Citrus Sinensis ID: 002586

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-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900----

MELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLDHDVQIEDVEEYFTNYIVNDSLGIIANAHTVFADREPRKARSEPCLQLAEKFSIAVDFPKTGVPAEIPPHLYVKEYPDFMEKPDKPTYESQNVIGKLFRAVKDIAPHTSCIRLFTKEVARRSYDPDMEVDGFEDHIDDAIYHKGNYDYKLGNLMDYYGIKTEAEILTGSIMKMSKSFTKRRDAEAIGMAVRALRKEARAWFKEKSGSDTEDDAYAKASAWYHVTYHPDYWGCYNQGMNRDHFLSFPWCVYDRLVEIKKDKTSIGNAFPALEQQFRQGLRMY

cccccccccccHHHHccccccccccEEEEccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHcHHHHHHHccccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccccccccccccccEEEEEEEEcccEEEEcccEEccHHHHHHHcccccccEEEEEEEcccccccccccccccccccccccHHHHHHHHHHHHHccEEEEcEEEEEEEcccccccccEEEEEEccccccHHHHHHHHccccccccHHHHHHHHHcccccccccEEEEcccEEEEccEEEcccccEEEEccccccccHHHHHHHHHHcccccccccEEEEEEcccEEEEEEcccccccEEEcccccccccccccEEEEEcccccccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHccccEEcccccEEEEEcccccccccccEEEEEcccccccccccccccccccccccEEEEEEEEEEEccccccccEEEEEEEEcccccccccEEEEccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHcccccccccHHHHHHHHHHccc

cccccccccccccccccccccccccEEEEcccccccccccccccccccccccccHHHHHHHHHHHcccccHHHccHHHHHHHHHccccHHHHHHHHHHHHHcccccHcccHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEEcccEEEEcccccccccEEEEEcccccccEEEEEEEccccccccccccccccccccccccHHHHHHHHHHHHccEEEcccEEEEEEEccHHHHcccEEEEcccccccHHHHHHHHcccHHcccHHHHHHHHHHHcccccccEEcccccEEEEcccEEccccccEEEccccccccHHHHHHHHHHcccccccccEEEEEEcccEEEEEEEcccccEEEEEccHHHcccccccEEEEEccccccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccEEcccccEEEEEEcccccccccEEEEEEccccccccccccccccccccccEEEEEEEEEEEEccccccccEEEEEEcccHHHHHccEEEEEccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccccHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccHEEEEEHHHHccccccccHcHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHccccccccHHHHHccccEEcc

melpyrlelpdfkenFAYYKESEDRFVLETGsaysrsldlvpivgppdgialPYEILFKINLLVqngcvagplldsnfyrlvdpyrapvsISCIEHALDKLYHlkeccyepsrwltDQYRKYmtsrskpsspaislddglvYVHRvqvtpsrvyfcgpeinvsNRVLRHFRRDIDNFlrisfidedldkihstdlsprgssatditrTRIYTRILSTLRngiligdrKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLgqsfsssketlsvhmdeieiipdvkieigktkyvfsdgiGKVSAEFARKVAskcglkdnppsafqiryggykgvvaadptsskklslRDSMRKYESELTKLDVLawskyqpcflnRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALElmspgentNILKELLIcgykpdaePFLSMMLQTFRASKLLELRTKtrifipngrsmmgcldetrtlnyGQVFVQISGagyrqlhgesslfsssrSRQRFIVQGLVVvaknpclhpgdvrvlkavnvpalhhmvdcvvfpqkgmrphpnecsgsdldgdiyfvcwddelippqqdppmdytpaqsmqldhdvqIEDVEEYFTNYIVNDSLGIIANAHTvfadreprkarsepcLQLAEKFSiavdfpktgvpaeipphlyvkeypdfmekpdkptyesqNVIGKLFRAVkdiaphtsciRLFTKEVarrsydpdmevdgfedhiddaiyhkgnydyklGNLMDYYGIKTEAEILTGSIMKMSKSFTKRRDAEAIGMAVRALRKEARAWFkeksgsdteddAYAKASAWYHVtyhpdywgcynqgmnrdhflsfpwcvYDRLVEIkkdktsignaFPALEQQFRQGLRMY

melpyrlelpdfKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYMTSrskpsspaislddglVYVHRVQVtpsrvyfcgpeinvsnrvlRHFRRDIDNFLRisfidedldkihstdlsprgssatditrtriYTRILStlrngiligdRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLgqsfsssketlsvhMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVAskcglkdnppsaFQIRYGGYkgvvaadptsskklslrdSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRtktrifipngrsmmgCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLDHDVQIEDVEEYFTNYIVNDSLGIIANAHTVFADREPRKARSEPCLQLAEKFSIAVDFPKTGVPAEIPPHLYVKEYPDFMEKPDKPTYESQNVIGKLFRAvkdiaphtscirlftkevarrsydpdMEVDGFEDHIDDAIYHKGNYDYKLGNLMDYYGIKTEAEILTGSIMKMSKSFTKRRDAEAIGMAVRALRKEARAWfkeksgsdteddAYAKASAWYHVTYHPDYWGCYNQGMNRDHFLSFPWCVYDRLVEIKKdktsignafpaLEQQFRQGLRMY

MELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDitrtriytriLSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGEsslfsssrsrqrfIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLDHDVQIEDVEEYFTNYIVNDSLGIIANAHTVFADREPRKARSEPCLQLAEKFSIAVDFPKTGVPAEIPPHLYVKEYPDFMEKPDKPTYESQNVIGKLFRAVKDIAPHTSCIRLFTKEVARRSYDPDMEVDGFEDHIDDAIYHKGNYDYKLGNLMDYYGIKTEAEILTGSIMKMSKSFTKRRDAEAIGMAVRALRKEARAWFKEKSGSDTEDDAYAKASAWYHVTYHPDYWGCYNQGMNRDHFLSFPWCVYDRLVEIKKDKTSIGNAFPALEQQFRQGLRMY

*******ELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYM**********ISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIH***********TDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSF****ETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVA********************ELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHG**********RQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKG**********SDLDGDIYFVCWDDELI*******************HDVQIEDVEEYFTNYIVNDSLGIIANAHTVFAD*********PCLQLAEKFSIAVDFPKTGVPAEIPPHLYVKEYPDFM*******YESQNVIGKLFRAVKDIAPHTSCIRLFTKEVARRSYDPDMEVDGFEDHIDDAIYHKGNYDYKLGNLMDYYGIKTEAEILTGSIMKMS**F*****AEAIGMAVRALRKEARAWF***********AYAKASAWYHVTYHPDYWGCYNQGMNRDHFLSFPWCVYDRLVEIKKDKTSIGNAF**************

*******ELPDFKENFAYYKESEDRFVLETG*******DL*PIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKY***************DGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAF****LRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQI*G****************RSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPM*************VQIEDVEEYFTNYIVNDSLGIIANAHTVFADREPRKARSEPCLQLAEKFSIAVDFPKTGVPAEIPPHLYVKEYPDFMEK*****YESQNVIGKLFRAVKDIAPHTSCIRLFTKEVARRSYDPDMEVDGFEDHIDDAIYHKGNYDYKLGNLMDYYGIKTEAEILTGSI*****************MAVRALRKEARAWFKEKSG*DTEDDAYAKASAWYHVTYHPDYWG********DHFLSFPWCVYDRLVEIK************************

MELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRK***********AISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLDHDVQIEDVEEYFTNYIVNDSLGIIANAHTVFADREPRKARSEPCLQLAEKFSIAVDFPKTGVPAEIPPHLYVKEYPDFMEKPDKPTYESQNVIGKLFRAVKDIAPHTSCIRLFTKEVARRSYDPDMEVDGFEDHIDDAIYHKGNYDYKLGNLMDYYGIKTEAEILTGSIMKMSKSFTKRRDAEAIGMAVRALRKEARAWF***********AYAKASAWYHVTYHPDYWGCYNQGMNRDHFLSFPWCVYDRLVEIKKDKTSIGNAFPALEQQFRQGLRMY

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		904	2.2.26 [Sep-21-2011]
Q9LQV2		1107	RNA-dependent RNA polymer	yes	no	0.954	0.779	0.701	0.0
Q0DXS3		740	Probable RNA-dependent RN	yes	no	0.799	0.977	0.658	0.0
Q7XM31		1136	Probable RNA-dependent RN	yes	no	0.908	0.722	0.444	0.0
O82504		1133	RNA-dependent RNA polymer	no	no	0.945	0.754	0.430	0.0
Q8LHH9		1218	Probable RNA-dependent RN	no	no	0.896	0.665	0.403	1e-166
Q9SG02		1196	RNA-dependent RNA polymer	no	no	0.907	0.685	0.395	1e-158
O14227		1215	RNA-dependent RNA polymer	yes	no	0.806	0.6	0.312	1e-99
O82188		977	Probable RNA-dependent RN	no	no	0.605	0.559	0.242	5e-23
O82190		992	Probable RNA-dependent RN	no	no	0.532	0.484	0.243	1e-21
O82189		927	Probable RNA-dependent RN	no	no	0.594	0.579	0.237	6e-21

>sp\|Q9LQV2\|RDR1_ARATH RNA-dependent RNA polymerase 1 OS=Arabidopsis thaliana GN=RDR1 PE=2 SV=1	Back alignment and function desciption

 Score = 1279 bits (3310), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 624/889 (70%), Positives = 726/889 (81%), Gaps = 26/889 (2%)

Query: 1    MELPYRLELPDFKENFAYYKESE-DRFVLETGSAYSRSLD-LVPIVGPPDGIALPYEILF 58
            +ELP  L +PDF+ENFA Y E     F++E+GS+YS + + LVP+V PP G +LP+EILF
Sbjct: 225  LELPVHLNVPDFRENFANYAEHRASSFLIESGSSYSSNANTLVPVVDPPPGFSLPFEILF 284

Query: 59   KINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQ 118
            K+N LVQN C++GP LD +FYRL++  +   ++  I+H L+KL+HL ECCYEP+ WL D+
Sbjct: 285  KLNTLVQNACLSGPALDLDFYRLLNQKKYDRAL--IDHCLEKLFHLGECCYEPAHWLRDE 342

Query: 119  YRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFL 178
            Y+K+++    P SP ISLDDGLVY++RVQVTP+RVYF GPE+NVSNRVLRH+ + I+NFL
Sbjct: 343  YKKWISKGKLPLSPTISLDDGLVYMYRVQVTPARVYFSGPEVNVSNRVLRHYSKYINNFL 402

Query: 179  RISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQ 238
            R+SF+DEDL+K+ S DLSPR S+     RT++Y RI S LR+GI+IGD+KFEFLAFSSSQ
Sbjct: 403  RVSFVDEDLEKVRSMDLSPRSSTQR---RTKLYDRIYSVLRDGIVIGDKKFEFLAFSSSQ 459

Query: 239  LRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEI 298
            LRE+SAWMFA    +TAA IR WMG+F  IRNVAKYAARLGQSFSSS+ETL+V  DEIE+
Sbjct: 460  LRENSAWMFAPIDRITAAHIRAWMGDFDHIRNVAKYAARLGQSFSSSRETLNVRSDEIEV 519

Query: 299  IPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPT 358
            IPDV+I    T+YVFSDGIGK+SAEFARKVA KCGL +  PSAFQIRYGGYKGVVA DP 
Sbjct: 520  IPDVEIISLGTRYVFSDGIGKISAEFARKVARKCGLTEFSPSAFQIRYGGYKGVVAVDPN 579

Query: 359  SSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAV 418
            SSKKLSLR SM K+ESE TKLDVLAWSKYQPC++NRQLI+LLSTLG+ D +FEKKQRE V
Sbjct: 580  SSKKLSLRKSMSKFESENTKLDVLAWSKYQPCYMNRQLITLLSTLGVTDSVFEKKQREVV 639

Query: 419  RQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLEL 478
             +LDAILT PL+A EAL LM+PGENTNILK L++CGYKPDAEPFLSMMLQ FRASKLLEL
Sbjct: 640  DRLDAILTHPLEAHEALGLMAPGENTNILKALILCGYKPDAEPFLSMMLQNFRASKLLEL 699

Query: 479  RTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQ 538
            RTKTRIFI  GRSMMGCLDETRTL YGQV VQ S                 R  +RFI+ 
Sbjct: 700  RTKTRIFISGGRSMMGCLDETRTLEYGQVVVQYS--------------DPMRPGRRFIIT 745

Query: 539  GLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFV 598
            G VVVAKNPCLHPGDVRVL+AVNVPAL+HMVDCVVFPQKG+RPHPNECSGSDLDGDIYFV
Sbjct: 746  GPVVVAKNPCLHPGDVRVLQAVNVPALNHMVDCVVFPQKGLRPHPNECSGSDLDGDIYFV 805

Query: 599  CWDDELIPPQQDPPMDYTPAQSMQLDHDVQIEDVEEYFTNYIVNDSLGIIANAHTVFADR 658
            CWD EL+PP+   PMDYTP  +  LDHDV IE+VEEYF NYIVNDSLGIIANAHT FAD+
Sbjct: 806  CWDQELVPPRTSEPMDYTPEPTQILDHDVTIEEVEEYFANYIVNDSLGIIANAHTAFADK 865

Query: 659  EPRKARSEPCLQLAEKFSIAVDFPKTGVPAEIPPHLYVKEYPDFMEKPDKPTYESQNVIG 718
            EP KA S+PC++LA+KFS AVDFPKTGV A IP HLYVKEYPDFMEKPDKPTYES+NVIG
Sbjct: 866  EPLKAFSDPCIELAKKFSTAVDFPKTGVAAVIPQHLYVKEYPDFMEKPDKPTYESKNVIG 925

Query: 719  KLFRAVKDIAPHTSCIRLFTKEVARRSYDPDMEVDGFEDHIDDAIYHKGNYDYKLGNLMD 778
            KLFR VK+ AP    I+ FT +VA +SYD DMEVDGFE+++D+A Y K NYD+KLGNLMD
Sbjct: 926  KLFREVKERAPPLISIKSFTLDVASKSYDKDMEVDGFEEYVDEAFYQKANYDFKLGNLMD 985

Query: 779  YYGIKTEAEILTGSIMKMSKSFTKRRDAEAIGMAVRALRKEARAWFKEKSGSDTEDDAYA 838
            YYGIKTEAEIL+G IM+MSKSFTKRRDAE+IG AVRALRKE  + F      +      A
Sbjct: 986  YYGIKTEAEILSGGIMRMSKSFTKRRDAESIGRAVRALRKETLSLFNASEEEEN---ESA 1042

Query: 839  KASAWYHVTYHPDYWGCYNQGMNRDHFLSFPWCVYDRLVEIKKDKTSIG 887
            KASAWYHVTYH  YWG YN+G+NRDHFLSF WCVYD+LV IK  KT++G
Sbjct: 1043 KASAWYHVTYHSSYWGLYNEGLNRDHFLSFAWCVYDKLVRIK--KTNLG 1089

RNA-dependent direct polymerase involved in antiviral silencing. Required for the production of some small RNAs (mainly 21 and some 22 nucleotides) derived from the crucifer-infecting tobamovirus (TMV-cg). Required for turnip mosaic virus (TuMV) silencing and accumulation of viral siRNAs. Involved in cucumber mosaic virus (CMV) silencing. Required for the biogenesis of viral secondary siRNAs, process that follows the production of primary siRNAs derived from viral RNA replication. Specifically targets the positive-strand of the 3 RNA genomes of CMV and preferentially amplifies the 5'-terminal siRNAs of each viral genomic RNA. Not involved in the production of siRNAs derived from a single-stranded 336-nucleotide satellite RNA of CMV.
Arabidopsis thaliana (taxid: 3702)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 4EC: 8

>sp\|Q0DXS3\|RDR1_ORYSJ Probable RNA-dependent RNA polymerase 1 OS=Oryza sativa subsp. japonica GN=RDR1 PE=2 SV=2	Back alignment and function description

>sp\|Q7XM31\|RDR2_ORYSJ Probable RNA-dependent RNA polymerase 2 OS=Oryza sativa subsp. japonica GN=RDR2 PE=2 SV=1	Back alignment and function description

>sp\|O82504\|RDR2_ARATH RNA-dependent RNA polymerase 2 OS=Arabidopsis thaliana GN=RDR2 PE=3 SV=1	Back alignment and function description

>sp\|Q8LHH9\|SHL2_ORYSJ Probable RNA-dependent RNA polymerase SHL2 OS=Oryza sativa subsp. japonica GN=SHL2 PE=2 SV=1	Back alignment and function description

>sp\|Q9SG02\|RDR6_ARATH RNA-dependent RNA polymerase 6 OS=Arabidopsis thaliana GN=RDR6 PE=1 SV=1	Back alignment and function description

>sp\|O14227\|RDR1_SCHPO RNA-dependent RNA polymerase 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rdr1 PE=1 SV=1	Back alignment and function description

>sp\|O82188\|RDR5_ARATH Probable RNA-dependent RNA polymerase 5 OS=Arabidopsis thaliana GN=RDR5 PE=2 SV=2	Back alignment and function description

>sp\|O82190\|RDR3_ARATH Probable RNA-dependent RNA polymerase 3 OS=Arabidopsis thaliana GN=RDR3 PE=3 SV=2	Back alignment and function description

>sp\|O82189\|RDR4_ARATH Probable RNA-dependent RNA polymerase 4 OS=Arabidopsis thaliana GN=RDR4 PE=3 SV=2	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		904
224099571		1133	rna-dependent RNA polymerase [Populus tr	0.996	0.795	0.747	0.0
225424397		1121	PREDICTED: RNA-dependent RNA polymerase	0.991	0.799	0.740	0.0
146762448		1110	RNA-dependent RNA polymerase [Gossypium	0.974	0.793	0.735	0.0
90823307		1110	RNA-dependent RNA polymerase [Gossypium	0.974	0.793	0.729	0.0
225424395		1109	PREDICTED: RNA-dependent RNA polymerase	0.973	0.793	0.730	0.0
4138282		1116	RNA-directed RNA polymerase [Nicotiana t	0.970	0.785	0.712	0.0
157152684		1117	RNA-dependent RNA polymerase [Nicotiana	0.970	0.785	0.709	0.0
350537951		1114	RNA-directed RNA polymerase [Solanum lyc	0.961	0.780	0.709	0.0
356499585		1125	PREDICTED: RNA-dependent RNA polymerase	0.984	0.791	0.707	0.0
142942402		1115	putative RNA-dependent RNA-polymerase [S	0.961	0.779	0.705	0.0

>gi\|224099571\|ref\|XP_002311536.1\| rna-dependent RNA polymerase [Populus trichocarpa] gi\|222851356\|gb\|EEE88903.1\| rna-dependent RNA polymerase [Populus trichocarpa]	Back alignment and taxonomy information

 Score = 1428 bits (3696), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 679/908 (74%), Positives = 784/908 (86%), Gaps = 7/908 (0%)

Query: 1    MELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKI 60
            +ELP  L+LP+F ENF YYKE+E  FVLE+G  +SR+ DLVPIVGP  G+ LPY ILF++
Sbjct: 227  LELPNHLQLPNFNENFFYYKENEGTFVLESGLTFSRNPDLVPIVGPSSGVNLPYNILFRV 286

Query: 61   NLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYR 120
            NLLVQNGC+AG +LD  FYRLVDP R PV   CIE+AL+KLYHLKECCYEPS+W  +QY+
Sbjct: 287  NLLVQNGCLAGSMLDDIFYRLVDPNRMPVR--CIEYALEKLYHLKECCYEPSKWFNEQYK 344

Query: 121  KYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRI 180
            KY+TS + P SP +SLD GLVYV++VQ+TP +V+FCGPE+NVSNRVLR +R DIDNFLR+
Sbjct: 345  KYLTSGNPPRSPVLSLDAGLVYVYKVQITPCKVFFCGPEVNVSNRVLRQYREDIDNFLRV 404

Query: 181  SFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLR 240
            SF+DE+L+KIHSTD+SPR SS  ++ RT IY RILSTL+NGI+IGD+KFEFLAFSSSQLR
Sbjct: 405  SFVDEELEKIHSTDVSPRTSSRNELRRTAIYNRILSTLQNGIVIGDKKFEFLAFSSSQLR 464

Query: 241  ESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIP 300
            E+S WMFASR GLTAA+IR WMG+F +IRNVA+YAARLGQSF SS ETLSV   EIEIIP
Sbjct: 465  ENSCWMFASRLGLTAADIRAWMGSFHKIRNVARYAARLGQSFGSSTETLSVSSHEIEIIP 524

Query: 301  DVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSS 360
            D+++  G T+Y+FSDGIGK+SAEFARKVA KCG K   PSAFQIRY GYKGVVA DPTSS
Sbjct: 525  DIEVSRGGTRYLFSDGIGKISAEFARKVAIKCGCKGFTPSAFQIRYAGYKGVVAVDPTSS 584

Query: 361  KKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQ 420
            KKLSLR SM KYESE TKLDVLA SKYQPCFLNRQLI+LLSTLG+ D  FE+KQREAV Q
Sbjct: 585  KKLSLRRSMFKYESENTKLDVLAHSKYQPCFLNRQLITLLSTLGVPDHHFERKQREAVDQ 644

Query: 421  LDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRT 480
            LDA+LTDPL+AQEALELMSPGENTNILKE+L+CGY+PDAEPFLSMMLQTFRASKLLELRT
Sbjct: 645  LDAMLTDPLRAQEALELMSPGENTNILKEMLLCGYQPDAEPFLSMMLQTFRASKLLELRT 704

Query: 481  KTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGL 540
            KTRIFIPNGRSMMGCLDETRTL +GQVFV+ SG+ +R L+  S +FS     Q ++++G 
Sbjct: 705  KTRIFIPNGRSMMGCLDETRTLEHGQVFVKFSGSRFRNLYDSSDMFSERGRGQCYLIKGS 764

Query: 541  VVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFVCW 600
            VVVAKNPCLHPGD+R+LKAV+VPALHHMVDCVVFPQKG RPHPNECSGSDLDGDIYFVCW
Sbjct: 765  VVVAKNPCLHPGDLRILKAVDVPALHHMVDCVVFPQKGPRPHPNECSGSDLDGDIYFVCW 824

Query: 601  DDELIPPQQDPPMDYTPAQSMQLDHDVQIEDVEEYFTNYIVNDSLGIIANAHTVFADREP 660
            D ELIP QQ  PMDYTP   +QLDHDV IE+VEEYFTNYIVNDSLG+IANAHT  AD+E 
Sbjct: 825  DPELIPSQQISPMDYTPEPPLQLDHDVTIEEVEEYFTNYIVNDSLGVIANAHTAHADKES 884

Query: 661  RKARSEPCLQLAEKFSIAVDFPKTGVPAEIPPHLYVKEYPDFMEKPDKPTYESQNVIGKL 720
             KA SEPC++LA KFSIAVDFPKTGVPAEIP +L  +EYPDFMEKPDKP+YES+NVIGKL
Sbjct: 885  LKAMSEPCVELARKFSIAVDFPKTGVPAEIPSNLRAREYPDFMEKPDKPSYESRNVIGKL 944

Query: 721  FRAVKDIAPHTSCIRLFTKEVARRSYDPDMEVDGFEDHIDDAIYHKGNYDYKLGNLMDYY 780
            FR VKDIAP TS IR FT +VAR+ YDPDMEVDGFED+IDDA Y+K NYDYKLGNLM+YY
Sbjct: 945  FREVKDIAPRTSSIRSFTSDVARQCYDPDMEVDGFEDYIDDAFYYKSNYDYKLGNLMEYY 1004

Query: 781  GIKTEAEILTGSIMKMSKSFTKRRDAEAIGMAVRALRKEARAWFKEK-SGSDTE-DDAYA 838
            GIKTEAE+L+GS MKMSKSFTK+RDAEAIGMAVR+L+KEAR+WF EK SG D++ DD  A
Sbjct: 1005 GIKTEAELLSGSFMKMSKSFTKKRDAEAIGMAVRSLKKEARSWFNEKGSGLDSQADDVDA 1064

Query: 839  KASAWYHVTYHPDYWGCYNQGMNRDHFLSFPWCVYDRLVEIKKDKTS---IGNAFPALEQ 895
            KASAWYHVTYH +YWGCYN+GMNRDHFLSFPWCVYD+L++IK+  ++        P++E+
Sbjct: 1065 KASAWYHVTYHHNYWGCYNEGMNRDHFLSFPWCVYDKLIQIKRRNSARIRRSLILPSVER 1124

Query: 896  QFRQGLRM 903
            QF +GL +
Sbjct: 1125 QFSRGLHL 1132

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225424397\|ref\|XP_002284914.1\| PREDICTED: RNA-dependent RNA polymerase 1 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|146762448\|gb\|ABQ45352.1\| RNA-dependent RNA polymerase [Gossypium hirsutum]	Back alignment and taxonomy information

>gi\|90823307\|gb\|ABE01124.1\| RNA-dependent RNA polymerase [Gossypium hirsutum]	Back alignment and taxonomy information

>gi\|225424395\|ref\|XP_002281315.1\| PREDICTED: RNA-dependent RNA polymerase 1-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|4138282\|emb\|CAA09697.1\| RNA-directed RNA polymerase [Nicotiana tabacum]	Back alignment and taxonomy information

>gi\|157152684\|gb\|ABV24845.1\| RNA-dependent RNA polymerase [Nicotiana glutinosa] gi\|209420668\|gb\|ACI46982.1\| RNA-dependent RNA polymerase [Nicotiana glutinosa]	Back alignment and taxonomy information

>gi\|350537951\|ref\|NP_001234319.1\| RNA-directed RNA polymerase [Solanum lycopersicum] gi\|4038592\|emb\|CAA71421.1\| RNA-directed RNA polymerase [Solanum lycopersicum]	Back alignment and taxonomy information

>gi\|356499585\|ref\|XP_003518619.1\| PREDICTED: RNA-dependent RNA polymerase 1-like [Glycine max]	Back alignment and taxonomy information

>gi\|142942402\|gb\|ABO92977.1\| putative RNA-dependent RNA-polymerase [Solanum tuberosum]	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		904
TAIR\|locus:2006822		1107	RDR1 "AT1G14790" [Arabidopsis	0.721	0.588	0.745	3.8e-268
TAIR\|locus:2136068		1133	RDR2 "RNA-dependent RNA polyme	0.944	0.753	0.425	4.2e-182
UNIPROTKB\|Q8LHH9		1218	SHL2 "Probable RNA-dependent R	0.898	0.666	0.389	5.4e-150
TAIR\|locus:2114633		1196	RDR6 "AT3G49500" [Arabidopsis	0.867	0.655	0.4	3.9e-147
UNIPROTKB\|G4NJ50		1407	MGG_02748 "RNA-dependent RNA p	0.823	0.528	0.335	4.3e-109
POMBASE\|SPAC6F12.09		1215	rdp1 "RNA-directed RNA polymer	0.811	0.604	0.314	4.1e-88
WB\|WBGene00004510		1765	rrf-3 [Caenorhabditis elegans	0.731	0.374	0.315	8.7e-83
WB\|WBGene00004509		1579	rrf-2 [Caenorhabditis elegans	0.466	0.267	0.327	2.4e-71
ASPGD\|ASPL0000040001		1203	rrpC [Emericella nidulans (tax	0.703	0.528	0.295	2.2e-68
WB\|WBGene00004508		1601	rrf-1 [Caenorhabditis elegans	0.467	0.264	0.319	3.4e-68

TAIR\|locus:2006822 RDR1 "AT1G14790" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2579 (912.9 bits), Expect = 3.8e-268, P = 3.8e-268
 Identities = 502/673 (74%), Positives = 563/673 (83%)

Query:   216 STLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYA 275
             S LR+GI+IGD+KFEFLAFSSSQLRE+SAWMFA    +TAA IR WMG+F  IRNVAKYA
Sbjct:   437 SVLRDGIVIGDKKFEFLAFSSSQLRENSAWMFAPIDRITAAHIRAWMGDFDHIRNVAKYA 496

Query:   276 ARLGQSFSSSKETLSVHMDEIEIIPDVKI-EIGKTKYVFSDGIGKVSAEFARKVASKCGL 334
             ARLGQSFSSS+ETL+V  DEIE+IPDV+I  +G T+YVFSDGIGK+SAEFARKVA KCGL
Sbjct:   497 ARLGQSFSSSRETLNVRSDEIEVIPDVEIISLG-TRYVFSDGIGKISAEFARKVARKCGL 555

Query:   335 KDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNR 394
              +  PSAFQIRYGGYKGVVA DP SSKKLSLR SM K+ESE TKLDVLAWSKYQPC++NR
Sbjct:   556 TEFSPSAFQIRYGGYKGVVAVDPNSSKKLSLRKSMSKFESENTKLDVLAWSKYQPCYMNR 615

Query:   395 QLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICG 454
             QLI+LLSTLG+ D +FEKKQRE V +LDAILT PL+A EAL LM+PGENTNILK L++CG
Sbjct:   616 QLITLLSTLGVTDSVFEKKQREVVDRLDAILTHPLEAHEALGLMAPGENTNILKALILCG 675

Query:   455 YKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGA 514
             YKPDAEPFLSMMLQ FRASKLLELRTKTRIFI  GRSMMGCLDETRTL YGQV VQ S  
Sbjct:   676 YKPDAEPFLSMMLQNFRASKLLELRTKTRIFISGGRSMMGCLDETRTLEYGQVVVQYSDP 735

Query:   515 GYRQLHGEXXXXXXXXXXXXXIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVF 574
                   G              I+ G VVVAKNPCLHPGDVRVL+AVNVPAL+HMVDCVVF
Sbjct:   736 ---MRPGRRF-----------IITGPVVVAKNPCLHPGDVRVLQAVNVPALNHMVDCVVF 781

Query:   575 PQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLDHDVQIEDVEE 634
             PQKG+RPHPNECSGSDLDGDIYFVCWD EL+PP+   PMDYTP  +  LDHDV IE+VEE
Sbjct:   782 PQKGLRPHPNECSGSDLDGDIYFVCWDQELVPPRTSEPMDYTPEPTQILDHDVTIEEVEE 841

Query:   635 YFTNYIVNDSLGIIANAHTVFADREPRKARSEPCLQLAEKFSIAVDFPKTGVPAEIPPHL 694
             YF NYIVNDSLGIIANAHT FAD+EP KA S+PC++LA+KFS AVDFPKTGV A IP HL
Sbjct:   842 YFANYIVNDSLGIIANAHTAFADKEPLKAFSDPCIELAKKFSTAVDFPKTGVAAVIPQHL 901

Query:   695 YVKEYPDFMEKPDKPTYESQNVIGKLFRAVKDIAPHTSCIRLFTKEVARRSYDPDMEVDG 754
             YVKEYPDFMEKPDKPTYES+NVIGKLFR VK+ AP    I+ FT +VA +SYD DMEVDG
Sbjct:   902 YVKEYPDFMEKPDKPTYESKNVIGKLFREVKERAPPLISIKSFTLDVASKSYDKDMEVDG 961

Query:   755 FEDHIDDAIYHKGNYDYKLGNLMDYYGIKTEAEILTGSIMKMSKSFTKRRDAEAIGMAVR 814
             FE+++D+A Y K NYD+KLGNLMDYYGIKTEAEIL+G IM+MSKSFTKRRDAE+IG AVR
Sbjct:   962 FEEYVDEAFYQKANYDFKLGNLMDYYGIKTEAEILSGGIMRMSKSFTKRRDAESIGRAVR 1021

Query:   815 ALRKEARAWFKEKSGSDTEDDAYAKASAWYHVTYHPDYWGCYNQGMNRDHFLSFPWCVYD 874
             ALRKE  + F   + S+ E++  AKASAWYHVTYH  YWG YN+G+NRDHFLSF WCVYD
Sbjct:  1022 ALRKETLSLF---NASEEEENESAKASAWYHVTYHSSYWGLYNEGLNRDHFLSFAWCVYD 1078

Query:   875 RLVEIKKDKTSIG 887
             +LV IKK  T++G
Sbjct:  1079 KLVRIKK--TNLG 1089

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003968 "RNA-directed RNA polymerase activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0016441 "posttranscriptional gene silencing" evidence=ISS

GO:0009615 "response to virus" evidence=IMP

GO:0009751 "response to salicylic acid stimulus" evidence=IEP

GO:0060148 "positive regulation of posttranscriptional gene silencing" evidence=IMP

GO:0000165 "MAPK cascade" evidence=RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009617 "response to bacterium" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0010025 "wax biosynthetic process" evidence=IGI

TAIR\|locus:2136068 RDR2 "RNA-dependent RNA polymerase 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|Q8LHH9 SHL2 "Probable RNA-dependent RNA polymerase SHL2" [Oryza sativa Japonica Group (taxid:39947)]	Back alignment and assigned GO terms

TAIR\|locus:2114633 RDR6 "AT3G49500" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|G4NJ50 MGG_02748 "RNA-dependent RNA polymerase 1" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

POMBASE\|SPAC6F12.09 rdp1 "RNA-directed RNA polymerase Rdp1" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

WB\|WBGene00004510 rrf-3 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

WB\|WBGene00004509 rrf-2 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000040001 rrpC [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

WB\|WBGene00004508 rrf-1 [Caenorhabditis elegans (taxid:6239)]	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)
Q9LQV2	RDR1_ARATH	2, ., 7, ., 7, ., 4, 8	0.7019	0.9546	0.7795	yes	no
Q0DXS3	RDR1_ORYSJ	2, ., 7, ., 7, ., 4, 8	0.6581	0.7997	0.9770	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	RDR902	rna-dependent RNA polymerase (1133 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	DCL904	dicer-like protein (1492 aa)	•	0.683
	DCL905	dicer-like protein (1588 aa)	•	0.683
	DCL901	dicer-like protein (1408 aa)	•	0.683
	DCL903	dicer-like protein (1468 aa)	•	0.683
	DCL902	dicer-like protein (1817 aa)	•	0.683

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		904
pfam05183		508	pfam05183, RdRP, RNA dependent RNA polymerase	0.0

>gnl\|CDD\|218483 pfam05183, RdRP, RNA dependent RNA polymerase	Back alignment and domain information

 Score =  534 bits (1376), Expect = 0.0
 Identities = 236/583 (40%), Positives = 331/583 (56%), Gaps = 88/583 (15%)

Query: 151 SRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRI 210
           +RV    PE+  SNRVLR +    D FLR+ F DEDL    S D               +
Sbjct: 1   TRVILELPELERSNRVLRKYG-AADRFLRVKFPDEDLSGAISNDED-------------V 46

Query: 211 YTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRN 270
             R+   L+NGI+IGDR   +LAFS+SQLRE SAW FA    LTA +IR W+G+F  I  
Sbjct: 47  GDRVKRVLKNGIIIGDR---YLAFSNSQLREHSAWFFAED-RLTAEDIRNWLGDFENIEQ 102

Query: 271 V-AKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVA 329
           V AKYAAR+GQ FS+++ T  + + +IE IPD+     +  Y+F+DG+GK+S + ARK+A
Sbjct: 103 VPAKYAARIGQCFSTTRPTTGIRIRKIERIPDI---PERNGYIFTDGVGKISRDLARKIA 159

Query: 330 SKCGLKDNPPSAFQIRYGGYKGVVAADPT-SSKKLSLRDSMRKYE----SELTKLDVLAW 384
            + G  +  PSA+QIR+GGYKGV+  DP     ++ +R SM K++    + +  L+++  
Sbjct: 160 DELGTLEEDPSAYQIRFGGYKGVLVVDPDLPGNEIHIRPSMLKFDLLGDAAVNSLEIIRS 219

Query: 385 SKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENT 444
           SK  P +LNRQLI++LSTLG+ DE+F +  REA+++L   LTD  +A   L+L+    + 
Sbjct: 220 SKPTPAYLNRQLITVLSTLGVPDEVFIELLREALKELAEALTDWDQA---LDLLRKQADE 276

Query: 445 NILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNY 504
           N     L   + P  +PFL  +L+      L +L+ K RI +P   ++ G +DET  L  
Sbjct: 277 ND--FTLTLRFMPSEDPFLRKLLRALVKHTLKKLKEKLRIPVPKSAALFGVVDETGVLKE 334

Query: 505 GQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPA 564
           G+VFVQ+S                +   Q   ++G V+VA+NPCLHPGD+RV++AV+VP 
Sbjct: 335 GEVFVQVS--------------DGNDGGQYEYLEGDVLVARNPCLHPGDIRVVRAVDVPE 380

Query: 565 LHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLD 624
           L H+ D VVFP KG RP  +E SG DLDGDIYFVCWD +L                    
Sbjct: 381 LRHLKDVVVFPSKGDRPLASELSGGDLDGDIYFVCWDPDL-------------------- 420

Query: 625 HDVQIEDVEEYFTNYIVNDSLGIIANAHTVFADREPRKARSEPCLQLAEKFSIAVDFPKT 684
                               LG I+N+H   AD  P       CL+LA+  S AVD+PKT
Sbjct: 421 --------------------LGRISNSHLAIAD--PEGVGDPECLRLAKLHSQAVDYPKT 458

Query: 685 GVPAEIPPHLYVKEYPDFMEKPDKPTYESQNVIGKLFRAVKDI 727
           G+P E+   L  KE+PDFMEK +  +Y+S  ++GKL+R+V   
Sbjct: 459 GLPVEMKRLLRPKEWPDFMEKDEGKSYKSTRILGKLYRSVLAN 501

This family of proteins are eukaryotic RNA dependent RNA polymerases. These proteins are involved in post transcriptional gene silencing where they are thought to amplify dsRNA templates. Length = 508

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		904
KOG0988		1145	consensus RNA-directed RNA polymerase QDE-1 requir	100.0
PF05183		579	RdRP: RNA dependent RNA polymerase; InterPro: IPR0	100.0
smart00663		295	RPOLA_N RNA polymerase I subunit A N-terminus.	81.71

>KOG0988 consensus RNA-directed RNA polymerase QDE-1 required for posttranscriptional gene silencing and RNA interference [RNA processing and modification]	Back alignment and domain information

Probab=100.00  E-value=4.1e-178  Score=1566.03  Aligned_cols=852  Identities=41%  Similarity=0.615  Sum_probs=742.6

Q ss_pred             hhccccccccc-----cC--eeEEeeCCccc-cCCCcccccC-CCCCCCCCcchHHHHHHHHHhCcCCcccccHHHHHhh
Q 002586           12 FKENFAYYKES-----ED--RFVLETGSAYS-RSLDLVPIVG-PPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLV   82 (904)
Q Consensus        12 ~~~~~~~~~~~-----~~--~~~~~~~~~~~-~~~~~~~~~~-~~~~~~lpf~v~fql~~l~~~g~l~~~~~~~~f~~~l   82 (904)
                      +..++||+.++     .-  .+.++.|+.|. ++..++||++ ...++..+++++++.++||+.|.+.......+|+.++
T Consensus       257 i~~~lP~~r~~~~~~~~~~~s~~ir~~~~~~~~~~~~~~l~~~~~~git~~~e~l~~r~slv~dq~~~~~~~~~~f~~l~  336 (1145)
T KOG0988|consen  257 IWKDLPYNRYNGSTAEEFRLSVWIRLGSKYDVSSAQLVPLNDERDFGITHLYECLVSRGSLVKDQVLLEEAHLLEFLGLL  336 (1145)
T ss_pred             hhccCCcccccccchhhhhhhhheecccccccccceeeeccccccccceeehhhhhcccchhhhhHHhhhhHHHHHHHHH
Confidence            67888888875     33  67888999998 5777999988 4567889999999999999999999999999999999


Q ss_pred             CCCCCCCChHHHHHHHHHHHhccccccCcchhHHHHHHHhhhcCCCCCCCCccCCCCcEEEEEEEEcCCeeeeccccccc
Q 002586           83 DPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINV  162 (904)
Q Consensus        83 ~~~~~~~~~~~~~~~l~~l~~~~~~~~dp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~vTPtri~~~~P~~e~  162 (904)
                      ..... .....++..||+|.+...+|+||.-+....++....++.+  .....+.+|+++|+||.|||||||+.+||+++
T Consensus       337 ~~~~~-~d~~v~~a~LekL~~~~~~cfd~~~~~k~i~~~~~~ng~~--~~~~~~~~g~~~vrk~v~TPtrv~~~~PE~~~  413 (1145)
T KOG0988|consen  337 RHKVL-GDDNVLEAKLEKLLKLSTKCFDPYCQYKKIAKLNPSNGKL--VTTKEIMEGLRRVRKVVFTPTRVYLLAPEVEM  413 (1145)
T ss_pred             hhhhc-cchhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhcccCcc--ccchhhhhcceeEEEEEEcCceeEecCchhhh
Confidence            76332 1225667789999999999999999888877765445442  23345678999999999999999999999999


Q ss_pred             cCchhcccCcCCCcEEEEEEeeCCCCccccCCCCCCCCCCccchhhhHHHHHHHHHhcCeEEcceeEEEeeecCCCCCcC
Q 002586          163 SNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRES  242 (904)
Q Consensus       163 sNRvlR~f~~~~d~FlRV~F~DE~~~~l~~~~~~~r~~~~~~~~~~~i~~rv~~~L~~Gi~I~gr~y~FLa~S~SqlR~~  242 (904)
                      +|||+|+|..+.++||||+|+||+++ +..++.+++       .++.+|.||..+|++||+||+|.|+||||||||||+|
T Consensus       414 gNRVlR~f~~~~t~~lRvtF~De~~~-~~ir~~S~~-------~~t~l~~rv~~~L~~Gi~v~~r~y~FL~~s~sQlRdn  485 (1145)
T KOG0988|consen  414 GNRVLRKFDKDSTRFLRVTFRDEDNK-LKIRTLSTG-------SRTKLDMRVNSYLTDGISVANRRYEFLAFSNSQLRDN  485 (1145)
T ss_pred             cchhheeccccCceEEEEEEEccccc-cccccCCcc-------hhhHHHHHHHHHHhcccEEccceeEEEEecccccccC
Confidence            99999999999999999999999986 444333221       1689999999999999999999999999999999999


Q ss_pred             eEEEEEcCCCCCHHHHHHHhCCCCcccCHHHHHHHHcccccCCccceee-eCCcEEEccCcccccCCccccccccccccc
Q 002586          243 SAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSV-HMDEIEIIPDVKIEIGKTKYVFSDGIGKVS  321 (904)
Q Consensus       243 s~wf~a~~~~~t~~~Ir~~mG~F~~i~~~aK~aARlgq~FSsT~~t~~i-~~~~i~~i~Di~~~~~g~~~~fTDG~G~IS  321 (904)
                      |.||++.....++++||.|||+|++|.|++|||||||||||+|++|..+ +...+..+|||+.+++|++||||||||+||
T Consensus       486 gy~m~~~s~~~~i~~iR~wmG~F~~i~nv~K~aARmGqCFs~Sr~T~~~~~~~~~~~~~DI~~g~~g~~y~FSDGvG~iS  565 (1145)
T KOG0988|consen  486 GYFMARFSDKTKIEDIREWMGDFRDIDNVPKLAARMGQCFSQSRGTGYVLERLDRMCPPDIEGGKRGNNYCFSDGVGMIS  565 (1145)
T ss_pred             ceEEeecCCCccHHHHHHHhcchhhccCHHHHHhhcCcceeccccccccccccccccCCcccccccCCceeecCCccccc
Confidence            9888887777899999999999999999999999999999999999877 667788999999887889999999999999


Q ss_pred             HHHHHHHHHHcCCCCCCCceEEEeccCceEEEEeCCCCCcceeecccccccccCCCceeEeeecCcccccccHHHHHHHh
Q 002586          322 AEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLS  401 (904)
Q Consensus       322 ~~la~~I~~~l~l~~~~PSafQiR~gG~KGvL~vdp~~~~~I~lR~Sm~KF~s~~~~leI~~~S~~~p~~LNrQ~I~iL~  401 (904)
                      .++|++|++++++...+|||||||++|+||||+|||.....+.+|.||.||.|.+..++|+.|++++||+||||+|.+|+
T Consensus       566 ~~~a~~vsq~~~~~~~vPsaFQiR~~G~KGVvav~Ps~~~~~~~~~~~~~s~S~n~~~~v~~~~~f~~~~lnr~lI~Lls  645 (1145)
T KOG0988|consen  566 LQFAREVSQKRKFGKAVPSAFQIRYGGYKGVVAVDPSMDKVLKLRDSMNKSQSFNSLLEVTPSSKFQPAFLNRQLITLLS  645 (1145)
T ss_pred             HHHHHHHHHHHcccccCChheeeeccCCcceEEeCccHhhhhhhhhhhhhhhhhcceeeeeeccCCccccccHHHHHHHH
Confidence            99999999999998889999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             hCCCCHHHHHHHHHHHHHH--HHHHhcCHHHHHHHHHhcCCCCcHHHHHHHHHCCCCCCCchHHHHHHHHHHHHHHHHhc
Q 002586          402 TLGIWDEIFEKKQREAVRQ--LDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELR  479 (904)
Q Consensus       402 ~lGV~~evF~~lq~~~l~~--l~~~l~d~~~a~~~L~~~~~~~~~~~l~~ll~~Gf~~~~epfl~~~L~~~~~~~l~~lk  479 (904)
                      .+||++++|+++|+..++.  ....+.....+.++|......+..+.++.++..++.++.|||+++||..++++.++.+|
T Consensus       646 ~~gv~n~~F~~il~~vle~~r~~~n~~e~~~~~~~l~~~~~m~~en~a~~~l~~~~~~D~EPflr~mL~~~~k~~~~~~k  725 (1145)
T KOG0988|consen  646 YLGVLNKPFINILDQVLEKQRRITNRIEELLDRAALNYGEQMDDENIAAMILKGFPRIDSEPFLRSMLSSLLKFTLQLLK  725 (1145)
T ss_pred             hcCccchHHHHHHHHHHHHHHhhhhhhhHHHHHHHhhhhhhccchHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999983  33444555555666665544566676666666666688899999999999999999999


Q ss_pred             cccceeccCceeeeeecCCCCCCCCCcEEEEEcCCcccccCCCcccccccccccceEEeeeEEEEeCCCCCCCCeeEEEE
Q 002586          480 TKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKA  559 (904)
Q Consensus       480 ~K~rI~Vp~s~~l~GV~DetG~L~~gEVfvq~s~~~~~~~~~~~~~~~~~~~~~~~vi~G~VlV~RnP~lhPGDIr~v~A  559 (904)
                      +|.|||||.||+||||+||||+|||||||||++.+....           ......|++|+|+|||||||||||||+++|
T Consensus       726 ek~ripv~~Gr~lmGvvDETG~L~ygQVfVq~t~~~~~~-----------~~~~~~vitG~VlvtKNPcLhpGDVRVl~A  794 (1145)
T KOG0988|consen  726 EKIRIPVDLGRSLMGVVDETGILKYGQVFVQYTKTIRNS-----------DSGRKEVITGKVLVTKNPCLHPGDVRVLKA  794 (1145)
T ss_pred             hcccccCcCCceeEeeeccccccccCeEEEEEccccccc-----------ccCCceEEEeeEEEecCCCCCCCceEEEEe
Confidence            999999999999999999999999999999999863211           112347999999999999999999999999


Q ss_pred             ecCCCCCCCCCeEEecCCCCCCCCCCcCCCCCCCCeEEEeecCCCCCCCCCCCCCCCCCcccCCCCccCHHHHHHHHHHh
Q 002586          560 VNVPALHHMVDCVVFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLDHDVQIEDVEEYFTNY  639 (904)
Q Consensus       560 V~~P~L~hl~dvIVFp~kG~Rplps~lsGGDLDGD~y~ViWD~~Lv~~~~~~P~~y~~~~~~~l~~~vt~~di~~ffv~y  639 (904)
                      |++|+|+||+|||||||||+||||+||||||||||+|||||||+|+|+.+++||+|++++++.+++.++.++|.+||++|
T Consensus       795 V~vp~L~h~~dvVvFPQkGpRphpdE~aGsDLDGDeYfViWDqkLL~~~~~epmd~~~~~sk~~~~~~~~~~m~effv~y  874 (1145)
T KOG0988|consen  795 VYVPALEHMVDVVVFPQKGPRPHPDEMAGSDLDGDEYFVIWDQKLLPPRNEEPMDSSSEKSKILDGRVPLDEMSEFFVEY  874 (1145)
T ss_pred             eccHHHHhhcCEEEcCCCCCCCCccccccCCCCCceEEEEeChhhccCcCCCccccCccccccccCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccCcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHhhcccCCCCCCcccCCCCCCCCCCCCCCCCCCCCCccccchhcH
Q 002586          640 IVNDSLGIIANAHTVFADREPRKARSEPCLQLAEKFSIAVDFPKTGVPAEIPPHLYVKEYPDFMEKPDKPTYESQNVIGK  719 (904)
Q Consensus       640 m~~d~LG~isn~Hl~~aD~~~~g~~~~~Cl~LA~l~s~AVD~~KTG~~v~ip~~l~~~~~Pdfm~k~~~~~Y~S~~iLG~  719 (904)
                      |++|+||+|+|||+++||+  .|+.+..|+.||++||+||||||||+.+.||..++++++||||++.++|+|.|++++||
T Consensus       875 L~~DslG~isnAhl~~aD~--~G~~~~~Cl~LA~k~~~AVDF~KsG~d~~~~~~ek~e~~PDfm~~~d~p~Y~S~~l~Gk  952 (1145)
T KOG0988|consen  875 LKEDSLGLISNAHLANADV--YGLFSDVCLELAKKHSQAVDFPKSGADESMPEKEKPERYPDFMEKTDKPTYYSERLCGK  952 (1145)
T ss_pred             HHHHHHHHHhhccccchhh--cchhhHHHHHHHHhhcccccccccCCcccccchhchhhcchhhhCCCCceeecchhhhH
Confidence            9999999999999999999  59999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhhhcCCccccccchhhhhhccCCCCCccCChHHHHHHHHHHHHhHHHHHHHHHhhcCCCChhhhhhh--hhcccc
Q 002586          720 LFRAVKDIAPHTSCIRLFTKEVARRSYDPDMEVDGFEDHIDDAIYHKGNYDYKLGNLMDYYGIKTEAEILTG--SIMKMS  797 (904)
Q Consensus       720 Lyr~v~~~~~~~~~~~~~~~~~~~~~~d~~l~~~g~~~~~~~A~~~k~~Y~~~l~~lm~~y~i~tE~Ev~sG--~i~~~~  797 (904)
                      |||+++.+.............+. ..||++++++||++|+++|..+++.|+.+|++||++|||.+|+||+||  .+..|+
T Consensus       953 LfR~~~aid~~~~~~e~~~~~~~-i~yD~~l~v~gFe~yme~a~~~~~~y~~qL~slm~~ygi~~E~eI~sG~~~~ddms 1031 (1145)
T KOG0988|consen  953 LFREAKAIDAPLKGSEERSEQVE-VEYDEDLEVDGFEHYMERAKKQVASYNGQLRSLMDFYGISTEGEIFSGILDQDDMS 1031 (1145)
T ss_pred             HHHHHHhhcchhhcCccccCccc-ccCCcccCcCCcHHHHHHHHHHHhhhhhHHHHHHHHhCccchhhhhccCccccchh
Confidence            99988766544333233334444 789999999999999999999999999999999999999999999999  555677


Q ss_pred             chhhhhhhHHHHHHHHHHHHHHHHHHHhh-h----c----CCCC-hhhHHHHHHHHhh-hccccccccccccCCCCCccc
Q 002586          798 KSFTKRRDAEAIGMAVRALRKEARAWFKE-K----S----GSDT-EDDAYAKASAWYH-VTYHPDYWGCYNQGMNRDHFL  866 (904)
Q Consensus       798 ~~~~~~~~~e~i~~~~~~l~~~~r~~f~~-~----~----~~~~-~~~~~~~a~A~Y~-Vty~~~~~~~~~~~~~~~~~l  866 (904)
                      .+.+.+...+++...+..||+.|.+.|.. .    .    .+.+ .+.+.+||+|||+ ++|+...      .++..+.+
T Consensus      1032 ~~~t~~~~e~~~~~l~~~~r~~~~qef~~y~~~~e~l~~fe~~~~eE~~~kKa~aWY~v~~ye~~~------~~~~~~~~ 1105 (1145)
T KOG0988|consen 1032 FYNTERMIELKLERLVLKLREKFFQEFGAYKLEIEKLSCFEDSPEEEFIMKKASAWYRVYRYEMAQ------AMRETRKL 1105 (1145)
T ss_pred             hhcccccchhhhHHHHHHHHHHHHHHhhhhcchhhhccccccCchhHHHHHHHHHHHHHHHhhhhc------ccccCccc
Confidence            77776666667777888888777777741 1    0    1223 3338899999999 7776542      23566778


Q ss_pred             ccccchhHHHHHHHhh---ccccCCCchhHH
Q 002586          867 SFPWCVYDRLVEIKKD---KTSIGNAFPALE  894 (904)
Q Consensus       867 SFpWi~~d~l~~ik~~---~~~~~~~~~~~~  894 (904)
                      |||||++|+|++||++   +....+.+.+|+
T Consensus      1106 SF~wia~Dvl~~iK~~~~~~~g~a~p~~tl~ 1136 (1145)
T KOG0988|consen 1106 SFAWIAYDVLARIKQTFLGAIGGANPVYTLE 1136 (1145)
T ss_pred             chHHHHHHHHHHHHHHHHHhhcccCchHHHH
Confidence            9999999999999999   555444444443

>PF05183 RdRP: RNA dependent RNA polymerase; InterPro: IPR007855 This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; 2	Back alignment and domain information

>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus	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		904
2j7n_A		1022	Structure Of The Rnai Polymerase From Neurospora Cr		2e-16

>pdb|2J7N|A Chain A, Structure Of The Rnai Polymerase From Neurospora Crassa Length = 1022

Back alignment and structure

Iteration: 1

Score = 84.7 bits (208), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 96/383 (25%), Positives = 153/383 (39%), Gaps = 55/383 (14%) Query: 309 TKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKG--VVAADPTSSKK-LSL 365 T V +DG+G++S A+++ GL D P SA Q R+G KG V+ D T + + Sbjct: 323 TGEVMNDGVGRMSRSVAKRIRDVLGLGDVP-SAVQGRFGSAKGMWVIDVDDTGDEDWIET 381 Query: 366 RDSMRKYESELT-----KLDVLA-WSKYQPCFLNRQLISLLS---------TLGIWDEIF 410 S RK+E + L+V + S+ + LN QL+ +L I D + Sbjct: 382 YPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGDRLI 441 Query: 411 EKKQREAVRQLDAILTDPLK-AQEALELMS-----------------PGENTNILKELLI 452 QR+ Q A L P++ Q E S P L L+ Sbjct: 442 NDLQRQFSEQKHA-LNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNFLMN 500 Query: 453 CGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQIS 512 G+ P + +L + + K L++K I + + D L +V V S Sbjct: 501 SGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFS 560 Query: 513 GAGYRQLHGEXXXXXXXXXXXXXIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCV 572 + +R + V+VA++P P D++ ++AV P LH + D + Sbjct: 561 -SKFRD----------EEESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSLKDVI 609 Query: 573 VFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLDHDVQIEDV 632 +F KG P + SG D DGD+ +VCWD E++ + M P S L D Sbjct: 610 IFSTKGDVPLAKKLSGGDYDGDMAWVCWDPEIVDGFVNAEMPLEPDLSRYLKKD------ 663 Query: 633 EEYFTNYIVNDSLGIIANAHTVF 655 + F + + G A T + Sbjct: 664 KTTFKQLMASHGTGSAAKEQTTY 686

PyMOL of 2j7n

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		904
2j7n_A		1022	RNA-dependent RNA polymerase; RNAI response, RNA-d	1e-179
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-14
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-12

>2j7n_A RNA-dependent RNA polymerase; RNAI response, RNA-directed RNA polymerase, hydrolase; 2.30A {Neurospora crassa} PDB: 2j7o_A Length = 1022	Back alignment and structure

 Score =  545 bits (1405), Expect = e-179
 Identities = 167/951 (17%), Positives = 300/951 (31%), Gaps = 129/951 (13%)

Query: 46  PPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLK 105
           P      P  + +++  L  +  V     +S   +    +     ++ I   L +L   +
Sbjct: 26  PKWLHEAPLAVAWEVTRLFMHCKVD-LEDESLGLKYDPSWSTARDVTDIWKTLYRLDAFR 84

Query: 106 ECCYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPS--RVYFCGPEINVS 163
                P +   D +   MT   +    A+ L   L Y      T     V          
Sbjct: 85  GK-PFPEKPPNDVFVTAMTGNFESKGSAVVLSAVLDYNPDNSPTAPLYLVKLKPLMFEQG 143

Query: 164 NRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATD-----ITRTRIYT-----R 213
            R+ R F    D F  I              +  +  +A +     +T  +        R
Sbjct: 144 CRLTRRF--GPDRFFEILIPSPTSTSPSVPPVVSKQPAAVEEVIQWLTMGQHSLVGRQWR 201

Query: 214 ILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFA------------------------S 249
                  G     R+F+  A     + +     FA                         
Sbjct: 202 AFFAKDAGYRKPLREFQLRAEDPKPIIKERVHFFAETGITFRPDVFKTRSVVPAEEPVEQ 261

Query: 250 RYGLTAAEIREWMGNFRE--IRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIG 307
           R     +++ +W+        +   K  +R+    S +   +++   +I       +   
Sbjct: 262 RTEFKVSQMLDWLLQLDNNTWQPHLKLFSRIQLGLSKTYAIMTLEPHQIRHHKTDLLSPS 321

Query: 308 KTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKK---LS 364
            T  V +DG+G++S   A+++    GL  + PSA Q R+G  KG+   D   +     + 
Sbjct: 322 GTGEVMNDGVGRMSRSVAKRIRDVLGL-GDVPSAVQGRFGSAKGMWVIDVDDTGDEDWIE 380

Query: 365 LRDSMRKYESEL-----TKLDVL-AWSKYQPCFLNRQLISLLSTLG---------IWDEI 409
              S RK+E +        L+V    S+ +   LN QL+ +L             I D +
Sbjct: 381 TYPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGDRL 440

Query: 410 FEKKQREAVRQLDAILTDPLKAQEALELMS-----------------PGENTNILKELLI 452
               QR+   Q  A+       Q   E  S                 P      L  L+ 
Sbjct: 441 INDLQRQFSEQKHALNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNFLMN 500

Query: 453 CGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQIS 512
            G+ P  + +L  +    +  K   L++K  I +     +    D    L   +V V  S
Sbjct: 501 SGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFS 560

Query: 513 GAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCV 572
                      S F         +    V+VA++P   P D++ ++AV  P LH + D +
Sbjct: 561 -----------SKFRDEEESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSLKDVI 609

Query: 573 VFPQKGMRPHPNECSGSDLDGDIYFVCWDDELIPPQQDPPMDYTPAQSMQLDHDVQI--- 629
           +F  KG  P   + SG D DGD+ +VCWD E++    +  M   P  S  L  D      
Sbjct: 610 IFSTKGDVPLAKKLSGGDYDGDMAWVCWDPEIVDGFVNAEMPLEPDLSRYLKKDKTTFKQ 669

Query: 630 -----------------EDVEEYFTNYIVNDSLGIIANAHTVFADREPRKARSEPCLQLA 672
                            + +++ F   +  + LG+  N              ++P + L+
Sbjct: 670 LMASHGTGSAAKEQTTYDMIQKSFHFALQPNFLGMCTNYKERLCYIN-NSVSNKPAIILS 728

Query: 673 EKFSIAVDFPKTGVPAEIPP-HLYVKEYPDFMEKPDKPTYESQNVIGK---------LFR 722
                 VD  K G+           +E          P Y+S + +G+         L  
Sbjct: 729 SLVGNLVDQSKQGIVFNEASWAQLRRELLGGALSLPDPMYKSDSWLGRGEPTHIIDYLKF 788

Query: 723 AVKDIAPHTSCIRLFTKEVARRSYDPDMEVDGFEDHIDDAIYHKGNYDYKLGNLMDYYGI 782
           ++   A     +  F   +       D       D      + K   D    + + +  +
Sbjct: 789 SIARPA-IDKELEAFHNAMKAAKDTEDGAHFWDPDLASYYTFFKEISDKSRSSALLFTTL 847

Query: 783 KTEAEILTGSIMKMSKSFTKRRDAEAIGMAVRALRKEARAWFKE---KSGSDTEDDAYAK 839
           K     +     ++ K+   R   +   + V  + ++  A   E   KSG++ +      
Sbjct: 848 KNRIGEVEKEYGRLVKNKEMRDSKDPYPVRVNQVYEKWCAITPEAMDKSGANYDSKVIRL 907

Query: 840 ASAWYHVTYHPDYW----GCYNQGMNRDHFLSFPWCVYDR-LVEIKKDKTS 885
               +      + W          +       F W +  R L  IK   TS
Sbjct: 908 LELSFLADREMNTWALLRASTAFKLYYHKSPKFVWQMAGRQLAYIKAQMTS 958

PyMOL of 2j7n

>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

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00