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Conserved domains on  [gi|27901694|gb|AAO26683|]
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gag-pol polyprotein, partial [Vitis vinifera]

Protein Classification

Ty1/Copia family ribonuclease HI( domain architecture ID 10276979)

Ty1/Copia family ribonuclease HI in long-term repeat (LTR) retroelements is involved in the 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

EC:  2.7.7.49
Gene Ontology:  GO:0003964|GO:0032197|GO:0003723

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 169-307 1.89e-84

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 250.85  E-value: 1.89e-84
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27901694 169 ECFSDADWAGSKFDRRSTTGYCVFFGGNLVAWKSKKQSVVSRSSAESEYRAMSRATCEIIWIHQLLCEVGMKCTMPAKLW 248
Cdd:cd09272   1 EGYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIY 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 27901694 249 CDNQAALHIAANPVYHERTKHIEVDCHFIREKIEENLVSTGYVKTGEQLGDIFTKALNG 307
Cdd:cd09272  81 CDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 4-85 1.30e-14

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


The actual alignment was detected with superfamily member pfam07727:

Pssm-ID: 400190  Cd Length: 243  Bit Score: 72.24  E-value: 1.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27901694     4 ILLVVYVDDIVITGNEHAGISELKTFMHSKFHTKDLGELKYFLGIEVSRSKKGMFLSQRKYVLDLLKETGKIEAKPCTTP 83
Cdd:pfam07727 162 LIVGLYVDDMFITGSDITIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQHNYLNSVIKKFNLTNNNGKYTP 241


                  ..
gi 27901694    84 MV 85
Cdd:pfam07727 242 II 243
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 169-307 1.89e-84

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 250.85  E-value: 1.89e-84
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27901694 169 ECFSDADWAGSKFDRRSTTGYCVFFGGNLVAWKSKKQSVVSRSSAESEYRAMSRATCEIIWIHQLLCEVGMKCTMPAKLW 248
Cdd:cd09272   1 EGYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIY 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 27901694 249 CDNQAALHIAANPVYHERTKHIEVDCHFIREKIEENLVSTGYVKTGEQLGDIFTKALNG 307
Cdd:cd09272  81 CDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 4-85 1.30e-14

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 400190  Cd Length: 243  Bit Score: 72.24  E-value: 1.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27901694     4 ILLVVYVDDIVITGNEHAGISELKTFMHSKFHTKDLGELKYFLGIEVSRSKKGMFLSQRKYVLDLLKETGKIEAKPCTTP 83
Cdd:pfam07727 162 LIVGLYVDDMFITGSDITIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQHNYLNSVIKKFNLTNNNGKYTP 241


                  ..
gi 27901694    84 MV 85
Cdd:pfam07727 242 II 243
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 169-307 1.89e-84

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 250.85  E-value: 1.89e-84
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27901694 169 ECFSDADWAGSKFDRRSTTGYCVFFGGNLVAWKSKKQSVVSRSSAESEYRAMSRATCEIIWIHQLLCEVGMKCTMPAKLW 248
Cdd:cd09272   1 EGYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIY 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 27901694 249 CDNQAALHIAANPVYHERTKHIEVDCHFIREKIEENLVSTGYVKTGEQLGDIFTKALNG 307
Cdd:cd09272  81 CDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 4-85 1.30e-14

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 400190  Cd Length: 243  Bit Score: 72.24  E-value: 1.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27901694     4 ILLVVYVDDIVITGNEHAGISELKTFMHSKFHTKDLGELKYFLGIEVSRSKKGMFLSQRKYVLDLLKETGKIEAKPCTTP 83
Cdd:pfam07727 162 LIVGLYVDDMFITGSDITIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQHNYLNSVIKKFNLTNNNGKYTP 241


                  ..
gi 27901694    84 MV 85
Cdd:pfam07727 242 II 243
 
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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