Conserved Protein Domain Family
TM_Y_HKU9-like_Nsp3_C

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cd21715: TM_Y_HKU9-like_Nsp3_C 
C-terminus of non-structural protein 3, including transmembrane and Y domains, from Rousettus bat coronavirus HKU9 and betacoronavirus in the D lineage
This model represents the C-terminus of non-structural protein 3 (Nsp3) from betacoronavirus in the nobecovirus subgenus (D lineage), including Rousettus bat coronavirus HKU9. 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: 409663
Aligned: 10 rows
Threshold Bit Score: 1033.66
Created: 30-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      ######################                                                          
P0C6T6    2084 YIWFVWTCLTICGVWLSEPYAPSLVTRFKYFLGIVMPCDYVLVNETGTGWLHHLCMAGMDSLDYPALRMQQHRYGSPYNY 2163 Rousettus bat co...
QEH60462  2016 YLWFLWTCLAIMGVWVSEPYAPTLLTRLKNFLGLVMPCDYVVANETGSGWLHHLCMAGMDNLDYPSLKMQQFRYGSPYDY 2095 Bat coronavirus
AOG30811  2128 YMWFTWTCLAIVGVWVSEPYAPSLLTKVKQYFGFVFPCDYLTVNETSEGWFHHMCMSGMDGLDYPALKMQQRRYGSPYDW 2207 Rousettus bat co...
AWV67038  2043 TLWFAWTLLMVLSVWLSEPYAPTWLTGLRHKVGISMPCDYVLTDDNVTGWFHNLCMAGMDNLAYPALRVVQQRMGSPYDY 2122 Bat coronavirus
AWV67054  2084 YIWFVWTCLTICGVWLSEPYAPSLLTRLKQFLGIVMPCDYVLVNETGTGWLHHLCMAGMDSLDYPALRMQQHRYGSPYNY 2163 Bat coronavirus
ADM33565  2059 YIWFVWTCLVITGVWLSEPYTMSIISRFKHFFGIVMPCDYVLVNETGSGWLHHLCMSGMDGFNYPALRMQQQRYGSPYDY 2138 Bat coronavirus ...
AVP25405  2071 YMWFVWTCVTIWGVWLSEPYAPELLTRFKHFLGLVMPCDYVLVNETGTGWLHHLCMAGMDGLDYPALHMQQYRYGSPYDY 2150 Rousettus bat co...
ABN10926  2079 YVWFVWTCLTICGVWLSEPYAPDWLNRVRSFIGLVMPCDYVLVNETGTGWLHHLCMAGMDNLDYPALRMQQHRYGSPYDY 2158 Bat coronavirus ...
QDF43839  2082 YLWFLWTCLAIMGVWVSEPYAPTLLTRFKNFLGLVMPCDYVVANETGSGWLHHLCMAGMDTLDYPALKMQQFRYGSPYDY 2161 Coronavirus BtRt...
ABN10934  2079 YMWFIWTCLAICGVWLSEPYAPNLLNRFKNFIGIVMPCDYVLVNETGAGWLHHLCMAGMDGLDYPALRMQQHRYGSPYDY 2158 Bat coronavirus ...
Feature 1                                                                                      
P0C6T6    2164 TYILMLLEAFFAYLLYTPALPIVGILAVLHLIVLYLPIPLGNSWLVVFLYYIIrlVPFTSMLRMYIVIAFLWLCYKGFLH 2243 Rousettus bat co...
QEH60462  2096 TFLLLLLEIFAAYLLYTPVFPALGIFAVLHFLILYVPLPLNNSWLLVFIYYFIkwVPFTTMVRMYIVTSFLRLCYKGFVH 2175 Bat coronavirus
AOG30811  2208 TYMVMFLEAFVAYLLYTPVLPLVGIIGCLHALVLYLPISLGNSWLVVFFYYFVklIPLSSLLRMYIVSAFLWLCYKGFVH 2287 Rousettus bat co...
AWV67038  2123 TSFLFVLEIVLAYVLYTPLLPGVGIFAVMHTLLNWFPNMLGSSWLMVFIYHVVrlVPLISLLRLYIALSFLWVCYRGLCH 2202 Bat coronavirus
AWV67054  2164 TYILMLLEAFFAYLLYTPALPIVGILAVLHLIVLYLPIPLGNSWLVVFLYYIIrlVPFTSMLRMYIVIAFLWLCYKGFLH 2243 Bat coronavirus
ADM33565  2139 TYILMLLEAFCAYLLYTPALPIVGVLAVLHLVVLYLPIPLGNSWLVVFLYYVIrlVPFTSMLRMYIVIAFLWLCYKGFVH 2218 Bat coronavirus ...
AVP25405  2151 TYVLMILEAFCAYLLYTPALPMVGILAVLHLIVLYLPVPLGNSWLVVFLYYIIrlVPFTSMLRMYIVIAFLWLCYKGFVH 2230 Rousettus bat co...
ABN10926  2159 TYILMLLEAFLAYLLYTPALPIVGVLAVLHLVVLYLPIPLGNSWLVVFLYYLIrlVPFTSMLRMYIVMAFLWLCYKGFLH 2238 Bat coronavirus ...
QDF43839  2162 TFLLLLLEIFAAYLLYTPVFPALGIFAVLHFLILYVPLPLNNSWLLVFFYYFIkwVPFTTMVRMYIVTSFLWLCYKGFVH 2241 Coronavirus BtRt...
ABN10934  2159 TYVLMLLEAFCAYLLYTPALPIVGILAVLHLIVLYLPIPLGNSWLVVFLYYIIrlVPFTSMLRMYIVIAFLWLCYKGFLH 2238 Bat coronavirus ...
Feature 1                                                                                      
P0C6T6    2244 VRYGCNNVACLMCYKKNVAKRIECSTVVNGVKRMFYVNANGGThFCTKHNWNCVSCDTYTVDSTFICRQVALDLSAQFKR 2323 Rousettus bat co...
QEH60462  2176 VRYGCNNVACLMCYKKNVAKRIECSTIVNGVKRVFYVNANGGThFCTKHNWNCVSCDTYNVDSTFISRPVALDLSAQFKR 2255 Bat coronavirus
AOG30811  2288 VRYGCTNVSCLMCYKRNIATRVECSTVVNGVKRVFYVNANGGTyYCTKHNWNCVNCDTYTVDSTFISRPVALDLSAQFKR 2367 Rousettus bat co...
AWV67038  2203 VRFGCNNVSCLMCYKRNGATRVECSTIVAGVKRSFYVNANGGTyFCTKHNWNCVNCDSYSVDSTFISRPVALDLSAQFKR 2282 Bat coronavirus
AWV67054  2244 VRYGCNNVACLMCYKKNVAKRIECSTVVNGVKRMFYVNANGGTrFCTKHNWNCVSCDTYTVDSTFICRQVALDLSAQFKR 2323 Bat coronavirus
ADM33565  2219 VRYGCNNVSCLMCYKKNVAKRIECSTVVNGVKRIFYVNANGGTyFCTKHNWNCVSCDTYTVDSTFISRQVALDLSTQFKR 2298 Bat coronavirus ...
AVP25405  2231 VRYGCNNVACLMCYKKNVARRIECSTVVNGVKRMFYVNANGGThFCTKHNWNCVSCDTYTVDSTFISRQVALDLSAQFKR 2310 Rousettus bat co...
ABN10926  2239 VRYGCNNVACLMCYKKNVARRIECSTVVNGVKRMFYVNANGGThFCTKHNWNCVSCDTYTVDSTFISRQVALDLSAQFKR 2318 Bat coronavirus ...
QDF43839  2242 VRYGCNNVACLMCYKKNVAKRIECSTIVNGVKRVFYVNANGGThFCTKHNWNCVSCDTYNVDSTFISRPVALDLSAQFKR 2321 Coronavirus BtRt...
ABN10934  2239 VRYGCNNVACLMCYKKNVAKRIECSTVVNGVKRMFYVNANGGTyFCTKHNWNCVSCDTYTVDSTFISRQVALDLSAQFKR 2318 Bat coronavirus ...
Feature 1                                                                                      
P0C6T6    2324 PIIHTDEAYYEVTSVEVRNGYVYCYFESDGQRsYERFPMDAFTNVSKLHYSELKGAAPAFNVLVFDATNRIEENavKTAA 2403 Rousettus bat co...
QEH60462  2256 PINPTDEAYYEVTSVEVRKGYVYCYFDLDGQRsYERFPMDAFTNVNKLHYSELKGAAPALNVLVFDATNSIEENavKTSA 2335 Bat coronavirus
AOG30811  2368 PINHTDEAYYEVTSVQVRNGYVYCYFDSEGEQsYERFPVDSFTNVSKLYYSELKGNPPAFNVLIFDATNRIEENavKTAA 2447 Rousettus bat co...
AWV67038  2283 PINHTDEAYYEVTSVEVKHGYVYAYFDLEGKRsYEKFPMDKFANPSKYYFSELKGVAPSLNVIIFDASNTIEENaaKTSA 2362 Bat coronavirus
AWV67054  2324 PIIHTDEAYYEVTSVEVRNGYVYCYFESDGQRsYERFPMDAFTNVSKLQYSELKGAAPAFNVLVFDATNRIEENavKAAA 2403 Bat coronavirus
ADM33565  2299 PIIHTDEAYYEVTSVEVRNGYVYCYFDSDGERsYERFPMDAFTNVSKLHYSELKGAAPSFNVLIFDATNRIEETavKNAA 2378 Bat coronavirus ...
AVP25405  2311 PIVHTDEAYYEVTSVEVRNGYVYCYFESDGQRsYERFPMDAFTNVSKLHYAELKGAAPSFNVLVFDATNRIEENavKAAA 2390 Rousettus bat co...
ABN10926  2319 PILPTDEAYYEVTSVEVRNGYVYCYFDSDGQRsYERFPMDAFTNVSKLHYAELKGAAPAFNVLVFDATNRIEENavKAAA 2398 Bat coronavirus ...
QDF43839  2322 PINPTDEAYYEVTSVEVRKGYVYCYFDLDGQRsYERFPMDAFTNVNKLYYAELKGAAPALNVLVFDATNSIEENavKTSA 2401 Coronavirus BtRt...
ABN10934  2319 PIIHTDEAYYEVTSVEVRNGYVYCYFESDGQRsYERFPMDAFTNVSKLHYSELKGAAPAFNVLVFDATNRIEENavKTAA 2398 Bat coronavirus ...
Feature 1                                                                                      
P0C6T6    2404 IYYAQLACKPILLVDKRMVGVVGDDAtiarAMFEAYAQNYLLKYSIAMDKVKHLYSTALQQISSGMTVESVLKVFVGSTR 2483 Rousettus bat co...
QEH60462  2336 IYYAQLACKPILLVDKRMVGVVGDDAtiskAMFEAYAQNYLMKYSIPMDKVKSLYATALQQLAAGSSVESVLKVFVGSTR 2415 Bat coronavirus
AOG30811  2448 IYYSQLACKPILLVDKRMVGVVGDDTaiakTMFEAYAQSYLLKYNIAMDKVKSLYATALQQIASGTSVEAVLKVFVGSTR 2527 Rousettus bat co...
AWV67038  2363 VFFAQLACRPMLLIDKRMIGVVGDEAgiskAMFEAYAQNYLLRFSIPMDKVKALYTTALQQIASGSSVESVLKVFVGSTR 2442 Bat coronavirus
AWV67054  2404 IYYAQLACKPILLVDKRMVGVVGDDAaiakAMFEAYAQNYLLKYSIAMDKVKHLYSTALQQISSGMTVEAVLKVFVGSTR 2483 Bat coronavirus
ADM33565  2379 IYYAQLACKPILLVDKRMVGVVGDDAtiakTMFEAYAQNYLLKYSINMEKVKHLYTTALQQIASGMTVEAVLKVFVGSTR 2458 Bat coronavirus ...
AVP25405  2391 IYYAQLACKPILLVDKRMVGVVGDDAtisrAMFEAYAQNYLLKYSITMEKVKHLYTTALQQIASGMTVESVLKVFVGSTR 2470 Rousettus bat co...
ABN10926  2399 IYFAQLACKPILLVDKRMVGVVGDDAtiakAMFEAYAQNYLLKYNIAMDKVKHLYSTALQQISSGMTVEAVLKVFVGSTR 2478 Bat coronavirus ...
QDF43839  2402 IYYAQLACKPILLVDKRMVGVVGDDAtiskAMFEAYAQNYLMKYSIPMDKVKHLYSTALQQLAAGSSVESVLKVFVGSTR 2481 Coronavirus BtRt...
ABN10934  2399 IYYAQLACKPILLVDKRMVGVVGDDAtiakAMFEAYAQNYLLKYSIAMDKVKHLYSTALQQISSGMTVEAVLKVFVGSTR 2478 Bat coronavirus ...
Feature 1                                                                                      
P0C6T6    2484 AEAKDLESDVDTNDLVSCIRLCHQEGWEWTTDSWNNLVPTYIKQDTLSTLEVGQFMTANAKYVNANIAKGAAVNLIWRYA 2563 Rousettus bat co...
QEH60462  2416 AEAKDLESDVDTNDLVSCLRLCHQEGWEWTTVSWNNLVPTYVKQDTLTTLEVGQFITSNARYINANVAKGAAVNLVWRYA 2495 Bat coronavirus
AOG30811  2528 EEARDLESDVDTNELVSCIRMCHQDGWEWTTASWNNLVPTYLKQETLSTLEVGQLITSNARYINANMAKSAAVQIVWRYA 2607 Rousettus bat co...
AWV67038  2443 NESKDIESDVETTDIVSCLRFCHQESWDWSVGPYNNLIPTYLKQDTLTTLEVGQLISCSARYVNANIAKSSAINIVWRFS 2522 Bat coronavirus
AWV67054  2484 AEAKDLESDVDTNDLVSCIRLCHQEGWEWTTDSWNNLVPTYIKQDTLSTLEVGQFMTANAKYVNANIAKGAAVNLIWRYA 2563 Bat coronavirus
ADM33565  2459 AEAKDLESDVDTNDVVSCIRLCHQEGWDWSTDSWNNLVPTYIKQDTLSTLEVGQFMTASARYVNANVAKSAAVNLIWRYA 2538 Bat coronavirus ...
AVP25405  2471 AEAKDLESDVDTNDLVSCIRLCHQEGWDWTTDSWNNLVPTYLKQDTLSTLEVGQFMTANARYVNANVAKGAAVNLVWRYA 2550 Rousettus bat co...
ABN10926  2479 SEAKDLESDVDTNDLVSCMRLCHQEGWDWTTDSWNNLVPTYIKQDTLSTLEVGQFMTANARYVNANVAKGAAVNLVWRYA 2558 Bat coronavirus ...
QDF43839  2482 AEAKDLESDVDTNDLVSCLRLCHQEGWEWTTMSWNNLVPTYVKQDTLTALEVGQFITSNARYINANVAKSAAVNLVWRYA 2561 Coronavirus BtRt...
ABN10934  2479 TEAKDLESDVDTNDLVSCIRLCHQEGWDWTTDSWNNLVPTYIKQDTLSTLEVGQFMTANARYVNANVAKGAAVNLVWRYT 2558 Bat coronavirus ...
Feature 1                                                    
P0C6T6    2564 DFIKLSESMRRQLKVAARKTGLNLLVTTSSLKADVPCMVTPFKIIG 2609 Rousettus bat coronavirus HKU9
QEH60462  2496 DFVKLSETMRRQLKVAARKTGLNLLLTTSSLRAEVPCVVTPFKIVG 2541 Bat coronavirus
AOG30811  2608 DFARLSESVRRQLKIAARKTGLSLQLTTSNLKADVACVVTPFKVVG 2653 Rousettus bat coronavirus
AWV67038  2523 DFIKLSESLRRQIRIAARKTGLNLQLTTSSLKADVTCVVTPIRVVG 2568 Bat coronavirus
AWV67054  2564 DFVKLSESMRRQLKVAARKTGLNLLVTTSSLKADVPCMVTPFKIIG 2609 Bat coronavirus
ADM33565  2539 DFIKLSESVRRQLRVAARKTGLNLFVTTSSLKADVPCVVTPFKIVG 2584 Bat coronavirus HKU9-5-2
AVP25405  2551 DFIKLSESMRRQLRVAARKTGLSLFVTTSSLKADVPCMVTPFKIIG 2596 Rousettus bat coronavirus HKU9
ABN10926  2559 DFVKLSESVRRQLRVAARKTGLNLLVTTSSLKADVPCMVTPFKIIG 2604 Bat coronavirus HKU9-3
QDF43839  2562 DFIKLSETMRRQLKVAARKTGLNLLLTTSSLRAEVPCVVTPFKIVG 2607 Coronavirus BtRt-BetaCoV/GX2018
ABN10934  2559 DFIKLSESVRRQLRVAARKTGLNLLVTTSSLKADVPCMVTPFKIIG 2604 Bat coronavirus HKU9-4

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