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Conserved domains on  [gi|392896661|ref|NP_499438|]
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Ku domain-containing protein [Caenorhabditis elegans]

Protein Classification

vWA_ku and KU70 domain-containing protein( domain architecture ID 10509362)

vWA_ku and KU70 domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
KU70 cd00788
Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in ...
241-583 4.81e-66

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: 219.07  E-value: 4.81e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 241 RSHATLTVNVGPG--VTFDVSVFSMVMEAKPldhSQKYTRDTEEKIVKTSgyVKKESK-MELESTeietqdsvldetqkm 317
Cdd:cd00788    1 RALFRLPLELGPGnkLVISVKGYSLVSHAKK---PRKYKLDREKNEERRE--VKSKRKfFDVESG--------------- 60
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 318 lircKFLEDSirnrrDLKKSIEIGGEKIILDGDQYEYMNEVNSKGVDFVGFCSMSRVDRETSVVSSKIIQPNDQTTLGST 397
Cdd:cd00788   61 ----KTLEKA-----DIKKGYKIGGEKIIFTKEELKKIKSFGEPGLRLIGFKPRSTLKPYHNIKKSYFIYPDESDYKGST 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 398 AIYRTFLDRCWARQQAIVCKYQSRSKQKMRLMALVPFKKDMTliekrhengeddddmedkkpdllrleqqraqADSSEWL 477
Cdd:cd00788  132 RLFAALLRSCLKKNKVAICWYILRKNSPPRLVALVPQEEELD-------------------------------EPDGQVL 180
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 478 HEGFMLVGQPFREELRDDFKRFEEqqNVLTEPSTEEQVNTMKQFVKRLTM-SYNPSFYENPRLLSERSALCLEATGEELI 556
Cdd:cd00788  181 PPGFHLVPLPFADDIRKLPSLLEE--NASAESASDELVDKAKQIIKKLRLlSYDPDKFPNPSLQKHYKILEALALDEEDP 258
                        330       340
                 ....*....|....*....|....*....
gi 392896661 557 ERR-DTLEPYY-QIPKRLQRVGTEIEKIV 583
Cdd:cd00788  259 EKPdDLTLPDTeGIDKRLGDLIEEFKKLL 287
Ku_N pfam03731
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
20-243 2.70e-60

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: 201.43  E-value: 2.70e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   20 YTFFIIDGNPAMFETSKAGEPPeFKLALKLILDEIVRVCCSRSlNNHIGVIVTSTKNSE-TEGLENSTLLVPMGVLGQEE 98
Cdd:pfam03731   1 AILFVIDVSPAMFESSKLLEAP-FDMALKCIRELLKSKIISRD-KDLIGVVLYGTDNSEnSEGLPNITVLRDLDLPGAEL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   99 VNKIKEIAEEENLlsAVNNYGGDHHKSDLSNVLNYCKRVFA-SCSNTRHQSVIYLTNNRNPFERDDFLESSHFKRTkaav 177
Cdd:pfam03731  79 ILELDQFVESFGR--DVRGFSGDSSDGSLLSALWVCLELLQkTGKKLSHKRIFLFTDLDDPFEDQDKLDIALQRLL---- 152
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392896661  178 tkiiGEGHRKTLGEFSVIML-------PEDGYKPQDKDEKRKEPWYDLDTEVFStECDAAARIRQKITAQRSH 243
Cdd:pfam03731 153 ----AEDLRDTRGEFDLIHLpnadgfdPNLFYKDIIKLGSDEVLNVMLDLEGQK-LEDLLAKIRAKKTAKRAH 220
 
Name Accession Description Interval E-value
KU70 cd00788
Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in ...
241-583 4.81e-66

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: 219.07  E-value: 4.81e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 241 RSHATLTVNVGPG--VTFDVSVFSMVMEAKPldhSQKYTRDTEEKIVKTSgyVKKESK-MELESTeietqdsvldetqkm 317
Cdd:cd00788    1 RALFRLPLELGPGnkLVISVKGYSLVSHAKK---PRKYKLDREKNEERRE--VKSKRKfFDVESG--------------- 60
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 318 lircKFLEDSirnrrDLKKSIEIGGEKIILDGDQYEYMNEVNSKGVDFVGFCSMSRVDRETSVVSSKIIQPNDQTTLGST 397
Cdd:cd00788   61 ----KTLEKA-----DIKKGYKIGGEKIIFTKEELKKIKSFGEPGLRLIGFKPRSTLKPYHNIKKSYFIYPDESDYKGST 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 398 AIYRTFLDRCWARQQAIVCKYQSRSKQKMRLMALVPFKKDMTliekrhengeddddmedkkpdllrleqqraqADSSEWL 477
Cdd:cd00788  132 RLFAALLRSCLKKNKVAICWYILRKNSPPRLVALVPQEEELD-------------------------------EPDGQVL 180
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 478 HEGFMLVGQPFREELRDDFKRFEEqqNVLTEPSTEEQVNTMKQFVKRLTM-SYNPSFYENPRLLSERSALCLEATGEELI 556
Cdd:cd00788  181 PPGFHLVPLPFADDIRKLPSLLEE--NASAESASDELVDKAKQIIKKLRLlSYDPDKFPNPSLQKHYKILEALALDEEDP 258
                        330       340
                 ....*....|....*....|....*....
gi 392896661 557 ERR-DTLEPYY-QIPKRLQRVGTEIEKIV 583
Cdd:cd00788  259 EKPdDLTLPDTeGIDKRLGDLIEEFKKLL 287
Ku_N pfam03731
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
20-243 2.70e-60

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: 201.43  E-value: 2.70e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   20 YTFFIIDGNPAMFETSKAGEPPeFKLALKLILDEIVRVCCSRSlNNHIGVIVTSTKNSE-TEGLENSTLLVPMGVLGQEE 98
Cdd:pfam03731   1 AILFVIDVSPAMFESSKLLEAP-FDMALKCIRELLKSKIISRD-KDLIGVVLYGTDNSEnSEGLPNITVLRDLDLPGAEL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   99 VNKIKEIAEEENLlsAVNNYGGDHHKSDLSNVLNYCKRVFA-SCSNTRHQSVIYLTNNRNPFERDDFLESSHFKRTkaav 177
Cdd:pfam03731  79 ILELDQFVESFGR--DVRGFSGDSSDGSLLSALWVCLELLQkTGKKLSHKRIFLFTDLDDPFEDQDKLDIALQRLL---- 152
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392896661  178 tkiiGEGHRKTLGEFSVIML-------PEDGYKPQDKDEKRKEPWYDLDTEVFStECDAAARIRQKITAQRSH 243
Cdd:pfam03731 153 ----AEDLRDTRGEFDLIHLpnadgfdPNLFYKDIIKLGSDEVLNVMLDLEGQK-LEDLLAKIRAKKTAKRAH 220
vWA_ku cd01458
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to ...
18-302 3.88e-41

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: 149.44  E-value: 3.88e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  18 KKYTFFIIDGNPAMFETSKAGEPPEFKLALKLILDEIVRVCCSRSlNNHIGVIVTSTKNSET-EGLENSTLLVPMGVLGQ 96
Cdd:cd01458    1 KESVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSP-KDLVGVVFYGTEESKNpVGYENIYVLLDLDTPGA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  97 EEVNKIKEIAEEENLLSAvnNYGGDHHKSDLSNVLNYCKRVFASC-SNTRHQSVIYLTNNRNPFErddflessHFKRTKA 175
Cdd:cd01458   80 ERVEDLKELIEPGGLSFA--GQVGDSGQVSLSDALWVCLDLFSKGkKKKSHKRIFLFTNNDDPHG--------GDSIKDS 149
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 176 AVTKIIGEGHRKtLGEFSVIMLPEDGYKpqdkdekrkepwydldtevfstecdaaarirqkitaqrshatltvnvgpgvt 255
Cdd:cd01458  150 QAAVKAEDLKDK-GIELELFPLSSPGKK---------------------------------------------------- 176
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 392896661 256 FDVSVFSMVMEAKPLDHsqkytRDTEEKIVKTSGYVKKESKMELEST 302
Cdd:cd01458  177 FDVSKFYKDIIALVEDA-----NEELLDEFTEPSKDLEDLLKRLRAK 218
Ku pfam02735
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
251-516 1.79e-25

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: 104.25  E-value: 1.79e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  251 GPGVTFDVSVFSMVMEAKPLDHSQKYTRDTEEKIVKTSgYVKKESKMELESTEIetqdsvldetqkmlirckfledsirn 330
Cdd:pfam02735   2 GGLVSIPVKLYSATEEEKKPSFKKLDRETNDGVRIKYK-YVCEDTGKEVEKEDI-------------------------- 54
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  331 rrdlKKSIEIGGEKIILDGDQYEYMNEVNSKGVDFVGFCSMSRVDRET-SVVSSKIIQPNDQTTLGSTAIYRTFLDRCWA 409
Cdd:pfam02735  55 ----VKGYEYGGTYVPLSDEELEELKPESTKGLDLLGFVPLDEIDPIYfMGDKSYFLYPDKGDIAGSTKAFSALREALLE 130
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  410 RQQAIVCKYQSRSKQKMRLMALVPFKKDmtliekrhengeddddmedkkpdllrleqqraqadssewLHEGFMLVGQPFR 489
Cdd:pfam02735 131 TDKVAIARFVLRRREHPRLVALRPQEEE---------------------------------------PDPGLVLITLPFA 171
                         250       260
                  ....*....|....*....|....*..
gi 392896661  490 EELRDDFkrFEEQQNVLTEPSTEEQVN 516
Cdd:pfam02735 172 DDVREEF--FPIPSLLEKPKPTEEQLD 196
ku70 TIGR00578
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in ...
12-669 4.06e-25

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: 110.37  E-value: 4.06e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   12 EGSTANKKYT-----FFIIDGNPAMFETSKAGEP-PEFKLALKLILDEIVRVCCSrSLNNHIGVIVTST-KNSETEGLEN 84
Cdd:TIGR00578   1 PEATGDYKYSgrdslIFLVDASKAMFEESQGEDElTPFDMSIQCIQSVYTSKIIS-SDKDLLAVVFYGTeKDKNSVNFKN 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   85 STLLVPMGVLGQEEVNKIKEIAEEENLLSAVNNYGgdhHKSD--LSNVLNYCKRVFA-SCSNTRHQSVIYLTNNRNPFER 161
Cdd:TIGR00578  80 IYVLQDLDNPGAKRVLELDQFKGDQGPKKFRDTYG---HGSDysLSEVLWVCANLFSdVQVRMSHKRIMLFTNEDDPHGN 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  162 DDFLESShfKRTKAAVTK----IIGEGHRKTLGEFSVIMLPEDGYKPQDKDEKRKEPwydldtEVFSTECDAAARIRQKI 237
Cdd:TIGR00578 157 DSAKASR--ARTKAGDLRdtgiFLDLMHLKKPGGFDISLFYRDIITDAEDEDLGVHP------EESSKLEDLLRKVRAKE 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  238 TAQRSHATLTVNVGPGVTFDVSVFSMVMEA-KPldHSQKYTRDTEEKI-VKTSGYVKKESKMELESteietqdsvldetq 315
Cdd:TIGR00578 229 TKKRALSRLKFKLGKDVVMSVGIYNLVQKAgKP--APVRLYRETNEPVkTKTRTFNMDTGSLLLPS-------------- 292
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  316 kmlirckfledsirnrrDLKKSIEIGGEKIILDGDQYEYMNEVNSKGVDFVGFCSMSRVDRETSVVSSKIIQPNDQTTLG 395
Cdd:TIGR00578 293 -----------------DTKRSQTYGGRQIYLEKEETEELKRFDPPGLQLMGFKPLSMLKKQHHLRPSLFVYPEESLVRG 355
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  396 STAIYRTFLDRCWARQQAIVCKYQSRSKQKMRLMALVPFKKDmtliekrhengeddddmedkkpdllrLEQQRAQADSSe 475
Cdd:TIGR00578 356 STTLFSALLQKCLEKEVAALCRYISRRNQPPYFVALVPQEEE--------------------------LDDQKIQVTPP- 408
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  476 wlheGFMLVGQPFreelRDDFKRFEEQQNVltePSTEEQVNTMKQFVKRLTMSYNPSFYENPRLLSERSalCLEATGEEL 555
Cdd:TIGR00578 409 ----GFHLVFLPF----ADDKRKVPFTEKV---KATPEQVDKMKAIVEKLRFTYRSDSFENPVLQQHFR--NLEALALDM 475
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  556 IER---RDTLEPYYQIPKRlqRVGTEIEKIVETFALNDEIKETKpkasaGRKRKtDDDEPSTSKKATM-----TIRDCIA 627
Cdd:TIGR00578 476 MEPeqaVDLTLPKVEAMKK--RLGSLVDEFKELVYPPGYNPEGK-----VAKRK-QAGEGSQSKKPKVenseeELREHAK 547
                         650       660       670       680
                  ....*....|....*....|....*....|....*....|..
gi 392896661  628 ADKIGKFKkdelLSMAVEHCEASKSLKSKTKNDIIAVIEAYL 669
Cdd:TIGR00578 548 KGTLGKLT----VSVLKDFCKAYGLRSGSKKQELLDALTKHL 585
Ku78 smart00559
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single ...
331-433 7.62e-13

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: 66.16  E-value: 7.62e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   331 RRDLKKSIEIGGEKIILDGDQYEYMNEVNSKGVDFVGFCSMSRVDRETSVVSSKIIQPNDQTTLGSTAIYRTFLDRCWAR 410
Cdd:smart00559   6 PEDIVKGYEYGGRYVPLSDEELEQLKYKSEPGLELLGFKPLSSLPPYYFLRPSYFLVPDDKSVIGSTKAFSALVEALLET 85
                           90       100
                   ....*....|....*....|...
gi 392896661   411 QQAIVCKYQSRSKQKMRLMALVP 433
Cdd:smart00559  86 DKIAIARYTLRTKSNPRLVALRP 108
 
Name Accession Description Interval E-value
KU70 cd00788
Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in ...
241-583 4.81e-66

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: 219.07  E-value: 4.81e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 241 RSHATLTVNVGPG--VTFDVSVFSMVMEAKPldhSQKYTRDTEEKIVKTSgyVKKESK-MELESTeietqdsvldetqkm 317
Cdd:cd00788    1 RALFRLPLELGPGnkLVISVKGYSLVSHAKK---PRKYKLDREKNEERRE--VKSKRKfFDVESG--------------- 60
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 318 lircKFLEDSirnrrDLKKSIEIGGEKIILDGDQYEYMNEVNSKGVDFVGFCSMSRVDRETSVVSSKIIQPNDQTTLGST 397
Cdd:cd00788   61 ----KTLEKA-----DIKKGYKIGGEKIIFTKEELKKIKSFGEPGLRLIGFKPRSTLKPYHNIKKSYFIYPDESDYKGST 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 398 AIYRTFLDRCWARQQAIVCKYQSRSKQKMRLMALVPFKKDMTliekrhengeddddmedkkpdllrleqqraqADSSEWL 477
Cdd:cd00788  132 RLFAALLRSCLKKNKVAICWYILRKNSPPRLVALVPQEEELD-------------------------------EPDGQVL 180
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 478 HEGFMLVGQPFREELRDDFKRFEEqqNVLTEPSTEEQVNTMKQFVKRLTM-SYNPSFYENPRLLSERSALCLEATGEELI 556
Cdd:cd00788  181 PPGFHLVPLPFADDIRKLPSLLEE--NASAESASDELVDKAKQIIKKLRLlSYDPDKFPNPSLQKHYKILEALALDEEDP 258
                        330       340
                 ....*....|....*....|....*....
gi 392896661 557 ERR-DTLEPYY-QIPKRLQRVGTEIEKIV 583
Cdd:cd00788  259 EKPdDLTLPDTeGIDKRLGDLIEEFKKLL 287
Ku_N pfam03731
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
20-243 2.70e-60

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: 201.43  E-value: 2.70e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   20 YTFFIIDGNPAMFETSKAGEPPeFKLALKLILDEIVRVCCSRSlNNHIGVIVTSTKNSE-TEGLENSTLLVPMGVLGQEE 98
Cdd:pfam03731   1 AILFVIDVSPAMFESSKLLEAP-FDMALKCIRELLKSKIISRD-KDLIGVVLYGTDNSEnSEGLPNITVLRDLDLPGAEL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   99 VNKIKEIAEEENLlsAVNNYGGDHHKSDLSNVLNYCKRVFA-SCSNTRHQSVIYLTNNRNPFERDDFLESSHFKRTkaav 177
Cdd:pfam03731  79 ILELDQFVESFGR--DVRGFSGDSSDGSLLSALWVCLELLQkTGKKLSHKRIFLFTDLDDPFEDQDKLDIALQRLL---- 152
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392896661  178 tkiiGEGHRKTLGEFSVIML-------PEDGYKPQDKDEKRKEPWYDLDTEVFStECDAAARIRQKITAQRSH 243
Cdd:pfam03731 153 ----AEDLRDTRGEFDLIHLpnadgfdPNLFYKDIIKLGSDEVLNVMLDLEGQK-LEDLLAKIRAKKTAKRAH 220
vWA_ku cd01458
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to ...
18-302 3.88e-41

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: 149.44  E-value: 3.88e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  18 KKYTFFIIDGNPAMFETSKAGEPPEFKLALKLILDEIVRVCCSRSlNNHIGVIVTSTKNSET-EGLENSTLLVPMGVLGQ 96
Cdd:cd01458    1 KESVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSP-KDLVGVVFYGTEESKNpVGYENIYVLLDLDTPGA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  97 EEVNKIKEIAEEENLLSAvnNYGGDHHKSDLSNVLNYCKRVFASC-SNTRHQSVIYLTNNRNPFErddflessHFKRTKA 175
Cdd:cd01458   80 ERVEDLKELIEPGGLSFA--GQVGDSGQVSLSDALWVCLDLFSKGkKKKSHKRIFLFTNNDDPHG--------GDSIKDS 149
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 176 AVTKIIGEGHRKtLGEFSVIMLPEDGYKpqdkdekrkepwydldtevfstecdaaarirqkitaqrshatltvnvgpgvt 255
Cdd:cd01458  150 QAAVKAEDLKDK-GIELELFPLSSPGKK---------------------------------------------------- 176
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 392896661 256 FDVSVFSMVMEAKPLDHsqkytRDTEEKIVKTSGYVKKESKMELEST 302
Cdd:cd01458  177 FDVSKFYKDIIALVEDA-----NEELLDEFTEPSKDLEDLLKRLRAK 218
KU cd00594
Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the ...
241-583 4.59e-36

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: 137.02  E-value: 4.59e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 241 RSHATLTVNVGPGVTFDVSVFSMVMEAKPLDHSQKYTRDTEEKIVKTSgyvkkesKMELESTEIEtqdsvldetqkmlir 320
Cdd:cd00594    1 RAIWKGALSLGLDVSIPVKLYSAATEEKPPSFKQLDRKTGERVKVKRV-------CKYTGGKEVE--------------- 58
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 321 ckfledsirnRRDLKKSIEIGGEKIILDGDQYEYMNEVNSKGVDFVGFCSMSRVDRETSVVSSKIIQPNDQTTlGSTAIY 400
Cdd:cd00594   59 ----------KEDIVKGYEYGGDYVPLTEEELEQLKLETSKGLDILGFVPASEIPPYYFDKESYYLVPDDSDK-GSEKAF 127
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 401 RTFLDRCWARQQAIVCKYQSRSKQKMRLMALVPFKKDmtliekrhengeddddmedkkpdllrleqqraqadssewLHEG 480
Cdd:cd00594  128 SALRRALLEKDKVAIARYVLRRNSRPRLVALRPQEEE---------------------------------------DPEG 168
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661 481 FMLVGQPFREELRDDfkRFEEQQNVLTEPSTEEQVNTMKQFVKRLTM-SYNPSFYENPRLLSERSALCLEATGEELIERR 559
Cdd:cd00594  169 LVLVTLPFADDVRSY--PFPLLLDIKTEKPTDEELELAKQLIDSLDLdDFDPEKFPNPYLQRLYALLEAKALGEEIPEPP 246
                        330       340
                 ....*....|....*....|....*.
gi 392896661 560 D--TLEPYYQIPKRLQRVGTEIEKIV 583
Cdd:cd00594  247 EdlTLPPPEEIPKRVIDLLEALKKSL 272
Ku pfam02735
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
251-516 1.79e-25

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: 104.25  E-value: 1.79e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  251 GPGVTFDVSVFSMVMEAKPLDHSQKYTRDTEEKIVKTSgYVKKESKMELESTEIetqdsvldetqkmlirckfledsirn 330
Cdd:pfam02735   2 GGLVSIPVKLYSATEEEKKPSFKKLDRETNDGVRIKYK-YVCEDTGKEVEKEDI-------------------------- 54
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  331 rrdlKKSIEIGGEKIILDGDQYEYMNEVNSKGVDFVGFCSMSRVDRET-SVVSSKIIQPNDQTTLGSTAIYRTFLDRCWA 409
Cdd:pfam02735  55 ----VKGYEYGGTYVPLSDEELEELKPESTKGLDLLGFVPLDEIDPIYfMGDKSYFLYPDKGDIAGSTKAFSALREALLE 130
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  410 RQQAIVCKYQSRSKQKMRLMALVPFKKDmtliekrhengeddddmedkkpdllrleqqraqadssewLHEGFMLVGQPFR 489
Cdd:pfam02735 131 TDKVAIARFVLRRREHPRLVALRPQEEE---------------------------------------PDPGLVLITLPFA 171
                         250       260
                  ....*....|....*....|....*..
gi 392896661  490 EELRDDFkrFEEQQNVLTEPSTEEQVN 516
Cdd:pfam02735 172 DDVREEF--FPIPSLLEKPKPTEEQLD 196
ku70 TIGR00578
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in ...
12-669 4.06e-25

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: 110.37  E-value: 4.06e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   12 EGSTANKKYT-----FFIIDGNPAMFETSKAGEP-PEFKLALKLILDEIVRVCCSrSLNNHIGVIVTST-KNSETEGLEN 84
Cdd:TIGR00578   1 PEATGDYKYSgrdslIFLVDASKAMFEESQGEDElTPFDMSIQCIQSVYTSKIIS-SDKDLLAVVFYGTeKDKNSVNFKN 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   85 STLLVPMGVLGQEEVNKIKEIAEEENLLSAVNNYGgdhHKSD--LSNVLNYCKRVFA-SCSNTRHQSVIYLTNNRNPFER 161
Cdd:TIGR00578  80 IYVLQDLDNPGAKRVLELDQFKGDQGPKKFRDTYG---HGSDysLSEVLWVCANLFSdVQVRMSHKRIMLFTNEDDPHGN 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  162 DDFLESShfKRTKAAVTK----IIGEGHRKTLGEFSVIMLPEDGYKPQDKDEKRKEPwydldtEVFSTECDAAARIRQKI 237
Cdd:TIGR00578 157 DSAKASR--ARTKAGDLRdtgiFLDLMHLKKPGGFDISLFYRDIITDAEDEDLGVHP------EESSKLEDLLRKVRAKE 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  238 TAQRSHATLTVNVGPGVTFDVSVFSMVMEA-KPldHSQKYTRDTEEKI-VKTSGYVKKESKMELESteietqdsvldetq 315
Cdd:TIGR00578 229 TKKRALSRLKFKLGKDVVMSVGIYNLVQKAgKP--APVRLYRETNEPVkTKTRTFNMDTGSLLLPS-------------- 292
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  316 kmlirckfledsirnrrDLKKSIEIGGEKIILDGDQYEYMNEVNSKGVDFVGFCSMSRVDRETSVVSSKIIQPNDQTTLG 395
Cdd:TIGR00578 293 -----------------DTKRSQTYGGRQIYLEKEETEELKRFDPPGLQLMGFKPLSMLKKQHHLRPSLFVYPEESLVRG 355
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  396 STAIYRTFLDRCWARQQAIVCKYQSRSKQKMRLMALVPFKKDmtliekrhengeddddmedkkpdllrLEQQRAQADSSe 475
Cdd:TIGR00578 356 STTLFSALLQKCLEKEVAALCRYISRRNQPPYFVALVPQEEE--------------------------LDDQKIQVTPP- 408
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  476 wlheGFMLVGQPFreelRDDFKRFEEQQNVltePSTEEQVNTMKQFVKRLTMSYNPSFYENPRLLSERSalCLEATGEEL 555
Cdd:TIGR00578 409 ----GFHLVFLPF----ADDKRKVPFTEKV---KATPEQVDKMKAIVEKLRFTYRSDSFENPVLQQHFR--NLEALALDM 475
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  556 IER---RDTLEPYYQIPKRlqRVGTEIEKIVETFALNDEIKETKpkasaGRKRKtDDDEPSTSKKATM-----TIRDCIA 627
Cdd:TIGR00578 476 MEPeqaVDLTLPKVEAMKK--RLGSLVDEFKELVYPPGYNPEGK-----VAKRK-QAGEGSQSKKPKVenseeELREHAK 547
                         650       660       670       680
                  ....*....|....*....|....*....|....*....|..
gi 392896661  628 ADKIGKFKkdelLSMAVEHCEASKSLKSKTKNDIIAVIEAYL 669
Cdd:TIGR00578 548 KGTLGKLT----VSVLKDFCKAYGLRSGSKKQELLDALTKHL 585
Ku_C pfam03730
Ku70/Ku80 C-terminal arm; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
528-618 3.55e-14

Ku70/Ku80 C-terminal arm; 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 C terminal arm. This alpha helical region embraces the beta-barrel domain pfam02735 of the opposite subunit.


Pssm-ID: 461029  Cd Length: 79  Bit Score: 68.07  E-value: 3.55e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661  528 SYNPSFYENPRLLSERSALCLEATGEELIErrdtlEPYYQIPKRLQRVGTEIEKIVETFALNDEIKETKPKasagrkrkt 607
Cdd:pfam03730   1 SYNPDKFPNPSLQRHYQNLQALALDEDEPE-----EPEDLTLPKYEAIDKRIGKLLEEFKELFELEDYKPD--------- 66
                          90
                  ....*....|.
gi 392896661  608 DDDEPSTSKKA 618
Cdd:pfam03730  67 EDEEGPAAKKA 77
Ku78 smart00559
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single ...
331-433 7.62e-13

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: 66.16  E-value: 7.62e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896661   331 RRDLKKSIEIGGEKIILDGDQYEYMNEVNSKGVDFVGFCSMSRVDRETSVVSSKIIQPNDQTTLGSTAIYRTFLDRCWAR 410
Cdd:smart00559   6 PEDIVKGYEYGGRYVPLSDEELEQLKYKSEPGLELLGFKPLSSLPPYYFLRPSYFLVPDDKSVIGSTKAFSALVEALLET 85
                           90       100
                   ....*....|....*....|...
gi 392896661   411 QQAIVCKYQSRSKQKMRLMALVP 433
Cdd:smart00559  86 DKIAIARYTLRTKSNPRLVALRP 108
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
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