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Conserved domains on  [gi|1585141376]
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Chain A, Gag-Pol polyprotein

Protein Classification

RNA-dependent RNA polymerase family protein; pol protein pepsin-like aspartate protease and reverse transcriptase( domain architecture ID 10132841)

RNA-dependent RNA polymerase (RdRp) family protein similar to the RdRp catalytic domain of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2; pol protein pepsin-like aspartate protease and reverse transcriptase; the retropepsin-like (A2 family) peptidase is an aspartic protease that hydrolyzes the peptide bonds of substrates

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 39-254 2.10e-130

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: 367.44  E-value: 2.10e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376  39 PVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLS 118
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376 119 GLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDpemgisGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDL 198
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1585141376 199 ILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLL 254
Cdd:cd03715   155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
 
Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 39-254 2.10e-130

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: 367.44  E-value: 2.10e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376  39 PVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLS 118
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376 119 GLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDpemgisGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDL 198
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1585141376 199 ILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLL 254
Cdd:cd03715   155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 82-252 3.09e-36

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: 127.03  E-value: 3.09e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376  82 VKKPGTNDYRPV----QDLREVNKRVED-IHPTVPNPYNLlSGLPP------SHQWYTVLDLKDAFFCLRLHPTSQPLFA 150
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrLKPENLDSPPQ-PGFRPglaklkKAKWFLKLDLKKAFDQVPLDELDRKLTA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376 151 F----EWRDPEMGISGQL-TWTRLPQGFKNSPTLFDEALHRDLADFRiQHPDLILLQYVDDLLLAATSELDCQQGTRALL 225
Cdd:pfam00078  80 FttppININWNGELSGGRyEWKGLPQGLVLSPALFQLFMNELLRPLR-KRAGLTLVRYADDILIFSKSEEEHQEALEEVL 158

                         170       180
                  ....*....|....*....|....*....
gi 1585141376 226 QTLGNLGYRASAKKAQIC--QKQVKYLGY 252
Cdd:pfam00078 159 EWLKESGLKINPEKTQFFlkSKEVKYLGV 187
 
Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 39-254 2.10e-130

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: 367.44  E-value: 2.10e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376  39 PVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLS 118
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376 119 GLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDpemgisGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDL 198
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1585141376 199 ILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLL 254
Cdd:cd03715   155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 39-254 6.10e-46

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: 152.82  E-value: 6.10e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376  39 PVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPgTNDYRPVQDLREVNKRVED---IHPTVPNPyn 115
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKK-SGKWRLLHDLRAVNAQTQDmgaLQPGLPHP-- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376 116 llSGLPpsHQWY-TVLDLKDAFFCLRLHPTSQPLFAFEWrdPEMGISG---QLTWTRLPQGFKNSPTLFDEALHRDLADF 191
Cdd:cd01645    78 --AALP--KGWPlIVLDLKDCFFSIPLHPDDRERFAFTV--PSINNKGpakRYQWKVLPQGMKNSPTICQSFVAQALEPF 151

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1585141376 192 RIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQIcQKQVKYLGYLL 254
Cdd:cd01645   152 RKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQK-EPPFQYLGYEL 213
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 66-253 6.72e-38

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: 130.79  E-value: 6.72e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376  66 GILVPCQSPWNTPLLPVKKPGtNDYRPVQDLREVNKRVE-DIHPtVPNPYNLLSGLPPSHqWYTVLDLKDAFFCLRLHPT 144
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKD-GKLRLCVDYRKLNKVTIkDRYP-LPTIDELLEELAGAK-VFSKLDLRSGYHQIPLAEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376 145 SQPLFAFEWRDpemgisGQLTWTRLPQGFKNSPTLF----DEALHRDLADFriqhpdliLLQYVDDLLLAATSELDCQQG 220
Cdd:cd01647    78 SRPKTAFRTPF------GLYEYTRMPFGLKNAPATFqrlmNKILGDLLGDF--------VEVYLDDILVYSKTEEEHLEH 143

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1585141376 221 TRALLQTLGNLGYRASAKKAQICQKQVKYLGYL 253
Cdd:cd01647   144 LREVLERLREAGLKLNPEKCEFGVPEVEFLGHI 176
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 82-252 3.09e-36

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: 127.03  E-value: 3.09e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376  82 VKKPGTNDYRPV----QDLREVNKRVED-IHPTVPNPYNLlSGLPP------SHQWYTVLDLKDAFFCLRLHPTSQPLFA 150
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrLKPENLDSPPQ-PGFRPglaklkKAKWFLKLDLKKAFDQVPLDELDRKLTA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376 151 F----EWRDPEMGISGQL-TWTRLPQGFKNSPTLFDEALHRDLADFRiQHPDLILLQYVDDLLLAATSELDCQQGTRALL 225
Cdd:pfam00078  80 FttppININWNGELSGGRyEWKGLPQGLVLSPALFQLFMNELLRPLR-KRAGLTLVRYADDILIFSKSEEEHQEALEEVL 158

                         170       180
                  ....*....|....*....|....*....
gi 1585141376 226 QTLGNLGYRASAKKAQIC--QKQVKYLGY 252
Cdd:pfam00078 159 EWLKESGLKINPEKTQFFlkSKEVKYLGV 187
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 168-254 1.74e-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: 78.16  E-value: 1.74e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376 168 RLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSElDCQQGTRALLQTLGNLGYRASAKKAQ--ICQK 245
Cdd:cd00304    11 PLPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE-QQAVKKRELEEFLARLGLNLSDEKTQftEKEK 89


                  ....*....
gi 1585141376 246 QVKYLGYLL 254
Cdd:cd00304    90 KFKFLGILV 98
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 130-251 1.07e-11

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: 60.44  E-value: 1.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376 130 LDLKDAFFCLRLHPTSQPLFAFEWRDPemgisgQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILlqYVDDLLL 209
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGFAWQGE------TYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFS--YLDDLLI 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1585141376 210 AATSELDCQQGTRALLQT-LGNLGYRASAKKAQIC-QKQVKYLG 251
Cdd:cd03714    73 IASSIKTSEAVLRHLRATlLANLGFTLNLEKSKLGpTQRITFLG 116
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 131-229 2.28e-04

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: 41.14  E-value: 2.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585141376 131 DLKDAFFCLRLHPTSQPLFAFEWR-DPEMGISGQLTWTRLPQGFKNSPTLFDEALHRDLADFriQHPDL--ILLQ--YVD 205
Cdd:cd01644    65 DIEKMFHQVKVRPEDRDVLRFLWRkDGDEPKPIEYRMTVVPFGAASAPFLANRALKQHAEDH--PHEAAakIIKRnfYVD 142

                          90       100
                  ....*....|....*....|....*..
gi 1585141376 206 DLLLAATSELDCQ---QGTRALLQTLG 229
Cdd:cd01644   143 DILVSTDTLNEAVnvaKRLIALLKKGG 169
 
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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