NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1234543341|ref|NP_001341659|]
View 

DNA repair protein complementing XP-C cells isoform 6 [Homo sapiens]

Protein Classification

RAD4 DNA repair family protein( domain architecture ID 1003424)

RAD4 DNA repair family protein such as DNA repair protein RAD4, a DNA damage recognition protein that is involved in the nucleotide excision repair (NER) pathway, which is responsible for removing a wide range of DNA lesions, including UV-induced photoproducts and chemical adducts.

CATH:  2.20.20.120
PubMed:  17882165

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
rad4 super family cl36705
DNA repair protein rad4; All proteins in this family for which functions are known are ...
147-785 0e+00

DNA repair protein rad4; All proteins in this family for which functions are known are involved in targeting nucleotide excision repair to specific regions of the genome.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR00605:

Pssm-ID: 273170 [Multi-domain]  Cd Length: 713  Bit Score: 774.05  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 147 VRESTAFSRSLLpVKPVEIEIETPEQAKTRERseKIKLEFETYLRRAMKRFNKGVHEDTHKVHLLCLLANGFYRNNICSQ 226
Cdd:TIGR00605   1 MNEDLAKEYFEL-IRKVENEKEAEKQPKSRRR--KVRRENEPSLRRRKKRFKTGLNELPHEVVLMCNLDSTHSDDRVVSV 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 227 PDLHAIGlSIIPARFTRVLPRDVDTYYLSNLVKWFIGTFTVNAELSASEQDNLQTTLERRFAIYSARDDEELVHIFLLIL 306
Cdd:TIGR00605  78 PDSLSVS-EEIPSREEDYDSREFEDVYLSNLVAEFETISVEIKPSSKAESDDDAETLSRNVCSNEARKDRKYIHILYLLC 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 307 RALQLLTRLVLSLQpIPLKSATAKGKKPSKERLTADPG--GSSETSSQVLENHTKPKTSKGTKQEETFAKGtCRPSAKGK 384
Cdd:TIGR00605 157 LMVHLFTRNEWSLS-APLKSAKLSNLIPEKVRLLLHPSvrKSEELPSRSLRGLRKPLVEKLKKCMETWQKG-LRKTTKGL 234
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 385 R--NKGGRKKRSKpssseedegpGDKQEKATQRRPHGRERRVASRVSYKEESGSDEAGSGSDFELSSGEASDPSDEDSEP 462
Cdd:TIGR00605 235 LklLNGGRYSRSK----------WEEIEKSSNRKLGGRKYRTLKRGSILENLNVPTRLVFSDFLLSVSKGHNDPEISSEG 304
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 463 GPPKQRKAPAPQRTKAGSKSASRTHRGSHRKDPSLPAASSSSSSSKRGKKMCSDGEKAEKRSIAGIDQWLEVFCEQEEKW 542
Cdd:TIGR00605 305 FVPKLSACNANQRLIMSCESADRTSRFRMKKDPSLPGFSAYSDMDKSPIFTCEEGDKFIDRWITYVDFWVEVFIEQEEKW 384
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341     --------------------------------------------------------------------------------
Cdd:TIGR00605 385 vcvdavhsgvvpkgvtcfepatlmmtyvfaydrdgyvkdvtrrycdqwstkvrkrrvekadfgetwfrpifgalhkrkrt 464
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 543 --------FQAKHMDQPLPTAIGLYKNHPLYALKRHLLKYEAIYP-ETAAILGYCRGEA-VYSRDCVHTLHSRDTWLKKA 612
Cdd:TIGR00605 465 iddiedqeFLRRHESEGIPKSIQDLKNHPLYVLERHLKKTQALKPgKKACTLGFVNGKAgVYSRKDVHDLKSAEQWYKKG 544
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 613 RVVRLGEVPYKMVKGfsnRARKARLAEPQLREEnDLGLFGYWQTEEYQPPVAVDGKVPRNEFGNVYLFLPSMMPIGCVQL 692
Cdd:TIGR00605 545 RVIKLGEQPYKVVKA---RARTVRLPKGEAEEE-DLGLYSYEQTELYIPPPAVDGIVPKNAYGNIDLFVPSMIPKGAVHL 620
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 693 NLPNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLLTAWENEQAVIERKEKEKKEKRALGNWKLLAKG 772
Cdd:TIGR00605 621 RLPGAIKAAKKLNIDYAPAVTGFDFHRGYSKPVLDGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNWKTLLKG 700
                         730
                  ....*....|...
gi 1234543341 773 LLIRERLKRRYGP 785
Cdd:TIGR00605 701 LRIRERLKETYGK 713
 
Name Accession Description Interval E-value
rad4 TIGR00605
DNA repair protein rad4; All proteins in this family for which functions are known are ...
147-785 0e+00

DNA repair protein rad4; All proteins in this family for which functions are known are involved in targeting nucleotide excision repair to specific regions of the genome.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273170 [Multi-domain]  Cd Length: 713  Bit Score: 774.05  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 147 VRESTAFSRSLLpVKPVEIEIETPEQAKTRERseKIKLEFETYLRRAMKRFNKGVHEDTHKVHLLCLLANGFYRNNICSQ 226
Cdd:TIGR00605   1 MNEDLAKEYFEL-IRKVENEKEAEKQPKSRRR--KVRRENEPSLRRRKKRFKTGLNELPHEVVLMCNLDSTHSDDRVVSV 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 227 PDLHAIGlSIIPARFTRVLPRDVDTYYLSNLVKWFIGTFTVNAELSASEQDNLQTTLERRFAIYSARDDEELVHIFLLIL 306
Cdd:TIGR00605  78 PDSLSVS-EEIPSREEDYDSREFEDVYLSNLVAEFETISVEIKPSSKAESDDDAETLSRNVCSNEARKDRKYIHILYLLC 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 307 RALQLLTRLVLSLQpIPLKSATAKGKKPSKERLTADPG--GSSETSSQVLENHTKPKTSKGTKQEETFAKGtCRPSAKGK 384
Cdd:TIGR00605 157 LMVHLFTRNEWSLS-APLKSAKLSNLIPEKVRLLLHPSvrKSEELPSRSLRGLRKPLVEKLKKCMETWQKG-LRKTTKGL 234
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 385 R--NKGGRKKRSKpssseedegpGDKQEKATQRRPHGRERRVASRVSYKEESGSDEAGSGSDFELSSGEASDPSDEDSEP 462
Cdd:TIGR00605 235 LklLNGGRYSRSK----------WEEIEKSSNRKLGGRKYRTLKRGSILENLNVPTRLVFSDFLLSVSKGHNDPEISSEG 304
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 463 GPPKQRKAPAPQRTKAGSKSASRTHRGSHRKDPSLPAASSSSSSSKRGKKMCSDGEKAEKRSIAGIDQWLEVFCEQEEKW 542
Cdd:TIGR00605 305 FVPKLSACNANQRLIMSCESADRTSRFRMKKDPSLPGFSAYSDMDKSPIFTCEEGDKFIDRWITYVDFWVEVFIEQEEKW 384
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341     --------------------------------------------------------------------------------
Cdd:TIGR00605 385 vcvdavhsgvvpkgvtcfepatlmmtyvfaydrdgyvkdvtrrycdqwstkvrkrrvekadfgetwfrpifgalhkrkrt 464
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 543 --------FQAKHMDQPLPTAIGLYKNHPLYALKRHLLKYEAIYP-ETAAILGYCRGEA-VYSRDCVHTLHSRDTWLKKA 612
Cdd:TIGR00605 465 iddiedqeFLRRHESEGIPKSIQDLKNHPLYVLERHLKKTQALKPgKKACTLGFVNGKAgVYSRKDVHDLKSAEQWYKKG 544
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 613 RVVRLGEVPYKMVKGfsnRARKARLAEPQLREEnDLGLFGYWQTEEYQPPVAVDGKVPRNEFGNVYLFLPSMMPIGCVQL 692
Cdd:TIGR00605 545 RVIKLGEQPYKVVKA---RARTVRLPKGEAEEE-DLGLYSYEQTELYIPPPAVDGIVPKNAYGNIDLFVPSMIPKGAVHL 620
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 693 NLPNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLLTAWENEQAVIERKEKEKKEKRALGNWKLLAKG 772
Cdd:TIGR00605 621 RLPGAIKAAKKLNIDYAPAVTGFDFHRGYSKPVLDGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNWKTLLKG 700
                         730
                  ....*....|...
gi 1234543341 773 LLIRERLKRRYGP 785
Cdd:TIGR00605 701 LRIRERLKETYGK 713
BHD_3 smart01032
Rad4 beta-hairpin domain 3; This short domain is found in the Rad4 protein. This domain binds ...
669-743 9.22e-42

Rad4 beta-hairpin domain 3; This short domain is found in the Rad4 protein. This domain binds to DNA.


Pssm-ID: 198100 [Multi-domain]  Cd Length: 75  Bit Score: 146.55  E-value: 9.22e-42
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1234543341  669 VPRNEFGNVYLFLPSMMPIGCVQLNLPNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLLTAW 743
Cdd:smart01032   1 VPRNEYGNIDLFKPSMLPIGCVHLKLPGLIRVAKRLGIDYAPAVTGFDFKRGSAHPVIDGVVVAEEFAEALLAAW 75
RAD4 COG5535
DNA repair protein RAD4 [DNA replication, recombination, and repair];
539-786 1.23e-40

DNA repair protein RAD4 [DNA replication, recombination, and repair];


Pssm-ID: 227822 [Multi-domain]  Cd Length: 650  Bit Score: 159.63  E-value: 1.23e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 539 EEKWFQAKHMDQpLPTAIGLYKNHPLYALKRHLLKYEAIYP--ETAAIL--GYCRGEAVYSRDCVHTLHSRDTWLKKARV 614
Cdd:COG5535   407 DFDDLDERRSEG-IPKSVQDLKRHPKFVLESHLKWNQAIKPgaKPGFTLtkGKNSVEAVYLRRDVVRLKSAEQWYRMGRV 485
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 615 VRLGEVPYKMVKGFSNRARKarLAEPQLREendlgLFGYWQTEEYQPPVAVDGKVPRNEFGNVYLFLPSMMPIGCVQLNL 694
Cdd:COG5535   486 IKPGAQPLKIVKRMRERVRN--LDDKVIRE-----LYSPEQTELYGPPLVVAGIIPKNMYGNIDYYVPSMIPRGCVLIPN 558
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 695 PNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLLTAWENEQAVIERKEKEKKEKRALGNWKLLAKGLL 774
Cdd:COG5535   559 RNARDIARLLGIDYADAVTGFDFGRSTVKPVLRGIVVPKKNLEAISNFLAEYERIQEEKERSEVRLGGLKRWKILLRKLR 638
                         250
                  ....*....|..
gi 1234543341 775 IRERLKRRYGPK 786
Cdd:COG5535   639 IRLRINEEYGLK 650
BHD_3 pfam10405
Rad4 beta-hairpin domain 3; This short domain is found in the Rad4 protein. This domain binds ...
669-740 2.01e-33

Rad4 beta-hairpin domain 3; This short domain is found in the Rad4 protein. This domain binds to DNA.


Pssm-ID: 463079 [Multi-domain]  Cd Length: 73  Bit Score: 122.94  E-value: 2.01e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1234543341 669 VPRNEFGNVYLFLPSMMPIGCVQLNLPNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLL 740
Cdd:pfam10405   1 VPKNAYGNIDIFVPSMLPEGCVHIPLPGAARAAKKLGIDYAPAVTGFDFKGRRGKPVIDGIVVAEEDEEALL 72
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
321-516 2.39e-07

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 54.79  E-value: 2.39e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341  321 PIPLKSATAKGKKPSKERLTADPGGSSETSSQVLENHTKPKTSKGTKQEETFAKGTCRPSAKGKRNKGGRKKRSKPSSSE 400
Cdd:PHA03307   212 PISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSP 291
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341  401 EDEGPgdkqeKATQRRPHGRERRVASRVSyKEESGSDEAGSGSDfeLSSGEASDPSDedSEPGPPKQRkAPAPQRTKAGS 480
Cdd:PHA03307   292 RERSP-----SPSPSSPGSGPAPSSPRAS-SSSSSSRESSSSST--SSSSESSRGAA--VSPGPSPSR-SPSPSRPPPPA 360
                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1234543341  481 KSASRTHRGSHRKDPSLPAASSSSSSSKRGKKMCSD 516
Cdd:PHA03307   361 DPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAG 396
 
Name Accession Description Interval E-value
rad4 TIGR00605
DNA repair protein rad4; All proteins in this family for which functions are known are ...
147-785 0e+00

DNA repair protein rad4; All proteins in this family for which functions are known are involved in targeting nucleotide excision repair to specific regions of the genome.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273170 [Multi-domain]  Cd Length: 713  Bit Score: 774.05  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 147 VRESTAFSRSLLpVKPVEIEIETPEQAKTRERseKIKLEFETYLRRAMKRFNKGVHEDTHKVHLLCLLANGFYRNNICSQ 226
Cdd:TIGR00605   1 MNEDLAKEYFEL-IRKVENEKEAEKQPKSRRR--KVRRENEPSLRRRKKRFKTGLNELPHEVVLMCNLDSTHSDDRVVSV 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 227 PDLHAIGlSIIPARFTRVLPRDVDTYYLSNLVKWFIGTFTVNAELSASEQDNLQTTLERRFAIYSARDDEELVHIFLLIL 306
Cdd:TIGR00605  78 PDSLSVS-EEIPSREEDYDSREFEDVYLSNLVAEFETISVEIKPSSKAESDDDAETLSRNVCSNEARKDRKYIHILYLLC 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 307 RALQLLTRLVLSLQpIPLKSATAKGKKPSKERLTADPG--GSSETSSQVLENHTKPKTSKGTKQEETFAKGtCRPSAKGK 384
Cdd:TIGR00605 157 LMVHLFTRNEWSLS-APLKSAKLSNLIPEKVRLLLHPSvrKSEELPSRSLRGLRKPLVEKLKKCMETWQKG-LRKTTKGL 234
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 385 R--NKGGRKKRSKpssseedegpGDKQEKATQRRPHGRERRVASRVSYKEESGSDEAGSGSDFELSSGEASDPSDEDSEP 462
Cdd:TIGR00605 235 LklLNGGRYSRSK----------WEEIEKSSNRKLGGRKYRTLKRGSILENLNVPTRLVFSDFLLSVSKGHNDPEISSEG 304
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 463 GPPKQRKAPAPQRTKAGSKSASRTHRGSHRKDPSLPAASSSSSSSKRGKKMCSDGEKAEKRSIAGIDQWLEVFCEQEEKW 542
Cdd:TIGR00605 305 FVPKLSACNANQRLIMSCESADRTSRFRMKKDPSLPGFSAYSDMDKSPIFTCEEGDKFIDRWITYVDFWVEVFIEQEEKW 384
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341     --------------------------------------------------------------------------------
Cdd:TIGR00605 385 vcvdavhsgvvpkgvtcfepatlmmtyvfaydrdgyvkdvtrrycdqwstkvrkrrvekadfgetwfrpifgalhkrkrt 464
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 543 --------FQAKHMDQPLPTAIGLYKNHPLYALKRHLLKYEAIYP-ETAAILGYCRGEA-VYSRDCVHTLHSRDTWLKKA 612
Cdd:TIGR00605 465 iddiedqeFLRRHESEGIPKSIQDLKNHPLYVLERHLKKTQALKPgKKACTLGFVNGKAgVYSRKDVHDLKSAEQWYKKG 544
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 613 RVVRLGEVPYKMVKGfsnRARKARLAEPQLREEnDLGLFGYWQTEEYQPPVAVDGKVPRNEFGNVYLFLPSMMPIGCVQL 692
Cdd:TIGR00605 545 RVIKLGEQPYKVVKA---RARTVRLPKGEAEEE-DLGLYSYEQTELYIPPPAVDGIVPKNAYGNIDLFVPSMIPKGAVHL 620
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 693 NLPNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLLTAWENEQAVIERKEKEKKEKRALGNWKLLAKG 772
Cdd:TIGR00605 621 RLPGAIKAAKKLNIDYAPAVTGFDFHRGYSKPVLDGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNWKTLLKG 700
                         730
                  ....*....|...
gi 1234543341 773 LLIRERLKRRYGP 785
Cdd:TIGR00605 701 LRIRERLKETYGK 713
BHD_3 smart01032
Rad4 beta-hairpin domain 3; This short domain is found in the Rad4 protein. This domain binds ...
669-743 9.22e-42

Rad4 beta-hairpin domain 3; This short domain is found in the Rad4 protein. This domain binds to DNA.


Pssm-ID: 198100 [Multi-domain]  Cd Length: 75  Bit Score: 146.55  E-value: 9.22e-42
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1234543341  669 VPRNEFGNVYLFLPSMMPIGCVQLNLPNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLLTAW 743
Cdd:smart01032   1 VPRNEYGNIDLFKPSMLPIGCVHLKLPGLIRVAKRLGIDYAPAVTGFDFKRGSAHPVIDGVVVAEEFAEALLAAW 75
RAD4 COG5535
DNA repair protein RAD4 [DNA replication, recombination, and repair];
539-786 1.23e-40

DNA repair protein RAD4 [DNA replication, recombination, and repair];


Pssm-ID: 227822 [Multi-domain]  Cd Length: 650  Bit Score: 159.63  E-value: 1.23e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 539 EEKWFQAKHMDQpLPTAIGLYKNHPLYALKRHLLKYEAIYP--ETAAIL--GYCRGEAVYSRDCVHTLHSRDTWLKKARV 614
Cdd:COG5535   407 DFDDLDERRSEG-IPKSVQDLKRHPKFVLESHLKWNQAIKPgaKPGFTLtkGKNSVEAVYLRRDVVRLKSAEQWYRMGRV 485
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 615 VRLGEVPYKMVKGFSNRARKarLAEPQLREendlgLFGYWQTEEYQPPVAVDGKVPRNEFGNVYLFLPSMMPIGCVQLNL 694
Cdd:COG5535   486 IKPGAQPLKIVKRMRERVRN--LDDKVIRE-----LYSPEQTELYGPPLVVAGIIPKNMYGNIDYYVPSMIPRGCVLIPN 558
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 695 PNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLLTAWENEQAVIERKEKEKKEKRALGNWKLLAKGLL 774
Cdd:COG5535   559 RNARDIARLLGIDYADAVTGFDFGRSTVKPVLRGIVVPKKNLEAISNFLAEYERIQEEKERSEVRLGGLKRWKILLRKLR 638
                         250
                  ....*....|..
gi 1234543341 775 IRERLKRRYGPK 786
Cdd:COG5535   639 IRLRINEEYGLK 650
BHD_3 pfam10405
Rad4 beta-hairpin domain 3; This short domain is found in the Rad4 protein. This domain binds ...
669-740 2.01e-33

Rad4 beta-hairpin domain 3; This short domain is found in the Rad4 protein. This domain binds to DNA.


Pssm-ID: 463079 [Multi-domain]  Cd Length: 73  Bit Score: 122.94  E-value: 2.01e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1234543341 669 VPRNEFGNVYLFLPSMMPIGCVQLNLPNLHRVARKLDIDCVQAITGFDFHGGYSHPVTDGYIVCEEFKDVLL 740
Cdd:pfam10405   1 VPKNAYGNIDIFVPSMLPEGCVHIPLPGAARAAKKLGIDYAPAVTGFDFKGRRGKPVIDGIVVAEEDEEALL 72
BHD_2 smart01031
Rad4 beta-hairpin domain 2; This short domain is found in the Rad4 protein. This domain binds ...
602-661 2.76e-19

Rad4 beta-hairpin domain 2; This short domain is found in the Rad4 protein. This domain binds to DNA.


Pssm-ID: 214985 [Multi-domain]  Cd Length: 56  Bit Score: 81.96  E-value: 2.76e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341  602 LHSRDTWLKKARVVRLGEVPYKMVKgfsnRARKARLAEPQLREENDLGLFGYWQTEEYQP 661
Cdd:smart01031   1 LKSAEHWLRQGRVVKPGEQPYKVVK----RKRKKDRIPNDTGEEEELELYGEWQTELYIP 56
BHD_1 smart01030
Rad4 beta-hairpin domain 1; This short domain is found in the Rad4 protein. This domain binds ...
548-599 6.69e-18

Rad4 beta-hairpin domain 1; This short domain is found in the Rad4 protein. This domain binds to DNA.


Pssm-ID: 214984 [Multi-domain]  Cd Length: 54  Bit Score: 78.04  E-value: 6.69e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1234543341  548 MDQPLPTAIGLYKNHPLYALKRHLLKYEAIYPETAAI--LGYCRGEAVYSRDCV 599
Cdd:smart01030   1 LNEPIPTSIQDFKNHPLYVLERHLKKNEAIYPKAKPVgtFGYGKGEPVYLRSDV 54
BHD_2 pfam10404
Rad4 beta-hairpin domain 2; This short domain is found in the Rad4 protein. This domain binds ...
603-662 1.54e-15

Rad4 beta-hairpin domain 2; This short domain is found in the Rad4 protein. This domain binds to DNA.


Pssm-ID: 463078 [Multi-domain]  Cd Length: 63  Bit Score: 71.47  E-value: 1.54e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1234543341 603 HSRDTWLKKARVVRLGEVPYKMVKGFSNRARKARLAEPQL---REENDLGLFGYWQTEEYQPP 662
Cdd:pfam10404   1 KSAEKWYREGREVKPGEQPLKRVKARAVTKNRKREEEDAReedGEEGGVGLYAEWQTELYIPP 63
BHD_1 pfam10403
Rad4 beta-hairpin domain 1; This short domain is found in the Rad4 protein. This domain binds ...
551-599 2.44e-14

Rad4 beta-hairpin domain 1; This short domain is found in the Rad4 protein. This domain binds to DNA.


Pssm-ID: 463077  Cd Length: 54  Bit Score: 67.95  E-value: 2.44e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1234543341 551 PLPTAIGLYKNHPLYALKRHLLKYEAIYPeTAAILGYCR----GEAVYSRDCV 599
Cdd:pfam10403   3 PMPTNIQDFKNHPLYVLERHLKRNEVIYP-GAKPVGTFRykkkGEPVYRRSDV 54
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
321-516 2.39e-07

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 54.79  E-value: 2.39e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341  321 PIPLKSATAKGKKPSKERLTADPGGSSETSSQVLENHTKPKTSKGTKQEETFAKGTCRPSAKGKRNKGGRKKRSKPSSSE 400
Cdd:PHA03307   212 PISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSP 291
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341  401 EDEGPgdkqeKATQRRPHGRERRVASRVSyKEESGSDEAGSGSDfeLSSGEASDPSDedSEPGPPKQRkAPAPQRTKAGS 480
Cdd:PHA03307   292 RERSP-----SPSPSSPGSGPAPSSPRAS-SSSSSSRESSSSST--SSSSESSRGAA--VSPGPSPSR-SPSPSRPPPPA 360
                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1234543341  481 KSASRTHRGSHRKDPSLPAASSSSSSSKRGKKMCSD 516
Cdd:PHA03307   361 DPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAG 396
recX PRK14136
recombination regulator RecX; Provisional
355-499 3.83e-03

recombination regulator RecX; Provisional


Pssm-ID: 237620 [Multi-domain]  Cd Length: 309  Bit Score: 40.37  E-value: 3.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1234543341 355 ENHTKPKTSkGTKQEETFAKGTCRPSAKGKRNKGGRKKRSKPSS--SEEDEGPGDKQEKATQRRPHGRERRVASRVSYKE 432
Cdd:PRK14136   11 QEADHPARA-ARAGRPHASRETDRTVSGEGRPAGRTATRASDDAlvSFEIAAPDEPFDDDESFDAHDRARRRVSGVGVRD 89
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1234543341 433 E-SGSDEAGSGSDFELSSGEASDPSDED----SEPGPPKQRKAPAPQRTKAGSKSASRTHRGSHRKDPSLPA 499
Cdd:PRK14136   90 AgAPGGRAADARAANLSSAAKRAEAAGDvytrTSQHPRRTRRAAGPFHSDSSPSASSEDDGAARSRASSRPA 161
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH