NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|30696088|ref|NP_199979|]
View 

cleavage and polyadenylation specificity factor 160 [Arabidopsis thaliana]

Protein Classification

CPSF1 family protein( domain architecture ID 13419888)

CPSF1 family protein similar to Arabidopsis thaliana cleavage and polyadenylation specificity factor subunit 1 (CPSF1), the RNA recognition subunit of CPSF that plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A)polymerase and other factors to bring about cleavage and poly(A) addition

Gene Ontology:  GO:0003723|GO:0006397|GO:0005847
PubMed:  38986572|29358758|29074584|11421366
SCOP:  4000432

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 1083-1408 1.30e-92

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: 302.20  E-value: 1.30e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1083 FEIQILEPERsggpWETKAKIPMQTSEHALTVRVVTLLNAS-TGENETLLAVGTAYVQGEDVAAR-GRVLLFSFGKNGdN 1160
Cdd:pfam03178    2 SCIRLVDPIT----KEVIDTLELEENEAVLSVKSVNLEDSStTKGKEEYLVVGTAFDLGEDPAARsGRILVFEIIEVP-E 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1161 SQNVVTEVYSRELKGAISAVASIQGHLLISSGPKIILHKWN-GTELNGVAFFDAPpLYVVSMNVVKSFILLGDVHKSIYF 1239
Cdd:pfam03178   77 TNRKLKLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLGeDKSLLPKAFLDTG-VYVVDLKVFGNRIIVGDLMKSVTF 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1240 LSWKEQGSQLSLLAKDFESLDCFATEFLiDGSTlsLAVSDEQKNIQVFYYAPKMIESWKG-LKLLSRAEFHVGAHVSKFL 1318
Cdd:pfam03178  156 VGYDEEPYRLIEFARDTQPRWVTAAEFL-DGDT--VLVADKFGNLHVLRYDPDVPESLDGdPRLLVRAEFHLGETVTSFR 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1319 RLQMVSSGADKINRFALLFGTLDGSFGCIAP-LDEVTFRRLQSLQKKLVDAVPHVAGLNPLAFRQFRSSGKArrsgPDSI 1397
Cdd:pfam03178  233 KGSLVPGGSESPSSPQLLYGTLDGSIGLLVPfISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTPPRT----VKGV 308

                          330
                   ....*....|.
gi 30696088   1398 VDCELLCHYEM 1408
Cdd:pfam03178  309 IDGDLLERFLD 319
SFT1 super family cl34923
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
79-1442 5.39e-74

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


The actual alignment was detected with superfamily member COG5161:

Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 271.45  E-value: 5.39e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   79 GNTQELRNPKlakrggvmdgvYGVSLELVCHYRLHGNVESIAVLPmgggNSSKGRDSIILTFRDAKISVLEFDDSIHSLR 158
Cdd:COG5161   35 GNILAVRLWK-----------YDSGLVLVDEHMLLEKVTQIEKYP----QISSEQDGLLLLTHRAKISLLRFDSQANEFR 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  159 MTSMHCFEGPDWLHLKRGRESFPRgplVKVDPQGRCGGVLVYGLQMIILKTSQVGSGLVGDDDA--------------FS 224
Cdd:COG5161  100 TISLHYYEGKFKGKSLVELAKFST---LEFDIRSSCALLFNEDIGNFLPFHVNKNDDDEVRIDVdlgmfqmskrhfsiFP 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  225 SGGTVSARVESSYIINLR-------------DLEMKHVKDFVFLHGYIEPVIVILQEEEHTWAGRVSWKHHTCVLSALSI 291
Cdd:COG5161  177 SQGTNTFNKRKRTLFPGKfsapskvlkfselDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRKYTILKNPYNAIVFTL 256

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  292 NSTLKQHPVIWSAINLPHDAYklLAVPSPIGGVLVLCANTIHYHSQSASCALALNNYASSADSS---QELPASNFSVELD 368
Cdd:COG5161  257 DLGAGRSAVIDEFLVLPRDFR--VTVAGPVGALLFGSNELILIDSTGSSYTIPLNSMSEKYGGNkivEDISLSDVNCFSR 334

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  369 AAHGTWIS-----NDVALLSTKSGELLLLTLIYDGRAVQRLDLSK-------SKASVLASDITSVGNSLFFLGSRLGDSL 436
Cdd:COG5161  335 GTTSIWIPsskclIETLFLGDLNGDRYYLRISMDGKRIIGFDIASlefegdlLKKGSAVSCVGHVNNLLFFGGVGDSNSR 414

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  437 LVQFSCR-SGPAASLPGLRDEDEDIegeghqakrlrmTSDTFQDTIGNEELSLFGSTPNNSDSAQKSFSFAVRDSLVNVG 515
Cdd:COG5161  415 VLRIKSLlPTIETRASEGVGPLEGG------------NDEEMDDEYSAPENKLFGNKEQEVRRQDEPYDAELFNALSNAG 482

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  516 PVKDFAYGlrinaDANATGVSKQSN---YELVCCSGHGKNGALCVLRQSIRPEMITEVELPGCKGIWTVyhkSSRGHNAD 592
Cdd:COG5161  483 PITDFAVG-----KVDVEKGLPIPNiglLNLVVTKGSDSEAALAVEGTSLEPCICTVSSFIPLEIVWSQ---KIRGYLRC 554

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  593 SskmaadedEYHAYLIISLEARTMVLETADLLTEVTESvDYYVQGRTIAAGNLFGRRRVIQVFEHGARILDGSF-MNQEL 671
Cdd:COG5161  555 S--------RALDFYILSRVSDSRIFRWSEEFLLEVSG-EYTRDVNTLLFVEFGEENRVVQVTPSYLLRYDQDLrMLGRV 625

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  672 SFgasnsesnsgsESSTVSSVSIADPYVLLRMTDDSIRLLVGD-PSTCTVSISSPSVLEGSKRKISACTLYHDKGP-EPW 749
Cdd:COG5161  626 EF-----------ASRAVEARSVRDPLILVVRDSGKILTFYDReKNMRLFKIDLVTCLADAKNKSFVLSDSNSLGIfDIG 694

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  750 LRKASTDAWLSSGVG-------EAVDSVDGGPQDQG-----DIYCVVCYESGaLEIFDVPSFNcvfsvdkfasgrrhlsd 817
Cdd:COG5161  695 KRISQLEPCLVKGLPyaiqfspEASPAMDLAGEEDGddqltEISMSLTYNLI-DMLFRLPSIG----------------- 756

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  818 mpihelEYELNKNSEDNTsskeikntrvvelamqrwsghhtRPFLFAVLADGTILCYHAYLFDGVDSTKA---ENSLSSE 894
Cdd:COG5161  757 ------NYMVAYLGLDLK-----------------------EEYLFDNSLSSEIVFYKTHLPRHVSFNLNvtrNDLAITG 807

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  895 NPAALNSSGSSKLRNLKFlripldtstregtsdgvasqritMFKNISGHQGFFLSGSRPGWCmlfreRLRFHS-----QL 969
Cdd:COG5161  808 APDNADIKAFSSVGRIDM-----------------------VFIKAVGHSFMFVTGKGPFLC-----RSRYTSsskafHR 859

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  970 CDGSIAAFTVLHNvncnHGFIYVTAQGVLKICQLPSASIYD-NYWPVQKIPLKATPHQVTYYAEKNLYplIVSYPVSKPL 1048
Cdd:COG5161  860 GNIPLVSVIPLSK----RGYLMVDNVLGVRASQYVFDNGYVgNKNPVKRTPKHKTLQKLVYHCAGRYM--VVGSCEEAGF 933

                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1049 nqvlsslvdqEAGQQLDNHNMSSDDLQRTYTVEEFEIQILEPErsggPWETKAKIPMQTSEHALTVRVVTL-LNASTGEN 1127
Cdd:COG5161  934 ----------SPKGEDGESGIPVDTNVPHAEGYRFYVDLYSPK----SWEVIDTYEFDENEYVFHIKYLILdDMQGTKGK 999

                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1128 ETLLAVGTAYVQGEDVAARGRVLLF-------SFGKNGDNSQnvVTEVYSRELKGAISAVASIQGHLLISSGPKIILHKW 1200
Cdd:COG5161 1000 SPYILVGTTFIEGEDRPARGRLHVLeiisvvpSPGSPFTDCK--LKVLGIEETKGTVVRVCEVRGKIALCQGQKVMVRKI 1077

                       1210      1220      1230      1240      1250      1260      1270      1280
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1201 NGTE-LNGVAFFDAPpLYVVSMNVVKSFILLGDVHKSIYFLSWKEQGSQLSLLAKDFESLDCFATEFLIDGSTLSLAVSD 1279
Cdd:COG5161 1078 DRSSgIIPVGFYDLH-IFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLRNATSTEFLVTGNELYFLCCD 1156

                       1290      1300      1310      1320      1330      1340      1350      1360
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1280 EQKNIQVFYYAPKMIESWKGLKLLSRAEFHVGAHVSKFLRL-QMVSSGADKINRFALLFGTLDGSFGCIAPLDEVTFRRL 1358
Cdd:COG5161 1157 AKGNIHGLTYSPNNPISMSGARLVKRSSFTLHSAEIKMNLLpRNSEFGAGFKKNFIMVYSRSDGMLIHVVPISDAHYRRL 1236

                       1370      1380      1390      1400      1410      1420      1430      1440
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1359 QSLQKKLVDAVPHVAGLNPLAFR---QFRSSGKARRsgpdSIVDCELLCHYEMLPLEEQLELAHQIGTTRYSILKDLVDL 1435
Cdd:COG5161 1237 LGIQTAIMARLKSVGGLNPRDYRlnsDIHLHSLSLR----SPLDLHIINLFSYFDMSTRESVASKAGRIDRKEISDMIAS 1312


                 ....*..
gi 30696088 1436 SVGTSFL 1442
Cdd:COG5161 1313 LNLLRSL 1319
 
Name Accession Description Interval E-value
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 1083-1408 1.30e-92

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: 302.20  E-value: 1.30e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1083 FEIQILEPERsggpWETKAKIPMQTSEHALTVRVVTLLNAS-TGENETLLAVGTAYVQGEDVAAR-GRVLLFSFGKNGdN 1160
Cdd:pfam03178    2 SCIRLVDPIT----KEVIDTLELEENEAVLSVKSVNLEDSStTKGKEEYLVVGTAFDLGEDPAARsGRILVFEIIEVP-E 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1161 SQNVVTEVYSRELKGAISAVASIQGHLLISSGPKIILHKWN-GTELNGVAFFDAPpLYVVSMNVVKSFILLGDVHKSIYF 1239
Cdd:pfam03178   77 TNRKLKLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLGeDKSLLPKAFLDTG-VYVVDLKVFGNRIIVGDLMKSVTF 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1240 LSWKEQGSQLSLLAKDFESLDCFATEFLiDGSTlsLAVSDEQKNIQVFYYAPKMIESWKG-LKLLSRAEFHVGAHVSKFL 1318
Cdd:pfam03178  156 VGYDEEPYRLIEFARDTQPRWVTAAEFL-DGDT--VLVADKFGNLHVLRYDPDVPESLDGdPRLLVRAEFHLGETVTSFR 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1319 RLQMVSSGADKINRFALLFGTLDGSFGCIAP-LDEVTFRRLQSLQKKLVDAVPHVAGLNPLAFRQFRSSGKArrsgPDSI 1397
Cdd:pfam03178  233 KGSLVPGGSESPSSPQLLYGTLDGSIGLLVPfISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTPPRT----VKGV 308

                          330
                   ....*....|.
gi 30696088   1398 VDCELLCHYEM 1408
Cdd:pfam03178  309 IDGDLLERFLD 319
SFT1 COG5161
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
79-1442 5.39e-74

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


Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 271.45  E-value: 5.39e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   79 GNTQELRNPKlakrggvmdgvYGVSLELVCHYRLHGNVESIAVLPmgggNSSKGRDSIILTFRDAKISVLEFDDSIHSLR 158
Cdd:COG5161   35 GNILAVRLWK-----------YDSGLVLVDEHMLLEKVTQIEKYP----QISSEQDGLLLLTHRAKISLLRFDSQANEFR 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  159 MTSMHCFEGPDWLHLKRGRESFPRgplVKVDPQGRCGGVLVYGLQMIILKTSQVGSGLVGDDDA--------------FS 224
Cdd:COG5161  100 TISLHYYEGKFKGKSLVELAKFST---LEFDIRSSCALLFNEDIGNFLPFHVNKNDDDEVRIDVdlgmfqmskrhfsiFP 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  225 SGGTVSARVESSYIINLR-------------DLEMKHVKDFVFLHGYIEPVIVILQEEEHTWAGRVSWKHHTCVLSALSI 291
Cdd:COG5161  177 SQGTNTFNKRKRTLFPGKfsapskvlkfselDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRKYTILKNPYNAIVFTL 256

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  292 NSTLKQHPVIWSAINLPHDAYklLAVPSPIGGVLVLCANTIHYHSQSASCALALNNYASSADSS---QELPASNFSVELD 368
Cdd:COG5161  257 DLGAGRSAVIDEFLVLPRDFR--VTVAGPVGALLFGSNELILIDSTGSSYTIPLNSMSEKYGGNkivEDISLSDVNCFSR 334

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  369 AAHGTWIS-----NDVALLSTKSGELLLLTLIYDGRAVQRLDLSK-------SKASVLASDITSVGNSLFFLGSRLGDSL 436
Cdd:COG5161  335 GTTSIWIPsskclIETLFLGDLNGDRYYLRISMDGKRIIGFDIASlefegdlLKKGSAVSCVGHVNNLLFFGGVGDSNSR 414

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  437 LVQFSCR-SGPAASLPGLRDEDEDIegeghqakrlrmTSDTFQDTIGNEELSLFGSTPNNSDSAQKSFSFAVRDSLVNVG 515
Cdd:COG5161  415 VLRIKSLlPTIETRASEGVGPLEGG------------NDEEMDDEYSAPENKLFGNKEQEVRRQDEPYDAELFNALSNAG 482

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  516 PVKDFAYGlrinaDANATGVSKQSN---YELVCCSGHGKNGALCVLRQSIRPEMITEVELPGCKGIWTVyhkSSRGHNAD 592
Cdd:COG5161  483 PITDFAVG-----KVDVEKGLPIPNiglLNLVVTKGSDSEAALAVEGTSLEPCICTVSSFIPLEIVWSQ---KIRGYLRC 554

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  593 SskmaadedEYHAYLIISLEARTMVLETADLLTEVTESvDYYVQGRTIAAGNLFGRRRVIQVFEHGARILDGSF-MNQEL 671
Cdd:COG5161  555 S--------RALDFYILSRVSDSRIFRWSEEFLLEVSG-EYTRDVNTLLFVEFGEENRVVQVTPSYLLRYDQDLrMLGRV 625

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  672 SFgasnsesnsgsESSTVSSVSIADPYVLLRMTDDSIRLLVGD-PSTCTVSISSPSVLEGSKRKISACTLYHDKGP-EPW 749
Cdd:COG5161  626 EF-----------ASRAVEARSVRDPLILVVRDSGKILTFYDReKNMRLFKIDLVTCLADAKNKSFVLSDSNSLGIfDIG 694

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  750 LRKASTDAWLSSGVG-------EAVDSVDGGPQDQG-----DIYCVVCYESGaLEIFDVPSFNcvfsvdkfasgrrhlsd 817
Cdd:COG5161  695 KRISQLEPCLVKGLPyaiqfspEASPAMDLAGEEDGddqltEISMSLTYNLI-DMLFRLPSIG----------------- 756

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  818 mpihelEYELNKNSEDNTsskeikntrvvelamqrwsghhtRPFLFAVLADGTILCYHAYLFDGVDSTKA---ENSLSSE 894
Cdd:COG5161  757 ------NYMVAYLGLDLK-----------------------EEYLFDNSLSSEIVFYKTHLPRHVSFNLNvtrNDLAITG 807

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  895 NPAALNSSGSSKLRNLKFlripldtstregtsdgvasqritMFKNISGHQGFFLSGSRPGWCmlfreRLRFHS-----QL 969
Cdd:COG5161  808 APDNADIKAFSSVGRIDM-----------------------VFIKAVGHSFMFVTGKGPFLC-----RSRYTSsskafHR 859

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  970 CDGSIAAFTVLHNvncnHGFIYVTAQGVLKICQLPSASIYD-NYWPVQKIPLKATPHQVTYYAEKNLYplIVSYPVSKPL 1048
Cdd:COG5161  860 GNIPLVSVIPLSK----RGYLMVDNVLGVRASQYVFDNGYVgNKNPVKRTPKHKTLQKLVYHCAGRYM--VVGSCEEAGF 933

                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1049 nqvlsslvdqEAGQQLDNHNMSSDDLQRTYTVEEFEIQILEPErsggPWETKAKIPMQTSEHALTVRVVTL-LNASTGEN 1127
Cdd:COG5161  934 ----------SPKGEDGESGIPVDTNVPHAEGYRFYVDLYSPK----SWEVIDTYEFDENEYVFHIKYLILdDMQGTKGK 999

                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1128 ETLLAVGTAYVQGEDVAARGRVLLF-------SFGKNGDNSQnvVTEVYSRELKGAISAVASIQGHLLISSGPKIILHKW 1200
Cdd:COG5161 1000 SPYILVGTTFIEGEDRPARGRLHVLeiisvvpSPGSPFTDCK--LKVLGIEETKGTVVRVCEVRGKIALCQGQKVMVRKI 1077

                       1210      1220      1230      1240      1250      1260      1270      1280
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1201 NGTE-LNGVAFFDAPpLYVVSMNVVKSFILLGDVHKSIYFLSWKEQGSQLSLLAKDFESLDCFATEFLIDGSTLSLAVSD 1279
Cdd:COG5161 1078 DRSSgIIPVGFYDLH-IFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLRNATSTEFLVTGNELYFLCCD 1156

                       1290      1300      1310      1320      1330      1340      1350      1360
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1280 EQKNIQVFYYAPKMIESWKGLKLLSRAEFHVGAHVSKFLRL-QMVSSGADKINRFALLFGTLDGSFGCIAPLDEVTFRRL 1358
Cdd:COG5161 1157 AKGNIHGLTYSPNNPISMSGARLVKRSSFTLHSAEIKMNLLpRNSEFGAGFKKNFIMVYSRSDGMLIHVVPISDAHYRRL 1236

                       1370      1380      1390      1400      1410      1420      1430      1440
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1359 QSLQKKLVDAVPHVAGLNPLAFR---QFRSSGKARRsgpdSIVDCELLCHYEMLPLEEQLELAHQIGTTRYSILKDLVDL 1435
Cdd:COG5161 1237 LGIQTAIMARLKSVGGLNPRDYRlnsDIHLHSLSLR----SPLDLHIINLFSYFDMSTRESVASKAGRIDRKEISDMIAS 1312


                 ....*..
gi 30696088 1436 SVGTSFL 1442
Cdd:COG5161 1313 LNLLRSL 1319
MMS1_N pfam10433
Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects ...
 134-665 1.24e-23

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: 106.58  E-value: 1.24e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    134 DSIILTFRDAKISVLEFDDSIHSLRmtSMHCFEGPDwlhlKRG-RESFPrGPLVKVDPQGRC-------GGVLVYGLQMI 205
Cdd:pfam10433    1 DHLVVGTDSGRLVFLSWDPEKNQFE--TIHSREDLG----KSGsRRSQP-GQYLAVDPKGRAiavsayeGVFLVYPLKQP 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    206 ILKTSqvgsglvgdDDAFSSGGTVSARVESSYIInlrdlemkhvkDFVFLH-GYIEPVIVILqEEEHTwaGRVswkhhTC 284
Cdd:pfam10433   74 QKLNR---------NEALLLSSPLEARKSEGFIL-----------SMVFLDpGYDNPIFALL-EQDRT--GKT-----HL 125

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    285 VLSALSINSTLKQHPVIWSAI-----NLPHDAYKLLAVPSPIGGVLVLCANTIHYHSQ-------SASCALALNNYASSA 352
Cdd:pfam10433  126 KLYEWDLGLNHVVRGPKWSEPldflpKEDRGANLLIPVPKGPGGVLVCGETIITYKDIldqpdirCPPVARPLRENATIF 205

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    353 DSSQELPASNFsveldaahgtwisndvaLLSTKSGELLLLTLIYD-GRAVQRLDLSK----SKASVLasdiTSVGNSLFF 427
Cdd:pfam10433  206 VAWHKLDNFFI-----------------LLADEYGDLYLLTIENDeDNVVTSIKIGYfgttSVASAL----VILDNGFLF 264

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    428 LGSRLGDSLLVQFscrsgpaaslpglrdedediegeghqakrlrmtsdtfqDTIGNEELSlfgstpnnsdsaqksfSFAV 507
Cdd:pfam10433  265 VASEFGDSQLYQI--------------------------------------DARGDDDLS----------------NLEL 290

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    508 RDSLVNVGPVKDFAYglrinadANATGvskQSNYELVCCSGHGKNGALCVLRQSI--RPEMITEVELPGCKGIWTVyhKS 585
Cdd:pfam10433  291 VQTFSNWAPILDFVV-------MDLGG---EDTARIYTCSGAGKRGSLRSLRHGVgaEELAVSEEPGSPITGVWTL--KS 358

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    586 SRghnadsskmaadEDEYHAYLIISLEARTMVLE-TADLLTEVTESVDYYVQGRTIAAGNLfGRRRVIQVFEHGARILDG 664
Cdd:pfam10433  359 SP------------EDEYDDYLVVSFVNETRVLSiDGDGVEEVDEDSGFLLSVPTLAAGNL-GDGRLLQVTPNGIRLIDS 425


                   .
gi 30696088    665 S 665
Cdd:pfam10433  426 D 426
 
Name Accession Description Interval E-value
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 1083-1408 1.30e-92

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: 302.20  E-value: 1.30e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1083 FEIQILEPERsggpWETKAKIPMQTSEHALTVRVVTLLNAS-TGENETLLAVGTAYVQGEDVAAR-GRVLLFSFGKNGdN 1160
Cdd:pfam03178    2 SCIRLVDPIT----KEVIDTLELEENEAVLSVKSVNLEDSStTKGKEEYLVVGTAFDLGEDPAARsGRILVFEIIEVP-E 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1161 SQNVVTEVYSRELKGAISAVASIQGHLLISSGPKIILHKWN-GTELNGVAFFDAPpLYVVSMNVVKSFILLGDVHKSIYF 1239
Cdd:pfam03178   77 TNRKLKLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLGeDKSLLPKAFLDTG-VYVVDLKVFGNRIIVGDLMKSVTF 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1240 LSWKEQGSQLSLLAKDFESLDCFATEFLiDGSTlsLAVSDEQKNIQVFYYAPKMIESWKG-LKLLSRAEFHVGAHVSKFL 1318
Cdd:pfam03178  156 VGYDEEPYRLIEFARDTQPRWVTAAEFL-DGDT--VLVADKFGNLHVLRYDPDVPESLDGdPRLLVRAEFHLGETVTSFR 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   1319 RLQMVSSGADKINRFALLFGTLDGSFGCIAP-LDEVTFRRLQSLQKKLVDAVPHVAGLNPLAFRQFRSSGKArrsgPDSI 1397
Cdd:pfam03178  233 KGSLVPGGSESPSSPQLLYGTLDGSIGLLVPfISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTPPRT----VKGV 308

                          330
                   ....*....|.
gi 30696088   1398 VDCELLCHYEM 1408
Cdd:pfam03178  309 IDGDLLERFLD 319
SFT1 COG5161
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
79-1442 5.39e-74

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


Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 271.45  E-value: 5.39e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088   79 GNTQELRNPKlakrggvmdgvYGVSLELVCHYRLHGNVESIAVLPmgggNSSKGRDSIILTFRDAKISVLEFDDSIHSLR 158
Cdd:COG5161   35 GNILAVRLWK-----------YDSGLVLVDEHMLLEKVTQIEKYP----QISSEQDGLLLLTHRAKISLLRFDSQANEFR 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  159 MTSMHCFEGPDWLHLKRGRESFPRgplVKVDPQGRCGGVLVYGLQMIILKTSQVGSGLVGDDDA--------------FS 224
Cdd:COG5161  100 TISLHYYEGKFKGKSLVELAKFST---LEFDIRSSCALLFNEDIGNFLPFHVNKNDDDEVRIDVdlgmfqmskrhfsiFP 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  225 SGGTVSARVESSYIINLR-------------DLEMKHVKDFVFLHGYIEPVIVILQEEEHTWAGRVSWKHHTCVLSALSI 291
Cdd:COG5161  177 SQGTNTFNKRKRTLFPGKfsapskvlkfselDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRKYTILKNPYNAIVFTL 256

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  292 NSTLKQHPVIWSAINLPHDAYklLAVPSPIGGVLVLCANTIHYHSQSASCALALNNYASSADSS---QELPASNFSVELD 368
Cdd:COG5161  257 DLGAGRSAVIDEFLVLPRDFR--VTVAGPVGALLFGSNELILIDSTGSSYTIPLNSMSEKYGGNkivEDISLSDVNCFSR 334

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  369 AAHGTWIS-----NDVALLSTKSGELLLLTLIYDGRAVQRLDLSK-------SKASVLASDITSVGNSLFFLGSRLGDSL 436
Cdd:COG5161  335 GTTSIWIPsskclIETLFLGDLNGDRYYLRISMDGKRIIGFDIASlefegdlLKKGSAVSCVGHVNNLLFFGGVGDSNSR 414

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  437 LVQFSCR-SGPAASLPGLRDEDEDIegeghqakrlrmTSDTFQDTIGNEELSLFGSTPNNSDSAQKSFSFAVRDSLVNVG 515
Cdd:COG5161  415 VLRIKSLlPTIETRASEGVGPLEGG------------NDEEMDDEYSAPENKLFGNKEQEVRRQDEPYDAELFNALSNAG 482

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  516 PVKDFAYGlrinaDANATGVSKQSN---YELVCCSGHGKNGALCVLRQSIRPEMITEVELPGCKGIWTVyhkSSRGHNAD 592
Cdd:COG5161  483 PITDFAVG-----KVDVEKGLPIPNiglLNLVVTKGSDSEAALAVEGTSLEPCICTVSSFIPLEIVWSQ---KIRGYLRC 554

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  593 SskmaadedEYHAYLIISLEARTMVLETADLLTEVTESvDYYVQGRTIAAGNLFGRRRVIQVFEHGARILDGSF-MNQEL 671
Cdd:COG5161  555 S--------RALDFYILSRVSDSRIFRWSEEFLLEVSG-EYTRDVNTLLFVEFGEENRVVQVTPSYLLRYDQDLrMLGRV 625

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  672 SFgasnsesnsgsESSTVSSVSIADPYVLLRMTDDSIRLLVGD-PSTCTVSISSPSVLEGSKRKISACTLYHDKGP-EPW 749
Cdd:COG5161  626 EF-----------ASRAVEARSVRDPLILVVRDSGKILTFYDReKNMRLFKIDLVTCLADAKNKSFVLSDSNSLGIfDIG 694

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  750 LRKASTDAWLSSGVG-------EAVDSVDGGPQDQG-----DIYCVVCYESGaLEIFDVPSFNcvfsvdkfasgrrhlsd 817
Cdd:COG5161  695 KRISQLEPCLVKGLPyaiqfspEASPAMDLAGEEDGddqltEISMSLTYNLI-DMLFRLPSIG----------------- 756

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  818 mpihelEYELNKNSEDNTsskeikntrvvelamqrwsghhtRPFLFAVLADGTILCYHAYLFDGVDSTKA---ENSLSSE 894
Cdd:COG5161  757 ------NYMVAYLGLDLK-----------------------EEYLFDNSLSSEIVFYKTHLPRHVSFNLNvtrNDLAITG 807

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  895 NPAALNSSGSSKLRNLKFlripldtstregtsdgvasqritMFKNISGHQGFFLSGSRPGWCmlfreRLRFHS-----QL 969
Cdd:COG5161  808 APDNADIKAFSSVGRIDM-----------------------VFIKAVGHSFMFVTGKGPFLC-----RSRYTSsskafHR 859

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088  970 CDGSIAAFTVLHNvncnHGFIYVTAQGVLKICQLPSASIYD-NYWPVQKIPLKATPHQVTYYAEKNLYplIVSYPVSKPL 1048
Cdd:COG5161  860 GNIPLVSVIPLSK----RGYLMVDNVLGVRASQYVFDNGYVgNKNPVKRTPKHKTLQKLVYHCAGRYM--VVGSCEEAGF 933

                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1049 nqvlsslvdqEAGQQLDNHNMSSDDLQRTYTVEEFEIQILEPErsggPWETKAKIPMQTSEHALTVRVVTL-LNASTGEN 1127
Cdd:COG5161  934 ----------SPKGEDGESGIPVDTNVPHAEGYRFYVDLYSPK----SWEVIDTYEFDENEYVFHIKYLILdDMQGTKGK 999

                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1128 ETLLAVGTAYVQGEDVAARGRVLLF-------SFGKNGDNSQnvVTEVYSRELKGAISAVASIQGHLLISSGPKIILHKW 1200
Cdd:COG5161 1000 SPYILVGTTFIEGEDRPARGRLHVLeiisvvpSPGSPFTDCK--LKVLGIEETKGTVVRVCEVRGKIALCQGQKVMVRKI 1077

                       1210      1220      1230      1240      1250      1260      1270      1280
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1201 NGTE-LNGVAFFDAPpLYVVSMNVVKSFILLGDVHKSIYFLSWKEQGSQLSLLAKDFESLDCFATEFLIDGSTLSLAVSD 1279
Cdd:COG5161 1078 DRSSgIIPVGFYDLH-IFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLRNATSTEFLVTGNELYFLCCD 1156

                       1290      1300      1310      1320      1330      1340      1350      1360
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1280 EQKNIQVFYYAPKMIESWKGLKLLSRAEFHVGAHVSKFLRL-QMVSSGADKINRFALLFGTLDGSFGCIAPLDEVTFRRL 1358
Cdd:COG5161 1157 AKGNIHGLTYSPNNPISMSGARLVKRSSFTLHSAEIKMNLLpRNSEFGAGFKKNFIMVYSRSDGMLIHVVPISDAHYRRL 1236

                       1370      1380      1390      1400      1410      1420      1430      1440
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088 1359 QSLQKKLVDAVPHVAGLNPLAFR---QFRSSGKARRsgpdSIVDCELLCHYEMLPLEEQLELAHQIGTTRYSILKDLVDL 1435
Cdd:COG5161 1237 LGIQTAIMARLKSVGGLNPRDYRlnsDIHLHSLSLR----SPLDLHIINLFSYFDMSTRESVASKAGRIDRKEISDMIAS 1312


                 ....*..
gi 30696088 1436 SVGTSFL 1442
Cdd:COG5161 1313 LNLLRSL 1319
MMS1_N pfam10433
Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects ...
 134-665 1.24e-23

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: 106.58  E-value: 1.24e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    134 DSIILTFRDAKISVLEFDDSIHSLRmtSMHCFEGPDwlhlKRG-RESFPrGPLVKVDPQGRC-------GGVLVYGLQMI 205
Cdd:pfam10433    1 DHLVVGTDSGRLVFLSWDPEKNQFE--TIHSREDLG----KSGsRRSQP-GQYLAVDPKGRAiavsayeGVFLVYPLKQP 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    206 ILKTSqvgsglvgdDDAFSSGGTVSARVESSYIInlrdlemkhvkDFVFLH-GYIEPVIVILqEEEHTwaGRVswkhhTC 284
Cdd:pfam10433   74 QKLNR---------NEALLLSSPLEARKSEGFIL-----------SMVFLDpGYDNPIFALL-EQDRT--GKT-----HL 125

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    285 VLSALSINSTLKQHPVIWSAI-----NLPHDAYKLLAVPSPIGGVLVLCANTIHYHSQ-------SASCALALNNYASSA 352
Cdd:pfam10433  126 KLYEWDLGLNHVVRGPKWSEPldflpKEDRGANLLIPVPKGPGGVLVCGETIITYKDIldqpdirCPPVARPLRENATIF 205

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    353 DSSQELPASNFsveldaahgtwisndvaLLSTKSGELLLLTLIYD-GRAVQRLDLSK----SKASVLasdiTSVGNSLFF 427
Cdd:pfam10433  206 VAWHKLDNFFI-----------------LLADEYGDLYLLTIENDeDNVVTSIKIGYfgttSVASAL----VILDNGFLF 264

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    428 LGSRLGDSLLVQFscrsgpaaslpglrdedediegeghqakrlrmtsdtfqDTIGNEELSlfgstpnnsdsaqksfSFAV 507
Cdd:pfam10433  265 VASEFGDSQLYQI--------------------------------------DARGDDDLS----------------NLEL 290

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    508 RDSLVNVGPVKDFAYglrinadANATGvskQSNYELVCCSGHGKNGALCVLRQSI--RPEMITEVELPGCKGIWTVyhKS 585
Cdd:pfam10433  291 VQTFSNWAPILDFVV-------MDLGG---EDTARIYTCSGAGKRGSLRSLRHGVgaEELAVSEEPGSPITGVWTL--KS 358

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30696088    586 SRghnadsskmaadEDEYHAYLIISLEARTMVLE-TADLLTEVTESVDYYVQGRTIAAGNLfGRRRVIQVFEHGARILDG 664
Cdd:pfam10433  359 SP------------EDEYDDYLVVSFVNETRVLSiDGDGVEEVDEDSGFLLSVPTLAAGNL-GDGRLLQVTPNGIRLIDS 425


                   .
gi 30696088    665 S 665
Cdd:pfam10433  426 D 426
 
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