Citrus Sinensis ID: 041141

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-----
Protein Sequence
MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQDQAIIARYLATLKGPETNNSQREHRTIGVSASIRREVIPYGDARSLNSLQHQNWHCIPFYPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPSLVEEPVSLVPEIGPFLYFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGGSDCWQNNCPSNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQLRNQTEQYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNSTMVSSSGSVGGSVPPSFAAPMTIRASATASTASLRPQSSNPLVRAPPPRRTAASFCSSRPWPEGMRNQGGMPSRHYMAPAVHIRSVVPVCSAPPSKKYPDPSREKRTEEQRGDISAT
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHccccccEEEEcccccccccEEEEEEEccEEEccccccccHHHHHHHHHHHHHHHHHccccccHHHHHcccccccHHHHHHHHHHHcccccccEEEEEEcccccccEEEEEEEccEEEcccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccHHcccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHccccccEEEEEccccccccEEEEEEEEccEEcccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHccccccEEEEEccccccccEEEEEEEEccEEEcccccccHHHHHHHHHHHHHHHHHHHcHHccccccccccccccccccccHHHHHHHHHHHccccHcccccHHHccccccccccccccccccccccccccccccccccccHHHHHHHHccHHHHHHccccccEEccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccccHHcccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccEEccccccccEccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcEccccccccccccccHcccccccccccccc
Coil and Loop (DISEMBL)
MYKNQLQELAQRscfnlpsysciregpdhaprfkaavnfngetfesptfcSTLRQAEHAAAEVALDVlskkgpskvLAARVLDETGVYKNLLQetshraglklpvyttvrsgpghgpvFSCTVElagvsftgepaktKKQAQKNAALAAWSALKKQAKsafssssfsppssesgtndeqDQAIIARYLATlkgpetnnsqrehrtigvsasirrevipygdarslnslqhqnwhcipfypelslyqtcpqeRVFRQQENLlalsslpsssprpqifpfirsmfqpdhgyyfpslveepvslvpeigpflyfsnrvmpvpvrnvsQVSIQeieenprmeedwrkgdggsdcwqnncpsnvprlsqseipnslvsfNSQSEQRMQEglqgkgeeksvssapnaeiSNQLRNqteqynwfspgfidarfrpttiskdgdkfrlqntvsldylqsdsrprnstmvsssgsvggsvppsfaapmtirasatastaslrpqssnplvrappprrtaasfcssrpwpegmrnqggmpsrhymapavhirsvvpvcsappskkypdpsrekrteeqrgdisat
Flexible Loop (DISEMBL)
myknqlqeLAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVAldvlskkgpsKVLAARVLDETGVYKNLlqetshraglklPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSsssfsppssesgtndeqDQAIIARYLATlkgpetnnsqrehrtigvsasirREVIPYGDARSLNSLQHQNWHCIPFYPELSLYQTCPQERVFRQQENLLAlsslpssspRPQIFPFIRSMFQPDHGYYFPSLVEEPVSLVPEIGPFLYFSNRVMPVPVRNVSQVSiqeieenprmeedwRKGDGGSDCWQNNCPSNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQLRNQTEQYNWFSPGFIDARFRPTTiskdgdkfrlqNTVSldylqsdsrprnSTMVsssgsvggsvPPSFAAPMTIRASATastaslrpqssnplvrappprrtaasfcssrpwpEGMRNQGGMPSRHYMAPAVHIRSvvpvcsappskkypdpsrekrteeqrgdisat
Low Complexity Region (SEG)
MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPaktkkqaqknaalaawsalkkqaksafssssfsppssesGTNDEQDQAIIARYLATLKGPETNNSQREHRTIGVSASIRREVIPYGDARSLNSLQHQNWHCIPFYPELSLYQTCPQERVFRQQENllalsslpssspRPQIFPFIRSMFQPDHGYYFPSLVEEPVSLVPEIGPFLYFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGGSDCWQNNCPSNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQLRNQTEQYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNSTMvsssgsvggsvppsFAAPMTIRasatastasLRPQSSNPLVRAPPPRRTAASFCSSRPWPEGMRNQGGMPSRHYMAPAVHIRSVVPVCSAPPSKKYPDPSREKRTEEQRGDISAT
Disordered region (IsUnstruct)
************SCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFT***************************************************IIARYLAT***************IGVSASIRREVIPYGDARSLNSLQHQNWHCIPFYPELSLYQTCPQERVFRQQENLL************QIFPFIRSMFQPDHGYYFPSLVEEPVSLVPEIGPFLYFSNRVMPVPVRNVSQV**************************************************************************************QYNWFSPGFIDARFRPTTISK***KFRLQ***********************************************************************************************PAVHIRSVVPV****************************
Disordered Region (DISOPRED)
MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGET*****************AEVALDVL***************ETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFT**********QKNAALAAWS**********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************YMAPAVHIRSVVPV****************************
Disordered Region (DISEMBL)
MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEP*******************************************EQDQAIIARYLATLKGPETNNSQREHRTIGVSASIRREVIPYGDARSLNSLQHQNWHCIPFYPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPSLVEEPVSLVPEIGPFLYFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGGSDCWQNNCPSNVPRLSQSEIPNSLVSFNSQ**********************NAEISNQLRNQTEQYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQS*******************VPPSFAAPMTIRA******************************CSSRPWPEGMRNQGGMPSRHYMAPAVHIRSVVPVCS**************************
Disordered Region (DISPRO)
MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK*******ARV*DETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA***********************************************************IPYGDARSLNSLQHQNWHCIPFYPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPSLVEEPVSLVPEIGPFLYFSNRVMPVPVRNVSQVSIQEIEEN**MEE**R**DGGSDCWQN*********************************************************************************GDKFR***T************************GGSVPPSFAAPMTIRASATASTASLRPQSSNPLVRAPPPRRTAASFCSSRPWPEGMRNQGGMPSRHYMAPAVHIRSVVPVCSAP************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQDQAIIARYLATLKGPETNNSQREHRTIGVSASIRREVIPYGDARSLNSLQHQNWHCIPFYPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPSLVEEPVSLVPEIGPFLYFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGGSDCWQNNCPSNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQLRNQTEQYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNSTMVSSSGSVGGSVPPSFAAPMTIRASATASTASLRPQSSNPLVRAPPPRRTAASFCSSRPWPEGMRNQGGMPSRHYMAPAVHIRSVVPVCSAPPSKKYPDPSREKRTEEQRGDISAT
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	575	2.2.26 [Sep-21-2011]
Q0DKP4	593	Double-stranded RNA-bindi	yes	no	0.886	0.860	0.395	9e-87
Q8GY79	393	Double-stranded RNA-bindi	yes	no	0.318	0.465	0.693	1e-75
Q9LJF5	359	Double-stranded RNA-bindi	no	no	0.32	0.512	0.698	4e-75
Q9SKN2	434	Double-stranded RNA-bindi	no	no	0.316	0.419	0.723	6e-73
B7E321	404	Double-stranded RNA-bindi	no	no	0.269	0.383	0.819	3e-71
Q9AV50	514	Double-stranded RNA-bindi	no	no	0.316	0.354	0.707	4e-65
Q8H1D4	355	Double-stranded RNA-bindi	no	no	0.253	0.411	0.467	1e-30
Q5N8Z0	441	Double-stranded RNA-bindi	no	no	0.297	0.387	0.448	1e-29
Q0IV63	473	Double-stranded RNA-bindi	no	no	0.281	0.342	0.373	6e-22
Q0IQN6	424	Double-stranded RNA-bindi	no	no	0.281	0.382	0.373	6e-22

>sp|Q0DKP4|DRB2_ORYSJ Double-stranded RNA-binding protein 2 OS=Oryza sativa subsp. japonica GN=DRB2 PE=2 SV=1

 Score =  321 bits (823), Expect = 9e-87,   Method: Compositional matrix adjust.
 Identities = 232/587 (39%), Positives = 312/587 (53%), Gaps = 77/587 (13%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLPSY+CIREGPDHAPRFKA VNFNGETFESP FCSTLR AEHAA
Sbjct: 1   MYKNQLQELAQRSCFNLPSYACIREGPDHAPRFKATVNFNGETFESPAFCSTLRLAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+ LSK+GPS  LAA+VLDETG+YKNLLQET+HRAGLKLPVYTT+RSGPGH PVF+
Sbjct: 61  AEVALNELSKRGPSSSLAAKVLDETGIYKNLLQETAHRAGLKLPVYTTIRSGPGHTPVFT 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTVELAG++FTG P KTKKQAQKNAA+AAWS LK+  +    SSS  PP  +   +D+Q+
Sbjct: 121 CTVELAGMTFTGNPGKTKKQAQKNAAMAAWSELKQLPRVGEPSSSSCPPDHD---DDDQE 177

Query: 181 QAIIARYLATLKGPETNNS----QREHRTIGVSASIRREVIPYGDARSLNSLQHQNWHCI 236
           Q I+AR LA+L   +TN      Q+E +      S RR   P  +A     L H   H  
Sbjct: 178 QIIVARTLASLN--QTNGGKTPQQKEKQQSSNRPSSRRPSYPKSNASFYGRL-HLQKHAY 234

Query: 237 PFY-PELSLYQTCPQERVFRQQENLLALSSLPSSS-PRPQIFPFIRSMFQPDHGYYFPSL 294
           P   PE ++Y    Q +  +Q+ +   + ++ S+  P P   P +  M+ P  G +    
Sbjct: 235 PSVPPEQAMYHMWHQVQATQQKPHFPMVPTMGSTGFPPP---PTVLHMYPPPRGQFTMPS 291

Query: 295 VEEPVSLV---PEIGPFL--YFSNRVMPVPVRNVSQ----VSIQEIEENPRMEEDWRKGD 345
            ++ + L+   PE  P L  YFS    P P   V +    V++ +I E   +  D  +  
Sbjct: 292 SQDGLGLIPCYPEASPVLPRYFS----PYPASFVPRRPLPVNVHKIHEKRLVGADMVELP 347

Query: 346 GGSDCWQNNCP-------SNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSA 398
             +   +   P       + V    + E   S  +   +S+         +   + + S 
Sbjct: 348 DAAVFSRYTAPDFSGTSENAVQDNKKEEYTESSPASEQESKSHTASSSATRSPSQQLESN 407

Query: 399 PNAEISNQLRNQTEQYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNS 458
            + EI   LR ++++     P    +R  P  + + G +    +    D +      RNS
Sbjct: 408 QDIEIMGGLRLESKKPAEQPPESSPSRVNPVLLCETGQRHHYSSVRHGDPVH-----RNS 462

Query: 459 TMVSSSGSVGGSVPPSFAAPMTIRASATAS------TASLRPQSSNPLVRAPPPRRTAAS 512
             +S + S           P  IR    A       + +  P+  +P  +APP       
Sbjct: 463 PQISVATS-----------PSPIRRGDPAHINIPQISVATPPECRSPRAQAPP------R 505

Query: 513 FCSSRPWPEGMRNQGGMPSRHY------MAPAVHIRSVVPVCSAPPS 553
           F        G R    +PS  Y      +A +V IR+ +PVCSA P+
Sbjct: 506 F--------GTRMPVNLPSSLYQQRPPWLAASVTIRTTIPVCSARPN 544

Binds double-stranded RNA.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8GY79|DRB5_ARATH Double-stranded RNA-binding protein 5 OS=Arabidopsis thaliana GN=DRB5 PE=1 SV=1

 Score =  284 bits (727), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 136/196 (69%), Positives = 159/196 (81%), Gaps = 13/196 (6%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLPSY+CIREGPDHAPRFKA+VNFNGE FESPT+CSTLRQAEHAA
Sbjct: 1   MYKNQLQELAQRSCFNLPSYTCIREGPDHAPRFKASVNFNGEIFESPTYCSTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEV+L+VLS + PSK L A++LDETG+YKNLLQET+HRAGL LP+YT+VRSG  H P FS
Sbjct: 61  AEVSLNVLSSRVPSKSLTAKILDETGIYKNLLQETAHRAGLDLPMYTSVRSGSCHFPGFS 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTVELAG++FTGE AKTKKQA+KNAA+AAWS+LKK              SS    ++E++
Sbjct: 121 CTVELAGMTFTGESAKTKKQAEKNAAIAAWSSLKKM-------------SSLDSQDEEKE 167

Query: 181 QAIIARYLATLKGPET 196
           Q  +AR L+  K  E 
Sbjct: 168 QEAVARVLSRFKPKEV 183

Binds double-stranded RNA. May be involved in RNA-mediated silencing.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LJF5|DRB3_ARATH Double-stranded RNA-binding protein 3 OS=Arabidopsis thaliana GN=DRB3 PE=2 SV=1

 Score =  282 bits (722), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 137/196 (69%), Positives = 157/196 (80%), Gaps = 12/196 (6%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCF+LPSY+C REGPDHAPRFKA+VNFNGE FESPT+CSTLRQAEH+A
Sbjct: 1   MYKNQLQELAQRSCFSLPSYTCTREGPDHAPRFKASVNFNGEIFESPTYCSTLRQAEHSA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL  LS KGPSK L ARVLDETG+YKNLLQET+HRAGL LPVYT+VRSGPGH P FS
Sbjct: 61  AEVALSALSSKGPSKSLTARVLDETGIYKNLLQETAHRAGLDLPVYTSVRSGPGHIPTFS 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTVELAG+SF GE AKTKKQA+KNAA+AAW +L+K             P  +    +E++
Sbjct: 121 CTVELAGMSFNGESAKTKKQAEKNAAIAAWFSLRKM------------PRLDPLRGEEKE 168

Query: 181 QAIIARYLATLKGPET 196
           Q I+AR L+  +  E 
Sbjct: 169 QEIVARVLSRFRPKEV 184

Binds double-stranded RNA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SKN2|DRB2_ARATH Double-stranded RNA-binding protein 2 OS=Arabidopsis thaliana GN=DRB2 PE=1 SV=1

 Score =  275 bits (704), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 136/188 (72%), Positives = 154/188 (81%), Gaps = 6/188 (3%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLPSY+CIREGPDHAPRFKA VNFNGE FESP +CSTLRQAEH+A
Sbjct: 1   MYKNQLQELAQRSCFNLPSYTCIREGPDHAPRFKATVNFNGEIFESPQYCSTLRQAEHSA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+ LS +GPS  LAAR+LDETGVYKNLLQE + R G  LP YTT RSG GH PVF+
Sbjct: 61  AEVALNALSNRGPSHSLAARILDETGVYKNLLQEIAQRVGAPLPRYTTFRSGLGHQPVFT 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
            TVELAG++FTG+PAK KKQA+KNAA+AAWS+LK+ AK   +SSS   P +     DE +
Sbjct: 121 GTVELAGITFTGDPAKNKKQAEKNAAMAAWSSLKQLAKE--TSSSMPEPEN----IDELE 174

Query: 181 QAIIARYL 188
           Q IIAR L
Sbjct: 175 QVIIARAL 182

Binds double-stranded RNA. May be involved in RNA-mediated silencing.

Arabidopsis thaliana (taxid: 3702)

>sp|B7E321|DRB5_ORYSJ Double-stranded RNA-binding protein 5 OS=Oryza sativa subsp. japonica GN=DRB5 PE=2 SV=1

 Score =  270 bits (689), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 127/155 (81%), Positives = 139/155 (89%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCF+LPSY C REGPDHAPRFKA V FNGETF+ P+ C+TLRQAEHAA
Sbjct: 1   MYKNQLQELAQRSCFSLPSYVCTREGPDHAPRFKATVTFNGETFDGPSNCTTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL  LS +GPS  L ARVLDETGVYKNLLQET+HRAGLKLPVYTTVRSGPGH PVFS
Sbjct: 61  AEVALARLSLRGPSSSLTARVLDETGVYKNLLQETAHRAGLKLPVYTTVRSGPGHSPVFS 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK 155
            TVELAG+SF G+PAKTKK A+KNAA+AAWS+LK+
Sbjct: 121 STVELAGMSFAGDPAKTKKHAEKNAAMAAWSSLKQ 155

Binds double-stranded RNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9AV50|DRB6_ORYSJ Double-stranded RNA-binding protein 6 OS=Oryza sativa subsp. japonica GN=DRB6 PE=2 SV=1

 Score =  249 bits (636), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 133/188 (70%), Positives = 154/188 (81%), Gaps = 6/188 (3%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLP+Y+C+REGPDHAPRFKAAVNFNGE FESP F +TLRQAEHAA
Sbjct: 1   MYKNQLQELAQRSCFNLPAYTCLREGPDHAPRFKAAVNFNGEQFESPGFFTTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL  L+++GPS  LAAR+LDETGVYKNLLQE + R G  LP YTT RSG GH PVF+
Sbjct: 61  AEVALAALARRGPSYSLAARILDETGVYKNLLQEVAQRVGAPLPSYTTERSGLGHLPVFT 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTVELAG++FTG+PAK KKQA+KNAA AAWS+L++  +   SS      S+E  +NDEQ+
Sbjct: 121 CTVELAGITFTGDPAKNKKQAEKNAASAAWSSLRQLVRQEASS------SNEPESNDEQE 174

Query: 181 QAIIARYL 188
           Q  IAR L
Sbjct: 175 QIRIARAL 182

Binds double-stranded RNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8H1D4|DRB4_ARATH Double-stranded RNA-binding protein 4 OS=Arabidopsis thaliana GN=DBR4 PE=1 SV=1

 Score =  135 bits (339), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 72/154 (46%), Positives = 94/154 (61%), Gaps = 8/154 (5%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           +YK QLQ  A +    LP Y+  REGP HAPRF+  V F G+TF+S  F  TL+ AEHAA
Sbjct: 4   VYKGQLQAYALQHNLELPVYANEREGPPHAPRFRCNVTFCGQTFQSSEFFPTLKSAEHAA 63

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           A++A+  L+ + P  +  A        YKNLLQE + +    LP Y T  SGP H P F+
Sbjct: 64  AKIAVASLTPQSPEGIDVA--------YKNLLQEIAQKESSLLPFYATATSGPSHAPTFT 115

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALK 154
            TVE AG  F+GE AKTKK A+ +AA  A+ ++K
Sbjct: 116 STVEFAGKVFSGEEAKTKKLAEMSAAKVAFMSIK 149

Double-stranded RNA-binding protein involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the trans-acting small interfering RNAs (ta-siRNAs) biogenesis by binding and assisting DICER-LIKE 4 (DCL4). Required for DCL4 activity. Required for the 21 nucleotide ta-siRNAs production of the TAS3 transcript in leaves but not in flowers. Plays an important role in silencing RNA of both DNA and RNA viruses. Involved with argonaute 7 (AGO7) and RDR6 in turnip crinkle virus (TCV) silencing. May not be directly involved in viral siRNA production. May stabilize the 21 nucleotide viral siRNAs and deliver them to the RISC complex. Targeted by the viral silencing suppressor (VSR) transactivator/viroplasmin (TAV) protein of the cauliflower mosaic virus (CaMV) that inactivates DRB4 function in RNA silencing. Probably not involved in the guide strand selection from RNA duplexes. Involved in leaf morphology through its function in ta-siRNA-mediated silencing.

Arabidopsis thaliana (taxid: 3702)

>sp|Q5N8Z0|DRB1_ORYSJ Double-stranded RNA-binding protein 1 OS=Oryza sativa subsp. japonica GN=DRB1 PE=2 SV=1

 Score =  132 bits (331), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 78/174 (44%), Positives = 104/174 (59%), Gaps = 3/174 (1%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
           YK+QLQ  AQ+    LPSY  IREGP HA RFK+ V  +G+ FESP +  T+++AE AAA
Sbjct: 87  YKSQLQIYAQKKGKLLPSYQTIREGPGHASRFKSVVTVDGKAFESPEYFHTVKEAESAAA 146

Query: 62  EVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSC 121
           ++AL  L ++  S   + +V  +   YKNLLQE + + G  LPVY+T   G    P+F  
Sbjct: 147 KLALMSLPQEASS---SEQVPVQPLSYKNLLQELAQKHGFSLPVYSTTSDGSVQVPMFKS 203

Query: 122 TVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGT 175
           TV     SF GEPA TKKQA+ NAA  A+   + + K+A SS+    P    GT
Sbjct: 204 TVVFQDGSFQGEPANTKKQAEMNAARVAFQHFEDRRKNALSSTVLRGPHLGQGT 257

Binds double-stranded RNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q0IV63|DRB7_ORYSJ Double-stranded RNA-binding protein 7 OS=Oryza sativa subsp. japonica GN=DRB7 PE=2 SV=1

 Score =  106 bits (264), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 62/166 (37%), Positives = 96/166 (57%), Gaps = 4/166 (2%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFES-PTFCSTLRQAEHA 59
           ++K++LQE AQ++    P Y   +EGP H P FK+ V  N  +++S P F +  + AE +
Sbjct: 33  VFKSRLQEYAQKAGLQTPEYHTFKEGPSHEPVFKSTVVINNTSYDSLPGFFNR-KAAEQS 91

Query: 60  AAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVF 119
           AAEVAL  + K  P+      V  ETG+ KNLLQE + +    +P Y   +S  G  P F
Sbjct: 92  AAEVALMEIVKSIPANANIPAV-QETGLCKNLLQEYAQKMNYAIPSYICTKSASGLAP-F 149

Query: 120 SCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSS 165
            CTVE+ G+ + G  A+TKK A+  AA  A  A++ Q++ + + ++
Sbjct: 150 ICTVEIGGIQYIGAAARTKKDAEIKAARTALLAIQGQSEGSANGAT 195

Binds double-stranded RNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q0IQN6|DRB8_ORYSJ Double-stranded RNA-binding protein 8 OS=Oryza sativa subsp. japonica GN=DRB8 PE=2 SV=1

 Score =  106 bits (264), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 62/166 (37%), Positives = 96/166 (57%), Gaps = 4/166 (2%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFES-PTFCSTLRQAEHA 59
           ++K++LQE AQ++    P Y   +EGP H P FK+ V  N  +++S P F +  + AE +
Sbjct: 33  VFKSRLQEYAQKTGLQTPEYHTFKEGPSHEPVFKSTVVINNTSYDSLPGFFNR-KAAEQS 91

Query: 60  AAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVF 119
           AAEVAL  + K  P+      V  ETG+ KNLLQE + +    +P Y   +S  G  P F
Sbjct: 92  AAEVALMEIVKSIPANANIPAV-QETGLCKNLLQEYAQKMNYAIPSYICTKSASGLAP-F 149

Query: 120 SCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSS 165
            CTVE+ G+ + G  A+TKK A+  AA  A  A++ Q++ + + ++
Sbjct: 150 ICTVEIGGIQYIGAAARTKKDAEIKAARTALLAIQGQSEGSANGAT 195

Binds double-stranded RNA.

Oryza sativa subsp. japonica (taxid: 39947)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	575
225432380	563	PREDICTED: double-stranded RNA-binding p	0.954	0.975	0.583	1e-164
297736909	826	unnamed protein product [Vitis vinifera]	0.956	0.665	0.581	1e-164
298204936	551	unnamed protein product [Vitis vinifera]	0.914	0.954	0.495	1e-126
359487919	532	PREDICTED: double-stranded RNA-binding p	0.890	0.962	0.491	1e-126
255542426	568	hypothetical protein RCOM_1429110 [Ricin	0.92	0.931	0.466	1e-109
356571155	538	PREDICTED: double-stranded RNA-binding p	0.883	0.944	0.440	1e-102
356504084	539	PREDICTED: double-stranded RNA-binding p	0.885	0.944	0.440	1e-101
357512161	505	Double-stranded RNA binding protein [Med	0.563	0.641	0.563	2e-88
102139807	610	double-stranded RNA-binding (DsRBD) doma	0.928	0.875	0.393	1e-86
115462131	593	Os05g0150400 [Oryza sativa Japonica Grou	0.886	0.860	0.395	6e-85

>gi|225432380|ref|XP_002276654.1| PREDICTED: double-stranded RNA-binding protein 2-like [Vitis vinifera]

 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 331/567 (58%), Positives = 403/567 (71%), Gaps = 18/567 (3%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLPSY+CIREGPDHAPRFKA VNFNGE FESPTFC+TLRQAEHAA
Sbjct: 1   MYKNQLQELAQRSCFNLPSYACIREGPDHAPRFKATVNFNGEVFESPTFCNTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+VLSK GPSK LAA+VLDETGVYKNLLQET+HRAGLKLPVYTTVRSGPGH PVF 
Sbjct: 61  AEVALNVLSKNGPSKALAAKVLDETGVYKNLLQETAHRAGLKLPVYTTVRSGPGHIPVFF 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTV++A +SFTGEPAKTKKQAQKNAA+AAWSALK+ ++++ S+SS      ESG NDE +
Sbjct: 121 CTVDIAKMSFTGEPAKTKKQAQKNAAMAAWSALKRLSQASSSTSSA---PLESGGNDELE 177

Query: 181 QAIIARYLATLKGPETNNSQREHRTIGVSAS-IRREVIPYGDARSLNSLQHQNW-HCIPF 238
           Q  +ARYLA+L+ PE N S +    +G  ++  RR+++P  +A SL S+  ++W H  P 
Sbjct: 178 QVTVARYLASLQPPEANKSAQRDGLLGQGSTPCRRDLMPNDNAISLYSMHCRDWSHSAPL 237

Query: 239 YPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPSLVEEP 298
             +L+ +Q+ P+ER  +QQ +LLAL S P++ PRPQ+ P IRS+FQPDHG  F    +EP
Sbjct: 238 I-QLA-HQSWPKERASQQQNHLLALPSAPTTLPRPQMSPIIRSIFQPDHGPCFLPREQEP 295

Query: 299 VSLVPEIGPFLYFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGGSDCWQNNCPSN 358
             L P IGPFLYFSN  MPVPV N+SQV+IQEIEE P++E++W   D  S CW+ N PSN
Sbjct: 296 APLSPGIGPFLYFSNGSMPVPVSNLSQVTIQEIEEKPKVEQEWLNVDANSGCWKINFPSN 355

Query: 359 VPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQL-RNQTEQYNWF 417
           +  LS  EIP   +S NS SE  +QE LQGK EE S  +      S QL  NQ ++  W 
Sbjct: 356 LSGLSLVEIPKCPISPNSHSEP-IQEALQGKEEENSAGN------SAQLGTNQIQRLAWT 408

Query: 418 SPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNSTMVSSSGSVGGSVPPSFAA 477
           SP F D   R +  + D     LQN   LDYLQS+ R +N+ M +  GS      PS AA
Sbjct: 409 SPRFADT--RSSAGASDEANLWLQNQQFLDYLQSNIRSQNAPMATYPGSSRVYTRPS-AA 465

Query: 478 PMTIRASATASTASLRPQSSNPLVRAPPPRRTAASFCSSRPWPEGMRNQGGMPSRHYMAP 537
           P+TIR+S  +S    RP SS+  V APPP R AA   S+RP  EG +  G  P   +MAP
Sbjct: 466 PVTIRSSDASSIRKPRPMSSSLFVSAPPPTRYAAPTWSTRPTLEGAKYTGVRPCSRFMAP 525

Query: 538 AVHIRSVVPVCSAPPSKKYPDPSREKR 564
           AV+IRSVVPVCSAPP+K     S+E+R
Sbjct: 526 AVNIRSVVPVCSAPPAKDRAGGSQEER 552

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736909|emb|CBI26110.3| unnamed protein product [Vitis vinifera]

 Score =  584 bits (1505), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 329/566 (58%), Positives = 404/566 (71%), Gaps = 16/566 (2%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLPSY+CIREGPDHAPRFKA VNFNGE FESPTFC+TLRQAEHAA
Sbjct: 1   MYKNQLQELAQRSCFNLPSYACIREGPDHAPRFKATVNFNGEVFESPTFCNTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+VLSK GPSK LAA+VLDETGVYKNLLQET+HRAGLKLPVYTTVRSGPGH PVF 
Sbjct: 61  AEVALNVLSKNGPSKALAAKVLDETGVYKNLLQETAHRAGLKLPVYTTVRSGPGHIPVFF 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTV++A +SFTGEPAKTKKQAQKNAA+AAWSALK+ ++++ S+SS      ESG NDE +
Sbjct: 121 CTVDIAKMSFTGEPAKTKKQAQKNAAMAAWSALKRLSQASSSTSSA---PLESGGNDELE 177

Query: 181 QAIIARYLATLKGPETNNSQREHRTIGVSAS-IRREVIPYGDARSLNSLQHQNW-HCIPF 238
           Q  +ARYLA+L+ PE N S +    +G  ++  RR+++P  +A SL S+  ++W H  P 
Sbjct: 178 QVTVARYLASLQPPEANKSAQRDGLLGQGSTPCRRDLMPNDNAISLYSMHCRDWSHSAPL 237

Query: 239 YPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPSLVEEP 298
             +L+ +Q+ P+ER  +QQ +LLAL S P++ PRPQ+ P IRS+FQPDHG  F    +EP
Sbjct: 238 I-QLA-HQSWPKERASQQQNHLLALPSAPTTLPRPQMSPIIRSIFQPDHGPCFLPREQEP 295

Query: 299 VSLVPEIGPFLYFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGGSDCWQNNCPSN 358
             L P IGPFLYFSN  MPVPV N+SQV+IQEIEE P++E++W   D  S CW+ N PSN
Sbjct: 296 APLSPGIGPFLYFSNGSMPVPVSNLSQVTIQEIEEKPKVEQEWLNVDANSGCWKINFPSN 355

Query: 359 VPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQLRNQTEQYNWFS 418
           +  LS  EIP   +S NS SE  +QE LQGK EE S  ++  A++     NQ ++  W S
Sbjct: 356 LSGLSLVEIPKCPISPNSHSEP-IQEALQGKEEENSAGNS--AQLGT---NQIQRLAWTS 409

Query: 419 PGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNSTMVSSSGSVGGSVPPSFAAP 478
           P F D   R +  + D     LQN   LDYLQS+ R +N+ M +  GS      PS AAP
Sbjct: 410 PRFADT--RSSAGASDEANLWLQNQQFLDYLQSNIRSQNAPMATYPGSSRVYTRPS-AAP 466

Query: 479 MTIRASATASTASLRPQSSNPLVRAPPPRRTAASFCSSRPWPEGMRNQGGMPSRHYMAPA 538
           +TIR+S  +S    RP SS+  V APPP R AA   S+RP  EG +  G  P   +MAPA
Sbjct: 467 VTIRSSDASSIRKPRPMSSSLFVSAPPPTRYAAPTWSTRPTLEGAKYTGVRPCSRFMAPA 526

Query: 539 VHIRSVVPVCSAPPSKKYPDPSREKR 564
           V+IRSVVPVCSAPP+K     S+E+R
Sbjct: 527 VNIRSVVPVCSAPPAKDRAGGSQEER 552

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298204936|emb|CBI34243.3| unnamed protein product [Vitis vinifera]

 Score =  460 bits (1183), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 284/573 (49%), Positives = 356/573 (62%), Gaps = 47/573 (8%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKA VNFNGETFESP+FCSTLRQAEHAA
Sbjct: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKATVNFNGETFESPSFCSTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+ L+ +GPSK LAARVLDETGVYKNLLQET+HRAGL LPVYTT+RSGPGH PVFS
Sbjct: 61  AEVALNTLANRGPSKALAARVLDETGVYKNLLQETAHRAGLNLPVYTTIRSGPGHVPVFS 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTVE+AG+SFTGE AKTKKQAQKNAA+ AWSAL+K ++    SS     S ES  N+EQ+
Sbjct: 121 CTVEIAGMSFTGEAAKTKKQAQKNAAMTAWSALRKLSQRGSPSSP----SVESECNEEQE 176

Query: 181 QAIIARYLATLKGPETNNSQ--REHRTIGVSASIRREVIPYGDARSLNSLQHQNWHCIPF 238
           Q IIAR LA+L+  ++NN Q  R+H     S SI R+  P        S+Q+Q+     F
Sbjct: 177 QVIIARVLASLRPSKSNNKQNDRQHGQ-QRSGSICRDSTPQTPISC--SMQYQSTVDPSF 233

Query: 239 YPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPSLVEEP 298
           +PE+++YQ   QE++ + Q  LLAL    +  P P  FPF++SMF+PDH  YFP+ V++P
Sbjct: 234 FPEMAMYQMWQQEQLAQLQNRLLALPVPLAPQPSPHFFPFMQSMFRPDHCLYFPTEVQQP 293

Query: 299 VSLVPEI-----GPFLYFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGGSDCWQN 353
           +++ P       G   Y SN ++P P+R  S V+IQEIEE      ++            
Sbjct: 294 ITMGPRFSIAASGSSFYLSNHLVPEPMRGRSMVTIQEIEEKTEERSEF------------ 341

Query: 354 NCPSNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQL-RNQTE 412
                    S SE+  S    ++ +E   QE +Q   ++ +         S QL RNQ  
Sbjct: 342 ---------SPSEVSVSPALGDNNTEAINQEPIQEDNKQNTEELGGKIATSVQLERNQPG 392

Query: 413 QYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNSTMVSSSGSVGGSVP 472
           Q+ W S   +D+R  P        +F+LQ     D  QS+ RP +   +SS  S      
Sbjct: 393 QFGWTSRRSVDSRLGPI-------EFQLQRPHGFDSSQSNPRPYHPPGLSSYRSSRPPS- 444

Query: 473 PSFAAPMTIRASATASTASLRPQSSNPLVRAPPPRRTAASFCSSRPWPEGMRNQGGMPSR 532
            + AAP+  R     S+  LRPQ+    + APP  RT     S RP PE M    G P  
Sbjct: 445 -TVAAPVMTRTGDPVSSVGLRPQNLANQMPAPPRMRTGIPPYSFRPRPERMDFGRGPP-- 501

Query: 533 HYMAPAVHIRSVVPVCSAPPSKKYPDPSREKRT 565
             MAPAV IR+VVPVCSAPP++K P PS ++ T
Sbjct: 502 RAMAPAVQIRTVVPVCSAPPARKIPRPSSKEMT 534

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487919|ref|XP_002271134.2| PREDICTED: double-stranded RNA-binding protein 2 [Vitis vinifera]

 Score =  458 bits (1179), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 280/570 (49%), Positives = 349/570 (61%), Gaps = 58/570 (10%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKA VNFNGETFESP+FCSTLRQAEHAA
Sbjct: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKATVNFNGETFESPSFCSTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+ L+ +GPSK LAARVLDETGVYKNLLQET+HRAGL LPVYTT+RSGPGH PVFS
Sbjct: 61  AEVALNTLANRGPSKALAARVLDETGVYKNLLQETAHRAGLNLPVYTTIRSGPGHVPVFS 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTVE+AG+SFTGE AKTKKQAQKNAA+ AWSAL+K                ES  N+EQ+
Sbjct: 121 CTVEIAGMSFTGEAAKTKKQAQKNAAMTAWSALRK---------------LESECNEEQE 165

Query: 181 QAIIARYLATLKGPETNNSQ--REHRTIGVSASIRREVIPYGDARSLNSLQHQNWHCIPF 238
           Q IIAR LA+L+  ++NN Q  R+H     S SI R+  P        S+Q+Q+     F
Sbjct: 166 QVIIARVLASLRPSKSNNKQNDRQHGQ-QRSGSICRDSTPQTPISC--SMQYQSTVDPSF 222

Query: 239 YPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPSLVEEP 298
           +PE+++YQ   QE++ + Q  LLAL    +  P P  FPF++SMF+PDH  YFP+ V++P
Sbjct: 223 FPEMAMYQMWQQEQLAQLQNRLLALPVPLAPQPSPHFFPFMQSMFRPDHCLYFPTEVQQP 282

Query: 299 VSLVPEI-----GPFLYFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGGSDCWQN 353
           +++ P       G   Y SN ++P P+R  S V+IQEIEE      ++            
Sbjct: 283 ITMGPRFSIAASGSSFYLSNHLVPEPMRGRSMVTIQEIEEKTEERSEF------------ 330

Query: 354 NCPSNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQL-RNQTE 412
                    S SE+  S    ++ +E   QE +Q   ++ +         S QL RNQ  
Sbjct: 331 ---------SPSEVSVSPALGDNNTEAINQEPIQEDNKQNTEELGGKIATSVQLERNQPG 381

Query: 413 QYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNSTMVSSSGSVGGSVP 472
           Q+ W S   +D+R  P        +F+LQ     D  QS+ RP +   +SS  S      
Sbjct: 382 QFGWTSRRSVDSRLGPI-------EFQLQRPHGFDSSQSNPRPYHPPGLSSYRSSRPPS- 433

Query: 473 PSFAAPMTIRASATASTASLRPQSSNPLVRAPPPRRTAASFCSSRPWPEGMRNQGGMPSR 532
            + AAP+  R     S+  LRPQ+    + APP  RT     S RP PE M    G P  
Sbjct: 434 -TVAAPVMTRTGDPVSSVGLRPQNLANQMPAPPRMRTGIPPYSFRPRPERMDFGRGPP-- 490

Query: 533 HYMAPAVHIRSVVPVCSAPPSKKYPDPSRE 562
             MAPAV IR+VVPVCSAPP++K P  S+E
Sbjct: 491 RAMAPAVQIRTVVPVCSAPPARKIPSSSQE 520

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255542426|ref|XP_002512276.1| hypothetical protein RCOM_1429110 [Ricinus communis] gi|223548237|gb|EEF49728.1| hypothetical protein RCOM_1429110 [Ricinus communis]

 Score =  402 bits (1032), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 274/587 (46%), Positives = 337/587 (57%), Gaps = 58/587 (9%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKA VNFNGETFESP FCSTLRQAEHAA
Sbjct: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKATVNFNGETFESPAFCSTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+ L+ +GPS+ LAARVLDETGVYKNLLQET+HRAGLKLPVYTTVRSGPGH PVFS
Sbjct: 61  AEVALNTLASRGPSRALAARVLDETGVYKNLLQETAHRAGLKLPVYTTVRSGPGHVPVFS 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK--QAKSAFSSSSFSPPSSESGTNDE 178
           CTVELAG+SFTGEPA+TKKQAQKNAA+AAWSALK+  Q  S+ SSS  S        ++E
Sbjct: 121 CTVELAGMSFTGEPARTKKQAQKNAAMAAWSALKRLVQHGSSSSSSLSSSLVENRKGSEE 180

Query: 179 QDQAIIARYLAT-----LKGPETNNSQREH-RTIGVSASIRREVIPYGDARSLNSLQHQN 232
           Q+Q +IAR+LA+     LK  + N+ Q  H R I V     +++ P     SL  +Q QN
Sbjct: 181 QEQVVIARFLASVQPSELKINKQNDCQTGHERFIPVC----KDLTP--PTPSLYPMQSQN 234

Query: 233 WHCIPFYPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFP 292
           W    F PE+++YQ   QE++ +    LL L   P+  P P + P+++S+  P+   +FP
Sbjct: 235 WAYPSFSPEIAIYQMWQQEQLLQLHNRLLTLQVPPAPPPAPPMLPYMQSVLPPNSHLFFP 294

Query: 293 SLVEEPVSLVPEI-----GPFLYFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGG 347
              +E V + P I     GP L  S+ V    VR  S V+IQEI E         K +  
Sbjct: 295 LRKQETVPVGPRITIASSGPLLCLSDNVDSDSVRGKSAVTIQEINEE--------KPEDL 346

Query: 348 SDCWQNNCPSNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQL 407
           SDC            S S I +  V  N  +E R +E           S   N  ++   
Sbjct: 347 SDC------------SPSIISDPPVLGNLSAEARFKESHDDDKNNAVESKVENVRLAENP 394

Query: 408 RNQTEQYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDS--RPRNSTMVSSSG 465
             Q+   N  S G+    FR   +   G       +      QS +  RP  + M+ +  
Sbjct: 395 SGQSSHRNTDS-GYSQVDFR---VQSPGVFVSCHASSQFSPRQSSTSCRPPPTVMIRNV- 449

Query: 466 SVGGSVPPSFAAPMTIRASATASTASLRPQSSNPLVRAPPPRRTAASFCSSRPWPEGMRN 525
              G  P   A P+ IR     S+   RP      +  PP  RT A   S+RP P+ M  
Sbjct: 450 ---GPRPLPAAPPVRIRTMGPVSSVP-RPHDLAAQIPGPPRMRTGAPSYSARPQPQRMDF 505

Query: 526 QGGMPSRHYMAPAVHIRSVVPVCSAPPSKKYPDPSREKRTEEQRGDI 572
            G  P   +MAPAV IRSVVPVCSAPP      P+R+  T  Q G +
Sbjct: 506 VGVHP--RFMAPAVRIRSVVPVCSAPP------PARKMPTAGQEGAL 544

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571155|ref|XP_003553745.1| PREDICTED: double-stranded RNA-binding protein 2-like [Glycine max]

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 256/581 (44%), Positives = 335/581 (57%), Gaps = 73/581 (12%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKN+LQELAQRSCFNLP+YSCIREGPDHAPRFKA VNFNGETFESPTFCSTLRQAEHAA
Sbjct: 1   MYKNRLQELAQRSCFNLPAYSCIREGPDHAPRFKATVNFNGETFESPTFCSTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+ ++K+GPS  LAARVLDETGVYKNLLQET+HRAGL LPVYTT+RSGPGHGP FS
Sbjct: 61  AEVALNTIAKRGPSGALAARVLDETGVYKNLLQETAHRAGLNLPVYTTIRSGPGHGPNFS 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           C+VE+AG+ FTG+P++TKKQAQKNAA+AAWSAL+K ++   SSS+ S  S ES  N+EQ+
Sbjct: 121 CSVEIAGMHFTGDPSRTKKQAQKNAAMAAWSALRKLSEHHLSSSTSSSFSRESKANEEQE 180

Query: 181 QAIIARYLATLKGPETNNSQREHRTIGVSASIRREVIPYGDARSLNSLQHQNWHC--IPF 238
           Q IIA  LA+L    + N       +G   S    ++       L  +Q   WHC    F
Sbjct: 181 QVIIAGVLASLHPSGSKNFSTSDSQLGWQKSTTTSLVSTQSTADLYPMQ---WHCGISSF 237

Query: 239 YPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPSLVEEP 298
            PE++LYQT  Q+++ +QQ  LL L+  P     P+I+P ++S+FQPDH  YFP+     
Sbjct: 238 SPEVALYQTWQQQQIMQQQNRLLELTIQPIIPSTPEIYPLMQSVFQPDHCLYFPARELAS 297

Query: 299 VSLVPEI-----GPFLYFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGGSDCWQN 353
           V L P++      P  Y SN+++P      S ++I+EI+E         K +    C  +
Sbjct: 298 VPLGPKLSIATSNPSFYSSNQIVPELNTGRSTLTIREIQEE--------KTEDPPVCTFS 349

Query: 354 NCPSNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQLRNQTE- 412
           N                +++   + E +   G  G+          NAE+  +   +TE 
Sbjct: 350 N-------------ETRVLTPAPEDEIQKHGGSGGRSR--------NAELVGEHCEKTEC 388

Query: 413 QYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNSTMVSSSGSVGGSVP 472
             +W +   I    RP           LQN  S+D     S  R  +  SS+ S     P
Sbjct: 389 DSHWSTRSVI----RPVNT-------ELQNPSSID----SSVLRAHSQASSNRSFR---P 430

Query: 473 PSFAAPMTIRASATASTASLRPQSSNPLVRAPPPRR----TAASFCSSRPWPEGMRNQGG 528
           P+ A+   +R     S+   RPQ +   +R   PR     T+  F   R           
Sbjct: 431 PAAASSSIVRTMCPTSSVGSRPQHAASRLRTGTPRSPGIPTSERFGMIR----------- 479

Query: 529 MPSRHYMAPAVHIRSVVPVCSAPPSKKYPDPSREKRTEEQR 569
            P+  +MAPAV IRSVVPVCSAPP +   + S+ K  E+ +
Sbjct: 480 APTPLFMAPAVRIRSVVPVCSAPPRRSMAEVSQSKEKEDLK 520

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504084|ref|XP_003520829.1| PREDICTED: double-stranded RNA-binding protein 2-like [Glycine max]

 Score =  374 bits (960), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 256/581 (44%), Positives = 335/581 (57%), Gaps = 72/581 (12%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKN+LQELAQRSCFNLP+YSCIREGPDHAPRFKA VNFNGETFESPTFCSTLRQAEHAA
Sbjct: 1   MYKNRLQELAQRSCFNLPAYSCIREGPDHAPRFKATVNFNGETFESPTFCSTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+ L+K+GPS+ LAARVLDETGVYKNLLQET+HRAGL LPVYTT+RSGPGHGP FS
Sbjct: 61  AEVALNTLAKRGPSRALAARVLDETGVYKNLLQETAHRAGLNLPVYTTIRSGPGHGPNFS 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTVE+AG+ FTG+P++TKKQAQKNAA+AAWSAL+K ++   SSS+ S  S ES  N+EQ+
Sbjct: 121 CTVEIAGMHFTGDPSRTKKQAQKNAAMAAWSALRKLSEHHLSSSTSSSFSLESKGNEEQE 180

Query: 181 QAIIARYLATLKGPETNNSQREHRTIGVSASIRREVIPYGDARSLNSLQHQNWHCIPFYP 240
           Q IIAR LA+L    + N  +    +G   S    ++       L  +  Q++    F P
Sbjct: 181 QVIIARVLASLHPSGSKNFSKSDIQLGWQKSTTTSLVSTQPTTDLYPMHCQHFGISSFSP 240

Query: 241 ELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPSLVEEPVS 300
           E++LYQ   Q+++ +QQ  LLAL+  P      QI+P ++S+FQPDH  YFP+     ++
Sbjct: 241 EVALYQIWQQQQIMQQQNRLLALTIQPIIPSTSQIYPLMQSVFQPDHCLYFPA---RELA 297

Query: 301 LVPEIGPFL---------YFSNRVMPVPVRNVSQVSIQEIEENPRMEEDWRKGDGGSDCW 351
            VP +GP L         Y SN++ P      S ++I+EI+E  ++E+            
Sbjct: 298 SVP-VGPKLSIPSSSPSFYSSNQIGPELNTGRSTLTIKEIQEE-KIEDP----------- 344

Query: 352 QNNCPSNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSAPNAEISNQLRNQT 411
                   P  S S     L        QR      G    +S+    NAE+  +   ++
Sbjct: 345 --------PVCSFSNETRVLTPATEDESQR-----HGGSGSRSI----NAELGGEHCEKS 387

Query: 412 EQYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNSTMVSSSGSVGGSV 471
           E  + +  G +     P           LQN  S+D     S  R  +  SS+ S     
Sbjct: 388 ECDSHWGTGSVHRPVNP----------ELQNPSSID----SSVLRAHSQASSNRSFR--- 430

Query: 472 PPSFAAPMTIRASATASTASLRPQSSNPLVRAPPPRRTAASFCSSRPWPEGMRNQGGM-- 529
           PP+ ++   +R     S    RPQ   P +R   PR               +  + GM  
Sbjct: 431 PPAASSSSIVRTMCPTSFVGSRPQHVAPRLRTGTPRSPGIP----------IYERFGMIR 480

Query: 530 -PSRHYMAPAVHIRSVVPVCSAPPSKKYPDPSREKRTEEQR 569
            P+  +MAPAV IRSVVPVCSAPP +   + S+ K  E+ +
Sbjct: 481 APTPLFMAPAVRIRSVVPVCSAPPRRSMAEVSQSKEKEDLK 521

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357512161|ref|XP_003626369.1| Double-stranded RNA binding protein [Medicago truncatula] gi|355501384|gb|AES82587.1| Double-stranded RNA binding protein [Medicago truncatula]

 Score =  333 bits (853), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 194/344 (56%), Positives = 244/344 (70%), Gaps = 20/344 (5%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKN+LQELAQRSCFNLP+YSCIREGPDHAPRFK  VNFNGETFESPTFCSTLRQAEHAA
Sbjct: 1   MYKNRLQELAQRSCFNLPAYSCIREGPDHAPRFKVTVNFNGETFESPTFCSTLRQAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+ L+ +GPS+ LAARVLDETGVYKNLLQET+HRAGL LPVY T+R+GPGH P F 
Sbjct: 61  AEVALNTLATRGPSRTLAARVLDETGVYKNLLQETAHRAGLNLPVYRTIRAGPGHVPNFY 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTVE+AG+ FTG+PA+TKKQAQKNAA+AAWSAL+K + +  SSS+ S  SSES +N+EQ+
Sbjct: 121 CTVEIAGMHFTGDPARTKKQAQKNAAIAAWSALRKLSANQLSSSTSSSFSSESKSNEEQE 180

Query: 181 QAIIARYLATLKG------PETNNSQREHRTIGVSASIRREVIPYGDARSLNSLQHQNWH 234
             IIAR LA+L+       PE ++  R  ++   S      ++       +  +Q+Q+  
Sbjct: 181 HVIIARVLASLQSSGSKNFPECDHQHRWQKSTTTS------LVSTQPTPGMYPMQYQHCG 234

Query: 235 CIPFYPELSLYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRSMFQPDHGYYFPS- 293
              F PEL+LYQT  QE   +  + ++AL+  P   P PQI+P ++S+ QPD   YFPS 
Sbjct: 235 ISNFSPELALYQTWQQE---QIMQQMMALTIQPIIPPAPQIYPLMQSVIQPDRYLYFPSK 291

Query: 294 -LVEEPVSLVPEIG---PFLYFSNRVMPVPVRNVSQVSIQEIEE 333
            L   PV     I    P  Y+SN+++P      S V+I+EI+E
Sbjct: 292 ELSSFPVGPNFSIATPRPPFYYSNQIVPQLNTGRSTVTIREIQE 335

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|102139807|gb|ABF69992.1| double-stranded RNA-binding (DsRBD) domain-containing protein [Musa acuminata]

 Score =  327 bits (838), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 251/638 (39%), Positives = 343/638 (53%), Gaps = 104/638 (16%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLPSY+ IREGPDHAPRFKA VNFNGE FESPTFCSTLRQAEH+A
Sbjct: 1   MYKNQLQELAQRSCFNLPSYASIREGPDHAPRFKATVNFNGEAFESPTFCSTLRQAEHSA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+ LSK+GPS+ LAA+VLDETG+YKNLLQET+HRAGLKLPVYTTVRSGPGH P+F+
Sbjct: 61  AEVALNTLSKRGPSRSLAAKVLDETGIYKNLLQETAHRAGLKLPVYTTVRSGPGHTPIFT 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSP-----------P 169
           CTVELAG+SFTG+PAKTKKQAQKNAA+AAWSALK         ++ +P            
Sbjct: 121 CTVELAGMSFTGDPAKTKKQAQKNAAMAAWSALKHFKSYLVDGANAAPRLGSSSSPSAPS 180

Query: 170 SSESGTNDEQDQAIIARYLATLKGPETNNSQREHRTIGVSASIRREVIPYGDARSLNSLQ 229
            SES  N+EQ+  I+A  LA L+  E N S  ++         RR        +S++   
Sbjct: 181 LSESEKNEEQEPVILAHALAKLQRSEENWSSSQN-------GRRRGQQRSPPQKSMHPTS 233

Query: 230 HQNWHCIPF----YPELS----LYQTCPQERVFRQQENLLALSSLPSSSPRPQIFPFIRS 281
           +  +  IPF    YP+LS     YQ   +     QQ +     SL   +   + FP +  
Sbjct: 234 NVCFCPIPFQNLVYPDLSSESEFYQMWHRAHASPQQSHF----SLTPHARDHRSFPILH- 288

Query: 282 MFQPDHGYYFPSLVEEPVSLV-------PEIGPFLYFSNRVMPVPVRNVSQVSIQEI--E 332
            F P    + PS+ ++PVS +       P +   + FS+  + V   + SQ +IQ+I  E
Sbjct: 289 YFYPSQVLHTPSVEQDPVSSLRCSTGSSPSL--LVCFSDHPVSVASGSWSQFTIQQIHGE 346

Query: 333 ENPRMEEDWRKGDGGSDCWQNNCPSNVPRLSQSEIP-NSLVSFNSQSEQRMQEGLQGKGE 391
           +N R+ ++W              PS+    S  ++  +SL S N      +Q+  + + +
Sbjct: 347 QNQRVGKEWLI-----------LPSSAEAYSALDVSGSSLQSDNISDASTVQKSHEDQEK 395

Query: 392 EKSVSSAPNAEISNQLRNQTEQYNWFSPGF--IDARFRPTTISKDGDKFRLQNTVSLDYL 449
           E S+  A  A +        E+ N    GF  + +   PT +     +  +Q   + +  
Sbjct: 396 ECSLGGA-EAHLE-------EEANSSCHGFKSVASASCPTMVQDPAGRTEMQERKTAEKS 447

Query: 450 QSDS-------------RPRNSTMVSSSGSVGGSVPPSFAAP----MTIRASATASTASL 492
           Q  S              P N +++ +  S       S  +P    +  +   +A +AS+
Sbjct: 448 QGKSYGWMPRASVWPGPSPPNHSLLYNLNSDSSPTQFSHGSPNSSSLDRKFRPSAVSASM 507

Query: 493 RPQSSN----------------PLVRAPPPRRTAASFCSSRPWPEGMRNQGGM-PSRHYM 535
           RP SS                 P   AP   RT    CS+R    G  N G +  S  ++
Sbjct: 508 RPISSALLHPSGLRYEAFRRQVPSPAAPVTIRTTIPVCSAR---AGAVNPGTLVSSTSFV 564

Query: 536 APAVHIRSVVPVCSAPPSKKYPDPSREKRTEEQRGDIS 573
           AP V++RSVVPVCSAPP +K   P + +++ E++  +S
Sbjct: 565 APPVNVRSVVPVCSAPPVRK---PEQNQKSIEEKETMS 599

Source: Musa acuminata

Species: Musa acuminata

Genus: Musa

Family: Musaceae

Order: Zingiberales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115462131|ref|NP_001054665.1| Os05g0150400 [Oryza sativa Japonica Group] gi|122169532|sp|Q0DKP4.1|DRB2_ORYSJ RecName: Full=Double-stranded RNA-binding protein 2; AltName: Full=dsRNA-binding protein 2; AltName: Full=dsRNA-binding protein 3; Short=OsDRB3 gi|113578216|dbj|BAF16579.1| Os05g0150400 [Oryza sativa Japonica Group]

 Score =  321 bits (823), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 232/587 (39%), Positives = 312/587 (53%), Gaps = 77/587 (13%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           MYKNQLQELAQRSCFNLPSY+CIREGPDHAPRFKA VNFNGETFESP FCSTLR AEHAA
Sbjct: 1   MYKNQLQELAQRSCFNLPSYACIREGPDHAPRFKATVNFNGETFESPAFCSTLRLAEHAA 60

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
           AEVAL+ LSK+GPS  LAA+VLDETG+YKNLLQET+HRAGLKLPVYTT+RSGPGH PVF+
Sbjct: 61  AEVALNELSKRGPSSSLAAKVLDETGIYKNLLQETAHRAGLKLPVYTTIRSGPGHTPVFT 120

Query: 121 CTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDEQD 180
           CTVELAG++FTG P KTKKQAQKNAA+AAWS LK+  +    SSS  PP  +   +D+Q+
Sbjct: 121 CTVELAGMTFTGNPGKTKKQAQKNAAMAAWSELKQLPRVGEPSSSSCPPDHD---DDDQE 177

Query: 181 QAIIARYLATLKGPETNNS----QREHRTIGVSASIRREVIPYGDARSLNSLQHQNWHCI 236
           Q I+AR LA+L   +TN      Q+E +      S RR   P  +A     L H   H  
Sbjct: 178 QIIVARTLASLN--QTNGGKTPQQKEKQQSSNRPSSRRPSYPKSNASFYGRL-HLQKHAY 234

Query: 237 PFY-PELSLYQTCPQERVFRQQENLLALSSLPSSS-PRPQIFPFIRSMFQPDHGYYFPSL 294
           P   PE ++Y    Q +  +Q+ +   + ++ S+  P P   P +  M+ P  G +    
Sbjct: 235 PSVPPEQAMYHMWHQVQATQQKPHFPMVPTMGSTGFPPP---PTVLHMYPPPRGQFTMPS 291

Query: 295 VEEPVSLV---PEIGPFL--YFSNRVMPVPVRNVSQ----VSIQEIEENPRMEEDWRKGD 345
            ++ + L+   PE  P L  YFS    P P   V +    V++ +I E   +  D  +  
Sbjct: 292 SQDGLGLIPCYPEASPVLPRYFS----PYPASFVPRRPLPVNVHKIHEKRLVGADMVELP 347

Query: 346 GGSDCWQNNCP-------SNVPRLSQSEIPNSLVSFNSQSEQRMQEGLQGKGEEKSVSSA 398
             +   +   P       + V    + E   S  +   +S+         +   + + S 
Sbjct: 348 DAAVFSRYTAPDFSGTSENAVQDNKKEEYTESSPASEQESKSHTASSSATRSPSQQLESN 407

Query: 399 PNAEISNQLRNQTEQYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQSDSRPRNS 458
            + EI   LR ++++     P    +R  P  + + G +    +    D +      RNS
Sbjct: 408 QDIEIMGGLRLESKKPAEQPPESSPSRVNPVLLCETGQRHHYSSVRHGDPVH-----RNS 462

Query: 459 TMVSSSGSVGGSVPPSFAAPMTIRASATAS------TASLRPQSSNPLVRAPPPRRTAAS 512
             +S + S           P  IR    A       + +  P+  +P  +APP       
Sbjct: 463 PQISVATS-----------PSPIRRGDPAHINIPQISVATPPECRSPRAQAPP------R 505

Query: 513 FCSSRPWPEGMRNQGGMPSRHY------MAPAVHIRSVVPVCSAPPS 553
           F        G R    +PS  Y      +A +V IR+ +PVCSA P+
Sbjct: 506 F--------GTRMPVNLPSSLYQQRPPWLAASVTIRTTIPVCSARPN 544

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	575
TAIR|locus:2829928	359	DRB3 "dsRNA-binding protein 3"	0.231	0.370	0.849	1.8e-71
TAIR|locus:2163016	393	DRB5 "dsRNA-binding protein 5"	0.231	0.338	0.819	1.5e-66
TAIR|locus:2057491	434	DRB2 "dsRNA-binding protein 2"	0.233	0.308	0.791	1.8e-62
TAIR|locus:2081620	355	DRB4 "double-stranded-RNA-bind	0.217	0.352	0.466	1.6e-24
UNIPROTKB|Q0IQN6	424	DRB8 "Double-stranded RNA-bind	0.224	0.304	0.390	2.6e-16
TAIR|locus:2024407	419	HYL1 "HYPONASTIC LEAVES 1" [Ar	0.227	0.312	0.358	3.6e-14

TAIR|locus:2829928 DRB3 "dsRNA-binding protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 604 (217.7 bits), Expect = 1.8e-71, Sum P(3) = 1.8e-71
 Identities = 113/133 (84%), Positives = 122/133 (91%)

Query:     1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
             MYKNQLQELAQRSCF+LPSY+C REGPDHAPRFKA+VNFNGE FESPT+CSTLRQAEH+A
Sbjct:     1 MYKNQLQELAQRSCFSLPSYTCTREGPDHAPRFKASVNFNGEIFESPTYCSTLRQAEHSA 60

Query:    61 AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
             AEVAL  LS KGPSK L ARVLDETG+YKNLLQET+HRAGL LPVYT+VRSGPGH P FS
Sbjct:    61 AEVALSALSSKGPSKSLTARVLDETGIYKNLLQETAHRAGLDLPVYTSVRSGPGHIPTFS 120

Query:   121 CTVELAGVSFTGE 133
             CTVELAG+SF GE
Sbjct:   121 CTVELAGMSFNGE 133

GO:0003723 "RNA binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0010267 "production of ta-siRNAs involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0051607 "defense response to virus" evidence=RCA

TAIR|locus:2163016 DRB5 "dsRNA-binding protein 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 583 (210.3 bits), Expect = 1.5e-66, Sum P(3) = 1.5e-66
 Identities = 109/133 (81%), Positives = 123/133 (92%)

Query:     1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
             MYKNQLQELAQRSCFNLPSY+CIREGPDHAPRFKA+VNFNGE FESPT+CSTLRQAEHAA
Sbjct:     1 MYKNQLQELAQRSCFNLPSYTCIREGPDHAPRFKASVNFNGEIFESPTYCSTLRQAEHAA 60

Query:    61 AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
             AEV+L+VLS + PSK L A++LDETG+YKNLLQET+HRAGL LP+YT+VRSG  H P FS
Sbjct:    61 AEVSLNVLSSRVPSKSLTAKILDETGIYKNLLQETAHRAGLDLPMYTSVRSGSCHFPGFS 120

Query:   121 CTVELAGVSFTGE 133
             CTVELAG++FTGE
Sbjct:   121 CTVELAGMTFTGE 133

GO:0003723 "RNA binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA;ISS;IDA

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005515 "protein binding" evidence=IPI

GO:0010267 "production of ta-siRNAs involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0051607 "defense response to virus" evidence=RCA

TAIR|locus:2057491 DRB2 "dsRNA-binding protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 561 (202.5 bits), Expect = 1.8e-62, Sum P(3) = 1.8e-62
 Identities = 106/134 (79%), Positives = 117/134 (87%)

Query:     1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
             MYKNQLQELAQRSCFNLPSY+CIREGPDHAPRFKA VNFNGE FESP +CSTLRQAEH+A
Sbjct:     1 MYKNQLQELAQRSCFNLPSYTCIREGPDHAPRFKATVNFNGEIFESPQYCSTLRQAEHSA 60

Query:    61 AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
             AEVAL+ LS +GPS  LAAR+LDETGVYKNLLQE + R G  LP YTT RSG GH PVF+
Sbjct:    61 AEVALNALSNRGPSHSLAARILDETGVYKNLLQEIAQRVGAPLPRYTTFRSGLGHQPVFT 120

Query:   121 CTVELAGVSFTGEP 134
              TVELAG++FTG+P
Sbjct:   121 GTVELAGITFTGDP 134

GO:0003723 "RNA binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA;ISS;IDA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA;IMP

GO:0070919 "production of siRNA involved in chromatin silencing by small RNA" evidence=IMP

GO:0010267 "production of ta-siRNAs involved in RNA interference" evidence=RCA

GO:0051607 "defense response to virus" evidence=RCA

TAIR|locus:2081620 DRB4 "double-stranded-RNA-binding protein 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 285 (105.4 bits), Expect = 1.6e-24, P = 1.6e-24
 Identities = 62/133 (46%), Positives = 79/133 (59%)

Query:     1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
             +YK QLQ  A +    LP Y+  REGP HAPRF+  V F G+TF+S  F  TL+ AEHAA
Sbjct:     4 VYKGQLQAYALQHNLELPVYANEREGPPHAPRFRCNVTFCGQTFQSSEFFPTLKSAEHAA 63

Query:    61 AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
             A++A+  L+ + P  +  A        YKNLLQE + +    LP Y T  SGP H P F+
Sbjct:    64 AKIAVASLTPQSPEGIDVA--------YKNLLQEIAQKESSLLPFYATATSGPSHAPTFT 115

Query:   121 CTVELAGVSFTGE 133
              TVE AG  F+GE
Sbjct:   116 STVEFAGKVFSGE 128

GO:0003723 "RNA binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA;ISS;IDA

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0010267 "production of ta-siRNAs involved in RNA interference" evidence=RCA;IMP

GO:0060145 "viral gene silencing in virus induced gene silencing" evidence=IMP

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA;IMP

GO:0070919 "production of siRNA involved in chromatin silencing by small RNA" evidence=IMP

GO:0051607 "defense response to virus" evidence=RCA

UNIPROTKB|Q0IQN6 DRB8 "Double-stranded RNA-binding protein 8" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 229 (85.7 bits), Expect = 2.6e-16, P = 2.6e-16
 Identities = 52/133 (39%), Positives = 76/133 (57%)

Query:     1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFES-PTFCSTLRQAEHA 59
             ++K++LQE AQ++    P Y   +EGP H P FK+ V  N  +++S P F +  + AE +
Sbjct:    33 VFKSRLQEYAQKTGLQTPEYHTFKEGPSHEPVFKSTVVINNTSYDSLPGFFNR-KAAEQS 91

Query:    60 AAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVF 119
             AAEVAL  + K  P+      V  ETG+ KNLLQE + +    +P Y   +S  G  P F
Sbjct:    92 AAEVALMEIVKSIPANANIPAV-QETGLCKNLLQEYAQKMNYAIPSYICTKSASGLAP-F 149

Query:   120 SCTVELAGVSFTG 132
              CTVE+ G+ + G
Sbjct:   150 ICTVEIGGIQYIG 162

GO:0003725 "double-stranded RNA binding" evidence=IDA

TAIR|locus:2024407 HYL1 "HYPONASTIC LEAVES 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 210 (79.0 bits), Expect = 3.6e-14, P = 3.6e-14
 Identities = 48/134 (35%), Positives = 76/134 (56%)

Query:     1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFES-PTFCSTLRQAEHA 59
             ++K++LQE AQ+     P Y  ++EGP H   F++ V  +G  + S P F +  + AE +
Sbjct:    15 VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNR-KAAEQS 73

Query:    60 AAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGP-GHGPV 118
             AAEVAL  L+K        ++ + ETG+ KNLLQE + +    +P+Y   +    G    
Sbjct:    74 AAEVALRELAKSSELSQCVSQPVHETGLCKNLLQEYAQKMNYAIPLYQCQKVETLGRVTQ 133

Query:   119 FSCTVELAGVSFTG 132
             F+CTVE+ G+ +TG
Sbjct:   134 FTCTVEIGGIKYTG 147


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.131   0.396    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      575       501   0.00085  119 3  11 22  0.43    34
                                                     35  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  616 (65 KB)
  Total size of DFA:  303 KB (2156 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  42.66u 0.08s 42.74t   Elapsed:  00:00:03
  Total cpu time:  42.66u 0.08s 42.74t   Elapsed:  00:00:03
  Start:  Thu May  9 23:28:41 2013   End:  Thu May  9 23:28:44 2013

GO:0003723 "RNA binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA;IDA

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0009733 "response to auxin stimulus" evidence=IMP

GO:0009735 "response to cytokinin stimulus" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA;IMP

GO:0005515 "protein binding" evidence=IPI

GO:0035279 "mRNA cleavage involved in gene silencing by miRNA" evidence=IMP

GO:0031054 "pre-miRNA processing" evidence=IMP

GO:0010267 "production of ta-siRNAs involved in RNA interference" evidence=RCA;IMP

GO:0015030 "Cajal body" evidence=IDA

GO:0035198 "miRNA binding" evidence=IDA

GO:0010445 "nuclear dicing body" evidence=IDA

GO:0051607 "defense response to virus" evidence=RCA

GO:0010305 "leaf vascular tissue pattern formation" evidence=IMP

GO:0010589 "leaf proximal/distal pattern formation" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q0DKP4	DRB2_ORYSJ	No assigned EC number	0.3952	0.8869	0.8600	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	575
cd00048	68	cd00048, DSRM, Double-stranded RNA binding motif	1e-17
cd00048	68	cd00048, DSRM, Double-stranded RNA binding motif	1e-16
pfam00035	66	pfam00035, dsrm, Double-stranded RNA binding motif	3e-16
pfam00035	66	pfam00035, dsrm, Double-stranded RNA binding motif	2e-15
smart00358	67	smart00358, DSRM, Double-stranded RNA binding moti	7e-14
smart00358	67	smart00358, DSRM, Double-stranded RNA binding moti	6e-13
PRK00102	229	PRK00102, rnc, ribonuclease III; Reviewed	1e-12
TIGR02191	220	TIGR02191, RNaseIII, ribonuclease III, bacterial	2e-11
PRK00102	229	PRK00102, rnc, ribonuclease III; Reviewed	5e-11
TIGR02191	220	TIGR02191, RNaseIII, ribonuclease III, bacterial	7e-11
COG0571	235	COG0571, Rnc, dsRNA-specific ribonuclease [Transcr	2e-10
COG0571	235	COG0571, Rnc, dsRNA-specific ribonuclease [Transcr	8e-09
PRK12371	235	PRK12371, PRK12371, ribonuclease III; Reviewed	2e-06
PHA03103	183	PHA03103, PHA03103, double-strand RNA-binding prot	2e-05
PRK12371	235	PRK12371, PRK12371, ribonuclease III; Reviewed	6e-05
TIGR04238	201	TIGR04238, seadorna_dsRNA, seadornavirus double-st	0.003

>gnl|CDD|238007 cd00048, DSRM, Double-stranded RNA binding motif

 Score = 76.9 bits (190), Expect = 1e-17
 Identities = 29/68 (42%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 2  YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           K+ LQELAQ+    LP Y  +  EGPDHAPRF   V   G         S+ ++A+  A
Sbjct: 2  PKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGG-KITGEGEGSSKKEAKQNA 60

Query: 61 AEVALDVL 68
          AE AL  L
Sbjct: 61 AEAALRKL 68

Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases. Length = 68

>gnl|CDD|238007 cd00048, DSRM, Double-stranded RNA binding motif

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 26/67 (38%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
            K+LLQE + + G  LP Y  V   GP H P F+  V + G         +KK+A++NAA
Sbjct: 2   PKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGKITGEGEGSSKKEAKQNAA 61

Query: 147 LAAWSAL 153
            AA   L
Sbjct: 62  EAALRKL 68

Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases. Length = 68

>gnl|CDD|215670 pfam00035, dsrm, Double-stranded RNA binding motif

 Score = 72.7 bits (179), Expect = 3e-16
 Identities = 23/66 (34%), Positives = 32/66 (48%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
            K+LLQE   + G K P       GP H P F+ TV + G  +      +KK+A++ AA 
Sbjct: 1   PKSLLQELCQKKGPKPPYEYVEEEGPPHSPTFTVTVTVNGKKYGTGTGSSKKEAKQLAAE 60

Query: 148 AAWSAL 153
            A   L
Sbjct: 61  KALQKL 66

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 localisation 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. Length = 66

>gnl|CDD|215670 pfam00035, dsrm, Double-stranded RNA binding motif

 Score = 70.8 bits (174), Expect = 2e-15
 Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
           K+ LQEL Q+     P      EGP H+P F   V  NG+ + +    S+ ++A+  AA
Sbjct: 1  PKSLLQELCQKKGPKPPYEYVEEEGPPHSPTFTVTVTVNGKKYGT-GTGSSKKEAKQLAA 59

Query: 62 EVALDVL 68
          E AL  L
Sbjct: 60 EKALQKL 66

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 localisation 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. Length = 66

>gnl|CDD|214634 smart00358, DSRM, Double-stranded RNA binding motif

 Score = 66.1 bits (162), Expect = 7e-14
 Identities = 28/68 (41%), Positives = 36/68 (52%), Gaps = 3/68 (4%)

Query: 2  YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           K+ LQELAQ+     P Y  +  EGPDHAPRF   V   G+        S+ ++A+  A
Sbjct: 1  PKSLLQELAQKRKLP-PEYELVKEEGPDHAPRFTVTVKVGGKRTGEGE-GSSKKEAKQRA 58

Query: 61 AEVALDVL 68
          AE AL  L
Sbjct: 59 AEAALRSL 66

Length = 67

>gnl|CDD|214634 smart00358, DSRM, Double-stranded RNA binding motif

 Score = 63.8 bits (156), Expect = 6e-13
 Identities = 26/68 (38%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
            K+LLQE + +  L  P Y  V   GP H P F+ TV++ G         +KK+A++ AA
Sbjct: 1   PKSLLQELAQKRKLP-PEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAA 59

Query: 147 LAAWSALK 154
            AA  +LK
Sbjct: 60  EAALRSLK 67

Length = 67

>gnl|CDD|234633 PRK00102, rnc, ribonuclease III; Reviewed

 Score = 67.1 bits (165), Expect = 1e-12
 Identities = 32/100 (32%), Positives = 44/100 (44%), Gaps = 7/100 (7%)

Query: 59  AAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVR-SGPGHGP 117
           AA +  L +   +     L   V D    YK  LQE     GL LP Y  V+  GP H  
Sbjct: 135 AARKFILRLFEPRIEEIDLGDLVKD----YKTRLQELLQGRGLPLPEYELVKEEGPAHDK 190

Query: 118 VFSCTVELAG-VSFTGEPAKTKKQAQKNAALAAWSALKKQ 156
            F+  V + G     G    +KK+A++ AA  A   LK++
Sbjct: 191 EFTVEVTVNGKELGEGT-GSSKKEAEQAAAKQALKKLKEK 229

Length = 229

>gnl|CDD|233772 TIGR02191, RNaseIII, ribonuclease III, bacterial

 Score = 63.8 bits (156), Expect = 2e-11
 Identities = 28/69 (40%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 2   YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQ-AEHA 59
           YK  LQE AQ     LP Y  I  EGPDH   F   V+ NGE +         ++ AE  
Sbjct: 154 YKTALQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGE--GKGKSKKEAEQN 211

Query: 60  AAEVALDVL 68
           AA+ AL+ L
Sbjct: 212 AAKAALEKL 220

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]. Length = 220

>gnl|CDD|234633 PRK00102, rnc, ribonuclease III; Reviewed

 Score = 62.4 bits (153), Expect = 5e-11
 Identities = 28/73 (38%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFC--STLRQAEH 58
           YK +LQEL Q     LP Y  ++E GP H   F   V  NG+          S+ ++AE 
Sbjct: 160 YKTRLQELLQGRGLPLPEYELVKEEGPAHDKEFTVEVTVNGKE---LGEGTGSSKKEAEQ 216

Query: 59  AAAEVALDVLSKK 71
           AAA+ AL  L +K
Sbjct: 217 AAAKQALKKLKEK 229

Length = 229

>gnl|CDD|233772 TIGR02191, RNaseIII, ribonuclease III, bacterial

 Score = 61.8 bits (151), Expect = 7e-11
 Identities = 31/72 (43%), Positives = 37/72 (51%), Gaps = 11/72 (15%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEP-----AKTKKQA 141
           YK  LQE +   G  LP Y  +   GP H   F  TVE   VS  GEP      K+KK+A
Sbjct: 154 YKTALQEWAQARGKPLPEYRLIKEEGPDHDKEF--TVE---VSVNGEPYGEGKGKSKKEA 208

Query: 142 QKNAALAAWSAL 153
           ++NAA AA   L
Sbjct: 209 EQNAAKAALEKL 220

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]. Length = 220

>gnl|CDD|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription]

 Score = 60.7 bits (148), Expect = 2e-10
 Identities = 27/73 (36%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 2   YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
            K +LQEL Q     LP Y  +  EGP H   F   V   G+   +     + ++AE AA
Sbjct: 163 PKTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGKELGTGK-GRSKKEAEQAA 221

Query: 61  AEVALDVLSKKGP 73
           AE AL  L  K P
Sbjct: 222 AEQALKKLGVKEP 234

Length = 235

>gnl|CDD|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription]

 Score = 56.1 bits (136), Expect = 8e-09
 Identities = 30/105 (28%), Positives = 43/105 (40%), Gaps = 7/105 (6%)

Query: 53  LRQAEHAAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTV-RS 111
           L     AA +  L +       ++      D+    K  LQE     GL LP Y  V   
Sbjct: 132 LDSGLEAARKFILKLF----LPRLEEIDAGDQFKDPKTRLQELLQAQGLVLPEYRLVKEE 187

Query: 112 GPGHGPVFSCTVELAG-VSFTGEPAKTKKQAQKNAALAAWSALKK 155
           GP H   F+  V + G    TG+  ++KK+A++ AA  A   L  
Sbjct: 188 GPAHDKEFTVEVAVGGKELGTGK-GRSKKEAEQAAAEQALKKLGV 231

Length = 235

>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed

 Score = 48.5 bits (116), Expect = 2e-06
 Identities = 25/60 (41%), Positives = 33/60 (55%), Gaps = 3/60 (5%)

Query: 89  KNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGV-SFTGEPAKTKKQAQKNAA 146
           K  LQE +H      PVY    RSGP H P F+  VE+ G    TGE  ++K+ A++ AA
Sbjct: 164 KTELQEWAHAQFGVTPVYRVDSRSGPDHDPRFTVEVEVKGFAPETGE-GRSKRAAEQVAA 222

Length = 235

>gnl|CDD|222987 PHA03103, PHA03103, double-strand RNA-binding protein; Provisional

 Score = 44.8 bits (106), Expect = 2e-05
 Identities = 16/37 (43%), Positives = 23/37 (62%)

Query: 110 RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
            SGP H P F+ +V ++G+ F      TKK+A+ NAA
Sbjct: 132 SSGPSHSPTFTASVIISGIKFKPAIGSTKKEAKNNAA 168

Length = 183

>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed

 Score = 44.3 bits (105), Expect = 6e-05
 Identities = 26/64 (40%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 3   KNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
           K +LQE A       P Y    R GPDH PRF   V   G   E+    S  R AE  AA
Sbjct: 164 KTELQEWAHAQFGVTPVYRVDSRSGPDHDPRFTVEVEVKGFAPETGEGRSK-RAAEQVAA 222

Query: 62  EVAL 65
           E  L
Sbjct: 223 EKML 226

Length = 235

>gnl|CDD|234517 TIGR04238, seadorna_dsRNA, seadornavirus double-stranded RNA-binding protein

 Score = 38.8 bits (90), Expect = 0.003
 Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 12/92 (13%)

Query: 3  KNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
             LQELA +    LP Y  + +EGPDHAP F   +  N    E     S+ +QAE  AA
Sbjct: 3  VGMLQELAVKRGLELPVYEKVGKEGPDHAPTFTIKLTAND--IEVIEAASSKKQAEKLAA 60

Query: 62 ---------EVALDVLSKKGPSKVLAARVLDE 84
                      L+V   +    +++  ++ +
Sbjct: 61 ATIYEDMKENGLLEVHDTRKSVSIMSILLVSK 92

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. Length = 201

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	575
KOG3732	339	consensus Staufen and related double-stranded-RNA-	99.88
COG0571	235	Rnc dsRNA-specific ribonuclease [Transcription]	99.76
PRK12371	235	ribonuclease III; Reviewed	99.75
PRK14718	467	ribonuclease III; Provisional	99.73
PRK12372	413	ribonuclease III; Reviewed	99.7
PRK00102	229	rnc ribonuclease III; Reviewed	99.61
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	99.58
cd00048	68	DSRM Double-stranded RNA binding motif. Binding is	99.57
TIGR02191	220	RNaseIII ribonuclease III, bacterial. This family	99.57
smart00358	67	DSRM Double-stranded RNA binding motif.	99.54
PHA03103	183	double-strand RNA-binding protein; Provisional	99.53
PF00035	67	dsrm: Double-stranded RNA binding motif; InterPro:	99.53
PF14709	80	DND1_DSRM: double strand RNA binding domain from D	99.2
smart00358	67	DSRM Double-stranded RNA binding motif.	99.17
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	99.17
KOG3732	339	consensus Staufen and related double-stranded-RNA-	99.16
cd00048	68	DSRM Double-stranded RNA binding motif. Binding is	99.15
KOG2777	542	consensus tRNA-specific adenosine deaminase 1 [RNA	99.1
PF00035	67	dsrm: Double-stranded RNA binding motif; InterPro:	99.09
PHA03103	183	double-strand RNA-binding protein; Provisional	99.07
PRK12371	235	ribonuclease III; Reviewed	99.03
PRK14718	467	ribonuclease III; Provisional	98.93
COG0571	235	Rnc dsRNA-specific ribonuclease [Transcription]	98.9
PRK12372	413	ribonuclease III; Reviewed	98.87
PF14709	80	DND1_DSRM: double strand RNA binding domain from D	98.86
PRK00102	229	rnc ribonuclease III; Reviewed	98.73
KOG1817	533	consensus Ribonuclease [RNA processing and modific	98.72
TIGR02191	220	RNaseIII ribonuclease III, bacterial. This family	98.63
KOG4334	650	consensus Uncharacterized conserved protein, conta	98.32
KOG3769	333	consensus Ribonuclease III domain proteins [Transl	97.71
KOG4334	650	consensus Uncharacterized conserved protein, conta	97.43
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	97.4
KOG1817	533	consensus Ribonuclease [RNA processing and modific	96.67
KOG3792	816	consensus Transcription factor NFAT, subunit NF90	96.61
KOG2777	542	consensus tRNA-specific adenosine deaminase 1 [RNA	96.54
PF03368	90	Dicer_dimer: Dicer dimerisation domain; InterPro:	96.34
KOG3769	333	consensus Ribonuclease III domain proteins [Transl	94.55
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	93.24
PF14954	252	LIX1: Limb expression 1	90.02
KOG2334	477	consensus tRNA-dihydrouridine synthase [Translatio	83.96

>KOG3732 consensus Staufen and related double-stranded-RNA-binding proteins [Intracellular trafficking, secretion, and vesicular transport; Transcription]

Probab=99.88  E-value=5.4e-22  Score=204.67  Aligned_cols=153  Identities=27%  Similarity=0.280  Sum_probs=130.4

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhh--
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLA--   78 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~--   78 (575)
                      ..+.|||+|.++++. |.|+++ ++|+.|.+.|+++|+|...  ++.|.|.+||.|++.||..+|..|....+...+.  
T Consensus        40 ~IS~l~E~~~r~~~~-v~fevl~eeGp~H~~~fv~rvtvg~~--~a~GeG~sKK~AKh~AA~~~L~~lk~l~~l~~v~k~  116 (339)
T KOG3732|consen   40 PISLLQEYGLRRGLT-PVYEVLREEGPPHMPNFVFRVTVGEI--TATGEGKSKKLAKHRAAEALLKELKKLPPLANVRKD  116 (339)
T ss_pred             hHHHHHHHHHHhCCC-cceeeeeccCCccCCCeEEEEEEeee--EEecCCCchhHHHHHHHHHHHHHHhcCCCccccccC
Confidence            468999999999875 699998 6999999999999999954  4457999999999999999999998764321110  


Q ss_pred             -------h-------hcc----cccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHH
Q 041141           79 -------A-------RVL----DETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKK  139 (575)
Q Consensus        79 -------~-------~i~----de~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKK  139 (575)
                             .       ...    +...|++++|+||||+++|.+|.|+++ +.|++|.++|++.|.|++.+ ..|.|.|||
T Consensus       117 ~~~~~~~~~~~~~~~q~~d~~~~~~~NPI~~L~e~~q~k~~k~P~yelv~E~G~~~~rEFv~q~sv~~~~-~~GkG~sKK  195 (339)
T KOG3732|consen  117 SLKFAKMKSSGVKKDQPGDPEYGQVLNPIGRLQELAQAKKWKLPEYELVQESGVPHRREFVIQCSVENFT-EEGKGPSKK  195 (339)
T ss_pred             cccccccccCCccccCCCCcccccccChHHHHHHHHHHhCCCCCceEEEeccCCCccceEEEEEEeccee-eecCCchHH
Confidence                   0       000    135799999999999999999999999 89999999999999999996 469999999


Q ss_pred             HHHHHHHHHHHHHHHhhhc
Q 041141          140 QAQKNAALAAWSALKKQAK  158 (575)
Q Consensus       140 eAEQ~AAk~ALe~L~~~~~  158 (575)
                      .||++||.+||+.|.-...
T Consensus       196 iAKRnAAeamLe~l~~~~~  214 (339)
T KOG3732|consen  196 IAKRNAAEAMLESLGFVKP  214 (339)
T ss_pred             HHHHHHHHHHHHHhccCCC
Confidence            9999999999999986553

>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]

Probab=99.76  E-value=7.5e-19  Score=175.72  Aligned_cols=146  Identities=25%  Similarity=0.289  Sum_probs=126.5

Q ss_pred             HHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhhhhccc
Q 041141            4 NQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVLD   83 (575)
Q Consensus         4 S~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~d   83 (575)
                      ..|.+++...  ++..|..+..|+.....|. +.+|-++.||+..+|.|+|.+.+.|.+++.+.+.........    ..
T Consensus        86 ~~La~ia~~l--~l~~~l~lg~ge~~~gg~~-~~silaD~~EAligAiylD~g~~~~~~~i~~l~~~~~~~~~~----~~  158 (235)
T COG0571          86 ESLAEIAREL--GLGDYLRLGKGEEKSGGRR-RESILADAFEALIGAIYLDSGLEAARKFILKLFLPRLEEIDA----GD  158 (235)
T ss_pred             HHHHHHHHHh--CccchhhccCChhhcCCCC-chhHHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHhhccc----cc
Confidence            4688999985  5679999888887777766 577888899999999999999999999999998876543221    12


Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ...|||++||||||+.++.+|.|.++ +.||+|++.|++.|.|+|..++.|.|+|||+|||.||+.||+.|...
T Consensus       159 ~~~D~Kt~LQe~~q~~~~~~p~Y~~v~~~g~~h~~~F~v~v~v~~~~~g~G~G~skk~AEq~AA~~al~~l~~~  232 (235)
T COG0571         159 QFKDPKTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGKELGTGKGRSKKEAEQAAAEQALKKLGVK  232 (235)
T ss_pred             cccChhHHHHHHHHhcCCCCCeEEEeeccCCCCCceEEEEEEECCeeEEEecccCHHHHHHHHHHHHHHHhccc
Confidence            34799999999999999999999999 67999999999999999999999999999999999999999999765

>PRK12371 ribonuclease III; Reviewed

Probab=99.75  E-value=1.7e-18  Score=172.71  Aligned_cols=144  Identities=22%  Similarity=0.171  Sum_probs=114.9

Q ss_pred             HHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhhhhccc
Q 041141            4 NQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVLD   83 (575)
Q Consensus         4 S~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~d   83 (575)
                      ..|.++|.+.|  ++.|.....+...... .....+-++.||+..+|.|+|.+.+.|.+++.+.|.+......      .
T Consensus        88 ~~La~ia~~lg--L~~~i~~~~~~~~~~~-~~~~~ilad~~EAliGAiylD~G~~~a~~~i~~~~~~~~~~~~------~  158 (235)
T PRK12371         88 ETCAAIADEIG--LHDLIRTGSDVKKLTG-KRLLNVRADVVEALIAAIYLDGGLEAARPFIQRYWQKRALETD------A  158 (235)
T ss_pred             HHHHHHHHHCC--cHHHhccCcchhhcCC-cccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhccc------c
Confidence            56888998854  5677765333211100 0112456888999999999999999999999988876532111      2


Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ...|||+.||||||+.+...|.|+++ +.||+|.+.|+|+|.|+|..++.|.|+|||+||++||++||+.|...
T Consensus       159 ~~~d~Ks~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~v~v~v~~~~~~~g~G~sKK~Ae~~AA~~al~~~~~~  232 (235)
T PRK12371        159 ARRDAKTELQEWAHAQFGVTPVYRVDSRSGPDHDPRFTVEVEVKGFAPETGEGRSKRAAEQVAAEKMLEREGVW  232 (235)
T ss_pred             ccCCHHHHHHHHHHhcCCCCCeEEEEEeecCCCCCeEEEEEEECCEEEEEeeeCCHHHHHHHHHHHHHHHhhhh
Confidence            34599999999999999999999998 78999999999999999999999999999999999999999998653

>PRK14718 ribonuclease III; Provisional

Probab=99.73  E-value=4.1e-18  Score=182.18  Aligned_cols=146  Identities=21%  Similarity=0.176  Sum_probs=117.8

Q ss_pred             HHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhhhhcc
Q 041141            3 KNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVL   82 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~   82 (575)
                      ...|.+++.+.|+  ..|.++..|......+. .-.|-++.||+.++++|+|.+.+.+.+++...|.......+.    .
T Consensus        75 netLA~IAr~LGL--~d~Lrlg~gE~~sgG~~-~~sILADvFEALIGAIYLDsG~e~a~~fI~~ll~p~i~~~d~----~  147 (467)
T PRK14718         75 QQSLYEIAQALNI--SDGLRLGEGELRSGGFR-RPSILADAFEAIIGAVFLDGGFEAAQGVIKRLYVPILDHIDP----R  147 (467)
T ss_pred             hHHHHHHHHHcCc--hHHHhhCCcccccCCCC-ChhHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhhhcc----c
Confidence            3578899998655  47777665544333333 456778899999999999999999998888888754322111    1


Q ss_pred             cccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEe-eeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           83 DETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVS-FTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        83 de~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~-fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      ....|||+.||||||++++.+|.|.++ +.||+|.+.|++.|.|+|.. ++.|.|.|||+|||+||+.||++|..
T Consensus       148 ~~~kDyKS~LQE~~Qk~~~~~PeY~li~esGPdH~k~F~V~V~v~g~~~~G~G~G~SKKeAEQ~AAk~AL~kL~~  222 (467)
T PRK14718        148 TLGKDAKTLLQEYLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDIKVSGSGASRRAAEQAAAKKALDEVTA  222 (467)
T ss_pred             ccccCHHHHHHHHHHhcCCCCCeeEEeeeecCCCCCeEEEEEEECCeeeEEEEEcCCHHHHHHHHHHHHHHHhcc
Confidence            224699999999999999999999998 78999999999999999964 47899999999999999999999973

>PRK12372 ribonuclease III; Reviewed

Probab=99.70  E-value=2.1e-17  Score=175.62  Aligned_cols=146  Identities=21%  Similarity=0.168  Sum_probs=117.0

Q ss_pred             HHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhhhhcc
Q 041141            3 KNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVL   82 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~   82 (575)
                      ...|.++|.+.|+  ..|.++..|......|. ...|-++.||+.++++|+|.+.+.+..++.+.|.........    .
T Consensus        75 n~tLA~IA~~LgL--~~~Lrlg~ge~~sgg~~-~~kILADvfEALIGAIYLDsG~e~a~~fV~~ll~p~l~~~~~----~  147 (413)
T PRK12372         75 QQSLYEIAQALNI--SEGLRLGEGELRSGGFR-RPSILADAFEAIIGAVFLDGGFEAAQGVIKRLYVPILDHIDP----R  147 (413)
T ss_pred             hHHHHHHHHHcCc--hHhhhcCcchhhcCCCC-CccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhccc----c
Confidence            3578999998654  57776655543333333 456778899999999999999998888888887654322110    1


Q ss_pred             cccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCE-eeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           83 DETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGV-SFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        83 de~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~-~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      ....|||+.||||||++++..|.|.++ +.|++|.+.|+|.|.|+|. .++.|.|.|||+|||+||+.||+.|..
T Consensus       148 ~~~~D~KS~LQE~~Q~~~~~~P~Y~lv~e~Gp~h~~~F~V~V~v~g~~~~g~G~G~SKKeAEQ~AAr~AL~kL~~  222 (413)
T PRK12372        148 TLGKDAKTLLQEYLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDVKVSGSGASRRAAEQAAAKKALDEVMA  222 (413)
T ss_pred             cccCCHHHHHHHHHHhcCCCCCeeEEeeeecCCCCceEEEEEEECCeEEEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            224589999999999999999999998 7899999999999999985 457899999999999999999999984

>PRK00102 rnc ribonuclease III; Reviewed

Probab=99.61  E-value=8.4e-16  Score=150.21  Aligned_cols=146  Identities=27%  Similarity=0.343  Sum_probs=113.7

Q ss_pred             HHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhhhhcc
Q 041141            3 KNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVL   82 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~   82 (575)
                      ...|..+|.+.|  +..|.....|...... .....+-++.||+..+|.|++.+.+.|.+++...+.........    .
T Consensus        82 n~~la~~a~~lg--l~~~i~~~~~~~~~~~-~~~~k~~ad~~EA~iGAiyld~g~~~~~~~i~~~~~~~l~~~~~----~  154 (229)
T PRK00102         82 EESLAEIARELG--LGEYLLLGKGEEKSGG-RRRPSILADAFEALIGAIYLDQGLEAARKFILRLFEPRIEEIDL----G  154 (229)
T ss_pred             HHHHHHHHHHCC--cHHHHccCcHHHHcCC-CCCccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcc----c
Confidence            457889998855  4566654333211111 11235567789999999999999998888888777654322211    1


Q ss_pred             cccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           83 DETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        83 de~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      ....|||+.|+||||+.++..|.|.++ ++|+.|.+.|+|+|.++|..++.|.|.|||+||++||+.||+.|+.
T Consensus       155 ~~~~~pk~~L~e~~~~~~~~~p~y~~~~~~g~~~~~~f~~~v~i~~~~~~~g~g~skk~Ae~~AA~~Al~~l~~  228 (229)
T PRK00102        155 DLVKDYKTRLQELLQGRGLPLPEYELVKEEGPAHDKEFTVEVTVNGKELGEGTGSSKKEAEQAAAKQALKKLKE  228 (229)
T ss_pred             cccCCHHHHHHHHHHHcCCCCCceEEeeccCCCCCceEEEEEEECCEEEEEeeeCCHHHHHHHHHHHHHHHHhh
Confidence            345699999999999999999999987 6899999999999999999999999999999999999999999864

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=99.58  E-value=6.3e-15  Score=142.31  Aligned_cols=72  Identities=24%  Similarity=0.314  Sum_probs=67.1

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ...|||+.||||||+.+..+ .|.++ +.||+|.+.|++.|.|+|..++.|.|+|||+|||+||+.||+.|...
T Consensus       106 k~~DpKS~LQE~~Q~~~~~l-~Y~li~~~GpdH~~~Ftv~V~V~g~~~g~G~G~SKKeAEQ~AAk~AL~~L~~~  178 (183)
T PHA02701        106 KTLNPVSAVNEFCMRTHRPL-EFCETRSGGHDHCPLFTCTIVVSGKVVATASGCSKKLARHAACADALTILINN  178 (183)
T ss_pred             CCCCccHHHHHHHHhcCCCC-eEEEEEeECCCCCceEEEEEEECCEEEEEEEeCCHHHHHHHHHHHHHHHHHhh
Confidence            45699999999999999888 89887 77999999999999999999999999999999999999999999654

>cd00048 DSRM Double-stranded RNA binding motif

Probab=99.57  E-value=1.1e-14  Score=114.52  Aligned_cols=67  Identities=39%  Similarity=0.534  Sum_probs=63.0

Q ss_pred             chhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHH
Q 041141           87 VYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSAL  153 (575)
Q Consensus        87 nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L  153 (575)
                      |||+.|+||||++++..|.|++. ..|+.|.+.|+|.|.|+|..++.|.|.|||+||+.||+.||..|
T Consensus         1 ~p~~~L~e~~~~~~~~~~~y~~~~~~g~~~~~~f~~~v~i~~~~~~~g~g~sKk~Ak~~AA~~al~~L   68 (68)
T cd00048           1 NPKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGKITGEGEGSSKKEAKQNAAEAALRKL   68 (68)
T ss_pred             ChHHHHHHHHHHcCCCCCeEEEeeeeCCCCCCeEEEEEEECCEEEEEeecCCHHHHHHHHHHHHHHhC
Confidence            68999999999999999999996 78999999999999999988888999999999999999999875

Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.

>TIGR02191 RNaseIII ribonuclease III, bacterial

Probab=99.57  E-value=3.3e-15  Score=144.75  Aligned_cols=144  Identities=26%  Similarity=0.335  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhhhhcc
Q 041141            3 KNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVL   82 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~   82 (575)
                      ...|..+|.+.|  +..|.....+...... .....+-++.||+..+|.|++.+.+.|.+++...|.........    .
T Consensus        76 n~~la~~a~~~g--l~~~i~~~~~~~~~~~-~~~~k~~ad~~eAliGAiyld~g~~~~~~~i~~~~~~~~~~~~~----~  148 (220)
T TIGR02191        76 EESLAEVARELG--LGKFLLLGKGEEKSGG-RRRESILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIEK----E  148 (220)
T ss_pred             HHHHHHHHHHCC--cHHHhccCchHhhcCC-cccchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhc----c
Confidence            357889998865  4566554322111101 11234567889999999999999988888888777654322111    1


Q ss_pred             cccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHH
Q 041141           83 DETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSAL  153 (575)
Q Consensus        83 de~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L  153 (575)
                      ....|||+.|+||||++++..|.|+++ ..|++|.+.|+|.|.++|..++.|.|.|||+||++||+.||+.|
T Consensus       149 ~~~~~pk~~L~e~~~~~~~~~p~y~~~~~~g~~~~~~f~~~v~~~~~~~~~g~g~skk~A~~~AA~~Al~~l  220 (220)
T TIGR02191       149 ETLKDYKTALQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEKL  220 (220)
T ss_pred             cccCChHHHHHHHHHHcCCCCceEEEecccCCCCCceEEEEEEECCEEEEEeeeCCHHHHHHHHHHHHHHhC
Confidence            245699999999999999999999998 67999999999999999999999999999999999999999875

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.

>smart00358 DSRM Double-stranded RNA binding motif

Probab=99.54  E-value=2.7e-14  Score=112.77  Aligned_cols=65  Identities=40%  Similarity=0.572  Sum_probs=61.5

Q ss_pred             hhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHH
Q 041141           88 YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSAL  153 (575)
Q Consensus        88 yKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L  153 (575)
                      ||+.|+||||++++ .|.|++. ..|+.|.+.|+|.|.|+|..++.|.|.|||+||++||+.||..|
T Consensus         1 p~~~L~e~~~~~~~-~~~y~~~~~~g~~~~~~f~~~v~i~~~~~~~g~g~sKk~Ak~~AA~~al~~L   66 (67)
T smart00358        1 PKSLLQELAQKRGL-PPEYELVKEEGPDHAPRFTVTVKVGGEYTGEGEGSSKKEAKQRAAEAALRSL   66 (67)
T ss_pred             CchHHHHHHHHCCC-CCEEEEEeeeCCCCCCcEEEEEEECCEEEEEeccCCHHHHHHHHHHHHHHhc
Confidence            68999999999999 8999998 58999999999999999998889999999999999999999887

>PHA03103 double-strand RNA-binding protein; Provisional

Probab=99.53  E-value=2.5e-14  Score=138.49  Aligned_cols=71  Identities=25%  Similarity=0.353  Sum_probs=64.5

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ..|||+.||||||+.+... .|.+.+.||+|.+.|++.|.|+|..++.|.|+|||+|||+||+.||..|...
T Consensus       108 ~kNpKS~LQE~~Qk~~~~~-y~~i~~~Gp~H~p~F~v~V~I~g~~~g~G~G~SKKeAEQ~AAk~AL~~L~~~  178 (183)
T PHA03103        108 DKNPCTVINEYCQITSRDW-SINITSSGPSHSPTFTASVIISGIKFKPAIGSTKKEAKNNAAKLAMDKILNY  178 (183)
T ss_pred             cCChhHHHHHHHHHhCCCe-EEEEEeeCCCCCceEEEEEEECCEEEEEeeeCCHHHHHHHHHHHHHHHHHhc
Confidence            5689999999999998875 5555588999999999999999999999999999999999999999999653

>PF00035 dsrm: Double-stranded RNA binding motif; InterPro: IPR001159 The DsRBD domain is found in a variety of RNA-binding proteins with different structures and exhibiting a diversity of functions []

Probab=99.53  E-value=3.3e-14  Score=112.97  Aligned_cols=66  Identities=32%  Similarity=0.484  Sum_probs=60.2

Q ss_pred             hhhHHHHHHHHcCCCCCeEEEeecCCCCC-CeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHH
Q 041141           88 YKNLLQETSHRAGLKLPVYTTVRSGPGHG-PVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSAL  153 (575)
Q Consensus        88 yKS~LQE~cQK~gl~lP~Yev~esGP~H~-p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L  153 (575)
                      ||+.|+|||+++++.+++|.+...|+.|. +.|.|+|.|+|..++.|.|.|||+||+.||+.||+.|
T Consensus         1 ~~~~L~e~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~i~~~~~~~g~g~sKk~Ak~~AA~~al~~L   67 (67)
T PF00035_consen    1 PKSRLNEYCQKNKFPPPYYYIEEEGPSHHRPRFICTVYIDGKEYGEGEGSSKKEAKQQAAKKALQKL   67 (67)
T ss_dssp             HHHHHHHHHHHCTSSEEEEEEEEESSSSSSEEEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCCCEEEEEEeCCCCCCceEEEEEEECCEEEeEeccCCHHHHHHHHHHHHHHhC
Confidence            78999999999999888888876666554 8999999999999999999999999999999999987

It is involved in localisation of at least five different mRNAs in the early Drosophila embryo and by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.; GO: 0003725 double-stranded RNA binding, 0005622 intracellular; PDB: 1EKZ_A 1STU_A 1QU6_A 2L2M_A 3ADJ_A 1WHN_A 3LLH_B 2B7V_A 2L3J_A 1UHZ_A ....

>PF14709 DND1_DSRM: double strand RNA binding domain from DEAD END PROTEIN 1

Probab=99.20  E-value=3.8e-11  Score=102.18  Aligned_cols=68  Identities=35%  Similarity=0.528  Sum_probs=60.8

Q ss_pred             chhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeee---------e-cccCCHHHHHHHHHHHHHHHHH
Q 041141           87 VYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFT---------G-EPAKTKKQAQKNAALAAWSALK  154 (575)
Q Consensus        87 nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg---------~-G~G~SKKeAEQ~AAk~ALe~L~  154 (575)
                      ++++.|+|+|+|++|..|.|++. +.||+|.+.|++.|.|.+..+.         . -...+||+||..||+.||..|+
T Consensus         2 ~a~~~L~elC~k~~W~~P~y~l~~~~Gp~~~~~F~ykV~i~~~~~~~~~~~~~~~p~~~~~~~k~Ak~~AA~~~L~~Lg   80 (80)
T PF14709_consen    2 SAVSLLNELCQKNKWGPPVYELVSESGPDHRKLFLYKVVIPGLEYPFEGSIECFGPTKPSSTKKEAKESAAQQALQALG   80 (80)
T ss_pred             CHHHHHHHHHHhcCCCCCeEEEEeccCCCccEEEEEEEEEcCCCCCCcceEEEccCCCcCccHHHHHHHHHHHHHHhcC
Confidence            68999999999999999999998 7899999999999999987762         2 3457899999999999999874

>smart00358 DSRM Double-stranded RNA binding motif

Probab=99.17  E-value=1e-10  Score=92.39  Aligned_cols=65  Identities=45%  Similarity=0.610  Sum_probs=59.1

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVL   68 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L   68 (575)
                      +|+.|+||||++++ .|.|.++ ..|++|.+.|++.|.|+|..+.. |.|.+||.|++.||+.+|..|
T Consensus         1 p~~~L~e~~~~~~~-~~~y~~~~~~g~~~~~~f~~~v~i~~~~~~~-g~g~sKk~Ak~~AA~~al~~L   66 (67)
T smart00358        1 PKSLLQELAQKRGL-PPEYELVKEEGPDHAPRFTVTVKVGGEYTGE-GEGSSKKEAKQRAAEAALRSL   66 (67)
T ss_pred             CchHHHHHHHHCCC-CCEEEEEeeeCCCCCCcEEEEEEECCEEEEE-eccCCHHHHHHHHHHHHHHhc
Confidence            68999999999999 7899988 47999999999999999987765 579999999999999999876

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=99.17  E-value=6.2e-11  Score=114.88  Aligned_cols=67  Identities=24%  Similarity=0.354  Sum_probs=61.9

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      ||+.||||||+.+..+ .|.++ ..|++|.+.|++.|.|+|..++. |.|.+||+|+++||+.||..|..
T Consensus       110 pKS~LQE~~Q~~~~~l-~Y~li~~~GpdH~~~Ftv~V~V~g~~~g~-G~G~SKKeAEQ~AAk~AL~~L~~  177 (183)
T PHA02701        110 PVSAVNEFCMRTHRPL-EFCETRSGGHDHCPLFTCTIVVSGKVVAT-ASGCSKKLARHAACADALTILIN  177 (183)
T ss_pred             ccHHHHHHHHhcCCCC-eEEEEEeECCCCCceEEEEEEECCEEEEE-EEeCCHHHHHHHHHHHHHHHHHh
Confidence            7999999999998888 89887 67999999999999999999987 48999999999999999998864

>KOG3732 consensus Staufen and related double-stranded-RNA-binding proteins [Intracellular trafficking, secretion, and vesicular transport; Transcription]

Probab=99.16  E-value=5e-11  Score=124.13  Aligned_cols=105  Identities=36%  Similarity=0.401  Sum_probs=86.6

Q ss_pred             cccccHHHHHHHHHHHHHHHhcCCChhhhhhccccc-CchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECC
Q 041141           50 CSTLRQAEHAAAEVALDVLSKKGPSKVLAARVLDET-GVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAG  127 (575)
Q Consensus        50 G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~de~-~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G  127 (575)
                      |.+..+|++.||..+|..|........... ..|.. ..+++.|||||.|+++ .|.|++. ++||.|.+.|+++|.|+.
T Consensus         2 g~t~~~a~~daaa~al~~l~~~~~~~~~~~-~~~~g~KS~IS~l~E~~~r~~~-~v~fevl~eeGp~H~~~fv~rvtvg~   79 (339)
T KOG3732|consen    2 GKTMQQAKHDAAAKALQVLQNGLISEGVML-NADPGAKSPISLLQEYGLRRGL-TPVYEVLREEGPPHMPNFVFRVTVGE   79 (339)
T ss_pred             ccchhhhhccccccchhhccCCCcchhccc-ccCcccCChHHHHHHHHHHhCC-CcceeeeeccCCccCCCeEEEEEEee
Confidence            567889999999999999987653322100 01222 6889999999999987 4688988 799999999999999996


Q ss_pred             EeeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141          128 VSFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus       128 ~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      .. +.|.|+|||.||+.||.++|..|+.+.
T Consensus        80 ~~-a~GeG~sKK~AKh~AA~~~L~~lk~l~  108 (339)
T KOG3732|consen   80 IT-ATGEGKSKKLAKHRAAEALLKELKKLP  108 (339)
T ss_pred             eE-EecCCCchhHHHHHHHHHHHHHHhcCC
Confidence            65 569999999999999999999999986

>cd00048 DSRM Double-stranded RNA binding motif

Probab=99.15  E-value=1.5e-10  Score=90.98  Aligned_cols=66  Identities=44%  Similarity=0.589  Sum_probs=58.9

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVL   68 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L   68 (575)
                      +|+.|+||||++++..|.|.+. ..|+.|.+.|++.|.|+|..+.. |.|.+||+|++.||+.+|..|
T Consensus         2 p~~~L~e~~~~~~~~~~~y~~~~~~g~~~~~~f~~~v~i~~~~~~~-g~g~sKk~Ak~~AA~~al~~L   68 (68)
T cd00048           2 PKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGKITGE-GEGSSKKEAKQNAAEAALRKL   68 (68)
T ss_pred             hHHHHHHHHHHcCCCCCeEEEeeeeCCCCCCeEEEEEEECCEEEEE-eecCCHHHHHHHHHHHHHHhC
Confidence            7999999999998888999996 68899999999999999965555 578999999999999999765

Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.

>KOG2777 consensus tRNA-specific adenosine deaminase 1 [RNA processing and modification]

Probab=99.10  E-value=7.8e-10  Score=121.61  Aligned_cols=157  Identities=29%  Similarity=0.373  Sum_probs=122.2

Q ss_pred             CceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCCh-----------hh----hhh-
Q 041141           18 PSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSK-----------VL----AAR-   80 (575)
Q Consensus        18 PeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~-----------~~----~~~-   80 (575)
                      ++|..+ ..||.|.+.|...|.|+|..|.       +|.|+..||+.+++.+.+..+..           +.    .+. 
T Consensus        10 ~~~~~~~q~~p~~~p~~~~~~~v~~~~~~-------~k~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (542)
T KOG2777|consen   10 LQYNLVSQTGPVHAPLFPFSVEVNGQEFP-------KKKAKQRAAEKALRVFLQFPEAHLSMGGTEGVNEDLTSDQADAF   82 (542)
T ss_pred             cccccccccCCCCCCcccceEEecccccc-------cccccchhhhHHHHHHhhcCCcccccCCCCccccccchhhhHHH
Confidence            478776 7899999999999999998765       88999999999999988754321           00    000 


Q ss_pred             --cccccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141           81 --VLDETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        81 --i~de~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                        ......|+++.|.|+++     -++|++. +.|+.|.+.|.|.|.|+|+.|..| |.|||+||+.||+.||+.|....
T Consensus        83 ~~~~~~~~npv~ll~e~~~-----~~~~~~~~~~~~~~~~~F~~~~~vdg~~~~~~-~~sKk~ak~~aa~~al~~l~~~~  156 (542)
T KOG2777|consen   83 LSLGKEGKNPVSLLHELAN-----GLFFDFVNESGPQHAPKFVMSVVVDGRWFEGG-GRSKKEAKQEAAMAALQVLFKID  156 (542)
T ss_pred             HhhhhccCCchHHHHHHhc-----ccceeeeccCCCCCCceEEEEEEECCEEccCC-CcchHHHHHHHHHHHHHHHHhcc
Confidence              01236799999999999     5678888 889999999999999999999877 99999999999999999999987


Q ss_pred             cccCCCCCCCCCCCCCCCChhhHHHHHHHHHhhc
Q 041141          158 KSAFSSSSFSPPSSESGTNDEQDQAIIARYLATL  191 (575)
Q Consensus       158 ~~~~sss~~~~~~~~~~~~~~qeq~~~a~~l~~~  191 (575)
                      .+....  .....  -+........+...++..+
T Consensus       157 ~~~~~~--~~~~~--~e~~~~~~~~Ia~lv~~kF  186 (542)
T KOG2777|consen  157 ENPERP--SEALT--LENPSTLGDEIAELVLEKF  186 (542)
T ss_pred             CCcccc--ccccc--ccCCChHHHHHHHHHHHHH
Confidence            664432  12222  2244556666777777766

>PF00035 dsrm: Double-stranded RNA binding motif; InterPro: IPR001159 The DsRBD domain is found in a variety of RNA-binding proteins with different structures and exhibiting a diversity of functions []

Probab=99.09  E-value=2.6e-10  Score=90.56  Aligned_cols=66  Identities=35%  Similarity=0.523  Sum_probs=56.7

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCC-CceEEEEEECCeeeecccccccccHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHA-PRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVL   68 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Ha-p~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L   68 (575)
                      ||+.|+|||++.++.++.|.....|+.|. +.|.+.|.|+|..++. |.|.+||+|++.||+.+|+.|
T Consensus         1 ~~~~L~e~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~i~~~~~~~-g~g~sKk~Ak~~AA~~al~~L   67 (67)
T PF00035_consen    1 PKSRLNEYCQKNKFPPPYYYIEEEGPSHHRPRFICTVYIDGKEYGE-GEGSSKKEAKQQAAKKALQKL   67 (67)
T ss_dssp             HHHHHHHHHHHCTSSEEEEEEEEESSSSSSEEEEEEEEETTEEEEE-EEESSHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCCCEEEEEEeCCCCCCceEEEEEEECCEEEeE-eccCCHHHHHHHHHHHHHHhC
Confidence            69999999999998775555556666555 8999999999999976 578999999999999999876

It is involved in localisation of at least five different mRNAs in the early Drosophila embryo and by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.; GO: 0003725 double-stranded RNA binding, 0005622 intracellular; PDB: 1EKZ_A 1STU_A 1QU6_A 2L2M_A 3ADJ_A 1WHN_A 3LLH_B 2B7V_A 2L3J_A 1UHZ_A ....

>PHA03103 double-strand RNA-binding protein; Provisional

Probab=99.07  E-value=3.2e-10  Score=110.18  Aligned_cols=68  Identities=28%  Similarity=0.408  Sum_probs=59.9

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ||+.||||||+.+..+ .|.+...|++|.+.|++.|.|+|..++. |.|.+||+|++.||+.||..|...
T Consensus       111 pKS~LQE~~Qk~~~~~-y~~i~~~Gp~H~p~F~v~V~I~g~~~g~-G~G~SKKeAEQ~AAk~AL~~L~~~  178 (183)
T PHA03103        111 PCTVINEYCQITSRDW-SINITSSGPSHSPTFTASVIISGIKFKP-AIGSTKKEAKNNAAKLAMDKILNY  178 (183)
T ss_pred             hhHHHHHHHHHhCCCe-EEEEEeeCCCCCceEEEEEEECCEEEEE-eeeCCHHHHHHHHHHHHHHHHHhc
Confidence            6799999999998775 4444478999999999999999999987 489999999999999999998653

>PRK12371 ribonuclease III; Reviewed

Probab=99.03  E-value=5.4e-10  Score=112.00  Aligned_cols=68  Identities=37%  Similarity=0.424  Sum_probs=62.9

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      ||+.||||||+.+...|.|.++ ..||+|.+.|++.|.|+|..++. |.|.+||+|++.||+.||..+..
T Consensus       163 ~Ks~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~v~v~v~~~~~~~-g~G~sKK~Ae~~AA~~al~~~~~  231 (235)
T PRK12371        163 AKTELQEWAHAQFGVTPVYRVDSRSGPDHDPRFTVEVEVKGFAPET-GEGRSKRAAEQVAAEKMLEREGV  231 (235)
T ss_pred             HHHHHHHHHHhcCCCCCeEEEEEeecCCCCCeEEEEEEECCEEEEE-eeeCCHHHHHHHHHHHHHHHhhh
Confidence            7999999999988888999988 67999999999999999998876 48999999999999999998864

>PRK14718 ribonuclease III; Provisional

Probab=98.93  E-value=1.8e-09  Score=116.57  Aligned_cols=71  Identities=28%  Similarity=0.364  Sum_probs=63.3

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      ||+.||||||++++.+|+|.++ ..|++|.+.|++.|+|+|..+...|.|.|||+|++.||+.+|..|....
T Consensus       153 yKS~LQE~~Qk~~~~~PeY~li~esGPdH~k~F~V~V~v~g~~~~G~G~G~SKKeAEQ~AAk~AL~kL~~~~  224 (467)
T PRK14718        153 AKTLLQEYLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDIKVSGSGASRRAAEQAAAKKALDEVTAVA  224 (467)
T ss_pred             HHHHHHHHHHhcCCCCCeeEEeeeecCCCCCeEEEEEEECCeeeEEEEEcCCHHHHHHHHHHHHHHHhcccc
Confidence            7999999999999999999998 6899999999999999996543225899999999999999999998543

>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]

Probab=98.90  E-value=3.5e-09  Score=106.66  Aligned_cols=69  Identities=38%  Similarity=0.511  Sum_probs=64.4

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ||+.||||||+.++.+|.|.++ .+|++|++.|++.|.++|..++. |.|.+||+|++.||+.+|..|...
T Consensus       163 ~Kt~LQe~~q~~~~~~p~Y~~v~~~g~~h~~~F~v~v~v~~~~~g~-G~G~skk~AEq~AA~~al~~l~~~  232 (235)
T COG0571         163 PKTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGKELGT-GKGRSKKEAEQAAAEQALKKLGVK  232 (235)
T ss_pred             hhHHHHHHHHhcCCCCCeEEEeeccCCCCCceEEEEEEECCeeEEE-ecccCHHHHHHHHHHHHHHHhccc
Confidence            7999999999999999999998 66999999999999999988887 489999999999999999998754

>PRK12372 ribonuclease III; Reviewed

Probab=98.87  E-value=4.6e-09  Score=112.60  Aligned_cols=72  Identities=29%  Similarity=0.382  Sum_probs=63.7

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGP   73 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~p   73 (575)
                      ||+.||||||++++.+|+|.++ ..|++|.+.|++.|+|+|..+...|.|.+||+|++.||+.+|..|....+
T Consensus       153 ~KS~LQE~~Q~~~~~~P~Y~lv~e~Gp~h~~~F~V~V~v~g~~~~g~G~G~SKKeAEQ~AAr~AL~kL~~~~~  225 (413)
T PRK12372        153 AKTLLQEYLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDVKVSGSGASRRAAEQAAAKKALDEVMAAAP  225 (413)
T ss_pred             HHHHHHHHHHhcCCCCCeeEEeeeecCCCCceEEEEEEECCeEEEEEEEeCCHHHHHHHHHHHHHHHHhcccc
Confidence            7999999999999999999988 78999999999999999864432358999999999999999999985443

>PF14709 DND1_DSRM: double strand RNA binding domain from DEAD END PROTEIN 1

Probab=98.86  E-value=6e-09  Score=88.82  Aligned_cols=67  Identities=31%  Similarity=0.444  Sum_probs=58.8

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeee---------cccccccccHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFE---------SPTFCSTLRQAEHAAAEVALDVL   68 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fE---------AgG~G~SKKeAeq~AAk~AL~~L   68 (575)
                      .++.|+|+|+|++|+.|.|.+. ..||+|.+.|.++|.|.+..+.         ......++|+|++.||+.+|..|
T Consensus         3 a~~~L~elC~k~~W~~P~y~l~~~~Gp~~~~~F~ykV~i~~~~~~~~~~~~~~~p~~~~~~~k~Ak~~AA~~~L~~L   79 (80)
T PF14709_consen    3 AVSLLNELCQKNKWGPPVYELVSESGPDHRKLFLYKVVIPGLEYPFEGSIECFGPTKPSSTKKEAKESAAQQALQAL   79 (80)
T ss_pred             HHHHHHHHHHhcCCCCCeEEEEeccCCCccEEEEEEEEEcCCCCCCcceEEEccCCCcCccHHHHHHHHHHHHHHhc
Confidence            4789999999999999999997 7899999999999999987662         11346789999999999999887

>PRK00102 rnc ribonuclease III; Reviewed

Probab=98.73  E-value=2.9e-08  Score=97.36  Aligned_cols=68  Identities=40%  Similarity=0.593  Sum_probs=62.3

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      +|+.|+||||++++..|+|.++ ..|+.|.+.|++.|.++|..++. |.|.+||.|++.||+.||..|..
T Consensus       160 pk~~L~e~~~~~~~~~p~y~~~~~~g~~~~~~f~~~v~i~~~~~~~-g~g~skk~Ae~~AA~~Al~~l~~  228 (229)
T PRK00102        160 YKTRLQELLQGRGLPLPEYELVKEEGPAHDKEFTVEVTVNGKELGE-GTGSSKKEAEQAAAKQALKKLKE  228 (229)
T ss_pred             HHHHHHHHHHHcCCCCCceEEeeccCCCCCceEEEEEEECCEEEEE-eeeCCHHHHHHHHHHHHHHHHhh
Confidence            6899999999999999999987 57999999999999999998887 48999999999999999998864

>KOG1817 consensus Ribonuclease [RNA processing and modification]

Probab=98.72  E-value=1.9e-08  Score=107.78  Aligned_cols=141  Identities=15%  Similarity=0.126  Sum_probs=106.9

Q ss_pred             HHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhhhhcccccC
Q 041141            7 QELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVLDETG   86 (575)
Q Consensus         7 QElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~de~~   86 (575)
                      ..||...|  .++|.+.........  .-+.+...++||++++|.+.|.+.+.+.+++-..+.....+...    ...-.
T Consensus       356 akva~~lg--f~e~li~n~~~k~~~--~lk~K~~ADlfEAfiGaLyvD~~le~~~qf~~~l~~Prl~~fi~----nq~wn  427 (533)
T KOG1817|consen  356 AKVADDLG--FHEYLITNFDLKDFQ--NLKLKDYADLFEAFIGALYVDKGLEYCRQFLRVLFFPRLKEFIR----NQDWN  427 (533)
T ss_pred             HHHHHHhC--CchhhhhCcchhhhh--hhhHHHHHHHHHHHHHHHhhcCCcHHHHHHHHHHhhHHHHHHHH----hhhcc
Confidence            35666644  457776532211100  11244556789999999999999999999988887765432211    12234


Q ss_pred             chhhHHHHHHHHcCC------CCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           87 VYKNLLQETSHRAGL------KLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        87 nyKS~LQE~cQK~gl------~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      |+|+.||.+|.....      .+|.|.+. ..||.+.+.|++.|+++|+.++.|.|.|.|+|+..||+.||+.+..
T Consensus       428 dpkskLqq~cl~~rys~~~epdip~y~V~~~~gpa~~r~y~Vavyf~gkrlat~~G~nik~Ae~rAA~~ALe~~~~  503 (533)
T KOG1817|consen  428 DPKSKLQQCCLTLRYSLGGEPDIPLYKVLGAKGPANDRNYKVAVYFKGKRLATGVGSNIKQAEMRAAMQALENLKM  503 (533)
T ss_pred             CcHHHHHHHHHHHhcccCCCCCCceEEEecccCCCCCCceEEEEEECCEEEeeccCchHhHHHHHHHHHHHHHHHh
Confidence            799999999987753      47888888 7899999999999999999999999999999999999999999874

>TIGR02191 RNaseIII ribonuclease III, bacterial

Probab=98.63  E-value=7.3e-08  Score=93.69  Aligned_cols=66  Identities=42%  Similarity=0.611  Sum_probs=60.1

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVL   68 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L   68 (575)
                      +|+.|+||||++++..|.|.++ ..|+.|.+.|.+.|.++|+.++.+ .|.+||.|++.||+.|++.|
T Consensus       154 pk~~L~e~~~~~~~~~p~y~~~~~~g~~~~~~f~~~v~~~~~~~~~g-~g~skk~A~~~AA~~Al~~l  220 (220)
T TIGR02191       154 YKTALQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEG-KGKSKKEAEQNAAKAALEKL  220 (220)
T ss_pred             hHHHHHHHHHHcCCCCceEEEecccCCCCCceEEEEEEECCEEEEEe-eeCCHHHHHHHHHHHHHHhC
Confidence            6899999999998888999988 568999999999999999998874 79999999999999999764

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.

>KOG4334 consensus Uncharacterized conserved protein, contains double-stranded RNA-binding motif and WW domain [General function prediction only]

Probab=98.32  E-value=2.9e-06  Score=92.40  Aligned_cols=150  Identities=19%  Similarity=0.184  Sum_probs=102.1

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCC-hh---
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPS-KV---   76 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps-~~---   76 (575)
                      |....|+||+|+.-..+|.|++.+.- ...-.|.+.|.+++..|++| .|.+||.|+..||+.+|..|...... .+   
T Consensus       376 s~vCiLhEy~q~~lk~~pvyef~e~~-n~stpysa~v~~d~~~yGsG-~g~sKK~Ak~~AAR~tLeiLIPd~~~~~~n~~  453 (650)
T KOG4334|consen  376 SKVCILHEYAQQCLKSLPVYEFAEND-NNSTPYSAGVLPDLFPYGSG-VGASKKTAKLVAARDTLEILIPDLRVSEDNVC  453 (650)
T ss_pred             eeeehHHHHHHHHhhhcceeehhhcc-CCCCcccccccccccccccc-cccchHHHHHHHHHHHHHHhcchhhhcccccc
Confidence            45568999999988888999776432 34556999999999999985 89999999999999999998754210 00   


Q ss_pred             ---------------hhhhcccc------------cCchhhHHHHHHHHc-CCC-CC-eEEEeecCCCCCCeEEEEEEEC
Q 041141           77 ---------------LAARVLDE------------TGVYKNLLQETSHRA-GLK-LP-VYTTVRSGPGHGPVFSCTVELA  126 (575)
Q Consensus        77 ---------------~~~~i~de------------~~nyKS~LQE~cQK~-gl~-lP-~Yev~esGP~H~p~Ftv~V~V~  126 (575)
                                     +-+.+..+            ...+-+.|.++.+++ ||. +- .++++..| .....|++.|   
T Consensus       454 d~k~~~~~k~q~~le~F~~I~Iedprv~e~ctk~~~psPy~iL~~cl~Rn~g~~d~~ik~E~i~~~-nqkse~im~~---  529 (650)
T KOG4334|consen  454 DGKVEEDGKQQGFLELFKKIKIEDPRVVEMCTKCAIPSPYNILRDCLSRNLGWNDLVIKKEMIGNG-NQKSEVIMIL---  529 (650)
T ss_pred             cccccccccchhHHHHhhcccccCchHHHHhhhcCCCCHHHHHHHHHHhhcCCcceeeeeeccCCC-CccceeEeee---
Confidence                           00011111            224566777777765 342 11 22222222 2334565554   


Q ss_pred             CEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141          127 GVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus       127 G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      |..-..|.+++|++++|.|.++.|++|.-.
T Consensus       530 Gkht~~~~cknkr~gkQlASQ~ilq~lHPh  559 (650)
T KOG4334|consen  530 GKHTEEAECKNKRQGKQLASQRILQKLHPH  559 (650)
T ss_pred             ccceeeeeeechhHHHHHHHHHHHHHhCHH
Confidence            444456999999999999999999998654

>KOG3769 consensus Ribonuclease III domain proteins [Translation, ribosomal structure and biogenesis]

Probab=97.71  E-value=6.3e-05  Score=78.32  Aligned_cols=73  Identities=23%  Similarity=0.234  Sum_probs=66.7

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCC-CCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGP-GHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP-~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      -.+|...|-++|+++++..|+|.+. ++|- ...+.|.|.++-|.+.+|.|.|.|-|.|++.||..||.+|....
T Consensus       231 l~~P~~~L~~lckr~~l~epe~Rll~esGr~S~~PvyvVgiYs~kkllGqG~Gesl~~A~e~AA~dAL~k~y~~t  305 (333)
T KOG3769|consen  231 LQWPRRLLSRLCKRRGLKEPESRLLAESGRNSAEPVYVVGIYSGKKLLGQGQGESLKLAEEQAARDALIKLYDHT  305 (333)
T ss_pred             ccchHHHHHHHHHHcCCCCchhHHHHHhccCccCceEEEEeecCchhhccCcchHHHHHHHHHHHHHHHHHHcCC
Confidence            3589999999999999999999998 6664 46789999999999999999999999999999999999998775

>KOG4334 consensus Uncharacterized conserved protein, contains double-stranded RNA-binding motif and WW domain [General function prediction only]

Probab=97.43  E-value=0.00011  Score=80.41  Aligned_cols=69  Identities=20%  Similarity=0.182  Sum_probs=59.4

Q ss_pred             chhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           87 VYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        87 nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ...-.|.||+|+-...+|.|++.+.. ...--|.+.|.+++.+||.|.|.|||.||..||+++|+.|.-.
T Consensus       376 s~vCiLhEy~q~~lk~~pvyef~e~~-n~stpysa~v~~d~~~yGsG~g~sKK~Ak~~AAR~tLeiLIPd  444 (650)
T KOG4334|consen  376 SKVCILHEYAQQCLKSLPVYEFAEND-NNSTPYSAGVLPDLFPYGSGVGASKKTAKLVAARDTLEILIPD  444 (650)
T ss_pred             eeeehHHHHHHHHhhhcceeehhhcc-CCCCcccccccccccccccccccchHHHHHHHHHHHHHHhcch
Confidence            34568999999999999999887432 3455799999999999999999999999999999999999543

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=97.40  E-value=0.00021  Score=83.01  Aligned_cols=156  Identities=19%  Similarity=0.207  Sum_probs=124.3

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCC--hh---
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPS--KV---   76 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps--~~---   76 (575)
                      -|..|..||-|+.+. |.|++..+|.+...+|.|.|.+.+..+...+....||.|+.+|++...+.|...+.-  .+   
T Consensus         3 ~k~fly~~~~k~~~~-p~~d~~~~~~~~rqrf~ce~~~~~~~~~~~~~stnkKda~knac~dfv~ylvr~Gk~n~~d~p~   81 (1282)
T KOG0921|consen    3 VKEFLYAWLGKNKYG-PTYDIRSEGRKGRQRFLCEVRVEGFGYTAVGNSTNKKDAATNAAQDFCQYLVREGKMQQSDIPT   81 (1282)
T ss_pred             HHHHHHHHHhhhccC-cceehhhhcccchhheeeeeeccCCcceeeecccccchhhHHHHHHHHHHhhhhccccccCCcc
Confidence            378899999999887 899999889999999999999999888777788999999999999999988654210  00   


Q ss_pred             ------------------------------------h-----------------------hhh--------cc-------
Q 041141           77 ------------------------------------L-----------------------AAR--------VL-------   82 (575)
Q Consensus        77 ------------------------------------~-----------------------~~~--------i~-------   82 (575)
                                                          .                       +.+        ..       
T Consensus        82 ~~s~s~~~~~~l~~~~~a~~~~~~~~g~~~q~~~qd~p~~~~p~~~d~~~~~~g~~~~~~~qkae~~~e~ea~d~~~~ih  161 (1282)
T KOG0921|consen   82 LTSSSLEASSTWQDSETATMFCGGEDGNSFQESQQPIPQKRFPWSNNAYQRNEGTHEQYITQKAEEIAESETVDLNAEIH  161 (1282)
T ss_pred             cccccccCcccccccccccccccccccccCCCCCCCcccccccccccccccCCCCCchhHHHHhhhhhhhhhhccCcccc
Confidence                                                0                       000        00       


Q ss_pred             --cccCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEEC-----CEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           83 --DETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELA-----GVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        83 --de~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~-----G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                        +...|-|..|+++-|+..+ .-.|+....|++|.+.|+.+..+-     -.....+.|.+||.|+...|...+..|.+
T Consensus       162 g~wt~eN~K~~ln~~~q~~~~-~~~y~~~~~g~~~~~s~~~e~si~v~~~~~~~~~~~~gsnkk~~~~~ca~s~vrqm~h  240 (1282)
T KOG0921|consen  162 GNWTMENAKKALNEYLQKMRI-QDNYKYTIVGPEHVRSFEAEASIYVPQLNRNLVAKETGSNKKVAEASCALSLVRQLFH  240 (1282)
T ss_pred             CCCCcchhHHHHhHHHhhhhh-ccccceeecCCccccchhhhHHHhhhhhchhhhhhhccccceecCcchHHHHHHHHHH
Confidence              0135889999999999998 667888888999999999887664     22345688999999999999999888877


Q ss_pred             hhcc
Q 041141          156 QAKS  159 (575)
Q Consensus       156 ~~~~  159 (575)
                      +..-
T Consensus       241 l~~~  244 (1282)
T KOG0921|consen  241 LNVM  244 (1282)
T ss_pred             Hhhh
Confidence            6544

>KOG1817 consensus Ribonuclease [RNA processing and modification]

Probab=96.67  E-value=0.005  Score=67.28  Aligned_cols=69  Identities=30%  Similarity=0.475  Sum_probs=60.3

Q ss_pred             cHHHHHHHHHHcCCC------CCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFN------LPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~------LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      .|+.||.+|..+...      +|.|.+. ..|+.+.+.|++.|+++|..++.+ .|.+.++|+..||+.||+.+...
T Consensus       429 pkskLqq~cl~~rys~~~epdip~y~V~~~~gpa~~r~y~Vavyf~gkrlat~-~G~nik~Ae~rAA~~ALe~~~~d  504 (533)
T KOG1817|consen  429 PKSKLQQCCLTLRYSLGGEPDIPLYKVLGAKGPANDRNYKVAVYFKGKRLATG-VGSNIKQAEMRAAMQALENLKMD  504 (533)
T ss_pred             cHHHHHHHHHHHhcccCCCCCCceEEEecccCCCCCCceEEEEEECCEEEeec-cCchHhHHHHHHHHHHHHHHHhh
Confidence            589999999887543      6777777 689999999999999999998874 89999999999999999998863

>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]

Probab=96.61  E-value=0.0017  Score=73.92  Aligned_cols=133  Identities=22%  Similarity=0.179  Sum_probs=93.1

Q ss_pred             ceE------Ee-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc----------C--C------
Q 041141           19 SYS------CI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK----------G--P------   73 (575)
Q Consensus        19 eY~------li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~----------~--p------   73 (575)
                      +|.      ++ ..||.|.++|+.++.+|+..+++  .|.++|.|+-.|+...|......          .  +      
T Consensus       387 QYk~kv~p~Lvv~t~P~~~~~~t~e~r~~~~~~~a--~gps~~~~~wh~~~k~lq~~~~p~ga~~r~~~~ge~~a~~p~~  464 (816)
T KOG3792|consen  387 QYKQKVDPDLVVDTKPSHRPRRTMEVRVNGLPAEA--EGPSKKTAKWHAARKRLQNEGRPTGAAQRFGRMGEDPASMPEP  464 (816)
T ss_pred             eeccccCCCceeccCCcccchhhhhhhhcCCcccc--CCcccccchHHHHHHHhhccCCCccccccccccCCCcccCCCC
Confidence            677      54 78999999999999999999996  59999999999999988776310          0  0      


Q ss_pred             ------Chh---hh-------------hhc----ccccCchhhHHHHHHHHcCCCCCeEEEe-ecC-CCCCCeEEEEEEE
Q 041141           74 ------SKV---LA-------------ARV----LDETGVYKNLLQETSHRAGLKLPVYTTV-RSG-PGHGPVFSCTVEL  125 (575)
Q Consensus        74 ------s~~---~~-------------~~i----~de~~nyKS~LQE~cQK~gl~lP~Yev~-esG-P~H~p~Ftv~V~V  125 (575)
                            +.+   ..             .++    .+.+..-|....|++.++.  --.|++. +.| -.|.++|...|.+
T Consensus       465 ~~r~~as~ddr~a~~~~a~~~Pt~~~l~nVqr~vs~~~~alK~vsd~L~Ek~r--g~k~El~set~~gs~~~R~v~gV~r  542 (816)
T KOG3792|consen  465 KGRRPASVDDRHANEKHAGIYPTEEELENVQRQVSHLERALKLVSDELAEKRR--GDKYELPSETGTGSHDKRFVKGVMR  542 (816)
T ss_pred             CCcccCCCcchhhhccccccCccHHHHHHHHHhhhHHHHhhcchhHHHhhhcc--ccceecccccCCCCCCceeeeeeee
Confidence                  000   00             000    0011122223333443332  2358877 665 7899999999999


Q ss_pred             CCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141          126 AGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus       126 ~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      .|+.+ .|.+.+||-|+..||..|++.+..+
T Consensus       543 vG~~a-kG~~~~gd~a~~~a~Lca~~pt~~l  572 (816)
T KOG3792|consen  543 VGILA-KGLLLNGDRAVELALLCAEKPTSGL  572 (816)
T ss_pred             eehhh-ccccccchHHHHHHHHhccCccccc
Confidence            99986 5999999999999999888776443

>KOG2777 consensus tRNA-specific adenosine deaminase 1 [RNA processing and modification]

Probab=96.54  E-value=0.0056  Score=68.60  Aligned_cols=65  Identities=34%  Similarity=0.442  Sum_probs=56.4

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGP   73 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~p   73 (575)
                      +.+.|+|++.  +   +.|+++ ..|+.|.+.|.+.|.|||..|+.  +|.+||+|++.||..+|+.|.....
T Consensus        92 pv~ll~e~~~--~---~~~~~~~~~~~~~~~~F~~~~~vdg~~~~~--~~~sKk~ak~~aa~~al~~l~~~~~  157 (542)
T KOG2777|consen   92 PVSLLHELAN--G---LFFDFVNESGPQHAPKFVMSVVVDGRWFEG--GGRSKKEAKQEAAMAALQVLFKIDE  157 (542)
T ss_pred             chHHHHHHhc--c---cceeeeccCCCCCCceEEEEEEECCEEccC--CCcchHHHHHHHHHHHHHHHHhccC
Confidence            3578999998  2   377877 78999999999999999999985  3999999999999999999987643

>PF03368 Dicer_dimer: Dicer dimerisation domain; InterPro: IPR005034 This domain is found in members of the Dicer protein family of dsRNA nucleases

Probab=96.34  E-value=0.015  Score=50.67  Aligned_cols=67  Identities=28%  Similarity=0.362  Sum_probs=45.1

Q ss_pred             hhHHHHHHHHcCC-----CCCeEEEeecCCCCCCeEEEEEEECCE----eeeecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           89 KNLLQETSHRAGL-----KLPVYTTVRSGPGHGPVFSCTVELAGV----SFTGEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        89 KS~LQE~cQK~gl-----~lP~Yev~esGP~H~p~Ftv~V~V~G~----~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      ++.|+.||++..-     ..|.|.+...+.    .|.|+|.+-..    .+.+..-.|||.||+.||-.|...|.+.+.-
T Consensus         2 i~lL~~yC~~Lp~d~~~~~~P~~~~~~~~~----~~~c~v~LP~~~pi~~i~g~~~~sk~~AK~sAAf~Ac~~L~~~g~l   77 (90)
T PF03368_consen    2 ISLLNRYCSTLPSDSFTNLKPEFEIEKIGS----GFICTVILPINSPIRSIEGPPMRSKKLAKRSAAFEACKKLHEAGEL   77 (90)
T ss_dssp             HHHHHHHHTTSSS-TT--SS-EEEEEE--G-----EEEEEE--TT-SS--EEEE--SSHHHHHHHHHHHHHHHHHHH-S-
T ss_pred             HHHHHHHHhcCCCCCCccCCceEEEEEcCC----cEEEEEECCCCCCCCeEEccccccHHHHHHHHHHHHHHHHHHcCCC
Confidence            5689999988642     468899885442    79999998532    2333467999999999999999999998754

This entry represents a dsRNA-binding domain. RNA interference (RNAi) is an ancient gene-silencing process that plays a fundamental role in diverse eukaryotic functions including viral defence, chromatin remodelling, genome rearrangement, developmental timing, brain morphogenesis, and stem cell maintenance. All RNAi pathways require the multidomain ribonuclease Dicer, which initiates RNAi by cleaving double-stranded RNA (dsRNA) substrates into small fragments ~25 nuleotides in length. A typical eukaryotic Dicer consists of a helicase domain (PDOC51192 from PROSITEDOC), a domain of unknown function, and a PAZ domain (PDOC50821 from PROSITEDOC) at the amino (N)-terminus as well as two ribonuclease III domains (PDOC00448 from PROSITEDOC) and a dsRNA-binding domain (dsRBD) (PDOC50137 from PROSITEDOC) at the carboxy (C)-terminus. The domain of unknown function of ~100 amino acids is predicted to adopt the canonical alpha-beta-beta-beta-alpha-fold found in all dsRBDs [, , , ].; GO: 0016891 endoribonuclease activity, producing 5'-phosphomonoesters; PDB: 2KOU_A.

>KOG3769 consensus Ribonuclease III domain proteins [Translation, ribosomal structure and biogenesis]

Probab=94.55  E-value=0.048  Score=57.47  Aligned_cols=69  Identities=20%  Similarity=0.239  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHcCCCCCceEEe-ecC-CCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            3 KNQLQELAQRSCFNLPSYSCI-REG-PDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li-~eG-P~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      ...|-++|+++|+.-|++.++ +.| ....+.|.+.++-+.+.++. |.|.+++.|++.||..+|..|...-
T Consensus       235 ~~~L~~lckr~~l~epe~Rll~esGr~S~~PvyvVgiYs~kkllGq-G~Gesl~~A~e~AA~dAL~k~y~~t  305 (333)
T KOG3769|consen  235 RRLLSRLCKRRGLKEPESRLLAESGRNSAEPVYVVGIYSGKKLLGQ-GQGESLKLAEEQAARDALIKLYDHT  305 (333)
T ss_pred             HHHHHHHHHHcCCCCchhHHHHHhccCccCceEEEEeecCchhhcc-CcchHHHHHHHHHHHHHHHHHHcCC
Confidence            568999999999999999998 455 35678999999999888887 4899999999999999999988764

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=93.24  E-value=0.16  Score=60.32  Aligned_cols=72  Identities=25%  Similarity=0.296  Sum_probs=63.4

Q ss_pred             chhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeee-ecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           87 VYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFT-GEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        87 nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg-~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      |-|..|-.||-|+.+. |.|++..+|+.....|.|.|.+.+..+. .|...+||.|+++||+.-.+.|...++-
T Consensus         2 d~k~fly~~~~k~~~~-p~~d~~~~~~~~rqrf~ce~~~~~~~~~~~~~stnkKda~knac~dfv~ylvr~Gk~   74 (1282)
T KOG0921|consen    2 DVKEFLYAWLGKNKYG-PTYDIRSEGRKGRQRFLCEVRVEGFGYTAVGNSTNKKDAATNAAQDFCQYLVREGKM   74 (1282)
T ss_pred             cHHHHHHHHHhhhccC-cceehhhhcccchhheeeeeeccCCcceeeecccccchhhHHHHHHHHHHhhhhccc
Confidence            5688999999999987 9999998898999999999999988764 4777889999999999999999776554

>PF14954 LIX1: Limb expression 1

Probab=90.02  E-value=0.69  Score=47.13  Aligned_cols=67  Identities=31%  Similarity=0.332  Sum_probs=46.9

Q ss_pred             cCchhhHHHHHHHHc---CCCCCeEEEe--ecCCCCCCeEEEEEEECCEe-eee-cccCCHHHHHHHHHHHHHH
Q 041141           85 TGVYKNLLQETSHRA---GLKLPVYTTV--RSGPGHGPVFSCTVELAGVS-FTG-EPAKTKKQAQKNAALAAWS  151 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~---gl~lP~Yev~--esGP~H~p~Ftv~V~V~G~~-fg~-G~G~SKKeAEQ~AAk~ALe  151 (575)
                      ..|-+..||||=|.+   +..++.-.++  +..|...+-|.|-|++-|-. ||. -...||-+|++.||+.||-
T Consensus        20 ~vnvV~~LqeFWq~Kq~r~a~~~~~~lv~YEs~ps~~ppyVcyVTLPGGSCFGnfq~C~tkAEARR~AAKiALm   93 (252)
T PF14954_consen   20 DVNVVEALQEFWQMKQSRGADLKSEALVVYESVPSPSPPYVCYVTLPGGSCFGNFQNCPTKAEARRSAAKIALM   93 (252)
T ss_pred             cchHHHHHHHHHHHHHhccccCCCCCeeeeeccCCCCCCeEEEEeCCCCCccCccccCCcHHHHHhhhHHHHHH
Confidence            457889999976543   3333322221  45566678899999996544 443 5689999999999999874

>KOG2334 consensus tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]

Probab=83.96  E-value=0.34  Score=53.41  Aligned_cols=71  Identities=23%  Similarity=0.267  Sum_probs=60.1

Q ss_pred             CchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeeccc-CCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           86 GVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPA-KTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        86 ~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G-~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      ..+|..|-+||-+.+..-|.|+++..   -++.|...+.++|..|..+.+ ++||.|+|.||..+|........+
T Consensus       375 ~~~k~~l~~~~~~~~~~~~~ye~~~~---~d~lf~si~~~~~~~~~ssi~~~n~k~aeq~aa~~~l~~s~l~e~~  446 (477)
T KOG2334|consen  375 DTPKMVLADLCVKTKANGPVYETVQR---TDKLFSSIATARGQKYNSSIWSPNKKSAEQDAAIVALRKSNLWEAD  446 (477)
T ss_pred             CCHHHHHHHhhhhhcCCCcchhhhhh---hhhhhHHHhhhhhhhhhccccCcchhhHHHHHHHHHHHhcCcchhh
Confidence            46899999999999999999999843   457899999999999987654 899999999999998877655433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	575
2l2n_A	103	Backbone 1h, 13c, And 15n Chemical Shift Assignment		4e-06
3adg_A	73	Structure Of Arabidopsis Hyl1 And Its Molecular Imp		7e-06
3n3w_A	248	2.2 Angstrom Resolution Crystal Structure Of Nuclea		4e-04
2l2m_A	77	Solution Structure Of The Second Dsrbd Of Hyl1 Leng		5e-04

>pdb|2L2N|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For The First Dsrbd Of Protein Hyl1 Length = 103

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 31/87 (35%), Positives = 49/87 (56%), Gaps = 2/87 (2%)
Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFES-PTFCSTLRQAEHA 59
           ++K++LQE AQ+     P Y  ++EGP H   F++ V  +G  + S P F +  + AE +
Sbjct: 18  VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNR-KAAEQS 76
Query: 60  AAEVALDVLSKKGPSKVLAARVLDETG 86
           AAEVAL  L+K        ++ + ETG
Sbjct: 77  AAEVALRELAKSSELSQCVSQPVHETG 103

>pdb|3ADG|A Chain A, Structure Of Arabidopsis Hyl1 And Its Molecular Implications For Mirna Processing Length = 73

Iteration: 1
 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 43/71 (60%), Gaps = 2/71 (2%)
Query: 1  MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFES-PTFCSTLRQAEHA 59
          ++K++LQE AQ+     P Y  ++EGP H   F++ V  +G  + S P F +  + AE +
Sbjct: 4  VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNR-KAAEQS 62
Query: 60 AAEVALDVLSK 70
          AAEVAL  L+K
Sbjct: 63 AAEVALRELAK 73

>pdb|3N3W|A Chain A, 2.2 Angstrom Resolution Crystal Structure Of Nuclease Domain Ribonuclase Iii (Rnc) From Campylobacter Jejuni Length = 248

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 2   YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           YK +LQE+ Q      P Y  +R  GPDH  +F+ A+  +G+   +     + ++A+  A
Sbjct: 179 YKTKLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKEL-ARAIAGSKKEAQQMA 237
Query: 61  AEVALDVL 68
           A++AL+ L
Sbjct: 238 AKIALEKL 245

>pdb|2L2M|A Chain A, Solution Structure Of The Second Dsrbd Of Hyl1 Length = 77

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 82  LDETGVYKNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVSFTG 132
           + ETG+ KNLLQE + +    +P+Y   +    G    F+CTVE+ G+ +TG
Sbjct: 3   MHETGLCKNLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTG 54

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	575
1qu6_A	179	Protein kinase PKR; dsRNA-binding domain, solution	1e-44
1qu6_A	179	Protein kinase PKR; dsRNA-binding domain, solution	5e-15
1qu6_A	179	Protein kinase PKR; dsRNA-binding domain, solution	8e-09
2l2n_A	103	Hyponastic leave 1; DSRBD, miRNA, RNA binding prot	5e-31
2l2n_A	103	Hyponastic leave 1; DSRBD, miRNA, RNA binding prot	2e-20
3adj_A	76	F21M12.9 protein; HYL1, miRNA processing, RNA bind	4e-30
3adj_A	76	F21M12.9 protein; HYL1, miRNA processing, RNA bind	3e-19
3adg_A	73	F21M12.9 protein; HYL1, miRNA processing mechanism	3e-29
3adg_A	73	F21M12.9 protein; HYL1, miRNA processing mechanism	1e-18
2yt4_A	232	Protein DGCR8; DSRBD, RNA binding domain, RNA bind	1e-19
1whn_A	128	Hypothetical protein riken cDNA 2310016K04; double	6e-18
1whn_A	128	Hypothetical protein riken cDNA 2310016K04; double	3e-13
1x49_A	97	Interferon-induced, double-stranded RNA- activated	8e-17
1x49_A	97	Interferon-induced, double-stranded RNA- activated	8e-13
1whq_A	99	RNA helicase A; double-stranded RNA binding domain	7e-16
1whq_A	99	RNA helicase A; double-stranded RNA binding domain	1e-11
2nug_A	221	Ribonuclease III, RNAse III; dsRNA, RNA interferen	8e-15
2nug_A	221	Ribonuclease III, RNAse III; dsRNA, RNA interferen	1e-12
2cpn_A	89	TAR RNA-binding protein 2; double-stranded RNA bin	2e-14
2cpn_A	89	TAR RNA-binding protein 2; double-stranded RNA bin	4e-11
3adl_A	88	RISC-loading complex subunit tarbp2; TRBP2, miRNA	5e-14
3adl_A	88	RISC-loading complex subunit tarbp2; TRBP2, miRNA	9e-12
1di2_A	69	XLRBPA, double stranded RNA binding protein A; pro	1e-13
1di2_A	69	XLRBPA, double stranded RNA binding protein A; pro	1e-10
3llh_A	90	RISC-loading complex subunit tarbp2; DSRBD, DSRM,	1e-13
3llh_A	90	RISC-loading complex subunit tarbp2; DSRBD, DSRM,	4e-12
2dix_A	84	Interferon-inducible double stranded RNA- dependen	3e-13
2dix_A	84	Interferon-inducible double stranded RNA- dependen	4e-12
2a11_A	242	Ribonuclease III, RNAse III; nuclease domain, stru	3e-13
2a11_A	242	Ribonuclease III, RNAse III; nuclease domain, stru	2e-12
1uhz_A	89	Staufen (RNA binding protein) homolog 2; DSRM, sta	8e-13
1uhz_A	89	Staufen (RNA binding protein) homolog 2; DSRM, sta	1e-12
3n3w_A	248	Ribonuclease III; nuclease domain, ribonuclase III	8e-13
3n3w_A	248	Ribonuclease III; nuclease domain, ribonuclase III	7e-12
1o0w_A	252	Ribonuclease III, RNAse III; TM1102, structural ge	1e-12
1o0w_A	252	Ribonuclease III, RNAse III; TM1102, structural ge	1e-12
1x47_A	98	DGCR8 protein; structural genomics, DSRM domain, N	8e-12
1x47_A	98	DGCR8 protein; structural genomics, DSRM domain, N	2e-09
1ekz_A	76	DSRBDIII, maternal effect protein (staufen); struc	2e-11
1ekz_A	76	DSRBDIII, maternal effect protein (staufen); struc	4e-11
2l33_A	91	Interleukin enhancer-binding factor 3; structural	3e-11
2l33_A	91	Interleukin enhancer-binding factor 3; structural	6e-10
2khx_A	85	Ribonuclease 3; drosha, RNA binding domain, hydrol	4e-11
2khx_A	85	Ribonuclease 3; drosha, RNA binding domain, hydrol	5e-11
3p1x_A	75	Interleukin enhancer-binding factor 3; structural	1e-10
3p1x_A	75	Interleukin enhancer-binding factor 3; structural	3e-10
2dmy_A	97	Spermatid perinuclear RNA-binding protein; DSRM do	2e-10
2dmy_A	97	Spermatid perinuclear RNA-binding protein; DSRM do	4e-10
2b7v_A	71	Double-stranded RNA-specific editase 1; RNA editin	3e-10
2b7v_A	71	Double-stranded RNA-specific editase 1; RNA editin	2e-09
2b7t_A	73	Double-stranded RNA-specific editase 1; RNA editin	4e-10
2b7t_A	73	Double-stranded RNA-specific editase 1; RNA editin	7e-10
2ljh_A	114	Double-stranded RNA-specific editase ADAR; DSRBD,	6e-10
2ljh_A	114	Double-stranded RNA-specific editase ADAR; DSRBD,	7e-10
3c4b_A	265	Endoribonuclease dicer; RNAse, dsRNA binding prote	2e-09
3c4b_A	265	Endoribonuclease dicer; RNAse, dsRNA binding prote	9e-09
3rv0_A	341	K. polysporus DCR1; RNAse III enzyme, RNA binding	3e-08
3rv0_A	341	K. polysporus DCR1; RNAse III enzyme, RNA binding	3e-06
2l3j_A	236	Double-stranded RNA-specific editase 1; editing, d	1e-07
2l3j_A	236	Double-stranded RNA-specific editase 1; editing, d	2e-07
2l3j_A	236	Double-stranded RNA-specific editase 1; editing, d	2e-05
2l3j_A	236	Double-stranded RNA-specific editase 1; editing, d	3e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
2qvw_A	756	GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral	1e-05
1x48_A	88	Interferon-induced, double-stranded RNA- activated	5e-05

>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1 Length = 179

 Score =  155 bits (393), Expect = 1e-44
 Identities = 32/165 (19%), Positives = 65/165 (39%), Gaps = 8/165 (4%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
           +  +L    Q+    L        GP H  RF   V  +G  F      S  ++A++AAA
Sbjct: 15  FMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRS-KKEAKNAAA 73

Query: 62  EVALDVLSKKGPSKVLAARVLDETG------VYKNLLQETSHRAGLKLPVYTTVRSGPGH 115
           ++A+++L+K+  +          +        Y  L+   + +  L +  Y    SG   
Sbjct: 74  KLAVEILNKEKKAVSPLLLTTTNSSEGLSMGNYIGLINRIAQKKRLTVN-YEQCASGVHG 132

Query: 116 GPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSA 160
              F    ++    ++     TK++A++ AA  A+  +  +   +
Sbjct: 133 PEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQILSEETGS 177

>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1 Length = 179

 Score = 72.2 bits (177), Expect = 5e-15
 Identities = 30/162 (18%), Positives = 51/162 (31%), Gaps = 17/162 (10%)

Query: 72  GPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFT 131
           G    +A  +    G +   L     + G+ L       SGP H   F+  V + G  F 
Sbjct: 1   GSHMEMAGDL--SAGFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDGREFP 58

Query: 132 GEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESGTNDE---------QDQA 182
               ++KK+A+  AA  A   L K+ K+       +  SSE  +            Q + 
Sbjct: 59  EGEGRSKKEAKNAAAKLAVEILNKEKKAVSPLLLTTTNSSEGLSMGNYIGLINRIAQKKR 118

Query: 183 IIARYLATLKGPETNNSQREHRTIGVSASIRREVIPYGDARS 224
           +   Y     G                  + ++    G   +
Sbjct: 119 LTVNYEQCASGVH------GPEGFHYKCKMGQKEYSIGTGST 154

>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1 Length = 179

 Score = 54.5 bits (131), Expect = 8e-09
 Identities = 13/74 (17%), Positives = 26/74 (35%), Gaps = 2/74 (2%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
            Y   +  +AQ+    +  Y     G      F        + +   T  ST ++A+  A
Sbjct: 105 NYIGLINRIAQKKRLTVN-YEQCASGVHGPEGFHYKCKMGQKEYSIGT-GSTKQEAKQLA 162

Query: 61  AEVALDVLSKKGPS 74
           A++A   +  +   
Sbjct: 163 AKLAYLQILSEETG 176

>2l2n_A Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, plant protein; NMR {Arabidopsis thaliana} Length = 103

 Score =  115 bits (289), Expect = 5e-31
 Identities = 29/86 (33%), Positives = 46/86 (53%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           ++K++LQE AQ+     P Y  ++EGP H   F++ V  +G  + S       + AE +A
Sbjct: 18  VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQSA 77

Query: 61  AEVALDVLSKKGPSKVLAARVLDETG 86
           AEVAL  L+K        ++ + ETG
Sbjct: 78  AEVALRELAKSSELSQCVSQPVHETG 103

>2l2n_A Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, plant protein; NMR {Arabidopsis thaliana} Length = 103

 Score = 85.6 bits (212), Expect = 2e-20
 Identities = 31/103 (30%), Positives = 49/103 (47%), Gaps = 4/103 (3%)

Query: 73  PSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSF-T 131
            +    +  +    V+K+ LQE + +  L  PVY  V+ GP H  +F  TV L GV + +
Sbjct: 4   MTSTDVSSGVSNCYVFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNS 63

Query: 132 GEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSPPSSESG 174
                 +K A+++AA  A   L K ++    S   S P  E+G
Sbjct: 64  LPGFFNRKAAEQSAAEVALRELAKSSE---LSQCVSQPVHETG 103

>3adj_A F21M12.9 protein; HYL1, miRNA processing, RNA binding protein, gene regulation; 3.00A {Arabidopsis thaliana} PDB: 2l2m_A Length = 76

 Score =  111 bits (280), Expect = 4e-30
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 84  ETGVYKNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQ 142
             G+ KNLLQE + +    +P+Y   +    G    F+CTVE+ G+ +TG   +TKK A+
Sbjct: 2   SHGLCKNLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTGAATRTKKDAE 61

Query: 143 KNAALAAWSALKKQA 157
            +A   A  A++   
Sbjct: 62  ISAGRTALLAIQSDT 76

>3adj_A F21M12.9 protein; HYL1, miRNA processing, RNA binding protein, gene regulation; 3.00A {Arabidopsis thaliana} PDB: 2l2m_A Length = 76

 Score = 81.2 bits (201), Expect = 3e-19
 Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 2/69 (2%)

Query: 1  MYKNQLQELAQRSCFNLPSYSCIR-EGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHA 59
          + KN LQE AQ+  + +P Y C + E      +F   V   G  +       T + AE +
Sbjct: 5  LCKNLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTGAA-TRTKKDAEIS 63

Query: 60 AAEVALDVL 68
          A   AL  +
Sbjct: 64 AGRTALLAI 72

>3adg_A F21M12.9 protein; HYL1, miRNA processing mechanism, RNA binding protein, gene regulation; 1.70A {Arabidopsis thaliana} PDB: 3adi_A Length = 73

 Score =  109 bits (274), Expect = 3e-29
 Identities = 26/70 (37%), Positives = 40/70 (57%)

Query: 1  MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
          ++K++LQE AQ+     P Y  ++EGP H   F++ V  +G  + S       + AE +A
Sbjct: 4  VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQSA 63

Query: 61 AEVALDVLSK 70
          AEVAL  L+K
Sbjct: 64 AEVALRELAK 73

>3adg_A F21M12.9 protein; HYL1, miRNA processing mechanism, RNA binding protein, gene regulation; 1.70A {Arabidopsis thaliana} PDB: 3adi_A Length = 73

 Score = 79.2 bits (196), Expect = 1e-18
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSF-TGEPAKTKKQAQKNAA 146
           +K+ LQE + +  L  PVY  V+ GP H  +F  TV L GV + +      +K A+++AA
Sbjct: 5   FKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQSAA 64

Query: 147 LAAWSALKK 155
             A   L K
Sbjct: 65  EVALRELAK 73

>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein; 2.60A {Homo sapiens} Length = 232

 Score = 87.5 bits (216), Expect = 1e-19
 Identities = 36/211 (17%), Positives = 62/211 (29%), Gaps = 27/211 (12%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
               L E  QR     P Y+         P F A+V  +G T+      S+ + A++ AA
Sbjct: 24  EVCILHEYMQRVLKVRPVYNFFECENPSEP-FGASVTIDGVTY-GSGTASSKKLAKNKAA 81

Query: 62  EVALDVL--------SKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPV-------- 105
              L++L        S++ P         +   +  + + E + +AGL  P         
Sbjct: 82  RATLEILIPDFVKQTSEEKPKDSEELEYFNHISIEDSRVYELTSKAGLLSPYQILHECLK 141

Query: 106 --------YTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA 157
                          PG        +     +  G   K K+  ++ A+      L    
Sbjct: 142 RNHGMGDTSIKFEVVPGKNQKSEYVMACGKHTVRGW-CKNKRVGKQLASQKILQLLHPHV 200

Query: 158 KSAFSSSSFSPPSSESGTNDEQDQAIIARYL 188
           K+  S        S      E     +    
Sbjct: 201 KNWGSLLRMYGRESSKMVKQETSDKSVIELQ 231

>1whn_A Hypothetical protein riken cDNA 2310016K04; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1 Length = 128

 Score = 79.2 bits (195), Expect = 6e-18
 Identities = 25/117 (21%), Positives = 41/117 (35%), Gaps = 16/117 (13%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
             K  L E  +R     P Y  ++   D    F + V    + ++S  +  + + AE  A
Sbjct: 27  TPKMCLLEWCRREKLPQPVYETVQRTIDR--MFCSVVTVAEQKYQSTLWDKSKKLAEQTA 84

Query: 61  AEVALDVLSKKGPSKVLAARVLDETG-VYKNLLQETSHRAGLKLPVYTTVRSGPGHG 116
           A V L          +   R+ +E+  + K   +      G         RSGP  G
Sbjct: 85  AIVCLRSQ------GLPEGRLGEESPSLNKRKREAPDQDPG-------GPRSGPSSG 128

>1whn_A Hypothetical protein riken cDNA 2310016K04; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1 Length = 128

 Score = 65.7 bits (160), Expect = 3e-13
 Identities = 23/94 (24%), Positives = 37/94 (39%), Gaps = 4/94 (4%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSF-TGEPAKTKKQAQKNAA 146
            K  L E   R  L  PVY TV+       +F   V +A   + +    K+KK A++ AA
Sbjct: 28  PKMCLLEWCRREKLPQPVYETVQR--TIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAA 85

Query: 147 LAAWSAL-KKQAKSAFSSSSFSPPSSESGTNDEQ 179
           +    +    + +    S S +    E+   D  
Sbjct: 86  IVCLRSQGLPEGRLGEESPSLNKRKREAPDQDPG 119

>1x49_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1 Length = 97

 Score = 75.1 bits (185), Expect = 8e-17
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 3/89 (3%)

Query: 83  DETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQ 142
           D  G Y + L +     G+ +       SGP H   F+  V +    F     ++K++A+
Sbjct: 11  DTPGFYMDKLNKYRQMHGVAITYKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSKQEAR 70

Query: 143 KNAALAAWSALKKQAKSAFSSSSFSPPSS 171
             AA  A   L  + K        S PSS
Sbjct: 71  NAAAKLAVDILDNENK---VDCHTSGPSS 96

>1x49_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1 Length = 97

 Score = 63.6 bits (155), Expect = 8e-13
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
          Y ++L +  Q       +Y  +   GP H  RF   V  + + F      S  ++A +AA
Sbjct: 16 YMDKLNKYRQMHG-VAITYKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSK-QEARNAA 73

Query: 61 AEVALDVLSKKGPS 74
          A++A+D+L  +   
Sbjct: 74 AKLAVDILDNENKV 87

>1whq_A RNA helicase A; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Mus musculus} SCOP: d.50.1.1 PDB: 2rs6_A Length = 99

 Score = 72.6 bits (178), Expect = 7e-16
 Identities = 22/92 (23%), Positives = 34/92 (36%), Gaps = 5/92 (5%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGE-PAKTKKQAQKNAA 146
            KN L     +  +  P Y     G  +   F C V + G ++ G   +  KK AQ NAA
Sbjct: 8   IKNFLYAWCGKRKMT-PAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAA 66

Query: 147 LAAWSALKKQAK---SAFSSSSFSPPSSESGT 175
               + L +  +       +    PP S   +
Sbjct: 67  RDFVNYLVRINEVKSEEVPAVGIVPPPSGPSS 98

>1whq_A RNA helicase A; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Mus musculus} SCOP: d.50.1.1 PDB: 2rs6_A Length = 99

 Score = 60.3 bits (146), Expect = 1e-11
 Identities = 13/71 (18%), Positives = 24/71 (33%), Gaps = 1/71 (1%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
           KN L     +     P+Y     G  +  +F   V   G  +      +  + A+  AA
Sbjct: 8  IKNFLYAWCGKRKM-TPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAA 66

Query: 62 EVALDVLSKKG 72
             ++ L +  
Sbjct: 67 RDFVNYLVRIN 77

>2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference, endonucleolytic cleavage, hydrolase/RNA complex; 1.70A {Aquifex aeolicus} SCOP: a.149.1.1 d.50.1.1 PDB: 1yyw_A 2nue_A 2nuf_A 1yyk_A 1yz9_A 1yyo_A 2ez6_A 1rc7_A 1i4s_A 1jfz_A 1rc5_A Length = 221

 Score = 72.9 bits (180), Expect = 8e-15
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
           YK +LQE + +   + P Y  +   GP H   F    ++      GE  K+KK+A++ AA
Sbjct: 152 YKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGE-GKSKKEAEQRAA 210

Query: 147 LAAWSALKKQ 156
                 L++ 
Sbjct: 211 EELIKLLEES 220

>2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference, endonucleolytic cleavage, hydrolase/RNA complex; 1.70A {Aquifex aeolicus} SCOP: a.149.1.1 d.50.1.1 PDB: 1yyw_A 2nue_A 2nuf_A 1yyk_A 1yz9_A 1yyo_A 2ez6_A 1rc7_A 1i4s_A 1jfz_A 1rc5_A Length = 221

 Score = 66.4 bits (163), Expect = 1e-12
 Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 3/71 (4%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           YK  LQE+ Q+     P Y  I   GP H  +F                  + ++AE  A
Sbjct: 152 YKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLG--EGKSKKEAEQRA 209

Query: 61  AEVALDVLSKK 71
           AE  + +L + 
Sbjct: 210 AEELIKLLEES 220

>2cpn_A TAR RNA-binding protein 2; double-stranded RNA binding domain, DSRBD, DSRM., structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 89

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
               LQE   + G +LP YT    SGP H   F+ T  +      G    +KK A++NAA
Sbjct: 18  PVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGS-GTSKKLAKRNAA 76

Query: 147 LAAWSALKKQA 157
                 +   +
Sbjct: 77  AKMLLRVSGPS 87

>2cpn_A TAR RNA-binding protein 2; double-stranded RNA binding domain, DSRBD, DSRM., structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 89

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 3/71 (4%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
              LQEL  +  + LP Y+  +E GP H   F                 ++ + A+  A
Sbjct: 18 PVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIG--SGTSKKLAKRNA 75

Query: 61 AEVALDVLSKK 71
          A   L  +S  
Sbjct: 76 AAKMLLRVSGP 86

>3adl_A RISC-loading complex subunit tarbp2; TRBP2, miRNA processing, gene regulation-RNA complex; 2.20A {Homo sapiens} Length = 88

 Score = 66.6 bits (163), Expect = 5e-14
 Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
               LQE   + G +LP YT    SGP H   F+ T  +      G    +KK A++NAA
Sbjct: 17  EVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGS-GTSKKLAKRNAA 75

Query: 147 LAAWSALKK 155
                 +  
Sbjct: 76  AKMLLRVHT 84

>3adl_A RISC-loading complex subunit tarbp2; TRBP2, miRNA processing, gene regulation-RNA complex; 2.20A {Homo sapiens} Length = 88

 Score = 60.4 bits (147), Expect = 9e-12
 Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 3/70 (4%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
              LQEL  +  + LP Y+  +E GP H   F                 ++ + A+  A
Sbjct: 17 EVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIG--SGTSKKLAKRNA 74

Query: 61 AEVALDVLSK 70
          A   L  +  
Sbjct: 75 AAKMLLRVHT 84

>1di2_A XLRBPA, double stranded RNA binding protein A; protein-RNA complex, protein-RNA interactions, RNA-bining protein; 1.90A {Xenopus laevis} SCOP: d.50.1.1 Length = 69

 Score = 64.9 bits (159), Expect = 1e-13
 Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 89  KNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
              LQE + + G +LP YT    SGP H   F+ T  +     TG    +K+ A++ AA 
Sbjct: 3   VGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGS-GTSKQVAKRVAAE 61

Query: 148 AAWSALK 154
              +  K
Sbjct: 62  KLLTKFK 68

>1di2_A XLRBPA, double stranded RNA binding protein A; protein-RNA complex, protein-RNA interactions, RNA-bining protein; 1.90A {Xenopus laevis} SCOP: d.50.1.1 Length = 69

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 17/67 (25%), Positives = 24/67 (35%), Gaps = 3/67 (4%)

Query: 3  KNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
             LQELA +  + LP Y+     GP H   F                 ++ + A+  AA
Sbjct: 3  VGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETG--SGTSKQVAKRVAA 60

Query: 62 EVALDVL 68
          E  L   
Sbjct: 61 EKLLTKF 67

>3llh_A RISC-loading complex subunit tarbp2; DSRBD, DSRM, microrna, RNA binding protein; 2.14A {Homo sapiens} Length = 90

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 26/71 (36%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
             +LLQE   R G K PVY  +   G  H P F+  V +   S TG+   +KK A+  AA
Sbjct: 16  PISLLQEYGTRIG-KTPVYDLLKAEGQAHQPNFTFRVTVGDTSCTGQ-GPSKKAAKHKAA 73

Query: 147 LAAWSALKKQA 157
             A   LK  +
Sbjct: 74  EVALKHLKGGS 84

>3llh_A RISC-loading complex subunit tarbp2; DSRBD, DSRM, microrna, RNA binding protein; 2.14A {Homo sapiens} Length = 90

 Score = 61.6 bits (150), Expect = 4e-12
 Identities = 21/73 (28%), Positives = 27/73 (36%), Gaps = 4/73 (5%)

Query: 2  YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
            + LQE   R     P Y  +  EG  H P F   V     +        + + A+H A
Sbjct: 16 PISLLQEYGTRI-GKTPVYDLLKAEGQAHQPNFTFRVTVGDTSCTG--QGPSKKAAKHKA 72

Query: 61 AEVALDVLSKKGP 73
          AEVAL  L     
Sbjct: 73 AEVALKHLKGGSM 85

>2dix_A Interferon-inducible double stranded RNA- dependent protein kinase activator A; structure genomics, DSRM domain, hypothetical protein PRKRA; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 84

 Score = 64.7 bits (158), Expect = 3e-13
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 89  KNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
             +L E   +    +PVY         H P F+  V +  ++ TGE   +KK A+  AA 
Sbjct: 11  IQVLHEYGMKTK-NIPVYECERSDVQIHVPTFTFRVTVGDITCTGE-GTSKKLAKHRAAE 68

Query: 148 AAWSALKKQA 157
           AA + LK  A
Sbjct: 69  AAINILKANA 78

>2dix_A Interferon-inducible double stranded RNA- dependent protein kinase activator A; structure genomics, DSRM domain, hypothetical protein PRKRA; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 84

 Score = 61.2 bits (149), Expect = 4e-12
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 4/72 (5%)

Query: 3  KNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
             L E   ++  N+P Y C   +   H P F   V     T       ++ + A+H AA
Sbjct: 11 IQVLHEYGMKTK-NIPVYECERSDVQIHVPTFTFRVTVGDITCTG--EGTSKKLAKHRAA 67

Query: 62 EVALDVLSKKGP 73
          E A+++L     
Sbjct: 68 EAAINILKANAS 79

>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomic protein structure initiative; 2.10A {Mycobacterium tuberculosis} Length = 242

 Score = 68.8 bits (169), Expect = 3e-13
 Identities = 31/108 (28%), Positives = 47/108 (43%), Gaps = 6/108 (5%)

Query: 59  AAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPV 118
            A EV L +      +       LD    +K  LQE +   GL  P Y    +GP H   
Sbjct: 139 KAREVILRLFGPLLDAAPTLGAGLD----WKTSLQELTAARGLGAPSYLVTSTGPDHDKE 194

Query: 119 FSCTVELAG-VSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSS 165
           F+  V +      +G   ++KK+A++ AA AAW AL+    +    +S
Sbjct: 195 FTAVVVVMDSEYGSGV-GRSKKEAEQKAAAAAWKALEVLDNAMPGKTS 241

>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomic protein structure initiative; 2.10A {Mycobacterium tuberculosis} Length = 242

 Score = 66.5 bits (163), Expect = 2e-12
 Identities = 22/73 (30%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
           +K  LQEL        PSY     GPDH   F A V      + S     + ++AE  AA
Sbjct: 164 WKTSLQELTAARGLGAPSYLVTSTGPDHDKEFTAVVVVMDSEYGSGV-GRSKKEAEQKAA 222

Query: 62  EVALDVLSKKGPS 74
             A   L     +
Sbjct: 223 AAAWKALEVLDNA 235

>1uhz_A Staufen (RNA binding protein) homolog 2; DSRM, staufen homolog 2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1 Length = 89

 Score = 63.1 bits (154), Expect = 8e-13
 Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 2/79 (2%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
             + L +       K P Y  +   G      F   V++     TG     KK A+KNAA
Sbjct: 8   PISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGT-GPNKKIAKKNAA 66

Query: 147 LAAWSALKKQAKSAFSSSS 165
            A    L  +A ++   S 
Sbjct: 67  EAMLLQLGYKASTSLQDSG 85

>1uhz_A Staufen (RNA binding protein) homolog 2; DSRM, staufen homolog 2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1 Length = 89

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 16/74 (21%), Positives = 24/74 (32%), Gaps = 3/74 (4%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
            ++L ++ Q      P Y  + E G      F   V    E           + A+  A
Sbjct: 8  PISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATG--TGPNKKIAKKNA 65

Query: 61 AEVALDVLSKKGPS 74
          AE  L  L  K  +
Sbjct: 66 AEAMLLQLGYKAST 79

>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862, csgid, structura genomics; 2.21A {Campylobacter jejuni subsp} Length = 248

 Score = 67.6 bits (166), Expect = 8e-13
 Identities = 30/99 (30%), Positives = 40/99 (40%), Gaps = 7/99 (7%)

Query: 59  AAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGP 117
            A  +AL ++ K  P       + D    YK  LQE +     + P Y TV   GP H  
Sbjct: 154 FAKTIALRLIEKNFPQIDAKILIKD----YKTKLQEITQGKIGQTPQYETVRAFGPDHLK 209

Query: 118 VFSCTVELAG-VSFTGEPAKTKKQAQKNAALAAWSALKK 155
            F   + L G        A +KK+AQ+ AA  A   L  
Sbjct: 210 QFEIALMLDGKELARAI-AGSKKEAQQMAAKIALEKLGA 247

>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862, csgid, structura genomics; 2.21A {Campylobacter jejuni subsp} Length = 248

 Score = 64.9 bits (159), Expect = 7e-12
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           YK +LQE+ Q      P Y  +R  GPDH  +F+ A+  +G+         + ++A+  A
Sbjct: 179 YKTKLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKELARAI-AGSKKEAQQMA 237

Query: 61  AEVALDVLSK 70
           A++AL+ L  
Sbjct: 238 AKIALEKLGA 247

>1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; 2.00A {Thermotoga maritima} SCOP: a.149.1.1 d.50.1.1 Length = 252

 Score = 67.2 bits (165), Expect = 1e-12
 Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           YK  LQE+ Q      P Y  +R    D    F   V  NG+T  +     T ++AE  A
Sbjct: 181 YKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGK-GRTKKEAEKEA 239

Query: 61  AEVALDVLSKK 71
           A +A + L K+
Sbjct: 240 ARIAYEKLLKE 250

>1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; 2.00A {Thermotoga maritima} SCOP: a.149.1.1 d.50.1.1 Length = 252

 Score = 67.2 bits (165), Expect = 1e-12
 Identities = 25/101 (24%), Positives = 36/101 (35%), Gaps = 7/101 (6%)

Query: 59  AAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGP 117
              E+            +    + D    YK  LQE         P Y  V         
Sbjct: 156 KIKELFEQEFEFYIEKIMKGEMLFD----YKTALQEIVQSEHKVPPEYILVRTEKNDGDR 211

Query: 118 VFSCTVELAG-VSFTGEPAKTKKQAQKNAALAAWSALKKQA 157
           +F   V + G    TG+  +TKK+A+K AA  A+  L K+ 
Sbjct: 212 IFVVEVRVNGKTIATGK-GRTKKEAEKEAARIAYEKLLKER 251

>1x47_A DGCR8 protein; structural genomics, DSRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 98

 Score = 61.0 bits (148), Expect = 8e-12
 Identities = 20/78 (25%), Positives = 27/78 (34%), Gaps = 1/78 (1%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
              +L E   R     PVY            F  +V + GV++    A +KK A+  AA 
Sbjct: 18  EVCILHEYMQRVLKVRPVYNFF-ECENPSEPFGASVTIDGVTYGSGTASSKKLAKNKAAR 76

Query: 148 AAWSALKKQAKSAFSSSS 165
           A    L        S S 
Sbjct: 77  ATLEILIPDFVKQTSESG 94

>1x47_A DGCR8 protein; structural genomics, DSRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 98

 Score = 54.1 bits (130), Expect = 2e-09
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
              L E  QR     P Y+   E  + +  F A+V  +G T+      S+ + A++ AA
Sbjct: 18 EVCILHEYMQRVLKVRPVYNFF-ECENPSEPFGASVTIDGVTY-GSGTASSKKLAKNKAA 75

Query: 62 EVALDVL 68
             L++L
Sbjct: 76 RATLEIL 82

>1ekz_A DSRBDIII, maternal effect protein (staufen); structure, protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila melanogaster} SCOP: d.50.1.1 PDB: 1stu_A Length = 76

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 4/70 (5%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
            +Q+ E+  +       +  +RE GP H   F  A        E     +  + ++  A
Sbjct: 9  PISQVHEIGIKRNMT-VHFKVLREEGPAHMKNFITACIVGSIVTEG--EGNGKKVSKKRA 65

Query: 61 AEVALDVLSK 70
          AE  L  L K
Sbjct: 66 AEKMLVELQK 75

>1ekz_A DSRBDIII, maternal effect protein (staufen); structure, protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila melanogaster} SCOP: d.50.1.1 PDB: 1stu_A Length = 76

 Score = 58.1 bits (141), Expect = 4e-11
 Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 3/69 (4%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
             + + E   +  +    +  +R  GP H   F     +  +   GE    KK ++K AA
Sbjct: 9   PISQVHEIGIKRNMT-VHFKVLREEGPAHMKNFITACIVGSIVTEGE-GNGKKVSKKRAA 66

Query: 147 LAAWSALKK 155
                 L+K
Sbjct: 67  EKMLVELQK 75

>2l33_A Interleukin enhancer-binding factor 3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, DRBM; NMR {Homo sapiens} Length = 91

 Score = 59.0 bits (143), Expect = 3e-11
 Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
           KN + EL ++       Y  I E G  H  RF   V  +G+ F+     S  + A+  A
Sbjct: 16 GKNPVMELNEK--RRGLKYELISETGGSHDKRFVMEVEVDGQKFQG--AGSNKKVAKAYA 71

Query: 61 AEVALDVLSKKGPSKVLAAR 80
          A  AL+ L    P  + A +
Sbjct: 72 ALAALEKLFPDTPLALDANK 91

>2l33_A Interleukin enhancer-binding factor 3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, DRBM; NMR {Homo sapiens} Length = 91

 Score = 55.1 bits (133), Expect = 6e-10
 Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 6/94 (6%)

Query: 72  GPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVSF 130
           G      + +L + G  KN + E + +   +   Y  +  +G  H   F   VE+ G  F
Sbjct: 2   GHHHHHHSHMLTKHG--KNPVMELNEKR--RGLKYELISETGGSHDKRFVMEVEVDGQKF 57

Query: 131 TGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSS 164
            G     KK A+  AALAA   L      A  ++
Sbjct: 58  QGA-GSNKKVAKAYAALAALEKLFPDTPLALDAN 90

>2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene regulation, NUCL protein, gene regulation,nuclear protein; NMR {Homo sapiens} Length = 85

 Score = 58.1 bits (141), Expect = 4e-11
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 8/74 (10%)

Query: 88  YKNLLQETSHRAGLK-----LPVYTTV-RSGPGHGPVFSCTVELAG-VSFTGEPAKTKKQ 140
            K+ LQ+       +     +P+Y T+   GP H   ++  V   G     G+   + +Q
Sbjct: 3   PKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGK-GPSIQQ 61

Query: 141 AQKNAALAAWSALK 154
           A+  AA+ A     
Sbjct: 62  AEMGAAMDALEKYN 75

>2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene regulation, NUCL protein, gene regulation,nuclear protein; NMR {Homo sapiens} Length = 85

 Score = 58.1 bits (141), Expect = 5e-11
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 2  YKNQLQELA-----QRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQ 55
           K+QLQ+       +    ++P Y  ++  GP HA  +  AV F GE         +++Q
Sbjct: 3  PKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGK-GPSIQQ 61

Query: 56 AEHAAAEVALDVLS 69
          AE  AA  AL+  +
Sbjct: 62 AEMGAAMDALEKYN 75

>3p1x_A Interleukin enhancer-binding factor 3; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 1.90A {Homo sapiens} Length = 75

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 8/73 (10%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
             +L E  +        Y  I E G  H  RF   V  +G+ F+     S  + A+  A
Sbjct: 9  PVMELNEKRRG-----LKYELISETGGSHDKRFVMEVEVDGQKFQG--AGSNKKVAKAYA 61

Query: 61 AEVALDVLSKKGP 73
          A  AL+ L    P
Sbjct: 62 ALAALEKLFPDTP 74

>3p1x_A Interleukin enhancer-binding factor 3; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 1.90A {Homo sapiens} Length = 75

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 24/71 (33%), Positives = 28/71 (39%), Gaps = 7/71 (9%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
               L E   R GLK   Y  +  +G  H   F   VE+ G  F G     KK A+  AA
Sbjct: 9   PVMELNEK--RRGLK---YELISETGGSHDKRFVMEVEVDGQKFQGA-GSNKKVAKAYAA 62

Query: 147 LAAWSALKKQA 157
           LAA   L    
Sbjct: 63  LAALEKLFPDT 73

>2dmy_A Spermatid perinuclear RNA-binding protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 97

 Score = 57.1 bits (138), Expect = 2e-10
 Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 5/99 (5%)

Query: 72  GPSKVLAARVLDETGV-YKNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVS 129
           G S     ++LD   +   N L   +         Y  +  SGP H PVF+ +V++ G +
Sbjct: 1   GSSGSSGRKILDSKAIDLMNALMRLNQIR--PGLQYKLLSQSGPVHAPVFTMSVDVDGTT 58

Query: 130 FTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSP 168
           +      +KK A+ + A+    A+          S  S 
Sbjct: 59  YEAS-GPSKKTAKLHVAVKVLQAMGYPTGFDADISGPSS 96

>2dmy_A Spermatid perinuclear RNA-binding protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 97

 Score = 56.0 bits (135), Expect = 4e-10
 Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 5/68 (7%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
            N L  L Q        Y  + + GP HAP F  +V+ +G T+E+     + + A+   
Sbjct: 18 LMNALMRLNQIR--PGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEA--SGPSKKTAKLHV 73

Query: 61 AEVALDVL 68
          A   L  +
Sbjct: 74 AVKVLQAM 81

>2b7v_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 PDB: 2l2k_B Length = 71

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 7/69 (10%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
              +L E   R GLK   Y  +  SG  H   F  +V + G  F G   + KK A+  AA
Sbjct: 6   PVMILNEL--RPGLK---YDFLSESGESHAKSFVMSVVVDGQFFEGS-GRNKKLAKARAA 59

Query: 147 LAAWSALKK 155
            +A + +  
Sbjct: 60  QSALATVFN 68

>2b7v_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 PDB: 2l2k_B Length = 71

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 18/68 (26%), Positives = 26/68 (38%), Gaps = 8/68 (11%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
              L EL          Y  + E G  HA  F  +V  +G+ FE        + A+  A
Sbjct: 6  PVMILNELRPG-----LKYDFLSESGESHAKSFVMSVVVDGQFFEG--SGRNKKLAKARA 58

Query: 61 AEVALDVL 68
          A+ AL  +
Sbjct: 59 AQSALATV 66

>2b7t_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 PDB: 2l3c_A Length = 73

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 5/69 (7%)

Query: 3  KNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
          KN L +L +        Y  + + GP HAP F  +V  NG+ FE      T ++A+  AA
Sbjct: 7  KNALMQLNEI--KPGLQYMLLSQTGPVHAPLFVMSVEVNGQVFEG--SGPTKKKAKLHAA 62

Query: 62 EVALDVLSK 70
          E AL    +
Sbjct: 63 EKALRSFVQ 71

>2b7t_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 PDB: 2l3c_A Length = 73

 Score = 54.6 bits (132), Expect = 7e-10
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 102 KLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK 155
               Y  + ++GP H P+F  +VE+ G  F G    TKK+A+ +AA  A  +  +
Sbjct: 18  PGLQYMLLSQTGPVHAPLFVMSVEVNGQVFEGS-GPTKKKAKLHAAEKALRSFVQ 71

>2ljh_A Double-stranded RNA-specific editase ADAR; DSRBD, DSRBM, editing, hydrolase; NMR {Drosophila melanogaster} Length = 114

 Score = 56.1 bits (135), Expect = 6e-10
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 5/70 (7%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
            KN +  L +    +   Y    + GP HAP F  +V  +G+ +       + + A   A
Sbjct: 36  PKNTVAMLNELR--HGLIYKLESQTGPVHAPLFTISVEVDGQKYLG--QGRSKKVARIEA 91

Query: 61  AEVALDVLSK 70
           A  AL    +
Sbjct: 92  AATALRSFIQ 101

>2ljh_A Double-stranded RNA-specific editase ADAR; DSRBD, DSRBM, editing, hydrolase; NMR {Drosophila melanogaster} Length = 114

 Score = 55.7 bits (134), Expect = 7e-10
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
            KN +   +        +Y    ++GP H P+F+ +VE+ G  + G+  ++KK A+  AA
Sbjct: 36  PKNTVAMLNELR--HGLIYKLESQTGPVHAPLFTISVEVDGQKYLGQ-GRSKKVARIEAA 92

Query: 147 LAAWSALKKQAKSAFSSS 164
             A  +  +    A  S 
Sbjct: 93  ATALRSFIQFKDGAVLSP 110

>3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding, endonuclease, HEL hydrolase, nucleotide-binding, phosphoprotein, RN binding; HET: MSE; 1.68A {Mus musculus} PDB: 3c4t_A 2eb1_A Length = 265

 Score = 57.8 bits (140), Expect = 2e-09
 Identities = 13/72 (18%), Positives = 26/72 (36%), Gaps = 6/72 (8%)

Query: 1   MYKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHA 59
           + ++ ++EL +      P  +        +  + +  V   G+         + R A+ A
Sbjct: 198 VPRSPVRELLEM----EPETAKFSPAERTYDGKVRVTVEVVGKGKFKGV-GRSYRIAKSA 252

Query: 60  AAEVALDVLSKK 71
           AA  AL  L   
Sbjct: 253 AARRALRSLKAN 264

>3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding, endonuclease, HEL hydrolase, nucleotide-binding, phosphoprotein, RN binding; HET: MSE; 1.68A {Mus musculus} PDB: 3c4t_A 2eb1_A Length = 265

 Score = 55.5 bits (134), Expect = 9e-09
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 7/71 (9%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAG-VSFTGEPAKTKKQAQKNA 145
            ++ ++E         P       +   +      TVE+ G   F G   ++ + A+  A
Sbjct: 199 PRSPVRELLE----MEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGV-GRSYRIAKSAA 253

Query: 146 ALAAWSALKKQ 156
           A  A  +LK  
Sbjct: 254 ARRALRSLKAN 264

>3rv0_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 2.29A {Vanderwaltozyma polyspora} Length = 341

 Score = 54.8 bits (132), Expect = 3e-08
 Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 5/74 (6%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSF-TGEPAKTKKQAQKNAA 146
            KN L E      L   ++          P F   V++  +     E   + ++A+  AA
Sbjct: 256 AKNELAELLQINKLGHKLHYRK---LTEMPPFRVEVKIGDILLDEAE-GNSIREAEHRAA 311

Query: 147 LAAWSALKKQAKSA 160
           +      +   K +
Sbjct: 312 MKVLENDELLRKYS 325

>3rv0_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 2.29A {Vanderwaltozyma polyspora} Length = 341

 Score = 48.6 bits (116), Expect = 3e-06
 Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
            KN+L EL Q +      +          P F+  V       +     +++R+AEH AA
Sbjct: 256 AKNELAELLQINKLGHKLHY---RKLTEMPPFRVEVKIGDILLDEAE-GNSIREAEHRAA 311

Query: 62  EVALD---VLSKKGPSKV 76
              L+   +L K     +
Sbjct: 312 MKVLENDELLRKYSVYDL 329

>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus} Length = 236

 Score = 52.2 bits (124), Expect = 1e-07
 Identities = 28/141 (19%), Positives = 47/141 (33%), Gaps = 3/141 (2%)

Query: 102 KLPVYTTVR-SGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSA 160
               Y  +  +GP H P+F  +VE+ G  F G    TKK+A+ +AA  A  +  +   ++
Sbjct: 18  PGLQYMLLSQTGPVHAPLFVMSVEVNGQVFEGS-GPTKKKAKLHAAEKALRSFVQFPNAS 76

Query: 161 FSSSSFSPPSSESGTNDEQDQAIIARYLATLKGPETNNSQREHRTIGVSASIRREVIPYG 220
             +      +    T+   DQA     L         +    +       S         
Sbjct: 77  -EAHLAMGRTLSVNTDFTSDQADFPDTLFNGFETPDKSEPPFYVGSNGDDSFSSSGDVSL 135

Query: 221 DARSLNSLQHQNWHCIPFYPE 241
            A  + +   Q    IP    
Sbjct: 136 SASPVPASLTQPPLPIPPPFP 156

>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus} Length = 236

 Score = 51.1 bits (121), Expect = 2e-07
 Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 104 PVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK 155
             Y  +  SG  H   F  +V + G  F G   + KK A+  AA +A + +  
Sbjct: 174 LKYDFLSESGESHAKSFVMSVVVDGQFFEGS-GRNKKLAKARAAQSALATVFN 225

>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus} Length = 236

 Score = 44.9 bits (105), Expect = 2e-05
 Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 3/57 (5%)

Query: 15  FNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK 70
                Y  + E G  HA  F  +V  +G+ FE        + A+  AA+ AL  +  
Sbjct: 171 RPGLKYDFLSESGESHAKSFVMSVVVDGQFFEG--SGRNKKLAKARAAQSALATVFN 225

>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus} Length = 236

 Score = 44.5 bits (104), Expect = 3e-05
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 3  KNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
          KN L +L +        Y  + + GP HAP F  +V  NG+ FE      T ++A+  AA
Sbjct: 7  KNALMQLNEI--KPGLQYMLLSQTGPVHAPLFVMSVEVNGQVFEG--SGPTKKKAKLHAA 62

Query: 62 EVALDVLSKKGPS 74
          E AL    +   +
Sbjct: 63 EKALRSFVQFPNA 75

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.5 bits (112), Expect = 1e-05
 Identities = 71/543 (13%), Positives = 139/543 (25%), Gaps = 167/543 (30%)

Query: 2   YK---NQLQELAQRSCFNLPSYSCIRE---------GPDHAPRFKAAVNFNGETFESPTF 49
           YK   + ++   ++       Y   R+            +  R +  +            
Sbjct: 91  YKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLR--------- 141

Query: 50  CSTLRQAEHAAAEVALDVLSKKGPSK-VLAARVLDETGVYKNLLQETSHRAGLKLPVYTT 108
              L +   A   V +D     G  K  +A  V              S++   K+     
Sbjct: 142 -QALLELRPAKN-VLID--GVLGSGKTWVALDVCL------------SYKVQCKMD---- 181

Query: 109 VRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFSSSSFSP 168
                    +F   +              K        L     L  Q    ++S S   
Sbjct: 182 -------FKIFWLNL--------------KNCNSPETVLEMLQKLLYQIDPNWTSRSDHS 220

Query: 169 PSSESGTNDEQDQAIIARYLATLKGPET-----NNSQREH--------------RTIGVS 209
            + +   +  Q +  + R L +           N    +               R   V+
Sbjct: 221 SNIKLRIHSIQAE--LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVT 278

Query: 210 ASIRREVIPYGDARSLNSLQHQNWHCIPFYPELSLYQTCPQERVFRQQENLLA--LSSLP 267
             +           +  SL H +       P+                 +LL   L   P
Sbjct: 279 DFLS------AATTTHISLDHHSM---TLTPDEVK--------------SLLLKYLDCRP 315

Query: 268 SSSPR--PQIFPFIRSMF------QPDHGYYFPSLVEEPVS---------LVPEIGPFLY 310
              PR      P   S+              +  +  + ++         L P     ++
Sbjct: 316 QDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMF 375

Query: 311 FSNRVMP----VPVRNVSQVSIQEIEENPR--MEEDWRKGDGGSDCWQNNCPSNVPRLSQ 364
               V P    +P   +S +    I+ +    + +  +     S   +    S       
Sbjct: 376 DRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY----SLVEKQPKES------T 425

Query: 365 SEIPNSLVSFNSQSE------QRMQEGLQGKGEEKSVSSAPNAE-------ISNQLRN-- 409
             IP+  +    + E      + + +         S    P          I + L+N  
Sbjct: 426 ISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIE 485

Query: 410 QTEQYNWFSPGFIDARFRPTTISKDGDKFRLQNTVSLDYLQ---------SDSRPRNSTM 460
             E+   F   F+D RF    I  D   +    ++ L+ LQ          D+ P+   +
Sbjct: 486 HPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSI-LNTLQQLKFYKPYICDNDPKYERL 544

Query: 461 VSS 463
           V++
Sbjct: 545 VNA 547

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 2e-04
 Identities = 30/259 (11%), Positives = 72/259 (27%), Gaps = 73/259 (28%)

Query: 225 LNSLQHQNWHCIP-----FYPELSLYQTCPQER-VFRQQE--NLLALSSLPS-------- 268
               Q+Q    +      F             + +  ++E  +++      S        
Sbjct: 11  TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWT 70

Query: 269 --SSPRPQIFPFIRSMFQPDHGYYFPSLVEEPVSLVPEIGPFLYFSNRVMPVPVRNVSQV 326
             S     +  F+  + + ++ +    +  E     P +   +Y   R     + N +QV
Sbjct: 71  LLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQ--PSMMTRMYIEQR---DRLYNDNQV 125

Query: 327 SIQEIEENPRMEEDWRKGDGGSDCWQNNCPSNVPRLSQ-SEIPNSLVSFNSQSEQRMQ-E 384
                                          NV RL    ++  +L     +  + +  +
Sbjct: 126 FA---------------------------KYNVSRLQPYLKLRQAL--LELRPAKNVLID 156

Query: 385 GLQGKGEEKSVSSAPNAEISNQLRNQTEQYN---WFSPGFIDARFRPTTISKDGDKFRLQ 441
           G+ G G  K+  +    ++    + Q +      W +    +    P T+ +      LQ
Sbjct: 157 GVLGSG--KTWVA---LDVCLSYKVQCKMDFKIFWLNLKNCN---SPETVLE-----MLQ 203

Query: 442 N---TVSLDYLQSDSRPRN 457
                +  ++        N
Sbjct: 204 KLLYQIDPNWTSRSDHSSN 222

>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A Length = 756

 Score = 47.6 bits (113), Expect = 1e-05
 Identities = 24/180 (13%), Positives = 40/180 (22%), Gaps = 47/180 (26%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
              +  +           +  + +   +       +   +    E         +   A 
Sbjct: 449 AVTKASKRVCMGEAGAHEFRSLVDYACEQGISVFCSSRVSTMFLER-------LRDIPAE 501

Query: 61  AEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFS 120
             +    L  +                        SHR+GL  P         G   V  
Sbjct: 502 DMLDWYRLGIQ-----------------------FSHRSGLSGP--------GGVVSVID 530

Query: 121 CTVELAGVSFTGEPA-KTKKQAQKN--AALAAWSALKKQAKSAFSSSSFSPPSSESGTND 177
               LA   + G P    ++Q  KN  A       L       +  S   P    S T  
Sbjct: 531 IMTHLARGLWLGSPGFYVEQQTDKNESACPPTIPVL-----YIYHRSVQCPVLYGSLTET 585

>1x48_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1 Length = 88

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 1/85 (1%)

Query: 83  DETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQ 142
             +  Y  L+   + +  L +  Y            F C  ++    +      TK++A+
Sbjct: 3   SGSSGYIGLVNSFAQKKKLSVN-YEQCEPNSELPQRFICKCKIGQTMYGTGSGVTKQEAK 61

Query: 143 KNAALAAWSALKKQAKSAFSSSSFS 167
           + AA  A+  L K       +S  S
Sbjct: 62  QLAAKEAYQKLLKSPPKTAGTSGPS 86

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	575
1qu6_A	179	Protein kinase PKR; dsRNA-binding domain, solution	99.96
2yt4_A	232	Protein DGCR8; DSRBD, RNA binding domain, RNA bind	99.93
2l3j_A	236	Double-stranded RNA-specific editase 1; editing, d	99.9
3adg_A	73	F21M12.9 protein; HYL1, miRNA processing mechanism	99.78
3adj_A	76	F21M12.9 protein; HYL1, miRNA processing, RNA bind	99.77
3adl_A	88	RISC-loading complex subunit tarbp2; TRBP2, miRNA	99.75
1di2_A	69	XLRBPA, double stranded RNA binding protein A; pro	99.75
2cpn_A	89	TAR RNA-binding protein 2; double-stranded RNA bin	99.74
1uhz_A	89	Staufen (RNA binding protein) homolog 2; DSRM, sta	99.73
2dix_A	84	Interferon-inducible double stranded RNA- dependen	99.73
1ekz_A	76	DSRBDIII, maternal effect protein (staufen); struc	99.72
2khx_A	85	Ribonuclease 3; drosha, RNA binding domain, hydrol	99.72
1x49_A	97	Interferon-induced, double-stranded RNA- activated	99.72
2l2n_A	103	Hyponastic leave 1; DSRBD, miRNA, RNA binding prot	99.72
2b7t_A	73	Double-stranded RNA-specific editase 1; RNA editin	99.71
1whq_A	99	RNA helicase A; double-stranded RNA binding domain	99.71
1x48_A	88	Interferon-induced, double-stranded RNA- activated	99.7
3llh_A	90	RISC-loading complex subunit tarbp2; DSRBD, DSRM,	99.7
2nug_A	221	Ribonuclease III, RNAse III; dsRNA, RNA interferen	99.7
1x47_A	98	DGCR8 protein; structural genomics, DSRM domain, N	99.68
1uil_A	113	Double-stranded RNA-binding motif; structural geno	99.68
3n3w_A	248	Ribonuclease III; nuclease domain, ribonuclase III	99.66
1t4n_A	94	Ribonuclease III; DSRBD, RNA-binding, hydrolase; N	99.66
2dmy_A	97	Spermatid perinuclear RNA-binding protein; DSRM do	99.66
1o0w_A	252	Ribonuclease III, RNAse III; TM1102, structural ge	99.65
1t4o_A	117	Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydro	99.63
2l33_A	91	Interleukin enhancer-binding factor 3; structural	99.63
1whn_A	128	Hypothetical protein riken cDNA 2310016K04; double	99.62
2ljh_A	114	Double-stranded RNA-specific editase ADAR; DSRBD,	99.59
2a11_A	242	Ribonuclease III, RNAse III; nuclease domain, stru	99.58
1di2_A	69	XLRBPA, double stranded RNA binding protein A; pro	99.57
2b7v_A	71	Double-stranded RNA-specific editase 1; RNA editin	99.56
3adg_A	73	F21M12.9 protein; HYL1, miRNA processing mechanism	99.55
1qu6_A	179	Protein kinase PKR; dsRNA-binding domain, solution	99.55
3adj_A	76	F21M12.9 protein; HYL1, miRNA processing, RNA bind	99.53
3p1x_A	75	Interleukin enhancer-binding factor 3; structural	99.49
2l2n_A	103	Hyponastic leave 1; DSRBD, miRNA, RNA binding prot	99.46
3adl_A	88	RISC-loading complex subunit tarbp2; TRBP2, miRNA	99.46
2cpn_A	89	TAR RNA-binding protein 2; double-stranded RNA bin	99.46
1uhz_A	89	Staufen (RNA binding protein) homolog 2; DSRM, sta	99.45
2khx_A	85	Ribonuclease 3; drosha, RNA binding domain, hydrol	99.43
2yt4_A	232	Protein DGCR8; DSRBD, RNA binding domain, RNA bind	99.43
3rv0_A	341	K. polysporus DCR1; RNAse III enzyme, RNA binding	99.42
2dix_A	84	Interferon-inducible double stranded RNA- dependen	99.42
1ekz_A	76	DSRBDIII, maternal effect protein (staufen); struc	99.41
1x49_A	97	Interferon-induced, double-stranded RNA- activated	99.39
2b7t_A	73	Double-stranded RNA-specific editase 1; RNA editin	99.39
3llh_A	90	RISC-loading complex subunit tarbp2; DSRBD, DSRM,	99.36
1whq_A	99	RNA helicase A; double-stranded RNA binding domain	99.36
1x48_A	88	Interferon-induced, double-stranded RNA- activated	99.34
1uil_A	113	Double-stranded RNA-binding motif; structural geno	99.33
2l33_A	91	Interleukin enhancer-binding factor 3; structural	99.32
2dmy_A	97	Spermatid perinuclear RNA-binding protein; DSRM do	99.31
1t4n_A	94	Ribonuclease III; DSRBD, RNA-binding, hydrolase; N	99.3
1x47_A	98	DGCR8 protein; structural genomics, DSRM domain, N	99.29
1whn_A	128	Hypothetical protein riken cDNA 2310016K04; double	99.27
1t4o_A	117	Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydro	99.25
2l3j_A	236	Double-stranded RNA-specific editase 1; editing, d	99.21
2ljh_A	114	Double-stranded RNA-specific editase ADAR; DSRBD,	99.15
2b7v_A	71	Double-stranded RNA-specific editase 1; RNA editin	99.1
3p1x_A	75	Interleukin enhancer-binding factor 3; structural	99.08
3c4b_A	265	Endoribonuclease dicer; RNAse, dsRNA binding prote	99.08
2nug_A	221	Ribonuclease III, RNAse III; dsRNA, RNA interferen	99.02
1o0w_A	252	Ribonuclease III, RNAse III; TM1102, structural ge	99.02
2a11_A	242	Ribonuclease III, RNAse III; nuclease domain, stru	98.85
3n3w_A	248	Ribonuclease III; nuclease domain, ribonuclase III	98.85
3rv0_A	341	K. polysporus DCR1; RNAse III enzyme, RNA binding	98.15
3c4b_A	265	Endoribonuclease dicer; RNAse, dsRNA binding prote	97.5
2qvw_A	756	GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral	96.24
2kou_A	102	Dicer-like protein 4; ATP-binding, endonuclease, h	95.39
3htx_A	950	HEN1; HEN1, small RNA methyltransferase, protein-R	89.3
2db2_A	119	KIAA0890 protein; DSRM domain, structural genomics	88.08

>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1

Probab=99.96  E-value=2.5e-29  Score=237.90  Aligned_cols=154  Identities=21%  Similarity=0.303  Sum_probs=133.2

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhh-
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLA-   78 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~-   78 (575)
                      .||+.||||||++++. |.|.++ ..||+|.+.|++.|.|+|..++. |.|.+||.|++.||+.+|..|.......... 
T Consensus        14 n~ks~LqE~~q~~~~~-p~Y~~~~~~Gp~h~~~F~~~v~v~g~~~~~-G~G~sKK~Aeq~AA~~al~~L~~~~~~~~p~~   91 (179)
T 1qu6_A           14 FFMEELNTYRQKQGVV-LKYQELPNSGPPHDRRFTFQVIIDGREFPE-GEGRSKKEAKNAAAKLAVEILNKEKKAVSPLL   91 (179)
T ss_dssp             SHHHHHHHHHHHHTCC-CEEEEEESCBTTTBCCEEEEEESSSSCCCE-EECCSSHHHHHHHHHHHHHHHHSCCSCCSCSS
T ss_pred             CHHHHHHHHHHhCCCC-CeEEEeeccCCCCCCeEEEEEEECCEEEEe-cCCCCHHHHHHHHHHHHHHHHhcccccCCCcc
Confidence            3899999999999987 899988 68999999999999999988866 5899999999999999999998654211100 


Q ss_pred             ----hhc-ccccCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHH
Q 041141           79 ----ARV-LDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSAL  153 (575)
Q Consensus        79 ----~~i-~de~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L  153 (575)
                          ... .....|||++|+||||++++.+ .|++.+.|++|.+.|+|+|.|+|..|+.|.|.|||+||++||+.||..|
T Consensus        92 ~~~~~~~e~~~~~n~~~~L~E~~qk~~~~~-~Y~~~~~G~~h~~~F~~~v~v~~~~~~~g~g~sKK~Ak~~AA~~al~~L  170 (179)
T 1qu6_A           92 LTTTNSSEGLSMGNYIGLINRIAQKKRLTV-NYEQCASGVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQI  170 (179)
T ss_dssp             CCCSCSSCCCCCCCCHHHHHHHHHHSCCEE-EEEEEEECSSSSSEEEEEEEEETTBCCEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcccccCCCCHHHHHHHHHHhcCCcc-eEEecCcCCCCCCeEEEEEEECCEEEeeEEECCHHHHHHHHHHHHHHHH
Confidence                000 1135699999999999999987 8998899999999999999999999899999999999999999999999


Q ss_pred             Hhhh
Q 041141          154 KKQA  157 (575)
Q Consensus       154 ~~~~  157 (575)
                      ....
T Consensus       171 ~~~~  174 (179)
T 1qu6_A          171 LSEE  174 (179)
T ss_dssp             HHCC
T ss_pred             hccc
Confidence            8764

>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein; 2.60A {Homo sapiens}

Probab=99.93  E-value=2.2e-25  Score=219.67  Aligned_cols=149  Identities=18%  Similarity=0.125  Sum_probs=119.8

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCC-hhh-
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPS-KVL-   77 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps-~~~-   77 (575)
                      .||+.||||||++++.+|.|.++ ..|++  +.|++.|.|+|..++. |.|.+||.|++.||+.||..|....+. ... 
T Consensus        23 d~ks~LqE~~q~~~~~~p~Y~~~~~~Gp~--~~F~~~v~v~g~~~~~-G~G~SKK~Aeq~AA~~aL~~L~~~~~~~~~~~   99 (232)
T 2yt4_A           23 SEVCILHEYMQRVLKVRPVYNFFECENPS--EPFGASVTIDGVTYGS-GTASSKKLAKNKAARATLEILIPDFVKQTSEE   99 (232)
T ss_dssp             CHHHHHHHHHHHTTCCCCEEEEEECSCTT--SCEEEEEEETTEEEEE-EEESSHHHHHHHHHHHHHHHHSTTTTTC----
T ss_pred             CHHHHHHHHHHHcCCCCCeEEEEeeECCC--CcEEEEEEECCEEEee-cCCCCHHHHHHHHHHHHHHHHHhhccccCCcc
Confidence            38999999999999999999998 67887  9999999999998877 489999999999999999999774321 000 


Q ss_pred             ----------hhh------------cccccCchhhHHHHHHHHcCCCCCeEE--Ee-ecCCCCCCeEEEEEEECCEeeee
Q 041141           78 ----------AAR------------VLDETGVYKNLLQETSHRAGLKLPVYT--TV-RSGPGHGPVFSCTVELAGVSFTG  132 (575)
Q Consensus        78 ----------~~~------------i~de~~nyKS~LQE~cQK~gl~lP~Ye--v~-esGP~H~p~Ftv~V~V~G~~fg~  132 (575)
                                .+.            ......|||+.||| ||++++.+|.|+  ++ +.||+|.+.|+|+|.  +. ++.
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~kt~LqE-~~~~~~~~p~Y~~~~~~~~Gp~h~~~F~~~v~--~~-~~~  175 (232)
T 2yt4_A          100 KPKDSEELEYFNHISIEDSRVYELTSKAGLLSPYQILHE-CLKRNHGMGDTSIKFEVVPGKNQKSEYVMACG--KH-TVR  175 (232)
T ss_dssp             ----CCGGGGGGGSBTTCTTHHHHHHHHTCCCHHHHHHH-HHHTSSSCCCEEEECC------CCEEEEEEET--TE-EEE
T ss_pred             ccccccchhhcccccccCCcccccccccCCCChhHHHHH-HHHcCCCCCceEEEEeecCCCCCCCEEEEEEE--EE-EEE
Confidence                      000            01124599999999 999999999999  55 789999999999886  44 567


Q ss_pred             cccCCHHHHHHHHHHHHHHHHHhh
Q 041141          133 EPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus       133 G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      |.|.|||+|||+||+.||..|...
T Consensus       176 G~G~sKK~Aeq~AA~~aL~~L~~~  199 (232)
T 2yt4_A          176 GWCKNKRVGKQLASQKILQLLHPH  199 (232)
T ss_dssp             EEESSHHHHHHHHHHHHHHHHSTT
T ss_pred             EEeCCHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999753

>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus}

Probab=99.90  E-value=6e-23  Score=202.56  Aligned_cols=146  Identities=27%  Similarity=0.280  Sum_probs=121.3

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCC------
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGP------   73 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~p------   73 (575)
                      .+|+.|++|++.  +.+|.|+++ ..|++|.+.|++.|.|+|..++  |.|.+||.|++.||+.||..|.....      
T Consensus         5 ~~K~~l~~l~e~--~~~p~Y~~~~~~Gp~H~~~F~~~v~v~g~~~~--G~G~SKK~Aeq~AA~~al~~l~~~~~~~~~~~   80 (236)
T 2l3j_A            5 LPKNALMQLNEI--KPGLQYMLLSQTGPVHAPLFVMSVEVNGQVFE--GSGPTKKKAKLHAAEKALRSFVQFPNASEAHL   80 (236)
T ss_dssp             CTHHHHHHHHHH--CSSCEEEEEEEESCTTSCEEEEEEEETTEEEE--EEESHHHHHHHHHHHHHHHHHTTCSSCSCCCC
T ss_pred             CCcCHHHHHhhc--CCCceEEEEeccCCCCCCeEEEEEEECCEEEE--EecCChHHHHHHHHHHHHHHHHhccccccchh
Confidence            489999999987  467899998 6899999999999999998863  58999999999999999999875310      


Q ss_pred             ------------Chhhh----------------h-------------------hc----------c-----------ccc
Q 041141           74 ------------SKVLA----------------A-------------------RV----------L-----------DET   85 (575)
Q Consensus        74 ------------s~~~~----------------~-------------------~i----------~-----------de~   85 (575)
                                  ..+..                .                   .+          .           ...
T Consensus        81 amg~~~~~~~d~~~d~~~~p~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~p~~~~~~~~~~  160 (236)
T 2l3j_A           81 AMGRTLSVNTDFTSDQADFPDTLFNGFETPDKSEPPFYVGSNGDDSFSSSGDVSLSASPVPASLTQPPLPIPPPFPPPSG  160 (236)
T ss_dssp             SCCCCCCCTTSCCSCCSCCCCCCCCCCCCSSSSCCCSSCSSSCSSSSSCSCCCSSCCCCCCCCSSSCSSSSCCCCCCCSS
T ss_pred             hhccCCCCCCCCcccccccchhhcccccccccccccccccccccccccccchhhccccccccccccccCccccccCCCCC
Confidence                        00000                0                   00          0           023


Q ss_pred             CchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           86 GVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        86 ~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      .|||++||||     +..|.|+++ +.||+|.+.|+|+|.|+|+.+ .|.|+|||+|||+||+.||..|...
T Consensus       161 ~d~ks~LqE~-----~~~p~Y~~~~~~Gp~h~~~F~~~v~v~~~~~-~G~G~sKK~Aeq~AA~~al~~L~~~  226 (236)
T 2l3j_A          161 KNPVMILNEL-----RPGLKYDFLSESGESHAKSFVMSVVVDGQFF-EGSGRNKKLAKARAAQSALATVFNL  226 (236)
T ss_dssp             CCHHHHHHHH-----CCCEEEEEECCSSSSSSCCEEEEEEETTEEE-EEEESSHHHHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHhc-----CCCCcEEEEEeeCCCCCCeEEEEEEECCEEE-EeeeCCHHHHHHHHHHHHHHHHccc
Confidence            5999999999     568999988 789999999999999999986 7999999999999999999999643

>3adg_A F21M12.9 protein; HYL1, miRNA processing mechanism, RNA binding protein, gene regulation; 1.70A {Arabidopsis thaliana} PDB: 3adi_A

Probab=99.78  E-value=7.6e-19  Score=144.16  Aligned_cols=69  Identities=38%  Similarity=0.576  Sum_probs=66.2

Q ss_pred             CchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeeccc-CCHHHHHHHHHHHHHHHHH
Q 041141           86 GVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPA-KTKKQAQKNAALAAWSALK  154 (575)
Q Consensus        86 ~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G-~SKKeAEQ~AAk~ALe~L~  154 (575)
                      .|||+.||||||++++.+|.|+++.+||+|.+.|+|.|.|+|..++.|.| +|||+||++||+.||..|.
T Consensus         3 ~d~Kt~LqE~~q~~~~~~p~Y~~~~~Gp~h~~~F~~~v~v~g~~~~~G~G~~sKK~Aeq~AA~~al~~L~   72 (73)
T 3adg_A            3 HVFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQSAAEVALRELA   72 (73)
T ss_dssp             CSHHHHHHHHHHHTTCCCCEEEEEEESSTTSCEEEEEEEETTEEEECCSCBSSHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHcCCCCCEEEEEeECCCCCCeEEEEEEECCEEEEeeeccCCHHHHHHHHHHHHHHHhh
Confidence            59999999999999999999999966999999999999999999999999 9999999999999999985

>3adj_A F21M12.9 protein; HYL1, miRNA processing, RNA binding protein, gene regulation; 3.00A {Arabidopsis thaliana} PDB: 2l2m_A

Probab=99.77  E-value=7.8e-19  Score=145.45  Aligned_cols=70  Identities=36%  Similarity=0.609  Sum_probs=66.9

Q ss_pred             CchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           86 GVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        86 ~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      .|||+.||||||++++.+|.|+++ ++||+|.+.|+|.|.|+|..++.|.|+|||+|||+||+.||..|..
T Consensus         4 ~n~Kt~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~~~v~v~g~~~~~G~G~sKK~Aeq~AA~~al~~L~~   74 (76)
T 3adj_A            4 GLCKNLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTGAATRTKKDAEISAGRTALLAIQS   74 (76)
T ss_dssp             HHHHHHHHHHHHTTTCCCCEEEEEEEECSSSCEEEEEEEEETTEEEECCCBSSHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHhCCCCCeEEEeeccCCCCCCcEEEEEEECCEEEEEeccCCHHHHHHHHHHHHHHHHhh
Confidence            589999999999999999999998 7899999999999999999999999999999999999999999963

>3adl_A RISC-loading complex subunit tarbp2; TRBP2, miRNA processing, gene regulation-RNA complex; 2.20A {Homo sapiens}

Probab=99.75  E-value=2.6e-18  Score=146.82  Aligned_cols=72  Identities=28%  Similarity=0.338  Sum_probs=67.0

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      ..|||+.||||||++++.+|.|+++ ++||+|.+.|+|.|.|+|. ++.|.|+|||+|||+||+.||..|...+
T Consensus        14 ~~d~Ks~LqE~~Q~~~~~~P~Y~~~~~~Gp~H~~~F~~~v~v~g~-~~~G~G~SKK~Aeq~AA~~AL~~L~~~p   86 (88)
T 3adl_A           14 GSHEVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERF-IEIGSGTSKKLAKRNAAAKMLLRVHTVP   86 (88)
T ss_dssp             TCCHHHHHHHHHHHTTCCCCEEEEEEEESCTTSCEEEEEEEETTE-EEEEEESSHHHHHHHHHHHHHHHHHC--
T ss_pred             CCCHHHHHHHHHHHcCCCCCEEEEEEeECCCCCCeEEEEEEECCE-EEEEeeCCHHHHHHHHHHHHHHHHHccC
Confidence            4699999999999999999999998 7899999999999999998 8999999999999999999999998654

>1di2_A XLRBPA, double stranded RNA binding protein A; protein-RNA complex, protein-RNA interactions, RNA-bining protein; 1.90A {Xenopus laevis} SCOP: d.50.1.1

Probab=99.75  E-value=2.3e-18  Score=139.70  Aligned_cols=66  Identities=29%  Similarity=0.375  Sum_probs=63.7

Q ss_pred             hhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHH
Q 041141           88 YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALK  154 (575)
Q Consensus        88 yKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~  154 (575)
                      ||+.||||||++++.+|.|+++ ++||+|++.|+|.|.|+|. ++.|.|+|||+|||+||+.||..|.
T Consensus         2 p~s~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~~~v~v~~~-~~~G~G~sKK~Aeq~AA~~al~~L~   68 (69)
T 1di2_A            2 PVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETF-VETGSGTSKQVAKRVAAEKLLTKFK   68 (69)
T ss_dssp             HHHHHHHHHHHHTCCCCEEEEEEEESCGGGCEEEEEEEETTE-EEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCCCEEEEEEeECCCCCCeEEEEEEECCE-EEEeecCCHHHHHHHHHHHHHHHHh
Confidence            7999999999999999999997 7899999999999999998 9999999999999999999999986

>2cpn_A TAR RNA-binding protein 2; double-stranded RNA binding domain, DSRBD, DSRM., structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.50.1.1

Probab=99.74  E-value=6e-18  Score=144.78  Aligned_cols=70  Identities=29%  Similarity=0.336  Sum_probs=66.6

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      ..|||++||||||++++.+|.|+++ +.||+|.+.|+|+|.|+|. ++.|.|+|||+|||+||+.||..|.+
T Consensus        15 ~~d~Kt~LqE~~Qk~~~~~P~Y~~~~~~Gp~h~~~F~~~v~i~g~-~~~G~G~SKK~Aeq~AA~~AL~~L~~   85 (89)
T 2cpn_A           15 ECNPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERF-IEIGSGTSKKLAKRNAAAKMLLRVSG   85 (89)
T ss_dssp             CCCHHHHHHHHHHHHTCCCCEEEEEEEECCSSSCEEEEEEEETTE-EEEEEESSHHHHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHHcCCCCCeEEEEeeECCCCCCeEEEEEEECCE-EEEeeeCCHHHHHHHHHHHHHHHHHh
Confidence            4699999999999999999999997 7899999999999999998 89999999999999999999999963

>1uhz_A Staufen (RNA binding protein) homolog 2; DSRM, staufen homolog 2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1

Probab=99.73  E-value=8.9e-18  Score=143.69  Aligned_cols=70  Identities=23%  Similarity=0.156  Sum_probs=66.3

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      ..|||++||||||++++.+|.|+++ +.||+|.+.|+|.|.|+|. ++.|.|+|||+|||+||+.||+.|..
T Consensus         5 ~~d~Kt~LqE~~Q~~~~~~P~Y~~~~~~Gp~H~~~F~~~v~v~g~-~~~G~G~SKK~Aeq~AA~~AL~~L~~   75 (89)
T 1uhz_A            5 SSGPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNE-VATGTGPNKKIAKKNAAEAMLLQLGY   75 (89)
T ss_dssp             SSCHHHHHHHHHHHTTSCCCEEEEEEEESCSTTCEEEEEEEETTE-EEEEEESSHHHHHHHHHHHHHHHHTS
T ss_pred             CCCHHHHHHHHHHHhCCCCCeEEEEEeECCCCCCeEEEEEEECCE-EEEEeeCCHHHHHHHHHHHHHHHHhc
Confidence            4699999999999999999999997 7899999999999999997 88999999999999999999999964

>2dix_A Interferon-inducible double stranded RNA- dependent protein kinase activator A; structure genomics, DSRM domain, hypothetical protein PRKRA; NMR {Homo sapiens} SCOP: d.50.1.1

Probab=99.73  E-value=1.2e-17  Score=141.12  Aligned_cols=72  Identities=26%  Similarity=0.275  Sum_probs=66.4

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      ...|||+.||||||+++ ..|.|+++ +.||+|.+.|+|.|.|+| .++.|.|+|||+|||+||+.||+.|....
T Consensus         6 ~~~d~Ks~LqE~~q~~~-~~p~Y~~~~~~Gp~h~~~F~~~v~v~~-~~~~G~G~SKK~Aeq~AA~~aL~~L~~~~   78 (84)
T 2dix_A            6 SGKTPIQVLHEYGMKTK-NIPVYECERSDVQIHVPTFTFRVTVGD-ITCTGEGTSKKLAKHRAAEAAINILKANA   78 (84)
T ss_dssp             CCCCHHHHHHHHHHHTT-CCCEEEEEEEECSSSSCEEEEEEEETT-EEEEECSSCTTHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHHcC-CCCeEEEEEeECCCCCCeEEEEEEECC-EEEEeeeCCHHHHHHHHHHHHHHHHhccc
Confidence            34699999999999998 68999997 789999999999999999 88999999999999999999999997543

>1ekz_A DSRBDIII, maternal effect protein (staufen); structure, protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila melanogaster} SCOP: d.50.1.1 PDB: 1stu_A

Probab=99.72  E-value=2.4e-18  Score=142.15  Aligned_cols=69  Identities=19%  Similarity=0.210  Sum_probs=65.5

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      ..|||+.||||||++++. |.|+++ ++||+|.+.|+|+|.|+| .++.|.|+|||+|||+||+.||..|.+
T Consensus         6 ~~d~ks~LqE~~q~~~~~-p~Y~~~~~~Gp~h~~~F~~~v~i~~-~~~~G~G~sKK~Aeq~AA~~aL~~L~~   75 (76)
T 1ekz_A            6 KKSPISQVHEIGIKRNMT-VHFKVLREEGPAHMKNFITACIVGS-IVTEGEGNGKKVSKKRAAEKMLVELQK   75 (76)
T ss_dssp             CSCHHHHHHHHHHHTTCC-CEEEESSSCCSSSCSCSSEEEEETT-EEEEECCCSTTSSSHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHcCCC-CEEEEEEeECCCCCCcEEEEEEECC-EEEEEeeCCHHHHHHHHHHHHHHHHhh
Confidence            469999999999999999 999998 789999999999999999 889999999999999999999999965

>2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene regulation, NUCL protein, gene regulation,nuclear protein; NMR {Homo sapiens}

Probab=99.72  E-value=4.7e-18  Score=144.26  Aligned_cols=71  Identities=23%  Similarity=0.313  Sum_probs=65.3

Q ss_pred             CchhhHHHHHHHH-----cCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           86 GVYKNLLQETSHR-----AGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        86 ~nyKS~LQE~cQK-----~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      .|||+.||||||+     .++.+|.|+++ ++||+|.+.|+|.|.|+|..++.|.|+|||+|||+||+.||..|...
T Consensus         1 ~d~Kt~LQE~~Q~~~~~~~~~~~p~Y~~~~~~Gp~H~~~F~v~V~v~g~~~~~G~G~SKK~AEq~AA~~AL~~L~~~   77 (85)
T 2khx_A            1 NDPKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYNFP   77 (85)
T ss_dssp             CCSCHHHHHHHHHCCCSSSCCCCCCEEECCCCCSSSCCCEEEEEEETTEECCCEEESSHHHHHHHHHHHHHTTCCSS
T ss_pred             CCHHHHHHHHHhhhhhhcCCCCCceEEEEEeECCCCCCcEEEEEEECCEEEEEEeeCCHHHHHHHHHHHHHHHHhHh
Confidence            3899999999998     46789999998 78999999999999999999999999999999999999999887543

>1x49_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1

Probab=99.72  E-value=1.1e-17  Score=145.25  Aligned_cols=75  Identities=25%  Similarity=0.393  Sum_probs=68.5

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      ...|||++||||||++++. |.|+++ +.||+|.+.|+|.|.|+|..++.|.|+|||+|||+||+.||+.|......
T Consensus        12 ~~~n~Kt~LqE~~Q~~~~~-p~Y~~~~~~Gp~H~~~F~v~v~i~g~~~~~G~G~SKK~Aeq~AA~~AL~~L~~~~~~   87 (97)
T 1x49_A           12 TPGFYMDKLNKYRQMHGVA-ITYKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSKQEARNAAAKLAVDILDNENKV   87 (97)
T ss_dssp             CTTHHHHHHHHHHHHHTCC-EEEEEEEEESCSSSCEEEEEEEESSCCCCCEEESSHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             CCCCHHHHHHHHHHHcCCC-CeEEEEEeeCCCCCCcEEEEEEECCEEEEEEeeCCHHHHHHHHHHHHHHHHHhhcCC
Confidence            3569999999999999997 899987 78999999999999999999999999999999999999999999755433

>2l2n_A Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, plant protein; NMR {Arabidopsis thaliana}

Probab=99.72  E-value=1.8e-17  Score=145.21  Aligned_cols=74  Identities=36%  Similarity=0.548  Sum_probs=67.0

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeeccc-CCHHHHHHHHHHHHHHHHHhhh
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPA-KTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G-~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      ...|||+.||||||++++.+|.|+++..||+|.+.|+|.|.|+|..++.|.| +|||+|||+||+.||..|....
T Consensus        15 ~~~d~Kt~LqE~~Q~~~~~~P~Y~~~~~Gp~H~~~F~~~V~v~g~~~~~G~G~~SKK~Aeq~AA~~AL~~L~~~~   89 (103)
T 2l2n_A           15 NCYVFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQSAAEVALRELAKSS   89 (103)
T ss_dssp             ----CTTHHHHHHHHTTCCCCEEEEEEESCSSSCEEEEEEEETTEEEECCSCBSSHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHcCCCCCeEEEEeEcCCCCCeEEEEEEECCEEEEEeecCCCHHHHHHHHHHHHHHHHhccc
Confidence            3569999999999999999999999966999999999999999999999999 9999999999999999998654

>2b7t_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 PDB: 2l3c_A

Probab=99.71  E-value=1.8e-17  Score=136.13  Aligned_cols=68  Identities=29%  Similarity=0.353  Sum_probs=63.6

Q ss_pred             CchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           86 GVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        86 ~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      .|||+.||||||+  +..|.|+++ ++||+|++.|+|.|.|+|..+ .|.|+|||+|||+||+.||+.|..+
T Consensus         4 ~d~Ks~Lqe~~q~--~~~p~Y~~~~~~Gp~h~~~F~~~v~v~g~~~-~G~G~SKK~Aeq~AA~~al~~L~~~   72 (73)
T 2b7t_A            4 VLPKNALMQLNEI--KPGLQYMLLSQTGPVHAPLFVMSVEVNGQVF-EGSGPTKKKAKLHAAEKALRSFVQF   72 (73)
T ss_dssp             SSSHHHHHHHHHH--CSCCEEEEEEEECSSSSCEEEEEEESSSSEE-EEEESSHHHHHHHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHHcC--CCCceEEEEEeeCCCCCCeEEEEEEECCEEE-EeecCCHHHHHHHHHHHHHHHHhcC
Confidence            5899999999996  778999997 789999999999999999987 8999999999999999999999864

>1whq_A RNA helicase A; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Mus musculus} SCOP: d.50.1.1 PDB: 2rs6_A

Probab=99.71  E-value=3e-17  Score=143.18  Aligned_cols=77  Identities=23%  Similarity=0.203  Sum_probs=70.0

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECC-EeeeecccCCHHHHHHHHHHHHHHHHHhhhcccCC
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAG-VSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAFS  162 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G-~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~~~s  162 (575)
                      ..|||++||||||++ +..|.|++.+.||+|.+.|+|.|.|+| ..++.|.|+|||+|||+||+.||+.|........+
T Consensus         5 ~~d~Kt~LqE~~Qk~-~~~P~Y~~~~~Gp~H~~~F~~~V~v~g~~~~~~G~G~SKK~Aeq~AA~~AL~~L~~~~~~~~~   82 (99)
T 1whq_A            5 SSGIKNFLYAWCGKR-KMTPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAARDFVNYLVRINEVKSE   82 (99)
T ss_dssp             CCSSHHHHHHHHHHT-TCCCEEEEEEEECSSSEEEEEEEECTTCSCCEEEEESSHHHHHHHHHHHHHHHHHHHTSSCTT
T ss_pred             CCCHHHHHHHHHHHC-CCCCeEEEeeecCCCCCeEEEEEEECCeEEEEEeccCCHHHHHHHHHHHHHHHHHhhCCCCcc
Confidence            359999999999999 889999998889999999999999999 68899999999999999999999999876654333

>1x48_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1

Probab=99.70  E-value=3.8e-17  Score=139.43  Aligned_cols=73  Identities=21%  Similarity=0.302  Sum_probs=67.0

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEeecCCCCCC-eEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGP-VFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p-~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      ..|||++||||||++++.+ .|+ .+.||+|.+ .|+|.|.|+|..++.|.|+|||+|||+||+.||+.|......
T Consensus         5 ~~d~Kt~LqE~~Q~~~~~~-~Y~-~~~Gp~H~~~~F~~~v~v~g~~~~~G~G~SKK~Aeq~AA~~AL~~L~~~~~~   78 (88)
T 1x48_A            5 SSGYIGLVNSFAQKKKLSV-NYE-QCEPNSELPQRFICKCKIGQTMYGTGSGVTKQEAKQLAAKEAYQKLLKSPPK   78 (88)
T ss_dssp             SSCHHHHHHHHHHHTTCCE-EEE-ECCCSSSSSCCEEEEEEESSCEEEEEEESSHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCHHHHHHHHHHHcCCCC-eeE-EeeCCCCCCceEEEEEEECCEEEEEeecCCHHHHHHHHHHHHHHHHHhcCCC
Confidence            3599999999999999976 999 888999999 799999999999999999999999999999999999876433

>3llh_A RISC-loading complex subunit tarbp2; DSRBD, DSRM, microrna, RNA binding protein; 2.14A {Homo sapiens}

Probab=99.70  E-value=2.3e-17  Score=141.06  Aligned_cols=74  Identities=30%  Similarity=0.341  Sum_probs=59.0

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      ...|||+.||||||+++. .|.|+++ ++||+|++.|+|+|.|+|. ++.|.|+|||+|||+||+.||+.|......
T Consensus        12 ~~kd~Ks~LqE~~q~~~~-~p~Y~~~~~~Gp~H~~~F~~~v~v~g~-~~~G~G~SKK~Aeq~AA~~aL~~L~~~~~~   86 (90)
T 3llh_A           12 PGKTPISLLQEYGTRIGK-TPVYDLLKAEGQAHQPNFTFRVTVGDT-SCTGQGPSKKAAKHKAAEVALKHLKGGSML   86 (90)
T ss_dssp             -CCCHHHHHHHHHHHTTC-CCEEEEEEEC-----CCEEEEEEETTE-EEEEEESSHHHHHHHHHHHHHHHHC-----
T ss_pred             cCCCHHHHHHHHHHhcCC-CCEEEEEEeECCCCCCcEEEEEEECCE-EEEEEeCCHHHHHHHHHHHHHHHHHhcccc
Confidence            356999999999999975 7999997 8899999999999999998 678999999999999999999999776543

>2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference, endonucleolytic cleavage, hydrolase/RNA complex; 1.70A {Aquifex aeolicus} SCOP: a.149.1.1 d.50.1.1 PDB: 1yyw_A 2nue_A 2nuf_A 1yyk_A 1yz9_A 1yyo_A 2ez6_A 1rc7_A 1i4s_A 1jfz_A 1rc5_A

Probab=99.70  E-value=3e-18  Score=166.24  Aligned_cols=138  Identities=21%  Similarity=0.226  Sum_probs=110.7

Q ss_pred             HHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHH--HHHHHHHHHHhcCC-Chhhhh
Q 041141            3 KNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHA--AAEVALDVLSKKGP-SKVLAA   79 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~--AAk~AL~~L~k~~p-s~~~~~   79 (575)
                      ...|.++|.+.|+  ..|.....|...       ..+-++.||+..++.|++.+.+.  |.+++...+..... ...   
T Consensus        77 ~~~la~~a~~l~l--~~~l~~~~~~~~-------~~~lad~~EAliGAiyld~g~~~~~~~~~i~~~~~~~~~~~~~---  144 (221)
T 2nug_A           77 EEFFNLLAQKLEL--HKFIRIKRGKIN-------ETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIK---  144 (221)
T ss_dssp             HHHHHHHHHTTTG--GGTCBSCTTCCC-------HHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH---
T ss_pred             HHHHHHHHHHcCh--HHhhccCCCccc-------chHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhhhhh---
Confidence            3568899988654  466655544322       45567789998889999999888  88888777754321 111   


Q ss_pred             hcccccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHH
Q 041141           80 RVLDETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALK  154 (575)
Q Consensus        80 ~i~de~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~  154 (575)
                       ......|||+.||||||++++..|.|+++ +.||+|.+.|+|.|.|+|. ++.|.|.|||+||++||+.||+.|.
T Consensus       145 -~~~~~~~pks~LqE~~q~~~~~~p~Y~~~~~~G~~h~~~F~v~v~v~~~-~~~G~G~skK~Ae~~AA~~AL~~L~  218 (221)
T 2nug_A          145 -EGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEY-RTLGEGKSKKEAEQRAAEELIKLLE  218 (221)
T ss_dssp             -TTCSCCCHHHHHHHHHHHHHSCCCEEEEEEEESCGGGCEEEEEEEETTE-EEEEEESSHHHHHHHHHHHHHHHHC
T ss_pred             -ccccccCHHHHHHHHHHHcCCCCceEEEEEeeCCCCCceEEEEEEECCE-EEEEecCCHHHHHHHHHHHHHHHhh
Confidence             01224699999999999999999999997 7899999999999999999 9999999999999999999999985

>1x47_A DGCR8 protein; structural genomics, DSRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1

Probab=99.68  E-value=1.2e-16  Score=138.86  Aligned_cols=76  Identities=25%  Similarity=0.272  Sum_probs=69.3

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhhcccC
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSAF  161 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~~~  161 (575)
                      ...|||+.||||||++++.+|.|+++ +.||+  +.|+|.|.|+|..++.|.|+|||+|||+||+.||..|.....+..
T Consensus        14 ~~kd~Kt~LqE~~Q~~~~~~P~Y~~~~~~Gp~--~~F~~~V~v~g~~~~~G~G~SKK~Aeq~AA~~AL~~L~~~~~~~~   90 (98)
T 1x47_A           14 NGKSEVCILHEYMQRVLKVRPVYNFFECENPS--EPFGASVTIDGVTYGSGTASSKKLAKNKAARATLEILIPDFVKQT   90 (98)
T ss_dssp             TCCCHHHHHHHHHHHHTCSCCEEEEEECSSSS--CCEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHCSSSSCCC
T ss_pred             CCCCHHHHHHHHHHHcCCCCCeEEEEEeECCC--CcEEEEEEECCEEEEEeeeCCHHHHHHHHHHHHHHHHHhhhhhhh
Confidence            45699999999999999999999998 68987  999999999999999999999999999999999999986655544

>1uil_A Double-stranded RNA-binding motif; structural genomics, DSRM, riken structural genomics/proteomics initiative, RSGI RNA binding protein; NMR {Mus musculus} SCOP: d.50.1.1 PDB: 2rs7_A

Probab=99.68  E-value=1.3e-16  Score=142.18  Aligned_cols=75  Identities=20%  Similarity=0.213  Sum_probs=69.2

Q ss_pred             CchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEE-----CCEeeeecccCCHHHHHHHHHHHHHHHHHhhhccc
Q 041141           86 GVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVEL-----AGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSA  160 (575)
Q Consensus        86 ~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V-----~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~~  160 (575)
                      .|||++||||||++++ .|.|++.+.||+|.+.|+|.|.|     +|..++.|.|+|||+|||+||+.||..|......+
T Consensus        26 ~d~Kt~LqE~~Qk~~~-~p~Y~~~~~Gp~H~~~F~~~V~v~~~~~~~~~~~~G~G~SKK~AEq~AA~~AL~~L~~~~~ie  104 (113)
T 1uil_A           26 ENAKARLNQYFQKEKI-QGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYHLGVIE  104 (113)
T ss_dssp             HHHHHHHHHHHHHSCC-CCCCEEEEESCSTTCEEEEEEEEEETTTTEEEEEECCCSSHHHHHHHHHHHHHHHHHHHTSSC
T ss_pred             CCHHHHHHHHHHHCCC-CCeEEEeeECCCCCCcEEEEEEEeeeccCCEEEEEEeeCCHHHHHHHHHHHHHHHHHhcCCcc
Confidence            4899999999999999 99999668999999999999999     68888999999999999999999999999886654


Q ss_pred             C
Q 041141          161 F  161 (575)
Q Consensus       161 ~  161 (575)
                      +
T Consensus       105 ~  105 (113)
T 1uil_A          105 A  105 (113)
T ss_dssp             C
T ss_pred             c
Confidence            4

>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862, csgid, structura genomics; 2.21A {Campylobacter jejuni subsp}

Probab=99.66  E-value=9e-19  Score=173.78  Aligned_cols=147  Identities=23%  Similarity=0.208  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhhhhcc
Q 041141            3 KNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVL   82 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~   82 (575)
                      ...|.++|.+.|  +..|.....|...... ...-.+-++.||+.++|.|++.+.+.|.+++...+.........    .
T Consensus       101 ~~~La~~a~~lg--L~~~l~~~~~e~~~~g-~~~~~~lad~fEAliGAiyld~G~~~~~~~i~~~~~~~l~~~~~----~  173 (248)
T 3n3w_A          101 EKSFAKIANSLN--LGDFILMSVAEENNGG-KEKPSILSDALEAIIGAIHLEAGFEFAKTIALRLIEKNFPQIDA----K  173 (248)
T ss_dssp             HHHHHHHHHHTT--GGGTCBCCHHHHHTTG-GGCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCC---------
T ss_pred             HHHHHHHHHHcC--cHHHhhcCchhhhcCC-CCCccHHHHHHHHHHHHHHHHCChHHHHHHHHHHHHHHHHHhhc----c
Confidence            357889999865  4577665433111100 01123567789999999999999999999999888876543221    1


Q ss_pred             cccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           83 DETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        83 de~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ....|||+.||||||++++.+|.|+++ ++||+|.+.|+|.|.|+|+.++.|.|.|||+||++||+.||+.|+.+
T Consensus       174 ~~~~dpks~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~v~v~v~g~~~~~G~G~SKK~Aeq~AA~~AL~~L~~l  248 (248)
T 3n3w_A          174 ILIKDYKTKLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKELARAIAGSKKEAQQMAAKIALEKLGAL  248 (248)
T ss_dssp             ---------------------------------------------------------------------------
T ss_pred             ccccCHHHHHHHHHHHcCCCCCceEEeeccCCCCCceEEEEEEECCEEEEEeeeCCHHHHHHHHHHHHHHHHHcC
Confidence            234699999999999999999999998 88999999999999999999999999999999999999999998753

>1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.50.1.1

Probab=99.66  E-value=5.7e-17  Score=140.75  Aligned_cols=73  Identities=18%  Similarity=-0.035  Sum_probs=66.4

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCE-eeeecccCCHHHHHHHHHHHHHHHHHhhhc
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGV-SFTGEPAKTKKQAQKNAALAAWSALKKQAK  158 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~-~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~  158 (575)
                      ..|||+.||||||+. ...|.|++++.||+|++.|++.|.|+|. .++.|.|+|||+|||+||+.||..|.-+.+
T Consensus         5 ~~D~KT~LQE~~Q~~-~~~p~Y~v~~~GpdH~k~F~v~v~i~~~~~~g~G~G~SKK~AEQ~AA~~AL~~l~~l~k   78 (94)
T 1t4n_A            5 DMNAKRQLYSLIGYA-SLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDF   78 (94)
T ss_dssp             CHHHHHHHHHHTCSS-SSCCEEEECCCCSSSCCSEEEEEECSSSCEEEEEEESSHHHHHHHHHHHHHHCHHHHHH
T ss_pred             CCCchHHHHHHHcCC-CCCCEEEEeeeCCCCCCeEEEEEEECCEEEEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Confidence            359999999999997 4689999996699999999999999999 899999999999999999999998876644

>2dmy_A Spermatid perinuclear RNA-binding protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1

Probab=99.66  E-value=2.4e-16  Score=136.67  Aligned_cols=69  Identities=25%  Similarity=0.360  Sum_probs=64.1

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      ...|||+.||||||++  ..|.|+++ +.||+|.+.|+|.|.|+|..+ .|.|+|||+|||+||+.||..|..
T Consensus        14 ~~~d~Kt~LqE~~Q~~--~~p~Y~~~~~~Gp~H~~~F~~~v~v~g~~~-~G~G~SKK~Aeq~AA~~aL~~L~~   83 (97)
T 2dmy_A           14 KAIDLMNALMRLNQIR--PGLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAMGY   83 (97)
T ss_dssp             CSSSCTHHHHHHHHHS--CSCCCEEEEEESCSSSCEEEEEEEETTEEE-EEEESSHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHhcC--CCceEEEEEeeCCCCCCeEEEEEEECCEEE-EEeeCCHHHHHHHHHHHHHHHhCC
Confidence            3569999999999996  68999998 789999999999999999998 899999999999999999999954

>1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; 2.00A {Thermotoga maritima} SCOP: a.149.1.1 d.50.1.1

Probab=99.65  E-value=7e-17  Score=160.01  Aligned_cols=147  Identities=19%  Similarity=0.189  Sum_probs=111.8

Q ss_pred             HHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhhhhcc
Q 041141            3 KNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVL   82 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~   82 (575)
                      ...|.++|.+.|+  ..|.....|...... ...-.+-++.||+..++.|++.+.+.|.+++...+........    ..
T Consensus       103 ~~~la~~a~~lgL--~~~l~~~~~e~~~~~-~~~~~~lad~~EAliGAiyld~g~~~~~~~i~~~~~~~~~~~~----~~  175 (252)
T 1o0w_A          103 EEVLAMVSRKMNL--GKFLFLGKGEEKTGG-RDRDSILADAFEALLAAIYLDQGYEKIKELFEQEFEFYIEKIM----KG  175 (252)
T ss_dssp             HHHHHHHHHHTTH--HHHCBCCHHHHHTTG-GGCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH----TT
T ss_pred             HHHHHHHHHHcCc--HHhhccCchhhhcCC-CCCccHHHhHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhh----hc
Confidence            3568899998654  466654332111000 0113455678999889999999999888888877765422111    01


Q ss_pred             cccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           83 DETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        83 de~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ....|||+.||||||++++..|.|+++ +.||+|.+.|+|.|.|+|+.++.|.|.|||+||++||+.||+.|...
T Consensus       176 ~~~~dpkt~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~v~v~v~g~~~~~G~G~SKK~Aeq~AA~~AL~~L~~~  250 (252)
T 1o0w_A          176 EMLFDYKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEKLLKE  250 (252)
T ss_dssp             CCCSCHHHHHHHHHHHHHSSCCEEEEEEEECCTTSCEEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHC--
T ss_pred             ccccCHHHHHHHHHHHcCCCCceEEEEeeeCCCCCCeEEEEEEECCEEEEEEeeCCHHHHHHHHHHHHHHHHhhc
Confidence            234699999999999999999999998 78999999999999999999999999999999999999999999643

>1t4o_A Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2.50A {Saccharomyces cerevisiae} SCOP: d.50.1.1 PDB: 1t4l_B 2lbs_B

Probab=99.63  E-value=2.6e-16  Score=141.47  Aligned_cols=74  Identities=18%  Similarity=-0.043  Sum_probs=67.6

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCE-eeeecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGV-SFTGEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~-~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      ..|||+.||||||+. ..+|.|++++.||+|++.|++.|.|+|. .++.|.|.|||+|||+||+.||..|.-+.+.
T Consensus         7 ~~D~KT~LQE~~Q~~-~~~P~Y~vv~~GPdH~k~F~v~V~i~g~~~~g~G~G~SKK~AEQ~AA~~AL~~l~~l~Ky   81 (117)
T 1t4o_A            7 DMNAKRQLYSLIGYA-SLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFY   81 (117)
T ss_dssp             CTTHHHHHHHHHCCG-GGCCEEEEEECCCSSCCCEEEEEECTTCCEEEEEEESSHHHHHHHHHHHHHHCHHHHHHH
T ss_pred             CCCchHHHHHHHcCC-CCCCEEEEeeeCCCCCCeEEEEEEECCEEEEEEEEeCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999995 4789999986699999999999999999 8999999999999999999999998777655

>2l33_A Interleukin enhancer-binding factor 3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, DRBM; NMR {Homo sapiens}

Probab=99.63  E-value=5.3e-16  Score=133.69  Aligned_cols=68  Identities=31%  Similarity=0.308  Sum_probs=63.3

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      ..++|+.||||||+++  .|.|+++ ++||+|++.|+|.|.|+|..+ .|.|+|||+|||+||+.||+.|..
T Consensus        13 ~~~~K~~LqEl~Qk~~--~p~Y~~v~~~Gp~H~~~F~v~V~v~g~~~-~G~G~SKK~AEq~AA~~AL~~L~~   81 (91)
T 2l33_A           13 TKHGKNPVMELNEKRR--GLKYELISETGGSHDKRFVMEVEVDGQKF-QGAGSNKKVAKAYAALAALEKLFP   81 (91)
T ss_dssp             CSSTTCHHHHHHHHCS--SCEEEEEEEEECSSCEEEEEEEEETTEEE-EEEESSHHHHHHHHHHHHHHHHCC
T ss_pred             ccCCCCHHHHHHHhCC--CCeEEEEEeeCCCCCCeEEEEEEECCEEE-EeeeCCHHHHHHHHHHHHHHHHhh
Confidence            3589999999999998  8899998 789999999999999999987 799999999999999999999963

>1whn_A Hypothetical protein riken cDNA 2310016K04; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1

Probab=99.62  E-value=7e-16  Score=140.46  Aligned_cols=72  Identities=26%  Similarity=0.251  Sum_probs=66.8

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeeccc-CCHHHHHHHHHHHHHHHHHhhhc
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPA-KTKKQAQKNAALAAWSALKKQAK  158 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G-~SKKeAEQ~AAk~ALe~L~~~~~  158 (575)
                      ..|||+.||||||++++.+|.|+++..  +|.+.|+|.|.|+|..++.|.| +|||+|||+||+.||+.|.....
T Consensus        25 ~~d~Kt~LQE~~Qk~~~~~P~Y~~v~~--~H~~~F~v~V~v~g~~~g~G~G~~SKK~AEQ~AA~~AL~~L~~~~~   97 (128)
T 1whn_A           25 QITPKMCLLEWCRREKLPQPVYETVQR--TIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGLPEG   97 (128)
T ss_dssp             TCCHHHHHHHHHHHTTCCCCCCCEEEC--SSSCCEEEEEEETTEEEEESSCBSSHHHHHHHHHHHHHHHHTCSSS
T ss_pred             CCCHHHHHHHHHHHcCCCCCeEEEEee--cCCCcEEEEEEECCEEEEEEeccCCHHHHHHHHHHHHHHHHhcccc
Confidence            469999999999999999999999965  8999999999999999999999 99999999999999999975443

>2ljh_A Double-stranded RNA-specific editase ADAR; DSRBD, DSRBM, editing, hydrolase; NMR {Drosophila melanogaster}

Probab=99.59  E-value=1.2e-15  Score=136.46  Aligned_cols=70  Identities=26%  Similarity=0.407  Sum_probs=64.0

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      ...|||++||||||+     |.|+++ ++||+|++.|+|+|.|+|+.+ .|.|+|||+|||+||+.||+.|......
T Consensus        35 ~~kd~Ks~LQE~~q~-----p~Y~~v~~~Gp~H~k~F~v~V~v~g~~~-~G~G~SKK~AEq~AA~~AL~~L~~~~~~  105 (114)
T 2ljh_A           35 QPKNTVAMLNELRHG-----LIYKLESQTGPVHAPLFTISVEVDGQKY-LGQGRSKKVARIEAAATALRSFIQFKDG  105 (114)
T ss_dssp             CCSCHHHHHHHHCSC-----CEEEEEEEECCSSSCEEEEEEEETTEEE-EEEESSHHHHHHHHHHHHHHHHCCCTTC
T ss_pred             CCCCHHHHHHHHccC-----CeEEEEEeeCCCCCCeEEEEEEECCEEE-EeeeCCHHHHHHHHHHHHHHHHHcCCCC
Confidence            356999999999984     899997 789999999999999999999 8999999999999999999999876544

>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomic protein structure initiative; 2.10A {Mycobacterium tuberculosis}

Probab=99.58  E-value=4.6e-17  Score=159.90  Aligned_cols=151  Identities=25%  Similarity=0.324  Sum_probs=43.3

Q ss_pred             HHHHHHHHHcCC-CCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCCChhhhhhcc
Q 041141            4 NQLQELAQRSCF-NLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGPSKVLAARVL   82 (575)
Q Consensus         4 S~LQElcQK~gl-~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~ps~~~~~~i~   82 (575)
                      ..|.++|.+.+. ++..|.....|...... ...-++-++.||+..++.|++.+.+.|.+++...+........    ..
T Consensus        84 ~~la~~a~~l~~~gL~~~l~~~~~e~~~~~-~~~~~~lad~~EAliGAiyld~g~~~~~~~i~~~~~~~~~~~~----~~  158 (242)
T 2a11_A           84 QALADVARRLCAEGLGVHVLLGRGEANTGG-ADKSSILADGMESLLGAIYLQHGMEKAREVILRLFGPLLDAAP----TL  158 (242)
T ss_dssp             HHHHHHHHHHSSSCSGGGCBCCHHHHHTTG-GGCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTHHHHHHTT----C-
T ss_pred             HHHHHHHHHhhhhChHHHhhcCchhhhcCC-CCCccHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHhh----hc
Confidence            568899999610 34467665433211110 0013445678899888999999999888888777654321100    01


Q ss_pred             cccCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           83 DETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        83 de~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      ....|||+.||||||++++..|.|+++..||+|.+.|+|.|.|+|+.++.|.|.|||+||++||+.||+.|......
T Consensus       159 ~~~~dpkt~Lqe~~q~~~~~~p~Y~~~~~Gp~h~~~F~v~v~v~g~~~~~G~G~skk~Ae~~AA~~AL~~L~~~~~~  235 (242)
T 2a11_A          159 GAGLDWKTSLQELTAARGLGAPSYLVTSTGPDHDKEFTAVVVVMDSEYGSGVGRSKKEAEQKAAAAAWKALEVLDNA  235 (242)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             cccCChHHHHHHHHHHhCCCCCeEEEeccCCCCCCeEEEEEEECCEEEEEeeeCCHHHHHHHHHHHHHHHHhhcccc
Confidence            12469999999999999999999999889999999999999999999999999999999999999999999866533

>1di2_A XLRBPA, double stranded RNA binding protein A; protein-RNA complex, protein-RNA interactions, RNA-bining protein; 1.90A {Xenopus laevis} SCOP: d.50.1.1

Probab=99.57  E-value=3.8e-15  Score=120.74  Aligned_cols=67  Identities=28%  Similarity=0.379  Sum_probs=62.8

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHH
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLS   69 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~   69 (575)
                      |+|+.||||||++++.+|.|.++ ..||+|.+.|++.|.|+|. ++. |.|.+||.|++.||+.+|..|.
T Consensus         1 ~p~s~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~~~v~v~~~-~~~-G~G~sKK~Aeq~AA~~al~~L~   68 (69)
T 1di2_A            1 MPVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETF-VET-GSGTSKQVAKRVAAEKLLTKFK   68 (69)
T ss_dssp             CHHHHHHHHHHHHTCCCCEEEEEEEESCGGGCEEEEEEEETTE-EEE-EEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHcCCCCCEEEEEEeECCCCCCeEEEEEEECCE-EEE-eecCCHHHHHHHHHHHHHHHHh
Confidence            89999999999999999999987 6899999999999999997 766 5899999999999999999885

>2b7v_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 PDB: 2l2k_B

Probab=99.56  E-value=7.2e-15  Score=119.86  Aligned_cols=66  Identities=24%  Similarity=0.234  Sum_probs=60.5

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ..|||+.|||||     ..|.|+++ ++||+|.+.|+|.|.|+|..+ .|.|+|||+|||+||+.||+.|...
T Consensus         3 ~knp~s~L~E~~-----~~p~Y~~~~~~Gp~h~~~F~~~v~v~~~~~-~G~G~SKK~Aeq~AA~~al~~L~~~   69 (71)
T 2b7v_A            3 GKNPVMILNELR-----PGLKYDFLSESGESHAKSFVMSVVVDGQFF-EGSGRNKKLAKARAAQSALATVFNL   69 (71)
T ss_dssp             SSCHHHHHHHHC-----CSCEEEEEECCCCTTTCCEEEEEECSSCEE-EEEESSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhC-----CCCEEEEEEeECCCCCceEEEEEEECCEEE-EEeeCCHHHHHHHHHHHHHHHHHhc
Confidence            468999999993     68999987 789999999999999999976 7999999999999999999999764

>3adg_A F21M12.9 protein; HYL1, miRNA processing mechanism, RNA binding protein, gene regulation; 1.70A {Arabidopsis thaliana} PDB: 3adi_A

Probab=99.55  E-value=9.8e-15  Score=119.66  Aligned_cols=68  Identities=37%  Similarity=0.559  Sum_probs=63.2

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeeccccc-ccccHHHHHHHHHHHHHHH
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFC-STLRQAEHAAAEVALDVLS   69 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G-~SKKeAeq~AAk~AL~~L~   69 (575)
                      .||+.||||||++++.+|.|+++.+||+|.+.|++.|.|+|..++.+ .| .+||.|++.||+.||..|.
T Consensus         4 d~Kt~LqE~~q~~~~~~p~Y~~~~~Gp~h~~~F~~~v~v~g~~~~~G-~G~~sKK~Aeq~AA~~al~~L~   72 (73)
T 3adg_A            4 VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSL-PGFFNRKAAEQSAAEVALRELA   72 (73)
T ss_dssp             SHHHHHHHHHHHTTCCCCEEEEEEESSTTSCEEEEEEEETTEEEECC-SCBSSHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHcCCCCCEEEEEeECCCCCCeEEEEEEECCEEEEee-eccCCHHHHHHHHHHHHHHHhh
Confidence            38999999999999999999999779999999999999999988774 78 8999999999999999885

>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1

Probab=99.55  E-value=3.9e-15  Score=140.76  Aligned_cols=72  Identities=28%  Similarity=0.435  Sum_probs=67.3

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      ..|||+.||||||++++. |.|+++ +.||+|.+.|+|.|.|+|..++.|.|.|||+|||+||+.||+.|....
T Consensus        12 ~~n~ks~LqE~~q~~~~~-p~Y~~~~~~Gp~h~~~F~~~v~v~g~~~~~G~G~sKK~Aeq~AA~~al~~L~~~~   84 (179)
T 1qu6_A           12 AGFFMEELNTYRQKQGVV-LKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKNAAAKLAVEILNKEK   84 (179)
T ss_dssp             SCSHHHHHHHHHHHHTCC-CEEEEEESCBTTTBCCEEEEEESSSSCCCEEECCSSHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCHHHHHHHHHHhCCCC-CeEEEeeccCCCCCCeEEEEEEECCEEEEecCCCCHHHHHHHHHHHHHHHHhccc
Confidence            368999999999999987 899998 789999999999999999999999999999999999999999998653

>3adj_A F21M12.9 protein; HYL1, miRNA processing, RNA binding protein, gene regulation; 3.00A {Arabidopsis thaliana} PDB: 2l2m_A

Probab=99.53  E-value=1.8e-14  Score=119.27  Aligned_cols=68  Identities=29%  Similarity=0.441  Sum_probs=63.4

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      ||+.||||||++++.+|.|.++ ..||+|.+.|++.|.|+|..++. |.|.+||.|++.||+.||..|..
T Consensus         6 ~Kt~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~~~v~v~g~~~~~-G~G~sKK~Aeq~AA~~al~~L~~   74 (76)
T 3adj_A            6 CKNLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTG-AATRTKKDAEISAGRTALLAIQS   74 (76)
T ss_dssp             HHHHHHHHHHTTTCCCCEEEEEEEECSSSCEEEEEEEEETTEEEEC-CCBSSHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCCCeEEEeeccCCCCCCcEEEEEEECCEEEEE-eccCCHHHHHHHHHHHHHHHHhh
Confidence            8999999999999999999997 68999999999999999988877 47999999999999999998863

>3p1x_A Interleukin enhancer-binding factor 3; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 1.90A {Homo sapiens}

Probab=99.49  E-value=6.2e-14  Score=116.09  Aligned_cols=67  Identities=30%  Similarity=0.329  Sum_probs=58.0

Q ss_pred             chhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           87 VYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        87 nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      +.|+.|++|+|..  ..|.|+++ ++||+|++.|++.|.|+|..+ .|.|+|||+|||+||+.||+.|...
T Consensus         5 ~~K~pl~~L~q~~--~~p~Y~~~~~~Gp~H~~~F~~~v~v~g~~~-~G~G~SKK~Aeq~AA~~al~~L~~~   72 (75)
T 3p1x_A            5 HGKNPVMELNEKR--RGLKYELISETGGSHDKRFVMEVEVDGQKF-QGAGSNKKVAKAYAALAALEKLFPD   72 (75)
T ss_dssp             -CCCHHHHHHHHS--TTCCEEEEEEESCTTSCEEEEEEEETTEEE-EEEESSHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCHHHHHHHcC--CCCEEEEEEeeCCCCCceEEEEEEECCEEE-EEEECCHHHHHHHHHHHHHHHHHcc
Confidence            3456666777765  58999998 799999999999999999988 7999999999999999999999643

>2l2n_A Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, plant protein; NMR {Arabidopsis thaliana}

Probab=99.46  E-value=1.1e-13  Score=121.39  Aligned_cols=72  Identities=36%  Similarity=0.543  Sum_probs=65.3

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeeccccc-ccccHHHHHHHHHHHHHHHhcCC
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFC-STLRQAEHAAAEVALDVLSKKGP   73 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G-~SKKeAeq~AAk~AL~~L~k~~p   73 (575)
                      .||+.||||||++++.+|.|+++.+||+|.+.|++.|.|+|..++.+ .| .+||.|++.||+.||..|.....
T Consensus        18 d~Kt~LqE~~Q~~~~~~P~Y~~~~~Gp~H~~~F~~~V~v~g~~~~~G-~G~~SKK~Aeq~AA~~AL~~L~~~~~   90 (103)
T 2l2n_A           18 VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSL-PGFFNRKAAEQSAAEVALRELAKSSE   90 (103)
T ss_dssp             -CTTHHHHHHHHTTCCCCEEEEEEESCSSSCEEEEEEEETTEEEECC-SCBSSHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CHHHHHHHHHHHcCCCCCeEEEEeEcCCCCCeEEEEEEECCEEEEEe-ecCCCHHHHHHHHHHHHHHHHhcccc
Confidence            48999999999999999999999779999999999999999988874 78 89999999999999999986543

>3adl_A RISC-loading complex subunit tarbp2; TRBP2, miRNA processing, gene regulation-RNA complex; 2.20A {Homo sapiens}

Probab=99.46  E-value=1.1e-13  Score=118.28  Aligned_cols=68  Identities=24%  Similarity=0.291  Sum_probs=62.6

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ||+.||||||++++.+|.|+++ ..||+|.+.|++.|.|+|. ++. |.|.+||.|++.||+.||..|...
T Consensus        17 ~Ks~LqE~~Q~~~~~~P~Y~~~~~~Gp~H~~~F~~~v~v~g~-~~~-G~G~SKK~Aeq~AA~~AL~~L~~~   85 (88)
T 3adl_A           17 EVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERF-IEI-GSGTSKKLAKRNAAAKMLLRVHTV   85 (88)
T ss_dssp             HHHHHHHHHHHTTCCCCEEEEEEEESCTTSCEEEEEEEETTE-EEE-EEESSHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHcCCCCCEEEEEEeECCCCCCeEEEEEEECCE-EEE-EeeCCHHHHHHHHHHHHHHHHHcc
Confidence            7999999999999999999997 6899999999999999997 666 589999999999999999999754

>2cpn_A TAR RNA-binding protein 2; double-stranded RNA binding domain, DSRBD, DSRM., structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.50.1.1

Probab=99.46  E-value=1.1e-13  Score=118.24  Aligned_cols=68  Identities=25%  Similarity=0.300  Sum_probs=62.8

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ||+.||||||++++.+|.|+++ ..|++|.+.|++.|.|+|. ++. |.|.+||+|++.||+.||..|.+.
T Consensus        18 ~Kt~LqE~~Qk~~~~~P~Y~~~~~~Gp~h~~~F~~~v~i~g~-~~~-G~G~SKK~Aeq~AA~~AL~~L~~~   86 (89)
T 2cpn_A           18 PVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERF-IEI-GSGTSKKLAKRNAAAKMLLRVSGP   86 (89)
T ss_dssp             HHHHHHHHHHHHTCCCCEEEEEEEECCSSSCEEEEEEEETTE-EEE-EEESSHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHcCCCCCeEEEEeeECCCCCCeEEEEEEECCE-EEE-eeeCCHHHHHHHHHHHHHHHHHhh
Confidence            7999999999999999999997 6899999999999999997 666 589999999999999999999743

>1uhz_A Staufen (RNA binding protein) homolog 2; DSRM, staufen homolog 2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1

Probab=99.45  E-value=1.6e-13  Score=117.42  Aligned_cols=68  Identities=21%  Similarity=0.177  Sum_probs=62.4

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      .||+.||||||++++.+|.|+++ ..|++|.+.|++.|.|+|. +.. |.|.+||+|++.||+.||..|..
T Consensus         7 d~Kt~LqE~~Q~~~~~~P~Y~~~~~~Gp~H~~~F~~~v~v~g~-~~~-G~G~SKK~Aeq~AA~~AL~~L~~   75 (89)
T 1uhz_A            7 GPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNE-VAT-GTGPNKKIAKKNAAEAMLLQLGY   75 (89)
T ss_dssp             CHHHHHHHHHHHTTSCCCEEEEEEEESCSTTCEEEEEEEETTE-EEE-EEESSHHHHHHHHHHHHHHHHTS
T ss_pred             CHHHHHHHHHHHhCCCCCeEEEEEeECCCCCCeEEEEEEECCE-EEE-EeeCCHHHHHHHHHHHHHHHHhc
Confidence            38999999999999999999997 6899999999999999996 655 58999999999999999999964

>2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene regulation, NUCL protein, gene regulation,nuclear protein; NMR {Homo sapiens}

Probab=99.43  E-value=1.2e-13  Score=117.16  Aligned_cols=68  Identities=32%  Similarity=0.411  Sum_probs=61.7

Q ss_pred             cHHHHHHHHHH-----cCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQR-----SCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK-----~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      ||+.||||||+     .++.+|.|.++ ..||+|.+.|++.|.|+|..++. |.|.+||+|++.||+.||..|..
T Consensus         3 ~Kt~LQE~~Q~~~~~~~~~~~p~Y~~~~~~Gp~H~~~F~v~V~v~g~~~~~-G~G~SKK~AEq~AA~~AL~~L~~   76 (85)
T 2khx_A            3 PKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGC-GKGPSIQQAEMGAAMDALEKYNF   76 (85)
T ss_dssp             SCHHHHHHHHHCCCSSSCCCCCCEEECCCCCSSSCCCEEEEEEETTEECCC-EEESSHHHHHHHHHHHHHTTCCS
T ss_pred             HHHHHHHHHhhhhhhcCCCCCceEEEEEeECCCCCCcEEEEEEECCEEEEE-EeeCCHHHHHHHHHHHHHHHHhH
Confidence            89999999998     46778999998 68999999999999999988876 58999999999999999988754

>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein; 2.60A {Homo sapiens}

Probab=99.43  E-value=2.9e-13  Score=133.45  Aligned_cols=71  Identities=27%  Similarity=0.320  Sum_probs=66.1

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ...|||+.||||||++++.+|.|+++ +.||+  +.|+|.|.|+|..++.|.|.|||+||++||+.||..|...
T Consensus        20 ~~kd~ks~LqE~~q~~~~~~p~Y~~~~~~Gp~--~~F~~~v~v~g~~~~~G~G~SKK~Aeq~AA~~aL~~L~~~   91 (232)
T 2yt4_A           20 NGKSEVCILHEYMQRVLKVRPVYNFFECENPS--EPFGASVTIDGVTYGSGTASSKKLAKNKAARATLEILIPD   91 (232)
T ss_dssp             TTSCHHHHHHHHHHHTTCCCCEEEEEECSCTT--SCEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHSTT
T ss_pred             CCCCHHHHHHHHHHHcCCCCCeEEEEeeECCC--CcEEEEEEECCEEEeecCCCCHHHHHHHHHHHHHHHHHhh
Confidence            34699999999999999999999998 78987  9999999999999999999999999999999999999653

>3rv0_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 2.29A {Vanderwaltozyma polyspora}

Probab=99.42  E-value=2.4e-15  Score=156.01  Aligned_cols=150  Identities=13%  Similarity=0.025  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccH---HHHHHHHHHHHHHHhcCCChhhhh
Q 041141            3 KNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQ---AEHAAAEVALDVLSKKGPSKVLAA   79 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKe---Aeq~AAk~AL~~L~k~~ps~~~~~   79 (575)
                      ...|.++|.+.|+  ..|.....|+.....-...-.|-++.||+..+|.|+|.   +.+.|.+++...+...........
T Consensus       170 ~~~La~iA~~lgL--~~~l~~~~g~~~~~~~~~~~~ilaD~fEAlIGAIylD~~~~G~~~a~~fi~~l~~~~l~~~~~~~  247 (341)
T 3rv0_A          170 NNNLFDWSTKLNF--TKRLQGNIATPTRVVKDKMSKRYADCVEAYIGALVIDRFGTEFLDIKEWLEELSEKKLAKSSQMV  247 (341)
T ss_dssp             HHHHHHHHHHTTT--TTTTCCSSCCC----CCHHHHHHHHHHHHHHHHHHHHHCSSTTHHHHHHHHHHTHHHHHCGGGC-
T ss_pred             HHHHHHHHHHcCc--HHHhhhcCChhhhccCCccccHHHHHHHHHHHHHhhcCccCCHHHHHHHHHHHHHHHHHHHhhhh
Confidence            4578999999654  56765322322110000012344578999999999999   899999998887765432211000


Q ss_pred             hcccccCchhhHHHHHHHHcCCCC-CeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141           80 RVLDETGVYKNLLQETSHRAGLKL-PVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        80 ~i~de~~nyKS~LQE~cQK~gl~l-P~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      .......|||+.||||||++++.. |.|+++ +.||     |++.|.|+|+.++.|.|.|||+|||+||+.||+.|+...
T Consensus       248 ~~~~~~~d~Kt~LqE~~Q~~~~~~~~~Y~~~~~~Gp-----F~v~v~i~~~~~g~G~G~SKK~AEq~AA~~AL~~L~~~~  322 (341)
T 3rv0_A          248 IKEPLNKNAKNELAELLQINKLGHKLHYRKLTEMPP-----FRVEVKIGDILLDEAEGNSIREAEHRAAMKVLENDELLR  322 (341)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hccccccCHHHHHHHHHHHcCCCCCceEEEEeccCC-----EEEEEEECCEEEEEEEeCCHHHHHHHHHHHHHHHhhhhh
Confidence            001124699999999999998766 599988 6675     999999999999999999999999999999999998775


Q ss_pred             cc
Q 041141          158 KS  159 (575)
Q Consensus       158 ~~  159 (575)
                      ..
T Consensus       323 k~  324 (341)
T 3rv0_A          323 KY  324 (341)
T ss_dssp             --
T ss_pred             hh
Confidence            44

>2dix_A Interferon-inducible double stranded RNA- dependent protein kinase activator A; structure genomics, DSRM domain, hypothetical protein PRKRA; NMR {Homo sapiens} SCOP: d.50.1.1

Probab=99.42  E-value=3.6e-13  Score=113.72  Aligned_cols=67  Identities=25%  Similarity=0.371  Sum_probs=61.1

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ||+.||||||+++ .+|.|+++ ..||+|.+.|++.|.|+| .+.. |.|.+||+|++.||+.||..|...
T Consensus        10 ~Ks~LqE~~q~~~-~~p~Y~~~~~~Gp~h~~~F~~~v~v~~-~~~~-G~G~SKK~Aeq~AA~~aL~~L~~~   77 (84)
T 2dix_A           10 PIQVLHEYGMKTK-NIPVYECERSDVQIHVPTFTFRVTVGD-ITCT-GEGTSKKLAKHRAAEAAINILKAN   77 (84)
T ss_dssp             HHHHHHHHHHHTT-CCCEEEEEEEECSSSSCEEEEEEEETT-EEEE-ECSSCTTHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcC-CCCeEEEEEeECCCCCCeEEEEEEECC-EEEE-eeeCCHHHHHHHHHHHHHHHHhcc
Confidence            7999999999998 68999997 689999999999999999 6665 589999999999999999999753

>1ekz_A DSRBDIII, maternal effect protein (staufen); structure, protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila melanogaster} SCOP: d.50.1.1 PDB: 1stu_A

Probab=99.41  E-value=1.3e-13  Score=113.81  Aligned_cols=66  Identities=21%  Similarity=0.257  Sum_probs=60.9

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      ||+.||||||++++. |.|.++ ..||+|.+.|++.|.|+| .++. |.|.+||.|++.||+.+|..|..
T Consensus         9 ~ks~LqE~~q~~~~~-p~Y~~~~~~Gp~h~~~F~~~v~i~~-~~~~-G~G~sKK~Aeq~AA~~aL~~L~~   75 (76)
T 1ekz_A            9 PISQVHEIGIKRNMT-VHFKVLREEGPAHMKNFITACIVGS-IVTE-GEGNGKKVSKKRAAEKMLVELQK   75 (76)
T ss_dssp             HHHHHHHHHHHTTCC-CEEEESSSCCSSSCSCSSEEEEETT-EEEE-ECCCSTTSSSHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCC-CEEEEEEeECCCCCCcEEEEEEECC-EEEE-EeeCCHHHHHHHHHHHHHHHHhh
Confidence            899999999999998 999997 689999999999999999 6666 58999999999999999998864

>1x49_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1

Probab=99.39  E-value=4.1e-13  Score=116.57  Aligned_cols=69  Identities=26%  Similarity=0.434  Sum_probs=63.2

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      ||+.||||||++++. |.|+++ ..||+|.+.|++.|.|+|..++. |.|.+||+|++.||+.||..|....
T Consensus        16 ~Kt~LqE~~Q~~~~~-p~Y~~~~~~Gp~H~~~F~v~v~i~g~~~~~-G~G~SKK~Aeq~AA~~AL~~L~~~~   85 (97)
T 1x49_A           16 YMDKLNKYRQMHGVA-ITYKELSTSGPPHDRRFTFQVLIDEKEFPE-AKGRSKQEARNAAAKLAVDILDNEN   85 (97)
T ss_dssp             HHHHHHHHHHHHTCC-EEEEEEEEESCSSSCEEEEEEEESSCCCCC-EEESSHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHcCCC-CeEEEEEeeCCCCCCcEEEEEEECCEEEEE-EeeCCHHHHHHHHHHHHHHHHHhhc
Confidence            899999999999987 799987 68999999999999999988876 5899999999999999999997553

>2b7t_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 PDB: 2l3c_A

Probab=99.39  E-value=6.3e-13  Score=109.04  Aligned_cols=65  Identities=34%  Similarity=0.404  Sum_probs=59.8

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      ||+.||||||+  +.+|.|.++ ..||+|++.|++.|.|+|..+ . |.|.+||.|++.||+.||..|..
T Consensus         6 ~Ks~Lqe~~q~--~~~p~Y~~~~~~Gp~h~~~F~~~v~v~g~~~-~-G~G~SKK~Aeq~AA~~al~~L~~   71 (73)
T 2b7t_A            6 PKNALMQLNEI--KPGLQYMLLSQTGPVHAPLFVMSVEVNGQVF-E-GSGPTKKKAKLHAAEKALRSFVQ   71 (73)
T ss_dssp             SHHHHHHHHHH--CSCCEEEEEEEECSSSSCEEEEEEESSSSEE-E-EEESSHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcC--CCCceEEEEEeeCCCCCCeEEEEEEECCEEE-E-eecCCHHHHHHHHHHHHHHHHhc
Confidence            89999999997  678999997 689999999999999999987 4 58999999999999999999874

>3llh_A RISC-loading complex subunit tarbp2; DSRBD, DSRM, microrna, RNA binding protein; 2.14A {Homo sapiens}

Probab=99.36  E-value=1e-12  Score=112.31  Aligned_cols=67  Identities=31%  Similarity=0.344  Sum_probs=54.6

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ||+.||||||+++. .|.|+++ .+|++|++.|++.|.|+|. ++. |.|.+||+|++.||+.||..|...
T Consensus        16 ~Ks~LqE~~q~~~~-~p~Y~~~~~~Gp~H~~~F~~~v~v~g~-~~~-G~G~SKK~Aeq~AA~~aL~~L~~~   83 (90)
T 3llh_A           16 PISLLQEYGTRIGK-TPVYDLLKAEGQAHQPNFTFRVTVGDT-SCT-GQGPSKKAAKHKAAEVALKHLKGG   83 (90)
T ss_dssp             HHHHHHHHHHHTTC-CCEEEEEEEC-----CCEEEEEEETTE-EEE-EEESSHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHhcCC-CCEEEEEEeECCCCCCcEEEEEEECCE-EEE-EEeCCHHHHHHHHHHHHHHHHHhc
Confidence            79999999999875 7999987 7899999999999999998 444 589999999999999999999765

>1whq_A RNA helicase A; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Mus musculus} SCOP: d.50.1.1 PDB: 2rs6_A

Probab=99.36  E-value=7.4e-13  Score=115.41  Aligned_cols=69  Identities=19%  Similarity=0.206  Sum_probs=63.0

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECC-eeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNG-ETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG-~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      ||+.||||||++ +.+|.|++...|++|.+.|++.|.|+| ..++. |.|.+||+|++.||+.||..|....
T Consensus         8 ~Kt~LqE~~Qk~-~~~P~Y~~~~~Gp~H~~~F~~~V~v~g~~~~~~-G~G~SKK~Aeq~AA~~AL~~L~~~~   77 (99)
T 1whq_A            8 IKNFLYAWCGKR-KMTPAYEIRAVGNKNRQKFMCEVRVEGFNYAGM-GNSTNKKDAQSNAARDFVNYLVRIN   77 (99)
T ss_dssp             SHHHHHHHHHHT-TCCCEEEEEEEECSSSEEEEEEEECTTCSCCEE-EEESSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHC-CCCCeEEEeeecCCCCCeEEEEEEECCeEEEEE-eccCCHHHHHHHHHHHHHHHHHhhC
Confidence            899999999999 888999997789999999999999999 67766 5899999999999999999998653

>1x48_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1

Probab=99.34  E-value=1.7e-12  Score=110.64  Aligned_cols=68  Identities=22%  Similarity=0.285  Sum_probs=62.4

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCC-ceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAP-RFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap-~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      ||+.||||||++++.+ .|+ ...||+|.+ .|++.|.|+|..++. |.|.+||+|++.||+.||..|....
T Consensus         8 ~Kt~LqE~~Q~~~~~~-~Y~-~~~Gp~H~~~~F~~~v~v~g~~~~~-G~G~SKK~Aeq~AA~~AL~~L~~~~   76 (88)
T 1x48_A            8 YIGLVNSFAQKKKLSV-NYE-QCEPNSELPQRFICKCKIGQTMYGT-GSGVTKQEAKQLAAKEAYQKLLKSP   76 (88)
T ss_dssp             HHHHHHHHHHHTTCCE-EEE-ECCCSSSSSCCEEEEEEESSCEEEE-EEESSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHcCCCC-eeE-EeeCCCCCCceEEEEEEECCEEEEE-eecCCHHHHHHHHHHHHHHHHHhcC
Confidence            8999999999999976 999 778999999 799999999998877 4899999999999999999998653

>1uil_A Double-stranded RNA-binding motif; structural genomics, DSRM, riken structural genomics/proteomics initiative, RSGI RNA binding protein; NMR {Mus musculus} SCOP: d.50.1.1 PDB: 2rs7_A

Probab=99.33  E-value=2.7e-12  Score=114.35  Aligned_cols=68  Identities=22%  Similarity=0.277  Sum_probs=61.6

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEE-----CCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNF-----NGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtI-----nG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ||+.||||||++++ +|.|.+...||+|.+.|++.|.|     +|..++. |.|.+||.|++.||+.||..|...
T Consensus        28 ~Kt~LqE~~Qk~~~-~p~Y~~~~~Gp~H~~~F~~~V~v~~~~~~~~~~~~-G~G~SKK~AEq~AA~~AL~~L~~~  100 (113)
T 1uil_A           28 AKARLNQYFQKEKI-QGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAR-EHGSNKKLAAQSCALSLVRQLYHL  100 (113)
T ss_dssp             HHHHHHHHHHHSCC-CCCCEEEEESCSTTCEEEEEEEEEETTTTEEEEEE-CCCSSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCC-CCeEEEeeECCCCCCcEEEEEEEeeeccCCEEEEE-EeeCCHHHHHHHHHHHHHHHHHhc
Confidence            69999999999999 89999558999999999999999     5777766 589999999999999999999865

>2l33_A Interleukin enhancer-binding factor 3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, DRBM; NMR {Homo sapiens}

Probab=99.32  E-value=2.2e-12  Score=111.21  Aligned_cols=69  Identities=30%  Similarity=0.349  Sum_probs=62.2

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCC
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGP   73 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~p   73 (575)
                      ++|+.||||||+++  .|.|+++ ..||+|++.|++.|.|+|..+ . |.|.+||+|++.||+.+|..|....+
T Consensus        15 ~~K~~LqEl~Qk~~--~p~Y~~v~~~Gp~H~~~F~v~V~v~g~~~-~-G~G~SKK~AEq~AA~~AL~~L~~~~~   84 (91)
T 2l33_A           15 HGKNPVMELNEKRR--GLKYELISETGGSHDKRFVMEVEVDGQKF-Q-GAGSNKKVAKAYAALAALEKLFPDTP   84 (91)
T ss_dssp             STTCHHHHHHHHCS--SCEEEEEEEEECSSCEEEEEEEEETTEEE-E-EEESSHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCHHHHHHHhCC--CCeEEEEEeeCCCCCCeEEEEEEECCEEE-E-eeeCCHHHHHHHHHHHHHHHHhhcCC
Confidence            47999999999987  7899987 689999999999999999887 4 58999999999999999999986544

>2dmy_A Spermatid perinuclear RNA-binding protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1

Probab=99.31  E-value=3.3e-12  Score=110.71  Aligned_cols=65  Identities=26%  Similarity=0.372  Sum_probs=59.9

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      ||+.||||||++  .+|.|.++ ..||+|.+.|++.|.|+|..+ . |.|.+||.|++.||+.||..|..
T Consensus        18 ~Kt~LqE~~Q~~--~~p~Y~~~~~~Gp~H~~~F~~~v~v~g~~~-~-G~G~SKK~Aeq~AA~~aL~~L~~   83 (97)
T 2dmy_A           18 LMNALMRLNQIR--PGLQYKLLSQSGPVHAPVFTMSVDVDGTTY-E-ASGPSKKTAKLHVAVKVLQAMGY   83 (97)
T ss_dssp             CTHHHHHHHHHS--CSCCCEEEEEESCSSSCEEEEEEEETTEEE-E-EEESSHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHhcC--CCceEEEEEeeCCCCCCeEEEEEEECCEEE-E-EeeCCHHHHHHHHHHHHHHHhCC
Confidence            899999999996  68999998 689999999999999999988 4 58999999999999999999964

>1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.50.1.1

Probab=99.30  E-value=1.2e-12  Score=113.59  Aligned_cols=66  Identities=18%  Similarity=0.102  Sum_probs=59.9

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCe-eeecccccccccHHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGE-TFESPTFCSTLRQAEHAAAEVALDVLS   69 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~-~fEAgG~G~SKKeAeq~AAk~AL~~L~   69 (575)
                      ||+.||||+|+. ..+|.|.++.+||+|++.|++.|.|+|. .++. |.|.|||+|++.||+.||..|.
T Consensus         8 ~KT~LQE~~Q~~-~~~p~Y~v~~~GpdH~k~F~v~v~i~~~~~~g~-G~G~SKK~AEQ~AA~~AL~~l~   74 (94)
T 1t4n_A            8 AKRQLYSLIGYA-SLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGT-GVGRNIKIAGIRAAENALRDKK   74 (94)
T ss_dssp             HHHHHHHHTCSS-SSCCEEEECCCCSSSCCSEEEEEECSSSCEEEE-EEESSHHHHHHHHHHHHHHCHH
T ss_pred             chHHHHHHHcCC-CCCCEEEEeeeCCCCCCeEEEEEEECCEEEEEE-EEeCCHHHHHHHHHHHHHHHHH
Confidence            799999999997 4689999997799999999999999998 7776 5899999999999999987665

>1x47_A DGCR8 protein; structural genomics, DSRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1

Probab=99.29  E-value=4.6e-12  Score=110.08  Aligned_cols=67  Identities=30%  Similarity=0.367  Sum_probs=61.6

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ||+.||||||++++.+|.|.++ ..|++  +.|++.|.|+|..++. |.|.+||+|++.||+.||..|...
T Consensus        18 ~Kt~LqE~~Q~~~~~~P~Y~~~~~~Gp~--~~F~~~V~v~g~~~~~-G~G~SKK~Aeq~AA~~AL~~L~~~   85 (98)
T 1x47_A           18 EVCILHEYMQRVLKVRPVYNFFECENPS--EPFGASVTIDGVTYGS-GTASSKKLAKNKAARATLEILIPD   85 (98)
T ss_dssp             HHHHHHHHHHHHTCSCCEEEEEECSSSS--CCEEEEEEETTEEEEE-EEESSHHHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHHHcCCCCCeEEEEEeECCC--CcEEEEEEECCEEEEE-eeeCCHHHHHHHHHHHHHHHHHhh
Confidence            7999999999999999999998 57887  9999999999998877 489999999999999999999754

>1whn_A Hypothetical protein riken cDNA 2310016K04; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1

Probab=99.27  E-value=7.2e-12  Score=114.09  Aligned_cols=66  Identities=23%  Similarity=0.266  Sum_probs=61.5

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeeccccc-ccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFC-STLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G-~SKKeAeq~AAk~AL~~L~k   70 (575)
                      ||+.||||||++++.+|.|.++.+  +|.+.|++.|.|+|..++.+ .| .+||+|++.||+.||..|..
T Consensus        28 ~Kt~LQE~~Qk~~~~~P~Y~~v~~--~H~~~F~v~V~v~g~~~g~G-~G~~SKK~AEQ~AA~~AL~~L~~   94 (128)
T 1whn_A           28 PKMCLLEWCRREKLPQPVYETVQR--TIDRMFCSVVTVAEQKYQST-LWDKSKKLAEQTAAIVCLRSQGL   94 (128)
T ss_dssp             HHHHHHHHHHHTTCCCCCCCEEEC--SSSCCEEEEEEETTEEEEES-SCBSSHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHcCCCCCeEEEEee--cCCCcEEEEEEECCEEEEEE-eccCCHHHHHHHHHHHHHHHHhc
Confidence            899999999999999999999866  89999999999999988774 78 99999999999999999964

>1t4o_A Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2.50A {Saccharomyces cerevisiae} SCOP: d.50.1.1 PDB: 1t4l_B 2lbs_B

Probab=99.25  E-value=3.7e-12  Score=114.59  Aligned_cols=66  Identities=18%  Similarity=0.102  Sum_probs=59.4

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCe-eeecccccccccHHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGE-TFESPTFCSTLRQAEHAAAEVALDVLS   69 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~-~fEAgG~G~SKKeAeq~AAk~AL~~L~   69 (575)
                      ||+.||||||+. ..+|.|.++.+||+|++.|++.|.|+|. .++. |.|.+||+|++.||+.||..+.
T Consensus        10 ~KT~LQE~~Q~~-~~~P~Y~vv~~GPdH~k~F~v~V~i~g~~~~g~-G~G~SKK~AEQ~AA~~AL~~l~   76 (117)
T 1t4o_A           10 AKRQLYSLIGYA-SLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGT-GVGRNIKIAGIRAAENALRDKK   76 (117)
T ss_dssp             HHHHHHHHHCCG-GGCCEEEEEECCCSSCCCEEEEEECTTCCEEEE-EEESSHHHHHHHHHHHHHHCHH
T ss_pred             chHHHHHHHcCC-CCCCEEEEeeeCCCCCCeEEEEEEECCEEEEEE-EEeCCHHHHHHHHHHHHHHHHH
Confidence            799999999995 4789999987799999999999999998 7776 5899999999999999986654

>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus}

Probab=99.21  E-value=2.1e-11  Score=120.25  Aligned_cols=69  Identities=29%  Similarity=0.350  Sum_probs=63.0

Q ss_pred             CchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141           86 GVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        86 ~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      .|+|+.|++|++.  +..|.|+++ +.||+|.+.|+|+|.|+|..+ .|.|.|||+|||+||+.||..|....
T Consensus         4 ~~~K~~l~~l~e~--~~~p~Y~~~~~~Gp~H~~~F~~~v~v~g~~~-~G~G~SKK~Aeq~AA~~al~~l~~~~   73 (236)
T 2l3j_A            4 VLPKNALMQLNEI--KPGLQYMLLSQTGPVHAPLFVMSVEVNGQVF-EGSGPTKKKAKLHAAEKALRSFVQFP   73 (236)
T ss_dssp             CCTHHHHHHHHHH--CSSCEEEEEEEESCTTSCEEEEEEEETTEEE-EEEESHHHHHHHHHHHHHHHHHTTCS
T ss_pred             CCCcCHHHHHhhc--CCCceEEEEeccCCCCCCeEEEEEEECCEEE-EEecCChHHHHHHHHHHHHHHHHhcc
Confidence            4899999999976  467999998 789999999999999999986 79999999999999999999998764

>2ljh_A Double-stranded RNA-specific editase ADAR; DSRBD, DSRBM, editing, hydrolase; NMR {Drosophila melanogaster}

Probab=99.15  E-value=2.5e-11  Score=108.62  Aligned_cols=64  Identities=27%  Similarity=0.319  Sum_probs=58.4

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      ||+.||||||+     |.|+++ +.|++|++.|++.|.|+|..+ . |.|.+||+|++.||+.||..|....
T Consensus        39 ~Ks~LQE~~q~-----p~Y~~v~~~Gp~H~k~F~v~V~v~g~~~-~-G~G~SKK~AEq~AA~~AL~~L~~~~  103 (114)
T 2ljh_A           39 TVAMLNELRHG-----LIYKLESQTGPVHAPLFTISVEVDGQKY-L-GQGRSKKVARIEAAATALRSFIQFK  103 (114)
T ss_dssp             HHHHHHHHCSC-----CEEEEEEEECCSSSCEEEEEEEETTEEE-E-EEESSHHHHHHHHHHHHHHHHCCCT
T ss_pred             HHHHHHHHccC-----CeEEEEEeeCCCCCCeEEEEEEECCEEE-E-eeeCCHHHHHHHHHHHHHHHHHcCC
Confidence            79999999985     799987 689999999999999999998 5 5899999999999999999997643

>2b7v_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 PDB: 2l2k_B

Probab=99.10  E-value=1.5e-10  Score=94.27  Aligned_cols=62  Identities=26%  Similarity=0.270  Sum_probs=55.9

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      +|+.|||||     .+|.|.++ ..|++|.+.|++.|.|+|..+ . |.|.+||.|++.||+.+|..|..
T Consensus         6 p~s~L~E~~-----~~p~Y~~~~~~Gp~h~~~F~~~v~v~~~~~-~-G~G~SKK~Aeq~AA~~al~~L~~   68 (71)
T 2b7v_A            6 PVMILNELR-----PGLKYDFLSESGESHAKSFVMSVVVDGQFF-E-GSGRNKKLAKARAAQSALATVFN   68 (71)
T ss_dssp             HHHHHHHHC-----CSCEEEEEECCCCTTTCCEEEEEECSSCEE-E-EEESSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhC-----CCCEEEEEEeECCCCCceEEEEEEECCEEE-E-EeeCCHHHHHHHHHHHHHHHHHh
Confidence            689999993     57899987 689999999999999999976 4 58999999999999999998875

>3p1x_A Interleukin enhancer-binding factor 3; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 1.90A {Homo sapiens}

Probab=99.08  E-value=2e-10  Score=94.95  Aligned_cols=67  Identities=31%  Similarity=0.398  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCC
Q 041141            3 KNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGP   73 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~p   73 (575)
                      |+-|++|+|..  ..|.|.++ .+||+|++.|++.|.|+|..+ . |.|.+||.|++.||+.||..|....+
T Consensus         7 K~pl~~L~q~~--~~p~Y~~~~~~Gp~H~~~F~~~v~v~g~~~-~-G~G~SKK~Aeq~AA~~al~~L~~~~~   74 (75)
T 3p1x_A            7 KNPVMELNEKR--RGLKYELISETGGSHDKRFVMEVEVDGQKF-Q-GAGSNKKVAKAYAALAALEKLFPDTP   74 (75)
T ss_dssp             CCHHHHHHHHS--TTCCEEEEEEESCTTSCEEEEEEEETTEEE-E-EEESSHHHHHHHHHHHHHHHHCTTCC
T ss_pred             CCHHHHHHHcC--CCCEEEEEEeeCCCCCceEEEEEEECCEEE-E-EEECCHHHHHHHHHHHHHHHHHccCC
Confidence            67899999985  57899998 699999999999999999988 4 58999999999999999999976543

>3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding, endonuclease, HEL hydrolase, nucleotide-binding, phosphoprotein, RN binding; HET: MSE; 1.68A {Mus musculus} PDB: 3c4t_A 2eb1_A

Probab=99.08  E-value=3.2e-11  Score=119.58  Aligned_cols=107  Identities=16%  Similarity=0.074  Sum_probs=80.2

Q ss_pred             EECCeeeecccccccccHHH--HHHHHHHHHHHHhcCCChhhhhhcccccCchhhHHHHHHHHcCCCCCeEEEeecCCCC
Q 041141           38 NFNGETFESPTFCSTLRQAE--HAAAEVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGH  115 (575)
Q Consensus        38 tInG~~fEAgG~G~SKKeAe--q~AAk~AL~~L~k~~ps~~~~~~i~de~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H  115 (575)
                      ++-++.||+.++|.|+|.+.  +.|.+++...|........        ..++|+.|+||++.... .+.|.  ..|+.|
T Consensus       155 ~~laD~~EAliGAiylD~G~~~~~~~~~i~~~~~~~i~~~~--------~~~~k~~l~el~~~~~~-~~~~~--~~~~~~  223 (265)
T 3c4b_A          155 KAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMQPLIEKFS--------ANVPRSPVRELLEMEPE-TAKFS--PAERTY  223 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH--------HHSCCCHHHHHHHHCTT-TEEEC--CCEECT
T ss_pred             hHHHHHHHHHhhheeeecCCCHHHHHHHHHHHHHHHHHhHh--------hcCCCCHHHHHHHhccC-Cceee--eccccC
Confidence            34567799998999999998  7777777777765421111        12566666666666542 22332  345578


Q ss_pred             CCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141          116 GPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus       116 ~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      .+.|+|.|.|+|..++.|.|.|||+|||+||+.||+.|..
T Consensus       224 ~~~f~v~v~v~~~~~~~G~G~SkK~Aeq~AA~~AL~~l~~  263 (265)
T 3c4b_A          224 DGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLKA  263 (265)
T ss_dssp             TSCEEEEEEETTTEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEecceEEEEeeCCHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999999999999999999974

>2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference, endonucleolytic cleavage, hydrolase/RNA complex; 1.70A {Aquifex aeolicus} SCOP: a.149.1.1 d.50.1.1 PDB: 1yyw_A 2nue_A 2nuf_A 1yyk_A 1yz9_A 1yyo_A 2ez6_A 1rc7_A 1i4s_A 1jfz_A 1rc5_A

Probab=99.02  E-value=2.4e-10  Score=110.72  Aligned_cols=66  Identities=30%  Similarity=0.413  Sum_probs=61.8

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLS   69 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~   69 (575)
                      ||+.||||||++++.+|.|.++ ..|++|.+.|++.|.|+|. ++. |.|.+||.|++.||+.||..|.
T Consensus       152 pks~LqE~~q~~~~~~p~Y~~~~~~G~~h~~~F~v~v~v~~~-~~~-G~G~skK~Ae~~AA~~AL~~L~  218 (221)
T 2nug_A          152 YKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEY-RTL-GEGKSKKEAEQRAAEELIKLLE  218 (221)
T ss_dssp             HHHHHHHHHHHHHSCCCEEEEEEEESCGGGCEEEEEEEETTE-EEE-EEESSHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcCCCCceEEEEEeeCCCCCceEEEEEEECCE-EEE-EecCCHHHHHHHHHHHHHHHhh
Confidence            7999999999999999999987 6899999999999999999 776 5899999999999999999886

>1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; 2.00A {Thermotoga maritima} SCOP: a.149.1.1 d.50.1.1

Probab=99.02  E-value=3.1e-10  Score=112.46  Aligned_cols=69  Identities=33%  Similarity=0.403  Sum_probs=62.7

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ||+.||||||++++..|.|.++ ..|++|.+.|++.|.|+|..++. |.|.+||+|++.||+.||..|...
T Consensus       181 pkt~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~v~v~v~g~~~~~-G~G~SKK~Aeq~AA~~AL~~L~~~  250 (252)
T 1o0w_A          181 YKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIAT-GKGRTKKEAEKEAARIAYEKLLKE  250 (252)
T ss_dssp             HHHHHHHHHHHHHSSCCEEEEEEEECCTTSCEEEEEEEETTEEEEE-EEESSHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHcCCCCceEEEEeeeCCCCCCeEEEEEEECCEEEEE-EeeCCHHHHHHHHHHHHHHHHhhc
Confidence            7999999999999989999998 68999999999999999988876 589999999999999999998643

>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomic protein structure initiative; 2.10A {Mycobacterium tuberculosis}

Probab=98.85  E-value=2.7e-10  Score=111.83  Aligned_cols=70  Identities=31%  Similarity=0.433  Sum_probs=0.0

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      ||+.||||||++++..|.|.++..|++|.+.|++.|.|+|..++. |.|.+||.|++.||+.||..|....
T Consensus       164 pkt~Lqe~~q~~~~~~p~Y~~~~~Gp~h~~~F~v~v~v~g~~~~~-G~G~skk~Ae~~AA~~AL~~L~~~~  233 (242)
T 2a11_A          164 WKTSLQELTAARGLGAPSYLVTSTGPDHDKEFTAVVVVMDSEYGS-GVGRSKKEAEQKAAAAAWKALEVLD  233 (242)
T ss_dssp             -----------------------------------------------------------------------
T ss_pred             hHHHHHHHHHHhCCCCCeEEEeccCCCCCCeEEEEEEECCEEEEE-eeeCCHHHHHHHHHHHHHHHHhhcc
Confidence            799999999999998999999889999999999999999988776 4799999999999999999997654

>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862, csgid, structura genomics; 2.21A {Campylobacter jejuni subsp}

Probab=98.85  E-value=2.9e-10  Score=112.83  Aligned_cols=68  Identities=31%  Similarity=0.562  Sum_probs=0.0

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      ||+.||||||++++.+|.|.++ ..|++|.+.|++.|.|+|..++. |.|.+||+|++.||+.||+.|..
T Consensus       179 pks~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~v~v~v~g~~~~~-G~G~SKK~Aeq~AA~~AL~~L~~  247 (248)
T 3n3w_A          179 YKTKLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKELAR-AIAGSKKEAQQMAAKIALEKLGA  247 (248)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCCCCCceEEeeccCCCCCceEEEEEEECCEEEEE-eeeCCHHHHHHHHHHHHHHHHHc
Confidence            7999999999999999999997 78999999999999999988877 48999999999999999988753

>3rv0_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 2.29A {Vanderwaltozyma polyspora}

Probab=98.15  E-value=2.8e-07  Score=95.83  Aligned_cols=64  Identities=27%  Similarity=0.298  Sum_probs=0.0

Q ss_pred             cHHHHHHHHHHcCCCC-CceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNL-PSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~L-PeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ||+.||||||++++.+ |.|.++ ..|+     |++.|.|+|..++. |.|.+||+|++.||+.||..|...
T Consensus       256 ~Kt~LqE~~Q~~~~~~~~~Y~~~~~~Gp-----F~v~v~i~~~~~g~-G~G~SKK~AEq~AA~~AL~~L~~~  321 (341)
T 3rv0_A          256 AKNELAELLQINKLGHKLHYRKLTEMPP-----FRVEVKIGDILLDE-AEGNSIREAEHRAAMKVLENDELL  321 (341)
T ss_dssp             ------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCCCCCceEEEEeccCC-----EEEEEEECCEEEEE-EEeCCHHHHHHHHHHHHHHHhhhh
Confidence            7999999999998766 599987 4564     99999999998877 589999999999999999988754

>3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding, endonuclease, HEL hydrolase, nucleotide-binding, phosphoprotein, RN binding; HET: MSE; 1.68A {Mus musculus} PDB: 3c4t_A 2eb1_A

Probab=97.50  E-value=0.00011  Score=72.77  Aligned_cols=65  Identities=20%  Similarity=0.155  Sum_probs=51.3

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      +|+.|+||.+.... .+.|.  ..|..|.+.|++.|.|+|+.++. |.|.+||.|++.||+.||+.|..
T Consensus       199 ~k~~l~el~~~~~~-~~~~~--~~~~~~~~~f~v~v~v~~~~~~~-G~G~SkK~Aeq~AA~~AL~~l~~  263 (265)
T 3c4b_A          199 PRSPVRELLEMEPE-TAKFS--PAERTYDGKVRVTVEVVGKGKFK-GVGRSYRIAKSAAARRALRSLKA  263 (265)
T ss_dssp             CCCHHHHHHHHCTT-TEEEC--CCEECTTSCEEEEEEETTTEEEE-EEESSHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhccC-Cceee--eccccCCCcEEEEEEEecceEEE-EeeCCHHHHHHHHHHHHHHHHhh
Confidence            57788888887532 22222  34557899999999999988776 58999999999999999999864

>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A

Probab=96.24  E-value=0.00053  Score=78.00  Aligned_cols=113  Identities=12%  Similarity=-0.024  Sum_probs=82.2

Q ss_pred             HHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeeccccccccc-HHHHHHHHHHHHHHHhcCCChhhhhhc
Q 041141            3 KNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLR-QAEHAAAEVALDVLSKKGPSKVLAARV   81 (575)
Q Consensus         3 KS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKK-eAeq~AAk~AL~~L~k~~ps~~~~~~i   81 (575)
                      ...|.++|.+.|  +..|.....|+.      ..-++-++.||+..+|.|++ .+.+.|.+++...+.........    
T Consensus       375 n~~La~~A~~lg--L~~~l~~~~~e~------~~~~ilaD~~EAliGAiylD~~G~~~a~~~v~~~~~~~~~~~~~----  442 (756)
T 2qvw_A          375 NEALNYLVQTLG--LPQLAEFSNNLV------AKSKTWADMYEEIVGSIFTGPNGIYGCEEFLAKTLMSPEHSKTV----  442 (756)
T ss_dssp             HHHHHHHHHHTT--CTTTCBCCSCC--------CCCCHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHBCGGGSCC-----
T ss_pred             chHHHHHHHHcC--hHHHhccCCCCC------CcccHHHhHHHHHhCcccccccChHHHHHHHHHHHHhhhhcccc----
Confidence            357899999955  568887666653      12345677899998999999 99998888888887765432211    


Q ss_pred             ccccCch-hhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeecccCCHHHHH---------HHHHHHHHH
Q 041141           82 LDETGVY-KNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQ---------KNAALAAWS  151 (575)
Q Consensus        82 ~de~~ny-KS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAE---------Q~AAk~ALe  151 (575)
                      .....|| |+.||||||++++                             +.|.+.+.+.||         -.||+.||+
T Consensus       443 ~~~~~Dp~Kt~LqE~~q~~~i-----------------------------a~~v~~~~~~ak~~~~~~~~~~~aa~~aL~  493 (756)
T 2qvw_A          443 GSACPDAVTKASKRVCMGEAG-----------------------------AHEFRSLVDYACEQGISVFCSSRVSTMFLE  493 (756)
T ss_dssp             --CCCHHHHHHHHHHHTSCCC-----------------------------HHHHHHHHHHTTTTTCCCBSSSHHHHHHHH
T ss_pred             cccccCchHHHHHHHHhccch-----------------------------hhhhhhhhhHHhhhccccchhhHHHHHHHH
Confidence            1234578 9999999996653                             457778888888         679999998


Q ss_pred             HHHhh
Q 041141          152 ALKKQ  156 (575)
Q Consensus       152 ~L~~~  156 (575)
                      +|...
T Consensus       494 ~l~~~  498 (756)
T 2qvw_A          494 RLRDI  498 (756)
T ss_dssp             HHHHS
T ss_pred             hhccc
Confidence            88765

>2kou_A Dicer-like protein 4; ATP-binding, endonuclease, helicase, hydrolase, nuclease, nucleotide-binding, nucleus, RNA- binding; NMR {Arabidopsis thaliana}

Probab=95.39  E-value=0.041  Score=48.02  Aligned_cols=71  Identities=15%  Similarity=0.190  Sum_probs=51.6

Q ss_pred             chhhHHHHHHHHcC-----CCCCeEEEeecCCCCCCeEEEEEEECCE----eeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141           87 VYKNLLQETSHRAG-----LKLPVYTTVRSGPGHGPVFSCTVELAGV----SFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        87 nyKS~LQE~cQK~g-----l~lP~Yev~esGP~H~p~Ftv~V~V~G~----~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      +.++.|+.||++..     ...|.|.+.+... ....| |+|.+-..    .+.+..-.|||.||+.||-.|...|.+.+
T Consensus         5 sAi~lL~~yC~~Lp~d~~~~~~P~~~~~~~~~-~~~~~-c~v~LP~~splr~i~g~~~~sk~~AK~sAAf~Ac~~L~~~G   82 (102)
T 2kou_A            5 SSISMMYKYCSRLPHDEFFQPKPEFQFKPVDE-FGGTI-CRITLPANAPISEIESSLLPSTEAAKKDACLKAVHELHNLG   82 (102)
T ss_dssp             HHHHHHHHHHTTSSSCTTCCSSCEEEEEECCG-GGCEE-EEEECCTTCSSCCEEEEEESSHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCccccCccceEEEeEeec-CCCeE-EEEECCCCCCCCeeeCCccccHHHHHHHHHHHHHHHHHHCC
Confidence            56889999999873     3578899752211 12367 88888541    22233459999999999999999999987


Q ss_pred             cc
Q 041141          158 KS  159 (575)
Q Consensus       158 ~~  159 (575)
                      .-
T Consensus        83 ~L   84 (102)
T 2kou_A           83 VL   84 (102)
T ss_dssp             SC
T ss_pred             CC
Confidence            55

>3htx_A HEN1; HEN1, small RNA methyltransferase, protein-RNA complex; HET: SAH; 3.10A {Arabidopsis thaliana}

Probab=89.30  E-value=0.45  Score=55.38  Aligned_cols=69  Identities=28%  Similarity=0.473  Sum_probs=48.9

Q ss_pred             chhhHHHHHHHHcCCCCCeEEEee------cC------CCCCC-eEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHH
Q 041141           87 VYKNLLQETSHRAGLKLPVYTTVR------SG------PGHGP-VFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSAL  153 (575)
Q Consensus        87 nyKS~LQE~cQK~gl~lP~Yev~e------sG------P~H~p-~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L  153 (575)
                      .||..++   ||.|- ...|++.+      .|      |..-+ .|.|.+.+-+..+-.|..+.||+|||.||..||++|
T Consensus        18 ~pk~~~~---q~~~~-~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~lp~~~~~~~~~~~kkd~eq~aa~~al~~~   93 (950)
T 3htx_A           18 TPKAIIH---QKFGA-KASYTVEEVHDSSQSGCPGLAIPQKGPCLYRCHLQLPEFSVVSNVFKKKKDSEQSAAELALDKL   93 (950)
T ss_dssp             CCHHHHH---HTTGG-GSEEEEEEECCSCSCCCTTCCSCCCCCCEEEEEEECSSCEEECCCBSCHHHHHHHHHHHHHTTT
T ss_pred             CHHHHHH---HHhCc-ceeeeehhhhcccCCCCCccccCCCCCeeEEEEeeCCCceEecchhhccccHHHHHHHHHHHHh
Confidence            5676554   33332 36787752      12      12222 789999987776667999999999999999999999


Q ss_pred             Hhhhcc
Q 041141          154 KKQAKS  159 (575)
Q Consensus       154 ~~~~~~  159 (575)
                      +..+..
T Consensus        94 g~~~~~   99 (950)
T 3htx_A           94 GIRPQN   99 (950)
T ss_dssp             TSTTTS
T ss_pred             CCCccc
Confidence            886544

>2db2_A KIAA0890 protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.08  E-value=1.1  Score=40.28  Aligned_cols=74  Identities=26%  Similarity=0.140  Sum_probs=50.0

Q ss_pred             ccCchhhHHHHHHHHcCC-----CCCeEEEeecCCCCCCeEEEEEEEC---CEeeeecccCCHHHHHHHHHHHHHHHHHh
Q 041141           84 ETGVYKNLLQETSHRAGL-----KLPVYTTVRSGPGHGPVFSCTVELA---GVSFTGEPAKTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl-----~lP~Yev~esGP~H~p~Ftv~V~V~---G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      +-..+|++|....|+.--     +.-.|-. .+|   .++=.|++++.   -.+| .|.|+.|-+||.+||.+|+++|+.
T Consensus        15 ~Fp~PKnLL~~ViqrA~~ss~~kd~l~~~~-t~g---~k~K~~tl~l~WP~~mef-~a~G~rK~eAE~kAAA~AC~kLK~   89 (119)
T 2db2_A           15 EFPQPKNLLNSVIGRALGISHAKDKLVYVH-TNG---PKKKKVTLHIKWPKSVEV-EGYGSKKIDAERQAAAAACQLFKG   89 (119)
T ss_dssp             TCSCHHHHHHHHHHHHTTHHHHHHHEEEEE-CCS---SSSEEEEEEECSSSCEEE-EEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             hCCChHHHHHHHHHHHHccCchhhheeEEe-ecC---CceeEEEEEecCCCcEEE-EeeccchHHHHHHHHHHHHHHHHH
Confidence            345799999987776421     1112322 233   23335666654   3344 599999999999999999999999


Q ss_pred             hhcccCC
Q 041141          156 QAKSAFS  162 (575)
Q Consensus       156 ~~~~~~s  162 (575)
                      ++..++.
T Consensus        90 Lgll~p~   96 (119)
T 2db2_A           90 WGLLGPR   96 (119)
T ss_dssp             HTSSCTT
T ss_pred             cCccCCC
Confidence            9877554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	575
d2nuga2	68	d.50.1.1 (A:151-218) RNase III, C-terminal domain	3e-15
d2nuga2	68	d.50.1.1 (A:151-218) RNase III, C-terminal domain	4e-13
d1x48a1	76	d.50.1.1 (A:8-83) dsRNA-dependent protein kinase p	4e-15
d1x48a1	76	d.50.1.1 (A:8-83) dsRNA-dependent protein kinase p	1e-13
d1o0wa2	69	d.50.1.1 (A:168-236) RNase III, C-terminal domain	4e-15
d1o0wa2	69	d.50.1.1 (A:168-236) RNase III, C-terminal domain	7e-15
d1x49a1	85	d.50.1.1 (A:8-92) dsRNA-dependent protein kinase p	5e-15
d1x49a1	85	d.50.1.1 (A:8-92) dsRNA-dependent protein kinase p	3e-12
d1qu6a1	90	d.50.1.1 (A:1-90) dsRNA-dependent protein kinase p	7e-14
d1qu6a1	90	d.50.1.1 (A:1-90) dsRNA-dependent protein kinase p	3e-12
d1x47a1	85	d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapie	8e-12
d1x47a1	85	d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapie	1e-10
d2b7ta1	73	d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (R	3e-11
d2b7ta1	73	d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (R	6e-09
d2b7va1	71	d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (R	5e-11
d2b7va1	71	d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (R	3e-09
d2dmya1	84	d.50.1.1 (A:8-91) Spermatid perinuclear RNA-bindin	6e-11
d2dmya1	84	d.50.1.1 (A:8-91) Spermatid perinuclear RNA-bindin	1e-09
d1di2a_	69	d.50.1.1 (A:) Double-stranded RNA-binding protein	3e-10
d1di2a_	69	d.50.1.1 (A:) Double-stranded RNA-binding protein	7e-09
d1t4oa_	81	d.50.1.1 (A:) RNase III, C-terminal domain {Baker'	4e-10
d1t4oa_	81	d.50.1.1 (A:) RNase III, C-terminal domain {Baker'	2e-06
d1ekza_	76	d.50.1.1 (A:) Staufen, domain III {Fruit fly (Dros	4e-10
d1ekza_	76	d.50.1.1 (A:) Staufen, domain III {Fruit fly (Dros	8e-09
d1whna_	128	d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like,	3e-09
d1whna_	128	d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like,	8e-08
d1whqa_	99	d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {	4e-09
d1whqa_	99	d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {	6e-08
d1qu6a2	89	d.50.1.1 (A:91-179) dsRNA-dependent protein kinase	2e-08
d1qu6a2	89	d.50.1.1 (A:91-179) dsRNA-dependent protein kinase	4e-08
d2cpna1	76	d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Hu	8e-08
d2cpna1	76	d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Hu	9e-07
d1uila_	113	d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {	1e-07
d1uila_	113	d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {	2e-07
d2dixa1	73	d.50.1.1 (A:7-79) Interferon-inducible double stra	7e-07
d2dixa1	73	d.50.1.1 (A:7-79) Interferon-inducible double stra	3e-06
d1uhza_	89	d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus muscul	5e-06
d1uhza_	89	d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus muscul	1e-04

>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 68

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

 Score = 68.5 bits (167), Expect = 3e-15
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRS-GPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
           YK +LQE + +   + P Y  +   GP H   F    ++      GE  K+KK+A++ AA
Sbjct: 2   YKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGE-GKSKKEAEQRAA 60

Query: 147 LAAWSALK 154
                 L+
Sbjct: 61  EELIKLLE 68

>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 68

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

 Score = 62.3 bits (151), Expect = 4e-13
 Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 3/68 (4%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
          YK  LQE+ Q+     P Y  I   GP H  +F                  + ++AE  A
Sbjct: 2  YKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLG--EGKSKKEAEQRA 59

Query: 61 AEVALDVL 68
          AE  + +L
Sbjct: 60 AEELIKLL 67

>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Length = 76

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.1 bits (166), Expect = 4e-15
 Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
          Y   +   AQ+   ++  Y       +   RF          + + +   T ++A+  AA
Sbjct: 1  YIGLVNSFAQKKKLSVN-YEQCEPNSELPQRFICKCKIGQTMYGTGS-GVTKQEAKQLAA 58

Query: 62 EVALDVLSKKGPS 74
          + A   L K  P 
Sbjct: 59 KEAYQKLLKSPPK 71

>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Length = 76

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.3 bits (156), Expect = 1e-13
 Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 1/77 (1%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
           Y  L+   + +  L +               F C  ++    +      TK++A++ AA 
Sbjct: 1   YIGLVNSFAQKKKLSVNYEQC-EPNSELPQRFICKCKIGQTMYGTGSGVTKQEAKQLAAK 59

Query: 148 AAWSALKKQAKSAFSSS 164
            A+  L K       +S
Sbjct: 60  EAYQKLLKSPPKTAGTS 76

>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 69

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 68.0 bits (166), Expect = 4e-15
 Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 1/67 (1%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
           YK  LQE         P Y  V         +F   V + G +      +TKK+A+K AA
Sbjct: 2   YKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAA 61

Query: 147 LAAWSAL 153
             A+  L
Sbjct: 62  RIAYEKL 68

>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 69

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 67.2 bits (164), Expect = 7e-15
 Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
          YK  LQE+ Q      P Y  +R    D    F   V  NG+T  +     T ++AE  A
Sbjct: 2  YKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGK-GRTKKEAEKEA 60

Query: 61 AEVALDVL 68
          A +A + L
Sbjct: 61 ARIAYEKL 68

>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.1 bits (166), Expect = 5e-15
 Identities = 20/82 (24%), Positives = 33/82 (40%)

Query: 83  DETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQ 142
           D  G Y + L +     G+ +       SGP H   F+  V +    F     ++K++A+
Sbjct: 4   DTPGFYMDKLNKYRQMHGVAITYKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSKQEAR 63

Query: 143 KNAALAAWSALKKQAKSAFSSS 164
             AA  A   L  + K    +S
Sbjct: 64  NAAAKLAVDILDNENKVDCHTS 85

>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.4 bits (146), Expect = 3e-12
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
          Y ++L +  Q       +Y  +   GP H  RF   V  + + F      S  ++A +AA
Sbjct: 9  YMDKLNKYRQMHGV-AITYKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSK-QEARNAA 66

Query: 61 AEVALDVLSKKG 72
          A++A+D+L  + 
Sbjct: 67 AKLAVDILDNEN 78

>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 7e-14
 Identities = 21/75 (28%), Positives = 32/75 (42%)

Query: 86  GVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNA 145
           G +   L     + G+ L       SGP H   F+  V + G  F     ++KK+A+  A
Sbjct: 13  GFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKNAA 72

Query: 146 ALAAWSALKKQAKSA 160
           A  A   L K+ K+ 
Sbjct: 73  AKLAVEILNKEKKAV 87

>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 3e-12
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 2  YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
          +  +L    Q+    +  Y  +   GP H  RF   V  +G  F      S  ++A++AA
Sbjct: 15 FMEELNTYRQKQGV-VLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSK-KEAKNAA 72

Query: 61 AEVALDVLSKKGPS 74
          A++A+++L+K+  +
Sbjct: 73 AKLAVEILNKEKKA 86

>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Dgcr8 protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 8e-12
 Identities = 19/75 (25%), Positives = 26/75 (34%), Gaps = 1/75 (1%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
              +L E   R     PVY            F  +V + GV++    A +KK A+  AA 
Sbjct: 11  EVCILHEYMQRVLKVRPVYNFF-ECENPSEPFGASVTIDGVTYGSGTASSKKLAKNKAAR 69

Query: 148 AAWSALKKQAKSAFS 162
           A    L        S
Sbjct: 70  ATLEILIPDFVKQTS 84

>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Dgcr8 protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 1e-10
 Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
              L E  QR     P Y+   E  + +  F A+V  +G T+ S T  S  + A++ AA
Sbjct: 11 EVCILHEYMQRVLKVRPVYNFF-ECENPSEPFGASVTIDGVTYGSGTASSK-KLAKNKAA 68

Query: 62 EVALDVL 68
             L++L
Sbjct: 69 RATLEIL 75

>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 73

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-specific editase 1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 57.2 bits (138), Expect = 3e-11
 Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 5/69 (7%)

Query: 3  KNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
          KN L +L +        Y  + + GP HAP F  +V  NG+ FE      T ++A+  AA
Sbjct: 7  KNALMQLNEI--KPGLQYMLLSQTGPVHAPLFVMSVEVNGQVFEGS--GPTKKKAKLHAA 62

Query: 62 EVALDVLSK 70
          E AL    +
Sbjct: 63 EKALRSFVQ 71

>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 73

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-specific editase 1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 50.7 bits (121), Expect = 6e-09
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 4/68 (5%)

Query: 89  KNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
           KN L + +         Y  + ++GP H P+F  +VE+ G  F G    TKK+A+ +AA 
Sbjct: 7   KNALMQLNEIK--PGLQYMLLSQTGPVHAPLFVMSVEVNGQVFEGS-GPTKKKAKLHAAE 63

Query: 148 AAWSALKK 155
            A  +  +
Sbjct: 64  KALRSFVQ 71

>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-specific editase 1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 56.4 bits (136), Expect = 5e-11
 Identities = 17/68 (25%), Positives = 25/68 (36%), Gaps = 8/68 (11%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
              L EL          Y  + E G  HA  F  +V  +G+ F         + A+  A
Sbjct: 6  PVMILNELRPG-----LKYDFLSESGESHAKSFVMSVVVDGQFF--EGSGRNKKLAKARA 58

Query: 61 AEVALDVL 68
          A+ AL  +
Sbjct: 59 AQSALATV 66

>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-specific editase 1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 51.4 bits (123), Expect = 3e-09
 Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 7/68 (10%)

Query: 88  YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
              +L E   R GLK   Y  +  SG  H   F  +V + G  F G   + KK A+  AA
Sbjct: 6   PVMILNE--LRPGLK---YDFLSESGESHAKSFVMSVVVDGQFFEGS-GRNKKLAKARAA 59

Query: 147 LAAWSALK 154
            +A + + 
Sbjct: 60  QSALATVF 67

>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Spermatid perinuclear RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (136), Expect = 6e-11
 Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 5/68 (7%)

Query: 2  YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
            N L  L Q        Y  + + GP HAP F  +V+ +G T+E+     + + A+   
Sbjct: 11 LMNALMRLNQI--RPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEA--SGPSKKTAKLHV 66

Query: 61 AEVALDVL 68
          A   L  +
Sbjct: 67 AVKVLQAM 74

>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Spermatid perinuclear RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.9 bits (127), Expect = 1e-09
 Identities = 19/82 (23%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 80  RVLDETGV-YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKT 137
           ++LD   +   N L   +         Y  + +SGP H PVF+ +V++ G ++      +
Sbjct: 2   KILDSKAIDLMNALMRLNQIR--PGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEA-SGPS 58

Query: 138 KKQAQKNAALAAWSALKKQAKS 159
           KK A+ + A+    A+      
Sbjct: 59  KKTAKLHVAVKVLQAMGYPTGF 80

>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]} Length = 69

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Double-stranded RNA-binding protein A, second dsRBD
species: Xenopus laevis [TaxId: 8355]

 Score = 54.3 bits (130), Expect = 3e-10
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 89  KNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
              LQE + + G +LP YT  + SGP H   F+ T  +     TG    +K+ A++ AA 
Sbjct: 3   VGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGSG-TSKQVAKRVAAE 61

Query: 148 AAWSALK 154
              +  K
Sbjct: 62  KLLTKFK 68

>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]} Length = 69

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Double-stranded RNA-binding protein A, second dsRBD
species: Xenopus laevis [TaxId: 8355]

 Score = 50.5 bits (120), Expect = 7e-09
 Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 3/69 (4%)

Query: 1  MYKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHA 59
          M    LQELA +  + LP Y+  +E GP H   F                 ++ + A+  
Sbjct: 1  MPVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGS--GTSKQVAKRV 58

Query: 60 AAEVALDVL 68
          AAE  L   
Sbjct: 59 AAEKLLTKF 67

>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.3 bits (130), Expect = 4e-10
 Identities = 13/65 (20%), Positives = 19/65 (29%), Gaps = 1/65 (1%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
           K QL  L   +      Y  +++     P           T         ++ A   AA
Sbjct: 8  AKRQLYSLIGYASLR-LHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAA 66

Query: 62 EVALD 66
          E AL 
Sbjct: 67 ENALR 71

>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 15/72 (20%), Positives = 20/72 (27%), Gaps = 2/72 (2%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEP-AKTKKQAQKNAA 146
            K  L      A L+   Y TV+      P       +   +  G    +  K A   AA
Sbjct: 8   AKRQLYSLIGYASLR-LHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAA 66

Query: 147 LAAWSALKKQAK 158
             A    K    
Sbjct: 67  ENALRDKKMLDF 78

>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 76

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Staufen, domain III
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 53.8 bits (129), Expect = 4e-10
 Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 4/70 (5%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
            +Q+ E+  +       +  +RE GP H   F  A        E     +  + ++  A
Sbjct: 9  PISQVHEIGIKRNMT-VHFKVLREEGPAHMKNFITACIVGSIVTEGE--GNGKKVSKKRA 65

Query: 61 AEVALDVLSK 70
          AE  L  L K
Sbjct: 66 AEKMLVELQK 75

>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 76

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Staufen, domain III
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 50.4 bits (120), Expect = 8e-09
 Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 1/68 (1%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
             + + E   +  + +        GP H   F     +  +   GE    KK ++K AA 
Sbjct: 9   PISQVHEIGIKRNMTVHFKVLREEGPAHMKNFITACIVGSIVTEGEG-NGKKVSKKRAAE 67

Query: 148 AAWSALKK 155
                L+K
Sbjct: 68  KMLVELQK 75

>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 128

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.2 bits (127), Expect = 3e-09
 Identities = 24/115 (20%), Positives = 36/115 (31%), Gaps = 14/115 (12%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
            K  L E  +R     P Y  ++        F + V    + ++S  +  + + AE  AA
Sbjct: 28  PKMCLLEWCRREKLPQPVYETVQ--RTIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAA 85

Query: 62  EVALDVLSKKGPSKVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHG 116
            V L                    G     L +    A  + P     RSGP  G
Sbjct: 86  IVCLRSQGLP----------EGRLGEESPSLNKRKREAPDQDP--GGPRSGPSSG 128

>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 128

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.0 bits (116), Expect = 8e-08
 Identities = 18/69 (26%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
            K  L E   R  L  PVY TV+           TV       +    K+KK A++ AA+
Sbjct: 28  PKMCLLEWCRREKLPQPVYETVQRTIDRMFCSVVTVAEQKY-QSTLWDKSKKLAEQTAAI 86

Query: 148 AAWSALKKQ 156
               +    
Sbjct: 87  VCLRSQGLP 95

>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: ATP-dependent RNA helicase A, Dhx9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.7 bits (123), Expect = 4e-09
 Identities = 14/74 (18%), Positives = 25/74 (33%), Gaps = 1/74 (1%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
           KN L     +     P+Y     G  +  +F   V   G  +      +  + A+  AA
Sbjct: 8  IKNFLYAWCGKRKM-TPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAA 66

Query: 62 EVALDVLSKKGPSK 75
             ++ L +    K
Sbjct: 67 RDFVNYLVRINEVK 80

>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: ATP-dependent RNA helicase A, Dhx9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.6 bits (115), Expect = 6e-08
 Identities = 22/92 (23%), Positives = 34/92 (36%), Gaps = 5/92 (5%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEP-AKTKKQAQKNAA 146
            KN L     +  +  P Y     G  +   F C V + G ++ G   +  KK AQ NAA
Sbjct: 8   IKNFLYAWCGKRKM-TPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAA 66

Query: 147 LAAWSALKKQAK---SAFSSSSFSPPSSESGT 175
               + L +  +       +    PP S   +
Sbjct: 67  RDFVNYLVRINEVKSEEVPAVGIVPPPSGPSS 98

>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
          Y   +  +AQ+    +    C   G      F        + +   T  ST ++A+  AA
Sbjct: 16 YIGLINRIAQKKRLTVNYEQC-ASGVHGPEGFHYKCKMGQKEYSIGT-GSTKQEAKQLAA 73

Query: 62 EVALDVLSKKGPS 74
          ++A   +  +   
Sbjct: 74 KLAYLQILSEETG 86

>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (116), Expect = 4e-08
 Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 86  GVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNA 145
           G Y  L+   + +  L +       SG      F    ++    ++     TK++A++ A
Sbjct: 14  GNYIGLINRIAQKKRLTVNYEQC-ASGVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLA 72

Query: 146 ALAAWSALKKQ 156
           A  A+  +  +
Sbjct: 73  AKLAYLQILSE 83

>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: TAR RNA-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.5 bits (112), Expect = 8e-08
 Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 3/68 (4%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
              LQEL  +  + LP Y+  +E GP H   F                 ++ + A+  A
Sbjct: 11 PVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIE--IGSGTSKKLAKRNA 68

Query: 61 AEVALDVL 68
          A   L  +
Sbjct: 69 AAKMLLRV 76

>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: TAR RNA-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 9e-07
 Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRS-GPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAA 146
               LQE   + G +LP YT  +  GP H   F+ T  +      G    +KK A++NAA
Sbjct: 11  PVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSG-TSKKLAKRNAA 69

Query: 147 LAAWSAL 153
                 +
Sbjct: 70  AKMLLRV 76

>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 113

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: ATP-dependent RNA helicase A, Dhx9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.1 bits (114), Expect = 1e-07
 Identities = 17/89 (19%), Positives = 26/89 (29%), Gaps = 9/89 (10%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGE-----PAKTKKQAQ 142
            K  L +   +       Y   + GP H   F   + +                 KK A 
Sbjct: 28  AKARLNQYFQKEK-IQGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAA 86

Query: 143 KNAALAAWSALKKQAKSAFSSSSFSPPSS 171
           ++ AL+    L          +  S PSS
Sbjct: 87  QSCALSLVRQLYHLGV---IEAYSSGPSS 112

>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 113

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: ATP-dependent RNA helicase A, Dhx9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.7 bits (113), Expect = 2e-07
 Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 5/75 (6%)

Query: 2   YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTF----CSTLRQAE 57
            K +L +  Q+       Y   + GPDH   F A +    +      F     S  + A 
Sbjct: 28  AKARLNQYFQKE-KIQGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAA 86

Query: 58  HAAAEVALDVLSKKG 72
            + A   +  L   G
Sbjct: 87  QSCALSLVRQLYHLG 101

>d2dixa1 d.50.1.1 (A:7-79) Interferon-inducible double stranded RNA-dependent protein kinase activator A {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Interferon-inducible double stranded RNA-dependent protein kinase activator A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 7e-07
 Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 2/67 (2%)

Query: 2  YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
              L E   ++           +   H P F   V     T       ++ + A+H AA
Sbjct: 4  PIQVLHEYGMKTKNIPVYECERSDVQIHVPTFTFRVTVGDITCT--GEGTSKKLAKHRAA 61

Query: 62 EVALDVL 68
          E A+++L
Sbjct: 62 EAAINIL 68

>d2dixa1 d.50.1.1 (A:7-79) Interferon-inducible double stranded RNA-dependent protein kinase activator A {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Interferon-inducible double stranded RNA-dependent protein kinase activator A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 3e-06
 Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 88  YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
              +L E   +                H P F+  V +  ++ TGE   +KK A+  AA 
Sbjct: 4   PIQVLHEYGMKTKNIPVYECERSDVQIHVPTFTFRVTVGDITCTGEG-TSKKLAKHRAAE 62

Query: 148 AAWSALKKQA 157
           AA + LK  A
Sbjct: 63  AAINILKANA 72

>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: staufen homolog 2
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.9 bits (100), Expect = 5e-06
 Identities = 15/74 (20%), Positives = 22/74 (29%), Gaps = 3/74 (4%)

Query: 3  KNQLQELAQRSCFNLPSY-SCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAA 61
           ++L ++ Q      P Y      G      F   V    E           + A+  AA
Sbjct: 9  ISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVA--TGTGPNKKIAKKNAA 66

Query: 62 EVALDVLSKKGPSK 75
          E  L  L  K  + 
Sbjct: 67 EAMLLQLGYKASTS 80

>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: staufen homolog 2
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.1 bits (90), Expect = 1e-04
 Identities = 20/78 (25%), Positives = 29/78 (37%), Gaps = 2/78 (2%)

Query: 89  KNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAAL 147
            + L +       K P Y  +   G      F   V++     TG     KK A+KNAA 
Sbjct: 9   ISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGTG-PNKKIAKKNAAE 67

Query: 148 AAWSALKKQAKSAFSSSS 165
           A    L  +A ++   S 
Sbjct: 68  AMLLQLGYKASTSLQDSG 85

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	575
d1o0wa2	69	RNase III, C-terminal domain {Thermotoga maritima	99.77
d1x48a1	76	dsRNA-dependent protein kinase pkr {Mouse (Mus mus	99.73
d2nuga2	68	RNase III, C-terminal domain {Aquifex aeolicus [Ta	99.73
d1di2a_	69	Double-stranded RNA-binding protein A, second dsRB	99.72
d1x49a1	85	dsRNA-dependent protein kinase pkr {Mouse (Mus mus	99.72
d1whqa_	99	ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus mus	99.72
d1qu6a1	90	dsRNA-dependent protein kinase pkr {Human (Homo sa	99.72
d2dixa1	73	Interferon-inducible double stranded RNA-dependent	99.71
d2cpna1	76	TAR RNA-binding protein 2 {Human (Homo sapiens) [T	99.71
d1uhza_	89	staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10	99.69
d1qu6a2	89	dsRNA-dependent protein kinase pkr {Human (Homo sa	99.67
d1uila_	113	ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus mus	99.67
d1ekza_	76	Staufen, domain III {Fruit fly (Drosophila melanog	99.65
d1x47a1	85	Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1whna_	128	tRNA-dihydrouridine synthase 2-like, Dus2l (231001	99.55
d1di2a_	69	Double-stranded RNA-binding protein A, second dsRB	99.54
d2b7va1	71	dsRNA-specific editase 1 {Rat (Rattus norvegicus)	99.53
d1o0wa2	69	RNase III, C-terminal domain {Thermotoga maritima	99.52
d1t4oa_	81	RNase III, C-terminal domain {Baker's yeast (Sacch	99.51
d2nuga2	68	RNase III, C-terminal domain {Aquifex aeolicus [Ta	99.47
d1qu6a1	90	dsRNA-dependent protein kinase pkr {Human (Homo sa	99.44
d1x48a1	76	dsRNA-dependent protein kinase pkr {Mouse (Mus mus	99.44
d1whqa_	99	ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus mus	99.42
d2b7ta1	73	dsRNA-specific editase 1 {Rat (Rattus norvegicus)	99.41
d2cpna1	76	TAR RNA-binding protein 2 {Human (Homo sapiens) [T	99.41
d2dixa1	73	Interferon-inducible double stranded RNA-dependent	99.4
d1x49a1	85	dsRNA-dependent protein kinase pkr {Mouse (Mus mus	99.4
d1uhza_	89	staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10	99.39
d2dmya1	84	Spermatid perinuclear RNA-binding protein {Human (	99.38
d1whna_	128	tRNA-dihydrouridine synthase 2-like, Dus2l (231001	99.31
d1ekza_	76	Staufen, domain III {Fruit fly (Drosophila melanog	99.29
d1qu6a2	89	dsRNA-dependent protein kinase pkr {Human (Homo sa	99.29
d1uila_	113	ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus mus	99.26
d1x47a1	85	Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]}	99.23
d2b7va1	71	dsRNA-specific editase 1 {Rat (Rattus norvegicus)	99.02
d1t4oa_	81	RNase III, C-terminal domain {Baker's yeast (Sacch	98.99
d2b7ta1	73	dsRNA-specific editase 1 {Rat (Rattus norvegicus)	98.95
d2dmya1	84	Spermatid perinuclear RNA-binding protein {Human (	98.76

>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.77  E-value=3.9e-19  Score=142.13  Aligned_cols=67  Identities=30%  Similarity=0.371  Sum_probs=64.9

Q ss_pred             chhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHH
Q 041141           87 VYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSAL  153 (575)
Q Consensus        87 nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L  153 (575)
                      |||+.||||||++++.+|.|+++ .+|++|.+.|++.|.|+|..++.|.|+|||+|||+||+.||+.|
T Consensus         1 d~Ks~LqE~~Qk~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~~~~g~g~sKK~Aeq~AA~~aL~~L   68 (69)
T d1o0wa2           1 DYKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEKL   68 (69)
T ss_dssp             CHHHHHHHHHHHHHSSCCEEEEEEEECCTTSCEEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHcCCCCCEEEEEEeeCCCCCceEEEEEEECCEEEEEEEeCCHHHHHHHHHHHHHHHh
Confidence            79999999999999999999988 78999999999999999999999999999999999999999987

>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=3.6e-18  Score=140.28  Aligned_cols=71  Identities=20%  Similarity=0.312  Sum_probs=65.8

Q ss_pred             hhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           88 YKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        88 yKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      ||++||||||++++.+ .|++.++||+|.+.|+|.|.|+|+.|+.|.|+|||+|||+||+.||+.|......
T Consensus         1 Y~s~L~E~~Qk~~~~~-~~~~~~~G~~h~~~F~~~v~v~~~~~~~g~G~sKK~Aeq~AA~~Al~~L~~~~~~   71 (76)
T d1x48a1           1 YIGLVNSFAQKKKLSV-NYEQCEPNSELPQRFICKCKIGQTMYGTGSGVTKQEAKQLAAKEAYQKLLKSPPK   71 (76)
T ss_dssp             HHHHHHHHHHHTTCCE-EEEECCCSSSSSCCEEEEEEESSCEEEEEEESSHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             ChHHHHHHHHHhCCCC-ccccCCcCCCCCCcEEEEEEECCEEeCCcCccHHHHHHHHHHHHHHHHHHccCCC
Confidence            8999999999999866 6777788999999999999999999999999999999999999999999988644

>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.73  E-value=3.3e-18  Score=136.83  Aligned_cols=67  Identities=28%  Similarity=0.366  Sum_probs=63.3

Q ss_pred             chhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHH
Q 041141           87 VYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALK  154 (575)
Q Consensus        87 nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~  154 (575)
                      |||+.||||||++++.+|.|+++ ..|++|.+.|+|.|.|+|.. +.|.|+|||+|||+||+.||+.|+
T Consensus         1 d~Ks~LqE~~q~~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~-~~g~g~sKK~Aeq~AA~~aL~~Lk   68 (68)
T d2nuga2           1 DYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYR-TLGEGKSKKEAEQRAAEELIKLLE   68 (68)
T ss_dssp             CHHHHHHHHHHHHHSCCCEEEEEEEESCGGGCEEEEEEEETTEE-EEEEESSHHHHHHHHHHHHHHHHC
T ss_pred             CcHHHHHHHHHHcCCCCCEEEEEEeeCCCCCcEEEEEEEECCEE-EEEecCCHHHHHHHHHHHHHHHhC
Confidence            79999999999999999999987 88999999999999999975 679999999999999999999883

>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Double-stranded RNA-binding protein A, second dsRBD
species: Xenopus laevis [TaxId: 8355]

Probab=99.72  E-value=5.2e-18  Score=136.32  Aligned_cols=66  Identities=29%  Similarity=0.350  Sum_probs=63.0

Q ss_pred             hhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHH
Q 041141           88 YKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALK  154 (575)
Q Consensus        88 yKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~  154 (575)
                      ||+.||||||++++++|.|+++ ++|++|.+.|+|.|.|+|..+ .|.|+|||+||++||+.||+.|+
T Consensus         2 Pv~~LqE~~q~~~~~~P~Y~~~~~~G~~h~~~F~~~v~v~~~~~-~g~g~sKK~Aeq~AA~~aL~~L~   68 (69)
T d1di2a_           2 PVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVE-TGSGTSKQVAKRVAAEKLLTKFK   68 (69)
T ss_dssp             HHHHHHHHHHHHTCCCCEEEEEEEESCGGGCEEEEEEEETTEEE-EEEESSHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHcCCCCCeEEEEEeeCCCCCcceEEEEEEeeEEE-ecCcCcHHHHHHHHHHHHHHHhc
Confidence            7999999999999999999998 789999999999999999875 79999999999999999999986

>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=4.3e-18  Score=142.15  Aligned_cols=76  Identities=26%  Similarity=0.405  Sum_probs=69.2

Q ss_pred             cccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           83 DETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        83 de~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      |.-.|||++||||||++++ .|.|+++ +.||+|.+.|+|.|.|+|..++.|.|+|||+||++||+.||+.|......
T Consensus         4 ~~~~~yk~~L~E~~Qk~~~-~~~y~~~~~~Gp~h~~~F~~~v~v~g~~~~~g~g~sKK~Aeq~AA~~aL~~L~~~~~~   80 (85)
T d1x49a1           4 DTPGFYMDKLNKYRQMHGV-AITYKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSKQEARNAAAKLAVDILDNENKV   80 (85)
T ss_dssp             CCTTHHHHHHHHHHHHHTC-CEEEEEEEEESCSSSCEEEEEEEESSCCCCCEEESSHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             CCchhHHHHHHHHHHhcCC-CCeEEEEEecCCCCCceEEEEEecCceEeeccccccHHHHHHHHHHHHHHHHHHcCcc
Confidence            4456999999999999999 5888887 88999999999999999999999999999999999999999999887543

>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: ATP-dependent RNA helicase A, Dhx9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=8.1e-18  Score=144.65  Aligned_cols=75  Identities=24%  Similarity=0.298  Sum_probs=68.6

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEee-eecccCCHHHHHHHHHHHHHHHHHhhhccc
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSF-TGEPAKTKKQAQKNAALAAWSALKKQAKSA  160 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~f-g~G~G~SKKeAEQ~AAk~ALe~L~~~~~~~  160 (575)
                      ..|||+.||||||++++ .|.|++.+.|++|.+.|+|+|.|+|..| +.|.|.|||+|||+||+.||+.|.+.+...
T Consensus         5 ~~~~Ks~LqE~~qk~k~-~P~Y~~~~~G~~h~~~F~~~v~v~g~~~~~~g~g~sKK~AEq~AA~~al~~L~~~~~~~   80 (99)
T d1whqa_           5 SSGIKNFLYAWCGKRKM-TPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAARDFVNYLVRINEVK   80 (99)
T ss_dssp             CCSSHHHHHHHHHHTTC-CCEEEEEEEECSSSEEEEEEEECTTCSCCEEEEESSHHHHHHHHHHHHHHHHHHHTSSC
T ss_pred             CccHHHHHHHHHHhCCC-CCeEEEecccCCCCceEEEEEEeccccceeccCCccHHHHHHHHHHHHHHHHHHcCCCC
Confidence            46999999999999988 5999988889999999999999999876 779999999999999999999998886643

>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=3.8e-18  Score=144.02  Aligned_cols=74  Identities=28%  Similarity=0.458  Sum_probs=68.0

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhhcc
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKS  159 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~  159 (575)
                      ..+||++||||||++++ .|.|.++ ++||+|.+.|+|.|.|+|..++.|.|.|||+||++||+.||+.|......
T Consensus        12 ~~~y~s~LqE~~Qk~~~-~p~y~~~~~~Gp~h~~~F~v~v~v~~~~~~~g~G~sKK~Aeq~AA~~aL~~L~~~~~~   86 (90)
T d1qu6a1          12 AGFFMEELNTYRQKQGV-VLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKNAAAKLAVEILNKEKKA   86 (90)
T ss_dssp             SCSHHHHHHHHHHHHTC-CCEEEEEESCBTTTBCCEEEEEESSSSCCCEEECCSSHHHHHHHHHHHHHHHHSCCSC
T ss_pred             CCCHHHHHHHHHHHhCC-CCcEEEEEeeCCCCCceEEEEEEECceeeeccCCCcHHHHHHHHHHHHHHHHHhhCCC
Confidence            45999999999999988 6888877 88999999999999999999999999999999999999999999877543

>d2dixa1 d.50.1.1 (A:7-79) Interferon-inducible double stranded RNA-dependent protein kinase activator A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Interferon-inducible double stranded RNA-dependent protein kinase activator A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.1e-17  Score=135.63  Aligned_cols=69  Identities=26%  Similarity=0.285  Sum_probs=64.5

Q ss_pred             CchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           86 GVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        86 ~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      .|||+.||||||++++ .|.|+++ ++||+|++.|+|.|.|++. ++.|.|+|||+||++||+.||..|+..
T Consensus         2 K~Pis~L~E~~qk~~~-~p~y~~~~~~Gp~h~~~F~~~v~v~~~-~~~g~g~sKK~Aeq~AA~~al~~L~~~   71 (73)
T d2dixa1           2 KTPIQVLHEYGMKTKN-IPVYECERSDVQIHVPTFTFRVTVGDI-TCTGEGTSKKLAKHRAAEAAINILKAN   71 (73)
T ss_dssp             CCHHHHHHHHHHHTTC-CCEEEEEEEECSSSSCEEEEEEEETTE-EEEECSSCTTHHHHHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHHhCCC-CCEEEEeeeeCCCCCcEEEEEEEEEEE-EEEeccccHHHHHHHHHHHHHHHHHhc
Confidence            5899999999999987 8999987 8899999999999999998 568999999999999999999999865

>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: TAR RNA-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.3e-17  Score=136.00  Aligned_cols=69  Identities=29%  Similarity=0.333  Sum_probs=64.8

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHH
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSAL  153 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L  153 (575)
                      ...|||+.||||||++++.+|.|+++ +.|++|.+.|+|.|.|++.. +.|.|+|||+||++||+.||+.|
T Consensus         7 ~~~npks~LqE~~q~~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~-~~g~G~SKK~Aeq~AA~~aL~~L   76 (76)
T d2cpna1           7 SECNPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFI-EIGSGTSKKLAKRNAAAKMLLRV   76 (76)
T ss_dssp             CCCCHHHHHHHHHHHHTCCCCEEEEEEEECCSSSCEEEEEEEETTEE-EEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHcCCCCCEEEEeeeeccCCCccEEEEEEeccee-eccccccHHHHHHHHHHHHHHhC
Confidence            35699999999999999999999988 79999999999999999986 77999999999999999999987

>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: staufen homolog 2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=3.9e-17  Score=137.58  Aligned_cols=71  Identities=23%  Similarity=0.142  Sum_probs=66.5

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ..|||+.||||||++++.+|.|+++ ++|++|.+.|+|.|.|+|+.+ .|.|.|||+||+.||+.||+.|...
T Consensus         5 ~~~P~s~LqE~~Q~~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~~-~g~g~SKK~Ae~~AA~~aL~~l~~~   76 (89)
T d1uhza_           5 SSGPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVA-TGTGPNKKIAKKNAAEAMLLQLGYK   76 (89)
T ss_dssp             SSCHHHHHHHHHHHTTSCCCEEEEEEEESCSTTCEEEEEEEETTEEE-EEEESSHHHHHHHHHHHHHHHHTSS
T ss_pred             CCCcHHHHHHHHHhcCCCCCEEEeccccccCCceeEEEEEEEeeeec-cccchHHHHHHHHHHHHHHHHhCcc
Confidence            4599999999999999999999988 789999999999999999986 6999999999999999999999654

>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=3e-17  Score=138.06  Aligned_cols=72  Identities=19%  Similarity=0.264  Sum_probs=67.5

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      ..|||++||||||++++. +.|++.+.|++|.+.|+|.|.|+|+.|+.|.|+|||+||++||+.||+.|....
T Consensus        13 ~~n~~s~L~E~~Qk~~~~-~~y~~~~~g~~h~~~F~~~v~i~g~~~~~g~G~sKK~Akq~AA~~Al~~L~~~~   84 (89)
T d1qu6a2          13 MGNYIGLINRIAQKKRLT-VNYEQCASGVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQILSEE   84 (89)
T ss_dssp             CCCCHHHHHHHHHHSCCE-EEEEEEEECSSSSSEEEEEEEEETTBCCEEEESSHHHHHHHHHHHHHHHHHHCC
T ss_pred             ccCHHHHHHHHHHhcCCC-cceeeeccCCCCCCceEEEEEECCccccccccchHHHHHHHHHHHHHHHHHccC
Confidence            569999999999999985 678888899999999999999999999999999999999999999999999875

>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: ATP-dependent RNA helicase A, Dhx9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=7.5e-17  Score=141.71  Aligned_cols=76  Identities=20%  Similarity=0.216  Sum_probs=68.9

Q ss_pred             CchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEE-----CCEeeeecccCCHHHHHHHHHHHHHHHHHhhhccc
Q 041141           86 GVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVEL-----AGVSFTGEPAKTKKQAQKNAALAAWSALKKQAKSA  160 (575)
Q Consensus        86 ~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V-----~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~~~  160 (575)
                      .|||++||||||++++. |.|++.+.||+|.+.|+|+|.|     ++..++.|.|+|||+|||+||+.||+.|.+++...
T Consensus        26 ~n~Ks~LqE~~Qk~k~~-p~Y~i~~~Gp~H~~~F~~~v~i~~~~~~~~~~~~G~G~sKK~AEq~AA~~~l~~L~~~g~i~  104 (113)
T d1uila_          26 ENAKARLNQYFQKEKIQ-GEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYHLGVIE  104 (113)
T ss_dssp             HHHHHHHHHHHHHSCCC-CCCEEEEESCSTTCEEEEEEEEEETTTTEEEEEECCCSSHHHHHHHHHHHHHHHHHHHTSSC
T ss_pred             cCHHHHHHHHHHhCCCC-CceEEeeeccCCCCeEEEEEEEeeeccCCeEEeecccchHHHHHHHHHHHHHHHHHHcCCcC
Confidence            48999999999999885 9999888899999999999999     56667789999999999999999999999998775


Q ss_pred             CC
Q 041141          161 FS  162 (575)
Q Consensus       161 ~s  162 (575)
                      +.
T Consensus       105 ~~  106 (113)
T d1uila_         105 AY  106 (113)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Staufen, domain III
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.65  E-value=3.3e-17  Score=133.95  Aligned_cols=70  Identities=19%  Similarity=0.222  Sum_probs=64.3

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ..||++.||||||+++++ |.|+++ +.||+|++.|+|+|.|+|. ++.|.|.|||+|||+||+.||+.|+++
T Consensus         6 ~k~Pvs~L~E~~q~~~~~-~~y~~~~~~G~~h~~~F~~~v~v~~~-~~~g~G~SKK~Aeq~AA~~al~~L~~l   76 (76)
T d1ekza_           6 KKSPISQVHEIGIKRNMT-VHFKVLREEGPAHMKNFITACIVGSI-VTEGEGNGKKVSKKRAAEKMLVELQKL   76 (76)
T ss_dssp             CSCHHHHHHHHHHHTTCC-CEEEESSSCCSSSCSCSSEEEEETTE-EEEECCCSTTSSSHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHhCCCC-CeEEEEEeeCCCCCeEEEEEEEEeee-EeeeccCcHHHHHHHHHHHHHHHHHcC
Confidence            469999999999999997 889987 7899999999999999887 467999999999999999999999763

>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Dgcr8 protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=4.5e-16  Score=129.63  Aligned_cols=70  Identities=26%  Similarity=0.282  Sum_probs=62.6

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHH
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALK  154 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~  154 (575)
                      ...|||+.||||||+.++.+|.|.+.. +.+|...|+|+|.|+|..++.|.|+|||.||++||+.||+.|.
T Consensus         7 ~~K~p~s~LqE~~Qk~~~~~p~Y~~~~-~~g~~~~F~~~v~i~g~~~~~g~G~sKK~Aeq~AA~~AL~~L~   76 (85)
T d1x47a1           7 NGKSEVCILHEYMQRVLKVRPVYNFFE-CENPSEPFGASVTIDGVTYGSGTASSKKLAKNKAARATLEILI   76 (85)
T ss_dssp             TCCCHHHHHHHHHHHHTCSCCEEEEEE-CSSSSCCEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHC
T ss_pred             CCcCHHHHHHHHHHHhCCCCCCeEEEe-cCCCCCCEEEEEEECCEEEecCCcchHHHHHHHHHHHHHHHHH
Confidence            356999999999999999999999873 2335567999999999999999999999999999999999984

>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=4.5e-15  Score=132.89  Aligned_cols=70  Identities=27%  Similarity=0.262  Sum_probs=63.3

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEECCEeeeeccc-CCHHHHHHHHHHHHHHHHHh
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEPA-KTKKQAQKNAALAAWSALKK  155 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~G~~fg~G~G-~SKKeAEQ~AAk~ALe~L~~  155 (575)
                      ...|||+.||||||++++.+|.|+++..  .|.+.|+|+|.|+|..|+.+.| +|||+|||+||+.||+.|..
T Consensus        24 ~~~~pKs~LqE~~Qk~~~~~P~Y~~~~~--~~~~~F~~~V~v~g~~~~s~~g~~SKK~AEq~AA~~AL~~Lg~   94 (128)
T d1whna_          24 PQITPKMCLLEWCRREKLPQPVYETVQR--TIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL   94 (128)
T ss_dssp             TTCCHHHHHHHHHHHTTCCCCCCCEEEC--SSSCCEEEEEEETTEEEEESSCBSSHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHhcCCCCCeEEEeec--ccCCCCEEEEEECCeEeeccCCcccHHHHHHHHHHHHHHHhCC
Confidence            3579999999999999999999998865  3778999999999999988776 89999999999999999953

>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Double-stranded RNA-binding protein A, second dsRBD
species: Xenopus laevis [TaxId: 8355]

Probab=99.54  E-value=5.6e-15  Score=118.37  Aligned_cols=67  Identities=27%  Similarity=0.333  Sum_probs=62.5

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHH
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLS   69 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~   69 (575)
                      |+|+.||||||++++.+|.|+++ .+|++|++.|++.|.|+|..+.  |.|.+||.|++.||+.||+.|.
T Consensus         1 ~Pv~~LqE~~q~~~~~~P~Y~~~~~~G~~h~~~F~~~v~v~~~~~~--g~g~sKK~Aeq~AA~~aL~~L~   68 (69)
T d1di2a_           1 MPVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVET--GSGTSKQVAKRVAAEKLLTKFK   68 (69)
T ss_dssp             CHHHHHHHHHHHHTCCCCEEEEEEEESCGGGCEEEEEEEETTEEEE--EEESSHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHcCCCCCeEEEEEeeCCCCCcceEEEEEEeeEEEe--cCcCcHHHHHHHHHHHHHHHhc
Confidence            89999999999999999999988 6799999999999999998764  5799999999999999999885

>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-specific editase 1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.53  E-value=4.8e-15  Score=119.96  Aligned_cols=67  Identities=24%  Similarity=0.241  Sum_probs=61.1

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhhh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQA  157 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~  157 (575)
                      ..|+++.|||||++     +.|+++ ++||+|.+.|+|.|.|+|..| .|.|.|||+||++||+.||+.|.++.
T Consensus         3 ~Knpv~~L~E~~~~-----~~y~~~~~~G~~h~~~F~~~v~v~~~~~-~g~G~SKK~Ak~~AA~~aL~~L~~~~   70 (71)
T d2b7va1           3 GKNPVMILNELRPG-----LKYDFLSESGESHAKSFVMSVVVDGQFF-EGSGRNKKLAKARAAQSALATVFNLH   70 (71)
T ss_dssp             SSCHHHHHHHHCCS-----CEEEEEECCCCTTTCCEEEEEECSSCEE-EEEESSHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHccC-----CeEEEeeeeCCCCCCeEEEEEEECCEEE-EecCCCHHHHHHHHHHHHHHHHHccC
Confidence            46999999999864     479988 889999999999999999998 69999999999999999999998763

>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.52  E-value=9e-15  Score=116.45  Aligned_cols=66  Identities=33%  Similarity=0.410  Sum_probs=62.2

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVL   68 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L   68 (575)
                      ||+.||||||++++.+|.|.++ ..|++|.+.|++.|.|+|..++. |.|.+||+|++.||+.||+.|
T Consensus         2 ~Ks~LqE~~Qk~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~~~~-g~g~sKK~Aeq~AA~~aL~~L   68 (69)
T d1o0wa2           2 YKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIAT-GKGRTKKEAEKEAARIAYEKL   68 (69)
T ss_dssp             HHHHHHHHHHHHHSSCCEEEEEEEECCTTSCEEEEEEEETTEEEEE-EEESSHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCCCCEEEEEEeeCCCCCceEEEEEEECCEEEEE-EEeCCHHHHHHHHHHHHHHHh
Confidence            8999999999999999999987 67999999999999999999876 589999999999999999887

>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.51  E-value=8.1e-15  Score=121.03  Aligned_cols=74  Identities=20%  Similarity=0.058  Sum_probs=63.4

Q ss_pred             ccCchhhHHHHHHHHcCCCCCeEEEeecCCCCCCeEEEEEEEC-CEeeeecccCCHHHHHHHHHHHHHHHHHhhhc
Q 041141           84 ETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELA-GVSFTGEPAKTKKQAQKNAALAAWSALKKQAK  158 (575)
Q Consensus        84 e~~nyKS~LQE~cQK~gl~lP~Yev~esGP~H~p~Ftv~V~V~-G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~~~  158 (575)
                      .+.|+|+.|+||||+.++. |.|++++.|.+|...|++.|.|. |..++.|.|.|||+|||+||+.||+.++.+.+
T Consensus         4 id~~~K~~L~e~~~~~g~~-P~Y~~~~~~~~~~~~f~v~~~v~~~~~~~~g~g~SKK~AEq~AA~~aL~~~~~l~k   78 (81)
T d1t4oa_           4 LDMNAKRQLYSLIGYASLR-LHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDF   78 (81)
T ss_dssp             CCTTHHHHHHHHHCCGGGC-CEEEEEECCCSSCCCEEEEEECTTCCEEEEEEESSHHHHHHHHHHHHHHCHHHHHH
T ss_pred             cccCHHHHHHHHHhcCCCC-cEEEEeccCCCCCCCEEEEEEEecCceEEecccchhhHHHHHHHHHHHHhccHHHH
Confidence            3569999999999999986 99999976666667777888774 66778899999999999999999999887654

>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.47  E-value=2.9e-14  Score=113.63  Aligned_cols=65  Identities=31%  Similarity=0.420  Sum_probs=60.3

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVL   68 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L   68 (575)
                      ||+.||||||++++.+|.|.++ ..|++|++.|++.|.|+|..+.  |.|.+||.|++.||+.||+.|
T Consensus         2 ~Ks~LqE~~q~~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~~~--g~g~sKK~Aeq~AA~~aL~~L   67 (68)
T d2nuga2           2 YKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTL--GEGKSKKEAEQRAAEELIKLL   67 (68)
T ss_dssp             HHHHHHHHHHHHHSCCCEEEEEEEESCGGGCEEEEEEEETTEEEE--EEESSHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHcCCCCCEEEEEEeeCCCCCcEEEEEEEECCEEEE--EecCCHHHHHHHHHHHHHHHh
Confidence            8999999999999999999987 7899999999999999997644  579999999999999999987

>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=5.9e-14  Score=118.00  Aligned_cols=71  Identities=25%  Similarity=0.460  Sum_probs=64.7

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCC
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGP   73 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~p   73 (575)
                      .||+.||||||++++ +|.|.++ ..|++|.+.|++.|.|+|..+.. |.|.+||+|++.||+.||+.|.+...
T Consensus        14 ~y~s~LqE~~Qk~~~-~p~y~~~~~~Gp~h~~~F~v~v~v~~~~~~~-g~G~sKK~Aeq~AA~~aL~~L~~~~~   85 (90)
T d1qu6a1          14 FFMEELNTYRQKQGV-VLKYQELPNSGPPHDRRFTFQVIIDGREFPE-GEGRSKKEAKNAAAKLAVEILNKEKK   85 (90)
T ss_dssp             SHHHHHHHHHHHHTC-CCEEEEEESCBTTTBCCEEEEEESSSSCCCE-EECCSSHHHHHHHHHHHHHHHHSCCS
T ss_pred             CHHHHHHHHHHHhCC-CCcEEEEEeeCCCCCceEEEEEEECceeeec-cCCCcHHHHHHHHHHHHHHHHHhhCC
Confidence            489999999999987 6899987 78999999999999999999866 58999999999999999999987754

>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.44  E-value=8.4e-14  Score=113.90  Aligned_cols=70  Identities=20%  Similarity=0.284  Sum_probs=64.3

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcCC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKGP   73 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~p   73 (575)
                      ||+.||||||++++.+ .|.+...|++|.+.|++.|.|+|..|+. |.|.+||+|++.||+.||..|....+
T Consensus         1 Y~s~L~E~~Qk~~~~~-~~~~~~~G~~h~~~F~~~v~v~~~~~~~-g~G~sKK~Aeq~AA~~Al~~L~~~~~   70 (76)
T d1x48a1           1 YIGLVNSFAQKKKLSV-NYEQCEPNSELPQRFICKCKIGQTMYGT-GSGVTKQEAKQLAAKEAYQKLLKSPP   70 (76)
T ss_dssp             HHHHHHHHHHHTTCCE-EEEECCCSSSSSCCEEEEEEESSCEEEE-EEESSHHHHHHHHHHHHHHHHHHSCC
T ss_pred             ChHHHHHHHHHhCCCC-ccccCCcCCCCCCcEEEEEEECCEEeCC-cCccHHHHHHHHHHHHHHHHHHccCC
Confidence            8999999999998876 7877788999999999999999999977 58999999999999999999998754

>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: ATP-dependent RNA helicase A, Dhx9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=7e-14  Score=119.83  Aligned_cols=70  Identities=19%  Similarity=0.248  Sum_probs=63.4

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      ||+.||||||++++ +|.|.+...|++|.+.|++.|.|+|..|..-|.|.+||.|++.||+.+|..|.+..
T Consensus         8 ~Ks~LqE~~qk~k~-~P~Y~~~~~G~~h~~~F~~~v~v~g~~~~~~g~g~sKK~AEq~AA~~al~~L~~~~   77 (99)
T d1whqa_           8 IKNFLYAWCGKRKM-TPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAARDFVNYLVRIN   77 (99)
T ss_dssp             SHHHHHHHHHHTTC-CCEEEEEEEECSSSEEEEEEEECTTCSCCEEEEESSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCC-CCeEEEecccCCCCceEEEEEEeccccceeccCCccHHHHHHHHHHHHHHHHHHcC
Confidence            89999999999988 59999888899999999999999998774435899999999999999999998764

>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-specific editase 1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.41  E-value=1.9e-13  Score=110.81  Aligned_cols=67  Identities=30%  Similarity=0.375  Sum_probs=56.5

Q ss_pred             chhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           87 VYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        87 nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ++|+.|+++.+.  ...|.|+++ ++|++|.+.|+|.|.|+|..| .|.|.|||+||++||+.||+.|.++
T Consensus         5 ~pK~~l~~L~e~--~~~~~y~~~~~~G~~h~~~F~~~v~v~~~~~-~g~G~SKK~Aeq~AA~~aL~~l~~~   72 (73)
T d2b7ta1           5 LPKNALMQLNEI--KPGLQYMLLSQTGPVHAPLFVMSVEVNGQVF-EGSGPTKKKAKLHAAEKALRSFVQF   72 (73)
T ss_dssp             SSHHHHHHHHHH--CSCCEEEEEEEECSSSSCEEEEEEESSSSEE-EEEESSHHHHHHHHHHHHHHHHHTC
T ss_pred             CCcCHHHHHHhc--CCCCEEEEEEeeCCCCCceEEEEEEECCEEE-EcCCCcHHHHHHHHHHHHHHHHhhC
Confidence            455555555443  256899998 789999999999999999988 6999999999999999999999764

>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: TAR RNA-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=2e-13  Score=110.79  Aligned_cols=65  Identities=23%  Similarity=0.265  Sum_probs=59.8

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVL   68 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L   68 (575)
                      ||+.||||||++++.+|.|.++ ..|++|.+.|++.|.|++... . |.|.+||.|++.||+.||..|
T Consensus        11 pks~LqE~~q~~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~~-~-g~G~SKK~Aeq~AA~~aL~~L   76 (76)
T d2cpna1          11 PVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIE-I-GSGTSKKLAKRNAAAKMLLRV   76 (76)
T ss_dssp             HHHHHHHHHHHHTCCCCEEEEEEEECCSSSCEEEEEEEETTEEE-E-EEESSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCEEEEeeeeccCCCccEEEEEEecceee-c-cccccHHHHHHHHHHHHHHhC
Confidence            7999999999999999999988 789999999999999998764 3 589999999999999999876

>d2dixa1 d.50.1.1 (A:7-79) Interferon-inducible double stranded RNA-dependent protein kinase activator A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Interferon-inducible double stranded RNA-dependent protein kinase activator A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=3.3e-13  Score=108.92  Aligned_cols=67  Identities=25%  Similarity=0.350  Sum_probs=60.3

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      +++.||||||++++ +|.|.++ .+|++|++.|++.|.|++.. .. |.|.+||+|++.||+.||..|...
T Consensus         4 Pis~L~E~~qk~~~-~p~y~~~~~~Gp~h~~~F~~~v~v~~~~-~~-g~g~sKK~Aeq~AA~~al~~L~~~   71 (73)
T d2dixa1           4 PIQVLHEYGMKTKN-IPVYECERSDVQIHVPTFTFRVTVGDIT-CT-GEGTSKKLAKHRAAEAAINILKAN   71 (73)
T ss_dssp             HHHHHHHHHHHTTC-CCEEEEEEEECSSSSCEEEEEEEETTEE-EE-ECSSCTTHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCC-CCEEEEeeeeCCCCCcEEEEEEEEEEEE-EE-eccccHHHHHHHHHHHHHHHHHhc
Confidence            68999999999987 7999987 78999999999999999874 44 589999999999999999999753

>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.40  E-value=1.7e-13  Score=113.93  Aligned_cols=69  Identities=26%  Similarity=0.430  Sum_probs=63.4

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      ||+.||||||++++ .|.|.++ ..|++|.+.|++.|.|+|..++. |.|.+||.|++.||+.+|..|....
T Consensus         9 yk~~L~E~~Qk~~~-~~~y~~~~~~Gp~h~~~F~~~v~v~g~~~~~-g~g~sKK~Aeq~AA~~aL~~L~~~~   78 (85)
T d1x49a1           9 YMDKLNKYRQMHGV-AITYKELSTSGPPHDRRFTFQVLIDEKEFPE-AKGRSKQEARNAAAKLAVDILDNEN   78 (85)
T ss_dssp             HHHHHHHHHHHHTC-CEEEEEEEEESCSSSCEEEEEEEESSCCCCC-EEESSHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHhcCC-CCeEEEEEecCCCCCceEEEEEecCceEeec-cccccHHHHHHHHHHHHHHHHHHcC
Confidence            89999999999998 4899887 78999999999999999999876 5899999999999999999998764

>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: staufen homolog 2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=3e-13  Score=113.48  Aligned_cols=68  Identities=22%  Similarity=0.190  Sum_probs=62.7

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      +|+.||||||++++.+|.|+++ ..|++|.+.|++.|+|+|..++  |.|.+||.|++.||+.||+.|...
T Consensus         8 P~s~LqE~~Q~~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~~~--g~g~SKK~Ae~~AA~~aL~~l~~~   76 (89)
T d1uhza_           8 PISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVAT--GTGPNKKIAKKNAAEAMLLQLGYK   76 (89)
T ss_dssp             HHHHHHHHHHHTTSCCCEEEEEEEESCSTTCEEEEEEEETTEEEE--EEESSHHHHHHHHHHHHHHHHTSS
T ss_pred             cHHHHHHHHHhcCCCCCEEEeccccccCCceeEEEEEEEeeeecc--ccchHHHHHHHHHHHHHHHHhCcc
Confidence            6899999999999999999988 6899999999999999999875  579999999999999999999643

>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Spermatid perinuclear RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=3.4e-13  Score=112.27  Aligned_cols=66  Identities=24%  Similarity=0.331  Sum_probs=57.4

Q ss_pred             cCchhhHHHHHHHHcCCCCCeEEEe-ecCCCCCCeEEEEEEECCEeeeecccCCHHHHHHHHHHHHHHHHHhh
Q 041141           85 TGVYKNLLQETSHRAGLKLPVYTTV-RSGPGHGPVFSCTVELAGVSFTGEPAKTKKQAQKNAALAAWSALKKQ  156 (575)
Q Consensus        85 ~~nyKS~LQE~cQK~gl~lP~Yev~-esGP~H~p~Ftv~V~V~G~~fg~G~G~SKKeAEQ~AAk~ALe~L~~~  156 (575)
                      ..|+++.|+|+     .+.|.|+++ ++||+|.+.|+|.|.|+|..| .|.|.|||+|||+||+.||+.|+..
T Consensus        11 ~~n~~~~L~e~-----~~~~~Y~~~~~~Gp~h~~~F~~~v~v~g~~~-~g~G~SKK~Aeq~AA~~aL~~L~~~   77 (84)
T d2dmya1          11 LMNALMRLNQI-----RPGLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAMGYP   77 (84)
T ss_dssp             CTHHHHHHHHH-----SCSCCCEEEEEESCSSSCEEEEEEEETTEEE-EEEESSHHHHHHHHHHHHHHHHTCC
T ss_pred             ccCHHHHHHHh-----CCCCeEEEEEeeCCCCCCeEEEEEEECCEEE-EcCCCCHHHHHHHHHHHHHHHhCCC
Confidence            34777777776     356789998 889999999999999999987 5999999999999999999999543

>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.31  E-value=1.7e-12  Score=115.92  Aligned_cols=68  Identities=22%  Similarity=0.241  Sum_probs=61.6

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      +||+.||||||++++.+|.|.++.++  |.+.|++.|.|+|..|.+++++.+||.||+.||+.||..|..
T Consensus        27 ~pKs~LqE~~Qk~~~~~P~Y~~~~~~--~~~~F~~~V~v~g~~~~s~~g~~SKK~AEq~AA~~AL~~Lg~   94 (128)
T d1whna_          27 TPKMCLLEWCRREKLPQPVYETVQRT--IDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL   94 (128)
T ss_dssp             CHHHHHHHHHHHTTCCCCCCCEEECS--SSCCEEEEEEETTEEEEESSCBSSHHHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHhcCCCCCeEEEeecc--cCCCCEEEEEECCeEeeccCCcccHHHHHHHHHHHHHHHhCC
Confidence            58999999999999999999987654  778999999999999988655689999999999999999964

>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Staufen, domain III
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.29  E-value=9.9e-13  Score=107.02  Aligned_cols=66  Identities=23%  Similarity=0.252  Sum_probs=59.3

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      +++.||||||++++. |.|.++ ..|++|++.|++.|.|+|..+.  |.|.+||.|++.||+.+|..|..
T Consensus         9 Pvs~L~E~~q~~~~~-~~y~~~~~~G~~h~~~F~~~v~v~~~~~~--g~G~SKK~Aeq~AA~~al~~L~~   75 (76)
T d1ekza_           9 PISQVHEIGIKRNMT-VHFKVLREEGPAHMKNFITACIVGSIVTE--GEGNGKKVSKKRAAEKMLVELQK   75 (76)
T ss_dssp             HHHHHHHHHHHTTCC-CEEEESSSCCSSSCSCSSEEEEETTEEEE--ECCCSTTSSSHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCCCC-CeEEEEEeeCCCCCeEEEEEEEEeeeEee--eccCcHHHHHHHHHHHHHHHHHc
Confidence            689999999999997 899988 6799999999999999886543  57999999999999999999864

>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-dependent protein kinase pkr
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=1.4e-12  Score=109.18  Aligned_cols=69  Identities=17%  Similarity=0.227  Sum_probs=63.3

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      ||+.||||||++++. +.|.+.+.|++|.+.|.+.|.|+|..|+. |.|.+||+|++.||+.||..|....
T Consensus        16 ~~s~L~E~~Qk~~~~-~~y~~~~~g~~h~~~F~~~v~i~g~~~~~-g~G~sKK~Akq~AA~~Al~~L~~~~   84 (89)
T d1qu6a2          16 YIGLINRIAQKKRLT-VNYEQCASGVHGPEGFHYKCKMGQKEYSI-GTGSTKQEAKQLAAKLAYLQILSEE   84 (89)
T ss_dssp             CHHHHHHHHHHSCCE-EEEEEEEECSSSSSEEEEEEEEETTBCCE-EEESSHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHhcCCC-cceeeeccCCCCCCceEEEEEECCccccc-cccchHHHHHHHHHHHHHHHHHccC
Confidence            899999999999886 58988889999999999999999999977 4899999999999999999998753

>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: ATP-dependent RNA helicase A, Dhx9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.26  E-value=4.7e-12  Score=110.79  Aligned_cols=69  Identities=23%  Similarity=0.307  Sum_probs=60.2

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEEC-----CeeeecccccccccHHHHHHHHHHHHHHHhcC
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFN-----GETFESPTFCSTLRQAEHAAAEVALDVLSKKG   72 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtIn-----G~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~~   72 (575)
                      +|+.||||||++++. |.|.+...|++|.+.|+++|.|+     +..++. |.|.+||.|++.||+.+|+.|...+
T Consensus        28 ~Ks~LqE~~Qk~k~~-p~Y~i~~~Gp~H~~~F~~~v~i~~~~~~~~~~~~-G~G~sKK~AEq~AA~~~l~~L~~~g  101 (113)
T d1uila_          28 AKARLNQYFQKEKIQ-GEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAR-EHGSNKKLAAQSCALSLVRQLYHLG  101 (113)
T ss_dssp             HHHHHHHHHHHSCCC-CCCEEEEESCSTTCEEEEEEEEEETTTTEEEEEE-CCCSSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCC-CceEEeeeccCCCCeEEEEEEEeeeccCCeEEee-cccchHHHHHHHHHHHHHHHHHHcC
Confidence            699999999999875 99998788999999999999993     444444 5899999999999999999998754

>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Dgcr8 protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=8.8e-12  Score=103.33  Aligned_cols=69  Identities=26%  Similarity=0.302  Sum_probs=59.8

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      .||+.||||||+.++.+|.|.++. +.+|...|.+.|.|+|..++. |.|.+||.|++.||+.||+.|...
T Consensus        10 ~p~s~LqE~~Qk~~~~~p~Y~~~~-~~g~~~~F~~~v~i~g~~~~~-g~G~sKK~Aeq~AA~~AL~~L~~~   78 (85)
T d1x47a1          10 SEVCILHEYMQRVLKVRPVYNFFE-CENPSEPFGASVTIDGVTYGS-GTASSKKLAKNKAARATLEILIPD   78 (85)
T ss_dssp             CHHHHHHHHHHHHTCSCCEEEEEE-CSSSSCCEEEEEEETTEEEEE-EEESSHHHHHHHHHHHHHHHHCSS
T ss_pred             CHHHHHHHHHHHhCCCCCCeEEEe-cCCCCCCEEEEEEECCEEEec-CCcchHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999873 233556799999999999876 589999999999999999998654

>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-specific editase 1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.02  E-value=1.2e-10  Score=93.73  Aligned_cols=63  Identities=27%  Similarity=0.294  Sum_probs=56.3

Q ss_pred             cHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141            2 YKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      +++.|||||++     +.|+++ .+|++|.+.|++.|.|+|..|.  |.|.+||.|+++||+.||+.|...
T Consensus         6 pv~~L~E~~~~-----~~y~~~~~~G~~h~~~F~~~v~v~~~~~~--g~G~SKK~Ak~~AA~~aL~~L~~~   69 (71)
T d2b7va1           6 PVMILNELRPG-----LKYDFLSESGESHAKSFVMSVVVDGQFFE--GSGRNKKLAKARAAQSALATVFNL   69 (71)
T ss_dssp             HHHHHHHHCCS-----CEEEEEECCCCTTTCCEEEEEECSSCEEE--EEESSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccC-----CeEEEeeeeCCCCCCeEEEEEEECCEEEE--ecCCCHHHHHHHHHHHHHHHHHcc
Confidence            57899999875     379988 7899999999999999999985  579999999999999999998753

>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: RNase III, C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.99  E-value=1.4e-10  Score=95.31  Aligned_cols=66  Identities=20%  Similarity=0.190  Sum_probs=55.6

Q ss_pred             cHHHHHHHHHHcCCCCCceEEeecCCCCCCceEEEEEEC-CeeeecccccccccHHHHHHHHHHHHHHH
Q 041141            2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFN-GETFESPTFCSTLRQAEHAAAEVALDVLS   69 (575)
Q Consensus         2 yKS~LQElcQK~gl~LPeY~li~eGP~Hap~Fta~VtIn-G~~fEAgG~G~SKKeAeq~AAk~AL~~L~   69 (575)
                      +|+.|+||||+.|+. |.|+++..|..|...|.+.|.|. +..++. |.|.+||.|++.||+.||+.+.
T Consensus         8 ~K~~L~e~~~~~g~~-P~Y~~~~~~~~~~~~f~v~~~v~~~~~~~~-g~g~SKK~AEq~AA~~aL~~~~   74 (81)
T d1t4oa_           8 AKRQLYSLIGYASLR-LHYVTVKKPTAVDPNSIVECRVGDGTVLGT-GVGRNIKIAGIRAAENALRDKK   74 (81)
T ss_dssp             HHHHHHHHHCCGGGC-CEEEEEECCCSSCCCEEEEEECTTCCEEEE-EEESSHHHHHHHHHHHHHHCHH
T ss_pred             HHHHHHHHHhcCCCC-cEEEEeccCCCCCCCEEEEEEEecCceEEe-cccchhhHHHHHHHHHHHHhcc
Confidence            799999999999986 99999977767777888888875 455444 5899999999999999997654

>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: dsRNA-specific editase 1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.95  E-value=8e-10  Score=89.17  Aligned_cols=66  Identities=35%  Similarity=0.446  Sum_probs=57.3

Q ss_pred             CcHHHHHHHHHHcCCCCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHh
Q 041141            1 MYKNQLQELAQRSCFNLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSK   70 (575)
Q Consensus         1 myKS~LQElcQK~gl~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k   70 (575)
                      ++|+.|+++-+..  ..|.|+++ ..|++|.+.|++.|.|+|..|+  |.|.+||.|++.||+.||+.|.+
T Consensus         5 ~pK~~l~~L~e~~--~~~~y~~~~~~G~~h~~~F~~~v~v~~~~~~--g~G~SKK~Aeq~AA~~aL~~l~~   71 (73)
T d2b7ta1           5 LPKNALMQLNEIK--PGLQYMLLSQTGPVHAPLFVMSVEVNGQVFE--GSGPTKKKAKLHAAEKALRSFVQ   71 (73)
T ss_dssp             SSHHHHHHHHHHC--SCCEEEEEEEECSSSSCEEEEEEESSSSEEE--EEESSHHHHHHHHHHHHHHHHHT
T ss_pred             CCcCHHHHHHhcC--CCCEEEEEEeeCCCCCceEEEEEEECCEEEE--cCCCcHHHHHHHHHHHHHHHHhh
Confidence            4688888886653  55799998 6799999999999999999985  57999999999999999999865

>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: dsRNA-binding domain-like
family: Double-stranded RNA-binding domain (dsRBD)
domain: Spermatid perinuclear RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.76  E-value=8.4e-09  Score=85.29  Aligned_cols=54  Identities=26%  Similarity=0.406  Sum_probs=48.5

Q ss_pred             CCCceEEe-ecCCCCCCceEEEEEECCeeeecccccccccHHHHHHHHHHHHHHHhc
Q 041141           16 NLPSYSCI-REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVALDVLSKK   71 (575)
Q Consensus        16 ~LPeY~li-~eGP~Hap~Fta~VtInG~~fEAgG~G~SKKeAeq~AAk~AL~~L~k~   71 (575)
                      ..|+|.++ ..|++|.+.|++.|.|+|..|.  |.|.+||.|++.||+.||+.|...
T Consensus        23 ~~~~Y~~~~~~Gp~h~~~F~~~v~v~g~~~~--g~G~SKK~Aeq~AA~~aL~~L~~~   77 (84)
T d2dmya1          23 PGLQYKLLSQSGPVHAPVFTMSVDVDGTTYE--ASGPSKKTAKLHVAVKVLQAMGYP   77 (84)
T ss_dssp             CSCCCEEEEEESCSSSCEEEEEEEETTEEEE--EEESSHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCeEEEEEeeCCCCCCeEEEEEEECCEEEE--cCCCCHHHHHHHHHHHHHHHhCCC
Confidence            45799987 7899999999999999999885  589999999999999999999643