third double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1433354021 430 TNPVGGLLEYARSHGFAAEFKLVDQSGPPHEPKFVYQAKVGGRWFPAVCAHSKKQGKQEAADAALRVLIGE 500
Cdd:cd19915     1 TNPVSGLLEYARSKGFAAEFKLVDQSGPPHEPKFVYQAKVGGRWFPAVCAHNKKQGKQEAADAALRVLIGE 71

second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA 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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1433354021 318 KSPVTTLLECMHKLGNSCEFRLLSKEGPAHEPKFQYCVAVGAQTFPSVSAPSKKVAKQMAAEEAMKALHGE 388
Cdd:cd19914     1 KNPISVLMEHSQKSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTFPSVVANSKKVAKQMAAEEAVKELMGE 71

Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1433354021 565 SLGTGNRCVKGDSLSLKGETVNDCHAEIISRRGFIRFLYSELMKYNSQTAKDSIFEPAKGGEKLQIKKTVSFHLYISTAP 644
Cdd:pfam02137   1 ALGTGTKCIGGSKLSPSGRVLNDSHAEVIARRSLLRYLYSQLLLALSGNPSKSIFEPNPDSGKLRLKPGISFHLYISQTP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1433354021 645 CGDGALFDKSCSdramESTESRHYPVFENPkqGKLRTKVENGEGTIPVESSDIvPTWDGIRLGERLRTMSCSDKILRWNV 724
Cdd:pfam02137  81 CGDARIFSPLEL----EPESSPAHPVRRFR--GQLRLKVETGAKTIPVESSED-QTWDGVKPGRRTLSMSCSDKLARWNV 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1433354021 725 LGLQGALLTHFLQPIYLKSVTL-GYLFSQGHLTRAICCRVTRdgsaFEDGLRHPFIVNHPKVGRVSiydskrqsgktket 803
Cdd:pfam02137 154 LGVQGALLSHFIEPIYLSSITVgGSLYDTEHLERAIYQRLDG----VLDSLPPPYRVNKPLIGQVA-------------- 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1433354021 804 svnwcladgydleildgtrgtvdgprnelSRVSKKNIFLLFKKLCSFRYRRDLLR-LSYGEAKKAARDYETAKNYFKKGL 882
Cdd:pfam02137 216 -----------------------------SRLCKAALFSRFLKLLSELSREDLLApLTYHEAKAAAKDYQEAKQQLKSLL 266

                         330
                  ....*....|..
gi 1433354021 883 KDMGYGNWISKP 894
Cdd:pfam02137 267 RQQGLGSWIRKP 278

first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA); DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA 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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1433354021 207 KNPISGLLEYAQFASQTCEFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAMTILLEE 277
Cdd:cd19913     1 KNPVSGLMEYAQFLGQTCEFLLLEQSGPSHDPRFKFQAVIDGRRFPPAEASSKKVAKKDAAAIALKILLRE 71

Adenosine deaminase z-alpha domain; This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1433354021   1 MAEIKEKICDYLFNVSD-SSALNLAKNIGLTK-ARDINAVLIDMERQGDVYRQGTTPPIWHLTDKK 64
Cdd:pfam02295   2 AQECAEKILELLENLGEgKAATAIALERGLSTpKREINRVLYDLERKGDVYREDGTPPRWFLTCAK 67

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1433354021  209 PISGLLEYAQFASQTCEFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAMTIL 274
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1433354021  432 PVGGLLEYARSHGFAAEFKLVDQSGPPHEPKFVYQAKVGGRWFPAVCAHSKKQGKQEAADAALRVL 497
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66

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 1433354021 209 PISGLLEYAQFASQTCEFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAMTIL 274
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

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 1433354021 432 PVGGLLEYARSHGFAAEFKLVDQSGPPHEPKFVYQAKVGGRWFPAVCAHSKKQGKQEAADAALRVL 497
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

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 1433354021 206 LKNPISGLLEYAQfASQTC--EFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAM 271
Cdd:TIGR02191 151 LKDYKTALQEWAQ-ARGKPlpEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAAL 217

dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1433354021 436 LLEYARSHGFAA-EFKLVDQSGPPHEPKFVYQAKVGGRWFPAVCAHSKKQGKQEAADAALRVLIGEN 501
Cdd:COG0571   163 LQEWLQARGLPLpEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229

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
                  ....*....|....*....|....*....|....*....|....*....|
gi 1433354021 336 EFRLLSKEGPAHEPKFQYCVAVGAQTFPSVSAPSKKVAKQMAAEEAMKAL 385
Cdd:TIGR02191 171 EYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEKL 220

Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1433354021 565 SLGTGNRCVKGDSLSLKGETVNDCHAEIISRRGFIRFLYSELMKYNSQTAKDSIFEPAKGGEKLQIKKTVSFHLYISTAP 644
Cdd:pfam02137   1 ALGTGTKCIGGSKLSPSGRVLNDSHAEVIARRSLLRYLYSQLLLALSGNPSKSIFEPNPDSGKLRLKPGISFHLYISQTP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1433354021 645 CGDGALFDKSCSdramESTESRHYPVFENPkqGKLRTKVENGEGTIPVESSDIvPTWDGIRLGERLRTMSCSDKILRWNV 724
Cdd:pfam02137  81 CGDARIFSPLEL----EPESSPAHPVRRFR--GQLRLKVETGAKTIPVESSED-QTWDGVKPGRRTLSMSCSDKLARWNV 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1433354021 725 LGLQGALLTHFLQPIYLKSVTL-GYLFSQGHLTRAICCRVTRdgsaFEDGLRHPFIVNHPKVGRVSiydskrqsgktket 803
Cdd:pfam02137 154 LGVQGALLSHFIEPIYLSSITVgGSLYDTEHLERAIYQRLDG----VLDSLPPPYRVNKPLIGQVA-------------- 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1433354021 804 svnwcladgydleildgtrgtvdgprnelSRVSKKNIFLLFKKLCSFRYRRDLLR-LSYGEAKKAARDYETAKNYFKKGL 882
Cdd:pfam02137 216 -----------------------------SRLCKAALFSRFLKLLSELSREDLLApLTYHEAKAAAKDYQEAKQQLKSLL 266

                         330
                  ....*....|..
gi 1433354021 883 KDMGYGNWISKP 894
Cdd:pfam02137 267 RQQGLGSWIRKP 278

first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA); DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA 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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1433354021 207 KNPISGLLEYAQFASQTCEFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAMTILLEE 277
Cdd:cd19913     1 KNPVSGLMEYAQFLGQTCEFLLLEQSGPSHDPRFKFQAVIDGRRFPPAEASSKKVAKKDAAAIALKILLRE 71

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1433354021 207 KNPISGLLEYAQFASQTCEFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAMTILLEE 277
Cdd:cd19902     1 KNPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGRRFPSVEASSKKDAKQEAADLALRALIAE 71

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1433354021 318 KSPVTTLLECMHKLGNSCEFRLLSKEGPAHEPKFQYCVAVGAQTFPSVSAPSKKVAKQMAAEEAMKALHGE 388
Cdd:cd19902     1 KNPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGRRFPSVEASSKKDAKQEAADLALRALIAE 71

second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA 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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1433354021 207 KNPISGLLEYAQFASQTCEFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAMTILLEE 277
Cdd:cd19914     1 KNPISVLMEHSQKSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTFPSVVANSKKVAKQMAAEEAVKELMGE 71

Z-DNA-binding domain in adenosine deaminases; Helix-turn-helix-containing domain. Also known as Zab.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1433354021    1 MAEIKEKICDYLFNVSD--SSALNLAKNIGLTKaRDINAVLIDMERQGDVYRQGTTPPIWHLTDKK 64
Cdd:smart00550   4 QDSLEEKILEFLENSGDetSTALQLAKNLGLPK-KEVNRVLYSLEKKGKVCKQGGTPPLWKLTDKA 68

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 1433354021 431 NPVGGLLEYARSHGFAAEFKLVdQSGPPHEPKFVYQAKVGGRWFPAVCAHSKKQGKQEAADAALRVL 497
Cdd:cd19875     2 NPVSALNEYCQKRGLSLEFVDV-SVGPDHCPGFTASATIDGIVFASATGTSKKEAKRAAAKLALKKL 67

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1433354021  209 PISGLLEYAQFASQTCEFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAMTIL 274
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1433354021  320 PVTTLLECMHKLGNSCEFRLLSKEGPAHEPKFQYCVAVGAQTFPSVSAPSKKVAKQMAAEEAMKAL 385
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66

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 1433354021 208 NPISGLLEYAQFASQTCEFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAMTIL 274
Cdd:cd19903     2 NYMGKLNEYCQKQKVVLDYVEVPTSGPSHDPRFTFQVVIDGKEYPEGEGKSKKEAKQAAAKLALEIL 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 1433354021 430 TNPVGGLLEYARSHGFAAEFKLVDQSGPPHEPKFVYQAKVGGRWFPAVCAHSKKQGKQEAADAALRVL 497
Cdd:cd19903     1 GNYMGKLNEYCQKQKVVLDYVEVPTSGPSHDPRFTFQVVIDGKEYPEGEGKSKKEAKQAAAKLALEIL 68

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 1433354021 209 PISGLLEYAQFASQTCEFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAMTIL 274
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1433354021 318 KSPVTTLLECMHKLGNSCEFRLLSKEGPAHEPKFQYCVAVGAQTFPSvSAPSKKVAKQMAAEEAMKALHG 387
Cdd:cd19862     1 KTPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGDITATG-SGTSKKKAKHAAAENALEQLKG 69

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.

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gi 1433354021 431 NPVGGLLEYARSHGFAAEFKLVDQSGPPHEPKFVYQAKVGGrwfpAVC---AHSKKQGKQEAADAALRVLIG 499
Cdd:cd19862     2 TPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGD----ITAtgsGTSKKKAKHAAAENALEQLKG 69

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.

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gi 1433354021 430 TNPVGGLLEYARSHGFAA-EFKLVDQSGPPHEPKFVYQAKVGGRWFPAVCAHSKKQGKQEAADAALRVL 497
Cdd:cd10845     1 KDYKTALQEYLQKRGLPLpEYELVEEEGPDHNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69

dsRNA-specific ribonuclease [Transcription];

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gi 1433354021 207 KNPISGLLEYAQ-FASQTCEFNMIEQSGPPHEPRFKFQVVINGREFPPAEAGSKKVAKQDAAMKAMTILLEE 277
Cdd:COG0571   157 KDYKTALQEWLQaRGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLGKK 228

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.

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gi 1433354021 320 PVTTLLECMHKLGNSCEFRLLSKEGPAHEPKFQYCVAVGAQTFPSVSAPSKKVAKQMAAEEAMKAL 385
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

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.

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gi 1433354021 318 KSPVTTLLE-CMhKLGNSCEFRLLSkEGPAHEPKFQYCVAVGAQTFPSVSAPSKKVAKQMAAEEAMKAL 385
Cdd:cd19875     1 KNPVSALNEyCQ-KRGLSLEFVDVS-VGPDHCPGFTASATIDGIVFASATGTSKKEAKRAAAKLALKKL 67

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 1433354021 318 KSPVTTLLECMHKLgnscEFRLLSKEGPAHEPKFQYCVAVGAQTFPSvSAPSKKVAKQMAAEEAMKAL 385
Cdd:cd19865     1 KNALMQLNELRPGL----QYKLTSQTGPVHAPVFTMSVEVNGQTFEG-TGRSKKKAKLEAAEKALRSF 63