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Conserved domains on  [gi|301016564|emb|CBV35857|]
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gag-pol fusion polyprotein precursor, partial [HIV-1 M:URF(U/A/D):07CD2682]

Protein Classification

pol protein( domain architecture ID 11082152)

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
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 117-333 2.87e-116

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member cd01645:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 213  Bit Score: 340.03  E-value: 2.87e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 117 GPRIKQWPLTEEKIKALTEICKEMEEEGKISRIGpeNPYNTPIFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 196
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 197 AGLKKKKSVTVLDVGDAYFSVPLH*DFRKYTAFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRSQNPG 276
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 301016564 277 IIIYQYMDDLYVGSDLEiGQHRAK*EELRDHLLKWGFTTPDKKHQKEPPFLWMGYEL 333
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 5-98 4.84e-33

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: 120.55  E-value: 4.84e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564    5 LWQRPLVTVKIGGQLREALLDTGADDTVLE*INLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKKAIGTV--LVG 78
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 301016564   79 PT-PVNIIGRNMLTQIGCTLN 98
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 ...
 340-395 1.69e-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: 76.59  E-value: 1.69e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 301016564  340 VQPIQLPNKDSWTVNDLQKLVGKLNWASQIYQ--GIKVKQLCRCLKGAKALTEVVPLT 395
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLT 58
RVT_connect super family cl06054
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 417-470 5.88e-10

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


The actual alignment was detected with superfamily member pfam06815:

Pssm-ID: 462013  Cd Length: 102  Bit Score: 56.30  E-value: 5.88e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 301016564  417 YYDPSKELIAEIQKQGQDQWTYQIYQEPFKNLKTGKYARKRSAHTNDVKQLTEV 470
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEA 54
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 117-333 2.87e-116

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: 340.03  E-value: 2.87e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 117 GPRIKQWPLTEEKIKALTEICKEMEEEGKISRIGpeNPYNTPIFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 196
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 197 AGLKKKKSVTVLDVGDAYFSVPLH*DFRKYTAFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRSQNPG 276
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 301016564 277 IIIYQYMDDLYVGSDLEiGQHRAK*EELRDHLLKWGFTTPDKKHQKEPPFLWMGYEL 333
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 162-333 1.84e-43

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: 151.30  E-value: 1.84e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564  162 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLH*DFRKYTAF 229
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564  230 TIPSTNN----ETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRSQnPGIIIYQYMDDLYVGSDlEIGQHRAK*EELR 305
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 301016564  306 DHLLKWGFTTPDKKHQ---KEPPFLWMGYEL 333
Cdd:pfam00078 159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 5-98 4.84e-33

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: 120.55  E-value: 4.84e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564    5 LWQRPLVTVKIGGQLREALLDTGADDTVLE*INLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKKAIGTV--LVG 78
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 301016564   79 PT-PVNIIGRNMLTQIGCTLN 98
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 11-91 1.71e-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: 93.87  E-value: 1.71e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564  11 VTVKIGGQLREALLDTGADDTVLE*INLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKKAIGTVLVGP--TPVNI 84
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                 ....*..
gi 301016564  85 IGRNMLT 91
Cdd:cd05482   81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 340-395 1.69e-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: 76.59  E-value: 1.69e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 301016564  340 VQPIQLPNKDSWTVNDLQKLVGKLNWASQIYQ--GIKVKQLCRCLKGAKALTEVVPLT 395
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLT 58
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 417-470 5.88e-10

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: 56.30  E-value: 5.88e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 301016564  417 YYDPSKELIAEIQKQGQDQWTYQIYQEPFKNLKTGKYARKRSAHTNDVKQLTEV 470
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEA 54
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 117-333 2.87e-116

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: 340.03  E-value: 2.87e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 117 GPRIKQWPLTEEKIKALTEICKEMEEEGKISRIGpeNPYNTPIFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 196
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 197 AGLKKKKSVTVLDVGDAYFSVPLH*DFRKYTAFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRSQNPG 276
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 301016564 277 IIIYQYMDDLYVGSDLEiGQHRAK*EELRDHLLKWGFTTPDKKHQKEPPFLWMGYEL 333
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 162-333 1.84e-43

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: 151.30  E-value: 1.84e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564  162 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLH*DFRKYTAF 229
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564  230 TIPSTNN----ETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRSQnPGIIIYQYMDDLYVGSDlEIGQHRAK*EELR 305
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 301016564  306 DHLLKWGFTTPDKKHQ---KEPPFLWMGYEL 333
Cdd:pfam00078 159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 118-321 4.29e-35

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: 129.78  E-value: 4.29e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 118 PRIKQWPLTEEKIKALTEICKEMEEEGKIsrIGPENPYNTPIFAIKKKDSTKWRKLVDFRELNKRTQDfweVQLGIPHPA 197
Cdd:cd03715    2 VNQKQYPLPREAREGITPHIQELLEAGIL--VPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 198 GL-----KKKKSVTVLDVGDAYFSVPLH*DFRKYTAFTIPstnnetpGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRS 272
Cdd:cd03715   77 TLlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 301016564 273 QNPGIIIYQYMDDLYVGSDLEIGQHRAK*EELRdHLLKWGFTTPDKKHQ 321
Cdd:cd03715  150 EHEGTILLQYVDDLLLAADSEEDCLKGTDALLT-HLGELGYKVSPKKAQ 197
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 5-98 4.84e-33

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: 120.55  E-value: 4.84e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564    5 LWQRPLVTVKIGGQLREALLDTGADDTVLE*INLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKKAIGTV--LVG 78
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                          90       100
                  ....*....|....*....|.
gi 301016564   79 PT-PVNIIGRNMLTQIGCTLN 98
Cdd:pfam00077  81 PTcPVNIIGRDLLQQLGGRLT 101
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 154-310 2.12e-25

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: 102.29  E-value: 2.12e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 154 PYNTPIFAIKKKDStKWRKLVDFRELNKRT-QDFWEvqlgIPHPAG----LKKKKSVTVLDVGDAYFSVPLH*DFRKYTA 228
Cdd:cd01647    9 PYASPVVVVKKKDG-KLRLCVDYRKLNKVTiKDRYP----LPTIDElleeLAGAKVFSKLDLRSGYHQIPLAEESRPKTA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 229 FTipstnneTPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRsqnpGIIIYQYMDDLYVGSDlEIGQHRAK*EE----L 304
Cdd:cd01647   84 FR-------TPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLL----GDFVEVYLDDILVYSK-TEEEHLEHLREvlerL 151


                 ....*.
gi 301016564 305 RDHLLK 310
Cdd:cd01647  152 REAGLK 157
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 11-91 1.71e-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: 93.87  E-value: 1.71e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564  11 VTVKIGGQLREALLDTGADDTVLE*INLPGKW----KPKMIGGIGGFIKVRQYDQILIEICGKKAIGTVLVGP--TPVNI 84
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                 ....*..
gi 301016564  85 IGRNMLT 91
Cdd:cd05482   81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 340-395 1.69e-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: 76.59  E-value: 1.69e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 301016564  340 VQPIQLPNKDSWTVNDLQKLVGKLNWASQIYQ--GIKVKQLCRCLKGAKALTEVVPLT 395
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLT 58
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 248-333 1.12e-16

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: 75.08  E-value: 1.12e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 248 LPQGWKGSPAIFQCSMTKILEPFRSQNPGIIIYQYMDDLYVGSDLEigQHRAK*EELRDHLLKWGFTTPDKKHQ---KEP 324
Cdd:cd00304   12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE--QQAVKKRELEEFLARLGLNLSDEKTQfteKEK 89


                 ....*....
gi 301016564 325 PFLWMGYEL 333
Cdd:cd00304   90 KFKFLGILV 98
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 417-470 5.88e-10

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: 56.30  E-value: 5.88e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 301016564  417 YYDPSKELIAEIQKQGQDQWTYQIYQEPFKNLKTGKYARKRSAHTNDVKQLTEV 470
Cdd:pfam06815   1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEA 54
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 208-324 2.15e-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: 2.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564 208 LDVGDAYFSVPLH*DFRKYTAFtIPStnnetpGIRYQYNVLPQGWKGSPAIFqcsmTKILEPFRS--QNPGIIIYQYMDD 285
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVF----TKVVEALLAplRLLGVRIFSYLDD 69

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 301016564 286 -LYVGSDLEIGQHRAK*EELRDhLLKWGFTTPDKKHQKEP 324
Cdd:cd03714   70 lLIIASSIKTSEAVLRHLRATL-LANLGFTLNLEKSKLGP 108
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 11-92 7.84e-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: 7.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564   11 VTVKIGGQLREALLDTGADDTVL-----E*INLP--GKWKPKMIGGIGGFIKVRQYDQILIEICGKKA---IGTVLVGPT 80
Cdd:pfam13975   1 VDVTINGRPVRFLVDTGASVTVIsealaERLGLDrlVDAYPVTVRTANGTVRAARVRLDSVKIGGIELrnvPAVVLPGDL 80

                          90
                  ....*....|..
gi 301016564   81 PVNIIGRNMLTQ 92
Cdd:pfam13975  81 DDVLLGMDFLKR 92
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 11-91 3.95e-03

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


Pssm-ID: 133159  Cd Length: 86  Bit Score: 36.54  E-value: 3.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 301016564  11 VTVKIGGQLREALLDTGADDTVLE*iNLPGKWKPKM----IGGIGGFIK--VRQYDQiLIEICGKKAIGTVLVGPT-PVN 83
Cdd:cd06095    1 VTITVEGVPIVFLVDTGATHSVLKS-DLGPKQELSTtsvlIRGVSGQSQqpVTTYRT-LVDLGGHTVSHSFLVVPNcPDP 78


                 ....*...
gi 301016564  84 IIGRNMLT 91
Cdd:cd06095   79 LLGRDLLS 86
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 11-57 5.80e-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: 36.11  E-value: 5.80e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 301016564   11 VTVKIGGQLREALLDTGADDTVL-----E*INLPGKWK--PKMIGGIGGFIKVR 57
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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