYELSQTGGEFVEQVIRPTGLVDPKVVVKPTKGQIDDLIGEIRTRADADQRVLVTTLTKKMAEDLTDYLLEMGIRVRYLHSEVDTLRRVELLRQLRLGDYDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSSRSLIQTIGRAARNVSGEVHMYADKITDSMREAIDETERRRAKQIAYNEANGIDPQPLRKKIADILDQVYREADDTAVVEVGGSGRNASRGRRAQGEPGRAVSAGVFEGRDTSAMPRAELADLIKDLTAQMMAAARDLQFELAARFRDEIADLKRELRGMDAAGLK