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Conserved domains on  [gi|7270688|emb|CAB77850|]
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putative reverse transcriptase [Arabidopsis thaliana]

Protein Classification

retrotransposon gag family protein; reverse transcriptase family protein( domain architecture ID 10509553)

retrotransposon gag family protein that may also contain retropepsin-like aspartic protease and reverse transcriptase (RT) domains; reverse transcriptase family protein (RT) from retrotransposons catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 515-619 1.72e-50

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: 175.09  E-value: 1.72e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688  515 LLAEADVRKTAFRTRYGHFEFVVMPFGLTNAPAAFMRLMNSVFQEFLDEFVIIFIDDILVYSKSPEEHEVHLRRVMEKLR 594
Cdd:cd01647  73 PLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLR 152

                        90       100
                ....*....|....*....|....*
gi 7270688  595 EQKLFAKLSKCSFWQREMGFLGHIV 619
Cdd:cd01647 153 EAGLKLNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 714-813 1.73e-45

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: 158.81  E-value: 1.73e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688  714 VYTDASGVGLGCALMQR-----GKVIAYASRQLRKHEGNYPTHDLEMAAVIFALKIWRSYLYGGKVQVFTDHKSLKYIFT 788
Cdd:cd09274   2 LETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                        90       100
                ....*....|....*....|....*
gi 7270688  789 QPELNLRQRRWMELVADYDLEIAYH 813
Cdd:cd09274  82 QKDLNGRLARWLLLLSEFDFEIEYR 106
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 188-284 3.66e-35

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


:

Pssm-ID: 367628  Cd Length: 97  Bit Score: 128.60  E-value: 3.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688    188 DLTVHFLEGDAHLWWRSVTARRRQADMSWADFMAEFNAKYFPREALDRMEARFLELTQGVRSVREYDRKFNRLLVYAGRG 267
Cdd:pfam03732   1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                          90
                  ....*....|....*..
gi 7270688    268 MEDDQAQMRRFLRGLRP 284
Cdd:pfam03732  81 GRDEEALISAFLRGLRP 97
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 373-427 8.41e-12

Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin 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. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family).


The actual alignment was detected with superfamily member pfam08284:

Pssm-ID: 472175  Cd Length: 134  Bit Score: 63.22  E-value: 8.41e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 7270688    373 KGVDIQIAGESLPADLIISHVELYDVILGMDWLDHYRVHLDCHRGRVSFERPEGS 427
Cdd:pfam08284  80 PSCPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKEREK 134
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 515-619 1.72e-50

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: 175.09  E-value: 1.72e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688  515 LLAEADVRKTAFRTRYGHFEFVVMPFGLTNAPAAFMRLMNSVFQEFLDEFVIIFIDDILVYSKSPEEHEVHLRRVMEKLR 594
Cdd:cd01647  73 PLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLR 152

                        90       100
                ....*....|....*....|....*
gi 7270688  595 EQKLFAKLSKCSFWQREMGFLGHIV 619
Cdd:cd01647 153 EAGLKLNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 714-813 1.73e-45

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: 158.81  E-value: 1.73e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688  714 VYTDASGVGLGCALMQR-----GKVIAYASRQLRKHEGNYPTHDLEMAAVIFALKIWRSYLYGGKVQVFTDHKSLKYIFT 788
Cdd:cd09274   2 LETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                        90       100
                ....*....|....*....|....*
gi 7270688  789 QPELNLRQRRWMELVADYDLEIAYH 813
Cdd:cd09274  82 QKDLNGRLARWLLLLSEFDFEIEYR 106
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 709-805 9.04e-40

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: 141.88  E-value: 9.04e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688    709 GEPYMVYTDASGVGLGCALMQRG-----KVIAYASRQLRKHEGNYPTHDLEMAAVIFALKIWRSYLYGGKVQVFTDHKSL 783
Cdd:pfam17917   3 SKPFILETDASDYGIGAVLSQKDedgkeRPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPL 82

                          90       100
                  ....*....|....*....|..
gi 7270688    784 KYIFTQPELNLRQRRWMELVAD 805
Cdd:pfam17917  83 KYLFTPKELNGRLARWALFLQE 104
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 188-284 3.66e-35

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 128.60  E-value: 3.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688    188 DLTVHFLEGDAHLWWRSVTARRRQADMSWADFMAEFNAKYFPREALDRMEARFLELTQGVRSVREYDRKFNRLLVYAGRG 267
Cdd:pfam03732   1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                          90
                  ....*....|....*..
gi 7270688    268 MEDDQAQMRRFLRGLRP 284
Cdd:pfam03732  81 GRDEEALISAFLRGLRP 97
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 516-619 7.65e-24

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: 99.68  E-value: 7.65e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688    516 LAEADVRKTAFRTR-----------YGHFEFVVMPFGLTNAPAAFMRLMNSVFQEFL---DEFVIIFIDDILVYSKSPEE 581
Cdd:pfam00078  70 LDELDRKLTAFTTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEE 149

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 7270688    582 HEVHLRRVMEKLREQKLFAKLSKCSF--WQREMGFLGHIV 619
Cdd:pfam00078 150 HQEALEEVLEWLKESGLKINPEKTQFflKSKEVKYLGVTL 189
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 373-427 8.41e-12

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.


Pssm-ID: 400537  Cd Length: 134  Bit Score: 63.22  E-value: 8.41e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 7270688    373 KGVDIQIAGESLPADLIISHVELYDVILGMDWLDHYRVHLDCHRGRVSFERPEGS 427
Cdd:pfam08284  80 PSCPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKEREK 134
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 337-405 6.74e-08

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: 50.80  E-value: 6.74e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 7270688  337 LPPESASRGNIRGDPGEQLGAVKVAGGQFLAVLGGAKGVDIQIAGESLPADLIISHVELYDVILGMDWL 405
Cdd:cd00303  23 ISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVILGRPWL 91
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 515-619 1.72e-50

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: 175.09  E-value: 1.72e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688  515 LLAEADVRKTAFRTRYGHFEFVVMPFGLTNAPAAFMRLMNSVFQEFLDEFVIIFIDDILVYSKSPEEHEVHLRRVMEKLR 594
Cdd:cd01647  73 PLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLR 152

                        90       100
                ....*....|....*....|....*
gi 7270688  595 EQKLFAKLSKCSFWQREMGFLGHIV 619
Cdd:cd01647 153 EAGLKLNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 714-813 1.73e-45

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: 158.81  E-value: 1.73e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688  714 VYTDASGVGLGCALMQR-----GKVIAYASRQLRKHEGNYPTHDLEMAAVIFALKIWRSYLYGGKVQVFTDHKSLKYIFT 788
Cdd:cd09274   2 LETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                        90       100
                ....*....|....*....|....*
gi 7270688  789 QPELNLRQRRWMELVADYDLEIAYH 813
Cdd:cd09274  82 QKDLNGRLARWLLLLSEFDFEIEYR 106
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 709-805 9.04e-40

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: 141.88  E-value: 9.04e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688    709 GEPYMVYTDASGVGLGCALMQRG-----KVIAYASRQLRKHEGNYPTHDLEMAAVIFALKIWRSYLYGGKVQVFTDHKSL 783
Cdd:pfam17917   3 SKPFILETDASDYGIGAVLSQKDedgkeRPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPL 82

                          90       100
                  ....*....|....*....|..
gi 7270688    784 KYIFTQPELNLRQRRWMELVAD 805
Cdd:pfam17917  83 KYLFTPKELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
682-776 1.94e-35

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 129.54  E-value: 1.94e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688    682 WSPECEEGFVSLKEMLTSTPVLALPEHGEPYMVYTDASGVGLGCALMQRG-----KVIAYASRQLRKHEGNYPTHDLEMA 756
Cdd:pfam17919   1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDddggeRPIAYASRKLSPAERNYSTTEKELL 80

                          90       100
                  ....*....|....*....|
gi 7270688    757 AVIFALKIWRSYLYGGKVQV 776
Cdd:pfam17919  81 AIVFALKKFRHYLLGRKFTV 100
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 188-284 3.66e-35

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 128.60  E-value: 3.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688    188 DLTVHFLEGDAHLWWRSVTARRRQADMSWADFMAEFNAKYFPREALDRMEARFLELTQGVRSVREYDRKFNRLLVYAGRG 267
Cdd:pfam03732   1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                          90
                  ....*....|....*..
gi 7270688    268 MEDDQAQMRRFLRGLRP 284
Cdd:pfam03732  81 GRDEEALISAFLRGLRP 97
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 516-619 7.65e-24

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: 99.68  E-value: 7.65e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688    516 LAEADVRKTAFRTR-----------YGHFEFVVMPFGLTNAPAAFMRLMNSVFQEFL---DEFVIIFIDDILVYSKSPEE 581
Cdd:pfam00078  70 LDELDRKLTAFTTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEE 149

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 7270688    582 HEVHLRRVMEKLREQKLFAKLSKCSF--WQREMGFLGHIV 619
Cdd:pfam00078 150 HQEALEEVLEWLKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 536-619 4.27e-14

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: 68.53  E-value: 4.27e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688  536 VVMPFGLTNAPAAFMRLMNSVFQEF----LDEFVIIFIDDILVYSKSpEEHEVHLRRVMEKLREQKLFAKLSKCSF--WQ 609
Cdd:cd00304  10 IPLPQGSPLSPALANLYMEKLEAPIlkqlLDITLIRYVDDLVVIAKS-EQQAVKKRELEEFLARLGLNLSDEKTQFteKE 88

                        90
                ....*....|
gi 7270688  610 REMGFLGHIV 619
Cdd:cd00304  89 KKFKFLGILV 98
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 373-427 8.41e-12

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.


Pssm-ID: 400537  Cd Length: 134  Bit Score: 63.22  E-value: 8.41e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 7270688    373 KGVDIQIAGESLPADLIISHVELYDVILGMDWLDHYRVHLDCHRGRVSFERPEGS 427
Cdd:pfam08284  80 PSCPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKEREK 134
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 337-405 6.74e-08

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: 50.80  E-value: 6.74e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 7270688  337 LPPESASRGNIRGDPGEQLGAVKVAGGQFLAVLGGAKGVDIQIAGESLPADLIISHVELYDVILGMDWL 405
Cdd:cd00303  23 ISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVILGRPWL 91
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 516-592 3.05e-06

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: 48.82  E-value: 3.05e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688  516 LAEADVRKTAF-------RTRYGHFEFVVMPFGLTNAPAAFMRLMNSVFQEFLDEF----VIIFIDDILVYSKSPEEHEV 584
Cdd:cd01645 100 LHPDDRERFAFtvpsinnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYpdivIYHYMDDILIASDLEGQLRE 179

                        90
                ....*....|.
gi 7270688  585 ---HLRRVMEK 592
Cdd:cd01645 180 iyeELRQTLLR 190
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 715-779 3.29e-06

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: 46.89  E-value: 3.29e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 7270688  715 YTDASGVGLGCALMqrgkvIAYASRQLRKHEGNYPTHDLEMAAVIFALKIWRSYLYGGKVQVFTD 779
Cdd:cd09275   3 FTDASLSGWGAYLL-----NSRAHGPWSADERNKHINLLELKAVLLALQHFAAELKNRKILIRTD 62
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 525-616 7.10e-05

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: 43.10  E-value: 7.10e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7270688  525 AFRTRYGHFEFVVMPFGLTNAPAAFMRLMNSVFQEFLDEFVIIF--IDDILVYSKSpEEHEVHLRRVMEKLREQKLFAKL 602
Cdd:cd03714  21 GFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFsyLDDLLIIASS-IKTSEAVLRHLRATLLANLGFTL 99

                        90
                ....*....|....*..
gi 7270688  603 SKC-SFW--QREMGFLG 616
Cdd:cd03714 100 NLEkSKLgpTQRITFLG 116
 
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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