HHsearch 1.5 NAME c9d8lC_ FAM FILE c9d8lC_ COM /bmm/www/servers/phyre2/HH/hhmake -i c9d8lC_.a3m DATE Sat Nov 1 10:01:18 2025 LENG 1105 match states, 1105 columns in multiple alignment FILT 22 out of 24 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100) NEFF 3.2 EVD 0.3162 -9.8688 SEQ >ss_pred CCCCHHHHHCCCCEEEECCCCCEEECCCEEEECEEEEECEEEEEEECCCEEEEEEECCCCCEECCCCEEEEECCEEEECCCCCCEEEEEEEECCCCCCEE EEEEECCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEECCCEEEEECCCCCCCCCCEEEEEEECCCEEEEEECCCCCCCCCCC CCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEECCCEEEEEEECCCCCHHHHEEEECCCCCCCCEEECCC CEEEEEEEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCEEEEEEECCCCCEECCCEECCCCCCCCCHHHHCCCEEEEEEEEEEEECCCCEEEECCCCCCC CEEEECCCCCCCCCCCCCHHCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCEEEEEEEEEEECCCEEEEEEEEEECCC CCCCCCCCCCCCCEEEECCEEEEEECCEEEEEEEEECEEEEECCEEEEEECCCCEEEEEECCCCCEEEEEECCCCCEEEEEECCCCCCCEEEEECCCCCC EEEEECCCCCCCCEEECCCCCCCCCCCCEEEEECCCCCCCCEEECCCCCCCCCCCCCCCCCEEEEEEECCCCCCCEECCCEEEECCCEEEEEEEEEEEEE CCCEEEEECCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHHHHHHCEEEEEE CEEEECCCCCHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCC CCEEEEEEEEECCCCEEEEEEEEEEEECCCEEEEECCEEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEEEEEEECCHHHCCCCCCCCCCHHHHHHHHH HHHCC >ss_conf 9661343310110010000001011232103010466110463220551332255245554010572147506435420247650367876212367359 9999624102655532011214898523257777630235202321454011210472567512443421221024687149549999658852013555 6655311489844044120223334665321476554333554310023551223169999715753787875265414442111024456887210467 5555325899814665447704320777765433432114654103610101031112110256463441122000134203663155112212676764 2042026765433333310000235334565523788504777766643310011220000133455667651000478887513420004799973058 8854445653232255421144785435889999601002764458997158825788753788379998425345067761345664025664044321 2554101100111000002467643221025641345775025213100441133236652244421113455320035504744521578888899864 4625996120450883799999999989989999999885555257799999875420034555645762202105788776642145644202013440 1066367678889888889999987411011002321113189899875140213288899889999999999999999888999999999999997448 9999999997511013577899999987544441014565566799999999999999999999999999999899751211015446876899970249 9818999997546875999986556654836554220689878989995313126416764556999410269996553336643777668688899986 42059 >Consensus xxxxxxxxxxxtxxxxxxxxxxxxxxdxxxxxxxxxlxxxxxxxxxxxxxxxxxxxgtxxxxxfxxxxxpxxxgxxxxxxxxxxxxxgxxfgxtxxxxxx xxxxxxnxxnxxxxvcxxxxcxxpxxxxxxxxxxxxxxxxxxxxxxxxnxtxxxvxxxxxxxxxxxxxxxxxxxxfxfxxxxgxxxxyxxxxxxxxxxxx xxxxxxxxxxxlxxgxxxxxxxxxxxxxxsxxxxxxxxxxxxxxxxxxxvxxLxxxxxLlxydxnGxitxavdCxxxxxxxLkCxxxsfxxxdGfYxxsx xxvxxxxtfVxvpxxxxxcxxxxxxxxtxxpsxxxwxrxxxxncnxnxsxxxsxxxxxxfkCxxVxxxxlxxxcfssvxxdxfxixxxxxxxlxxgxxxx xxxxnykxxdxxxxcxxxxxxxxxxxxxxxxxxxxxxxxxxgxxxxxxxxixxxxxxxxxkxxsxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxixxxxx xxpxtxxgxxxxsxixxdxCvxYnIYGxtGxGVixxxnsxxxxgxxxxxdxsgxLxgfknxtTgxiyxVxPCxxxxxxvvxxgxxxsxxxaxlxxxxxcx xxxxxxxxxxxxxxxxxxxtxxxxxxtxxgcxixaxxxxxxxnCxxpxxxxxcxxxxxxxxxxxxxxtxxxxxxxxxxxxnIxIPtnFtlsvtxEylQxx xxkvsIDCaxYVCngnxrCxxLLxQYgsfCxxIexaLxxxaxledxxxxxxxxxxxxxxxxxxxxxxgxxNfsxiLpxxsxxxxRSaIEDLLFxKVvTYN GImVLPgVvdaexmamYTasLxGgmaxggxTagxxsAxaIPFaxavQaRlNylalttxVLxeNQkilAnsFNxAignIqxgfxtvsxALxKIQdVVNxqx xALxxLxxQLsxNFgAISSSixdIyxRLDxleAdaQVDRLItGRLxALnafVtQxLxxxxevraSrxLAqqKINECVKSQSxRygFCGNGtHixSlxQxA PnGixFlHxxlvPtxxvxVxaxxGlCvxxxxxvpkxgxfvxxxxxwxiTxRxxyxPrxiTxsdxvxixsCxVxyxnxtxxxlxxxxpdxxDfnxelxexf xNxts >c9d8lC_ CVMPLFNLITTTQSYTNSFTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQ SLLIVNNATNVFIKVCEFQFCNDPFLDVYHKNNKSWMESESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIGRDFP QGFSALEPLVDLPIGINITRFQTLLALNRSYLTPGDSSSGWTAGAADYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSN FRVQPTESIVRFPNVTNLCPFHEVFNATTFASVYAWNRTRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTGN IADYNYKLPDDFTGCVIAWNSNKLDSKHSGNYDYWYRSLRKSKLKPFERDISTEIYQAGNKPCKGKGPNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELL HAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTKSNKKFLPFQQFGRDIVDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCT EVSVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVS MTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTKFN GLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLFSTASALGKLQDVVNHNA QALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSA PHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFLTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQLELDSFKEELDKYF KNHTS >UniRef50_Q02385(38-1264:1376) Spike protein S2 n=160 Tax=Coronavirinae RepID=SPIKE_CVMJC E=0 s/c=0.85 id=35% cov=94% ----------STEAVDVSKGLGTYYVlDRVYLNATLLLTG--YYPVDGSNYRNLALTGTNtlSLTWFKPPFLsEFNDGIFAkvqnlktntptgATSYFPT IVIGSLFGNT--SYTVVLEPYNNI--IMASVCTYTICQLPYTPCKPNTNGNRvigfwhTDVKPPICLLKRNFTFN-VNAPWLY--------------FHF YQQGGTFYAYYADKP----------SATTFLFSVYIGDILTQYFVLPFIC----TPTAGSTLLP----LYWVTPLLKRQYLFNFNEKGVITSAVDCASSY ISEIKCKTQSLLPSTGVYDLSGYTVQPVGVVYrRVPNLPD-CKIEEWLTAKSVPSPLNWERRTFQNCNFNLSSLLRYVQAESLSCNNIDASKVYGMCFGS VSVDKFAIPRSRQIDLQIGNSGFLQTANYKIDTAATSCQLyyslpknnvtinnynpsSWNRRYgfndagvfGKSKHDVAYAQQCFIVRPSYCPCAQPDIV SAC-TSQTKPMSAYCPTGtihrecslwngphlrsarvgsgtytcectckPNPFDTYDLRcgqikTIVNVGDHCEGLGVLEDKCGNsDPHKGCscahdsfi GWSHDTCLVNDhsqifanillnginsgttcstdlqlpntevatgVCVRYDLYGITGQGVFKEVKADYYNsWQALLYDVNGNLNGFRDLTTNKTYTIRSCY SGRVSAAY--HKEAPEPALLYRNINCSYVFTNNISREENPL--------NYFDSYLGCVVNADNRPDEAlpNCDLRMGAGLCVDYSKSRRarrsvSTGYR LTTFEPYMPMLVNDSVqsvgglyemQIPTNFTIGHHEEFIQIRAPKVTIDCAAFVCGDNAACRQQLVEYGSFCDNVNAILNEVNNLLDNMQLQVASALMQ gvtISSRLPDGISGpidDINFSPLLGcigstcaedgnGPSAMRGRSAIEDLLFDKvklsdvgfveaynnctggqevrdllcVQSFNGIKVLPPVLSESQI SGYTAGATAAAMFPPWTAAAG----VPFSLNVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQEGFDATNSALGKIQSVVNANAEALNNLLNQLSNRF GAISASLQEILTRLDRVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKFSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLCFIHFSYVPT SFKTANVSPGLCISGdRGLAPKAGYFVQDNGEWKFTGSNYYYPEPITDKNSVVMISCAVNYTKAPEVFLNNSIPNLPDFKEELDKWFKNQTS >UniRef50_B2BW33(473-1343:1472) Spike protein n=1 Tax=Beluga Whale coronavirus SW1 RepID=B2BW33_9GAMC E=0 s/c=0.83 id=27% cov=71% ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- ------------------------------------------------FISTLNYTTALVTFD-KGNVRSVIDCnSEKPFDRLRCDLQTDVVSDGFYPVN ikTNEAKENTTFIDVPATLANLTL-EVFVSSPEQSPA---------CV-----------IKSYKC--VDTRYFYISDYS--------------------- ---YSCAENGIPNDAAGAA------YCRGVLDQINNYGVRGMDfKGKCPFAGSKVNSgltfdkICFGVYEQGCqSDKACRFGFYFDNVQFSqYGNKLYYK PQDLGFIDYQFGTLFKNSL---VQSNIIQEGCHDYDIYGYKGTGVVKPFSdySYLQTGGLIMLDSGGFPSLFRYN--FALYEVTQC-----------TRE VAQLAVASNNAIGYYLPKQVTIDGVNASTSCNTTGAFKYCYYDDVIhVGRDVSNVTINVCNPslmMENSHCINIQGNFMVNEPAITFnsTQYQPLLGVSG DVQLPRTLMLHTTTEFIQTHSPKIVIDCTKYVCGSSERCRRILVKYGGFCESIMRLLNGVNMADDvsvTDFLDNFNSFDNISVSLqnlnaSFGQFEGYGF QKFLPksfdfDGSDPRdARSTIEDILFDKVTTvglgtvdadydkctkglsvadlvcaqyYNGIMVLPGVADAEKMAMYTGALVGGMVLG----GITSAAA IPFATQIQARVNYLALTQNAIQENQKIIVQQFNKAIDSMTsafqsvnEGFSAVSSAITEVQNAVNAQSQALTKLLGQLNYNFGATTSSIKELYERLAKLE ADVQVDRLINGRLTALSAFVAARQVEAAKVASQRVLAAEKINECVKSTSNRYGFCGNGAHIISFPQNAPNGMLFVHFSLVPNETITVKGIIGLCLNNSiG IVPAkdRGMFIQcsngtycpefensfneskNGNVTFpfaITSREQYNPRQITTGDIQMLTSCNSGYTHIEWSQLPLVAPPYDDFDKEFDKLYE---- >UniRef50_B3FHU5(115-1066:1226) Spike n=17 Tax=Coronavirinae RepID=B3FHU5_CVTKE E=0 s/c=0.76 id=28% cov=70% ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------DTTINKLRCAYQQFNFSTGFYDID- -------TFVPVTSNITYLPYPDLKDNTGQEVCDFYVALKGDHVIYNQSCVDSKYPFFKLKCNNTYSWDNDKLCIlgSEIYVPGYNVYTNTQHSYAGTIP NYPTCSSKGLSLENIYNNIGFNRFCVTKLLTT------------------RDISSITQYTCVYVVSVEG------FDSYNQGIVYSYVGVNFDFGTAMYS VKTAPMQF--------IYTEQCHKYNIYNIRGVGqilnVTGKDNTTLVDGGLVITSGSG-LLAFRNN--GSLFSVQPCRTVSTQAVI----VNGSFVGLF VPASCwlaDQFNLGNHTEYVD----GGCLISNKTISRKRRSTNAVYTGECTGLFAAMGTSCIYSNGTVLNRTLPQPSVQTSvQPLLGVVANVSIPKELTL AVTTEYLQTRYQKVTIDCAKYVCGDSTRCRTLLQQYGSFCQSVNAILSGVNENEDNGLLQYAEAINTGYTLNFTGYNvsnlGGFDLSLVLPKNltlAQNQ GRSTIEDLLFDKVVTlgvsevdqnydkciasrggsftnladltcaqfYNGVMVLPGVVDPGLMAVYTGSLIGGMALGGITA----AASIPFATQIQARVN YLALTQSVLLDNQNLIANSFNKALKGIQsaldtvsqgfvevaRGFESVTVALNKVQDVVNTHSDILNKLMAQLSVNFGAVSSSLNEIYLKLDQINADAQV DRLITGRLTALSTYVASLQLAAYKADQSRRLALQKVEECVKSQSMRYGFCGNGSHVLTIPQSAPNGIFFIHYTYQPTSYVTIEAVPGLCVTtpsgKYGVM PKtgSGIIFRQNDTFFVTSTQLYEPKLLSYSEVVNLTSCEANYYNVSESE-TPFQPALPNFDDEFNDIF----- >UniRef50_Q65984(376-1325:1453) Spike glycoprotein n=344 Tax=Alphacoronavirus RepID=SPIKE_CVCAK E=0 s/c=0.74 id=27% cov=69% ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------SHINNIKCSQLTANLQNGFYPVAS SEVGLVnKSVVLLPSFYSHTSVNITIDLGMKRSGYG-QPIASTLSNITLPMQDNNTDVYCIRSNRFS-VYFHSTCKSSLWDDVFNSDCTDVLYA----TA VIKTGTCPFSFDKLNNYLTFNKFCLSLNPVGANCKFDVAARTRTNE----QVVRSLYVIYEEG----------------------------------DNI VGVPSDNSGLHDLSVLHLDSCTDYNIYGITGVGIIRQTNSTLLSGLYYT-SLSGDLLGFKNVSDGVIYSVTPCDVSAHAAVIDGAIVGAMTSINSELLGL THWTT-------TPNFYYYSIYNYTNERTRGTAIDSNDVDCE-----PIITYSNIGVCKNGALVFINVTHSDGDVQPISTGNVTIPTNFTISVQVEYIQV YTTPVSIDCSRYVCNGNPRCNKLLTQYVSACQTIEQALAMGARLENMEIDSMLFVSENALKLASVEAFNSTetldpiykewpniggswlgGLKDILPShN SKRKYRSAIEDLLFDKVVTsglgtvdedykrctggydiadlvcaqyYNGIMVLPGVANDDKMAMYTASLAGGITLGSL---GGGAVSIPFAIAVQARLNY VALQTDVLNKNQQILANAFNQAIGNITQAFGKVNDAihqtsqglatvakvLAKVQDVVNTQGQALSHLTLQLQNNFQAISSSISDIYNRLDELSADAQVD RLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFFHTVLLPTAYETVTAWSGICASDgdrtFGLVV KDvqlTLFRNLDDKFYLTPRTMYQPIVATSSDFVQIEGCDVLFVNATVIDLPSIIPDYIDINQTVQDILEN--- >UniRef50_A6N252(130-904:1035) Spike protein n=3 Tax=Guangxi coronaviridae RepID=A6N252_9NIDO E=0 s/c=0.88 id=28% cov=66% ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------CDKSVVDSIACQRSSHQVEDGFYSDPK SAVRaRQRTIVTLPKLPEL--------------------------------------------EVVQLNISAHMDFGEARLDSVTINGNTSYCV--TKPY FRLETNFLCRGCTMSLRTDTCSFDLSAVNNGmSFSQFCLSTESGACEM-----------------------------KIIVTYVWNYLLRQRLYVTAVEG QTHTGTTAVHATDTSSVVTDVCTDYTIYGVSGTGIIKPSDLLLHNGIAFT-SPTGELYAFKNITTGKTLQVLPCETPSQLIVI-------------NNTV VGAITSSNSTEN-NRFTTTIVTPTFFYSTNA----------TTFNCTKPVLSYGPISVCSDGAIAGtSTLQNTRPSIVSLYDGEVEIPSAFSLSVQTEYL QVQAEQVIVDCPQYVCNGNSRCLQLLAQYTSACSNIEAALHSSAQLDSREIINMFQTSTQSLQLANITNFkGDYNFSSIL--TTRVGGRSAIEDLLFNKV VTsglgtvdqdykscsrdmaiadlvcsqyYNGIMVLPGVVDAEKMAMYTGSLTGAMVFGGLTAAAAIPFA----TAVQARLNYVALQTNVLQENQKILAE SFNQAVGNIslalssvndaiqqtSEALNTVAIAIKKIQTVVNQQGEALSHLTAQLSNNFQAISTSIQDIYNRLEEVEANQQVDRLITGRLAALNAYVTQL LNQMSQIRQSRLLAQQKXNECVKSQSSRYGFCGNGTHIFSLTQAAPNGIFFMHAVLVPNKFTRVNASAGICVDNtRGYSLQpQLILYQFNNSWRVTPRNM YEPRLPRQADFIQLTDCSVTFYNTTAANLPNIIPDVIDVNQTVSDIIDN--- >UniRef50_A3EXG6(19-1160:1274) Spike protein S2 n=4 Tax=Rousettus bat coronavirus HKU9 RepID=SPIKE_BCHK9 E=0 s/c=0.89 id=34% cov=96% CFNPRFTLtpLNHTLNYTSikAKVSNVLLPDPYIAYSGQTLRQNLFMADMSNTILYPVTppaNGANGGFIYNTSIIPVSAGLFvntwmyrqpASSRAYCQ EPFGVAFGDTFENDRIAILIMapdnlgswsavapRNQTNIYLLVCsNATLCINPGFNRWGPAG-SFIAPDALV-DHSNSC---FVNNTFSVNISTSRISL A----FLFK--DGDLLIYHSGwlpTSNFEHGFSRGSHPMTYFMSLPVGGNLPRAQFFQSIVRSnAIDKGDGMC--TNFDVNLHVAHLINRDLLVSYFNNG SVANAADCADSAAEELYCVTGSFDPPTGVYPLSRYRAQ-VAGFVRVTQRGSYCtPPYSVLQDPPQPVV--WRRYMLYDCVFDFTVVVDSLPTHQLQCYGV SPRRLASMCYGSVTLDVMRINETHLNNLFNRVPDTFSLYNYALPDNFYGCLHAFYLNSTAP---------YAVANRFPIKPGGRQSNSA----------- -------FIDTVINAAHYSPFSYVYGLAVITLKPAAGSKLVCPVANDTVVITDRCVQYNLYGYTGTGVLSKNTSLVIPdGKVFTASSTGTIIGVSINST- -TYSIMPCVTVPVSV---GYHPNFERALLFNGLSCSQRSRAV-TEPVSVLWSASATAQDAFDTPSGCVVNVELRNTTIvnTCAMPIGNSLCfinGSIATA NADSLPRLQLVNYDPLYdNSTATpmtpvywVKVPTNFTLSATEEYIQTTAPKITIDCARYLCGDSSRCLNVLLHYGTFCNDINKALSRVSTILDSALLSL VKelSINTRDEVTTFSFDGDYNFTGLMgclgPNCGATTYRSAFSDLLYDKVritdpgfmqsyqkcidsqwggsirdllctQTYNGIAVLPPIVSPAMQAL YTSLLVGAVASSGYTFGITSAGVIPFATQLQFRLNGIGVTTQVLVENQKLIASSFNNALVNIQKGFTETSIALSKMQDVINQHAAQLHTLVVQLGNSFGA ISSSINEIFSRLEGLAANAEVDRLINGRMMVLNTYVTQLLIQASEAKAQNALAAQKISECVKAQSLRNDFCGNGTHVLSIPQLAPNGVLFIHYAYTPTEY AFVQTSAGLCHNGTGYAPRQGMFVlpNNTNMWHFTTMQFYNPVNISASNTQVLTSCSVNYTSVNYTVLEPSVPGDYDFQKEFDKFYKNLST >UniRef50_A3EXD0(235-1245:1352) Spike protein S2 n=12 Tax=root RepID=SPIKE_BCHK5 E=0 s/c=0.81 id=35% cov=77% ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- ---------------------------------------------AAFYIYKLHPLTYLLNFDVEGYITKAVDCGYDDLAQLQCSYESFEVETGVYSVSS FEASPRGEFIE-QATTQECDFTPMLTGTP-PPIYNFKRLVFTNCNYNLTKLLSLFQVSEFSCHQVSPSSLATGCYSSLTVDYFAYSTDMSSYLQPGSAGA IVQFNYKQDFSNPTCRVLATVPQNLTTITKPSNYAYLTECYKTSAYGKNYLYNAPGA--YTPClslasrgfsTKYQSHSDGELTTTG--YIYPVTGNLQM AFIISVQYGTDTNSVCPMqalRNDTSIEdkLDVCVEYSLHGITGRGVFHNCTSVGLRNQRFVYDTFDNLVGYHSDN-GNYYCVRPCVSVPVSVIYD--KA SNSHATLFGSVACSHVTTMMSQfSRMTKTNLLARTTPGPLQTTVGCAMGFINSSMVVdECQLPLGQSLCAippttssrvRRATSGASDVFQIATLNFTSP ltlAPINSTgfvVAVPTNFTFGVTQEFIETTIQKITVDCKQYVCNGFKKCEDLLKEYGQFCSKINQALHGANLRQDESIANLFSSIKtQNTQPLQAGLNG DFNLTMLqIPQvtTGERKYRSTIEDLLFNKVTIADpgymqgydecmqqgpqsardlicaqyvaGYKVLPPLYDPYMEAAYTSSLLGSIAGASWTAGLSSF AAIPFAQSIFYRLNGVGITQQVLSENQKIIANKFNQALGAMQTGFTTTNLAFNKVQDAVNANAMALSKLAAELSNTFGAISSSISDILARLDTVEQEAQI DRLINGRLTSLNAFVAQQLVRTEAAARSAQLAQDKVNECVKSQSKRNGFCGTGTHIVSFAINAPNGLYFFHVGYQPTSHVNATAAYGLCNTenpQKCIAP IDGYFVLNQTtstvadsdqQWYYTGSSFFHPEPITEANSKYV-SMDVKFENLTNRLPPPLLSNstDLDFKEELEEFFKNVSS >UniRef50_P05135(208-1040:1163) Spike protein S2 n=1237 Tax=Avian coronavirus RepID=SPIKE_IBV6 E=0 s/c=0.88 id=29% cov=71% ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- -----------------------------------------------------------LAYFVNGTAQDVILCDGSPTGLLACQYNTGNFSDGFYPFTN SSlVKEKFIVYRESSV----------------------NTTLELTNFTFSNVSNATPNTG----GVQTIQLYQTI-------------TAQSGYYNLNFS FLSSFIYKASDYMYGSYHPSCKFRLETINNGLwFNSLSVSLGYGPIQGGCKQ---SVFANRATCCYAYSYNGP-SLCKGVYRGELTKSFECGLLVFVTKT DGSRIQTRNEPftltqHNYNNITLDRCVEYNIYGRVGQGFITNVTNYAINY-NYLADG-----GMAILDTSGAIDIF-VVQGEYGLNYYKVNPCEDV--- ------NQQFVVSGGKLVGILTSRNETGSQPLENQFYIKIINGTRrsrrsitGNVTNCPYVTYGKFCIKPDGSISTIVPKELEHFVAPLLNVTENVLIPD SFNLTVTDEYIQTRMDKVQINCLQYVCGNSLECRKLFQQYGPVCDNILSVVNSVGQKEDMELLYFYSSTKPSgFNTPVLSNvsTGEFNISLLLTPPSSAS GRSFIEDLLFTSVESvglptddaykkctagplgflkdlacareYNGLLVLPPIITAEMQTLYTSSLVASMAFGGIT----SAGAIPFATQLQARINHLGI TQSLLFKNQEKIAASFNKAIGHMQEGFRSTSLALQQIQDVVNKQSSILTETMASLNKNFGAISSVLQDIYQQLDSIQADAQVDRIITGRLSSLSVLASAK QAEYYRVSQQRELATQKINECVKSQSIRYSFCGNGRHVLTIPQNAPNGIVFIHFTYTPESFVNVTAIVGFCVNPanasqYAIVPAngRGIFIQVNGSYYI TARDMYMPRDITAGDIVTLTSCQANYVSVNKTVITTfVDNDDFDFDDELSKWWND--- >UniRef50_A8JP00(219-1017:1128) Spike glycoprotein n=3 Tax=Rhinolophus bat coronavirus HKU2 RepID=A8JP00_9ALPC E=0 s/c=0.81 id=29% cov=68% ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- --------------------------------------------------------------DQSGAVTRYSYCADGFVNGLQCKLRLFDIPPGVY--SN SEVEYPVALYTVVHNMSVCPqrPESYCGSNYCP----FKRVVFSNCVVNYTSWTSGL-----------------------------LRDYQHLVLPNGKF NPFTECNglNRIVDD---CVTGFVLRVGRGTA----------------------VNRTVITPYLKPNECFG----WSWNDYqDSIYDWWIADFVSTGAFV CEKNPDAPRTG------------VCITYTIEKVTFQGVLYESNFTFAQYYNVLY-FGSQLKYVRIL--GKVYEVAPCFEASYDVLF---RSSSSFGLLYR SFDCNQlrISASRFAERLLPSHNGTATA-------LGCLFNATYAPNDTmvNCTNPLGDGFCADLLSN--VVVRRMTFEKHDTTYVAPVTIerftELPLD HQLVLTEQFLQTTMPKFSISCETYICDVSKACKNLLFRYGGFCQKIEADIRGAGVLLDSDVSGLYSTIAAKTSSIMPTTD-RFNVSQfFLPKVQSTSErf esRSVIEDLLFSKIETtgpgfygdyynckknaiqdltcaqyHNGILVIPPVMDAETLGMY-----GGIAAASLTLGIfgGQAGITTWSLAMAGRLNALGV VQNALVDDVNKLANGFNQLTASVSKLALTTSSALQAIQAVVNQNAAQVESLVSGITENFGAISTNFKVISQRLDKLEADVQMDRLINGRMNVLQLFVTNY KLKIAELRNTHRYVQSLINECVYAQSLRNGFCGQGLHVLSLMQNAPSGIMFFHYSLIPNNTIIVKTTPGLCESDelgsKCIVAKDGVLVSaNLSYWQWSP RNLYKPENLTFAN-VIAVSRGANYTTLNRTFDIPELNNTFPIEEEFREYFQNMSS # NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665 HMM A C D E F G H I K L M N P Q R S T V W Y M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D 0 * * 0 * 0 * * * * C 1 * 0 * * * * * * * * * * * * * * * * * * 1 0 * * * * * * 1546 0 0 V 2 * * * * 1065 * * * * * * * * * * * * 937 * * 2 0 * * * * * * 1546 0 0 M 3 * * * * * * * * * * 937 1065 * * * * * * * * 3 0 * * * * * * 1546 0 0 P 4 * * * * * * * * * * * * 0 * * * * * * * 4 0 * * * * * * 1546 0 0 L 5 * * * * * * * * * 937 * * * * 1065 * * * * * 5 0 * * * * * * 1546 0 0 F 6 * * * * 0 * * * * * * * * * * * * * * * 6 0 * * * * * * 1546 0 0 N 7 * * * * * * * * * * * 937 * * * * 1065 * * * 7 0 * * * * * * 1546 0 0 L 8 * * * * * * * * * 0 * * * * * * * * * * 8 937 1065 * 1000 1000 * * 1546 1000 0 I 9 * * * * * * * 937 * 1065 * * * * * * * * * * 9 0 * * * * * * 1546 0 0 T 10 * * * * * * * * * * * 1065 * * * * 937 * * * 10 0 * * * * * * 1546 0 0 T 11 * * * * * * 1600 * * * * * * * * 1624 1532 * * * 11 0 * * * * * * 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2216 0 0 L 37 * * * * * * * * * 0 * * * * * * * * * * 37 0 * * * * * * 2216 0 0 T 38 * * * * * * * * * * * 2378 * * 2044 * 823 * * * 38 0 * * * * * * 2216 0 0 Q 39 * * * * * 1405 * * * * * * * 684 * * * * * * 39 684 * 1405 * * * * 2216 0 0 D 40 * * 707 * * * * * * * * 1369 * * * * * * * * 40 0 * * * * * 0 1686 0 1250 L 41 * * * * * * * * * 0 * * * * * * * * * * 41 0 * * * * 0 * 1686 0 1250 F 42 * * * * 684 * * * * * * * * * * * * * * 1405 42 0 * * * * * * 2216 0 0 L 43 * * * * * * * * * 1397 2044 * * * * * * * * 1405 43 0 * * * * * * 2216 0 0 P 44 2044 * * * * * * * * * * * 401 * * * * * * * 44 0 * * * * * * 2216 0 0 F 45 * * 2044 * 1397 * * 2378 * * * * * * * * * 2431 * * 45 0 * * * * * * 2216 0 0 F 46 * * 2431 * 2402 * * * * * 2044 * * * * 2378 * * * 2391 46 0 * * * * * * 2216 0 0 S 47 * * * * * 1405 * * * * * * * * * 684 * * * * 47 0 * * * * * * 2216 0 0 N 48 2378 * * * * * * * * * * 684 * * * 2431 * * * * 48 0 * * * * * * 2216 0 0 V 49 * * * * * * * * * * * 2431 * * * * 1202 1397 * 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* * * * * * * * * * * 2044 1385 1417 * * * 99 0 * * * * * * 2216 0 0 Q 100 * * * * * * * 1202 * * * * * 1397 * * * 2431 * * 100 0 * * * * * * 2216 0 0 S 101 2044 * * * * * * * * * * * * * * 1397 * 1405 * * 101 0 * * * * * * 2216 0 0 L 102 * * * * * * * 2044 * 1417 * * * * * * * 1385 * * 102 0 * * * * * * 2216 0 0 L 103 * * * 1405 * * * 2391 * 1212 * * * * * * * * * * 103 0 * * * * * * 2216 0 0 I 104 * * * * * * * 684 * * * * 1405 * * * * * * * 104 0 * * * * * * 2216 0 0 V 105 * * * * * * 2378 2391 * * 2044 * * * * * * 2402 * 2431 105 401 2044 * 3700 115 * * 2216 1000 0 N 106 * * * * * * * * * * * 823 * * 2044 * 2378 * * * 106 0 * * * * * * 2216 0 0 N 107 * * * * * * * * * * * 308 * * * 2378 * * * * 107 0 * * * * * * 2216 0 0 A 108 2402 * * * * * * 2431 * 2378 * * * 2044 * 2391 * * * * 108 296 * 2431 * * * * 2216 0 0 T 109 * * * * * * * 1829 * * * * * * * * 477 * * * 109 0 * * * * * 0 2090 0 1000 N 110 * * * * * * * * * * * 0 * * * * * * * * 110 477 1829 * 2585 263 0 * 2090 1000 1000 V 111 * * * * * * * 1225 * 2378 * * * * * * * 1397 * * 111 0 * * * * * * 2216 0 0 F 112 * * * * 2402 * * * * * 2431 * * 2378 * * * 2391 * 2044 112 0 * * * * * * 2216 0 0 I 113 2431 * * * * * * 806 * 2044 * * * * * * * * * * 113 0 * * * * * * 2216 0 0 K 114 * * * * * * * * 2402 2044 * * * * 2391 1405 * * * * 114 0 * * * * * * 2216 0 0 V 115 2391 * * * * * * * * * * * * * * * * 305 * * 115 0 * * * * * * 2216 0 0 C 116 * 0 * * * * * * * * * * * * * * * * * * 116 401 2044 * 0 * * * 2216 1000 0 E 117 * * * 2402 * * * * * * * 1207 * 2378 * * 2431 * * * 117 0 * * * * * * 2216 0 0 F 118 2044 * * * 1397 * * * * * * * * * * * * * * 1405 118 0 * * * * * * 2216 0 0 Q 119 * * * 2391 * * * * * * * * * 2402 * * 689 * * * 119 0 * * * * * * 2216 0 0 F 120 * * * * 2402 * * 2431 * 1207 2378 * * * * * * * * * 120 0 * * * * * * 2216 0 0 C 121 * 0 * * * * * * * * * * * * * * * * * * 121 0 * * * * * * 2216 0 0 N 122 * * 2391 2378 * * * 2044 * * * 2402 * 2431 * * * * * * 122 0 * * * * * * 2216 0 0 D 123 * * 2402 * * * * * * 2431 * 1207 * * * * * * * 2378 123 0 * * * * * * 2216 0 0 P 124 * * * * * * * * * * * * 0 * * * * * * * 124 0 * * * * * * 2216 0 0 F 125 * * * * 1397 2044 2378 * * * * * * * * * * * * 2431 125 0 * * * * * * 2216 0 0 L 126 * * * * 1207 * * * * 2402 * * * * * * 1405 * * * 126 0 * * * * * * 2216 0 0 D 127 2391 * 2402 * * * * 2378 * * * 2044 2431 * * * * * * * 127 0 * * * * * * 2216 0 0 V 128 * 1405 * * * * * * * * * * * * 2044 * * 1397 * * 128 305 * 2391 * * * * 2216 0 0 Y 129 * * * * * * 2193 * 2231 * * * * * * * * * 1847 1784 129 0 * * * * * 0 2110 0 1000 H 130 * * * * * 1847 1784 * * * * * 1212 * * * * * * * 130 0 * * * * * 0 2110 0 1000 K 131 * * * * * * * * 1784 * * 1212 1847 * * * * * * * 131 0 * * * * 0 * 2110 0 1000 N 132 2044 * * * * * * * * 2378 * 2402 * * * 2391 2431 * * * 132 0 * * * * * * 2216 0 0 N 133 * * * * * 1202 * * 2391 * * 1417 * * * * * * * * 133 401 * 2044 * * * * 2216 0 0 K 134 * * * * * 2048 * * 1979 * * 1996 1978 * * * * * * * 134 0 * * * * 0 * 1857 0 1000 S 135 * * * * * * * * * * 2391 2431 * 2378 * 1212 * * * * 135 0 * * * * * * 2216 0 0 W 136 * * * * 2044 2391 * * * * * * * * 1405 * * * 2402 * 136 296 2431 * 2585 263 * * 2216 1000 0 M 137 * * * * * * * 1202 * * 2402 * * * * * 1411 * * * 137 308 2378 * 2322 322 * * 2216 1000 0 E 138 2044 * 1405 2402 * * * * * * * * * 2391 * * * * * * 138 0 * * * * * * 2216 0 0 S 139 * * * * * * * * * * * * 2044 * * 2402 1385 2431 * * 139 0 * * * * * * 2216 0 0 E 140 * * 1202 2402 * * 2391 * 2431 * * * * * * * * * * * 140 0 * * * * * * 2216 0 0 S 141 2044 * * * * * * * * * * * 2431 * * 2402 2391 2378 * * 141 0 * * * * * * 2216 0 0 G 142 * * * * * 2402 * * * 2044 2391 * 2431 * * * * 2378 * * 142 0 * * * * * * 2216 0 0 V 143 * * * * * * * 1411 * * * * * * * 2378 * 1212 * * 143 401 * 2044 * * * * 2216 0 0 Y 144 * 1022 * * 1978 * * * * * * * * * * * * * * 1979 144 0 * * * * 0 * 1857 0 1000 S 145 * * 1207 * * * * * * 1405 * * * * * 2402 * * * * 145 0 * * * * * * 2216 0 0 S 146 * * * * * * 2044 * 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* * * 2044 * * * 158 0 * * * * * * 2216 0 0 F 159 * * * * 684 * * * * * * * * * * * * * 2431 2378 159 0 * * * * * * 2216 0 0 L 160 * * * * * * * * * 819 * * * * * 1207 * * * * 160 0 * * * * * * 2216 0 0 M 161 * * * * * * * * * 2391 2402 * * * * * * 2044 * 1405 161 684 * 1405 * * * * 2216 0 0 D 162 * * 707 * * * * * * * * 1369 * * * * * * * * 162 0 * * * * * 0 1686 0 1250 L 163 * * * * * * * 1369 * 1694 * * * * * * * 1719 * * 163 0 * * * * * 0 1686 0 1250 E 164 * * * 1694 * * * * * * * * * * * 533 * * * * 164 0 * * * * * 0 1686 0 1250 G 165 * * * 1719 * 1694 * * * * * * * * * * 1369 * * * 165 0 * * * * * 0 1686 0 1250 K 166 * * * * * * * * 707 * * * * * * 1369 * * * * 166 0 * * * * * 0 1686 0 1250 Q 167 * * * * * * * * * * * * * 1694 1369 1719 * * * * 167 0 * * * * * 0 1686 0 1250 G 168 * * * * * 707 * 1369 * * * * * * * * * * * * 168 0 * * * * * 0 1686 0 1250 N 169 * * * * * * * * * * * 707 * * * 1369 * * * * 169 0 * * * * * 0 1686 0 1250 F 170 * * * * 707 * * * * 1369 * * * * * * * * 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* * * * * * 1093 0 * * * * * * 3571 0 0 E 1094 4657 * 3012 1578 * * * * 1534 * * * * 2678 * * * * * * 1094 0 * * * * * * 3571 0 0 E 1095 * * * 767 * * * * * * * * * * * * 1278 * * * 1095 63 4538 * 2000 415 * * 3568 1000 0 L 1096 * * * * 1955 * * * * 715 * * * * * * * 2911 * * 1096 0 * * * * * * 3568 0 0 D 1097 * * 1586 2765 * * * * 4492 * * 3349 * 3485 3606 2678 * * * 4334 1097 0 * * * * * * 3568 0 0 K 1098 * * 2399 1383 * * * * 1580 * * * * 3433 * * * * * * 1098 0 * * * * * * 3568 0 0 Y 1099 * * * * 2080 * * 2195 * 3891 * * * * * * * * 2103 2030 1099 0 * * * * * * 3539 0 0 F 1100 4220 * * * 975 * * 4192 * 3151 * * * * * 4191 * * 3674 2866 1100 0 * * * * * * 3506 0 0 K 1101 3995 * 3973 2724 * * * * 1300 * * 3485 3947 2626 * * * * * * 1101 0 * * * * * * 3419 0 0 N 1102 * * 3342 * * * * * * * * 150 * * * * * * * * 1102 0 * * * * * * 3314 0 0 H 1103 * * * * 3016 * 2435 * 3126 3102 2781 * * 2374 * * * 3033 * * 1103 0 * * * * * * 2911 0 0 T 1104 * * * * * * * * * * * * * * * 1050 951 * * * 1104 0 * * * * * * 2911 0 0 S 1105 * * * * * * * * * * * * * * * 246 2673 * * * 1105 0 * * 0 * * * 2704 0 0 //