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Conserved domains on  [gi|699030863|emb|CDI27931|]
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Gag-Pol, protease region, partial [HIV-1 M:CRF06_cpx_MAU60-PROT]

Protein Classification

retropepsin-like aspartic protease( domain architecture ID 10442194)

retropepsin-like (A2 family) peptidase is an aspartic protease that hydrolyzes the peptide bonds of substrates, such as HIV-1 protease

CATH:  2.40.70.10
EC:  3.4.23.-
Gene Ontology:  GO:0004190|GO:0006508
MEROPS:  A2
PubMed:  2194475|7674916
SCOP:  4002288

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 4-97 3.95e-32

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: 107.84  E-value: 3.95e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699030863    4 LWQRPLVTVKVGGQLIEALLDTGADDTVLEDINLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKRAIGTV--LVG 77
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 699030863   78 PT-PINIIGRNMLTQIGCTLN 97
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
 
Name Accession Description Interval E-value
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 4-97 3.95e-32

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: 107.84  E-value: 3.95e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699030863    4 LWQRPLVTVKVGGQLIEALLDTGADDTVLEDINLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKRAIGTV--LVG 77
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 699030863   78 PT-PINIIGRNMLTQIGCTLN 97
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 10-90 1.32e-23

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: 85.78  E-value: 1.32e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699030863 10 VTVKVGGQLIEALLDTGADDTVLEDINLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKRAIGTVLVGP--TPINI 83
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                ....*..
gi 699030863 84 IGRNMLT 90
Cdd:cd05482  81 WGRDILS 87
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
8-32 2.02e-03

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 34.92  E-value: 2.02e-03
                         10        20
                 ....*....|....*....|....*
gi 699030863   8 PLVTVKVGGQLIEALLDTGADDTVL 32
Cdd:COG3577   42 FVVEGTINGQPVRFLVDTGASTVVL 66
 
Name Accession Description Interval E-value
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 4-97 3.95e-32

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: 107.84  E-value: 3.95e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699030863    4 LWQRPLVTVKVGGQLIEALLDTGADDTVLEDINLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKRAIGTV--LVG 77
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 699030863   78 PT-PINIIGRNMLTQIGCTLN 97
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 10-90 1.32e-23

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: 85.78  E-value: 1.32e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699030863 10 VTVKVGGQLIEALLDTGADDTVLEDINLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKRAIGTVLVGP--TPINI 83
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                ....*..
gi 699030863 84 IGRNMLT 90
Cdd:cd05482  81 WGRDILS 87
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 10-90 3.69e-04

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: 36.16  E-value: 3.69e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699030863 10 VTVKVGGQLIEALLDTGADDTVL-EDINLPGKWKPK--MIGGIGGFIKVR-QYDQILIEICGKRAIGTVLVGPT-PINII 84
Cdd:cd06095   1 VTITVEGVPIVFLVDTGATHSVLkSDLGPKQELSTTsvLIRGVSGQSQQPvTTYRTLVDLGGHTVSHSFLVVPNcPDPLL 80


                ....*.
gi 699030863 85 GRNMLT 90
Cdd:cd06095  81 GRDLLS 86
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 10-91 7.36e-04

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: 35.24  E-value: 7.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699030863  10 VTVKVGGQLIEALLDTGADDTVL-----EDINLP--GKWKPKMIGGIGGFIKVRQYDQILIEICGKRA---IGTVLVGPT 79
Cdd:pfam13975  1 VDVTINGRPVRFLVDTGASVTVIsealaERLGLDrlVDAYPVTVRTANGTVRAARVRLDSVKIGGIELrnvPAVVLPGDL 80

                         90
                 ....*....|..
gi 699030863  80 PINIIGRNMLTQ 91
Cdd:pfam13975 81 DDVLLGMDFLKR 92
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
8-32 2.02e-03

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 34.92  E-value: 2.02e-03
                         10        20
                 ....*....|....*....|....*
gi 699030863   8 PLVTVKVGGQLIEALLDTGADDTVL 32
Cdd:COG3577   42 FVVEGTINGQPVRFLVDTGASTVVL 66
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 10-56 2.49e-03

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: 34.18  E-value: 2.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 699030863  10 VTVKVGGQLIEALLDTGADDTVL-----EDINLPGKWK--PKMIGGIGGFIKVR 56
Cdd:pfam13650  1 VPVTINGKPVRFLVDTGASGTVIspslaERLGLKVRGLayTVRVSTAGGRVSAA 54
 
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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