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Conserved domains on  [gi|130592|sp|P03554|]
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RecName: Full=Enzymatic polyprotein; Includes: RecName: Full=Aspartic protease; Includes: RecName: Full=Endonuclease; Includes: RecName: Full=Reverse transcriptase

Protein Classification

reverse transcriptase/ribonuclease H family protein( domain architecture ID 10490038)

reverse transcriptase (RT)/ribonuclease H (RNase H) family protein from retrotransposons catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements, and may be an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_A3 pfam02160
Cauliflower mosaic virus peptidase (A3);
20-224 2.69e-116

Cauliflower mosaic virus peptidase (A3);


:

Pssm-ID: 280345  Cd Length: 208  Bit Score: 347.08  E-value: 2.69e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592      20 NPNSIYIKGRLYFKGYKKIELHCFVDTGASLCIASKFVIPEEHWVNAERPIMVKIADGSSITISKVCKDIDLIIAGEIFR 99
Cdd:pfam02160   1 NPNSIFIKGRIGFKGFKAIELHCFIDTGASLCFAKKFIIPEEHWEIAEQPIEIIIADGSKHTIREACKDIDLIIAGEEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592     100 IPTVYQQESGIDFIIGNNFCQLYEPFIQFTDRVIFTKNKS-YPVHIAKLTRAVRVGTEGFLESMKKRSKTQQPEPVNIST 178
Cdd:pfam02160  81 IPIIYLHDSGIDFIIGNNFCKLYEPFIQFLDRIEFRKKKLnNPKEIAKISRAILTGNEGFKESFEKIHICLEKELFFISI 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 130592     179 NKIENPLEEIAILSEGRRLSEEKLFITQQ-RMQKIEELLEK-VCSENP 224
Cdd:pfam02160 161 EEIENPLEEIAIEHEGDRLSEEKLFIGLLiEIQKIDELLEInVCNEIP 208
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 273-452 1.02e-60

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: 200.90  E-value: 1.02e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   273 KVIKPSKSPHMAPAFLVNneaeKRRGKKRMVVNYKAMNKATVGDAYNLPNKDELLTLIRGKKIFSSFDCKSGFWQVLLDQ 352
Cdd:cd01647   1 GIIEPSSSPYASPVVVVK----KKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAE 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   353 ESRPLTAFTCPQGHYEWNVVPFGLKQAPSIFQRHMDEAFR-VFRKFCCVYVDDILVFSNNEEDHLLHVAMILQKCNQHGI 431
Cdd:cd01647  77 ESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGdLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGL 156

                       170       180
                ....*....|....*....|.
gi 130592   432 ILSKKKAQLFKKKINFLGLEI 452
Cdd:cd01647 157 KLNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 547-672 2.33e-33

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


:

Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 124.14  E-value: 2.33e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   547 IIETDASDDYWGGMLKaikINEGTNTELICRYASGSFKAAEKNYHSNDKETLAVINTIKKFSIYLTPVHFLIRTDN---T 623
Cdd:cd09274   1 ILETDASDYGIGAVLS---QEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHkalK 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 130592   624 HFKSFVNLNykgdsklGRNIRWQAWLSHYSFDVEHIKGTDNHFADFLSR 672
Cdd:cd09274  78 YLLTQKDLN-------GRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
 
Name Accession Description Interval E-value
Peptidase_A3 pfam02160
Cauliflower mosaic virus peptidase (A3);
20-224 2.69e-116

Cauliflower mosaic virus peptidase (A3);


Pssm-ID: 280345  Cd Length: 208  Bit Score: 347.08  E-value: 2.69e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592      20 NPNSIYIKGRLYFKGYKKIELHCFVDTGASLCIASKFVIPEEHWVNAERPIMVKIADGSSITISKVCKDIDLIIAGEIFR 99
Cdd:pfam02160   1 NPNSIFIKGRIGFKGFKAIELHCFIDTGASLCFAKKFIIPEEHWEIAEQPIEIIIADGSKHTIREACKDIDLIIAGEEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592     100 IPTVYQQESGIDFIIGNNFCQLYEPFIQFTDRVIFTKNKS-YPVHIAKLTRAVRVGTEGFLESMKKRSKTQQPEPVNIST 178
Cdd:pfam02160  81 IPIIYLHDSGIDFIIGNNFCKLYEPFIQFLDRIEFRKKKLnNPKEIAKISRAILTGNEGFKESFEKIHICLEKELFFISI 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 130592     179 NKIENPLEEIAILSEGRRLSEEKLFITQQ-RMQKIEELLEK-VCSENP 224
Cdd:pfam02160 161 EEIENPLEEIAIEHEGDRLSEEKLFIGLLiEIQKIDELLEInVCNEIP 208
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 273-452 1.02e-60

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: 200.90  E-value: 1.02e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   273 KVIKPSKSPHMAPAFLVNneaeKRRGKKRMVVNYKAMNKATVGDAYNLPNKDELLTLIRGKKIFSSFDCKSGFWQVLLDQ 352
Cdd:cd01647   1 GIIEPSSSPYASPVVVVK----KKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAE 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   353 ESRPLTAFTCPQGHYEWNVVPFGLKQAPSIFQRHMDEAFR-VFRKFCCVYVDDILVFSNNEEDHLLHVAMILQKCNQHGI 431
Cdd:cd01647  77 ESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGdLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGL 156

                       170       180
                ....*....|....*....|.
gi 130592   432 ILSKKKAQLFKKKINFLGLEI 452
Cdd:cd01647 157 KLNPEKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 297-452 1.27e-39

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: 143.98  E-value: 1.27e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592     297 RGKKRMV----VNYKAMNKATVG-------DAYNLPNKDELLTLIRGKKIFSSFDCKSGFWQVLLDQESRPLTAFTCP-- 363
Cdd:pfam00078   6 KGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPpi 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592     364 ---------QGHYEWNVVPFGLKQAPSIFQRHMDEAFRVFRK----FCCVYVDDILVFSNNEEDHLLHVAMILQKCNQHG 430
Cdd:pfam00078  86 ninwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKraglTLVRYADDILIFSKSEEEHQEALEEVLEWLKESG 165

                         170       180
                  ....*....|....*....|....
gi 130592     431 IILSKK--KAQLFKKKINFLGLEI 452
Cdd:pfam00078 166 LKINPEktQFFLKSKEVKYLGVTL 189
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 547-672 2.33e-33

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 124.14  E-value: 2.33e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   547 IIETDASDDYWGGMLKaikINEGTNTELICRYASGSFKAAEKNYHSNDKETLAVINTIKKFSIYLTPVHFLIRTDN---T 623
Cdd:cd09274   1 ILETDASDYGIGAVLS---QEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHkalK 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 130592   624 HFKSFVNLNykgdsklGRNIRWQAWLSHYSFDVEHIKGTDNHFADFLSR 672
Cdd:cd09274  78 YLLTQKDLN-------GRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 542-651 5.65e-27

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 105.28  E-value: 5.65e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592     542 PEEKLIIETDASDDYWGGMLKAIKINegtNTELICRYASGSFKAAEKNYHSNDKETLAVINTIKKFSIYLTPVHFLIRTD 621
Cdd:pfam17917   2 PSKPFILETDASDYGIGAVLSQKDED---GKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTD 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 130592     622 NTHFKSFvnlnYKGDSKLGRNIRWQAWLSH 651
Cdd:pfam17917  79 HKPLKYL----FTPKELNGRLARWALFLQE 104
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 36-120 3.31e-06

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, 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: 133136  Cd Length: 92  Bit Score: 45.79  E-value: 3.31e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592    36 KKIELHCFVDTGASLCIASKFVIPEEH--WVNAERPIMVKIADGSSITISKVCKDIDLIIAGEIFRIPTVYQQESGIDFI 113
Cdd:cd00303   6 NGVPVRALVDSGASVNFISESLAKKLGlpPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVI 85


                ....*..
gi 130592   114 IGNNFCQ 120
Cdd:cd00303  86 LGRPWLE 92
 
Name Accession Description Interval E-value
Peptidase_A3 pfam02160
Cauliflower mosaic virus peptidase (A3);
20-224 2.69e-116

Cauliflower mosaic virus peptidase (A3);


Pssm-ID: 280345  Cd Length: 208  Bit Score: 347.08  E-value: 2.69e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592      20 NPNSIYIKGRLYFKGYKKIELHCFVDTGASLCIASKFVIPEEHWVNAERPIMVKIADGSSITISKVCKDIDLIIAGEIFR 99
Cdd:pfam02160   1 NPNSIFIKGRIGFKGFKAIELHCFIDTGASLCFAKKFIIPEEHWEIAEQPIEIIIADGSKHTIREACKDIDLIIAGEEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592     100 IPTVYQQESGIDFIIGNNFCQLYEPFIQFTDRVIFTKNKS-YPVHIAKLTRAVRVGTEGFLESMKKRSKTQQPEPVNIST 178
Cdd:pfam02160  81 IPIIYLHDSGIDFIIGNNFCKLYEPFIQFLDRIEFRKKKLnNPKEIAKISRAILTGNEGFKESFEKIHICLEKELFFISI 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 130592     179 NKIENPLEEIAILSEGRRLSEEKLFITQQ-RMQKIEELLEK-VCSENP 224
Cdd:pfam02160 161 EEIENPLEEIAIEHEGDRLSEEKLFIGLLiEIQKIDELLEInVCNEIP 208
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 273-452 1.02e-60

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: 200.90  E-value: 1.02e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   273 KVIKPSKSPHMAPAFLVNneaeKRRGKKRMVVNYKAMNKATVGDAYNLPNKDELLTLIRGKKIFSSFDCKSGFWQVLLDQ 352
Cdd:cd01647   1 GIIEPSSSPYASPVVVVK----KKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAE 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   353 ESRPLTAFTCPQGHYEWNVVPFGLKQAPSIFQRHMDEAFR-VFRKFCCVYVDDILVFSNNEEDHLLHVAMILQKCNQHGI 431
Cdd:cd01647  77 ESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGdLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGL 156

                       170       180
                ....*....|....*....|.
gi 130592   432 ILSKKKAQLFKKKINFLGLEI 452
Cdd:cd01647 157 KLNPEKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 297-452 1.27e-39

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: 143.98  E-value: 1.27e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592     297 RGKKRMV----VNYKAMNKATVG-------DAYNLPNKDELLTLIRGKKIFSSFDCKSGFWQVLLDQESRPLTAFTCP-- 363
Cdd:pfam00078   6 KGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPpi 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592     364 ---------QGHYEWNVVPFGLKQAPSIFQRHMDEAFRVFRK----FCCVYVDDILVFSNNEEDHLLHVAMILQKCNQHG 430
Cdd:pfam00078  86 ninwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKraglTLVRYADDILIFSKSEEEHQEALEEVLEWLKESG 165

                         170       180
                  ....*....|....*....|....
gi 130592     431 IILSKK--KAQLFKKKINFLGLEI 452
Cdd:pfam00078 166 LKINPEktQFFLKSKEVKYLGVTL 189
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 547-672 2.33e-33

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 124.14  E-value: 2.33e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   547 IIETDASDDYWGGMLKaikINEGTNTELICRYASGSFKAAEKNYHSNDKETLAVINTIKKFSIYLTPVHFLIRTDN---T 623
Cdd:cd09274   1 ILETDASDYGIGAVLS---QEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHkalK 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 130592   624 HFKSFVNLNykgdsklGRNIRWQAWLSHYSFDVEHIKGTDNHFADFLSR 672
Cdd:cd09274  78 YLLTQKDLN-------GRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 542-651 5.65e-27

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 105.28  E-value: 5.65e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592     542 PEEKLIIETDASDDYWGGMLKAIKINegtNTELICRYASGSFKAAEKNYHSNDKETLAVINTIKKFSIYLTPVHFLIRTD 621
Cdd:pfam17917   2 PSKPFILETDASDYGIGAVLSQKDED---GKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTD 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 130592     622 NTHFKSFvnlnYKGDSKLGRNIRWQAWLSH 651
Cdd:pfam17917  79 HKPLKYL----FTPKELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
516-618 1.04e-20

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 87.17  E-value: 1.04e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592     516 WTKEDTLYMQKVKKNLQGFPPLHHPLPEEKLIIETDASDDYWGGMLKAIKINEGtntELICRYASGSFKAAEKNYHSNDK 595
Cdd:pfam17919   1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGG---ERPIAYASRKLSPAERNYSTTEK 77

                          90       100
                  ....*....|....*....|...
gi 130592     596 ETLAVINTIKKFSIYLTPVHFLI 618
Cdd:pfam17919  78 ELLAIVFALKKFRHYLLGRKFTV 100
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 249-414 9.80e-20

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: 88.17  E-value: 9.80e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   249 VKPMKYSPMDREEFDKQIKELLDLKVIKPSKSPHMAPAFLVnneaEKRRGKK-RMVVNYKAMNKATVGDAYNLPNKDELL 327
Cdd:cd03715   4 QKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPV----KKPGGNDyRMVQDLRLVNQAVLPIHPAVPNPYTLL 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   328 TLIRGK-KIFSSFDCKSGFWQVLLDQESRPLTAFTCPQGHYEWNVVPFGLKQAPSIFQR--HMD-EAFRVFRKFCCV--Y 401
Cdd:cd03715  80 SLLPPKhQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEalARDlAPFPLEHEGTILlqY 159

                       170
                ....*....|...
gi 130592   402 VDDILVFSNNEED 414
Cdd:cd03715 160 VDDLLLAADSEED 172
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 266-434 2.61e-17

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: 81.18  E-value: 2.61e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   266 IKELLDLKVIKPSKSPHMAPAFLVnneaEKRRGKKRMVVNYKAMNKATV-------GdaynLPNkdelLTLIRGKKIFSS 338
Cdd:cd01645  21 VTEQLKEGHIEPSTSPWNTPVFVI----KKKSGKWRLLHDLRAVNAQTQdmgalqpG----LPH----PAALPKGWPLIV 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   339 FDCKSGFWQVLLDQESRPLTAFTCP----QG---HYEWNVVPFGLKQAPSIFQRHMDEAFRVFRK---FCCV--YVDDIL 406
Cdd:cd01645  89 LDLKDCFFSIPLHPDDRERFAFTVPsinnKGpakRYQWKVLPQGMKNSPTICQSFVAQALEPFRKqypDIVIyhYMDDIL 168

                       170       180
                ....*....|....*....|....*...
gi 130592   407 VFSNNEEDHLLHVAMILQKCNQHGIILS 434
Cdd:cd01645 169 IASDLEGQLREIYEELRQTLLRWGLTIP 196
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 547-675 1.32e-10

DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 59.22  E-value: 1.32e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   547 IIETDASDDYWGGMLKaikinegtnteliCRYASGSFKAAEKNYHSNDKETLAVINTIKKFSIYLTPVHFLIRTDNTHFK 626
Cdd:cd09275   1 VLFTDASLSGWGAYLL-------------NSRAHGPWSADERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTAV 67

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 130592   627 SFVN----LNYKGDSKLGRNIRWQA-----WLSHysfdvEHIKGTDNHFADFLSREFN 675
Cdd:cd09275  68 AYINkqggTSSPPLLALARQILLWCeqrniWLRA-----SHIPGVLNTEADRLSRLGL 120
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 339-452 1.33e-10

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: 59.28  E-value: 1.33e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   339 FDCKSGFWQVLLDQESRPLTAFtCPQG-HYEWNVVPFGLKQAPSIFQRHMDEAFRVFRKF---CCVYVDDILVFSNNeED 414
Cdd:cd03714   1 VDLKDAYFHIPILPRSRDLLGF-AWQGeTYQFKALPFGLSLAPRVFTKVVEALLAPLRLLgvrIFSYLDDLLIIASS-IK 78

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 130592   415 HLLHVAMILQKCN--QHGIILSKKKAQLF-KKKINFLGLEI 452
Cdd:cd03714  79 TSEAVLRHLRATLlaNLGFTLNLEKSKLGpTQRITFLGLEL 119
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 36-120 3.31e-06

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, 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: 133136  Cd Length: 92  Bit Score: 45.79  E-value: 3.31e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592    36 KKIELHCFVDTGASLCIASKFVIPEEH--WVNAERPIMVKIADGSSITISKVCKDIDLIIAGEIFRIPTVYQQESGIDFI 113
Cdd:cd00303   6 NGVPVRALVDSGASVNFISESLAKKLGlpPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVI 85


                ....*..
gi 130592   114 IGNNFCQ 120
Cdd:cd00303  86 LGRPWLE 92
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 340-415 2.86e-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: 39.60  E-value: 2.86e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130592   340 DCKSGFWQVLLDQESRPLTAF-------TCPQGHYEWNVVPFGLKQAPSIFQR----------HMDEAFRVFRKFccvYV 402
Cdd:cd01644  65 DIEKMFHQVKVRPEDRDVLRFlwrkdgdEPKPIEYRMTVVPFGAASAPFLANRalkqhaedhpHEAAAKIIKRNF---YV 141

                        90
                ....*....|...
gi 130592   403 DDILVFSNNEEDH 415
Cdd:cd01644 142 DDILVSTDTLNEA 154
 
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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