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Conserved domains on  [gi|28876544|ref|NP_579894|]
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Envelope surface glycoprotein gp120 [Human immunodeficiency virus 1]

Protein Classification

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 CD4 and ...
6-483 0e+00

Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with CD4 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: 855.23  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544     6 LWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWD 85
Cdd:pfam00516   1 LWVTVFYGIPAWKEASIPLFCASDAKAYDTENHDTWATHACLPDDDDPQEIILVNVTEAFDAWKNDMTEQAHEDIIHLFD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544    86 QSLKPCVKLTPLCVSLKCTDLKNDTNT-------------NSSSGRMIMEKG--------------EIKNCSFNISTSIR 138
Cdd:pfam00516  81 QSIKPCVKLTPLCVALKCSDLKGDTNTpnprtsssttsrpNSSAARIIMEKGncienntcaglgyeEIKNCEFNIKTGIE 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   139 GKVQKEYAFFYKLDIIPIDNDT--TSYKLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGP-CTNVS 215
Cdd:pfam00516 161 GDKKKEYADFWKLDDIPCDNDTagTCYKLRHCNTSIIKEACDKHSFDAIPFHYCAPAGFAILKCNDKNFNGFEPkCTKVS 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   216 TVQCTHGIRPVVSTQLLLNGSLAEEEVVI----RSVNFTDNAKTIIVQLNT--SVEINCTRPNNNTRKRIRIQRGPGRAF 289
Cdd:pfam00516 241 AAQCTHGIEPQTSTQFGFNGSLAEEETVIywhgRSVNFTDNAKTIIVQLNKyyNLEINCKRPGNKTRKPIRIMRGPGRAF 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   290 VTIGKIGNM--RQAHCNISRAKWNNTLKQIASKLREQ-----FGNNKTIIF-KQSSGGDPEIVTHSFNCGGEFFYCNSTQ 361
Cdd:pfam00516 321 VFHGKIGNMrpRQAHCNFGRAKWNEALKEIAQKLREHprykgFGDNGKIIFtKPGAGGDPEIAFHSFNCGGEFFYCNMTQ 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   362 LFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEI-F 440
Cdd:pfam00516 401 FFNSTWFNSTWSTEDKNNTEGNDTITLPCHIKQIINMWHKVGKAMYAPPIEGEIACESNITGIIANIDGDKNNNESEItF 480
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*
gi 28876544   441 RPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKR--RVVQREKR 483
Cdd:pfam00516 481 RPGGADMADLWRLELGDYKLIEIEPIGFAPTDAKRysRTPQREKR 525
 
Name Accession Description Interval E-value
GP120 pfam00516
Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with CD4 and ...
6-483 0e+00

Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with CD4 and a chemokine receptor on the cell surface.


Pssm-ID: 278917  Cd Length: 525  Bit Score: 855.23  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544     6 LWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWD 85
Cdd:pfam00516   1 LWVTVFYGIPAWKEASIPLFCASDAKAYDTENHDTWATHACLPDDDDPQEIILVNVTEAFDAWKNDMTEQAHEDIIHLFD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544    86 QSLKPCVKLTPLCVSLKCTDLKNDTNT-------------NSSSGRMIMEKG--------------EIKNCSFNISTSIR 138
Cdd:pfam00516  81 QSIKPCVKLTPLCVALKCSDLKGDTNTpnprtsssttsrpNSSAARIIMEKGncienntcaglgyeEIKNCEFNIKTGIE 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   139 GKVQKEYAFFYKLDIIPIDNDT--TSYKLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGP-CTNVS 215
Cdd:pfam00516 161 GDKKKEYADFWKLDDIPCDNDTagTCYKLRHCNTSIIKEACDKHSFDAIPFHYCAPAGFAILKCNDKNFNGFEPkCTKVS 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   216 TVQCTHGIRPVVSTQLLLNGSLAEEEVVI----RSVNFTDNAKTIIVQLNT--SVEINCTRPNNNTRKRIRIQRGPGRAF 289
Cdd:pfam00516 241 AAQCTHGIEPQTSTQFGFNGSLAEEETVIywhgRSVNFTDNAKTIIVQLNKyyNLEINCKRPGNKTRKPIRIMRGPGRAF 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   290 VTIGKIGNM--RQAHCNISRAKWNNTLKQIASKLREQ-----FGNNKTIIF-KQSSGGDPEIVTHSFNCGGEFFYCNSTQ 361
Cdd:pfam00516 321 VFHGKIGNMrpRQAHCNFGRAKWNEALKEIAQKLREHprykgFGDNGKIIFtKPGAGGDPEIAFHSFNCGGEFFYCNMTQ 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   362 LFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEI-F 440
Cdd:pfam00516 401 FFNSTWFNSTWSTEDKNNTEGNDTITLPCHIKQIINMWHKVGKAMYAPPIEGEIACESNITGIIANIDGDKNNNESEItF 480
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*
gi 28876544   441 RPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKR--RVVQREKR 483
Cdd:pfam00516 481 RPGGADMADLWRLELGDYKLIEIEPIGFAPTDAKRysRTPQREKR 525
 
Name Accession Description Interval E-value
GP120 pfam00516
Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with CD4 and ...
6-483 0e+00

Envelope glycoprotein GP120; The entry of HIV requires interaction of viral GP120 with CD4 and a chemokine receptor on the cell surface.


Pssm-ID: 278917  Cd Length: 525  Bit Score: 855.23  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544     6 LWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWD 85
Cdd:pfam00516   1 LWVTVFYGIPAWKEASIPLFCASDAKAYDTENHDTWATHACLPDDDDPQEIILVNVTEAFDAWKNDMTEQAHEDIIHLFD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544    86 QSLKPCVKLTPLCVSLKCTDLKNDTNT-------------NSSSGRMIMEKG--------------EIKNCSFNISTSIR 138
Cdd:pfam00516  81 QSIKPCVKLTPLCVALKCSDLKGDTNTpnprtsssttsrpNSSAARIIMEKGncienntcaglgyeEIKNCEFNIKTGIE 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   139 GKVQKEYAFFYKLDIIPIDNDT--TSYKLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGP-CTNVS 215
Cdd:pfam00516 161 GDKKKEYADFWKLDDIPCDNDTagTCYKLRHCNTSIIKEACDKHSFDAIPFHYCAPAGFAILKCNDKNFNGFEPkCTKVS 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   216 TVQCTHGIRPVVSTQLLLNGSLAEEEVVI----RSVNFTDNAKTIIVQLNT--SVEINCTRPNNNTRKRIRIQRGPGRAF 289
Cdd:pfam00516 241 AAQCTHGIEPQTSTQFGFNGSLAEEETVIywhgRSVNFTDNAKTIIVQLNKyyNLEINCKRPGNKTRKPIRIMRGPGRAF 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   290 VTIGKIGNM--RQAHCNISRAKWNNTLKQIASKLREQ-----FGNNKTIIF-KQSSGGDPEIVTHSFNCGGEFFYCNSTQ 361
Cdd:pfam00516 321 VFHGKIGNMrpRQAHCNFGRAKWNEALKEIAQKLREHprykgFGDNGKIIFtKPGAGGDPEIAFHSFNCGGEFFYCNMTQ 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28876544   362 LFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEI-F 440
Cdd:pfam00516 401 FFNSTWFNSTWSTEDKNNTEGNDTITLPCHIKQIINMWHKVGKAMYAPPIEGEIACESNITGIIANIDGDKNNNESEItF 480
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*
gi 28876544   441 RPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKR--RVVQREKR 483
Cdd:pfam00516 481 RPGGADMADLWRLELGDYKLIEIEPIGFAPTDAKRysRTPQREKR 525
 
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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