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Conserved domains on  [gi|4101775|gb|AAD01290|]
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gp41, partial [Human immunodeficiency virus 1]

Protein Classification

envelope glycoprotein( domain architecture ID 10177626)

envelope glycoprotein on the surface of an envelope virus is responsible for receptor binding and fusion

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 1-111 5.86e-34

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: 114.42  E-value: 5.86e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4101775    1 LLRAIEAQQHMLRLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKL-ICTTNVPWNSSWSNKSQ*EIWDNMTWLQWDK 79
Cdd:cd09909  17 LIDAIEKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNLWGCVTKQpYCHTDVPWNRSWNHLQGNDNWISLTWQEWEN 96

                        90       100       110
                ....*....|....*....|....*....|..
gi 4101775   80 EISNYTQIIFNLIEESQNQQEKNEQDLLALDK 111
Cdd:cd09909  97 KIDDLEEKILNLLEEAQNQLEKLADGLLSLDP 128
 
Name Accession Description Interval E-value
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 1-111 5.86e-34

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: 114.42  E-value: 5.86e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4101775    1 LLRAIEAQQHMLRLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKL-ICTTNVPWNSSWSNKSQ*EIWDNMTWLQWDK 79
Cdd:cd09909  17 LIDAIEKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNLWGCVTKQpYCHTDVPWNRSWNHLQGNDNWISLTWQEWEN 96

                        90       100       110
                ....*....|....*....|....*....|..
gi 4101775   80 EISNYTQIIFNLIEESQNQQEKNEQDLLALDK 111
Cdd:cd09909  97 KIDDLEEKILNLLEEAQNQLEKLADGLLSLDP 128
GP41 pfam00517
Retroviral envelope protein; This family includes envelope protein from a variety of ...
 1-127 7.65e-28

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: 101.21  E-value: 7.65e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4101775      1 LLRAIEAQQHMlrltvwgIKQLQARVLAVERY----------LKDQQLLGIWGcSGKLICTTNVPWNSS----WSNKSQ* 66
Cdd:pfam00517  23 VTKVMGTQQDI-------DKKLEARLSALEDVvrvlgeqvqsLKFRMKLQCHA-NYKWICVTKVPYNASdpwdKVKKHLQ 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4101775     67 EIWDNMtwlqwdkEISNYTQIIFNLIEESQNQQEKNEQDLLALDKWA-NLWNWFSISN--WLWY 127
Cdd:pfam00517  95 GIWNNT-------EVSYDLLQLHNLIEDIQNQQEKTLNELDTLDNWAqSLFNWFPSLNslWRSY 151
 
Name Accession Description Interval E-value
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 1-111 5.86e-34

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: 114.42  E-value: 5.86e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4101775    1 LLRAIEAQQHMLRLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKL-ICTTNVPWNSSWSNKSQ*EIWDNMTWLQWDK 79
Cdd:cd09909  17 LIDAIEKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNLWGCVTKQpYCHTDVPWNRSWNHLQGNDNWISLTWQEWEN 96

                        90       100       110
                ....*....|....*....|....*....|..
gi 4101775   80 EISNYTQIIFNLIEESQNQQEKNEQDLLALDK 111
Cdd:cd09909  97 KIDDLEEKILNLLEEAQNQLEKLADGLLSLDP 128
GP41 pfam00517
Retroviral envelope protein; This family includes envelope protein from a variety of ...
 1-127 7.65e-28

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: 101.21  E-value: 7.65e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4101775      1 LLRAIEAQQHMlrltvwgIKQLQARVLAVERY----------LKDQQLLGIWGcSGKLICTTNVPWNSS----WSNKSQ* 66
Cdd:pfam00517  23 VTKVMGTQQDI-------DKKLEARLSALEDVvrvlgeqvqsLKFRMKLQCHA-NYKWICVTKVPYNASdpwdKVKKHLQ 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4101775     67 EIWDNMtwlqwdkEISNYTQIIFNLIEESQNQQEKNEQDLLALDKWA-NLWNWFSISN--WLWY 127
Cdd:pfam00517  95 GIWNNT-------EVSYDLLQLHNLIEDIQNQQEKTLNELDTLDNWAqSLFNWFPSLNslWRSY 151
 
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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