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retrotransposon-like protein 1 [Homo sapiens]
List of domain hits
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Name | Accession | Description | Interval | E-value | ||||
RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
607-782 | 1.07e-39 | ||||
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: 145.43 E-value: 1.07e-39
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RT_RNaseH_2 | pfam17919 | RNase H-like domain found in reverse transcriptase; |
845-942 | 5.99e-23 | ||||
RNase H-like domain found in reverse transcriptase; : Pssm-ID: 465567 [Multi-domain] Cd Length: 100 Bit Score: 94.49 E-value: 5.99e-23
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retropepsin_like | cd00303 | Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ... |
413-510 | 3.34e-19 | ||||
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: 83.54 E-value: 3.34e-19
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Retrotrans_gag super family | cl46289 | Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ... |
200-278 | 1.27e-12 | ||||
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. The actual alignment was detected with superfamily member pfam16297: Pssm-ID: 480629 Cd Length: 112 Bit Score: 65.71 E-value: 1.27e-12
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Retrotrans_gag super family | cl46289 | Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ... |
240-332 | 3.44e-11 | ||||
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. The actual alignment was detected with superfamily member pfam03732: Pssm-ID: 480629 Cd Length: 97 Bit Score: 60.81 E-value: 3.44e-11
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PHA03169 super family | cl27451 | hypothetical protein; Provisional |
14-160 | 9.36e-04 | ||||
hypothetical protein; Provisional The actual alignment was detected with superfamily member PHA03169: Pssm-ID: 223003 [Multi-domain] Cd Length: 413 Bit Score: 43.42 E-value: 9.36e-04
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Name | Accession | Description | Interval | E-value | ||||
RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
607-782 | 1.07e-39 | ||||
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: 145.43 E-value: 1.07e-39
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RT_RNaseH_2 | pfam17919 | RNase H-like domain found in reverse transcriptase; |
845-942 | 5.99e-23 | ||||
RNase H-like domain found in reverse transcriptase; Pssm-ID: 465567 [Multi-domain] Cd Length: 100 Bit Score: 94.49 E-value: 5.99e-23
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retropepsin_like | cd00303 | Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ... |
413-510 | 3.34e-19 | ||||
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: 83.54 E-value: 3.34e-19
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DUF4939 | pfam16297 | Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ... |
200-278 | 1.27e-12 | ||||
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown. Pssm-ID: 465086 Cd Length: 112 Bit Score: 65.71 E-value: 1.27e-12
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Retrotrans_gag | pfam03732 | Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ... |
240-332 | 3.44e-11 | ||||
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: 60.81 E-value: 3.44e-11
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RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
650-782 | 5.89e-08 | ||||
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: 54.23 E-value: 5.89e-08
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Asp_protease_2 | pfam13650 | Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ... |
413-465 | 5.47e-04 | ||||
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Pssm-ID: 433378 Cd Length: 90 Bit Score: 40.35 E-value: 5.47e-04
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RNase_HI_RT_Ty3 | cd09274 | Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ... |
876-985 | 5.68e-04 | ||||
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: 40.94 E-value: 5.68e-04
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PHA03169 | PHA03169 | hypothetical protein; Provisional |
14-160 | 9.36e-04 | ||||
hypothetical protein; Provisional Pssm-ID: 223003 [Multi-domain] Cd Length: 413 Bit Score: 43.42 E-value: 9.36e-04
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Name | Accession | Description | Interval | E-value | ||||
RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
607-782 | 1.07e-39 | ||||
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: 145.43 E-value: 1.07e-39
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RT_RNaseH_2 | pfam17919 | RNase H-like domain found in reverse transcriptase; |
845-942 | 5.99e-23 | ||||
RNase H-like domain found in reverse transcriptase; Pssm-ID: 465567 [Multi-domain] Cd Length: 100 Bit Score: 94.49 E-value: 5.99e-23
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retropepsin_like | cd00303 | Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ... |
413-510 | 3.34e-19 | ||||
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: 83.54 E-value: 3.34e-19
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DUF4939 | pfam16297 | Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ... |
200-278 | 1.27e-12 | ||||
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown. Pssm-ID: 465086 Cd Length: 112 Bit Score: 65.71 E-value: 1.27e-12
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Retrotrans_gag | pfam03732 | Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ... |
240-332 | 3.44e-11 | ||||
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: 60.81 E-value: 3.44e-11
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RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
650-782 | 5.89e-08 | ||||
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: 54.23 E-value: 5.89e-08
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Asp_protease_2 | pfam13650 | Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ... |
413-465 | 5.47e-04 | ||||
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Pssm-ID: 433378 Cd Length: 90 Bit Score: 40.35 E-value: 5.47e-04
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RNase_HI_RT_Ty3 | cd09274 | Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ... |
876-985 | 5.68e-04 | ||||
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: 40.94 E-value: 5.68e-04
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PHA03169 | PHA03169 | hypothetical protein; Provisional |
14-160 | 9.36e-04 | ||||
hypothetical protein; Provisional Pssm-ID: 223003 [Multi-domain] Cd Length: 413 Bit Score: 43.42 E-value: 9.36e-04
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gag-asp_proteas | pfam13975 | gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ... |
415-510 | 1.04e-03 | ||||
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins. Pssm-ID: 464060 Cd Length: 92 Bit Score: 39.48 E-value: 1.04e-03
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Ty3_capsid | pfam19259 | Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ... |
199-353 | 2.40e-03 | ||||
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements. Pssm-ID: 437091 [Multi-domain] Cd Length: 197 Bit Score: 40.92 E-value: 2.40e-03
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Blast search parameters | ||||
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