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Conserved domains on  [gi|1985421139|ref|XP_039351097|]
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X-ray repair cross-complementing protein 5 isoform X2 [Mauremys reevesii]

Protein Classification

ATP-dependent DNA helicase 2 subunit KU80( domain architecture ID 10208075)

ATP-dependent DNA helicase 2 subunit KU80 is part of a single-stranded DNA-dependent, ATP-dependent helicase involved in non-homologous end joining (NHEJ) DNA double strand break repair

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
KU80 cd00873
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
230-528 1.56e-126

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: 378.17  E-value: 1.56e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 230 PMPWPCQLTIGSNLSIRIVAYKSFTEEKLKKSWTLVDA-KTLKK--EDVQKETVYCLNDDDETEVPKDDLVQGFRYGSDI 306
Cdd:cd00873     1 VAAFKGQLTLGSPLSIAVELYKKTKEERPPKLKKVSDAeKTGEDafEDVKSERSYDVNDDDKTEVEKEDLIKGYRYGRDI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 307 VPFSKVDEEQMKYKTEaKCFSVLGFSRSSQIQRHHYMGnQVLKVFAAKDDEAAAVALSALIHALDELDVVAIVRYAYDRR 386
Cdd:cd00873    81 VPLSEEDEEATKLSTS-KGLDILGFIKASNVPRYYLMG-ESSYVVPQQDDEAAALAFSALVRALAELDKYAIARYVYKDN 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 387 ANPQVGVAFPCIKDAYECLIYVQLPYMEDLRQYMFSSLKNNK-KYTPTEDQLSAVDSLIDSMSLvyEDDDGETTEDIFKT 465
Cdd:cd00873   159 SEPQLGVLFPRIKEDYECLVLVRLPFAEDVRQYRFPSLDKLKtPNLPTEEQLEAMDDLVDSMDL--DDDEEDDPEEALKP 236
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1985421139 466 SKIPNPQFQRLYQCLQHKAFHPDKPLPPIEQHLLEMLETPQEVSERCQAPLEKIKALFPLKDA 528
Cdd:cd00873   237 DETPNPVLQRIYQALRHRALHPDEPLPPLLQVLLRYLEPPEEVLEKSKEALKKIKEKFPLKEV 299
vWFA super family cl00057
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation ...
1-229 2.35e-44

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: 158.68  E-value: 2.35e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139   1 MDVGFAMSNSAPGEESPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTENTlasgDQYQNITVQRHLMLPDFDLLED 80
Cdd:pfam03731   6 IDVSPAMFESSKLLEAPFDMALKCIRELLKSKIISRDKDLIGVVLYGTDNSENS----EGLPNITVLRDLDLPGAELILE 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139  81 IQNAIQPG----------SEQADFLDALVVCMDLLQKetIGKKYEKRHIEVFTDLSSPF-SEDQLEIIIANLKKtgislq 149
Cdd:pfam03731  82 LDQFVESFgrdvrgfsgdSSDGSLLSALWVCLELLQK--TGKKLSHKRIFLFTDLDDPFeDQDKLDIALQRLLA------ 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 150 fflpfpvDDEEGSGDTGDGRHSDMYRNSFPRKGLTEQQKEGICMVRKLMFALEEEggldeiyTFRESLERLSMFKKIERR 229
Cdd:pfam03731 154 -------EDLRDTRGEFDLIHLPNADGFDPNLFYKDIIKLGSDEVLNVMLDLEGQ-------KLEDLLAKIRAKKTAKRA 219
Ku_PK_bind pfam08785
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by ...
580-693 1.54e-36

Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs.


:

Pssm-ID: 462604  Cd Length: 117  Bit Score: 133.09  E-value: 1.54e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 580 NPAENFCVLVRQKNAN--FKEVSQQLVNRIEQFLETK-GLQYYMKSINCIRVFREEAIKLSEVQCFNDFLQALKEEVEDK 656
Cdd:pfam08785   1 NPVPDFKQLLARGDDVdaVEKAVKQMGNIIEDLVRDSfGDSNYDKALECLRALREECIEEEEPDLYNDFLRDLKKKLLEG 80
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1985421139 657 TLADFWEILIQDGISLITKDEAEGSSVTSDEAKKFLA 693
Cdd:pfam08785  81 DRREFWELVRKNKLGLITKDEAEDSDVTEEEAKEFLS 117
 
Name Accession Description Interval E-value
KU80 cd00873
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
230-528 1.56e-126

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: 378.17  E-value: 1.56e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 230 PMPWPCQLTIGSNLSIRIVAYKSFTEEKLKKSWTLVDA-KTLKK--EDVQKETVYCLNDDDETEVPKDDLVQGFRYGSDI 306
Cdd:cd00873     1 VAAFKGQLTLGSPLSIAVELYKKTKEERPPKLKKVSDAeKTGEDafEDVKSERSYDVNDDDKTEVEKEDLIKGYRYGRDI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 307 VPFSKVDEEQMKYKTEaKCFSVLGFSRSSQIQRHHYMGnQVLKVFAAKDDEAAAVALSALIHALDELDVVAIVRYAYDRR 386
Cdd:cd00873    81 VPLSEEDEEATKLSTS-KGLDILGFIKASNVPRYYLMG-ESSYVVPQQDDEAAALAFSALVRALAELDKYAIARYVYKDN 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 387 ANPQVGVAFPCIKDAYECLIYVQLPYMEDLRQYMFSSLKNNK-KYTPTEDQLSAVDSLIDSMSLvyEDDDGETTEDIFKT 465
Cdd:cd00873   159 SEPQLGVLFPRIKEDYECLVLVRLPFAEDVRQYRFPSLDKLKtPNLPTEEQLEAMDDLVDSMDL--DDDEEDDPEEALKP 236
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1985421139 466 SKIPNPQFQRLYQCLQHKAFHPDKPLPPIEQHLLEMLETPQEVSERCQAPLEKIKALFPLKDA 528
Cdd:cd00873   237 DETPNPVLQRIYQALRHRALHPDEPLPPLLQVLLRYLEPPEEVLEKSKEALKKIKEKFPLKEV 299
Ku pfam02735
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
239-439 1.68e-59

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: 199.01  E-value: 1.68e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 239 IGSNLSIRIVAYKSFTEEKlKKSWTLVDAKTlkKEDVQKETVYClNDDDETEVPKDDLVQGFRYGSDIVPFSKVDEEQMK 318
Cdd:pfam02735   1 IGGLVSIPVKLYSATEEEK-KPSFKKLDRET--NDGVRIKYKYV-CEDTGKEVEKEDIVKGYEYGGTYVPLSDEELEELK 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 319 YKTEaKCFSVLGFSRSSQIQRHHYMGNQVLKVFAAKDDEAAAV-ALSALIHALDELDVVAIVRYAYDRRANPQVGVAFPC 397
Cdd:pfam02735  77 PEST-KGLDLLGFVPLDEIDPIYFMGDKSYFLYPDKGDIAGSTkAFSALREALLETDKVAIARFVLRRREHPRLVALRPQ 155
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1985421139 398 IKDAYECLIYVQLPYMEDLRQYMFSSLKNNKKYTPTEDQLSA 439
Cdd:pfam02735 156 EEEPDPGLVLITLPFADDVREEFFPIPSLLEKPKPTEEQLDL 197
Ku_N pfam03731
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
1-229 2.35e-44

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: 158.68  E-value: 2.35e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139   1 MDVGFAMSNSAPGEESPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTENTlasgDQYQNITVQRHLMLPDFDLLED 80
Cdd:pfam03731   6 IDVSPAMFESSKLLEAPFDMALKCIRELLKSKIISRDKDLIGVVLYGTDNSENS----EGLPNITVLRDLDLPGAELILE 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139  81 IQNAIQPG----------SEQADFLDALVVCMDLLQKetIGKKYEKRHIEVFTDLSSPF-SEDQLEIIIANLKKtgislq 149
Cdd:pfam03731  82 LDQFVESFgrdvrgfsgdSSDGSLLSALWVCLELLQK--TGKKLSHKRIFLFTDLDDPFeDQDKLDIALQRLLA------ 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 150 fflpfpvDDEEGSGDTGDGRHSDMYRNSFPRKGLTEQQKEGICMVRKLMFALEEEggldeiyTFRESLERLSMFKKIERR 229
Cdd:pfam03731 154 -------EDLRDTRGEFDLIHLPNADGFDPNLFYKDIIKLGSDEVLNVMLDLEGQ-------KLEDLLAKIRAKKTAKRA 219
Ku78 smart00559
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single ...
288-427 3.08e-43

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: 152.45  E-value: 3.08e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139  288 ETEVPKDDLVQGFRYGSDIVPFSKVDEEQMKYKTEaKCFSVLGFSRSSQIQRHHYMGNQVLKVFAAKDDEAAAVALSALI 367
Cdd:smart00559   1 GKEVKPEDIVKGYEYGGRYVPLSDEELEQLKYKSE-PGLELLGFKPLSSLPPYYFLRPSYFLVPDDKSVIGSTKAFSALV 79
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1985421139  368 HALDELDVVAIVRYAYDRRANPQVGVAFPCI-KDAYECLIYVQLPYMEDLRQYMFSSLKNN 427
Cdd:smart00559  80 EALLETDKIAIARYTLRTKSNPRLVALRPYDeEDDGEGLVLVQLPFADDVRKLDFPELNTT 140
vWA_ku cd01458
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to ...
1-223 2.82e-39

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: 144.43  E-value: 2.82e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139   1 MDVGFAMSNSAPGE-ESPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTENTlasgDQYQNITVQRHLMLPDFDLLE 79
Cdd:cd01458     8 VDVSPSMFESKDGEyESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKNP----VGYENIYVLLDLDTPGAERVE 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139  80 DIQNAIQPG----------SEQADFLDALVVCMDLLQKetIGKKYEKRHIEVFTDLSSPFSED-----QLEIIIANLKKT 144
Cdd:cd01458    84 DLKELIEPGglsfagqvgdSGQVSLSDALWVCLDLFSK--GKKKKSHKRIFLFTNNDDPHGGDsikdsQAAVKAEDLKDK 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 145 GISLQFFLPFPVDDeegsgdtgdgrhsdmyrnsfprkglteqQKEGICMVRKLMFALEE--EGGLDEIYTFR----ESLE 218
Cdd:cd01458   162 GIELELFPLSSPGK----------------------------KFDVSKFYKDIIALVEDanEELLDEFTEPSkdleDLLK 213

                  ....*
gi 1985421139 219 RLSMF 223
Cdd:cd01458   214 RLRAK 218
Ku_PK_bind pfam08785
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by ...
580-693 1.54e-36

Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs.


Pssm-ID: 462604  Cd Length: 117  Bit Score: 133.09  E-value: 1.54e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 580 NPAENFCVLVRQKNAN--FKEVSQQLVNRIEQFLETK-GLQYYMKSINCIRVFREEAIKLSEVQCFNDFLQALKEEVEDK 656
Cdd:pfam08785   1 NPVPDFKQLLARGDDVdaVEKAVKQMGNIIEDLVRDSfGDSNYDKALECLRALREECIEEEEPDLYNDFLRDLKKKLLEG 80
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1985421139 657 TLADFWEILIQDGISLITKDEAEGSSVTSDEAKKFLA 693
Cdd:pfam08785  81 DRREFWELVRKNKLGLITKDEAEDSDVTEEEAKEFLS 117
VWA smart00327
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
2-151 1.35e-08

von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.


Pssm-ID: 214621 [Multi-domain]  Cd Length: 175  Bit Score: 54.77  E-value: 1.35e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139    2 DVGFAMSNSAPGEESPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTenTLASGDQYQNITvqrhlmlpdfDLLEDI 81
Cdd:smart00327   1 DVVFLLDGSGSMGGNRFELAKEFVLKLVEQLDIGPDGDRVGLVTFSDDAR--VLFPLNDSRSKD----------ALLEAL 68
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1985421139   82 QNAIQPGSEQADFLDALVVCMDLLQKETIG-KKYEKRHIEVFTDLSSPFSEDQLEIIIANLKKTGISLQFF 151
Cdd:smart00327  69 ASLSYKLGGGTNLGAALQYALENLFSKSAGsRRGAPKVVILITDGESNDGPKDLLKAAKELKRSGVKVFVV 139
ku70 TIGR00578
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in ...
1-562 4.63e-08

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: 56.44  E-value: 4.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139   1 MDVGFAMSNSAPGEE--SPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTENTlasgDQYQNITVQRHLMLPDFD-L 77
Cdd:TIGR00578  19 VDASKAMFEESQGEDelTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTEKDKNS----VNFKNIYVLQDLDNPGAKrV 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139  78 LEDIQNAIQPGSEQ--------ADFL--DALVVCMDLLQKetIGKKYEKRHIEVFTDLSSPFSEDQLEIIIA-----NLK 142
Cdd:TIGR00578  95 LELDQFKGDQGPKKfrdtyghgSDYSlsEVLWVCANLFSD--VQVRMSHKRIMLFTNEDDPHGNDSAKASRArtkagDLR 172
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 143 KTGISLQFF-LPFPvddeegsgdtGDGRHSDMYRNSFPRKgltEQQKEGIcmvrklmfALEEEGGLDEIytfresLERLS 221
Cdd:TIGR00578 173 DTGIFLDLMhLKKP----------GGFDISLFYRDIITDA---EDEDLGV--------HPEESSKLEDL------LRKVR 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 222 MFKKIERRPMPWPcqLTIGSNLSIRIVAYKSFteEKLKKSWTLVDAKTLKKEDVQKETVYclNDDDETEVPKDDLVQGFR 301
Cdd:TIGR00578 226 AKETKKRALSRLK--FKLGKDVVMSVGIYNLV--QKAGKPAPVRLYRETNEPVKTKTRTF--NMDTGSLLLPSDTKRSQT 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 302 YGSDIVPFSKVDEEQMKYKTEAKCFsVLGFSRSSQIQRHHYMgNQVLKVFAAKDDEAAAVAL-SALIHALDELDVVAIVR 380
Cdd:TIGR00578 300 YGGRQIYLEKEETEELKRFDPPGLQ-LMGFKPLSMLKKQHHL-RPSLFVYPEESLVRGSTTLfSALLQKCLEKEVAALCR 377
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 381 YAYDRRANPQVGVAFPCIKDAYECLI--------YVQLPYMEDLRQYMFSslknnKKYTPTEDQLSAVDSLIDSMSLVYE 452
Cdd:TIGR00578 378 YISRRNQPPYFVALVPQEEELDDQKIqvtppgfhLVFLPFADDKRKVPFT-----EKVKATPEQVDKMKAIVEKLRFTYR 452
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 453 DDDGEttedifktskipNPQFQRLYQCLQHKAFHPDKPLPPIEQHLLEMLETPQEVSERCQAPLEkikALFPLKDAGKKK 532
Cdd:TIGR00578 453 SDSFE------------NPVLQQHFRNLEALALDMMEPEQAVDLTLPKVEAMKKRLGSLVDEFKE---LVYPPGYNPEGK 517
                         570       580       590
                  ....*....|....*....|....*....|
gi 1985421139 533 EQKTAQgvfkdnNEDGPSTKKANAENEEGS 562
Cdd:TIGR00578 518 VAKRKQ------AGEGSQSKKPKVENSEEE 541
 
Name Accession Description Interval E-value
KU80 cd00873
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
230-528 1.56e-126

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: 378.17  E-value: 1.56e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 230 PMPWPCQLTIGSNLSIRIVAYKSFTEEKLKKSWTLVDA-KTLKK--EDVQKETVYCLNDDDETEVPKDDLVQGFRYGSDI 306
Cdd:cd00873     1 VAAFKGQLTLGSPLSIAVELYKKTKEERPPKLKKVSDAeKTGEDafEDVKSERSYDVNDDDKTEVEKEDLIKGYRYGRDI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 307 VPFSKVDEEQMKYKTEaKCFSVLGFSRSSQIQRHHYMGnQVLKVFAAKDDEAAAVALSALIHALDELDVVAIVRYAYDRR 386
Cdd:cd00873    81 VPLSEEDEEATKLSTS-KGLDILGFIKASNVPRYYLMG-ESSYVVPQQDDEAAALAFSALVRALAELDKYAIARYVYKDN 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 387 ANPQVGVAFPCIKDAYECLIYVQLPYMEDLRQYMFSSLKNNK-KYTPTEDQLSAVDSLIDSMSLvyEDDDGETTEDIFKT 465
Cdd:cd00873   159 SEPQLGVLFPRIKEDYECLVLVRLPFAEDVRQYRFPSLDKLKtPNLPTEEQLEAMDDLVDSMDL--DDDEEDDPEEALKP 236
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1985421139 466 SKIPNPQFQRLYQCLQHKAFHPDKPLPPIEQHLLEMLETPQEVSERCQAPLEKIKALFPLKDA 528
Cdd:cd00873   237 DETPNPVLQRIYQALRHRALHPDEPLPPLLQVLLRYLEPPEEVLEKSKEALKKIKEKFPLKEV 299
KU cd00594
Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the ...
232-523 1.46e-81

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: 260.28  E-value: 1.46e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 232 PWPCQLTIGSNLSIRIVAYKSFTEEKlKKSWTLVDAKTLKKEDVQKETVYClnddDETEVPKDDLVQGFRYGSDIVPFSK 311
Cdd:cd00594     3 IWKGALSLGLDVSIPVKLYSAATEEK-PPSFKQLDRKTGERVKVKRVCKYT----GGKEVEKEDIVKGYEYGGDYVPLTE 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 312 VDEEQMKYKTEaKCFSVLGFSRSSQIQRHHYMGnQVLKVFAAKDDEAAAVALSALIHALDELDVVAIVRYAYDRRANPQV 391
Cdd:cd00594    78 EELEQLKLETS-KGLDILGFVPASEIPPYYFDK-ESYYLVPDDSDKGSEKAFSALRRALLEKDKVAIARYVLRRNSRPRL 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 392 GVAFPCIKDAYECLIYVQLPYMEDLRQYMFSSLKNNKKYTPTEDQLSAVDSLIDSMSLvyedddgetteDIFKTSKIPNP 471
Cdd:cd00594   156 VALRPQEEEDPEGLVLVTLPFADDVRSYPFPLLLDIKTEKPTDEELELAKQLIDSLDL-----------DDFDPEKFPNP 224
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1985421139 472 QFQRLYQCLQHKAFHPDKPLPPIEQhlleMLETPQEVSERCQAPLEKIKALF 523
Cdd:cd00594   225 YLQRLYALLEAKALGEEIPEPPEDL----TLPPPEEIPKRVIDLLEALKKSL 272
Ku pfam02735
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
239-439 1.68e-59

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: 199.01  E-value: 1.68e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 239 IGSNLSIRIVAYKSFTEEKlKKSWTLVDAKTlkKEDVQKETVYClNDDDETEVPKDDLVQGFRYGSDIVPFSKVDEEQMK 318
Cdd:pfam02735   1 IGGLVSIPVKLYSATEEEK-KPSFKKLDRET--NDGVRIKYKYV-CEDTGKEVEKEDIVKGYEYGGTYVPLSDEELEELK 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 319 YKTEaKCFSVLGFSRSSQIQRHHYMGNQVLKVFAAKDDEAAAV-ALSALIHALDELDVVAIVRYAYDRRANPQVGVAFPC 397
Cdd:pfam02735  77 PEST-KGLDLLGFVPLDEIDPIYFMGDKSYFLYPDKGDIAGSTkAFSALREALLETDKVAIARFVLRRREHPRLVALRPQ 155
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1985421139 398 IKDAYECLIYVQLPYMEDLRQYMFSSLKNNKKYTPTEDQLSA 439
Cdd:pfam02735 156 EEEPDPGLVLITLPFADDVREEFFPIPSLLEKPKPTEEQLDL 197
Ku_N pfam03731
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
1-229 2.35e-44

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: 158.68  E-value: 2.35e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139   1 MDVGFAMSNSAPGEESPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTENTlasgDQYQNITVQRHLMLPDFDLLED 80
Cdd:pfam03731   6 IDVSPAMFESSKLLEAPFDMALKCIRELLKSKIISRDKDLIGVVLYGTDNSENS----EGLPNITVLRDLDLPGAELILE 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139  81 IQNAIQPG----------SEQADFLDALVVCMDLLQKetIGKKYEKRHIEVFTDLSSPF-SEDQLEIIIANLKKtgislq 149
Cdd:pfam03731  82 LDQFVESFgrdvrgfsgdSSDGSLLSALWVCLELLQK--TGKKLSHKRIFLFTDLDDPFeDQDKLDIALQRLLA------ 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 150 fflpfpvDDEEGSGDTGDGRHSDMYRNSFPRKGLTEQQKEGICMVRKLMFALEEEggldeiyTFRESLERLSMFKKIERR 229
Cdd:pfam03731 154 -------EDLRDTRGEFDLIHLPNADGFDPNLFYKDIIKLGSDEVLNVMLDLEGQ-------KLEDLLAKIRAKKTAKRA 219
Ku78 smart00559
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single ...
288-427 3.08e-43

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: 152.45  E-value: 3.08e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139  288 ETEVPKDDLVQGFRYGSDIVPFSKVDEEQMKYKTEaKCFSVLGFSRSSQIQRHHYMGNQVLKVFAAKDDEAAAVALSALI 367
Cdd:smart00559   1 GKEVKPEDIVKGYEYGGRYVPLSDEELEQLKYKSE-PGLELLGFKPLSSLPPYYFLRPSYFLVPDDKSVIGSTKAFSALV 79
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1985421139  368 HALDELDVVAIVRYAYDRRANPQVGVAFPCI-KDAYECLIYVQLPYMEDLRQYMFSSLKNN 427
Cdd:smart00559  80 EALLETDKIAIARYTLRTKSNPRLVALRPYDeEDDGEGLVLVQLPFADDVRKLDFPELNTT 140
vWA_ku cd01458
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to ...
1-223 2.82e-39

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: 144.43  E-value: 2.82e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139   1 MDVGFAMSNSAPGE-ESPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTENTlasgDQYQNITVQRHLMLPDFDLLE 79
Cdd:cd01458     8 VDVSPSMFESKDGEyESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKNP----VGYENIYVLLDLDTPGAERVE 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139  80 DIQNAIQPG----------SEQADFLDALVVCMDLLQKetIGKKYEKRHIEVFTDLSSPFSED-----QLEIIIANLKKT 144
Cdd:cd01458    84 DLKELIEPGglsfagqvgdSGQVSLSDALWVCLDLFSK--GKKKKSHKRIFLFTNNDDPHGGDsikdsQAAVKAEDLKDK 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 145 GISLQFFLPFPVDDeegsgdtgdgrhsdmyrnsfprkglteqQKEGICMVRKLMFALEE--EGGLDEIYTFR----ESLE 218
Cdd:cd01458   162 GIELELFPLSSPGK----------------------------KFDVSKFYKDIIALVEDanEELLDEFTEPSkdleDLLK 213

                  ....*
gi 1985421139 219 RLSMF 223
Cdd:cd01458   214 RLRAK 218
Ku_PK_bind pfam08785
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by ...
580-693 1.54e-36

Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs.


Pssm-ID: 462604  Cd Length: 117  Bit Score: 133.09  E-value: 1.54e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 580 NPAENFCVLVRQKNAN--FKEVSQQLVNRIEQFLETK-GLQYYMKSINCIRVFREEAIKLSEVQCFNDFLQALKEEVEDK 656
Cdd:pfam08785   1 NPVPDFKQLLARGDDVdaVEKAVKQMGNIIEDLVRDSfGDSNYDKALECLRALREECIEEEEPDLYNDFLRDLKKKLLEG 80
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1985421139 657 TLADFWEILIQDGISLITKDEAEGSSVTSDEAKKFLA 693
Cdd:pfam08785  81 DRREFWELVRKNKLGLITKDEAEDSDVTEEEAKEFLS 117
Ku_C pfam03730
Ku70/Ku80 C-terminal arm; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
463-556 4.78e-21

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: 87.71  E-value: 4.78e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 463 FKTSKIPNPQFQRLYQCLQHKAFHPDKPlppiEQHLLEMLETPQEVSERCQAPLEKIKALFPLKDAGkkkeqktaqgvfK 542
Cdd:pfam03730   2 YNPDKFPNPSLQRHYQNLQALALDEDEP----EEPEDLTLPKYEAIDKRIGKLLEEFKELFELEDYK------------P 65
                          90
                  ....*....|....
gi 1985421139 543 DNNEDGPSTKKANA 556
Cdd:pfam03730  66 DEDEEGPAAKKAKI 79
KU70 cd00788
Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in ...
235-493 1.62e-17

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: 83.48  E-value: 1.62e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 235 CQLTIG--SNLSIRIVAYKSFTEEKLKKSWTLVDAKTLKKEDVQKETVYcLNDDDETEVPKDDLVQGFRYGSDIVPFSKV 312
Cdd:cd00788     6 LPLELGpgNKLVISVKGYSLVSHAKKPRKYKLDREKNEERREVKSKRKF-FDVESGKTLEKADIKKGYKIGGEKIIFTKE 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 313 DEEQMKYKTEaKCFSVLGFSRSSQIQRHHymgnqVLK--VFAAKDDE---AAAVALSALIHALDELDVVAIVRYAydRRA 387
Cdd:cd00788    85 ELKKIKSFGE-PGLRLIGFKPRSTLKPYH-----NIKksYFIYPDESdykGSTRLFAALLRSCLKKNKVAICWYI--LRK 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 388 N---------PQVGVAFPCIKDAYECLIY-VQLPYMEDLRQYMFSSLKNNKKYTPTEDQLSAVDSLIDSMSLVYedddge 457
Cdd:cd00788   157 NspprlvalvPQEEELDEPDGQVLPPGFHlVPLPFADDIRKLPSLLEENASAESASDELVDKAKQIIKKLRLLS------ 230
                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1985421139 458 ttediFKTSKIPNPQFQRLYQCLQHKAFHPDKPLPP 493
Cdd:cd00788   231 -----YDPDKFPNPSLQKHYKILEALALDEEDPEKP 261
VWA smart00327
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
2-151 1.35e-08

von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.


Pssm-ID: 214621 [Multi-domain]  Cd Length: 175  Bit Score: 54.77  E-value: 1.35e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139    2 DVGFAMSNSAPGEESPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTenTLASGDQYQNITvqrhlmlpdfDLLEDI 81
Cdd:smart00327   1 DVVFLLDGSGSMGGNRFELAKEFVLKLVEQLDIGPDGDRVGLVTFSDDAR--VLFPLNDSRSKD----------ALLEAL 68
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1985421139   82 QNAIQPGSEQADFLDALVVCMDLLQKETIG-KKYEKRHIEVFTDLSSPFSEDQLEIIIANLKKTGISLQFF 151
Cdd:smart00327  69 ASLSYKLGGGTNLGAALQYALENLFSKSAGsRRGAPKVVILITDGESNDGPKDLLKAAKELKRSGVKVFVV 139
ku70 TIGR00578
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in ...
1-562 4.63e-08

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: 56.44  E-value: 4.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139   1 MDVGFAMSNSAPGEE--SPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTENTlasgDQYQNITVQRHLMLPDFD-L 77
Cdd:TIGR00578  19 VDASKAMFEESQGEDelTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTEKDKNS----VNFKNIYVLQDLDNPGAKrV 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139  78 LEDIQNAIQPGSEQ--------ADFL--DALVVCMDLLQKetIGKKYEKRHIEVFTDLSSPFSEDQLEIIIA-----NLK 142
Cdd:TIGR00578  95 LELDQFKGDQGPKKfrdtyghgSDYSlsEVLWVCANLFSD--VQVRMSHKRIMLFTNEDDPHGNDSAKASRArtkagDLR 172
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 143 KTGISLQFF-LPFPvddeegsgdtGDGRHSDMYRNSFPRKgltEQQKEGIcmvrklmfALEEEGGLDEIytfresLERLS 221
Cdd:TIGR00578 173 DTGIFLDLMhLKKP----------GGFDISLFYRDIITDA---EDEDLGV--------HPEESSKLEDL------LRKVR 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 222 MFKKIERRPMPWPcqLTIGSNLSIRIVAYKSFteEKLKKSWTLVDAKTLKKEDVQKETVYclNDDDETEVPKDDLVQGFR 301
Cdd:TIGR00578 226 AKETKKRALSRLK--FKLGKDVVMSVGIYNLV--QKAGKPAPVRLYRETNEPVKTKTRTF--NMDTGSLLLPSDTKRSQT 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 302 YGSDIVPFSKVDEEQMKYKTEAKCFsVLGFSRSSQIQRHHYMgNQVLKVFAAKDDEAAAVAL-SALIHALDELDVVAIVR 380
Cdd:TIGR00578 300 YGGRQIYLEKEETEELKRFDPPGLQ-LMGFKPLSMLKKQHHL-RPSLFVYPEESLVRGSTTLfSALLQKCLEKEVAALCR 377
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 381 YAYDRRANPQVGVAFPCIKDAYECLI--------YVQLPYMEDLRQYMFSslknnKKYTPTEDQLSAVDSLIDSMSLVYE 452
Cdd:TIGR00578 378 YISRRNQPPYFVALVPQEEELDDQKIqvtppgfhLVFLPFADDKRKVPFT-----EKVKATPEQVDKMKAIVEKLRFTYR 452
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139 453 DDDGEttedifktskipNPQFQRLYQCLQHKAFHPDKPLPPIEQHLLEMLETPQEVSERCQAPLEkikALFPLKDAGKKK 532
Cdd:TIGR00578 453 SDSFE------------NPVLQQHFRNLEALALDMMEPEQAVDLTLPKVEAMKKRLGSLVDEFKE---LVYPPGYNPEGK 517
                         570       580       590
                  ....*....|....*....|....*....|
gi 1985421139 533 EQKTAQgvfkdnNEDGPSTKKANAENEEGS 562
Cdd:TIGR00578 518 VAKRKQ------AGEGSQSKKPKVENSEEE 541
vWFA cd00198
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation ...
7-148 5.25e-06

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.


Pssm-ID: 238119 [Multi-domain]  Cd Length: 161  Bit Score: 47.18  E-value: 5.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139   7 MSNSAPGEesPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTEntLASGDQYQNitvqrhlmlpDFDLLEDIQNAIQ 86
Cdd:cd00198     9 VSGSMGGE--KLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARV--VLPLTTDTD----------KADLLEAIDALKK 74
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1985421139  87 PGSEQADFLDALVVCMDLLQKETigKKYEKRHIEVFTDLSSPFSEDQLEIIIANLKKTGISL 148
Cdd:cd00198    75 GLGGGTNIGAALRLALELLKSAK--RPNARRVIILLTDGEPNDGPELLAEAARELRKLGITV 134
VWA pfam00092
von Willebrand factor type A domain;
2-148 3.11e-04

von Willebrand factor type A domain;


Pssm-ID: 459670 [Multi-domain]  Cd Length: 174  Bit Score: 42.26  E-value: 3.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985421139   2 DVGFAMSNSAPGEESPFEQAKKMMTMFVQRQVFAESKDEVSVVLFGTDGTenTLASGDQYQNITvqrhlmlpdfDLLEDI 81
Cdd:pfam00092   1 DIVFLLDGSGSIGGDNFEKVKEFLKKLVESLDIGPDGTRVGLVQYSSDVR--TEFPLNDYSSKE----------ELLSAV 68
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1985421139  82 QNAIQPGSEQADFLDALVVCMDLLQKETIGKKYE-KRHIEVFTDLSSpfSEDQLEIIIANLKKTGISL 148
Cdd:pfam00092  69 DNLRYLGGGTTNTGKALKYALENLFSSAAGARPGaPKVVVLLTDGRS--QDGDPEEVARELKSAGVTV 134
 
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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