Conserved Protein Domain Family
TM_Y_alphaCoV_Nsp3_C

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cd21712: TM_Y_alphaCoV_Nsp3_C 
C-terminus of alphacoronavirus non-structural protein 3, including transmembrane and Y domains
This model represents the C-terminus of non-structural protein 3 (Nsp3) from alphacoronavirus, including Porcine epidemic diarrhea virus and Human coronavirus 229E, among others. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In the related betacoronaviruses, Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain.
Statistics
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PSSM-Id: 409660
Aligned: 85 rows
Threshold Bit Score: 626.192
Created: 28-Apr-2020
Updated: 25-Oct-2021
Structure
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Aligned Rows:
 
TM1 [structuralTM2 [structural
Feature 1:TM1 [structural motif]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1         ######################                                                          
SNQ27886     2015 FFKLKLYWFKVLGKFSLGIYALYallfmtirFTPIGGPVCDDVVAGYANSSFDK-NEYCNSVICKVCLYGYQELSDFSHT 2093 Porcine epide...
YP_009380519 1859 ERRNWFYAFGVFASFFYICYAVVs-------AGLRFSSLCTEWTDGYANSTFVKqDYCNGSLICYECLRGYEELSDFAHI 1931 Coronavirus A...
YP_009336483 1956 AASGIYAKRRWFYIFGIVASAFYigys-llfTTLRFSSLCKGWTDGYANSTFIKqDYCNGSLICYECLRGYEELSDFPHT 2034 Lucheng Rn ra...
ATP66766     1944 AASGIYAKRSWFYIFGIVASAFYigys-llfTTLRFSSLCKGWTKGYANSTFIKqDYCNGSLICYECLRGYEELSDFPHT 2022 Rodent corona...
QBG64654     1951 AASGICAKRRWFYMFGIVASAFYigys-llfTTLRFSSLCKGWTDGYANSTFIKqDYCNGSLICYECLRGYEELSDFPHT 2029 Alphacoronavi...
QBG64644      295 SVYSRCCWFYIFGIIANILYCVYsl----lfTGLRFSSFCSSWTSGYANSTFVKsEYCNGSLICYECLRGYEELADFPHT 370  Alphacoronavi...
ASF90443     1598 GIKKKKKKISFCYKTGILLFGLFq-------LLLLVSQLDHSYYDEYSQSNFNKkEFCGKNFWCYLTLWNVDGLEDFPHL 1670 Wencheng Sm s...
ASF90459     1585 VIKKKRKKISFCYKIGILLFGLFq-------LLLLGAQLDHSYYDEYSQSNFNKkEFCGKNFWCYLTLWNVDGLEDFLHL 1657 Wencheng Sm s...
ASF90474     1599 GIKKKKKKISFCYKTGILLFGLFq-------VLLLVAQLDHSYYDEYSQSNFNKkEFCGKNFWCYLTLWNVDGLESFPHL 1671 Wencheng Sm s...
ASF90490     1596 GIKKKKKKISLCYKTGILLFGFFq-------LLLIAAQFDYSYYDEYSQSNFNKkEFCGKNFWCYLTLWNVDGLEDFSHL 1668 Wencheng Sm s...
Feature 1                                                                                         
SNQ27886     2094 QVVWQHLr-dPLIGNVMPFFYLAFLAIFGGVYVKAITLYFICQYLnilgvFLGLQQSIWFLQlvpFDVFGDEIVVFFIVT 2172 Porcine epide...
YP_009380519 1932 HVRWSFTynlSEFFIFYHALTFTIMWVFGSKYVKTGLFYFVLQCWnnamcWFDNTEPIWLLNivkFSSVSVHFFSLFCVY 2011 Coronavirus A...
YP_009336483 2035 QVKWSFTynlSEFALFYHVLTFTIMWVFGNKYVKALLFYFVLQCWnsamcWFDETEPIWFLNfikFSSISAHGFSLFCVF 2114 Lucheng Rn ra...
ATP66766     2023 QVKWSFTynlSEFALFYHVLTFTIMWVFGNKYVKALLFYFVLQCWnsamcWFDKTEPIWFLNfikFSSISAHGFSLFCVF 2102 Rodent corona...
QBG64654     2030 QVKWSFTynlSEFALFYHVLTFTIMWVFGNKYVKALLFYFVLQCWngamcWFDKTEPIWFLSfikFSSISTHGFSLFCVF 2109 Alphacoronavi...
QBG64644      371 RIKWSFTynlSEFVVFYHAMAFVIMWCFGNKYVKLFLLYFVLQVWnhvmcWFDNTEPMFLLNlvkFNTISTHAFSLFCVF 450  Alphacoronavi...
ASF90443     1671 NIQWNVFk-gGFSFTILPLFYMAIMFCFGSFYLQGFLIAMLFQWF-----SSVMGLSIEVLDivnLTQFLEPVFCCFIFV 1744 Wencheng Sm s...
ASF90459     1658 NIQWNVFk-gGFSFTILPLFYMAIMFCFGNIYLQGFLIAMLFQWF-----SSVMGLNVEMLDfvnLTQFLEPLFCCFIFV 1731 Wencheng Sm s...
ASF90474     1672 NIQWNVFk-gGFSFTILPLFYMAIMFCFGNFYLQGFLIAMLFQWF-----SSMMGVNVEVLDfvnLTQFLEPVFCCFIFI 1745 Wencheng Sm s...
ASF90490     1669 NIQWNVFk-gGFSFTILPLFYMVIMFCFGNFYLQGFLIAMLLQWF-----SSMMGVNVEMLDfvnLTQFLEPVFCCFIFI 1742 Wencheng Sm s...
Feature 1                                                                                         
SNQ27886     2173 RVLMFLKHVFFGCDKASCVACSRSARLKRVPVQTIFQGTSKSFYVHANGGsKFCKKHNFFCLNCDSYGPGCTFINDVIAT 2252 Porcine epide...
YP_009380519 2012 KLACFVKHVLFGCSKPNCLSCSRSAKYDRVPCDTIVNGVKRSFYVTANGGrKFCDKHQFFCQNCDSLGVGCTFINEHVAK 2091 Coronavirus A...
YP_009336483 2115 KIACFVKHVVFGCNDVKCLSCSRSAKYDRISCDTIVNGVKRSFYVKANGGkSFCEKHQFFCQNCDSYGVGCTFINDHVAK 2194 Lucheng Rn ra...
ATP66766     2103 KIACFVKHVVFGCNDAKCLSCSRSAKYDRISCDTIVNGVKRSFYVKANGGkSFCEKHQFFCQNCDSYGVGCTFINDHVAK 2182 Rodent corona...
QBG64654     2110 KMACFVKHVIFGCSDVKCLSCSRSAKYDRISCDTIVNGVKRSFYVTANGGkSFCERHQFFCQNCDSYGVGCTFINDHVAK 2189 Alphacoronavi...
QBG64644      451 KLLCFFKHVIFGCNDPKCPSCSRSAKYDRITCDTIVNGMKRSFYVKANGGqSFCEKHQFFCHNCDTYGVGSTFINDHVAK 530  Alphacoronavi...
ASF90443     1745 KIFRFFHHVVFGCTKSFCKYCSKAAKQKKFLVSTIVNGSSKSFYVNANGGgKFCNKHNFYCKGCESYGVGNTFINESVAD 1824 Wencheng Sm s...
ASF90459     1732 KIFKFFHHVIFGCTKSFCKYCSKAAKQKKFLVSTVVNGSSKSFYVNANGGgKFCNKHNFYCKSCESYGVGNTFINESVAD 1811 Wencheng Sm s...
ASF90474     1746 KIFKFFHHVCFGCTKSFCKYCSKAAKQKKFLVSTVVNGSSKSFYVNANGGgKVCNKHNFYCKSCESYGVGNTFINESVAD 1825 Wencheng Sm s...
ASF90490     1743 KIFKFFHHVCFGCTKSFCKYCSKAAKQKKFLVSTVVNGSSKSFYVNANGGgKFCNKHNFYCKSCESYGVGNTFINESVAD 1822 Wencheng Sm s...
Feature 1                                                                                         
SNQ27886     2253 EVGNvvKLNVQPTGPATILIDKVEFsNGFYYLYSGDTFWKYNFDITDsKYTCKESLKNCSIitDFIVFNNNgSNVNQVKN 2332 Porcine epide...
YP_009380519 2092 EVSNvtKTNVRATGPAYVEIDKVTFdDGFYYLHAGDQFWKYDFDVSSkKFDSEVCIKDLSLtaDFMVFNDSgTARANAVN 2171 Coronavirus A...
YP_009336483 2195 EVANvtRTAVRATGPAYVEVDKVTFeDGFYYLYSGEQFWKYEFDVSSkKFDSENCIKDLSLgaDFMVYNDNgTARANALN 2274 Lucheng Rn ra...
ATP66766     2183 EVANvtRTAVRATGPAYVEVDKVTFeDGFYYLYSGDQFWKYEFDVSSkKFDSENCIKDLSLgaDFMVYNDNgTARANALN 2262 Rodent corona...
QBG64654     2190 EVANvtRTAVRATGPAYVEVDRVTFeDGFYYLYSGEQFWKYEFDVSSkKFDSENCIKDLSLgaDFMVYNDNgTARANALN 2269 Alphacoronavi...
QBG64644      531 EVANvtRTAVRATGPAYIEIDKVSFeDGFYYLYSGDQFWKYDFDISSkKFDADNCIKDLSVssDFLVYNDSgTCRANALN 610  Alphacoronavi...
ASF90443     1825 YLSDyvKHRVVATAPASKVVDKVAFeNGKWKLYVGDEFISITEDLTSsSYTIESVLKNNLMvsNVVVVSDN-SNMGVVDN 1903 Wencheng Sm s...
ASF90459     1812 YLSDyvKHRVVATAPASKVVDKVAFeNGKWKLYVGDEFISITDDLTSsSYTIESVLKSNLMasNVVVVSDN-SNMGVVDN 1890 Wencheng Sm s...
ASF90474     1826 YLSDyvKHRVLATAPASKIVDKVVFeNGKWKLYAGGEFISITEDLTSsSYTIESVLKNNLManNVVVVSDN-SNMGVVDN 1904 Wencheng Sm s...
ASF90490     1823 YLSDyvKHRVLATAPASKIVDKVVFeNGRWKLYVGDEFISITEDLTSsSYTIESVLKNNLManNVVVVSDN-SNMGVVDN 1901 Wencheng Sm s...
Feature 1                                                                                         
SNQ27886     2333 ACVYFSQMLCKPVKLVDSALLASLSVDFGasLHSAFVSVLSNSFGKDLSSCNDMQDCKSTLGFDDVPLDTFNAavaeaHR 2412 Porcine epide...
YP_009380519 2172 ASVYFSQLLCKPIKLVNKVLLSSLTIDHGgaMHDAYCKVLHNSFNKDFAKCGDLQSCKRCVGVDCRDAVFEQGvk-laHK 2250 Coronavirus A...
YP_009336483 2275 ASVYFSQLLCKPIKVVNRVLLSSLTIDHGsaMHEAYCKVLHNSFNKDFTRCTDLQNCKSVAGIECRDSTFETGvk-laHK 2353 Lucheng Rn ra...
ATP66766     2263 ASVYFSQLLCKPIKVVNRVLLSSLTIDHGsaMHEAYCKVLHNSFNKDFTRCTDLQNCKNVAGIECRDSTFETGvk-laHK 2341 Rodent corona...
QBG64654     2270 ASVYFSQLLCKPIKVVNRVLLSSLTIDHGsaMHEAYCKVLHNSFNKDFTRCTDLQNCKSVAGIECRDSTFETGvk-laHK 2348 Alphacoronavi...
QBG64644      611 ACVYFSQLACKPIKVVNRVLLSSLTIDHGhaMHEAYCRVLHNSFNKDFGKCNDLQSCKSVAGVECRDSIFESGvk-laHK 689  Alphacoronavi...
ASF90443     1904 ACVYYSQLFCKPIFVVDRQLLFSLDIDYNtaVFDSLIKVCANSFNKDFTNCKTLEDCKKELDFSVNTQAFVDAvk-maHK 1982 Wencheng Sm s...
ASF90459     1891 ACVYYSQLFCKPIFVVDRQLLLSLDIDYNtaVFDSLIKVCANSFNKDFTNCKTLEECKKELDFSVNTQAFVDAvk-maHK 1969 Wencheng Sm s...
ASF90474     1905 ACVYYSQLFCKPIFVVDRQLLLSLDIDYNtaVFDSLIKVCANSFNKDFTNCKTLEECKKELDFSVNTQAFVDAvk-maHK 1983 Wencheng Sm s...
ASF90490     1902 ACVYYSQLFCKPIFVVDRQLLLSLDIDYNtaVFDSLIKVCANSFNKDFTNCKTLEECKKELDFSVNTQAFVDAvk-maHK 1980 Wencheng Sm s...
Feature 1                                                                                         
SNQ27886     2413 YDVLLTDMSFNNFTTSYAKPEEKLpvHDIATCMRVGAKIVNHNVLVKDSIPVVWLVRDFiALSEETRKYIIRTTKVKGIt 2492 Porcine epide...
YP_009380519 2251 YDVLLCNDSANNFVTTYAKAGTRVgtADLAVFNRESVREINHAVLTRNKVTVVWSVNVFsKLSTDTQDYIVKTTKAKGLl 2330 Coronavirus A...
YP_009336483 2354 FDILLCNDSANNFVTTYAKAGTRIgtADLAVFNRESVREVSHAVLARNKTTIVWSVNVFsKLSGDTQDYIVRTTKAKGLl 2433 Lucheng Rn ra...
ATP66766     2342 FDVLLCNDSANNFVTTYAKAGTRVgtADLAVFNRESVREVSHAVLARNKTTIVWSVNVFsKLSGDTQDYIVRTTKAKGLl 2421 Rodent corona...
QBG64654     2349 FDILLCNDSANNFVTTYAKAGTRVgtADLAVFNRESVREVSHAVLARNKTTIVWSVNVFsKLSGDTQDYIVRTTKAKGLl 2428 Alphacoronavi...
QBG64644      690 YDVLLCNDSANNFVTTYAKVSQRVgtADLAVFNRESVREINHAVLARNKTTIVWSVAVFsKLSSDTQDYVVKTTKAKGLl 769  Alphacoronavi...
ASF90443     1983 YDVLLTDRSYNNFTITYAKIGDKLskTDQAVCLRANVGIINHNVAVKENISVVWYYKNFlQLSEEGKKYIVKTTKAKGVg 2062 Wencheng Sm s...
ASF90459     1970 YDVLLTDRSYNNFTITYAKIGDKLskTDQAVCLRANVGVLNHNVAVKENISVVWYYKNFlQLSEEGKKYIVKTTKAKGVg 2049 Wencheng Sm s...
ASF90474     1984 YDILLTDRSYNNFTITYAKIGDKLskTDQSVCLRANVGVINHNVAVKENISVVWYYKNFlQLSEEGKKYIVKTTKAKGVg 2063 Wencheng Sm s...
ASF90490     1981 YDILLTDRSYNNFTITYAKIGDKLskTDQSVCLRANVGVINHNVAVKEHISVVWYYKNFlQLSEEGKKYIVKTTKAKGVg 2060 Wencheng Sm s...
Feature 1                                
SNQ27886     2493 FMLTFNDCRMHTTIPTVCIANKK 2515 Porcine epidemic diarrhea virus
YP_009380519 2331 FLLTFNDHVNTQNLPCNMVNSKN 2353 Coronavirus AcCoV-JC34
YP_009336483 2434 FLLTFNDHVNTQNLPCTMVNSKS 2456 Lucheng Rn rat coronavirus
ATP66766     2422 FLLTFNDHVNTQNLPCTMVNSKS 2444 Rodent coronavirus
QBG64654     2429 FLLTFNDHVNTQNLPCTMVNSKS 2451 Alphacoronavirus UKRn3
QBG64644      770 FLLTFNDHVNTQNLPCSAIGVKS 792  Alphacoronavirus UKMa1
ASF90443     2063 FYITFNDIEANTQAPVTRFQKNA 2085 Wencheng Sm shrew coronavirus
ASF90459     2050 FYITFNDIEATIQAPITRFQKNA 2072 Wencheng Sm shrew coronavirus
ASF90474     2064 FYITFNDIEATIQAPITRFQKNA 2086 Wencheng Sm shrew coronavirus
ASF90490     2061 FYITFNDIEATIQAPITRFQKNA 2083 Wencheng Sm shrew coronavirus

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