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Conserved domains on  [gi|578815943|ref|XP_006716611|]
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cleavage and polyadenylation specificity factor subunit 1 isoform X1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SFT1 super family cl34923
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
1-1434 7.48e-114

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: 390.48  E-value: 7.48e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943    1 MYAVYKQAHPPTGLEFSMYCNFFNNSERNLVVAGTSQLYVYRLNRDaealtkndrstegkahrEKLELAASFSFFGNVMS 80
Cdd:COG5161     1 MNYLYSDESDWTVTEGCSAGLFTPSRTCSLLVYNGNILAVRLWKYD-----------------SGLVLVDEHMLLEKVTQ 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943   81 MASVQLAGAKRDALLLSFKDAKLSVVEYDPGTHDLKTLSLHYFE-----------------EPELRDG------------ 131
Cdd:COG5161    64 IEKYPQISSEQDGLLLLTHRAKISLLRFDSQANEFRTISLHYYEgkfkgkslvelakfstlEFDIRSScallfnedignf 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  132 FVQNVHTP-RVRVDPDGRCAAMLVYGTRLVVLPFRRESLAEEHEGLVGEGQRSSflPSYIIDVRALDEKLLNIIDLQFLH 210
Cdd:COG5161   144 LPFHVNKNdDDEVRIDVDLGMFQMSKRHFSIFPSQGTNTFNKRKRTLFPGKFSA--PSKVLKFSELDGKIKNIIDFVFLE 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  211 GYYEPTLLILFEPNQTWPGRVAVRQDTCSIVAISLNITQKVHPVIWSLTSLPFDCTQALAVPKpigGVVVFAVNSLLYLN 290
Cdd:COG5161   222 NYSIPTVALLYDPKLSLPRKYTILKNPYNAIVFTLDLGAGRSAVIDEFLVLPRDFRVTVAGPV---GALLFGSNELILID 298

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  291 QSVPPYGVALNSLTTGTTAFPlRTQEGVRITLDCAQATFISY---------DKMVISLKGGEIYVLTLITDGmRSVRAFH 361
Cdd:COG5161   299 STGSSYTIPLNSMSEKYGGNK-IVEDISLSDVNCFSRGTTSIwipsskcliETLFLGDLNGDRYYLRISMDG-KRIIGFD 376

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  362 -----------FDKAAASVLTTSMVTMepgyLFLGSRLGNSLLLKYTEKLqepPASAVREAadkeeppskkKRVDATAGW 430
Cdd:COG5161   377 iaslefegdllKKGSAVSCVGHVNNLL----FFGGVGDSNSRVLRIKSLL---PTIETRAS----------EGVGPLEGG 439

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  431 SAAGKSVPQDEVDEIEVYGSEAQSGTQLATYSFEVCDSILNIGPCANAAVGEPAFLSEEFQNSPEPdLEIVVCSGHGKNG 510
Cdd:COG5161   440 NDEEMDDEYSAPENKLFGNKEQEVRRQDEPYDAELFNALSNAGPITDFAVGKVDVEKGLPIPNIGL-LNLVVTKGSDSEA 518

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  511 ALSVLQKSIRPQVVTTFELPGCYDMWTVIAPVRkeeednpkgegteqepsttpeaDDDGRRHGFLILSREDSTMILQTGQ 590
Cdd:COG5161   519 ALAVEGTSLEPCICTVSSFIPLEIVWSQKIRGY----------------------LRCSRALDFYILSRVSDSRIFRWSE 576

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  591 EIMELDTSGFATQGPTVFAGNIGDNRYIVQVSPLGIRLLEG-VNQLHFIPVDLGApIVQCAVADPYVVIMSAEGHVTMFL 669
Cdd:COG5161   577 EFLLEVSGEYTRDVNTLLFVEFGEENRVVQVTPSYLLRYDQdLRMLGRVEFASRA-VEARSVRDPLILVVRDSGKILTFY 655

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  670 LKSDSyggrhhrLALHKPPLHH--QSKVITLCLYRD--LSGMFTTESRLGgARDELGGRSGPEAEGLGSETSPTVDDEEE 745
Cdd:COG5161   656 DREKN-------MRLFKIDLVTclADAKNKSFVLSDsnSLGIFDIGKRIS-QLEPCLVKGLPYAIQFSPEASPAMDLAGE 727

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  746 mLYGDSGslfspskeearrssqppadrdpapfraepthwcllVRENGTMEIYQLPDwrLVFlvknfpvgqrvlvdssfgq 825
Cdd:COG5161   728 -EDGDDQ-----------------------------------LTEISMSLTYNLID--MLF------------------- 750

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  826 pttqgearreeatrqgELPLVKEVLLVALGSRQSRPYL-LVHVDQELLIYEAFPhdsqlgqgnlkvrfkkvPHNINFREK 904
Cdd:COG5161   751 ----------------RLPSIGNYMVAYLGLDLKEEYLfDNSLSSEIVFYKTHL-----------------PRHVSFNLN 797

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  905 KPKPSKKKAEGGGAEEGAGARGRVARFRYFEDIYGYSGVFICGPSPHWLLVTGRGALRLHPMAiDGPVDSFAPFHNvncp 984
Cdd:COG5161   798 VTRNDLAITGAPDNADIKAFSSVGRIDMVFIKAVGHSFMFVTGKGPFLCRSRYTSSSKAFHRG-NIPLVSVIPLSK---- 872

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  985 RGFLYFNRQGELRISVLPAYLSYDA-PWPVRKIPLRCTAHYVAYHVESKVYAVATstntpCARIPRMTGEEKEFETIERD 1063
Cdd:COG5161   873 RGYLMVDNVLGVRASQYVFDNGYVGnKNPVKRTPKHKTLQKLVYHCAGRYMVVGS-----CEEAGFSPKGEDGESGIPVD 947

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1064 ERYIHPQQEAFSIQLISPVSWEAIPnaRIELQEWEHVTCMKTVSLRSEETVSGLKGYVAAGTCLMQGEEVTCRGRILIMD 1143
Cdd:COG5161   948 TNVPHAEGYRFYVDLYSPKSWEVID--TYEFDENEYVFHIKYLILDDMQGTKGKSPYILVGTTFIEGEDRPARGRLHVLE 1025

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1144 VIEVVPEPGQPLTKNKFKVLYEKEQKGPVTALCHCNGHLVSAIGQKIFLWSL-RASELTGMAFIDTQLYIHQMISVKNFI 1222
Cdd:COG5161  1026 IISVVPSPGSPFTDCKLKVLGIEETKGTVVRVCEVRGKIALCQGQKVMVRKIdRSSGIIPVGFYDLHIFTSSIKVVKNLL 1105

                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1223 LAADVMKSISLLRYQEESKTLSLDAKPLE---VYSVDFMVDNAQLGFLVSDRDRNLMVYMYLPEAKESFGGMRLLRRADF 1299
Cdd:COG5161  1106 LAGDIYQGLSFFGFQSEPYRMHLISSSEPlrnATSTEFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSF 1185

                        1370      1380      1390      1400      1410      1420      1430      1440
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1300 HVGAhVNTFWRTPCRGATEGLSKKsvvweNKHITWFATLDGGIGLLLPMQEKTYRRLLMLQNALTTMLPHHAGLNPRAFR 1379
Cdd:COG5161  1186 TLHS-AEIKMNLLPRNSEFGAGFK-----KNFIMVYSRSDGMLIHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYR 1259

                        1450      1460      1470      1480      1490
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 578815943 1380 mLHVDRRTLQNAVRNVLDGELLNRYLYLSTMERSELAKKIGTTPDIILDDLLETD 1434
Cdd:COG5161  1260 -LNSDIHLHSLSLRSPLDLHIINLFSYFDMSTRESVASKAGRIDRKEISDMIASL 1313
 
Name Accession Description Interval E-value
SFT1 COG5161
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
1-1434 7.48e-114

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


Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 390.48  E-value: 7.48e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943    1 MYAVYKQAHPPTGLEFSMYCNFFNNSERNLVVAGTSQLYVYRLNRDaealtkndrstegkahrEKLELAASFSFFGNVMS 80
Cdd:COG5161     1 MNYLYSDESDWTVTEGCSAGLFTPSRTCSLLVYNGNILAVRLWKYD-----------------SGLVLVDEHMLLEKVTQ 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943   81 MASVQLAGAKRDALLLSFKDAKLSVVEYDPGTHDLKTLSLHYFE-----------------EPELRDG------------ 131
Cdd:COG5161    64 IEKYPQISSEQDGLLLLTHRAKISLLRFDSQANEFRTISLHYYEgkfkgkslvelakfstlEFDIRSScallfnedignf 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  132 FVQNVHTP-RVRVDPDGRCAAMLVYGTRLVVLPFRRESLAEEHEGLVGEGQRSSflPSYIIDVRALDEKLLNIIDLQFLH 210
Cdd:COG5161   144 LPFHVNKNdDDEVRIDVDLGMFQMSKRHFSIFPSQGTNTFNKRKRTLFPGKFSA--PSKVLKFSELDGKIKNIIDFVFLE 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  211 GYYEPTLLILFEPNQTWPGRVAVRQDTCSIVAISLNITQKVHPVIWSLTSLPFDCTQALAVPKpigGVVVFAVNSLLYLN 290
Cdd:COG5161   222 NYSIPTVALLYDPKLSLPRKYTILKNPYNAIVFTLDLGAGRSAVIDEFLVLPRDFRVTVAGPV---GALLFGSNELILID 298

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  291 QSVPPYGVALNSLTTGTTAFPlRTQEGVRITLDCAQATFISY---------DKMVISLKGGEIYVLTLITDGmRSVRAFH 361
Cdd:COG5161   299 STGSSYTIPLNSMSEKYGGNK-IVEDISLSDVNCFSRGTTSIwipsskcliETLFLGDLNGDRYYLRISMDG-KRIIGFD 376

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  362 -----------FDKAAASVLTTSMVTMepgyLFLGSRLGNSLLLKYTEKLqepPASAVREAadkeeppskkKRVDATAGW 430
Cdd:COG5161   377 iaslefegdllKKGSAVSCVGHVNNLL----FFGGVGDSNSRVLRIKSLL---PTIETRAS----------EGVGPLEGG 439

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  431 SAAGKSVPQDEVDEIEVYGSEAQSGTQLATYSFEVCDSILNIGPCANAAVGEPAFLSEEFQNSPEPdLEIVVCSGHGKNG 510
Cdd:COG5161   440 NDEEMDDEYSAPENKLFGNKEQEVRRQDEPYDAELFNALSNAGPITDFAVGKVDVEKGLPIPNIGL-LNLVVTKGSDSEA 518

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  511 ALSVLQKSIRPQVVTTFELPGCYDMWTVIAPVRkeeednpkgegteqepsttpeaDDDGRRHGFLILSREDSTMILQTGQ 590
Cdd:COG5161   519 ALAVEGTSLEPCICTVSSFIPLEIVWSQKIRGY----------------------LRCSRALDFYILSRVSDSRIFRWSE 576

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  591 EIMELDTSGFATQGPTVFAGNIGDNRYIVQVSPLGIRLLEG-VNQLHFIPVDLGApIVQCAVADPYVVIMSAEGHVTMFL 669
Cdd:COG5161   577 EFLLEVSGEYTRDVNTLLFVEFGEENRVVQVTPSYLLRYDQdLRMLGRVEFASRA-VEARSVRDPLILVVRDSGKILTFY 655

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  670 LKSDSyggrhhrLALHKPPLHH--QSKVITLCLYRD--LSGMFTTESRLGgARDELGGRSGPEAEGLGSETSPTVDDEEE 745
Cdd:COG5161   656 DREKN-------MRLFKIDLVTclADAKNKSFVLSDsnSLGIFDIGKRIS-QLEPCLVKGLPYAIQFSPEASPAMDLAGE 727

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  746 mLYGDSGslfspskeearrssqppadrdpapfraepthwcllVRENGTMEIYQLPDwrLVFlvknfpvgqrvlvdssfgq 825
Cdd:COG5161   728 -EDGDDQ-----------------------------------LTEISMSLTYNLID--MLF------------------- 750

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  826 pttqgearreeatrqgELPLVKEVLLVALGSRQSRPYL-LVHVDQELLIYEAFPhdsqlgqgnlkvrfkkvPHNINFREK 904
Cdd:COG5161   751 ----------------RLPSIGNYMVAYLGLDLKEEYLfDNSLSSEIVFYKTHL-----------------PRHVSFNLN 797

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  905 KPKPSKKKAEGGGAEEGAGARGRVARFRYFEDIYGYSGVFICGPSPHWLLVTGRGALRLHPMAiDGPVDSFAPFHNvncp 984
Cdd:COG5161   798 VTRNDLAITGAPDNADIKAFSSVGRIDMVFIKAVGHSFMFVTGKGPFLCRSRYTSSSKAFHRG-NIPLVSVIPLSK---- 872

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  985 RGFLYFNRQGELRISVLPAYLSYDA-PWPVRKIPLRCTAHYVAYHVESKVYAVATstntpCARIPRMTGEEKEFETIERD 1063
Cdd:COG5161   873 RGYLMVDNVLGVRASQYVFDNGYVGnKNPVKRTPKHKTLQKLVYHCAGRYMVVGS-----CEEAGFSPKGEDGESGIPVD 947

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1064 ERYIHPQQEAFSIQLISPVSWEAIPnaRIELQEWEHVTCMKTVSLRSEETVSGLKGYVAAGTCLMQGEEVTCRGRILIMD 1143
Cdd:COG5161   948 TNVPHAEGYRFYVDLYSPKSWEVID--TYEFDENEYVFHIKYLILDDMQGTKGKSPYILVGTTFIEGEDRPARGRLHVLE 1025

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1144 VIEVVPEPGQPLTKNKFKVLYEKEQKGPVTALCHCNGHLVSAIGQKIFLWSL-RASELTGMAFIDTQLYIHQMISVKNFI 1222
Cdd:COG5161  1026 IISVVPSPGSPFTDCKLKVLGIEETKGTVVRVCEVRGKIALCQGQKVMVRKIdRSSGIIPVGFYDLHIFTSSIKVVKNLL 1105

                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1223 LAADVMKSISLLRYQEESKTLSLDAKPLE---VYSVDFMVDNAQLGFLVSDRDRNLMVYMYLPEAKESFGGMRLLRRADF 1299
Cdd:COG5161  1106 LAGDIYQGLSFFGFQSEPYRMHLISSSEPlrnATSTEFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSF 1185

                        1370      1380      1390      1400      1410      1420      1430      1440
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1300 HVGAhVNTFWRTPCRGATEGLSKKsvvweNKHITWFATLDGGIGLLLPMQEKTYRRLLMLQNALTTMLPHHAGLNPRAFR 1379
Cdd:COG5161  1186 TLHS-AEIKMNLLPRNSEFGAGFK-----KNFIMVYSRSDGMLIHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYR 1259

                        1450      1460      1470      1480      1490
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 578815943 1380 mLHVDRRTLQNAVRNVLDGELLNRYLYLSTMERSELAKKIGTTPDIILDDLLETD 1434
Cdd:COG5161  1260 -LNSDIHLHSLSLRSPLDLHIINLFSYFDMSTRESVASKAGRIDRKEISDMIASL 1313
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 1073-1405 1.73e-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: 299.12  E-value: 1.73e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  1073 AFSIQLISPVSWEAIPnaRIELQEWEHVTCMKTVSLRSEETVSGLKGYVAAGTCLMQGEEVTCR-GRILIMDVIEVvpep 1151
Cdd:pfam03178    1 ASCIRLVDPITKEVID--TLELEENEAVLSVKSVNLEDSSTTKGKEEYLVVGTAFDLGEDPAARsGRILVFEIIEV---- 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  1152 gqPLTKNKFKVLYEKEQKGPVTALCHCNGHLVSAIGQKIFLWSL-RASELTGMAFIDTQLYIHQMISVKNFILAADVMKS 1230
Cdd:pfam03178   75 --PETNRKLKLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLgEDKSLLPKAFLDTGVYVVDLKVFGNRIIVGDLMKS 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  1231 ISLLRYQEESKTLSLDAK---PLEVYSVDFMVDNaqlGFLVSDRDRNLMVYMYLPEAKESFGG-MRLLRRADFHVGAHVN 1306
Cdd:pfam03178  153 VTFVGYDEEPYRLIEFARdtqPRWVTAAEFLDGD---TVLVADKFGNLHVLRYDPDVPESLDGdPRLLVRAEFHLGETVT 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  1307 TFWRTPC-RGATEGLSKKSVVWenkhitwfATLDGGIGLLLP-MQEKTYRRLLMLQNALTTMLPHHAGLNPRAFRMLHVD 1384
Cdd:pfam03178  230 SFRKGSLvPGGSESPSSPQLLY--------GTLDGSIGLLVPfISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTP 301

                          330       340
                   ....*....|....*....|.
gi 578815943  1385 RRTlqnaVRNVLDGELLNRYL 1405
Cdd:pfam03178  302 PRT----VKGVIDGDLLERFL 318
 
Name Accession Description Interval E-value
SFT1 COG5161
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
1-1434 7.48e-114

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


Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 390.48  E-value: 7.48e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943    1 MYAVYKQAHPPTGLEFSMYCNFFNNSERNLVVAGTSQLYVYRLNRDaealtkndrstegkahrEKLELAASFSFFGNVMS 80
Cdd:COG5161     1 MNYLYSDESDWTVTEGCSAGLFTPSRTCSLLVYNGNILAVRLWKYD-----------------SGLVLVDEHMLLEKVTQ 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943   81 MASVQLAGAKRDALLLSFKDAKLSVVEYDPGTHDLKTLSLHYFE-----------------EPELRDG------------ 131
Cdd:COG5161    64 IEKYPQISSEQDGLLLLTHRAKISLLRFDSQANEFRTISLHYYEgkfkgkslvelakfstlEFDIRSScallfnedignf 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  132 FVQNVHTP-RVRVDPDGRCAAMLVYGTRLVVLPFRRESLAEEHEGLVGEGQRSSflPSYIIDVRALDEKLLNIIDLQFLH 210
Cdd:COG5161   144 LPFHVNKNdDDEVRIDVDLGMFQMSKRHFSIFPSQGTNTFNKRKRTLFPGKFSA--PSKVLKFSELDGKIKNIIDFVFLE 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  211 GYYEPTLLILFEPNQTWPGRVAVRQDTCSIVAISLNITQKVHPVIWSLTSLPFDCTQALAVPKpigGVVVFAVNSLLYLN 290
Cdd:COG5161   222 NYSIPTVALLYDPKLSLPRKYTILKNPYNAIVFTLDLGAGRSAVIDEFLVLPRDFRVTVAGPV---GALLFGSNELILID 298

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  291 QSVPPYGVALNSLTTGTTAFPlRTQEGVRITLDCAQATFISY---------DKMVISLKGGEIYVLTLITDGmRSVRAFH 361
Cdd:COG5161   299 STGSSYTIPLNSMSEKYGGNK-IVEDISLSDVNCFSRGTTSIwipsskcliETLFLGDLNGDRYYLRISMDG-KRIIGFD 376

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  362 -----------FDKAAASVLTTSMVTMepgyLFLGSRLGNSLLLKYTEKLqepPASAVREAadkeeppskkKRVDATAGW 430
Cdd:COG5161   377 iaslefegdllKKGSAVSCVGHVNNLL----FFGGVGDSNSRVLRIKSLL---PTIETRAS----------EGVGPLEGG 439

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  431 SAAGKSVPQDEVDEIEVYGSEAQSGTQLATYSFEVCDSILNIGPCANAAVGEPAFLSEEFQNSPEPdLEIVVCSGHGKNG 510
Cdd:COG5161   440 NDEEMDDEYSAPENKLFGNKEQEVRRQDEPYDAELFNALSNAGPITDFAVGKVDVEKGLPIPNIGL-LNLVVTKGSDSEA 518

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  511 ALSVLQKSIRPQVVTTFELPGCYDMWTVIAPVRkeeednpkgegteqepsttpeaDDDGRRHGFLILSREDSTMILQTGQ 590
Cdd:COG5161   519 ALAVEGTSLEPCICTVSSFIPLEIVWSQKIRGY----------------------LRCSRALDFYILSRVSDSRIFRWSE 576

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  591 EIMELDTSGFATQGPTVFAGNIGDNRYIVQVSPLGIRLLEG-VNQLHFIPVDLGApIVQCAVADPYVVIMSAEGHVTMFL 669
Cdd:COG5161   577 EFLLEVSGEYTRDVNTLLFVEFGEENRVVQVTPSYLLRYDQdLRMLGRVEFASRA-VEARSVRDPLILVVRDSGKILTFY 655

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  670 LKSDSyggrhhrLALHKPPLHH--QSKVITLCLYRD--LSGMFTTESRLGgARDELGGRSGPEAEGLGSETSPTVDDEEE 745
Cdd:COG5161   656 DREKN-------MRLFKIDLVTclADAKNKSFVLSDsnSLGIFDIGKRIS-QLEPCLVKGLPYAIQFSPEASPAMDLAGE 727

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  746 mLYGDSGslfspskeearrssqppadrdpapfraepthwcllVRENGTMEIYQLPDwrLVFlvknfpvgqrvlvdssfgq 825
Cdd:COG5161   728 -EDGDDQ-----------------------------------LTEISMSLTYNLID--MLF------------------- 750

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  826 pttqgearreeatrqgELPLVKEVLLVALGSRQSRPYL-LVHVDQELLIYEAFPhdsqlgqgnlkvrfkkvPHNINFREK 904
Cdd:COG5161   751 ----------------RLPSIGNYMVAYLGLDLKEEYLfDNSLSSEIVFYKTHL-----------------PRHVSFNLN 797

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  905 KPKPSKKKAEGGGAEEGAGARGRVARFRYFEDIYGYSGVFICGPSPHWLLVTGRGALRLHPMAiDGPVDSFAPFHNvncp 984
Cdd:COG5161   798 VTRNDLAITGAPDNADIKAFSSVGRIDMVFIKAVGHSFMFVTGKGPFLCRSRYTSSSKAFHRG-NIPLVSVIPLSK---- 872

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  985 RGFLYFNRQGELRISVLPAYLSYDA-PWPVRKIPLRCTAHYVAYHVESKVYAVATstntpCARIPRMTGEEKEFETIERD 1063
Cdd:COG5161   873 RGYLMVDNVLGVRASQYVFDNGYVGnKNPVKRTPKHKTLQKLVYHCAGRYMVVGS-----CEEAGFSPKGEDGESGIPVD 947

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1064 ERYIHPQQEAFSIQLISPVSWEAIPnaRIELQEWEHVTCMKTVSLRSEETVSGLKGYVAAGTCLMQGEEVTCRGRILIMD 1143
Cdd:COG5161   948 TNVPHAEGYRFYVDLYSPKSWEVID--TYEFDENEYVFHIKYLILDDMQGTKGKSPYILVGTTFIEGEDRPARGRLHVLE 1025

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1144 VIEVVPEPGQPLTKNKFKVLYEKEQKGPVTALCHCNGHLVSAIGQKIFLWSL-RASELTGMAFIDTQLYIHQMISVKNFI 1222
Cdd:COG5161  1026 IISVVPSPGSPFTDCKLKVLGIEETKGTVVRVCEVRGKIALCQGQKVMVRKIdRSSGIIPVGFYDLHIFTSSIKVVKNLL 1105

                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1223 LAADVMKSISLLRYQEESKTLSLDAKPLE---VYSVDFMVDNAQLGFLVSDRDRNLMVYMYLPEAKESFGGMRLLRRADF 1299
Cdd:COG5161  1106 LAGDIYQGLSFFGFQSEPYRMHLISSSEPlrnATSTEFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSF 1185

                        1370      1380      1390      1400      1410      1420      1430      1440
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943 1300 HVGAhVNTFWRTPCRGATEGLSKKsvvweNKHITWFATLDGGIGLLLPMQEKTYRRLLMLQNALTTMLPHHAGLNPRAFR 1379
Cdd:COG5161  1186 TLHS-AEIKMNLLPRNSEFGAGFK-----KNFIMVYSRSDGMLIHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYR 1259

                        1450      1460      1470      1480      1490
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 578815943 1380 mLHVDRRTLQNAVRNVLDGELLNRYLYLSTMERSELAKKIGTTPDIILDDLLETD 1434
Cdd:COG5161  1260 -LNSDIHLHSLSLRSPLDLHIINLFSYFDMSTRESVASKAGRIDRKEISDMIASL 1313
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 1073-1405 1.73e-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: 299.12  E-value: 1.73e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  1073 AFSIQLISPVSWEAIPnaRIELQEWEHVTCMKTVSLRSEETVSGLKGYVAAGTCLMQGEEVTCR-GRILIMDVIEVvpep 1151
Cdd:pfam03178    1 ASCIRLVDPITKEVID--TLELEENEAVLSVKSVNLEDSSTTKGKEEYLVVGTAFDLGEDPAARsGRILVFEIIEV---- 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  1152 gqPLTKNKFKVLYEKEQKGPVTALCHCNGHLVSAIGQKIFLWSL-RASELTGMAFIDTQLYIHQMISVKNFILAADVMKS 1230
Cdd:pfam03178   75 --PETNRKLKLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLgEDKSLLPKAFLDTGVYVVDLKVFGNRIIVGDLMKS 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  1231 ISLLRYQEESKTLSLDAK---PLEVYSVDFMVDNaqlGFLVSDRDRNLMVYMYLPEAKESFGG-MRLLRRADFHVGAHVN 1306
Cdd:pfam03178  153 VTFVGYDEEPYRLIEFARdtqPRWVTAAEFLDGD---TVLVADKFGNLHVLRYDPDVPESLDGdPRLLVRAEFHLGETVT 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943  1307 TFWRTPC-RGATEGLSKKSVVWenkhitwfATLDGGIGLLLP-MQEKTYRRLLMLQNALTTMLPHHAGLNPRAFRMLHVD 1384
Cdd:pfam03178  230 SFRKGSLvPGGSESPSSPQLLY--------GTLDGSIGLLVPfISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTP 301

                          330       340
                   ....*....|....*....|.
gi 578815943  1385 RRTlqnaVRNVLDGELLNRYL 1405
Cdd:pfam03178  302 PRT----VKGVIDGDLLERFL 318
MMS1_N pfam10433
Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects ...
 92-672 1.54e-27

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: 118.52  E-value: 1.54e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943    92 DALLLSFKDAKLSVVEYDPGTHDLKTLslHYFE---EPELRDGFVQNvhtpRVRVDPDGRCAAMLVYGTRLVVLPFRRES 168
Cdd:pfam10433    1 DHLVVGTDSGRLVFLSWDPEKNQFETI--HSREdlgKSGSRRSQPGQ----YLAVDPKGRAIAVSAYEGVFLVYPLKQPQ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943   169 LAEEHEglvgEGQRSSFLPSYIIDvraldeklLNIIDLQFLH-GYYEPTLLILFEPNQtwpGRVAVrqdTCSIVAISLNI 247
Cdd:pfam10433   75 KLNRNE----ALLLSSPLEARKSE--------GFILSMVFLDpGYDNPIFALLEQDRT---GKTHL---KLYEWDLGLNH 136

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943   248 TQKvhPVIWSLTS--LPFDCTQA---LAVPKPIGGVVVFAVNSLLYLNQSVPPYgvalnsLTTGTTAFPLRTQEGVritl 322
Cdd:pfam10433  137 VVR--GPKWSEPLdfLPKEDRGAnllIPVPKGPGGVLVCGETIITYKDILDQPD------IRCPPVARPLRENATI---- 204

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943   323 dcaqatFISYDKM-----VISLKGGEIYVLTLITD------GMRSVRAFHFDKAaasvltTSMVTMEPGYLFLGSRLGNS 391
Cdd:pfam10433  205 ------FVAWHKLdnffiLLADEYGDLYLLTIENDednvvtSIKIGYFGTTSVA------SALVILDNGFLFVASEFGDS 272

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943   392 LLLKYTEKLQEPPASavreaadkeeppskkkrvdatagwsaagksvpqdevdeievygseaqsgtqlatysFEVCDSILN 471
Cdd:pfam10433  273 QLYQIDARGDDDLSN--------------------------------------------------------LELVQTFSN 296

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943   472 IGPCANAAVgepAFLSEEfqnspePDLEIVVCSGHGKNGALSVLQKSIRPQVVTTFELPG--CYDMWTViapvrkeeedn 549
Cdd:pfam10433  297 WAPILDFVV---MDLGGE------DTARIYTCSGAGKRGSLRSLRHGVGAEELAVSEEPGspITGVWTL----------- 356

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578815943   550 pkgegteqePSTTPEADDDgrrhgFLILSREDSTMILQ-TGQEIMELDT-SGFATQGPTVFAGNIGDNRyIVQVSPLGIR 627
Cdd:pfam10433  357 ---------KSSPEDEYDD-----YLVVSFVNETRVLSiDGDGVEEVDEdSGFLLSVPTLAAGNLGDGR-LLQVTPNGIR 421

                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*
gi 578815943   628 LLEGVNQLHFIPVDLGAPIVQCAVADPYVVIMSAEGHVTMFLLKS 672
Cdd:pfam10433  422 LIDSDKRISEWKPPGGKSITAAAANGRQVLLALSGGELVYFEIST 466
 
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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