Conserved Protein Domain Family
CoV_S2

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pfam01601: CoV_S2 (This model is not part of the current CDD release)
Coronavirus spike glycoprotein S2
The coronavirus spike glycoprotein forms the characteristic 'corona' after which the group is named. The Spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 pfam01600 and S2,. The S2 subunit normally contains multiple key components, including one or more fusion peptides (FP), a second proteolytic site (S2') and two conserved heptad repeats (HRs), driving membrane penetration and virus-cell fusion. The HRs can trimerize into a coiled-coil structure built of three HR1-HR2 helical hairpins presenting as a canonical six-helix bundle and drag the virus envelope and the host cell bilayer into close proximity, preparing for fusion to occur.
Statistics
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PSSM-Id: 514379
Aligned: 32 rows
Threshold Bit Score: 378.165
Created: 13-Feb-2025
Updated: 28-Apr-2025
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
YP_009199609  795 GNISVPTNFTFSVQVEYIQ----LMLKPVTVDCSVYVCNGNPRCLQLLAQYA--SACRTIEQALQLSARLESVEVNSMIS 868 
YP_009505583  701 GYASTPIYSGYLTHTEVISkppfCTSFTSLPSCAELICGSNSLCYTKLTEFGklNMCTALGDAISV-------------- 766 
YP_009389425  587 SFVELALDHVLVSESEYFQ----TEMPVFDIDCEKYICDNSESCRMLLEQYA--GFCSKITSDVKGNSQLLNANTLAMYK 660 
YP_009336484  580 QQIELPIDHYVSVKEQFIQ----TSTPKFDVDCERYICDVSSDCRELLVKYG--GYCSKILADIKSSSIQLDYQILGLYK 653 
YP_009380521  573 QIVSLPLDHVINVKEQFVQ----TSAPKFDVDCERYICDVSVQCKELLAKYG--GYCPKIVSDIKSSSLQLDYQVQGIYK 646 
4_pfamImport    1 YWVRVPTNFTLTATTEFIE----TTAPKITIDCARYLCGDSSRCLAVLEQYG--TFCDDVNTALQRVNTMLDAAVVSLTS 74  
A3EXG6        698 YWVKVPTNFTLSATEEYIQ----TTAPKITIDCARYLCGDSSRCLNVLLHYG--TFCNDINKALSRVSTILDSALLSLVK 771  Rousettus bat...
YP_009513010  759 FQVSIPQNFSFGITEEFIE----TSIQKVTVDCKQYVCNGFERCEQLLVQYG--QFCSKINQALHGVNLRQDDATKSLFE 832 
P59594        692 NTIAIPTNFSISITTEVMP----VSMAKTSVDCNMYICGDSTECANLLLQYG--SFCTQLNRALSGIAAEQDRNTREVFA 765  Severe acute ...
YP_009072440  757 STLQIPINFTIGIEYETIP----VTMPKVTVDCAQYVCGDNSECRTLLVQYG--TFCETINDALRGVALQQDVNQKDVFS 830 
YP_009199609  869 ISQEALALGV---IDNFKHDF-----NLTNVLPA--SVG------AKSAVEDLLFDKVVTSGLGTVDAdYKECASr-tAN 931 
YP_009505583  767 ---------------------------------------------YNSVITDIVESQATLDAL------Y---------T 786 
YP_009389425  661 NIVPSDSIKP---IENFG-DF-----NMSMFIDK--S--------GRSVLEDLLFDKIVTTGPGFYED-YYKCRT----T 716 
YP_009336484  654 TLAVDFKVP----------DIdfgdfNFSMYMSE--AN-------GRSFIEDLLFDKIVTTGPGFYQD-YYDCKK----M 709 
YP_009380521  647 TLNVDVKVPD----VDFGAf------NFSMFESE--PN-------GRSFIEDILFDKIVTTGPGFYQD-YYDCKK----M 702 
4_pfamImport   75 QLVSDIVPTE---NSNFDSTY-----NFTALMGC--LGSsc--nsKRSAISDLLYNKVKIADPGFMDS-YQKCIDsqwGG 141 
A3EXG6        772 EL--SINTRDevtTFSFDGDY-----NFTGLMGC--LGPncgattYRSAFSDLLYDKVRITDPGFMQS-YQKCIDsqwGG 841  Rousettus bat...
YP_009513010  833 DIKVPQSVPL---MTSLTGDYnlslfEAPNIGSG--NNN------YRSALEDLLFDKVTLSDPGYMKG-YDECMKk-gPP 899 
P59594        766 QVKQMYKTPT---LKYFGG-F-----NFSQILPD--PLKp----tKRSFIEDLLFNKVTLADAGFMKQ-YGECLG---DI 826  Severe acute ...
YP_009072440  831 SVRRLAKVSS---PMNLGnln---gfNFSSILNQeaINGnn--fqARSAIEDLFFDKIETADVGFQKK-YDECTG---GS 898 
YP_009199609  932 TVAEVGCVQYYNGIMVLPGVVDQSLLAQYSAALTGAMVFGGVT----AGAAVPFSIAVQSRLNYLALQTDVLQR----NQ 1003
YP_009505583  787 EMLDVAMTKF--------GTVAQTRKKRFVEFIALGVASVALVe---ATVAIGLAVANANDIRELRGDVKNLRDesaaNF 855 
YP_009389425  717 TVKDLVCAQYYNGIMIIPPIQDAETIGMYGGIVAAGMTMGLFGg---QATMGTWQIAMSARLNAVGVTQGMIME----DV 789 
YP_009336484  710 NLQDLTCKQYYNGIMVIPPVMDDTLITFWSSAVAGSMTAGLFGg---QAGMVSWTVALAGRLNALGVMQDALVE----DV 782 
YP_009380521  703 NLEDITCKQYYNGIMVIPPVMDDTLITFWSSAVAGSMTAGLFGg---QAGMVSWSIAVAGRLNALGVMQDALVN----DV 775 
4_pfamImport  142 NIRDLICTQVFNGIAVLPPIVSPGMQALYTSLLVGAVASSGYTfgitSVGVIPFATQLQFRLNGIGVTTQVLVD----NQ 217 
A3EXG6        842 SIRDLLCTQTYNGIAVLPPIVSPAMQALYTSLLVGAVASSGYTfgitSAGVIPFATQLQFRLNGIGVTTQVLVE----NQ 917  Rousettus bat...
YP_009513010  900 SARDLICAQYVSGYKVLPPLYDANMEAMYTASLTGSIAGSFWTgglsSAAALPFAQSMFYRMNGIGITQNVLMK----NQ 975 
P59594        827 NARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTfgagAALQIPFAMQMAYRFNGIGVTQNVLYE----NQ 902  Severe acute ...
YP_009072440  899 VVKDLGCAQSFNGLMVLPPQMTDAHVAAYTTSAALG-----------SFFSIPNTMQMAYRFNGIAVTQKVLVD----NQ 963 
YP_009199609 1004 QQLANSFNAAMGNITeafgrvndaieqtsHAISTVAQALDKVQTVVNDQGLALSQLTKQLASNFQAISSSIEDLYNRLDR 1083
YP_009505583  856 KAIEEKHNAFVKTTA--------------DGFAAQNEVNKGFNSNIDTLQNSLKDMAIVTSQKFKELDQAIQSLVSSINS 921 
YP_009389425  790 QKLANGFNTLATSVS--------------KMASVTADALSRIQGVVNANALQVELLARATMDNFGAISSNFEIIEKRLKQ 855 
YP_009336484  783 NKLANGFNNLTQYVS--------------DGFKTTSQALSTIQAVVNNNAQQVSQLVQGLSENFGAISNNFALIAERLER 848 
YP_009380521  776 NKLANGFNNLTQYVA--------------DGFKTTSQALSAIQSVVNNNAQQISQLVQGLSENFGAISNNFLVIAERLER 841 
4_pfamImport  218 KLIASSFNNALNQIQ--------------KGFDATNSALSKIQAVINQHATQLQTLVLQLGNTFGAISSSINIIFSRLEG 283 
A3EXG6        918 KLIASSFNNALVNIQ--------------KGFTETSIALSKMQDVINQHAAQLHTLVVQLGNSFGAISSSINEIFSRLEG 983  Rousettus bat...
YP_009513010  976 REIANKFNQALGAMQ--------------TGFTATNQAFQKVQDVVNANAQALSKLASELANTFGAISSSIGDILKRLDV 1041
P59594        903 KQIANQFNKAISQIQ--------------ESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDK 968  Severe acute ...
YP_009072440  964 KQIANKFNQAMMSVQ--------------TGFKATSSALEKLQKVVNDNAQALNNLVAQLTNNFGAISSAINDITQRLDK 1029
YP_009199609 1084 VEADLQVDRLITGRLAALNAFVAQQLTKYTDVRASRQLAQDKINECVKS-QSFRYGFCGN-GTHVFSVVNAAPDG----- 1156
YP_009505583  922 LQLKLDTEIQLSANSDSALARVLTALSLGHRTNRNLDRHISQVRTCLASiQQNSLAGCVNqGSNSIPLGIRVFNEtgdlk 1001
YP_009389425  856 VQAEQQMDRVINGKMNALLNFVSNYKLKVSELTSIQQLVKQKVQECVHA-QSLRNGFCGS-GLHVMSIPQLVPNG----- 928 
YP_009336484  849 IEAAMQMDRLINGRMNILQNFVTNYKLSISELKSQQALAQSLINECVYA-QSSRNGFCGD-GLHLFSLMQRAPDG----- 921 
YP_009380521  842 LEAQMQMDRLINGRMNILQNFVTNYKLSISELKSQQILAQSLVNECVYA-QSNRNGFCGD-GLHLFSLMQRAPDG----- 914 
4_pfamImport  284 LEADAEVDRLISGRMVVLNTYVTQLLVQASRIKAQSDLALQKINECVKS-QTLRNEFCGN-GTHVLSVPQLAPNG----- 356 
A3EXG6        984 LAANAEVDRLINGRMMVLNTYVTQLLIQASEAKAQNALAAQKISECVKA-QSLRNDFCGN-GTHVLSIPQLAPNG----- 1056 Rousettus bat...
YP_009513010 1042 LEQEVQIDRLINGRLTSLNAFVSQQLVRSEAAARSSQLAKEKINECVKA-QSTRSGFCGQ-GTHIVSFVINAPNG----- 1114
P59594        969 VEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLG-QSKRVDFCGK-GYHLMSFPQAAPHG----- 1041 Severe acute ...
YP_009072440 1030 LEADAQIDRLINGRLQVLQTFVTQQLIRASEIRASAKLAAQKMSECVQG-QSQRLDFCGR-GMHLMSFPQAAPYG----- 1102
YP_009199609 1157 MMFFHSVLLPTAYMEVAAFSGLCVEGN--GYVLRDTGNVLF-EKNg--qYLITARKMFEPRVPQTSDF--VQITGCDVVY 1229
YP_009505583 1002 IVFFYATRQRLGYLQFKATSAFCTNGTl-VTAAPGCIFTAN-GTQ-------IEHSKIGPLTPCGSSFvsLPIATCPTGS 1072
YP_009389425  929 VMFLHFSLVKNNSIIVKQTPGLCKEDKinCIVPKSGIFVSK-NDSn---WYITPRNKYVPKNITNSD---IIFTTYSENF 1001
YP_009336484  922 IMFFHYTLKPNNTIIVETTPGLCLSNDv-CIAPKDGLFVRL-STArdtdWHFTTRNRYSPEPITVNNT--LTISG-GVNF 996 
YP_009380521  915 IMFFHYTLVPNNTIDVETTPGLCLGNNv-CIAPRDGLFVKT-NIRsd-vWHFTTRNLYNPQAITVNNS--VIVNG-GVNF 988 
4_pfamImport  357 IMFIHYSYTPTQYATVQTAAGLCFNGT--GYAPRNGLFILPnNSNf---WYFTQANFYNPVNISNSNT--QVLESCSVNY 429 
A3EXG6       1057 VLFIHYAYTPTEYAFVQTSAGLCHNGT--GYAPRQGMFVLPnNTNm---WHFTTMQFYNPVNISASNT--QVLTSCSVNY 1129 Rousettus bat...
YP_009513010 1115 FYFIHVGYHPQDYVNQTAAYGLCDSSSskCIAAKNGYFVKN-DSDsd-sWSYTGSSFYQPEPITSFNS--RFVQP-EFTF 1189
P59594       1042 VVFLHVTYVPSQERNFTTAPAICHEGK--AYFPREGVFVFN-GTS----WFITQRNFFSPQIITTDNT--FVSGNCDVVI 1112 Severe acute ...
YP_009072440 1103 MVFLHVLYKPTDYINVTTVPAICSNDV--AYFPVDGVFVYY-NNS----LMFTKRNYFEPEIITIDNI--RSAGSCNVDV 1173
YP_009199609 1230 LNVTRDE-LPTV-IPD--YIDVNSTVEDILSKLpNRT---T-PEFD---LDIFNATYLNLTGEIADLtarseslknttLE 1298
YP_009505583 1073 VDIEGVK--PSL-TPN--FEVPQLELKp--------------PKLE------VNLTNVNLSDYIRPItpvd---lskiED 1124
YP_009389425 1002 TVINNTIqFPGIeFPQ--DGDFDGQIKNVTLEL---------QSLK---DVVANMSYLDLSNHT--------------AL 1053
YP_009336484  997 TVVNSTI-DGIE-PPA--NPSFDEEFAELYKNV-TLEleqL-KNIS------FDPEMLNLTYYI--------------DR 1050
YP_009380521  989 TSLNQTI-EGIE-PPT--IPSFDEEFEDLYKNI-TLEleqL-KNIT------FDPELLNLTYYI--------------DR 1042
4_pfamImport  430 TTVNYTI-LSPQ-EPL--YNNFDEEFNKFYKNL-SSVf--N-NTFN---PGAFNFSTVELQSEI--------------AT 484 
A3EXG6       1130 TSVNYTV-LEPS-VPG--DYDFQKEFDKFYKNL-STIf--N-NTFN---PNDFNFSTVDVTAQI--------------KS 1184 Rousettus bat...
YP_009513010 1190 QNLTNNL-PPPL-LSNnsDVTFEDELEEFYKNI-TSE---I-PNFGs--ISQINTTMLNLSREM--------------SI 1246
P59594       1113 GIINNTV-YDPL-QPE--LDSFKEELDKYFKNH-------TsPDVDlgdISGINASVVNIQKEI--------------DR 1167 Severe acute ...
YP_009072440 1174 TYVNHTI-YNPE-MPE--LEDFKQELEEIRKNF-STGlpnR-PNFTlpgLEGINASMVDLSEEV--------------KI 1233
YP_009199609 1299 LKELIANINATLVDLEWLNRVETYIKWPWWVWL--IIVLVLILFTCL 1343
YP_009505583 1125 LQARFDKLNLTLTELSHISSSGSGLP-TWAIIF--IVCVAVVIVLVF 1168
YP_009389425 1054 LKNISEEVKKMNITVSQFKQYVKYVKWPWYVWL--LIVMALIAFGLV 1098
YP_009336484 1051 LDELATNVSQLHVDVSEFNKFVQYIKWPWYVWL--AIFLVLVLFSFL 1095
YP_009380521 1043 LDELSTNVSQLHVDISEFNKYVQYIKWPWYVWL--AIFLVLVLFSFM 1087
4_pfamImport  485 LNEVVQQLNKSFIDLKQMNVYEQTIKWPWYVWLamIAGLVGLALAVV 531 
A3EXG6       1185 LHDVVNQLNQSFIDLKKLNVYEKTIKWPWYVWLamIAGIVGLVLAVI 1231 Rousettus bat coronavirus HKU9
YP_009513010 1247 LQQVVKDLNNSYIELKELGNYTYYQKSPWYVWLgfIAGLVALALCLF 1293
P59594       1168 LNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLgfIAGLIAIVMVTI 1214 Severe acute respiratory syndrome-related coro...
YP_009072440 1234 LNDVVKELNASLINLQELGVNSQYIKWPWYIWLgfIAGLIAIVMATI 1280
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