Citrus Sinensis ID: 004909

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----

MKKFAVLWRGVNVTVNFGFGMRKINFLLSHLGEEYRLELDYENIWEIELHCPRWQMTKYLLIQLLGAPRIFQKGIRSPDLLYESPVFNFFKEVPDDQWVRTTDFTPSNFIGQSTGLCMELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILTMLKPRLLWYELNSSHALPRFIVV

cccEEEEEEEccEEEEEcccEEEEEEEEccccEEEEEEEEcccccEEEEEcccccccEEEEEEEcccccEEEEccccccccccccccccccccccccEEEEcccccccccccEEEEEEEEcccccccHHHHHHHHHHHccccEEEEccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHccHHHHHHHccccccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHccccccccccccccccEEEEEEEEcccEEEEcccEEEcHHHHHcccccccccEEEEEEEEcccccccccccccccccccccccHHHHHHHHHHHHccEEEEEEEEEEEEccccccccccEEEEEccccccHHHHHHHHccccccccHHHHHHHHccccccccccEEEEcccEEEEEcEEEcccccEEEEccccccccHHHHHHHHHHcccccccccEEEEEEccccEEEEEcccccccEEEcccccccccccccEEEEEccccccccccHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHcccEEccccEEEEEEEccccccccccEEEEEcccccccccccccccccccccccEEEEcEEEEEEccccccccEEEEEEEEcccccccccEEEEccccccccccccccccccccccccccccccccc

ccEEEEEEcccEEEEEEcccEEEEEEEEEccccEEEEEEEEccEEEEEEEEccccccEEEEEEEccccEEEEEccccccHHccccccccccccccccEEEEEcccccccccEEEEEEEEEccccccHHHHHHHHHHHHcccccEccccccccccHHHHHHccccccccccHHHHHHHHHHHHcccccHHHccHHHHHHHHHcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEEcccEEEEcccccccccEEEEEcccccccEEEEEEEccccccccccccccccccccccccHHHHHHHHHHHHcccEEcccEEEEEEEccHHHHcccEEEEcccccccHHHHHHHHcccHHcccHHHHHHHHHHHcccccccEEcccccEEEEcccEEccccccEEEccccccccHHHHHHHHHHcccccccccEEEEEEcccEEEEEEccccccEEEEEccHHHcccccccEEEEEcccccccHHcHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccEEcccccEEEEEEcccccccccEEEEEEccccccccccccccccccccccEEEEEEEEEEEEccccccccEEEEEEcccHHHHHccEEEEEcccccccccccccccEEEEEEccccccccEEEc

MKKFAVLWRGVNVTVNFGFGMRKINFLLSHLGeeyrleldyENIWEIELHCPRWQMTKYLLIQLLgaprifqkgirspdllyespvfnffkevpddqwvrttdftpsnfigqstglcmelpyrlelpdfkenFAYYKESEDRFVLETGsaysrsldlvpivgppdgialPYEILFKINLLVqngcvagplldsnfyrlvdpyrapvsISCIEHALDKLYHlkeccyepsrwltDQYRKYmtsrskpsspaislddglvYVHRvqvtpsrvyfcgpeinvsNRVLRHFRRDIDNFlrisfidedldkihstdlsprgssatditrTRIYTRILSTLRngiligdrKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLgqsfsssketlsvhmdeieiipdvkieigktkyvfsdgiGKVSAEFARKVAskcglkdnppsafqiryggykgvvaadptsskklslRDSMRKYESELTKLDVLawskyqpcflnRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALElmspgentNILKELLIcgykpdaePFLSMMLQTFRASKLLELRTKtrifipngrsmmgcldetrtlnyGQVFVQISGagyrqlhgesslfsssrSRQRFIVQGLVVvaknpclhpgdvrvlkavnvpalhhmvdcvvfpqkgMRYILTMLKPRLLWYElnsshalprfivv

mkkfavlwrgVNVTVNFGFGMRKINFLLSHLGEEYRLELDYENIWEIELHCPRWQMTKYLLIQLLGAPRIFQKGIRSPDLLYESPVFNFFKEVPDDQWVRTTDftpsnfigqstGLCMELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYMTSrskpsspaislddglVYVHRVQVtpsrvyfcgpeinvsnrvlRHFRRDIDNFLRisfidedldkihstdlsprgssatditrtriYTRILStlrngiligdRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLgqsfsssketlsvhMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVAskcglkdnppsaFQIRYGGYkgvvaadptsskklslrdSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRtktrifipngrsmmgCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILTMLKPRLLWYelnsshalprfivv

MKKFAVLWRGVNVTVNFGFGMRKINFLLSHLGEEYRLELDYENIWEIELHCPRWQMTKYLLIQLLGAPRIFQKGIRSPDLLYESPVFNFFKEVPDDQWVRTTDFTPSNFIGQSTGLCMELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDitrtriytriLSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGEsslfsssrsrqrfIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILTMLKPRLLWYELNSSHALPRFIVV

***FAVLWRGVNVTVNFGFGMRKINFLLSHLGEEYRLELDYENIWEIELHCPRWQMTKYLLIQLLGAPRIFQKGIRSPDLLYESPVFNFFKEVPDDQWVRTTDFTPSNFIGQSTGLCMELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYM**********ISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIH***********TDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSF****ETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVA********************ELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHG**********RQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILTMLKPRLLWYELNSSHALPRFI**

*KKFAVLWRGVNVTVNFGFGMRKINFLLSHLGEEYRLELDYENIWEIELHCPRWQMTKYLLIQLLGAPRIFQKGIRSPDLLYESPVFNFFKEVPDDQWVRTTDFTPSNFIGQSTGLCMELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKY****************GLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAF****LRE*SAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAG****************RQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILTMLKPRLLWYELNSSHALPRFIVV

MKKFAVLWRGVNVTVNFGFGMRKINFLLSHLGEEYRLELDYENIWEIELHCPRWQMTKYLLIQLLGAPRIFQKGIRSPDLLYESPVFNFFKEVPDDQWVRTTDFTPSNFIGQSTGLCMELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRK***********AISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILTMLKPRLLWYELNSSHALPRFIVV

*KKFAVLWRGVNVTVNFGFGMRKINFLLSHLGEEYRLELDYENIWEIELHCPRWQMTKYLLIQLLGAPRIFQKGIRSPDLLYESPVFNFFKEVPDDQWVRTTDFTPSNFIGQSTGLCMELPYRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILTMLKPRLLWYELNSSHALPRFIVV

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		724	2.2.26 [Sep-21-2011]
Q9LQV2		1107	RNA-dependent RNA polymer	yes	no	0.932	0.609	0.656	0.0
Q0DXS3		740	Probable RNA-dependent RN	no	no	0.570	0.558	0.655	1e-162
O82504		1133	RNA-dependent RNA polymer	no	no	0.951	0.608	0.387	1e-137
Q7XM31		1136	Probable RNA-dependent RN	no	no	0.937	0.597	0.396	1e-137
Q8LHH9		1218	Probable RNA-dependent RN	no	no	0.831	0.494	0.377	1e-105
Q9SG02		1196	RNA-dependent RNA polymer	no	no	0.838	0.507	0.363	1e-103
O14227		1215	RNA-dependent RNA polymer	yes	no	0.589	0.351	0.321	1e-60
O82188		977	Probable RNA-dependent RN	no	no	0.558	0.413	0.254	1e-12
O82190		992	Probable RNA-dependent RN	no	no	0.465	0.339	0.248	2e-09
O82189		927	Probable RNA-dependent RN	no	no	0.545	0.426	0.235	4e-09

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

 Score =  934 bits (2415), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 458/698 (65%), Positives = 558/698 (79%), Gaps = 23/698 (3%)

Query: 2   KKFAVLWRGVNVTVNFGFGMRKINFLLSHLGEEYRLELDYENIWEIELHCPRWQMTKYLL 61
           KKF  LW   +V V+FG GMRK++F  S   ++YRLEL YENIW+I+LH P+ + +K+L+
Sbjct: 111 KKFLTLWSAQDVCVSFGIGMRKLHFSFSWYQKDYRLELSYENIWQIDLHSPQGRSSKFLV 170

Query: 62  IQLLGAPRIFQKGIRSPDLLYESPVFNFFKEVPDDQWVRTTDFTPSNFIGQSTGLCMELP 121
           IQ++GAP+IF+K  +  +LL+   + +F+ +  D+QW+RTTDFT S+ IGQST  C+ELP
Sbjct: 171 IQVIGAPKIFEKEDQPINLLFG--IMDFYSDGSDEQWIRTTDFTSSSCIGQSTAFCLELP 228

Query: 122 YRLELPDFKENFAYYKESE-DRFVLETGSAYSRSLD-LVPIVGPPDGIALPYEILFKINL 179
             L +PDF+ENFA Y E     F++E+GS+YS + + LVP+V PP G +LP+EILFK+N 
Sbjct: 229 VHLNVPDFRENFANYAEHRASSFLIESGSSYSSNANTLVPVVDPPPGFSLPFEILFKLNT 288

Query: 180 LVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKY 239
           LVQN C++GP LD +FYRL++  +   ++  I+H L+KL+HL ECCYEP+ WL D+Y+K+
Sbjct: 289 LVQNACLSGPALDLDFYRLLNQKKYDRAL--IDHCLEKLFHLGECCYEPAHWLRDEYKKW 346

Query: 240 MTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISF 299
           ++    P SP ISLDDGLVY++RVQVTP+RVYF GPE+NVSNRVLRH+ + I+NFLR+SF
Sbjct: 347 ISKGKLPLSPTISLDDGLVYMYRVQVTPARVYFSGPEVNVSNRVLRHYSKYINNFLRVSF 406

Query: 300 IDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRES 359
           +DEDL+K+ S DLSPR S+     RT++Y RI S LR+GI+IGD+KFEFLAFSSSQLRE+
Sbjct: 407 VDEDLEKVRSMDLSPRSSTQR---RTKLYDRIYSVLRDGIVIGDKKFEFLAFSSSQLREN 463

Query: 360 SAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDV 419
           SAWMFA    +TAA IR WMG+F  IRNVAKYAARLGQSFSSS+ETL+V  DEIE+IPDV
Sbjct: 464 SAWMFAPIDRITAAHIRAWMGDFDHIRNVAKYAARLGQSFSSSRETLNVRSDEIEVIPDV 523

Query: 420 KIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKK 479
           +I    T+YVFSDGIGK+SAEFARKVA KCGL +  PSAFQIRYGGYKGVVA DP SSKK
Sbjct: 524 EIISLGTRYVFSDGIGKISAEFARKVARKCGLTEFSPSAFQIRYGGYKGVVAVDPNSSKK 583

Query: 480 LSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLD 539
           LSLR SM K+ESE TKLDVLAWSKYQPC++NRQLI+LLSTLG+ D +FEKKQRE V +LD
Sbjct: 584 LSLRKSMSKFESENTKLDVLAWSKYQPCYMNRQLITLLSTLGVTDSVFEKKQREVVDRLD 643

Query: 540 AILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKT 599
           AILT PL+A EAL LM+PGENTNILK L++CGYKPDAEPFLSMMLQ FRASKLLELRTKT
Sbjct: 644 AILTHPLEAHEALGLMAPGENTNILKALILCGYKPDAEPFLSMMLQNFRASKLLELRTKT 703

Query: 600 RIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVV 659
           RIFI  GRSMMGCLDETRTL YGQV VQ S                 R  +RFI+ G VV
Sbjct: 704 RIFISGGRSMMGCLDETRTLEYGQVVVQYS--------------DPMRPGRRFIITGPVV 749

Query: 660 VAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMR 697
           VAKNPCLHPGDVRVL+AVNVPAL+HMVDCVVFPQKG+R
Sbjct: 750 VAKNPCLHPGDVRVLQAVNVPALNHMVDCVVFPQKGLR 787

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\|O82504\|RDR2_ARATH RNA-dependent RNA polymerase 2 OS=Arabidopsis thaliana GN=RDR2 PE=3 SV=1	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\|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		724
224099571		1133	rna-dependent RNA polymerase [Populus tr	0.958	0.612	0.719	0.0
225424397		1121	PREDICTED: RNA-dependent RNA polymerase	0.943	0.609	0.713	0.0
90823307		1110	RNA-dependent RNA polymerase [Gossypium	0.929	0.606	0.718	0.0
146762448		1110	RNA-dependent RNA polymerase [Gossypium	0.929	0.606	0.718	0.0
225424395		1109	PREDICTED: RNA-dependent RNA polymerase	0.941	0.614	0.700	0.0
356499585		1125	PREDICTED: RNA-dependent RNA polymerase	0.946	0.608	0.672	0.0
4138282		1116	RNA-directed RNA polymerase [Nicotiana t	0.941	0.611	0.669	0.0
157152684		1117	RNA-dependent RNA polymerase [Nicotiana	0.941	0.610	0.667	0.0
15223906		1107	RNA-dependent RNA polymerase 1 [Arabidop	0.932	0.609	0.656	0.0
24935275		1107	RNA-dependent RNA polymerase 1 [Arabidop	0.932	0.609	0.654	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 = 1056 bits (2730), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 501/696 (71%), Positives = 591/696 (84%), Gaps = 2/696 (0%)

Query: 2   KKFAVLWRGVNVTVNFGFGMRKINFLLSHLGEEYRLELDYENIWEIELHCPRWQMTKYLL 61
           +KF+ +W G NV+VNFG GMRK++F LSH   EY+L L +ENIW+IELH PR Q  KYLL
Sbjct: 111 EKFSAVWSGNNVSVNFGLGMRKLHFFLSHNLAEYKLNLLFENIWQIELHRPRGQTVKYLL 170

Query: 62  IQLLGAPRIFQKGIRSPDLLYESPVFNFFKEVPDDQWVRTTDFTPSNFIGQSTGLCMELP 121
           IQL GAPRI+++ + S   ++E P+ N+F++VPD+QWVRTTDFTPS  IG S+ LC+ELP
Sbjct: 171 IQLYGAPRIYERDVPSSSNVFEDPLLNYFRDVPDEQWVRTTDFTPSCGIGHSSSLCLELP 230

Query: 122 YRLELPDFKENFAYYKESEDRFVLETGSAYSRSLDLVPIVGPPDGIALPYEILFKINLLV 181
             L+LP+F ENF YYKE+E  FVLE+G  +SR+ DLVPIVGP  G+ LPY ILF++NLLV
Sbjct: 231 NHLQLPNFNENFFYYKENEGTFVLESGLTFSRNPDLVPIVGPSSGVNLPYNILFRVNLLV 290

Query: 182 QNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKYMT 241
           QNGC+AG +LD  FYRLVDP R PV   CIE+AL+KLYHLKECCYEPS+W  +QY+KY+T
Sbjct: 291 QNGCLAGSMLDDIFYRLVDPNRMPVR--CIEYALEKLYHLKECCYEPSKWFNEQYKKYLT 348

Query: 242 SRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFID 301
           S + P SP +SLD GLVYV++VQ+TP +V+FCGPE+NVSNRVLR +R DIDNFLR+SF+D
Sbjct: 349 SGNPPRSPVLSLDAGLVYVYKVQITPCKVFFCGPEVNVSNRVLRQYREDIDNFLRVSFVD 408

Query: 302 EDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSA 361
           E+L+KIHSTD+SPR SS  ++ RT IY RILSTL+NGI+IGD+KFEFLAFSSSQLRE+S 
Sbjct: 409 EELEKIHSTDVSPRTSSRNELRRTAIYNRILSTLQNGIVIGDKKFEFLAFSSSQLRENSC 468

Query: 362 WMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKI 421
           WMFASR GLTAA+IR WMG+F +IRNVA+YAARLGQSF SS ETLSV   EIEIIPD+++
Sbjct: 469 WMFASRLGLTAADIRAWMGSFHKIRNVARYAARLGQSFGSSTETLSVSSHEIEIIPDIEV 528

Query: 422 EIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKKLS 481
             G T+Y+FSDGIGK+SAEFARKVA KCG K   PSAFQIRY GYKGVVA DPTSSKKLS
Sbjct: 529 SRGGTRYLFSDGIGKISAEFARKVAIKCGCKGFTPSAFQIRYAGYKGVVAVDPTSSKKLS 588

Query: 482 LRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAI 541
           LR SM KYESE TKLDVLA SKYQPCFLNRQLI+LLSTLG+ D  FE+KQREAV QLDA+
Sbjct: 589 LRRSMFKYESENTKLDVLAHSKYQPCFLNRQLITLLSTLGVPDHHFERKQREAVDQLDAM 648

Query: 542 LTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRI 601
           LTDPL+AQEALELMSPGENTNILKE+L+CGY+PDAEPFLSMMLQTFRASKLLELRTKTRI
Sbjct: 649 LTDPLRAQEALELMSPGENTNILKEMLLCGYQPDAEPFLSMMLQTFRASKLLELRTKTRI 708

Query: 602 FIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVA 661
           FIPNGRSMMGCLDETRTL +GQVFV+ SG+ +R L+  S +FS     Q ++++G VVVA
Sbjct: 709 FIPNGRSMMGCLDETRTLEHGQVFVKFSGSRFRNLYDSSDMFSERGRGQCYLIKGSVVVA 768

Query: 662 KNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMR 697
           KNPCLHPGD+R+LKAV+VPALHHMVDCVVFPQKG R
Sbjct: 769 KNPCLHPGDLRILKAVDVPALHHMVDCVVFPQKGPR 804

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

>gi\|146762448\|gb\|ABQ45352.1\| 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\|356499585\|ref\|XP_003518619.1\| PREDICTED: RNA-dependent RNA polymerase 1-like [Glycine max]	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|15223906|ref|NP_172932.1| RNA-dependent RNA polymerase 1 [Arabidopsis thaliana] gi|75335341|sp|Q9LQV2.1|RDR1_ARATH RecName: Full=RNA-dependent RNA polymerase 1; Short=AtRDRP1; AltName: Full=RNA-directed RNA polymerase 1 gi|8778232|gb|AAF79241.1|AC006917_26 F10B6.19 [Arabidopsis thaliana] gi|110737376|dbj|BAF00633.1| putative RNA-directed RNA polymerase [Arabidopsis thaliana] gi|332191105|gb|AEE29226.1| RNA-dependent RNA polymerase 1 [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|24935275\|gb\|AAN64409.1\| RNA-dependent RNA polymerase 1 [Arabidopsis thaliana]	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		724
TAIR\|locus:2006822		1107	RDR1 "AT1G14790" [Arabidopsis	0.930	0.608	0.648	2.9e-238
TAIR\|locus:2136068		1133	RDR2 "RNA-dependent RNA polyme	0.950	0.607	0.382	8e-124
UNIPROTKB\|Q8LHH9		1218	SHL2 "Probable RNA-dependent R	0.885	0.526	0.350	5.2e-97
TAIR\|locus:2114633		1196	RDR6 "AT3G49500" [Arabidopsis	0.882	0.534	0.350	4.7e-96
UNIPROTKB\|G4NJ50		1407	MGG_02748 "RNA-dependent RNA p	0.707	0.363	0.332	9.2e-72
POMBASE\|SPAC6F12.09		1215	rdp1 "RNA-directed RNA polymer	0.593	0.353	0.323	1.1e-51
WB\|WBGene00004510		1765	rrf-3 [Caenorhabditis elegans	0.610	0.250	0.314	3.7e-50
ASPGD\|ASPL0000040001		1203	rrpC [Emericella nidulans (tax	0.698	0.420	0.286	3.8e-40
WB\|WBGene00004509		1579	rrf-2 [Caenorhabditis elegans	0.524	0.240	0.258	7.2e-37
WB\|WBGene00004508		1601	rrf-1 [Caenorhabditis elegans	0.295	0.133	0.304	1.9e-34

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

 Score = 2297 (813.6 bits), Expect = 2.9e-238, P = 2.9e-238
 Identities = 453/699 (64%), Positives = 551/699 (78%)

Query:     2 KKFAVLWRGVNVTVNFGFGMRKINFLLSHLGEEYRLELDYENIWEIELHCPRWQMTKYLL 61
             KKF  LW   +V V+FG GMRK++F  S   ++YRLEL YENIW+I+LH P+ + +K+L+
Sbjct:   111 KKFLTLWSAQDVCVSFGIGMRKLHFSFSWYQKDYRLELSYENIWQIDLHSPQGRSSKFLV 170

Query:    62 IQLLGAPRIFQKGIRSPDLLYESPVFNFFKEVPDDQWVRTTDFTPSNFIGQSTGLCMELP 121
             IQ++GAP+IF+K  +  +LL+   + +F+ +  D+QW+RTTDFT S+ IGQST  C+ELP
Sbjct:   171 IQVIGAPKIFEKEDQPINLLFG--IMDFYSDGSDEQWIRTTDFTSSSCIGQSTAFCLELP 228

Query:   122 YRLELPDFKENFAYYKESE-DRFVLETGSAYSRSLD-LVPIVGPPDGIALPYEILFKINL 179
               L +PDF+ENFA Y E     F++E+GS+YS + + LVP+V PP G +LP+EILFK+N 
Sbjct:   229 VHLNVPDFRENFANYAEHRASSFLIESGSSYSSNANTLVPVVDPPPGFSLPFEILFKLNT 288

Query:   180 LVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKECCYEPSRWLTDQYRKY 239
             LVQN C++GP LD +FYRL++  +   ++  I+H L+KL+HL ECCYEP+ WL D+Y+K+
Sbjct:   289 LVQNACLSGPALDLDFYRLLNQKKYDRAL--IDHCLEKLFHLGECCYEPAHWLRDEYKKW 346

Query:   240 MTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISF 299
             ++    P SP ISLDDGLVY++RVQVTP+RVYF GPE+NVSNRVLRH+ + I+NFLR+SF
Sbjct:   347 ISKGKLPLSPTISLDDGLVYMYRVQVTPARVYFSGPEVNVSNRVLRHYSKYINNFLRVSF 406

Query:   300 IDEDLDKIHSTDLSPRGSSATDXXXXXXXXXXLSTLRNGILIGDRKFEFLAFSSSQLRES 359
             +DEDL+K+ S DLSPR S+              S LR+GI+IGD+KFEFLAFSSSQLRE+
Sbjct:   407 VDEDLEKVRSMDLSPRSSTQR---RTKLYDRIYSVLRDGIVIGDKKFEFLAFSSSQLREN 463

Query:   360 SAWMFASRYGLTAAEIREWMGNFREIRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDV 419
             SAWMFA    +TAA IR WMG+F  IRNVAKYAARLGQSFSSS+ETL+V  DEIE+IPDV
Sbjct:   464 SAWMFAPIDRITAAHIRAWMGDFDHIRNVAKYAARLGQSFSSSRETLNVRSDEIEVIPDV 523

Query:   420 KI-EIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSK 478
             +I  +G T+YVFSDGIGK+SAEFARKVA KCGL +  PSAFQIRYGGYKGVVA DP SSK
Sbjct:   524 EIISLG-TRYVFSDGIGKISAEFARKVARKCGLTEFSPSAFQIRYGGYKGVVAVDPNSSK 582

Query:   479 KLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQL 538
             KLSLR SM K+ESE TKLDVLAWSKYQPC++NRQLI+LLSTLG+ D +FEKKQRE V +L
Sbjct:   583 KLSLRKSMSKFESENTKLDVLAWSKYQPCYMNRQLITLLSTLGVTDSVFEKKQREVVDRL 642

Query:   539 DAILTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTK 598
             DAILT PL+A EAL LM+PGENTNILK L++CGYKPDAEPFLSMMLQ FRASKLLELRTK
Sbjct:   643 DAILTHPLEAHEALGLMAPGENTNILKALILCGYKPDAEPFLSMMLQNFRASKLLELRTK 702

Query:   599 TRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGEXXXXXXXXXXXXXIVQGLV 658
             TRIFI  GRSMMGCLDETRTL YGQV VQ S    R   G              I+ G V
Sbjct:   703 TRIFISGGRSMMGCLDETRTLEYGQVVVQYSDP-MRP--GRRF-----------IITGPV 748

Query:   659 VVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMR 697
             VVAKNPCLHPGDVRVL+AVNVPAL+HMVDCVVFPQKG+R
Sbjct:   749 VVAKNPCLHPGDVRVLQAVNVPALNHMVDCVVFPQKGLR 787

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

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

WB\|WBGene00004509 rrf-2 [Caenorhabditis elegans (taxid:6239)]	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	0.6561	0.9323	0.6097	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		724
pfam05183		508	pfam05183, RdRP, RNA dependent RNA polymerase	1e-135

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

 Score =  408 bits (1050), Expect = e-135
 Identities = 182/442 (41%), Positives = 262/442 (59%), Gaps = 46/442 (10%)

Query: 268 SRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRI 327
           +RV    PE+  SNRVLR +    D FLR+ F DEDL    S D               +
Sbjct: 1   TRVILELPELERSNRVLRKYG-AADRFLRVKFPDEDLSGAISNDED-------------V 46

Query: 328 YTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIRN 387
             R+   L+NGI+IGDR   +LAFS+SQLRE SAW FA    LTA +IR W+G+F  I  
Sbjct: 47  GDRVKRVLKNGIIIGDR---YLAFSNSQLREHSAWFFAED-RLTAEDIRNWLGDFENIEQ 102

Query: 388 V-AKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVA 446
           V AKYAAR+GQ FS+++ T  + + +IE IPD+     +  Y+F+DG+GK+S + ARK+A
Sbjct: 103 VPAKYAARIGQCFSTTRPTTGIRIRKIERIPDI---PERNGYIFTDGVGKISRDLARKIA 159

Query: 447 SKCGLKDNPPSAFQIRYGGYKGVVAADPT-SSKKLSLRDSMRKYE----SELTKLDVLAW 501
            + G  +  PSA+QIR+GGYKGV+  DP     ++ +R SM K++    + +  L+++  
Sbjct: 160 DELGTLEEDPSAYQIRFGGYKGVLVVDPDLPGNEIHIRPSMLKFDLLGDAAVNSLEIIRS 219

Query: 502 SKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENT 561
           SK  P +LNRQLI++LSTLG+ DE+F +  REA+++L   LTD  +A   L+L+    + 
Sbjct: 220 SKPTPAYLNRQLITVLSTLGVPDEVFIELLREALKELAEALTDWDQA---LDLLRKQADE 276

Query: 562 NILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNY 621
           N     L   + P  +PFL  +L+      L +L+ K RI +P   ++ G +DET  L  
Sbjct: 277 ND--FTLTLRFMPSEDPFLRKLLRALVKHTLKKLKEKLRIPVPKSAALFGVVDETGVLKE 334

Query: 622 GQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPA 681
           G+VFVQ+S                +   Q   ++G V+VA+NPCLHPGD+RV++AV+VP 
Sbjct: 335 GEVFVQVS--------------DGNDGGQYEYLEGDVLVARNPCLHPGDIRVVRAVDVPE 380

Query: 682 LHHMVDCVVFPQKGMRYILTML 703
           L H+ D VVFP KG R + + L
Sbjct: 381 LRHLKDVVVFPSKGDRPLASEL 402

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		724
KOG0988		1145	consensus RNA-directed RNA polymerase QDE-1 requir	100.0
PF05183		579	RdRP: RNA dependent RNA polymerase; InterPro: IPR0	100.0

>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=1.3e-128  Score=1120.55  Aligned_cols=692  Identities=36%  Similarity=0.479  Sum_probs=580.4

Q ss_pred             eEEEEEec---ccceEEEcccceEEEEEEeecCe-eEEEEEeccchhhhhhcCCCCCc----ccEEEEEEccCCeEEEec
Q 004909            3 KFAVLWRG---VNVTVNFGFGMRKINFLLSHLGE-EYRLELDYENIWEIELHCPRWQM----TKYLLIQLLGAPRIFQKG   74 (724)
Q Consensus         3 ~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~-~~k~~~~~~~i~~~~~~~~~~~~----~~~~~~~l~~~P~i~~~~   74 (724)
                      .|..+|.+   ..+.|+.....+.+.+.+...+. ++..|++++.+-+...++.+..+    .+....-..+.|.+++..
T Consensus       127 ~~~~~~~~~v~~~v~V~~~~~~~~~~~p~~~~~~~~v~f~~~~~~~i~~~~~D~~~~s~~~~~~~~~~~~~G~~k~~~~~  206 (1145)
T KOG0988|consen  127 TFDCLESYKVNDQVTVRGSPVRRIVESPVVEYCKLCVPFEHSCRVLIETVSLDLDKPSIIRYPKSRRYLDNGGSKYFRFA  206 (1145)
T ss_pred             eecceEEEeecceEEEeccceeeeeecccccccccccchhhcchhheeeEEeccCcchhccCcchhhhhhcCccceeecc
Confidence            58889999   99999999999999999766444 77777777766654444333322    111112225666666664


Q ss_pred             CCCCCccccCccccccccCC-CCCceEeeccCCCCCccceeeEEEEecCCCCcchHHHhhhhcccc-----cc--eeeee
Q 004909           75 IRSPDLLYESPVFNFFKEVP-DDQWVRTTDFTPSNFIGQSTGLCMELPYRLELPDFKENFAYYKES-----ED--RFVLE  146 (724)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~-~~~w~R~~df~~~~~ig~~~~~~l~~~~~~~~~~~~~~~~~~~~~-----~~--~~~~~  146 (724)
                      ..|.+-.+.++.+.+.+++. +++|+|++||++..++|+++++|++++.+     +.++++|++..     ..  .+..+
T Consensus       207 ~~p~~~~~~~~~~Ef~k~~~~~~~~i~~~~~~~~~~v~~eta~~~eI~~~-----i~~~lP~~r~~~~~~~~~~~s~~ir  281 (1145)
T KOG0988|consen  207 FSPLLLALGDSELEFKKDFLADLLYIRTTDLRSRTGVGIETASCDEIRVP-----IWKDLPYNRYNGSTAEEFRLSVWIR  281 (1145)
T ss_pred             cccHHHhhccceeeeecccccccceeeecceeccccccceeeccceecch-----hhccCCcccccccchhhhhhhhhee
Confidence            44444444444677677766 88999999999999999999999999874     44444555443     12  24456


Q ss_pred             cCCccc-cCCCcccccCC-CCCCCCCcchHHHHHHHHHcCccCcccccHHHHHhhCCCCCCCChHHHHHHHHHHHhcccc
Q 004909          147 TGSAYS-RSLDLVPIVGP-PDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKEC  224 (724)
Q Consensus       147 ~~~~~~-~~~~~~~~~~~-~~~~~lpf~v~fql~~lv~~g~l~~~~~~~~f~~~l~~~~~~~~~~~~~~al~~l~~~~~~  224 (724)
                      .|..|. ++.+++|+... ..++..+++.+++.++||+.|.+.......+|+.++..... .....++++||+|.+...+
T Consensus       282 ~~~~~~~~~~~~~~l~~~~~~git~~~e~l~~r~slv~dq~~~~~~~~~~f~~l~~~~~~-~d~~v~~a~LekL~~~~~~  360 (1145)
T KOG0988|consen  282 LGSKYDVSSAQLVPLNDERDFGITHLYECLVSRGSLVKDQVLLEEAHLLEFLGLLRHKVL-GDDNVLEAKLEKLLKLSTK  360 (1145)
T ss_pred             cccccccccceeeeccccccccceeehhhhhcccchhhhhHHhhhhHHHHHHHHHhhhhc-cchhHHHHHHHHHhhhhhh
Confidence            777776 34456777663 34677899999999999999999999999999999976433 1125566789999999999


Q ss_pred             ccCchhHHHHHHHHhhhcCCCCCCCCccCCCCcEEEEEEEEcCCeeeeccccccccCceecccCCCCCcEEEEEEecCCC
Q 004909          225 CYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDL  304 (724)
Q Consensus       225 ~~dp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~iTPtri~l~~P~~e~sNRvlR~y~~~~d~FLRV~F~DE~~  304 (724)
                      ||||.-+.+..++...++.++  .+...+.+|+.+|++|.|||||+|+.+||++++|||+|+|..+.++||||+|+||++
T Consensus       361 cfd~~~~~k~i~~~~~~ng~~--~~~~~~~~g~~~vrk~v~TPtrv~~~~PE~~~gNRVlR~f~~~~t~~lRvtF~De~~  438 (1145)
T KOG0988|consen  361 CFDPYCQYKKIAKLNPSNGKL--VTTKEIMEGLRRVRKVVFTPTRVYLLAPEVEMGNRVLRKFDKDSTRFLRVTFRDEDN  438 (1145)
T ss_pred             hhhHHHHHHHHHHHhcccCcc--ccchhhhhcceeEEEEEEcCceeEecCchhhhcchhheeccccCceEEEEEEEcccc
Confidence            999999988887765555542  233456799999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCCCCCCCCCccchhhhHHHHHHHHHhcCeEEcceeEEEEeecCCCCCcceEEEEEeCCCCCHHHHHHHhcCCCc
Q 004909          305 DKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFRE  384 (724)
Q Consensus       305 ~~l~~~~~~pr~~~~~~~~~~~i~~Rv~~~L~~Gi~I~gR~y~FLafS~SqLR~~s~wFfa~~~~lt~~~Ir~wmGdF~~  384 (724)
                      + +..+++++       ..++.+|.||..+|++||.||+|+|+||||||||||+||.||++.....++++||.|||+|++
T Consensus       439 ~-~~ir~~S~-------~~~t~l~~rv~~~L~~Gi~v~~r~y~FL~~s~sQlRdngy~m~~~s~~~~i~~iR~wmG~F~~  510 (1145)
T KOG0988|consen  439 K-LKIRTLST-------GSRTKLDMRVNSYLTDGISVANRRYEFLAFSNSQLRDNGYFMARFSDKTKIEDIREWMGDFRD  510 (1145)
T ss_pred             c-cccccCCc-------chhhHHHHHHHHHHhcccEEccceeEEEEecccccccCceEEeecCCCccHHHHHHHhcchhh
Confidence            6 44433321       226899999999999999999999999999999999999998887777899999999999999


Q ss_pred             ccCHHHHHHHhccccCCCccceee-ecCcEEEeCCeeccccCcceeeccccccccHHHHHHHHHHcCCCCCCCeEEEEee
Q 004909          385 IRNVAKYAARLGQSFSSSKETLSV-HMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRY  463 (724)
Q Consensus       385 i~~vaK~aARlgq~FSsT~~tv~v-~~~~i~~i~DI~~~~~g~~~~FTDG~G~IS~~lA~~I~~~l~l~~~~PSAfQiR~  463 (724)
                      |.|++|||||||||||+|+.|..+ +..++..+|||+..++|++||||||||+||.++|++|++++++...+||||||||
T Consensus       511 i~nv~K~aARmGqCFs~Sr~T~~~~~~~~~~~~~DI~~g~~g~~y~FSDGvG~iS~~~a~~vsq~~~~~~~vPsaFQiR~  590 (1145)
T KOG0988|consen  511 IDNVPKLAARMGQCFSQSRGTGYVLERLDRMCPPDIEGGKRGNNYCFSDGVGMISLQFAREVSQKRKFGKAVPSAFQIRY  590 (1145)
T ss_pred             ccCHHHHHhhcCcceeccccccccccccccccCCcccccccCCceeecCCcccccHHHHHHHHHHHcccccCChheeeec
Confidence            999999999999999999999877 5667889999997777889999999999999999999999999888999999999


Q ss_pred             cCceEEEEeCCCCCcceeeccccccccCCCCcEEEEeecCcccccccHHHHHHHhcCCCChHHHHHHHHHHHHHH--HHH
Q 004909          464 GGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQL--DAI  541 (724)
Q Consensus       464 gG~KGvl~vdp~~~~~I~lR~Sm~KF~s~~~~LeI~~~S~~~p~~LNRQ~I~iLs~lGV~devF~~lq~~~l~~l--~~~  541 (724)
                      ||+||||+|||.....+.+|.||.||.|.+..++|+.|++++||+||||+|++|+.+||++++|+++|+..+++-  ...
T Consensus       591 ~G~KGVvav~Ps~~~~~~~~~~~~~s~S~n~~~~v~~~~~f~~~~lnr~lI~Lls~~gv~n~~F~~il~~vle~~r~~~n  670 (1145)
T KOG0988|consen  591 GGYKGVVAVDPSMDKVLKLRDSMNKSQSFNSLLEVTPSSKFQPAFLNRQLITLLSYLGVLNKPFINILDQVLEKQRRITN  670 (1145)
T ss_pred             cCCcceEEeCccHhhhhhhhhhhhhhhhhcceeeeeeccCCccccccHHHHHHHHhcCccchHHHHHHHHHHHHHHhhhh
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999943  344


Q ss_pred             hcCHHHHHHHHHhcCCCCcHHHHHHHHHCCCCCCCchHHHHHHHHHHHHHHHhhccccceeecCceeeeeeeCCCCCCCC
Q 004909          542 LTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNY  621 (724)
Q Consensus       542 l~d~~~a~~~l~~~~~~~~~~~l~~ml~~Gf~p~~epfl~~~L~~~~~~~L~~Lk~K~RI~Vp~s~~L~GV~DetG~L~~  621 (724)
                      +.....++++|......+.+++++.++..++.++.|||+++||..++++.++.+|+|.||||+.|++||||+||||+||+
T Consensus       671 ~~e~~~~~~~l~~~~~m~~en~a~~~l~~~~~~D~EPflr~mL~~~~k~~~~~~kek~ripv~~Gr~lmGvvDETG~L~y  750 (1145)
T KOG0988|consen  671 RIEELLDRAALNYGEQMDDENIAAMILKGFPRIDSEPFLRSMLSSLLKFTLQLLKEKIRIPVDLGRSLMGVVDETGILKY  750 (1145)
T ss_pred             hhhHHHHHHHhhhhhhccchHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHhcccccCcCCceeEeeecccccccc
Confidence            45555566777654445666766666666666888999999999999999999999999999999999999999999999


Q ss_pred             CcEEEEEeCCccccccCCCccccccccccceeEeeEEEEEeCCCCCCCceEEEEeeeCCCCccCCCeEEeCCCCCCCccc
Q 004909          622 GQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILT  701 (724)
Q Consensus       622 gEVfvq~s~~~~~~~~~~~~~~~~~~~~~~~vi~G~VlV~RnP~lHPGDIrvv~AV~~P~L~hL~dvIVFp~kG~Rpl~s  701 (724)
                      ||||||++.+....           ...+..+++|+|+||||||||||||||++||++|+|+||+|||||||||+||||+
T Consensus       751 gQVfVq~t~~~~~~-----------~~~~~~vitG~VlvtKNPcLhpGDVRVl~AV~vp~L~h~~dvVvFPQkGpRphpd  819 (1145)
T KOG0988|consen  751 GQVFVQYTKTIRNS-----------DSGRKEVITGKVLVTKNPCLHPGDVRVLKAVYVPALEHMVDVVVFPQKGPRPHPD  819 (1145)
T ss_pred             CeEEEEEccccccc-----------ccCCceEEEeeEEEecCCCCCCCceEEEEeeccHHHHhhcCEEEcCCCCCCCCcc
Confidence            99999999862111           1122479999999999999999999999999999999999999999999999999


Q ss_pred             ccCCC----ceEEEecccCcCCCc
Q 004909          702 MLKPR----LLWYELNSSHALPRF  721 (724)
Q Consensus       702 ~LSGg----~~~~~~~~~~~~p~~  721 (724)
                      +||||    |.|-++||+.++|.+
T Consensus       820 E~aGsDLDGDeYfViWDqkLL~~~  843 (1145)
T KOG0988|consen  820 EMAGSDLDGDEYFVIWDQKLLPPR  843 (1145)
T ss_pred             ccccCCCCCceEEEEeChhhccCc
Confidence            99998    559999999999976

>PF05183 RdRP: RNA dependent RNA polymerase; InterPro: IPR007855 This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; 2	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		724
2j7n_A		1022	Structure Of The Rnai Polymerase From Neurospora Cr		3e-08

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

Back alignment and structure

Iteration: 1

Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust. Identities = 75/306 (24%), Positives = 122/306 (39%), Gaps = 49/306 (16%) Query: 426 TKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKG--VVAADPTSSKK-LSL 482 T V +DG+G++S A+++ GL D PSA Q R+G KG V+ D T + + Sbjct: 323 TGEVMNDGVGRMSRSVAKRIRDVLGLGDV-PSAVQGRFGSAKGMWVIDVDDTGDEDWIET 381 Query: 483 RDSMRKYESELTK-----LDVLA-WSKYQPCFLNRQLISLLST---------LGIWDEIF 527 S RK+E + L+V + S+ + LN QL+ +L I D + Sbjct: 382 YPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGDRLI 441 Query: 528 EKKQREAVRQLDAILTDPLK-AQEALELMS-----------------PGENTNILKELLI 569 QR+ Q A L P++ Q E S P L L+ Sbjct: 442 NDLQRQFSEQKHA-LNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNFLMN 500 Query: 570 CGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQIS 629 G+ P + +L + + K L++K I + + D L +V V S Sbjct: 501 SGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFS 560 Query: 630 GAGYRQLHGEXXXXXXXXXXXXXIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCV 689 + +R + V+VA++P P D++ ++AV P LH + D + Sbjct: 561 -SKFRD----------EEESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSLKDVI 609 Query: 690 VFPQKG 695 +F KG Sbjct: 610 IFSTKG 615

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		724
2j7n_A		1022	RNA-dependent RNA polymerase; RNAI response, RNA-d	1e-113
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-12
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-11

>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 =  365 bits (938), Expect = e-113
 Identities = 110/608 (18%), Positives = 195/608 (32%), Gaps = 89/608 (14%)

Query: 163 PPDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLK 222
           P      P  + +++  L  +  V     +S   +    +     ++ I   L +L   +
Sbjct: 26  PKWLHEAPLAVAWEVTRLFMHCKVD-LEDESLGLKYDPSWSTARDVTDIWKTLYRLDAFR 84

Query: 223 ECCYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPS--RVYFCGPEINVS 280
                P +   D +   MT   +    A+ L   L Y      T     V          
Sbjct: 85  GK-PFPEKPPNDVFVTAMTGNFESKGSAVVLSAVLDYNPDNSPTAPLYLVKLKPLMFEQG 143

Query: 281 NRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATD-----ITRTRIYT-----R 330
            R+ R F    D F  I              +  +  +A +     +T  +        R
Sbjct: 144 CRLTRRF--GPDRFFEILIPSPTSTSPSVPPVVSKQPAAVEEVIQWLTMGQHSLVGRQWR 201

Query: 331 ILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFA------------------------S 366
                  G     R+F+  A     + +     FA                         
Sbjct: 202 AFFAKDAGYRKPLREFQLRAEDPKPIIKERVHFFAETGITFRPDVFKTRSVVPAEEPVEQ 261

Query: 367 RYGLTAAEIREWMGNFRE--IRNVAKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIEIG 424
           R     +++ +W+        +   K  +R+    S +   +++   +I       +   
Sbjct: 262 RTEFKVSQMLDWLLQLDNNTWQPHLKLFSRIQLGLSKTYAIMTLEPHQIRHHKTDLLSPS 321

Query: 425 KTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSSKK---LS 481
            T  V +DG+G++S   A+++    GL  + PSA Q R+G  KG+   D   +     + 
Sbjct: 322 GTGEVMNDGVGRMSRSVAKRIRDVLGL-GDVPSAVQGRFGSAKGMWVIDVDDTGDEDWIE 380

Query: 482 LRDSMRKYESEL-----TKLDVL-AWSKYQPCFLNRQLISLLSTLG---------IWDEI 526
              S RK+E +        L+V    S+ +   LN QL+ +L             I D +
Sbjct: 381 TYPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGDRL 440

Query: 527 FEKKQREAVRQLDAILTDPLKAQEALELMS-----------------PGENTNILKELLI 569
               QR+   Q  A+       Q   E  S                 P      L  L+ 
Sbjct: 441 INDLQRQFSEQKHALNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNFLMN 500

Query: 570 CGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQIS 629
            G+ P  + +L  +    +  K   L++K  I +     +    D    L   +V V  S
Sbjct: 501 SGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFS 560

Query: 630 GAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCV 689
                      S F         +    V+VA++P   P D++ ++AV  P LH + D +
Sbjct: 561 -----------SKFRDEEESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSLKDVI 609

Query: 690 VFPQKGMR 697
           +F  KG  
Sbjct: 610 IFSTKGDV 617

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

ID	Alignment Graph	Length	Definition	Probability
Query		724
2j7n_A		1022	RNA-dependent RNA polymerase; RNAI response, RNA-d	100.0

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

Probab=100.00  E-value=1.5e-99  Score=899.72  Aligned_cols=432  Identities=20%  Similarity=0.258  Sum_probs=357.9

Q ss_pred             CeeeeccccccccCceecccCCCCCcEEEEEEecCCCcccccCCCCCCCCCCccchhhhHHHHHHHHHhcC-eEEcceeE
Q 004909          268 SRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNG-ILIGDRKF  346 (724)
Q Consensus       268 tri~l~~P~~e~sNRvlR~y~~~~d~FLRV~F~DE~~~~l~~~~~~pr~~~~~~~~~~~i~~Rv~~~L~~G-i~I~gR~y  346 (724)
                      .++.|.+|+++.|||+.|+|++  ||||||+|++++.....   ++++.. .    ....+++|..+|.+| +.++||+|
T Consensus       131 ~~l~L~p~~l~~s~R~~RrfGs--DrFL~V~fp~~~~~~~~---~~~~~~-~----~~~~~~~v~~~l~~~~~~~~gr~~  200 (1022)
T 2j7n_A          131 YLVKLKPLMFEQGCRLTRRFGP--DRFFEILIPSPTSTSPS---VPPVVS-K----QPAAVEEVIQWLTMGQHSLVGRQW  200 (1022)
T ss_dssp             EEEEECCCEEEECBHHHHHHCG--GGEEEEEEECTTCCCSS---SCTTSS-S----SSSCHHHHHHHHHSSCEEETTEEE
T ss_pred             eEEEecCCccCCCceEEEeeCC--ceeEEEEecCCcccccc---ccchhc-c----chHHHHHHHHHHhcCcEEEeccee
Confidence            4788999999999999999996  89999999998644221   111111 0    122467888888877 67888888


Q ss_pred             EEEeec---------CCCCC--------cceEEEEEeC------------------------CCCCHHHHHHHhcCCCcc
Q 004909          347 EFLAFS---------SSQLR--------ESSAWMFASR------------------------YGLTAAEIREWMGNFREI  385 (724)
Q Consensus       347 ~FLafS---------~SqLR--------~~s~wFfa~~------------------------~~lt~~~Ir~wmGdF~~i  385 (724)
                      +.+-.-         ..|+|        ...||||+.+                        .++|+++||+|||+|+++
T Consensus       201 r~f~~~d~~~r~~~~~~~l~~~~~~~~~~~Rv~~f~~~G~~i~~~~f~fl~~s~lre~s~~~~~ls~~~ir~wmg~f~~n  280 (1022)
T 2j7n_A          201 RAFFAKDAGYRKPLREFQLRAEDPKPIIKERVHFFAETGITFRPDVFKTRSVVPAEEPVEQRTEFKVSQMLDWLLQLDNN  280 (1022)
T ss_dssp             EEEEEEECC--------------CCCCCEEEEEEEEEEETTCBCCCC-------------CCBCCCHHHHHHHHHCGGGC
T ss_pred             EEEeeccccccccccccccccccccccccceEEEEeccCccccCccccccccccccccccccCCCCHHHHHHhccChhhc
Confidence            843221         12332        1457777732                        248999999999999987


Q ss_pred             c--CHHHHHHHhccccCCCccceeeecCcEEEe-CCeeccccCcceeeccccccccHHHHHHHHHHcCCCCCCCeEEEEe
Q 004909          386 R--NVAKYAARLGQSFSSSKETLSVHMDEIEII-PDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIR  462 (724)
Q Consensus       386 ~--~vaK~aARlgq~FSsT~~tv~v~~~~i~~i-~DI~~~~~g~~~~FTDG~G~IS~~lA~~I~~~l~l~~~~PSAfQiR  462 (724)
                      +  ++||||||||||||+|.+|+.+.+++|.++ |||+. .+|++|+||||||+||++||++||+++++ ..+|||||||
T Consensus       281 ~~q~~aK~aARigq~FS~T~~tv~v~~~~I~~~~dDI~~-~~g~g~vFTDGvG~IS~~lA~~I~~~l~l-~~~PSAfQiR  358 (1022)
T 2j7n_A          281 TWQPHLKLFSRIQLGLSKTYAIMTLEPHQIRHHKTDLLS-PSGTGEVMNDGVGRMSRSVAKRIRDVLGL-GDVPSAVQGR  358 (1022)
T ss_dssp             TTSBHHHHHHTTHHHHSBCEEEEECCGGGEEECSSCCBC-TTSSCCBSSTTEEEECHHHHHHHHHHHTC-SSCCSEEEEE
T ss_pred             ccchHHHHHHHhhhhhcCccCcEEechHHEEEcCCcccc-CCCCCCeecCCchHhhHHHHHHHHHHcCC-CCCCcEEEEE
Confidence            4  599999999999999999999999999985 78872 34678999999999999999999999999 6899999999


Q ss_pred             ecCceEEEEeCCCC---CcceeeccccccccC-----CCCcEEEEeec-CcccccccHHHHHHHhcCCCChHHHHHHHHH
Q 004909          463 YGGYKGVVAADPTS---SKKLSLRDSMRKYES-----ELTKLDVLAWS-KYQPCFLNRQLISLLSTLGIWDEIFEKKQRE  533 (724)
Q Consensus       463 ~gG~KGvl~vdp~~---~~~I~lR~Sm~KF~s-----~~~~LeI~~~S-~~~p~~LNRQ~I~iLs~lGV~devF~~lq~~  533 (724)
                      ||||||||+|||++   +.+|+|||||+||++     .+++||||++| ++.|++||||+|+||+++||++++|++++++
T Consensus       359 ~gGaKGvl~vdp~~~~~~~~I~lRpSm~KF~~~~~d~~~~~LEIv~~s~~~~~~~LNRQlI~lL~~lGV~~~~f~~~i~~  438 (1022)
T 2j7n_A          359 FGSAKGMWVIDVDDTGDEDWIETYPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGD  438 (1022)
T ss_dssp             ETTEEEEEEECTTCCSCCCCEEECTTTBCSCCCCCSGGGSEEEEEEECCCCCCCCBCTTTHHHHHHTBSSHHHHHHHHHH
T ss_pred             eccceEEEEECcccCCCcceEEeCCcceeecCCCCCcccCeEEEEeecCCCCCceecHHHHHHHHhCCcCHHHHHHHHHH
Confidence            99999999999986   346999999999986     36799999997 5899999999999999999999999887554


Q ss_pred             HH-H-------HHHHHhcCHHHHHHHHHhcC------------------CCCcHHHHHHHHHCCCCCCCchHHHHHHHHH
Q 004909          534 AV-R-------QLDAILTDPLKAQEALELMS------------------PGENTNILKELLICGYKPDAEPFLSMMLQTF  587 (724)
Q Consensus       534 ~l-~-------~l~~~l~d~~~a~~~l~~~~------------------~~~~~~~l~~ml~~Gf~p~~epfl~~~L~~~  587 (724)
                      ++ +       ....+++++..++.++....                  +...++++..|+.+||+|.++|||+++++.+
T Consensus       439 ~~~~~L~~~l~~~~~al~~~~~~r~~l~~~~~~~~~r~~~g~~~~~~glp~s~~~~l~~Ll~aGf~p~~epfL~~~l~~~  518 (1022)
T 2j7n_A          439 RLINDLQRQFSEQKHALNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNFLMNSGFDPKKQKYLQDIAWDL  518 (1022)
T ss_dssp             HHHHHHHHHHHHHHHHTTSHHHHHHHHHHHSCCHHHHHHHTSCCEETTEESSHHHHHHHHHHTTCCTTTBHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhCHHHHHHHHHhhccccccccccccchhhccCccchHHHHHHHHHcCCCccccHHHHHHHHHH
Confidence            42 2       23455778777777664321                  1223467899999999999999999999999


Q ss_pred             HHHHHHhhccccceeecCceeeeeeeCCCCCCCCCcEEEEEeCCccccccCCCccccccccccceeEe-eEEEEEeCCCC
Q 004909          588 RASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQ-GLVVVAKNPCL  666 (724)
Q Consensus       588 ~~~~L~~Lk~K~RI~Vp~s~~L~GV~DetG~L~~gEVfvq~s~~~~~~~~~~~~~~~~~~~~~~~vi~-G~VlV~RnP~l  666 (724)
                      +..+|+.||+|+||+||+|++||||+||||+|+||||||+++.....           . .....++. |+|+|+|||||
T Consensus       519 ~~~~l~~LK~k~rI~V~~s~~L~GV~DetG~L~eGEVfv~~s~~~~~-----------~-~~~~~~l~gg~VlVtRnP~l  586 (1022)
T 2j7n_A          519 QKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFSSKFRD-----------E-EESFTLLSDCDVLVARSPAH  586 (1022)
T ss_dssp             HHHHHHHHHHHCCBCCSSEEEEEEEECTTSCCCTTEEEEEEEEEEEE-----------T-TEEEEEECSEEEEEECSSCC
T ss_pred             HHHHHHHHHHhhccccccceEEEEEecCCCccCCCeEEEEecccccc-----------C-CCCceeecCceEEEEeCCCc
Confidence            99999999999999999999999999999999999999999964211           0 11233554 69999999999


Q ss_pred             CCCceEEEEeeeCCCCccCCCeEEeCCCCCCCcccccCCCc----eEEEecccCcCCCccc
Q 004909          667 HPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILTMLKPRL----LWYELNSSHALPRFIV  723 (724)
Q Consensus       667 HPGDIrvv~AV~~P~L~hL~dvIVFp~kG~Rpl~s~LSGg~----~~~~~~~~~~~p~~~~  723 (724)
                      ||||||+++||++|+||||+|||||||+|+||+||||||||    .++++||+.|||.|.|
T Consensus       587 hPGDIrvv~AV~~PeL~hL~DvIVFp~kG~Rplps~lSGGDLDGD~Y~ViWD~~Lv~~f~n  647 (1022)
T 2j7n_A          587 FPSDIQRVRAVFKPELHSLKDVIIFSTKGDVPLAKKLSGGDYDGDMAWVCWDPEIVDGFVN  647 (1022)
T ss_dssp             SGGGEEEEEECCCGGGTTCCSEEEECSCSSSCHHHHTTTCCSSSCEEEEECCHHHHHTBCC
T ss_pred             CcCceeEEEeccChhhhccCCeEEccCCCCCCChhHhcCCCCCCCeEEEEechhhcccccC
Confidence            99999999999999999999999999999999999999984    6999999999998865

PyMOL of 2j7n

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