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Conserved domains on  [gi|306517593|emb|CBH29271|]
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gag-pol fusion polyprotein precursor, partial [HIV-1 CRF26_A5U:08GQ323]

Protein Classification

pol protein( domain architecture ID 10442199)

HIV-1 pol protein containing the pepsin-like aspartate protease, reverse transcriptase (RT), RT thumb, and RT connection domains; RT catalyzes the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes

CATH:  3.10.10.10|2.40.70.10
EC:  2.7.7.49
Gene Ontology:  GO:0003964|GO:0004190|GO:0006508
MEROPS:  A2
PubMed:  1698615|2194475|7674916
SCOP:  4002796|4002288

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 ...
 172-388 9.20e-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: 9.20e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 172 GPKVKQWPLTEEKIKALTEICDEMEKEGKISRIGpeNPYNTPIFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 251
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 252 AGLKKKKSVTVLDVGDAYFSVPLDPDFRKYTAFTIPSINNEKPGVRYQYNVLPQGWKGSPAIFQSSMTKILEPFRSQNPE 331
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 306517593 332 IVIYQYMDDLYVGSDLEiGQHRAKIEELREHLLKWGFTTPDKKHQKEPPFLWMGYEL 388
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 472-573 1.16e-35

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: 129.49  E-value: 1.16e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593  472 YYDPSKDLIAEIQKQGQDQWTYQIYQEPFKNLKTGKYAKRKSAHTNDVKQLAEVVQKVVLESIVIWGKTPKFRLPIQKET 551
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                          90       100
                  ....*....|....*....|..
gi 306517593  552 WDTWWMDYWQATWIPEWEFVNT 573
Cdd:pfam06815  81 WETWWTEYWQATWIPEWEFVNT 102
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 60-153 6.57e-31

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: 115.93  E-value: 6.57e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593   60 LWQRPIVTVKIEGQLREALLDTGADDTVLEDINLPGKW----KPRMIGGIGGFIKVRQYDQVTIDICGQKAIGTV--LVG 133
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 306517593  134 PT-PVNIIGRNMLTQIGCTLN 153
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 395-458 5.33e-21

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: 86.61  E-value: 5.33e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 306517593  395 VQPIQLPEQDNWTVNDIQKLVGKLNWASQIY--PGIKVKQMCKLLRGAKALTDIVPLTREAELELE 458
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 172-388 9.20e-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: 9.20e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 172 GPKVKQWPLTEEKIKALTEICDEMEKEGKISRIGpeNPYNTPIFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 251
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 252 AGLKKKKSVTVLDVGDAYFSVPLDPDFRKYTAFTIPSINNEKPGVRYQYNVLPQGWKGSPAIFQSSMTKILEPFRSQNPE 331
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 306517593 332 IVIYQYMDDLYVGSDLEiGQHRAKIEELREHLLKWGFTTPDKKHQKEPPFLWMGYEL 388
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 217-388 1.10e-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: 157.08  E-value: 1.10e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593  217 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLDPDFRKYTAF 284
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593  285 TIPSINN----EKPGVRYQYNVLPQGWKGSPAIFQSSMTKILEPFRSQnPEIVIYQYMDDLYVGSDlEIGQHRAKIEELR 360
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 306517593  361 EHLLKWGFTTPDKKHQ---KEPPFLWMGYEL 388
Cdd:pfam00078 159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 472-573 1.16e-35

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: 129.49  E-value: 1.16e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593  472 YYDPSKDLIAEIQKQGQDQWTYQIYQEPFKNLKTGKYAKRKSAHTNDVKQLAEVVQKVVLESIVIWGKTPKFRLPIQKET 551
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                          90       100
                  ....*....|....*....|..
gi 306517593  552 WDTWWMDYWQATWIPEWEFVNT 573
Cdd:pfam06815  81 WETWWTEYWQATWIPEWEFVNT 102
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 60-153 6.57e-31

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: 115.93  E-value: 6.57e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593   60 LWQRPIVTVKIEGQLREALLDTGADDTVLEDINLPGKW----KPRMIGGIGGFIKVRQYDQVTIDICGQKAIGTV--LVG 133
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 306517593  134 PT-PVNIIGRNMLTQIGCTLN 153
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 66-146 3.19e-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: 88.09  E-value: 3.19e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593  66 VTVKIEGQLREALLDTGADDTVLEDINLPGKW----KPRMIGGIGGFIKVRQYDQVTIDICGQKAIGTVLVGP--TPVNI 139
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                 ....*..
gi 306517593 140 IGRNMLT 146
Cdd:cd05482   81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 395-458 5.33e-21

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: 86.61  E-value: 5.33e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 306517593  395 VQPIQLPEQDNWTVNDIQKLVGKLNWASQIY--PGIKVKQMCKLLRGAKALTDIVPLTREAELELE 458
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 172-388 9.20e-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: 9.20e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 172 GPKVKQWPLTEEKIKALTEICDEMEKEGKISRIGpeNPYNTPIFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 251
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 252 AGLKKKKSVTVLDVGDAYFSVPLDPDFRKYTAFTIPSINNEKPGVRYQYNVLPQGWKGSPAIFQSSMTKILEPFRSQNPE 331
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 306517593 332 IVIYQYMDDLYVGSDLEiGQHRAKIEELREHLLKWGFTTPDKKHQKEPPFLWMGYEL 388
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 217-388 1.10e-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: 157.08  E-value: 1.10e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593  217 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLDPDFRKYTAF 284
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593  285 TIPSINN----EKPGVRYQYNVLPQGWKGSPAIFQSSMTKILEPFRSQnPEIVIYQYMDDLYVGSDlEIGQHRAKIEELR 360
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 306517593  361 EHLLKWGFTTPDKKHQ---KEPPFLWMGYEL 388
Cdd:pfam00078 159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 472-573 1.16e-35

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: 129.49  E-value: 1.16e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593  472 YYDPSKDLIAEIQKQGQDQWTYQIYQEPFKNLKTGKYAKRKSAHTNDVKQLAEVVQKVVLESIVIWGKTPKFRLPIQKET 551
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                          90       100
                  ....*....|....*....|..
gi 306517593  552 WDTWWMDYWQATWIPEWEFVNT 573
Cdd:pfam06815  81 WETWWTEYWQATWIPEWEFVNT 102
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 173-376 1.33e-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: 124.38  E-value: 1.33e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 173 PKVKQWPLTEEKIKALTEICDEMEKEGKIsrIGPENPYNTPIFAIKKKDSTKWRKLVDFRELNKRTQDfweVQLGIPHPA 252
Cdd:cd03715    2 VNQKQYPLPREAREGITPHIQELLEAGIL--VPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 253 GL-----KKKKSVTVLDVGDAYFSVPLDPDFRKYTAFTIPsinnekpGVRYQYNVLPQGWKGSPAIFQSSMTKILEPFRS 327
Cdd:cd03715   77 TLlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 306517593 328 QNPEIVIYQYMDDLYVGSDLEIGQHRAKIEELReHLLKWGFTTPDKKHQ 376
Cdd:cd03715  150 EHEGTILLQYVDDLLLAADSEEDCLKGTDALLT-HLGELGYKVSPKKAQ 197
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 60-153 6.57e-31

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: 115.93  E-value: 6.57e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593   60 LWQRPIVTVKIEGQLREALLDTGADDTVLEDINLPGKW----KPRMIGGIGGFIKVRQYDQVTIDICGQKAIGTV--LVG 133
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 306517593  134 PT-PVNIIGRNMLTQIGCTLN 153
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 209-365 6.41e-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: 107.30  E-value: 6.41e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 209 PYNTPIFAIKKKDStKWRKLVDFRELNKRT-QDFWEvqlgIPHPAG----LKKKKSVTVLDVGDAYFSVPLDPDFRKYTA 283
Cdd:cd01647    9 PYASPVVVVKKKDG-KLRLCVDYRKLNKVTiKDRYP----LPTIDElleeLAGAKVFSKLDLRSGYHQIPLAEESRPKTA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 284 FTIPSinnekpGvRYQYNVLPQGWKGSPAIFQSSMTKILEPFRSQNPEIviyqYMDDLYVGSDlEIGQHRAKIEE----L 359
Cdd:cd01647   84 FRTPF------G-LYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEV----YLDDILVYSK-TEEEHLEHLREvlerL 151


                 ....*.
gi 306517593 360 REHLLK 365
Cdd:cd01647  152 REAGLK 157
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 66-146 3.19e-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: 88.09  E-value: 3.19e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593  66 VTVKIEGQLREALLDTGADDTVLEDINLPGKW----KPRMIGGIGGFIKVRQYDQVTIDICGQKAIGTVLVGP--TPVNI 139
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                 ....*..
gi 306517593 140 IGRNMLT 146
Cdd:cd05482   81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 395-458 5.33e-21

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: 86.61  E-value: 5.33e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 306517593  395 VQPIQLPEQDNWTVNDIQKLVGKLNWASQIY--PGIKVKQMCKLLRGAKALTDIVPLTREAELELE 458
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 303-388 2.22e-17

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: 77.39  E-value: 2.22e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 303 LPQGWKGSPAIFQSSMTKILEPFRSQNPEIVIYQYMDDLYVGSDLEigQHRAKIEELREHLLKWGFTTPDKKHQ---KEP 379
Cdd:cd00304   12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE--QQAVKKRELEEFLARLGLNLSDEKTQfteKEK 89


                 ....*....
gi 306517593 380 PFLWMGYEL 388
Cdd:cd00304   90 KFKFLGILV 98
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 263-379 2.98e-08

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: 52.35  E-value: 2.98e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 263 LDVGDAYFSVPLDPDFRKYTAFtIPSinnekpGVRYQYNVLPQGWKGSPAIFQSSMTKILEPFRSQNpeIVIYQYMDD-L 341
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLG--VRIFSYLDDlL 71

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 306517593 342 YVGSDLEIGQHRAKieELREHLL-KWGFTTPDKKHQKEP 379
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 ...
 66-146 4.90e-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: 41.93  E-value: 4.90e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593  66 VTVKIEGQLREALLDTGADDTVL-EDINLPGKWKPR--MIGGIGGFIKVRQYDQVT-IDICGQKAIGTVLVGPT-PVNII 140
Cdd:cd06095    1 VTITVEGVPIVFLVDTGATHSVLkSDLGPKQELSTTsvLIRGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNcPDPLL 80


                 ....*.
gi 306517593 141 GRNMLT 146
Cdd:cd06095   81 GRDLLS 86
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 66-147 7.37e-05

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: 41.79  E-value: 7.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593   66 VTVKIEGQLREALLDTGADDTVL-----EDINLP--GKWKPRMIGGIGGFIKVRQYDQVTIDICG---QKAIGTVLVGPT 135
Cdd:pfam13975   1 VDVTINGRPVRFLVDTGASVTVIsealaERLGLDrlVDAYPVTVRTANGTVRAARVRLDSVKIGGielRNVPAVVLPGDL 80

                          90
                  ....*....|..
gi 306517593  136 PVNIIGRNMLTQ 147
Cdd:pfam13975  81 DDVLLGMDFLKR 92
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 66-143 3.61e-04

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: 3.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593   66 VTVKIEGQLREALLDTGADDTVL-----EDINLPGKWK--PRMIGGIGGFIKVRQYDQVTIDICGQKAIG-TVLV---GP 134
Cdd:pfam13650   1 VPVTINGKPVRFLVDTGASGTVIspslaERLGLKVRGLayTVRVSTAGGRVSAARVRLDSLRLGGLTLENvPALVldlGD 80


                  ....*....
gi 306517593  135 TPVNIIGRN 143
Cdd:pfam13650  81 LIDGLLGMD 89
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 264-346 8.56e-03

RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.


Pssm-ID: 238822  Cd Length: 213  Bit Score: 38.05  E-value: 8.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 306517593 264 DVGDAYFSVPLDPDFRKYTAFTIPSINNEKPGVRYQYNVLPQGWKGSPAIFQSSMTKILE--PFRSQNPEIVIYQYMDDL 341
Cdd:cd01644   65 DIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFLANRALKQHAEdhPHEAAAKIIKRNFYVDDI 144


                 ....*
gi 306517593 342 YVGSD 346
Cdd:cd01644  145 LVSTD 149
 
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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