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Conserved domains on  [gi|1983930778|gb|QRN75109|]
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spike protein [Feline coronavirus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TGEV-like_Spike_SD1-2_S1-S2_S2 cd22377
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
680-1418 0e+00

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from transmissible gastroenteritis virus and related alphacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine transmissible gastroenteritis virus (TGEV), canine coronavirus (CCoV), and feline coronavirus (FCoV). They display greater than 96% sequence identity and have been grouped in the same species, alphacoronavirus 1, within the Alphacoronavirus genus. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


:

Pssm-ID: 411964 [Multi-domain]  Cd Length: 751  Bit Score: 1258.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  680 DLSVLHLDSCTDYNIYGRTGVGIIRRTNSTLLSGLYYTSLSGDLLGFKNVSDGVIYSVTPCDVSAQAAVIDGAIVGAMTS 759
Cdd:cd22377      1 DISVLVKDECTDYNIYGFQGTGIIRNTTSRLVAGLYYTSISGDLLAFKNSTTGEIFTVVPCDLTAQAAVINDEIVGAITS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  760 INSE-----------------LLGLTHWTTTPNFYYYSIYNytsertrdtaiDSNDVDCEPVITYSNIGVCKNGALVFIN 822
Cdd:cd22377     81 VNQTdlfefvnhtqsrrsrrsTLGLVHTYTMPQFYYITKWN-----------NDTSTNCTSVITYSSFAICNTGEIKYVN 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  823 VTHSDGDV------QPISTGNVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMG 896
Cdd:cd22377    150 VTHVEIVDdsigviKPISTGNITIPKNFTVAVQAEYIQIQVKPVVVDCAKYVCNGNRHCLKLLTQYTSACQTIENALNLG 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  897 ARLENMEVDSMLFVSENALKLASVEAFNSTENLDsiykewPSIGGSWLGGLKDILPSHNSKRkygSAIEDLLFDKVVTSG 976
Cdd:cd22377    230 ARLESLMLNDMITVSDRSLELATVEKFNSTVLGG------EKLGGFYFDGLKDLLPPRIGKR---SAIEDLLFNKVVTSG 300
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  977 LGTVDEDYKRCTGGYDIADLVCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGAlGGGAVAIPFAVAVQARLNYVALQ 1056
Cdd:cd22377    301 LGTVDDDYKKCSAGTDVADLVCAQYYNGIMVLPGVVDDNKMAMYTASLIGGMALGS-ITSAVAVPFAMQVQARLNYVALQ 379
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1057 TDVLNKNQQILANAFNQAIGNITQAFGKVNDAIHQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSIS 1136
Cdd:cd22377    380 TDVLQENQKILANAFNNAIGNITLALGKVSNAITTTSDGFNTMASALTKIQSVVNQQGEALSQLTSQLQKNFQAISSSIA 459
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1137 DIYNRLDELSADAQVDRLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPN 1216
Cdd:cd22377    460 EIYNRLEKVEADAQVDRLITGRLAALNAYVSQTLTQYAEVKASRQLAMEKVNECVKSQSDRYGFCGNGTHLFSLVNSAPD 539
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1217 GMIFFHTVLLPTAYETVTAWSGICASDGDRTFGLvvkdVQLTLFRNLDDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFV 1296
Cdd:cd22377    540 GLLFFHTVLLPTEWEEVTAWSGICVNDTYAYVLK----DFLTSIFSYNGTYMVTPRNMFQPRKPQMSDFVQITSCEVTFL 615
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1297 NATVIDLPSIIPDYIDINQTVQDILENYRPNWTVPEF--TLDIFNATYLNLTGEIDDLEFRSEKLHNTTVELAILIDNIN 1374
Cdd:cd22377    616 NTTYTTFQEIVIDYIDINKTIADMLEQYNPNYTVPELdlQLEIFNQTKLNLTAEIDQLEQRADNLTNIAHELQQYIDNLN 695
                          730       740       750       760
                   ....*....|....*....|....*....|....*....|....
gi 1983930778 1375 NTLVNLEWLNRIETYVKWPWYVWLLIGLVVVFCIPLLLFCCFST 1418
Cdd:cd22377    696 KTLVDLEWLNRIETYVKWPWYVWLLIGLVVVFCIPLLLFCCLST 739
CoV_S1 pfam01600
Coronavirus spike glycoprotein S1; This family represents the spike glycoprotein (S) of ...
249-673 2.24e-166

Coronavirus spike glycoprotein S1; This family represents the spike glycoprotein (S) of coronaviruses. The spike protein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilize both the S1 NTD and S1 RBD for viral entry. This entry contains spike protein from both alpha and gamma coronaviruses but excludes the spike protein from beta-coronaviruses such as SARS-CoV.


:

Pssm-ID: 460262  Cd Length: 412  Bit Score: 505.34  E-value: 2.24e-166
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  249 YELCEdyeHCTGYATNVFAPTSGGYIPDGFSFNNWFLLTNSSTFVSGRFVTNQPLLINCLWPVPSFGVAAQEFCFEGA-Q 327
Cdd:pfam01600    1 YSVCT---NCDGFPDNVFAVEEGGYIPPSFSFNNWFYLTNSSTPVDGRVVSNQPLLLNCLWPIPSLNGTTLKVYFNGSiP 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  328 FSQCNGVSL-NNTVDVIRFNLNFTADVQSGMGATVFSLNTTGGVILEISCYSDTVSESSSYSygeIPFGITDGPRYCYVL 406
Cdd:pfam01600   78 NGRCNGYSNkNGTVDAIRFNLNFTASDSVFAGAGSISLNTVGGVTYSFSCSNSSTPVGASHQ---IPFGATDQPYYCFVN 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  407 YNG---TALKYLGTLPPSVKEIAISKWGHFYINGYNFFSTFPIGCISFNLTTGVSGAFWTIAYTSYTEALVQVENTAIKN 483
Cdd:pfam01600  155 YNGnisTTSQFVGILPPVVREIVISRYGDFYVNGYRYFSTPPLESVNFNLTSGDTSDFWTVAFANYTDVLVNINNTSIQR 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  484 VTYCNSHINNIKCSQLTANLNNGFYPVASSEVGFVNKSVVLLPSFFTYTAVNITIDLGMKLSGyGQPIASTLSNITLPMQ 563
Cdd:pfam01600  235 ILYCDSPLNSIKCQQLSFSLPDGFYSTSSVEVVQLPRTFVTLPKFATHSFVNLTVSVSFDGGG-GPPSLSALSEVNLTIN 313
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  564 DNNTDVYCIRSNQFSVYVHSTCKSSlwdnifnqdctdVLEATAVIKTGTCPFSFDKLNNYLTFNKFCLSLSPVGANCKFD 643
Cdd:pfam01600  314 GTNNTSLCVNTSQFTVNLNFTCTST------------AYGYTAEIRTGTCPFSFDKLNNYLSFGSICFSLVPSGGGCTMD 381
                          410       420       430
                   ....*....|....*....|....*....|.
gi 1983930778  644 V-AARTRTNEQVVRSLYVIYEEGDNIVGVPS 673
Cdd:pfam01600  382 IvTKYWNGSFVKVGSLYVSYSEGDNITGVPK 412
 
Name Accession Description Interval E-value
TGEV-like_Spike_SD1-2_S1-S2_S2 cd22377
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
680-1418 0e+00

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from transmissible gastroenteritis virus and related alphacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine transmissible gastroenteritis virus (TGEV), canine coronavirus (CCoV), and feline coronavirus (FCoV). They display greater than 96% sequence identity and have been grouped in the same species, alphacoronavirus 1, within the Alphacoronavirus genus. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411964 [Multi-domain]  Cd Length: 751  Bit Score: 1258.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  680 DLSVLHLDSCTDYNIYGRTGVGIIRRTNSTLLSGLYYTSLSGDLLGFKNVSDGVIYSVTPCDVSAQAAVIDGAIVGAMTS 759
Cdd:cd22377      1 DISVLVKDECTDYNIYGFQGTGIIRNTTSRLVAGLYYTSISGDLLAFKNSTTGEIFTVVPCDLTAQAAVINDEIVGAITS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  760 INSE-----------------LLGLTHWTTTPNFYYYSIYNytsertrdtaiDSNDVDCEPVITYSNIGVCKNGALVFIN 822
Cdd:cd22377     81 VNQTdlfefvnhtqsrrsrrsTLGLVHTYTMPQFYYITKWN-----------NDTSTNCTSVITYSSFAICNTGEIKYVN 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  823 VTHSDGDV------QPISTGNVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMG 896
Cdd:cd22377    150 VTHVEIVDdsigviKPISTGNITIPKNFTVAVQAEYIQIQVKPVVVDCAKYVCNGNRHCLKLLTQYTSACQTIENALNLG 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  897 ARLENMEVDSMLFVSENALKLASVEAFNSTENLDsiykewPSIGGSWLGGLKDILPSHNSKRkygSAIEDLLFDKVVTSG 976
Cdd:cd22377    230 ARLESLMLNDMITVSDRSLELATVEKFNSTVLGG------EKLGGFYFDGLKDLLPPRIGKR---SAIEDLLFNKVVTSG 300
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  977 LGTVDEDYKRCTGGYDIADLVCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGAlGGGAVAIPFAVAVQARLNYVALQ 1056
Cdd:cd22377    301 LGTVDDDYKKCSAGTDVADLVCAQYYNGIMVLPGVVDDNKMAMYTASLIGGMALGS-ITSAVAVPFAMQVQARLNYVALQ 379
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1057 TDVLNKNQQILANAFNQAIGNITQAFGKVNDAIHQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSIS 1136
Cdd:cd22377    380 TDVLQENQKILANAFNNAIGNITLALGKVSNAITTTSDGFNTMASALTKIQSVVNQQGEALSQLTSQLQKNFQAISSSIA 459
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1137 DIYNRLDELSADAQVDRLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPN 1216
Cdd:cd22377    460 EIYNRLEKVEADAQVDRLITGRLAALNAYVSQTLTQYAEVKASRQLAMEKVNECVKSQSDRYGFCGNGTHLFSLVNSAPD 539
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1217 GMIFFHTVLLPTAYETVTAWSGICASDGDRTFGLvvkdVQLTLFRNLDDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFV 1296
Cdd:cd22377    540 GLLFFHTVLLPTEWEEVTAWSGICVNDTYAYVLK----DFLTSIFSYNGTYMVTPRNMFQPRKPQMSDFVQITSCEVTFL 615
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1297 NATVIDLPSIIPDYIDINQTVQDILENYRPNWTVPEF--TLDIFNATYLNLTGEIDDLEFRSEKLHNTTVELAILIDNIN 1374
Cdd:cd22377    616 NTTYTTFQEIVIDYIDINKTIADMLEQYNPNYTVPELdlQLEIFNQTKLNLTAEIDQLEQRADNLTNIAHELQQYIDNLN 695
                          730       740       750       760
                   ....*....|....*....|....*....|....*....|....
gi 1983930778 1375 NTLVNLEWLNRIETYVKWPWYVWLLIGLVVVFCIPLLLFCCFST 1418
Cdd:cd22377    696 KTLVDLEWLNRIETYVKWPWYVWLLIGLVVVFCIPLLLFCCLST 739
CoV_S2 pfam01601
Coronavirus spike glycoprotein S2; The coronavirus spike glycoprotein forms the characteriztic ...
836-1391 0e+00

Coronavirus spike glycoprotein S2; The coronavirus spike glycoprotein forms the characteriztic '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.


Pssm-ID: 460263  Cd Length: 502  Bit Score: 775.68  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  836 GNVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMGARLENMEVDSMLFVSENAL 915
Cdd:pfam01601    1 GNISIPTNFTISVQTEYIQTTSPKVSVDCAQYVCNGNERCLQLLVQYGSFCSTIEQALQGSARLEDVEVLSMLSISNRAL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  916 KLASVEAFNSTENLDSIykewpsiggswlgglkdiLPSHNSKRkygSAIEDLLFDKVVTSGLGTVDeDYKRCTGGYDIAD 995
Cdd:pfam01601   81 TLATISNFGSDFNFSSF------------------LPCLNSGR---SAIEDLLFDKVVTSGLGTVD-AYKKCTKGTSIAD 138
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  996 LVCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGALGGGAVAIPFAVAVQARLNYVALQTDVLNKNQQILANAFNQAI 1075
Cdd:pfam01601  139 LVCAQYYNGIMVLPGVVDAEKMAMYTASLTGGMAFGGLTGAAAAIPFALAVQARLNYLGLQTDVLQENQKILANAFNNAV 218
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1076 GNITQAFgkvndaihqtsqglATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDELSADAQVDRLI 1155
Cdd:pfam01601  219 GNITDGF--------------TTTASALSKIQDVVNANAQALNQLTQQLSNNFGAISSSIQDIYSRLDQLEADAQVDRLI 284
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1156 TGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFFHTVLLPTAYETVTA 1235
Cdd:pfam01601  285 NGRLAALNAFVTQQLTKASEVKASRQLAQQKVNECVKSQSSRYGFCGNGTHLFSLPQAAPNGIMFLHTVLVPTEYITVKA 364
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1236 WSGICASDgdrTFGLVVKDVQLTLFRNldDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFVNATVIDLPSIIPDYIDINQ 1315
Cdd:pfam01601  365 TPGLCVNG---TTGYAPRDGQFVLNNT--SNWYITPRNMYQPRPITGSDFVQISSCDVNFVNITNTKLPPLIPDYVDFNK 439
                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1983930778 1316 TVQDILENYrpNWTVPEFTLDIFNATYLNLTGEIDDLEfrseklhnttvELAILIDNINNTLVNLEWLNRIETYVK 1391
Cdd:pfam01601  440 ELEDIYKNL--NSTLPDLDLDIFNATILNLTDEIKDLE-----------RLQELIDNLNQTLVDLEWLNRYETYIK 502
CoV_S1 pfam01600
Coronavirus spike glycoprotein S1; This family represents the spike glycoprotein (S) of ...
249-673 2.24e-166

Coronavirus spike glycoprotein S1; This family represents the spike glycoprotein (S) of coronaviruses. The spike protein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilize both the S1 NTD and S1 RBD for viral entry. This entry contains spike protein from both alpha and gamma coronaviruses but excludes the spike protein from beta-coronaviruses such as SARS-CoV.


Pssm-ID: 460262  Cd Length: 412  Bit Score: 505.34  E-value: 2.24e-166
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  249 YELCEdyeHCTGYATNVFAPTSGGYIPDGFSFNNWFLLTNSSTFVSGRFVTNQPLLINCLWPVPSFGVAAQEFCFEGA-Q 327
Cdd:pfam01600    1 YSVCT---NCDGFPDNVFAVEEGGYIPPSFSFNNWFYLTNSSTPVDGRVVSNQPLLLNCLWPIPSLNGTTLKVYFNGSiP 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  328 FSQCNGVSL-NNTVDVIRFNLNFTADVQSGMGATVFSLNTTGGVILEISCYSDTVSESSSYSygeIPFGITDGPRYCYVL 406
Cdd:pfam01600   78 NGRCNGYSNkNGTVDAIRFNLNFTASDSVFAGAGSISLNTVGGVTYSFSCSNSSTPVGASHQ---IPFGATDQPYYCFVN 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  407 YNG---TALKYLGTLPPSVKEIAISKWGHFYINGYNFFSTFPIGCISFNLTTGVSGAFWTIAYTSYTEALVQVENTAIKN 483
Cdd:pfam01600  155 YNGnisTTSQFVGILPPVVREIVISRYGDFYVNGYRYFSTPPLESVNFNLTSGDTSDFWTVAFANYTDVLVNINNTSIQR 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  484 VTYCNSHINNIKCSQLTANLNNGFYPVASSEVGFVNKSVVLLPSFFTYTAVNITIDLGMKLSGyGQPIASTLSNITLPMQ 563
Cdd:pfam01600  235 ILYCDSPLNSIKCQQLSFSLPDGFYSTSSVEVVQLPRTFVTLPKFATHSFVNLTVSVSFDGGG-GPPSLSALSEVNLTIN 313
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  564 DNNTDVYCIRSNQFSVYVHSTCKSSlwdnifnqdctdVLEATAVIKTGTCPFSFDKLNNYLTFNKFCLSLSPVGANCKFD 643
Cdd:pfam01600  314 GTNNTSLCVNTSQFTVNLNFTCTST------------AYGYTAEIRTGTCPFSFDKLNNYLSFGSICFSLVPSGGGCTMD 381
                          410       420       430
                   ....*....|....*....|....*....|.
gi 1983930778  644 V-AARTRTNEQVVRSLYVIYEEGDNIVGVPS 673
Cdd:pfam01600  382 IvTKYWNGSFVKVGSLYVSYSEGDNITGVPK 412
PHA03332 PHA03332
membrane glycoprotein; Provisional
1011-1196 1.34e-03

membrane glycoprotein; Provisional


Pssm-ID: 223047 [Multi-domain]  Cd Length: 1328  Bit Score: 43.42  E-value: 1.34e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1011 VANADKMT---MYTASLAGGI-TLGALGGGAVAIPFAVAVQARLNYvALQTDVLNKNQQILAnafnqaigniTQAFGKVN 1086
Cdd:PHA03332   829 VLDLWHETvkmFAPRRFGGSVmAGDAIGLSAAAFTMASAALNAATQ-ALAVATLYVNQLLQA----------TAATAEMA 897
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1087 DAIHQTSqglatvaKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDE--LSADAQVDRLITGrLTALNA 1164
Cdd:PHA03332   898 SKIGGLN-------ARVDKTSDVITKLGDTIAKISATLDNNIRAVNGRVSDLEDQVNLrfLAVATNFNTLATQ-LKELGT 969
                          170       180       190
                   ....*....|....*....|....*....|..
gi 1983930778 1165 FVSQTLTRQAEVRASRQLAKDKVNECVRSQSQ 1196
Cdd:PHA03332   970 TTNERIEEVMAAALYYQQLNSLTNQVTQSASK 1001
Tar COG0840
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
1067-1189 2.84e-03

Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];


Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 41.93  E-value: 2.84e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1067 LANAFNQAIGNITQAFGKVNDAIHQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNnfqaISSSISDIYNRLDELS 1146
Cdd:COG0840    240 LADAFNRMIENLRELVGQVRESAEQVASASEELAASAEELAAGAEEQAASLEETAAAMEE----LSATVQEVAENAQQAA 315
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1983930778 1147 ADAQ--VDRLITGRLTalnafVSQTLTRQAEVRASRQLAKDKVNE 1189
Cdd:COG0840    316 ELAEeaSELAEEGGEV-----VEEAVEGIEEIRESVEETAETIEE 355
 
Name Accession Description Interval E-value
TGEV-like_Spike_SD1-2_S1-S2_S2 cd22377
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
680-1418 0e+00

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from transmissible gastroenteritis virus and related alphacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine transmissible gastroenteritis virus (TGEV), canine coronavirus (CCoV), and feline coronavirus (FCoV). They display greater than 96% sequence identity and have been grouped in the same species, alphacoronavirus 1, within the Alphacoronavirus genus. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411964 [Multi-domain]  Cd Length: 751  Bit Score: 1258.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  680 DLSVLHLDSCTDYNIYGRTGVGIIRRTNSTLLSGLYYTSLSGDLLGFKNVSDGVIYSVTPCDVSAQAAVIDGAIVGAMTS 759
Cdd:cd22377      1 DISVLVKDECTDYNIYGFQGTGIIRNTTSRLVAGLYYTSISGDLLAFKNSTTGEIFTVVPCDLTAQAAVINDEIVGAITS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  760 INSE-----------------LLGLTHWTTTPNFYYYSIYNytsertrdtaiDSNDVDCEPVITYSNIGVCKNGALVFIN 822
Cdd:cd22377     81 VNQTdlfefvnhtqsrrsrrsTLGLVHTYTMPQFYYITKWN-----------NDTSTNCTSVITYSSFAICNTGEIKYVN 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  823 VTHSDGDV------QPISTGNVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMG 896
Cdd:cd22377    150 VTHVEIVDdsigviKPISTGNITIPKNFTVAVQAEYIQIQVKPVVVDCAKYVCNGNRHCLKLLTQYTSACQTIENALNLG 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  897 ARLENMEVDSMLFVSENALKLASVEAFNSTENLDsiykewPSIGGSWLGGLKDILPSHNSKRkygSAIEDLLFDKVVTSG 976
Cdd:cd22377    230 ARLESLMLNDMITVSDRSLELATVEKFNSTVLGG------EKLGGFYFDGLKDLLPPRIGKR---SAIEDLLFNKVVTSG 300
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  977 LGTVDEDYKRCTGGYDIADLVCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGAlGGGAVAIPFAVAVQARLNYVALQ 1056
Cdd:cd22377    301 LGTVDDDYKKCSAGTDVADLVCAQYYNGIMVLPGVVDDNKMAMYTASLIGGMALGS-ITSAVAVPFAMQVQARLNYVALQ 379
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1057 TDVLNKNQQILANAFNQAIGNITQAFGKVNDAIHQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSIS 1136
Cdd:cd22377    380 TDVLQENQKILANAFNNAIGNITLALGKVSNAITTTSDGFNTMASALTKIQSVVNQQGEALSQLTSQLQKNFQAISSSIA 459
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1137 DIYNRLDELSADAQVDRLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPN 1216
Cdd:cd22377    460 EIYNRLEKVEADAQVDRLITGRLAALNAYVSQTLTQYAEVKASRQLAMEKVNECVKSQSDRYGFCGNGTHLFSLVNSAPD 539
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1217 GMIFFHTVLLPTAYETVTAWSGICASDGDRTFGLvvkdVQLTLFRNLDDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFV 1296
Cdd:cd22377    540 GLLFFHTVLLPTEWEEVTAWSGICVNDTYAYVLK----DFLTSIFSYNGTYMVTPRNMFQPRKPQMSDFVQITSCEVTFL 615
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1297 NATVIDLPSIIPDYIDINQTVQDILENYRPNWTVPEF--TLDIFNATYLNLTGEIDDLEFRSEKLHNTTVELAILIDNIN 1374
Cdd:cd22377    616 NTTYTTFQEIVIDYIDINKTIADMLEQYNPNYTVPELdlQLEIFNQTKLNLTAEIDQLEQRADNLTNIAHELQQYIDNLN 695
                          730       740       750       760
                   ....*....|....*....|....*....|....*....|....
gi 1983930778 1375 NTLVNLEWLNRIETYVKWPWYVWLLIGLVVVFCIPLLLFCCFST 1418
Cdd:cd22377    696 KTLVDLEWLNRIETYVKWPWYVWLLIGLVVVFCIPLLLFCCLST 739
alphaCoV_Spike_SD1-2_S1-S2_S2 cd22369
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
680-1383 0e+00

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) protein from alphacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from alphacoronaviruses including human coronaviruses (HCoVs), HCoV-NL63, and HCoV-229E, and porcine coronaviruses, transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV), among others. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP), and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1 the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411956 [Multi-domain]  Cd Length: 666  Bit Score: 1171.68  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  680 DLSVLHLDSCTDYNIYGRTGVGIIRRTNSTLLSGLYYTSLSGDLLGFKNVSDGVIYSVTPCDVSAQAAVIDGAIVGAMTS 759
Cdd:cd22369      1 DPSVVHLNVCTDYTIYGITGRGIIRKSNSTYIAGLYYTSNSGQLLGFKNSTTGEVFSVTPCQLSSQVAVVSDNIVGVMSA 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  760 INSELLGLTHWTTTPNFYYYSIynytsertrdtaidsNDVDC-EPVITYSNIGVCKNGALV-FINVTHSDGDVQPISTGN 837
Cdd:cd22369     81 TNNVSLGFNNTIETPSFYYHSN---------------GAENCtEPVLTYGSIGVCADGSITeVTPRSVSPEPVSPIITGN 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  838 VTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMGARLENMEVDSMLFVSENALKL 917
Cdd:cd22369    146 ISIPSNFTVSVQVEYLQMYLKPVSVDCSTYVCNGNPRCLQLLTQYASACRTIEEALQLSARLESVEVNSMITVSEEALRL 225
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  918 ASVEAFNSTENLDSIykewpsiggswlgglkdiLPSHNSKRkygSAIEDLLFDKVVTSGLGTVDEDYKRCTGGYDIA--D 995
Cdd:cd22369    226 ANISTFFDDYNLSAV------------------LPAGVGGR---SAIEDLLFDKVVTSGLGTVDEDYKACTKGLGIAaaD 284
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  996 LVCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGALGGGAvAIPFAVAVQARLNYVALQTDVLNKNQQILANAFNQAI 1075
Cdd:cd22369    285 VACAQYYNGIMVLPGVVDAEKMALYTASLTGGMVLGGFTAAA-AIPFSLAVQSRLNYVALQTDVLQRNQQILANSFNSAM 363
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1076 GNITQAFGKVNDAIHQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDELSADAQVDRLI 1155
Cdd:cd22369    364 GNITVAFSEVNDAIQQTSDAINTVAQALNKVQNVVNEQGQALSQLTKQLASNFQAISSSIEDIYNRLDGLAADAQVDRLI 443
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1156 TGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFFHTVLLPTAYETVTA 1235
Cdd:cd22369    444 TGRLAALNAFVTQTLTKYTEVRASRQLAQQKINECVKSQSSRYGFCGNGTHLFSIVNAAPDGIMFLHTVLLPTEYVTVAA 523
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1236 WSGICASDgdrtFGLVVKDVQLTLFRNLDDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFVNATVIDLPSIIPDYIDINQ 1315
Cdd:cd22369    524 WAGLCVDG----KAYVLRDDVVLTLFKLNDKYYVTPRDMFEPRVPVSSDFVQISNCNVTYVNITSDELPEVIPDYIDVNK 599
                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1983930778 1316 TVQDILENyRPNWTVPEFTLDIFNATYLNLTGEIDDLEFRSEKLHNTTVELAILIDNINNTLVNLEWL 1383
Cdd:cd22369    600 TLEEFLAN-LPNYTLPDLPLDIFNATYLNLTGEIADLENKSESLLNTTVELQELIDNINNTLVDLEWL 666
PDEV-like_Spike_SD1-2_S1-2_S2 cd22376
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
680-1388 0e+00

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Porcine epidemic diarrhea virus and related alphacoronavirus; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from alphacoronaviruses, including porcine epidemic diarrhea virus (PEDV), Scotophilus bat coronavirus, and swine enteric coronavirus, among others. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1 the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411963 [Multi-domain]  Cd Length: 673  Bit Score: 978.09  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  680 DLSVLHLDSCTDYNIYGRTGVGIIRRTNSTLLSGLYYTSLSGDLLGFKNVSDGVIYSVTPCDVSAQAAVIDGAIVGAMTS 759
Cdd:cd22376      1 DVSFMTLDVCTKYTIYGFKGEGIITLTNSSLLGGVYYTSDSGQLLAFKNVTSGAIYSVTPCSFSQQAAYVDDDIVGVISS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  760 INSELLGLThwTTTPNFYYYSiyNYTSERTrdtaidsndvdcEPVITYSNIGVCKNGALVFINVTHSDGDVQPISTGNVT 839
Cdd:cd22376     81 LSNSTFNST--RELPGFFYHS--NDGSNCT------------EPVLVYSNIGVCKSGSIGYVPSQSGQPKIAPMVTGNIS 144
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  840 IPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMGARLENMEVDSMLFVSENALKLAS 919
Cdd:cd22376    145 IPTNFTMSIRTEYLQLYNTPVSVDCAMYVCNGNSRCKQLLTQYTSACKTIESALQLSARLESVEVNSMLTISEEALQLAT 224
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  920 VEAFNstenldsiykewpsiGGSWlgGLKDILPSHNSKRkygSAIEDLLFDKVVTSGLGTVDEDYKRCTGGYDIADLVCA 999
Cdd:cd22376    225 ISSFN---------------GGGY--NFTNVLGASVQKR---SFIEDLLFNKVVTNGLGTVDEDYKRCSNGLSVADLVCA 284
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1000 QYYNGIMVLPGVANADKMTMYTASLAGGITLGALGGGAvAIPFAVAVQARLNYVALQTDVLNKNQQILANAFNQAIGNIT 1079
Cdd:cd22376    285 QYYSGVMVLPGVVDAEKLHMYSASLIGGMVLGGITAAA-ALPFSYAVQARLNYVALQTDVLQRNQQLLAESFNSAIGNIT 363
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1080 QAFGKVNDAIHQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDELSADAQVDRLITGRL 1159
Cdd:cd22376    364 SAFESVKEAISQTSQGLNTVAHALTKVQDVVNSQGAALNQLTVQLQHNFQAISSSIDDIYSRLDQLSADAQVDRLITGRL 443
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1160 TALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGN-GTHLFSLANAAPNGMIFFHTVLLPTAYETVTAWSG 1238
Cdd:cd22376    444 SALNAFVAQTLTKYTEVQASRKLAQQKVNECVKSQSQRYGFCGGdGEHIFSLVQAAPQGLLFLHTVLVPGDFVNVTAIAG 523
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1239 ICASDgdrTFGLVVKDVQLTLFRNL----DDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFVNATVIDLPSIIPDYIDIN 1314
Cdd:cd22376    524 LCVDD---EIALTLREPGVLFTHEVltytATEYFVSPRKMFEPRKPTVSDFVQIESCVVTYVNLTSDQLPDVIPDYIDVN 600
                          650       660       670       680       690       700       710
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1983930778 1315 QTVQDILENYrPNWTVPEFTLDIFNATYLNLTGEIDDLEFRSEKLHNTTVELAILIDNINNTLVNLEWLNRIET 1388
Cdd:cd22376    601 KTLDEILASL-PNRTGPSLPLDVFNATYLNLTGEIADLEQRSESLRNTTEELRSLIYNINNTLVDLEWLNRVET 673
delta-PiCoV-like_Spike_SD1-2_S1-S2_S2 cd22374
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
662-1415 0e+00

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Pigeon coronavirus UAE-HKU29, and related avian deltacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Pigeon coronavirus UAE-HKU29, and related avian deltacoronaviruses including Falcon coronavirus UAE-HKU27, Magpie-robin coronavirus HKU18, Sparrow coronavirus HKU17, and Night heron coronavirus HKU19. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the (C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411961 [Multi-domain]  Cd Length: 739  Bit Score: 910.81  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  662 YEEGDNIVGVPSDNSGLHDLSVLHLDSCTDYNIYGRTGVGIIRRTNSTLLSGLYYTSLSGDLLGFKNVSDGVIYSVTPCD 741
Cdd:cd22374      1 YQPGNSITAMPQPSTGTTDISTVYLDVCTKYNIYGKTGTGIIRLTNQSYIAGLYYTSPSGDLLAFKNVTTQTVYSVTPCR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  742 VSAQAAVIDGAIVGAMTSI-NSELLGLTHWTTTPNFYYYSIynytsertrdtaidSNDVDCEPVITYSNIGVCKNGALVF 820
Cdd:cd22374     81 LSSQVAVYNGSIIAAFTSTeNFTIADFTYSRATPMFYYHSI--------------GNDTCETPVITFGSIGVCPGGGLHF 146
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  821 INVTHSDGD-VQPISTGNVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMGARL 899
Cdd:cd22374    147 VDPTSNEFTnVVPISTQNISIPKNFTVSIQTEYIQIEQQPVTVDCRQYVCNGNPRCLQLLMQYTSACSTIEQALSLNARL 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  900 ENMEVDSMLFVSENALKLASVEAFNStenldsiykewpsigGSWLGGLKDILPSHNSKRkygSAIEDLLFDKVVTSGLGT 979
Cdd:cd22374    227 EAASIQTMLTYSPETLKLANITNFQS---------------DDVNYNLTNILPKKYQGR---SAIEDLLFDKVVTNGLGT 288
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  980 VDEDYKRCTGGYDIADLVCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGALGGGAvAIPFAVAVQARLNYVALQTDV 1059
Cdd:cd22374    289 VDQDYKACTNGVSIADLVCAQYYNGIMVLPGVADPEKMAQYTASLTGGMVFGGLTSAA-AIPFSLAVQSRLNYVALQTDV 367
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1060 LNKNQQILANAFNQAIGNITQAFGKVNDAIHQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIY 1139
Cdd:cd22374    368 LQQNQQILADSFNNAMGNITLAFKEVSEGLSQVSGAITTVANALTKIQTVVNSQGQALATLTEQLANNFQAISASIADIY 447
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1140 NRLDELSADAQVDRLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMI 1219
Cdd:cd22374    448 NRLNQLEADAQVDRLITGRLAALNAFVTQTLSKLAEVRQARQLALDKINECVKSQSSRYGFCGNGTHLFSIVNAAPYGFV 527
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1220 FFHTVLLPTAYETVTAWSGICASDgdrtFGLVVKDVQLTLFRNlDDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFVNAT 1299
Cdd:cd22374    528 FFHTVLLPTQYATVQAYSGICQNG----RALALKDPSLALFRG-TDKYLVTPRNMYQPRTAAQADFVYIESCTVTYLNLT 602
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1300 VIDLPSIIPDYIDINQTVQDILENYrPNWTVPEFTLDIFNATYLNLTGEIDDLEFRSEKLHNTTVELAILIDNINNTLVN 1379
Cdd:cd22374    603 DTTIDAVIPDYVDVNKTVEDILNNL-PNYTKPDLDIGRYNNTILNLTTEINDLNGRAENLSQIVENLEEYIKKINATLVD 681
                          730       740       750
                   ....*....|....*....|....*....|....*...
gi 1983930778 1380 LEWLNRIETYVKWPWYVWLLIGLVVV--FCIPLLLFCC 1415
Cdd:cd22374    682 LEWLNRVETYIKWPWWVWLLIALAITafVCILVTIFLC 719
HCoV-NL63-229E-like_Spike_SD1-2_S1-S2_S2 cd22375
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
680-1391 0e+00

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoproteins from HCoV-NL63, HCoV-229E, and related alphacoronavirus; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from alphacoronaviruses, including human coronaviruses (HCoVs), HCoV-NL63 and HCoV-229E. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411962 [Multi-domain]  Cd Length: 677  Bit Score: 869.60  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  680 DLSVLHLDSCTDYNIYGRTGVGIIRRTNSTLLSGLYYTSLSGDLLGFKNVSDGVIYSVTPCDVSAQAAVIDGAIVGAMTS 759
Cdd:cd22375      1 SFSNVVLNNCTKYNIYDYSGTGVIRSSNDSFIGGITYTSNSGNLLGFKDVSTGTIYSITPCNPPDQVVVYQQAIVGAMLS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  760 INSELLGLTHWTTTPNFYYYSIYNYTSErtrdtaidsndvdcEPVITYSNIGVCKNGALVFI---NVthSDGDVQPISTG 836
Cdd:cd22375     81 ENETRYGLSNVVELPNFYYASNGTYNCT--------------DAVLTYSNFGICADGSIIPVrprNV--SDNGVSAIVTA 144
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  837 NVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMGARLENMEVDSMLFVSENALK 916
Cdd:cd22375    145 NLSIPSNWTTSVQVEYLQITSTPIVVDCSTYVCNGNPRCVELLKQYTSACKTIEDALRLSARLESADVSSMLTFDSNAFT 224
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  917 LASVEAFNSTeNLDSIYkewPSiggswlgglkdiLPSHNSKRKYGSAIEDLLFDKVVTSGLGTVDEDYKRCTGGYDIADL 996
Cdd:cd22375    225 LANVSSFGDY-NLSSVL---PQ------------LPTSGSRIAGRSAIEDLLFSKVVTSGLGTVDADYKSCTKGLSIADL 288
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  997 VCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGALGGgAVAIPFAVAVQARLNYVALQTDVLNKNQQILANAFNQAIG 1076
Cdd:cd22375    289 ACAQYYNGIMVLPGVADAERMAMYTGSLIGGMALGGLTS-AAAIPFSLALQARLNYVALQTDVLQENQKILAASFNKAMT 367
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1077 NITQAFGKVNDAIHQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDELSADAQVDRLIT 1156
Cdd:cd22375    368 NIVDAFTGVNDAITQTSQAIQTVATALNKIQDVVNQQGNALNHLTSQLRQNFQAISSSIQAIYDRLDTIQADQQVDRLIT 447
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1157 GRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFFHTVLLPTAYETVTAW 1236
Cdd:cd22375    448 GRLAALNAFVSQTLTKYTEVRASRQLAQQKVNECVKSQSNRYGFCGNGTHIFSIVNAAPEGLVFLHTVLLPTQYKDVEAW 527
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1237 SGICAsdgDRTFGLVVKDVQLTLFRNlDDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFVNATVIDLPSIIPDYIDINQT 1316
Cdd:cd22375    528 SGLCV---DGVNGYVLRQPNLALYKD-GGVFRITSRVMFEPRIPTMADFVQIENCNVTFVNISRSELQTIVPEYVDVNKT 603
                          650       660       670       680       690       700       710
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1983930778 1317 VQDILENYrPNWTVPEFTLDIFNATYLNLTGEIDDLEFRSEKLHNTTVELAILIDNINNTLVNLEWLNRIETYVK 1391
Cdd:cd22375    604 LQELIEKL-PNYTVPDLDLDQYNQTILNLTSEISTLENKSAELNYTVQKLQTLIDNINSTLVDLKWLNRVETYIK 677
delta-PDCoV-like_Spike_SD1-2_S1-S2_S2 cd22373
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
687-1374 0e+00

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine coronavirus HKU15, avian coronaviruses, and related deltacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine coronavirus PDCoV, and several avian coronaviruses such as quail deltacoronavirus (QdCoV) UAE-HKU30, white-eye coronavirus HKU16, common moorhen coronavirus HKU21, thrush CoV HKU12, and munia CoV HKU13, all from the Buldecovirus subgenus of deltacoronaviruses. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411960 [Multi-domain]  Cd Length: 648  Bit Score: 814.45  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  687 DSCTDYNIYGRTGVGIIRRTNSTLLSGLYYTSLSGDLLGFKNVSDGVIYSVTPCDVSAQAAVIDGAIVGAMTSINSELLG 766
Cdd:cd22373      1 DVCTDYTIYGVSGTGIIKPSDLQLHNGIAFTSPTGELYAFKNITTGKTYQVLPCETPSQLIVINNTIVGAITSSNSTENG 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  767 LTHWTTTPNFYYYSiyNYTSertrdtaidsndVDC-EPVITYSNIGVCKNGALVFINVTH-SDGDVQPISTGNVTIPTNF 844
Cdd:cd22373     81 FTTTIVTPTFYYST--NATS------------FNCtKPVLSYGPISVCSDGAIVGTSTLQdTRPSIVSLYDGEVEIPSAF 146
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  845 TISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMGARLENMEVDSMLFVSENALKLASVEAFN 924
Cdd:cd22373    147 TLSVQTEYLQVQAEQVVVDCPQYVCNGNSRCLQLLAQYTSACSNIESALHSSAQLDSREITNMFQTSTQSLELANITNFK 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  925 STENLDSIykewpsiggswlgglkdiLPSHNSKRkygSAIEDLLFDKVVTSGLGTVDEDYKRCTGGYDIADLVCAQYYNG 1004
Cdd:cd22373    227 GDYNFTSI------------------LTTKIGGR---SAIEDLLFNKVVTNGLGTVDQDYKSCSKDMAIADLVCSQYYNG 285
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1005 IMVLPGVANADKMTMYTASLAGGITLGALGGGAvAIPFAVAVQARLNYVALQTDVLNKNQQILANAFNQAIGNITQAFGK 1084
Cdd:cd22373    286 IMVLPGVVDAEKMAMYTGSLTGAMVFGGLTAAA-AIPFSTAVQARLNYVALQTNVLQENQKILAESFNQAVGNISLALSS 364
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1085 VNDAIHQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDELSADAQVDRLITGRLTALNA 1164
Cdd:cd22373    365 VNDAIQQTSEALNTVANAINKIQTVVNQQGEALSHLTAQLSNNFQAISTSIQDIYNRLDEVEANQQVDRLITGRLAALNA 444
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1165 FVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFFHTVLLPTAYETVTAWSGICAsDG 1244
Cdd:cd22373    445 YVTQLLNQMSQIRQSRLLAQQKINECVKSQSSRYGFCGNGTHLFSITQAAPNGIFFMHAVLVPTKFTRVNASAGICV-DN 523
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1245 DRTFGLvvkDVQLTLFrNLDDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFVNATVIDLPSIIPDYIDINQTVQDILENY 1324
Cdd:cd22373    524 TKGYSL---QPQLILY-QFNNSWRVTPRNMYEPRLPRQADFIPLTDCSVTFYNTTAADLPNIIPDYVDVNQTVSDIIDNL 599
                          650       660       670       680       690
                   ....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1325 rPNWTVPEFTLDIFNATYLNLTGEIDDLEFRSEKLHNTTVELAILIDNIN 1374
Cdd:cd22373    600 -PTPTPPQLDVDIYNNTILNLTQEINDLQERSKNLSQIADRLQQYIDNLN 648
CoV_S2 pfam01601
Coronavirus spike glycoprotein S2; The coronavirus spike glycoprotein forms the characteriztic ...
836-1391 0e+00

Coronavirus spike glycoprotein S2; The coronavirus spike glycoprotein forms the characteriztic '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.


Pssm-ID: 460263  Cd Length: 502  Bit Score: 775.68  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  836 GNVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMGARLENMEVDSMLFVSENAL 915
Cdd:pfam01601    1 GNISIPTNFTISVQTEYIQTTSPKVSVDCAQYVCNGNERCLQLLVQYGSFCSTIEQALQGSARLEDVEVLSMLSISNRAL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  916 KLASVEAFNSTENLDSIykewpsiggswlgglkdiLPSHNSKRkygSAIEDLLFDKVVTSGLGTVDeDYKRCTGGYDIAD 995
Cdd:pfam01601   81 TLATISNFGSDFNFSSF------------------LPCLNSGR---SAIEDLLFDKVVTSGLGTVD-AYKKCTKGTSIAD 138
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  996 LVCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGALGGGAVAIPFAVAVQARLNYVALQTDVLNKNQQILANAFNQAI 1075
Cdd:pfam01601  139 LVCAQYYNGIMVLPGVVDAEKMAMYTASLTGGMAFGGLTGAAAAIPFALAVQARLNYLGLQTDVLQENQKILANAFNNAV 218
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1076 GNITQAFgkvndaihqtsqglATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDELSADAQVDRLI 1155
Cdd:pfam01601  219 GNITDGF--------------TTTASALSKIQDVVNANAQALNQLTQQLSNNFGAISSSIQDIYSRLDQLEADAQVDRLI 284
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1156 TGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFFHTVLLPTAYETVTA 1235
Cdd:pfam01601  285 NGRLAALNAFVTQQLTKASEVKASRQLAQQKVNECVKSQSSRYGFCGNGTHLFSLPQAAPNGIMFLHTVLVPTEYITVKA 364
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1236 WSGICASDgdrTFGLVVKDVQLTLFRNldDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFVNATVIDLPSIIPDYIDINQ 1315
Cdd:pfam01601  365 TPGLCVNG---TTGYAPRDGQFVLNNT--SNWYITPRNMYQPRPITGSDFVQISSCDVNFVNITNTKLPPLIPDYVDFNK 439
                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1983930778 1316 TVQDILENYrpNWTVPEFTLDIFNATYLNLTGEIDDLEfrseklhnttvELAILIDNINNTLVNLEWLNRIETYVK 1391
Cdd:pfam01601  440 ELEDIYKNL--NSTLPDLDLDIFNATILNLTDEIKDLE-----------RLQELIDNLNQTLVDLEWLNRYETYIK 502
CoV_Spike_S1-S2_S2 cd21698
S1/S2 cleavage region and the S2 fusion subunit of coronavirus spike (S) proteins; This model ...
807-1369 0e+00

S1/S2 cleavage region and the S2 fusion subunit of coronavirus spike (S) proteins; This model represents the S1/S2 cleavage region and the S2 subunit of the spike (S) glycoprotein from coronavirus (CoVs), including three highly pathogenic human CoVs, Middle East respiratory syndrome coronavirus (MERS-CoV), Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS coronavirus 2 (SARS-CoV-2), also known as a 2019 novel coronavirus (2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect S1 and S2. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV, and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP), and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. Notably, SARS-CoV-2 has a functional polybasic (furin) cleavage site through the insertion of PRRAR*SV (* indicates the cleavage site) at the S1/S2 interface, which is absent in SARS-CoV and other SARS-related CoVs. The S1/S2 cleavage region and the S2 fusion subunit play an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411955 [Multi-domain]  Cd Length: 523  Bit Score: 668.35  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  807 YSNIGVCKNGALVFINVTH-SDGDVQPISTGNVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSA 885
Cdd:cd21698      1 YGGICICYDGAIYTVSTGQeESPSIVAISTENIAIPSNFTLSVTTEYLQVTMTKVSVDCTTYVCGGSPRCKNLLLQYGSA 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  886 CQTIEQALAMGARLENMEVDSMLFVSENALKLASVEAFNSTeNLDSIykewpsiggswlgglkdiLPSHNSKRKYgSAIE 965
Cdd:cd21698     81 CDTIEQALRGIAVLEDSEVSNMFSTSKQALKLAIIKSFGGF-NFSQI------------------LPTPSRPSGR-SAIE 140
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  966 DLLFDKVVTSGLGTVDeDYKRCTGGYDIADLVCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGALGGgAVAIPFAVA 1045
Cdd:cd21698    141 DLLFTKVVTAGLGTVD-QYKNCTKGIAIADLACAQYYNGIMVLPPVADAEKMAMYTGSLTAGMVFGGITA-AAAIPFSLA 218
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1046 VQARLNYVALQTDVLNKNQQILANAFNQAIGNITQAFGKVNDAihqtsqglatvakaLAKVQDVVNTQGQALSHLTVQLQ 1125
Cdd:cd21698    219 MQARLNYVGLQQNVLLENQKLLANSFNKAIGNISDAFSSTSSA--------------LQKIQDVVNQQAQALNTLTSQLS 284
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1126 NNFQAISSSISDIYNRLDELSADAQVDRLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGT 1205
Cdd:cd21698    285 NNFGAISSSIQDIYQRLDKLEADVQVDRLITGRLAALNAFVTQQLIKAAEVRQSRRLAQQKINECVKSQSSRYGFCGNGT 364
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1206 HLFSLANAAPNGMIFFHTVLLPTAYETVTAWSGICASDgdrTFGLvVKDVQLTLFRNLdDKFYLTPRTMYQPRVATSSDF 1285
Cdd:cd21698    365 HLFSIPQSAPSGIVFLHTVLVPTSYKNVTAYPGICVDG---KAGS-PLEGPLVFIQNN-NHWFVTPRNMYEPRIITTADF 439
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1286 VQIEGCD--VLFVNATVIDLPsIIPDYIDINQTVQDILENYrPNWTVPEFTLDIFNATYLNLTGEIDDLEFRSEKLHNTT 1363
Cdd:cd21698    440 VQITSCDanVTIVNNTVNLDP-VIPDYVDVNEELDDYIQNL-PNHTLPDLDLSGYNATILNISSEIDRLNEVAKNLNQSV 517

                   ....*.
gi 1983930778 1364 VELAIL 1369
Cdd:cd21698    518 VELQEY 523
CoV_S1 pfam01600
Coronavirus spike glycoprotein S1; This family represents the spike glycoprotein (S) of ...
249-673 2.24e-166

Coronavirus spike glycoprotein S1; This family represents the spike glycoprotein (S) of coronaviruses. The spike protein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilize both the S1 NTD and S1 RBD for viral entry. This entry contains spike protein from both alpha and gamma coronaviruses but excludes the spike protein from beta-coronaviruses such as SARS-CoV.


Pssm-ID: 460262  Cd Length: 412  Bit Score: 505.34  E-value: 2.24e-166
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  249 YELCEdyeHCTGYATNVFAPTSGGYIPDGFSFNNWFLLTNSSTFVSGRFVTNQPLLINCLWPVPSFGVAAQEFCFEGA-Q 327
Cdd:pfam01600    1 YSVCT---NCDGFPDNVFAVEEGGYIPPSFSFNNWFYLTNSSTPVDGRVVSNQPLLLNCLWPIPSLNGTTLKVYFNGSiP 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  328 FSQCNGVSL-NNTVDVIRFNLNFTADVQSGMGATVFSLNTTGGVILEISCYSDTVSESSSYSygeIPFGITDGPRYCYVL 406
Cdd:pfam01600   78 NGRCNGYSNkNGTVDAIRFNLNFTASDSVFAGAGSISLNTVGGVTYSFSCSNSSTPVGASHQ---IPFGATDQPYYCFVN 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  407 YNG---TALKYLGTLPPSVKEIAISKWGHFYINGYNFFSTFPIGCISFNLTTGVSGAFWTIAYTSYTEALVQVENTAIKN 483
Cdd:pfam01600  155 YNGnisTTSQFVGILPPVVREIVISRYGDFYVNGYRYFSTPPLESVNFNLTSGDTSDFWTVAFANYTDVLVNINNTSIQR 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  484 VTYCNSHINNIKCSQLTANLNNGFYPVASSEVGFVNKSVVLLPSFFTYTAVNITIDLGMKLSGyGQPIASTLSNITLPMQ 563
Cdd:pfam01600  235 ILYCDSPLNSIKCQQLSFSLPDGFYSTSSVEVVQLPRTFVTLPKFATHSFVNLTVSVSFDGGG-GPPSLSALSEVNLTIN 313
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  564 DNNTDVYCIRSNQFSVYVHSTCKSSlwdnifnqdctdVLEATAVIKTGTCPFSFDKLNNYLTFNKFCLSLSPVGANCKFD 643
Cdd:pfam01600  314 GTNNTSLCVNTSQFTVNLNFTCTST------------AYGYTAEIRTGTCPFSFDKLNNYLSFGSICFSLVPSGGGCTMD 381
                          410       420       430
                   ....*....|....*....|....*....|.
gi 1983930778  644 V-AARTRTNEQVVRSLYVIYEEGDNIVGVPS 673
Cdd:pfam01600  382 IvTKYWNGSFVKVGSLYVSYSEGDNITGVPK 412
gammaCoV_Spike_SD1-2_S1-S2_S2 cd22372
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
683-1383 4.61e-166

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from avian infectious bronchitis coronavirus (IBV) and related gammacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from gammacoronaviruses, including avian infectious bronchitis virus, and Beluga whale coronavirus SW1 (whale-CoV SW1). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411959 [Multi-domain]  Cd Length: 661  Bit Score: 514.15  E-value: 4.61e-166
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  683 VLHLDSCTDYNIYGRTGVGII------RRTNSTLL-SGLYYTSLSGDLLGFKNVSDGVI--YSVTPC-DVSAQAAVIDGA 752
Cdd:cd22372      3 NITLNKCVDYNIYGRVGQGFItnvtdsAADYNYLAdGGLAILDTSGAIDIFVVQGEYGLnyYKVNPCeDVNQQFVVSGGN 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  753 IVGAMTSINSellglTHWTTTPNFYYYSIYNYTseRTRDTAIDSNDVDCePVITYSNIGVCKNGALVFINVTHSDGDVQP 832
Cdd:cd22372     83 LVGILTSRNE-----TGSQLLENQFYIKLTNGT--RRRRRSISENVTSC-PYVSYGKFCIKPDGSISTIVPQELETFVAP 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  833 I--STGNVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMGARLENMEVDSMLfv 910
Cdd:cd22372    155 LlnVTENVLIPNSFNLTVTDEYIQTRMDKVQINCLQYVCGNSLECRKLFQQYGPVCDNILSIVNSVNQKEDMELLSFY-- 232
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  911 senalklasveafnstENLDSIYKEWPSIGGSWLGGL-KDILPSHNSKRKYGSAIEDLLFDKVVTSGLGTVDEdYKRCTG 989
Cdd:cd22372    233 ----------------SSTKPGGFNTPVFNNVSTGGFnISLLLPPPSSPQGRSFIEDLLFTKVETVGLPTDDA-YKKCTA 295
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  990 GY--DIADLVCAQYYNGIMVLPGVANADKMTMYTASLAGGItlgALGG--GAVAIPFAVAVQARLNYVALQTDVLNKNQQ 1065
Cdd:cd22372    296 GPlgFLKDLVCAQEYNGLLVLPPIITAEMQTMYTGSLVASM---AFGGitAAGAIPFATQIQARINHLGITQSLLLKNQE 372
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1066 ILANAFNQAIGNITQAFgkvndaihqtsqglATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDEL 1145
Cdd:cd22372    373 KIAASFNKAIGHMQEGF--------------RSTSLALQQIQDVVNKQSAILTETMASLNKNFGAISSVIQDIYQQLDAI 438
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1146 SADAQVDRLITGRLTALNAFVSqtlTRQAE---VRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFFH 1222
Cdd:cd22372    439 QADAQVDRLITGRLSSLSVLAS---AKQAEyykVSQQRELATQKINECVKSQSNRYGFCGNGRHVLTIPQNAPNGIVFIH 515
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1223 TVLLPTAYETVTAWSGICASDGDRTFGLVVKDVQLTLFRNLDDKFYLTPRTMYQPRVATSSDFVQIEGCDVLF--VNATV 1300
Cdd:cd22372    516 FTYTPESFVNVTAIVGFCVNPANGSQYAIVPANGRGIFIQVNGTYYITARDMYMPRDITAGDIVTLTSCQANYvsVNKTV 595
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1301 IDLPsIIPDYIDINQTVQDILenyrpNWTVPEF-TLDIFNAT--YLNLTGEIDDLEFrseklhnttvelaiLIDNINNTL 1377
Cdd:cd22372    596 ITTF-VDNDDFDFDDELSKWW-----NETKHELpDFDQFNYTipILNISNEIDRIQE--------------VIQGLNDSL 655

                   ....*.
gi 1983930778 1378 VNLEWL 1383
Cdd:cd22372    656 IDLETL 661
betaCoV_Spike_SD1-2_S1-S2_S2 cd22370
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
694-1352 3.15e-134

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses; This family contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses, including three highly pathogenic human coronaviruses (CoVs), Middle East respiratory syndrome coronavirus (MERS-CoV), Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS coronavirus 2 (SARS-CoV-2), also known as a 2019 novel coronavirus (2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411957 [Multi-domain]  Cd Length: 667  Bit Score: 429.59  E-value: 3.15e-134
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  694 IYGRTGVGIIRRTNSTLLS--GLYYTSlSGDLLGFKNVSDGVIYSVTPC---DVSA--------QAAVIDGAIVGAMTSI 760
Cdd:cd22370      1 LYGYTGTGVLTETNATFLPfqNFGYDS-NGNLIAFKDPQTNTIYTILPCvsgPVSVitpgnntnEVAVLYNGLNCSEVPS 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  761 NSELLGLTHW----TTTPNFY-------YYSIYNYTSERTRDTAIDSNDvdCEPVITYSNIGVCKNGA----LVFINVTH 825
Cdd:cd22370     80 AISAVSLTPWwrvySSTSNYFdtpvgclLGAVNSSNNSYECDLPLGAGL--CASYTTQSVLRSRSVASrsirLTTMSFFA 157
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  826 SDGDVQPISTGN--VTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALamgaRLENME 903
Cdd:cd22370    158 ENSVDVEVAYSNfsIQIPTNFTIAVTEEFIPTTMPKVTVDCAQYVCGDSSECSNLLLQYGTFCDNINRAL----TGVALL 233
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  904 VDSMLfvsenalklasVEAFNSTENLDSIYKEWPSIGGSWLGGLKDILPSHNSKRKYgSAIEDLLFDKVVTSGLGTVdED 983
Cdd:cd22370    234 QDKNQ-----------LEVFASVKQIVKTPAPLKDFGGFNFSSLLPCLGSNGGSSAR-SAIEDLLFNKVTLADVGFM-KQ 300
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  984 YKRCTGGYDIADLVCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGALGGG---AVAIPFAVAVQARLNYVALQTDVL 1060
Cdd:cd22370    301 YDDCTGGSAARDLICAQSFNGLKVLPPLLTDEMIAAYTSALLGGTATSGWTFGassAAQIPFAMQMAYRFNGIGVTQQVL 380
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1061 NKNQQILANAFNQAIGNItqafgkvndaihqtSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYN 1140
Cdd:cd22370    381 VENQKLIANKFNQALGSI--------------QTGFTATNSALAKLQDVVNQNAQALNTLVKQLSNNFGAISSSLNDILS 446
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1141 RLDELSADAQVDRLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIF 1220
Cdd:cd22370    447 RLDKLEADVQIDRLINGRLQVLQTYVTQQLIRASEIRASAQLAAQKMSECVKGQSKRVDFCGNGTHLMSFPQSAPNGVVF 526
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1221 FHTVLLPTAYETVTAWSGICaSDGDRTF---GLVVKDvqltlfrnlDDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFVN 1297
Cdd:cd22370    527 LHVTYKPTSYKNVTTAPAIC-HNGKAYFpkeGVFVKN---------NNSWMFTGRNFYEPEIITTDNTFYSGSCDVNFTY 596
                          650       660       670       680       690
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1983930778 1298 ATVIDLPSIIPDYIDINQTVQDILENY-RPNWTVPEftLDIFNATYLNLTGEIDDL 1352
Cdd:cd22370    597 VNNTVYNPLQPELDDFKAELDKFFKNHtSPDPNLGD--LSGINASFVDLQKEMDTL 650
MERS-CoV-like_Spike_SD1-2_S1-S2_S2 cd22379
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
694-1366 2.76e-104

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Middle East respiratory syndrome coronavirus and related betacoronaviruses in the C lineage; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the merbecovirus subgenus (C lineage), including Middle East respiratory syndrome coronavirus (MERS-CoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411966 [Multi-domain]  Cd Length: 682  Bit Score: 347.94  E-value: 2.76e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  694 IYGRTGVGIIRRTNSTLLSG--LYYTSLsGDLLGFKNvSDGVIYSVTPCdVSAQAAVI-DGAivgamTSINSELLG---L 767
Cdd:cd22379      1 LYGVTGRGVFQNCTAVGIRQqrFVYDSF-DNLVGYHS-DDGNYYCVRPC-VSVPVSVIyDKS-----TNTHATLFGsvaC 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  768 THWTTTPNfyYYSIYNYTSERTRDTA-------------IDSNDV--DCE-----------PVITYSNIGVCKNGALVFI 821
Cdd:cd22379     73 EHISTMMS--QFSRSTQSMLRRRSTNgplqtavgcviglVNTSLTveDCKlplgqslcavpPTLTPRSVSSVPGEQLASI 150
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  822 NVTHSDgDVQPI-STG-NVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALaMGARL 899
Cdd:cd22379    151 NFNHPL-QVDQLnSSGfKVSIPTNFSFGVTQEYIQTTIQKVTVDCKQYVCNGFEKCEQLLREYGQFCSKINQAL-HGANL 228
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  900 ENMEVDSMLFVSENALKLASVEA-FNSTENLDSIykEWPSIGGSwlgglkdilpshnsKRKYGSAIEDLLFDKVVTSGLG 978
Cdd:cd22379    229 RQDDSVRNLFASIKTSQSQPLIAgLGGDFNLTLL--EPPSISTG--------------SRSYRSAIEDLLFDKVTIADPG 292
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  979 TVdEDYKRCT--GGYDIADLVCAQYYNGIMVLPGVANADKMTMYTASLAGGITLGALGGG---AVAIPFAVAVQARLNYV 1053
Cdd:cd22379    293 YM-QGYDECMkqGPPSARDLICAQYVAGYKVLPPLYDVNMEAAYTSSLLGSIAGAGWTAGlssFAAIPFAQSIFYRLNGV 371
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1054 ALQTDVLNKNQQILANAFNQAIGNItqafgkvndaihQTsqGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISS 1133
Cdd:cd22379    372 GITQQVLSENQKLIANKFNQALGAM------------QT--GFTTTNLAFQKVQDAVNANAQALSKLASELSNTFGAISS 437
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1134 SISDIYNRLDELSADAQVDRLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANA 1213
Cdd:cd22379    438 SIGDILKRLDVLEQEAQIDRLINGRLTSLNAFVAQQLVRSETAARSAQLAKDKVNECVKSQSKRNGFCGQGTHIVSFVIN 517
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1214 APNGMIFFHTVLLPTAYETVTAWSGICASDGDRTF-----GLVVKDVQLTlfrnLDDKFYLTPRTMYQPRVATSSDFVQI 1288
Cdd:cd22379    518 APNGLYFFHVGYVPTNHVNVTAAYGLCDSANPTNCiapvnGYFIKNNTTR----IVDEWSYTGSSFYAPEPITSANTRYV 593
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1289 EGcDVLFVNATVIDLPSIIPDYIDInqTVQDILENYRPNWT--VPEF-TLDIFNATYLNLTGEIDDLEFRSEKLHNTTVE 1365
Cdd:cd22379    594 SP-DVTFQNLSNNLPPPLLSNSTDI--DFKDELEEFFKNVSsqIPNFgSISQINTTLLDLSDEMLSLQQVVKALNESYID 670

                   .
gi 1983930778 1366 L 1366
Cdd:cd22379    671 L 671
bat-HKU9-CoV-like_Spike_SD1-2_S1-S2_S2 cd22381
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
694-1415 3.50e-102

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Rousettus bat coronavirus HKU9 and related betacoronaviruses in the D lineage; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the nobecovirus subgenus (D lineage), including Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411968 [Multi-domain]  Cd Length: 731  Bit Score: 343.66  E-value: 3.50e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  694 IYGRTGVGIIRRTNSTLLSG-LYYTSLSGDLLGFKnvSDGVIYSVTPCdVSAQAAVidgaivGAMTSINSELL--GL--- 767
Cdd:cd22381      1 LYGYTGTGVLSTSNLTIPDSkVFSASSTGDIIAVS--VNGTVYSISPC-VSVPISV------GYDPGFERALLfnGLscs 71
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  768 -----------THWTT-----------TPNFYYYSIYNYTSERTRDTAIDSNDVDC-EPVITYSNIGVCKNG-ALVFINV 823
Cdd:cd22381     72 eraravsepasDYWRAsvsdganntfdTPSGCVYNVINRTTITVNQCSMPLGNSLClVNNTTAVSARGSLSLlSLVTYDP 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  824 ThSDGDVQPIS-TGNVTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALA-MGARLEN 901
Cdd:cd22381    152 L-YDSSVTPLTpVYWVSIPTNFTLAATTEYIQTTAPKINIDCAKYLCGDSSRCLTVLLQYGTFCDDVNKALArVSTILDA 230
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  902 MEVDSMLFVSENALKLASVeAFNSTENLDsiykewpsiggswlgGLKDILPSHNSKRKYGSAIEDLLFDKVVTSGLGTVD 981
Cdd:cd22381    231 SLVSLVSELTSDVVRSENL-AFDGDYNFT---------------GLMGCLGSNCNSKSYRSALSDLLYNKVKVADPGFMQ 294
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  982 EdYKRCTG---GYDIADLVCAQYYNGIMVLPGVANADKMTMYTASLAGGI-----TLGALGGGAvaIPFAVAVQARLNYV 1053
Cdd:cd22381    295 S-YQKCIDsqwGGNIRDLICTQTFNGISVLPPIVSPGMQALYTSLLVGAVassgyTFGITSVGV--IPFATQLQFRLNGL 371
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1054 ALQTDVLNKNQQILANAFNQAIGNITQAFGKVNdaihqtsqglatvaKALAKVQDVVNTQGQALSHLTVQLQNNFQAISS 1133
Cdd:cd22381    372 GVTTQVLVENQKLIANSFNKALVSIQKGFDATN--------------QALSKMQTVINQHAQQLQTLVQQLGNSFGAISS 437
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1134 SISDIYNRLDELSADAQVDRLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANA 1213
Cdd:cd22381    438 SINEIFSRLDGLEANAEVDRLINGRMVVLNTYVTQLLIQASEVRAQAALAKQKISECVKAQSLRNDFCGNGTHVLSIPQL 517
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1214 APNGMIFFHTVLLPTAYETVTAWSGICASDGdrtfGLVVKDvQLTLFRNLDDKFYLTPRTMYQPRVATSSDFVQIEGCDV 1293
Cdd:cd22381    518 APNGVLFIHYSYQPTAYALVQTAAGLCFNGT----GYAPRG-GLFVLPNNSNLWHFTKMNFYNPVNISYSNTQVLTSCSV 592
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1294 LF--VNATVIDlPSIIPDYidinqTVQDILENYRPNwtvpeftldifNATYLNLTGEIDDLEFRSEKLHNTTVELAILID 1371
Cdd:cd22381    593 NYttVNYTVLN-PSEPSDF-----NFQEEFDKWYKN-----------QSSQFNNTFNPSDFNFSTVDVNEQLATLTDVVK 655
                          730       740       750       760       770
                   ....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1372 NINNTLVNLEWLNRIETYVKWPWYVWL-----LIGLVV-VFCIPLLLFCC 1415
Cdd:cd22381    656 QLNESFIDLKKLNVYEQTIKWPWYVWLamiagLVGLALaVVMLLCMTNCC 705
alphaCoV-HKU2-like_Spike_SD1-2_S1-S2_S2 cd22371
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the CoV ...
694-1418 1.13e-99

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the CoV spike (S) glycoprotein from Rhinolophus bat coronavirus HKU2 and related alphacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Wencheng shrew coronavirus (WESV), Lucheng Rn rat coronavirus (LRNV), and two bat viruses (Rhinolophus bat coronavirus HKU2 and BtRf-AlphaCoV/YN2012). Members of this group form a distinct cluster that is separated from the other alphacoronaviruses. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411958 [Multi-domain]  Cd Length: 686  Bit Score: 335.22  E-value: 1.13e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  694 IYGRTGVGIIRRTNSTLLSglYYTSL-SGDLLGFKNVsDGVIYSVTPCdVSAQAAVIDGAIVGAMTSINSELLGLTHWTT 772
Cdd:cd22371      1 IDGVTFQGILYETNFTFDS--FYNLLyKGSMVKYVRI-LGVVYEVEPC-NEFSYSVLKNNSSSYGTLYSGADCNQIDTKT 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  773 tpnfyyySIYNYTSERTRDTAI---------DSNDVDCEPVITYSNIGVCKNGALV---FINVTHSDGDVQPISTG-NVT 839
Cdd:cd22371     77 -------FRFKARSHTGTNTSLgclfnasytNDTYTTCLNPLGNGFCADVNVTSPVvgnIGIQKHDTDYVRPILTEqFIE 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  840 IPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMGARLENMEVDSML--FVSENALKL 917
Cdd:cd22371    150 LPLDHQLVVKEQFLQTSMPKFDVDCERYICDVSKACRELLFKYGGFCSKITADIKGSSILLDSQILGLYktIAVDFSSPD 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  918 ASVEAFNSTEnldsiykewpsiggswlgglkdILPSHNSKrkygSAIEDLLFDKVVTSGLGTVDeDYKRCTGGyDIADLV 997
Cdd:cd22371    230 VDFGDFNFSM----------------------FMSEKNGR----SFIEDLLFDKIVTTGPGFYQ-DYYDCKKM-NLQDLT 281
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  998 CAQYYNGIMVLPGVANADKMTMYTASLAGGITLGALGGGAVAIPFAVAVQARLNYVALQTDVLNKNQQILANAFNQaign 1077
Cdd:cd22371    282 CAQYYNGIMVIPPIMDDETIGMYGGIVAASMTAGLFGGQAGMVTWNTAMAGRLNALGVTQDALVEDVNKLANGFNN---- 357
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1078 ITQafgkvndaihQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDELSADAQVDRLITG 1157
Cdd:cd22371    358 LTQ----------SVSKLAKTTSQALSAIQAVVNQNAAQVEQLVQGLSENFGAISNNFEVIAERLEKLEADQQMDRLING 427
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1158 RLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFFHTVLLPTAYETVTAWS 1237
Cdd:cd22371    428 RMNVLQNFVTNYKLKISELKSTQRLVQSLINECVYAQSLRNGFCGDGLHVMSLMQNAPDGIMFFHYTLKPNNTIIVKTTP 507
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1238 GICASDGDRTFGLVVKDVQLTLFRnlDDKFYLTPRTMYQPRVATSSDFVQIE-GCDVLFVNATV--IDLPSIIP---DYI 1311
Cdd:cd22371    508 GLCLSNEVCIKPIDAKFGVLVSAN--DSYWHFTPRNIYNPENITNSNIIAVSgGANYTTVNNTIdiIEPPQNPPideEFR 585
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1312 DINQTVQDILENYRpNWTvpeftldiFNATYLNLTGEIDDLEfrseklhnttvELAiliDNINNTLVNLEWLNRIETYVK 1391
Cdd:cd22371    586 ELYKNVTLELEQLK-NIT--------FDMSKLNLTYEIDRLN-----------EIA---ENVSKLHVTVSEFNKYVQYVK 642
                          730       740
                   ....*....|....*....|....*..
gi 1983930778 1392 WPWYVWLLIGLVVVFCIPLLLFCCFST 1418
Cdd:cd22371    643 WPWYVWLAIFLVLILFSFLMLWCCCAT 669
HKU1-CoV-like_Spike_SD1-2_S1-S2_S2 cd22380
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
840-1366 2.63e-95

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from human HKU1 and OC43 coronaviruses and related betacoronaviruses in the A lineage; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the embecovirus subgenus (A lineage), including highly pathogenic human coronaviruses (CoVs), HKU1 and OC43 CoVs, as well as murine hepatitis virus (MHV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of MHV is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411967 [Multi-domain]  Cd Length: 663  Bit Score: 322.11  E-value: 2.63e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  840 IPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAmgarlenmEVDSMLFVSENALKLAS 919
Cdd:cd22380    167 IPTNFTIGNHEEFIQTSSPKVTIDCAAFVCGDYAACRQQLVEYGSFCDNINAILN--------EVNELLDTTQLQVANSL 238
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  920 VEAFNSTENL-DSIYKEWPSIGGSWLGGlkdILPSHNSKRKYGSAIEDLLFDKVVTSGLGTVdEDYKRCTGGYDIADLVC 998
Cdd:cd22380    239 MQGVTLSSRLkDGINFNVDDINFSPVLG---CLGSDCNAASSRSAIEDLLFDKVKLSDVGFV-EAYNNCTGGAEIRDLLC 314
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  999 AQYYNGIMVLPGVANADKMTMYTASlAGGITLGALGGGAVAIPFAVAVQARLNYVALQTDVLNKNQQILANAFNQAIGNI 1078
Cdd:cd22380    315 VQSFNGIKVLPPVLSENQISGYTTA-ATAASLFPPWSAAAGVPFSLNVQYRINGLGVTMDVLSQNQKLIANAFNNALGAI 393
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1079 TQAFGKVNdaihqtsqglatvaKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDELSADAQVDRLITGR 1158
Cdd:cd22380    394 QEGFDATN--------------SALAKIQSVVNANAEALNNLLQQLSNRFGAISASLQEILSRLDALEAQAQIDRLINGR 459
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1159 LTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFFHTVLLPTAYETVTAWSG 1238
Cdd:cd22380    460 LTALNAYVSQQLSDSTLVKFSAAQAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLYFIHFSYVPTSFVTAKVSPG 539
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1239 ICASdGDRtfGLVVKDvqlTLFRNLDDKFYLTPRTMYQPRVATSSDFVQIEGCDVLFVNATVIDLPSIIPDYIDINQTVQ 1318
Cdd:cd22380    540 LCIA-GDR--GIAPKS---GYFVNVNNEWMFTGSGYYYPEPITDKNVVVMSSCAVNYTKAPDVMLNTSIPNLPDFKEELD 613
                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*....
gi 1983930778 1319 DILENYRPnwTVPEFTLDIF-NATYLNLTGEIDDLEFRSEKLHNTTVEL 1366
Cdd:cd22380    614 QWFKNQTS--VAPDLSLDEYiNVTFLDLQDEMNRIQEAIKVLNESYINL 660
SARS-CoV-like_Spike_SD1-2_S1-S2_S2 cd22378
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ...
696-1387 6.28e-93

SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from SARS-CoV-2 (COVID-19) and related betacoronaviruses in the B lineage; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic human CoVs such as Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS-CoV-2 (also known as a 2019 novel coronavirus or 2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. Notably, SARS-CoV-2 has a functional polybasic (furin) cleavage site through the insertion of PRRAR*SV (* indicates the cleavage site) at the S1/S2 interface, which is absent in SARS-CoV and other SARS-related coronaviruses. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.


Pssm-ID: 411965 [Multi-domain]  Cd Length: 662  Bit Score: 315.40  E-value: 6.28e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  696 GRTGVGIIRRTNSTLLSglyYTSLSGDLLGFknvSDGV-------IYSVTPCDVSAQAAVIDGAIVGAMTSINSELLGLT 768
Cdd:cd22378      3 GLTGTGVLTPSSKRFQP---FQQFGRDVSDF---TDSVrdpktleILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCT 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  769 HWTT-------TPNFYYYSIYNYTSERTRDTAI----DSNDVDCEPVI------TYSNIGVCK-NGALVFINVTHSDGDV 830
Cdd:cd22378     77 DVPTaihadqlTPAWRVYSTGSNVFQTQAGCLIgaehVNTSYECDIPIgagicaSYHTVSLLRsTSQKSIVAYTMSLGAE 156
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  831 QPISTGN--VTIPTNFTISVQVEYMQVYTTPVSIDCARYVCNGNPRCNKLLTQYVSACQTIEQALAMGArlenMEVDSml 908
Cdd:cd22378    157 NSIAYSNnsIAIPTNFSISVTTEVMPVSMAKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALSGIA----VEQDK-- 230
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  909 fvsenalklASVEAFNSTEnldSIYKEwPSIggSWLGGLK--DILPShNSKRKYGSAIEDLLFDKVVTSGLGTVDEdYKR 986
Cdd:cd22378    231 ---------NTQEVFAQVK---QMYKT-PTI--KDFGGFNfsQILPD-PSKPTKRSFIEDLLFNKVTLADAGFMKQ-YGD 293
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778  987 CTGGYDIADLVCAQYYNGIMVLPGVANADKMTMYTASL-----AGGITLGAlgGGAVAIPFAVAVQARLNYVALQTDVLN 1061
Cdd:cd22378    294 CLGDINARDLICAQKFNGLTVLPPLLTDEMIAAYTAALvsgtaTAGWTFGA--GAALQIPFAMQMAYRFNGIGVTQNVLY 371
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1062 KNQQILANAFNQAIGNITQAfgkvndaihqtsqgLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNR 1141
Cdd:cd22378    372 ENQKQIANQFNKAISQIQES--------------LTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSR 437
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1142 LDELSADAQVDRLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFF 1221
Cdd:cd22378    438 LDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFL 517
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1222 HTVLLPTAYETVTAWSGICaSDGDRTF---GLVVKDvqltlfrnlDDKFYLTPRTMYQPRVATSSDFVQIEGCDVL--FV 1296
Cdd:cd22378    518 HVTYVPSQERNFTTAPAIC-HEGKAYFpreGVFVSN---------GTSWFITQRNFYSPQIITTDNTFVSGNCDVVigII 587
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1297 NATVIDlpSIIPDYidinQTVQDILENYRPNWTVPEFTL-DI--FNATYLNLTGEIDDLEfrseklhnttvELAiliDNI 1373
Cdd:cd22378    588 NNTVYD--PLQPEL----DSFKEELDKYFKNHTSPDVDLgDIsgINASVVNIQKEIDRLN-----------EVA---KNL 647
                          730
                   ....*....|....
gi 1983930778 1374 NNTLVNLEWLNRIE 1387
Cdd:cd22378    648 NESLIDLQELGKYE 661
CoV_S1_C pfam19209
Coronavirus spike glycoprotein S1, C-terminal; This entry represents a domain found at the ...
687-743 2.84e-22

Coronavirus spike glycoprotein S1, C-terminal; This entry represents a domain found at the C-terminus of the Coronavirus S1 protein. It is found across a range of alpha, beta and gamma coronaviruses. This small all beta stranded domain is known as subdomain 2 in the structure of the porcine epidemic diarrhea virus spike protein.


Pssm-ID: 437047 [Multi-domain]  Cd Length: 57  Bit Score: 91.14  E-value: 2.84e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1983930778  687 DSCTDYNIYGRTGVGIIRRTNSTLLSGLYYTSLSGDLLGFKNVSDGVIYSVTPCDVS 743
Cdd:pfam19209    1 NVCTDYTIYGITGTGVIRETNSTIPSGLYYTSSSGDLLGFKNSTTGTVYSVTPCVSS 57
PHA03332 PHA03332
membrane glycoprotein; Provisional
1011-1196 1.34e-03

membrane glycoprotein; Provisional


Pssm-ID: 223047 [Multi-domain]  Cd Length: 1328  Bit Score: 43.42  E-value: 1.34e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1011 VANADKMT---MYTASLAGGI-TLGALGGGAVAIPFAVAVQARLNYvALQTDVLNKNQQILAnafnqaigniTQAFGKVN 1086
Cdd:PHA03332   829 VLDLWHETvkmFAPRRFGGSVmAGDAIGLSAAAFTMASAALNAATQ-ALAVATLYVNQLLQA----------TAATAEMA 897
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1087 DAIHQTSqglatvaKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDE--LSADAQVDRLITGrLTALNA 1164
Cdd:PHA03332   898 SKIGGLN-------ARVDKTSDVITKLGDTIAKISATLDNNIRAVNGRVSDLEDQVNLrfLAVATNFNTLATQ-LKELGT 969
                          170       180       190
                   ....*....|....*....|....*....|..
gi 1983930778 1165 FVSQTLTRQAEVRASRQLAKDKVNECVRSQSQ 1196
Cdd:PHA03332   970 TTNERIEEVMAAALYYQQLNSLTNQVTQSASK 1001
PRK10920 PRK10920
putative uroporphyrinogen III C-methyltransferase; Provisional
1031-1134 2.73e-03

putative uroporphyrinogen III C-methyltransferase; Provisional


Pssm-ID: 236795  Cd Length: 390  Bit Score: 42.01  E-value: 2.73e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1031 GALGGGAVAIPFAVAVQARLNYVAlqtdvlnKNQQILANAFNQAIGNITQAFGKVNDaihQTSQGLATVAKALAKVQDVV 1110
Cdd:PRK10920    35 TGLVLSAVAIAIALAAGAGLYYHG-------KQQAQNQTATNDALANQLTALQKAQE---SQKQELEGILKQQAKALDQA 104
                           90       100
                   ....*....|....*....|....
gi 1983930778 1111 NTQGQALSHLTVQLQNNFQAISSS 1134
Cdd:PRK10920   105 NRQQAALAKQLDELQQKVATISGS 128
Tar COG0840
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
1067-1189 2.84e-03

Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];


Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 41.93  E-value: 2.84e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983930778 1067 LANAFNQAIGNITQAFGKVNDAIHQTSQGLATVAKALAKVQDVVNTQGQALSHLTVQLQNnfqaISSSISDIYNRLDELS 1146
Cdd:COG0840    240 LADAFNRMIENLRELVGQVRESAEQVASASEELAASAEELAAGAEEQAASLEETAAAMEE----LSATVQEVAENAQQAA 315
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1983930778 1147 ADAQ--VDRLITGRLTalnafVSQTLTRQAEVRASRQLAKDKVNE 1189
Cdd:COG0840    316 ELAEeaSELAEEGGEV-----VEEAVEGIEEIRESVEETAETIEE 355
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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