dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1178041721   1 LRSLLVKGVTLAEIGKEFKLGDYLNLGGGELKSGGFRRESIIADALEAVIGAIYLDSDHSTCREVVLSWYEPRFANLSLD 80
Cdd:COG0571    74 LRAALVSEETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPG 153

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1178041721  81 NTEKDPKTRLQEYLQSIKKDLPKYEVIKVTGEAHDQTFFVECEVASmSIRTNSEGPSRRIAEQKSAKQALAILEEKS 157
Cdd:COG0571   154 GAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGG-KVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229

dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1178041721   1 LRSLLVKGVTLAEIGKEFKLGDYLNLGGGELKSGGFRRESIIADALEAVIGAIYLDSDHSTCREVVLSWYEPRFANLSLD 80
Cdd:COG0571    74 LRAALVSEETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPG 153

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1178041721  81 NTEKDPKTRLQEYLQSIKKDLPKYEVIKVTGEAHDQTFFVECEVASmSIRTNSEGPSRRIAEQKSAKQALAILEEKS 157
Cdd:COG0571   154 GAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGG-KVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1178041721   1 LRSLLVKGVTLAEIGKEFKLGDYLNLGGGELKSGGFRRESIIADALEAVIGAIYLDSDHSTCREVVLSWYEPRFANLSL 79
Cdd:cd00593    55 LRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133

Ribonuclease III family;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1178041721    1 LRSLLVKGVTLAEIGKEFKLGDYLNLGGGELKSGGFRRESIIADALEAVIGAIYLDSDHSTCREVVLSWYEPR 73
Cdd:smart00535  53 LRSALVSNETLARLAKKLGLGEFIRLGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPR 125

dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1178041721   1 LRSLLVKGVTLAEIGKEFKLGDYLNLGGGELKSGGFRRESIIADALEAVIGAIYLDSDHSTCREVVLSWYEPRFANLSLD 80
Cdd:COG0571    74 LRAALVSEETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPG 153

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1178041721  81 NTEKDPKTRLQEYLQSIKKDLPKYEVIKVTGEAHDQTFFVECEVASmSIRTNSEGPSRRIAEQKSAKQALAILEEKS 157
Cdd:COG0571   154 GAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGG-KVLGEGTGRSKKEAEQAAAKAALEKLGKKE 229

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1178041721   1 LRSLLVKGVTLAEIGKEFKLGDYLNLGGGELKSGGFRRESIIADALEAVIGAIYLDSDHSTCREVVLSWYEPRFANLSL 79
Cdd:cd00593    55 LRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1178041721   1 LRSLLVKGVTLAEIGKEFKLGDYLNLGGGELKSGGFRRESIIADALEAVIGAIYLDSDHSTCREVVLSWYEPR 73
Cdd:pfam14622  54 LRASIVSEESLAEIAREIGLGKYLRLGKGEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILKKILPD 126

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1178041721   86 PKTRLQEYLQSIKKdLPKYEVIKVTGEAHDQTFFVECEVASmSIRTNSEGPSRRIAEQKSAKQALAILE 154
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKEEGPDHAPRFTVTVKVGG-KRTGEGEGSSKKEAKQRAAEAALRSLK 67

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 1178041721  91 QEYLQSIKKDLPKYEVIKVTGeAHDQTFFVECEVASMSIRtnSEGPSRRIAEQKSAKQAL 150
Cdd:cd00048     1 NELCQKNKWPPPEYETVEEGG-PHNPRFTCTVTVNGQTFE--GEGKSKKEAKQAAAEKAL 57

double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as Drosha, or ribonuclease 3) is a double-stranded RNA (dsRNA)-specific endoribonuclease that is involved in the initial step of microRNA (miRNA) biogenesis. It is a component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, RNase III cleaves the 3' and 5' strands of a stem-loop in pri-miRNAs (processing center 11 bp from the dsRNA-ssRNA junction) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. It is also involved in pre-rRNA processing. Metazoan RNase III is a larger protein than bacterial RNase III. It contains two RNase III domains in the C-terminal half of the protein followed by a 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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1178041721  84 KDPKTRLQEYLQSIKK------DLPKYEVIKVTGEAHDQTFFVECEVASMSIRTnSEGPSRRIAEQKSAKQALAIL 153
Cdd:cd19877     1 NDPKSQLQQCCLTLRTegkkepDIPEYKVLQKSGPTNTRVYTVAVYFRGERIAT-GTGSSIQQAEMNAAEKALEKL 75

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 1178041721  84 KDPKTRLQEYLQSIKKDlPKYEVIKVTGEAHDQTFFVECEVASMSirTNSEGPSRRIAEQKSAKQALAIL 153
Cdd:cd19862     1 KTPISVLQELCAKRGIT-PKYELISSEGAVHEPTFTFRVTVGDIT--ATGSGTSKKKAKHAAAENALEQL 67

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1178041721  87 KTRLQEYLQSIKKDLPKYEVIKvTGEAHDQTFFVECEVAsmSIRTNSEG-PSRRIAEQKSAKQAL 150
Cdd:cd19878     2 KNLLQEYAQKKKIPLPKYESAK-SGPSHQPTFVSTVIVL--GVRFSSEGaKNKKQAEQSAAKVAL 63

first 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 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 1178041721  84 KDPKTRLQEYLQSIKKdLPKYEVIKVTGEAHDQTFFVECEVASmsIRTNSEGPSRRIAEQKSAKQALAILE 154
Cdd:cd19889     2 KTPIQLLHEYGTKTGN-IPVYELEKSEGQAHLPSFTFRVTVGD--ITCTGEGTSKKLAKHRAAEAALNILK 69

seadornavirus double-stranded RNA-binding protein; This protein family occurs in the seadornavirus virus group, with an N-terminal domain for binding double-stranded RNA, is designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1178041721  85 DPKTRLQEYLQSIKKDLPKYEVIKVTGEAHDQTFFVECEVasMSIRTNSEGPSRRIAEQKSA 146
Cdd:TIGR04238   1 NVVGMLQELAVKRGLELPVYEKVGKEGPDHAPTFTIKLTA--NDIEVIEAASSKKQAEKLAA 60

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1178041721  97 IKKDLP-KYEVIKVTGEAHDQTFFVECEVAsmSIRTNSEGPSRRIAEQKSAKqalAILEE 155
Cdd:cd19859    10 LKRNLTvNFEVLRESGPPHMKNFITRCTVG--SFVTEGEGNSKKVSKKRAAE---KMLEE 64

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1178041721  87 KTRLQEYLQSIKKDLPKYEVIKVtGEAHDQTFFVECEVASMSIrTNSEGPSRRIAEQKSAKQALAILE 154
Cdd:cd19908     4 KNLLQEYAQKAGLPLPLYTTVRS-GPGHVPTFTCTVEIAGITF-TGEAAKTKKQAEKSAARTAWSSIK 69

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1178041721 103 KYEVIKVTGEAHDQTFFVECEVASMSIRtnSEGPSRRIAEQKSAKQALAIL 153
Cdd:cd19866    15 KYKCLSESGESHAKSFVMSVTVDGQTFE--GTGRSKKLAKAAAAQAALAKL 63

Family of unknown function (DUF5385); This is a family of unknown function found in Mycoplasmataceae. Family members are predicted to have one trans-membrane region.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1178041721  82 TEKDPKTRLQEYLQSIKKDLPK--YEVIKVTGEAHDQTFF----VECEVASMSIRTNSEGPSRRI 140
Cdd:pfam17359  97 EHKLSKKDKKQYLKNRKKEKPRelYCIYFQTKDAKTQATDepriIEAEVLTVPAKSKKDVPERKI 161