Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
244-583
5.82e-72
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
:
Pssm-ID: 238445 [Multi-domain] Cd Length: 300 Bit Score: 234.11 E-value: 5.82e-72
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation ...
5-232
3.29e-46
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.
The actual alignment was detected with superfamily member pfam03731:
Pssm-ID: 469594 Cd Length: 220 Bit Score: 162.53 E-value: 3.29e-46
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
244-583
5.82e-72
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
Pssm-ID: 238445 [Multi-domain] Cd Length: 300 Bit Score: 234.11 E-value: 5.82e-72
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
5-232
3.29e-46
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold.
Pssm-ID: 427470 Cd Length: 220 Bit Score: 162.53 E-value: 3.29e-46
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to ...
3-212
7.00e-42
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Pssm-ID: 238735 Cd Length: 218 Bit Score: 150.98 E-value: 7.00e-42
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single ...
307-453
1.60e-41
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single stranded DNA- and ATP-depedent helicase that has a role in chromosome translocation. This is a domain of unknown function C-terminal to its von Willebrand factor A domain, that also occurs in bacterial hypothetical proteins.
Pssm-ID: 128831 [Multi-domain] Cd Length: 140 Bit Score: 147.05 E-value: 1.60e-41
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
238-456
1.87e-24
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 and Ku80 proteins that form a DNA binding heterodimer.
Pssm-ID: 460669 Cd Length: 197 Bit Score: 101.17 E-value: 1.87e-24
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in ...
299-447
5.13e-04
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273151 [Multi-domain] Cd Length: 586 Bit Score: 42.96 E-value: 5.13e-04
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
244-583
5.82e-72
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
Pssm-ID: 238445 [Multi-domain] Cd Length: 300 Bit Score: 234.11 E-value: 5.82e-72
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
5-232
3.29e-46
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold.
Pssm-ID: 427470 Cd Length: 220 Bit Score: 162.53 E-value: 3.29e-46
Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the ...
255-487
2.39e-42
Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen recognized by the sera of patients with an autoimmunity disease. In eukaryotes, the Ku heterodimer contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by non-homologous end-joining. The bacterial Ku homologs does not contain the conserved N-terminal extension that is present in the eukaryotic Ku protein.
Pssm-ID: 238334 [Multi-domain] Cd Length: 272 Bit Score: 153.97 E-value: 2.39e-42
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to ...
3-212
7.00e-42
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Pssm-ID: 238735 Cd Length: 218 Bit Score: 150.98 E-value: 7.00e-42
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single ...
307-453
1.60e-41
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single stranded DNA- and ATP-depedent helicase that has a role in chromosome translocation. This is a domain of unknown function C-terminal to its von Willebrand factor A domain, that also occurs in bacterial hypothetical proteins.
Pssm-ID: 128831 [Multi-domain] Cd Length: 140 Bit Score: 147.05 E-value: 1.60e-41
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
238-456
1.87e-24
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 and Ku80 proteins that form a DNA binding heterodimer.
Pssm-ID: 460669 Cd Length: 197 Bit Score: 101.17 E-value: 1.87e-24
Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in ...
307-452
6.11e-16
Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in the nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
Pssm-ID: 238407 [Multi-domain] Cd Length: 287 Bit Score: 78.48 E-value: 6.11e-16
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in ...
299-447
5.13e-04
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273151 [Multi-domain] Cd Length: 586 Bit Score: 42.96 E-value: 5.13e-04
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
