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Conserved domains on  [gi|685953734|ref|XP_009270530|]
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Retrotransposable element Tf2 kDa protein type 1 [Wallemia ichthyophaga EXF-994]

Protein Classification

Graphical summary

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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) ...
 105-223 1.25e-52

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: 169.98  E-value: 1.25e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 685953734 105 IVTTDASGSAVGAVLEQE-EDGETRPVAYLSQKLNGSQLNWSIRDKELYAIIVAITKWKHYLLGRSIKVITDHKTIETF- 182
Cdd:cd09274    1 ILETDASDYGIGAVLSQEdDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLl 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 685953734 183 GKAEFSSRIAKWSEIWAEFDIEVVYKPGKTNKAADALSRIA 223
Cdd:cd09274   81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 298-339 5.91e-11

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 57.26  E-value: 5.91e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 685953734  298 REIILHDFHDApvAGHQGTDKVHSSIARHYYWPRMYEDIKKY 339
Cdd:pfam17921   6 RKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKY 45
 
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) ...
 105-223 1.25e-52

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: 169.98  E-value: 1.25e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 685953734 105 IVTTDASGSAVGAVLEQE-EDGETRPVAYLSQKLNGSQLNWSIRDKELYAIIVAITKWKHYLLGRSIKVITDHKTIETF- 182
Cdd:cd09274    1 ILETDASDYGIGAVLSQEdDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLl 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 685953734 183 GKAEFSSRIAKWSEIWAEFDIEVVYKPGKTNKAADALSRIA 223
Cdd:cd09274   81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
74-172 2.84e-41

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 139.94  E-value: 2.84e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 685953734   74 WGEEQQRSFDLLKEKLASAPVLKIPTRTGRFIVTTDASGSAVGAVLEQE-EDGETRPVAYLSQKLNGSQLNWSIRDKELY 152
Cdd:pfam17919   1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEdDDGGERPIAYASRKLSPAERNYSTTEKELL 80

                          90       100
                  ....*....|....*....|
gi 685953734  153 AIIVAITKWKHYLLGRSIKV 172
Cdd:pfam17919  81 AIVFALKKFRHYLLGRKFTV 100
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 298-339 5.91e-11

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 57.26  E-value: 5.91e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 685953734  298 REIILHDFHDApvAGHQGTDKVHSSIARHYYWPRMYEDIKKY 339
Cdd:pfam17921   6 RKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKY 45
 
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) ...
 105-223 1.25e-52

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: 169.98  E-value: 1.25e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 685953734 105 IVTTDASGSAVGAVLEQE-EDGETRPVAYLSQKLNGSQLNWSIRDKELYAIIVAITKWKHYLLGRSIKVITDHKTIETF- 182
Cdd:cd09274    1 ILETDASDYGIGAVLSQEdDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLl 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 685953734 183 GKAEFSSRIAKWSEIWAEFDIEVVYKPGKTNKAADALSRIA 223
Cdd:cd09274   81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
74-172 2.84e-41

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 139.94  E-value: 2.84e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 685953734   74 WGEEQQRSFDLLKEKLASAPVLKIPTRTGRFIVTTDASGSAVGAVLEQE-EDGETRPVAYLSQKLNGSQLNWSIRDKELY 152
Cdd:pfam17919   1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEdDDGGERPIAYASRKLSPAERNYSTTEKELL 80

                          90       100
                  ....*....|....*....|
gi 685953734  153 AIIVAITKWKHYLLGRSIKV 172
Cdd:pfam17919  81 AIVFALKKFRHYLLGRKFTV 100
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 104-200 2.73e-38

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: 132.25  E-value: 2.73e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 685953734  104 FIVTTDASGSAVGAVLEQ-EEDGETRPVAYLSQKLNGSQLNWSIRDKELYAIIVAITKWKHYLLGRSIKVITDHKTIET- 181
Cdd:pfam17917   6 FILETDASDYGIGAVLSQkDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPLKYl 85

                          90
                  ....*....|....*....
gi 685953734  182 FGKAEFSSRIAKWSEIWAE 200
Cdd:pfam17917  86 FTPKELNGRLARWALFLQE 104
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 105-222 2.26e-12

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: 63.07  E-value: 2.26e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 685953734 105 IVTTDASGSAVGAVLEQEEDGETRPVaylsqklngSQLNWSIRDKELYAIIVAITKWKHYLLGRSIKVITDHKT----IE 180
Cdd:cd09275    1 VLFTDASLSGWGAYLLNSRAHGPWSA---------DERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTavayIN 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 685953734 181 TFGKAEFSSRIAKWSEIWA---EFDIEV--VYKPGKTNKAADALSRI 222
Cdd:cd09275   72 KQGGTSSPPLLALARQILLwceQRNIWLraSHIPGVLNTEADRLSRL 118
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 298-339 5.91e-11

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 57.26  E-value: 5.91e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 685953734  298 REIILHDFHDApvAGHQGTDKVHSSIARHYYWPRMYEDIKKY 339
Cdd:pfam17921   6 RKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKY 45
 
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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