Retrovirus-related Pol polyprotein from transposon 17.6 [Vitis vinifera]
Protein Classification
pol polyprotein( domain architecture ID 10084787)
retrovirus-related pol polyprotein is a polyprotein supplying protease, reverse transcriptase, RNase H and integrase functions.
List of domain hits
| Name | Accession | Description | Interval | E-value | |||
| RNase_HI_RT_Ty3 | cd09274 | Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ... |
800-919 | 2.08e-64 | |||
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: 212.74 E-value: 2.08e-64
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| RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
569-706 | 3.74e-57 | |||
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: 194.74 E-value: 3.74e-57
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| retropepsin_like | cd00303 | Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ... |
327-400 | 5.04e-05 | |||
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: 43.09 E-value: 5.04e-05
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| Name | Accession | Description | Interval | E-value | ||||
| RNase_HI_RT_Ty3 | cd09274 | Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ... |
800-919 | 2.08e-64 | ||||
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: 212.74 E-value: 2.08e-64
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| RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
569-706 | 3.74e-57 | ||||
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: 194.74 E-value: 3.74e-57
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| RT_RNaseH | pfam17917 | RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ... |
794-896 | 2.95e-46 | ||||
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: 160.75 E-value: 2.95e-46
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| RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
552-706 | 1.33e-20 | ||||
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: 90.44 E-value: 1.33e-20
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| retropepsin_like | cd00303 | Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ... |
327-400 | 5.04e-05 | ||||
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: 43.09 E-value: 5.04e-05
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| Name | Accession | Description | Interval | E-value | ||||
| RNase_HI_RT_Ty3 | cd09274 | Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ... |
800-919 | 2.08e-64 | ||||
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: 212.74 E-value: 2.08e-64
|
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| RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
569-706 | 3.74e-57 | ||||
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: 194.74 E-value: 3.74e-57
|
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| RT_RNaseH | pfam17917 | RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ... |
794-896 | 2.95e-46 | ||||
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: 160.75 E-value: 2.95e-46
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| RT_RNaseH_2 | pfam17919 | RNase H-like domain found in reverse transcriptase; |
769-867 | 6.01e-41 | ||||
RNase H-like domain found in reverse transcriptase; Pssm-ID: 465567 [Multi-domain] Cd Length: 100 Bit Score: 145.72 E-value: 6.01e-41
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| RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
552-706 | 1.33e-20 | ||||
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: 90.44 E-value: 1.33e-20
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| RNase_HI_RT_DIRS1 | cd09275 | DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ... |
800-918 | 3.00e-11 | ||||
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: 61.53 E-value: 3.00e-11
|
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| retropepsin_like | cd00303 | Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ... |
327-400 | 5.04e-05 | ||||
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: 43.09 E-value: 5.04e-05
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| RT_DIRS1 | cd03714 | RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ... |
596-706 | 6.67e-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: 43.49 E-value: 6.67e-05
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| RT_like | cd00304 | RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ... |
624-706 | 9.60e-03 | ||||
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: 36.56 E-value: 9.60e-03
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| Blast search parameters | ||||
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