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Conserved domains on  [gi|1954541451|gb|KAG1528820|]
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hypothetical protein G6F52_000310 [Rhizopus delemar]

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];
5-1458 5.66e-164

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: 530.69  E-value: 5.66e-164
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451    5 TIYQELFPPQTVEYVETSQFTSPDATNLIVAKASLLQIYefveyvpeaveeeeetpsdnelanerlndtedinltypklK 84
Cdd:COG5161      3 YLYSDESDWTVTEGCSAGLFTPSRTCSLLVYNGNILAVR----------------------------------------L 42

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451   85 PLKKGGMIsdttlgrleLVAQFKMNGIITTMGTVrtnsPRGREGCDSLLLGFSDAKMSLLEWSSSTNSIITVSIHYYERD 164
Cdd:COG5161     43 WKYDSGLV---------LVDEHMLLEKVTQIEKY----PQISSEQDGLLLLTHRAKISLLRFDSQANEFRTISLHYYEGK 109

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  165 EFKKEFLTNPYPSAIHIDPQQRCAVFnFYDNKLAVLPFR----QSDKLDERQGEGEEDEEK-----WPY----------- 224
Cdd:COG5161    110 FKGKSLVELAKFSTLEFDIRSSCALL-FNEDIGNFLPFHvnknDDDEVRIDVDLGMFQMSKrhfsiFPSqgtntfnkrkr 188

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  225 --------YPSFIIDLATLDSRIKNVIDMTFLSDYYEPTLAILFQPEQTWTGRLGNNKDTVSLVVISLDITAKIYPIIYS 296
Cdd:COG5161    189 tlfpgkfsAPSKVLKFSELDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRKYTILKNPYNAIVFTLDLGAGRSAVIDE 268

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  297 IDKLPYDCFKLVAMPkpvTGMLVIAANSILHVSQGSPGMGVAVNGYTKKTTDFPGMIyEPSLIELGLSLEGAKALAFGGD 376
Cdd:COG5161    269 FLVLPRDFRVTVAGP---VGALLFGSNELILIDSTGSSYTIPLNSMSEKYGGNKIVE-DISLSDVNCFSRGTTSIWIPSS 344

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  377 RCLI-FMQNGHWA----LVEVRRDGNKVVGMAISEIKHDLPVMEKKPPrfdtppllasvPSCVTNVKAGEyFFLGSRVGD 451
Cdd:COG5161    345 KCLIeTLFLGDLNgdryYLRISMDGKRIIGFDIASLEFEGDLLKKGSA-----------VSCVGHVNNLL-FFGGVGDSN 412

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  452 SLLIK-------------------YDAN--------------------RVNHQSVAPPVFRVCDTMLNTGPIVDMAVGDV 492
Cdd:COG5161    413 SRVLRiksllptietrasegvgplEGGNdeemddeysapenklfgnkeQEVRRQDEPYDAELFNALSNAGPITDFAVGKV 492

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  493 DTVE--QQEDWPQLELVSSSGHGKNGALCVFQRHIYPQTSFAFhQFDS-QAIWSIKCRKNDQQQNEDDdfdkLLFISKSK 569
Cdd:COG5161    493 DVEKglPIPNIGLLNLVVTKGSDSEAALAVEGTSLEPCICTVS-SFIPlEIVWSQKIRGYLRCSRALD----FYILSRVS 567

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  570 STLVLSAGDELQEVKTGFYTRGS-TIAVSTLFDATRIVQVYATGVMVLTPEGKRIQTVPIPRGAkIVEASIHDPYILLTL 648
Cdd:COG5161    568 DSRIFRWSEEFLLEVSGEYTRDVnTLLFVEFGEENRVVQVTPSYLLRYDQDLRMLGRVEFASRA-VEARSVRDPLILVVR 646

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  649 DNNKILALQGDASTKDIIHIQLPNHIKDVgIIMSGIFAD--ASGLFMSvseriktteaakaaaseaqrqKKRKAEEEnQS 726
Cdd:COG5161    647 DSGKILTFYDREKNMRLFKIDLVTCLADA-KNKSFVLSDsnSLGIFDI---------------------GKRISQLE-PC 703

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  727 MKKKMSKTIATFEFDEIDMDLYGEdiLDAVEPNNEEkkaeekpvkeeqvkkesikeevdeanvslqgtginmtqvtfwcf 806
Cdd:COG5161    704 LVKGLPYAIQFSPEASPAMDLAGE--EDGDDQLTEI-------------------------------------------- 737

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  807 tytttGILRIYSLPDfkehfacpqfsiapdLIVDDSGVKsriptnniqEILMTHIGKERKDPHLVVRTDTNDIIIYKAFT 886
Cdd:COG5161    738 -----SMSLTYNLID---------------MLFRLPSIG---------NYMVAYLGLDLKEEYLFDNSLSSEIVFYKTHL 788

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  887 YldesspdrlalrfsrvqheyvsRKSSSHESKPKKKRGIIDEfeiPDTdlneeeedlklSTKKMDKKIQRkLLIPFTDVA 966
Cdd:COG5161    789 P----------------------RHVSFNLNVTRNDLAITGA---PDN-----------ADIKAFSSVGR-IDMVFIKAV 831

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  967 GYAGVFVAGAQPAWLMCSCKSFVRVHPMkTEHEIVGFTQFHnvncQHGFITVDSKSTIQLSRLRTEGINYDLDWVIQKVL 1046
Cdd:COG5161    832 GHSFMFVTGKGPFLCRSRYTSSSKAFHR-GNIPLVSVIPLS----KRGYLMVDNVLGVRASQYVFDNGYVGNKNPVKRTP 906

                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1047 LGQTVHKIQYHPVMRVYAVLVSSSVPTRMKNDDNQYIDGkeTDERGPgefLPEMEQFSMILVSPVTWEIVDKVEFEEFEQ 1126
Cdd:COG5161    907 KHKTLQKLVYHCAGRYMVVGSCEEAGFSPKGEDGESGIP--VDTNVP---HAEGYRFYVDLYSPKSWEVIDTYEFDENEY 981

                         1210      1220      1230      1240      1250      1260      1270      1280
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1127 CFSLECALLDSKQTSTGRKYYMIIGTGTLKGEDTTMKGSIRMYDIIEVVPEPDNPQTNHKFKPVLTEDVKGAVTAMCTVS 1206
Cdd:COG5161    982 VFHIKYLILDDMQGTKGKSPYILVGTTFIEGEDRPARGRLHVLEIISVVPSPGSPFTDCKLKVLGIEETKGTVVRVCEVR 1061

                         1290      1300      1310      1320      1330      1340      1350      1360
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1207 GHLAACIGSKVIVWSLEDDERLVGVAFIDVQIYVTSMSSIKNFILIGDAQKSIWFLGFQLEPAKLTLLGKDYQSFDVGCV 1286
Cdd:COG5161   1062 GKIALCQGQKVMVRKIDRSSGIIPVGFYDLHIFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLRNATST 1141

                         1370      1380      1390      1400      1410      1420      1430      1440
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1287 DFIIDDKSLYLIVGDTNENIDLYQYAPFNLQSFGGQKLMRRGDFHVGSQVQTMVRLPQIEktEKGFEYSRRHFCLCGTFN 1366
Cdd:COG5161   1142 EFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSFTLHSAEIKMNLLPRNS--EFGAGFKKNFIMVYSRSD 1219

                         1450      1460      1470      1480      1490      1500      1510      1520
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1367 GSIAVISSISEKTFKRLNTLYGHLVNNLQHVAGLNPRAFRLIKGPKQRmsTNRTKAVLDGDLIFEFAGLSIEEQKETTKQ 1446
Cdd:COG5161   1220 GMLIHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYRLNSDIHLH--SLSLRSPLDLHIINLFSYFDMSTRESVASK 1297

                         1530
                   ....*....|..
gi 1954541451 1447 IGTTVTRIMEDL 1458
Cdd:COG5161   1298 AGRIDRKEISDM 1309
S1_S28E cd04457
S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 1465-1524 1.61e-35

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: 129.29  E-value: 1.61e-35
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1465 KLARVTKVLGRTGSRGGVTQVRVEFMDDTNRSIIRNVKGPVRENDILCLLESEREARRLR 1524
Cdd:cd04457      1 KLAEVIKVLGRTGSRGEVTQVRVEFMDDKGRSIIRNVKGPVREGDILMLLETEREARRLR 60
 
Name Accession Description Interval E-value
SFT1 COG5161
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
5-1458 5.66e-164

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


Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 530.69  E-value: 5.66e-164
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451    5 TIYQELFPPQTVEYVETSQFTSPDATNLIVAKASLLQIYefveyvpeaveeeeetpsdnelanerlndtedinltypklK 84
Cdd:COG5161      3 YLYSDESDWTVTEGCSAGLFTPSRTCSLLVYNGNILAVR----------------------------------------L 42

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451   85 PLKKGGMIsdttlgrleLVAQFKMNGIITTMGTVrtnsPRGREGCDSLLLGFSDAKMSLLEWSSSTNSIITVSIHYYERD 164
Cdd:COG5161     43 WKYDSGLV---------LVDEHMLLEKVTQIEKY----PQISSEQDGLLLLTHRAKISLLRFDSQANEFRTISLHYYEGK 109

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  165 EFKKEFLTNPYPSAIHIDPQQRCAVFnFYDNKLAVLPFR----QSDKLDERQGEGEEDEEK-----WPY----------- 224
Cdd:COG5161    110 FKGKSLVELAKFSTLEFDIRSSCALL-FNEDIGNFLPFHvnknDDDEVRIDVDLGMFQMSKrhfsiFPSqgtntfnkrkr 188

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  225 --------YPSFIIDLATLDSRIKNVIDMTFLSDYYEPTLAILFQPEQTWTGRLGNNKDTVSLVVISLDITAKIYPIIYS 296
Cdd:COG5161    189 tlfpgkfsAPSKVLKFSELDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRKYTILKNPYNAIVFTLDLGAGRSAVIDE 268

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  297 IDKLPYDCFKLVAMPkpvTGMLVIAANSILHVSQGSPGMGVAVNGYTKKTTDFPGMIyEPSLIELGLSLEGAKALAFGGD 376
Cdd:COG5161    269 FLVLPRDFRVTVAGP---VGALLFGSNELILIDSTGSSYTIPLNSMSEKYGGNKIVE-DISLSDVNCFSRGTTSIWIPSS 344

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  377 RCLI-FMQNGHWA----LVEVRRDGNKVVGMAISEIKHDLPVMEKKPPrfdtppllasvPSCVTNVKAGEyFFLGSRVGD 451
Cdd:COG5161    345 KCLIeTLFLGDLNgdryYLRISMDGKRIIGFDIASLEFEGDLLKKGSA-----------VSCVGHVNNLL-FFGGVGDSN 412

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  452 SLLIK-------------------YDAN--------------------RVNHQSVAPPVFRVCDTMLNTGPIVDMAVGDV 492
Cdd:COG5161    413 SRVLRiksllptietrasegvgplEGGNdeemddeysapenklfgnkeQEVRRQDEPYDAELFNALSNAGPITDFAVGKV 492

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  493 DTVE--QQEDWPQLELVSSSGHGKNGALCVFQRHIYPQTSFAFhQFDS-QAIWSIKCRKNDQQQNEDDdfdkLLFISKSK 569
Cdd:COG5161    493 DVEKglPIPNIGLLNLVVTKGSDSEAALAVEGTSLEPCICTVS-SFIPlEIVWSQKIRGYLRCSRALD----FYILSRVS 567

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  570 STLVLSAGDELQEVKTGFYTRGS-TIAVSTLFDATRIVQVYATGVMVLTPEGKRIQTVPIPRGAkIVEASIHDPYILLTL 648
Cdd:COG5161    568 DSRIFRWSEEFLLEVSGEYTRDVnTLLFVEFGEENRVVQVTPSYLLRYDQDLRMLGRVEFASRA-VEARSVRDPLILVVR 646

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  649 DNNKILALQGDASTKDIIHIQLPNHIKDVgIIMSGIFAD--ASGLFMSvseriktteaakaaaseaqrqKKRKAEEEnQS 726
Cdd:COG5161    647 DSGKILTFYDREKNMRLFKIDLVTCLADA-KNKSFVLSDsnSLGIFDI---------------------GKRISQLE-PC 703

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  727 MKKKMSKTIATFEFDEIDMDLYGEdiLDAVEPNNEEkkaeekpvkeeqvkkesikeevdeanvslqgtginmtqvtfwcf 806
Cdd:COG5161    704 LVKGLPYAIQFSPEASPAMDLAGE--EDGDDQLTEI-------------------------------------------- 737

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  807 tytttGILRIYSLPDfkehfacpqfsiapdLIVDDSGVKsriptnniqEILMTHIGKERKDPHLVVRTDTNDIIIYKAFT 886
Cdd:COG5161    738 -----SMSLTYNLID---------------MLFRLPSIG---------NYMVAYLGLDLKEEYLFDNSLSSEIVFYKTHL 788

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  887 YldesspdrlalrfsrvqheyvsRKSSSHESKPKKKRGIIDEfeiPDTdlneeeedlklSTKKMDKKIQRkLLIPFTDVA 966
Cdd:COG5161    789 P----------------------RHVSFNLNVTRNDLAITGA---PDN-----------ADIKAFSSVGR-IDMVFIKAV 831

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  967 GYAGVFVAGAQPAWLMCSCKSFVRVHPMkTEHEIVGFTQFHnvncQHGFITVDSKSTIQLSRLRTEGINYDLDWVIQKVL 1046
Cdd:COG5161    832 GHSFMFVTGKGPFLCRSRYTSSSKAFHR-GNIPLVSVIPLS----KRGYLMVDNVLGVRASQYVFDNGYVGNKNPVKRTP 906

                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1047 LGQTVHKIQYHPVMRVYAVLVSSSVPTRMKNDDNQYIDGkeTDERGPgefLPEMEQFSMILVSPVTWEIVDKVEFEEFEQ 1126
Cdd:COG5161    907 KHKTLQKLVYHCAGRYMVVGSCEEAGFSPKGEDGESGIP--VDTNVP---HAEGYRFYVDLYSPKSWEVIDTYEFDENEY 981

                         1210      1220      1230      1240      1250      1260      1270      1280
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1127 CFSLECALLDSKQTSTGRKYYMIIGTGTLKGEDTTMKGSIRMYDIIEVVPEPDNPQTNHKFKPVLTEDVKGAVTAMCTVS 1206
Cdd:COG5161    982 VFHIKYLILDDMQGTKGKSPYILVGTTFIEGEDRPARGRLHVLEIISVVPSPGSPFTDCKLKVLGIEETKGTVVRVCEVR 1061

                         1290      1300      1310      1320      1330      1340      1350      1360
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1207 GHLAACIGSKVIVWSLEDDERLVGVAFIDVQIYVTSMSSIKNFILIGDAQKSIWFLGFQLEPAKLTLLGKDYQSFDVGCV 1286
Cdd:COG5161   1062 GKIALCQGQKVMVRKIDRSSGIIPVGFYDLHIFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLRNATST 1141

                         1370      1380      1390      1400      1410      1420      1430      1440
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1287 DFIIDDKSLYLIVGDTNENIDLYQYAPFNLQSFGGQKLMRRGDFHVGSQVQTMVRLPQIEktEKGFEYSRRHFCLCGTFN 1366
Cdd:COG5161   1142 EFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSFTLHSAEIKMNLLPRNS--EFGAGFKKNFIMVYSRSD 1219

                         1450      1460      1470      1480      1490      1500      1510      1520
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1367 GSIAVISSISEKTFKRLNTLYGHLVNNLQHVAGLNPRAFRLIKGPKQRmsTNRTKAVLDGDLIFEFAGLSIEEQKETTKQ 1446
Cdd:COG5161   1220 GMLIHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYRLNSDIHLH--SLSLRSPLDLHIINLFSYFDMSTRESVASK 1297

                         1530
                   ....*....|..
gi 1954541451 1447 IGTTVTRIMEDL 1458
Cdd:COG5161   1298 AGRIDRKEISDM 1309
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 1102-1432 3.20e-89

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: 292.96  E-value: 3.20e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1102 QFSMILVSPVTWEIVDKVEFEEFEQCFSLECALLDSKQTSTGRKYYMIIGTGTLKGED-TTMKGSIRMYDIIEVvpepdn 1180
Cdd:pfam03178    1 ASCIRLVDPITKEVIDTLELEENEAVLSVKSVNLEDSSTTKGKEEYLVVGTAFDLGEDpAARSGRILVFEIIEV------ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1181 PQTNHKFKPVLTEDVKGAVTAMCTVSGHLAACIGSKVIVWSLEDDERLVGVAFIDVQIYVTSMSSIKNFILIGDAQKSIW 1260
Cdd:pfam03178   75 PETNRKLKLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLGEDKSLLPKAFLDTGVYVVDLKVFGNRIIVGDLMKSVT 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1261 FLGFQLEPAKLTLLGKDYQSFDVGCVDFIIDDkslYLIVGDTNENIDLYQYAPFNLQSFGGQ-KLMRRGDFHVGSQVQTM 1339
Cdd:pfam03178  155 FVGYDEEPYRLIEFARDTQPRWVTAAEFLDGD---TVLVADKFGNLHVLRYDPDVPESLDGDpRLLVRAEFHLGETVTSF 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1340 VRLPQIektEKGFEYSRRHFCLCGTFNGSI-AVISSISEKTFKRLNTLYGHLVNNLQHVAGLNPRAFRLIKGPKQRMstn 1418
Cdd:pfam03178  232 RKGSLV---PGGSESPSSPQLLYGTLDGSIgLLVPFISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTPPRTV--- 305

                          330
                   ....*....|....
gi 1954541451 1419 rtKAVLDGDLIFEF 1432
Cdd:pfam03178  306 --KGVIDGDLLERF 317
S1_S28E cd04457
S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 1465-1524 1.61e-35

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: 129.29  E-value: 1.61e-35
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1465 KLARVTKVLGRTGSRGGVTQVRVEFMDDTNRSIIRNVKGPVRENDILCLLESEREARRLR 1524
Cdd:cd04457      1 KLAEVIKVLGRTGSRGEVTQVRVEFMDDKGRSIIRNVKGPVREGDILMLLETEREARRLR 60
PTZ00085 PTZ00085
40S ribosomal protein S28; Provisional
 1462-1524 2.93e-35

40S ribosomal protein S28; Provisional


Pssm-ID: 240261  Cd Length: 73  Bit Score: 128.72  E-value: 2.93e-35
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1954541451 1462 TPVKLARVTKVLGRTGSRGGVTQVRVEFMDDT---NRSIIRNVKGPVRENDILCLLESEREARRLR 1524
Cdd:PTZ00085     8 EQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEgdaGRTLIRNVKGPVREGDILSLMETEREARRLR 73
Ribosomal_S28e pfam01200
Ribosomal protein S28e;
1463-1523 6.24e-33

Ribosomal protein S28e;


Pssm-ID: 460109  Cd Length: 64  Bit Score: 121.97  E-value: 6.24e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954541451 1463 PVKLARVTKVLGRTGSRGGVTQVRVEFMD--DTNRSIIRNVKGPVRENDILCLLESEREARRL 1523
Cdd:pfam01200    2 KAQPAEVIKVLGRTGSRGEVTQVRVEILEgrDKGRIITRNVKGPVRVGDILMLLETEREARRL 64
RPS28A COG2053
Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]; Ribosomal ...
 1455-1524 1.65e-19

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: 83.87  E-value: 1.65e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1954541451 1455 MEDLDTKTPVKlARVTKVLGRTGSRGGVTQVRVEFMD--DTNRSIIRNVKGPVRENDILCLLESEREARRLR 1524
Cdd:COG2053      1 MSEVTEEDGVP-AEVIEIIGRTGMTGEVTQVRVRILEgrDKGRIITRNVKGPVRVGDILMLRETEREARKLK 71
 
Name Accession Description Interval E-value
SFT1 COG5161
Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification];
5-1458 5.66e-164

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


Pssm-ID: 227490 [Multi-domain]  Cd Length: 1319  Bit Score: 530.69  E-value: 5.66e-164
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451    5 TIYQELFPPQTVEYVETSQFTSPDATNLIVAKASLLQIYefveyvpeaveeeeetpsdnelanerlndtedinltypklK 84
Cdd:COG5161      3 YLYSDESDWTVTEGCSAGLFTPSRTCSLLVYNGNILAVR----------------------------------------L 42

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451   85 PLKKGGMIsdttlgrleLVAQFKMNGIITTMGTVrtnsPRGREGCDSLLLGFSDAKMSLLEWSSSTNSIITVSIHYYERD 164
Cdd:COG5161     43 WKYDSGLV---------LVDEHMLLEKVTQIEKY----PQISSEQDGLLLLTHRAKISLLRFDSQANEFRTISLHYYEGK 109

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  165 EFKKEFLTNPYPSAIHIDPQQRCAVFnFYDNKLAVLPFR----QSDKLDERQGEGEEDEEK-----WPY----------- 224
Cdd:COG5161    110 FKGKSLVELAKFSTLEFDIRSSCALL-FNEDIGNFLPFHvnknDDDEVRIDVDLGMFQMSKrhfsiFPSqgtntfnkrkr 188

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  225 --------YPSFIIDLATLDSRIKNVIDMTFLSDYYEPTLAILFQPEQTWTGRLGNNKDTVSLVVISLDITAKIYPIIYS 296
Cdd:COG5161    189 tlfpgkfsAPSKVLKFSELDGKIKNIIDFVFLENYSIPTVALLYDPKLSLPRKYTILKNPYNAIVFTLDLGAGRSAVIDE 268

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  297 IDKLPYDCFKLVAMPkpvTGMLVIAANSILHVSQGSPGMGVAVNGYTKKTTDFPGMIyEPSLIELGLSLEGAKALAFGGD 376
Cdd:COG5161    269 FLVLPRDFRVTVAGP---VGALLFGSNELILIDSTGSSYTIPLNSMSEKYGGNKIVE-DISLSDVNCFSRGTTSIWIPSS 344

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  377 RCLI-FMQNGHWA----LVEVRRDGNKVVGMAISEIKHDLPVMEKKPPrfdtppllasvPSCVTNVKAGEyFFLGSRVGD 451
Cdd:COG5161    345 KCLIeTLFLGDLNgdryYLRISMDGKRIIGFDIASLEFEGDLLKKGSA-----------VSCVGHVNNLL-FFGGVGDSN 412

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  452 SLLIK-------------------YDAN--------------------RVNHQSVAPPVFRVCDTMLNTGPIVDMAVGDV 492
Cdd:COG5161    413 SRVLRiksllptietrasegvgplEGGNdeemddeysapenklfgnkeQEVRRQDEPYDAELFNALSNAGPITDFAVGKV 492

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  493 DTVE--QQEDWPQLELVSSSGHGKNGALCVFQRHIYPQTSFAFhQFDS-QAIWSIKCRKNDQQQNEDDdfdkLLFISKSK 569
Cdd:COG5161    493 DVEKglPIPNIGLLNLVVTKGSDSEAALAVEGTSLEPCICTVS-SFIPlEIVWSQKIRGYLRCSRALD----FYILSRVS 567

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  570 STLVLSAGDELQEVKTGFYTRGS-TIAVSTLFDATRIVQVYATGVMVLTPEGKRIQTVPIPRGAkIVEASIHDPYILLTL 648
Cdd:COG5161    568 DSRIFRWSEEFLLEVSGEYTRDVnTLLFVEFGEENRVVQVTPSYLLRYDQDLRMLGRVEFASRA-VEARSVRDPLILVVR 646

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  649 DNNKILALQGDASTKDIIHIQLPNHIKDVgIIMSGIFAD--ASGLFMSvseriktteaakaaaseaqrqKKRKAEEEnQS 726
Cdd:COG5161    647 DSGKILTFYDREKNMRLFKIDLVTCLADA-KNKSFVLSDsnSLGIFDI---------------------GKRISQLE-PC 703

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  727 MKKKMSKTIATFEFDEIDMDLYGEdiLDAVEPNNEEkkaeekpvkeeqvkkesikeevdeanvslqgtginmtqvtfwcf 806
Cdd:COG5161    704 LVKGLPYAIQFSPEASPAMDLAGE--EDGDDQLTEI-------------------------------------------- 737

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  807 tytttGILRIYSLPDfkehfacpqfsiapdLIVDDSGVKsriptnniqEILMTHIGKERKDPHLVVRTDTNDIIIYKAFT 886
Cdd:COG5161    738 -----SMSLTYNLID---------------MLFRLPSIG---------NYMVAYLGLDLKEEYLFDNSLSSEIVFYKTHL 788

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  887 YldesspdrlalrfsrvqheyvsRKSSSHESKPKKKRGIIDEfeiPDTdlneeeedlklSTKKMDKKIQRkLLIPFTDVA 966
Cdd:COG5161    789 P----------------------RHVSFNLNVTRNDLAITGA---PDN-----------ADIKAFSSVGR-IDMVFIKAV 831

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  967 GYAGVFVAGAQPAWLMCSCKSFVRVHPMkTEHEIVGFTQFHnvncQHGFITVDSKSTIQLSRLRTEGINYDLDWVIQKVL 1046
Cdd:COG5161    832 GHSFMFVTGKGPFLCRSRYTSSSKAFHR-GNIPLVSVIPLS----KRGYLMVDNVLGVRASQYVFDNGYVGNKNPVKRTP 906

                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1047 LGQTVHKIQYHPVMRVYAVLVSSSVPTRMKNDDNQYIDGkeTDERGPgefLPEMEQFSMILVSPVTWEIVDKVEFEEFEQ 1126
Cdd:COG5161    907 KHKTLQKLVYHCAGRYMVVGSCEEAGFSPKGEDGESGIP--VDTNVP---HAEGYRFYVDLYSPKSWEVIDTYEFDENEY 981

                         1210      1220      1230      1240      1250      1260      1270      1280
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1127 CFSLECALLDSKQTSTGRKYYMIIGTGTLKGEDTTMKGSIRMYDIIEVVPEPDNPQTNHKFKPVLTEDVKGAVTAMCTVS 1206
Cdd:COG5161    982 VFHIKYLILDDMQGTKGKSPYILVGTTFIEGEDRPARGRLHVLEIISVVPSPGSPFTDCKLKVLGIEETKGTVVRVCEVR 1061

                         1290      1300      1310      1320      1330      1340      1350      1360
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1207 GHLAACIGSKVIVWSLEDDERLVGVAFIDVQIYVTSMSSIKNFILIGDAQKSIWFLGFQLEPAKLTLLGKDYQSFDVGCV 1286
Cdd:COG5161   1062 GKIALCQGQKVMVRKIDRSSGIIPVGFYDLHIFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLRNATST 1141

                         1370      1380      1390      1400      1410      1420      1430      1440
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1287 DFIIDDKSLYLIVGDTNENIDLYQYAPFNLQSFGGQKLMRRGDFHVGSQVQTMVRLPQIEktEKGFEYSRRHFCLCGTFN 1366
Cdd:COG5161   1142 EFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSFTLHSAEIKMNLLPRNS--EFGAGFKKNFIMVYSRSD 1219

                         1450      1460      1470      1480      1490      1500      1510      1520
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1367 GSIAVISSISEKTFKRLNTLYGHLVNNLQHVAGLNPRAFRLIKGPKQRmsTNRTKAVLDGDLIFEFAGLSIEEQKETTKQ 1446
Cdd:COG5161   1220 GMLIHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYRLNSDIHLH--SLSLRSPLDLHIINLFSYFDMSTRESVASK 1297

                         1530
                   ....*....|..
gi 1954541451 1447 IGTTVTRIMEDL 1458
Cdd:COG5161   1298 AGRIDRKEISDM 1309
CPSF_A pfam03178
CPSF A subunit region; This family includes a region that lies towards the C-terminus of the ...
 1102-1432 3.20e-89

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: 292.96  E-value: 3.20e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1102 QFSMILVSPVTWEIVDKVEFEEFEQCFSLECALLDSKQTSTGRKYYMIIGTGTLKGED-TTMKGSIRMYDIIEVvpepdn 1180
Cdd:pfam03178    1 ASCIRLVDPITKEVIDTLELEENEAVLSVKSVNLEDSSTTKGKEEYLVVGTAFDLGEDpAARSGRILVFEIIEV------ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1181 PQTNHKFKPVLTEDVKGAVTAMCTVSGHLAACIGSKVIVWSLEDDERLVGVAFIDVQIYVTSMSSIKNFILIGDAQKSIW 1260
Cdd:pfam03178   75 PETNRKLKLVHKTEVKGAVTALAEFQGRLLAGQGQKLRVYDLGEDKSLLPKAFLDTGVYVVDLKVFGNRIIVGDLMKSVT 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1261 FLGFQLEPAKLTLLGKDYQSFDVGCVDFIIDDkslYLIVGDTNENIDLYQYAPFNLQSFGGQ-KLMRRGDFHVGSQVQTM 1339
Cdd:pfam03178  155 FVGYDEEPYRLIEFARDTQPRWVTAAEFLDGD---TVLVADKFGNLHVLRYDPDVPESLDGDpRLLVRAEFHLGETVTSF 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1340 VRLPQIektEKGFEYSRRHFCLCGTFNGSI-AVISSISEKTFKRLNTLYGHLVNNLQHVAGLNPRAFRLIKGPKQRMstn 1418
Cdd:pfam03178  232 RKGSLV---PGGSESPSSPQLLYGTLDGSIgLLVPFISEEDYRFLQSLQQQLRDELPHLGGLDHRAFRSYYTPPRTV--- 305

                          330
                   ....*....|....
gi 1954541451 1419 rtKAVLDGDLIFEF 1432
Cdd:pfam03178  306 --KGVIDGDLLERF 317
S1_S28E cd04457
S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 1465-1524 1.61e-35

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: 129.29  E-value: 1.61e-35
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1465 KLARVTKVLGRTGSRGGVTQVRVEFMDDTNRSIIRNVKGPVRENDILCLLESEREARRLR 1524
Cdd:cd04457      1 KLAEVIKVLGRTGSRGEVTQVRVEFMDDKGRSIIRNVKGPVREGDILMLLETEREARRLR 60
PTZ00085 PTZ00085
40S ribosomal protein S28; Provisional
 1462-1524 2.93e-35

40S ribosomal protein S28; Provisional


Pssm-ID: 240261  Cd Length: 73  Bit Score: 128.72  E-value: 2.93e-35
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1954541451 1462 TPVKLARVTKVLGRTGSRGGVTQVRVEFMDDT---NRSIIRNVKGPVRENDILCLLESEREARRLR 1524
Cdd:PTZ00085     8 EQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEgdaGRTLIRNVKGPVREGDILSLMETEREARRLR 73
Ribosomal_S28e pfam01200
Ribosomal protein S28e;
1463-1523 6.24e-33

Ribosomal protein S28e;


Pssm-ID: 460109  Cd Length: 64  Bit Score: 121.97  E-value: 6.24e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954541451 1463 PVKLARVTKVLGRTGSRGGVTQVRVEFMD--DTNRSIIRNVKGPVRENDILCLLESEREARRL 1523
Cdd:pfam01200    2 KAQPAEVIKVLGRTGSRGEVTQVRVEILEgrDKGRIITRNVKGPVRVGDILMLLETEREARRL 64
MMS1_N pfam10433
Mono-functional DNA-alkylating methyl methanesulfonate N-term; MMS1 is a protein that protects ...
 130-657 5.41e-30

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: 125.84  E-value: 5.41e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  130 DSLLLGfSDA-KMSLLEWSSSTNSIITvsIHYYERdefkkefLTNPYPSA------IHIDPQQRCAVFNFYDNKLAVLPF 202
Cdd:pfam10433    1 DHLVVG-TDSgRLVFLSWDPEKNQFET--IHSRED-------LGKSGSRRsqpgqyLAVDPKGRAIAVSAYEGVFLVYPL 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  203 RQSDKLDErqgeGEEDEEKWPyypsfiidlatLDSRIKN--VIDMTFL-SDYYEPTLAILFQpeqtwtgrlgNNKDTVSL 279
Cdd:pfam10433   71 KQPQKLNR----NEALLLSSP-----------LEARKSEgfILSMVFLdPGYDNPIFALLEQ----------DRTGKTHL 125

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  280 VVISLDIT----AKIYPIIYSIDKLPYDCFK---LVAMPKPVTGMLVIAANSILHVSQGSPGMGVAVNGYTKKTTDFPGM 352
Cdd:pfam10433  126 KLYEWDLGlnhvVRGPKWSEPLDFLPKEDRGanlLIPVPKGPGGVLVCGETIITYKDILDQPDIRCPPVARPLRENATIF 205

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  353 IYEPSLielglslegakalafggDRCLIFMQ--NGHWALVEVRRDGNKVVgmaiSEIKHDlpvmekkppRFDTppllASV 430
Cdd:pfam10433  206 VAWHKL-----------------DNFFILLAdeYGDLYLLTIENDEDNVV----TSIKIG---------YFGT----TSV 251

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  431 PSCVTNVKAGeYFFLGSRVGDSLLIKYDANRVNHQSVappvFRVCDTMLNTGPIVDMAVGDVdtveQQEDWPQleLVSSS 510
Cdd:pfam10433  252 ASALVILDNG-FLFVASEFGDSQLYQIDARGDDDLSN----LELVQTFSNWAPILDFVVMDL----GGEDTAR--IYTCS 320

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451  511 GHGKNGALCVFqRHIYPQTSFAFHQFDSQ---AIWSIKcrkndqqQNEDDDFDKLLFISKSKSTLVLS-AGDELQEVKT- 585
Cdd:pfam10433  321 GAGKRGSLRSL-RHGVGAEELAVSEEPGSpitGVWTLK-------SSPEDEYDDYLVVSFVNETRVLSiDGDGVEEVDEd 392

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954541451  586 -GFYTRGSTIAVSTLfDATRIVQVYATGVmVLTPEGKRIQTVPIPRGAKIVEASIHDPYILLTLDNNKILALQ 657
Cdd:pfam10433  393 sGFLLSVPTLAAGNL-GDGRLLQVTPNGI-RLIDSDKRISEWKPPGGKSITAAAANGRQVLLALSGGELVYFE 463
RPS28A COG2053
Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]; Ribosomal ...
 1455-1524 1.65e-19

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: 83.87  E-value: 1.65e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1954541451 1455 MEDLDTKTPVKlARVTKVLGRTGSRGGVTQVRVEFMD--DTNRSIIRNVKGPVRENDILCLLESEREARRLR 1524
Cdd:COG2053      1 MSEVTEEDGVP-AEVIEIIGRTGMTGEVTQVRVRILEgrDKGRIITRNVKGPVRVGDILMLRETEREARKLK 71
rps28e PRK04007
30S ribosomal protein S28e; Validated
 1467-1524 5.53e-18

30S ribosomal protein S28e; Validated


Pssm-ID: 235197  Cd Length: 70  Bit Score: 79.63  E-value: 5.53e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954541451 1467 ARVTKVLGRTGSRGGVTQVRVEFMD--DTNRSIIRNVKGPVRENDILCLLESEREARRLR 1524
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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