Citrus Sinensis ID: 001183

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-------910-------920-------930-------940-------950-------960-------970-------980-------990------1000------1010------1020------1030------1040------1050------1060------1070------1080------1090------1100------1110------1120------1130-
MVLATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSKAQNLSLNDKLVFNSQNLKISETHSDIVPRPVKAQHRVEDGVLHVGVMCKEERLRVLQTFEGVRGWLLPDRRRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLDEGATVNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSIGCSTSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRPGFNLSHEVLFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFVKTQLHVLGRNCKSIPLSSHKRLIDHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQTLVVPVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGVIAVDRNSFRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELESKDQSFFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTAHLVHADRDPDKARSSKCLHLATLHSMAVDFAKTGAPAEMPLALKPKEFPDFMEREDKPRYISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEEEMNALMNYYGASTEDEILTGNLRNRASYLQRDNRRYGDMKDRILLSAKNLQNEAKEWFGSSCKENEHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNIKSVNSRKA
ccEEEEEEEcccccccHHHHHHHHHHccccccEEEEEEEEccccccccccEEEEEcccHHHHHHHHHcccccEEEccEEEEEcccccccccccccccccccccEEEEEEEEcccEEEEEEEEcccEEEEEccccEEEEEEccccccccccccccccccccccEEEEEEEccccEEEEEEEcccccccEEEEEEEcccccEEEEcccccccccccccccccccccccccEEEEccccccccccccEEEEEEEccccccccHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccccccccccccccccccEEEEEEEEcccEEEEcccEEccHHHHHHHcccccccEEEEEEEcccccccccccccccHHccccccccHHHHHHHHHHHHHccEEEccEEEEEEEEccccccccEEEEEEccccccHHHHHHHHccccccccHHHHHHHHHccccccccccccccccEEEEEccccccccccEEEEcccccccHHHHHHHHHHHcccccccEEEEEccccccEEEEEcccccEEEEcccccccccccccEEEEEcccccccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHcccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHcccEEcccccEEEEEcccccccccccEEEEEccccccccccccccccccccccEEEEEEEEEEEcccccccccEEEEEEEcccccccccccEEEEccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHcccc
cEEEEEEEccccccccHHHHHHHHHHHcccEEEEEEEEcccccccccccEEEEEEcccHHHHHHHHHHcccEEEEcccccEccccccccccccccccccccccEEEEEcEccccEEEEEEEccccEEEEEccccEEEEEEEEEEEEEcccccccccccccccEEEEEEEEccHHHEEEEEcccccccEEEEEEEccccEEEEEccccccccccccccccccccccccccEEEEccccccccccEEEEEEEEcccccccHHHHHHHHHHHccccEEEccccccccccccccccccccccccccHHHHHHHHHHHcccccHccccHHHHHHHHHccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccccccccccccccccccEEEEEEEEcccEEEEcccccccccEEEEEcccccccEEEEEEEcccccccccccccccccccccccccHHHHHHHHHHHHHcccEEcccEEEEEEEcccHHHcccEEEEcccccccHHHHHHHHcccHHcccHHHHHHHHHHHcccccccEEcccccEEEEccEEEccccccEEEccccccccHHHHHHHHHHccccccccEEEEEEcccEEEEEEccccccEEEEEcccHHcccccccEEEEEccccccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccEEcccccEEEEEEcccccccccEEEEEEcccccccccccccccccccccEEEEEEEEEEEEccccccccEEEEEEEcccccccccccEEEEEccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccccccccccccccccccccccHcccccccccccHHHHHHHHHHHHHcccccccccccccHHcccccccHcccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccHEEEEEHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccHHcccccccccHHHHHHHHHHHHHHHHcccc
MVLATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITdrsnwksrgigrvqftsLDFKSkaqnlslndklvfnsqnlkisethsdivprpvkaqhrvedgvlhvgvmcKEERLRVLQTFEGvrgwllpdrrrlefwvwpkhngewqkgiqecqsdssdccfkVEILFEDVLETVgfsldegatvNGILFklkygpkiyqkvsgphvaskfpsdryhickedfdffwvrttdfsvtksigcstSFFWEIKNGllasdisnifpfykedktdLILEEgeefcttseivplvkcrpgfnlshEVLFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLksicydpvsfVKTQLHVlgrncksiplsshkrlidhNVMSCYRALVTpmkiyclgpeletsnyVVKNFAKYASDFMRVTFVeedwsklpanaLSTSIqrgifskpyrtKIYSRILTILQDGIVIGDKHYEFLAFSAsqlrnnsvwmfasndevsaedVRGWMGCFNKIRSVSKCAARMGqlfssskqtlvvpvqdvemipdvevtsdgntycfsdgiGKISLSFARQVAQkcglshtpsafqiryggykgviavdrnsfRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLqgyepnvePYLSMMLLSHHENQLSDLksrcriyvpkgrlligcfdetgilnyGQVFVRVTMTReeleskdqsffhrvddktsivkgkvlvtknpclhpgdvRVLEAVYEMKLeekdyvdciifpqkgerphpnecsggdldgdiffiswdndlipceteppmdytgrrsrimdhdvTLEEIHKFFVDYMINDTLGAISTAHLvhadrdpdkarsskclhLATLHSMAVDfaktgapaemplalkpkefpdfmeredkpryisfgVLGKLYRATLDSIMQIRSNAIWSEKIAeasydhdlevdgFEAFLGVAESHKEMYEEEMNALMNYygastedeiltgnLRNRasylqrdnrrygdmKDRILLSAKNLQNEAKEWfgssckenehpqlasawyhvtyspsycKERMALlsfpwivgdILLNIKSVNSRKA
MVLATVwvsnipqtaIAKDLLLFLESKLGKNSVFALEiitdrsnwksrgiGRVQFTSLDFKSKAQNLSLNDKLVFNSQNLKisethsdivprpvkAQHRVEDGVLHVGVMCKEERLRVLQTfegvrgwllpdrrRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLDEGATVNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSIGCSTSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRPGFNLSHEVLFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFVKTQLHVLGRNCKSiplsshkrlidHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKlpanalstsiqrgifskpyrTKIYSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLfssskqtlvvpVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLshtpsafqiryGGYKGVIAVDRNSFRKLSLrrsmlkfesrnrmlnvtkwsesmPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELeskdqsffhrvddktsivkgkvlvtknpclhpgdvRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTAHLVHADRDPDKARSSKCLHLATLHSMAVDFAKTGAPAEMPLALKPKEFPDFMEREDKPRYISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEEEMNALMNYYGASTEDEILtgnlrnrasylqrdnrrygdMKDRILLSAKNLQNEAKEWFGSSCKENEHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNIKSVNSRKA
MVLATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSKAQNLSLNDKLVFNSQNLKISETHSDIVPRPVKAQHRVEDGVLHVGVMCKEERLRVLQTFEGVRGWLLPDRRRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLDEGATVNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSIGCSTSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRPGFNLSHEVLFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFVKTQLHVLGRNCKSIPLSSHKRLIDHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQTLVVPVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGVIAVDRNSFRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELESKDQSFFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTAHLVHADRDPDKARSSKCLHLATLHSMAVDFAKTGAPAEMPLALKPKEFPDFMEREDKPRYISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEEEMNALMNYYGASTEDEILTGNLRNRASYLQRDNRRYGDMKDRILLSAKNLQNEAKEWFGSSCKENEHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNIKSVNSRKA
**LATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSKAQNLSLNDKLVFNSQNLKISETHSDIVPRPVKAQHRVEDGVLHVGVMCKEERLRVLQTFEGVRGWLLPDRRRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLDEGATVNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSIGCSTSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRPGFNLSHEVLFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFVKTQLHVLGRNCKSIPLSSHKRLIDHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQTLVVPVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGVIAVDRNSFRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELE**DQSFFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQ**********SGGDLDGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTAHLVHA**********KCLHLATLHSMAVDFAKT************************PRYISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEEEMNALMNYYGASTEDEILTGNLRNRASYLQRDNRRYGDMKDRILLSAKNLQNEAKEWFGSSCKENEHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNIK*******
*VLATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSKAQNLSLNDKLVFNSQNLKISET**D**PRPVKAQHRVEDGVLHVGVMCKEERLRVLQTFEGVRGWLLPDRRRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLDEGATVNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSIGCSTSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRPGFNLSHEVLFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFVKTQLHVLGR***************HNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQTLVVPVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGVIAVDRNSFRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTR*********FFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPM**************TLEEIHKFFVDYMINDTLGAISTAHLVHADRDPDKARSSKCLHLATLHSMAVDFAKTGAPAEMPLALKPKEFPDFMEREDK*RYISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEEEMNALMNYYGASTEDEILTGNLR*****************DRILLSAKNLQNEAKEWFGSSCKENEHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNI*SV*****
MVLATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSKAQNLSLNDKLVFNSQNLKISETHSDIVPRPVKAQHRVEDGVLHVGVMCKEERLRVLQTFEGVRGWLLPDRRRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLDEGATVNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSIGCSTSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRPGFNLSHEVLFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFVKTQLHVLGRNCKSIPLSSHKRLIDHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQTLVVPVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGVIAVDRNSFRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELESKDQSFFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTAHLVH**********SKCLHLATLHSMAVDFAKTGAPAEMPLALKPKEFPDFMEREDKPRYISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEEEMNALMNYYGASTEDEILTGNLRNRASYLQRDNRRYGDMKDRILLSAKNLQNEAKEWFGSSCKENEHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNIKSVNSRKA
MVLATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSKAQNLSLNDKLVFNSQNLKISETHSDIVPRPVKAQHRVEDGVLHVGVMCKEERLRVLQTFEGVRGWLLPDRRRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLDEGATVNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSIGCSTSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRPGFNLSHEVLFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFVKTQLHVLGRNCKSIPLSSHKRLIDHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQTLVVPVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGVIAVDRNSFRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELESKDQSFFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTAHLVHADRDPDKARSSKCLHLATLHSMAVDFAKTGAPAEMPLALKPKEFPDFMEREDKPRYISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEEEMNALMNYYGASTEDEILTGNLRNRASYLQRDNRRYGDMKDRILLSAKNLQNEAKEWFGSSCKENEHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNIKSVNS***
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiii
SSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVLATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSKAQNLSLNDKLVFNSQNLKISETHSDIVPRPVKAQHRVEDGVLHVGVMCKEERLRVLQTFEGVRGWLLPDRRRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLDEGATVNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSIGCSTSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRPGFNLSHEVLFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFVKTQLHVLGRNCKSIPLSSHKRLIDHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQTLVVPVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGVIAVDRNSFRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELESKDQSFFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTAHLVHADRDPDKARSSKCLHLATLHSMAVDFAKTGAPAEMPLALKPKEFPDFMEREDKPRYISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEEEMNALMNYYGASTEDEILTGNLRNRASYLQRDNRRYGDMKDRILLSAKNLQNEAKEWFGSSCKENEHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNIKSVNSRKA
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 ?
Query1131 2.2.26 [Sep-21-2011]
O825041133 RNA-dependent RNA polymer yes no 0.977 0.976 0.635 0.0
Q7XM311136 Probable RNA-dependent RN yes no 0.966 0.962 0.515 0.0
Q9LQV21107 RNA-dependent RNA polymer no no 0.945 0.965 0.403 0.0
Q0DXS3740 Probable RNA-dependent RN yes no 0.617 0.943 0.466 0.0
Q8LHH91218 Probable RNA-dependent RN yes no 0.713 0.662 0.393 1e-155
Q9SG021196 RNA-dependent RNA polymer no no 0.907 0.857 0.331 1e-152
O142271215 RNA-dependent RNA polymer yes no 0.625 0.581 0.321 4e-90
O82188977 Probable RNA-dependent RN no no 0.431 0.499 0.261 3e-26
O82190992 Probable RNA-dependent RN no no 0.445 0.508 0.256 1e-25
O82189927 Probable RNA-dependent RN no no 0.424 0.517 0.253 1e-24
>sp|O82504|RDR2_ARATH RNA-dependent RNA polymerase 2 OS=Arabidopsis thaliana GN=RDR2 PE=3 SV=1 Back     alignment and function desciption
 Score = 1502 bits (3888), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 719/1132 (63%), Positives = 895/1132 (79%), Gaps = 26/1132 (2%)

Query: 4    ATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSK 63
            +TV +SN+PQT +A +LL FLE  LG+++VFALEI T R NWK R   RVQFT+L+ KS+
Sbjct: 10   STVKISNVPQTIVADELLRFLELHLGEDTVFALEIPTTRDNWKPRDFARVQFTTLEVKSR 69

Query: 64   AQNLSLNDKLVFNSQNLKISETHSDIVPRPVKAQHRVEDGVLHVGV-MCKEERLRVLQTF 122
            AQ LS   KL+F + NL++SE + DI+PRPV  + R++D VL VG     E+R   L+ +
Sbjct: 70   AQLLSSQSKLLFKTHNLRLSEAYDDIIPRPVDPRKRLDDIVLTVGFPESDEKRFCALEKW 129

Query: 123  EGVRGWLLPDRRRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLD 182
            +GVR W+L ++RR+EFWVW                +S DC +K+E+ FED++ET+   ++
Sbjct: 130  DGVRCWILTEKRRVEFWVW----------------ESGDC-YKIEVRFEDIIETLSCCVN 172

Query: 183  EGAT-VNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSI 241
              A+ ++  L KLKYGPK++++V+  H+A+KF SDRY  CKEDFDF W+RTTDFS +KSI
Sbjct: 173  GDASEIDAFLLKLKYGPKVFKRVT-VHIATKFKSDRYRFCKEDFDFMWIRTTDFSGSKSI 231

Query: 242  GCSTSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRP-GFNL 300
            G ST F  E+ NG    DI +  P+Y+ED   L   +G+ F + ++IVPL+     G   
Sbjct: 232  GTSTCFCLEVHNGSTMLDIFSGLPYYREDTLSLTYVDGKTFASAAQIVPLLNAAILGLEF 291

Query: 301  SHEVLFQLNSLVHNQKVSLVAA-DAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFV 359
             +E+LFQLN+LVH QK+SL AA D ELI+IL G+S+ETAL++L+KLH+  SICYDPV FV
Sbjct: 292  PYEILFQLNALVHAQKISLFAASDMELIKILRGMSLETALVILKKLHQQSSICYDPVFFV 351

Query: 360  KTQLHVLGRNCKSIPLSSHKRLIDHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKY 419
            KTQ+  + +  K  P S++KRL + N+MSC RA VTP KIY LGPELET+NYVVKNFA++
Sbjct: 352  KTQMQSVVKKMKHSPASAYKRLTEQNIMSCQRAYVTPSKIYLLGPELETANYVVKNFAEH 411

Query: 420  ASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTILQDGIVIGDKHYEF 479
             SDFMRVTFVEEDWSKLPANALS + + G F KP RT IY+R+L+IL +GI +G K +EF
Sbjct: 412  VSDFMRVTFVEEDWSKLPANALSVNSKEGYFVKPSRTNIYNRVLSILGEGITVGPKRFEF 471

Query: 480  LAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQTLVV 539
            LAFSASQLR NSVWMFASN++V AED+R WMGCF KIRS+SKCAARMGQLFS+S+QTL+V
Sbjct: 472  LAFSASQLRGNSVWMFASNEKVKAEDIREWMGCFRKIRSISKCAARMGQLFSASRQTLIV 531

Query: 540  PVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGV 599
              QDVE IPD+EVT+DG  YCFSDGIGKISL+FA+QVAQKCGLSH PSAFQIRYGGYKGV
Sbjct: 532  RAQDVEQIPDIEVTTDGADYCFSDGIGKISLAFAKQVAQKCGLSHVPSAFQIRYGGYKGV 591

Query: 600  IAVDRNSFRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEA 659
            IAVDR+SFRKLSLR SMLKF+S NRMLNVT+W+ESMPCFLNREII LLSTLG++D +FEA
Sbjct: 592  IAVDRSSFRKLSLRDSMLKFDSNNRMLNVTRWTESMPCFLNREIICLLSTLGIEDAMFEA 651

Query: 660  MQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHE 719
            MQ   L +LG ML +R+AAL+VLQKL+G +SKN+LVKMLLQGY P+ EPYLSMML  HHE
Sbjct: 652  MQAVHLSMLGNMLEDRDAALNVLQKLSGENSKNLLVKMLLQGYAPSSEPYLSMMLRVHHE 711

Query: 720  NQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELESKDQSFFHRVDDK 779
            +QLS+LKSRCRI VPKGR+LIGC DE GIL YGQV+VRVT+T+ EL+S+DQS+F ++D++
Sbjct: 712  SQLSELKSRCRILVPKGRILIGCMDEMGILEYGQVYVRVTLTKAELKSRDQSYFRKIDEE 771

Query: 780  TSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDL 839
            TS+V GKV+VTKNPCLHPGD+RVL+A+YE+  EEK Y+DCIIFPQKGERPHPNECSGGDL
Sbjct: 772  TSVVIGKVVVTKNPCLHPGDIRVLDAIYEVHFEEKGYLDCIIFPQKGERPHPNECSGGDL 831

Query: 840  DGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTA 899
            DGD FF+SWD  +IP E +PPMDY G R R+MDHDVTLEEIHKFFVDYMI+DTLG ISTA
Sbjct: 832  DGDQFFVSWDEKIIPSEMDPPMDYAGSRPRLMDHDVTLEEIHKFFVDYMISDTLGVISTA 891

Query: 900  HLVHADRDPDKARSSKCLHLATLHSMAVDFAKTGAPAEMPLALKPKEFPDFMEREDKPRY 959
            HLVHADRDP+KARS KCL LA LHS AVDFAKTGAPAEMP ALKP+EFPDF+ER +KP Y
Sbjct: 892  HLVHADRDPEKARSQKCLELANLHSRAVDFAKTGAPAEMPYALKPREFPDFLERFEKPTY 951

Query: 960  ISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEE 1019
            IS  V GKLYRA   S+ Q +  A   + +A   YD  LE  GFE+F+  A++H++MY E
Sbjct: 952  ISESVFGKLYRAVKSSLAQRKPEAESEDTVA---YDVTLEEAGFESFIETAKAHRDMYGE 1008

Query: 1020 EMNALMNYYGASTEDEILTGNLRNRASYLQRDNRRYGDMKDRILLSAKNLQNEAKEWFGS 1079
            ++ +LM YYGA+ E+EILTG L+ +  YL RDNRRYGDMKDRI LS K+L  EA  WF  
Sbjct: 1009 KLTSLMIYYGAANEEEILTGILKTKEMYLARDNRRYGDMKDRITLSVKDLHKEAMGWFEK 1068

Query: 1080 SCK-ENEHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNIKSVNSRK 1130
            SC+ E +  +LASAWY+VTY+P++  E++  LSFPWIVGD+LL+IK+ N+++
Sbjct: 1069 SCEDEQQKKKLASAWYYVTYNPNHRDEKLTFLSFPWIVGDVLLDIKAENAQR 1120
RNA-dependent direct polymerase involved in the production of small interfering RNAs (siRNAs). Required for the biogenesis of endogenous siRNAs of 24 nucleotide which derive from heterochromatin and DNA repeats such as transposons or endogenous gene tandem repeats, such as repeats present in FWA gene. Involved in transcriptional gene silencing (TGS). Component of the RNA-directed DNA methylation (RdDM) silencing pathway that utilizes siRNAs to guide DNA methyltransferases to asymmetric cytosines. Involved in control of flowering time through RdDM of FWA locus. Required for reception of long-distance mRNA silencing in the shoot. Required for the formation of telomeric siRNAs and the RNA-dependent DNA methylation of asymmetric cytosines in telomeric (5'-CCCTAAA-3') repeats.
Arabidopsis thaliana (taxid: 3702)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 4EC: 8
>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|Q9LQV2|RDR1_ARATH RNA-dependent RNA polymerase 1 OS=Arabidopsis thaliana GN=RDR1 PE=2 SV=1 Back     alignment and function description
>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|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 ?
Query1131
2241334961110 rna-dependent RNA polymerase [Populus tr 0.974 0.992 0.705 0.0
3153074841147 hypothetical protein [Gossypium hirsutum 0.974 0.960 0.698 0.0
3153074781147 hypothetical protein [Gossypium hirsutum 0.974 0.960 0.696 0.0
4494406901117 PREDICTED: RNA-dependent RNA polymerase 0.979 0.991 0.684 0.0
4495189491117 PREDICTED: RNA-dependent RNA polymerase 0.979 0.991 0.684 0.0
2254570891127 PREDICTED: RNA-dependent RNA polymerase 0.979 0.983 0.682 0.0
356513586 1262 PREDICTED: RNA-dependent RNA polymerase 0.977 0.875 0.675 0.0
357477317 1308 Rna-dependent RNA polymerase [Medicago t 0.977 0.845 0.658 0.0
3565650221120 PREDICTED: RNA-dependent RNA polymerase 0.975 0.984 0.671 0.0
2978093351134 RNA-dependent RNA polymerase 2 [Arabidop 0.978 0.976 0.636 0.0
>gi|224133496|ref|XP_002321582.1| rna-dependent RNA polymerase [Populus trichocarpa] gi|222868578|gb|EEF05709.1| rna-dependent RNA polymerase [Populus trichocarpa] Back     alignment and taxonomy information
 Score = 1644 bits (4256), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 795/1127 (70%), Positives = 932/1127 (82%), Gaps = 25/1127 (2%)

Query: 5    TVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSKA 64
            +V V+NIPQT  AK++L +L ++LGK+SVFA+EI T R NW SRG GRVQF+SL+ K +A
Sbjct: 9    SVRVTNIPQTITAKEILQYLVAQLGKDSVFAIEISTVRKNWNSRGFGRVQFSSLEVKHEA 68

Query: 65   QNLSLNDKLVFNSQNLKISETHSDIVPRPVKAQHRVEDGVLHVGVMCKEERLRVLQTFEG 124
             +LSL +KLV  SQNLK+SET+ DI+PRPVK Q+R+E+GVL+VG M KE  L VL+ +EG
Sbjct: 69   LSLSLKNKLVLKSQNLKLSETYDDIIPRPVKDQNRMENGVLYVGFMKKETTLCVLEYWEG 128

Query: 125  VRGWLLPDRRRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLDEG 184
            VRGW +P+RRR+EFW+         +  QE +       +K+ + FED+LE VG+ LD G
Sbjct: 129  VRGWFMPERRRIEFWI---------RVGQEFR-------YKLVVEFEDILEAVGYPLD-G 171

Query: 185  ATVNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSIGCS 244
              VN ++ KL+YGP+IYQK+SGP +ASKF ++RY  CKEDFDF WVRTTD S  KSIG S
Sbjct: 172  DKVNAVVLKLRYGPRIYQKISGPGIASKFSTNRYFYCKEDFDFLWVRTTDISAIKSIGQS 231

Query: 245  TSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRPGFNLSHEV 304
            TSF WEI  GL ASD    FP+Y+ED   L LE+GEEFC+ SE VPL++C     L++EV
Sbjct: 232  TSFCWEIGEGLEASDTFRNFPYYQEDMNRLDLEDGEEFCSASETVPLIRCGSD-KLAYEV 290

Query: 305  LFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFVKTQLH 364
            LFQLNSLVH QK+SL A D++LI+IL  L++ TA+++LQKLHKLK  CYDP+SFVK  L 
Sbjct: 291  LFQLNSLVHTQKISLAAVDSDLIKILRNLTVNTAIIILQKLHKLKMTCYDPLSFVKQSL- 349

Query: 365  VLGRNCKSIPLSSHKRLIDHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKYASDFM 424
               R   S P    K L ++N+MSC+RAL+TP KI+CLGPE ETSNYVVK+FA+YASDF+
Sbjct: 350  ---RESLSSP---PKSLTENNIMSCHRALITPSKIFCLGPEYETSNYVVKHFAQYASDFI 403

Query: 425  RVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTILQDGIVIGDKHYEFLAFSA 484
            RVTFVEEDWSKLPANA+STSIQRGIF+KP+RT IY RIL+IL+DG VIG K +EFLAFSA
Sbjct: 404  RVTFVEEDWSKLPANAISTSIQRGIFAKPFRTGIYHRILSILRDGFVIGAKRFEFLAFSA 463

Query: 485  SQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQTLVVPVQDV 544
            SQLR+NSVWMFASN+ V AED+R WMGCF+KIRSVSKCAARMGQLFSSS QT VVPVQDV
Sbjct: 464  SQLRSNSVWMFASNNGVKAEDIRKWMGCFDKIRSVSKCAARMGQLFSSSLQTFVVPVQDV 523

Query: 545  EMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGVIAVDR 604
            E+IPD+EVT+DG  YCFSDGIGKISLSFA+QVA KCGLSHTPSAFQIRYGGYKGV+AVDR
Sbjct: 524  EIIPDIEVTTDGIDYCFSDGIGKISLSFAKQVAHKCGLSHTPSAFQIRYGGYKGVVAVDR 583

Query: 605  NSFRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQ 664
            NSFRKLSLR SMLKF+S NRMLNVTKWSESMPC+LNREIISLLSTLGV DE+F+A+QQ+Q
Sbjct: 584  NSFRKLSLRSSMLKFDSENRMLNVTKWSESMPCYLNREIISLLSTLGVADEIFQALQQKQ 643

Query: 665  LILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHENQLSD 724
            L  L KML N+E+ALDVL+ L   DSKNILV+MLLQGYEPNVEPYLSMML ++HEN L +
Sbjct: 644  LYRLRKMLTNKESALDVLENLAWADSKNILVQMLLQGYEPNVEPYLSMMLQAYHENSLME 703

Query: 725  LKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELESKDQSFFHRVDDKTSIVK 784
            L+SRCRI+VPKGR+LIGC DE+GIL+YGQV+VR+TMT+ EL+  DQSFF +VD+ TS + 
Sbjct: 704  LRSRCRIFVPKGRILIGCLDESGILDYGQVYVRITMTKAELQCCDQSFFRKVDESTSTII 763

Query: 785  GKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIF 844
            G+V VTKNPCLHPGD+RVLEAVY+++LEEK  VDCIIFPQ G RPHPNECSGGDLDGD F
Sbjct: 764  GEVAVTKNPCLHPGDIRVLEAVYDVELEEKGLVDCIIFPQNGGRPHPNECSGGDLDGDQF 823

Query: 845  FISWDNDLIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTAHLVHA 904
            FISWD  L+PC TE PMDY G R RIMDH+VTLEEI +FFVDYMINDTLGAISTAHLVHA
Sbjct: 824  FISWDEGLLPCHTEAPMDYVGGRQRIMDHNVTLEEIQRFFVDYMINDTLGAISTAHLVHA 883

Query: 905  DRDPDKARSSKCLHLATLHSMAVDFAKTGAPAEMPLALKPKEFPDFMEREDKPRYISFGV 964
            D +PDKARS KCL LATLHSMAVDFAKTGAPAEMPL LKP+EFPDFMER +K  YIS GV
Sbjct: 884  DCEPDKARSEKCLQLATLHSMAVDFAKTGAPAEMPLYLKPREFPDFMERAEKQMYISDGV 943

Query: 965  LGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEEEMNAL 1024
            LGKLYR   DS  Q RSN +WS+KIAEA+YD DLEV GFE FLG+A  +KE Y E+M+ L
Sbjct: 944  LGKLYRDIHDSTRQERSNFMWSKKIAEATYDQDLEVKGFEDFLGIASIYKEKYMEKMSTL 1003

Query: 1025 MNYYGASTEDEILTGNLRNRASYLQRDNRRYGDMKDRILLSAKNLQNEAKEWFGSSCKEN 1084
            M+YYGA TEDEILTGNLR+R +YLQRDNR+YGD+KDRIL+S KNL+ EAKEWF SSC   
Sbjct: 1004 MDYYGAKTEDEILTGNLRHRPTYLQRDNRKYGDVKDRILVSLKNLKKEAKEWFESSCNPT 1063

Query: 1085 EHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNIKSVNSRKA 1131
            EH  +ASAWYHVTY P+Y  ERM  LSFPWIVGDILLNIKS+NSR A
Sbjct: 1064 EHQCMASAWYHVTYHPTYFHERMNCLSFPWIVGDILLNIKSLNSRNA 1110

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|315307484|gb|ADU04145.1| hypothetical protein [Gossypium hirsutum] Back     alignment and taxonomy information
>gi|315307478|gb|ADU04140.1| hypothetical protein [Gossypium hirsutum] Back     alignment and taxonomy information
>gi|449440690|ref|XP_004138117.1| PREDICTED: RNA-dependent RNA polymerase 2-like [Cucumis sativus] gi|316989905|gb|ADU77018.1| RNA-dependent RNA polymerase 2 [Cucumis sativus] Back     alignment and taxonomy information
>gi|449518949|ref|XP_004166498.1| PREDICTED: RNA-dependent RNA polymerase 2-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|225457089|ref|XP_002280099.1| PREDICTED: RNA-dependent RNA polymerase 2 [Vitis vinifera] gi|297733815|emb|CBI15062.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|356513586|ref|XP_003525493.1| PREDICTED: RNA-dependent RNA polymerase 2-like [Glycine max] Back     alignment and taxonomy information
>gi|357477317|ref|XP_003608944.1| Rna-dependent RNA polymerase [Medicago truncatula] gi|355509999|gb|AES91141.1| Rna-dependent RNA polymerase [Medicago truncatula] Back     alignment and taxonomy information
>gi|356565022|ref|XP_003550744.1| PREDICTED: RNA-dependent RNA polymerase 2-like [Glycine max] Back     alignment and taxonomy information
>gi|297809335|ref|XP_002872551.1| RNA-dependent RNA polymerase 2 [Arabidopsis lyrata subsp. lyrata] gi|297318388|gb|EFH48810.1| RNA-dependent RNA polymerase 2 [Arabidopsis lyrata subsp. lyrata] 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 ?
Query1131
TAIR|locus:21360681133 RDR2 "RNA-dependent RNA polyme 0.977 0.976 0.635 0.0
TAIR|locus:20068221107 RDR1 "AT1G14790" [Arabidopsis 0.577 0.589 0.489 6.7e-173
UNIPROTKB|Q8LHH91218 SHL2 "Probable RNA-dependent R 0.811 0.753 0.372 4.6e-150
TAIR|locus:21146331196 RDR6 "AT3G49500" [Arabidopsis 0.907 0.857 0.334 8.4e-145
UNIPROTKB|G4NJ50 1407 MGG_02748 "RNA-dependent RNA p 0.630 0.506 0.342 8e-110
POMBASE|SPAC6F12.091215 rdp1 "RNA-directed RNA polymer 0.788 0.734 0.288 2.5e-88
WB|WBGene00004510 1765 rrf-3 [Caenorhabditis elegans 0.633 0.405 0.297 7.9e-76
WB|WBGene00004508 1601 rrf-1 [Caenorhabditis elegans 0.402 0.284 0.282 6.4e-65
WB|WBGene00004509 1579 rrf-2 [Caenorhabditis elegans 0.389 0.278 0.287 2.1e-61
ASPGD|ASPL00000400011203 rrpC [Emericella nidulans (tax 0.558 0.525 0.307 2.7e-59
TAIR|locus:2136068 RDR2 "RNA-dependent RNA polymerase 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 3768 (1331.5 bits), Expect = 0., P = 0.
 Identities = 719/1132 (63%), Positives = 895/1132 (79%)

Query:     4 ATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSK 63
             +TV +SN+PQT +A +LL FLE  LG+++VFALEI T R NWK R   RVQFT+L+ KS+
Sbjct:    10 STVKISNVPQTIVADELLRFLELHLGEDTVFALEIPTTRDNWKPRDFARVQFTTLEVKSR 69

Query:    64 AQNLSLNDKLVFNSQNLKISETHSDIVPRPVKAQHRVEDGVLHVGVM-CKEERLRVLQTF 122
             AQ LS   KL+F + NL++SE + DI+PRPV  + R++D VL VG     E+R   L+ +
Sbjct:    70 AQLLSSQSKLLFKTHNLRLSEAYDDIIPRPVDPRKRLDDIVLTVGFPESDEKRFCALEKW 129

Query:   123 EGVRGWLLPDRRRLEFWVWPKHNGEWQKGIQECQSDSSDCCFKVEILFEDVLETVGFSLD 182
             +GVR W+L ++RR+EFWVW                +S DC +K+E+ FED++ET+   ++
Sbjct:   130 DGVRCWILTEKRRVEFWVW----------------ESGDC-YKIEVRFEDIIETLSCCVN 172

Query:   183 EGAT-VNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDFDFFWVRTTDFSVTKSI 241
               A+ ++  L KLKYGPK++++V+  H+A+KF SDRY  CKEDFDF W+RTTDFS +KSI
Sbjct:   173 GDASEIDAFLLKLKYGPKVFKRVT-VHIATKFKSDRYRFCKEDFDFMWIRTTDFSGSKSI 231

Query:   242 GCSTSFFWEIKNGLLASDISNIFPFYKEDKTDLILEEGEEFCTTSEIVPLVKCRP-GFNL 300
             G ST F  E+ NG    DI +  P+Y+ED   L   +G+ F + ++IVPL+     G   
Sbjct:   232 GTSTCFCLEVHNGSTMLDIFSGLPYYREDTLSLTYVDGKTFASAAQIVPLLNAAILGLEF 291

Query:   301 SHEVLFQLNSLVHNQKVSLVAA-DAELIQILSGLSMETALMVLQKLHKLKSICYDPVSFV 359
              +E+LFQLN+LVH QK+SL AA D ELI+IL G+S+ETAL++L+KLH+  SICYDPV FV
Sbjct:   292 PYEILFQLNALVHAQKISLFAASDMELIKILRGMSLETALVILKKLHQQSSICYDPVFFV 351

Query:   360 KTQLHVLGRNCKSIPLSSHKRLIDHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKY 419
             KTQ+  + +  K  P S++KRL + N+MSC RA VTP KIY LGPELET+NYVVKNFA++
Sbjct:   352 KTQMQSVVKKMKHSPASAYKRLTEQNIMSCQRAYVTPSKIYLLGPELETANYVVKNFAEH 411

Query:   420 ASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTILQDGIVIGDKHYEF 479
              SDFMRVTFVEEDWSKLPANALS + + G F KP RT IY+R+L+IL +GI +G K +EF
Sbjct:   412 VSDFMRVTFVEEDWSKLPANALSVNSKEGYFVKPSRTNIYNRVLSILGEGITVGPKRFEF 471

Query:   480 LAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQTLVV 539
             LAFSASQLR NSVWMFASN++V AED+R WMGCF KIRS+SKCAARMGQLFS+S+QTL+V
Sbjct:   472 LAFSASQLRGNSVWMFASNEKVKAEDIREWMGCFRKIRSISKCAARMGQLFSASRQTLIV 531

Query:   540 PVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGV 599
               QDVE IPD+EVT+DG  YCFSDGIGKISL+FA+QVAQKCGLSH PSAFQIRYGGYKGV
Sbjct:   532 RAQDVEQIPDIEVTTDGADYCFSDGIGKISLAFAKQVAQKCGLSHVPSAFQIRYGGYKGV 591

Query:   600 IAVDRNSFRKLSLRRSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEA 659
             IAVDR+SFRKLSLR SMLKF+S NRMLNVT+W+ESMPCFLNREII LLSTLG++D +FEA
Sbjct:   592 IAVDRSSFRKLSLRDSMLKFDSNNRMLNVTRWTESMPCFLNREIICLLSTLGIEDAMFEA 651

Query:   660 MQQQQLILLGKMLINREAALDVLQKLNGVDSKNILVKMLLQGYEPNVEPYLSMMLLSHHE 719
             MQ   L +LG ML +R+AAL+VLQKL+G +SKN+LVKMLLQGY P+ EPYLSMML  HHE
Sbjct:   652 MQAVHLSMLGNMLEDRDAALNVLQKLSGENSKNLLVKMLLQGYAPSSEPYLSMMLRVHHE 711

Query:   720 NQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELESKDQSFFHRVDDK 779
             +QLS+LKSRCRI VPKGR+LIGC DE GIL YGQV+VRVT+T+ EL+S+DQS+F ++D++
Sbjct:   712 SQLSELKSRCRILVPKGRILIGCMDEMGILEYGQVYVRVTLTKAELKSRDQSYFRKIDEE 771

Query:   780 TSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDL 839
             TS+V GKV+VTKNPCLHPGD+RVL+A+YE+  EEK Y+DCIIFPQKGERPHPNECSGGDL
Sbjct:   772 TSVVIGKVVVTKNPCLHPGDIRVLDAIYEVHFEEKGYLDCIIFPQKGERPHPNECSGGDL 831

Query:   840 DGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTA 899
             DGD FF+SWD  +IP E +PPMDY G R R+MDHDVTLEEIHKFFVDYMI+DTLG ISTA
Sbjct:   832 DGDQFFVSWDEKIIPSEMDPPMDYAGSRPRLMDHDVTLEEIHKFFVDYMISDTLGVISTA 891

Query:   900 HLVHADRDPDKARSSKCLHLATLHSMAVDFAKTGAPAEMPLALKPKEFPDFMEREDKPRY 959
             HLVHADRDP+KARS KCL LA LHS AVDFAKTGAPAEMP ALKP+EFPDF+ER +KP Y
Sbjct:   892 HLVHADRDPEKARSQKCLELANLHSRAVDFAKTGAPAEMPYALKPREFPDFLERFEKPTY 951

Query:   960 ISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAESHKEMYEE 1019
             IS  V GKLYRA   S+ Q +  A   + +A   YD  LE  GFE+F+  A++H++MY E
Sbjct:   952 ISESVFGKLYRAVKSSLAQRKPEAESEDTVA---YDVTLEEAGFESFIETAKAHRDMYGE 1008

Query:  1020 EMNALMNYYGASTEDEILTGNLRNRASYLQRDNRRYGDMKDRILLSAKNLQNEAKEWFGS 1079
             ++ +LM YYGA+ E+EILTG L+ +  YL RDNRRYGDMKDRI LS K+L  EA  WF  
Sbjct:  1009 KLTSLMIYYGAANEEEILTGILKTKEMYLARDNRRYGDMKDRITLSVKDLHKEAMGWFEK 1068

Query:  1080 SCK-ENEHPQLASAWYHVTYSPSYCKERMALLSFPWIVGDILLNIKSVNSRK 1130
             SC+ E +  +LASAWY+VTY+P++  E++  LSFPWIVGD+LL+IK+ N+++
Sbjct:  1069 SCEDEQQKKKLASAWYYVTYNPNHRDEKLTFLSFPWIVGDVLLDIKAENAQR 1120
GO:0003968 "RNA-directed RNA polymerase activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0016441 "posttranscriptional gene silencing" evidence=ISS
GO:0009751 "response to salicylic acid stimulus" evidence=IEP
GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA;IMP
GO:0016458 "gene silencing" evidence=IMP
GO:0007267 "cell-cell signaling" evidence=RCA;IMP
GO:0016246 "RNA interference" evidence=RCA;IMP
GO:0005730 "nucleolus" evidence=IDA
GO:0010495 "long-distance posttranscriptional gene silencing" evidence=IMP
GO:0050832 "defense response to fungus" evidence=IMP
GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA
GO:0006306 "DNA methylation" evidence=RCA
GO:0006342 "chromatin silencing" evidence=RCA
GO:0006346 "methylation-dependent chromatin silencing" evidence=RCA
GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA
GO:0009616 "virus induced gene silencing" evidence=RCA
GO:0009855 "determination of bilateral symmetry" evidence=RCA
GO:0010014 "meristem initiation" evidence=RCA
GO:0010073 "meristem maintenance" evidence=RCA
GO:0010267 "production of ta-siRNAs involved in RNA interference" evidence=RCA
GO:0016569 "covalent chromatin modification" evidence=RCA
GO:0031047 "gene silencing by RNA" evidence=RCA
GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA
GO:0043687 "post-translational protein modification" evidence=RCA
GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA
TAIR|locus:2006822 RDR1 "AT1G14790" [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|WBGene00004508 rrf-1 [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

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) ?
O82504RDR2_ARATH2, ., 7, ., 7, ., 4, 80.63510.97780.9761yesno
Q7XM31RDR2_ORYSJ2, ., 7, ., 7, ., 4, 80.51510.96640.9621yesno

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:
RDR904
rna-dependent RNA polymerase (1110 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 ?
Query1131
pfam05183508 pfam05183, RdRP, RNA dependent RNA polymerase 1e-151
cd1228373 cd12283, RRM1_RBM39_like, RNA recognition motif 1 2e-05
cd1239378 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc 0.003
smart0036073 smart00360, RRM, RNA recognition motif 0.003
>gnl|CDD|218483 pfam05183, RdRP, RNA dependent RNA polymerase Back     alignment and domain information 
 Score =  461 bits (1189), Expect = e-151
 Identities = 222/581 (38%), Positives = 323/581 (55%), Gaps = 92/581 (15%)

Query: 398 KIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTK 457
           ++    PELE SN V++ +   A  F+RV F +ED S   +N                  
Sbjct: 2   RVILELPELERSNRVLRKYGA-ADRFLRVKFPDEDLSGAISN---------------DED 45

Query: 458 IYSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIR 517
           +  R+  +L++GI+IGD+   +LAFS SQLR +S W FA  D ++AED+R W+G F  I 
Sbjct: 46  VGDRVKRVLKNGIIIGDR---YLAFSNSQLREHSAWFFAE-DRLTAEDIRNWLGDFENIE 101

Query: 518 SV-SKCAARMGQLFSSSKQTLVVPVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQV 576
            V +K AAR+GQ FS+++ T  + ++ +E IPD+    + N Y F+DG+GKIS   AR++
Sbjct: 102 QVPAKYAARIGQCFSTTRPTTGIRIRKIERIPDIP---ERNGYIFTDGVGKISRDLARKI 158

Query: 577 AQKCGL-SHTPSAFQIRYGGYKGVIAVD-RNSFRKLSLRRSMLKFESRN----RMLNVTK 630
           A + G     PSA+QIR+GGYKGV+ VD      ++ +R SMLKF+         L + +
Sbjct: 159 ADELGTLEEDPSAYQIRFGGYKGVLVVDPDLPGNEIHIRPSMLKFDLLGDAAVNSLEIIR 218

Query: 631 WSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLGKMLINREAALDVLQKLNGVDS 690
            S+  P +LNR++I++LSTLGV DEVF  + ++ L  L + L + + ALD+L+K    + 
Sbjct: 219 SSKPTPAYLNRQLITVLSTLGVPDEVFIELLREALKELAEALTDWDQALDLLRKQADEN- 277

Query: 691 KNILVKMLLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILN 750
                  L   + P+ +P+L  +L +  ++ L  LK + RI VPK   L G  DETG+L 
Sbjct: 278 ----DFTLTLRFMPSEDPFLRKLLRALVKHTLKKLKEKLRIPVPKSAALFGVVDETGVLK 333

Query: 751 YGQVFVRVTMTREELESKDQSFFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMK 810
            G+VFV+V+   +  + +              ++G VLV +NPCLHPGD+RV+ AV   +
Sbjct: 334 EGEVFVQVSDGNDGGQYE-------------YLEGDVLVARNPCLHPGDIRVVRAVDVPE 380

Query: 811 LEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPMDYTGRRSRI 870
           L  +   D ++FP KG+RP  +E SGGDLDGDI+F+ WD DL                  
Sbjct: 381 L--RHLKDVVVFPSKGDRPLASELSGGDLDGDIYFVCWDPDL------------------ 420

Query: 871 MDHDVTLEEIHKFFVDYMINDTLGAISTAHLVHADRDPDKARSSKCLHLATLHSMAVDFA 930
                                 LG IS +HL  A  DP+     +CL LA LHS AVD+ 
Sbjct: 421 ----------------------LGRISNSHLAIA--DPEGVGDPECLRLAKLHSQAVDYP 456

Query: 931 KTGAPAEMPLALKPKEFPDFMEREDKPRYISFGVLGKLYRA 971
           KTG P EM   L+PKE+PDFME+++   Y S  +LGKLYR+
Sbjct: 457 KTGLPVEMKRLLRPKEWPDFMEKDEGKSYKSTRILGKLYRS 497

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
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins Back     alignment and domain information
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins Back     alignment and domain information
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 1131
KOG09881145 consensus RNA-directed RNA polymerase QDE-1 requir 100.0
PF05183579 RdRP: RNA dependent RNA polymerase; InterPro: IPR0 100.0
PLN03134144 glycine-rich RNA-binding protein 4; Provisional 99.53
PLN03213759 repressor of silencing 3; Provisional 99.39
KOG0149247 consensus Predicted RNA-binding protein SEB4 (RRM 99.37
TIGR01661352 ELAV_HUD_SF ELAV/HuD family splicing factor. These 99.36
PF0007670 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or 99.32
TIGR01661352 ELAV_HUD_SF ELAV/HuD family splicing factor. These 99.3
TIGR01659346 sex-lethal sex-lethal family splicing factor. This 99.28
PLN03120260 nucleic acid binding protein; Provisional 99.27
PF1425970 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or 99.24
TIGR01645612 half-pint poly-U binding splicing factor, half-pin 99.21
TIGR01645612 half-pint poly-U binding splicing factor, half-pin 99.19
KOG0122270 consensus Translation initiation factor 3, subunit 99.13
TIGR01659346 sex-lethal sex-lethal family splicing factor. This 99.13
smart0036071 RRM RNA recognition motif. 99.1
smart0036272 RRM_2 RNA recognition motif. 99.06
TIGR01648578 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein 99.04
TIGR01628562 PABP-1234 polyadenylate binding protein, human typ 99.03
TIGR01642509 U2AF_lg U2 snRNP auxilliary factor, large subunit, 99.02
KOG0108435 consensus mRNA cleavage and polyadenylation factor 99.02
COG0724306 RNA-binding proteins (RRM domain) [General functio 99.02
TIGR01628562 PABP-1234 polyadenylate binding protein, human typ 99.01
KOG0125376 consensus Ataxin 2-binding protein (RRM superfamil 99.0
TIGR01622457 SF-CC1 splicing factor, CC1-like family. A homolog 99.0
TIGR01622457 SF-CC1 splicing factor, CC1-like family. A homolog 98.99
PLN03121243 nucleic acid binding protein; Provisional 98.98
KOG0148321 consensus Apoptosis-promoting RNA-binding protein 98.95
smart0036170 RRM_1 RNA recognition motif. 98.93
KOG0117506 consensus Heterogeneous nuclear ribonucleoprotein 98.9
cd0059074 RRM RRM (RNA recognition motif), also known as RBD 98.89
TIGR01649481 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor 98.88
KOG4207256 consensus Predicted splicing factor, SR protein su 98.85
KOG0111298 consensus Cyclophilin-type peptidyl-prolyl cis-tra 98.84
TIGR01649481 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor 98.79
KOG0131203 consensus Splicing factor 3b, subunit 4 [RNA proce 98.77
KOG0107195 consensus Alternative splicing factor SRp20/9G8 (R 98.77
TIGR01648578 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein 98.77
KOG0113335 consensus U1 small nuclear ribonucleoprotein (RRM 98.76
KOG4208214 consensus Nucleolar RNA-binding protein NIFK [Gene 98.72
KOG0145360 consensus RNA-binding protein ELAV/HU (RRM superfa 98.7
KOG0126219 consensus Predicted RNA-binding protein (RRM super 98.66
KOG0127678 consensus Nucleolar protein fibrillarin NOP77 (RRM 98.65
KOG0145360 consensus RNA-binding protein ELAV/HU (RRM superfa 98.64
TIGR01642509 U2AF_lg U2 snRNP auxilliary factor, large subunit, 98.63
KOG0127678 consensus Nucleolar protein fibrillarin NOP77 (RRM 98.56
KOG0105241 consensus Alternative splicing factor ASF/SF2 (RRM 98.55
KOG0130170 consensus RNA-binding protein RBM8/Tsunagi (RRM su 98.5
KOG4212608 consensus RNA-binding protein hnRNP-M [RNA process 98.45
KOG0144510 consensus RNA-binding protein CUGBP1/BRUNO (RRM su 98.45
KOG0147549 consensus Transcriptional coactivator CAPER (RRM s 98.45
KOG0121153 consensus Nuclear cap-binding protein complex, sub 98.44
KOG0148321 consensus Apoptosis-promoting RNA-binding protein 98.43
PF1389356 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or 98.43
KOG4205311 consensus RNA-binding protein musashi/mRNA cleavag 98.41
KOG0124544 consensus Polypyrimidine tract-binding protein PUF 98.39
KOG0117506 consensus Heterogeneous nuclear ribonucleoprotein 98.37
KOG0123369 consensus Polyadenylate-binding protein (RRM super 98.33
KOG0109346 consensus RNA-binding protein LARK, contains RRM a 98.31
KOG0146371 consensus RNA-binding protein ETR-3 (RRM superfami 98.3
KOG4205311 consensus RNA-binding protein musashi/mRNA cleavag 98.27
KOG0114124 consensus Predicted RNA-binding protein (RRM super 98.11
KOG4661940 consensus Hsp27-ERE-TATA-binding protein/Scaffold 98.06
KOG0124544 consensus Polypyrimidine tract-binding protein PUF 98.02
KOG0110725 consensus RNA-binding protein (RRM superfamily) [G 97.95
KOG0132894 consensus RNA polymerase II C-terminal domain-bind 97.88
KOG0109346 consensus RNA-binding protein LARK, contains RRM a 97.88
KOG4209231 consensus Splicing factor RNPS1, SR protein superf 97.84
KOG0123369 consensus Polyadenylate-binding protein (RRM super 97.84
KOG0131203 consensus Splicing factor 3b, subunit 4 [RNA proce 97.83
KOG4211510 consensus Splicing factor hnRNP-F and related RNA- 97.83
KOG0533243 consensus RRM motif-containing protein [RNA proces 97.8
KOG0153377 consensus Predicted RNA-binding protein (RRM super 97.74
KOG4206221 consensus Spliceosomal protein snRNP-U1A/U2B [RNA 97.73
KOG0116419 consensus RasGAP SH3 binding protein rasputin, con 97.73
KOG4454267 consensus RNA binding protein (RRM superfamily) [G 97.64
KOG0144510 consensus RNA-binding protein CUGBP1/BRUNO (RRM su 97.53
KOG0415479 consensus Predicted peptidyl prolyl cis-trans isom 97.48
KOG0110725 consensus RNA-binding protein (RRM superfamily) [G 97.45
KOG0226290 consensus RNA-binding proteins [General function p 97.33
KOG0106216 consensus Alternative splicing factor SRp55/B52/SR 97.14
KOG1457284 consensus RNA binding protein (contains RRM repeat 97.1
KOG4212608 consensus RNA-binding protein hnRNP-M [RNA process 96.91
KOG0147549 consensus Transcriptional coactivator CAPER (RRM s 96.87
KOG0146371 consensus RNA-binding protein ETR-3 (RRM superfami 96.76
PF0405997 RRM_2: RNA recognition motif 2; InterPro: IPR00720 96.75
KOG0120500 consensus Splicing factor U2AF, large subunit (RRM 96.7
KOG0151877 consensus Predicted splicing regulator, contains R 96.53
KOG0129520 consensus Predicted RNA-binding protein (RRM super 96.52
KOG1548382 consensus Transcription elongation factor TAT-SF1 96.49
KOG4660549 consensus Protein Mei2, essential for commitment t 96.4
KOG4210285 consensus Nuclear localization sequence binding pr 96.38
PF1160890 Limkain-b1: Limkain b1; InterPro: IPR024582 This e 96.12
KOG1995351 consensus Conserved Zn-finger protein [General fun 96.12
KOG4211510 consensus Splicing factor hnRNP-F and related RNA- 96.04
KOG4849498 consensus mRNA cleavage factor I subunit/CPSF subu 95.53
KOG1190492 consensus Polypyrimidine tract-binding protein [RN 94.56
KOG1365508 consensus RNA-binding protein Fusilli, contains RR 94.13
KOG1190492 consensus Polypyrimidine tract-binding protein [RN 93.95
KOG1365508 consensus RNA-binding protein Fusilli, contains RR 93.71
KOG0106216 consensus Alternative splicing factor SRp55/B52/SR 93.33
PF1460553 Nup35_RRM_2: Nup53/35/40-type RNA recognition moti 92.94
PF08777105 RRM_3: RNA binding motif; InterPro: IPR014886 This 92.82
COG5175480 MOT2 Transcriptional repressor [Transcription] 91.61
KOG1457284 consensus RNA binding protein (contains RRM repeat 91.38
KOG4307944 consensus RNA binding protein RBM12/SWAN [General 90.91
KOG4307944 consensus RNA binding protein RBM12/SWAN [General 90.5
KOG3152278 consensus TBP-binding protein, activator of basal 90.22
KOG4206221 consensus Spliceosomal protein snRNP-U1A/U2B [RNA 88.63
KOG1548382 consensus Transcription elongation factor TAT-SF1 87.36
KOG0120500 consensus Splicing factor U2AF, large subunit (RRM 86.36
KOG1855484 consensus Predicted RNA-binding protein [General f 85.59
KOG2202260 consensus U2 snRNP splicing factor, small subunit, 84.75
PF05172100 Nup35_RRM: Nup53/35/40-type RNA recognition motif; 84.35
KOG0128881 consensus RNA-binding protein SART3 (RRM superfami 83.93
KOG2314698 consensus Translation initiation factor 3, subunit 80.9
KOG0128881 consensus RNA-binding protein SART3 (RRM superfami 80.67
KOG1996378 consensus mRNA splicing factor [RNA processing and 80.57
>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=2.4e-182  Score=1636.15  Aligned_cols=1070  Identities=37%  Similarity=0.538  Sum_probs=853.8

Q ss_pred             cccEEEEeCCCCcCCHHHHHHHHhhccCCceEEEEEEeecCCCCCccceEEEEeCChHHHHHHHHhhcCCCceecCce-e
Q 001183            2 VLATVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSKAQNLSLNDKLVFNSQN-L   80 (1131)
Q Consensus         2 m~~ti~Vgnl~~~~t~~~L~~~fe~~~G~G~V~~~~i~~dr~tg~sRgfgfV~f~~~e~A~~Ai~~~~~~~~~~~gr~-L   80 (1131)
                      |+.++.+++||.+.++.+|.+|+|..+|.++|+..++-+++..+..+-|+-++|.+.+.--.++.... ....|+.-+ +
T Consensus         9 ~~~~~~~~~f~e~~~~~~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~f~~i~l~~~~~~~~~-a~v~f~~~~~~   87 (1145)
T KOG0988|consen    9 VVEEQDCNGFPESNSAVELGDFLELLIGAITVYLLKMNTTKPYRPNRVYHGSDFTSIALDCSGIETPL-AKVYFKHNQGL   87 (1145)
T ss_pred             eeeeeeccCcccchhHHHhhhHHHHHhcchHHHHHhcCCCCCCCCccccccccccccccccccchhhH-HHHhhccCCCC
Confidence            46789999999999999999999999999999999999988665677899999987665544344332 123444444 7


Q ss_pred             EeecCCC--CCCCCCCCCcceecCeEEEEeeeec---ccceEEEeee---cccceeeccCceeEEEEEecCCCCcccccc
Q 001183           81 KISETHS--DIVPRPVKAQHRVEDGVLHVGVMCK---EERLRVLQTF---EGVRGWLLPDRRRLEFWVWPKHNGEWQKGI  152 (1131)
Q Consensus        81 ~V~~a~~--~i~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (1131)
                      +..++..  ++++.+...++.+..+++++++--.   .-.|..+|++   +++.+...+..+.++..+..+.+ .     
T Consensus        88 ~~~e~~~~~~~l~~~a~~~~~l~~i~~~~~F~~~~~~t~~~~~~~~~~v~~~v~V~~~~~~~~~~~p~~~~~~-~-----  161 (1145)
T KOG0988|consen   88 NPWEVETSRRILSSLAVIRESLNQIVLEKVFDKPDGITKTFDCLESYKVNDQVTVRGSPVRRIVESPVVEYCK-L-----  161 (1145)
T ss_pred             CccchhhhhhhccccccchHHHhhHHHhhccCcccceeeeecceEEEeecceEEEeccceeeeeecccccccc-c-----
Confidence            7777777  6667665567777777776665333   3467777777   66777777766666666652222 1     


Q ss_pred             cccCCCCCCcceEEEEecccchheeeeccCCCCc----eeEEEEEeccCCeeEEEccCccccccccCccccccccCC-CC
Q 001183          153 QECQSDSSDCCFKVEILFEDVLETVGFSLDEGAT----VNGILFKLKYGPKIYQKVSGPHVASKFPSDRYHICKEDF-DF  227 (1131)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~----~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~  227 (1131)
                                ++..+..+..+.+...++. +...    ..+...-.+..|.+++....|.. ..+.++.+.+.+.+. +.
T Consensus       162 ----------~v~f~~~~~~~i~~~~~D~-~~~s~~~~~~~~~~~~~G~~k~~~~~~~p~~-~~~~~~~~Ef~k~~~~~~  229 (1145)
T KOG0988|consen  162 ----------CVPFEHSCRVLIETVSLDL-DKPSIIRYPKSRRYLDNGGSKYFRFAFSPLL-LALGDSELEFKKDFLADL  229 (1145)
T ss_pred             ----------ccchhhcchhheeeEEecc-CcchhccCcchhhhhhcCccceeecccccHH-Hhhccceeeeeccccccc
Confidence                      2333333333333222222 1100    00111112555555544333321 223334555566666 88


Q ss_pred             ceeEeeCCCCCCcccceeEEEEEEcCCCChhhhhhhhhhhhhh-------cCCceeecCCcccc-cccccccccC-CCCC
Q 001183          228 FWVRTTDFSVTKSIGCSTSFFWEIKNGLLASDISNIFPFYKED-------KTDLILEEGEEFCT-TSEIVPLVKC-RPGF  298 (1131)
Q Consensus       228 ~w~R~td~~~~~~iG~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~-~~~~~~~~~~-~~~~  298 (1131)
                      +|+|++||++..++|++|++++++...     +.+.+||++..       ...+.++.+..|.+ +.+.+++.+. ..+.
T Consensus       230 ~~i~~~~~~~~~~v~~eta~~~eI~~~-----i~~~lP~~r~~~~~~~~~~~s~~ir~~~~~~~~~~~~~~l~~~~~~gi  304 (1145)
T KOG0988|consen  230 LYIRTTDLRSRTGVGIETASCDEIRVP-----IWKDLPYNRYNGSTAEEFRLSVWIRLGSKYDVSSAQLVPLNDERDFGI  304 (1145)
T ss_pred             ceeeecceeccccccceeeccceecch-----hhccCCcccccccchhhhhhhhheecccccccccceeeeccccccccc
Confidence            999999999999999999999999985     44455555431       12456677777764 4556777552 2456


Q ss_pred             CCchhhHHHHHHHHhcCCCChhhhhHHHHHHHhCCC---HHHHHHHHHhccccCCCcCChhHHHHHHHHHhcccCCCCCC
Q 001183          299 NLSHEVLFQLNSLVHNQKVSLVAADAELIQILSGLS---METALMVLQKLHKLKSICYDPVSFVKTQLHVLGRNCKSIPL  375 (1131)
Q Consensus       299 ~l~f~v~fql~~lv~~g~l~~~~~~~~~~~~l~~~~---~~~~~~~l~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~  375 (1131)
                      ..+++.+++.++||+.|.+.......+|+.++....   .......|++|.....+||||.-+.+.+....-.+-+    
T Consensus       305 t~~~e~l~~r~slv~dq~~~~~~~~~~f~~l~~~~~~~d~~v~~a~LekL~~~~~~cfd~~~~~k~i~~~~~~ng~----  380 (1145)
T KOG0988|consen  305 THLYECLVSRGSLVKDQVLLEEAHLLEFLGLLRHKVLGDDNVLEAKLEKLLKLSTKCFDPYCQYKKIAKLNPSNGK----  380 (1145)
T ss_pred             eeehhhhhcccchhhhhHHhhhhHHHHHHHHHhhhhccchhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhcccCc----
Confidence            677788888888888999988888999999888643   3555566999999999999999988887753211111    


Q ss_pred             CCcccccCCCeEEEEEEEEcCCeEEecCCcccccCceecccCcCCCcEEEEEEeeCCCCCCCCCcccccccccccCcchh
Q 001183          376 SSHKRLIDHNVMSCYRALVTPMKIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYR  455 (1131)
Q Consensus       376 ~~~~~~~~~~~~~v~~v~vTPt~i~~~~P~~e~sNRvlR~y~~~~d~FLRV~F~DE~~~~l~~~~~~~~~~~~~~~~~~~  455 (1131)
                      -.+..+...|+..|+||+|||||+|+.+||++++|||+|+|..++++||||+|+|||.+ +..+..+..         .+
T Consensus       381 ~~~~~~~~~g~~~vrk~v~TPtrv~~~~PE~~~gNRVlR~f~~~~t~~lRvtF~De~~~-~~ir~~S~~---------~~  450 (1145)
T KOG0988|consen  381 LVTTKEIMEGLRRVRKVVFTPTRVYLLAPEVEMGNRVLRKFDKDSTRFLRVTFRDEDNK-LKIRTLSTG---------SR  450 (1145)
T ss_pred             cccchhhhhcceeEEEEEEcCceeEecCchhhhcchhheeccccCceEEEEEEEccccc-cccccCCcc---------hh
Confidence            12344567899999999999999999999999999999999999999999999999985 333332221         15


Q ss_pred             hHHHHHHHHHhhcCeEEcCeEEEEeeecccccccCeEEEEecCCCCCHHHHHHHcCCCCCCCCHHHHHHHHhccccCCcc
Q 001183          456 TKIYSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRGWMGCFNKIRSVSKCAARMGQLFSSSKQ  535 (1131)
Q Consensus       456 ~~i~~Rv~~~L~~Gi~I~gr~y~FLafS~SqlR~~s~wff~~~~~~t~~~Ir~wmG~F~~i~~vaK~aARigq~FSsT~~  535 (1131)
                      +.+|.||..+|++||+||+|+|+||||||||||+||.||++.....++++||.|||+|.+|.|++|||||||||||+|+.
T Consensus       451 t~l~~rv~~~L~~Gi~v~~r~y~FL~~s~sQlRdngy~m~~~s~~~~i~~iR~wmG~F~~i~nv~K~aARmGqCFs~Sr~  530 (1145)
T KOG0988|consen  451 TKLDMRVNSYLTDGISVANRRYEFLAFSNSQLRDNGYFMARFSDKTKIEDIREWMGDFRDIDNVPKLAARMGQCFSQSRG  530 (1145)
T ss_pred             hHHHHHHHHHHhcccEEccceeEEEEecccccccCceEEeecCCCccHHHHHHHhcchhhccCHHHHHhhcCcceecccc
Confidence            88999999999999999999999999999999999999999888899999999999999999999999999999999999


Q ss_pred             eeee-eCCcEEEcCCccccCCCCccccccccceecHHHHHHHHHHcCC-CCCCceeEeecCCceEEEEeeCCCCceEEec
Q 001183          536 TLVV-PVQDVEMIPDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGL-SHTPSAFQIRYGGYKGVIAVDRNSFRKLSLR  613 (1131)
Q Consensus       536 t~~i-~~~~i~~I~DI~~~~~g~~~~FTDG~G~IS~~la~~I~~~l~l-~~~PSAfQiR~gG~KGvl~vdp~~~~~I~lR  613 (1131)
                      |..+ +..++..+|||+..++|++||||||||+||.++|++|++++++ +.+|||||||+||+||||+|||.....+.+|
T Consensus       531 T~~~~~~~~~~~~~DI~~g~~g~~y~FSDGvG~iS~~~a~~vsq~~~~~~~vPsaFQiR~~G~KGVvav~Ps~~~~~~~~  610 (1145)
T KOG0988|consen  531 TGYVLERLDRMCPPDIEGGKRGNNYCFSDGVGMISLQFAREVSQKRKFGKAVPSAFQIRYGGYKGVVAVDPSMDKVLKLR  610 (1145)
T ss_pred             ccccccccccccCCcccccccCCceeecCCcccccHHHHHHHHHHHcccccCChheeeeccCCcceEEeCccHhhhhhhh
Confidence            9987 5667889999998778889999999999999999999999999 7799999999999999999999998899999


Q ss_pred             cccccccccCcceeEEeecCCccccccHHHHHHHhhCCCCHHHHHHHHHHHHHHHH--HHhcCHHHHHHHHHhccCCChH
Q 001183          614 RSMLKFESRNRMLNVTKWSESMPCFLNREIISLLSTLGVKDEVFEAMQQQQLILLG--KMLINREAALDVLQKLNGVDSK  691 (1131)
Q Consensus       614 ~Sm~KF~s~~~~LeI~~~S~~~p~~LNRQ~I~iL~~lGV~~~vF~~lq~~~l~~l~--~~l~d~~~a~~~L~~~~~~~~~  691 (1131)
                      .||.||.|.|..++|+.|++++||+||||+|.+|+.+||++++|+++|+..+++-+  ..+.....+..+|.-....+.+
T Consensus       611 ~~~~~s~S~n~~~~v~~~~~f~~~~lnr~lI~Lls~~gv~n~~F~~il~~vle~~r~~~n~~e~~~~~~~l~~~~~m~~e  690 (1145)
T KOG0988|consen  611 DSMNKSQSFNSLLEVTPSSKFQPAFLNRQLITLLSYLGVLNKPFINILDQVLEKQRRITNRIEELLDRAALNYGEQMDDE  690 (1145)
T ss_pred             hhhhhhhhhcceeeeeeccCCccccccHHHHHHHHhcCccchHHHHHHHHHHHHHHhhhhhhhHHHHHHHhhhhhhccch
Confidence            99999999999999999999999999999999999999999999999999998442  3333333344455433223445


Q ss_pred             HHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHhhhcceeeeecCceEEEEEecCCCCCCCCcEEEEEccchhhhhccccc
Q 001183          692 NILVKMLLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELESKDQS  771 (1131)
Q Consensus       692 ~~l~~ml~~Gf~~~~epfl~~~L~~~~~~~l~~lk~K~rI~Vp~s~~l~GV~DetG~L~~GEVfv~~s~~~~~~~~~~~~  771 (1131)
                      ++.+.++..++.++.||||++||...+++.++.+|+|.|||||.|++||||+||||+||+||||||++.+...       
T Consensus       691 n~a~~~l~~~~~~D~EPflr~mL~~~~k~~~~~~kek~ripv~~Gr~lmGvvDETG~L~ygQVfVq~t~~~~~-------  763 (1145)
T KOG0988|consen  691 NIAAMILKGFPRIDSEPFLRSMLSSLLKFTLQLLKEKIRIPVDLGRSLMGVVDETGILKYGQVFVQYTKTIRN-------  763 (1145)
T ss_pred             HHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHhcccccCcCCceeEeeeccccccccCeEEEEEcccccc-------
Confidence            5544445445558889999999999999999999999999999999999999999999999999999975321       


Q ss_pred             cccccCCcceeEeeeEEEeeCCCCCCCCeeEEEEEccCcccccCCcceEEecCCCCCCCCCcCCCCCCCCCeEEEeecCC
Q 001183          772 FFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIFFISWDND  851 (1131)
Q Consensus       772 ~~~~~~~~~~vi~G~VlV~RnP~lhPGDIr~v~AV~~P~L~~~hl~dvIVFp~kG~Rplps~lSGGDLDGD~y~ViWD~~  851 (1131)
                         .+-++..||+|+|+|||||||||||||+++||++|+|  +||+|||||||||+||||+||||||||||+|+|||||+
T Consensus       764 ---~~~~~~~vitG~VlvtKNPcLhpGDVRVl~AV~vp~L--~h~~dvVvFPQkGpRphpdE~aGsDLDGDeYfViWDqk  838 (1145)
T KOG0988|consen  764 ---SDSGRKEVITGKVLVTKNPCLHPGDVRVLKAVYVPAL--EHMVDVVVFPQKGPRPHPDEMAGSDLDGDEYFVIWDQK  838 (1145)
T ss_pred             ---cccCCceEEEeeEEEecCCCCCCCceEEEEeeccHHH--HhhcCEEEcCCCCCCCCccccccCCCCCceEEEEeChh
Confidence               1113458999999999999999999999999999999  99999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCCCccccCCCCCCHHHHHHHHHHhhccCchhHHHHHHHHhcccCCCCCCCHHHHHHHHHHHhcccccC
Q 001183          852 LIPCETEPPMDYTGRRSRIMDHDVTLEEIHKFFVDYMINDTLGAISTAHLVHADRDPDKARSSKCLHLATLHSMAVDFAK  931 (1131)
Q Consensus       852 Lvp~~~~~P~~Y~~~~~~~l~~~vt~~di~~ffv~ym~~d~LG~is~~Hl~~aD~~~~g~~~~~cl~LA~L~S~AVD~~K  931 (1131)
                      |+|+.+++||+|++.+++.+++.+++++|.+||++||++|+||+|+|||+++||+  .|+.+..|+.||++||+||||||
T Consensus       839 LL~~~~~epmd~~~~~sk~~~~~~~~~~m~effv~yL~~DslG~isnAhl~~aD~--~G~~~~~Cl~LA~k~~~AVDF~K  916 (1145)
T KOG0988|consen  839 LLPPRNEEPMDSSSEKSKILDGRVPLDEMSEFFVEYLKEDSLGLISNAHLANADV--YGLFSDVCLELAKKHSQAVDFPK  916 (1145)
T ss_pred             hccCcCCCccccCccccccccCCCCHHHHHHHHHHHHHHHHHHHHhhccccchhh--cchhhHHHHHHHHhhcccccccc
Confidence            9999999999999999999999999999999999999999999999999999999  69999999999999999999999


Q ss_pred             CCCCCCCCccCCCCCCCcccCCCCCCcccccchhhHHHHHhhhhhhhhhccccchhhhhhccccccccccchhhhHHHHH
Q 001183          932 TGAPAEMPLALKPKEFPDFMEREDKPRYISFGVLGKLYRATLDSIMQIRSNAIWSEKIAEASYDHDLEVDGFEAFLGVAE 1011 (1131)
Q Consensus       932 TG~~v~lp~~l~~~~~PdFm~k~~~~~Y~S~kiLGkLYr~v~~~~~~~~~~~~~~~~~~~~~~d~~l~~~g~~~~l~~A~ 1011 (1131)
                      ||+.+.||..++|++|||||++.++|+|.|++++|||||.++.............+. .+..||++++++||++|++.|+
T Consensus       917 sG~d~~~~~~ek~e~~PDfm~~~d~p~Y~S~~l~GkLfR~~~aid~~~~~~e~~~~~-~~i~yD~~l~v~gFe~yme~a~  995 (1145)
T KOG0988|consen  917 SGADESMPEKEKPERYPDFMEKTDKPTYYSERLCGKLFREAKAIDAPLKGSEERSEQ-VEVEYDEDLEVDGFEHYMERAK  995 (1145)
T ss_pred             cCCcccccchhchhhcchhhhCCCCceeecchhhhHHHHHHHhhcchhhcCccccCc-ccccCCcccCcCCcHHHHHHHH
Confidence            999999999999999999999999999999999999999875432211111111222 3378999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCcchheeh--hhcccchhhhhcchhhhhhHHHHHHHHH-HHHHHHH---------HHhcc
Q 001183         1012 SHKEMYEEEMNALMNYYGASTEDEILTG--NLRNRASYLQRDNRRYGDMKDRILLSAK-NLQNEAK---------EWFGS 1079 (1131)
Q Consensus      1012 ~~~~~Y~~~l~~lm~~y~i~tE~Ev~sG--~i~~~~~~~~~d~~~~~~~~~~i~~~~~-~l~~e~~---------~~f~~ 1079 (1131)
                      ++++.|+.+|++||.+|||++|+||+||  .+..+..+..  ++..+...+++...++ .+.+|++         .+|+.
T Consensus       996 ~~~~~y~~qL~slm~~ygi~~E~eI~sG~~~~ddms~~~t--~~~~e~~~~~l~~~~r~~~~qef~~y~~~~e~l~~fe~ 1073 (1145)
T KOG0988|consen  996 KQVASYNGQLRSLMDFYGISTEGEIFSGILDQDDMSFYNT--ERMIELKLERLVLKLREKFFQEFGAYKLEIEKLSCFED 1073 (1145)
T ss_pred             HHHhhhhhHHHHHHHHhCccchhhhhccCccccchhhhcc--cccchhhhHHHHHHHHHHHHHHhhhhcchhhhcccccc
Confidence            9999999999999999999999999999  3333332221  1222233344444444 2334443         22333


Q ss_pred             CCCCCChhhHHHHHHH-hhcccccccCCCceeeeccchHHHHHHHHhh
Q 001183         1080 SCKENEHPQLASAWYH-VTYSPSYCKERMALLSFPWIVGDILLNIKSV 1126 (1131)
Q Consensus      1080 ~~~~~~~~~~a~AwY~-Vty~~~~~~~~~~~lSFpWi~~d~L~~ik~~ 1126 (1131)
                      .+..+.+.+||+|||+ ++|+.+...+..+.+|||||++|+|++||+.
T Consensus      1074 ~~~eE~~~kKa~aWY~v~~ye~~~~~~~~~~~SF~wia~Dvl~~iK~~ 1121 (1145)
T KOG0988|consen 1074 SPEEEFIMKKASAWYRVYRYEMAQAMRETRKLSFAWIAYDVLARIKQT 1121 (1145)
T ss_pred             CchhHHHHHHHHHHHHHHHhhhhcccccCcccchHHHHHHHHHHHHHH
Confidence            2233348899999999 9999887777788889999999999999998

>PF05183 RdRP: RNA dependent RNA polymerase; InterPro: IPR007855 This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; 2 Back     alignment and domain information
>PLN03134 glycine-rich RNA-binding protein 4; Provisional Back     alignment and domain information
>PLN03213 repressor of silencing 3; Provisional Back     alignment and domain information
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only] Back     alignment and domain information
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor Back     alignment and domain information
>PF00076 RRM_1: RNA recognition motif Back     alignment and domain information
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor Back     alignment and domain information
>TIGR01659 sex-lethal sex-lethal family splicing factor Back     alignment and domain information
>PLN03120 nucleic acid binding protein; Provisional Back     alignment and domain information
>PF14259 RRM_6: RNA recognition motif (a Back     alignment and domain information
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family Back     alignment and domain information
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family Back     alignment and domain information
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR01659 sex-lethal sex-lethal family splicing factor Back     alignment and domain information
>smart00360 RRM RNA recognition motif Back     alignment and domain information
>smart00362 RRM_2 RNA recognition motif Back     alignment and domain information
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family Back     alignment and domain information
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family Back     alignment and domain information
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor Back     alignment and domain information
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification] Back     alignment and domain information
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only] Back     alignment and domain information
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family Back     alignment and domain information
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only] Back     alignment and domain information
>TIGR01622 SF-CC1 splicing factor, CC1-like family Back     alignment and domain information
>TIGR01622 SF-CC1 splicing factor, CC1-like family Back     alignment and domain information
>PLN03121 nucleic acid binding protein; Provisional Back     alignment and domain information
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>smart00361 RRM_1 RNA recognition motif Back     alignment and domain information
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability Back     alignment and domain information
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family Back     alignment and domain information
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification] Back     alignment and domain information
>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family Back     alignment and domain information
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification] Back     alignment and domain information
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family Back     alignment and domain information
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only] Back     alignment and domain information
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only] Back     alignment and domain information
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor Back     alignment and domain information
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only] Back     alignment and domain information
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification] Back     alignment and domain information
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription] Back     alignment and domain information
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF13893 RRM_5: RNA recognition motif Back     alignment and domain information
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification] Back     alignment and domain information
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only] Back     alignment and domain information
>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification] Back     alignment and domain information
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only] Back     alignment and domain information
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription] Back     alignment and domain information
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only] Back     alignment and domain information
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription] Back     alignment and domain information
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only] Back     alignment and domain information
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification] Back     alignment and domain information
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification] Back     alignment and domain information
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification] Back     alignment and domain information
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification] Back     alignment and domain information
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only] Back     alignment and domain information
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification] Back     alignment and domain information
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms] Back     alignment and domain information
>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only] Back     alignment and domain information
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only] Back     alignment and domain information
>KOG0226 consensus RNA-binding proteins [General function prediction only] Back     alignment and domain information
>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only] Back     alignment and domain information
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification] Back     alignment and domain information
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription] Back     alignment and domain information
>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2 Back     alignment and domain information
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only] Back     alignment and domain information
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription] Back     alignment and domain information
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>KOG4210 consensus Nuclear localization sequence binding protein [Transcription] Back     alignment and domain information
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes Back     alignment and domain information
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only] Back     alignment and domain information
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification] Back     alignment and domain information
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification] Back     alignment and domain information
>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification] Back     alignment and domain information
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only] Back     alignment and domain information
>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification] Back     alignment and domain information
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only] Back     alignment and domain information
>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif Back     alignment and domain information
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation Back     alignment and domain information
>COG5175 MOT2 Transcriptional repressor [Transcription] Back     alignment and domain information
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only] Back     alignment and domain information
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only] Back     alignment and domain information
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only] Back     alignment and domain information
>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription] Back     alignment and domain information
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification] Back     alignment and domain information
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription] Back     alignment and domain information
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG1855 consensus Predicted RNA-binding protein [General function prediction only] Back     alignment and domain information
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification] Back     alignment and domain information
>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT [] Back     alignment and domain information
>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG1996 consensus mRNA splicing factor [RNA processing and modification] 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 ?
Query1131
2j7n_A 1022 Structure Of The Rnai Polymerase From Neurospora Cr 1e-15
>pdb|2J7N|A Chain A, Structure Of The Rnai Polymerase From Neurospora Crassa Length = 1022 Back     alignment and structure 
Iteration: 1

 Score = 82.4 bits (202), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 87/360 (24%), Positives = 153/360 (42%), Gaps = 47/360 (13%)
Query: 552 VTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGVIAVDRNSFRK-- 609
           ++  G     +DG+G++S S A+++    GL   PSA Q R+G  KG+  +D +      
Sbjct: 318 LSPSGTGEVMNDGVGRMSRSVAKRIRDVLGLGDVPSAVQGRFGSAKGMWVIDVDDTGDED 377
Query: 610 -LSLRRSMLKFE-----SRNRMLNV-TKWSESMPCFLNREIISLLSTLG---------VK 653
            +    S  K+E        R L V +  SE     LN +++ +L             + 
Sbjct: 378 WIETYPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIG 437
Query: 654 DEVFEAMQQQ---QLILLGKMLINREAALDVLQK------------LNGV-DSKNILVKM 697
           D +   +Q+Q   Q   L + +  R+   +                L G+ DS+   +  
Sbjct: 438 DRLINDLQRQFSEQKHALNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNF 497
Query: 698 LLQ-GYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFV 756
           L+  G++P  + YL  +     + +   LKS+  I V +   +    D  G+L   +V V
Sbjct: 498 LMNSGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHV 557
Query: 757 RVTMTREELESKDQSFFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDY 816
             +    +   +++SF       T +    VLV ++P   P D++ + AV++ +L     
Sbjct: 558 GFS---SKFRDEEESF-------TLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHS--L 605
Query: 817 VDCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDVT 876
            D IIF  KG+ P   + SGGD DGD+ ++ WD +++       M      SR +  D T
Sbjct: 606 KDVIIFSTKGDVPLAKKLSGGDYDGDMAWVCWDPEIVDGFVNAEMPLEPDLSRYLKKDKT 665

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query1131
2j7n_A1022 RNA-dependent RNA polymerase; RNAI response, RNA-d 1e-161
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-17
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-14
1vt4_I1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-05
2cq4_A114 RNA binding motif protein 23; RRM domain, structur 3e-04
2dng_A103 Eukaryotic translation initiation factor 4H; RRM d 3e-04
>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 =  503 bits (1296), Expect = e-161
 Identities = 147/957 (15%), Positives = 301/957 (31%), Gaps = 138/957 (14%)

Query: 293  KCRPGF-NLSHEVLFQLNSLVHNQKVSLVAADAELIQILSGLSMETALMVLQKLHKLKSI 351
            K           V +++  L  + KV L      L    S  +      + + L++L + 
Sbjct: 24   KFPKWLHEAPLAVAWEVTRLFMHCKVDLEDESLGLKYDPSWSTARDVTDIWKTLYRLDA- 82

Query: 352  CYDPVSFVKTQLHVLGRNCKSIPLSSHKRLIDHNVMSCYRALVTPM----KIYCLGPELE 407
             +    F +   + +     +    S    +  + +  Y    +P      +       E
Sbjct: 83   -FRGKPFPEKPPNDVFVTAMTGNFESKGSAVVLSAVLDYNPDNSPTAPLYLVKLKPLMFE 141

Query: 408  TSNYVVKNFAKYASD-FMRVTFVEEDWSKLPANALSTS-------IQRGIFSKPYRT-KI 458
                + +   ++  D F  +       +      + +        + + +    +     
Sbjct: 142  QGCRLTR---RFGPDRFFEILIPSPTSTSPSVPPVVSKQPAAVEEVIQWLTMGQHSLVGR 198

Query: 459  YSRILTILQDGIVIGDKHYEFLAFSASQLRNNSVWMFASND------------------- 499
              R       G     + ++  A     +    V  FA                      
Sbjct: 199  QWRAFFAKDAGYRKPLREFQLRAEDPKPIIKERVHFFAETGITFRPDVFKTRSVVPAEEP 258

Query: 500  -----EVSAEDVRGWMGCF--NKIRSVSKCAARMGQLFSSSKQTLVVPVQDVEMIPDVEV 552
                 E     +  W+     N  +   K  +R+    S +   + +    +       +
Sbjct: 259  VEQRTEFKVSQMLDWLLQLDNNTWQPHLKLFSRIQLGLSKTYAIMTLEPHQIRHHKTDLL 318

Query: 553  TSDGNTYCFSDGIGKISLSFARQVAQKCGLSHTPSAFQIRYGGYKGVIAVDRNSFRK--- 609
            +  G     +DG+G++S S A+++    GL   PSA Q R+G  KG+  +D +       
Sbjct: 319  SPSGTGEVMNDGVGRMSRSVAKRIRDVLGLGDVPSAVQGRFGSAKGMWVIDVDDTGDEDW 378

Query: 610  LSLRRSMLKFESR-----NRMLNVTKWS-ESMPCFLNREIISLLSTLGV---------KD 654
            +    S  K+E        R L V   + E     LN +++ +L               D
Sbjct: 379  IETYPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGD 438

Query: 655  EVFEAMQQQ---QLILLGKMLINREAALDVLQKLNGVDS--------------KNILVKM 697
             +   +Q+Q   Q   L + +  R+   +         S              +  L  +
Sbjct: 439  RLINDLQRQFSEQKHALNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNFL 498

Query: 698  LLQGYEPNVEPYLSMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVR 757
            +  G++P  + YL  +     + +   LKS+  I V +   +    D  G+L   +V V 
Sbjct: 499  MNSGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVG 558

Query: 758  VTMTREELESKDQSFFHRVDDKTSIVKGKVLVTKNPCLHPGDVRVLEAVYEMKLEEKDYV 817
             +    + E          +  T +    VLV ++P   P D++ + AV++ +L      
Sbjct: 559  FSSKFRDEE----------ESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHS--LK 606

Query: 818  DCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPMDYTGRRSRIMDHDV-- 875
            D IIF  KG+ P   + SGGD DGD+ ++ WD +++       M      SR +  D   
Sbjct: 607  DVIIFSTKGDVPLAKKLSGGDYDGDMAWVCWDPEIVDGFVNAEMPLEPDLSRYLKKDKTT 666

Query: 876  ------------------TLEEIHKFFVDYMINDTLGAISTAHLVHADRDPDKARSSKCL 917
                              T + I K F   +  + LG  +         + +   +   +
Sbjct: 667  FKQLMASHGTGSAAKEQTTYDMIQKSFHFALQPNFLGMCTNYKERLCYIN-NSVSNKPAI 725

Query: 918  HLATLHSMAVDFAKTGAPAEMPLALK-PKEFPDFMEREDKPRYISFGVLGK--------- 967
             L++L    VD +K G         +  +E          P Y S   LG+         
Sbjct: 726  ILSSLVGNLVDQSKQGIVFNEASWAQLRRELLGGALSLPDPMYKSDSWLGRGEPTHIIDY 785

Query: 968  LYRA----TLDSIMQIRSNAIWSEKIAE---ASYDHDL-----EVDGFEAFLGVAESHKE 1015
            L  +     +D  ++   NA+ + K  E     +D DL                +     
Sbjct: 786  LKFSIARPAIDKELEAFHNAMKAAKDTEDGAHFWDPDLASYYTFFKEISDKSRSSALLFT 845

Query: 1016 MYEEEMNALMNYYGASTEDEILTGNLRNRASYLQRDNRRYGDMKDRILLSAKNLQNEAKE 1075
              +  +  +   YG   +++ +  +       + +   ++  +    +  +    +    
Sbjct: 846  TLKNRIGEVEKEYGRLVKNKEMRDSKDPYPVRVNQVYEKWCAITPEAMDKSGANYDSKVI 905

Query: 1076 WFGSSCKENEHPQLASAWYHVTYSPSYCKERMALLSFPWIV-GDILLNIKSVNSRKA 1131
                     +     + W  +  S ++         F W + G  L  IK+  + + 
Sbjct: 906  RLLELSFLADREM--NTWALLRASTAFKLYYHKSPKFVWQMAGRQLAYIKAQMTSRP 960
>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
>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
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114 Back     alignment and structure
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query1131
2j7n_A1022 RNA-dependent RNA polymerase; RNAI response, RNA-d 100.0
4fxv_A99 ELAV-like protein 1; RNA recognition motif, putati 99.69
2lxi_A91 RNA-binding protein 10; NMR {Homo sapiens} 99.65
3p5t_L90 Cleavage and polyadenylation specificity factor S; 99.64
3s8s_A110 Histone-lysine N-methyltransferase SETD1A; chromat 99.61
3md1_A83 Nuclear and cytoplasmic polyadenylated RNA-bindin 99.6
2lkz_A95 RNA-binding protein 5; RRM; NMR {Homo sapiens} 99.6
3bs9_A87 Nucleolysin TIA-1 isoform P40; RNA recognition mot 99.59
4f25_A115 Polyadenylate-binding protein 1; RRM fold, transla 99.59
2j8a_A136 Histone-lysine N-methyltransferase, H3 lysine-4 sp 99.59
3ns6_A100 Eukaryotic translation initiation factor 3 subuni; 99.59
1whw_A99 Hypothetical protein riken cDNA 1200009A02; RNA re 99.58
2x1f_A96 MRNA 3'-END-processing protein RNA15; transcriptio 99.57
3ucg_A89 Polyadenylate-binding protein 2; ferredoxin-like, 99.57
2dnz_A95 Probable RNA-binding protein 23; RNA recognition m 99.56
2la6_A99 RNA-binding protein FUS; structural genomics, nort 99.56
3mdf_A85 Peptidyl-prolyl CIS-trans isomerase E; RRM domain, 99.56
2cq0_A103 Eukaryotic translation initiation factor 3 subunit 99.56
1s79_A103 Lupus LA protein; RRM, alpha/beta, RNA binding pro 99.56
3s7r_A87 Heterogeneous nuclear ribonucleoprotein A/B; ferre 99.55
3n9u_C156 Cleavage and polyadenylation specificity factor S; 99.55
2cqb_A102 Peptidyl-prolyl CIS-trans isomerase E; RNA recogni 99.55
2cpf_A98 RNA binding motif protein 19; RNA recognition moti 99.55
2dgs_A99 DAZ-associated protein 1; RRM domain, structural g 99.55
2cpz_A115 CUG triplet repeat RNA-binding protein 1; RRM doma 99.55
2cqc_A95 Arginine/serine-rich splicing factor 10; RNA recog 99.55
2div_A99 TRNA selenocysteine associated protein; structural 99.55
1p27_B106 RNA-binding protein 8A; nuclear protein, mRNA spli 99.54
1x5t_A96 Splicing factor 3B subunit 4; structure genomics, 99.54
2cqd_A116 RNA-binding region containing protein 1; RNA recog 99.54
2dgo_A115 Cytotoxic granule-associated RNA binding protein 1 99.54
2dnm_A103 SRP46 splicing factor; RRM domain, RBD, structural 99.54
1x5u_A105 Splicing factor 3B subunit 4 (spliceosome associat 99.54
1sjq_A105 Polypyrimidine tract-binding protein 1; babbab mot 99.54
2mss_A75 Protein (musashi1); RNA-binding domain, RNA bindin 99.54
2dgx_A96 KIAA0430 protein; RRM domain, structural genomics, 99.53
1oo0_B110 CG8781-PA, drosophila Y14; RNA recognition motif, 99.53
1uaw_A77 Mouse-musashi-1; RNP-type structure, RNA binding p 99.53
2ki2_A90 SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA 99.53
2jrs_A108 RNA-binding protein 39; RNA binding motif of RBM39 99.53
4a8x_A88 RNA-binding protein with serine-rich domain 1; tra 99.53
1x5s_A102 Cold-inducible RNA-binding protein; structure geno 99.53
1x4h_A111 RNA-binding protein 28; structural genomics, RRM d 99.53
2e5h_A94 Zinc finger CCHC-type and RNA-binding motif- conta 99.53
2krb_A81 Eukaryotic translation initiation factor 3 subunit 99.53
2kt5_A124 RNA and export factor-binding protein 2; chaperone 99.53
2dis_A109 Unnamed protein product; structural genomics, RRM 99.52
2do4_A100 Squamous cell carcinoma antigen recognized by T- c 99.52
2dnh_A105 Bruno-like 5, RNA binding protein; RRM domain, RBD 99.52
1p1t_A104 Cleavage stimulation factor, 64 kDa subunit; RNA r 99.52
2dhg_A104 TRNA selenocysteine associated protein (SECP43); R 99.52
1x4e_A85 RNA binding motif, single-stranded interacting pro 99.52
2dng_A103 Eukaryotic translation initiation factor 4H; RRM d 99.52
2rs2_A109 Musashi-1, RNA-binding protein musashi homolog 1; 99.51
2nlw_A105 Eukaryotic translation initiation factor 3 subunit 99.51
2dgp_A106 Bruno-like 4, RNA binding protein; RRM domain, str 99.51
2cph_A107 RNA binding motif protein 19; RNA recognition moti 99.51
2dh8_A105 DAZ-associated protein 1; RRM domain, structural g 99.51
2wbr_A89 GW182, gawky, LD47780P; DNA-binding protein, RRM, 99.51
2cpe_A113 RNA-binding protein EWS; RNA recognition motif, RR 99.51
2fy1_A116 RNA-binding motif protein, Y chromosome, family 1 99.51
2khc_A118 Testis-specific RNP-type RNA binding protein; RRM, 99.5
1u6f_A139 Tcubp1, RNA-binding protein UBP1; trypanosome, mRN 99.5
2ek1_A95 RNA-binding protein 12; RNA recognition motif, dim 99.5
2ywk_A95 Putative RNA-binding protein 11; RRM-domain, struc 99.5
1wi8_A104 EIF-4B, eukaryotic translation initiation factor 4 99.5
1iqt_A75 AUF1, heterogeneous nuclear ribonucleoprotein D0; 99.5
2cq4_A114 RNA binding motif protein 23; RRM domain, structur 99.5
2j76_E100 EIF-4B, EIF4B, eukaryotic translation initiation f 99.5
2d9p_A103 Polyadenylate-binding protein 3; RRM domain, struc 99.5
2jwn_A124 Embryonic polyadenylate-binding protein 2-B; epabp 99.49
3ex7_B126 RNA-binding protein 8A; protein-RNA complex, mRNA 99.49
2cqp_A98 RNA-binding protein 12; RNA recognition motif, RRM 99.49
1wez_A102 HnRNP H', FTP-3, heterogeneous nuclear ribonucleop 99.49
2m2b_A131 RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio 99.49
2cqi_A103 Nucleolysin TIAR; RNA recognition motif, RRM, RNA 99.49
2dgv_A92 HnRNP M, heterogeneous nuclear ribonucleoprotein M 99.49
2kn4_A158 Immunoglobulin G-binding protein G, splicing FACT 99.49
2kxn_B129 Transformer-2 protein homolog beta; SR protein, RR 99.48
3ulh_A107 THO complex subunit 4; nuclear protein, RNA bindin 99.48
1x4b_A116 Heterogeneous nuclear ribonucleoproteins A2/B1; st 99.48
1wg5_A104 Heterogeneous nuclear ribonucleoprotein H; structu 99.48
2ku7_A140 MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio 99.47
2do0_A114 HnRNP M, heterogeneous nuclear ribonucleoprotein M 99.47
2cpy_A114 RNA-binding protein 12; RRM domain, structural gen 99.47
2dnn_A109 RNA-binding protein 12; RRM domain, RBD, structura 99.47
2cqg_A103 TDP-43, TAR DNA-binding protein-43; RNA recognitio 99.47
2dgw_A91 Probable RNA-binding protein 19; RRM domain, struc 99.47
2cpi_A111 CCR4-NOT transcription complex subunit 4; RNA reco 99.46
2jvr_A111 Nucleolar protein 3; RNA recognition motif, nucleu 99.46
2hgl_A136 HNRPF protein, heterogeneous nuclear ribonucleopro 99.46
3r27_A100 HnRNP L, heterogeneous nuclear ribonucleoprotein L 99.46
2cq1_A101 PTB-like protein L; RRM domain, structural genomic 99.46
2cq3_A103 RNA-binding protein 9; RRM domain, structural geno 99.45
2lea_A135 Serine/arginine-rich splicing factor 2; SR protein 99.45
2db1_A118 Heterogeneous nuclear ribonucleoprotein F; RRM dom 99.45
3q2s_C229 Cleavage and polyadenylation specificity factor S; 99.45
2ad9_A119 Polypyrimidine tract-binding protein 1; RBD, RRM, 99.45
2err_A109 Ataxin-2-binding protein 1; protein-RNA complex, R 99.45
1h2v_Z156 20 kDa nuclear CAP binding protein; CAP-binding-co 99.45
2lmi_A107 GRSF-1, G-rich sequence factor 1; G-rich RNA seque 99.45
1wex_A104 Hypothetical protein (riken cDNA 2810036L13); stru 99.44
1fj7_A101 Nucleolin RBD1, protein C23; RNP, RRM, RNA binding 99.44
1x4a_A109 Splicing factor, arginine/serine-rich 1 (splicing 99.43
1x4d_A102 Matrin 3; structural genomics, RRM domain, NPPSFA, 99.43
1rk8_A165 CG8781-PA, CG8781-PA protein; mRNA processing, RRM 99.43
2xs2_A102 Deleted in azoospermia-like; RNA binding protein-R 99.42
2fc9_A101 NCL protein; structure genomics, RRM_1 domain, str 99.42
1wel_A124 RNA-binding protein 12; structural genomics, NPPSF 99.42
2hgm_A126 HNRPF protein, heterogeneous nuclear ribonucleopro 99.42
2dha_A123 FLJ20171 protein; RRM domain, structural genomics, 99.42
1x4f_A112 Matrin 3; structural genomics, RRM domain, NPPSFA, 99.41
4f02_A213 Polyadenylate-binding protein 1; mRNA, eukaryotic 99.41
1x5o_A114 RNA binding motif, single-stranded interacting pro 99.41
2a3j_A127 U1 small nuclear ribonucleoprotein A; computationa 99.4
2fc8_A102 NCL protein; structure genomics, RRM_1 domain, str 99.4
2cpx_A115 Hypothetical protein FLJ11016; RRM domain, structu 99.39
1nu4_A97 U1A RNA binding domain; RNA recognition motif, U1 99.39
2qfj_A216 FBP-interacting repressor; protein-DNA complex; HE 99.39
1fxl_A167 Paraneoplastic encephalomyelitis antigen HUD; prot 99.38
2hgn_A139 Heterogeneous nuclear ribonucleoprotein F; RNA rec 99.38
2e5j_A97 Methenyltetrahydrofolate synthetase domain contain 99.38
2la4_A101 Nuclear and cytoplasmic polyadenylated RNA-bindin 99.38
2lcw_A116 RNA-binding protein FUS; RRM, nucleic acid binding 99.08
1b7f_A168 Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP 99.38
2hvz_A101 Splicing factor, arginine/serine-rich 7; RRM, RNA 99.37
2dnl_A114 Cytoplasmic polyadenylation element binding protei 99.37
2dnq_A90 RNA-binding protein 4B; RRM domain,RBD, structural 99.37
1fjc_A96 Nucleolin RBD2, protein C23; RNP, RRM, RNA binding 99.37
1x4g_A109 Nucleolysin TIAR; structural genomics, RRM domain, 99.37
1x4c_A108 Splicing factor, arginine/serine-rich 1; structura 99.36
1l3k_A196 Heterogeneous nuclear ribonucleoprotein A1; nuclea 99.36
3md3_A166 Nuclear and cytoplasmic polyadenylated RNA-bindin 99.36
2e5g_A94 U6 snRNA-specific terminal uridylyltransferase 1; 99.36
2g4b_A172 Splicing factor U2AF 65 kDa subunit; protein-RNA c 99.36
2cpd_A99 Apobec-1 stimulating protein; RNA recognition moti 99.36
2xnq_A97 Nuclear polyadenylated RNA-binding protein 3; tran 99.36
3lqv_A115 PRE-mRNA branch site protein P14; cysless mutant, 99.35
2f3j_A177 RNA and export factor binding protein 2; RRM domai 99.35
1wg1_A88 KIAA1579 protein, homolog EXC-7; RBD, structural g 99.35
1whx_A111 Hypothetical protein riken cDNA 1200009A02; RNA re 99.34
1why_A97 Hypothetical protein riken cDNA 1810017N16; RNA re 99.34
3md3_A166 Nuclear and cytoplasmic polyadenylated RNA-bindin 99.34
2ytc_A85 PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s 99.34
2cjk_A167 Nuclear polyadenylated RNA-binding protein 4; HRP1 99.34
3d2w_A89 TAR DNA-binding protein 43; DP-43 proteinopathy, T 99.34
1wf1_A110 RNA-binding protein RALY; structural genomics, RRM 99.33
2dgt_A92 RNA-binding protein 30; RRM domain, structural gen 99.33
2dnp_A90 RNA-binding protein 14; RRM domain, RBD, structura 99.33
2kvi_A96 Nuclear polyadenylated RNA-binding protein 3; RNA- 99.33
2cqh_A93 IGF-II mRNA-binding protein 2 isoform A; RNA recog 99.32
2jvo_A108 Nucleolar protein 3; nucleus, phosphorylation, rib 99.32
2yh0_A198 Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli 99.32
3egn_A143 RNA-binding protein 40; RNA recognition motif (RRM 99.31
2cq2_A114 Hypothetical protein LOC91801; RRM domain, structu 99.31
1l3k_A196 Heterogeneous nuclear ribonucleoprotein A1; nuclea 99.31
2dgu_A103 Heterogeneous nuclear ribonucleoprotein Q; RRM dom 99.3
2qfj_A216 FBP-interacting repressor; protein-DNA complex; HE 99.3
2i2y_A150 Fusion protein consists of immunoglobin G- binding 99.3
2cjk_A167 Nuclear polyadenylated RNA-binding protein 4; HRP1 99.3
2cpj_A99 Non-POU domain-containing octamer-binding protein; 99.29
2e44_A96 Insulin-like growth factor 2 mRNA binding protein 99.29
4f02_A213 Polyadenylate-binding protein 1; mRNA, eukaryotic 99.29
2pe8_A105 Splicing factor 45; RRM, protein binding; 2.00A {H 99.28
2voo_A193 Lupus LA protein; RNA-binding protein, RNA recogni 99.28
3pgw_S437 U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM 99.27
1x5p_A97 Negative elongation factor E; structure genomics, 99.27
2hzc_A87 Splicing factor U2AF 65 kDa subunit; RNA splicing, 99.26
1b7f_A168 Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP 99.26
3nmr_A175 Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl 99.25
3beg_B115 Splicing factor, arginine/serine-rich 1; kinase, S 99.24
1sjr_A164 Polypyrimidine tract-binding protein 1; extended b 99.24
1wf0_A88 TDP-43, TAR DNA-binding protein-43; structural gen 99.23
3tyt_A205 Heterogeneous nuclear ribonucleoprotein L; ferredo 99.23
1fxl_A167 Paraneoplastic encephalomyelitis antigen HUD; prot 99.23
3nmr_A175 Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl 99.22
2diu_A96 KIAA0430 protein; structural genomics, RRM domain, 99.22
3zzy_A130 Polypyrimidine tract-binding protein 1; protein bi 99.21
2e5i_A124 Heterogeneous nuclear ribonucleoprotein L-like; RR 99.2
1fje_B175 Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin 99.19
3smz_A284 Protein raver-1, ribonucleoprotein PTB-binding 1; 99.18
1fje_B175 Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin 99.17
2bz2_A121 Negative elongation factor E; NELF E, RNA recognit 99.15
2yh0_A198 Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli 99.15
1jmt_A104 Splicing factor U2AF 35 kDa subunit; RRM, RNA spli 99.14
2ghp_A292 U4/U6 snRNA-associated splicing factor PRP24; RNA 99.14
3sde_A261 Paraspeckle component 1; RRM, anti parallel right 99.11
3pgw_A282 U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c 99.11
2g4b_A172 Splicing factor U2AF 65 kDa subunit; protein-RNA c 99.1
2adc_A229 Polypyrimidine tract-binding protein 1; RBD, RRM, 99.09
1qm9_A198 Polypyrimidine tract-binding protein; ribonucleopr 99.09
3smz_A284 Protein raver-1, ribonucleoprotein PTB-binding 1; 99.09
3u1l_A240 PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 99.09
3tyt_A205 Heterogeneous nuclear ribonucleoprotein L; ferredo 99.04
2ghp_A292 U4/U6 snRNA-associated splicing factor PRP24; RNA 99.04
3sde_A261 Paraspeckle component 1; RRM, anti parallel right 99.03
3v4m_A105 Splicing factor U2AF 65 kDa subunit; canonical RNA 99.02
3ue2_A118 Poly(U)-binding-splicing factor PUF60; RNA recogni 99.01
1qm9_A198 Polypyrimidine tract-binding protein; ribonucleopr 98.97
3pgw_A282 U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c 98.97
2adc_A229 Polypyrimidine tract-binding protein 1; RBD, RRM, 98.96
2dit_A112 HIV TAT specific factor 1 variant; structural geno 98.96
3tht_A345 Alkylated DNA repair protein ALKB homolog 8; struc 98.89
2d9o_A100 DNAJ (HSP40) homolog, subfamily C, member 17; RRM 98.8
3s6e_A114 RNA-binding protein 39; ferredoxin-like, structura 98.6
3dxb_A222 Thioredoxin N-terminally fused to PUF60(UHM); spli 98.53
1owx_A121 Lupus LA protein, SS-B, LA; RRM, transcription; NM 98.47
2dnr_A91 Synaptojanin-1; RRM domain, RBD, structural genomi 98.46
1ufw_A95 Synaptojanin 2; RNP domain, structural genomics, r 98.14
2dhx_A104 Poly (ADP-ribose) polymerase family, member 10 var 97.06
2l9w_A117 U4/U6 snRNA-associated-splicing factor PRP24; RRM, 96.98
2kn4_A158 Immunoglobulin G-binding protein G, splicing FACT 94.52
2i2y_A150 Fusion protein consists of immunoglobin G- binding 90.44
1wwh_A119 Nucleoporin 35, nucleoporin; structural genomics, 82.37
1wey_A104 Calcipressin 1; structural genomics, RRM domain, r 82.34
3pq1_A464 Poly(A) RNA polymerase; nucleotidyl transferase, R 80.96
>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=8.5e-122  Score=1143.26  Aligned_cols=537  Identities=19%  Similarity=0.266  Sum_probs=434.7

Q ss_pred             CeEEecCCcccccCceecccCcCCCcEEEEEEeeCCCCCCCCCcccccccccccCcchhhHHHHHHHHHh----------
Q 001183          397 MKIYCLGPELETSNYVVKNFAKYASDFMRVTFVEEDWSKLPANALSTSIQRGIFSKPYRTKIYSRILTIL----------  466 (1131)
Q Consensus       397 t~i~~~~P~~e~sNRvlR~y~~~~d~FLRV~F~DE~~~~l~~~~~~~~~~~~~~~~~~~~~i~~Rv~~~L----------  466 (1131)
                      .++.|.+|+++.|||++|+|+  +||||||+|.+++....+..+.   +.    ..+   ..+++|.++|          
T Consensus       131 ~~l~L~p~~l~~s~R~~RrfG--sDrFL~V~fp~~~~~~~~~~~~---~~----~~~---~~~~~v~~~l~~~~~~~~gr  198 (1022)
T 2j7n_A          131 YLVKLKPLMFEQGCRLTRRFG--PDRFFEILIPSPTSTSPSVPPV---VS----KQP---AAVEEVIQWLTMGQHSLVGR  198 (1022)
T ss_dssp             EEEEECCCEEEECBHHHHHHC--GGGEEEEEEECTTCCCSSSCTT---SS----SSS---SCHHHHHHHHHSSCEEETTE
T ss_pred             eEEEecCCccCCCceEEEeeC--CceeEEEEecCCccccccccch---hc----cch---HHHHHHHHHHhcCcEEEecc
Confidence            488999999999999999999  5999999999986542211100   00    000   1234444444          


Q ss_pred             --------------------------------------hcCeEEcCeEEEEeeecccccccCeEEEEecCCCCCHHHHHH
Q 001183          467 --------------------------------------QDGIVIGDKHYEFLAFSASQLRNNSVWMFASNDEVSAEDVRG  508 (1131)
Q Consensus       467 --------------------------------------~~Gi~I~gr~y~FLafS~SqlR~~s~wff~~~~~~t~~~Ir~  508 (1131)
                                                            .+|+.|++++|+||++  ||+|++++|    ...+|+++||+
T Consensus       199 ~~r~f~~~d~~~r~~~~~~~l~~~~~~~~~~~Rv~~f~~~G~~i~~~~f~fl~~--s~lre~s~~----~~~ls~~~ir~  272 (1022)
T 2j7n_A          199 QWRAFFAKDAGYRKPLREFQLRAEDPKPIIKERVHFFAETGITFRPDVFKTRSV--VPAEEPVEQ----RTEFKVSQMLD  272 (1022)
T ss_dssp             EEEEEEEEECC--------------CCCCCEEEEEEEEEEETTCBCCCC---------------C----CBCCCHHHHHH
T ss_pred             eeEEEeeccccccccccccccccccccccccceEEEEeccCccccCcccccccc--ccccccccc----cCCCCHHHHHH
Confidence                                                  4555555555555555  455555555    23589999999


Q ss_pred             HcCCCCCCC--CHHHHHHHHhccccCCcceeeeeCCcEEEc-CCccccCCCCccccccccceecHHHHHHHHHHcCCCCC
Q 001183          509 WMGCFNKIR--SVSKCAARMGQLFSSSKQTLVVPVQDVEMI-PDVEVTSDGNTYCFSDGIGKISLSFARQVAQKCGLSHT  585 (1131)
Q Consensus       509 wmG~F~~i~--~vaK~aARigq~FSsT~~t~~i~~~~i~~I-~DI~~~~~g~~~~FTDG~G~IS~~la~~I~~~l~l~~~  585 (1131)
                      |||+|++++  +++|||||||||||+|.+++.|++++|..+ |||+. .+|++|+||||||+||++||++|++++++...
T Consensus       273 wmg~f~~n~~q~~aK~aARigq~FS~T~~tv~v~~~~I~~~~dDI~~-~~g~g~vFTDGvG~IS~~lA~~I~~~l~l~~~  351 (1022)
T 2j7n_A          273 WLLQLDNNTWQPHLKLFSRIQLGLSKTYAIMTLEPHQIRHHKTDLLS-PSGTGEVMNDGVGRMSRSVAKRIRDVLGLGDV  351 (1022)
T ss_dssp             HHHCGGGCTTSBHHHHHHTTHHHHSBCEEEEECCGGGEEECSSCCBC-TTSSCCBSSTTEEEECHHHHHHHHHHHTCSSC
T ss_pred             hccChhhcccchHHHHHHHhhhhhcCccCcEEechHHEEEcCCcccc-CCCCCCeecCCchHhhHHHHHHHHHHcCCCCC
Confidence            999998764  599999999999999999999999999875 78863 45678999999999999999999999999999


Q ss_pred             CceeEeecCCceEEEEeeCCC-C--ceEEeccccccccc-----cCcceeEEeec-CCccccccHHHHHHHhhCCCCHHH
Q 001183          586 PSAFQIRYGGYKGVIAVDRNS-F--RKLSLRRSMLKFES-----RNRMLNVTKWS-ESMPCFLNREIISLLSTLGVKDEV  656 (1131)
Q Consensus       586 PSAfQiR~gG~KGvl~vdp~~-~--~~I~lR~Sm~KF~s-----~~~~LeI~~~S-~~~p~~LNRQ~I~iL~~lGV~~~v  656 (1131)
                      |||||||||||||||+|||++ +  .+|+|||||.||++     .+++|||+++| ++.|++||||+|+||+++||++++
T Consensus       352 PSAfQiR~gGaKGvl~vdp~~~~~~~~I~lRpSm~KF~~~~~d~~~~~LEIv~~s~~~~~~~LNRQlI~lL~~lGV~~~~  431 (1022)
T 2j7n_A          352 PSAVQGRFGSAKGMWVIDVDDTGDEDWIETYPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVK  431 (1022)
T ss_dssp             CSEEEEEETTEEEEEEECTTCCSCCCCEEECTTTBCSCCCCCSGGGSEEEEEEECCCCCCCCBCTTTHHHHHHTBSSHHH
T ss_pred             CcEEEEEeccceEEEEECcccCCCcceEEeCCcceeecCCCCCcccCeEEEEeecCCCCCceecHHHHHHHHhCCcCHHH
Confidence            999999999999999999986 2  35999999999986     46899999998 589999999999999999999999


Q ss_pred             HHHHHHHHH--------HHHHHHhcCHHHHHHHHHhccC------------------CChHHHHHHHHHcCCCCCCcHHH
Q 001183          657 FEAMQQQQL--------ILLGKMLINREAALDVLQKLNG------------------VDSKNILVKMLLQGYEPNVEPYL  710 (1131)
Q Consensus       657 F~~lq~~~l--------~~l~~~l~d~~~a~~~L~~~~~------------------~~~~~~l~~ml~~Gf~~~~epfl  710 (1131)
                      |++++.+++        .....++.++..+.+++.....                  ...++++..|+.+||+|.++|||
T Consensus       432 f~~~i~~~~~~~L~~~l~~~~~al~~~~~~r~~l~~~~~~~~~r~~~g~~~~~~glp~s~~~~l~~Ll~aGf~p~~epfL  511 (1022)
T 2j7n_A          432 MRQAIGDRLINDLQRQFSEQKHALNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNFLMNSGFDPKKQKYL  511 (1022)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSHHHHHHHHHHHSCCHHHHHHHTSCCEETTEESSHHHHHHHHHHTTCCTTTBHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhhccccccccccccchhhccCccchHHHHHHHHHcCCCccccHHH
Confidence            988765543        2334566777777776643211                  12346788999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhcceeeeecCceEEEEEecCCCCCCCCcEEEEEccchhhhhccccccccccCCcceeEe-eeEEE
Q 001183          711 SMMLLSHHENQLSDLKSRCRIYVPKGRLLIGCFDETGILNYGQVFVRVTMTREELESKDQSFFHRVDDKTSIVK-GKVLV  789 (1131)
Q Consensus       711 ~~~L~~~~~~~l~~lk~K~rI~Vp~s~~l~GV~DetG~L~~GEVfv~~s~~~~~~~~~~~~~~~~~~~~~~vi~-G~VlV  789 (1131)
                      +++++.+++.+|+.||+|+||+||+|++||||+||||+|+||||||+++....           .......++. |+|+|
T Consensus       512 ~~~l~~~~~~~l~~LK~k~rI~V~~s~~L~GV~DetG~L~eGEVfv~~s~~~~-----------~~~~~~~~l~gg~VlV  580 (1022)
T 2j7n_A          512 QDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFSSKFR-----------DEEESFTLLSDCDVLV  580 (1022)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCBCCSSEEEEEEEECTTSCCCTTEEEEEEEEEEE-----------ETTEEEEEECSEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHhhccccccceEEEEEecCCCccCCCeEEEEeccccc-----------cCCCCceeecCceEEE
Confidence            99999999999999999999999999999999999999999999999986311           1112334565 69999


Q ss_pred             eeCCCCCCCCeeEEEEEccCcccccCCcceEEecCCCCCCCCCcCCCCCCCCCeEEEeecCCCCCCCCCCCCCCCCC---
Q 001183          790 TKNPCLHPGDVRVLEAVYEMKLEEKDYVDCIIFPQKGERPHPNECSGGDLDGDIFFISWDNDLIPCETEPPMDYTGR---  866 (1131)
Q Consensus       790 ~RnP~lhPGDIr~v~AV~~P~L~~~hl~dvIVFp~kG~Rplps~lSGGDLDGD~y~ViWD~~Lvp~~~~~P~~Y~~~---  866 (1131)
                      +|||||||||||+|+||++|+|  |||+||||||++|+||+||||||||||||+|||||||+|||++.+.|+...+.   
T Consensus       581 tRnP~lhPGDIrvv~AV~~PeL--~hL~DvIVFp~kG~Rplps~lSGGDLDGD~Y~ViWD~~Lv~~f~na~~p~~p~~~~  658 (1022)
T 2j7n_A          581 ARSPAHFPSDIQRVRAVFKPEL--HSLKDVIIFSTKGDVPLAKKLSGGDYDGDMAWVCWDPEIVDGFVNAEMPLEPDLSR  658 (1022)
T ss_dssp             ECSSCCSGGGEEEEEECCCGGG--TTCCSEEEECSCSSSCHHHHTTTCCSSSCEEEEECCHHHHHTBCCCCCCCCCCCTT
T ss_pred             EeCCCcCcCceeEEEeccChhh--hccCCeEEccCCCCCCChhHhcCCCCCCCeEEEEechhhcccccCCCCCCCCchhh
Confidence            9999999999999999999999  99999999999999999999999999999999999999999987665543221   


Q ss_pred             ----ccccC----C--------CCCCHH-HHHHHHHHhhccCchhHHHHHHHHhcccCCCCCCCHHHHHHHHHHHhcccc
Q 001183          867 ----RSRIM----D--------HDVTLE-EIHKFFVDYMINDTLGAISTAHLVHADRDPDKARSSKCLHLATLHSMAVDF  929 (1131)
Q Consensus       867 ----~~~~l----~--------~~vt~~-di~~ffv~ym~~d~LG~is~~Hl~~aD~~~~g~~~~~cl~LA~L~S~AVD~  929 (1131)
                          ....+    +        ++++.+ .|.+||+.||++|.||+|||+|+..+|+. .|+.+++|++||+|||+||||
T Consensus       659 y~~k~~~~~~~~~~~~~~g~~~~~~~~~d~i~~ff~~~m~~d~LG~is~~h~~~~~~~-~g~~~~~cl~LA~L~S~AVD~  737 (1022)
T 2j7n_A          659 YLKKDKTTFKQLMASHGTGSAAKEQTTYDMIQKSFHFALQPNFLGMCTNYKERLCYIN-NSVSNKPAIILSSLVGNLVDQ  737 (1022)
T ss_dssp             TSEECCCBHHHHHTTTCSSHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHH-TCSSSHHHHHHHHHHHHHTTH
T ss_pred             hccccccchhhhhhccccccccCchhHHHHHHHHHHHhcCcchHHHHHHHHHHHHhhc-CCCCCHHHHHHHHHHHHhhCc
Confidence                11111    0        112334 45679999999999999999999888764 799999999999999999999


Q ss_pred             cCCCCCCCC--CccCCCCCCCcccCCCCCCcccccchhhH
Q 001183          930 AKTGAPAEM--PLALKPKEFPDFMEREDKPRYISFGVLGK  967 (1131)
Q Consensus       930 ~KTG~~v~l--p~~l~~~~~PdFm~k~~~~~Y~S~kiLGk  967 (1131)
                      ||||+|+++  ++.++|+.+||||+ .++|+|+|++++|+
T Consensus       738 ~KtG~pv~~~~~~~lr~~~~p~~m~-~~~p~Y~s~~~~g~  776 (1022)
T 2j7n_A          738 SKQGIVFNEASWAQLRRELLGGALS-LPDPMYKSDSWLGR  776 (1022)
T ss_dssp             HHHTEECCHHHHHHHHHHHSCCSSC-CCCCGGGSSSCCSS
T ss_pred             cccCcccChhhhhhhhHhhCCCCCC-CCCCccccCcccCC
Confidence            999999998  77889999999999 67899999988877
>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens} Back     alignment and structure
>2lxi_A RNA-binding protein 10; NMR {Homo sapiens} Back     alignment and structure
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Back     alignment and structure
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Back     alignment and structure
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0 Back     alignment and structure
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Back     alignment and structure
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Back     alignment and structure
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Back     alignment and structure
>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae} Back     alignment and structure
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Back     alignment and structure
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Back     alignment and structure
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Back     alignment and structure
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Back     alignment and structure
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A* Back     alignment and structure
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Back     alignment and structure
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Back     alignment and structure
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Back     alignment and structure
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Back     alignment and structure
>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Back     alignment and structure
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Back     alignment and structure
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Back     alignment and structure
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Back     alignment and structure
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Back     alignment and structure
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Back     alignment and structure
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Back     alignment and structure
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Back     alignment and structure
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Back     alignment and structure
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Back     alignment and structure
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Back     alignment and structure
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Back     alignment and structure
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Back     alignment and structure
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Back     alignment and structure
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Back     alignment and structure
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Back     alignment and structure
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Back     alignment and structure
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Back     alignment and structure
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Back     alignment and structure
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Back     alignment and structure
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Back     alignment and structure
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens} Back     alignment and structure
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Back     alignment and structure
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Back     alignment and structure
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Back     alignment and structure
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Back     alignment and structure
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Back     alignment and structure
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Back     alignment and structure
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Back     alignment and structure
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Back     alignment and structure
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Back     alignment and structure
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Back     alignment and structure
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Back     alignment and structure
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Back     alignment and structure
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Back     alignment and structure
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Back     alignment and structure
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Back     alignment and structure
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Back     alignment and structure
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Back     alignment and structure
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Back     alignment and structure
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Back     alignment and structure
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Back     alignment and structure
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Back     alignment and structure
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Back     alignment and structure
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Back     alignment and structure
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Back     alignment and structure
>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Back     alignment and structure
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Back     alignment and structure
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Back     alignment and structure
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Back     alignment and structure
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Back     alignment and structure
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Back     alignment and structure
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Back     alignment and structure
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B Back     alignment and structure
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Back     alignment and structure
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Back     alignment and structure
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Back     alignment and structure
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Back     alignment and structure
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Back     alignment and structure
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Back     alignment and structure
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Back     alignment and structure
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Back     alignment and structure
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Back     alignment and structure
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Back     alignment and structure
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Back     alignment and structure
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Back     alignment and structure
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Back     alignment and structure
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Back     alignment and structure
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Back     alignment and structure
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Back     alignment and structure
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Back     alignment and structure
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Back     alignment and structure
>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Back     alignment and structure
>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Back     alignment and structure
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Back     alignment and structure
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Back     alignment and structure
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Back     alignment and structure
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Back     alignment and structure
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Back     alignment and structure
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Back     alignment and structure
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Back     alignment and structure
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Back     alignment and structure
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E Back     alignment and structure
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Back     alignment and structure
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Back     alignment and structure
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Back     alignment and structure
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Back     alignment and structure
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Back     alignment and structure
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Back     alignment and structure
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Back     alignment and structure
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Back     alignment and structure
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Back     alignment and structure
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E Back     alignment and structure
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Back     alignment and structure
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Back     alignment and structure
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Back     alignment and structure
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Back     alignment and structure
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Back     alignment and structure
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A Back     alignment and structure
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Back     alignment and structure
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Back     alignment and structure
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Back     alignment and structure
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A* Back     alignment and structure
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Back     alignment and structure
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157} Back     alignment and structure
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Back     alignment and structure
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Back     alignment and structure
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens} Back     alignment and structure

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query1131
d1cvja180 Poly(A)-binding protein {Human (Homo sapiens) [Tax 99.68
d1b7fa182 Sex-lethal protein {Drosophila melanogaster [TaxId 99.66
d2cqda1103 RNA-binding region containing protein 1 {Human (Ho 99.65
d1fxla182 Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9 99.65
d2cqba189 Peptidyl-prolyl cis-trans isomerase E, N-terminal 99.65
d1x5ua193 Splicing factor 3B subunit 4 {Human (Homo sapiens) 99.63
d1l3ka184 Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human 99.63
d1hd0a_75 Heterogeneous nuclear ribonucleoprotein d0 {Human 99.63
d1h2vz_93 CBP20, 20KDa nuclear cap-binding protein {Human (H 99.63
d2cqca183 Arginine/serine-rich splicing factor 10 {Human (Ho 99.63
d2u2fa_85 Splicing factor U2AF 65 KDa subunit {Human (Homo s 99.62
d1whwa_99 Probable RNA-binding protein 19, Rbm19 {Mouse (Mus 99.62
d2cqga190 TAR DNA-binding protein 43, TDP-43 {Human (Homo sa 99.62
d1uawa_77 Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} 99.62
d2cq0a190 Eukaryotic translation initiation factor 3 subunit 99.62
d1p1ta_104 Cleavage stimulation factor, 64 kda subunit {Human 99.62
d1l3ka279 Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human 99.62
d2cq4a1101 RNA binding protein 23 {Human (Homo sapiens) [TaxI 99.61
d1x0fa175 Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s 99.61
d1rk8a_88 RNA-binding protein 8 {Fruit fly (Drosophila melan 99.61
d1fxla285 Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9 99.61
d1x5sa190 Cold-inducible RNA-binding protein {Human (Homo sa 99.6
d1b7fa285 Sex-lethal protein {Drosophila melanogaster [TaxId 99.6
d2cpza1102 CUG triplet repeat RNA-binding protein 1 {Human (H 99.6
d2cpha194 Probable RNA-binding protein 19, Rbm19 {Mouse (Mus 99.6
d1no8a_78 Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1 99.59
d2ghpa181 U4/U6 snRNA-associated-splicing factor PRP24 {Bake 99.59
d1x5ta183 Splicing factor 3B subunit 4 {Human (Homo sapiens) 99.59
d2cpfa185 Probable RNA-binding protein 19, Rbm19 {Mouse (Mus 99.59
d1u6fa1139 RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId 99.58
d2ghpa386 U4/U6 snRNA-associated-splicing factor PRP24 {Bake 99.58
d1x4ba1103 Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu 99.57
d1cvja289 Poly(A)-binding protein {Human (Homo sapiens) [Tax 99.57
d1x4ha198 RNA-binding protein 28 {Mouse (Mus musculus) [TaxI 99.57
d2msta_75 Neural RNA-binding protein Musashi-1 {Mouse (Mus m 99.56
d2cq3a193 RNA-binding protein 9 {Human (Homo sapiens) [TaxId 99.55
d2cqia190 Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960 99.54
d2cpea1101 RNA-binding protein EWS {Human (Homo sapiens) [Tax 99.53
d1zh5a285 Lupus LA protein {Human (Homo sapiens) [TaxId: 960 99.51
d1x4ea172 RNA-binding motif, single-stranded-interacting pro 99.51
d2disa196 Hypothetical protein FLJ20273 {Human (Homo sapiens 99.51
d2cpia189 E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc 99.5
d1x5oa1101 RNA-binding motif, single-stranded-interacting pro 99.49
d1fjeb191 Nucleolin {Golden hamster (Mesocricetus auratus) [ 99.49
d2f9da1114 Pre-mRNA branch site protein p14 {Human (Homo sapi 99.47
d2cpxa1102 RNA-binding protein 41, RBM41 {Human (Homo sapiens 99.47
d2ghpa275 U4/U6 snRNA-associated-splicing factor PRP24 {Bake 99.45
d2cqpa186 RNA-binding protein 12 {Mouse (Mus musculus) [TaxI 99.45
d2adca1109 Polypyrimidine tract-binding protein {Human (Homo 99.44
d1wi8a_104 Eukaryotic translation initiation factor 4B {Human 99.43
d1x4aa195 Splicing factor, arginine/serine-rich 1, SFRS1 {Hu 99.42
d1x4ga196 Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960 99.42
d2adca288 Polypyrimidine tract-binding protein {Human (Homo 99.41
d1whxa_111 Probable RNA-binding protein 19, Rbm19 {Mouse (Mus 99.41
d2cpya1103 RNA-binding protein 12 {Human (Homo sapiens) [TaxI 99.4
d2bz2a179 Negative elongation factor E, NELF-E {Human (Homo 99.39
d2cpda186 APOBEC1 stimulating protein {Human (Homo sapiens) 99.39
d1wg5a_104 Heterogeneous nuclear ribonucleoprotein H' {Human 99.38
d3begb187 Splicing factor, arginine/serine-rich 1, SFRS1 {Hu 99.38
d2cqha180 IGF-II mRNA-binding protein 2 isoform A {Human (Ho 99.38
d1fjca_96 Nucleolin {Golden hamster (Mesocricetus auratus) [ 99.38
d1wf2a_98 Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu 99.38
d1nu4a_91 Splicesomal U1A protein {Human (Homo sapiens) [Tax 99.37
d2cpja186 Non-POU domain-containing octamer-binding protein, 99.36
d1wi6a175 Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M 99.35
d1u2fa_90 Splicing factor U2AF 65 KDa subunit {Human (Homo s 99.35
d1wf0a_88 TAR DNA-binding protein 43, TDP-43 {Human (Homo sa 99.35
d1weza_102 Heterogeneous nuclear ribonucleoprotein H' {Human 99.34
d2cq1a188 Polypyrimidine tract-binding protein 2, PTBP2 {Hum 99.34
d1wg1a_88 Probable RNA-binding protein KIAA1579 {Human (Homo 99.34
d2b0ga183 Splicesomal U1A protein {Drosophila melanogaster [ 99.33
d1wexa_104 Heterogeneous nuclear ribonucleoprotein L-like {Mo 99.31
d1u1qa_183 Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human 99.3
d1wela1112 RNA-binding protein 12 {Human (Homo sapiens) [TaxI 99.29
d2adba1108 Polypyrimidine tract-binding protein {Human (Homo 99.28
d1wg4a_98 Splicing factor, arginine/serine-rich 9 (SFRS9) {M 99.28
d1whya_97 Putative RNA-binding protein 15B, Rbm15b {Mouse (M 99.26
d1x4fa199 Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} 99.25
d1x4da189 Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} 99.23
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_104 U2 99.12
d1u1qa_183 Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human 99.11
d1weya_104 Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090 99.07
d1wwha181 Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090 98.9
d1owxa_113 Lupus LA protein {Human (Homo sapiens) [TaxId: 960 98.89
d2cq2a1101 Alkylation repair AlkB homolog 8, ALKBH8 {Human (H 98.86
d2dita199 HIV Tat-specific factor 1 {Human (Homo sapiens) [T 98.77
d1o0pa_104 Splicing factor U2AF 65 KDa subunit {Human (Homo s 98.64
d2dgxa173 Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960 86.98
>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=5.3e-17  Score=144.78  Aligned_cols=79  Identities=14%  Similarity=0.207  Sum_probs=75.6

Q ss_pred             EEEEeCCCCcCCHHHHHHHHhhccCCceEEEEEEeecCCCCCccceEEEEeCChHHHHHHHHhhcCCCceecCceeEeec
Q 001183            5 TVWVSNIPQTAIAKDLLLFLESKLGKNSVFALEIITDRSNWKSRGIGRVQFTSLDFKSKAQNLSLNDKLVFNSQNLKISE   84 (1131)
Q Consensus         5 ti~Vgnl~~~~t~~~L~~~fe~~~G~G~V~~~~i~~dr~tg~sRgfgfV~f~~~e~A~~Ai~~~~~~~~~~~gr~L~V~~   84 (1131)
                      +|||||||+.+|+++|+++|+++   |.|.+|+|..|+.||++||||||+|.++++|..|++.+  ||..++||.|+|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~---G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l--~g~~~~gr~i~v~~   76 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPA---GPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM--NFDVIKGKPVRIMW   76 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGG---SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTS--TTCEETTEECEEEE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHh---CCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHc--CCCEECCEEEEEEE
Confidence            69999999999999999999997   69999999999999999999999999999999999999  48999999999999


Q ss_pred             CCCC
Q 001183           85 THSD   88 (1131)
Q Consensus        85 a~~~   88 (1131)
                      |..|
T Consensus        77 a~~d   80 (80)
T d1cvja1          77 SQRD   80 (80)
T ss_dssp             CCCC
T ss_pred             eCCC
Confidence            8765
>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Back     information, alignment and structure
>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Back     information, alignment and structure
>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Back     information, alignment and structure
>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure