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Conserved domains on  [gi|559105484|emb|CDK02573|]
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protease and reverse transcriptase, partial [HIV-1 M:URF(A/C/U/C)]

Protein Classification

pol protein( domain architecture ID 15830043)

HIV-1 pol protein containing the retroviral aspartyl protease, reverse transcriptase (RT), RT thumb, and RT connection domains

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 167-383 6.37e-118

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


:

Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 348.12  E-value: 6.37e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 167 GPKVKQWPLTEEKIKALTAICEEMEKEGKITKIGpeNPYNTPVFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 246
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 247 AGLKKKKSVTVLDVGDAYFSVPLHEDFRKYTAFTIPSINNETPGVRYQYNVLPQGWKGSPSIFQSSMTKILEPFRTQNPD 326
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 559105484 327 IVIYQYMDDLYVGSDLEiGQHRAKIEELREHLLRWGFTTPDKKHQKEPPFLWMGYEL 383
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 467-568 3.64e-37

Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains.


:

Pssm-ID: 462013  Cd Length: 102  Bit Score: 133.34  E-value: 3.64e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484  467 YYDPSKDLIAEIQKQGQDQWTYQIYQEPFKNLKTGKYAKMKNAHTNDVKQLTEAVQKIAMESIVIWGKIPKFRLPMQKET 546
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                          90       100
                  ....*....|....*....|..
gi 559105484  547 WETWWTDYWQATWIPEWEFINT 568
Cdd:pfam06815  81 WETWWTEYWQATWIPEWEFVNT 102
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 55-148 1.05e-30

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: 115.16  E-value: 1.05e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484   55 LWQRPLVTVKIEGQLREALLDTGADDTVLEDINLPGKW----KPRMIGGIGGFIKVKQYDQIIIEICGKKAIGTV--LVG 128
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 559105484  129 PT-PVNIIGRNMLTQIGCTLN 148
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
RVT_thumb super family cl06055
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 390-445 3.46e-17

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


The actual alignment was detected with superfamily member pfam06817:

Pssm-ID: 429135  Cd Length: 66  Bit Score: 75.82  E-value: 3.46e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 559105484  390 VQPIELPEKESWTVNDIQKLVGKLNWASQIY--SGIKVKQLCKLLRGAKALTDIVPLT 445
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 167-383 6.37e-118

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 348.12  E-value: 6.37e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 167 GPKVKQWPLTEEKIKALTAICEEMEKEGKITKIGpeNPYNTPVFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 246
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 247 AGLKKKKSVTVLDVGDAYFSVPLHEDFRKYTAFTIPSINNETPGVRYQYNVLPQGWKGSPSIFQSSMTKILEPFRTQNPD 326
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 559105484 327 IVIYQYMDDLYVGSDLEiGQHRAKIEELREHLLRWGFTTPDKKHQKEPPFLWMGYEL 383
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 212-383 1.33e-44

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 156.69  E-value: 1.33e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484  212 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLHEDFRKYTAF 279
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484  280 TIPSINN----ETPGVRYQYNVLPQGWKGSPSIFQSSMTKILEPFRTQnPDIVIYQYMDDLYVGSDlEIGQHRAKIEELR 355
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 559105484  356 EHLLRWGFTTPDKKHQ---KEPPFLWMGYEL 383
Cdd:pfam00078 159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 467-568 3.64e-37

Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains.


Pssm-ID: 462013  Cd Length: 102  Bit Score: 133.34  E-value: 3.64e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484  467 YYDPSKDLIAEIQKQGQDQWTYQIYQEPFKNLKTGKYAKMKNAHTNDVKQLTEAVQKIAMESIVIWGKIPKFRLPMQKET 546
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                          90       100
                  ....*....|....*....|..
gi 559105484  547 WETWWTDYWQATWIPEWEFINT 568
Cdd:pfam06815  81 WETWWTEYWQATWIPEWEFVNT 102
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 55-148 1.05e-30

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: 115.16  E-value: 1.05e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484   55 LWQRPLVTVKIEGQLREALLDTGADDTVLEDINLPGKW----KPRMIGGIGGFIKVKQYDQIIIEICGKKAIGTV--LVG 128
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 559105484  129 PT-PVNIIGRNMLTQIGCTLN 148
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 61-141 1.49e-22

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: 91.94  E-value: 1.49e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484  61 VTVKIEGQLREALLDTGADDTVLEDINLPGKW----KPRMIGGIGGFIKVKQYDQIIIEICGKKAIGTVLVGP--TPVNI 134
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                 ....*..
gi 559105484 135 IGRNMLT 141
Cdd:cd05482   81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 390-445 3.46e-17

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 75.82  E-value: 3.46e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 559105484  390 VQPIELPEKESWTVNDIQKLVGKLNWASQIY--SGIKVKQLCKLLRGAKALTDIVPLT 445
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 167-383 6.37e-118

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 348.12  E-value: 6.37e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 167 GPKVKQWPLTEEKIKALTAICEEMEKEGKITKIGpeNPYNTPVFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 246
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 247 AGLKKKKSVTVLDVGDAYFSVPLHEDFRKYTAFTIPSINNETPGVRYQYNVLPQGWKGSPSIFQSSMTKILEPFRTQNPD 326
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 559105484 327 IVIYQYMDDLYVGSDLEiGQHRAKIEELREHLLRWGFTTPDKKHQKEPPFLWMGYEL 383
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 212-383 1.33e-44

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 156.69  E-value: 1.33e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484  212 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLHEDFRKYTAF 279
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484  280 TIPSINN----ETPGVRYQYNVLPQGWKGSPSIFQSSMTKILEPFRTQnPDIVIYQYMDDLYVGSDlEIGQHRAKIEELR 355
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 559105484  356 EHLLRWGFTTPDKKHQ---KEPPFLWMGYEL 383
Cdd:pfam00078 159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 467-568 3.64e-37

Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains.


Pssm-ID: 462013  Cd Length: 102  Bit Score: 133.34  E-value: 3.64e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484  467 YYDPSKDLIAEIQKQGQDQWTYQIYQEPFKNLKTGKYAKMKNAHTNDVKQLTEAVQKIAMESIVIWGKIPKFRLPMQKET 546
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                          90       100
                  ....*....|....*....|..
gi 559105484  547 WETWWTDYWQATWIPEWEFINT 568
Cdd:pfam06815  81 WETWWTEYWQATWIPEWEFVNT 102
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 168-371 3.75e-32

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 123.23  E-value: 3.75e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 168 PKVKQWPLTEEKIKALTAICEEMEKEGKItkIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDfweVQLGIPHPA 247
Cdd:cd03715    2 VNQKQYPLPREAREGITPHIQELLEAGIL--VPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 248 GL-----KKKKSVTVLDVGDAYFSVPLHEDFRKYTAFTIPsinnetpGVRYQYNVLPQGWKGSPSIFQSSMTKILEPFRT 322
Cdd:cd03715   77 TLlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 559105484 323 QNPDIVIYQYMDDLYVGSDLEIGQHRAKIEELReHLLRWGFTTPDKKHQ 371
Cdd:cd03715  150 EHEGTILLQYVDDLLLAADSEEDCLKGTDALLT-HLGELGYKVSPKKAQ 197
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 55-148 1.05e-30

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: 115.16  E-value: 1.05e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484   55 LWQRPLVTVKIEGQLREALLDTGADDTVLEDINLPGKW----KPRMIGGIGGFIKVKQYDQIIIEICGKKAIGTV--LVG 128
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 559105484  129 PT-PVNIIGRNMLTQIGCTLN 148
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 204-377 2.61e-27

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 108.45  E-value: 2.61e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 204 PYNTPVFAIKKKDStKWRKLVDFRELNKRT-QDFWEvqlgIPHPAG----LKKKKSVTVLDVGDAYFSVPLHEDFRKYTA 278
Cdd:cd01647    9 PYASPVVVVKKKDG-KLRLCVDYRKLNKVTiKDRYP----LPTIDElleeLAGAKVFSKLDLRSGYHQIPLAEESRPKTA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 279 FTipsinneTPGVRYQYNVLPQGWKGSPSIFQSSMTKILEPFRtqnPDIVIyQYMDDLYVGSDlEIGQHRAKIEELREHL 358
Cdd:cd01647   84 FR-------TPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLL---GDFVE-VYLDDILVYSK-TEEEHLEHLREVLERL 151

                        170       180
                 ....*....|....*....|..
gi 559105484 359 LRWGFTTPDKK---HQKEPPFL 377
Cdd:cd01647  152 REAGLKLNPEKcefGVPEVEFL 173
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 61-141 1.49e-22

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: 91.94  E-value: 1.49e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484  61 VTVKIEGQLREALLDTGADDTVLEDINLPGKW----KPRMIGGIGGFIKVKQYDQIIIEICGKKAIGTVLVGP--TPVNI 134
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                 ....*..
gi 559105484 135 IGRNMLT 141
Cdd:cd05482   81 WGRDILS 87
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 298-383 6.47e-18

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 78.93  E-value: 6.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 298 LPQGWKGSPSIFQSSMTKILEPFRTQNPDIVIYQYMDDLYVGSDLEigQHRAKIEELREHLLRWGFTTPDKKHQ---KEP 374
Cdd:cd00304   12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE--QQAVKKRELEEFLARLGLNLSDEKTQfteKEK 89


                 ....*....
gi 559105484 375 PFLWMGYEL 383
Cdd:cd00304   90 KFKFLGILV 98
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 390-445 3.46e-17

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 75.82  E-value: 3.46e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 559105484  390 VQPIELPEKESWTVNDIQKLVGKLNWASQIY--SGIKVKQLCKLLRGAKALTDIVPLT 445
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 258-374 2.11e-07

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 49.65  E-value: 2.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484 258 LDVGDAYFSVPLHEDFRKYTAFtIPSinnetpGVRYQYNVLPQGWKGSPSIFQSSMTKILEPFRTQNpdIVIYQYMDD-L 336
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLG--VRIFSYLDDlL 71

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 559105484 337 YVGSDLEIGQHRAKieELREHLL-RWGFTTPDKKHQKEP 374
Cdd:cd03714   72 IIASSIKTSEAVLR--HLRATLLaNLGFTLNLEKSKLGP 108
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 61-141 6.15e-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: 38.85  E-value: 6.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484  61 VTVKIEGQLREALLDTGADDTVL-EDINLPGKWKPR--MIGGIGGFIK--VKQYDQiIIEICGKKAIGTVLVGPT-PVNI 134
Cdd:cd06095    1 VTITVEGVPIVFLVDTGATHSVLkSDLGPKQELSTTsvLIRGVSGQSQqpVTTYRT-LVDLGGHTVSHSFLVVPNcPDPL 79


                 ....*..
gi 559105484 135 IGRNMLT 141
Cdd:cd06095   80 LGRDLLS 86
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 61-142 7.27e-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: 38.71  E-value: 7.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559105484   61 VTVKIEGQLREALLDTGADDTVL-----EDINLP--GKWKPRMIGGIGGFIKVKQYDQIIIEICGKKA---IGTVLVGPT 130
Cdd:pfam13975   1 VDVTINGRPVRFLVDTGASVTVIsealaERLGLDrlVDAYPVTVRTANGTVRAARVRLDSVKIGGIELrnvPAVVLPGDL 80

                          90
                  ....*....|..
gi 559105484  131 PVNIIGRNMLTQ 142
Cdd:pfam13975  81 DDVLLGMDFLKR 92
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 61-106 8.19e-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: 35.72  E-value: 8.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 559105484   61 VTVKIEGQLREALLDTGADDTVL-----EDINLPGKWK--PRMIGGIGGFIKV 106
Cdd:pfam13650   1 VPVTINGKPVRFLVDTGASGTVIspslaERLGLKVRGLayTVRVSTAGGRVSA 53
 
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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