Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, ...
1-370
7.04e-122
Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.
Pssm-ID: 238082 [Multi-domain] Cd Length: 365 Bit Score: 356.05 E-value: 7.04e-122
DNA polymerase III, beta subunit; All proteins in this family for which functions are known ...
1-370
2.18e-94
DNA polymerase III, beta subunit; All proteins in this family for which functions are known are components of the DNA polymerase III complex (beta subunit). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273204 [Multi-domain] Cd Length: 367 Bit Score: 286.15 E-value: 2.18e-94
DNA polymerase III beta subunit, central domain; A dimer of the beta subunit of DNA polymerase ...
136-245
2.07e-33
DNA polymerase III beta subunit, central domain; A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.
Pssm-ID: 397061 [Multi-domain] Cd Length: 115 Bit Score: 120.10 E-value: 2.07e-33
Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, ...
1-370
7.04e-122
Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.
Pssm-ID: 238082 [Multi-domain] Cd Length: 365 Bit Score: 356.05 E-value: 7.04e-122
DNA polymerase III, beta subunit; All proteins in this family for which functions are known ...
1-370
2.18e-94
DNA polymerase III, beta subunit; All proteins in this family for which functions are known are components of the DNA polymerase III complex (beta subunit). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273204 [Multi-domain] Cd Length: 367 Bit Score: 286.15 E-value: 2.18e-94
DNA polymerase III beta subunit, central domain; A dimer of the beta subunit of DNA polymerase ...
136-245
2.07e-33
DNA polymerase III beta subunit, central domain; A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.
Pssm-ID: 397061 [Multi-domain] Cd Length: 115 Bit Score: 120.10 E-value: 2.07e-33
DNA polymerase III beta subunit, N-terminal domain; A dimer of the beta subunit of DNA ...
1-118
3.20e-31
DNA polymerase III beta subunit, N-terminal domain; A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.
Pssm-ID: 395580 [Multi-domain] Cd Length: 121 Bit Score: 114.70 E-value: 3.20e-31
DNA polymerase III beta subunit, C-terminal domain; A dimer of the beta subunit of DNA ...
258-369
1.05e-22
DNA polymerase III beta subunit, C-terminal domain; A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.
Pssm-ID: 426968 [Multi-domain] Cd Length: 118 Bit Score: 91.98 E-value: 1.05e-22
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These ...
161-345
2.45e-03
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].
Pssm-ID: 238322 [Multi-domain] Cd Length: 248 Bit Score: 39.15 E-value: 2.45e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
Click on the triangle to view details about the feature, including a multiple sequence alignment
of your query sequence and the protein sequences used to curate the domain model,
where hash marks (#) above the aligned sequences show the location of the conserved feature residues.
The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
Click here to see more details.
This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
(labeled illustration) or all hits
(labeled illustration).
Domains are color coded according to superfamilies
to which they have been assigned. Hits with scores that pass a domain-specific threshold
(specific hits) are drawn in bright colors.
Others (non-specific hits) and
superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features),
they are mapped to the query sequence and indicated through sets of triangles
with the same color and shade of the domain or superfamily that provides the annotation. Mouse over the colored bars or triangles to see descriptions of the domains and features.
click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
mapped to the query sequence.
Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
(CDART).
Modify your query to search against a different database and/or use advanced search options
