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Conserved domains on  [gi|19172954|ref|NP_579895|]
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Envelope transmembrane glycoprotein gp41 [Human immunodeficiency virus 1]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Ebola_HIV-1-like_HR1-HR2 super family cl02885
heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of various ...
19-215 1.86e-54

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: 177.10  E-value: 1.86e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172954    19 MGAASMTLTVQARQLLSGIvqqQNNLLRAIEAQQHLlqltvwgIKQLQARILAVERY----------LKDQQLLGIWGcS 88
Cdd:pfam00517   1 MAAVSLTLSIQAATLVDGL---QYNVTKVMGTQQDI-------DKKLEARLSALEDVvrvlgeqvqsLKFRMKLQCHA-N 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172954    89 GKLICTTAVPWNAS----WSNKSLEQIWNHTtwmewdrEINNYTSLIHSLIEESQNQQEKNEQELLELDKWA-SLWNWFN 163
Cdd:pfam00517  70 YKWICVTKVPYNASdpwdKVKKHLQGIWNNT-------EVSYDLLQLHNLIEDIQNQQEKTLNELDTLDNWAqSLFNWFP 142
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19172954   164 ITN--WLWYiklfimIVGGLVGLRIVFAVLSIVNRVRQGYSPLSFQTH-------LPTPRG 215
Cdd:pfam00517 143 SLNslWRSY------IIAGGVGLRIVLIVLCLAPCLFRSIVKELLQMHvlihknmLQKQKG 197
 
Name Accession Description Interval E-value
GP41 pfam00517
Retroviral envelope protein; This family includes envelope protein from a variety of ...
19-215 1.86e-54

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 tumor virus (MMTV) and human endogenous retroviruses (HERVs).


Pssm-ID: 395415  Cd Length: 197  Bit Score: 177.10  E-value: 1.86e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172954    19 MGAASMTLTVQARQLLSGIvqqQNNLLRAIEAQQHLlqltvwgIKQLQARILAVERY----------LKDQQLLGIWGcS 88
Cdd:pfam00517   1 MAAVSLTLSIQAATLVDGL---QYNVTKVMGTQQDI-------DKKLEARLSALEDVvrvlgeqvqsLKFRMKLQCHA-N 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172954    89 GKLICTTAVPWNAS----WSNKSLEQIWNHTtwmewdrEINNYTSLIHSLIEESQNQQEKNEQELLELDKWA-SLWNWFN 163
Cdd:pfam00517  70 YKWICVTKVPYNASdpwdKVKKHLQGIWNNT-------EVSYDLLQLHNLIEDIQNQQEKTLNELDTLDNWAqSLFNWFP 142
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19172954   164 ITN--WLWYiklfimIVGGLVGLRIVFAVLSIVNRVRQGYSPLSFQTH-------LPTPRG 215
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 ...
28-154 8.50e-44

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: 147.16  E-value: 8.50e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172954  28 VQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGKL-ICTTAVPWNASWSNK 106
Cdd:cd09909   1 VQARQLLVTRVQQQQSLIDAIEKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNLWGCVTKQpYCHTDVPWNRSWNHL 80
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 19172954 107 SLEQIWNHTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLELDK 154
Cdd:cd09909  81 QGNDNWISLTWQEWENKIDDLEEKILNLLEEAQNQLEKLADGLLSLDP 128
 
Name Accession Description Interval E-value
GP41 pfam00517
Retroviral envelope protein; This family includes envelope protein from a variety of ...
19-215 1.86e-54

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 tumor virus (MMTV) and human endogenous retroviruses (HERVs).


Pssm-ID: 395415  Cd Length: 197  Bit Score: 177.10  E-value: 1.86e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172954    19 MGAASMTLTVQARQLLSGIvqqQNNLLRAIEAQQHLlqltvwgIKQLQARILAVERY----------LKDQQLLGIWGcS 88
Cdd:pfam00517   1 MAAVSLTLSIQAATLVDGL---QYNVTKVMGTQQDI-------DKKLEARLSALEDVvrvlgeqvqsLKFRMKLQCHA-N 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172954    89 GKLICTTAVPWNAS----WSNKSLEQIWNHTtwmewdrEINNYTSLIHSLIEESQNQQEKNEQELLELDKWA-SLWNWFN 163
Cdd:pfam00517  70 YKWICVTKVPYNASdpwdKVKKHLQGIWNNT-------EVSYDLLQLHNLIEDIQNQQEKTLNELDTLDNWAqSLFNWFP 142
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19172954   164 ITN--WLWYiklfimIVGGLVGLRIVFAVLSIVNRVRQGYSPLSFQTH-------LPTPRG 215
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 ...
28-154 8.50e-44

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: 147.16  E-value: 8.50e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19172954  28 VQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGKL-ICTTAVPWNASWSNK 106
Cdd:cd09909   1 VQARQLLVTRVQQQQSLIDAIEKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNLWGCVTKQpYCHTDVPWNRSWNHL 80
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 19172954 107 SLEQIWNHTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLELDK 154
Cdd:cd09909  81 QGNDNWISLTWQEWENKIDDLEEKILNLLEEAQNQLEKLADGLLSLDP 128
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.19
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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