Raptor N-terminal CASPase like domain; This domain is found at the N-terminus of the Raptor protein. It has been identified to have a CASPase like structure. It conserves the characteriztic cys/his dyad of the caspases suggesting it may have a peptidase activity.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002272272 362 MKTGCVALVLCLNISVDPPDVIKISPCVRKECWIAP------KALETIGKTLHSQYERWQPKARYKLQLDPTLEEV 431
Cdd:pfam14538   1 LKTVSVALVLCLNIGVDPPDVVKTKPCARLECWIDPssmspqKALEEIGKNLQDQYESWQPRARYKQSLDPSVEDV 76

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002272272  35 VFKSRLQEYAQKAGLQTPEYHTSKEGPSHEPVFKSTVVINNTSYGSLPGFSNRKAAEQSAAEVALMEI 102
Cdd:cd19907     1 MYKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNSL 68

Raptor N-terminal CASPase like domain; This domain is found at the N-terminus of the Raptor protein. It has been identified to have a CASPase like structure. It conserves the characteriztic cys/his dyad of the caspases suggesting it may have a peptidase activity.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002272272 362 MKTGCVALVLCLNISVDPPDVIKISPCVRKECWIAP------KALETIGKTLHSQYERWQPKARYKLQLDPTLEEV 431
Cdd:pfam14538   1 LKTVSVALVLCLNIGVDPPDVVKTKPCARLECWIDPssmspqKALEEIGKNLQDQYESWQPRARYKQSLDPSVEDV 76

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002272272  35 VFKSRLQEYAQKAGLQTPEYHTSKEGPSHEPVFKSTVVINNTSYGSLPGFSNRKAAEQSAAEVALMEI 102
Cdd:cd19907     1 MYKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNSL 68

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]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002272272  36 FKSRLQEYAQKAGLQTPEYHTSKE-GPSHEPVFKSTVVINNTSYGSLPGFSnRKAAEQSAAEVAL 99
Cdd:TIGR02191 154 YKTALQEWAQARGKPLPEYRLIKEeGPDHDKEFTVEVSVNGEPYGEGKGKS-KKEAEQNAAKAAL 217

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002272272   37 KSRLQEYAQKAGLqTPEY-HTSKEGPSHEPVFKSTVVINNTSYGSLPGfSNRKAAEQSAAEVALMEI 102
Cdd:smart00358   2 KSLLQELAQKRKL-PPEYeLVKEEGPDHAPRFTVTVKVGGKRTGEGEG-SSKKEAKQRAAEAALRSL 66

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002272272  122 KNLLQEYAQKMNYaIPSYICTKpASGLAP---FLCTVEIGGIQYIGAAARTKKDAEIKAARTAL 182
Cdd:smart00358   2 KSLLQELAQKRKL-PPEYELVK-EEGPDHaprFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAAL 63

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]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002272272 122 KNLLQEYAQKMNYAIPSYICTKpASGLAP---FLCTVEIGGIQYIGAAARTKKDAEIKAARTALLAI 185
Cdd:TIGR02191 155 KTALQEWAQARGKPLPEYRLIK-EEGPDHdkeFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEKL 220

Raptor N-terminal CASPase like domain; This domain is found at the N-terminus of the Raptor protein. It has been identified to have a CASPase like structure. It conserves the characteriztic cys/his dyad of the caspases suggesting it may have a peptidase activity.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002272272 362 MKTGCVALVLCLNISVDPPDVIKISPCVRKECWIAP------KALETIGKTLHSQYERWQPKARYKLQLDPTLEEV 431
Cdd:pfam14538   1 LKTVSVALVLCLNIGVDPPDVVKTKPCARLECWIDPssmspqKALEEIGKNLQDQYESWQPRARYKQSLDPSVEDV 76

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002272272  35 VFKSRLQEYAQKAGLQTPEYHTSKEGPSHEPVFKSTVVINNTSYGSLPGFSNRKAAEQSAAEVALMEI 102
Cdd:cd19907     1 MYKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNSL 68

dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002272272  36 FKSRLQEYAQKAGLQTPEYH-TSKEGPSHEPVFKSTVVINNTSYGSLPGfSNRKAAEQSAAEVALMEI 102
Cdd:COG0571   159 YKTALQEWLQARGLPLPEYEvVEEEGPDHAKTFTVEVLVGGKVLGEGTG-RSKKEAEQAAAKAALEKL 225

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002272272  36 FKSRLQEYAQKAGLQTPEYH-TSKEGPSHEPVFKSTVVINNTSYGSLPGfSNRKAAEQSAAEVAL 99
Cdd:cd10845     3 YKTALQEYLQKRGLPLPEYElVEEEGPDHNKTFTVEVKVNGKVIGEGTG-RSKKEAEQAAAKAAL 66

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002272272   37 KSRLQEYAQKAGLqTPEY-HTSKEGPSHEPVFKSTVVINNTSYGSLPGfSNRKAAEQSAAEVALMEI 102
Cdd:smart00358   2 KSLLQELAQKRKL-PPEYeLVKEEGPDHAPRFTVTVKVGGKRTGEGEG-SSKKEAKQRAAEAALRSL 66

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two 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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002272272 124 LLQEYAQKMNYAIPSYICTKPASGLAPFLCTVEIGGIQYIGAAARTKKDAEIKAARTALLA 184
Cdd:cd19867    11 ILHEYCQRVLKVQPEYNFTETENAATPFSAEVFINGVEYGSGEASSKKLAKQKAARATLEI 71

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002272272 122 KNLLQEYAQKMNYAIPSYICTKPASGLAP-FLCTVEIGGIQYIGAAARTKKDAEIKAARTAL 182
Cdd:pfam00035   2 KSLLQEYAQKNGKPPPYEYVSEEGPPHSPkFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKAL 63

double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) and similar proteins; DUS2L (also known as dihydrouridine synthase 2 (DUS2), up-regulated in lung cancer protein 8 (URLC8), or tRNA-dihydrouridine synthase 2-like) catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. It negatively regulates the activation of EIF2AK2/PKR. DUS2L contains an N-terminal FMN-binding domain and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002272272  37 KSRLQEYAQKAGLQTPEYHTSKEGPSHepVFKSTVVINNTSYGSLPGFSNRKAAEQSAAEVAL 99
Cdd:cd19871     3 KMILNEWCRKNKLPQPVYETVQRPSDR--LFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCL 63

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002272272 126 QEYAQKMNYAIPSYICTKPASGLAP-FLCTVEIGGIQYIGAAaRTKKDAEIKAARTAL 182
Cdd:cd00048     1 NELCQKNKWPPPEYETVEEGGPHNPrFTCTVTVNGQTFEGEG-KSKKEAKQAAAEKAL 57

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two 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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002272272  36 FKSRLQEYAQKAgLQT-PEYHTSKEGPSHEPvFKSTVVINNTSYGSLPGfSNRKAAEQSAAEVAL 99
Cdd:cd19867     8 PVCILHEYCQRV-LKVqPEYNFTETENAATP-FSAEVFINGVEYGSGEA-SSKKLAKQKAARATL 69

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002272272  38 SRLQEYAQKAGLQTPEYHTSKE-GPSHEPVFKSTVVINNTSYGSLPGFSNRKAAEQSAAEVAL 99
Cdd:cd19870     6 SALMELCNKRKWGPPEFRLVEEsGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAATVAL 68

first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins 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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002272272  36 FKSRLQEYAQKAGLQTPEYHTSKEGPSHEPVFKSTVVINNTSYGSLPGfSNRKAAEQSAAEVALMEI 102
Cdd:cd19903     3 YMGKLNEYCQKQKVVLDYVEVPTSGPSHDPRFTFQVVIDGKEYPEGEG-KSKKEAKQAAAKLALEIL 68

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002272272  38 SRLQEYAQKAGLqTPEYH-TSKEGPSHEPVFKSTVVINN-TSYGSlpGFSnRKAAEQSAAEVAL 99
Cdd:cd19862     5 SVLQELCAKRGI-TPKYElISSEGAVHEPTFTFRVTVGDiTATGS--GTS-KKKAKHAAAENAL 64

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002272272  38 SRLQEYAQKAGLQTpEYHTSKEGPSHEPVFKSTVVINNTSYGSLPGfSNRKAAEQSAAEVAL 99
Cdd:cd19875     5 SALNEYCQKRGLSL-EFVDVSVGPDHCPGFTASATIDGIVFASATG-TSKKEAKRAAAKLAL 64

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1002272272 124 LLQEYAQKMNYAIPSYICTKPASGLAPFLCTVEIGGIQYIGAAARTKKDAEIKAARTAL 182
Cdd:cd19875     6 ALNEYCQKRGLSLEFVDVSVGPDHCPGFTASATIDGIVFASATGTSKKEAKRAAAKLAL 64

second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002272272  30 VENCyvfKSRLQEYAQKAGLQTpEYHTSKEGPSHEPVFKSTVVI-----NNTSYGSLPGfSNRKAAEQSAAevalMEIVK 104
Cdd:cd19855     1 LDNA---KSRLNEFLQKNKIPA-EYKYTSVGPDHNRSFIAELSIfvkqlGKTIYARETG-SNKKLASQSCA----LSLVR 71

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002272272 124 LLQEYAQKMNYAIpSYICTKPA--SGLAPFLCTVEIGGIQYIGAAARTKKDAEIKAARTALLAI 185
Cdd:cd20314     6 LLNEYCQKERLTV-KYEEEKRSgpTHKPRFFCKYIIDGKEYPEGEGKSKKEAKQAAARLAYEEL 68

first 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 first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002272272  38 SRLQEYAQKAGlQTPEYHTSK-EGPSHEPVFKSTVVINNTS-YGSLPgfsNRKAAEQSAAEVAL 99
Cdd:cd19890     7 SLLQEYGTRIG-KTPVYDLLKaEGQAHQPNFTFRVTVGDIScTGQGP---SKKAAKHKAAEVAL 66

double-strand RNA-binding protein; Provisional

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1002272272  60 GPSHEPVFKSTVVINNTSYGSLPGfSNRKAAEQSAAEVALMEIVKSI 106
Cdd:PHA03103  134 GPSHSPTFTASVIISGIKFKPAIG-STKKEAKNNAAKLAMDKILNYV 179

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two 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.

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gi 1002272272  56 TSKEGPSHEPVFKSTVVINNTSY-GSLPgfsNRKAAEQSAAEVAL 99
Cdd:cd19865    19 TSQTGPVHAPVFTMSVEVNGQTFeGTGR---SKKKAKLEAAEKAL 60