Psyllid ID: psy5350

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------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-------

MARVSNVSDEVEDKADINMPSTVSLDCNEVKVEENSPSRVLFDNNEIKQIPKVSTNNLPLEEAARLEVMRLNTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNAAKSVLDQLIGRDDEKLMCQKENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAALNMLKFLETVPIEIPEKKQGEDVDEKGESNGLKHTHDSTFLTPQILKKIQQYHTVFSQKTKGPLLEKLLSTRNLIDEVEDPILYLEDLSDELKYRVSFVDIEEKSKADGFQSLLQLTTTPVTVFCGTGASIEVAKIEAVYRALDFLQIMNR

ccccccccHHHHHHccccccccccccccccccccccccccccccHHHcccccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHcccccEEEEEEEEcccccccEEEEEEEcccccEEEEEcccccHHHHHHHHHHHHHHHHHcccHHHHHHHHcccccccccHHHHHHHHHHHccccccEEEEEEccccccccEEEEEEEEccEEEEEEEccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccHHHHHccccccccccccHHHHHHHHHHHcccEEEEEEEccccccccEEEEEEEEEcccEEEEEEEccHHHHHHHHHHHHHHHHHHHcc

ccEEcccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccHHHHHcccccccHHHHHHHHHHHcccccEEEEEEcccccccccEEEEEEEcccccEEEEEEccccHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHcccccEEEEEEEEccHHHcEEEEEEEEccEEEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccHHHHccccccccccccHHHHHHHHHHHcccEEEEEEccccccccEEEEEEEEcccccEEEccccccHHHHHHHHHHHHHHHHHHHcc

marvsnvsdevedkadinmpstvsldcnevkveenspsrvlfdnneikqipkvstnnlpleeAARLEVMrlntgdrtpVSLMQELLSrrgtapkyeLIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNAAKSVLDQligrddekLMCQkenlfkvepnpvgqlqeacmtrkwpppvyeteettglphermFTVCAYVNVYkeegmgksKKIAKREAALNMLKFLEtvpieipekkqgedvdekgesnglkhthdstfltpQILKKIQQYHTVFSQKTKGPLLEKLLSTrnlidevedpilYLEDLSDELKYRVSFVdieekskadGFQSLlqltttpvtvfcgtgasiEVAKIEAVYRALDFLQIMNR

marvsnvsdevedkadinmpstvsldcneVKVEenspsrvlfdnneikqipkvstnnlpleEAARLEvmrlntgdrtpVSLMQELLsrrgtapkyeliqiegainepIFKYRISLTSESRLYVAIGsgkskkeakhnAAKSVLDQLIGRDDEKLMCQKENLfkvepnpvgqLQEACMTRKWPPPVYETEettglphermFTVCAYVNVYKEEGMGKSKKIAKREAALNMLKFletvpieipekkqgedvDEKGesnglkhthdstfLTPQILKKIQQYHTVFSQKTKGPLLEKLLSTRNLIDEVEDPILYLEDLSDELKYRVSFVDIEEKSKADGFQSLLQLTTTPVTVFCGTGASIEVAKIEAVYRALDFLQIMNR

*********************************************************************************M*ELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIG*******************LIG****KLMCQKENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGM*****IAKREAALNMLKFLETVPI**************************TFLTPQILKKIQQYHTVFSQKTKGPLLEKLLSTRNLIDEVEDPILYLEDLSDELKYRVSFVDIEEKSKADGFQSLLQLTTTPVTVFCGTGASIEVAKIEAVYRALDFLQI***

*******************************************************************************SLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNAAKSVLDQLIGRDDEKLMCQKENLFKVEPNPVGQLQEACMTRKWPPPVY*********HERMFTVCAYVNVYKEEGMGKSKKIAKREAALNMLK*******************************************************************************LEDLSDELKYRVSFVDIEEKSKADGFQSLLQLTTTPVTVFCGTGASIEVAKIEAVYRALDFLQIMNR

************DKADINMPSTVSLDCNEVKVEENSPSRVLFDNNEIKQIPKVSTNNLPLEEAARLEVMRLNTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIG*************KSVLDQLIGRDDEKLMCQKENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAALNMLKFLETVPIEIPEKK***************HTHDSTFLTPQILKKIQQYHTVFSQKTKGPLLEKLLSTRNLIDEVEDPILYLEDLSDELKYRVSFVDIEEKSKADGFQSLLQLTTTPVTVFCGTGASIEVAKIEAVYRALDFLQIMNR

*****************************************************************LE****NTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNAAKSVLDQLIGRDDEKLMCQKEN***VEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAALNMLKFLETVPI*****************************************************EK*L***NLIDEVEDPILYLEDLSDELKYRVSFVDIEEKSKADGFQSLLQLTTTPVTVFCGTGASIEVAKIEAVYRALDFLQIMNR

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		377	2.2.26 [Sep-21-2011]
Q7ZYA5		309	Interferon-inducible doub	N/A	N/A	0.750	0.915	0.307	2e-30
Q91836		298	Interferon-inducible doub	N/A	N/A	0.737	0.932	0.304	2e-29
Q7SXR1		346	RISC-loading complex subu	yes	N/A	0.763	0.832	0.300	1e-26
P97473		365	RISC-loading complex subu	yes	N/A	0.779	0.805	0.280	1e-24
Q5BJ52		351	RISC-loading complex subu	yes	N/A	0.774	0.831	0.298	4e-24
Q4SS66		345	RISC-loading complex subu	N/A	N/A	0.750	0.820	0.293	2e-23
Q2HJ92		313	Interferon-inducible doub	yes	N/A	0.713	0.859	0.292	3e-22
Q6GPZ1		351	RISC-loading complex subu	N/A	N/A	0.755	0.811	0.290	4e-22
Q4V8C7		313	Interferon-inducible doub	yes	N/A	0.713	0.859	0.288	6e-22
Q9WTX2		313	Interferon-inducible doub	no	N/A	0.713	0.859	0.288	9e-22

>sp\|Q7ZYA5\|PRKAA_XENLA Interferon-inducible double stranded RNA-dependent protein kinase activator A homolog A OS=Xenopus laevis GN=prkra-a PE=2 SV=1	Back alignment and function desciption

 Score =  133 bits (334), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 104/338 (30%), Positives = 160/338 (47%), Gaps = 55/338 (16%)

Query: 51  PKVSTNNLPLEEAARLEVMRLNTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFK 110
           PK+S+     E+   L+ MR      TP+ L+ E  ++ G  P Y L + EG  + P F 
Sbjct: 10  PKMSS-----EKPTSLDAMRATNPCETPIQLLHEFGTKTGNHPVYTLEKAEGQAHNPSFT 64

Query: 111 YRISLTSESRLYVAIGSGKSKKEAKHNAAKSVLDQLIGRDDEKLMCQKENLF-------K 163
           +R+ +        ++G G SKK AK  AA+  L+ L G D  K +   + L        +
Sbjct: 65  FRLVIGD----ITSLGEGPSKKTAKQKAAEFALNILRG-DTSKCLPVTDTLRDPKKPPNQ 119

Query: 164 VEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKR 223
           ++ NPVG LQE  + + W  P Y   + +G PH+R FT+   V  + E G G SK++AKR
Sbjct: 120 MQENPVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGSGTSKQVAKR 179

Query: 224 EAALNMLKFLETVPIE-IP-----EKKQGEDVDEKGESNGLKHTHDSTFLTPQILKKIQQ 277
            AA  +L   +T+  + IP       K G   D    S+G K                  
Sbjct: 180 VAAEKLLTKFKTISTDNIPLNKLIGNKMGCTWDSMRNSSGEK------------------ 221

Query: 278 YHTVFSQKTKGPLLEKLLSTRNLIDEVEDPILYLEDLSDELKYRVSFVDIEEKSKADGFQ 337
                S   + P     LS  N      D +  L+D+++EL + ++++DI+E S    +Q
Sbjct: 222 ----ISMLKRSP-----LSIPN-----TDYVKMLKDVAEELDFNLTYLDIDELSVNGQYQ 267

Query: 338 SLLQLTTTPVTVFCGTGASIEVAKIEAVYRALDFLQIM 375
            L +L+T P+TV  GTG S   A  +A + AL +L+IM
Sbjct: 268 CLAELSTNPITVCHGTGISCGNAHNDAAHNALQYLKIM 305

Activates eif2ak2/pkr in the absence of double stranded RNA (dsRNA), leading to phosphorylation of eif2s1/efi2-alpha and inhibition of translation and induction of apoptosis. Required for siRNA production by dicer1 and for subsequent siRNA-mediated post-transcriptional gene silencing. Does not seem to be required for processing of pre-miRNA to miRNA by dicer1.
Xenopus laevis (taxid: 8355)

>sp\|Q91836\|PRKAB_XENLA Interferon-inducible double stranded RNA-dependent protein kinase activator A homolog B OS=Xenopus laevis GN=prkra-b PE=1 SV=1	Back alignment and function description

>sp\|Q7SXR1\|TRBP2_DANRE RISC-loading complex subunit tarbp2 OS=Danio rerio GN=tarbp2 PE=2 SV=1	Back alignment and function description

>sp\|P97473\|TRBP2_MOUSE RISC-loading complex subunit TARBP2 OS=Mus musculus GN=Tarbp2 PE=1 SV=2	Back alignment and function description

>sp\|Q5BJ52\|TRBP2_XENTR RISC-loading complex subunit tarbp2 OS=Xenopus tropicalis GN=tarbp2 PE=2 SV=2	Back alignment and function description

>sp\|Q4SS66\|TRBP2_TETNG RISC-loading complex subunit tarbp2 OS=Tetraodon nigroviridis GN=tarbp2 PE=3 SV=1	Back alignment and function description

>sp\|Q2HJ92\|PRKRA_BOVIN Interferon-inducible double stranded RNA-dependent protein kinase activator A OS=Bos taurus GN=PRKRA PE=2 SV=1	Back alignment and function description

>sp\|Q6GPZ1\|TRBP2_XENLA RISC-loading complex subunit tarbp2 OS=Xenopus laevis GN=tarbp2 PE=2 SV=2	Back alignment and function description

>sp\|Q4V8C7\|PRKRA_RAT Interferon-inducible double stranded RNA-dependent protein kinase activator A OS=Rattus norvegicus GN=Prkra PE=1 SV=1	Back alignment and function description

>sp\|Q9WTX2\|PRKRA_MOUSE Interferon-inducible double stranded RNA-dependent protein kinase activator A OS=Mus musculus GN=Prkra PE=1 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		377
425626950		353	loquacious [Mayetiola destructor]	0.779	0.832	0.439	3e-61
328784437		383	PREDICTED: RISC-loading complex subunit	0.822	0.809	0.426	4e-61
380016563		383	PREDICTED: RISC-loading complex subunit	0.822	0.809	0.426	5e-61
383849930		377	PREDICTED: RISC-loading complex subunit	0.824	0.824	0.424	2e-60
350399379		381	PREDICTED: RISC-loading complex subunit	0.832	0.824	0.421	4e-60
340721164		388	PREDICTED: RISC-loading complex subunit	0.830	0.806	0.417	9e-60
91091212		384	PREDICTED: similar to tar RNA binding pr	0.822	0.807	0.433	1e-58
195115174		454	GI17218 [Drosophila mojavensis] gi\|19391	0.843	0.700	0.386	2e-57
198476324		477	GA19915 [Drosophila pseudoobscura pseudo	0.782	0.618	0.395	1e-56
195156001		470	GL26052 [Drosophila persimilis] gi\|19411	0.782	0.627	0.395	2e-56

>gi\|425626950\|gb\|AFX89033.1\| loquacious [Mayetiola destructor]	Back alignment and taxonomy information

 Score =  241 bits (616), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 137/312 (43%), Positives = 200/312 (64%), Gaps = 18/312 (5%)

Query: 76  RTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAK 135
           +TPVS++QELLSRRG  P Y+L+QIEGAI+EP F+YR++  ++     A+G+GKSKKEAK
Sbjct: 49  KTPVSVLQELLSRRGITPTYDLVQIEGAIHEPTFRYRVTYGNKD----AMGAGKSKKEAK 104

Query: 136 HNAAKSVLDQLIGRD--DEKL-----MCQKENLFKVEPNPVGQLQEACMTRKWPPPVYET 188
           H AA++++D+L G    D+ L        KEN  KV  NP+G LQE CM R+WPPP YET
Sbjct: 105 HQAARNLIDKLTGIQIADQILPPATPNGNKENDSKVNGNPIGWLQELCMARRWPPPFYET 164

Query: 189 EETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAALNMLKFLETVPIEIPEKKQGED 248
           +   GLPHER FT+  +V++Y E G GKSKK AKR AA  M + L+ +P++  +    +D
Sbjct: 165 QSEVGLPHERQFTIACHVSIYCETGRGKSKKEAKRLAAHQMWQRLQDLPLD-GQDDANDD 223

Query: 249 VDEKGESN---GLKHTHDSTFLTPQILKKIQQYHTVFSQKTKGPLLEKLLSTRNLIDEVE 305
           ++     N    LK    ST LT Q   K+ Q+H      + G +L KL +T  L D   
Sbjct: 224 INRANNMNRYADLKEKRIST-LTNQHSYKVSQFHKTLKANS-GQILSKLQNT-CLNDPDV 280

Query: 306 DPILYLEDLSDELKYRVSFVDIEEKSKADGFQSLLQLTTTPVTVFCGTGASIEVAKIEAV 365
           + + +L++++ E ++ V++VDIEEKS +  FQ L+QL+T PV V  G+G + ++A+  A 
Sbjct: 281 NFVQFLQEIATEQQFEVTYVDIEEKSYSGQFQCLVQLSTLPVAVCQGSGKTSKIAQTCAA 340

Query: 366 YRALDFLQIMNR 377
             AL++L+IM +
Sbjct: 341 RNALEYLKIMTK 352

Source: Mayetiola destructor

Species: Mayetiola destructor

Genus: Mayetiola

Family: Cecidomyiidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|328784437\|ref\|XP_624606.3\| PREDICTED: RISC-loading complex subunit tarbp2-like [Apis mellifera]	Back alignment and taxonomy information

>gi\|380016563\|ref\|XP_003692250.1\| PREDICTED: RISC-loading complex subunit tarbp2-like [Apis florea]	Back alignment and taxonomy information

>gi\|383849930\|ref\|XP_003700586.1\| PREDICTED: RISC-loading complex subunit tarbp2-like [Megachile rotundata]	Back alignment and taxonomy information

>gi\|350399379\|ref\|XP_003485505.1\| PREDICTED: RISC-loading complex subunit tarbp2-like [Bombus impatiens]	Back alignment and taxonomy information

>gi\|340721164\|ref\|XP_003398995.1\| PREDICTED: RISC-loading complex subunit tarbp2-like [Bombus terrestris]	Back alignment and taxonomy information

>gi\|91091212\|ref\|XP_966668.1\| PREDICTED: similar to tar RNA binding protein [Tribolium castaneum] gi\|270013108\|gb\|EFA09556.1\| hypothetical protein TcasGA2_TC011666 [Tribolium castaneum]	Back alignment and taxonomy information

>gi\|195115174\|ref\|XP_002002139.1\| GI17218 [Drosophila mojavensis] gi\|193912714\|gb\|EDW11581.1\| GI17218 [Drosophila mojavensis]	Back alignment and taxonomy information

>gi\|198476324\|ref\|XP_001357331.2\| GA19915 [Drosophila pseudoobscura pseudoobscura] gi\|198137644\|gb\|EAL34400.2\| GA19915 [Drosophila pseudoobscura pseudoobscura]	Back alignment and taxonomy information

>gi\|195156001\|ref\|XP_002018889.1\| GL26052 [Drosophila persimilis] gi\|194115042\|gb\|EDW37085.1\| GL26052 [Drosophila persimilis]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		377
FB\|FBgn0032515		465	loqs "loquacious" [Drosophila	0.562	0.455	0.414	1.3e-57
ZFIN\|ZDB-GENE-030131-8085		346	tarbp2 "TAR (HIV) RNA binding	0.567	0.618	0.316	1.5e-35
UNIPROTKB\|Q7ZYA5		309	prkra-a "Interferon-inducible	0.488	0.595	0.331	1.7e-33
UNIPROTKB\|Q91836		298	prkra-b "Interferon-inducible	0.474	0.600	0.328	2e-32
ZFIN\|ZDB-GENE-050309-206		289	prkra "protein kinase, interfe	0.416	0.543	0.361	3e-30
UNIPROTKB\|Q0IIG6		366	TARBP2 "RISC-loading complex s	0.533	0.549	0.351	3.9e-30
MGI\|MGI:103027		365	Tarbp2 "TAR (HIV) RNA binding	0.533	0.550	0.337	7.8e-30
RGD\|1307375		365	Tarbp2 "TAR (HIV-1) RNA bindin	0.604	0.624	0.329	1.1e-29
UNIPROTKB\|Q3SWU0		365	Tarbp2 "RISC-loading complex s	0.604	0.624	0.329	1.1e-29
UNIPROTKB\|F1SFP3		366	TARBP2 "Uncharacterized protei	0.533	0.549	0.347	1.7e-29

FB\|FBgn0032515 loqs "loquacious" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

 Score = 368 (134.6 bits), Expect = 1.3e-57, Sum P(2) = 1.3e-57
 Identities = 92/222 (41%), Positives = 129/222 (58%)

Query:   163 KVEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTV-CAYVNVYKEEGMGKSKKIA 221
             K   NP+G LQE CM R+WPPP YETE   GLPHER+FT+ C+ +N Y+E G GKSKKIA
Sbjct:   246 KTVGNPIGWLQEMCMQRRWPPPSYETETEVGLPHERLFTIACSILN-YREMGKGKSKKIA 304

Query:   222 KREAALNMLKFLETVPIE---IPEKKQGE-DVDEKGESNGLKHTHDSTF--LTPQILKKI 275
             KR AA  M   L+  PI+   I +   GE + + +   N      D +   LT Q   K+
Sbjct:   305 KRLAAHRMWMRLQETPIDSGKISDSICGELEGEPRSSENYYGELKDISVPTLTTQHSNKV 364

Query:   276 QQYHTVFSQKTKGPLLEKLLSTRNLIDEVEDPILYLEDLSDELKYRVSFVDIEEKSKADG 335
              Q+H      T G  L KL  T    +++ D I  L +++ E ++ V++VDIEEK+ +  
Sbjct:   365 SQFHKTLKNAT-GKKLLKLQKTCLKNNKI-DYIKLLGEIATENQFEVTYVDIEEKTFSGQ 422

Query:   336 FQSLLQLTTTPVTVFCGTGASIEVAKIEAVYRALDFLQIMNR 377
             FQ L+QL+T PV V  G+G +   A+  A   AL++L+IM +
Sbjct:   423 FQCLVQLSTLPVGVCHGSGPTAADAQRHAAQNALEYLKIMTK 464

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

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0030718 "germ-line stem cell maintenance" evidence=IMP

GO:0048132 "female germ-line stem cell division" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0030422 "production of siRNA involved in RNA interference" evidence=IDA;IMP

GO:0007417 "central nervous system development" evidence=IMP

GO:0070918 "production of small RNA involved in gene silencing by RNA" evidence=IDA

GO:0010586 "miRNA metabolic process" evidence=IDA

GO:0070920 "regulation of production of small RNA involved in gene silencing by RNA" evidence=IDA

GO:0016442 "RNA-induced silencing complex" evidence=IPI

ZFIN\|ZDB-GENE-030131-8085 tarbp2 "TAR (HIV) RNA binding protein 2" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|Q7ZYA5 prkra-a "Interferon-inducible double stranded RNA-dependent protein kinase activator A homolog A" [Xenopus laevis (taxid:8355)]	Back alignment and assigned GO terms

UNIPROTKB\|Q91836 prkra-b "Interferon-inducible double stranded RNA-dependent protein kinase activator A homolog B" [Xenopus laevis (taxid:8355)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-050309-206 prkra "protein kinase, interferon-inducible double stranded RNA dependent activator" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|Q0IIG6 TARBP2 "RISC-loading complex subunit TARBP2" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

MGI\|MGI:103027 Tarbp2 "TAR (HIV) RNA binding protein 2" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1307375 Tarbp2 "TAR (HIV-1) RNA binding protein 2" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q3SWU0 Tarbp2 "RISC-loading complex subunit TARBP2" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SFP3 TARBP2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

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)
Q7SXR1	TRBP2_DANRE	No assigned EC number	0.3002	0.7639	0.8323	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		377
cd00048		68	cd00048, DSRM, Double-stranded RNA binding motif	2e-19
smart00358		67	smart00358, DSRM, Double-stranded RNA binding moti	8e-16
smart00358		67	smart00358, DSRM, Double-stranded RNA binding moti	3e-13
cd00048		68	cd00048, DSRM, Double-stranded RNA binding motif	6e-13
pfam00035		66	pfam00035, dsrm, Double-stranded RNA binding motif	5e-12
PRK00102		229	PRK00102, rnc, ribonuclease III; Reviewed	2e-11
pfam00035		66	pfam00035, dsrm, Double-stranded RNA binding motif	1e-10
PRK00102		229	PRK00102, rnc, ribonuclease III; Reviewed	2e-09
TIGR02191		220	TIGR02191, RNaseIII, ribonuclease III, bacterial	2e-09
TIGR02191		220	TIGR02191, RNaseIII, ribonuclease III, bacterial	2e-09
COG0571		235	COG0571, Rnc, dsRNA-specific ribonuclease [Transcr	4e-09
TIGR04238		201	TIGR04238, seadorna_dsRNA, seadornavirus double-st	2e-07
COG0571		235	COG0571, Rnc, dsRNA-specific ribonuclease [Transcr	2e-05
PRK12371		235	PRK12371, PRK12371, ribonuclease III; Reviewed	0.001

>gnl\|CDD\|238007 cd00048, DSRM, Double-stranded RNA binding motif	Back alignment and domain information

 Score = 80.8 bits (200), Expect = 2e-19
 Identities = 29/68 (42%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN-VYKEEGMGKSKKIAKREA 225
           NP   LQE    R  P P YE  E  G  H   FTV   V      EG G SKK AK+ A
Sbjct: 1   NPKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGKITGEGEGSSKKEAKQNA 60

Query: 226 ALNMLKFL 233
           A   L+ 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\|214634 smart00358, DSRM, Double-stranded RNA binding motif	Back alignment and domain information

>gnl\|CDD\|214634 smart00358, DSRM, Double-stranded RNA binding motif	Back alignment and domain information

>gnl\|CDD\|238007 cd00048, DSRM, Double-stranded RNA binding motif	Back alignment and domain information

>gnl\|CDD\|215670 pfam00035, dsrm, Double-stranded RNA binding motif	Back alignment and domain information

>gnl\|CDD\|234633 PRK00102, rnc, ribonuclease III; Reviewed	Back alignment and domain information

>gnl\|CDD\|215670 pfam00035, dsrm, Double-stranded RNA binding motif	Back alignment and domain information

>gnl\|CDD\|234633 PRK00102, rnc, ribonuclease III; Reviewed	Back alignment and domain information

>gnl\|CDD\|233772 TIGR02191, RNaseIII, ribonuclease III, bacterial	Back alignment and domain information

>gnl\|CDD\|233772 TIGR02191, RNaseIII, ribonuclease III, bacterial	Back alignment and domain information

>gnl\|CDD\|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription]	Back alignment and domain information

>gnl\|CDD\|234517 TIGR04238, seadorna_dsRNA, seadornavirus double-stranded RNA-binding protein	Back alignment and domain information

>gnl\|CDD\|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription]	Back alignment and domain information

>gnl\|CDD\|171444 PRK12371, PRK12371, ribonuclease III; Reviewed	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		377
KOG3732\|consensus		339		100.0
KOG3732\|consensus		339		99.97
COG0571		235	Rnc dsRNA-specific ribonuclease [Transcription]	99.96
PRK12371		235	ribonuclease III; Reviewed	99.95
PRK14718		467	ribonuclease III; Provisional	99.95
PRK12372		413	ribonuclease III; Reviewed	99.94
PRK00102		229	rnc ribonuclease III; Reviewed	99.9
TIGR02191		220	RNaseIII ribonuclease III, bacterial. This family	99.89
KOG1817\|consensus		533		99.77
PHA02701		183	ORF020 dsRNA-binding PKR inhibitor; Provisional	99.68
cd00048		68	DSRM Double-stranded RNA binding motif. Binding is	99.62
cd00048		68	DSRM Double-stranded RNA binding motif. Binding is	99.62
smart00358		67	DSRM Double-stranded RNA binding motif.	99.62
PHA03103		183	double-strand RNA-binding protein; Provisional	99.61
smart00358		67	DSRM Double-stranded RNA binding motif.	99.57
PHA02701		183	ORF020 dsRNA-binding PKR inhibitor; Provisional	99.57
PF00035		67	dsrm: Double-stranded RNA binding motif; InterPro:	99.56
PHA03103		183	double-strand RNA-binding protein; Provisional	99.51
PF00035		67	dsrm: Double-stranded RNA binding motif; InterPro:	99.48
PRK12371		235	ribonuclease III; Reviewed	99.43
COG0571		235	Rnc dsRNA-specific ribonuclease [Transcription]	99.42
PF14709		80	DND1_DSRM: double strand RNA binding domain from D	99.41
PRK14718		467	ribonuclease III; Provisional	99.37
PRK12372		413	ribonuclease III; Reviewed	99.32
KOG2777\|consensus		542		99.27
PRK00102		229	rnc ribonuclease III; Reviewed	99.26
PF14709		80	DND1_DSRM: double strand RNA binding domain from D	99.22
TIGR02191		220	RNaseIII ribonuclease III, bacterial. This family	99.2
KOG4334\|consensus		650		99.12
KOG2777\|consensus		542		98.99
KOG3769\|consensus		333		98.83
KOG4334\|consensus		650		98.68
PF14622		128	Ribonucleas_3_3: Ribonuclease-III-like; PDB: 1O0W_	98.63
smart00535		129	RIBOc Ribonuclease III family.	98.12
KOG0921\|consensus		1282		98.02
KOG1817\|consensus		533		98.0
KOG3792\|consensus		816		97.97
cd00593		133	RIBOc RIBOc. Ribonuclease III C terminal domain. T	97.92
KOG3792\|consensus		816		97.89
KOG3769\|consensus		333		97.41
PF00636		114	Ribonuclease_3: Ribonuclease III domain; InterPro:	97.25
PF03368		90	Dicer_dimer: Dicer dimerisation domain; InterPro:	96.28
PF03368		90	Dicer_dimer: Dicer dimerisation domain; InterPro:	96.27
KOG0921\|consensus		1282		96.15
PF14954		252	LIX1: Limb expression 1	94.0
PF14954		252	LIX1: Limb expression 1	92.19
KOG0701\|consensus		1606		90.8

>KOG3732\|consensus	Back alignment and domain information

Probab=100.00  E-value=3e-43  Score=327.27  Aligned_cols=281  Identities=33%  Similarity=0.450  Sum_probs=222.0

Q ss_pred             CChHHHHHHHHHhCCCCCeEEEEeeeCCCCCCeEEEEEEECCccceeEEEeeccchhHHHHHHHHHHHHHHhcCCCcccc
Q psy5350          76 RTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNAAKSVLDQLIGRDDEKLM  155 (377)
Q Consensus        76 ~~pks~L~E~~q~~~~~p~Y~~~~~~G~~h~~~F~~~v~v~~~~~~~~~~g~G~sKK~Ae~~AA~~aL~~L~~~~~~~~~  155 (377)
                      ++|+|.|||+|.+++..|.|++++++||.|++.|+++|.|++    +.+.|.|+|||.|+|+||..+|..|+..++....
T Consensus        38 KS~IS~l~E~~~r~~~~v~fevl~eeGp~H~~~fv~rvtvg~----~~a~GeG~sKK~AKh~AA~~~L~~lk~l~~l~~v  113 (339)
T KOG3732|consen   38 KSPISLLQEYGLRRGLTPVYEVLREEGPPHMPNFVFRVTVGE----ITATGEGKSKKLAKHRAAEALLKELKKLPPLANV  113 (339)
T ss_pred             CChHHHHHHHHHHhCCCcceeeeeccCCccCCCeEEEEEEee----eEEecCCCchhHHHHHHHHHHHHHHhcCCCcccc
Confidence            999999999999999999999999999999999999999997    8999999999999999999999999987653221


Q ss_pred             c------------------cccCCCCCCCChhHHHHHHHHhcCCCCCeeEeecccCCCCCceEEEEEEEccEEEEEecCC
Q psy5350         156 C------------------QKENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKS  217 (377)
Q Consensus       156 ~------------------~~~~~~~~~~n~~~~L~e~~q~~~~~~p~y~~~~~~Gp~h~~~F~~~v~v~~~~~~G~G~s  217 (377)
                      .                  ..++++....|||++|+||||+++|+.|.|+++.+.|++|.+.|+++|+|.+++.+|.|+|
T Consensus       114 ~k~~~~~~~~~~~~~~~~q~~d~~~~~~~NPI~~L~e~~q~k~~k~P~yelv~E~G~~~~rEFv~q~sv~~~~~~GkG~s  193 (339)
T KOG3732|consen  114 RKDSLKFAKMKSSGVKKDQPGDPEYGQVLNPIGRLQELAQAKKWKLPEYELVQESGVPHRREFVIQCSVENFTEEGKGPS  193 (339)
T ss_pred             ccCcccccccccCCccccCCCCcccccccChHHHHHHHHHHhCCCCCceEEEeccCCCccceEEEEEEecceeeecCCch
Confidence            0                  1124456789999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCCCccCCCCcccccccccCCCCCCCccccchhhhhhhhhhhhccccCCCCchh-Hhhhc
Q psy5350         218 KKIAKREAALNMLKFLETVPIEIPEKKQGEDVDEKGESNGLKHTHDSTFLTPQILKKIQQYHTVFSQKTKGPLL-EKLLS  296 (377)
Q Consensus       218 KK~Ak~~AA~~~l~~L~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~  296 (377)
                      ||.||++||++||..|.-.++....     ++.            .+....+...-...+.+....++-+..+. .+...
T Consensus       194 KKiAKRnAAeamLe~l~~~~~~~~p-----~~~------------~~~~~~p~~~~~~~~~~~s~~~s~~eel~~~k~~~  256 (339)
T KOG3732|consen  194 KKIAKRNAAEAMLESLGFVKPNKTP-----ENL------------KVSLLKPASGRALGCSDKSLDNSEGEELSRLKACL  256 (339)
T ss_pred             HHHHHHHHHHHHHHHhccCCCCcCc-----ccc------------cccccccccCcCCccCccccccchhhhhhhhhhhh
Confidence            9999999999999999866542100     000            00000000000000011111111111111 00000


Q ss_pred             cCCCCCCCCCHHHHHHHHHhhcCceEEEEeecccCCCCceEEEEEEecCCceEEEeecCCHHHHHHHHHHHHHHHHHhhh
Q psy5350         297 TRNLIDEVEDPILYLEDLSDELKYRVSFVDIEEKSKADGFQSLLQLTTTPVTVFCGTGASIEVAKIEAVYRALDFLQIMN  376 (377)
Q Consensus       297 ~~~~~~~~~n~i~~L~el~q~~~~~~~~~~~~~~g~~~~~~~~v~v~~~p~~~~~G~G~tkk~Ak~~AA~~aL~~L~~~~  376 (377)
                      ...+...+.+++..|+++.....|.+.|.++.+.+..+.++|.++.++.|..+|+|++.|-..|...||+++|+||+.|.
T Consensus       257 ~~~~~~~~~~~~~~~~~~~~e~~f~~~y~d~~~~t~sg~~~~~~e~s~~~~~~~~~s~~t~~~s~~~aa~~~L~yL~~~~  336 (339)
T KOG3732|consen  257 KVIFNSAGLAYIKLLSEIAPENQFTVTYPDIEELTLSGQNQCLVELSTSPATVCHGSSITPPSAQSEAAHNALEYLKIMA  336 (339)
T ss_pred             hhccccccccccccccccccccchheecchhHHhhhhhHHHHHHHhcCCCceeeeccCCCCCcccchhHHHHHHHHHHHh
Confidence            11233456789999999999999999999998888889999999999999999999999999999999999999999986


Q ss_pred             C
Q psy5350         377 R  377 (377)
Q Consensus       377 ~  377 (377)
                      .
T Consensus       337 ~  337 (339)
T KOG3732|consen  337 G  337 (339)
T ss_pred             c
Confidence            3

>KOG3732\|consensus	Back alignment and domain information

>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]	Back alignment and domain information

>PRK12371 ribonuclease III; Reviewed	Back alignment and domain information

>PRK14718 ribonuclease III; Provisional	Back alignment and domain information

>PRK12372 ribonuclease III; Reviewed	Back alignment and domain information

>PRK00102 rnc ribonuclease III; Reviewed	Back alignment and domain information

>TIGR02191 RNaseIII ribonuclease III, bacterial	Back alignment and domain information

>KOG1817\|consensus	Back alignment and domain information

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional	Back alignment and domain information

>cd00048 DSRM Double-stranded RNA binding motif	Back alignment and domain information

>cd00048 DSRM Double-stranded RNA binding motif	Back alignment and domain information

>smart00358 DSRM Double-stranded RNA binding motif	Back alignment and domain information

>PHA03103 double-strand RNA-binding protein; Provisional	Back alignment and domain information

>smart00358 DSRM Double-stranded RNA binding motif	Back alignment and domain information

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional	Back alignment and domain information

>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 []	Back alignment and domain information

>PHA03103 double-strand RNA-binding protein; Provisional	Back alignment and domain information

>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 []	Back alignment and domain information

>PRK12371 ribonuclease III; Reviewed	Back alignment and domain information

>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]	Back alignment and domain information

>PF14709 DND1_DSRM: double strand RNA binding domain from DEAD END PROTEIN 1	Back alignment and domain information

>PRK14718 ribonuclease III; Provisional	Back alignment and domain information

>PRK12372 ribonuclease III; Reviewed	Back alignment and domain information

>KOG2777\|consensus	Back alignment and domain information

>PRK00102 rnc ribonuclease III; Reviewed	Back alignment and domain information

>PF14709 DND1_DSRM: double strand RNA binding domain from DEAD END PROTEIN 1	Back alignment and domain information

>TIGR02191 RNaseIII ribonuclease III, bacterial	Back alignment and domain information

>KOG4334\|consensus	Back alignment and domain information

>KOG2777\|consensus	Back alignment and domain information

>KOG3769\|consensus	Back alignment and domain information

>KOG4334\|consensus	Back alignment and domain information

>PF14622 Ribonucleas_3_3: Ribonuclease-III-like; PDB: 1O0W_A 2A11_A 3N3W_B	Back alignment and domain information

>smart00535 RIBOc Ribonuclease III family	Back alignment and domain information

>KOG0921\|consensus	Back alignment and domain information

>KOG1817\|consensus	Back alignment and domain information

>KOG3792\|consensus	Back alignment and domain information

>cd00593 RIBOc RIBOc	Back alignment and domain information

>KOG3792\|consensus	Back alignment and domain information

>KOG3769\|consensus	Back alignment and domain information

>PF00636 Ribonuclease_3: Ribonuclease III domain; InterPro: IPR000999 Prokaryotic ribonuclease III (3	Back alignment and domain information

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

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

>KOG0921\|consensus	Back alignment and domain information

>PF14954 LIX1: Limb expression 1	Back alignment and domain information

>PF14954 LIX1: Limb expression 1	Back alignment and domain information

>KOG0701\|consensus	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		377
1di2_A		69	Crystal Structure Of A Dsrna-Binding Domain Complex		3e-08
3adl_A		88	Structure Of Trbp2 And Its Molecule Implications Fo		6e-08
2cpn_A		89	Solution Structure Of The Second Dsrbd Of Tar Rna-B		1e-07
3llh_A		90	Crystal Structure Of The First Dsrbd Of Tar Rna-Bin		2e-04

>pdb|1DI2|A Chain A, Crystal Structure Of A Dsrna-Binding Domain Complexed With Dsrna: Molecular Basis Of Double-Stranded Rna-Protein Interactions Length = 69

Back alignment and structure

Iteration: 1

Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust. Identities = 28/68 (41%), Positives = 39/68 (57%) Query: 168 PVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAAL 227 PVG LQE + + W P Y + +G PH+R FT+ V + E G G SK++AKR AA Sbjct: 2 PVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGSGTSKQVAKRVAAE 61 Query: 228 NMLKFLET 235 +L +T Sbjct: 62 KLLTKFKT 69

PyMOL of 1di2

>pdb|3ADL|A Chain A, Structure Of Trbp2 And Its Molecule Implications For Mirna Processing Length = 88

Back alignment and structure

>pdb|2CPN|A Chain A, Solution Structure Of The Second Dsrbd Of Tar Rna-Binding Protein 2 Length = 89

Back alignment and structure

>pdb|3LLH|A Chain A, Crystal Structure Of The First Dsrbd Of Tar Rna-Binding Protein 2 Length = 90

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		377
1qu6_A		179	Protein kinase PKR; dsRNA-binding domain, solution	2e-30
1qu6_A		179	Protein kinase PKR; dsRNA-binding domain, solution	1e-12
1qu6_A		179	Protein kinase PKR; dsRNA-binding domain, solution	5e-09
2yt4_A		232	Protein DGCR8; DSRBD, RNA binding domain, RNA bind	1e-27
2yt4_A		232	Protein DGCR8; DSRBD, RNA binding domain, RNA bind	1e-09
2yt4_A		232	Protein DGCR8; DSRBD, RNA binding domain, RNA bind	1e-07
1uhz_A		89	Staufen (RNA binding protein) homolog 2; DSRM, sta	1e-24
1uhz_A		89	Staufen (RNA binding protein) homolog 2; DSRM, sta	4e-14
3adl_A		88	RISC-loading complex subunit tarbp2; TRBP2, miRNA	3e-24
3adl_A		88	RISC-loading complex subunit tarbp2; TRBP2, miRNA	3e-13
1di2_A		69	XLRBPA, double stranded RNA binding protein A; pro	5e-23
1di2_A		69	XLRBPA, double stranded RNA binding protein A; pro	4e-14
2cpn_A		89	TAR RNA-binding protein 2; double-stranded RNA bin	5e-22
2cpn_A		89	TAR RNA-binding protein 2; double-stranded RNA bin	9e-13
2dix_A		84	Interferon-inducible double stranded RNA- dependen	3e-20
2dix_A		84	Interferon-inducible double stranded RNA- dependen	1e-17
1ekz_A		76	DSRBDIII, maternal effect protein (staufen); struc	4e-20
1ekz_A		76	DSRBDIII, maternal effect protein (staufen); struc	3e-16
2l3j_A		236	Double-stranded RNA-specific editase 1; editing, d	2e-19
2l3j_A		236	Double-stranded RNA-specific editase 1; editing, d	1e-09
3llh_A		90	RISC-loading complex subunit tarbp2; DSRBD, DSRM,	3e-18
3llh_A		90	RISC-loading complex subunit tarbp2; DSRBD, DSRM,	4e-17
2l33_A		91	Interleukin enhancer-binding factor 3; structural	1e-15
2l33_A		91	Interleukin enhancer-binding factor 3; structural	1e-12
2b7v_A		71	Double-stranded RNA-specific editase 1; RNA editin	4e-15
2b7v_A		71	Double-stranded RNA-specific editase 1; RNA editin	6e-13
3adj_A		76	F21M12.9 protein; HYL1, miRNA processing, RNA bind	3e-14
3adj_A		76	F21M12.9 protein; HYL1, miRNA processing, RNA bind	2e-11
1x49_A		97	Interferon-induced, double-stranded RNA- activated	4e-14
1x49_A		97	Interferon-induced, double-stranded RNA- activated	8e-14
3p1x_A		75	Interleukin enhancer-binding factor 3; structural	4e-14
3p1x_A		75	Interleukin enhancer-binding factor 3; structural	1e-12
2nug_A		221	Ribonuclease III, RNAse III; dsRNA, RNA interferen	1e-13
2nug_A		221	Ribonuclease III, RNAse III; dsRNA, RNA interferen	1e-08
2b7t_A		73	Double-stranded RNA-specific editase 1; RNA editin	2e-13
2b7t_A		73	Double-stranded RNA-specific editase 1; RNA editin	3e-12
3adg_A		73	F21M12.9 protein; HYL1, miRNA processing mechanism	7e-13
3adg_A		73	F21M12.9 protein; HYL1, miRNA processing mechanism	2e-09
1whn_A		128	Hypothetical protein riken cDNA 2310016K04; double	1e-12
1whn_A		128	Hypothetical protein riken cDNA 2310016K04; double	8e-08
2dmy_A		97	Spermatid perinuclear RNA-binding protein; DSRM do	1e-12
2dmy_A		97	Spermatid perinuclear RNA-binding protein; DSRM do	4e-11
1whq_A		99	RNA helicase A; double-stranded RNA binding domain	2e-12
1whq_A		99	RNA helicase A; double-stranded RNA binding domain	4e-09
1o0w_A		252	Ribonuclease III, RNAse III; TM1102, structural ge	3e-12
1o0w_A		252	Ribonuclease III, RNAse III; TM1102, structural ge	3e-09
2ljh_A		114	Double-stranded RNA-specific editase ADAR; DSRBD,	3e-12
2ljh_A		114	Double-stranded RNA-specific editase ADAR; DSRBD,	2e-09
1x47_A		98	DGCR8 protein; structural genomics, DSRM domain, N	3e-12
1x47_A		98	DGCR8 protein; structural genomics, DSRM domain, N	2e-11
2l2n_A		103	Hyponastic leave 1; DSRBD, miRNA, RNA binding prot	6e-12
2l2n_A		103	Hyponastic leave 1; DSRBD, miRNA, RNA binding prot	1e-08
2a11_A		242	Ribonuclease III, RNAse III; nuclease domain, stru	9e-12
2a11_A		242	Ribonuclease III, RNAse III; nuclease domain, stru	2e-07
3n3w_A		248	Ribonuclease III; nuclease domain, ribonuclase III	2e-11
3n3w_A		248	Ribonuclease III; nuclease domain, ribonuclase III	2e-09
2khx_A		85	Ribonuclease 3; drosha, RNA binding domain, hydrol	4e-11
2khx_A		85	Ribonuclease 3; drosha, RNA binding domain, hydrol	1e-08
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-10
3c4b_A		265	Endoribonuclease dicer; RNAse, dsRNA binding prote	1e-08
3c4b_A		265	Endoribonuclease dicer; RNAse, dsRNA binding prote	3e-08
1uil_A		113	Double-stranded RNA-binding motif; structural geno	7e-06
3rv0_A		341	K. polysporus DCR1; RNAse III enzyme, RNA binding	2e-05
3rv0_A		341	K. polysporus DCR1; RNAse III enzyme, RNA binding	1e-04
2qvw_A		756	GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral	8e-05
1x48_A		88	Interferon-induced, double-stranded RNA- activated	2e-04
1t4n_A		94	Ribonuclease III; DSRBD, RNA-binding, hydrolase; N	6e-04

>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	Back alignment and structure

 Score =  113 bits (285), Expect = 2e-30
 Identities = 30/170 (17%), Positives = 60/170 (35%), Gaps = 10/170 (5%)

Query: 69  MRLNTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSG 128
           M  +      +  +     ++G   KY+ +   G  ++  F +++ +          G G
Sbjct: 6   MAGDLSAGFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDGRE---FPEGEG 62

Query: 129 KSKKEAKHNAAKSVLDQL----IGRDDEKLMCQKENLFKVEPNPVGQLQEACMTRKWPPP 184
           +SKKEAK+ AAK  ++ L           L     +      N +G +      ++    
Sbjct: 63  RSKKEAKNAAAKLAVEILNKEKKAVSPLLLTTTNSSEGLSMGNYIGLINRIAQKKRLTVN 122

Query: 185 VYETEETTGLPHERMFTVCAYVNVYK-EEGMGKSKKIAKREAALNMLKFL 233
             +     G+     F     +   +   G G +K+ AK+ AA      +
Sbjct: 123 YEQCAS--GVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQI 170

PyMOL of 1qu6

>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	Back alignment and structure

>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	Back alignment and structure

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

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

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

>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	Back alignment and structure

>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	Back alignment and structure

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

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

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

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

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

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

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

>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	Back alignment and structure

>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	Back alignment and structure

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

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

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

>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	Back alignment and structure

>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	Back alignment and structure

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

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

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

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

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

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

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

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

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

>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	Back alignment and structure

>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	Back alignment and structure

>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 Length = 113	Back alignment and structure

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

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

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

>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	Back alignment and structure

>1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.50.1.1 Length = 94	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		377
1qu6_A		179	Protein kinase PKR; dsRNA-binding domain, solution	100.0
2yt4_A		232	Protein DGCR8; DSRBD, RNA binding domain, RNA bind	99.97
1qu6_A		179	Protein kinase PKR; dsRNA-binding domain, solution	99.96
2l3j_A		236	Double-stranded RNA-specific editase 1; editing, d	99.95
1o0w_A		252	Ribonuclease III, RNAse III; TM1102, structural ge	99.94
3n3w_A		248	Ribonuclease III; nuclease domain, ribonuclase III	99.93
2nug_A		221	Ribonuclease III, RNAse III; dsRNA, RNA interferen	99.92
2a11_A		242	Ribonuclease III, RNAse III; nuclease domain, stru	99.91
2yt4_A		232	Protein DGCR8; DSRBD, RNA binding domain, RNA bind	99.91
2l3j_A		236	Double-stranded RNA-specific editase 1; editing, d	99.88
3rv0_A		341	K. polysporus DCR1; RNAse III enzyme, RNA binding	99.85
3c4b_A		265	Endoribonuclease dicer; RNAse, dsRNA binding prote	99.81
3adl_A		88	RISC-loading complex subunit tarbp2; TRBP2, miRNA	99.81
3llh_A		90	RISC-loading complex subunit tarbp2; DSRBD, DSRM,	99.8
3adj_A		76	F21M12.9 protein; HYL1, miRNA processing, RNA bind	99.79
2dix_A		84	Interferon-inducible double stranded RNA- dependen	99.79
3adl_A		88	RISC-loading complex subunit tarbp2; TRBP2, miRNA	99.79
1di2_A		69	XLRBPA, double stranded RNA binding protein A; pro	99.79
3adg_A		73	F21M12.9 protein; HYL1, miRNA processing mechanism	99.78
2cpn_A		89	TAR RNA-binding protein 2; double-stranded RNA bin	99.78
1uhz_A		89	Staufen (RNA binding protein) homolog 2; DSRM, sta	99.78
1di2_A		69	XLRBPA, double stranded RNA binding protein A; pro	99.78
2khx_A		85	Ribonuclease 3; drosha, RNA binding domain, hydrol	99.77
2cpn_A		89	TAR RNA-binding protein 2; double-stranded RNA bin	99.77
1ekz_A		76	DSRBDIII, maternal effect protein (staufen); struc	99.77
1uhz_A		89	Staufen (RNA binding protein) homolog 2; DSRM, sta	99.77
2b7t_A		73	Double-stranded RNA-specific editase 1; RNA editin	99.77
3adj_A		76	F21M12.9 protein; HYL1, miRNA processing, RNA bind	99.77
1x49_A		97	Interferon-induced, double-stranded RNA- activated	99.77
1ekz_A		76	DSRBDIII, maternal effect protein (staufen); struc	99.77
2dix_A		84	Interferon-inducible double stranded RNA- dependen	99.76
3adg_A		73	F21M12.9 protein; HYL1, miRNA processing mechanism	99.76
1whq_A		99	RNA helicase A; double-stranded RNA binding domain	99.75
1t4n_A		94	Ribonuclease III; DSRBD, RNA-binding, hydrolase; N	99.75
3llh_A		90	RISC-loading complex subunit tarbp2; DSRBD, DSRM,	99.75
2b7t_A		73	Double-stranded RNA-specific editase 1; RNA editin	99.75
1x48_A		88	Interferon-induced, double-stranded RNA- activated	99.74
2dmy_A		97	Spermatid perinuclear RNA-binding protein; DSRM do	99.74
2khx_A		85	Ribonuclease 3; drosha, RNA binding domain, hydrol	99.74
1t4o_A		117	Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydro	99.73
2l33_A		91	Interleukin enhancer-binding factor 3; structural	99.73
2l2n_A		103	Hyponastic leave 1; DSRBD, miRNA, RNA binding prot	99.72
1x49_A		97	Interferon-induced, double-stranded RNA- activated	99.72
1x47_A		98	DGCR8 protein; structural genomics, DSRM domain, N	99.7
2dmy_A		97	Spermatid perinuclear RNA-binding protein; DSRM do	99.7
2l33_A		91	Interleukin enhancer-binding factor 3; structural	99.7
1uil_A		113	Double-stranded RNA-binding motif; structural geno	99.7
2ljh_A		114	Double-stranded RNA-specific editase ADAR; DSRBD,	99.7
2l2n_A		103	Hyponastic leave 1; DSRBD, miRNA, RNA binding prot	99.7
1whq_A		99	RNA helicase A; double-stranded RNA binding domain	99.69
1x48_A		88	Interferon-induced, double-stranded RNA- activated	99.68
2b7v_A		71	Double-stranded RNA-specific editase 1; RNA editin	99.68
2b7v_A		71	Double-stranded RNA-specific editase 1; RNA editin	99.66
1x47_A		98	DGCR8 protein; structural genomics, DSRM domain, N	99.66
1uil_A		113	Double-stranded RNA-binding motif; structural geno	99.64
1t4n_A		94	Ribonuclease III; DSRBD, RNA-binding, hydrolase; N	99.64
2ljh_A		114	Double-stranded RNA-specific editase ADAR; DSRBD,	99.63
3p1x_A		75	Interleukin enhancer-binding factor 3; structural	99.63
1whn_A		128	Hypothetical protein riken cDNA 2310016K04; double	99.62
3p1x_A		75	Interleukin enhancer-binding factor 3; structural	99.62
1t4o_A		117	Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydro	99.61
1whn_A		128	Hypothetical protein riken cDNA 2310016K04; double	99.57
2nug_A		221	Ribonuclease III, RNAse III; dsRNA, RNA interferen	99.48
1o0w_A		252	Ribonuclease III, RNAse III; TM1102, structural ge	99.45
3n3w_A		248	Ribonuclease III; nuclease domain, ribonuclase III	99.35
2a11_A		242	Ribonuclease III, RNAse III; nuclease domain, stru	99.26
2qvw_A		756	GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral	98.9
3rv0_A		341	K. polysporus DCR1; RNAse III enzyme, RNA binding	98.85
3o2r_A		170	Ribonuclease III; structural genomics, center for	98.75
3c4b_A		265	Endoribonuclease dicer; RNAse, dsRNA binding prote	98.46
1u61_A		138	Hypothetical protein; structural genomics, PSI, pr	98.44
3rv1_A		246	K. polysporus DCR1; RNAse III enzyme, RNA binding	98.1
2gsl_A		137	Hypothetical protein; alpha-helical protein, struc	97.97
2qvw_A		756	GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral	97.8
2kou_A		102	Dicer-like protein 4; ATP-binding, endonuclease, h	96.19
2kou_A		102	Dicer-like protein 4; ATP-binding, endonuclease, h	95.51
2db2_A		119	KIAA0890 protein; DSRM domain, structural genomics	95.34
2db2_A		119	KIAA0890 protein; DSRM domain, structural genomics	94.9
3htx_A		950	HEN1; HEN1, small RNA methyltransferase, protein-R	93.72

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

Probab=100.00  E-value=9e-34  Score=250.69  Aligned_cols=161  Identities=19%  Similarity=0.188  Sum_probs=139.1

Q ss_pred             CCCCCChHHHHHHHHHhCCCCCeEEEEeeeCCCCCCeEEEEEEECCccceeEEEeeccchhHHHHHHHHHHHHHHhcCCC
Q psy5350          72 NTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNAAKSVLDQLIGRDD  151 (377)
Q Consensus        72 ~~~~~~pks~L~E~~q~~~~~p~Y~~~~~~G~~h~~~F~~~v~v~~~~~~~~~~g~G~sKK~Ae~~AA~~aL~~L~~~~~  151 (377)
                      +....|||+.||||||+++..|.|+++.+.||+|.+.|+|+|.|+|.   .++.|.|.|||+|||.||+.||+.|.....
T Consensus         9 ~~~~~n~ks~LqE~~q~~~~~p~Y~~~~~~Gp~h~~~F~~~v~v~g~---~~~~G~G~sKK~Aeq~AA~~al~~L~~~~~   85 (179)
T 1qu6_A            9 DLSAGFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDGR---EFPEGEGRSKKEAKNAAAKLAVEILNKEKK   85 (179)
T ss_dssp             CSSSCSHHHHHHHHHHHHTCCCEEEEEESCBTTTBCCEEEEEESSSS---CCCEEECCSSHHHHHHHHHHHHHHHHSCCS
T ss_pred             ccCCCCHHHHHHHHHHhCCCCCeEEEeeccCCCCCCeEEEEEEECCE---EEEecCCCCHHHHHHHHHHHHHHHHhcccc
Confidence            34567999999999999986799999999999999999999999997   789999999999999999999999986543


Q ss_pred             ccccc----cccCCCCCCCChhHHHHHHHHhcCCCCCeeEeecccCCCCCceEEEEEEEccE-EEEEecCCHHHHHHHHH
Q psy5350         152 EKLMC----QKENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVY-KEEGMGKSKKIAKREAA  226 (377)
Q Consensus       152 ~~~~~----~~~~~~~~~~n~~~~L~e~~q~~~~~~p~y~~~~~~Gp~h~~~F~~~v~v~~~-~~~G~G~sKK~Ak~~AA  226 (377)
                      +..+.    .....+....||++.||||||+++|++ .|++. ++||+|.+.|+++|.|++. .++|.|+|||+||++||
T Consensus        86 ~~~p~~~~~~~~~e~~~~~n~~~~L~E~~qk~~~~~-~Y~~~-~~G~~h~~~F~~~v~v~~~~~~~g~g~sKK~Ak~~AA  163 (179)
T 1qu6_A           86 AVSPLLLTTTNSSEGLSMGNYIGLINRIAQKKRLTV-NYEQC-ASGVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAA  163 (179)
T ss_dssp             CCSCSSCCCSCSSCCCCCCCCHHHHHHHHHHSCCEE-EEEEE-EECSSSSSEEEEEEEEETTBCCEEEESSHHHHHHHHH
T ss_pred             cCCCccCCCCCcccccCCCCHHHHHHHHHHhcCCcc-eEEec-CcCCCCCCeEEEEEEECCEEEeeEEECCHHHHHHHHH
Confidence            21110    011123456899999999999999987 99975 7899999999999999997 48999999999999999


Q ss_pred             HHHHHHhhcCC
Q psy5350         227 LNMLKFLETVP  237 (377)
Q Consensus       227 ~~~l~~L~~~~  237 (377)
                      +.||..|....
T Consensus       164 ~~al~~L~~~~  174 (179)
T 1qu6_A          164 KLAYLQILSEE  174 (179)
T ss_dssp             HHHHHHHHHCC
T ss_pred             HHHHHHHhccc
Confidence            99999997654

PyMOL of 1qu6

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

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

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

>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	Back alignment and structure

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

>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	Back alignment and structure

>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomic protein structure initiative; 2.10A {Mycobacterium tuberculosis}	Back alignment and structure

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

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

>3rv0_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 2.29A {Vanderwaltozyma polyspora}	Back alignment and structure

>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	Back alignment and structure

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

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

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

>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	Back alignment and structure

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

>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	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

>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	Back alignment and structure

>1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.50.1.1	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

>1t4o_A Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2.50A {Saccharomyces cerevisiae} SCOP: d.50.1.1 PDB: 1t4l_B 2lbs_B	Back alignment and structure

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

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

>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	Back alignment and structure

>2ljh_A Double-stranded RNA-specific editase ADAR; DSRBD, DSRBM, editing, hydrolase; NMR {Drosophila melanogaster}	Back alignment and structure

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

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.50.1.1	Back alignment and structure

>2ljh_A Double-stranded RNA-specific editase ADAR; DSRBD, DSRBM, editing, hydrolase; NMR {Drosophila melanogaster}	Back alignment and structure

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

>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	Back alignment and structure

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

>1t4o_A Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2.50A {Saccharomyces cerevisiae} SCOP: d.50.1.1 PDB: 1t4l_B 2lbs_B	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

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

>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomic protein structure initiative; 2.10A {Mycobacterium tuberculosis}	Back alignment and structure

>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A	Back alignment and structure

>3rv0_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 2.29A {Vanderwaltozyma polyspora}	Back alignment and structure

>3o2r_A Ribonuclease III; structural genomics, center for structural genomics of infec diseases, csgid, nuclease domain, ribonuclase III; HET: MLZ; 1.25A {Campylobacter jejuni subsp} PDB: 3o2r_B*	Back alignment and structure

>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	Back alignment and structure

>1u61_A Hypothetical protein; structural genomics, PSI, protein STRU initiative, midwest center for structural genomics, MCSG, U function; 2.15A {Bacillus cereus} SCOP: a.149.1.1	Back alignment and structure

>3rv1_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 1.98A {Vanderwaltozyma polyspora}	Back alignment and structure

>2gsl_A Hypothetical protein; alpha-helical protein, structural genomics, PSI, protein STR initiative; 2.60A {Fusobacterium nucleatum subsp}	Back alignment and structure

>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A	Back alignment and structure

>2kou_A Dicer-like protein 4; ATP-binding, endonuclease, helicase, hydrolase, nuclease, nucleotide-binding, nucleus, RNA- binding; NMR {Arabidopsis thaliana}	Back alignment and structure

>2kou_A Dicer-like protein 4; ATP-binding, endonuclease, helicase, hydrolase, nuclease, nucleotide-binding, nucleus, RNA- binding; NMR {Arabidopsis thaliana}	Back alignment and structure

>2db2_A KIAA0890 protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2db2_A KIAA0890 protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3htx_A HEN1; HEN1, small RNA methyltransferase, protein-RNA complex; HET: SAH; 3.10A {Arabidopsis thaliana}	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		377
d2nuga2		68	d.50.1.1 (A:151-218) RNase III, C-terminal domain	7e-15
d2nuga2		68	d.50.1.1 (A:151-218) RNase III, C-terminal domain	6e-10
d1di2a_		69	d.50.1.1 (A:) Double-stranded RNA-binding protein	7e-15
d1di2a_		69	d.50.1.1 (A:) Double-stranded RNA-binding protein	1e-09
d1o0wa2		69	d.50.1.1 (A:168-236) RNase III, C-terminal domain	9e-15
d1o0wa2		69	d.50.1.1 (A:168-236) RNase III, C-terminal domain	4e-12
d2b7va1		71	d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (R	4e-13
d2b7va1		71	d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (R	5e-11
d2dmya1		84	d.50.1.1 (A:8-91) Spermatid perinuclear RNA-bindin	8e-13
d2dmya1		84	d.50.1.1 (A:8-91) Spermatid perinuclear RNA-bindin	8e-09
d2cpna1		76	d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Hu	2e-12
d2cpna1		76	d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Hu	5e-06
d1ekza_		76	d.50.1.1 (A:) Staufen, domain III {Fruit fly (Dros	2e-12
d1ekza_		76	d.50.1.1 (A:) Staufen, domain III {Fruit fly (Dros	4e-10
d2b7ta1		73	d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (R	7e-12
d2b7ta1		73	d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (R	1e-08
d2dixa1		73	d.50.1.1 (A:7-79) Interferon-inducible double stra	1e-11
d2dixa1		73	d.50.1.1 (A:7-79) Interferon-inducible double stra	6e-10
d1uhza_		89	d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus muscul	1e-11
d1uhza_		89	d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus muscul	1e-05
d1qu6a1		90	d.50.1.1 (A:1-90) dsRNA-dependent protein kinase p	8e-11
d1qu6a1		90	d.50.1.1 (A:1-90) dsRNA-dependent protein kinase p	2e-08
d1x47a1		85	d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapie	4e-09
d1x47a1		85	d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapie	2e-08
d1x49a1		85	d.50.1.1 (A:8-92) dsRNA-dependent protein kinase p	4e-09
d1x49a1		85	d.50.1.1 (A:8-92) dsRNA-dependent protein kinase p	1e-07
d1uila_		113	d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {	8e-09
d1uila_		113	d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {	1e-06
d1whqa_		99	d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {	6e-08
d1whqa_		99	d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {	9e-08
d1whna_		128	d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like,	3e-07
d1whna_		128	d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like,	1e-05
d1qu6a2		89	d.50.1.1 (A:91-179) dsRNA-dependent protein kinase	2e-06
d1qu6a2		89	d.50.1.1 (A:91-179) dsRNA-dependent protein kinase	0.001
d1x48a1		76	d.50.1.1 (A:8-83) dsRNA-dependent protein kinase p	3e-06
d1x48a1		76	d.50.1.1 (A:8-83) dsRNA-dependent protein kinase p	0.004
d1t4oa_		81	d.50.1.1 (A:) RNase III, C-terminal domain {Baker'	1e-05
d1t4oa_		81	d.50.1.1 (A:) RNase III, C-terminal domain {Baker'	6e-05

>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 68	Back information, alignment and structure


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 = 66.5 bits (162), Expect = 7e-15
 Identities = 24/68 (35%), Positives = 33/68 (48%)

Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
           +    LQE    R    P Y      G  H++ F V A +  Y+  G GKSKK A++ AA
Sbjct: 1   DYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAA 60

Query: 227 LNMLKFLE 234
             ++K LE
Sbjct: 61  EELIKLLE 68

PyMOL of d2nuga2

>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 68	Back information, alignment and structure

>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]} Length = 69	Back information, alignment and structure

>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]} Length = 69	Back information, alignment and structure

>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 69	Back information, alignment and structure

>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 69	Back information, alignment and structure

>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71	Back information, alignment and structure

>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71	Back information, alignment and structure

>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 84	Back information, alignment and structure

>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 84	Back information, alignment and structure

>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 76	Back information, alignment and structure

>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 76	Back information, alignment and structure

>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 76	Back information, alignment and structure

>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 76	Back information, alignment and structure

>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 73	Back information, alignment and structure

>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 73	Back information, alignment and structure

>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	Back information, alignment and structure

>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	Back information, alignment and structure

>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89	Back information, alignment and structure

>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89	Back information, alignment and structure

>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Length = 90	Back information, alignment and structure

>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Length = 90	Back information, alignment and structure

>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85	Back information, alignment and structure

>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85	Back information, alignment and structure

>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Length = 85	Back information, alignment and structure

>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Length = 85	Back information, alignment and structure

>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 113	Back information, alignment and structure

>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 113	Back information, alignment and structure

>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99	Back information, alignment and structure

>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99	Back information, alignment and structure

>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 128	Back information, alignment and structure

>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 128	Back information, alignment and structure

>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Length = 89	Back information, alignment and structure

>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Length = 89	Back information, alignment and structure

>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Length = 76	Back information, alignment and structure

>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Length = 76	Back information, alignment and structure

>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81	Back information, alignment and structure

>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		377
d1di2a_		69	Double-stranded RNA-binding protein A, second dsRB	99.81
d2dixa1		73	Interferon-inducible double stranded RNA-dependent	99.81
d2dixa1		73	Interferon-inducible double stranded RNA-dependent	99.8
d2cpna1		76	TAR RNA-binding protein 2 {Human (Homo sapiens) [T	99.8
d2nuga2		68	RNase III, C-terminal domain {Aquifex aeolicus [Ta	99.8
d1o0wa2		69	RNase III, C-terminal domain {Thermotoga maritima	99.79
d1uhza_		89	staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10	99.79
d1ekza_		76	Staufen, domain III {Fruit fly (Drosophila melanog	99.79
d1qu6a1		90	dsRNA-dependent protein kinase pkr {Human (Homo sa	99.78
d2nuga2		68	RNase III, C-terminal domain {Aquifex aeolicus [Ta	99.77
d1ekza_		76	Staufen, domain III {Fruit fly (Drosophila melanog	99.77
d1o0wa2		69	RNase III, C-terminal domain {Thermotoga maritima	99.77
d2cpna1		76	TAR RNA-binding protein 2 {Human (Homo sapiens) [T	99.76
d1di2a_		69	Double-stranded RNA-binding protein A, second dsRB	99.76
d1x49a1		85	dsRNA-dependent protein kinase pkr {Mouse (Mus mus	99.76
d1x48a1		76	dsRNA-dependent protein kinase pkr {Mouse (Mus mus	99.74
d1uhza_		89	staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10	99.73
d1qu6a1		90	dsRNA-dependent protein kinase pkr {Human (Homo sa	99.73
d1x49a1		85	dsRNA-dependent protein kinase pkr {Mouse (Mus mus	99.72
d1x48a1		76	dsRNA-dependent protein kinase pkr {Mouse (Mus mus	99.72
d1qu6a2		89	dsRNA-dependent protein kinase pkr {Human (Homo sa	99.71
d1whqa_		99	ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus mus	99.71
d2b7va1		71	dsRNA-specific editase 1 {Rat (Rattus norvegicus)	99.69
d1x47a1		85	Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]}	99.69
d1uila_		113	ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus mus	99.68
d1qu6a2		89	dsRNA-dependent protein kinase pkr {Human (Homo sa	99.67
d2b7va1		71	dsRNA-specific editase 1 {Rat (Rattus norvegicus)	99.67
d1x47a1		85	Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1whqa_		99	ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus mus	99.63
d1uila_		113	ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus mus	99.62
d2b7ta1		73	dsRNA-specific editase 1 {Rat (Rattus norvegicus)	99.62
d1t4oa_		81	RNase III, C-terminal domain {Baker's yeast (Sacch	99.61
d2dmya1		84	Spermatid perinuclear RNA-binding protein {Human (	99.6
d2dmya1		84	Spermatid perinuclear RNA-binding protein {Human (	99.55
d2b7ta1		73	dsRNA-specific editase 1 {Rat (Rattus norvegicus)	99.54
d1whna_		128	tRNA-dihydrouridine synthase 2-like, Dus2l (231001	99.5
d1t4oa_		81	RNase III, C-terminal domain {Baker's yeast (Sacch	99.48
d1whna_		128	tRNA-dihydrouridine synthase 2-like, Dus2l (231001	99.47
d1o0wa1		169	RNase III endonuclease catalytic domain {Thermotog	98.5
d2nuga1		148	RNase III endonuclease catalytic domain {Aquifex a	98.05
d1u61a_		127	Hypothetical protein BC0111 {Bacillus cereus [TaxI	97.94

>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]}	Back information, alignment and structure

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=99.81  E-value=2.4e-20  Score=136.71  Aligned_cols=67  Identities=40%  Similarity=0.706  Sum_probs=65.3

Q ss_pred             hhHHHHHHHHhcCCCCCeeEeecccCCCCCceEEEEEEEccEEEEEecCCHHHHHHHHHHHHHHHhh
Q psy5350         168 PVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAALNMLKFLE  234 (377)
Q Consensus       168 ~~~~L~e~~q~~~~~~p~y~~~~~~Gp~h~~~F~~~v~v~~~~~~G~G~sKK~Ak~~AA~~~l~~L~  234 (377)
                      ||+.||||||+++|++|.|+++.++||+|.+.|++.|.|+++.++|.|+|||+|+++||+.||+.|+
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 PVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGSGTSKQVAKRVAAEKLLTKFK   68 (69)
T ss_dssp             HHHHHHHHHHHHTCCCCEEEEEEEESCGGGCEEEEEEEETTEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHcCCCCCeEEEEEeeCCCCCcceEEEEEEeeEEEecCcCcHHHHHHHHHHHHHHHhc
Confidence            8999999999999999999999999999999999999999999999999999999999999999986

PyMOL of d1di2a_

>d2dixa1 d.50.1.1 (A:7-79) Interferon-inducible double stranded RNA-dependent protein kinase activator A {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2dixa1 d.50.1.1 (A:7-79) Interferon-inducible double stranded RNA-dependent protein kinase activator A {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]}	Back information, alignment and structure

>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]}	Back information, alignment and structure

>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]}	Back information, alignment and structure

>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2nuga1 a.149.1.1 (A:3-150) RNase III endonuclease catalytic domain {Aquifex aeolicus [TaxId: 63363]}	Back information, alignment and structure

>d1u61a_ a.149.1.1 (A:) Hypothetical protein BC0111 {Bacillus cereus [TaxId: 1396]}	Back information, alignment and structure