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Conserved domains on  [gi|2098254]
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Chain B, HIV-2 PROTEASE

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 11-91 1.42e-21

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


:

Pssm-ID: 133149  Cd Length: 87  Bit Score: 80.77  E-value: 1.42e-21
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254  11 VTAYIEGQPVEVLLDTGADDSIVAGIELGNN----YSPKIVGGIGGFINTLEYKNVEIEVLNKKVRATIMTG--DTPINI 84
Cdd:cd05482  1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNwpiqPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYvlSLPVNL 80


               ....*..
gi 2098254  85 FGRNILT 91
Cdd:cd05482 81 WGRDILS 87
 
Name Accession Description Interval E-value
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 11-91 1.42e-21

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 80.77  E-value: 1.42e-21
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254  11 VTAYIEGQPVEVLLDTGADDSIVAGIELGNN----YSPKIVGGIGGFINTLEYKNVEIEVLNKKVRATIMTG--DTPINI 84
Cdd:cd05482  1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNwpiqPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYvlSLPVNL 80


               ....*..
gi 2098254  85 FGRNILT 91
Cdd:cd05482 81 WGRDILS 87
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 5-98 7.69e-19

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 74.33  E-value: 7.69e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254      5 LWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNY----SPKIVGGIGGFINTLEYKNVEIEVLNKKVRATI---MT 77
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVsplIL 80

                          90       100
                  ....*....|....*....|.
gi 2098254     78 GDTPINIFGRNILTALGMSLN 98
Cdd:pfam00077  81 PTCPVNIIGRDLLQQLGGRLT 101
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
9-96 2.94e-05

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 39.93  E-value: 2.94e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254    9 PVVTAYIEGQPVEVLLDTGADDSIV-------AGIELGNNYSPKIVGGIGGFINTLEY--KNVEI-EVLNKKVRATIMTG 78
Cdd:COG3577  42 FVVEGTINGQPVRFLVDTGASTVVLsesdarrLGLDPEDLGRPVRVQTANGVVRAARVrlDSVRIgGITLRNVRAVVLPG 121

                        90
                ....*....|....*...
gi 2098254   79 DTPINIFgrniltaLGMS 96
Cdd:COG3577 122 GELDDGL-------LGMS 132
 
Name Accession Description Interval E-value
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 11-91 1.42e-21

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 80.77  E-value: 1.42e-21
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254  11 VTAYIEGQPVEVLLDTGADDSIVAGIELGNN----YSPKIVGGIGGFINTLEYKNVEIEVLNKKVRATIMTG--DTPINI 84
Cdd:cd05482  1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNwpiqPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYvlSLPVNL 80


               ....*..
gi 2098254  85 FGRNILT 91
Cdd:cd05482 81 WGRDILS 87
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 5-98 7.69e-19

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 74.33  E-value: 7.69e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254      5 LWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNY----SPKIVGGIGGFINTLEYKNVEIEVLNKKVRATI---MT 77
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVsplIL 80

                          90       100
                  ....*....|....*....|.
gi 2098254     78 GDTPINIFGRNILTALGMSLN 98
Cdd:pfam00077  81 PTCPVNIIGRDLLQQLGGRLT 101
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 11-90 1.94e-07

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.


Pssm-ID: 464060  Cd Length: 92  Bit Score: 44.87  E-value: 1.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254    11 VTAYIEGQPVEVLLDTGADDSIV-------AGIELGNNYSPKIVGGIGG-------FINTLEYKNVEIevlnKKVRATIM 76
Cdd:pfam13975  1 VDVTINGRPVRFLVDTGASVTVIsealaerLGLDRLVDAYPVTVRTANGtvraarvRLDSVKIGGIEL----RNVPAVVL 76

                         90
                 ....*....|....
gi 2098254    77 TGDTPINIFGRNIL 90
Cdd:pfam13975 77 PGDLDDVLLGMDFL 90
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 11-88 2.13e-05

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 39.58  E-value: 2.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254    11 VTAYIEGQPVEVLLDTGADDSIV-------AGIELGNNYSPKIVGGIGGFINTLEYKNVEIEVLN---KKVRATIM-TGD 79
Cdd:pfam13650  1 VPVTINGKPVRFLVDTGASGTVIspslaerLGLKVRGLAYTVRVSTAGGRVSAARVRLDSLRLGGltlENVPALVLdLGD 80


                 ....*....
gi 2098254    80 TPINIFGRN 88
Cdd:pfam13650 81 LIDGLLGMD 89
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
9-96 2.94e-05

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 39.93  E-value: 2.94e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254    9 PVVTAYIEGQPVEVLLDTGADDSIV-------AGIELGNNYSPKIVGGIGGFINTLEY--KNVEI-EVLNKKVRATIMTG 78
Cdd:COG3577  42 FVVEGTINGQPVRFLVDTGASTVVLsesdarrLGLDPEDLGRPVRVQTANGVVRAARVrlDSVRIgGITLRNVRAVVLPG 121

                        90
                ....*....|....*...
gi 2098254   79 DTPINIFgrniltaLGMS 96
Cdd:COG3577 122 GELDDGL-------LGMS 132
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 8-90 2.58e-03

Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133150  Cd Length: 96  Bit Score: 34.14  E-value: 2.58e-03
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254   8 RPVVTAYIEGQPVEVLLDTGADDSIV---AGIELGNNY---SPKIVGGIGGFINTLEYKNVEIEVLN---KKVRATIMTG 78
Cdd:cd05483  2 HFVVPVTINGQPVRFLLDTGASTTVIseeLAERLGLPLtlgGKVTVQTANGRVRAARVRLDSLQIGGitlRNVPAVVLPG 81

                       90
               ....*....|....
gi 2098254  79 DT--PINIFGRNIL 90
Cdd:cd05483 82 DAlgVDGLLGMDFL 95
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 11-33 4.54e-03

Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133159  Cd Length: 86  Bit Score: 33.46  E-value: 4.54e-03
                       10        20
               ....*....|....*....|...
gi 2098254  11 VTAYIEGQPVEVLLDTGADDSIV 33
Cdd:cd06095  1 VTITVEGVPIVFLVDTGATHSVL 23
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 11-91 9.97e-03

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 32.31  E-value: 9.97e-03
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098254  11 VTAYIEGQPVEVLLDTGADDSIVA-------GIELGNNYSPKIVGGIGG-FINTL-EYKNVEIEVLNKKVRATIM---TG 78
Cdd:cd00303  1 LKGKINGVPVRALVDSGASVNFISeslakklGLPPRLLPTPLKVKGANGsSVKTLgVILPVTIGIGGKTFTVDFYvldLL 80

                       90
               ....*....|...
gi 2098254  79 DTPInIFGRNILT 91
Cdd:cd00303 81 SYDV-ILGRPWLE 92
 
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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