TIM-like beta/alpha barrel domains; A large family of domains similar to triose phosphate isomerase (TIM) which, in general, share an eight beta/alpha closed barrel structure.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958746271  29 RNRDERPQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHLDIEDFRQATAASSVMVARAAMWNPSIF 96
Cdd:cd02801   160 RTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPWLF 223

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958746271  29 RNRDERPQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHLDIEDFRQATAASSVMVARAAMWNPSIF 96
Cdd:cd02801   160 RTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPWLF 223

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 1958746271 214 PKTCLLEWCRREKlPQPVYETVQR---PIDRMFCSVVTVAEQKYQSTlWDKSKKLAEQTAAIVCLR 276
Cdd:pfam00035   1 PKSLLQEYAQKNG-KPPPYEYVSEegpPHSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALE 64

Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746271  21 CQTLTRSRRNRDERPQHPVSCEVIRAIAETLSIPVIANGG--SHDHIQQHLDIedfrqaTAASSVMVARAAMWNPSIF-- 96
Cdd:pfam01207 152 AQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGDitDPEDAQRCLAY------TGADGVMIGRGALGNPWLFae 225

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1958746271  97 ---LKDGLR----PLEEVMQKyiryavqYDNHYTNTKY 127
Cdd:pfam01207 226 qhtVKTGEFgpspPLAEEAEK-------VLRHLPYLEE 256

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 1958746271 214 PKTCLLEWCRREKLPQPVYETVQR---PIDRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAAIVCL 275
Cdd:TIGR02191 154 YKTALQEWAQARGKPLPEYRLIKEegpDHDKEFTVEVSVNGEPY-GEGKGKSKKEAEQNAAKAAL 217

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958746271  29 RNRDERPQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHLDIEDFRQATAASSVMVARAAMWNPSIF 96
Cdd:cd02801   160 RTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPWLF 223

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 1958746271 214 PKTCLLEWCRREKLPQPVYETVQR---PIDRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAAIVCLR 276
Cdd:cd10845     3 YKTALQEYLQKRGLPLPEYELVEEegpDHNKTFTVEVKVNGKVI-GEGTGRSKKEAEQAAAKAALE 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 1958746271 215 KTCLLEWCRREKLPQPVYETVQRPIDR--MFCSVVTVAEQKYQSTLWdKSKKLAEQTAAIVCLRSQG 279
Cdd:cd19878     2 KNLLQEYAQKKKIPLPKYESAKSGPSHqpTFVSTVIVLGVRFSSEGA-KNKKQAEQSAAKVALKELG 67

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 1958746271 214 PKTCLLEWCRREKlPQPVYETVQR---PIDRMFCSVVTVAEQKYQSTlWDKSKKLAEQTAAIVCLR 276
Cdd:pfam00035   1 PKSLLQEYAQKNG-KPPPYEYVSEegpPHSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALE 64

Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746271  21 CQTLTRSRRNRDERPQHPVSCEVIRAIAETLSIPVIANGG--SHDHIQQHLDIedfrqaTAASSVMVARAAMWNPSIF-- 96
Cdd:pfam01207 152 AQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGDitDPEDAQRCLAY------TGADGVMIGRGALGNPWLFae 225

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1958746271  97 ---LKDGLR----PLEEVMQKyiryavqYDNHYTNTKY 127
Cdd:pfam01207 226 qhtVKTGEFgpspPLAEEAEK-------VLRHLPYLEE 256

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 1958746271 214 PKTCLLEWCRREKLPQPVYETVQR---PIDRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAAIVCL 275
Cdd:TIGR02191 154 YKTALQEWAQARGKPLPEYRLIKEegpDHDKEFTVEVSVNGEPY-GEGKGKSKKEAEQNAAKAAL 217

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 1958746271 213 TPKTCLLEWCRREKLPQPVYETVQRPIDRM-FCSVVTVAEQKYQSTLwDKSKKLAEQTAA 271
Cdd:cd19867     7 SPVCILHEYCQRVLKVQPEYNFTETENAATpFSAEVFINGVEYGSGE-ASSKKLAKQKAA 65

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 1958746271 214 PKTCLLEWCRREKLPQPVYETVQR---PIDRMFCSVVTVAEQKYQSTlwDKSKKLAEQTAA 271
Cdd:TIGR04238   2 VVGMLQELAVKRGLELPVYEKVGKegpDHAPTFTIKLTANDIEVIEA--ASSKKQAEKLAA 60