Conserved Protein Domain Family
TM_Y_MERS-CoV-like_Nsp3_C

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cd21716: TM_Y_MERS-CoV-like_Nsp3_C 
C-terminus of non-structural protein 3, including transmembrane and Y domains, from Middle East respiratory syndrome-related coronavirus and betacoronavirus in the C lineage
This model represents the C-terminus of non-structural protein 3 (Nsp3) from betacoronavirus in the merbecovirus subgenus (C lineage), including Middle East respiratory syndrome-related coronavirus (MERS-CoV) and Tylonycteris bat coronavirus HKU4. 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: 409664
Aligned: 23 rows
Threshold Bit Score: 1129.14
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      ######################                                                          
AVV62536  2203 LRLLLVLCTTGLLLSSIYHLYIFNQVVSSDAMLDDVTGFMAIYKEIRSYLHITSACDGLArDYRANSFDISNFCANRSAL 2282 Middle East resp...
P0C6F7    2227 LRLFLLLCTTILLLSSIYHLVIFNQVLSSDVMLEDATGILAMYKEVRSYLGIRTLCDGLAvEYRNTSFDVVDFCSNRSVL 2306 Bat coronavirus ...
P0C6T5    2266 LRLLFLICTTGLLLSSLYYLFLFHQVLTSDVMLDGAEGMLATYRELRSYLGIHSLCDGMVeAYRNVSYDVNDFCSNRSAL 2345 Pipistrellus bat...
QGA70691  2184 LRLLLFVLTTVVMLLSVYHLYIFNAVLTSDIIKEGRAGVRGVYNKLTSYIVSSSPCDGFSrSYRNASFNVDEYCEKYGYI 2263 Erinaceus hedgeh...
AUM60013  2173 LRLLLVICTTGLLLSSVYHLYVFNQVLSSDVMLEDATGLKWVYKEFRSYLGITSSCDGIAsDYRANSFDISSYCANRSAL 2252 Middle East resp...
QCC20712  2246 LRLLLFMLTTVIMLLSLYHLYVFNAVLTSDVIKEVNTGIKGVYYRISSYLGVTSVCDGFSsSYRNVSFNRDDYCEKFGYV 2325 Hedgehog coronav...
AIA62351  2228 LRLFLLLCTTILLLSSIYHLVIFNQVLSSDVMLEDATGILAFYKEVRSYLGIRTLCDGLAvEYRNTSFDVVDFCSNRSVL 2307 BtTp-BetaCoV/GX2012
ANA96038  2233 LRLFLLLCTTVLLLSSIYHLIIFNQVLSSDVMLEDATGILAIYKEVRSYLGISTLCDGLVaEYRNTSFDVVDFCSNRSVL 2312 Bat coronavirus
P0C6T4    2220 LRLFLLLCTTILLLSSIYHLVLFNQVLSSDVMLEDATGILAIYKEVRSYLGIRTLCDGLVvEYRNTSFDVMEFCSNRSVL 2299 Tylonycteris bat...
AIA62342  2266 LRLLFLICTTGLLLSSLYYLFLFHQVLTSDVMLDGAEGMLATYRELRSYLGIHSLCDGMVeAYRNVSFDVNDFCSNRSAL 2345 BtPa-BetaCoV/GD2013
Feature 1                                                                                      
AVV62536  2283 CKWCLLGQDSITHYSALKMVQTHISHYVLNVDWLWFALELLFAYVMYTAAFNWVLLACTLQYFFSQTSLFVDWRSYNYVV 2362 Middle East resp...
P0C6F7    2307 CQWCLIGQDSLTRYSALQMLQTHITSYVLNIDWIWFALEFFLAYVLYTSSFNVLLLVVTAQYFFAYTSAFVNWRAYNYIV 2386 Bat coronavirus ...
P0C6T5    2346 CNWCLIGQDSLTRYSAFQMIQTHVTSYVINIDWVWFVMEFALAYVLYTSTFNVLLLVVSSQYFFSYTGAFVNWRSYNYLV 2425 Pipistrellus bat...
QGA70691  2264 CRWCLKGQDSVTKYTALQMNQINLSHYVLNIDWFGFVFEVFIAYLMYTPAFNWVMLICTLQYFFSQTSHIVNWRSYNFLL 2343 Erinaceus hedgeh...
AUM60013  2253 CQWCLIGQDSLNRYSSLKMIQTHLSHYVLNIDWLWFVLELFVGYALYTAAFNWVLLACTLQYFFAQTSLFVDWRSYNYVM 2332 Middle East resp...
QCC20712  2326 CHWCLMRQDSLTQYSAIQIVQTNLSHYVLSIDWIWFWIELGIAYLMYTPAFNWVLLACTLQYFFSQTSHIISWRSYNFVM 2405 Hedgehog coronav...
AIA62351  2308 CQWCLIGQDSLTRYSALQMLQTHITSYVLNIDWIWFAFEFLLAYVLYTSSFNVLLLVVTAQYFFAYTSAFVNWRAYNYIV 2387 BtTp-BetaCoV/GX2012
ANA96038  2313 CQWCLIGQDSLTRYSALQMLQTHITSYVLNIDWIWFALEFLLAYVLYTSSFNVLLLVVTAQYFFAYTSAFVNWRAYNYIV 2392 Bat coronavirus
P0C6T4    2300 CQWCLIGQDSLTRYSALQMLQTHITSYVLNIDWIWFALEFFLAYVLYTSSFNVLLLVVTAQYFFAYTSAFVNWRAYNYIV 2379 Tylonycteris bat...
AIA62342  2346 CNWCLIGQDSLTRYSAFQMIQTHVTSYVINIDWVWFVMEFALAYVLYTSTFNVLLLVVSSQYFFSYTGAFVNWRSYNYLV 2425 BtPa-BetaCoV/GD2013
Feature 1                                                                                      
AVV62536  2363 SCIYLLFTHIPLDGLVRIYNVLACLWFLRKFYNHAINGCKDTACLLCYKRNRLTRVEASTVVCGTKRTFYIAANGGTSFC 2442 Middle East resp...
P0C6F7    2387 SGLFFLVTHIPLHGLVRVYNFLACLWFLRKFYSHVINGCKDTACLLCYKRNRLTRVEASTIVCGTKRTFYIAANGGTSYC 2466 Bat coronavirus ...
P0C6T5    2426 SGYFFCVTHIPLLGLVRIYNFLACLWFLRRFYNHVINGCKDTACLLCYKRNRLTRVEASTVVCGSKRTFYIVANGGTSFC 2505 Pipistrellus bat...
QGA70691  2344 SGIYILTTYIPLGGLLRVYNVLACLWLLRKFYNHVFNGCKDTACLLCYKRNRLTRVEASTVVCGVKRTFYITANGGTSFC 2423 Erinaceus hedgeh...
AUM60013  2333 SSIYLFFTHIPLDGLVRAYNIIACLWFLRRFYNHVINGCKDTACLLCYKRNRLTRIEASTVVCGAKRTFYITANGGTYFC 2412 Middle East resp...
QCC20712  2406 SGVYLLTTYIPLCGLLRVYNVLATLWYLRRFYNHVINGCKDTACMLCYKRNRLTRVEASTVVCGVKRTFYITANGGISFC 2485 Hedgehog coronav...
AIA62351  2388 SGLFFLVTHIPLHGLVRVYNFFACLWFLRKFYSHVINGCKDTACLLCYKRNRLTRVEASTIVCGIKRTFYIAANGGISYC 2467 BtTp-BetaCoV/GX2012
ANA96038  2393 SGIFFLVTHIPLHGLVRVYNFLACLWFLRKFYSHVINGCKDTACLLCYKRNRLTRVEASTIVCGTKRTFYIAANGGMSYC 2472 Bat coronavirus
P0C6T4    2380 SGLFFLVTHIPLHGLVRVYNFLACLWFLRKFYSHVINGCKDTACLLCYKRNRLTRVEASTIVCGTKRTFYIAANGGTSYC 2459 Tylonycteris bat...
AIA62342  2426 SGYFFCVTHIPLLGLVRIYNFLACLWFLRRFYNHVINGCKDTACLLCYKRNRLTRVEASTVVCGSKRTFYIVANGGTSFC 2505 BtPa-BetaCoV/GD2013
Feature 1                                                                                      
AVV62536  2443 CRHNWNCVDCDTAGIGNTFICEEVANDLTTGLRRLIKPTDRSHYYVNSVEVKDTVVQLNYTRDGQVcYERFSLCYFSNLD 2522 Middle East resp...
P0C6F7    2467 CKHNWNCVECDTAGVGNTFICTEVANDLTTTLRRLIKPTDQSHYYVDSVVVKDAVVELHYNRDGSScYERYPLCYFTNLE 2546 Bat coronavirus ...
P0C6T5    2506 CRHNWNCVDCDTAGIGNTFICEEVANDLTTSLRRLVKPTDKSHYYVESVTVKDSVVQLHYSREGAScYERYPLCYFTNLD 2585 Pipistrellus bat...
QGA70691  2424 SRHNWNCVDCDTTGVGNTFICEEVANDLTTSLRRLVKPTDKSHYYVESVELKDTAVQFNYTRGGQLcYERVPLCNFSNID 2503 Erinaceus hedgeh...
AUM60013  2413 CRHNWNCVDCDTAGIGSTFICEEVANDLTASLRRLVKPTDRSHYYVDSVVVKDTVVQLNYCRGDQAcYERFPLCSFTNLD 2492 Middle East resp...
QCC20712  2486 SRHNWNCVDCDTAGLGNTFICEEVANDLTTSLRRLVKPTDRSHYYVESVEVKNSVVQLNYTRDGQLcYERVPLCNFSNLD 2565 Hedgehog coronav...
AIA62351  2468 CKHNWNCVECDTAGVGNTFICTEVANDLTTTLRRLIKPTDQSHYYVDSVVVKDAVVELHYNRDGSScYERYPLCYFTNLE 2547 BtTp-BetaCoV/GX2012
ANA96038  2473 CKHNWNCVDCDTAGVGNTFICTEVANDLTTSLRRLIKPTDQSHYYVDSVVVKDAVVELHYNRDGSScYERYPLCYFTNLE 2552 Bat coronavirus
P0C6T4    2460 CKHNWNCVECDTAGVGNTFICTEVANDLTTTLRRLIKPTDQSHYYVDSVVVKDAVVELHYNRDGSScYERYPLCYFTNLE 2539 Tylonycteris bat...
AIA62342  2506 CRHNWNCVDCDTAGIGNTFICEEVANDLTTSLRRLVKPTDKSHYYVESVTVKDSVVQLHYSREGAScYERYPLCYFTNLD 2585 BtPa-BetaCoV/GD2013
Feature 1                                                                                      
AVV62536  2523 KLKFKEVCKSTTGIPEHNFIIYDASDRGQENLARSACVYYSQVLCKPILLVDSNLVTSVGDSTEIATKMFDSFVNSFVSL 2602 Middle East resp...
P0C6F7    2547 KLKFKEVCKTPTGIPEHNFLIYDTNDRGQENLARSACVYYSQVLCKPMLLVDVNLVTTVGDSREIAIKMLDSFINSFISL 2626 Bat coronavirus ...
P0C6T5    2586 KLKFKEVCKTPTGIPEHNFLIYDSSDRGQENLARSACVYYSQVLSKPMLLVDSNMVTTVGDSREIASKMLDSYVNSFISL 2665 Pipistrellus bat...
QGA70691  2504 KFKFKEVCKSTTGIPEFNFVIYDSSDRGQENLARSACVYYSQVLCRSILLIDSNLVTSVGDSSAIAIRLLDSFINTFANL 2583 Erinaceus hedgeh...
AUM60013  2493 KLKFKEVCKSTTGIPEHNLIIYDSSDRGQENLARSACVYYSQVLCKPILLVDSNLVTSVGDSCEIATKMFDSFVNSFVSL 2572 Middle East resp...
QCC20712  2566 KFKFKEVCKSTTGIPEFNFVIYDSTDRGQENLARAACVYYSQVLCKSILLVDSNLMNTVGDSSAIAIRMLDSFINSFASL 2645 Hedgehog coronav...
AIA62351  2548 KLKFKEVCKTPTGIPEHNFLIYDTNDRGQENLARSACVYYSQVLCKPMLLVDANLVTTVGDSREIAIKMLDSFINSFISL 2627 BtTp-BetaCoV/GX2012
ANA96038  2553 KLKFKEVCKTPTGIPEHNFLIYDTNDRGQENLARAACVYYSQVLCKPMLLVDANLVTTVGDSREIAIKMLDSFINSFISL 2632 Bat coronavirus
P0C6T4    2540 KLKFKEVCKTPTGIPEHNFLIYDTNDRGQENLARSACVYYSQVLCKPMLLVDVNLVTTVGDSREIAIKMLDSFINSFISL 2619 Tylonycteris bat...
AIA62342  2586 KLKFKEVCKTPTGIPEHNFLIYDSSDRGQENLARSACVYYSQVLSKPMLLVDSNMVTTVGDSREIASKMLDSYVNSFISL 2665 BtPa-BetaCoV/GD2013
Feature 1                                                                                      
AVV62536  2603 YNVTRDRLEKLISTARDGLKRGENLQPILKTFIDAARGPAGVESDIDTGDIVDAVQYAHKHDIQLTTEGYNNYVPSYVKP 2682 Middle East resp...
P0C6F7    2627 FSVSRDKLEKLINTARDCVRRGDDFQTVLKTFTDAARGHAGVESDVETTMVVDALQYAHKNDIQLTTECYNNYVPGYIKP 2706 Bat coronavirus ...
P0C6T5    2666 FGVNRDKLDKLVATARDCVKRGDDFQTVIKTFTDAARGPAGVESDVETSSIVDALQYAYKHDLQLTTEGFNNYVPSYIKP 2745 Pipistrellus bat...
QGA70691  2584 YNVSRDKLEKLIFTARDCVKRGENLQNVLKTFIQAARVHANVESDIEDKTIVDGIQYAQKYDIELVTDSFNNYVPSYVKP 2663 Erinaceus hedgeh...
AUM60013  2573 YNVTREKLDKLISTARDGVKRGENLQSVLKVFIDAARGPAGVESDVDTTELVDSVQYAHKHDINLTNEGFNNYVPSYIKP 2652 Middle East resp...
QCC20712  2646 YNVSRDKLEKLISTAKDCVKRGEDLQSVLKTFIQAARVHANVESDVETDSIVDGIQYAHKNDIELVTDSFNNYIPSYVKP 2725 Hedgehog coronav...
AIA62351  2628 FSVSRDKLEKLINTARDCVRRGDDFQNVLKTFTDAARGHAGVESDVETTMVVDALQYAHKNDIQLTTECYNNYVPGYIKP 2707 BtTp-BetaCoV/GX2012
ANA96038  2633 FSVSRDKLEKLINTARDCVRRGDDFQNVLKTFTDAARGHAGVESDVETTTVVDALQYAHKNDIQLTTEGYNNYVPGYIKP 2712 Bat coronavirus
P0C6T4    2620 FSVSRDKLEKLINTARDCVRRGDDFQNVLKTFTDAARGHAGVESDVETTMVVDALQYAHKNDIQLTTECYNNYVPGYIKP 2699 Tylonycteris bat...
AIA62342  2666 FGVNRDKLDKLVATARDCVKRGDDFQTVIKTFTDAARGPAGVESDVETSSIVDALQYAHKHDLQLTTEGFNNYVPSYIKP 2745 BtPa-BetaCoV/GD2013
Feature 1                                                                                      
AVV62536  2683 DSIATsDLGSLIDSNAASVNPANMRNANGACVWNAAAYLKLSDALKRQVRIACRKCNLnFRLTTSKLRACDNILSVRFSA 2762 Middle East resp...
P0C6F7    2707 DSINTlDLGCLIDLKAASVNQTSMRNANGACVWNSGDYMKLSDSFKRQIRIACRKCNIpFRLTTSKLRAADNILSVKFSA 2786 Bat coronavirus ...
P0C6T5    2746 DSVATaDLGCLIDLNAASVNQTSIRNANGACIWNSSDYMKLSDSLKRQIRIACRKCNIpFRLTTSRLRSADNILSVKFSA 2825 Pipistrellus bat...
QGA70691  2664 DSIATvDLGCLIDVKAASVNPASMRNANGSCIWNVDAFLKLSDSLKRQIRVACRKCNLnFKLTTSKLRAHDNILSVKYSV 2743 Erinaceus hedgeh...
AUM60013  2653 ESVATsDLGSLIDCNAASVNPASMRNANGACIWNCSAYMQLSDAMKRQIRIACRKCNLpFRLTTSKLRAHDNILSVKFSV 2732 Middle East resp...
QCC20712  2726 DSIATvDLGCLIDLKAASVNPASMRNANGACVWNIDAYLKLSDSLKRQIRVACRKCSLnFKLTTSKLRAQDNILSVKFSV 2805 Hedgehog coronav...
AIA62351  2708 DSINTlDLGCLIDLKAASVNQTSMRNANGACVWNSGDYMKLSDSFKRQIRIACRKCNIpFRLTTSKLRAADNILSVKFSA 2787 BtTp-BetaCoV/GX2012
ANA96038  2713 ESINTlDLGCLIDLKAASVNQTSMRNANGACVWNSGDYMKLSDSFKRQIRIACRKCTIpFRLTTSKLRAADNILSVKFSA 2792 Bat coronavirus
P0C6T4    2700 DSINTlDLGCLIDLKAASVNQTSMRNANGACVWNSGDYMKLSDSFKRQIRIACRKCNIpFRLTTSKLRAADNILSVKFSA 2779 Tylonycteris bat...
AIA62342  2746 DSVATaDLGCLIDLNAASVNQTSIRNANGACIWNSSDYMKLSDSLKRQIRIACRKCNIsFRLTTSRLRSADNILSVKFSA 2825 BtPa-BetaCoV/GD2013
Feature 1            
AVV62536  2763 TKTVGG 2768 Middle East respiratory syndrome-related coronavirus
P0C6F7    2787 TKIVGG 2792 Bat coronavirus (BtCoV/133/2005)
P0C6T5    2826 TKLSGG 2831 Pipistrellus bat coronavirus HKU5
QGA70691  2744 TKFVGG 2749 Erinaceus hedgehog coronavirus HKU31
AUM60013  2733 TKIVGG 2738 Middle East respiratory syndrome-related coronavirus
QCC20712  2806 TKFVGG 2811 Hedgehog coronavirus 1
AIA62351  2788 TKIVGG 2793 BtTp-BetaCoV/GX2012
ANA96038  2793 TKIVGG 2798 Bat coronavirus
P0C6T4    2780 TKIVGG 2785 Tylonycteris bat coronavirus HKU4
AIA62342  2826 TKLSGG 2831 BtPa-BetaCoV/GD2013

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