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Conserved domains on  [gi|1945602123|gb|KAG0172330|]
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Cleavage and polyadenylation specificity factor subunit 1 [Apophysomyces sp. BC1021]

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];
102-1483 1.22e-150

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: 494.87  E-value: 1.22e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  102 SGRLELVAQYKLNGSIATLGVVrtasPRGKEGCDSLLLGFNDAKMSLLEWSPATNSIVTVSIHYYERDELKKEFLTNPYP 181
Cdd:COG5161     46 DSGLVLVDEHMLLEKVTQIEKY----PQISSEQDGLLLLTHRAKISLLRFDSQANEFRTISLHYYEGKFKGKSLVELAKF 121

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  182 PTIHMDPQQRCAvMNFYDNKLAVLPFrQSEKRDGPISLLDVD--------DQAQKWPYSS-------------------S 234
Cdd:COG5161    122 STLEFDIRSSCA-LLFNEDIGNFLPF-HVNKNDDDEVRIDVDlgmfqmskRHFSIFPSQGtntfnkrkrtlfpgkfsapS 199

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  235 FVLDLESIDSRIKNVIDMVFLSGYYEPTLAILFQTEQTWTGQvcsiFPNAKDTVSVVVISLDLSAKIYPIIYSLDKLPYD 314
Cdd:COG5161    200 KVLKFSELDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRK----YTILKNPYNAIVFTLDLGAGRSAVIDEFLVLPRD 275

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  315 CLKLFAMPkpvDGLLIIASNSLLHVSQGSPGVGVAVNGYTKKTTEFAGMAyGDETIKMDLVLDGAKAFSLGGKRCVI--- 391
Cdd:COG5161    276 FRVTVAGP---VGALLFGSNELILIDSTGSSYTIPLNSMSEKYGGNKIVE-DISLSDVNCFSRGTTSIWIPSSKCLIetl 351

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  392 FLQD--GAWILVEMVLDGNKVVGMELVKMEHAQGKATapLAMVPSCVTSVKDGEyFFLGSRVGDSLLIKWRyNSDPVKRT 469
Cdd:COG5161    352 FLGDlnGDRYYLRISMDGKRIIGFDIASLEFEGDLLK--KGSAVSCVGHVNNLL-FFGGVGDSNSRVLRIK-SLLPTIET 427

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  470 KLSAGD------------------------------------LTFRVCDSLLNTGPIVDMAVGNV---EHAEVPDLTEat 510
Cdd:COG5161    428 RASEGVgpleggndeemddeysapenklfgnkeqevrrqdepYDAELFNALSNAGPITDFAVGKVdveKGLPIPNIGL-- 505

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  511 sitpdLELASCSGHGKNGSLCVFQRHIRPISTFSFTQSDCQSVWSIKCRKehyfegmqvgrgqgskgpaYLWNEDTADag 590
Cdd:COG5161    506 -----LNLVVTKGSDSEAALAVEGTSLEPCICTVSSFIPLEIVWSQKIRG-------------------YLRCSRALD-- 559

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  591 nafnnsfdkLLFISKSTSTLVLAAGEELQELGNSDFYTSGPTVTVSTLFDHTQIVQVYAHGVMLLSPEGKLLQTLPVKKS 670
Cdd:COG5161    560 ---------FYILSRVSDSRIFRWSEEFLLEVSGEYTRDVNTLLFVEFGEENRVVQVTPSYLLRYDQDLRMLGRVEFASR 630

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  671 RIVDASIYDPYILLSLEDQTILALQGNPDTRDLSHMQVPSSLNaeddtstSSTNKKTHSPPKDAVDSFDeIDLDLYGDQT 750
Cdd:COG5161    631 AVEARSVRDPLILVVRDSGKILTFYDREKNMRLFKIDLVTCLA-------DAKNKSFVLSDSNSLGIFD-IGKRISQLEP 702

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  751 DHVEKVKEDTPIADDSNktlaaepdyeddeemlyDDNETAPvhtvaggeEIDeinvsmkgGLSEVTQItfwcllyttdGT 830
Cdd:COG5161    703 CLVKGLPYAIQFSPEAS-----------------PAMDLAG--------EED--------GDDQLTEI----------SM 739

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  831 LQLHTLPDfracfafprfdllpgLIVDHPvrepssatlqqqtsavpgdtgttTIKELIIANIGKERKTPHLVARTHTDDI 910
Cdd:COG5161    740 SLTYNLID---------------MLFRLP-----------------------SIGNYMVAYLGLDLKEEYLFDNSLSSEI 781

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  911 IIYKAFGFVSTSdpstagdldrlalrfsrvHHEYVSRKTHAESEKKDDvMQIDEFEVPDedantpsdkpqpvpfrrHMLI 990
Cdd:COG5161    782 VFYKTHLPRHVS------------------FNLNVTRNDLAITGAPDN-ADIKAFSSVG-----------------RIDM 825

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  991 PFTDISGYAGVFVAGPQPAWLLCSCKSFVRVHPMkSDHEIIGFTQFHnvncKHGFISVDAESNIRLCGLPTGKATYDMDW 1070
Cdd:COG5161    826 VFIKAVGHSFMFVTGKGPFLCRSRYTSSSKAFHR-GNIPLVSVIPLS----KRGYLMVDNVLGVRASQYVFDNGYVGNKN 900

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1071 IMQKVPLGQTVHKIEYHPTMRVYAVLVSSPEAVRLRNEEGAPIDGKegerDVGEFLPVVDRYSLLMVSPVTWEVVDRVEF 1150
Cdd:COG5161    901 PVKRTPKHKTLQKLVYHCAGRYMVVGSCEEAGFSPKGEDGESGIPV----DTNVPHAEGYRFYVDLYSPKSWEVIDTYEF 976

                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1151 EEYEQGFSLQCVALESKQTSTGRKHFMAVGTGYLRGEDTAMRGSIYLFDIIEVVPEPNNPQTNHRFKHLHTEDVKGAVTA 1230
Cdd:COG5161    977 DENEYVFHIKYLILDDMQGTKGKSPYILVGTTFIEGEDRPARGRLHVLEIISVVPSPGSPFTDCKLKVLGIEETKGTVVR 1056

                         1210      1220      1230      1240      1250      1260      1270      1280
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1231 LCDASGHLVSCIGSKVIIWSFEDNESVVGVAFIDVQIYVTSICSIKNFIVLGDAQKSVWFLGFQLEPAKLVLLGKDYQSF 1310
Cdd:COG5161   1057 VCEVRGKIALCQGQKVMVRKIDRSSGIIPVGFYDLHIFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLR 1136

                         1290      1300      1310      1320      1330      1340      1350      1360
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1311 EVASVNFIIDDKSLYLLVGDTDDNMDIYQYAPFNLQSFGGQKLMRRGDFHVGAQVRTMVRLPQISQ-GEYNRRHF-CLCG 1388
Cdd:COG5161   1137 NATSTEFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSFTLHSAEIKMNLLPRNSEfGAGFKKNFiMVYS 1216

                         1370      1380      1390      1400      1410      1420      1430      1440
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1389 SFSGSISVVSPIPEKTFKRLNTLYGQLVNGLQHVAGLNPRAFRLIKGPKQRmsSNRTKAVLDGDLIFEFAGLAVNQQREM 1468
Cdd:COG5161   1217 RSDGMLIHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYRLNSDIHLH--SLSLRSPLDLHIINLFSYFDMSTRESV 1294

                         1450
                   ....*....|....*
gi 1945602123 1469 TKQIGTTVSRIMEDL 1483
Cdd:COG5161   1295 ASKAGRIDRKEISDM 1309
PTZ00085 PTZ00085
40S ribosomal protein S28; Provisional
 1481-1550 2.23e-36

40S ribosomal protein S28; Provisional


:

Pssm-ID: 240261  Cd Length: 73  Bit Score: 132.18  E-value: 2.23e-36
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1945602123 1481 EDLDAQKTPVKLAKVIKVLGRTGSRGGVTQVRVEFMDDT---NRSIIRNVKGPVRENDILCLLESEREARRLR 1550
Cdd:PTZ00085     1 EVVTQDTEQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEgdaGRTLIRNVKGPVREGDILSLMETEREARRLR 73
 
Name Accession Description Interval E-value
SFT1 COG5161
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
102-1483 1.22e-150

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


Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 494.87  E-value: 1.22e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  102 SGRLELVAQYKLNGSIATLGVVrtasPRGKEGCDSLLLGFNDAKMSLLEWSPATNSIVTVSIHYYERDELKKEFLTNPYP 181
Cdd:COG5161     46 DSGLVLVDEHMLLEKVTQIEKY----PQISSEQDGLLLLTHRAKISLLRFDSQANEFRTISLHYYEGKFKGKSLVELAKF 121

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  182 PTIHMDPQQRCAvMNFYDNKLAVLPFrQSEKRDGPISLLDVD--------DQAQKWPYSS-------------------S 234
Cdd:COG5161    122 STLEFDIRSSCA-LLFNEDIGNFLPF-HVNKNDDDEVRIDVDlgmfqmskRHFSIFPSQGtntfnkrkrtlfpgkfsapS 199

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  235 FVLDLESIDSRIKNVIDMVFLSGYYEPTLAILFQTEQTWTGQvcsiFPNAKDTVSVVVISLDLSAKIYPIIYSLDKLPYD 314
Cdd:COG5161    200 KVLKFSELDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRK----YTILKNPYNAIVFTLDLGAGRSAVIDEFLVLPRD 275

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  315 CLKLFAMPkpvDGLLIIASNSLLHVSQGSPGVGVAVNGYTKKTTEFAGMAyGDETIKMDLVLDGAKAFSLGGKRCVI--- 391
Cdd:COG5161    276 FRVTVAGP---VGALLFGSNELILIDSTGSSYTIPLNSMSEKYGGNKIVE-DISLSDVNCFSRGTTSIWIPSSKCLIetl 351

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  392 FLQD--GAWILVEMVLDGNKVVGMELVKMEHAQGKATapLAMVPSCVTSVKDGEyFFLGSRVGDSLLIKWRyNSDPVKRT 469
Cdd:COG5161    352 FLGDlnGDRYYLRISMDGKRIIGFDIASLEFEGDLLK--KGSAVSCVGHVNNLL-FFGGVGDSNSRVLRIK-SLLPTIET 427

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  470 KLSAGD------------------------------------LTFRVCDSLLNTGPIVDMAVGNV---EHAEVPDLTEat 510
Cdd:COG5161    428 RASEGVgpleggndeemddeysapenklfgnkeqevrrqdepYDAELFNALSNAGPITDFAVGKVdveKGLPIPNIGL-- 505

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  511 sitpdLELASCSGHGKNGSLCVFQRHIRPISTFSFTQSDCQSVWSIKCRKehyfegmqvgrgqgskgpaYLWNEDTADag 590
Cdd:COG5161    506 -----LNLVVTKGSDSEAALAVEGTSLEPCICTVSSFIPLEIVWSQKIRG-------------------YLRCSRALD-- 559

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  591 nafnnsfdkLLFISKSTSTLVLAAGEELQELGNSDFYTSGPTVTVSTLFDHTQIVQVYAHGVMLLSPEGKLLQTLPVKKS 670
Cdd:COG5161    560 ---------FYILSRVSDSRIFRWSEEFLLEVSGEYTRDVNTLLFVEFGEENRVVQVTPSYLLRYDQDLRMLGRVEFASR 630

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  671 RIVDASIYDPYILLSLEDQTILALQGNPDTRDLSHMQVPSSLNaeddtstSSTNKKTHSPPKDAVDSFDeIDLDLYGDQT 750
Cdd:COG5161    631 AVEARSVRDPLILVVRDSGKILTFYDREKNMRLFKIDLVTCLA-------DAKNKSFVLSDSNSLGIFD-IGKRISQLEP 702

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  751 DHVEKVKEDTPIADDSNktlaaepdyeddeemlyDDNETAPvhtvaggeEIDeinvsmkgGLSEVTQItfwcllyttdGT 830
Cdd:COG5161    703 CLVKGLPYAIQFSPEAS-----------------PAMDLAG--------EED--------GDDQLTEI----------SM 739

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  831 LQLHTLPDfracfafprfdllpgLIVDHPvrepssatlqqqtsavpgdtgttTIKELIIANIGKERKTPHLVARTHTDDI 910
Cdd:COG5161    740 SLTYNLID---------------MLFRLP-----------------------SIGNYMVAYLGLDLKEEYLFDNSLSSEI 781

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  911 IIYKAFGFVSTSdpstagdldrlalrfsrvHHEYVSRKTHAESEKKDDvMQIDEFEVPDedantpsdkpqpvpfrrHMLI 990
Cdd:COG5161    782 VFYKTHLPRHVS------------------FNLNVTRNDLAITGAPDN-ADIKAFSSVG-----------------RIDM 825

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  991 PFTDISGYAGVFVAGPQPAWLLCSCKSFVRVHPMkSDHEIIGFTQFHnvncKHGFISVDAESNIRLCGLPTGKATYDMDW 1070
Cdd:COG5161    826 VFIKAVGHSFMFVTGKGPFLCRSRYTSSSKAFHR-GNIPLVSVIPLS----KRGYLMVDNVLGVRASQYVFDNGYVGNKN 900

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1071 IMQKVPLGQTVHKIEYHPTMRVYAVLVSSPEAVRLRNEEGAPIDGKegerDVGEFLPVVDRYSLLMVSPVTWEVVDRVEF 1150
Cdd:COG5161    901 PVKRTPKHKTLQKLVYHCAGRYMVVGSCEEAGFSPKGEDGESGIPV----DTNVPHAEGYRFYVDLYSPKSWEVIDTYEF 976

                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1151 EEYEQGFSLQCVALESKQTSTGRKHFMAVGTGYLRGEDTAMRGSIYLFDIIEVVPEPNNPQTNHRFKHLHTEDVKGAVTA 1230
Cdd:COG5161    977 DENEYVFHIKYLILDDMQGTKGKSPYILVGTTFIEGEDRPARGRLHVLEIISVVPSPGSPFTDCKLKVLGIEETKGTVVR 1056

                         1210      1220      1230      1240      1250      1260      1270      1280
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1231 LCDASGHLVSCIGSKVIIWSFEDNESVVGVAFIDVQIYVTSICSIKNFIVLGDAQKSVWFLGFQLEPAKLVLLGKDYQSF 1310
Cdd:COG5161   1057 VCEVRGKIALCQGQKVMVRKIDRSSGIIPVGFYDLHIFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLR 1136

                         1290      1300      1310      1320      1330      1340      1350      1360
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1311 EVASVNFIIDDKSLYLLVGDTDDNMDIYQYAPFNLQSFGGQKLMRRGDFHVGAQVRTMVRLPQISQ-GEYNRRHF-CLCG 1388
Cdd:COG5161   1137 NATSTEFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSFTLHSAEIKMNLLPRNSEfGAGFKKNFiMVYS 1216

                         1370      1380      1390      1400      1410      1420      1430      1440
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1389 SFSGSISVVSPIPEKTFKRLNTLYGQLVNGLQHVAGLNPRAFRLIKGPKQRmsSNRTKAVLDGDLIFEFAGLAVNQQREM 1468
Cdd:COG5161   1217 RSDGMLIHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYRLNSDIHLH--SLSLRSPLDLHIINLFSYFDMSTRESV 1294

                         1450
                   ....*....|....*
gi 1945602123 1469 TKQIGTTVSRIMEDL 1483
Cdd:COG5161   1295 ASKAGRIDRKEISDM 1309
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 1131-1457 1.48e-88

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: 291.42  E-value: 1.48e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1131 RYSLLMVSPVTWEVVDRVEFEEYEQGFSLQCVALESKQTSTGRKHFMAVGTGYLRGEDTAMR-GSIYLFDIIEVvpepnn 1209
Cdd:pfam03178    1 ASCIRLVDPITKEVIDTLELEENEAVLSVKSVNLEDSSTTKGKEEYLVVGTAFDLGEDPAARsGRILVFEIIEV------ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1210 PQTNHRFKHLHTEDVKGAVTALCDASGHLVSCIGSKVIIWSFEDNESVVGVAFIDVQIYVTSICSIKNFIVLGDAQKSVW 1289
Cdd:pfam03178   75 PETNRKLKLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLGEDKSLLPKAFLDTGVYVVDLKVFGNRIIVGDLMKSVT 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1290 FLGFQLEPAKLVLLGKDYQSFEVASVNFIIDDkslYLLVGDTDDNMDIYQYAPFNLQSFGGQ-KLMRRGDFHVGAQVRTM 1368
Cdd:pfam03178  155 FVGYDEEPYRLIEFARDTQPRWVTAAEFLDGD---TVLVADKFGNLHVLRYDPDVPESLDGDpRLLVRAEFHLGETVTSF 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1369 VRLPQISQG-EYNRRHFCLCGSFSGSISVVSP-IPEKTFKRLNTLYGQLVNGLQHVAGLNPRAFRLIKGPKQRMssnrtK 1446
Cdd:pfam03178  232 RKGSLVPGGsESPSSPQLLYGTLDGSIGLLVPfISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTPPRTV-----K 306

                          330
                   ....*....|.
gi 1945602123 1447 AVLDGDLIFEF 1457
Cdd:pfam03178  307 GVIDGDLLERF 317
PTZ00085 PTZ00085
40S ribosomal protein S28; Provisional
 1481-1550 2.23e-36

40S ribosomal protein S28; Provisional


Pssm-ID: 240261  Cd Length: 73  Bit Score: 132.18  E-value: 2.23e-36
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1945602123 1481 EDLDAQKTPVKLAKVIKVLGRTGSRGGVTQVRVEFMDDT---NRSIIRNVKGPVRENDILCLLESEREARRLR 1550
Cdd:PTZ00085     1 EVVTQDTEQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEgdaGRTLIRNVKGPVREGDILSLMETEREARRLR 73
S1_S28E cd04457
S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 1491-1550 2.56e-36

S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28E might be involved in protein synthesis.


Pssm-ID: 239904  Cd Length: 60  Bit Score: 131.60  E-value: 2.56e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1491 KLAKVIKVLGRTGSRGGVTQVRVEFMDDTNRSIIRNVKGPVRENDILCLLESEREARRLR 1550
Cdd:cd04457      1 KLAEVIKVLGRTGSRGEVTQVRVEFMDDKGRSIIRNVKGPVREGDILMLLETEREARRLR 60
Ribosomal_S28e pfam01200
Ribosomal protein S28e;
1489-1549 3.75e-33

Ribosomal protein S28e;


Pssm-ID: 460109  Cd Length: 64  Bit Score: 122.36  E-value: 3.75e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1945602123 1489 PVKLAKVIKVLGRTGSRGGVTQVRVEFMD--DTNRSIIRNVKGPVRENDILCLLESEREARRL 1549
Cdd:pfam01200    2 KAQPAEVIKVLGRTGSRGEVTQVRVEILEgrDKGRIITRNVKGPVRVGDILMLLETEREARRL 64
RPS28A COG2053
Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]; Ribosomal ...
 1493-1550 3.70e-21

Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S28E/S33 is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 441656  Cd Length: 73  Bit Score: 88.49  E-value: 3.70e-21
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1493 AKVIKVLGRTGSRGGVTQVRVEFMD--DTNRSIIRNVKGPVRENDILCLLESEREARRLR 1550
Cdd:COG2053     12 AEVIEIIGRTGMTGEVTQVRVRILEgrDKGRIITRNVKGPVRVGDILMLRETEREARKLK 71
 
Name Accession Description Interval E-value
SFT1 COG5161
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
102-1483 1.22e-150

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


Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 494.87  E-value: 1.22e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  102 SGRLELVAQYKLNGSIATLGVVrtasPRGKEGCDSLLLGFNDAKMSLLEWSPATNSIVTVSIHYYERDELKKEFLTNPYP 181
Cdd:COG5161     46 DSGLVLVDEHMLLEKVTQIEKY----PQISSEQDGLLLLTHRAKISLLRFDSQANEFRTISLHYYEGKFKGKSLVELAKF 121

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  182 PTIHMDPQQRCAvMNFYDNKLAVLPFrQSEKRDGPISLLDVD--------DQAQKWPYSS-------------------S 234
Cdd:COG5161    122 STLEFDIRSSCA-LLFNEDIGNFLPF-HVNKNDDDEVRIDVDlgmfqmskRHFSIFPSQGtntfnkrkrtlfpgkfsapS 199

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  235 FVLDLESIDSRIKNVIDMVFLSGYYEPTLAILFQTEQTWTGQvcsiFPNAKDTVSVVVISLDLSAKIYPIIYSLDKLPYD 314
Cdd:COG5161    200 KVLKFSELDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRK----YTILKNPYNAIVFTLDLGAGRSAVIDEFLVLPRD 275

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  315 CLKLFAMPkpvDGLLIIASNSLLHVSQGSPGVGVAVNGYTKKTTEFAGMAyGDETIKMDLVLDGAKAFSLGGKRCVI--- 391
Cdd:COG5161    276 FRVTVAGP---VGALLFGSNELILIDSTGSSYTIPLNSMSEKYGGNKIVE-DISLSDVNCFSRGTTSIWIPSSKCLIetl 351

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  392 FLQD--GAWILVEMVLDGNKVVGMELVKMEHAQGKATapLAMVPSCVTSVKDGEyFFLGSRVGDSLLIKWRyNSDPVKRT 469
Cdd:COG5161    352 FLGDlnGDRYYLRISMDGKRIIGFDIASLEFEGDLLK--KGSAVSCVGHVNNLL-FFGGVGDSNSRVLRIK-SLLPTIET 427

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  470 KLSAGD------------------------------------LTFRVCDSLLNTGPIVDMAVGNV---EHAEVPDLTEat 510
Cdd:COG5161    428 RASEGVgpleggndeemddeysapenklfgnkeqevrrqdepYDAELFNALSNAGPITDFAVGKVdveKGLPIPNIGL-- 505

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  511 sitpdLELASCSGHGKNGSLCVFQRHIRPISTFSFTQSDCQSVWSIKCRKehyfegmqvgrgqgskgpaYLWNEDTADag 590
Cdd:COG5161    506 -----LNLVVTKGSDSEAALAVEGTSLEPCICTVSSFIPLEIVWSQKIRG-------------------YLRCSRALD-- 559

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  591 nafnnsfdkLLFISKSTSTLVLAAGEELQELGNSDFYTSGPTVTVSTLFDHTQIVQVYAHGVMLLSPEGKLLQTLPVKKS 670
Cdd:COG5161    560 ---------FYILSRVSDSRIFRWSEEFLLEVSGEYTRDVNTLLFVEFGEENRVVQVTPSYLLRYDQDLRMLGRVEFASR 630

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  671 RIVDASIYDPYILLSLEDQTILALQGNPDTRDLSHMQVPSSLNaeddtstSSTNKKTHSPPKDAVDSFDeIDLDLYGDQT 750
Cdd:COG5161    631 AVEARSVRDPLILVVRDSGKILTFYDREKNMRLFKIDLVTCLA-------DAKNKSFVLSDSNSLGIFD-IGKRISQLEP 702

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  751 DHVEKVKEDTPIADDSNktlaaepdyeddeemlyDDNETAPvhtvaggeEIDeinvsmkgGLSEVTQItfwcllyttdGT 830
Cdd:COG5161    703 CLVKGLPYAIQFSPEAS-----------------PAMDLAG--------EED--------GDDQLTEI----------SM 739

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  831 LQLHTLPDfracfafprfdllpgLIVDHPvrepssatlqqqtsavpgdtgttTIKELIIANIGKERKTPHLVARTHTDDI 910
Cdd:COG5161    740 SLTYNLID---------------MLFRLP-----------------------SIGNYMVAYLGLDLKEEYLFDNSLSSEI 781

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  911 IIYKAFGFVSTSdpstagdldrlalrfsrvHHEYVSRKTHAESEKKDDvMQIDEFEVPDedantpsdkpqpvpfrrHMLI 990
Cdd:COG5161    782 VFYKTHLPRHVS------------------FNLNVTRNDLAITGAPDN-ADIKAFSSVG-----------------RIDM 825

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  991 PFTDISGYAGVFVAGPQPAWLLCSCKSFVRVHPMkSDHEIIGFTQFHnvncKHGFISVDAESNIRLCGLPTGKATYDMDW 1070
Cdd:COG5161    826 VFIKAVGHSFMFVTGKGPFLCRSRYTSSSKAFHR-GNIPLVSVIPLS----KRGYLMVDNVLGVRASQYVFDNGYVGNKN 900

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1071 IMQKVPLGQTVHKIEYHPTMRVYAVLVSSPEAVRLRNEEGAPIDGKegerDVGEFLPVVDRYSLLMVSPVTWEVVDRVEF 1150
Cdd:COG5161    901 PVKRTPKHKTLQKLVYHCAGRYMVVGSCEEAGFSPKGEDGESGIPV----DTNVPHAEGYRFYVDLYSPKSWEVIDTYEF 976

                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1151 EEYEQGFSLQCVALESKQTSTGRKHFMAVGTGYLRGEDTAMRGSIYLFDIIEVVPEPNNPQTNHRFKHLHTEDVKGAVTA 1230
Cdd:COG5161    977 DENEYVFHIKYLILDDMQGTKGKSPYILVGTTFIEGEDRPARGRLHVLEIISVVPSPGSPFTDCKLKVLGIEETKGTVVR 1056

                         1210      1220      1230      1240      1250      1260      1270      1280
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1231 LCDASGHLVSCIGSKVIIWSFEDNESVVGVAFIDVQIYVTSICSIKNFIVLGDAQKSVWFLGFQLEPAKLVLLGKDYQSF 1310
Cdd:COG5161   1057 VCEVRGKIALCQGQKVMVRKIDRSSGIIPVGFYDLHIFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLR 1136

                         1290      1300      1310      1320      1330      1340      1350      1360
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1311 EVASVNFIIDDKSLYLLVGDTDDNMDIYQYAPFNLQSFGGQKLMRRGDFHVGAQVRTMVRLPQISQ-GEYNRRHF-CLCG 1388
Cdd:COG5161   1137 NATSTEFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSFTLHSAEIKMNLLPRNSEfGAGFKKNFiMVYS 1216

                         1370      1380      1390      1400      1410      1420      1430      1440
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1389 SFSGSISVVSPIPEKTFKRLNTLYGQLVNGLQHVAGLNPRAFRLIKGPKQRmsSNRTKAVLDGDLIFEFAGLAVNQQREM 1468
Cdd:COG5161   1217 RSDGMLIHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYRLNSDIHLH--SLSLRSPLDLHIINLFSYFDMSTRESV 1294

                         1450
                   ....*....|....*
gi 1945602123 1469 TKQIGTTVSRIMEDL 1483
Cdd:COG5161   1295 ASKAGRIDRKEISDM 1309
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 1131-1457 1.48e-88

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: 291.42  E-value: 1.48e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1131 RYSLLMVSPVTWEVVDRVEFEEYEQGFSLQCVALESKQTSTGRKHFMAVGTGYLRGEDTAMR-GSIYLFDIIEVvpepnn 1209
Cdd:pfam03178    1 ASCIRLVDPITKEVIDTLELEENEAVLSVKSVNLEDSSTTKGKEEYLVVGTAFDLGEDPAARsGRILVFEIIEV------ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1210 PQTNHRFKHLHTEDVKGAVTALCDASGHLVSCIGSKVIIWSFEDNESVVGVAFIDVQIYVTSICSIKNFIVLGDAQKSVW 1289
Cdd:pfam03178   75 PETNRKLKLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLGEDKSLLPKAFLDTGVYVVDLKVFGNRIIVGDLMKSVT 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1290 FLGFQLEPAKLVLLGKDYQSFEVASVNFIIDDkslYLLVGDTDDNMDIYQYAPFNLQSFGGQ-KLMRRGDFHVGAQVRTM 1368
Cdd:pfam03178  155 FVGYDEEPYRLIEFARDTQPRWVTAAEFLDGD---TVLVADKFGNLHVLRYDPDVPESLDGDpRLLVRAEFHLGETVTSF 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1369 VRLPQISQG-EYNRRHFCLCGSFSGSISVVSP-IPEKTFKRLNTLYGQLVNGLQHVAGLNPRAFRLIKGPKQRMssnrtK 1446
Cdd:pfam03178  232 RKGSLVPGGsESPSSPQLLYGTLDGSIGLLVPfISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTPPRTV-----K 306

                          330
                   ....*....|.
gi 1945602123 1447 AVLDGDLIFEF 1457
Cdd:pfam03178  307 GVIDGDLLERF 317
PTZ00085 PTZ00085
40S ribosomal protein S28; Provisional
 1481-1550 2.23e-36

40S ribosomal protein S28; Provisional


Pssm-ID: 240261  Cd Length: 73  Bit Score: 132.18  E-value: 2.23e-36
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1945602123 1481 EDLDAQKTPVKLAKVIKVLGRTGSRGGVTQVRVEFMDDT---NRSIIRNVKGPVRENDILCLLESEREARRLR 1550
Cdd:PTZ00085     1 EVVTQDTEQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEgdaGRTLIRNVKGPVREGDILSLMETEREARRLR 73
S1_S28E cd04457
S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 1491-1550 2.56e-36

S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28E might be involved in protein synthesis.


Pssm-ID: 239904  Cd Length: 60  Bit Score: 131.60  E-value: 2.56e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1491 KLAKVIKVLGRTGSRGGVTQVRVEFMDDTNRSIIRNVKGPVRENDILCLLESEREARRLR 1550
Cdd:cd04457      1 KLAEVIKVLGRTGSRGEVTQVRVEFMDDKGRSIIRNVKGPVREGDILMLLETEREARRLR 60
Ribosomal_S28e pfam01200
Ribosomal protein S28e;
1489-1549 3.75e-33

Ribosomal protein S28e;


Pssm-ID: 460109  Cd Length: 64  Bit Score: 122.36  E-value: 3.75e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1945602123 1489 PVKLAKVIKVLGRTGSRGGVTQVRVEFMD--DTNRSIIRNVKGPVRENDILCLLESEREARRL 1549
Cdd:pfam01200    2 KAQPAEVIKVLGRTGSRGEVTQVRVEILEgrDKGRIITRNVKGPVRVGDILMLLETEREARRL 64
MMS1_N pfam10433
Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects ...
 135-695 1.56e-22

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: 103.11  E-value: 1.56e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  135 DSLLLGFNDAKMSLLEWSPATNSIVTvsIHYYErdelkkefltnPYPPT----------IHMDPQQRCAVMNFYDNKLAV 204
Cdd:pfam10433    1 DHLVVGTDSGRLVFLSWDPEKNQFET--IHSRE-----------DLGKSgsrrsqpgqyLAVDPKGRAIAVSAYEGVFLV 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  205 LPFRQSEKRDGPIS-LLDVDDQAQKwpysssfvldLESIdsriknVIDMVFL-SGYYEPTLAILFQteqtwtgqvcsifp 282
Cdd:pfam10433   68 YPLKQPQKLNRNEAlLLSSPLEARK----------SEGF------ILSMVFLdPGYDNPIFALLEQ-------------- 117

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  283 NAKDTVSVVVISLDLS----AKIYPIIYSLDKLPYDCLK---LFAMPKPVDGLLIIASNSLLHVSQGSpGVGVAVNGYTK 355
Cdd:pfam10433  118 DRTGKTHLKLYEWDLGlnhvVRGPKWSEPLDFLPKEDRGanlLIPVPKGPGGVLVCGETIITYKDILD-QPDIRCPPVAR 196

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  356 KTTEFAGMAYGDETIKMDLVL----DGakafslggkrcVIFLqdgawILVEMVLDgNKVVGMELVKMEHAQgkataplam 431
Cdd:pfam10433  197 PLRENATIFVAWHKLDNFFILladeYG-----------DLYL-----LTIENDED-NVVTSIKIGYFGTTS--------- 250

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  432 VPSCVTSVKDGeYFFLGSRVGDSLLIkwrynsdpvKRTKLSAGDLT-FRVCDSLLNTGPIVDMAVGNVEHAEVPdlteat 510
Cdd:pfam10433  251 VASALVILDNG-FLFVASEFGDSQLY---------QIDARGDDDLSnLELVQTFSNWAPILDFVVMDLGGEDTA------ 314

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  511 sitpdlELASCSGHGKNGSLcvfqRHIR---PISTFSFTQSD---CQSVWSIKCRKEhyfegmqvgrgqgskgpaylwne 584
Cdd:pfam10433  315 ------RIYTCSGAGKRGSL----RSLRhgvGAEELAVSEEPgspITGVWTLKSSPE----------------------- 361

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123  585 dtadagnafnNSFDKLLFISKSTSTLVLA-AGEELQELGNSD-FYTSGPTVTVSTLfDHTQIVQVYAHGVMLLSPEGKLL 662
Cdd:pfam10433  362 ----------DEYDDYLVVSFVNETRVLSiDGDGVEEVDEDSgFLLSVPTLAAGNL-GDGRLLQVTPNGIRLIDSDKRIS 430

                          570       580       590
                   ....*....|....*....|....*....|...
gi 1945602123  663 QTLPVKKSRIVDASIYDPYILLSLEDQTILALQ 695
Cdd:pfam10433  431 EWKPPGGKSITAAAANGRQVLLALSGGELVYFE 463
RPS28A COG2053
Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]; Ribosomal ...
 1493-1550 3.70e-21

Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S28E/S33 is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 441656  Cd Length: 73  Bit Score: 88.49  E-value: 3.70e-21
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1493 AKVIKVLGRTGSRGGVTQVRVEFMD--DTNRSIIRNVKGPVRENDILCLLESEREARRLR 1550
Cdd:COG2053     12 AEVIEIIGRTGMTGEVTQVRVRILEgrDKGRIITRNVKGPVRVGDILMLRETEREARKLK 71
rps28e PRK04007
30S ribosomal protein S28e; Validated
 1493-1550 1.50e-19

30S ribosomal protein S28e; Validated


Pssm-ID: 235197  Cd Length: 70  Bit Score: 83.87  E-value: 1.50e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1945602123 1493 AKVIKVLGRTGSRGGVTQVRVEFMD--DTNRSIIRNVKGPVRENDILCLLESEREARRLR 1550
Cdd:PRK04007     9 AEVIEIIGRTGMTGEVTQVKCRILEgrDKGRIITRNVKGPVRVGDILMLRETEREARKLG 68
 
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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