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Conserved domains on  [gi|9843869|emb|CAB89874|]
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damage-specific DNA binding protein 1 [Rattus norvegicus]

Protein Classification

DDB1/RSE1 family protein( domain architecture ID 10564462)

DDB1/RSE1 family protein is a nucleic acid binding protein with a beta-propeller fold, such as human DNA damage-binding protein 1 (DDB1) and Neurospora crassa pre-mRNA-splicing factor RSE1

CATH:  2.130.10.10
Gene Ontology:  GO:0003676
SCOP:  4004169

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
MMS1_N pfam10433
Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects ...
 75-543 8.64e-130

Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects against replication-dependent DNA damage in Saccharomyces cerevisiae. MMS1 belongs to the DDB1 family of cullin 4 adaptors and the two proteins are homologous. MMS1 bridges the interaction of MMS22 and Crt10 with Cul8/Rtt101. Cul8/Rtt101 is a cullin protein involved in the regulation of DNA replication subsequent to DNA damage. The N-terminal region of MMS1 and the C-terminal of MMS22 are required for the the MMS1-MMS22 interaction. The human HIV-1 virion-associated protein Vpr assembles with DDB1 through interaction with DCAF1 (chromatin assembly factor) to form an E3 ubiquitin ligase that targets cellular substrates for proteasome-mediated degradation and subsequent G2 arrest.


:

Pssm-ID: 463091  Cd Length: 486  Bit Score: 404.72  E-value: 8.64e-130
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869      75 DLLFILTAKYNACILEYkqSGESIDIITRAH-GNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPL------DR 147
Cdd:pfam10433    1 DHLVVGTDSGRLVFLSW--DPEKNQFETIHSrEDLGKSGSRRSQPGQYLAVDPKGRAIAVSAYEGVFLVYPLkqpqklNR 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     148 DNKEL--KAFNIRLEELHVIDVKFLYGCQA-PTICFVYQDPQGR-HVKTYEVSL---------REKEFNKGPWKQEnveA 214
Cdd:pfam10433   79 NEALLlsSPLEARKSEGFILSMVFLDPGYDnPIFALLEQDRTGKtHLKLYEWDLglnhvvrgpKWSEPLDFLPKED---R 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     215 EASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPII------KQSTIVCHNRVDpnGSRYLLGDMEGRLFMLLLEKE 288
Cdd:pfam10433  156 GANLLIPVPKGPGGVLVCGETIITYKDILDQPDIRCPPVarplreNATIFVAWHKLD--NFFILLADEYGDLYLLTIEND 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     289 EqmDGTVTlkDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQPVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLE 368
Cdd:pfam10433  234 E--DNVVT--SIKIGYFGTTSVASALVILDNGFLFVASEFGDSQLYQIDARGDDDLSNLELVQTFSNWAPILDFVVMDLG 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     369 RQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPG--IKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEET 446
Cdd:pfam10433  310 GEDTARIYTCSGAGKRGSLRSLRHGVGAEELAVSEEPGspITGVWTLKSSPEDEYDDYLVVSFVNETRVLSIDGDGVEEV 389

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     447 -ELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPkaLVSEWKEPRAKNISVASCNSSQVVVAV-GRALYYLQIHPQ 524
Cdd:pfam10433  390 dEDSGFLLSVPTLAAGNLGDGRLLQVTPNGIRLIDSDK--RISEWKPPGGKSITAAAANGRQVLLALsGGELVYFEISTQ 467

                          490
                   ....*....|....*....
gi 9843869     525 ELRQISHTEMEHEVACLDV 543
Cdd:pfam10433  468 LIEVVERKDLSSQVSCISL 486
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 789-1099 5.20e-91

CPSF A subunit region; This family includes a region that lies towards the C-terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160 kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in pre-mRNA. CPSF has also been found to be necessary for splicing of single-intron pre-mRNAs. The function of the aligned region is unknown but may be involved in RNA/DNA binding.


:

Pssm-ID: 427182  Cd Length: 319  Bit Score: 294.88  E-value: 5.20e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     789 HNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKL-----GKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQY-----SGGKL 858
Cdd:pfam03178    2 SCIRLVDPITKEVIDTLELEENEAVLSVKSVNLedsstTKGKEEYLVVGTAFDLGEDPAARSGRILVFEIievpeTNRKL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     859 QTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPM 938
Cdd:pfam03178   82 KLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLGEDKSLLPKAFLDTGVYVVDLKVFGNRIIVGDLMKSVTFVGYDEE 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     939 EGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKD-SAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMqnl 1017
Cdd:pfam03178  162 PYRLIEFARDTQPRWVTAAEFLDGDTVLVADKFGNLHVLRYDpDVPESLDGDPRLLVRAEFHLGETVTSFRKGSLVP--- 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869    1018 GETSTPTQGSVLLGTVNGMIGLVTS-LSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERktEPATGFIDGDLIES 1096
Cdd:pfam03178  239 GGSESPSSPQLLYGTLDGSIGLLVPfISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTPP--RTVKGVIDGDLLER 316


                   ...
gi 9843869    1097 FLD 1099
Cdd:pfam03178  317 FLD 319
 
Name Accession Description Interval E-value
MMS1_N pfam10433
Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects ...
 75-543 8.64e-130

Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects against replication-dependent DNA damage in Saccharomyces cerevisiae. MMS1 belongs to the DDB1 family of cullin 4 adaptors and the two proteins are homologous. MMS1 bridges the interaction of MMS22 and Crt10 with Cul8/Rtt101. Cul8/Rtt101 is a cullin protein involved in the regulation of DNA replication subsequent to DNA damage. The N-terminal region of MMS1 and the C-terminal of MMS22 are required for the the MMS1-MMS22 interaction. The human HIV-1 virion-associated protein Vpr assembles with DDB1 through interaction with DCAF1 (chromatin assembly factor) to form an E3 ubiquitin ligase that targets cellular substrates for proteasome-mediated degradation and subsequent G2 arrest.


Pssm-ID: 463091  Cd Length: 486  Bit Score: 404.72  E-value: 8.64e-130
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869      75 DLLFILTAKYNACILEYkqSGESIDIITRAH-GNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPL------DR 147
Cdd:pfam10433    1 DHLVVGTDSGRLVFLSW--DPEKNQFETIHSrEDLGKSGSRRSQPGQYLAVDPKGRAIAVSAYEGVFLVYPLkqpqklNR 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     148 DNKEL--KAFNIRLEELHVIDVKFLYGCQA-PTICFVYQDPQGR-HVKTYEVSL---------REKEFNKGPWKQEnveA 214
Cdd:pfam10433   79 NEALLlsSPLEARKSEGFILSMVFLDPGYDnPIFALLEQDRTGKtHLKLYEWDLglnhvvrgpKWSEPLDFLPKED---R 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     215 EASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPII------KQSTIVCHNRVDpnGSRYLLGDMEGRLFMLLLEKE 288
Cdd:pfam10433  156 GANLLIPVPKGPGGVLVCGETIITYKDILDQPDIRCPPVarplreNATIFVAWHKLD--NFFILLADEYGDLYLLTIEND 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     289 EqmDGTVTlkDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQPVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLE 368
Cdd:pfam10433  234 E--DNVVT--SIKIGYFGTTSVASALVILDNGFLFVASEFGDSQLYQIDARGDDDLSNLELVQTFSNWAPILDFVVMDLG 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     369 RQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPG--IKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEET 446
Cdd:pfam10433  310 GEDTARIYTCSGAGKRGSLRSLRHGVGAEELAVSEEPGspITGVWTLKSSPEDEYDDYLVVSFVNETRVLSIDGDGVEEV 389

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     447 -ELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPkaLVSEWKEPRAKNISVASCNSSQVVVAV-GRALYYLQIHPQ 524
Cdd:pfam10433  390 dEDSGFLLSVPTLAAGNLGDGRLLQVTPNGIRLIDSDK--RISEWKPPGGKSITAAAANGRQVLLALsGGELVYFEISTQ 467

                          490
                   ....*....|....*....
gi 9843869     525 ELRQISHTEMEHEVACLDV 543
Cdd:pfam10433  468 LIEVVERKDLSSQVSCISL 486
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 789-1099 5.20e-91

CPSF A subunit region; This family includes a region that lies towards the C-terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160 kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in pre-mRNA. CPSF has also been found to be necessary for splicing of single-intron pre-mRNAs. The function of the aligned region is unknown but may be involved in RNA/DNA binding.


Pssm-ID: 427182  Cd Length: 319  Bit Score: 294.88  E-value: 5.20e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     789 HNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKL-----GKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQY-----SGGKL 858
Cdd:pfam03178    2 SCIRLVDPITKEVIDTLELEENEAVLSVKSVNLedsstTKGKEEYLVVGTAFDLGEDPAARSGRILVFEIievpeTNRKL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     859 QTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPM 938
Cdd:pfam03178   82 KLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLGEDKSLLPKAFLDTGVYVVDLKVFGNRIIVGDLMKSVTFVGYDEE 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     939 EGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKD-SAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMqnl 1017
Cdd:pfam03178  162 PYRLIEFARDTQPRWVTAAEFLDGDTVLVADKFGNLHVLRYDpDVPESLDGDPRLLVRAEFHLGETVTSFRKGSLVP--- 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869    1018 GETSTPTQGSVLLGTVNGMIGLVTS-LSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERktEPATGFIDGDLIES 1096
Cdd:pfam03178  239 GGSESPSSPQLLYGTLDGSIGLLVPfISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTPP--RTVKGVIDGDLLER 316


                   ...
gi 9843869    1097 FLD 1099
Cdd:pfam03178  317 FLD 319
SFT1 COG5161
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
13-1104 2.96e-23

Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];


Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 107.36  E-value: 2.96e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869    13 TAVNGCVTGHFTSAEDINLLIAKNTRLEIYVVT-AEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEY 91
Cdd:COG5161   12 TVTEGCSAGLFTPSRTCSLLVYNGNILAVRLWKyDSGLVLVDEHMLLEKVTQIEKYPQISSEQDGLLLLTHRAKISLLRF 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869    92 KQSGESIDIIT--------------------------------------------RAHGNVQDRIgRPSETgiIGIIDPE 127
Cdd:COG5161   92 DSQANEFRTISlhyyegkfkgkslvelakfstlefdirsscallfnedignflpfHVNKNDDDEV-RIDVD--LGMFQMS 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   128 CRMIGLRLYDGLFKVIPLDRD---------NKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTyevSLR 198
Cdd:COG5161  169 KRHFSIFPSQGTNTFNKRKRTlfpgkfsapSKVLKFSELDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRKY---TIL 245

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   199 EKEFNKGPWKQeNVEAEASMVIA------------VPEPFGGAIIIGQESITYHN------------GDKYLAiAPPIIK 254
Cdd:COG5161  246 KNPYNAIVFTL-DLGAGRSAVIDeflvlprdfrvtVAGPVGALLFGSNELILIDStgssytiplnsmSEKYGG-NKIVED 323

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   255 QST--IVCHNR----VDPNGSR-----YLLGDMEGRLFMLLLEkeeqMDGTVTLK------DLRVELLGETSIAECLTYL 317
Cdd:COG5161  324 ISLsdVNCFSRgttsIWIPSSKclietLFLGDLNGDRYYLRIS----MDGKRIIGfdiaslEFEGDLLKKGSAVSCVGHV 399

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   318 DNGVVFVGSRLGDSQPVKLN-------------VDSNEQGS------------------------------YVVAMETFT 354
Cdd:COG5161  400 NNLLFFGGVGDSNSRVLRIKsllptietrasegVGPLEGGNdeemddeysapenklfgnkeqevrrqdepyDAELFNALS 479

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   355 NLGPIVDMCV--VDLER------QGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPL---RSDPNRETDD 423
Cdd:COG5161  480 NAGPITDFAVgkVDVEKglpipnIGLLNLVVTKGSDSEAALAVEGTSLEPCICTVSSFIPLEIVWSQkirGYLRCSRALD 559

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   424 TLVLSFVGQTRVLmLNGEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLVSQEPKaLVSEWKEPRAKNISVAS 502
Cdd:COG5161  560 FYILSRVSDSRIF-RWSEEFLLEVSGEYTRDVNTLLFVEFgEENRVVQVTPSYLLRYDQDLR-MLGRVEFASRAVEARSV 637

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   503 CNSSQVVVAVG--RALYYLQIHPQELRQISHTEMEHEVA-----CLDVTPLGD-SNGLS-----PLCAIGLWTDISARIL 569
Cdd:COG5161  638 RDPLILVVRDSgkILTFYDREKNMRLFKIDLVTCLADAKnksfvLSDSNSLGIfDIGKRisqlePCLVKGLPYAIQFSPE 717

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   570 KLPSFELLhKEMLGGEIIPRSILMTTFESSHYL--LCALGDGALFYFGLNIETGLLSDRkkvTLGTQPTVLRTF--RSLS 645
Cdd:COG5161  718 ASPAMDLA-GEEDGDDQLTEISMSLTYNLIDMLfrLPSIGNYMVAYLGLDLKEEYLFDN---SLSSEIVFYKTHlpRHVS 793

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   646 -----TTNVFACSDRPTVIY-----SSNH-KLVFSNVN-------LKEVNYMC----------------------PLNSD 685
Cdd:COG5161  794 fnlnvTRNDLAITGAPDNADikafsSVGRiDMVFIKAVghsfmfvTGKGPFLCrsrytssskafhrgniplvsviPLSKR 873

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   686 GY--PDSLALANTSTLTIGTMNEIQKLHIRTVPIYESPRKICYQEVSQCFGVLSTR---IEVQDTSGGTTAlrpsastqa 760
Cdd:COG5161  874 GYlmVDNVLGVRASQYVFDNGYVGNKNPVKRTPKHKTLQKLVYHCAGRYMVVGSCEeagFSPKGEDGESGI--------- 944

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   761 lsssvsssklFSSSAAPHETSFgeeveVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKL-------GKDPntYFIVGT 833
Cdd:COG5161  945 ----------PVDTNVPHAEGY-----RFYVDLYSPKSWEVIDTYEFDENEYVFHIKYLILddmqgtkGKSP--YILVGT 1007

                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   834 AMVYPEEAePKQGRIVVFQ-----------YSGGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTE 902
Cdd:COG5161 1008 TFIEGEDR-PARGRLHVLEiisvvpspgspFTDCKLKVLGIEETKGTVVRVCEVRGKIALCQGQKVMVRKIDRSSGIIPV 1086

                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   903 CNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDN---FLGAENAFNLFVCQK 979
Cdd:COG5161 1087 GFYDLHIFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLRNATSTEFLVTGNelyFLCCDAKGNIHGLTY 1166

                       1210      1220      1230      1240      1250      1260      1270      1280
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   980 DSAATTDEERQHLQEVGLFHLGefvNVFCHGSLVMQNlGETSTPTQGS--VLLGTVNGMIGLVTSLSESWYNLLLDMQNR 1057
Cdd:COG5161 1167 SPNNPISMSGARLVKRSSFTLH---SAEIKMNLLPRN-SEFGAGFKKNfiMVYSRSDGMLIHVVPISDAHYRRLLGIQTA 1242

                       1290      1300      1310      1320      1330
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9843869  1058 LNKVIKSVGKIEHSFWR---SFHteRKTEPATGFIDGDLIESF--LDISRPK 1104
Cdd:COG5161 1243 IMARLKSVGGLNPRDYRlnsDIH--LHSLSLRSPLDLHIINLFsyFDMSTRE 1292
 
Name Accession Description Interval E-value
MMS1_N pfam10433
Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects ...
 75-543 8.64e-130

Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects against replication-dependent DNA damage in Saccharomyces cerevisiae. MMS1 belongs to the DDB1 family of cullin 4 adaptors and the two proteins are homologous. MMS1 bridges the interaction of MMS22 and Crt10 with Cul8/Rtt101. Cul8/Rtt101 is a cullin protein involved in the regulation of DNA replication subsequent to DNA damage. The N-terminal region of MMS1 and the C-terminal of MMS22 are required for the the MMS1-MMS22 interaction. The human HIV-1 virion-associated protein Vpr assembles with DDB1 through interaction with DCAF1 (chromatin assembly factor) to form an E3 ubiquitin ligase that targets cellular substrates for proteasome-mediated degradation and subsequent G2 arrest.


Pssm-ID: 463091  Cd Length: 486  Bit Score: 404.72  E-value: 8.64e-130
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869      75 DLLFILTAKYNACILEYkqSGESIDIITRAH-GNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPL------DR 147
Cdd:pfam10433    1 DHLVVGTDSGRLVFLSW--DPEKNQFETIHSrEDLGKSGSRRSQPGQYLAVDPKGRAIAVSAYEGVFLVYPLkqpqklNR 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     148 DNKEL--KAFNIRLEELHVIDVKFLYGCQA-PTICFVYQDPQGR-HVKTYEVSL---------REKEFNKGPWKQEnveA 214
Cdd:pfam10433   79 NEALLlsSPLEARKSEGFILSMVFLDPGYDnPIFALLEQDRTGKtHLKLYEWDLglnhvvrgpKWSEPLDFLPKED---R 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     215 EASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPII------KQSTIVCHNRVDpnGSRYLLGDMEGRLFMLLLEKE 288
Cdd:pfam10433  156 GANLLIPVPKGPGGVLVCGETIITYKDILDQPDIRCPPVarplreNATIFVAWHKLD--NFFILLADEYGDLYLLTIEND 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     289 EqmDGTVTlkDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQPVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLE 368
Cdd:pfam10433  234 E--DNVVT--SIKIGYFGTTSVASALVILDNGFLFVASEFGDSQLYQIDARGDDDLSNLELVQTFSNWAPILDFVVMDLG 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     369 RQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPG--IKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEET 446
Cdd:pfam10433  310 GEDTARIYTCSGAGKRGSLRSLRHGVGAEELAVSEEPGspITGVWTLKSSPEDEYDDYLVVSFVNETRVLSIDGDGVEEV 389

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     447 -ELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPkaLVSEWKEPRAKNISVASCNSSQVVVAV-GRALYYLQIHPQ 524
Cdd:pfam10433  390 dEDSGFLLSVPTLAAGNLGDGRLLQVTPNGIRLIDSDK--RISEWKPPGGKSITAAAANGRQVLLALsGGELVYFEISTQ 467

                          490
                   ....*....|....*....
gi 9843869     525 ELRQISHTEMEHEVACLDV 543
Cdd:pfam10433  468 LIEVVERKDLSSQVSCISL 486
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 789-1099 5.20e-91

CPSF A subunit region; This family includes a region that lies towards the C-terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160 kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in pre-mRNA. CPSF has also been found to be necessary for splicing of single-intron pre-mRNAs. The function of the aligned region is unknown but may be involved in RNA/DNA binding.


Pssm-ID: 427182  Cd Length: 319  Bit Score: 294.88  E-value: 5.20e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     789 HNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKL-----GKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQY-----SGGKL 858
Cdd:pfam03178    2 SCIRLVDPITKEVIDTLELEENEAVLSVKSVNLedsstTKGKEEYLVVGTAFDLGEDPAARSGRILVFEIievpeTNRKL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     859 QTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPM 938
Cdd:pfam03178   82 KLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLGEDKSLLPKAFLDTGVYVVDLKVFGNRIIVGDLMKSVTFVGYDEE 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869     939 EGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKD-SAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMqnl 1017
Cdd:pfam03178  162 PYRLIEFARDTQPRWVTAAEFLDGDTVLVADKFGNLHVLRYDpDVPESLDGDPRLLVRAEFHLGETVTSFRKGSLVP--- 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869    1018 GETSTPTQGSVLLGTVNGMIGLVTS-LSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERktEPATGFIDGDLIES 1096
Cdd:pfam03178  239 GGSESPSSPQLLYGTLDGSIGLLVPfISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTPP--RTVKGVIDGDLLER 316


                   ...
gi 9843869    1097 FLD 1099
Cdd:pfam03178  317 FLD 319
SFT1 COG5161
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
13-1104 2.96e-23

Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];


Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 107.36  E-value: 2.96e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869    13 TAVNGCVTGHFTSAEDINLLIAKNTRLEIYVVT-AEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEY 91
Cdd:COG5161   12 TVTEGCSAGLFTPSRTCSLLVYNGNILAVRLWKyDSGLVLVDEHMLLEKVTQIEKYPQISSEQDGLLLLTHRAKISLLRF 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869    92 KQSGESIDIIT--------------------------------------------RAHGNVQDRIgRPSETgiIGIIDPE 127
Cdd:COG5161   92 DSQANEFRTISlhyyegkfkgkslvelakfstlefdirsscallfnedignflpfHVNKNDDDEV-RIDVD--LGMFQMS 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   128 CRMIGLRLYDGLFKVIPLDRD---------NKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTyevSLR 198
Cdd:COG5161  169 KRHFSIFPSQGTNTFNKRKRTlfpgkfsapSKVLKFSELDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRKY---TIL 245

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   199 EKEFNKGPWKQeNVEAEASMVIA------------VPEPFGGAIIIGQESITYHN------------GDKYLAiAPPIIK 254
Cdd:COG5161  246 KNPYNAIVFTL-DLGAGRSAVIDeflvlprdfrvtVAGPVGALLFGSNELILIDStgssytiplnsmSEKYGG-NKIVED 323

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   255 QST--IVCHNR----VDPNGSR-----YLLGDMEGRLFMLLLEkeeqMDGTVTLK------DLRVELLGETSIAECLTYL 317
Cdd:COG5161  324 ISLsdVNCFSRgttsIWIPSSKclietLFLGDLNGDRYYLRIS----MDGKRIIGfdiaslEFEGDLLKKGSAVSCVGHV 399

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   318 DNGVVFVGSRLGDSQPVKLN-------------VDSNEQGS------------------------------YVVAMETFT 354
Cdd:COG5161  400 NNLLFFGGVGDSNSRVLRIKsllptietrasegVGPLEGGNdeemddeysapenklfgnkeqevrrqdepyDAELFNALS 479

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   355 NLGPIVDMCV--VDLER------QGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPL---RSDPNRETDD 423
Cdd:COG5161  480 NAGPITDFAVgkVDVEKglpipnIGLLNLVVTKGSDSEAALAVEGTSLEPCICTVSSFIPLEIVWSQkirGYLRCSRALD 559

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   424 TLVLSFVGQTRVLmLNGEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLVSQEPKaLVSEWKEPRAKNISVAS 502
Cdd:COG5161  560 FYILSRVSDSRIF-RWSEEFLLEVSGEYTRDVNTLLFVEFgEENRVVQVTPSYLLRYDQDLR-MLGRVEFASRAVEARSV 637

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   503 CNSSQVVVAVG--RALYYLQIHPQELRQISHTEMEHEVA-----CLDVTPLGD-SNGLS-----PLCAIGLWTDISARIL 569
Cdd:COG5161  638 RDPLILVVRDSgkILTFYDREKNMRLFKIDLVTCLADAKnksfvLSDSNSLGIfDIGKRisqlePCLVKGLPYAIQFSPE 717

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   570 KLPSFELLhKEMLGGEIIPRSILMTTFESSHYL--LCALGDGALFYFGLNIETGLLSDRkkvTLGTQPTVLRTF--RSLS 645
Cdd:COG5161  718 ASPAMDLA-GEEDGDDQLTEISMSLTYNLIDMLfrLPSIGNYMVAYLGLDLKEEYLFDN---SLSSEIVFYKTHlpRHVS 793

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   646 -----TTNVFACSDRPTVIY-----SSNH-KLVFSNVN-------LKEVNYMC----------------------PLNSD 685
Cdd:COG5161  794 fnlnvTRNDLAITGAPDNADikafsSVGRiDMVFIKAVghsfmfvTGKGPFLCrsrytssskafhrgniplvsviPLSKR 873

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   686 GY--PDSLALANTSTLTIGTMNEIQKLHIRTVPIYESPRKICYQEVSQCFGVLSTR---IEVQDTSGGTTAlrpsastqa 760
Cdd:COG5161  874 GYlmVDNVLGVRASQYVFDNGYVGNKNPVKRTPKHKTLQKLVYHCAGRYMVVGSCEeagFSPKGEDGESGI--------- 944

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   761 lsssvsssklFSSSAAPHETSFgeeveVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKL-------GKDPntYFIVGT 833
Cdd:COG5161  945 ----------PVDTNVPHAEGY-----RFYVDLYSPKSWEVIDTYEFDENEYVFHIKYLILddmqgtkGKSP--YILVGT 1007

                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   834 AMVYPEEAePKQGRIVVFQ-----------YSGGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTE 902
Cdd:COG5161 1008 TFIEGEDR-PARGRLHVLEiisvvpspgspFTDCKLKVLGIEETKGTVVRVCEVRGKIALCQGQKVMVRKIDRSSGIIPV 1086

                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   903 CNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDN---FLGAENAFNLFVCQK 979
Cdd:COG5161 1087 GFYDLHIFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLRNATSTEFLVTGNelyFLCCDAKGNIHGLTY 1166

                       1210      1220      1230      1240      1250      1260      1270      1280
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9843869   980 DSAATTDEERQHLQEVGLFHLGefvNVFCHGSLVMQNlGETSTPTQGS--VLLGTVNGMIGLVTSLSESWYNLLLDMQNR 1057
Cdd:COG5161 1167 SPNNPISMSGARLVKRSSFTLH---SAEIKMNLLPRN-SEFGAGFKKNfiMVYSRSDGMLIHVVPISDAHYRRLLGIQTA 1242

                       1290      1300      1310      1320      1330
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9843869  1058 LNKVIKSVGKIEHSFWR---SFHteRKTEPATGFIDGDLIESF--LDISRPK 1104
Cdd:COG5161 1243 IMARLKSVGGLNPRDYRlnsDIH--LHSLSLRSPLDLHIINLFsyFDMSTRE 1292
 
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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