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Conserved domains on  [gi|52000853|sp|P63122|]
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RecName: Full=Endogenous retrovirus group K member 8 Pro protein; AltName: Full=HERV-K115 Pro protein; AltName: Full=HERV-K_8p23.1 provirus ancestral Pro protein; AltName: Full=Protease; AltName: Full=Proteinase; Short=PR

Protein Classification

HIV_retropepsin_like and G-patch domain-containing protein( domain architecture ID 10442237)

HIV_retropepsin_like and G-patch domain-containing protein

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, ...
 6-105 4.60e-41

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: 132.88  E-value: 4.60e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000853     6 SENRPVCKAIIQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVIGLVGIGTASEVYQSMEILHCLGPDNQESTVQPMIT 85
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLIL 80

                          90       100
                  ....*....|....*....|.
gi 52000853    86 S-IPLNLWGRDLLQQWGAEIT 105
Cdd:pfam00077  81 PtCPVNIIGRDLLQQLGGRLT 101
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 111-155 2.91e-14

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


:

Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 62.91  E-value: 2.91e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 52000853   111 YSPTSQKIMTKRGYIPGKGLGKNEDGIKIPFEAKINQKREGIGYP 155
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
 
Name Accession Description Interval E-value
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 6-105 4.60e-41

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: 132.88  E-value: 4.60e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000853     6 SENRPVCKAIIQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVIGLVGIGTASEVYQSMEILHCLGPDNQESTVQPMIT 85
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLIL 80

                          90       100
                  ....*....|....*....|.
gi 52000853    86 S-IPLNLWGRDLLQQWGAEIT 105
Cdd:pfam00077  81 PtCPVNIIGRDLLQQLGGRLT 101
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 12-98 2.99e-31

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: 107.35  E-value: 2.99e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000853  12 CKAIIQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVIGLVGIGTASEVYQS-MEILHCLGpDNQESTVQPMITSIPLN 90
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSsVLLLEIDG-EGHLGTILVYVLSLPVN 79


                ....*...
gi 52000853  91 LWGRDLLQ 98
Cdd:cd05482  80 LWGRDILS 87
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 111-155 2.91e-14

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 62.91  E-value: 2.91e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 52000853   111 YSPTSQKIMTKRGYIPGKGLGKNEDGIKIPFEAKINQKREGIGYP 155
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 111-154 1.03e-11

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 56.40  E-value: 1.03e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 52000853    111 YSPTSQKIMTKRGYIPGKGLGKNEDGIKIPFEAKINQKREGIGY 154
Cdd:smart00443   3 TSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46
 
Name Accession Description Interval E-value
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 6-105 4.60e-41

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: 132.88  E-value: 4.60e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000853     6 SENRPVCKAIIQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVIGLVGIGTASEVYQSMEILHCLGPDNQESTVQPMIT 85
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLIL 80

                          90       100
                  ....*....|....*....|.
gi 52000853    86 S-IPLNLWGRDLLQQWGAEIT 105
Cdd:pfam00077  81 PtCPVNIIGRDLLQQLGGRLT 101
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 12-98 2.99e-31

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: 107.35  E-value: 2.99e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000853  12 CKAIIQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVIGLVGIGTASEVYQS-MEILHCLGpDNQESTVQPMITSIPLN 90
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSsVLLLEIDG-EGHLGTILVYVLSLPVN 79


                ....*...
gi 52000853  91 LWGRDLLQ 98
Cdd:cd05482  80 LWGRDILS 87
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 111-155 2.91e-14

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 62.91  E-value: 2.91e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 52000853   111 YSPTSQKIMTKRGYIPGKGLGKNEDGIKIPFEAKINQKREGIGYP 155
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 111-154 1.03e-11

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 56.40  E-value: 1.03e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 52000853    111 YSPTSQKIMTKRGYIPGKGLGKNEDGIKIPFEAKINQKREGIGY 154
Cdd:smart00443   3 TSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 16-98 8.68e-05

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: 39.24  E-value: 8.68e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000853  16 IQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVIgLVGIGTASEVYQSMEILHC-LGPdnqeSTVQP---MITSIPLNL 91
Cdd:cd06095   5 VEGVPIVFLVDTGATHSVLKSDLGPKQELSTTSVL-IRGVSGQSQQPVTTYRTLVdLGG----HTVSHsflVVPNCPDPL 79


                ....*..
gi 52000853  92 WGRDLLQ 98
Cdd:cd06095  80 LGRDLLS 86
 
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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