dicer-like 1 [Arabidopsis thaliana]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
248-447 | 1.93e-95 | ||||
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. : Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 306.50 E-value: 1.93e-95
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| PAZ_CAF_like | cd02844 | PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ... |
1176-1320 | 3.01e-63 | ||||
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA molecules. PAZ domains are named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. : Pssm-ID: 239210 Cd Length: 135 Bit Score: 211.51 E-value: 3.01e-63
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| SF2_C_dicer | cd18802 | C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
645-775 | 1.11e-56 | ||||
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. : Pssm-ID: 350189 [Multi-domain] Cd Length: 142 Bit Score: 193.19 E-value: 1.11e-56
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| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1575-1730 | 4.37e-44 | ||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. : Pssm-ID: 238333 Cd Length: 133 Bit Score: 156.62 E-value: 4.37e-44
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| DSRM_DCL_plant | cd19869 | double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ... |
1837-1906 | 5.74e-38 | ||||
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. : Pssm-ID: 380698 Cd Length: 70 Bit Score: 136.73 E-value: 5.74e-38
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| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1357-1536 | 2.28e-34 | ||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. : Pssm-ID: 238333 Cd Length: 133 Bit Score: 128.88 E-value: 2.28e-34
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| Dicer_dimer | pfam03368 | Dicer dimerization domain; This domain is found in members of the Dicer protein family which ... |
840-927 | 1.61e-29 | ||||
Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners. : Pssm-ID: 460900 Cd Length: 89 Bit Score: 113.36 E-value: 1.61e-29
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| DSRM | smart00358 | Double-stranded RNA binding motif; |
1734-1784 | 1.44e-04 | ||||
Double-stranded RNA binding motif; : Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 41.48 E-value: 1.44e-04
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| SF-CC1 super family | cl36939 | splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ... |
111-219 | 1.80e-03 | ||||
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. The actual alignment was detected with superfamily member TIGR01622: Pssm-ID: 273721 [Multi-domain] Cd Length: 494 Bit Score: 42.98 E-value: 1.80e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
248-447 | 1.93e-95 | |||||||||
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 306.50 E-value: 1.93e-95
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| PAZ_CAF_like | cd02844 | PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ... |
1176-1320 | 3.01e-63 | |||||||||
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA molecules. PAZ domains are named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. Pssm-ID: 239210 Cd Length: 135 Bit Score: 211.51 E-value: 3.01e-63
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| SF2_C_dicer | cd18802 | C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
645-775 | 1.11e-56 | |||||||||
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350189 [Multi-domain] Cd Length: 142 Bit Score: 193.19 E-value: 1.11e-56
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| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1575-1730 | 4.37e-44 | |||||||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. Pssm-ID: 238333 Cd Length: 133 Bit Score: 156.62 E-value: 4.37e-44
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| Rnc | COG0571 | dsRNA-specific ribonuclease [Transcription]; |
1562-1784 | 4.80e-39 | |||||||||
dsRNA-specific ribonuclease [Transcription]; Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 146.01 E-value: 4.80e-39
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| RIBOc | smart00535 | Ribonuclease III family; |
1575-1727 | 3.69e-38 | |||||||||
Ribonuclease III family; Pssm-ID: 197778 Cd Length: 129 Bit Score: 139.66 E-value: 3.69e-38
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| DSRM_DCL_plant | cd19869 | double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ... |
1837-1906 | 5.74e-38 | |||||||||
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380698 Cd Length: 70 Bit Score: 136.73 E-value: 5.74e-38
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
248-776 | 5.42e-37 | |||||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 151.04 E-value: 5.42e-37
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| RNaseIII | TIGR02191 | ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ... |
1562-1784 | 5.70e-37 | |||||||||
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing] Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 139.65 E-value: 5.70e-37
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| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1357-1536 | 2.28e-34 | |||||||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. Pssm-ID: 238333 Cd Length: 133 Bit Score: 128.88 E-value: 2.28e-34
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| PAZ | smart00949 | This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ... |
1189-1342 | 1.06e-30 | |||||||||
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway. Pssm-ID: 198017 Cd Length: 138 Bit Score: 118.54 E-value: 1.06e-30
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| Dicer_dimer | pfam03368 | Dicer dimerization domain; This domain is found in members of the Dicer protein family which ... |
840-927 | 1.61e-29 | |||||||||
Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners. Pssm-ID: 460900 Cd Length: 89 Bit Score: 113.36 E-value: 1.61e-29
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| RIBOc | smart00535 | Ribonuclease III family; |
1357-1534 | 2.29e-29 | |||||||||
Ribonuclease III family; Pssm-ID: 197778 Cd Length: 129 Bit Score: 114.24 E-value: 2.29e-29
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
248-799 | 7.88e-26 | |||||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 116.13 E-value: 7.88e-26
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| Ribonuclease_3 | pfam00636 | Ribonuclease III domain; |
1594-1707 | 2.03e-25 | |||||||||
Ribonuclease III domain; Pssm-ID: 459883 Cd Length: 101 Bit Score: 101.97 E-value: 2.03e-25
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
250-456 | 3.95e-20 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 90.63 E-value: 3.95e-20
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| PAZ | pfam02170 | PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ... |
1207-1336 | 7.78e-20 | |||||||||
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerization. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteriztic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway. Pssm-ID: 460472 Cd Length: 123 Bit Score: 86.86 E-value: 7.78e-20
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| Ribonuclease_3 | pfam00636 | Ribonuclease III domain; |
1375-1518 | 3.10e-19 | |||||||||
Ribonuclease III domain; Pssm-ID: 459883 Cd Length: 101 Bit Score: 84.63 E-value: 3.10e-19
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
648-764 | 1.29e-17 | |||||||||
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 79.95 E-value: 1.29e-17
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| DND1_DSRM | pfam14709 | double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ... |
1831-1904 | 1.34e-15 | |||||||||
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333) Pssm-ID: 405408 Cd Length: 80 Bit Score: 73.53 E-value: 1.34e-15
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| RNaseIII | TIGR02191 | ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ... |
1360-1548 | 1.02e-13 | |||||||||
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing] Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 72.24 E-value: 1.02e-13
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
250-415 | 2.77e-13 | |||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 69.62 E-value: 2.77e-13
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| Rnc | COG0571 | dsRNA-specific ribonuclease [Transcription]; |
1345-1537 | 1.09e-12 | |||||||||
dsRNA-specific ribonuclease [Transcription]; Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 69.36 E-value: 1.09e-12
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
707-768 | 5.54e-11 | |||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 60.30 E-value: 5.54e-11
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| DSRM | smart00358 | Double-stranded RNA binding motif; |
1836-1904 | 1.01e-10 | |||||||||
Double-stranded RNA binding motif; Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 59.20 E-value: 1.01e-10
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| PRK11192 | PRK11192 | ATP-dependent RNA helicase SrmB; Provisional |
652-777 | 1.88e-10 | |||||||||
ATP-dependent RNA helicase SrmB; Provisional Pssm-ID: 236877 [Multi-domain] Cd Length: 434 Bit Score: 65.35 E-value: 1.88e-10
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
657-822 | 8.74e-06 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 50.79 E-value: 8.74e-06
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| DSRM | smart00358 | Double-stranded RNA binding motif; |
1734-1784 | 1.44e-04 | |||||||||
Double-stranded RNA binding motif; Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 41.48 E-value: 1.44e-04
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| SF-CC1 | TIGR01622 | splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ... |
111-219 | 1.80e-03 | |||||||||
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Pssm-ID: 273721 [Multi-domain] Cd Length: 494 Bit Score: 42.98 E-value: 1.80e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
248-447 | 1.93e-95 | |||||||||
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 306.50 E-value: 1.93e-95
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| PAZ_CAF_like | cd02844 | PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ... |
1176-1320 | 3.01e-63 | |||||||||
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA molecules. PAZ domains are named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. Pssm-ID: 239210 Cd Length: 135 Bit Score: 211.51 E-value: 3.01e-63
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| SF2_C_dicer | cd18802 | C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
645-775 | 1.11e-56 | |||||||||
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350189 [Multi-domain] Cd Length: 142 Bit Score: 193.19 E-value: 1.11e-56
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| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1575-1730 | 4.37e-44 | |||||||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. Pssm-ID: 238333 Cd Length: 133 Bit Score: 156.62 E-value: 4.37e-44
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| Rnc | COG0571 | dsRNA-specific ribonuclease [Transcription]; |
1562-1784 | 4.80e-39 | |||||||||
dsRNA-specific ribonuclease [Transcription]; Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 146.01 E-value: 4.80e-39
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| DEXHc_RIG-I | cd17927 | DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
248-445 | 8.31e-39 | |||||||||
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 144.11 E-value: 8.31e-39
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| RIBOc | smart00535 | Ribonuclease III family; |
1575-1727 | 3.69e-38 | |||||||||
Ribonuclease III family; Pssm-ID: 197778 Cd Length: 129 Bit Score: 139.66 E-value: 3.69e-38
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| DSRM_DCL_plant | cd19869 | double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ... |
1837-1906 | 5.74e-38 | |||||||||
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380698 Cd Length: 70 Bit Score: 136.73 E-value: 5.74e-38
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
248-776 | 5.42e-37 | |||||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 151.04 E-value: 5.42e-37
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| RNaseIII | TIGR02191 | ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ... |
1562-1784 | 5.70e-37 | |||||||||
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing] Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 139.65 E-value: 5.70e-37
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| RIBOc | cd00593 | RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ... |
1357-1536 | 2.28e-34 | |||||||||
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. Pssm-ID: 238333 Cd Length: 133 Bit Score: 128.88 E-value: 2.28e-34
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| PAZ | smart00949 | This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ... |
1189-1342 | 1.06e-30 | |||||||||
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway. Pssm-ID: 198017 Cd Length: 138 Bit Score: 118.54 E-value: 1.06e-30
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| Dicer_dimer | pfam03368 | Dicer dimerization domain; This domain is found in members of the Dicer protein family which ... |
840-927 | 1.61e-29 | |||||||||
Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners. Pssm-ID: 460900 Cd Length: 89 Bit Score: 113.36 E-value: 1.61e-29
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| RIBOc | smart00535 | Ribonuclease III family; |
1357-1534 | 2.29e-29 | |||||||||
Ribonuclease III family; Pssm-ID: 197778 Cd Length: 129 Bit Score: 114.24 E-value: 2.29e-29
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| DEXHc_RLR | cd18036 | DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
250-415 | 4.07e-28 | |||||||||
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350794 [Multi-domain] Cd Length: 204 Bit Score: 113.72 E-value: 4.07e-28
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
248-799 | 7.88e-26 | |||||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 116.13 E-value: 7.88e-26
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| Ribonuclease_3 | pfam00636 | Ribonuclease III domain; |
1594-1707 | 2.03e-25 | |||||||||
Ribonuclease III domain; Pssm-ID: 459883 Cd Length: 101 Bit Score: 101.97 E-value: 2.03e-25
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| DEXHc_RIG-I_DDX58 | cd18073 | DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ... |
248-414 | 4.67e-24 | |||||||||
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called DEAD box protein 58 (DDX58), is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. The optimal ligand for RIG-I has been found to be base-paired or double-stranded RNA (dsRNA) molecules containing a 5' triphosphate (5'-ppp-dsRNA). RIG-I contains two N-terminal caspase activation and recruitment domains (CARDs), which are required for interaction with IPS-1, a superfamily 2 helicase/translocase/ATPase (SF2) domain and a C-terminal regulatory/repressor domain (RD). RIG-I is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350831 [Multi-domain] Cd Length: 202 Bit Score: 101.82 E-value: 4.67e-24
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
250-456 | 3.95e-20 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 90.63 E-value: 3.95e-20
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| PAZ | pfam02170 | PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ... |
1207-1336 | 7.78e-20 | |||||||||
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerization. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteriztic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway. Pssm-ID: 460472 Cd Length: 123 Bit Score: 86.86 E-value: 7.78e-20
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| Ribonucleas_3_3 | pfam14622 | Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ... |
1573-1710 | 1.07e-19 | |||||||||
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3. Pssm-ID: 434075 Cd Length: 127 Bit Score: 86.85 E-value: 1.07e-19
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| Ribonuclease_3 | pfam00636 | Ribonuclease III domain; |
1375-1518 | 3.10e-19 | |||||||||
Ribonuclease III domain; Pssm-ID: 459883 Cd Length: 101 Bit Score: 84.63 E-value: 3.10e-19
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| DEXDc_FANCM | cd18033 | DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ... |
250-435 | 1.18e-18 | |||||||||
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA), and Holliday junction substrates. Its ATP-dependent DNA branch migration activity can process branched DNA structures such as a movable replication fork. This activity is strongly stimulated in the presence of CENPS and CENPX. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, it strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA. FANCM is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350791 [Multi-domain] Cd Length: 182 Bit Score: 85.45 E-value: 1.18e-18
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| DEXHc_Hef | cd18035 | DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
248-415 | 9.41e-18 | |||||||||
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350793 [Multi-domain] Cd Length: 181 Bit Score: 82.95 E-value: 9.41e-18
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
648-764 | 1.29e-17 | |||||||||
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 79.95 E-value: 1.29e-17
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| DND1_DSRM | pfam14709 | double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ... |
1831-1904 | 1.34e-15 | |||||||||
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333) Pssm-ID: 405408 Cd Length: 80 Bit Score: 73.53 E-value: 1.34e-15
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| SF2_C_FANCM_Hef | cd18801 | C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
644-774 | 2.22e-15 | |||||||||
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350188 [Multi-domain] Cd Length: 143 Bit Score: 75.08 E-value: 2.22e-15
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
262-413 | 4.60e-14 | |||||||||
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region. Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 71.28 E-value: 4.60e-14
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| RNaseIII | TIGR02191 | ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ... |
1360-1548 | 1.02e-13 | |||||||||
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing] Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 72.24 E-value: 1.02e-13
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| DEXHc_RLR-3 | cd18075 | DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
250-415 | 2.33e-13 | |||||||||
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350833 [Multi-domain] Cd Length: 200 Bit Score: 70.66 E-value: 2.33e-13
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
250-415 | 2.77e-13 | |||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 69.62 E-value: 2.77e-13
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| PAZ_piwi_like | cd02845 | PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be ... |
1210-1314 | 9.87e-13 | |||||||||
PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be essential for the maintenance of germline stem cells. In the Drosophila male germline, Piwi was shown to be involved in the silencing of retrotransposons in the male gametes. The Piwi proteins share their domain architecture with other members of the argonaute family. The PAZ domain has been named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. Pssm-ID: 239211 Cd Length: 117 Bit Score: 66.51 E-value: 9.87e-13
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| Rnc | COG0571 | dsRNA-specific ribonuclease [Transcription]; |
1345-1537 | 1.09e-12 | |||||||||
dsRNA-specific ribonuclease [Transcription]; Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 69.36 E-value: 1.09e-12
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
648-768 | 3.25e-12 | |||||||||
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350174 [Multi-domain] Cd Length: 131 Bit Score: 65.61 E-value: 3.25e-12
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| DEXHc_RLR-2 | cd18074 | DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ... |
248-415 | 3.47e-12 | |||||||||
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma differentiation-associated protein 5 or Mda5 and IFIH1) is a viral double-stranded RNA (dsRNA) receptor that shares sequence similarity and signaling pathways with RIG-I, yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. RLR-2 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. RLR-2 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement. The signaling domain (tandem CARD), which decorates the outside of the core RLR-2 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. RLR-2 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling. LGP2 appears to positively and negatively regulate RLR-2 and RIG-I signaling, respectively. RLR-2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350832 [Multi-domain] Cd Length: 216 Bit Score: 67.96 E-value: 3.47e-12
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
707-768 | 5.54e-11 | |||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 60.30 E-value: 5.54e-11
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
250-416 | 7.43e-11 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 66.97 E-value: 7.43e-11
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| DSRM | smart00358 | Double-stranded RNA binding motif; |
1836-1904 | 1.01e-10 | |||||||||
Double-stranded RNA binding motif; Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 59.20 E-value: 1.01e-10
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| DEXHc_RE_I_III_res | cd18032 | DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
250-415 | 1.69e-10 | |||||||||
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350790 [Multi-domain] Cd Length: 163 Bit Score: 61.42 E-value: 1.69e-10
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| PRK11192 | PRK11192 | ATP-dependent RNA helicase SrmB; Provisional |
652-777 | 1.88e-10 | |||||||||
ATP-dependent RNA helicase SrmB; Provisional Pssm-ID: 236877 [Multi-domain] Cd Length: 434 Bit Score: 65.35 E-value: 1.88e-10
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| PAZ_dicer_like | cd02843 | PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ... |
1224-1295 | 1.98e-10 | |||||||||
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. Pssm-ID: 239209 Cd Length: 122 Bit Score: 60.15 E-value: 1.98e-10
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
250-381 | 2.10e-10 | |||||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 61.10 E-value: 2.10e-10
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| DEXHc_Ski2 | cd17921 | DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
251-381 | 3.93e-10 | |||||||||
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 60.74 E-value: 3.93e-10
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
250-415 | 5.13e-10 | |||||||||
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 59.63 E-value: 5.13e-10
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| Ribonucleas_3_3 | pfam14622 | Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ... |
1373-1522 | 1.20e-09 | |||||||||
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3. Pssm-ID: 434075 Cd Length: 127 Bit Score: 57.96 E-value: 1.20e-09
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| DSRM_SON-like | cd19870 | double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ... |
1834-1904 | 2.18e-08 | |||||||||
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380699 Cd Length: 75 Bit Score: 52.67 E-value: 2.18e-08
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| dsrm | pfam00035 | Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ... |
1833-1904 | 7.10e-08 | |||||||||
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA. Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 51.08 E-value: 7.10e-08
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| DSRM_RNAse_III_family | cd10845 | double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ... |
1836-1904 | 7.67e-08 | |||||||||
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380682 [Multi-domain] Cd Length: 69 Bit Score: 50.95 E-value: 7.67e-08
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| DSRM_SF | cd00048 | double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ... |
1837-1901 | 3.30e-07 | |||||||||
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis. Pssm-ID: 380679 [Multi-domain] Cd Length: 57 Bit Score: 48.82 E-value: 3.30e-07
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| DSRM_PRKRA-like_rpt1 | cd19862 | first double-stranded RNA binding motif of protein activator of the interferon-induced protein ... |
1836-1905 | 3.78e-07 | |||||||||
first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380691 [Multi-domain] Cd Length: 70 Bit Score: 49.18 E-value: 3.78e-07
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| PAZ | cd02825 | PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ... |
1214-1315 | 1.05e-06 | |||||||||
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain. Pssm-ID: 239207 Cd Length: 115 Bit Score: 49.38 E-value: 1.05e-06
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
725-771 | 7.41e-06 | |||||||||
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 45.77 E-value: 7.41e-06
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
657-822 | 8.74e-06 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 50.79 E-value: 8.74e-06
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| PLN00206 | PLN00206 | DEAD-box ATP-dependent RNA helicase; Provisional |
648-785 | 1.39e-05 | |||||||||
DEAD-box ATP-dependent RNA helicase; Provisional Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 49.79 E-value: 1.39e-05
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| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
648-768 | 2.46e-05 | |||||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 48.99 E-value: 2.46e-05
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| DEXHc_archSki2 | cd18028 | DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
261-381 | 3.62e-05 | |||||||||
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 46.17 E-value: 3.62e-05
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| DSRM_STAU1_rpt1 | cd19879 | first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ... |
1842-1897 | 6.27e-05 | |||||||||
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380708 Cd Length: 66 Bit Score: 42.76 E-value: 6.27e-05
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| DSRM_PRKRA-like_rpt2 | cd19863 | second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ... |
1835-1872 | 6.80e-05 | |||||||||
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. The family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380692 Cd Length: 67 Bit Score: 42.75 E-value: 6.80e-05
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| DEXHc_POLQ-like | cd18026 | DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ... |
263-423 | 1.12e-04 | |||||||||
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in the repair of genomic double-strand breaks (DSBs). POLQ contains an N-terminal type II DEAD box helicase domain which contains the ATP-binding region. Pssm-ID: 350784 [Multi-domain] Cd Length: 202 Bit Score: 45.28 E-value: 1.12e-04
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| DSRM | smart00358 | Double-stranded RNA binding motif; |
1734-1784 | 1.44e-04 | |||||||||
Double-stranded RNA binding motif; Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 41.48 E-value: 1.44e-04
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| DSRM_AtDRB-like_rpt1 | cd19907 | first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ... |
1836-1903 | 1.50e-04 | |||||||||
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380736 [Multi-domain] Cd Length: 69 Bit Score: 41.69 E-value: 1.50e-04
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| SF2_C_RecG_TRCF | cd18792 | C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
707-803 | 1.51e-04 | |||||||||
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350179 [Multi-domain] Cd Length: 160 Bit Score: 44.18 E-value: 1.51e-04
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| PRK11634 | PRK11634 | ATP-dependent RNA helicase DeaD; Provisional |
656-797 | 2.35e-04 | |||||||||
ATP-dependent RNA helicase DeaD; Provisional Pssm-ID: 236941 [Multi-domain] Cd Length: 629 Bit Score: 45.99 E-value: 2.35e-04
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| DSRM_STAU2_rpt1 | cd19880 | first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ... |
1839-1901 | 2.86e-04 | |||||||||
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380709 Cd Length: 68 Bit Score: 40.86 E-value: 2.86e-04
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| DSRM_PRKRA_rpt2 | cd19891 | second double-stranded RNA binding motif of protein activator of the interferon-induced ... |
1835-1872 | 3.44e-04 | |||||||||
second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. PRKRA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380720 Cd Length: 67 Bit Score: 40.69 E-value: 3.44e-04
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| DEADc_DDX28 | cd17948 | DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ... |
261-379 | 3.64e-04 | |||||||||
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350706 [Multi-domain] Cd Length: 231 Bit Score: 44.28 E-value: 3.64e-04
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| DSRM_TARBP2_rpt2 | cd10844 | second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ... |
1835-1870 | 4.41e-04 | |||||||||
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380681 Cd Length: 67 Bit Score: 40.48 E-value: 4.41e-04
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| DSRM_STAU_rpt1 | cd19857 | first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ... |
1836-1897 | 5.56e-04 | |||||||||
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380686 Cd Length: 64 Bit Score: 39.94 E-value: 5.56e-04
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| SF-CC1 | TIGR01622 | splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ... |
111-219 | 1.80e-03 | |||||||||
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Pssm-ID: 273721 [Multi-domain] Cd Length: 494 Bit Score: 42.98 E-value: 1.80e-03
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| SF2_C_SNF | cd18793 | C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
645-750 | 2.45e-03 | |||||||||
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350180 [Multi-domain] Cd Length: 135 Bit Score: 40.15 E-value: 2.45e-03
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| PTZ00110 | PTZ00110 | helicase; Provisional |
716-769 | 3.24e-03 | |||||||||
helicase; Provisional Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 42.45 E-value: 3.24e-03
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| SF2_C_RecG | cd18811 | C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
707-786 | 5.96e-03 | |||||||||
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350198 [Multi-domain] Cd Length: 159 Bit Score: 39.25 E-value: 5.96e-03
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| PAZ_argonaute_like | cd02846 | PAZ domain, argonaute_like subfamily. Argonaute is part of the RNA-induced silencing complex ... |
1216-1317 | 7.12e-03 | |||||||||
PAZ domain, argonaute_like subfamily. Argonaute is part of the RNA-induced silencing complex (RISC), and is an endonuclease that plays a key role in the RNA interference pathway. The PAZ domain has been named after the proteins Piwi,Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. Pssm-ID: 239212 [Multi-domain] Cd Length: 114 Bit Score: 38.07 E-value: 7.12e-03
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
250-392 | 8.54e-03 | |||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 40.98 E-value: 8.54e-03
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| DEADc | cd00268 | DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
259-380 | 9.61e-03 | |||||||||
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 39.35 E-value: 9.61e-03
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