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uncharacterized protein K02A2.6-like [Danio rerio]
List of domain hits
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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) ... |
159-284 | 2.96e-49 | ||||
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: 168.83 E-value: 2.96e-49
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ps-ssRNAv_RdRp-like super family | cl40470 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
1-65 | 1.07e-20 | ||||
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model. The actual alignment was detected with superfamily member cd01647: Pssm-ID: 477363 Cd Length: 177 Bit Score: 89.96 E-value: 1.07e-20
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transpos_IS481 super family | cl41329 | IS481 family transposase; null |
434-581 | 2.07e-17 | ||||
IS481 family transposase; null The actual alignment was detected with superfamily member NF033577: Pssm-ID: 468094 [Multi-domain] Cd Length: 283 Bit Score: 83.02 E-value: 2.07e-17
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Integrase_H2C2 | pfam17921 | Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ... |
367-422 | 1.42e-13 | ||||
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: 65.73 E-value: 1.42e-13
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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) ... |
159-284 | 2.96e-49 | ||||
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: 168.83 E-value: 2.96e-49
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RT_RNaseH | pfam17917 | RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ... |
153-259 | 6.66e-47 | ||||
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: 161.52 E-value: 6.66e-47
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RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
1-65 | 1.07e-20 | ||||
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: 89.96 E-value: 1.07e-20
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transpos_IS481 | NF033577 | IS481 family transposase; null |
434-581 | 2.07e-17 | ||||
IS481 family transposase; null Pssm-ID: 468094 [Multi-domain] Cd Length: 283 Bit Score: 83.02 E-value: 2.07e-17
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rve | pfam00665 | Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ... |
437-526 | 1.06e-16 | ||||
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site. Pssm-ID: 459897 [Multi-domain] Cd Length: 98 Bit Score: 75.81 E-value: 1.06e-16
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Integrase_H2C2 | pfam17921 | Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ... |
367-422 | 1.42e-13 | ||||
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: 65.73 E-value: 1.42e-13
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transpos_IS3 | NF033516 | IS3 family transposase; |
419-541 | 1.80e-13 | ||||
IS3 family transposase; Pssm-ID: 468052 [Multi-domain] Cd Length: 369 Bit Score: 72.60 E-value: 1.80e-13
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Tra5 | COG2801 | Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; |
421-541 | 1.33e-12 | ||||
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; Pssm-ID: 442053 [Multi-domain] Cd Length: 309 Bit Score: 69.41 E-value: 1.33e-12
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RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
1-65 | 3.79e-10 | ||||
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: 60.01 E-value: 3.79e-10
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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) ... |
159-284 | 2.96e-49 | ||||
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: 168.83 E-value: 2.96e-49
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RT_RNaseH | pfam17917 | RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ... |
153-259 | 6.66e-47 | ||||
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: 161.52 E-value: 6.66e-47
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RT_RNaseH_2 | pfam17919 | RNase H-like domain found in reverse transcriptase; |
128-227 | 1.42e-45 | ||||
RNase H-like domain found in reverse transcriptase; Pssm-ID: 465567 [Multi-domain] Cd Length: 100 Bit Score: 157.66 E-value: 1.42e-45
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RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
1-65 | 1.07e-20 | ||||
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: 89.96 E-value: 1.07e-20
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transpos_IS481 | NF033577 | IS481 family transposase; null |
434-581 | 2.07e-17 | ||||
IS481 family transposase; null Pssm-ID: 468094 [Multi-domain] Cd Length: 283 Bit Score: 83.02 E-value: 2.07e-17
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rve | pfam00665 | Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ... |
437-526 | 1.06e-16 | ||||
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site. Pssm-ID: 459897 [Multi-domain] Cd Length: 98 Bit Score: 75.81 E-value: 1.06e-16
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Integrase_H2C2 | pfam17921 | Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ... |
367-422 | 1.42e-13 | ||||
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: 65.73 E-value: 1.42e-13
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transpos_IS3 | NF033516 | IS3 family transposase; |
419-541 | 1.80e-13 | ||||
IS3 family transposase; Pssm-ID: 468052 [Multi-domain] Cd Length: 369 Bit Score: 72.60 E-value: 1.80e-13
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Tra5 | COG2801 | Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; |
421-541 | 1.33e-12 | ||||
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; Pssm-ID: 442053 [Multi-domain] Cd Length: 309 Bit Score: 69.41 E-value: 1.33e-12
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RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
1-65 | 3.79e-10 | ||||
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: 60.01 E-value: 3.79e-10
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RT_like | cd00304 | RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ... |
13-65 | 4.01e-04 | ||||
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: 40.03 E-value: 4.01e-04
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zf-H2C2 | pfam09337 | H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ... |
383-417 | 5.94e-04 | ||||
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters. Pssm-ID: 430537 Cd Length: 39 Bit Score: 38.08 E-value: 5.94e-04
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RT_Bac_retron_I | cd01646 | RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ... |
1-78 | 3.02e-03 | ||||
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome. Pssm-ID: 238824 [Multi-domain] Cd Length: 158 Bit Score: 38.85 E-value: 3.02e-03
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Lipoprotein_Ltp | pfam07553 | Host cell surface-exposed lipoprotein; This is a family of lipoproteins that is involved in ... |
486-509 | 9.82e-03 | ||||
Host cell surface-exposed lipoprotein; This is a family of lipoproteins that is involved in superinfection exclusion. Proteins in this family have been shown to act at the stage of DNA release from the phage head into the cell. Pssm-ID: 462206 Cd Length: 48 Bit Score: 34.86 E-value: 9.82e-03
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Blast search parameters | ||||
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