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Conserved domains on  [gi|6651485|gb|AAF22333|]
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envelope glycoprotein [Human immunodeficiency virus 1]

Protein Classification

envelope glycoprotein( domain architecture ID 343)

envelope glycoprotein similar to Human immunodeficiency virus envelope glycoprotein gp160, also called surface protein gp120, that attaches the virus to the host lymphoid cell by binding to the primary receptor CD4

Gene Ontology:  GO:0019031|GO:0019062
PubMed:  23389465|30935048

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
GP120 super family cl02884
Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with Swiss: ...
 30-493 0e+00

Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with Swiss:P01730 and a chemokine receptor on the cell surface.


The actual alignment was detected with superfamily member pfam00516:

Pssm-ID: 278917  Cd Length: 525  Bit Score: 724.26  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485     30 LWVTVYYGVPVWKEATTTLFCASDAKAYSKEVHNVWATYACVPTDPSPQEIPLENVTENFNMGKNNMVEQMHEDIISLWD 109
Cdd:pfam00516   1 LWVTVFYGIPAWKEASIPLFCASDAKAYDTENHDTWATHACLPDDDDPQEIILVNVTEAFDAWKNDMTEQAHEDIIHLFD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    110 QSLKPCVKLTPLCVTLNCTEVKTNDTSTNAS--------------------------------GIEMMKNCSFNITTDLR 157
Cdd:pfam00516  81 QSIKPCVKLTPLCVALKCSDLKGDTNTPNPRtsssttsrpnssaariimekgncienntcaglGYEEIKNCEFNIKTGIE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    158 DKVKKEHALFYKLDVVQIDND----SYRLISCNTSVVTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGP-CTNVS 232
Cdd:pfam00516 161 GDKKKEYADFWKLDDIPCDNDtagtCYKLRHCNTSIIKEACDKHSFDAIPFHYCAPAGFAILKCNDKNFNGFEPkCTKVS 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    233 TVQCTHGIKPVVSTQLLLNGSLAEEEVVI----RSVNFTDNTKTIIVQLKEP--VEINCTRPNNNTRKGIHI--GPGRAF 304
Cdd:pfam00516 241 AAQCTHGIEPQTSTQFGFNGSLAEEETVIywhgRSVNFTDNAKTIIVQLNKYynLEINCKRPGNKTRKPIRImrGPGRAF 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    305 YATGDIIG-DIRQAYCNISRTKWNNTLEQIVSKLRKQFR------NKTIVFN-QSSGGDPEIVMHSFNCGGEFFYCNTTK 376
Cdd:pfam00516 321 VFHGKIGNmRPRQAHCNFGRAKWNEALKEIAQKLREHPRykgfgdNGKIIFTkPGAGGDPEIAFHSFNCGGEFFYCNMTQ 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    377 LFNSTWNN----TEESNNTKG-DIVTLPCRIKQIINMWQEVGKAMYAPPIAGQIRCSSNITGLLLTRDGGNQNNVTEI-F 450
Cdd:pfam00516 401 FFNSTWFNstwsTEDKNNTEGnDTITLPCHIKQIINMWHKVGKAMYAPPIEGEIACESNITGIIANIDGDKNNNESEItF 480

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*
gi 6651485    451 RPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKR--RVVQREKR 493
Cdd:pfam00516 481 RPGGADMADLWRLELGDYKLIEIEPIGFAPTDAKRysRTPQREKR 525
Ebola_HIV-1-like_HR1-HR2 super family cl02885
heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of various ...
 512-708 3.84e-50

heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus and human immunodeficiency virus type 1 (HIV-1); This domain superfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus gp2, Rous sarcoma virus gp37, human immunodeficiency virus type 1 (HIV-1) gp41, and the envelope proteins of various ERVs. In the HR1-HR2 region of Ebola virus and RSV, the linker region between the two repeats includes a CKS17-like immunosuppressive region and a CX6C motif that forms an intra-subunit disulfide bond; MMTV, HIV-1, HERV-K endogenous retroviruses and related sequences lack a canonical CSK17-like sequence, and CX6C motif. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as Jaagsiekte sheep retrovirus (JSRV), feline leukemia virus (FeLV), and avian leukemia virus (ALV). Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Human ERVs (HERVs) belonging to this superfamily include Syncytin-1 (HERV-W_c7q21.2/ ERVWE1), and Syncytin-2 (HERV-FRD_6p24.1) which are expressed in the placenta, and are fusogenic, although they have a different cell specificity for fusion. Syncytin-2, but not Syncytin-1, is immunosuppressive; its immunosuppressive domain may protect the fetus from the mother's immune system. Syncytin-1 may participate in the formation of the placental trophoblast; it is also implicated in cell fusions between cancer and host cells and between cancer cell, and in human osteclast fusion. This superfamily also contains human HERV-R_c7q21.2 (ERV-3), which is also expressed in the placenta, but is not fusogenic, and has an immunosuppressive domain, but lacks a fusion peptide. It is unclear whether ERV-3 has a critical biological role. Included in this superfamily are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep; for example, enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development.


The actual alignment was detected with superfamily member pfam00517:

Pssm-ID: 413513  Cd Length: 197  Bit Score: 174.79  E-value: 3.84e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    512 MGAASITLTVQARQLLSGIvqqQNNLLRAIEAQQHLlqltvwgIKQLQARVLAVERY----------LKDQQLLGIWGcS 581
Cdd:pfam00517   1 MAAVSLTLSIQAATLVDGL---QYNVTKVMGTQQDI-------DKKLEARLSALEDVvrvlgeqvqsLKFRMKLQCHA-N 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    582 GKLICTTAVPWNTS----WSNKSLDKIWNNMtwmewerEINNYTGLIYNLIEESQNQQEKNEQELLALDKWA-SLWNWFD 656
Cdd:pfam00517  70 YKWICVTKVPYNASdpwdKVKKHLQGIWNNT-------EVSYDLLQLHNLIEDIQNQQEKTLNELDTLDNWAqSLFNWFP 142

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6651485    657 I--SKWLWYikifimIVGGLVGLRIIFAVLSIVNRVRQGYSPLSFQTR-------LPTQRG 708
Cdd:pfam00517 143 SlnSLWRSY------IIAGGVGLRIVLIVLCLAPCLFRSIVKELLQMHvlihknmLQKQKG 197
 
Name Accession Description Interval E-value
GP120 pfam00516
Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with Swiss: ...
 30-493 0e+00

Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with Swiss:P01730 and a chemokine receptor on the cell surface.


Pssm-ID: 278917  Cd Length: 525  Bit Score: 724.26  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485     30 LWVTVYYGVPVWKEATTTLFCASDAKAYSKEVHNVWATYACVPTDPSPQEIPLENVTENFNMGKNNMVEQMHEDIISLWD 109
Cdd:pfam00516   1 LWVTVFYGIPAWKEASIPLFCASDAKAYDTENHDTWATHACLPDDDDPQEIILVNVTEAFDAWKNDMTEQAHEDIIHLFD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    110 QSLKPCVKLTPLCVTLNCTEVKTNDTSTNAS--------------------------------GIEMMKNCSFNITTDLR 157
Cdd:pfam00516  81 QSIKPCVKLTPLCVALKCSDLKGDTNTPNPRtsssttsrpnssaariimekgncienntcaglGYEEIKNCEFNIKTGIE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    158 DKVKKEHALFYKLDVVQIDND----SYRLISCNTSVVTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGP-CTNVS 232
Cdd:pfam00516 161 GDKKKEYADFWKLDDIPCDNDtagtCYKLRHCNTSIIKEACDKHSFDAIPFHYCAPAGFAILKCNDKNFNGFEPkCTKVS 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    233 TVQCTHGIKPVVSTQLLLNGSLAEEEVVI----RSVNFTDNTKTIIVQLKEP--VEINCTRPNNNTRKGIHI--GPGRAF 304
Cdd:pfam00516 241 AAQCTHGIEPQTSTQFGFNGSLAEEETVIywhgRSVNFTDNAKTIIVQLNKYynLEINCKRPGNKTRKPIRImrGPGRAF 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    305 YATGDIIG-DIRQAYCNISRTKWNNTLEQIVSKLRKQFR------NKTIVFN-QSSGGDPEIVMHSFNCGGEFFYCNTTK 376
Cdd:pfam00516 321 VFHGKIGNmRPRQAHCNFGRAKWNEALKEIAQKLREHPRykgfgdNGKIIFTkPGAGGDPEIAFHSFNCGGEFFYCNMTQ 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    377 LFNSTWNN----TEESNNTKG-DIVTLPCRIKQIINMWQEVGKAMYAPPIAGQIRCSSNITGLLLTRDGGNQNNVTEI-F 450
Cdd:pfam00516 401 FFNSTWFNstwsTEDKNNTEGnDTITLPCHIKQIINMWHKVGKAMYAPPIEGEIACESNITGIIANIDGDKNNNESEItF 480

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*
gi 6651485    451 RPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKR--RVVQREKR 493
Cdd:pfam00516 481 RPGGADMADLWRLELGDYKLIEIEPIGFAPTDAKRysRTPQREKR 525
GP41 pfam00517
Retroviral envelope protein; This family includes envelope protein from a variety of ...
 512-708 3.84e-50

Retroviral envelope protein; This family includes envelope protein from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from human and simian immunodeficiency viruses (HIV and SIV) which mediate membrane fusion during viral entry. The family also includes bovine immunodeficiency virus, feline immunodeficiency virus and Equine infectious anaemia (EIAV). The family also includes the Gp36 protein from mouse mammary tumour virus (MMTV) and human endogenous retroviruses (HERVs).


Pssm-ID: 395415  Cd Length: 197  Bit Score: 174.79  E-value: 3.84e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    512 MGAASITLTVQARQLLSGIvqqQNNLLRAIEAQQHLlqltvwgIKQLQARVLAVERY----------LKDQQLLGIWGcS 581
Cdd:pfam00517   1 MAAVSLTLSIQAATLVDGL---QYNVTKVMGTQQDI-------DKKLEARLSALEDVvrvlgeqvqsLKFRMKLQCHA-N 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    582 GKLICTTAVPWNTS----WSNKSLDKIWNNMtwmewerEINNYTGLIYNLIEESQNQQEKNEQELLALDKWA-SLWNWFD 656
Cdd:pfam00517  70 YKWICVTKVPYNASdpwdKVKKHLQGIWNNT-------EVSYDLLQLHNLIEDIQNQQEKTLNELDTLDNWAqSLFNWFP 142

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6651485    657 I--SKWLWYikifimIVGGLVGLRIIFAVLSIVNRVRQGYSPLSFQTR-------LPTQRG 708
Cdd:pfam00517 143 SlnSLWRSY------IIAGGVGLRIVLIVLCLAPCLFRSIVKELLQMHvlihknmLQKQKG 197
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 521-647 9.78e-48

heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human immunodeficiency virus (HIV-1), and related domains; This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including human, simian, and feline immunodeficiency viruses (HIV, SIV, and FIV), bovine immunodeficiency-like virus (BIV), equine infectious anaemia virus (EIAV), and Jaagsiekte sheep retrovirus (JSRV), mouse mammary tumour virus (MMTV) and various ERVs including sheep enJSRV-26, and human ERVs (HERVs): HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs to a larger superfamily containing the HR1-HR2 domain of ERVs and infectious retroviruses, including Ebola virus, and Rous sarcoma virus. Proteins in this family lack the canonical CSK17-like immunosuppressive sequence, and the intrasubunit disulfide bond-forming CX6C motif found in linker region between HR1 and HR2 in the Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as JSRV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Included in this subgroup are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep, for example enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development. HERV-K_c12q14.1 is potentially a complete envelope protein; however, it does not appear to be fusogenic.


Pssm-ID: 197369  Cd Length: 128  Bit Score: 165.65  E-value: 9.78e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485  521 VQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKL-ICTTAVPWNTSWSNK 599
Cdd:cd09909   1 VQARQLLVTRVQQQQSLIDAIEKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNLWGCVTKQpYCHTDVPWNRSWNHL 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 6651485  600 SLDKIWNNMTWMEWEREINNYTGLIYNLIEESQNQQEKNEQELLALDK 647
Cdd:cd09909  81 QGNDNWISLTWQEWENKIDDLEEKILNLLEEAQNQLEKLADGLLSLDP 128
 
Name Accession Description Interval E-value
GP120 pfam00516
Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with Swiss: ...
 30-493 0e+00

Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with Swiss:P01730 and a chemokine receptor on the cell surface.


Pssm-ID: 278917  Cd Length: 525  Bit Score: 724.26  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485     30 LWVTVYYGVPVWKEATTTLFCASDAKAYSKEVHNVWATYACVPTDPSPQEIPLENVTENFNMGKNNMVEQMHEDIISLWD 109
Cdd:pfam00516   1 LWVTVFYGIPAWKEASIPLFCASDAKAYDTENHDTWATHACLPDDDDPQEIILVNVTEAFDAWKNDMTEQAHEDIIHLFD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    110 QSLKPCVKLTPLCVTLNCTEVKTNDTSTNAS--------------------------------GIEMMKNCSFNITTDLR 157
Cdd:pfam00516  81 QSIKPCVKLTPLCVALKCSDLKGDTNTPNPRtsssttsrpnssaariimekgncienntcaglGYEEIKNCEFNIKTGIE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    158 DKVKKEHALFYKLDVVQIDND----SYRLISCNTSVVTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGP-CTNVS 232
Cdd:pfam00516 161 GDKKKEYADFWKLDDIPCDNDtagtCYKLRHCNTSIIKEACDKHSFDAIPFHYCAPAGFAILKCNDKNFNGFEPkCTKVS 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    233 TVQCTHGIKPVVSTQLLLNGSLAEEEVVI----RSVNFTDNTKTIIVQLKEP--VEINCTRPNNNTRKGIHI--GPGRAF 304
Cdd:pfam00516 241 AAQCTHGIEPQTSTQFGFNGSLAEEETVIywhgRSVNFTDNAKTIIVQLNKYynLEINCKRPGNKTRKPIRImrGPGRAF 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    305 YATGDIIG-DIRQAYCNISRTKWNNTLEQIVSKLRKQFR------NKTIVFN-QSSGGDPEIVMHSFNCGGEFFYCNTTK 376
Cdd:pfam00516 321 VFHGKIGNmRPRQAHCNFGRAKWNEALKEIAQKLREHPRykgfgdNGKIIFTkPGAGGDPEIAFHSFNCGGEFFYCNMTQ 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    377 LFNSTWNN----TEESNNTKG-DIVTLPCRIKQIINMWQEVGKAMYAPPIAGQIRCSSNITGLLLTRDGGNQNNVTEI-F 450
Cdd:pfam00516 401 FFNSTWFNstwsTEDKNNTEGnDTITLPCHIKQIINMWHKVGKAMYAPPIEGEIACESNITGIIANIDGDKNNNESEItF 480

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*
gi 6651485    451 RPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKR--RVVQREKR 493
Cdd:pfam00516 481 RPGGADMADLWRLELGDYKLIEIEPIGFAPTDAKRysRTPQREKR 525
GP41 pfam00517
Retroviral envelope protein; This family includes envelope protein from a variety of ...
 512-708 3.84e-50

Retroviral envelope protein; This family includes envelope protein from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from human and simian immunodeficiency viruses (HIV and SIV) which mediate membrane fusion during viral entry. The family also includes bovine immunodeficiency virus, feline immunodeficiency virus and Equine infectious anaemia (EIAV). The family also includes the Gp36 protein from mouse mammary tumour virus (MMTV) and human endogenous retroviruses (HERVs).


Pssm-ID: 395415  Cd Length: 197  Bit Score: 174.79  E-value: 3.84e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    512 MGAASITLTVQARQLLSGIvqqQNNLLRAIEAQQHLlqltvwgIKQLQARVLAVERY----------LKDQQLLGIWGcS 581
Cdd:pfam00517   1 MAAVSLTLSIQAATLVDGL---QYNVTKVMGTQQDI-------DKKLEARLSALEDVvrvlgeqvqsLKFRMKLQCHA-N 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485    582 GKLICTTAVPWNTS----WSNKSLDKIWNNMtwmewerEINNYTGLIYNLIEESQNQQEKNEQELLALDKWA-SLWNWFD 656
Cdd:pfam00517  70 YKWICVTKVPYNASdpwdKVKKHLQGIWNNT-------EVSYDLLQLHNLIEDIQNQQEKTLNELDTLDNWAqSLFNWFP 142

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6651485    657 I--SKWLWYikifimIVGGLVGLRIIFAVLSIVNRVRQGYSPLSFQTR-------LPTQRG 708
Cdd:pfam00517 143 SlnSLWRSY------IIAGGVGLRIVLIVLCLAPCLFRSIVKELLQMHvlihknmLQKQKG 197
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 521-647 9.78e-48

heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human immunodeficiency virus (HIV-1), and related domains; This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including human, simian, and feline immunodeficiency viruses (HIV, SIV, and FIV), bovine immunodeficiency-like virus (BIV), equine infectious anaemia virus (EIAV), and Jaagsiekte sheep retrovirus (JSRV), mouse mammary tumour virus (MMTV) and various ERVs including sheep enJSRV-26, and human ERVs (HERVs): HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs to a larger superfamily containing the HR1-HR2 domain of ERVs and infectious retroviruses, including Ebola virus, and Rous sarcoma virus. Proteins in this family lack the canonical CSK17-like immunosuppressive sequence, and the intrasubunit disulfide bond-forming CX6C motif found in linker region between HR1 and HR2 in the Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as JSRV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Included in this subgroup are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep, for example enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development. HERV-K_c12q14.1 is potentially a complete envelope protein; however, it does not appear to be fusogenic.


Pssm-ID: 197369  Cd Length: 128  Bit Score: 165.65  E-value: 9.78e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6651485  521 VQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKL-ICTTAVPWNTSWSNK 599
Cdd:cd09909   1 VQARQLLVTRVQQQQSLIDAIEKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNLWGCVTKQpYCHTDVPWNRSWNHL 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 6651485  600 SLDKIWNNMTWMEWEREINNYTGLIYNLIEESQNQQEKNEQELLALDK 647
Cdd:cd09909  81 QGNDNWISLTWQEWENKIDDLEEKILNLLEEAQNQLEKLADGLLSLDP 128
Ebola_HIV-1-like_HR1-HR2 cd09947
heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of various ...
 544-617 1.30e-03

heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus and human immunodeficiency virus type 1 (HIV-1); This domain superfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus gp2, Rous sarcoma virus gp37, human immunodeficiency virus type 1 (HIV-1) gp41, and the envelope proteins of various ERVs. In the HR1-HR2 region of Ebola virus and RSV, the linker region between the two repeats includes a CKS17-like immunosuppressive region and a CX6C motif that forms an intra-subunit disulfide bond; MMTV, HIV-1, HERV-K endogenous retroviruses and related sequences lack a canonical CSK17-like sequence, and CX6C motif. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as Jaagsiekte sheep retrovirus (JSRV), feline leukemia virus (FeLV), and avian leukemia virus (ALV). Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Human ERVs (HERVs) belonging to this superfamily include Syncytin-1 (HERV-W_c7q21.2/ ERVWE1), and Syncytin-2 (HERV-FRD_6p24.1) which are expressed in the placenta, and are fusogenic, although they have a different cell specificity for fusion. Syncytin-2, but not Syncytin-1, is immunosuppressive; its immunosuppressive domain may protect the fetus from the mother's immune system. Syncytin-1 may participate in the formation of the placental trophoblast; it is also implicated in cell fusions between cancer and host cells and between cancer cell, and in human osteclast fusion. This superfamily also contains human HERV-R_c7q21.2 (ERV-3), which is also expressed in the placenta, but is not fusogenic, and has an immunosuppressive domain, but lacks a fusion peptide. It is unclear whether ERV-3 has a critical biological role. Included in this superfamily are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep; for example, enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development.


Pssm-ID: 197370  Cd Length: 73  Bit Score: 37.98  E-value: 1.30e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6651485  544 QQHLLQLTVWGIKQLQARVLAVERYLKDQQLLGIWGC---SGKLICTTAVPWNTSwsnksldKIWNNmTWMEWEREI 617
Cdd:cd09947   2 LQQLLRLTTQAIKNLHTNLTAIAKYLAQNRRGLDWLAarrGGTCVALTEVCCPFL-------SITNK-WWQDWIRKL 70
 
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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