Citrus Sinensis ID: 002823

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------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------
Protein Sequence
MGAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGNLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLAIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPPTESAFHLGISSSVPSLVRMESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIKPPEIIDSRHFSRVSSNGHSIGFTEVFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAESPEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMMFSGRGQTIPLMNSFDPPNERARNRRNEGAVNQADKKQYELDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVNFRTRPGKARSVIHEENHHGSPPNVEDLSNGDAPSGSAKESD
Secondary Structure (PSIPRED)
cccccccccccccHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHccccccHHcccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEccccccccccccccEEEEEEcccccccHHHHHHHHcccccEEEEEEccccccEEEEEEccHHHHHHHHHHHccccccccEEEEcccccHHHHHHHHHccccHHHHHHccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccHHHHccccccccEEEcccccccccHHHHHHHHHHcccccccEEEEccccccccccEEEEEEccccccHHHHHHHHcccccccccccEEEEEEEHHHHHHHHHHHHHccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccHHcccccccccccHHHHHHHHHccccccHHHHHHccccccccccccccccccccHHHHHHccccccEEEcccccccccccccEcccccccccccccccccccccccccccEEEEEEcccccccHHHHHHHHHHHccEEEEEEccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEEccccccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEEcccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEcccccccHHHHHccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccEEEcHHHHHccccccEEEEEEcccccccHHHHHHHHHHHccccEEEEEEEEcccccccEEEEEEEcccHHHHHHHHHHHccccccEcccHHHHHHHHHHHccHHHHHHHHccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mgaqyesslFSSSLSELFSRKLrlssdiasyghsvdtvsshyeeeepfeslEEIEAQTIgnllpddddlfsgvtdglectvhpsggsggddmddldffssvggmdlgndssyvaqkkseicigfsnhelgvcngavagehlndehpsRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLtrsgkldihysipkdnpsekeinqgTLVVFNLdssvsndelhHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIagkqiklepshLRGLRKClanqlppeleqeecgsyqqqnsppnkptnesagMITIVISLPLNVKSLAIIYLFTGafahgskssritdtcivsvvpsavkapptesafhlgisssvpslvrmesfgtqsalaepghlqgqlkfnirstpsfhphslpechdglnkgvrcnssgtkganinikppeiidsrhfsrvssnghsigftevfgsasngscprpghqyswnnsycpqlpgmmwpnspslvsgifntysptrvhglprapshmvntvlpigshhvgsaptvdpslweRQHAyvaespeasgfhlgshgsmrisnnslhsvefvshnifpcvggngmdmplpsknsvfqshhqrsmmfsgrgqtiplmnsfdppnerarnrrnegavnqadkkqYELDIDRIlrgednrttLMIKNIPNKYTSKMLLAAIDERhkgtydfiylpidfknkcnvgyafinmtdpsqivpfyqsfngkkwekfNSEKVASLAYARIQGKAALIAHFQnsslmnedkrcrpilfntdgpnagdqvpfpmgvnfrtrpgkarsviheenhhgsppnvedlsngdapsgsakesd
Flexible Loop (DISEMBL)
MGAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGNLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIhysipkdnpsekeiNQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLAIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPPTESAFHLGISSSVPSLVRMESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTkganinikppeiidSRHFSRVSSNGHSIGFTEVFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAESPEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMMFSGRGQTIPLMNSFDPPNERarnrrnegavnqadkkqyeldidrilrgednrttlmiknipnkytSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVNFRTRPGKARSVIHEENhhgsppnvedlsngdapsgsakesd
Low Complexity Region (SEG)
MGAQYesslfssslselfsrklrlssDIASYGHSVDTVSSHYeeeepfesleeieAQTIGNLLPDDDDLFSGVTDGLECTVHPsggsggddmddldffssVGGMDLGNDSSYVAQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLAIIYLFTGAFAHGSKSSRITDTCIvsvvpsavkappTESAFHLGISSSVPSLVRMESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIKPPEIIDSRHFSRVSSNGHSIGFTEVFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAESPEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMMFSGRGQTIPLMNSFDPPnerarnrrnegavnQADKKQYELDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVNFRTRPGKARSVIHEENHHGSPPNVEDLSNGDAPSGSAKESD
Disordered region (IsUnstruct)
**********************************************************IGNLLPDDDDLFSGVTDGLECTV**************DFFSSVGGMDLGNDSSYVAQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMK***********LDIHY************NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCL*******************************GMITIVISLPLNVKSLAIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVK*******FHLG*****************************************************************************************SIGFTEVFG**********GHQYSWNNSYCPQLPGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYV**********************SLHSVEFVSHNIFPCVGGN************************************************************ELDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNT*********************************************************
Disordered Region (DISOPRED)
*********FSSSLSE****************************************QTIGNLLPDDDDLFSGVTDGLECTV**************DFFSSVGG*********************************************TLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH*****************LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL*****************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************YELDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQV************************************************
Disordered Region (DISEMBL)
**************SELFSRKLRLSSDIASYGHSVD**************LEEIEAQTIGNLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPP*********************NESAGMITIVISLPLNVKSLAIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPPTESAFHLGISSSVPSLVRMESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIKPPEIIDSRHFSRVSSNGHSIGFTEVFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAESPEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMMFSGRGQTIPLMNSFDPPNERARNRRNEGAVNQADKKQYELDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVNFRTRPGKARSVIHEENHHGSPPNV*****************
Disordered Region (DISPRO)
**********************************************PFESLEEIEAQTIGNLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEICIGFSN********A****H**DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR**R***************C***********************************I*YL******H*SKSS**T*TCIVSVVPSA****************SVPSLVRMESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIKPPEIIDSRHFSRVSSNGHSIGFTEVFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAESPEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMMFSGRGQT***************************KKQYELDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTD********PFP*********************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGNLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLAIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPPTESAFHLGISSSVPSLVRMESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIKPPEIIDSRHFSRVSSNGHSIGFTEVFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAESPEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMMFSGRGQTIPLMNSFDPPNERARNRRNEGAVNQADKKQYELDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVNFRTRPGKARSVIHEENHHGSPPNVEDLSNGDAPSGSAKESD
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	876	2.2.26 [Sep-21-2011]
Q64M78	1001	Protein MEI2-like 4 OS=Or	yes	no	0.964	0.844	0.524	0.0
Q8W4I9	915	Protein MEI2-like 1 OS=Ar	yes	no	0.878	0.841	0.494	0.0
Q9LYN7	907	Protein MEI2-like 4 OS=Ar	no	no	0.866	0.836	0.474	1e-176
Q75M35	955	Protein MEI2-like 3 OS=Or	yes	no	0.884	0.811	0.432	1e-164
Q8VWF5	800	Protein MEI2-like 5 OS=Ar	no	no	0.372	0.407	0.521	1e-84
Q6ZI17	848	Protein MEI2-like 2 OS=Or	no	no	0.363	0.375	0.511	5e-82
Q9SVV9	759	Protein MEI2-like 3 OS=Ar	no	no	0.311	0.359	0.542	5e-79
Q6EQX3	811	Protein MEI2-like 5 OS=Or	no	no	0.323	0.348	0.505	2e-75
Q9SJG8	843	Protein MEI2-like 2 OS=Ar	no	no	0.325	0.338	0.471	7e-67
P08965	750	Meiosis protein mei2 OS=S	yes	no	0.184	0.216	0.490	5e-38

>sp|Q64M78|OML4_ORYSJ Protein MEI2-like 4 OS=Oryza sativa subsp. japonica GN=ML4 PE=2 SV=1

 Score =  773 bits (1996), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 468/893 (52%), Positives = 587/893 (65%), Gaps = 48/893 (5%)

Query: 2    GAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGN 61
            GA  E+ LFSSS+S++F +KLRL+S     G S++ V  ++ ++EPFE  EEIEAQ IGN
Sbjct: 137  GAYNENGLFSSSVSDIFDKKLRLTSKNGLVGQSIEKVDLNHVDDEPFELTEEIEAQIIGN 196

Query: 62   LLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEIC 121
            LLPDDDDL SGV D +    +P+  +  DD DD  F++  GGM+L  D +    KK +  
Sbjct: 197  LLPDDDDLLSGVVDEVG---YPTNANNRDDADDDIFYTG-GGMELETDEN----KKLQEF 248

Query: 122  IGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRAS 181
             G +N  +G+ NG + GEHL  E PSRTL +R INSN+EDSELK LFE +GD+R  Y A 
Sbjct: 249  NGSANDGIGLLNGVLNGEHLYREQPSRTLFVRNINSNVEDSELKLLFEHFGDIRALYTAC 308

Query: 182  KHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLD 241
            KH GFV ISYYDIR+A NA   LQNK  R  KLDIHYSIPKDNPSEK+INQGT+V+FN+D
Sbjct: 309  KHRGFVMISYYDIRSALNAKMELQNKALRRRKLDIHYSIPKDNPSEKDINQGTIVLFNVD 368

Query: 242  SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL 301
             S++ND+LH IFG YGEIKEIR+TPQK H K IEFYD RAAEAALR LN   IAGK+IKL
Sbjct: 369  LSLTNDDLHKIFGDYGEIKEIRDTPQKGHHKIIEFYDVRAAEAALRALNRNDIAGKKIKL 428

Query: 302  EPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLA 361
            E S L   R+ L+  +  EL QEE G  +  +   + P   S G   +        ++ +
Sbjct: 429  ETSRLGAARR-LSQHMSSELCQEEFGVCKLGSPSTSSPPIASFGSTNLATITSTGHENGS 487

Query: 362  IIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPPTESAFHLGISSSVPSLVRMESFGTQ 421
            I  + +G     S+    +   + S +P ++  P       +GISS         +   Q
Sbjct: 488  IQGMHSGLQTSISQFRETSFPGLSSTIPQSLSTP-------IGISSGA-------THSNQ 533

Query: 422  SALAEP----GHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGV--RCNSSGTKGANINIK 475
            +AL E     G + G + ++ +   + HPHSLPE H+G+N GV    NS        N +
Sbjct: 534  AALGEISQSLGRMNGHMNYSFQGMSALHPHSLPEVHNGVNNGVPYNLNSMAQVVNGTNSR 593

Query: 476  PPEIIDSRHFSRVSS---NGHSIGFTE-VFGSASNGSCPRPGHQYSWNNS----YCPQLP 527
              E +D+RH  +V S   NGHS    E   G + +GS    GHQ  WNNS    + P  P
Sbjct: 594  TAEAVDNRHLHKVGSGNLNGHSFDRAEGALGFSRSGSSSVRGHQLMWNNSSNFHHHPNSP 653

Query: 528  GMMWPNSPSLVSGIFNTYSPTRVHGLPRAPS-HMVNTVLPIGSHHVGSAPTVDPSLWERQ 586
             ++WP+  S V+ +  + SP ++HG+PRAPS HM++ VLP+   HVGSAP ++PSLW+R+
Sbjct: 654  -VLWPSPGSFVNNV-PSRSPAQMHGVPRAPSSHMIDNVLPMHHLHVGSAPAINPSLWDRR 711

Query: 587  HAYVAESPEASGFHLGSHGSMRISNN-SLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQ 645
            H Y  E  EA  FH GS GSM    +  LHS+E   +NI+P  GGN MD  +        
Sbjct: 712  HGYAGELTEAPNFHPGSVGSMGFPGSPQLHSMEL--NNIYPQTGGNCMDPTVSPAQIGGP 769

Query: 646  SHHQRSMMFSGRGQTIPLMNSFDPPNERARNRRNEGAVNQAD-KKQYELDIDRILRGEDN 704
            S  QR  MF GR   +PL  SFD P ER R+RRN+   NQ+D KKQYELD+DRI+RG+D+
Sbjct: 770  SPQQRGSMFHGRNPMVPLP-SFDSPGERMRSRRNDSNGNQSDNKKQYELDVDRIVRGDDS 828

Query: 705  RTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVP 764
            RTTLMIKNIPNKYTSKMLLAAIDE HKGTYDFIYLPIDFKNKCNVGYAFINMT+P  I+P
Sbjct: 829  RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFIYLPIDFKNKCNVGYAFINMTNPQHIIP 888

Query: 765  FYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNA 824
            FYQ+FNGKKWEKFNSEKVASLAYARIQGK+ALIAHFQNSSLMNEDKRCRPILF++DGPNA
Sbjct: 889  FYQTFNGKKWEKFNSEKVASLAYARIQGKSALIAHFQNSSLMNEDKRCRPILFHSDGPNA 948

Query: 825  GDQVPFPMGVNFRTRPGKARSVIHEENHHG---SPPNVEDLSNGDAPSGSAKE 874
            GDQ PFPMG N R R G++R+   EE+H     +  N +  +NG   +G AK+
Sbjct: 949  GDQEPFPMGTNIRARSGRSRASSGEESHQDISITSVNCDTSTNGVDTTGPAKD 1001

Probable RNA-binding protein that may play a role in growth regulation.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8W4I9|AML1_ARATH Protein MEI2-like 1 OS=Arabidopsis thaliana GN=ML1 PE=1 SV=1

 Score =  645 bits (1663), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 432/873 (49%), Positives = 529/873 (60%), Gaps = 103/873 (11%)

Query: 2   GAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGN 61
           G+Q+ESSLFSSS+S+LFSRKLRL         S +TV +H  EEEP ESLEEIEAQTIGN
Sbjct: 85  GSQWESSLFSSSMSDLFSRKLRLQGSDMLSTMSANTVVTH-REEEPSESLEEIEAQTIGN 143

Query: 62  LLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDS-SYVAQKKSEI 120
           LLPD+DDLF+ VT  +      S  + GD++D+ D FSSVGGM+L  D  S V+ +    
Sbjct: 144 LLPDEDDLFAEVTGEVG---RKSRANTGDELDEFDLFSSVGGMELDGDIFSSVSHR---- 196

Query: 121 CIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA 180
                N E G  N    GE    E PSRTLL+  I+SN+ED ELK LFEQ+GD++  + A
Sbjct: 197 -----NGERGGNNSV--GELNRGEIPSRTLLVGNISSNVEDYELKVLFEQFGDIQALHTA 249

Query: 181 SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNL 240
            K+ GF+ +SY DIRAA+NA ++LQNKL R  KLDI YSI K+NPS+K+ ++G L+V NL
Sbjct: 250 CKNRGFIMVSYCDIRAAQNAARALQNKLLRGTKLDIRYSISKENPSQKDTSKGALLVNNL 309

Query: 241 DSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK 300
           DSS+SN EL+ +   YGE+KEIR T     Q YIEF+D RAA AAL  LN   +AGK+++
Sbjct: 310 DSSISNQELNRLVKSYGEVKEIRRTMHDNSQIYIEFFDVRAAAAALGGLNGLEVAGKKLQ 369

Query: 301 LEPSHLRGLR---KCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNV 357
           L P++  G R   +C AN      + E C        P    +N S+G I          
Sbjct: 370 LVPTYPEGTRYTSQCAAN------DTEGC-------LPKTSYSNTSSGHI---------- 406

Query: 358 KSLAIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPPT---ESAFHLGISSSVPSLVR 414
                     G    G  SS  +D   + V+ +++ +P     E    L I    P    
Sbjct: 407 ----------GRHFPGMISSTSSDGGSMRVIHNSIGSPVNSFIERHRSLSIPIGFPPSAN 456

Query: 415 MESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINI 474
             S      L E GH        I+S P+ HPHS  E  D    G    SS         
Sbjct: 457 GISASKPVGLQEHGHHFDNSNMGIQSMPNLHPHSFSEYVDNFANGSPYTSSA-------- 508

Query: 475 KPPEIIDSRHFSRVSSNG---------HSIGFTEVFGSASNGSCPRPGHQYS------WN 519
                     FS + S+G         H++   E F   S G    P HQ S      W+
Sbjct: 509 ----------FSEMVSDGSKANEGFMIHNVRGVEGF---SGGGIGSPMHQSSRRPINLWS 555

Query: 520 NSYCPQL---PGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAP 576
           NS   Q     GMMWPNSPS ++ I     P  V    RAP  MVN       HH+GSAP
Sbjct: 556 NSNTQQQNPSSGMMWPNSPSHINSIPTQRPPVTV--FSRAPPIMVNMASSPVHHHIGSAP 613

Query: 577 TVDPSLWERQHAYVAESPEASGFHLGSHGSMRISNNS-LHSVEFVSHNIFPCVGGNGMDM 635
            ++   W+R+ AYVAES E+SGFH+GSHGSM I  +S  H ++  SH  F  VGGN MD 
Sbjct: 614 VLNSPFWDRRQAYVAESLESSGFHIGSHGSMGIPGSSPSHPMDIGSHKTF-SVGGNRMD- 671

Query: 636 PLPSKNSVFQSHHQRSMMFSGRGQTIPLMNSFDPPNERARN---RRNEGAVNQADKKQYE 692
            + S+N+V +S  Q S +F GR     +  SFD PNER RN   RR+E + + ADKK YE
Sbjct: 672 -VNSQNAVLRSPQQLSHLFPGRSPMGSMPGSFDSPNERYRNLSHRRSESSSSNADKKLYE 730

Query: 693 LDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYA 752
           LD+DRILRGED RTTLMIKNIPNKYTSKMLL+AIDE  KGTYDF+YLPIDFKNKCNVGYA
Sbjct: 731 LDVDRILRGEDRRTTLMIKNIPNKYTSKMLLSAIDEHCKGTYDFLYLPIDFKNKCNVGYA 790

Query: 753 FINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRC 812
           FIN+ +P +IVPF+++FNGKKWEKFNSEKVA+L YARIQGK ALIAHFQNSSLMNEDKRC
Sbjct: 791 FINLIEPEKIVPFFKAFNGKKWEKFNSEKVATLTYARIQGKTALIAHFQNSSLMNEDKRC 850

Query: 813 RPILFNTDGPNAGDQVPFPMGVNFRTRPGKARS 845
           RPILF+TDGPNAGDQ PFPMG N R+RPGK RS
Sbjct: 851 RPILFHTDGPNAGDQEPFPMGSNIRSRPGKPRS 883

Probable RNA-binding transcriptional activator that plays a role in meiosis and vegetative growth. May be a downstream effector of TOR signaling pathway and recruited by RAPTOR1 for TOR substrate.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LYN7|AML4_ARATH Protein MEI2-like 4 OS=Arabidopsis thaliana GN=ML4 PE=1 SV=1

 Score =  618 bits (1593), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 392/826 (47%), Positives = 497/826 (60%), Gaps = 67/826 (8%)

Query: 56  AQTIGNLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDS-SYVA 114
           AQTIGNLLPD+DDLF+ V   +   VH S  +GGDD+DD D FSSVGGM+L  D  S V+
Sbjct: 131 AQTIGNLLPDEDDLFAEV---VGEGVHKSRANGGDDLDDCDLFSSVGGMELDGDVFSSVS 187

Query: 115 QKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDV 174
           Q+  +             N +   EH   E  SR L +R ++S+IED EL  LF+Q+GDV
Sbjct: 188 QRDGKRG----------SNVSTVAEHPQGEILSRILFVRNVDSSIEDCELGVLFKQFGDV 237

Query: 175 RTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGT 234
           R  + A K+ GF+ +SYYDIRAA+ A ++L  +L R  KLDI YSIPK+NP E   ++G 
Sbjct: 238 RALHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDIRYSIPKENPKENS-SEGA 296

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYI 294
           L V NLDSS+SN+ELH IF  YGEI+E+R T  +  Q YIEF+D R A+ AL+ LN   +
Sbjct: 297 LWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQVYIEFFDVRKAKVALQGLNGLEV 356

Query: 295 AGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLP 354
           AG+Q+KL P+   G          P+   ++                   G+  +  +  
Sbjct: 357 AGRQLKLAPTCPEG------TSFWPQFASDDG----------------EGGLPKMAFN-- 392

Query: 355 LNVKSLAIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPPT---ESAFHLGISSSVPS 411
            N+ S  +   F G  A  S      D   +  + ++V +P     E    L +   +P 
Sbjct: 393 -NLSSAHMGRHFPGILASTS-----IDGGSIRGMHNSVGSPMNSFIERHQSLDVPIGLPP 446

Query: 412 LVRMESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGAN 471
             R+ S      L E G+     K  I+S P+ HPH  P+  D    G    SS T    
Sbjct: 447 SARVISASKPVGLQEFGNPFDNSKTGIQSMPNLHPH-FPDYLDNFASGSPYKSSTTFSEM 505

Query: 472 IN--IKPPEIIDSRHFSRVSSNGHSIGFTEVFGSASNGSCPRPGHQYSWNNSYCPQ---L 526
           ++   K  E     +   V  +G + G   V GS  N    R G+   W+NS   Q    
Sbjct: 506 VSDGQKANEGFMMSNVRGVGVDGFNGG---VIGSPINQGSHR-GNLNLWSNSNSQQHNQS 561

Query: 527 PGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQ 586
            GMMWPNSPS V+G+ +   P  V    RA   MVN       HH+GSAP ++   W+R+
Sbjct: 562 SGMMWPNSPSRVNGVPSQRIPP-VTAFSRASPLMVNMASSPVHHHIGSAPVLNSPFWDRR 620

Query: 587 HAYVAESPEASGFHLGSHGSMRISNNS-LHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQ 645
            AYVAESPE+SGFHLGS GSM    +S  H ++F SH +F  VGGN M+    SKN+V +
Sbjct: 621 QAYVAESPESSGFHLGSPGSMGFPGSSPSHPMDFGSHKVFSHVGGNRMEAN--SKNAVLR 678

Query: 646 SHHQRSMMFSGRGQTIPLMNSFDPPNERARN---RRNEGAVNQADKKQYELDIDRILRGE 702
           S  Q   +F+GR   + +  SFD PNER RN   RR+E   + A+KK YELD+DRILRGE
Sbjct: 679 SSRQMPHLFTGRSPMLSVSGSFDLPNERYRNLSHRRSESNSSNAEKKLYELDVDRILRGE 738

Query: 703 DNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQI 762
           D+RTTLMIKNIPNKYTSKMLLAAIDE  KGTYDF+YLPIDFKNKCNVGYAFIN+ +P  I
Sbjct: 739 DSRTTLMIKNIPNKYTSKMLLAAIDEYCKGTYDFLYLPIDFKNKCNVGYAFINLIEPENI 798

Query: 763 VPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGP 822
           VPFY++FNGKKWEKFNSEKVASLAY RIQGK+ALIAHFQNSSLMNEDKRCRPILF+T GP
Sbjct: 799 VPFYKAFNGKKWEKFNSEKVASLAYGRIQGKSALIAHFQNSSLMNEDKRCRPILFHTAGP 858

Query: 823 NAGDQVPFPMGVNFRTRPGKAR--SVIHEENHHGSPPNVEDLSNGD 866
           NAGDQ PFPMG N R+RPGK R  S+ +  N   S  N ++ +NG+
Sbjct: 859 NAGDQEPFPMGSNIRSRPGKHRTNSIENYTNFSSSSDNRDEPANGN 904

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q75M35|OML3_ORYSJ Protein MEI2-like 3 OS=Oryza sativa subsp. japonica GN=ML3 PE=2 SV=2

 Score =  579 bits (1492), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 378/874 (43%), Positives = 496/874 (56%), Gaps = 99/874 (11%)

Query: 16  ELFSRKLRLSSDIAS--YGHSVDTVSSHYEEEEPFESLEEIEAQTIGNLLPDDDDL-FSG 72
           E+FS K R   +I S     S  T +S Y+ +EP ES+E IEAQTIG+LLPDDDD   SG
Sbjct: 152 EVFSGKSR---EIVSGVLCQSTGTHTSIYDSDEPLESMEAIEAQTIGDLLPDDDDDLISG 208

Query: 73  VTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEICIGFSNHELGVC 132
           + DG E T    G S   D  D D F + GGM+L N+ S    K  +          G  
Sbjct: 209 IADGFEFT----GMSTNQDDADEDIFCTGGGMELENNDSVKGDKVQD----------GSF 254

Query: 133 NGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYY 192
              ++  H  ++ PSRTL++R I +NIEDS+L  LF+QYGD+R  Y + KH GFVT+SYY
Sbjct: 255 KSQISSGHSINKQPSRTLVVRNITANIEDSDLTVLFQQYGDIRMLYTSFKHHGFVTVSYY 314

Query: 193 DIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHI 252
           DIRAA+NAM++L +K     KLD+ +S PK+N   K+I++G LVV N+DSS+SND+L  +
Sbjct: 315 DIRAAQNAMRALHSKPLGLMKLDVQFSFPKENVPGKDIDKGMLVVSNIDSSISNDDLLQM 374

Query: 253 FGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKC 312
             VYG++KEI  +P    +K++EFYD RAAE AL +LN   I+G + K+E S       C
Sbjct: 375 LSVYGDVKEISSSPISCTKKFVEFYDVRAAEEALHDLNKGGISGPKFKVELSQHGEAGSC 434

Query: 313 LANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLAIIYLFTGAFAH 372
           L  Q   E +Q+         S P++P N S G I     L    +  + ++     F+ 
Sbjct: 435 LRQQHSREWKQD---------SLPHQPKNSSPGTIG---KLGTKCQDNSTVH---NLFSP 479

Query: 373 GSKSSRITDTCIVSVVPSAVKAPPTESAFHLGISSSVPSLVRMESFGTQSALAEPGHLQG 432
            ++       CI +  P  + +P                 +R++S    +  A  G L G
Sbjct: 480 VNQQLESPTQCISTTGPQILSSP-----------------IRIKSTLQHNNQASVGDLSG 522

Query: 433 QL-KFNI-RSTPSFHPHSLPECHD-------GLNKGVRCNSSGTKGANINIKP--PEIID 481
            L + N  R   + HP SLPE H+        +    R  SS   G + NI+   P    
Sbjct: 523 PLGQGNFGRGIQTLHPRSLPEHHNRICNNSKSMTVSGRNASSRQDGVDHNIQKVGPAGFC 582

Query: 482 SRHFSRVSSNGHSIGFTEVFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPNSPSLVSGI 541
              F +   N  + GFTE+      GSCP  G+ Y+WN++        ++P SPS     
Sbjct: 583 GHSFDQ---NNEAFGFTEI------GSCPLHGYHYTWNHTN-------VFPQSPSAPILW 626

Query: 542 FNTYSPTRVHGLPRAPSHMVNT-VLPIGSHHVGSAPTVDPSLWERQHAYVAESPEASGFH 600
            N   P  VH  P  P HM+NT   P+  HH+GSAP    S                 FH
Sbjct: 627 SNLQHPMHVHSYPGVPPHMLNTGSYPMDQHHLGSAPDNGGSFGN-----------VHSFH 675

Query: 601 LGSHGSMRISNN-SLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMMFSGRGQ 659
            GS GS+ +  +  L+  E  +   F    GN  +         FQS  Q     +GR  
Sbjct: 676 PGSLGSIGLHGSPQLYPSELSA---FASSRGNFREALFSPVGGGFQSLQQMCNAINGRNP 732

Query: 660 TIPLMNSFDPPNERARNRRNEGAVNQAD-KKQYELDIDRILRGEDNRTTLMIKNIPNKYT 718
            I +  S+D  N+R R+RR++G   Q++ K+Q+ELDIDRI +GED+RTTLMIKNIPNKY 
Sbjct: 733 MIHVSTSYDATNDRMRSRRHDGNPAQSENKRQFELDIDRIAKGEDSRTTLMIKNIPNKYN 792

Query: 719 SKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFN 778
            K+LLA IDE H+GTYDFIYLPIDFKNKCNVGYAFINMTDP  I+PFY++FNGKKWEKFN
Sbjct: 793 CKLLLAVIDENHRGTYDFIYLPIDFKNKCNVGYAFINMTDPQHIIPFYKTFNGKKWEKFN 852

Query: 779 SEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVNFRT 838
           SEKVASLAYARIQG++ALIAHFQNSSLMNEDK CRP+LF+ DGPNAGDQ PFP+G N R+
Sbjct: 853 SEKVASLAYARIQGRSALIAHFQNSSLMNEDKWCRPMLFHKDGPNAGDQEPFPVGNNVRS 912

Query: 839 RPGKARSVIHEENHHGSP---PNVEDLSNGDAPS 869
           R G+ RS+I  +    SP   P+ E  S G A S
Sbjct: 913 RAGRNRSLISLDTKDASPSSSPDQESNSVGTANS 946

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8VWF5|AML5_ARATH Protein MEI2-like 5 OS=Arabidopsis thaliana GN=ML5 PE=1 SV=1

 Score =  315 bits (807), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 184/353 (52%), Positives = 225/353 (63%), Gaps = 27/353 (7%)

Query: 6   ESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGNLLPD 65
           +++LFSSSL      KL+LS +   +    DT  S   +    ES ++ E+ +IGNLLPD
Sbjct: 27  DATLFSSSLPVFPRGKLQLSDNRDGFSLIDDTAVSRTNKFN--ESADDFESHSIGNLLPD 84

Query: 66  DDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEICIGFS 125
           ++DL +G+ D L+    P       D DD D F S GGM+L  D            +  S
Sbjct: 85  EEDLLTGMMDDLDLGELP-------DADDYDLFGSGGGMELDADFRDNLSMSGPPRLSLS 137

Query: 126 NH------ELGVCNGA--VAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTF 177
           +       +  + NGA  VAGEH   EHPSRTL +R INSN+EDSEL ALFEQYGD+RT 
Sbjct: 138 SLGGNAIPQFNIPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELTALFEQYGDIRTL 197

Query: 178 YRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVV 237
           Y   KH GFV ISYYDIR+AR AM+SLQNK  R  KLDIH+SIPKDNPSEK++NQGTLVV
Sbjct: 198 YTTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFSIPKDNPSEKDMNQGTLVV 257

Query: 238 FNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK 297
           FNLD S+SND+LH IFG +GEIKEIRETP K H K++EFYD R AEAAL+ LN   IAGK
Sbjct: 258 FNLDPSISNDDLHGIFGAHGEIKEIRETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGK 317

Query: 298 QIKLEPSHLRGLRKCLANQLPPELEQEEC------GSYQQQNSPP---NKPTN 341
           +IK+EPS   G R+ L  QL  +LE ++       GS    NSPP   N P N
Sbjct: 318 RIKVEPSRPGGARRSLMLQLNQDLENDDLHYLPMIGS-PMANSPPMQGNWPLN 369

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6ZI17|OML2_ORYSJ Protein MEI2-like 2 OS=Oryza sativa subsp. japonica GN=ML2 PE=2 SV=1

 Score =  306 bits (784), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 173/338 (51%), Positives = 226/338 (66%), Gaps = 20/338 (5%)

Query: 7   SSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEE----EEPFESLEEIEAQTIGNL 62
           +SLFS+SL  L   K+    D A     +D  S+  +E     E  +   + + + I +L
Sbjct: 48  ASLFSTSLPVLPHEKINFL-DSARGTPLMDDASAKLKELDDDPEGKDYKFDFDLRQIDDL 106

Query: 63  LPDDDDLFSGVTDGLECTVHPSGGSGG-DDMDDLDFFSSVGGMDLGND---SSYVAQKKS 118
           LP++DDLF+G+T+ +E    P+G +   +++++ D F S GGM+L  D   S       +
Sbjct: 107 LPNEDDLFAGITNEIE----PAGQTNSMEELEEFDVFGSGGGMELDTDPVESITAGLGNT 162

Query: 119 EICIGFS----NHELGVCNGA--VAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYG 172
            I  G      NH  G  N A  VAGEH   EHPSRTL +R INSN++D+EL++LFEQYG
Sbjct: 163 SIADGLRGNGVNH-FGPSNSASTVAGEHPYGEHPSRTLFVRNINSNVDDTELRSLFEQYG 221

Query: 173 DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQ 232
           D+RT Y A+KH GFV ISY+DIRAAR AM+ LQNK  R  KLDIH+SIPK+NPS+K++NQ
Sbjct: 222 DIRTLYTATKHRGFVMISYFDIRAARGAMRGLQNKPLRRRKLDIHFSIPKENPSDKDLNQ 281

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSR 292
           GTLV+FNLD SVSN+E+  IFG YGE+KEIRETP K H K+IEFYD RAAEAALR LN  
Sbjct: 282 GTLVIFNLDPSVSNEEVRQIFGTYGEVKEIRETPNKKHHKFIEFYDVRAAEAALRSLNKS 341

Query: 293 YIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQ 330
            IAGK+IKLEPS   G R+ L  QL  +++Q+E  SY+
Sbjct: 342 EIAGKRIKLEPSRPGGTRRNLMQQLGHDIDQDEPRSYR 379

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SVV9|AML3_ARATH Protein MEI2-like 3 OS=Arabidopsis thaliana GN=ML3 PE=2 SV=2

 Score =  296 bits (758), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 158/291 (54%), Positives = 205/291 (70%), Gaps = 18/291 (6%)

Query: 51  LEEIEAQTIGNLLPDDDD-LFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGND 109
           L++ ++  IGN+LPDD++ LFSG+ D L  +  P+     DD++D D F S GG++L  D
Sbjct: 63  LDDGDSHPIGNMLPDDEEELFSGLMDDLNLSSLPATL---DDLEDYDLFGSGGGLELETD 119

Query: 110 SSYVAQKKSEICIGFSNHEL-----------GVCNGAVAGEHLNDEHPSRTLLLRKINSN 158
             Y +  K    +GF++  +           GV  G++AGEH   EHPSRTL +R INSN
Sbjct: 120 P-YDSLNKGFSRMGFADSNVDNVMPQNIFQNGV--GSIAGEHPYGEHPSRTLFVRNINSN 176

Query: 159 IEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY 218
           +EDSEL+ALFEQYG +RT Y A K  GFV +SY DIRA+R AM++LQ KL +  KLDIH+
Sbjct: 177 VEDSELQALFEQYGHIRTLYTACKQRGFVMVSYNDIRASRAAMRALQGKLLKKRKLDIHF 236

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYD 278
           SIPKDNPSEK++NQGTLVVFNL  SVSN +L +IFGVYGEIKEIRETP K H K++EF+D
Sbjct: 237 SIPKDNPSEKDVNQGTLVVFNLAPSVSNRDLENIFGVYGEIKEIRETPNKRHHKFVEFFD 296

Query: 279 TRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSY 329
            R+A+AAL+ LN   IAGK+IKLE S   G R+ +  Q+ PELEQ++  SY
Sbjct: 297 VRSADAALKALNRTEIAGKRIKLEHSRPGGARRNMMLQMNPELEQDDSYSY 347

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6EQX3|OML5_ORYSJ Protein MEI2-like 5 OS=Oryza sativa subsp. japonica GN=ML5 PE=2 SV=1

 Score =  284 bits (727), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 151/299 (50%), Positives = 201/299 (67%), Gaps = 16/299 (5%)

Query: 51  LEEIEAQTIGNLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGND- 109
           ++++    IGNLLPDD++L +GV +  +   H    +  ++ ++ D F + GGM+L  D 
Sbjct: 92  MDDVAQHLIGNLLPDDEELLAGVIEDFD---HVKLRTQVEESEEYDVFRNSGGMELDIDP 148

Query: 110 --SSYVAQKKSEIC--IGFSNHELGVCNGA--VAGEHLNDEHPSRTLLLRKINSNIEDSE 163
             S      K+ +    G S ++  + NGA  V GEH   EHPSRTL +R INSN+EDSE
Sbjct: 149 LESITFGTAKASLVNGTGSSTNQYSIQNGAGTVTGEHPYGEHPSRTLFVRNINSNVEDSE 208

Query: 164 LKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD 223
           L++LFE +GD+R+ Y A+KH GFV ISYYDIR ARNA  +LQ+K  R  KLDIHYSIPK+
Sbjct: 209 LRSLFEPFGDIRSMYTATKHRGFVMISYYDIRHARNAKTALQSKPLRRRKLDIHYSIPKE 268

Query: 224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAE 283
           NPS+K++NQGTLV+FNL+ +VSN+EL  IFG +GE++EIRETP K H ++IEFYD RAAE
Sbjct: 269 NPSDKDMNQGTLVIFNLEPAVSNEELLQIFGAFGEVREIRETPHKRHHRFIEFYDVRAAE 328

Query: 284 AALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEEC--GSYQ----QQNSPP 336
           +ALR LN   IAGK++KLEPS   G R+        E EQ+E    S+Q      NSPP
Sbjct: 329 SALRSLNKSDIAGKRVKLEPSRPGGARRSFIQHFNHEFEQDETKHNSFQIGSPSANSPP 387

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SJG8|AML2_ARATH Protein MEI2-like 2 OS=Arabidopsis thaliana GN=ML2 PE=2 SV=2

 Score =  256 bits (653), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 143/303 (47%), Positives = 189/303 (62%), Gaps = 18/303 (5%)

Query: 49  ESLEEIEAQTIGNLLPDDD-DLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDL- 106
           +SLE++E   +  LLP+D+ +L  G+ D L  T  P      DD+++ D F + GGM+L 
Sbjct: 93  DSLEDVEPDALEILLPEDENELLPGLIDELNFTGLPDEL---DDLEECDVFCTGGGMELD 149

Query: 107 -------GNDSSYVAQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNI 159
                    D+S +          F   +     G V+ EH N EHPSRTL +R INS++
Sbjct: 150 VESQDNHAVDASGMQISDRGAANAFVPRKRPNTAGRVSVEHPNGEHPSRTLFVRNINSSV 209

Query: 160 EDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS 219
           EDSEL ALFE +G++R+ Y A K  GFV ISYYDIRAA  AM++LQN L R   LDIH+S
Sbjct: 210 EDSELSALFEPFGEIRSLYTACKSRGFVMISYYDIRAAHAAMRALQNTLLRKRTLDIHFS 269

Query: 220 IPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDT 279
           IPK+NPSEK++NQGTLV+FN+D++VSNDEL  +FG YGEI+EIRETP +   ++IE+YD 
Sbjct: 270 IPKENPSEKDMNQGTLVIFNVDTTVSNDELLQLFGAYGEIREIRETPNRRFHRFIEYYDV 329

Query: 280 RAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQ------N 333
           R AE AL+ LN   I GK IKLE S   G R+        +LE+ E  ++  Q      N
Sbjct: 330 RDAETALKALNRSEIGGKCIKLELSRPGGARRLSVPSQSQDLERTEVTNFYNQVGSHVAN 389

Query: 334 SPP 336
           SPP
Sbjct: 390 SPP 392

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|P08965|MEI2_SCHPO Meiosis protein mei2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mei2 PE=1 SV=1

 Score =  160 bits (404), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 81/165 (49%), Positives = 106/165 (64%), Gaps = 3/165 (1%)

Query: 693 LDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYA 752
           +D  +I  G D RTT+MIKNIPNK+T +ML   ID  +KGTYDF+YL IDF NKCNVGYA
Sbjct: 584 VDYAQIASGIDTRTTVMIKNIPNKFTQQMLRDYIDVTNKGTYDFLYLRIDFVNKCNVGYA 643

Query: 753 FINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRC 812
           FIN  +P  I+ F ++  G +W  F+SEK+  ++YA IQGK  LI  F+NS +M+E+   
Sbjct: 644 FINFIEPQSIITFGKARVGTQWNVFHSEKICDISYANIQGKDRLIEKFRNSCVMDENPAY 703

Query: 813 RPILFNTDGPNAGDQVPFPMGVNFRTRPGKARSVIHEENHHGSPP 857
           RP +F + GPN G + PFP   N R    K RS+   +     PP
Sbjct: 704 RPKIFVSHGPNRGMEEPFPAPNNARR---KLRSIASAQQIGLFPP 745

Crucial for commitment to meiosis but it is not sufficient itself for the commitment. May be a splicing regulator.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	876
359473863	965	PREDICTED: protein MEI2-like 4-like [Vit	0.966	0.877	0.662	0.0
296085525	986	unnamed protein product [Vitis vinifera]	0.966	0.859	0.662	0.0
224075455	976	predicted protein [Populus trichocarpa]	0.952	0.854	0.675	0.0
147775314	932	hypothetical protein VITISV_040729 [Viti	0.958	0.901	0.642	0.0
307135827	968	RNA-binding protein [Cucumis melo subsp.	0.938	0.849	0.661	0.0
449487385	968	PREDICTED: LOW QUALITY PROTEIN: protein	0.937	0.848	0.659	0.0
449445596	962	PREDICTED: LOW QUALITY PROTEIN: protein	0.918	0.836	0.654	0.0
350537385	971	AML1 [Solanum lycopersicum] gi|47834703|	0.937	0.845	0.603	0.0
297734509	998	unnamed protein product [Vitis vinifera]	0.956	0.839	0.585	0.0
255540053	972	RNA-binding protein, putative [Ricinus c	0.940	0.847	0.577	0.0

>gi|359473863|ref|XP_002267714.2| PREDICTED: protein MEI2-like 4-like [Vitis vinifera]

 Score = 1133 bits (2931), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 588/887 (66%), Positives = 679/887 (76%), Gaps = 40/887 (4%)

Query: 2   GAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGN 61
           G+QYE+ LFSSSLSELF+RKLRLSS+   YGHSVDTV+ H+EEE+ FESLEEIEAQTIGN
Sbjct: 107 GSQYENGLFSSSLSELFNRKLRLSSNNGLYGHSVDTVAPHHEEEDLFESLEEIEAQTIGN 166

Query: 62  LLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEIC 121
           LLP++DDL SGV D L+  V PS G   DD++D+D FSSVGGMDLG+D S   Q+ SE  
Sbjct: 167 LLPNEDDLLSGVADVLDYVVQPSNG---DDLEDIDLFSSVGGMDLGDDGSSAGQRNSEYP 223

Query: 122 IGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRAS 181
            G SN +LG  NG+  GEH   EHPSRTL +R INSN+EDSEL+ LFEQYGD+R  Y A 
Sbjct: 224 GGMSNGQLGGSNGSAVGEHPYGEHPSRTLFVRNINSNVEDSELRILFEQYGDIRALYTAC 283

Query: 182 KHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLD 241
           KH GFV ISYYDIRAARNAM++LQNK  R  KLDIHYSIPKDNP EK++NQGTLVVFNLD
Sbjct: 284 KHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPPEKDVNQGTLVVFNLD 343

Query: 242 SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL 301
            SV+NDEL  IFGVYGEIKEIRETP + H K++EFYD RAAEAALR LN   IAGK+IKL
Sbjct: 344 PSVTNDELLQIFGVYGEIKEIRETPHRSHHKFVEFYDIRAAEAALRALNRSDIAGKRIKL 403

Query: 302 EPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLA 361
           EPS   G R+ L  Q P ELE++E G Y QQN+ PN  T    G  ++            
Sbjct: 404 EPSRPGGARR-LMQQFPSELEEDESGLYLQQNNTPNNSTTGFPGPASL------------ 450

Query: 362 IIYLFTGAFAHGSKSSRITDTCIVSV---VPSAVKAPPTESAFHLGISSSVP----SLVR 414
                 GA      SS + +  I+ V   +P  ++ P  E+  H GISSSVP    SL+ 
Sbjct: 451 ------GAIT----SSSMENGTIMGVHSGIPFPIR-PFLENVSHHGISSSVPNTLPSLLS 499

Query: 415 MESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINI 474
           +ES G+QS LAE    QGQLKF+ R T S HPHSLPE +DGL  G  CN  GT  ANIN 
Sbjct: 500 VESVGSQSGLAESSRSQGQLKFDFRGTQSLHPHSLPEYNDGLANGAPCNPVGTMAANINP 559

Query: 475 KPPEIIDSRHFSRVSSNGHSIGFTE-VFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPN 533
           +P E I++R  S  +SNG ++   + VFGS+ NGSCP PGH Y W+NS+ PQ PGMMWPN
Sbjct: 560 RP-ERIENRQLSGANSNGLTVELNDGVFGSSGNGSCPLPGHHYMWSNSHHPQSPGMMWPN 618

Query: 534 SPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAES 593
           SPS ++GI   + P R+HGLPRAPSHM+NT+L I +HHVGSAPTV+PS+W+R+H Y  ES
Sbjct: 619 SPSFMNGIGTAHPPPRLHGLPRAPSHMLNTMLSINNHHVGSAPTVNPSIWDRRHTYAGES 678

Query: 594 PEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMM 653
            EASGFH GS GSMRISNNSLH +EF  HNIFP VGGN +D+ +P KN    SHHQR +M
Sbjct: 679 SEASGFHPGSLGSMRISNNSLHPLEFAPHNIFPSVGGNCIDLSIPPKNVGLHSHHQRCLM 738

Query: 654 FSGRGQTIPLMNSFDPPNERARNRRNEGAVNQAD-KKQYELDIDRILRGEDNRTTLMIKN 712
           F GR Q IP+M+SFDPPNER+R+RRN+ + NQ D KKQYELDIDRILRGED RTTLMIKN
Sbjct: 739 FPGRSQLIPMMSSFDPPNERSRSRRNDNSSNQVDNKKQYELDIDRILRGEDTRTTLMIKN 798

Query: 713 IPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGK 772
           IPNKYTSKMLLAAIDERH+GTYDFIYLPIDFKNKCNVGYAFINMTDP QI+PFYQ+FNGK
Sbjct: 799 IPNKYTSKMLLAAIDERHRGTYDFIYLPIDFKNKCNVGYAFINMTDPCQIIPFYQAFNGK 858

Query: 773 KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPM 832
           KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILF+TDGPNAGDQVPFPM
Sbjct: 859 KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDQVPFPM 918

Query: 833 GVNFRTRPGKARSVIHEENHHGSPPNV---EDLSNGDAPSGSAKESD 876
           GVN R+RPGK R+  +E+NH GSPPN+   ED SNGD+ SGS K+SD
Sbjct: 919 GVNVRSRPGKTRTSSNEDNHQGSPPNLTTGEDYSNGDSSSGSTKDSD 965

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296085525|emb|CBI29257.3| unnamed protein product [Vitis vinifera]

 Score = 1132 bits (2929), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 588/887 (66%), Positives = 679/887 (76%), Gaps = 40/887 (4%)

Query: 2   GAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGN 61
           G+QYE+ LFSSSLSELF+RKLRLSS+   YGHSVDTV+ H+EEE+ FESLEEIEAQTIGN
Sbjct: 128 GSQYENGLFSSSLSELFNRKLRLSSNNGLYGHSVDTVAPHHEEEDLFESLEEIEAQTIGN 187

Query: 62  LLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEIC 121
           LLP++DDL SGV D L+  V PS G   DD++D+D FSSVGGMDLG+D S   Q+ SE  
Sbjct: 188 LLPNEDDLLSGVADVLDYVVQPSNG---DDLEDIDLFSSVGGMDLGDDGSSAGQRNSEYP 244

Query: 122 IGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRAS 181
            G SN +LG  NG+  GEH   EHPSRTL +R INSN+EDSEL+ LFEQYGD+R  Y A 
Sbjct: 245 GGMSNGQLGGSNGSAVGEHPYGEHPSRTLFVRNINSNVEDSELRILFEQYGDIRALYTAC 304

Query: 182 KHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLD 241
           KH GFV ISYYDIRAARNAM++LQNK  R  KLDIHYSIPKDNP EK++NQGTLVVFNLD
Sbjct: 305 KHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPPEKDVNQGTLVVFNLD 364

Query: 242 SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL 301
            SV+NDEL  IFGVYGEIKEIRETP + H K++EFYD RAAEAALR LN   IAGK+IKL
Sbjct: 365 PSVTNDELLQIFGVYGEIKEIRETPHRSHHKFVEFYDIRAAEAALRALNRSDIAGKRIKL 424

Query: 302 EPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLA 361
           EPS   G R+ L  Q P ELE++E G Y QQN+ PN  T    G  ++            
Sbjct: 425 EPSRPGGARR-LMQQFPSELEEDESGLYLQQNNTPNNSTTGFPGPASL------------ 471

Query: 362 IIYLFTGAFAHGSKSSRITDTCIVSV---VPSAVKAPPTESAFHLGISSSVP----SLVR 414
                 GA      SS + +  I+ V   +P  ++ P  E+  H GISSSVP    SL+ 
Sbjct: 472 ------GAIT----SSSMENGTIMGVHSGIPFPIR-PFLENVSHHGISSSVPNTLPSLLS 520

Query: 415 MESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINI 474
           +ES G+QS LAE    QGQLKF+ R T S HPHSLPE +DGL  G  CN  GT  ANIN 
Sbjct: 521 VESVGSQSGLAESSRSQGQLKFDFRGTQSLHPHSLPEYNDGLANGAPCNPVGTMAANINP 580

Query: 475 KPPEIIDSRHFSRVSSNGHSIGFTE-VFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPN 533
           +P E I++R  S  +SNG ++   + VFGS+ NGSCP PGH Y W+NS+ PQ PGMMWPN
Sbjct: 581 RP-ERIENRQLSGANSNGLTVELNDGVFGSSGNGSCPLPGHHYMWSNSHHPQSPGMMWPN 639

Query: 534 SPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAES 593
           SPS ++GI   + P R+HGLPRAPSHM+NT+L I +HHVGSAPTV+PS+W+R+H Y  ES
Sbjct: 640 SPSFMNGIGTAHPPPRLHGLPRAPSHMLNTMLSINNHHVGSAPTVNPSIWDRRHTYAGES 699

Query: 594 PEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMM 653
            EASGFH GS GSMRISNNSLH +EF  HNIFP VGGN +D+ +P KN    SHHQR +M
Sbjct: 700 SEASGFHPGSLGSMRISNNSLHPLEFAPHNIFPSVGGNCIDLSIPPKNVGLHSHHQRCLM 759

Query: 654 FSGRGQTIPLMNSFDPPNERARNRRNEGAVNQAD-KKQYELDIDRILRGEDNRTTLMIKN 712
           F GR Q IP+M+SFDPPNER+R+RRN+ + NQ D KKQYELDIDRILRGED RTTLMIKN
Sbjct: 760 FPGRSQLIPMMSSFDPPNERSRSRRNDNSSNQVDNKKQYELDIDRILRGEDTRTTLMIKN 819

Query: 713 IPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGK 772
           IPNKYTSKMLLAAIDERH+GTYDFIYLPIDFKNKCNVGYAFINMTDP QI+PFYQ+FNGK
Sbjct: 820 IPNKYTSKMLLAAIDERHRGTYDFIYLPIDFKNKCNVGYAFINMTDPCQIIPFYQAFNGK 879

Query: 773 KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPM 832
           KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILF+TDGPNAGDQVPFPM
Sbjct: 880 KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDQVPFPM 939

Query: 833 GVNFRTRPGKARSVIHEENHHGSPPNV---EDLSNGDAPSGSAKESD 876
           GVN R+RPGK R+  +E+NH GSPPN+   ED SNGD+ SGS K+SD
Sbjct: 940 GVNVRSRPGKTRTSSNEDNHQGSPPNLTTGEDYSNGDSSSGSTKDSD 986

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224075455|ref|XP_002304641.1| predicted protein [Populus trichocarpa] gi|222842073|gb|EEE79620.1| predicted protein [Populus trichocarpa]

 Score = 1127 bits (2915), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 597/884 (67%), Positives = 682/884 (77%), Gaps = 50/884 (5%)

Query: 1   MGAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIG 60
           M  Q+E+SLFSSSLSELFSRKLRLSS  + YGHSVDT++SH+EEEEPF+SLEEIEAQTIG
Sbjct: 135 MATQHENSLFSSSLSELFSRKLRLSSTNSLYGHSVDTIASHFEEEEPFQSLEEIEAQTIG 194

Query: 61  NLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEI 120
           NLLP+DDDLFSGVTD +E   HPSGG   DDM+DLDFFSSVGGMDLG+D S VAQ  SE 
Sbjct: 195 NLLPNDDDLFSGVTDRVENINHPSGG---DDMEDLDFFSSVGGMDLGDDGS-VAQIDSEF 250

Query: 121 CIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA 180
             G SN +LG CN +VAGEH   EHPSRTL +R INSN+E+SEL+A+FEQYGD+RT Y A
Sbjct: 251 HGGASNGQLGACNLSVAGEHPYGEHPSRTLFVRNINSNVEESELRAIFEQYGDIRTLYTA 310

Query: 181 SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNL 240
            KH GFV ISYYDIRAA+NAMK+LQN+  R  KLDIHYSIPKDNPSEK+ NQGTL VFNL
Sbjct: 311 CKHRGFVMISYYDIRAAKNAMKALQNRPLRCRKLDIHYSIPKDNPSEKDFNQGTLAVFNL 370

Query: 241 DSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK 300
           DSSVSND+L  IFGVYGEIKEIRETP + H K++EFYD RAAEAAL  LN   IAGK+IK
Sbjct: 371 DSSVSNDDLRRIFGVYGEIKEIRETPHRNHHKFVEFYDVRAAEAALHALNKSDIAGKRIK 430

Query: 301 LEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSL 360
           LE S   GLR+ L +Q+PPELEQ+E G + QQ+SPPN  T E +G +             
Sbjct: 431 LEASCPGGLRRLL-HQIPPELEQDEFGPFVQQSSPPNNSTTEFSGTV------------- 476

Query: 361 AIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPPTESAFHLGI----SSSVPSLVRME 416
               + TG            D   +    SA +AP  ESA H GI     +S+ SL R+E
Sbjct: 477 ----ISTG-----------MDNGPILGAHSATQAPFFESALHHGISSSVPNSMSSLSRVE 521

Query: 417 SFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIKP 476
           S G Q+  AE  H  G LKF+I+ST +FHPHSLPE +DGLN GV CNS G   ANIN + 
Sbjct: 522 SAGNQTGFAELSHSPGHLKFDIQSTLNFHPHSLPE-YDGLNSGVHCNSPGAMAANINPRL 580

Query: 477 PEIIDSRHFSRVSSNGHSIGFTE-VFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPNSP 535
            E ID+RH +R+S NG+ I F+E VFGSA NGSC RPGH Y+W NSY  Q PGM+WPNSP
Sbjct: 581 LERIDTRHLARISPNGNPIEFSEGVFGSARNGSCSRPGHHYTWGNSYHHQPPGMIWPNSP 640

Query: 536 SLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAESPE 595
           S V+GI   +   R+HG PRAP  M+N VLPI + HVGS P V+PSLW+RQHAY  ESP+
Sbjct: 641 SFVNGISVAHPGPRLHGPPRAPPPMLNPVLPINNQHVGSVPAVNPSLWDRQHAYAGESPD 700

Query: 596 ASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMMFS 655
           ASGFH  S GSMRISNNSLHS+EF+S  +FP VGGN +++P+P +N  FQS  QRSM+F 
Sbjct: 701 ASGFHPCSLGSMRISNNSLHSMEFLSPKMFPHVGGNCLELPMPPQNVGFQSQQQRSMVFP 760

Query: 656 GRGQTIPLMNSFDPPNERARNRRNEGAVNQADKKQYELDIDRILRGEDNRTTLMIKNIPN 715
           GRGQ IP++N+FD P ERAR+RRNEG+ +QADKKQYELDIDRIL+GEDNRTTLMIKNIPN
Sbjct: 761 GRGQMIPMINTFDAPGERARSRRNEGSTSQADKKQYELDIDRILQGEDNRTTLMIKNIPN 820

Query: 716 KYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWE 775
           KYTSKMLLAAIDERHKGTY+F        NKCNVGYAFINM DP QI+PFYQ+FNGKKWE
Sbjct: 821 KYTSKMLLAAIDERHKGTYNF--------NKCNVGYAFINMIDPRQIIPFYQAFNGKKWE 872

Query: 776 KFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVN 835
           KFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVN
Sbjct: 873 KFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVN 932

Query: 836 FRTRPGKARSVIHEENHHGSPPNV---EDLSNGDAPSGSAKESD 876
            RTRPGK R++ HEEN  GSP N+   ED SNGDA SGS KESD
Sbjct: 933 VRTRPGKPRTITHEENQQGSPSNLAGGEDSSNGDASSGSGKESD 976

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147775314|emb|CAN72509.1| hypothetical protein VITISV_040729 [Vitis vinifera]

 Score = 1065 bits (2755), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 570/887 (64%), Positives = 660/887 (74%), Gaps = 47/887 (5%)

Query: 2   GAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGN 61
           G+QYE+ LFSSSLSELF+RKLRLSS+   YGHSVDTV+ H+EEE+ FESLEEIEAQTIGN
Sbjct: 81  GSQYENGLFSSSLSELFNRKLRLSSNNGLYGHSVDTVAPHHEEEDLFESLEEIEAQTIGN 140

Query: 62  LLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEIC 121
           LLP++DDL SGV D L+  V PS G   DD++D+D FSSVGGMDLG+D S   Q+ SE  
Sbjct: 141 LLPNEDDLLSGVADVLDYVVQPSNG---DDLEDIDLFSSVGGMDLGDDGSSAGQRNSEYP 197

Query: 122 IGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRAS 181
            G SN +LG  NG+  GEH   EHPSRTL +R INSN+EDSEL+ LFEQYGD+R  Y A 
Sbjct: 198 GGMSNGQLGGSNGSAVGEHPYGEHPSRTLFVRNINSNVEDSELRILFEQYGDIRALYTAC 257

Query: 182 KHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLD 241
           KH GFV ISYYDIRAARNAM++LQNK  R  KLDIHYSIPKDNP EK++NQGTLVVFNLD
Sbjct: 258 KHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPPEKDVNQGTLVVFNLD 317

Query: 242 SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL 301
            SV+NDEL  IFGVYGEIKEIRETP + H K++EFYD RAAEAALR LN   IAGK+IKL
Sbjct: 318 PSVTNDELLQIFGVYGEIKEIRETPHRSHHKFVEFYDIRAAEAALRALNRSDIAGKRIKL 377

Query: 302 EPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLA 361
           EPS   G R+ L  Q P ELE++E G Y QQN+ PN  T     ++T   SL        
Sbjct: 378 EPSRPGGARR-LMQQFPSELEEDESGLYLQQNNTPNNSTTGFPALLTGPASL-------- 428

Query: 362 IIYLFTGAFAHGSKSSRITDTCIVSV---VPSAVKAPPTESAFHLGISSSV----PSLVR 414
                 GA      SS + +  I+ V   +P  ++ P  E+  H GISSSV    PSL+ 
Sbjct: 429 ------GAIT----SSSMENGTIMGVHSGIPFPIR-PFLENVSHHGISSSVPNTLPSLLS 477

Query: 415 MESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINI 474
           +ES G+QS LAE    QGQLKF+ R T S HPHSLPE +DGL  G  CN  GT  ANIN 
Sbjct: 478 VESVGSQSGLAESSRSQGQLKFDFRGTQSLHPHSLPEYNDGLANGAPCNPVGTMAANINP 537

Query: 475 KPPEIIDSRHFSRVSSNGHSIGFTE-VFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPN 533
           + PE I++R  S  +SNG ++   + VFGS+ NGSCP PGH Y W+NS+ PQ PGMMWPN
Sbjct: 538 R-PERIENRQLSGANSNGLTVELNDGVFGSSGNGSCPLPGHHYMWSNSHHPQSPGMMWPN 596

Query: 534 SPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAES 593
           SPS  +GI   + P R+HGLPRAPSHM+NT+L I +HHVGSAPTV+PS+W+R+H Y  ES
Sbjct: 597 SPSFXNGIGTAHPPPRLHGLPRAPSHMLNTMLSINNHHVGSAPTVNPSIWDRRHTYAGES 656

Query: 594 PEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMM 653
            EASGFH GS GSMRISNNSLH +EF  HNIFP VGGN +D+ +P KN    SHHQR +M
Sbjct: 657 SEASGFHPGSLGSMRISNNSLHPLEFAPHNIFPSVGGNCIDLSIPPKNVGLHSHHQRCLM 716

Query: 654 FSGRGQTIPLMNSFDPPNERARNRRNEGAVNQAD-KKQYELDIDRILRGEDNRTTLMIKN 712
           F GR Q IP+M+SFDPPNER+R+RRN+ + NQ D KKQYELDIDRILRGED RTTLMIKN
Sbjct: 717 FPGRSQLIPMMSSFDPPNERSRSRRNDNSSNQVDNKKQYELDIDRILRGEDTRTTLMIKN 776

Query: 713 IPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGK 772
           IPNK   + LL  I E H   Y    L     NKCNVGYAFINMTDP QI+PFYQ+FNGK
Sbjct: 777 IPNK---RELL--ILELHY-CYSQCVL-----NKCNVGYAFINMTDPCQIIPFYQAFNGK 825

Query: 773 KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPM 832
           KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILF+TDGPNAGDQVPFPM
Sbjct: 826 KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDQVPFPM 885

Query: 833 GVNFRTRPGKARSVIHEENHHGSPPNV---EDLSNGDAPSGSAKESD 876
           GVN R+RPGK R+  +E+NH GSPPN+   ED SNGD+ SGS K+SD
Sbjct: 886 GVNVRSRPGKTRTSSNEDNHQGSPPNLTTGEDYSNGDSSSGSTKDSD 932

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307135827|gb|ADN33699.1| RNA-binding protein [Cucumis melo subsp. melo]

 Score = 1030 bits (2664), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 568/859 (66%), Positives = 655/859 (76%), Gaps = 37/859 (4%)

Query: 1   MGAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIG 60
           M +QYESSLFSSSLS++F+RKLR S   A YGHSVDTV+SH+EEEE FESLEE+EAQTIG
Sbjct: 106 MNSQYESSLFSSSLSDIFTRKLRFSPSNALYGHSVDTVASHFEEEEVFESLEELEAQTIG 165

Query: 61  NLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEI 120
           NLLPDDDDL +GVTDGL+C V  +G    DD +DLDFFS+VGGMDLG+D   V QK SE 
Sbjct: 166 NLLPDDDDLLAGVTDGLDCLVETTGE---DDAEDLDFFSNVGGMDLGDDGLSVGQKNSE- 221

Query: 121 CIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA 180
             G  N+  G+ NGA+AGEH   EHPSRTL +R INSN+EDSELK LFEQYGD+RT Y A
Sbjct: 222 SPGLFNNLPGMHNGAMAGEHPLGEHPSRTLFVRNINSNVEDSELKVLFEQYGDIRTLYTA 281

Query: 181 SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNL 240
            KH GFV ISYYDIRAARNAMK+LQNK  R  KLDIHYSIPKDNPSEK+INQGTLVVFNL
Sbjct: 282 CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDINQGTLVVFNL 341

Query: 241 DSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK 300
           +SSVSN+EL  IFGVYGEIKEIRE P + H K+IEFYD RAAEAAL  LN   IAGKQIK
Sbjct: 342 ESSVSNEELRQIFGVYGEIKEIREAPHRSHHKFIEFYDIRAAEAALCALNLSDIAGKQIK 401

Query: 301 LEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSL 360
           LEPS   G+R+ L  QL P+LE+E+ G Y QQ SPP    N SAG               
Sbjct: 402 LEPSRPGGVRRSLVQQLHPQLEREDIGLYLQQGSPP---VNCSAG--------------- 443

Query: 361 AIIYLFTGAFAHGS-KSSRITDTCIVSVVPSAVKAPPTESAFHLGISSSVPSL----VRM 415
                F+G    G+ KSS +++  ++ V  S ++AP  E+  H GISSSVPS     +R 
Sbjct: 444 -----FSGLVPSGTIKSSSLSNGSVLGV-HSMLRAPSLETVLHHGISSSVPSSLPSVMRS 497

Query: 416 ESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIK 475
           ES G QS   + GH   QLK  IR++ + HPHSLPE  DGLN  V CNS  T   NIN++
Sbjct: 498 ESTGNQSGFIDSGHSPSQLKLGIRASSAVHPHSLPEHPDGLNNNVHCNSLNTLAGNINLR 557

Query: 476 PPEIIDSRHFSRVSSNGHSIGFTE-VFGSASNGSCPRPGHQYSWNNSYCPQ--LPGMMWP 532
             E  DSR    V+ NG SI   E VF S  N +CP PG  Y+W NSY PQ   PG++WP
Sbjct: 558 SSERPDSRQLCGVNFNGRSIELNEDVFASGGNRTCPIPGPHYAWGNSYRPQPPAPGVVWP 617

Query: 533 NSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVAE 592
           NSPS ++GI   ++PT+VHG+PRA SH+++TV+P+ +HHVGSAP V+PS+W+RQHAY  E
Sbjct: 618 NSPSYMNGIAAAHTPTQVHGVPRAASHLMHTVMPMNNHHVGSAPAVNPSIWDRQHAYAGE 677

Query: 593 SPEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSM 652
             +ASGFH GS G+M +SNNS  S++F SH IFP VGGN +++P+P +N   QSHHQR M
Sbjct: 678 LSKASGFHSGSIGNMNLSNNSPQSMDFFSH-IFPQVGGNSVELPIPQRNVGLQSHHQRCM 736

Query: 653 MFSGRGQTIPLMNSFDPPNERARNRRNEGAVNQADKKQYELDIDRILRGEDNRTTLMIKN 712
           +F GRGQ +P+MNSFD  NER R+RRNE   NQADKKQYELDIDRI+RGEDNRTTLMIKN
Sbjct: 737 VFPGRGQILPMMNSFDSSNERGRSRRNEAVSNQADKKQYELDIDRIMRGEDNRTTLMIKN 796

Query: 713 IPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGK 772
           IPNKYTSKMLLAAIDERH+GTYDFIYLPIDFKNKCNVGYAFINMTDP  I+PFY++FNGK
Sbjct: 797 IPNKYTSKMLLAAIDERHRGTYDFIYLPIDFKNKCNVGYAFINMTDPGLIIPFYEAFNGK 856

Query: 773 KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPM 832
           KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPM
Sbjct: 857 KWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPM 916

Query: 833 GVNFRTRPGKARSVIHEEN 851
           GVN RTRPGK RS   +EN
Sbjct: 917 GVNVRTRPGKTRSNTPDEN 935

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449487385|ref|XP_004157600.1| PREDICTED: LOW QUALITY PROTEIN: protein MEI2-like 4-like [Cucumis sativus]

 Score = 1022 bits (2642), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 567/860 (65%), Positives = 655/860 (76%), Gaps = 39/860 (4%)

Query: 1   MGAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIG 60
           M +QYESSLFSSSLS++F+RKLR S   A YGHSVDTV+SH+EEEE FESLEE+EAQTIG
Sbjct: 106 MNSQYESSLFSSSLSDIFTRKLRFSPSNALYGHSVDTVASHFEEEEVFESLEELEAQTIG 165

Query: 61  NLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEI 120
           NLLPDDDDL +GVTDGL+C V  +G    DD +DLDFFS+VGGMDLG+D   V QK SE 
Sbjct: 166 NLLPDDDDLLAGVTDGLDCLVETTGE---DDAEDLDFFSNVGGMDLGDDGLSVGQKNSE- 221

Query: 121 CIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA 180
             G  N+  G+ NGA+AGEH   EHPSRTL +R INSN+EDSEL+ALFEQYGD+RT Y A
Sbjct: 222 SPGLFNNLPGMHNGAMAGEHPLGEHPSRTLFVRNINSNVEDSELEALFEQYGDIRTLYTA 281

Query: 181 SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNL 240
            KH GFV ISYYDIRAARNAMK+LQNK  R  KLDIHYSIPKDNPSEK+INQGTLVVFNL
Sbjct: 282 CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDINQGTLVVFNL 341

Query: 241 DSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK 300
           +SSVSN+EL  IFGVYGEIKEIRE P + H K+IEFYD RAAEAAL  LN   IAGKQIK
Sbjct: 342 ESSVSNEELRQIFGVYGEIKEIREAPHRSHHKFIEFYDIRAAEAALCALNLSDIAGKQIK 401

Query: 301 LEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSL 360
           LEPS   G+R+ L  QL P+LE+E+ G Y QQ SPP    N SAG               
Sbjct: 402 LEPSRPGGVRRSLVQQLHPQLEREDIGLYLQQGSPP---VNCSAG--------------- 443

Query: 361 AIIYLFTGAFAHGS-KSSRITDTCIVSVVPSAVKAPPTESAFHLGISSSVPSL----VRM 415
                F+G    G+ KSS +++  ++ V  S ++AP  ++  H GISSSVPS     +R 
Sbjct: 444 -----FSGLVPSGTIKSSSLSNGSVLGV-HSLLRAPSLDTVLHHGISSSVPSSLPSVMRS 497

Query: 416 ESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIK 475
           ES G QS   + GH   QLK  IR++ + HPHSLPE  DGLN  V CNS    G NIN++
Sbjct: 498 ESTGNQSGFIDSGHSPSQLKLGIRASSAVHPHSLPEHPDGLNNNVHCNSLNAIGGNINLR 557

Query: 476 PPEIIDSRHFSRVSSNGHSIGFTE-VFGSASNGSCPRPGHQYSWNNSYCPQ--LPGMMWP 532
           PPE  DSR    V+ NG SI   E VF S  N +CP PG  Y W NSY PQ   PG++WP
Sbjct: 558 PPERADSRQLCGVNFNGRSIELNEDVFASGGNRTCPIPGPHYGWGNSYRPQPPAPGVVWP 617

Query: 533 NSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDP-SLWERQHAYVA 591
           NSPS ++GI   ++PT+VHG+PRA SH+++TV+P+ +HHVGSAP V+P S+W+RQH Y  
Sbjct: 618 NSPSYMNGIAAGHTPTQVHGVPRAASHLMHTVMPMNNHHVGSAPAVNPPSIWDRQH-YAG 676

Query: 592 ESPEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRS 651
           E  +ASGFH GS G+M +SNNS  S++F  H IFP VGGN +++P+P +N   QSHHQR 
Sbjct: 677 ELSKASGFHSGSIGNMNLSNNSPQSMDFFXH-IFPQVGGNSVELPIPQRNVGLQSHHQRC 735

Query: 652 MMFSGRGQTIPLMNSFDPPNERARNRRNEGAVNQADKKQYELDIDRILRGEDNRTTLMIK 711
           M F GRGQ +P+MNSFD  NER R+RRNE A NQADKKQYELDIDRI+RGEDNRTTLMIK
Sbjct: 736 MXFPGRGQILPMMNSFDSSNERGRSRRNEAASNQADKKQYELDIDRIMRGEDNRTTLMIK 795

Query: 712 NIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNG 771
           NIPNKYTSKMLLAAIDERH+GTYDFIYLPIDFKNKCNVGYAFINMTDP  I+PFY++FNG
Sbjct: 796 NIPNKYTSKMLLAAIDERHRGTYDFIYLPIDFKNKCNVGYAFINMTDPGLIIPFYEAFNG 855

Query: 772 KKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFP 831
           KKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFP
Sbjct: 856 KKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFP 915

Query: 832 MGVNFRTRPGKARSVIHEEN 851
           MGVN RTRPGK R+   +EN
Sbjct: 916 MGVNVRTRPGKTRTNTPDEN 935

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449445596|ref|XP_004140558.1| PREDICTED: LOW QUALITY PROTEIN: protein MEI2-like 4-like [Cucumis sativus]

 Score = 1007 bits (2604), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 552/844 (65%), Positives = 639/844 (75%), Gaps = 39/844 (4%)

Query: 17  LFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGNLLPDDDDLFSGVTDG 76
           +F   +R S   A YGHSVDTV+SH+EEEE FESLEE+EAQTIGNLLPDDDDL +GVTDG
Sbjct: 116 VFIXAVRFSPSNALYGHSVDTVASHFEEEEVFESLEELEAQTIGNLLPDDDDLLAGVTDG 175

Query: 77  LECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEICIGFSNHELGVCNGAV 136
           L+C V  +G    DD +DLDFFS+VGGMDLG+D   V QK SE   G  N+  G+ NGA+
Sbjct: 176 LDCLVETTGE---DDAEDLDFFSNVGGMDLGDDGLSVGQKNSE-SPGLFNNLPGMHNGAM 231

Query: 137 AGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRA 196
           AGEH   EHPSRTL +R INSN+EDSEL+ALFEQYGD+RT Y A KH GFV ISYYDIRA
Sbjct: 232 AGEHPLGEHPSRTLFVRNINSNVEDSELEALFEQYGDIRTLYTACKHRGFVMISYYDIRA 291

Query: 197 ARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVY 256
           ARNAMK+LQNK  R  KLDIHYSIPKDNPSEK+INQGTLVVFNL+SSVSN+EL  IFGVY
Sbjct: 292 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDINQGTLVVFNLESSVSNEELRQIFGVY 351

Query: 257 GEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQ 316
           GEIKEIRE P + H K+IEFYD RAAEAAL  LN   IAGKQIKLEPS   G+R+ L  Q
Sbjct: 352 GEIKEIREAPHRSHHKFIEFYDIRAAEAALCALNLSDIAGKQIKLEPSRPGGVRRSLVQQ 411

Query: 317 LPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLAIIYLFTGAFAHGS-K 375
           L P+LE+E+ G Y QQ SPP    N SAG                    F+G    G+ K
Sbjct: 412 LHPQLEREDIGLYLQQGSPP---VNCSAG--------------------FSGLVPSGTIK 448

Query: 376 SSRITDTCIVSVVPSAVKAPPTESAFHLGISSSVPSL----VRMESFGTQSALAEPGHLQ 431
           SS +++  ++ V  S ++AP  ++  H GISSSVPS     +R ES G QS   + GH  
Sbjct: 449 SSSLSNGSVLGV-HSLLRAPSLDTVLHHGISSSVPSSLPSVMRSESTGNQSGFIDSGHSP 507

Query: 432 GQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIKPPEIIDSRHFSRVSSN 491
            QLK  IR++ + HPHSLPE  DGLN  V CNS    G NIN++PPE  DSR    V+ N
Sbjct: 508 SQLKLGIRASSAVHPHSLPEHPDGLNNNVHCNSLNAIGGNINLRPPERADSRQLCGVNFN 567

Query: 492 GHSIGFTE-VFGSASNGSCPRPGHQYSWNNSYCPQ--LPGMMWPNSPSLVSGIFNTYSPT 548
           G SI   E VF S  N +CP PG  Y W NSY PQ   PG++WPNSPS ++GI   ++PT
Sbjct: 568 GRSIELNEDVFASGGNRTCPIPGPHYGWGNSYRPQPPAPGVVWPNSPSYMNGIAAGHTPT 627

Query: 549 RVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDP-SLWERQHAYVAESPEASGFHLGSHGSM 607
           +VHG+PRA SH+++TV+P+ +HHVGSAP V+P S+W+RQH Y  E  +ASGFH GS G+M
Sbjct: 628 QVHGVPRAASHLMHTVMPMNNHHVGSAPAVNPPSIWDRQH-YAGELSKASGFHSGSIGNM 686

Query: 608 RISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMMFSGRGQTIPLMNSF 667
            +SNNS  S++F SH IFP VGGN +++P+P +N   QSHHQR M+F GRGQ +P+MNSF
Sbjct: 687 NLSNNSPQSMDFFSH-IFPQVGGNSVELPIPQRNVGLQSHHQRCMVFPGRGQILPMMNSF 745

Query: 668 DPPNERARNRRNEGAVNQADKKQYELDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAID 727
           D  NER R+RRNE A NQADKKQYELDIDRI+RGEDNRTTLMIKNIPNKYTSKMLLAAID
Sbjct: 746 DSSNERGRSRRNEAASNQADKKQYELDIDRIMRGEDNRTTLMIKNIPNKYTSKMLLAAID 805

Query: 728 ERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAY 787
           ERH+GTYDFIYLPIDFKNKCNVGYAFINMTDP  I+PFY++FNGKKWEKFNSEKVASLAY
Sbjct: 806 ERHRGTYDFIYLPIDFKNKCNVGYAFINMTDPGLIIPFYEAFNGKKWEKFNSEKVASLAY 865

Query: 788 ARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVNFRTRPGKARSVI 847
           ARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVN RTRPGK R+  
Sbjct: 866 ARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMGVNVRTRPGKTRTNT 925

Query: 848 HEEN 851
            +EN
Sbjct: 926 PDEN 929

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|350537385|ref|NP_001234547.1| AML1 [Solanum lycopersicum] gi|47834703|gb|AAT39005.1| AML1 [Solanum lycopersicum]

 Score =  942 bits (2434), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 520/862 (60%), Positives = 623/862 (72%), Gaps = 41/862 (4%)

Query: 1   MGAQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIG 60
           +G Q E+ LFSSSLSELFSRKLRL ++ + +GHSV    SHYEEE  FESL+E+EA  IG
Sbjct: 131 LGGQCENGLFSSSLSELFSRKLRLPTNYSPHGHSVGAADSHYEEER-FESLKELEAHAIG 189

Query: 61  NLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEI 120
           NLLPDDDDL +GVTDGL+    P  G   D+ +DLD FSSVGGMDLG D S   Q+ SE 
Sbjct: 190 NLLPDDDDLLAGVTDGLDYVGQPYAG---DETEDLDLFSSVGGMDLGEDGSSTGQQNSEY 246

Query: 121 CIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA 180
              ++   LG  N A+  +   +E+PSRTL +R +NS++EDSEL+ LFEQYGD+RT Y A
Sbjct: 247 AGNYT-LPLGDSNAAIGSQKPFEENPSRTLFVRNVNSSVEDSELQTLFEQYGDIRTLYTA 305

Query: 181 SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNL 240
            KH GFV ISYYDIRA++NAMK+LQN   R  KLDIH+SIPKDNPSEK  NQGTL+VFNL
Sbjct: 306 CKHRGFVMISYYDIRASQNAMKALQNNPLRRRKLDIHFSIPKDNPSEKNANQGTLLVFNL 365

Query: 241 DSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK 300
           DSSVSNDEL  IFGVYGEIKEIRET  + H KYIEFYD RAAEAALR LN   +AGKQI 
Sbjct: 366 DSSVSNDELRQIFGVYGEIKEIRETQHRSHHKYIEFYDVRAAEAALRALNRSDVAGKQIM 425

Query: 301 LEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSL 360
           +E  H  G R+ L+ Q P ELEQ+E G Y  QNSP +  T                    
Sbjct: 426 IEAIHPGGTRR-LSQQFPSELEQDEPGLYLHQNSPSSLATG------------------- 465

Query: 361 AIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPPT--ESAFHLGISSSVP-SLVRMES 417
                F+GA  HG     + +  I+    ++  A  +  ++AF  G+S SVP SL+R+ES
Sbjct: 466 -----FSGALPHGGHGLSMENGSILGRQSASGSAMNSYLDNAFDCGLSFSVPNSLLRLES 520

Query: 418 FG-TQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIKP 476
            G  Q+ + E GHLQ Q  F++R T   HPHSLPE HDGL+ G    S G   AN+NI+P
Sbjct: 521 KGGNQANVGETGHLQSQFNFDLRGTSGLHPHSLPEYHDGLSNGTTSISPGGISANMNIRP 580

Query: 477 PEIIDSRHFSRVSSNGHSIGFTEVFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPNSPS 536
            E I++R FSRV  NG  +   EVF      +CP PGHQY W+NS+  Q  GMMWPNSP+
Sbjct: 581 LEAIENRKFSRVGPNGQPVELNEVFTPNGTANCPSPGHQYMWSNSHQSQPQGMMWPNSPT 640

Query: 537 LVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSL--WERQHAYVAESP 594
            V G+  +  P ++H +PRAPSHM+N ++PI +HHVGSAP+V+PSL  W+R+HAY  ESP
Sbjct: 641 YVGGVCAS-RPQQLHSVPRAPSHMLNALVPINNHHVGSAPSVNPSLSLWDRRHAYAGESP 699

Query: 595 EASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRSMMF 654
           +ASGFH GS GSMRIS NS H +EF+ HN+F   GG+ +D+P+ S N     H QR++MF
Sbjct: 700 DASGFHPGSLGSMRISGNSPHPLEFIPHNVFSRTGGSCIDLPMSSSNV---GHQQRNLMF 756

Query: 655 SGRGQTIPLMNSFDPPNERARNRRNEGAVNQAD-KKQYELDIDRILRGEDNRTTLMIKNI 713
            GR Q IP+++SFD PNER R+RRNEG  +Q D KKQ+ELDI+RI RG+D RTTLMIKNI
Sbjct: 757 PGRAQIIPMISSFDSPNERMRSRRNEGNSSQTDNKKQFELDIERIARGDDKRTTLMIKNI 816

Query: 714 PNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKK 773
           PNKYTSKMLLAAIDERH+GTYDFIYLPIDFKNKCNVGYAFINMT+PS IVPFY +FNGKK
Sbjct: 817 PNKYTSKMLLAAIDERHRGTYDFIYLPIDFKNKCNVGYAFINMTEPSLIVPFYHAFNGKK 876

Query: 774 WEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMG 833
           WEKFNSEKVASLAYARIQGK+ALIAHFQNSSLMNEDKRCRPILF+TDGPNAGDQVPFPMG
Sbjct: 877 WEKFNSEKVASLAYARIQGKSALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDQVPFPMG 936

Query: 834 VNFRTRPGKARSVIHEENHHGS 855
           V+ R R  K R+   EE++  S
Sbjct: 937 VSMRPRSSKNRAGTSEESYQES 958

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297734509|emb|CBI15756.3| unnamed protein product [Vitis vinifera]

 Score =  890 bits (2300), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 526/899 (58%), Positives = 618/899 (68%), Gaps = 61/899 (6%)

Query: 2   GAQYESSLFSSSLSELFSRKLRLS-SDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIG 60
           GA YESSLFSSSLSE+F+RKLR+S SD+ S+  S  TV+ H EEE+ F+SLEEIE QT+G
Sbjct: 137 GALYESSLFSSSLSEIFNRKLRVSTSDVLSH-QSAGTVAPHSEEEKLFKSLEEIEVQTLG 195

Query: 61  NLLPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDL-GNDSSYVAQKKSE 119
           NLLPD+D+LFSGV D +    H    + GDD +D D FSS GGM+L G+D   ++Q+ S+
Sbjct: 196 NLLPDEDELFSGVVDDMGYNAH---ANNGDDFEDFDLFSSGGGMELEGDDHLCISQRHSD 252

Query: 120 ICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR 179
              G  N + G  NG++A EH   EHPSRTL +R INSN+EDSEL+ LFEQYGD+RT Y 
Sbjct: 253 FNGGIPNSQ-GGSNGSLASEHPYGEHPSRTLFVRNINSNVEDSELRDLFEQYGDIRTLYT 311

Query: 180 ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFN 239
           A KH GFV ISYYDIRAARNAM++LQNK  R  KLDIHYSIPKDNPSEK+INQGTLVVFN
Sbjct: 312 ACKHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPSEKDINQGTLVVFN 371

Query: 240 LDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQI 299
           LDSSVSND+L  IFG+YGEIKEIRETP K H K+IEF+D RAAEAALR LN   IAGK+I
Sbjct: 372 LDSSVSNDDLRQIFGIYGEIKEIRETPHKRHHKFIEFFDVRAAEAALRALNRSDIAGKRI 431

Query: 300 KLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKS 359
           KLEPS   G R+CL      ELEQ+E    Q  +       N S+G +            
Sbjct: 432 KLEPSRPGGSRRCLMQLCSSELEQDESILCQSPDD------NLSSGCM------------ 473

Query: 360 LAIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPP---TESAFHLGISS---SVPSLV 413
                    A + G K+S   D   +  + SAV+ P     E+A   G SS   ++PS +
Sbjct: 474 ---------AVSPGIKTSSCMDNVSIQDLHSAVRMPIGSFVENATSHGSSSVPNTLPSPM 524

Query: 414 RMESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKG---A 470
           R+ S   +  L E  +   Q+KF  +S P++HPHSLPE HD L   +R NSS T G    
Sbjct: 525 RVVSIINEFGLGETSNTLDQMKFGNQSFPNYHPHSLPEYHDNLANAIRYNSSSTIGDMTG 584

Query: 471 NINIKPPEIIDSRHFSRVSSNGHSIGFT-EVFGSASNGSCPRPGHQYSWNNSYCPQLPG- 528
           ++  +  E ID+RH  RV SNGH I      FGS+ NGSCP  G   +W NS   Q    
Sbjct: 585 HVGPRITEGIDNRHIHRVGSNGHPIELNGGAFGSSGNGSCPVHGLHRAWGNSSSYQHHSS 644

Query: 529 --MMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQ 586
             M+WPNSPS  +G+ +   PT+V G PR P HM+N V P+  HHVGSAP V+PSLW+R+
Sbjct: 645 SPMIWPNSPSFSNGV-HAQRPTQVPGFPRPPPHMLNIVSPVHHHHVGSAPAVNPSLWDRR 703

Query: 587 HAYVAESPEASGFHLGSHGSMRISNNS-LHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQ 645
           HAY  ESPE SGFHLGS GS+    +S LH +E  SH IFP VGGN MD+   S N   +
Sbjct: 704 HAYSGESPETSGFHLGSLGSVGFPGSSPLHPLEMASH-IFPHVGGNCMDI---SANVGLR 759

Query: 646 SHHQRSMMFSGRGQTIPLMNSFDPPNERARN---RRNEGAVNQADKKQYELDIDRILRGE 702
           S  Q   +F GR   + + +SFD P ER RN   RR E   N  DKKQYELDIDRILRGE
Sbjct: 760 SPQQICHVFPGRNSMLSIPSSFDLPMERVRNLSHRRTEANSNHTDKKQYELDIDRILRGE 819

Query: 703 DNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQI 762
           D RTTLMIKNIPNKYTSKMLLAAIDE H+GTYDFIYLPIDFKNKCNVGYAF+NM DP  I
Sbjct: 820 DCRTTLMIKNIPNKYTSKMLLAAIDEHHRGTYDFIYLPIDFKNKCNVGYAFVNMIDPLHI 879

Query: 763 VPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGP 822
           VPF+Q+FNGKKWEKFNSEKVASLAYARIQGK ALIAHFQNSSLMNEDKRCRPILF+TDGP
Sbjct: 880 VPFHQAFNGKKWEKFNSEKVASLAYARIQGKTALIAHFQNSSLMNEDKRCRPILFHTDGP 939

Query: 823 NAGDQVPFPMGVNFRTRPGKARSVIHEEN-HHGSP---PNVEDLSNGDAP-SGSAKESD 876
           NAGDQ PFPMG N R+RPGKAR+   EE+ H GSP    N E+ SNG     GSAK+SD
Sbjct: 940 NAGDQEPFPMGSNIRSRPGKARTSGGEESQHQGSPTTSANGEESSNGAVTLLGSAKDSD 998

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540053|ref|XP_002511091.1| RNA-binding protein, putative [Ricinus communis] gi|223550206|gb|EEF51693.1| RNA-binding protein, putative [Ricinus communis]

 Score =  887 bits (2291), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 512/886 (57%), Positives = 599/886 (67%), Gaps = 62/886 (6%)

Query: 3   AQYESSLFSSSLSELFSRKLRLSSDIASYGHSVDTVSSHYEEEEPFESLEEIEAQTIGNL 62
            Q+ESSLFSSSLSE+F+ KLRL  +          ++   EE+EPFESLEE+EAQTIGNL
Sbjct: 131 TQWESSLFSSSLSEVFNGKLRLLENDIQSRQPAKPIALPNEEDEPFESLEELEAQTIGNL 190

Query: 63  LPDDDDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDL-GNDSSYVAQKKSEIC 121
           LP +DDLFSGVTD L    H +GG   DD++D D F + GGM+L G+D   V Q+ S+  
Sbjct: 191 LPAEDDLFSGVTDELGHNAHTNGG---DDLEDFDLFITGGGMELEGDDRLCVGQRNSDFV 247

Query: 122 IGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRAS 181
              SN + G  NG+V GEH   EHPSRTL +R INSN+EDSELKALFEQYGD+RT Y A 
Sbjct: 248 GALSNLQ-GGSNGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQYGDIRTLYTAC 306

Query: 182 KHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLD 241
           KH GFV ISYYDIRAARNAM+SLQNK  R  KLDIHYSIPKDNPSEK+INQGTLV+FNLD
Sbjct: 307 KHRGFVMISYYDIRAARNAMRSLQNKPLRRRKLDIHYSIPKDNPSEKDINQGTLVIFNLD 366

Query: 242 SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL 301
           SSVS +ELH IFGVYGEIKEIRETP K H K+IE+YD R+AEAAL  LN   IAGKQIKL
Sbjct: 367 SSVSTEELHKIFGVYGEIKEIRETPHKRHHKFIEYYDIRSAEAALSALNRSDIAGKQIKL 426

Query: 302 EPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLA 361
           EPS   G R+ +     PE EQ+E G  Q   SP                      + L+
Sbjct: 427 EPSRPGGTRRLMTK---PEQEQDESGLCQ---SP---------------------FEDLS 459

Query: 362 IIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPP---TESAFHLGISSSVPSLVRMESF 418
              L T  F+ G  +S   +     V+ SA+++P     ES     + +++PS V + S 
Sbjct: 460 SGRLAT--FSPGVIASSCMENGSTQVIHSAIQSPVGSFIESHRSSSVPNNLPSPVSVTSI 517

Query: 419 GTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGA---NINIK 475
             Q  L EP     ++ F  +  PSFHPHSLPE  DGL  GV  NSS + G    ++  K
Sbjct: 518 SKQFGLHEPNRSMDEMMFGNQRIPSFHPHSLPEYPDGLANGVPFNSSSSIGGMAHSVGSK 577

Query: 476 PPEIIDSRHFSRVSSNGHSIGFTE-VFGSASNGSCPRPGHQYSWNNSYCPQL---PGMMW 531
             E I SRH   VSSNGH +     VFGS+ NGS P  GH Y WNNS   Q      M+W
Sbjct: 578 VTEGISSRHIQAVSSNGHLMELNGGVFGSSGNGSLP--GHHYMWNNSNTNQQHHSSRMIW 635

Query: 532 PNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSHHVGSAPTVDPSLWERQHAYVA 591
           PNS S  +G+   + P  + G PRAP  M+NTV     HHVGSAP+V+PS+WER+HAY  
Sbjct: 636 PNSSSFTNGVHAHHLP-HMPGFPRAPPVMLNTV--PAHHHVGSAPSVNPSVWERRHAYAG 692

Query: 592 ESPEASGFHLGSHGSMRISNNSLHSVEFVSHNIFPCVGGNGMDMPLPSKNSVFQSHHQRS 651
           ESPEAS FHLGS GS+     S H +E  SHNIF  VGGN MDM   +KN+  ++     
Sbjct: 693 ESPEASSFHLGSLGSV----GSPHPMEIASHNIFSHVGGNCMDM---TKNAGLRTAQPMC 745

Query: 652 MMFSGRGQTIPLMNSFDPPNERARN---RRNEGAVNQADKKQYELDIDRILRGEDNRTTL 708
            +F GR   I +  SFD PNER RN   RR +   N +DKKQYELD+DRI+RGED+RTTL
Sbjct: 746 HIFPGRNPMISMPASFDSPNERVRNLSHRRIDSNPNHSDKKQYELDLDRIMRGEDSRTTL 805

Query: 709 MIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQS 768
           MIKNIPNKYTSKMLLAAIDE  +GTYDFIYLPIDFKNKCNVGYAFINM DP QI+PF+++
Sbjct: 806 MIKNIPNKYTSKMLLAAIDEYCRGTYDFIYLPIDFKNKCNVGYAFINMIDPQQIIPFHKA 865

Query: 769 FNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQV 828
           FNGKKWEKFNSEKVASLAYARIQGK+ALIAHFQNSSLMNEDKRCRPILF+TDGPNAGD  
Sbjct: 866 FNGKKWEKFNSEKVASLAYARIQGKSALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPE 925

Query: 829 PFPMGVNFRTRPGKARSVIHEENHHGSP---PNVEDLSNGDAPSGS 871
           PFPMG N R+R GK R+   EENHHG+P    N ED S G   SGS
Sbjct: 926 PFPMGTNVRSRLGKLRTSGSEENHHGNPSTSANGEDSSVGTDSSGS 971

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (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)
Q75M35	OML3_ORYSJ	No assigned EC number	0.4324	0.8847	0.8115	yes	no
Q64M78	OML4_ORYSJ	No assigned EC number	0.5240	0.9646	0.8441	yes	no
Q8W4I9	AML1_ARATH	No assigned EC number	0.4948	0.8789	0.8415	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00031323 hypothetical protein (977 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	876
pfam04059	97	pfam04059, RRM_2, RNA recognition motif 2	3e-62
cd12531	86	cd12531, RRM3_MEI2_like, RNA recognition motif 3 i	9e-61
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	3e-42
cd12532	90	cd12532, RRM3_MEI2_fungi, RNA recognition motif 3	6e-38
cd12530	101	cd12530, RRM3_EAR1_like, RNA recognition motif 3 i	2e-37
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	9e-37
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	4e-34
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	2e-30
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	8e-26
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	5e-21
smart00360	73	smart00360, RRM, RNA recognition motif	2e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-11
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-10
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	1e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-09
cd12526	71	cd12526, RRM1_EAR1_like, RNA recognition motif 1 i	7e-09
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-07
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	2e-07
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-07
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-06
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-06
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	2e-06
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-06
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-06
cd12752	87	cd12752, RRM1_RBM5, RNA recognition motif 1 in ver	5e-06
smart00360	73	smart00360, RRM, RNA recognition motif	6e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	6e-06
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	6e-06
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	9e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	9e-06
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	1e-05
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	2e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	2e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-05
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-05
cd12525	72	cd12525, RRM1_MEI2_fungi, RNA recognition motif 1	2e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	4e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	6e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	8e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	8e-05
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	9e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-04
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	1e-04
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	1e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-04
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-04
cd12528	81	cd12528, RRM2_MEI2_fungi, RNA recognition motif 2	2e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-04
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-04
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	3e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	4e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	4e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	4e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	5e-04
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	5e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	5e-04
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	6e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	6e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	6e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	9e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	9e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.001
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	0.001
cd12696	107	cd12696, RRM3_PTBP2, RNA recognition motif 3 in ve	0.001
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	0.001
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	0.001
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.001
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.001
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	0.001
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.002
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	0.002
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.003
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	0.003
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.003
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.003
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	0.003
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.003
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	0.003
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	0.003
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.003
smart00360	73	smart00360, RRM, RNA recognition motif	0.004
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	0.004

>gnl|CDD|112856 pfam04059, RRM_2, RNA recognition motif 2

 Score =  204 bits (520), Expect = 3e-62
 Identities = 84/97 (86%), Positives = 91/97 (93%)

Query: 705 RTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVP 764
           RTTLMIKNIPNKYT KMLLAAIDE++KGTYDF+YLPIDFKNKCNVGYAFINM +P  I+P
Sbjct: 1   RTTLMIKNIPNKYTQKMLLAAIDEKNKGTYDFLYLPIDFKNKCNVGYAFINMIEPQSIIP 60

Query: 765 FYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQ 801
           F ++FNGKKWEKFNSEKVASLAYARIQGK ALIAHFQ
Sbjct: 61  FGKAFNGKKWEKFNSEKVASLAYARIQGKDALIAHFQ 97

Length = 97

>gnl|CDD|240975 cd12531, RRM3_MEI2_like, RNA recognition motif 3 in plant Mei2-like proteins

 Score =  199 bits (509), Expect = 9e-61
 Identities = 75/86 (87%), Positives = 79/86 (91%)

Query: 708 LMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQ 767
           LMIKNIPNKYT KMLLAAIDE+H+GTYDF YLPIDFKNKCNVGYAFINM  P  IVPFY+
Sbjct: 1   LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYK 60

Query: 768 SFNGKKWEKFNSEKVASLAYARIQGK 793
           +FNGKKWEKFNSEKV SLAYARIQGK
Sbjct: 61  AFNGKKWEKFNSEKVCSLAYARIQGK 86

This subgroup corresponds to the RRM3 of Mei2-like proteins, representing an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 86

>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like proteins and terminal EAR1-like proteins

 Score =  148 bits (375), Expect = 3e-42
 Identities = 56/86 (65%), Positives = 67/86 (77%), Gaps = 1/86 (1%)

Query: 708 LMIKNIPNKYTSKMLLAAIDERHKG-TYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFY 766
           +MI+NIPNKYT +MLL  +DE  KG  YDF+YLPIDFKNKCNVGYAFIN  +P     FY
Sbjct: 1   VMIRNIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFY 60

Query: 767 QSFNGKKWEKFNSEKVASLAYARIQG 792
           ++FNGKKW+ F S+KV  + YARIQG
Sbjct: 61  KAFNGKKWKNFKSKKVCDITYARIQG 86

This subfamily corresponds to the RRM3 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 86

>gnl|CDD|240976 cd12532, RRM3_MEI2_fungi, RNA recognition motif 3 in fungal Mei2-like proteins

 Score =  136 bits (343), Expect = 6e-38
 Identities = 52/89 (58%), Positives = 66/89 (74%)

Query: 705 RTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVP 764
           RTT+M+KNIPNK+T +ML   IDE + GTYDF+YL IDF N CNVGYAF+N  +P  I+ 
Sbjct: 1   RTTVMLKNIPNKFTQQMLRKYIDETNPGTYDFMYLRIDFNNSCNVGYAFVNFIEPISIIT 60

Query: 765 FYQSFNGKKWEKFNSEKVASLAYARIQGK 793
           F ++  G KW  F+SEKV  ++YA IQGK
Sbjct: 61  FGKARVGTKWNMFHSEKVCDISYANIQGK 89

This subgroup corresponds to the RRM3 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. . Length = 90

>gnl|CDD|240974 cd12530, RRM3_EAR1_like, RNA recognition motif 3 in terminal EAR1-like proteins

 Score =  134 bits (340), Expect = 2e-37
 Identities = 53/102 (51%), Positives = 69/102 (67%), Gaps = 15/102 (14%)

Query: 705 RTTLMIKNIPNKYTSKMLLAAIDERH--------------KGTYDFIYLPIDFKNKCNVG 750
           RTTLMIKNIPNKY+ K+LL  +D  H                +YDF+YLPIDFKNKCN+G
Sbjct: 1   RTTLMIKNIPNKYSQKLLLDMLD-THCIQCNQHIEDSSQPVSSYDFVYLPIDFKNKCNLG 59

Query: 751 YAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQG 792
           YAF+N T P     FY++F+ ++WE+FNS K+  + YAR+QG
Sbjct: 60  YAFVNFTSPEATWRFYKAFHNQQWEEFNSRKICQITYARVQG 101

This subgroup corresponds to the RRM3 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 101

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score =  132 bits (334), Expect = 9e-37
 Identities = 50/77 (64%), Positives = 60/77 (77%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN 206
           SRTL +R INSN+ED EL+ALFEQ+GD+RT Y A KH GF+ +SYYDIRAAR A ++LQ 
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 207 KLTRSGKLDIHYSIPKD 223
                 KLDIH+SIPKD
Sbjct: 61  TELGGRKLDIHFSIPKD 77

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score =  124 bits (313), Expect = 4e-34
 Identities = 55/71 (77%), Positives = 60/71 (84%)

Query: 232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS 291
           QGTLVVFNLD SVSND+LH IFG YGEIKEIRETP K H K+IEFYD R+AEAAL+ LN 
Sbjct: 1   QGTLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNR 60

Query: 292 RYIAGKQIKLE 302
             IAGK+IKLE
Sbjct: 61  SEIAGKRIKLE 71

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score =  113 bits (286), Expect = 2e-30
 Identities = 40/71 (56%), Positives = 54/71 (76%)

Query: 232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS 291
           QGTL+VFNLDS +S+ EL  +F  +GE+K+IRETP +  QK++EFYD RAAEAAL  LN 
Sbjct: 1   QGTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 292 RYIAGKQIKLE 302
           R   G ++K++
Sbjct: 61  RPFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score =  101 bits (252), Expect = 8e-26
 Identities = 38/71 (53%), Positives = 54/71 (76%)

Query: 232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS 291
           QGTLV+FNLD +VS++ L  IF VYG++KE+RETP K  Q+++EF+D R A  ALR +N 
Sbjct: 1   QGTLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNG 60

Query: 292 RYIAGKQIKLE 302
           + I+GK + +E
Sbjct: 61  KEISGKPVVIE 71

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 87.2 bits (216), Expect = 5e-21
 Identities = 24/71 (33%), Positives = 38/71 (53%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN 206
           SR+L +  +  ++ +S L+ LFE YGDVR         G VT+ +YDIR A+ A++ L  
Sbjct: 1   SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCG 60

Query: 207 KLTRSGKLDIH 217
           +  +   L   
Sbjct: 61  RHMQQQALGGS 71

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRE 288
           TL V NL    + +EL  +F  +G+++ +R    K   K     ++EF     AE AL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 289 LNSRYIAGKQIKL 301
           LN + + G+ +K+
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 59.6 bits (145), Expect = 3e-11
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIR-ETPQKIHQK---YIEFYDTRAAEAALRELN 290
           L V NL    + ++L  +F  +GEI+ +R    +    K   ++EF     AE AL  LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 291 SRYIAGKQIKLE 302
            + + G+++K+ 
Sbjct: 61  GKELDGRKLKVS 72

RRM, 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. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 56.9 bits (138), Expect = 3e-10
 Identities = 20/67 (29%), Positives = 37/67 (55%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
           TL V N++S+V ++EL  +F  +G+I+ +    +      + +YD RAA  A R L    
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTE 62

Query: 294 IAGKQIK 300
           + G+++ 
Sbjct: 63  LGGRKLD 69

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 149 TLLLRKINSNIEDSELKALFEQYGDVRTF--YRASKHCGFVTISYYDIRAARNAMKSLQN 206
           TLL+  ++S I D EL++LF Q+G+V+            FV   +YDIRAA  A+ +L  
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFV--EFYDIRAAEAALDALNG 60

Query: 207 KLTRSGKLDI 216
           +    G+L +
Sbjct: 61  RPFLGGRLKV 70

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 52.5 bits (127), Expect = 5e-09
 Identities = 15/56 (26%), Positives = 32/56 (57%)

Query: 249 LHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS 304
           L+ +F  +G +++I+   +K    ++EF    AAE A++ LN     G+ ++++ S
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIR----ETPQKIHQKYIEFYDTRAAEAALRELN 290
           L V NL    + ++L  +F  +G I+ IR    ET +     ++EF D   AE AL  LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 291 SRYIAGKQIK 300
            + + G++++
Sbjct: 61  GKELGGRELR 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal EAR1-like proteins

 Score = 52.7 bits (127), Expect = 7e-09
 Identities = 20/59 (33%), Positives = 36/59 (61%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ 205
           SR LLL  +  +I +++L+   EQ+G VR     +   G VT+ +YD+R A +A++ ++
Sbjct: 1   SRALLLSGVPPHIPETQLRRDLEQWGAVRAVQMDAMAEGIVTVHFYDLRHAEDALRDIR 59

This subgroup corresponds to the RRM1 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALREL 289
           L V  L  +V+ D L  IF  YG +K++     RE        Y+EF     AE A++ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 290 NSRYIAGKQIKLE 302
           +   I G+++ +E
Sbjct: 61  DGGQIDGQEVTVE 73

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 49.1 bits (117), Expect = 2e-07
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY----IEFYDTRAAEAALRELN 290
           L V NLD  V+ D L  IF V G ++ ++  P K ++      +E++ +  AE AL+ LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 291 SRYIAGKQIKL 301
            R I   +I++
Sbjct: 61  GRQIENNEIRV 71

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 49.1 bits (118), Expect = 2e-07
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALR 287
             L V  L +  +  EL  +F  +G ++E+         +     ++ F     A+AA+R
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 288 ELNSRYIAGKQIKLE 302
           +LN + + G+ IK+E
Sbjct: 62  DLNGKELEGRVIKVE 76

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 27/68 (39%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFYDTRAAEAALRELNSR 292
           L V NLD +V+ D L  +F   G IK  +   +  +  Y  +E+YD R+A AAL+ +N R
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 293 YIAGKQIK 300
            I G++IK
Sbjct: 61  LILGQEIK 68

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 47.9 bits (115), Expect = 3e-07
 Identities = 16/56 (28%), Positives = 23/56 (41%)

Query: 164 LKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS 219
           L  LF  +G+V       K  GF  + +    AA  A++ L   L     L + YS
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 237 VFNLDSSVSNDELHHIFGVYGEIKEI---RETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
           V NL    +  EL   F  YG ++ +   R  P      ++EF D R AE A+R L+ R 
Sbjct: 4   VGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGF---AFVEFEDPRDAEDAVRALDGRR 60

Query: 294 IAGKQIKLEPSH 305
           I G ++++E S 
Sbjct: 61  ICGNRVRVELSR 72

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 26/68 (38%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
           T+ V  LD +V+ DEL  +FG +GEI  ++  P K    +++F    AAEAA+++L    
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGK-GCGFVQFVHRAAAEAAIQQLQGTI 61

Query: 294 IAGKQIKL 301
           I G +I+L
Sbjct: 62  IGGSRIRL 69

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIR--ETPQKIHQK---YIEFYDTRAAEAALREL 289
           L V NL      D ++  FG YGEI  +R    P     K   Y+EF    AA+AAL  L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 290 NSRYIAGKQIKLE 302
               + G+ ++L+
Sbjct: 61  GGTDLLGRPVRLD 73

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 46.0 bits (110), Expect = 2e-06
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIH-QKYIEFYDTRAAEAALRELNSRY 293
           + + NL   V+ D LH +F  YG +++I    +    Q  ++F    +AE A + LN R 
Sbjct: 4   VTISNLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRN 63

Query: 294 IAGKQIKL--EPSHLRGLR 310
           I      L  + S L+ L 
Sbjct: 64  IYDGCCTLDIQFSRLKELT 82

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 8/74 (10%)

Query: 150 LLLRKINSNIEDSELKALFEQYGDV------RTFYRASKHCGFVTISYYDIRAARNAMKS 203
           L +  +  +  + +L+ LF ++G++      R     SK   FV   +     A  A+++
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVE--FESPEDAEKALEA 58

Query: 204 LQNKLTRSGKLDIH 217
           L  K     KL + 
Sbjct: 59  LNGKELDGRKLKVS 72

RRM, 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. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 45.2 bits (108), Expect = 3e-06
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 234 TLVVFNLDSSVSNDE----LHHIFGVYGEIKEI--RETPQKIHQKYIEFYDTRAAEAALR 287
           TL + NL+  +  DE    L+ +F  +G + +I   +T +   Q ++ F D  +A  ALR
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 288 ELNSRYIAGKQIKLE 302
            L       K ++++
Sbjct: 61  ALQGFPFYDKPMRIQ 75

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate RNA-binding protein 5 (RBM5)

 Score = 45.4 bits (107), Expect = 5e-06
 Identities = 29/87 (33%), Positives = 49/87 (56%), Gaps = 7/87 (8%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFE-----QYGDVRTFYRASKHC-GFVTISYYDIRA 196
           DE  S+T++LR +  NI +++++ L E     Q  DVR   R +    GF  + +Y ++ 
Sbjct: 1   DEKESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQD 60

Query: 197 ARNAMKSLQNKLTRSGK-LDIHYSIPK 222
           A + M++ Q KL   GK + +HYS P+
Sbjct: 61  ATSWMEANQKKLVIQGKTIAMHYSNPR 87

This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. . Length = 87

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 44.5 bits (106), Expect = 6e-06
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 5/64 (7%)

Query: 149 TLLLRKINSNIEDSELKALFEQYGDV-----RTFYRASKHCGFVTISYYDIRAARNAMKS 203
           TL +  +  +  + EL+ LF ++G V            K  GF  + +     A  A+++
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 204 LQNK 207
           L  K
Sbjct: 61  LNGK 64

Length = 73

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 44.6 bits (106), Expect = 6e-06
 Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAE-AALRELNSR 292
           TL V  L   V+  +L   F  +GEI+ I   P++    ++ F    AAE AA R  N  
Sbjct: 3   TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQ-QCAFVTFTTREAAEKAAERLFNKL 61

Query: 293 YIAGKQIKL 301
            I G+++KL
Sbjct: 62  IINGRRLKL 70

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 45.4 bits (108), Expect = 6e-06
 Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 13/82 (15%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIR-----ETPQKIHQKYIEFYD-----TRAAE 283
            +VV+    S S D + + F  +GEI EIR      T   +    I++Y       RAA+
Sbjct: 4   EIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDRAAK 63

Query: 284 AALRELN---SRYIAGKQIKLE 302
           AAL+ +       I G + K+E
Sbjct: 64  AALKAVRKAQDCRIGGAEFKVE 85

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 110

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 44.1 bits (105), Expect = 9e-06
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 149 TLLLRKINSNIEDSELK----ALFEQYG---DVRTFYRASKHCGFVTISYYDIRAARNAM 201
           TL +  +N  I+  ELK    ALF Q+G   D+    +  K  G   + + D+ +A NA+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVAS-KTLKMRGQAFVVFKDVESATNAL 59

Query: 202 KSLQNKLTRSGKLDIHYS 219
           ++LQ        + I Y+
Sbjct: 60  RALQGFPFYDKPMRIQYA 77

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 44.1 bits (105), Expect = 9e-06
 Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALREL 289
           L V +L   V+   L+ IF   G +  IR     I ++     Y+ F +   AE AL  L
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 290 NSRYIAGKQIKLEPSH 305
           N   I GK I++  S 
Sbjct: 62  NFDVIKGKPIRIMWSQ 77

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR----ETPQKIHQKYIEFYDTRAAEA 284
           EI + T+ V NLD + + D+L   F   GE+K +R    ET    +  ++EF +  +   
Sbjct: 2   EI-RRTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRY-AFVEFAEQTSVIN 59

Query: 285 ALRELNSRYIAGKQIKLEPS 304
           AL+ LN     G+ +K+  S
Sbjct: 60  ALK-LNGAMFGGRPLKVNHS 78

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 19/59 (32%), Positives = 31/59 (52%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSR 292
           +L V N+   V+   L  +F VYG+++ ++          + FYD R A+ A+REL  R
Sbjct: 3   SLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCGR 61

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 43.5 bits (103), Expect = 2e-05
 Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKE--IRETPQKIHQKYIEFYDTRAAEAALRELNS 291
           TL + NL+ + +  +L   F  +GEI +  I++        +I++ D  +   A+R+++ 
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63

Query: 292 RYIAGKQIKL 301
            Y+   ++KL
Sbjct: 64  EYLGNNRVKL 73

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 48.0 bits (114), Expect = 2e-05
 Identities = 44/185 (23%), Positives = 78/185 (42%), Gaps = 35/185 (18%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-------RASKHCGFVTISYYDIR 195
            E   RT+ + ++     + +L   F + G VR          R SK   +V   +YD+ 
Sbjct: 85  AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYV--EFYDVE 142

Query: 196 AARNAM--------------KSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLD 241
           +   A+              +S Q +  R+ K   H      N  +       L V NL 
Sbjct: 143 SVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLK-------LYVGNLH 195

Query: 242 SSVSNDELHHIFGVYGEIKEIR-----ETPQKIHQKYIEFYDTRAAEAALRELNSRYIAG 296
            +++  EL  IF  +G+I++++     ET +     +I+F+D   A+ AL  +N   +AG
Sbjct: 196 FNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAG 255

Query: 297 KQIKL 301
           + IK+
Sbjct: 256 RPIKV 260

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK---YIEFYDTRAAEAALRELN 290
           T+ V  +D S+S D+L   F   GE+  +R    + H     ++EF D  +A +AL  L+
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALN-LS 60

Query: 291 SRYIAGKQIKLEPS 304
              + G  +++ PS
Sbjct: 61  GTLLGGHPLRVSPS 74

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 43.5 bits (102), Expect = 2e-05
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 7/75 (9%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK------YIEFYDTRAAEAALR 287
           +L V N+  +   ++L   FG YG I ++   P   + +      YI+F D R AE AL 
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVY-VPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 288 ELNSRYIAGKQIKLE 302
            LN +++ G+QI+++
Sbjct: 61  NLNRKWVCGRQIEIQ 75

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal Mei2-like proteins

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVR-TFYRASKHCGFVTISYYDIRAARNAMKSLQ 205
           +R L +  +  ++  S LK +FE+ GDV+  F +     G V +S++D+R A  A K LQ
Sbjct: 1   TRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLLSKGIVIVSFHDLRQAIKAYKDLQ 60

Query: 206 NKL 208
           +K 
Sbjct: 61  SKR 63

This subgroup corresponds to the RRM1 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. . Length = 72

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIR--ETPQKIHQKYIEFYDTRAAEAALRELNSR 292
           L V NL   +S++EL+ +FG YG I++IR   T +     ++ + D   A+ A   L+  
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGF 64

Query: 293 YIAGK 297
            +A +
Sbjct: 65  NVANR 69

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 7/58 (12%)

Query: 244 VSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFYDTRAAEAALRELNSRYIAGKQI 299
           VS ++L  IF  YG+I  I      +H+ Y  ++F +   A AA+   N R IAG+++
Sbjct: 13  VSKEDLEEIFSKYGKILGIS-----LHKGYGFVQFDNEEDARAAVAGENGREIAGQKL 65

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
           T+ V NL   ++ +EL   F  +G I+E+R    K    ++ F    AA  A+  +N   
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK-GYAFVRFDTHEAAATAIVAVNGTS 60

Query: 294 IAGKQIK 300
           I G+ +K
Sbjct: 61  INGQTVK 67

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 42.3 bits (99), Expect = 6e-05
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 7/75 (9%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK------YIEFYDTRAAEAALR 287
           +L V N+     +++L   FG YG I ++   P   + +      Y++F D R AE AL 
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVY-VPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 288 ELNSRYIAGKQIKLE 302
            L+ ++I G+QI+++
Sbjct: 61  NLDRKWICGRQIEIQ 75

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 41.9 bits (99), Expect = 8e-05
 Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 5/71 (7%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRE 288
           TL V  L    + + L  +F  YG+I+ +R     +        ++E+   R A  A R+
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 289 LNSRYIAGKQI 299
            +   I G +I
Sbjct: 65  AHKLVIDGSEI 75

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 41.2 bits (97), Expect = 8e-05
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALREL 289
           L+V  L   ++ +EL  +F   G I+       R T Q +   ++++ D   A+ A+  L
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 290 NSRYIAGKQIK 300
           N   I  K++K
Sbjct: 63  NGFEIRNKRLK 73

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 41.8 bits (99), Expect = 9e-05
 Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRE 288
           TL V  L+   +  +L   F  YG IK IR    K   K     +IEF   R  +AA + 
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62

Query: 289 LNSRYIAGKQI 299
            + + I G+++
Sbjct: 63  ADGKKIDGRRV 73

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>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

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 5/72 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALRE 288
           T+ V NL  S++N++LH IF  YG++ ++     +ET +     +I F D   A   ++ 
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 289 LNSRYIAGKQIK 300
           LN++ + G+ +K
Sbjct: 63  LNNKELFGRTLK 74

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 41.2 bits (96), Expect = 1e-04
 Identities = 22/69 (31%), Positives = 38/69 (55%)

Query: 237 VFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAG 296
           V NL ++ +  EL   FG YG ++ +          ++EF D R A  A+REL+ R + G
Sbjct: 9   VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCG 68

Query: 297 KQIKLEPSH 305
            ++++E S+
Sbjct: 69  CRVRVELSN 77

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 235 LVVFNLDSS-VSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
           L+V NL+   V+ D L  +FGVYG++  ++    K     I+  D + A+ AL  LN   
Sbjct: 2   LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIR 61

Query: 294 IAGKQIKLEPS 304
           + GK++++  S
Sbjct: 62  LHGKKLRVTLS 72

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKE--IRETPQKIHQKY--IEFYDTRAAEAALREL 289
           TL V NL+ +++ +EL   F  YG +++  I+  P+     Y  ++F +   A  A   +
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 290 NSRYIAGKQIKL 301
           + +YI   QIK+
Sbjct: 64  SGQYIGRNQIKI 75

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 8/64 (12%)

Query: 150 LLLRKINSNIEDSELKALFEQYGDVRTFY------RASKHCGFVTISYYDIRAARNAMKS 203
           L +  +  +  + +LK LF ++G + +          SK   FV   + D   A  A+++
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVE--FEDEEDAEKALEA 58

Query: 204 LQNK 207
           L  K
Sbjct: 59  LNGK 62

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRE 288
            L+V N+    +  EL  +F  +G++K +R  P+K         ++EF   + A+ A+  
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 289 LNSRYIAGKQIKLEPS 304
           L S ++ G+ + LE +
Sbjct: 61  LKSTHLYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKE---IRETPQKIHQ--KYIEFYDTRAAEAALRE 288
           TL V NL    ++++L   F   G IK    +++   K  +   Y+ F     A+ AL E
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 289 LNSRYIAGKQIKLE 302
                  G++I +E
Sbjct: 61  KKKTKFGGRKIHVE 74

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|240972 cd12528, RRM2_MEI2_fungi, RNA recognition motif 2 in fungal Mei2-like proteins

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 3/57 (5%)

Query: 241 DSSVSNDELHHIFGVYGEIKEI---RETPQKIHQKYIEFYDTRAAEAALRELNSRYI 294
           +S +  + L ++   +G++K           + +   EF+DTR A+ A+ ELN R +
Sbjct: 17  NSDLVKNSLQNLLSTFGDLKAFKSLPSQQDNVKEFICEFFDTRDADNAVDELNGRVV 73

This subgroup corresponds to the RRM2 of fungal Mei2-like proteins.The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. . Length = 81

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 43.9 bits (103), Expect = 2e-04
 Identities = 44/171 (25%), Positives = 80/171 (46%), Gaps = 19/171 (11%)

Query: 134 GAVAGEHLNDEHPSRT-LLLRKINSNIEDSELKALFEQYGDVRTF-----YRASKHCGFV 187
               G   ND + S T L++  +  ++ D EL ALF   G + T      Y+     G+ 
Sbjct: 93  LGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYA 152

Query: 188 TISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSND 247
            + +     ++ A+K+L     R+ +L + Y+     P  + I    L V NL  ++++D
Sbjct: 153 FVDFGSEADSQRAIKNLNGITVRNKRLKVSYA----RPGGESIKDTNLYVTNLPRTITDD 208

Query: 248 ELHHIFGVYGEIKE---IRE----TPQKIHQKYIEFYDTRAAEAALRELNS 291
           +L  IFG YG+I +   +R+    TP+ +   ++ F     A+ A+  LN+
Sbjct: 209 QLDTIFGKYGQIVQKNILRDKLTGTPRGV--AFVRFNKREEAQEAISALNN 257

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALRE 288
            L V NL  +V+ ++L  +FG +GE+        RET +     ++E      A AA+ +
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 289 LNSRYIAGKQIK 300
           LN     G+ + 
Sbjct: 61  LNGTDFGGRTLT 72

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYR-ASKHCGFVTISYYDIRAARNAMKSLQN 206
            TL +  +   + + +L+  F Q+G++R+      + C FVT  +    AA  A + L N
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVT--FTTREAAEKAAERLFN 59

Query: 207 KLTRSGK 213
           KL  +G+
Sbjct: 60  KLIINGR 66

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 44.4 bits (105), Expect = 3e-04
 Identities = 27/123 (21%), Positives = 57/123 (46%), Gaps = 6/123 (4%)

Query: 185 GFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSV 244
           G+  +++ +   A  A++++  K      + I +S  + +PS +    G + V NLD SV
Sbjct: 43  GYGYVNFQNPADAERALETMNFKRLGGKPIRIMWS--QRDPSLRRSGVGNIFVKNLDKSV 100

Query: 245 SNDELHHIFGVYGEIKEIR----ETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK 300
            N  L   F  +G I   +    E  +     ++ F    +A+AA++++N   +  K++ 
Sbjct: 101 DNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY 160

Query: 301 LEP 303
           +  
Sbjct: 161 VGR 163

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 43.8 bits (102), Expect = 3e-04
 Identities = 22/88 (25%), Positives = 45/88 (51%), Gaps = 5/88 (5%)

Query: 222 KDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEF 276
             +  + +    TL V NL   V+ ++L  +F  +G +K +     RET +     ++EF
Sbjct: 105 PKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEF 164

Query: 277 YDTRAAEAALRELNSRYIAGKQIKLEPS 304
               +AE A+ ELN + + G+ ++++ +
Sbjct: 165 ESEESAEKAIEELNGKELEGRPLRVQKA 192

Length = 306

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 21/68 (30%), Positives = 34/68 (50%)

Query: 237 VFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAG 296
           V NL +     EL   F  YG ++ +          ++EF D R AE A+R L+ + I G
Sbjct: 4   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 63

Query: 297 KQIKLEPS 304
            ++++E S
Sbjct: 64  SRVRVELS 71

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 3/69 (4%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEI---RETPQKIHQKYIEFYDTRAAEAALRELNS 291
           L V NL  SV+ ++L   F  YG+++ +   R   +     ++EF     AEAAL++LN 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 292 RYIAGKQIK 300
             + G+ ++
Sbjct: 61  LVLDGRTLR 69

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 9/70 (12%)

Query: 150 LLLRKINSNIEDSELKALFEQYGDVRTFY-------RASKHCGFVTISYYDIRAARNAMK 202
           L + ++     + +++ALFE+YG++             SK C FV   +     A+ A++
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVK--FSSREEAQKAIE 59

Query: 203 SLQNKLTRSG 212
           +L  K+T  G
Sbjct: 60  ALHGKVTMPG 69

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALREL 289
           L+V NL    +  +L  +F  +G + E+   P+K   K     +++F     AE A++ +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEV-TIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 290 NSRYIAGKQI 299
           N + I G+ +
Sbjct: 61  NGKKIKGRPV 70

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 39.7 bits (93), Expect = 4e-04
 Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 9/78 (11%)

Query: 149 TLLLRKINSNIEDSELKALFEQYGDVRTFY-------RASKHCGFVTISYYDIRAARNAM 201
           +L +R +       +L+ LF +YG +   Y       R  +  GF  + + D+R A +A+
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPR--GFAYVQFEDVRDAEDAL 59

Query: 202 KSLQNKLTRSGKLDIHYS 219
             L        +++I ++
Sbjct: 60  YYLDRTRFLGREIEIQFA 77

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 5/69 (7%)

Query: 240 LDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQI 299
           L   V   ++   FG YG++ EI     K    ++EF D+R A+ A+ ELN + + G+++
Sbjct: 7   LSYHVREKDIQRFFGGYGKLLEI---DLKNGYGFVEFEDSRDADDAVYELNGKDLCGERV 63

Query: 300 KLEPSHLRG 308
            +E  H RG
Sbjct: 64  IVE--HARG 70

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIK--EIRETPQKIHQKYIEFYDTRAAEAALRELNSR 292
           L V  L  SV+  +L   F  +G +   EI +       +   + D R +EA L++  S 
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 293 Y----IAGKQIKLEPSH 305
                  G  +K+E + 
Sbjct: 62  LNGTKWKGSVLKIEEAK 78

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYI 294
           L V  L    S  EL   F  +G I+ I   P + +  YIE+    AA+AA   L    +
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNY-AYIEYESIEAAQAAKEALRGFPL 59

Query: 295 --AGKQIKLE 302
              G++++++
Sbjct: 60  GGPGRRLRVD 69

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 39.3 bits (91), Expect = 5e-04
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK---YIEFYDTRAAEAALRELN 290
           TL V NL   V+   +  +F   G  K  +   +        ++EFY+ R A AAL  +N
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 291 SRYIAGKQIKL 301
            R I GK++K+
Sbjct: 61  GRKILGKEVKV 71

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 39.3 bits (91), Expect = 5e-04
 Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKE---IRETPQKIHQKYIEFYDTRAAEAALRELN 290
           TL V NL   V+   +  +F   G  K    I +T       ++EF++ R A A+L  +N
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60

Query: 291 SRYIAGKQIKL 301
            R I GK++K+
Sbjct: 61  GRKIMGKEVKV 71

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 38.6 bits (90), Expect = 6e-04
 Identities = 19/67 (28%), Positives = 39/67 (58%), Gaps = 5/67 (7%)

Query: 149 TLLLRKINSNIEDSELKALFEQYGDVRTFYRA--SKHCGFVTISYYDIRAARNAMKSLQN 206
           TL++  ++ ++ + +L  +F  YG+++        +H  F  I +YD+R+A  A+K+L N
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKF--IEFYDVRSAEAALKAL-N 59

Query: 207 KLTRSGK 213
           +   +GK
Sbjct: 60  RSEIAGK 66

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 39.2 bits (92), Expect = 6e-04
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 237 VFNLDSSVSNDELHHIFGVYGEIKEIR-----ETPQKIHQK---YIEFYDTRAAEAALRE 288
           V NLD  +  D+L  IF  +GE++ IR     +  Q        ++ F D  +AE AL +
Sbjct: 5   VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL-Q 63

Query: 289 LNSRYIAGKQIKLEP 303
           LN   + G++I +  
Sbjct: 64  LNGTELGGRKISVSL 78

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKE--IRETPQKIHQK--YIEFYDTRAAEAALRELN 290
           L+V NL   +  D+L  +F  +G I +  ++ T     +K  ++ +     A+ AL+  N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 291 SRYIAGKQIKLEP 303
           + +I   +I +E 
Sbjct: 63  NSFIDTSKITVEI 75

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 38.9 bits (91), Expect = 6e-04
 Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALR 287
           G L V NL  S   D+L  +F  +GE+ E+     K   K     Y+ F D   A  A +
Sbjct: 3   GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

Query: 288 ELNSRYIAGKQIKLEP 303
           EL+ +   G+ I + P
Sbjct: 63  ELDGKVFQGRLIHILP 78

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 38.5 bits (90), Expect = 9e-04
 Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 11/80 (13%)

Query: 230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-------YIEFYDTRAA 282
           I++ ++ V  L   V+ +EL+  F  +G+I E+      I +        +I+F   +AA
Sbjct: 1   IDKYSIFVGQLSPDVTKEELNERFSRHGKILEV----NLIKRANHTNAFAFIKFEREQAA 56

Query: 283 EAALRELNSRYIAGKQIKLE 302
             A+   N   +  K + ++
Sbjct: 57  ARAVESENHSMLKNKTMHVQ 76

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 38.4 bits (90), Expect = 9e-04
 Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 8/59 (13%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK------YIEFYDTRAAEAAL 286
           T+ V NLD SV  DEL  +F   GEI ++R    K ++       Y+EF +  + + AL
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVR--LVKNYKGKSKGYAYVEFENEESVQEAL 57

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 42.5 bits (100), Expect = 0.001
 Identities = 33/165 (20%), Positives = 68/165 (41%), Gaps = 26/165 (15%)

Query: 159 IEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNK-LTRSGK 213
           + + +L+ LF ++G++ +       + +  GF  +++     A  A++ +  K +  + +
Sbjct: 190 VNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKE 249

Query: 214 LDIHYSIPKDNPSE----------------KEINQGT-LVVFNLDSSVSNDELHHIFGVY 256
               Y       +E                K   QG  L V NLD +V++++L  +F   
Sbjct: 250 GKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSEC 309

Query: 257 GEIKEIR----ETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK 297
           GEI   +    E        ++ F +   A  A+ E++ R + GK
Sbjct: 310 GEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGK 354

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 3/61 (4%)

Query: 150 LLLRKINSNIEDSELKALFEQYGDV---RTFYRASKHCGFVTISYYDIRAARNAMKSLQN 206
           L +R +  ++ + +L+  F  YG V   R      +  GF  + +     A  A+K L  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 207 K 207
            
Sbjct: 61  L 61

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)

 Score = 39.2 bits (91), Expect = 0.001
 Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 7/89 (7%)

Query: 233 GTLVVFNL-DSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS 291
             L+V NL +  V+   L  +FGVYG+++ ++    K     I+  D   ++ A+  LN 
Sbjct: 14  TVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNG 73

Query: 292 RYIAGKQIKLEPSHLRGLRKCLANQLPPE 320
           + + GK I++       L K    QLP E
Sbjct: 74  QKMYGKIIRVT------LSKHQTVQLPRE 96

This subgroup corresponds to the RRM3 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 107

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEI---RETPQKIHQKY--IEFYDTRAAEAALREL 289
           L V NL  +++ D+L  IF  +GEI+ +   R+      + Y  I+F D   A+ AL +L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 290 NSRYIAGKQIKL 301
           N   +AG+ IK+
Sbjct: 61  NGFELAGRPIKV 72

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTF-YRASKHCGFVTISYYDIRAARNAMKSL- 204
           SR + +  I+ ++ + +L+  F QYG++ +  Y   K+C FV  ++ +I  A  A+  + 
Sbjct: 3   SRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFV--NFTNISNAIKAIDGVK 60

Query: 205 QNKLTRSGKLDIHY 218
            + L +  K  I Y
Sbjct: 61  SHPLFK--KFKISY 72

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 4/67 (5%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK----YIEFYDTRAAEAALREL 289
           TL V N   S    ++  +F  YGEI  IR    + ++     Y++F    +A AA+  L
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALL 61

Query: 290 NSRYIAG 296
           N +   G
Sbjct: 62  NGKLGEG 68

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 5/71 (7%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALREL 289
           L V NL    + D+L  +F  YGE+ ++     R T +     ++ FYD R AE A+  +
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 290 NSRYIAGKQIK 300
           + + + G++++
Sbjct: 61  DGKELDGRELR 71

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 15/64 (23%), Positives = 36/64 (56%), Gaps = 5/64 (7%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDV---RTFY--RASKHCGFVTISYYDIRAARNA 200
           P R +    +N NI++  LK + ++YG+V   + ++  + +KH G   + +  +++A+  
Sbjct: 1   PPREVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRC 60

Query: 201 MKSL 204
           ++ L
Sbjct: 61  VEKL 64

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 5/56 (8%)

Query: 708 LMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKC---NVGYAFINMTDPS 760
           + ++N+ +    +  L  I  +  G  + I +P     K    N G+AF+   D S
Sbjct: 3   IYVRNL-DFKLDEDDLRGIFSKF-GEVESIRIPKKQDEKQGRLNNGFAFVTFKDAS 56

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALR 287
             ++V NL    +  ++  +F  YG++K +R  P+K  Q      ++EF   + A  A+ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMN 59

Query: 288 ELNSRYIAGKQIKLE 302
            L   ++ G+++ L+
Sbjct: 60  ALKDTHLLGRRLVLQ 74

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 239 NLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQ 298
            L       ++   F  YG I+EI     K    ++EF D R A+ A+ ELN + + G++
Sbjct: 6   RLPYRARERDVERFFKGYGRIREIN---LKNGFGFVEFEDPRDADDAVYELNGKELCGER 62

Query: 299 IKLEPSH 305
           + +E + 
Sbjct: 63  VIVEHAR 69

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAAL 286
           L V NL+  V+ + L   FG +G +  +     R   ++   +   ++ F +   AE AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 287 RELNSRYIAGKQIKL 301
            EL+ + + G ++KL
Sbjct: 64  DELDGKDVMGYELKL 78

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 9/70 (12%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIH-QKYIEF--YDTRA-AEAALRELN 290
           L V NL + ++ +E   +F  YGE+ E+      ++ +K   F   DTR  AE A  EL+
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVF-----LNKEKGFGFIRLDTRTNAEKAKAELD 58

Query: 291 SRYIAGKQIK 300
                G+Q++
Sbjct: 59  GIMRKGRQLR 68

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 10/82 (12%)

Query: 148 RTLLLRKINSNIEDSELKALFEQYGDVRTF----------YRASKHCGFVTISYYDIRAA 197
            TL ++ +N    +  LK  FE+ G VR+                  G+  + +    AA
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 198 RNAMKSLQNKLTRSGKLDIHYS 219
           + A+K LQ  +     L++  S
Sbjct: 61  QKALKRLQGTVLDGHALELKLS 82

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 37.0 bits (85), Expect = 0.003
 Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 5/78 (6%)

Query: 229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEI---KEIRE--TPQKIHQKYIEFYDTRAAE 283
           E ++  L+V  L  +++ +EL  +FG  GEI   K +R+  T Q +   ++ + D + AE
Sbjct: 1   EDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE 60

Query: 284 AALRELNSRYIAGKQIKL 301
            A+  LN   +  K IK+
Sbjct: 61  KAINTLNGLRLQTKTIKV 78

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYI 294
           + V N+D   S +EL  +F  YG +       Q     ++      AA+ A+ ELN R +
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ---FAFVHLRGEAAADRAIEELNGREL 59

Query: 295 AGKQIKLEPS 304
            G+++ +E S
Sbjct: 60  HGRKLVVEHS 69

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 10/76 (13%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQY-G--DVRTFYRASKHC-GFVTISYYDIRAARNAM 201
           P++ L L+ +        L+ LF Q+ G  +VR      +    FV   +     A  A+
Sbjct: 1   PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRL---VPRRGIAFV--EFETEEQATVAL 55

Query: 202 KSLQN-KLTRSGKLDI 216
           ++LQ  K+T    + I
Sbjct: 56  QALQGFKITPGHAMKI 71

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 37.1 bits (86), Expect = 0.003
 Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 14/76 (18%)

Query: 154 KINSNIEDSELKALFEQYG---------DVRTFYRASKHCGFVTISYYDIRAARNAMKSL 204
           +I  +  + +L+ LFEQYG         D       SK C FVT  +Y  +AA  A  +L
Sbjct: 8   QIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVT--FYTRKAALEAQNAL 65

Query: 205 QNKLTRSGKLDIHYSI 220
            N  T  G   +H+ I
Sbjct: 66  HNMKTLPG---MHHPI 78

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 18/77 (23%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTF-YRASKHCGFVTISYYDIRAARNAMKSLQ 205
           S TL +  ++  + + +LK LFE+YG++++      + C +V       + A  A++ L+
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVC--METRQDAHRALQKLR 59

Query: 206 NKLTRSGKLDIHYSIPK 222
           N      K+ + ++  K
Sbjct: 60  NVKLAGKKIKVAWAPNK 76

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 36.8 bits (86), Expect = 0.004
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 707 TLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFY 766
           TL + N+P   T + L         G  + + L  D +   + G+AF+            
Sbjct: 1   TLFVGNLPPDTTEEELRELF--SKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL 58

Query: 767 QSFNGKKWE 775
           ++ NGK+ +
Sbjct: 59  EALNGKELD 67

Length = 73

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 37.0 bits (86), Expect = 0.004
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 9/84 (10%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK------YIEFYDTRAAEAALR 287
           +L V N+  +   D+L  +FG YG I ++   P   + +      Y++F D R AE AL 
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVY-IPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 288 ELNSRYIAGKQIKLEPSHLRGLRK 311
            L+     G++I+++ +  +G RK
Sbjct: 61  YLDRTRFLGREIEIQFA--QGDRK 82

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	876
KOG4660	549	consensus Protein Mei2, essential for commitment t	100.0
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.95
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.94
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.93
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.93
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.92
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.92
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.91
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.91
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.9
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.9
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.9
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.9
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.88
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.88
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.87
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.85
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.85
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.83
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.83
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.82
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.82
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.81
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.77
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.77
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.75
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.73
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.72
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.71
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.66
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.66
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.66
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.65
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.65
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.64
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.62
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.57
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.47
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.45
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.44
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.43
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.41
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.38
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.36
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.32
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.31
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.28
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.28
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.26
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.25
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.23
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.21
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.19
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.19
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.16
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.13
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.12
PLN03120	260	nucleic acid binding protein; Provisional	99.11
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.1
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.1
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.09
PLN03120	260	nucleic acid binding protein; Provisional	99.08
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.07
smart00362	72	RRM_2 RNA recognition motif.	99.07
KOG0122	270	consensus Translation initiation factor 3, subunit	99.05
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.04
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.03
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.03
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.02
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.01
KOG0122	270	consensus Translation initiation factor 3, subunit	99.01
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.0
smart00362	72	RRM_2 RNA recognition motif.	99.0
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.99
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.98
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.97
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.96
smart00360	71	RRM RNA recognition motif.	98.95
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.94
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.94
PLN03213	759	repressor of silencing 3; Provisional	98.93
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.93
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.92
PLN03213	759	repressor of silencing 3; Provisional	98.9
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.9
PLN03121	243	nucleic acid binding protein; Provisional	98.89
smart00360	71	RRM RNA recognition motif.	98.89
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.88
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.87
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.86
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.86
PLN03121	243	nucleic acid binding protein; Provisional	98.84
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.83
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.82
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.82
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.8
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.8
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.77
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.76
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.73
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.71
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.7
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.69
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.67
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.66
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.64
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.63
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.61
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.61
smart00361	70	RRM_1 RNA recognition motif.	98.61
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.59
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.53
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.53
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.51
smart00361	70	RRM_1 RNA recognition motif.	98.48
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.38
KOG4210	285	consensus Nuclear localization sequence binding pr	98.3
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.23
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.23
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.19
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.13
KOG0226	290	consensus RNA-binding proteins [General function p	98.11
KOG0151	877	consensus Predicted splicing regulator, contains R	98.1
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.09
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.07
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.06
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.02
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	98.0
KOG0151	877	consensus Predicted splicing regulator, contains R	97.94
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.91
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.89
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.87
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	97.85
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.75
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.73
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.72
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.69
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.69
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.61
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.6
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.58
KOG0226	290	consensus RNA-binding proteins [General function p	97.53
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.49
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.49
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.43
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.4
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.25
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.16
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.83
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.82
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.74
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.72
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.55
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.54
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.5
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.29
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.26
KOG1295	376	consensus Nonsense-mediated decay protein Upf3 [RN	96.08
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.02
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.0
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.96
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	95.87
KOG4210	285	consensus Nuclear localization sequence binding pr	95.73
KOG3152	278	consensus TBP-binding protein, activator of basal	95.61
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.41
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.25
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.15
KOG3152	278	consensus TBP-binding protein, activator of basal	95.14
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.97
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.96
KOG1996	378	consensus mRNA splicing factor [RNA processing and	94.95
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	94.83
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.62
KOG2314	698	consensus Translation initiation factor 3, subunit	94.57
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.3
KOG2314	698	consensus Translation initiation factor 3, subunit	93.97
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	93.87
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	93.52
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	93.06
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	92.69
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.4
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.15
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	92.09
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	91.81
KOG2591	684	consensus c-Mpl binding protein, contains La domai	90.51
KOG2135	526	consensus Proteins containing the RNA recognition	90.27
KOG2591	684	consensus c-Mpl binding protein, contains La domai	90.23
KOG2068	327	consensus MOT2 transcription factor [Transcription	88.71
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	88.62
KOG1996	378	consensus mRNA splicing factor [RNA processing and	88.49
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	87.38
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	84.91
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	84.04
KOG4483	528	consensus Uncharacterized conserved protein [Funct	83.99
KOG2068	327	consensus MOT2 transcription factor [Transcription	83.91
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	83.09
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	82.87
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	82.86
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	82.5
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	80.91
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	80.61

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=100.00  E-value=8.3e-75  Score=646.15  Aligned_cols=525  Identities=45%  Similarity=0.621  Sum_probs=383.3

Q ss_pred             CCccccccCCCcccc-CCCcchhhccccccccCCCCCCCCcCCccccCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhc
Q 002823           92 MDDLDFFSSVGGMDL-GNDSSYVAQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQ  170 (876)
Q Consensus        92 ~dd~D~F~sgGGmEL-~D~s~s~g~~~~s~~~g~~nG~~~~~ng~~~ge~p~~e~pSrTLFVgNLP~~vTEeeL~elFsq  170 (876)
                      +||+|+|+++||||| +|.-......+..          ...++.+.+++|.++  +++ ||         .+|..+|++
T Consensus         1 ~~d~~lf~~~G~~el~~~~~~~~~~~~~~----------~n~~~~~~~~~P~~~--s~~-~~---------~~l~a~f~~   58 (549)
T KOG4660|consen    1 LEDCDLFSSGGGMELDADSFDNLSVRNSD----------RNSAGFVFPEHPPGE--SRT-FV---------SELSALFEP   58 (549)
T ss_pred             CCccccccCCCCCCcccccccchhhcccc----------cCCCccccCCCCCCC--CCC-Ch---------hhHHhhhhc
Confidence            478899999999999 6632221211110          134556778888877  667 88         788899998


Q ss_pred             cCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCCCCccccccceeEeecCCCCCcHHHHH
Q 002823          171 YGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELH  250 (876)
Q Consensus       171 fG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLr  250 (876)
                      |+                                  +.+.           ++.+.+++.++++|+|.|||.++++++|+
T Consensus        59 ~~----------------------------------~p~~-----------~~np~~~~~~~~~L~v~nl~~~Vsn~~L~   93 (549)
T KOG4660|consen   59 FN----------------------------------KPLR-----------PDNPSEKDMNQGTLVVFNLPRSVSNDTLL   93 (549)
T ss_pred             cC----------------------------------CCCC-----------cCCCCcccCccceEEEEecCCcCCHHHHH
Confidence            81                                  1111           15566677889999999999999999999


Q ss_pred             HHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchhHHHHhhcCCchhhhhhcCCCC
Q 002823          251 HIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQ  330 (876)
Q Consensus       251 eiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~Rr~l~qQ~~~q~~q~~~g~~~  330 (876)
                      ++|+.||+|++|+.+...++.+||+|.|+.+|++|+++|++.+|.|++|+    ++...++.+..|...+.      ...
T Consensus        94 ~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k----~~~~~~~~~~~~~~~~~------~~~  163 (549)
T KOG4660|consen   94 RIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK----RPGGARRAMGLQSGTSF------LNH  163 (549)
T ss_pred             HHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc----CCCcccccchhcccchh------hhh
Confidence            99999999999999999999999999999999999999999999999999    67777663323333111      112


Q ss_pred             CCCCCCCCCCCCcccceeeeccCchhhhHHHHHHhhccccccCCcCcccccCCccccccCCCCCCCCCCcccCCcccCCC
Q 002823          331 QQNSPPNKPTNESAGMITIVISLPLNVKSLAIIYLFTGAFAHGSKSSRITDTCIVSVVPSAVKAPPTESAFHLGISSSVP  410 (876)
Q Consensus       331 ~gsp~~~sp~~~~~~~~~~~fssP~n~~~~~l~~l~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (876)
                      .+.|.+++++++|.....+.+-.|                                         ..... +..+.+++ 
T Consensus       164 ~~~p~a~s~pgg~~~~~~~g~l~P-----------------------------------------~~s~~-~~~~~~~~-  200 (549)
T KOG4660|consen  164 FGSPLANSPPGGWPRGQLFGMLSP-----------------------------------------TRSSI-LLEHISSV-  200 (549)
T ss_pred             ccchhhcCCCCCCcCCcceeeecc-----------------------------------------chhhh-hhhcchhc-
Confidence            667888999999864111111111                                         11000 11111101 


Q ss_pred             CccccccccCcccccCCCCcccccccccCCCCCCCCCCCccccCCCCCCcccCCCCCCCcccCCCCcccccccccccccC
Q 002823          411 SLVRMESFGTQSALAEPGHLQGQLKFNIRSTPSFHPHSLPECHDGLNKGVRCNSSGTKGANINIKPPEIIDSRHFSRVSS  490 (876)
Q Consensus       411 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  490 (876)
                         -....+...+.-.|     |. +.  .....-+|.+++...                                    
T Consensus       201 ---~~~~~~~~~~~~~h-----q~-~~--~~~~~~s~a~~~~~~------------------------------------  233 (549)
T KOG4660|consen  201 ---DGSSPGRETPLLNH-----QR-FV--EFADNRSYAFSEPRG------------------------------------  233 (549)
T ss_pred             ---cCccccccccchhh-----hh-hh--hhccccchhhcccCC------------------------------------
Confidence               00000011111111     00 00  000000112222100                                    


Q ss_pred             CCCccccccccCCCCCCCCCCCCCcccCCCCCCCCCCCCccCCCCCCccccccCCCCCccCCCCCCCCccccCcCCCCCC
Q 002823          491 NGHSIGFTEVFGSASNGSCPRPGHQYSWNNSYCPQLPGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGSH  570 (876)
Q Consensus       491 ~g~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  570 (876)
                       |.       +.++..++.+++|+             +++|       |+++++ +            ++-+.+...+||
T Consensus       234 -G~-------~~s~~~~v~t~S~~-------------~g~~-------n~~~~~-r------------~~~~~~~~~~~~  272 (549)
T KOG4660|consen  234 -GF-------LISNSSGVITFSGP-------------GGVW-------NPFPSR-R------------QRQNSSSSHYEH  272 (549)
T ss_pred             -ce-------ecCCCCceEEecCC-------------Cccc-------CCcccc-c------------cccccCcccccC
Confidence             22       23344455555554             2466       344332 1            233344557799


Q ss_pred             CccCCCCCCCchhhhccccccCCcccccCcccCcCccccCCC-Cccccccc--ccCccccCCCCCCCCCCCCCCcccccc
Q 002823          571 HVGSAPTVDPSLWERQHAYVAESPEASGFHLGSHGSMRISNN-SLHSVEFV--SHNIFPCVGGNGMDMPLPSKNSVFQSH  647 (876)
Q Consensus       571 ~~gsap~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~  647 (876)
                      |||+||+                    ..|+.+-+++++.+. ..+.|+-+  ....|.+..|++++..  ++++++.+.
T Consensus       273 hi~~~Ps--------------------~~~l~~~~~~~f~~~s~~~~~~~~~~~n~g~~~~t~~~~e~~--s~n~~~e~~  330 (549)
T KOG4660|consen  273 HIGSAPS--------------------MHHLLSRISVGFNGGSGALEMNSNGQANQGFLTKTGNVTEFN--SKNVGMESS  330 (549)
T ss_pred             ccCCCcc--------------------cccccccCccccCCCCCCccccccccCCCCccccCccccccc--CCCcccccc
Confidence            9999998                    334556677777776 55555444  3446778899999998  999999999


Q ss_pred             cccccccCCCCcccccCCCCCCchhhhccccCCCCCCcccccccccchhHHhhCCCCceeEEeecCCCCCCHHHHHHHHH
Q 002823          648 HQRSMMFSGRGQTIPLMNSFDPPNERARNRRNEGAVNQADKKQYELDIDRILRGEDNRTTLMIKNIPNKYTSKMLLAAID  727 (876)
Q Consensus       648 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~i~~g~d~rTTvMirNIPnk~t~~~L~~~id  727 (876)
                      ++....|.++.-+...-.......+.++.||.+....+.+++++.+|+.+|++|++.|||+||||||||||++||++. |
T Consensus       331 ~rv~~~f~~~~~~~~~~~~~~~~~~~~~~~Rtt~~i~ni~n~~~~~dl~~Ildge~~rtt~~iknipNK~T~~ml~~~-d  409 (549)
T KOG4660|consen  331 PRVPKNFEGRRSYTSQNDYPVELILNYRDRRTTVMIKNIPNKYGQLDLLRILDGECPRTTLMIKNIPNKYTSKMLLAA-D  409 (549)
T ss_pred             CCCCcccccccccccccccccccccccccchhhhhhhccccchhHHHHHHHHhCcCchhhhHhhccCchhhHHhhhhh-h
Confidence            999999988875443333333344577889999887888899999999999999999999999999999999999999 9


Q ss_pred             hhCCCcccEEEecccccccceeEEEEEecCCccchHHHHHHhcCccccCCCCccEEEEEeeccccHHHHHHHcccCcccC
Q 002823          728 ERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMN  807 (876)
Q Consensus       728 e~~~g~yDF~Ylp~Df~~~~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~Kv~~v~yA~iQG~~ali~~f~~s~v~~  807 (876)
                      |.++|+|||+||||||+|+||||||||||++|++|++||++|||++|++|+|+|||+|+|||||||++|++|||||++|+
T Consensus       410 ~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQGk~~Li~hFqnS~lm~  489 (549)
T KOG4660|consen  410 EKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQGKEALIEHFQNSSLMC  489 (549)
T ss_pred             ccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhhchHHHHHHhhcccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccceEEecCCCCCCCcccCCCCCCCccCCCCCcccccc
Q 002823          808 EDKRCRPILFNTDGPNAGDQVPFPMGVNFRTRPGKARSVIHE  849 (876)
Q Consensus       808 ~~~~~rP~~f~~~g~~~g~~~pfp~~~n~~~~~~~~~~~~~~  849 (876)
                      |++.|+|++|++  |+.|.++++|...+++.+.+..+.....
T Consensus       490 E~e~y~Pvvf~p--p~dg~~~~~p~~~~~~a~~~~s~~~~~~  529 (549)
T KOG4660|consen  490 EDEAYRPVVFSP--PEDGREEPEPVKLNQDAGAGHSTNASLK  529 (549)
T ss_pred             cchhcCceEecC--cccccccCccccccccCCCCcccchhhh
Confidence            999999999987  8999999999999999877776655443

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=100.00  E-value=4.8e-46  Score=340.64  Aligned_cols=97  Identities=65%  Similarity=1.207  Sum_probs=96.4

Q ss_pred             ceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEecccccccceeEEEEEecCCccchHHHHHHhcCccccCCCCccEEE
Q 002823          705 RTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVAS  784 (876)
Q Consensus       705 rTTvMirNIPnk~t~~~L~~~ide~~~g~yDF~Ylp~Df~~~~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~Kv~~  784 (876)
                      |||||||||||||||+||+++||+.|+|+||||||||||+++||+|||||||++++++++|++.|+|++|+.++|+|||+
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEE
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccccHHHHHHHcc
Q 002823          785 LAYARIQGKAALIAHFQ  801 (876)
Q Consensus       785 v~yA~iQG~~ali~~f~  801 (876)
                      |+||||||++|||+|||
T Consensus        81 i~yAriQG~~alv~~f~   97 (97)
T PF04059_consen   81 ISYARIQGKDALVEHFR   97 (97)
T ss_pred             EehhHhhCHHHHHHhhC
Confidence            99999999999999997

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.95  E-value=7.7e-27  Score=259.10  Aligned_cols=164  Identities=23%  Similarity=0.425  Sum_probs=146.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ......++|||+|||+++|+++|+++|++||+|++|+     .+++++|||||+|.++++|++|++.|++..+.+++|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            3556679999999999999999999999999999887     36778999999999999999999999999999999999


Q ss_pred             eecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCC
Q 002823          217 HYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNS  291 (876)
Q Consensus       217 ~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG  291 (876)
                      .|+.+....    ....+|||+|||.++++++|+++|++||+|+.|++     ++++++||||+|.+.++|++||+.||+
T Consensus       182 ~~a~p~~~~----~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng  257 (346)
T TIGR01659       182 SYARPGGES----IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNN  257 (346)
T ss_pred             ecccccccc----cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            998765432    23568999999999999999999999999999876     456679999999999999999999999


Q ss_pred             ceeCC--eEEEEEeecCchh
Q 002823          292 RYIAG--KQIKLEPSHLRGL  309 (876)
Q Consensus       292 ~~I~G--r~IkVs~A~~k~~  309 (876)
                      ..+.+  ++|+|.+++....
T Consensus       258 ~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       258 VIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             CccCCCceeEEEEECCcccc
Confidence            98866  7999999987543

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=1.5e-26  Score=240.59  Aligned_cols=214  Identities=18%  Similarity=0.296  Sum_probs=178.3

Q ss_pred             HHHHhcCCCCCC-chhhhcccCCCCCCCCCCCCCCCCCCCccccccCCCccccCCCcchhhccccccccCCCCCCCCcCC
Q 002823           55 EAQTIGNLLPDD-DDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLGNDSSYVAQKKSEICIGFSNHELGVCN  133 (876)
Q Consensus        55 e~~~iG~llPdd-dellsgv~d~~~~~~~~~~~s~~dD~dd~D~F~sgGGmEL~D~s~s~g~~~~s~~~g~~nG~~~~~n  133 (876)
                      ..+++|||.++. ||+|+.++..++.+...+   ..-|  |           +                        +.+
T Consensus         7 rtlyvgnld~~vte~~i~~lf~qig~v~~~k---~i~~--e-----------~------------------------~v~   46 (321)
T KOG0148|consen    7 RTLYVGNLDSTVTEDFIATLFNQIGSVTKTK---VIFD--E-----------L------------------------KVN   46 (321)
T ss_pred             ceEEeeccChhhHHHHHHHHHHhccccccce---eehh--h-----------h------------------------ccc
Confidence            467899999998 999999999999988777   3222  1           2                        111


Q ss_pred             cccc-CCCCC-CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccc
Q 002823          134 GAVA-GEHLN-DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQN  206 (876)
Q Consensus       134 g~~~-ge~p~-~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng  206 (876)
                      |+.. +.... .-.....+||+.|.++++-++|++.|.+||+|.+++     .++|+|||+||.|.+.++|++||..|+|
T Consensus        47 wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnG  126 (321)
T KOG0148|consen   47 WATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNG  126 (321)
T ss_pred             cccCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCC
Confidence            1110 11111 112256899999999999999999999999998877     5899999999999999999999999999


Q ss_pred             cccCCceeeEeecCCCCCCC------------ccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEE
Q 002823          207 KLTRSGKLDIHYSIPKDNPS------------EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYI  274 (876)
Q Consensus       207 ~~l~Gr~L~V~~A~pk~~~~------------ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFV  274 (876)
                      +.|.+|.|+-.|+..|....            ......++|||+||+.-+++++|++.|++||.|.+||+ -+-+||+||
T Consensus       127 qWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRv-Fk~qGYaFV  205 (321)
T KOG0148|consen  127 QWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRV-FKDQGYAFV  205 (321)
T ss_pred             eeeccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEE-ecccceEEE
Confidence            99999999999998775322            11235679999999999999999999999999999998 456899999


Q ss_pred             EecCHHHHHHHHHHhCCceeCCeEEEEEeecCchh
Q 002823          275 EFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       275 eF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~  309 (876)
                      .|++.|+|.+||..+|+.+|.|..|+|.|.+....
T Consensus       206 rF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  206 RFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             EecchhhHHHHHHHhcCceeCceEEEEeccccCCC
Confidence            99999999999999999999999999999987653

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.93  E-value=4e-25  Score=243.78  Aligned_cols=159  Identities=21%  Similarity=0.374  Sum_probs=143.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      +..+|||+|||.++++++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|+.+.|++|+|+|+.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            467999999999999999999999999999987     357799999999999999999999999999999999999998


Q ss_pred             CCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeC
Q 002823          221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIA  295 (876)
Q Consensus       221 pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~  295 (876)
                      ++...    ....+|||+|||..+++++|+++|++||.|..+++     ++..++||||+|.+.++|++|++.|||..+.
T Consensus        82 ~~~~~----~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~  157 (352)
T TIGR01661        82 PSSDS----IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPS  157 (352)
T ss_pred             ccccc----cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccC
Confidence            76543    23458999999999999999999999999998776     3457899999999999999999999999988


Q ss_pred             C--eEEEEEeecCch
Q 002823          296 G--KQIKLEPSHLRG  308 (876)
Q Consensus       296 G--r~IkVs~A~~k~  308 (876)
                      |  .+|+|.|+..+.
T Consensus       158 g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       158 GCTEPITVKFANNPS  172 (352)
T ss_pred             CCceeEEEEECCCCC
Confidence            7  788999987654

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.93  E-value=7.2e-25  Score=241.78  Aligned_cols=166  Identities=16%  Similarity=0.288  Sum_probs=142.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCC--ceeeEe
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRS--GKLDIH  217 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G--r~L~V~  217 (876)
                      ...++|||+|||..+++++|+++|++||.|..++.     ++.++|||||+|.+.++|++|++.|+|..+.|  ++|.|.
T Consensus        87 ~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~  166 (352)
T TIGR01661        87 IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVK  166 (352)
T ss_pred             cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEE
Confidence            34679999999999999999999999999988772     46789999999999999999999999999877  578888


Q ss_pred             ecCCCCCCCc----------------c-----------------------------------------------------
Q 002823          218 YSIPKDNPSE----------------K-----------------------------------------------------  228 (876)
Q Consensus       218 ~A~pk~~~~e----------------k-----------------------------------------------------  228 (876)
                      |+........                .                                                     
T Consensus       167 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (352)
T TIGR01661       167 FANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASP  246 (352)
T ss_pred             ECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCC
Confidence            8753321000                0                                                     


Q ss_pred             -------------------ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHH
Q 002823          229 -------------------EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEA  284 (876)
Q Consensus       229 -------------------~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~k  284 (876)
                                         .....+|||+|||.++++++|+++|++||.|++|++     ++.+||||||+|.+.++|.+
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~  326 (352)
T TIGR01661       247 PATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAM  326 (352)
T ss_pred             ccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHH
Confidence                               000115999999999999999999999999999887     56789999999999999999


Q ss_pred             HHHHhCCceeCCeEEEEEeecCchhH
Q 002823          285 ALRELNSRYIAGKQIKLEPSHLRGLR  310 (876)
Q Consensus       285 AL~~LnG~~I~Gr~IkVs~A~~k~~R  310 (876)
                      |+..|||..|.||+|+|.|...+..|
T Consensus       327 Ai~~lnG~~~~gr~i~V~~~~~~~~~  352 (352)
T TIGR01661       327 AILSLNGYTLGNRVLQVSFKTNKAYR  352 (352)
T ss_pred             HHHHhCCCEECCeEEEEEEccCCCCC
Confidence            99999999999999999999987643

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.92  E-value=1.5e-24  Score=253.49  Aligned_cols=163  Identities=14%  Similarity=0.296  Sum_probs=143.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ...++|||+|||+++++++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|+.+.|++|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            3457999999999999999999999999999998     36789999999999999999999999999999999999875


Q ss_pred             CCCCCCC-------ccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHH
Q 002823          220 IPKDNPS-------EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALR  287 (876)
Q Consensus       220 ~pk~~~~-------ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~  287 (876)
                      .......       .......+|||+||+.++++++|+++|+.||.|+++++     ++..||||||+|.+.++|.+|++
T Consensus       185 ~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~  264 (612)
T TIGR01645       185 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA  264 (612)
T ss_pred             ccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHH
Confidence            4322111       11123469999999999999999999999999999887     34578999999999999999999


Q ss_pred             HhCCceeCCeEEEEEeecCc
Q 002823          288 ELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       288 ~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      .||+..|+|+.|+|.++.++
T Consensus       265 amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       265 SMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             HhCCCeeCCeEEEEEecCCC
Confidence            99999999999999988864

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.92  E-value=3.9e-24  Score=251.31  Aligned_cols=168  Identities=18%  Similarity=0.358  Sum_probs=149.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccC----Cceee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTR----SGKLD  215 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~----Gr~L~  215 (876)
                      ....++|||+|||.++|+++|+++|++||+|.+++    .+++++|||||+|.+.++|.+|++.|+++.+.    |+.|.
T Consensus       175 ~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~  254 (562)
T TIGR01628       175 LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLY  254 (562)
T ss_pred             ccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeE
Confidence            34457899999999999999999999999999987    34678999999999999999999999999999    99999


Q ss_pred             EeecCCCCCCCc--------------cccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEec
Q 002823          216 IHYSIPKDNPSE--------------KEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFY  277 (876)
Q Consensus       216 V~~A~pk~~~~e--------------k~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~  277 (876)
                      |.++.++.+...              ......+|||+||+..+++++|+++|++||.|++|++    ++.++|||||+|.
T Consensus       255 v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~  334 (562)
T TIGR01628       255 VGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFS  334 (562)
T ss_pred             eecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeC
Confidence            998877654310              0123458999999999999999999999999999887    5667899999999


Q ss_pred             CHHHHHHHHHHhCCceeCCeEEEEEeecCchhHH
Q 002823          278 DTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       278 d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~Rr  311 (876)
                      +.++|.+|++.|||..+.|++|+|.++.+++.|+
T Consensus       335 ~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~~  368 (562)
T TIGR01628       335 NPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRR  368 (562)
T ss_pred             CHHHHHHHHHHhcCCeeCCceeEEEeccCcHHHH
Confidence            9999999999999999999999999999998776

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=6.5e-24  Score=231.89  Aligned_cols=177  Identities=20%  Similarity=0.351  Sum_probs=150.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccc-cCC--ceeeE
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKL-TRS--GKLDI  216 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~-l~G--r~L~V  216 (876)
                      ...-+|||+-||+.++|.||+++|++||.|.+|.     .++.++|||||.|++.++|.+|+.+|+++. |.|  .+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            4567999999999999999999999999998886     578899999999999999999999999965 665  57888


Q ss_pred             eecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCc
Q 002823          217 HYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSR  292 (876)
Q Consensus       217 ~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~  292 (876)
                      +|+....+..   ....+|||+-|++.++|.|++++|++||.|++|++    .+.+||||||+|.+.|.|..||++|||.
T Consensus       112 k~Ad~E~er~---~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~  188 (510)
T KOG0144|consen  112 KYADGERERI---VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGT  188 (510)
T ss_pred             cccchhhhcc---ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccc
Confidence            8886654432   44678999999999999999999999999999887    5678999999999999999999999994


Q ss_pred             -eeCC--eEEEEEeecCchhHH--HHhhcCCchhhhh
Q 002823          293 -YIAG--KQIKLEPSHLRGLRK--CLANQLPPELEQE  324 (876)
Q Consensus       293 -~I~G--r~IkVs~A~~k~~Rr--~l~qQ~~~q~~q~  324 (876)
                       .+.|  .+|.|+|+.+++.|.  +++++...+..+.
T Consensus       189 ~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql  225 (510)
T KOG0144|consen  189 QTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQL  225 (510)
T ss_pred             eeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHh
Confidence             4555  799999998877655  5534444444433

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.91  E-value=2.4e-23  Score=238.06  Aligned_cols=163  Identities=23%  Similarity=0.374  Sum_probs=143.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .+.+.++|||+|||..+++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|+. |+|+.+.|++|.|+
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~  163 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQ  163 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEe
Confidence            4566899999999999999999999999999999883     57789999999999999999995 99999999999998


Q ss_pred             ecCCCCCCCc--------cccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHH
Q 002823          218 YSIPKDNPSE--------KEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEA  284 (876)
Q Consensus       218 ~A~pk~~~~e--------k~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~k  284 (876)
                      ++........        ......+|||+|||..+++++|+++|+.||.|..|++     ++..+|||||+|.+.++|.+
T Consensus       164 ~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~  243 (457)
T TIGR01622       164 SSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKE  243 (457)
T ss_pred             ecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHH
Confidence            8754332211        1123579999999999999999999999999999887     34678999999999999999


Q ss_pred             HHHHhCCceeCCeEEEEEeecC
Q 002823          285 ALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       285 AL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      |++.|+|..|.|++|+|.|+..
T Consensus       244 A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       244 ALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HHHhcCCcEECCEEEEEEEccC
Confidence            9999999999999999999883

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.90  E-value=2.2e-23  Score=244.89  Aligned_cols=291  Identities=17%  Similarity=0.200  Sum_probs=197.4

Q ss_pred             HHhcCCCCCC-chhhhcccCCCCCCCCCCCCCCCCCCCccccccCCCccccC--CCcchhhccccccccCCCCCCCCcCC
Q 002823           57 QTIGNLLPDD-DDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDLG--NDSSYVAQKKSEICIGFSNHELGVCN  133 (876)
Q Consensus        57 ~~iG~llPdd-dellsgv~d~~~~~~~~~~~s~~dD~dd~D~F~sgGGmEL~--D~s~s~g~~~~s~~~g~~nG~~~~~n  133 (876)
                      .++|||-++. ++.|..++..++.+....   ...|..    ....-|..++  ......-.+...++...-.|..-...
T Consensus         3 l~VgnLp~~vte~~L~~~F~~~G~v~~v~---v~~d~~----t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~   75 (562)
T TIGR01628         3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVR---VCRDSV----TRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIM   75 (562)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEE---EEecCC----CCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEee
Confidence            4689998886 777777777776554333   222211    1111233321  11111111111222222223222333


Q ss_pred             ccccCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHcccccc
Q 002823          134 GAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLT  209 (876)
Q Consensus       134 g~~~ge~p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l  209 (876)
                      |+... .........+|||+|||.++++++|+++|++||.|.+|+    .+++++|||||+|.+.++|++|++.++|..+
T Consensus        76 ~s~~~-~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~  154 (562)
T TIGR01628        76 WSQRD-PSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLL  154 (562)
T ss_pred             ccccc-ccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEe
Confidence            32211 111223356899999999999999999999999999987    3467899999999999999999999999999


Q ss_pred             CCceeeEeecCCCCCCC-ccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHH
Q 002823          210 RSGKLDIHYSIPKDNPS-EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEA  284 (876)
Q Consensus       210 ~Gr~L~V~~A~pk~~~~-ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~k  284 (876)
                      .++.|.|....++.... ......++|||+||+.++++++|+++|+.||+|.++++    ++..+|||||+|.+.++|.+
T Consensus       155 ~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~  234 (562)
T TIGR01628       155 NDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAK  234 (562)
T ss_pred             cCceEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHH
Confidence            99999998776655442 22334568999999999999999999999999999877    44568899999999999999


Q ss_pred             HHHHhCCceeC----CeEEEEEeecCchhHHHHhhcCCchhhhhhcCCCCCCCCCCCCCCCCcccceeeeccCchhhhHH
Q 002823          285 ALRELNSRYIA----GKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSL  360 (876)
Q Consensus       285 AL~~LnG~~I~----Gr~IkVs~A~~k~~Rr~l~qQ~~~q~~q~~~g~~~~gsp~~~sp~~~~~~~~~~~fssP~n~~~~  360 (876)
                      |++.|+|..+.    |+.|.|.++..+.+|.........+..+.....              .....-..-+.|.+++..
T Consensus       235 Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~--------------~~~~~l~V~nl~~~~~~~  300 (562)
T TIGR01628       235 AVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMK--------------AQGVNLYVKNLDDTVTDE  300 (562)
T ss_pred             HHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcc--------------cCCCEEEEeCCCCccCHH
Confidence            99999999999    999999999888766411011111111110000              001112334677788888


Q ss_pred             HHHHhhccc
Q 002823          361 AIIYLFTGA  369 (876)
Q Consensus       361 ~l~~l~~~~  369 (876)
                      .|..+|...
T Consensus       301 ~L~~~F~~~  309 (562)
T TIGR01628       301 KLRELFSEC  309 (562)
T ss_pred             HHHHHHHhc
Confidence            899999764

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.90  E-value=6.3e-23  Score=237.40  Aligned_cols=162  Identities=19%  Similarity=0.226  Sum_probs=139.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHc--cccccCCceeeEeecCCCC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSL--QNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~L--ng~~l~Gr~L~V~~A~pk~  223 (876)
                      |+++|||+|||+++++++|+++|++||+|.+|+.. +.|+||||+|.+.++|++|++.+  ++..+.|++|+|+|+..+.
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~-~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~   79 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMML-PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQE   79 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEE-CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcc
Confidence            68999999999999999999999999999999853 57899999999999999999874  6788999999999997653


Q ss_pred             CCCcc--------ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecC-CcccEEEEEecCHHHHHHHHHHhCCcee
Q 002823          224 NPSEK--------EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETP-QKIHQKYIEFYDTRAAEAALRELNSRYI  294 (876)
Q Consensus       224 ~~~ek--------~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg-~skG~AFVeF~d~E~A~kAL~~LnG~~I  294 (876)
                      .....        .....+|||.||+..+++++|+++|+.||+|.+|.+.. ..+++|||+|.+.++|.+|++.|||..|
T Consensus        80 ~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i  159 (481)
T TIGR01649        80 IKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADI  159 (481)
T ss_pred             cccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcc
Confidence            21111        01223799999999999999999999999999988733 3347999999999999999999999999


Q ss_pred             CC--eEEEEEeecCch
Q 002823          295 AG--KQIKLEPSHLRG  308 (876)
Q Consensus       295 ~G--r~IkVs~A~~k~  308 (876)
                      .+  ++|+|.|++.+.
T Consensus       160 ~~~~~~l~v~~sk~~~  175 (481)
T TIGR01649       160 YNGCCTLKIEYAKPTR  175 (481)
T ss_pred             cCCceEEEEEEecCCC
Confidence            64  699999998743

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=1.1e-22  Score=223.33  Aligned_cols=164  Identities=22%  Similarity=0.415  Sum_probs=141.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccC-CceeeEee
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTR-SGKLDIHY  218 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~-Gr~L~V~~  218 (876)
                      .-.+.|||+.||.++.|++|.-+|++.|+|.+++     .++.+||||||.|.+.++|++|++.||+.+|+ ||.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            4468999999999999999999999999999998     47889999999999999999999999999885 78777744


Q ss_pred             cC------------------------------------------------------------------------------
Q 002823          219 SI------------------------------------------------------------------------------  220 (876)
Q Consensus       219 A~------------------------------------------------------------------------------  220 (876)
                      +.                                                                              
T Consensus       161 Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~  240 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAI  240 (506)
T ss_pred             eeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcc
Confidence            31                                                                              


Q ss_pred             ------CCCCCCcccc-ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCce
Q 002823          221 ------PKDNPSEKEI-NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY  293 (876)
Q Consensus       221 ------pk~~~~ek~~-~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~  293 (876)
                            |+.+..+... .-+.|||+||+.++|+|.|+++|++||.|..|+.   .|.||||+|.++++|.+|++.+||++
T Consensus       241 tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk---~rDYaFVHf~eR~davkAm~~~ngke  317 (506)
T KOG0117|consen  241 TVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKK---PRDYAFVHFAEREDAVKAMKETNGKE  317 (506)
T ss_pred             eeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeec---ccceeEEeecchHHHHHHHHHhcCce
Confidence                  1111111100 2247999999999999999999999999999886   36799999999999999999999999


Q ss_pred             eCCeEEEEEeecCchhHH
Q 002823          294 IAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       294 I~Gr~IkVs~A~~k~~Rr  311 (876)
                      |.|..|.|.+++|.+.++
T Consensus       318 ldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  318 LDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             ecCceEEEEecCChhhhc
Confidence            999999999999987665

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.90  E-value=1e-22  Score=235.69  Aligned_cols=164  Identities=22%  Similarity=0.257  Sum_probs=141.6

Q ss_pred             CCCCcEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          144 EHPSRTLLLRKINS-NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       144 e~pSrTLFVgNLP~-~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ..++++|||+|||+ .+|+++|+++|++||.|.+|+.....+|||||+|.+.++|++|++.|+|..|.|++|+|.++..+
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            45788999999998 69999999999999999999965556899999999999999999999999999999999998543


Q ss_pred             CCCCc------------c---------------------ccccceeEeecCCCCCcHHHHHHHhhhcCC--eEEEEecCC
Q 002823          223 DNPSE------------K---------------------EINQGTLVVFNLDSSVSNDELHHIFGVYGE--IKEIRETPQ  267 (876)
Q Consensus       223 ~~~~e------------k---------------------~~~~~tLfV~NLP~svTeedLreiFs~fG~--I~sVritg~  267 (876)
                      .....            +                     ..+..+|||+|||.++++++|+++|+.||.  |+.|++...
T Consensus       352 ~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~  431 (481)
T TIGR01649       352 NVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPK  431 (481)
T ss_pred             cccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecC
Confidence            11000            0                     013458999999999999999999999998  888887333


Q ss_pred             ---cccEEEEEecCHHHHHHHHHHhCCceeCCeE------EEEEeecCc
Q 002823          268 ---KIHQKYIEFYDTRAAEAALRELNSRYIAGKQ------IKLEPSHLR  307 (876)
Q Consensus       268 ---skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~------IkVs~A~~k  307 (876)
                         ++++|||+|.+.++|.+||..||+..|.++.      |+|.|++++
T Consensus       432 ~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       432 DNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             CCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence               3789999999999999999999999999985      999999874

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.88  E-value=3.2e-22  Score=233.52  Aligned_cols=161  Identities=20%  Similarity=0.307  Sum_probs=139.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCC-eEE-EE-----eCCCccceEeeecCCHHHHHHHHHHccc--cccCCceeeE
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGD-VRT-FY-----RASKHCGFVTISYYDIRAARNAMKSLQN--KLTRSGKLDI  216 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~-I~s-V~-----~tgksrGfAFV~F~d~edA~kAl~~Lng--~~l~Gr~L~V  216 (876)
                      ..++|||+|||+++++++|.++|++++. |.. +.     ..++++|||||+|.+.++|.+|++.|+.  ..+.|+.|.|
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~V  216 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV  216 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEE
Confidence            3689999999999999999999999863 333 32     2457899999999999999999998864  3578999999


Q ss_pred             eecCCCCCCCccc-cccceeEeecCCCCCcHHHHHHHhhhc--CCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCce
Q 002823          217 HYSIPKDNPSEKE-INQGTLVVFNLDSSVSNDELHHIFGVY--GEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY  293 (876)
Q Consensus       217 ~~A~pk~~~~ek~-~~~~tLfV~NLP~svTeedLreiFs~f--G~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~  293 (876)
                      .|+.++....+.. ...++|||+||+.++++++|+++|++|  |+|+.|++   .++||||+|++.++|++|++.||+..
T Consensus       217 dwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~---~rgfAFVeF~s~e~A~kAi~~lnG~~  293 (578)
T TIGR01648       217 DWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKK---IRDYAFVHFEDREDAVKAMDELNGKE  293 (578)
T ss_pred             EeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEe---ecCeEEEEeCCHHHHHHHHHHhCCCE
Confidence            9998876543322 234689999999999999999999999  99999987   36799999999999999999999999


Q ss_pred             eCCeEEEEEeecCchh
Q 002823          294 IAGKQIKLEPSHLRGL  309 (876)
Q Consensus       294 I~Gr~IkVs~A~~k~~  309 (876)
                      |.|++|+|+|++++..
T Consensus       294 i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       294 LEGSEIEVTLAKPVDK  309 (578)
T ss_pred             ECCEEEEEEEccCCCc
Confidence            9999999999998653

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.88  E-value=8.2e-22  Score=228.22  Aligned_cols=162  Identities=15%  Similarity=0.233  Sum_probs=136.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcc------------CCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQY------------GDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTR  210 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqf------------G~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~  210 (876)
                      .....++|||+|||+++|+++|+++|.+|            +.|..+.. .+.+|||||+|.+.++|.+|| +|+|..+.
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~-~~~kg~afVeF~~~e~A~~Al-~l~g~~~~  248 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-NKEKNFAFLEFRTVEEATFAM-ALDSIIYS  248 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE-CCCCCEEEEEeCCHHHHhhhh-cCCCeEee
Confidence            45667999999999999999999999975            34444444 678999999999999999999 69999999


Q ss_pred             CceeeEeecCCCCCCC-------------------------ccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-
Q 002823          211 SGKLDIHYSIPKDNPS-------------------------EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-  264 (876)
Q Consensus       211 Gr~L~V~~A~pk~~~~-------------------------ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-  264 (876)
                      |+.|+|..........                         .......+|||+|||..+++++|+++|+.||.|+.+.+ 
T Consensus       249 g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~  328 (509)
T TIGR01642       249 NVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLI  328 (509)
T ss_pred             CceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEE
Confidence            9999996432211000                         00112358999999999999999999999999999776 


Q ss_pred             ----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          265 ----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       265 ----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                          ++..+|||||+|.+.++|.+|++.|+|..|.|++|+|.++..
T Consensus       329 ~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~  374 (509)
T TIGR01642       329 KDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV  374 (509)
T ss_pred             ecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECcc
Confidence                466789999999999999999999999999999999999865

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.87  E-value=8.5e-22  Score=203.93  Aligned_cols=163  Identities=21%  Similarity=0.373  Sum_probs=148.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .....|.|.-||..+|++||+.+|...|+|++|+     .++.+.||+||.|-++++|++|+..|+|..+..+.|+|.|+
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyA  118 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYA  118 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEec
Confidence            3446899999999999999999999999999998     67889999999999999999999999999999999999999


Q ss_pred             CCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCcee
Q 002823          220 IPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYI  294 (876)
Q Consensus       220 ~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I  294 (876)
                      +|..+..    ....|||.+||..+|..||.++|++||.|..-|+     ++.+||.+||.|+.+++|++||+.|||.+-
T Consensus       119 RPSs~~I----k~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P  194 (360)
T KOG0145|consen  119 RPSSDSI----KDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKP  194 (360)
T ss_pred             cCChhhh----cccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCC
Confidence            9876543    3457999999999999999999999999987554     788999999999999999999999999988


Q ss_pred             CC--eEEEEEeecCchhHH
Q 002823          295 AG--KQIKLEPSHLRGLRK  311 (876)
Q Consensus       295 ~G--r~IkVs~A~~k~~Rr  311 (876)
                      .|  .+|.|+|+....+++
T Consensus       195 ~g~tepItVKFannPsq~t  213 (360)
T KOG0145|consen  195 SGCTEPITVKFANNPSQKT  213 (360)
T ss_pred             CCCCCCeEEEecCCccccc
Confidence            76  799999998876665

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.85  E-value=1.8e-20  Score=217.07  Aligned_cols=163  Identities=18%  Similarity=0.305  Sum_probs=136.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ...++|||+|||..+++++|+++|++||.|..+.     .+++++|||||+|.+.++|.+|++.|+|..|.|++|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3468999999999999999999999999998876     35779999999999999999999999999999999999998


Q ss_pred             CCCCCCCc------------------------cccccceeEeecCCCC--C--------cHHHHHHHhhhcCCeEEEEec
Q 002823          220 IPKDNPSE------------------------KEINQGTLVVFNLDSS--V--------SNDELHHIFGVYGEIKEIRET  265 (876)
Q Consensus       220 ~pk~~~~e------------------------k~~~~~tLfV~NLP~s--v--------TeedLreiFs~fG~I~sVrit  265 (876)
                      ........                        ...+..+|+|.|+...  +        ..++|+++|++||.|+.|++.
T Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~  452 (509)
T TIGR01642       373 CVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIP  452 (509)
T ss_pred             ccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEee
Confidence            54321100                        0123567899999632  1        236799999999999999883


Q ss_pred             C--------CcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          266 P--------QKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       266 g--------~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      .        ..+|++||+|.++++|++|+..|||..|.|+.|.|.|....
T Consensus       453 ~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~~  502 (509)
T TIGR01642       453 RPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGED  502 (509)
T ss_pred             ccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCHH
Confidence            1        23589999999999999999999999999999999998653

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.85  E-value=5.7e-21  Score=189.90  Aligned_cols=163  Identities=20%  Similarity=0.294  Sum_probs=143.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ....||||+||+..++++.|.++|-+.|+|..++     .+.+.+|||||+|.++|+|+-|++-|+...+.||+|+|.-+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            3457999999999999999999999999999998     56789999999999999999999999999999999999887


Q ss_pred             CCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEE----EEe--cCCcccEEEEEecCHHHHHHHHHHhCCce
Q 002823          220 IPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKE----IRE--TPQKIHQKYIEFYDTRAAEAALRELNSRY  293 (876)
Q Consensus       220 ~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~s----Vri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~  293 (876)
                      ...   ..+......|||+||++.+++..|.+.|+.||.|..    ++.  ++.+++||||.|.+.|.+.+|+..+||..
T Consensus        87 s~~---~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~  163 (203)
T KOG0131|consen   87 SAH---QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQY  163 (203)
T ss_pred             ccc---cccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccch
Confidence            621   112223468999999999999999999999999876    232  67889999999999999999999999999


Q ss_pred             eCCeEEEEEeecCchhH
Q 002823          294 IAGKQIKLEPSHLRGLR  310 (876)
Q Consensus       294 I~Gr~IkVs~A~~k~~R  310 (876)
                      ++.++|.|.++..++.+
T Consensus       164 l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  164 LCNRPITVSYAFKKDTK  180 (203)
T ss_pred             hcCCceEEEEEEecCCC
Confidence            99999999999876533

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.83  E-value=5.9e-20  Score=214.67  Aligned_cols=153  Identities=20%  Similarity=0.291  Sum_probs=132.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccC-CceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTR-SGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~-Gr~L~V~~A~  220 (876)
                      ..++|||+|||++++|++|+++|++||.|.+++    .++++||||||+|.+.++|++|++.|++..+. ++.|.|..+.
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc
Confidence            458999999999999999999999999999987    36789999999999999999999999999885 7888776653


Q ss_pred             CCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCC-eEEEEe------cCCcccEEEEEecCHHHHHHHHHHhCC--
Q 002823          221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGE-IKEIRE------TPQKIHQKYIEFYDTRAAEAALRELNS--  291 (876)
Q Consensus       221 pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~-I~sVri------tg~skG~AFVeF~d~E~A~kAL~~LnG--  291 (876)
                                ..++|||+|||.++++++|++.|++++. |+++.+      ..+.++||||+|.+.++|.+|++.|+.  
T Consensus       137 ----------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gk  206 (578)
T TIGR01648       137 ----------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGR  206 (578)
T ss_pred             ----------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccc
Confidence                      2468999999999999999999999974 333322      235689999999999999999998864  


Q ss_pred             ceeCCeEEEEEeecCch
Q 002823          292 RYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       292 ~~I~Gr~IkVs~A~~k~  308 (876)
                      ..+.|+.|+|+|+.++.
T Consensus       207 i~l~Gr~I~VdwA~p~~  223 (578)
T TIGR01648       207 IQLWGHVIAVDWAEPEE  223 (578)
T ss_pred             eEecCceEEEEeecccc
Confidence            46789999999998754

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.83  E-value=9.1e-21  Score=199.28  Aligned_cols=148  Identities=24%  Similarity=0.343  Sum_probs=138.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCCCCc
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSE  227 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~~~e  227 (876)
                      -+|||+|||.++++.+|+.+|++||+|.+|.+   -|.||||..++...|+.|++.|++..|+|..|.|+-++.|.    
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDI---vKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs----   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDI---VKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS----   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeee---ecccceEEeecccccHHHHhhcccceecceEEEEEeccccC----
Confidence            47999999999999999999999999999986   56799999999999999999999999999999999887662    


Q ss_pred             cccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          228 KEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       228 k~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                        +...+|+|+||.+.++.+||+..|++||.|.+++|   -|+|+||.|+..++|..|++.||+.++.|++++|..+..+
T Consensus        76 --k~stkl~vgNis~tctn~ElRa~fe~ygpviecdi---vkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen   76 --KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDI---VKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             --CCccccccCCCCccccCHHHhhhhcccCCceeeee---ecceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence              34678999999999999999999999999999998   4789999999999999999999999999999999998764

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.82  E-value=1.8e-19  Score=206.16  Aligned_cols=162  Identities=22%  Similarity=0.333  Sum_probs=137.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      .++|||+|||..+++++|+++|++||.|..|..     +++++|||||+|.+.++|.+|++.|+|..|.|++|.|.|+..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            689999999999999999999999999998872     457899999999999999999999999999999999999531


Q ss_pred             CCCCC---------------------------------------------------------------------------
Q 002823          222 KDNPS---------------------------------------------------------------------------  226 (876)
Q Consensus       222 k~~~~---------------------------------------------------------------------------  226 (876)
                      .....                                                                           
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (457)
T TIGR01622       266 STYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALA  345 (457)
T ss_pred             CCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccc
Confidence            10000                                                                           


Q ss_pred             ---------c--cccccceeEeecCCCCCc----------HHHHHHHhhhcCCeEEEEec-CCcccEEEEEecCHHHHHH
Q 002823          227 ---------E--KEINQGTLVVFNLDSSVS----------NDELHHIFGVYGEIKEIRET-PQKIHQKYIEFYDTRAAEA  284 (876)
Q Consensus       227 ---------e--k~~~~~tLfV~NLP~svT----------eedLreiFs~fG~I~sVrit-g~skG~AFVeF~d~E~A~k  284 (876)
                               .  .......|+|.||....+          .+||++.|++||.|+.|.+. +...|++||+|.+.++|.+
T Consensus       346 ~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F~~~e~A~~  425 (457)
T TIGR01622       346 IMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDAALA  425 (457)
T ss_pred             cccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCCCceeEEEEECCHHHHHH
Confidence                     0  001335788888855433          36899999999999999884 7778999999999999999


Q ss_pred             HHHHhCCceeCCeEEEEEeecCch
Q 002823          285 ALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       285 AL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      |++.|||..++|+.|.|.|.....
T Consensus       426 A~~~lnGr~f~gr~i~~~~~~~~~  449 (457)
T TIGR01622       426 AFQALNGRYFGGKMITAAFVVNDV  449 (457)
T ss_pred             HHHHhcCcccCCeEEEEEEEcHHH
Confidence            999999999999999999987654

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.82  E-value=6.9e-20  Score=204.89  Aligned_cols=164  Identities=16%  Similarity=0.284  Sum_probs=144.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      .||||++||+.++.++|.++|+.+|+|..++     .+..+|||+||.|.-.+++++|++...+..+.|+.|+|.++.++
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            7999999999999999999999999999887     23458999999999999999999999999999999999998766


Q ss_pred             CCCCcc----------------------ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEe
Q 002823          223 DNPSEK----------------------EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEF  276 (876)
Q Consensus       223 ~~~~ek----------------------~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF  276 (876)
                      ....+.                      +.+.-+|.|+|||+.+...+|+.+|+.||.|.+|.|    .+.-.|||||.|
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~f  165 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQF  165 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEE
Confidence            432200                      002348999999999999999999999999999998    333459999999


Q ss_pred             cCHHHHHHHHHHhCCceeCCeEEEEEeecCchhHH
Q 002823          277 YDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       277 ~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~Rr  311 (876)
                      .+..+|.+|++.+|+.+|.||+|-|.|+.+++.-+
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye  200 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYE  200 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeeccccccc
Confidence            99999999999999999999999999999987443

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.81  E-value=3.1e-19  Score=199.77  Aligned_cols=184  Identities=18%  Similarity=0.330  Sum_probs=151.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      --.|.|+|||+.+.+.+|+.+|++||.|..|.+    .++-.|||||.|.+..+|.+|++.+|+..|.||+|.|.||.+|
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            568999999999999999999999999999983    4556699999999999999999999999999999999999665


Q ss_pred             CCCCc-----------------------------------------c--c------------------------------
Q 002823          223 DNPSE-----------------------------------------K--E------------------------------  229 (876)
Q Consensus       223 ~~~~e-----------------------------------------k--~------------------------------  229 (876)
                      +....                                         .  +                              
T Consensus       197 d~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~  276 (678)
T KOG0127|consen  197 DTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKES  276 (678)
T ss_pred             ccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcc
Confidence            31000                                         0  0                              


Q ss_pred             -------------cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHh--
Q 002823          230 -------------INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALREL--  289 (876)
Q Consensus       230 -------------~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~L--  289 (876)
                                   ....+|||+|||+++|+++|.+.|++||+|.++.+     +++++|.|||.|.+..+|.+||...  
T Consensus       277 ~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Asp  356 (678)
T KOG0127|consen  277 DKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASP  356 (678)
T ss_pred             cchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCc
Confidence                         01148999999999999999999999999999665     8889999999999999999999977  


Q ss_pred             ---CC-ceeCCeEEEEEeecCchhHHHHhhcCCchhhhhhcCCCC
Q 002823          290 ---NS-RYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQ  330 (876)
Q Consensus       290 ---nG-~~I~Gr~IkVs~A~~k~~Rr~l~qQ~~~q~~q~~~g~~~  330 (876)
                         .| ..+.||.|+|..+..+++...|++.........-+.+|+
T Consensus       357 a~e~g~~ll~GR~Lkv~~Av~RkeA~dmeqkk~~Kk~~gkrNLyL  401 (678)
T KOG0127|consen  357 ASEDGSVLLDGRLLKVTLAVTRKEAADMEQKKKRKKPKGKRNLYL  401 (678)
T ss_pred             cCCCceEEEeccEEeeeeccchHHHHHHHHHhhhhccCCccceee
Confidence               34 678999999999999887665644422223333344444

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.77  E-value=3.4e-18  Score=177.44  Aligned_cols=165  Identities=15%  Similarity=0.274  Sum_probs=140.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCC--ceee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRS--GKLD  215 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G--r~L~  215 (876)
                      +......|||.+||+.+|..||+.+|++||.|..-+     .++.+||.+||.|...++|++|++.|+|..-.|  .+|.
T Consensus       123 ~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepIt  202 (360)
T KOG0145|consen  123 DSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPIT  202 (360)
T ss_pred             hhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeE
Confidence            345567999999999999999999999999886544     678999999999999999999999999988655  5788


Q ss_pred             EeecCCCCCCC------------------------ccc----------------------------------c-ccceeE
Q 002823          216 IHYSIPKDNPS------------------------EKE----------------------------------I-NQGTLV  236 (876)
Q Consensus       216 V~~A~pk~~~~------------------------ek~----------------------------------~-~~~tLf  236 (876)
                      |+|+.......                        .+.                                  . ..-.||
T Consensus       203 VKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciF  282 (360)
T KOG0145|consen  203 VKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIF  282 (360)
T ss_pred             EEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEE
Confidence            98874321100                        000                                  0 112899


Q ss_pred             eecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          237 VFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       237 V~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      |.||.++.++.-|+++|.+||.|..|++     +.+.|||+||.+.+.++|..||..|||..+++|.|.|.|...+
T Consensus       283 vYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  283 VYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             EEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            9999999999999999999999999887     5678999999999999999999999999999999999998764

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.77  E-value=3e-18  Score=191.95  Aligned_cols=150  Identities=19%  Similarity=0.331  Sum_probs=136.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDN  224 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~  224 (876)
                      ..|||+   +++|+..|.++|+++|+|.+++   ... +.|||||.|.++++|++|+++++...+.|++|+|-|+.....
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~   77 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDAT-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPS   77 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCC-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCc
Confidence            468999   9999999999999999999887   334 999999999999999999999999999999999999864322


Q ss_pred             CCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 002823          225 PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL  301 (876)
Q Consensus       225 ~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkV  301 (876)
                               .|||.||+++++..+|.++|+.||+|.+|++   ....+|| ||+|++.++|.+|+..+||..+.|++|.|
T Consensus        78 ---------~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~v  147 (369)
T KOG0123|consen   78 ---------LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYV  147 (369)
T ss_pred             ---------eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEE
Confidence                     2999999999999999999999999999988   2237889 99999999999999999999999999999


Q ss_pred             EeecCchhHH
Q 002823          302 EPSHLRGLRK  311 (876)
Q Consensus       302 s~A~~k~~Rr  311 (876)
                      ....++..|.
T Consensus       148 g~~~~~~er~  157 (369)
T KOG0123|consen  148 GLFERKEERE  157 (369)
T ss_pred             eeccchhhhc
Confidence            9999887664

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.75  E-value=3.6e-18  Score=183.45  Aligned_cols=160  Identities=15%  Similarity=0.327  Sum_probs=140.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      +.|||+.|.+++.|+.|+..|..||+|++|.     .++++||||||+|+-+|.|+-|++.|||..++||.|+|.....-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            6899999999999999999999999999998     68999999999999999999999999999999999999743211


Q ss_pred             CC--C-----CccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhC
Q 002823          223 DN--P-----SEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELN  290 (876)
Q Consensus       223 ~~--~-----~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~Ln  290 (876)
                      ..  +     .+....-.+|||..+.++++++||+.+|+.||+|++|.+     ....|||+||||.+..+-..|+..||
T Consensus       194 pQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMN  273 (544)
T KOG0124|consen  194 PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN  273 (544)
T ss_pred             cccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcc
Confidence            11  1     011224569999999999999999999999999999998     34568999999999999999999999


Q ss_pred             CceeCCeEEEEEeecCc
Q 002823          291 SRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       291 G~~I~Gr~IkVs~A~~k  307 (876)
                      -..++|.-|+|..+...
T Consensus       274 lFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  274 LFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             hhhcccceEecccccCC
Confidence            99999999999876553

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.73  E-value=1e-17  Score=192.92  Aligned_cols=160  Identities=22%  Similarity=0.366  Sum_probs=139.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEeCC--------CccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          150 LLLRKINSNIEDSELKALFEQYGDVRTFYRAS--------KHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       150 LFVgNLP~~vTEeeL~elFsqfG~I~sV~~tg--------ksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      |||.||+++.+.++|..+|.++|.|.++.+..        .+.|||||+|.+.++|++|++.|+|+.|.|+.|.|+++..
T Consensus       518 lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~  597 (725)
T KOG0110|consen  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISEN  597 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccC
Confidence            99999999999999999999999999996311        1449999999999999999999999999999999999972


Q ss_pred             CCCC-----CccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCC-----cccEEEEEecCHHHHHHHHHHhCC
Q 002823          222 KDNP-----SEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQ-----KIHQKYIEFYDTRAAEAALRELNS  291 (876)
Q Consensus       222 k~~~-----~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~-----skG~AFVeF~d~E~A~kAL~~LnG  291 (876)
                      +...     .......+.|+|+|||...+..+++++|..||.|++|++..+     .+|||||+|-+.++|.+|+.+|..
T Consensus       598 k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~S  677 (725)
T KOG0110|consen  598 KPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGS  677 (725)
T ss_pred             ccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcc
Confidence            2211     111123468999999999999999999999999999998332     478999999999999999999999


Q ss_pred             ceeCCeEEEEEeecCchh
Q 002823          292 RYIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       292 ~~I~Gr~IkVs~A~~k~~  309 (876)
                      ..+.||+|.++|+.....
T Consensus       678 THlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  678 THLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             cceechhhheehhccchH
Confidence            999999999999988653

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.72  E-value=7.7e-17  Score=165.83  Aligned_cols=163  Identities=24%  Similarity=0.384  Sum_probs=145.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHH----HhhccCCeEEEE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKA----LFEQYGDVRTFY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~e----lFsqfG~I~sV~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      +..|..||||.||+..+..++|++    +|++||.|..|.  .+.+.||.|||.|.+.+.|-.|+++|+|..+.|+.++|
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            445667999999999999999987    999999999998  67889999999999999999999999999999999999


Q ss_pred             eecCCCCCCCcc----------------------------------------------ccccceeEeecCCCCCcHHHHH
Q 002823          217 HYSIPKDNPSEK----------------------------------------------EINQGTLVVFNLDSSVSNDELH  250 (876)
Q Consensus       217 ~~A~pk~~~~ek----------------------------------------------~~~~~tLfV~NLP~svTeedLr  250 (876)
                      +||..+.+...+                                              ..+..+||+.|||..++.+.|.
T Consensus        85 qyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~  164 (221)
T KOG4206|consen   85 QYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLS  164 (221)
T ss_pred             ecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHH
Confidence            999665332111                                              1244589999999999999999


Q ss_pred             HHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEeec
Q 002823          251 HIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIA-GKQIKLEPSH  305 (876)
Q Consensus       251 eiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~-Gr~IkVs~A~  305 (876)
                      .+|.+|...++|++....++.|||+|.+...|..|...+.+..|. ...++|.+++
T Consensus       165 ~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  165 DLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            999999999999998888899999999999999999999999887 7888888875

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.71  E-value=6.8e-17  Score=181.14  Aligned_cols=234  Identities=15%  Similarity=0.234  Sum_probs=179.6

Q ss_pred             HHHhcCCCCCC-chhhhcccCCCCCCCCCCCCCCCCCCCccccccCCCcccc--CCCcchhhccccccccCCCCCCCCcC
Q 002823           56 AQTIGNLLPDD-DDLFSGVTDGLECTVHPSGGSGGDDMDDLDFFSSVGGMDL--GNDSSYVAQKKSEICIGFSNHELGVC  132 (876)
Q Consensus        56 ~~~iG~llPdd-dellsgv~d~~~~~~~~~~~s~~dD~dd~D~F~sgGGmEL--~D~s~s~g~~~~s~~~g~~nG~~~~~  132 (876)
                      ..++|   |+. +..|-+.+...+.+..+.   -..|     . + +-|...  .........+...++.....|...+.
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~r---vc~d-----~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~ri   69 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIR---VCRD-----A-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRI   69 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEE---Eeec-----C-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEe
Confidence            34667   776 777777777777666665   3332     2 2 334333  22223333444455554455554454


Q ss_pred             CccccCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe---CCCccceEeeecCCHHHHHHHHHHcccccc
Q 002823          133 NGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR---ASKHCGFVTISYYDIRAARNAMKSLQNKLT  209 (876)
Q Consensus       133 ng~~~ge~p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~---tgksrGfAFV~F~d~edA~kAl~~Lng~~l  209 (876)
                      -|...       +++ .|||.||++++|..+|.++|+.||.|.+|+.   ..-++|| ||+|.++++|++|++.+||..+
T Consensus        70 m~s~r-------d~~-~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll  140 (369)
T KOG0123|consen   70 MWSQR-------DPS-LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLL  140 (369)
T ss_pred             ehhcc-------CCc-eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCccc
Confidence            44421       222 2999999999999999999999999999992   2338999 9999999999999999999999


Q ss_pred             CCceeeEeecCCCCCCCccc----cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHH
Q 002823          210 RSGKLDIHYSIPKDNPSEKE----INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRA  281 (876)
Q Consensus       210 ~Gr~L~V~~A~pk~~~~ek~----~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~  281 (876)
                      .+++|.|.....+..+....    ..-..++|.|++.++++++|..+|..||.|..+.+    .+++++|+||+|++.++
T Consensus       141 ~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~  220 (369)
T KOG0123|consen  141 NGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPED  220 (369)
T ss_pred             CCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhH
Confidence            99999998887765543222    23448999999999999999999999999999776    45578999999999999


Q ss_pred             HHHHHHHhCCceeCCeEEEEEeecCchhHH
Q 002823          282 AEAALRELNSRYIAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       282 A~kAL~~LnG~~I~Gr~IkVs~A~~k~~Rr  311 (876)
                      |..|++.|++..+.++.+.|..+..+.++.
T Consensus       221 a~~av~~l~~~~~~~~~~~V~~aqkk~e~~  250 (369)
T KOG0123|consen  221 AKKAVETLNGKIFGDKELYVGRAQKKSERE  250 (369)
T ss_pred             HHHHHHhccCCcCCccceeecccccchhhH
Confidence            999999999999999999999998866665

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=1.3e-16  Score=166.26  Aligned_cols=165  Identities=17%  Similarity=0.324  Sum_probs=139.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccc-cCC--ceeeEee
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKL-TRS--GKLDIHY  218 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~-l~G--r~L~V~~  218 (876)
                      ..|+|||+-|.+.-.|+|++.+|..||.|.+|.    ..+.+||||||.|.+..+|+.||..|+|.. +.|  ..|.|+|
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            468999999999999999999999999999988    467899999999999999999999999964 444  3455655


Q ss_pred             cCCCCCCCc-----------------------------------------------------------------------
Q 002823          219 SIPKDNPSE-----------------------------------------------------------------------  227 (876)
Q Consensus       219 A~pk~~~~e-----------------------------------------------------------------------  227 (876)
                      +...+++.-                                                                       
T Consensus        98 ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A~  177 (371)
T KOG0146|consen   98 ADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAAA  177 (371)
T ss_pred             ccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcccccC
Confidence            422211000                                                                       


Q ss_pred             --------------------------------------------------------------------------------
Q 002823          228 --------------------------------------------------------------------------------  227 (876)
Q Consensus       228 --------------------------------------------------------------------------------  227 (876)
                                                                                                      
T Consensus       178 Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aay  257 (371)
T KOG0146|consen  178 PVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAAY  257 (371)
T ss_pred             CcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhhc
Confidence                                                                                            


Q ss_pred             -----------------------cccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCH
Q 002823          228 -----------------------KEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDT  279 (876)
Q Consensus       228 -----------------------k~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~  279 (876)
                                             ..+..+.|||..||....+.||.+.|-.||.|++.++     +..+|.|+||.|+++
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence                                   0003358999999999999999999999999999655     778999999999999


Q ss_pred             HHHHHHHHHhCCceeCCeEEEEEeecCchhH
Q 002823          280 RAAEAALRELNSRYIAGKQIKLEPSHLRGLR  310 (876)
Q Consensus       280 E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~R  310 (876)
                      .+|++||.+|||..|+-|+|+|.+.++|++.
T Consensus       338 ~SaQaAIqAMNGFQIGMKRLKVQLKRPkdan  368 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIGMKRLKVQLKRPKDAN  368 (371)
T ss_pred             hhHHHHHHHhcchhhhhhhhhhhhcCccccC
Confidence            9999999999999999999999999998754

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=2.2e-16  Score=173.46  Aligned_cols=163  Identities=16%  Similarity=0.348  Sum_probs=141.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccc-cCC--ceeeEee
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKL-TRS--GKLDIHY  218 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~-l~G--r~L~V~~  218 (876)
                      ..++|||+-|++.++|.|++++|.+||.|++|+    ..+.+||||||+|.+.|.|..||++||+.. +.|  .+|.|+|
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkF  202 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKF  202 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEe
Confidence            368999999999999999999999999999998    457899999999999999999999999965 655  5899999


Q ss_pred             cCCCCCCCcccc--------------------------------------------------------------------
Q 002823          219 SIPKDNPSEKEI--------------------------------------------------------------------  230 (876)
Q Consensus       219 A~pk~~~~ek~~--------------------------------------------------------------------  230 (876)
                      +.+++++..+..                                                                    
T Consensus       203 ADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~~~  282 (510)
T KOG0144|consen  203 ADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAALAA  282 (510)
T ss_pred             cccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHhhh
Confidence            876654211000                                                                    


Q ss_pred             --------------------------------------------------------------------------------
Q 002823          231 --------------------------------------------------------------------------------  230 (876)
Q Consensus       231 --------------------------------------------------------------------------------  230 (876)
                                                                                                      
T Consensus       283 ~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~aa  362 (510)
T KOG0144|consen  283 AATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPVAA  362 (510)
T ss_pred             hcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCcccc
Confidence                                                                                            


Q ss_pred             ------------------------------------------------------------ccceeEeecCCCCCcHHHHH
Q 002823          231 ------------------------------------------------------------NQGTLVVFNLDSSVSNDELH  250 (876)
Q Consensus       231 ------------------------------------------------------------~~~tLfV~NLP~svTeedLr  250 (876)
                                                                                  ....|||.+||.+.-+.+|.
T Consensus       363 ~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~l~  442 (510)
T KOG0144|consen  363 SLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQDLI  442 (510)
T ss_pred             cccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHHHH
Confidence                                                                        12379999999999999999


Q ss_pred             HHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          251 HIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       251 eiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..|..||.|++.++     ++-+|.|+||.|++..+|..||..|||..|+.++++|...+.+.
T Consensus       443 ~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~  505 (510)
T KOG0144|consen  443 ATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRN  505 (510)
T ss_pred             HHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccC
Confidence            99999999998554     67789999999999999999999999999999999999988764

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.66  E-value=2.4e-15  Score=176.61  Aligned_cols=76  Identities=14%  Similarity=0.348  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ...++|||+|||+++++++|+++|++||+|.+++     .++++||||||+|.+.++|.+|++.||+..+.|+.|+|.++
T Consensus       202 ~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA  281 (612)
T TIGR01645       202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  281 (612)
T ss_pred             cccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence            3457999999999999999999999999999987     35679999999999999999999999999999999999776


Q ss_pred             C
Q 002823          220 I  220 (876)
Q Consensus       220 ~  220 (876)
                      .
T Consensus       282 i  282 (612)
T TIGR01645       282 V  282 (612)
T ss_pred             C
Confidence            5

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.65  E-value=4.2e-16  Score=163.09  Aligned_cols=135  Identities=20%  Similarity=0.390  Sum_probs=113.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      +...|||||+||+++|||+-|..||.+.|.|+.+++-          |+                    .|+|.|+....
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i----------~~--------------------e~~v~wa~~p~   52 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVI----------FD--------------------ELKVNWATAPG   52 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceee----------hh--------------------hhccccccCcc
Confidence            3456899999999999999999999999999998741          11                    44555654433


Q ss_pred             CCCccccc-cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCe
Q 002823          224 NPSEKEIN-QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK  297 (876)
Q Consensus       224 ~~~ek~~~-~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr  297 (876)
                      ........ .-.+||+.|...++.++|++.|.+||+|.+.|+     +.++|||+||.|.+.++|++||..|||..|++|
T Consensus        53 nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R  132 (321)
T KOG0148|consen   53 NQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRR  132 (321)
T ss_pred             cCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccc
Confidence            33222222 338999999999999999999999999998766     788999999999999999999999999999999


Q ss_pred             EEEEEeecCch
Q 002823          298 QIKLEPSHLRG  308 (876)
Q Consensus       298 ~IkVs~A~~k~  308 (876)
                      .|+-.|+.+|-
T Consensus       133 ~IRTNWATRKp  143 (321)
T KOG0148|consen  133 TIRTNWATRKP  143 (321)
T ss_pred             eeeccccccCc
Confidence            99999998876

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.65  E-value=2.5e-13  Score=149.43  Aligned_cols=158  Identities=18%  Similarity=0.286  Sum_probs=131.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhh-ccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFE-QYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFs-qfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      .|.+||.|||+++...+|++||. +.|+|+.|.    ..+|.||||.|+|+++|.+++|++.|+...+.||+|.|+-...
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            46799999999999999999998 788999887    6799999999999999999999999999999999999843211


Q ss_pred             ----------------------------------------------CCC-CCc---------------------------
Q 002823          222 ----------------------------------------------KDN-PSE---------------------------  227 (876)
Q Consensus       222 ----------------------------------------------k~~-~~e---------------------------  227 (876)
                                                                    +++ ...                           
T Consensus       124 ~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~F  203 (608)
T KOG4212|consen  124 EQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASF  203 (608)
T ss_pred             hhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhh
Confidence                                                          000 000                           


Q ss_pred             -------cccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC
Q 002823          228 -------KEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG  296 (876)
Q Consensus       228 -------k~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G  296 (876)
                             ..+...++||.||...+..+.|++.|.-.|+|..|.+    .+.+++++.++|..+-+|..||..|++.-+..
T Consensus       204 lr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~~  283 (608)
T KOG4212|consen  204 LRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLFD  283 (608)
T ss_pred             hhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCcc
Confidence                   0002347999999999999999999999999988665    56678999999999999999999999877777


Q ss_pred             eEEEEEee
Q 002823          297 KQIKLEPS  304 (876)
Q Consensus       297 r~IkVs~A  304 (876)
                      ++..+...
T Consensus       284 ~~~~~Rl~  291 (608)
T KOG4212|consen  284 RRMTVRLD  291 (608)
T ss_pred             ccceeecc
Confidence            77666653

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.64  E-value=1.7e-15  Score=151.21  Aligned_cols=149  Identities=18%  Similarity=0.253  Sum_probs=127.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCC--ccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASK--HCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgk--srGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ..+++|||+|||.++.+.+|+++|-+||.|+.|.....  .-.||||+|+++.+|+.||..-+|..+.|..|+|+|+..-
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            45789999999999999999999999999999984333  4689999999999999999999999999999999998654


Q ss_pred             CCCC----------------------ccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHH
Q 002823          223 DNPS----------------------EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTR  280 (876)
Q Consensus       223 ~~~~----------------------ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E  280 (876)
                      ....                      ........|.|.+||++.+++||++++.+-|.|....+.  ..+++.|+|...|
T Consensus        84 r~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~--rDg~GvV~~~r~e  161 (241)
T KOG0105|consen   84 RSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQ--RDGVGVVEYLRKE  161 (241)
T ss_pred             CcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeee--cccceeeeeeehh
Confidence            2110                      111244589999999999999999999999999987764  3469999999999


Q ss_pred             HHHHHHHHhCCceeC
Q 002823          281 AAEAALRELNSRYIA  295 (876)
Q Consensus       281 ~A~kAL~~LnG~~I~  295 (876)
                      +.+-|++.|+...+.
T Consensus       162 DMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  162 DMKYAVRKLDDQKFR  176 (241)
T ss_pred             hHHHHHHhhcccccc
Confidence            999999999887764

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.62  E-value=1.1e-15  Score=166.80  Aligned_cols=162  Identities=10%  Similarity=0.269  Sum_probs=141.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ..++|||++|+++++++.|++.|.+||+|..+.     .+++++||+||+|.+++...+++.. ....|.|+.|.+.-+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            578999999999999999999999999999987     4688999999999999999988843 4467999999999999


Q ss_pred             CCCCCCcccc--ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCce
Q 002823          221 PKDNPSEKEI--NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRY  293 (876)
Q Consensus       221 pk~~~~ek~~--~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~  293 (876)
                      ++.+..+...  ...+|||++||.+++++++++.|.+||.|..+.+     +.+.++|+||.|.+++.+.+++. ..-..
T Consensus        84 ~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~  162 (311)
T KOG4205|consen   84 SREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHD  162 (311)
T ss_pred             CcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceee
Confidence            8876654333  3569999999999999999999999998877544     55678999999999999999876 67789


Q ss_pred             eCCeEEEEEeecCchh
Q 002823          294 IAGKQIKLEPSHLRGL  309 (876)
Q Consensus       294 I~Gr~IkVs~A~~k~~  309 (876)
                      |.|+.+.|..|.+++.
T Consensus       163 ~~gk~vevkrA~pk~~  178 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKEV  178 (311)
T ss_pred             ecCceeeEeeccchhh
Confidence            9999999999999763

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.57  E-value=1.9e-15  Score=170.79  Aligned_cols=163  Identities=22%  Similarity=0.310  Sum_probs=140.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .++..||+|+--|+..++..+|.++|+.+|+|+.|.     .++.++|.|||+|.|.+....|+ .|.|+.+.|.+|.|+
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEec
Confidence            445579999999999999999999999999999987     46779999999999999999999 799999999999997


Q ss_pred             ecCCCCCCCcc----------ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHH
Q 002823          218 YSIPKDNPSEK----------EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAA  282 (876)
Q Consensus       218 ~A~pk~~~~ek----------~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A  282 (876)
                      ......+....          ..+-..|||+||-.++++++|+.+|+.||.|..|.+     ++..+||+||+|.+.++|
T Consensus       254 ~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~a  333 (549)
T KOG0147|consen  254 LSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDA  333 (549)
T ss_pred             ccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHH
Confidence            76433221100          001123999999999999999999999999999776     677899999999999999


Q ss_pred             HHHHHHhCCceeCCeEEEEEeecC
Q 002823          283 EAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       283 ~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .+|+..|||.+|.|+.|+|.....
T Consensus       334 r~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  334 RKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             HHHHHHhccceecCceEEEEEeee
Confidence            999999999999999999887654

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.47  E-value=2e-13  Score=154.52  Aligned_cols=161  Identities=20%  Similarity=0.329  Sum_probs=128.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      +.|||+||-.++++++|+.+|+.||+|..|.     .++.++||+||+|.+.++|++|++.|||..|-|+.|+|.....+
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            3499999999999999999999999999987     38999999999999999999999999999999999998443211


Q ss_pred             CCCCcc-------c------------------------------------------------------------------
Q 002823          223 DNPSEK-------E------------------------------------------------------------------  229 (876)
Q Consensus       223 ~~~~ek-------~------------------------------------------------------------------  229 (876)
                      -...+.       +                                                                  
T Consensus       359 ~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~  438 (549)
T KOG0147|consen  359 VDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPA  438 (549)
T ss_pred             cccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccc
Confidence            000000       0                                                                  


Q ss_pred             --cccceeEeecCCC--CCc--------HHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCe
Q 002823          230 --INQGTLVVFNLDS--SVS--------NDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK  297 (876)
Q Consensus       230 --~~~~tLfV~NLP~--svT--------eedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr  297 (876)
                        .++.++.+.|+=.  ..|        .+|+.+.+.+||+|..|.++..+-|+.||.|.+.++|..|+++|||..|.||
T Consensus       439 ~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrWF~gr  518 (549)
T KOG0147|consen  439 FDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRWFAGR  518 (549)
T ss_pred             cCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhhhccc
Confidence              0111223333311  111        2678889999999999999888889999999999999999999999999999


Q ss_pred             EEEEEeecCch
Q 002823          298 QIKLEPSHLRG  308 (876)
Q Consensus       298 ~IkVs~A~~k~  308 (876)
                      .|.+.|-....
T Consensus       519 ~Ita~~~~~~~  529 (549)
T KOG0147|consen  519 MITAKYLPLER  529 (549)
T ss_pred             eeEEEEeehhh
Confidence            99999976543

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.45  E-value=8.5e-14  Score=144.49  Aligned_cols=151  Identities=21%  Similarity=0.347  Sum_probs=130.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCCC--
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNP--  225 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~~--  225 (876)
                      ..+||++||+.+.+.+|.++|..||.|..+.+   ..||+||.|.+..+|..|+..++++.|.+..+.|+|+..+...  
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m---k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g   78 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADM---KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRG   78 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccccccee---ecccceeccCchhhhhcccchhcCceecceeeeeecccccccccC
Confidence            36899999999999999999999999999876   4578899999999999999999999999988999998753110  


Q ss_pred             ----C----------ccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCC
Q 002823          226 ----S----------EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS  291 (876)
Q Consensus       226 ----~----------ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG  291 (876)
                          .          ........++|.++...+.+.+|.+.|..+|++.+...   ..+++||+|.+.++|.+|+..|++
T Consensus        79 ~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~  155 (216)
T KOG0106|consen   79 RPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEKLDG  155 (216)
T ss_pred             CCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchhccc
Confidence                0          00123447899999999999999999999999965544   678999999999999999999999


Q ss_pred             ceeCCeEEEEEee
Q 002823          292 RYIAGKQIKLEPS  304 (876)
Q Consensus       292 ~~I~Gr~IkVs~A  304 (876)
                      ..+.+++|.+...
T Consensus       156 ~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  156 KKLNGRRISVEKN  168 (216)
T ss_pred             hhhcCceeeeccc
Confidence            9999999999443

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.44  E-value=6.5e-13  Score=136.20  Aligned_cols=151  Identities=17%  Similarity=0.277  Sum_probs=119.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE--eCCCc----cceEeeecCCHHHHHHHHHHccccccC---Cceee
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY--RASKH----CGFVTISYYDIRAARNAMKSLQNKLTR---SGKLD  215 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~--~tgks----rGfAFV~F~d~edA~kAl~~Lng~~l~---Gr~L~  215 (876)
                      ..-|||||.+||.++...||..+|..|--.+...  .+.+.    +.+|||.|.+..+|..|+.+|||..++   +..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            3469999999999999999999999886555443  33443    479999999999999999999999875   67888


Q ss_pred             EeecCCCCCCC----------------------cc-----------------------------c---------------
Q 002823          216 IHYSIPKDNPS----------------------EK-----------------------------E---------------  229 (876)
Q Consensus       216 V~~A~pk~~~~----------------------ek-----------------------------~---------------  229 (876)
                      |++++......                      ..                             +               
T Consensus       112 iElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P  191 (284)
T KOG1457|consen  112 IELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAP  191 (284)
T ss_pred             eeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCC
Confidence            87774221100                      00                             0               


Q ss_pred             ----------------cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-cCCcccEEEEEecCHHHHHHHHHHhCCc
Q 002823          230 ----------------INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-TPQKIHQKYIEFYDTRAAEAALRELNSR  292 (876)
Q Consensus       230 ----------------~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-tg~skG~AFVeF~d~E~A~kAL~~LnG~  292 (876)
                                      ....||||.||...+++++|+++|+.|-....+++ ....-..|||+|++.+.|..|+..|.|.
T Consensus       192 ~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~  271 (284)
T KOG1457|consen  192 SANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGN  271 (284)
T ss_pred             cccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcc
Confidence                            02348999999999999999999999988777776 2334468999999999999999999998


Q ss_pred             eeC
Q 002823          293 YIA  295 (876)
Q Consensus       293 ~I~  295 (876)
                      .|.
T Consensus       272 ~~s  274 (284)
T KOG1457|consen  272 LLS  274 (284)
T ss_pred             eec
Confidence            763

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.43  E-value=7.1e-13  Score=130.80  Aligned_cols=81  Identities=19%  Similarity=0.315  Sum_probs=74.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ...+++|||+|||+++++++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|++..|.|++|+|++
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            35578999999999999999999999999999987     3578899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 002823          219 SIPKDN  224 (876)
Q Consensus       219 A~pk~~  224 (876)
                      +.++..
T Consensus       111 a~~~~~  116 (144)
T PLN03134        111 ANDRPS  116 (144)
T ss_pred             CCcCCC
Confidence            976654

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.41  E-value=9.7e-13  Score=129.81  Aligned_cols=78  Identities=22%  Similarity=0.418  Sum_probs=72.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||+|||..+++++|+++|++||.|++|++     ++++++||||+|.+.++|++|++.||+..|.|++|+|++++
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            4568999999999999999999999999999877     45679999999999999999999999999999999999998


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      ++.
T Consensus       113 ~~~  115 (144)
T PLN03134        113 DRP  115 (144)
T ss_pred             cCC
Confidence            643

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.38  E-value=2.4e-12  Score=149.29  Aligned_cols=161  Identities=22%  Similarity=0.392  Sum_probs=133.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC---
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI---  220 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~---  220 (876)
                      +...+.|+|+|||..+..++|...|..||+|..+... ..--.|+|.|.+..+|++|.+.|....+...++++.|+.   
T Consensus       382 ~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp-~~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dv  460 (725)
T KOG0110|consen  382 ERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP-PGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDV  460 (725)
T ss_pred             hhhcceeeeccCccccccHHHHHHhhcccccceeecC-cccceeeeeecCccchHHHHHHhchhhhccCccccccChhhh
Confidence            4456889999999999999999999999999998653 333459999999999999999999999888888887652   


Q ss_pred             ----CCCC-------------CC------------ccc--------------cccceeEeecCCCCCcHHHHHHHhhhcC
Q 002823          221 ----PKDN-------------PS------------EKE--------------INQGTLVVFNLDSSVSNDELHHIFGVYG  257 (876)
Q Consensus       221 ----pk~~-------------~~------------ek~--------------~~~~tLfV~NLP~svTeedLreiFs~fG  257 (876)
                          |+..             ..            +.+              ....+|||.||+.+++.++|...|..+|
T Consensus       461 f~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G  540 (725)
T KOG0110|consen  461 FTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQG  540 (725)
T ss_pred             ccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcC
Confidence                1100             00            000              0122499999999999999999999999


Q ss_pred             CeEEEEecCC--------cccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          258 EIKEIRETPQ--------KIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       258 ~I~sVritg~--------skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      .|.++.|..+        +.|||||+|.+.++|.+|++.|+|..|.|+.|.|+++.
T Consensus       541 ~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  541 TVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             eEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            9999877222        23999999999999999999999999999999999998

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.36  E-value=1.2e-11  Score=133.82  Aligned_cols=161  Identities=14%  Similarity=0.236  Sum_probs=131.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEE----------E--eCCCccceEeeecCCHHHHHHHHHHccccccCCc
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTF----------Y--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSG  212 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV----------~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr  212 (876)
                      .-...|||.|||.++|.+++.++|++||-|..-          +  ..|+.+|-|.|.|-..++++-|++.|++..++|+
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            345679999999999999999999999977542          2  4588899999999999999999999999999999


Q ss_pred             eeeEeecCCC---------CC-------------------------CCccccccceeEeecCCC----CCc-------HH
Q 002823          213 KLDIHYSIPK---------DN-------------------------PSEKEINQGTLVVFNLDS----SVS-------ND  247 (876)
Q Consensus       213 ~L~V~~A~pk---------~~-------------------------~~ek~~~~~tLfV~NLP~----svT-------ee  247 (876)
                      +|+|+.|.-.         ..                         ...+....++|.+.|+=.    ..+       .+
T Consensus       212 ~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlke  291 (382)
T KOG1548|consen  212 KLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKE  291 (382)
T ss_pred             EEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHH
Confidence            9999776311         00                         011112455899999832    222       36


Q ss_pred             HHHHHhhhcCCeEEEEe-cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          248 ELHHIFGVYGEIKEIRE-TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       248 dLreiFs~fG~I~sVri-tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      +|++-+++||.|..|.+ ..++.|.+-|.|.+.++|..||+.|+|+.+.||+|..+...
T Consensus       292 dl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~D  350 (382)
T KOG1548|consen  292 DLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWD  350 (382)
T ss_pred             HHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeC
Confidence            77788999999999877 67789999999999999999999999999999999877653

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.32  E-value=1.8e-11  Score=134.39  Aligned_cols=160  Identities=23%  Similarity=0.260  Sum_probs=136.8

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCCC
Q 002823          147 SRTLLLRKINS-NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNP  225 (876)
Q Consensus       147 SrTLFVgNLP~-~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~~  225 (876)
                      +..|.|.||.. .||.+.|..+|.-||+|.+|++-.+.+--|.|+|.|...|+-|++.|+|..+.|++|+|.+++...-.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq  376 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ  376 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc
Confidence            57889999965 59999999999999999999966666789999999999999999999999999999999888533211


Q ss_pred             ------Cc---------------c----------ccccceeEeecCCCCCcHHHHHHHhhhcCCe-EEEEecCCcccEEE
Q 002823          226 ------SE---------------K----------EINQGTLVVFNLDSSVSNDELHHIFGVYGEI-KEIRETPQKIHQKY  273 (876)
Q Consensus       226 ------~e---------------k----------~~~~~tLfV~NLP~svTeedLreiFs~fG~I-~sVritg~skG~AF  273 (876)
                            .+               +          -+++.+|.+.|+|.++++|+|+..|..-|-. +-.+..++.+.+++
T Consensus       377 lp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal  456 (492)
T KOG1190|consen  377 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMAL  456 (492)
T ss_pred             CCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceee
Confidence                  00               0          0145589999999999999999999988765 55666777888999


Q ss_pred             EEecCHHHHHHHHHHhCCceeCCe-EEEEEeecC
Q 002823          274 IEFYDTRAAEAALRELNSRYIAGK-QIKLEPSHL  306 (876)
Q Consensus       274 VeF~d~E~A~kAL~~LnG~~I~Gr-~IkVs~A~~  306 (876)
                      +++.++|+|..|+..++...+++. .++|+|++.
T Consensus       457 ~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  457 PQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             cccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            999999999999999999999864 999999875

>PF00076 RRM_1: RNA recognition motif

Probab=99.31  E-value=9.7e-12  Score=104.94  Aligned_cols=66  Identities=35%  Similarity=0.580  Sum_probs=61.8

Q ss_pred             eEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       235 LfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      |||+|||.++++++|+++|++||.|..+++    .+..+++|||+|.+.++|++|++.|+|..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999877    345789999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>PF00076 RRM_1: RNA recognition motif

Probab=99.28  E-value=8.7e-12  Score=105.23  Aligned_cols=66  Identities=20%  Similarity=0.455  Sum_probs=61.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          150 LLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       150 LFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      |||+|||+++++++|+++|++||+|..+.    ..++.++||||+|.+.++|++|++.++|..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            79999999999999999999999998887    2467899999999999999999999999999999885

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.28  E-value=2.4e-11  Score=124.63  Aligned_cols=118  Identities=22%  Similarity=0.378  Sum_probs=101.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC-
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI-  220 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~-  220 (876)
                      .++|||+|||.++++++|+++|.+||.|..+.     .+++.+|||||+|.+.++|..|++.+++..+.|++|.|.++. 
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            69999999999999999999999999997776     368899999999999999999999999999999999999954 


Q ss_pred             ---CCCCCCc----------------cccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe
Q 002823          221 ---PKDNPSE----------------KEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE  264 (876)
Q Consensus       221 ---pk~~~~e----------------k~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri  264 (876)
                         ++.....                .......+++.+++..++..++...|..+|.+..+.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  257 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASL  257 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeec
Confidence               2222210                0113458999999999999999999999999977666

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.26  E-value=6.4e-11  Score=130.19  Aligned_cols=165  Identities=24%  Similarity=0.375  Sum_probs=135.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccce-EeeecCCHHHHHHHHHHccccccC--CceeeEeecC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGF-VTISYYDIRAARNAMKSLQNKLTR--SGKLDIHYSI  220 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGf-AFV~F~d~edA~kAl~~Lng~~l~--Gr~L~V~~A~  220 (876)
                      ..+--.++|.|+-.-|+-+.|..+|++||.|..|.+-.|..+| |.|+|.+.+.|+.|...|+|..|.  -+.|+|+|++
T Consensus       147 ~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sk  226 (492)
T KOG1190|consen  147 PNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSK  226 (492)
T ss_pred             CceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhh
Confidence            3445677899999999999999999999999999865566665 999999999999999999998864  3577776652


Q ss_pred             CC----------CC-------CCc--------------------------------------c--ccc--cceeEeecCC
Q 002823          221 PK----------DN-------PSE--------------------------------------K--EIN--QGTLVVFNLD  241 (876)
Q Consensus       221 pk----------~~-------~~e--------------------------------------k--~~~--~~tLfV~NLP  241 (876)
                      -.          ..       +..                                      .  ...  ...|.|.||.
T Consensus       227 lt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln  306 (492)
T KOG1190|consen  227 LTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLN  306 (492)
T ss_pred             cccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCc
Confidence            11          00       000                                      0  001  3477888886


Q ss_pred             C-CCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          242 S-SVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       242 ~-svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      . .+|.+.|.-+|+.||.|..|++-.+++..|+|+|.|...|+-|+..|+|..+.||+|+|.+++-..
T Consensus       307 ~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  307 EEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             hhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcc
Confidence            5 589999999999999999999977777899999999999999999999999999999999998643

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.25  E-value=1.1e-11  Score=123.63  Aligned_cols=77  Identities=31%  Similarity=0.447  Sum_probs=73.2

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..+|||+||+..+++.||..+|..||.|..|.+...+.|||||||+++.+|+.|+..|||+.|+|.+|+|+++....
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            56899999999999999999999999999999988899999999999999999999999999999999999997643

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.23  E-value=1.5e-11  Score=122.67  Aligned_cols=78  Identities=22%  Similarity=0.406  Sum_probs=74.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDN  224 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~  224 (876)
                      .++|||+||+..+++.||+.+|..||+|.+|++.....|||||+|+++.+|+.|+..|+|+.|.|..|+|+++.-...
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            689999999999999999999999999999999899999999999999999999999999999999999999865543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.21  E-value=3.5e-11  Score=134.49  Aligned_cols=108  Identities=19%  Similarity=0.258  Sum_probs=88.4

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|+.||+|++|++     ++++++||||+|.++++|++|++.|++..+.+++|+|.|+
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            34679999999999999999999999999999887     4567899999999999999999999999999999999998


Q ss_pred             cCchhHHHHhhcCCchhhhhhcCCCCCCCCCCCCCCCCcccceeeeccCchhhhHHHHHHhhccc
Q 002823          305 HLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLAIIYLFTGA  369 (876)
Q Consensus       305 ~~k~~Rr~l~qQ~~~q~~q~~~g~~~~gsp~~~sp~~~~~~~~~~~fssP~n~~~~~l~~l~~~~  369 (876)
                      ++.....      .                     .     ..-+.-+.|.+++...|..+|...
T Consensus       185 ~p~~~~~------~---------------------~-----~~lfV~nLp~~vtee~L~~~F~~f  217 (346)
T TIGR01659       185 RPGGESI------K---------------------D-----TNLYVTNLPRTITDDQLDTIFGKY  217 (346)
T ss_pred             ccccccc------c---------------------c-----ceeEEeCCCCcccHHHHHHHHHhc
Confidence            7643110      0                     0     012334678888888888888654

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.19  E-value=7.5e-11  Score=135.27  Aligned_cols=164  Identities=16%  Similarity=0.311  Sum_probs=128.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ....++||++||..+++.+++++.+.||+++...     .++.++||||.+|.+......|+..|+|+.+.+++|.|+.+
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            4457999999999999999999999999998765     45789999999999999999999999999999999999888


Q ss_pred             CCCCCCCccc--------------------cccceeEeecCC--CCC-cH-------HHHHHHhhhcCCeEEEEecCC--
Q 002823          220 IPKDNPSEKE--------------------INQGTLVVFNLD--SSV-SN-------DELHHIFGVYGEIKEIRETPQ--  267 (876)
Q Consensus       220 ~pk~~~~ek~--------------------~~~~tLfV~NLP--~sv-Te-------edLreiFs~fG~I~sVritg~--  267 (876)
                      .+........                    .+...|.+.|+=  .++ .+       |+++..+.+||.|..|.+...  
T Consensus       367 ~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~  446 (500)
T KOG0120|consen  367 IVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYP  446 (500)
T ss_pred             hccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCC
Confidence            6543221110                    122233333331  111 11       446667889999999998221  


Q ss_pred             ------cccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          268 ------KIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       268 ------skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                            ..|..||+|.+.+++++|.++|+|.++.|+.|...|....+
T Consensus       447 ~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeDk  493 (500)
T KOG0120|consen  447 DENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDEDK  493 (500)
T ss_pred             CCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHHH
Confidence                  34789999999999999999999999999999999986643

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.19  E-value=1.6e-10  Score=129.93  Aligned_cols=163  Identities=14%  Similarity=0.221  Sum_probs=128.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ...-|-+++|||++|++||.++|+.++ |+.+.   .+++..|-|||+|.+.+++++|++ .+...+..|-|.|--+.++
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCc
Confidence            345788899999999999999999887 44443   668999999999999999999996 5777788888888555433


Q ss_pred             CCCC-------ccccccceeEeecCCCCCcHHHHHHHhhhcCCeEE-EEe----cCCcccEEEEEecCHHHHHHHHHHhC
Q 002823          223 DNPS-------EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKE-IRE----TPQKIHQKYIEFYDTRAAEAALRELN  290 (876)
Q Consensus       223 ~~~~-------ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~s-Vri----tg~skG~AFVeF~d~E~A~kAL~~Ln  290 (876)
                      +...       ....+...|-+++||..||++||.++|+..-.|.. |.+    .+++.+-|||+|++.+.|++|+. -|
T Consensus        87 e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rh  165 (510)
T KOG4211|consen   87 EADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RH  165 (510)
T ss_pred             cccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HH
Confidence            3211       01124558999999999999999999997655544 322    34466889999999999999997 46


Q ss_pred             CceeCCeEEEEEeecCchhHH
Q 002823          291 SRYIAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       291 G~~I~Gr~IkVs~A~~k~~Rr  311 (876)
                      ...|+-+-|.|-.+...+.++
T Consensus       166 re~iGhRYIEvF~Ss~~e~~~  186 (510)
T KOG4211|consen  166 RENIGHRYIEVFRSSRAEVKR  186 (510)
T ss_pred             HHhhccceEEeehhHHHHHHh
Confidence            778888999998887766665

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.16  E-value=1.7e-10  Score=106.42  Aligned_cols=83  Identities=20%  Similarity=0.299  Sum_probs=77.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..+.|||+|||.++|.|++.++|.+||.|..||+  +...+|.|||.|++..+|.+|+..|+|..+.++.+.|-|..+.+
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHH
Confidence            4568999999999999999999999999999999  66678999999999999999999999999999999999999887


Q ss_pred             hHHHH
Q 002823          309 LRKCL  313 (876)
Q Consensus       309 ~Rr~l  313 (876)
                      ..+.+
T Consensus        97 ~~~~~  101 (124)
T KOG0114|consen   97 AFKLM  101 (124)
T ss_pred             HHHHH
Confidence            76644

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.13  E-value=1.2e-10  Score=125.50  Aligned_cols=100  Identities=16%  Similarity=0.239  Sum_probs=81.1

Q ss_pred             cccccCCceeeEeecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHH
Q 002823          205 QNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRA  281 (876)
Q Consensus       205 ng~~l~Gr~L~V~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~  281 (876)
                      ++....|..+.++-+.    ..+.....++|+|.|||....+-||+.+|++||+|.+|.|   ...+||||||+|++.++
T Consensus        73 ~~~~t~g~~~~~~~st----~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~d  148 (376)
T KOG0125|consen   73 NGAPTDGQPIQTQPST----NSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPAD  148 (376)
T ss_pred             CCCCCCCCccccCCCC----cCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhh
Confidence            3344555555543322    1222234568999999999999999999999999999888   55689999999999999


Q ss_pred             HHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          282 AEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       282 A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      |++|.++|||..|.||+|+|..+..+-
T Consensus       149 adRARa~LHgt~VEGRkIEVn~ATarV  175 (376)
T KOG0125|consen  149 ADRARAELHGTVVEGRKIEVNNATARV  175 (376)
T ss_pred             HHHHHHHhhcceeeceEEEEeccchhh
Confidence            999999999999999999999988753

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.12  E-value=7.7e-11  Score=112.30  Aligned_cols=77  Identities=19%  Similarity=0.407  Sum_probs=71.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      -..+.||||+||...++|++|.+||+++|+|+.|.     .+....|||||+|.+.++|+.|++.+++..+..++|+|.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            35689999999999999999999999999999998     4566889999999999999999999999999999999988


Q ss_pred             cC
Q 002823          219 SI  220 (876)
Q Consensus       219 A~  220 (876)
                      ..
T Consensus       113 D~  114 (153)
T KOG0121|consen  113 DA  114 (153)
T ss_pred             cc
Confidence            53

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.11  E-value=2.7e-10  Score=121.47  Aligned_cols=74  Identities=22%  Similarity=0.393  Sum_probs=68.1

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+||++.+++++|+++|+.||+|++|++  .+..++||||+|.+.++|+.|+. |+|..|.|++|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            468999999999999999999999999999988  33357999999999999999995 999999999999999764

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.10  E-value=2.6e-10  Score=105.22  Aligned_cols=81  Identities=26%  Similarity=0.393  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      +..-.+-|||+|||.++|.++..++|.+||.|+.|+  .+...+|.|||.|++..+|++|++.|.|..+.++.|.|.|..
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            455678999999999999999999999999999999  456689999999999999999999999999999999999987


Q ss_pred             CCC
Q 002823          221 PKD  223 (876)
Q Consensus       221 pk~  223 (876)
                      +.+
T Consensus        94 ~~~   96 (124)
T KOG0114|consen   94 PED   96 (124)
T ss_pred             HHH
Confidence            653

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.10  E-value=3.9e-10  Score=96.32  Aligned_cols=66  Identities=26%  Similarity=0.500  Sum_probs=59.1

Q ss_pred             eEeecCCCCCcHHHHHHHhhhcCCeEEEEec----CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRET----PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       235 LfV~NLP~svTeedLreiFs~fG~I~sVrit----g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      |||+|||+++++++|+++|+.||.|..+++.    +..+++|||+|.+.++|.+|++.+++..+.|++|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999999998883    33579999999999999999999999999999985

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.09  E-value=7.9e-10  Score=119.98  Aligned_cols=161  Identities=16%  Similarity=0.344  Sum_probs=126.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      +.-..|||..+.++.+|+||+..|+-||+|..|.     ..+.+|||+||+|.+..+-..|+..||-..++|.-|+|.-+
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccc
Confidence            3357999999999999999999999999999998     45779999999999999999999999999999998888322


Q ss_pred             CCCCC---------------------------------------------------------------------------
Q 002823          220 IPKDN---------------------------------------------------------------------------  224 (876)
Q Consensus       220 ~pk~~---------------------------------------------------------------------------  224 (876)
                      ....+                                                                           
T Consensus       288 vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~l~qa~~a~~~pgvi~~  367 (544)
T KOG0124|consen  288 VTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGTLPQAVMAAQAPGVITG  367 (544)
T ss_pred             cCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCCCCccccchhccCCceecc
Confidence            00000                                                                           


Q ss_pred             ------------------------------------CCc-----------------------------------cccccc
Q 002823          225 ------------------------------------PSE-----------------------------------KEINQG  233 (876)
Q Consensus       225 ------------------------------------~~e-----------------------------------k~~~~~  233 (876)
                                                          ..+                                   +...++
T Consensus       368 vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~sARhlvMqkLmR~~~S~  447 (544)
T KOG0124|consen  368 VTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSSARHLVMQKLMRKQEST  447 (544)
T ss_pred             CCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccCccHHHHHHHHHhccccCc
Confidence                                                000                                   000344


Q ss_pred             eeEeecC--CCCCc---HHHHHHHhhhcCCeEEEEecCCcc---------cEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 002823          234 TLVVFNL--DSSVS---NDELHHIFGVYGEIKEIRETPQKI---------HQKYIEFYDTRAAEAALRELNSRYIAGKQI  299 (876)
Q Consensus       234 tLfV~NL--P~svT---eedLreiFs~fG~I~sVritg~sk---------G~AFVeF~d~E~A~kAL~~LnG~~I~Gr~I  299 (876)
                      .|+++|+  |.+++   +.+|.+.+++||.|..|-+.....         -.-||+|....++.+|+.+|||+.|+|+++
T Consensus       448 VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~~rak~ALdGRfFgGr~V  527 (544)
T KOG0124|consen  448 VIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASETHRAKQALDGRFFGGRKV  527 (544)
T ss_pred             EEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhHHHHHHHhhccceecCcee
Confidence            6777887  44554   458999999999999977732221         257999999999999999999999999999


Q ss_pred             EEEeec
Q 002823          300 KLEPSH  305 (876)
Q Consensus       300 kVs~A~  305 (876)
                      ..+...
T Consensus       528 vAE~YD  533 (544)
T KOG0124|consen  528 VAEVYD  533 (544)
T ss_pred             ehhhhh
Confidence            876543

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.08  E-value=4e-10  Score=120.19  Aligned_cols=76  Identities=14%  Similarity=0.232  Sum_probs=68.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe--CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYR--ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~--tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      .++|||+|||+.+++++|+++|+.||+|.+|++  .+..+|||||+|.++++|+.|+. |+|..|.|+.|.|.++....
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~~   81 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDYQ   81 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCCC
Confidence            579999999999999999999999999999984  33368999999999999999994 99999999999999986443

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.07  E-value=3.2e-10  Score=96.90  Aligned_cols=66  Identities=18%  Similarity=0.391  Sum_probs=58.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          150 LLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       150 LFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      |||+|||+++++++|+++|+.||.|..++.    .+..+++|||+|.+.++|++|++.+++..++|++|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999998882    245789999999999999999999999999999875

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>smart00362 RRM_2 RNA recognition motif

Probab=99.07  E-value=7.4e-10  Score=91.82  Aligned_cols=69  Identities=28%  Similarity=0.523  Sum_probs=63.1

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCC---cccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQ---KIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLE  302 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVritg~---skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs  302 (876)
                      +|||+|||..+++++|+++|++||.|..+++...   .+++|||+|.+.++|++|++.+++..+.|++|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            5899999999999999999999999999887432   46999999999999999999999999999999873

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.05  E-value=4.7e-10  Score=116.98  Aligned_cols=78  Identities=18%  Similarity=0.369  Sum_probs=74.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ....+|-|.||+.+++|++|++||.+||.|..++     .++.+||||||.|.+.++|.+||+.|+|.-+..--|+|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            3568999999999999999999999999999988     68999999999999999999999999999999999999999


Q ss_pred             CCC
Q 002823          220 IPK  222 (876)
Q Consensus       220 ~pk  222 (876)
                      +|+
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            986

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.04  E-value=4e-10  Score=121.43  Aligned_cols=80  Identities=19%  Similarity=0.337  Sum_probs=72.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      .-.++|+|.|||+...|-||+..|++||+|.+|.   ..+-+|||+||+|++.++|++|.++|||..|.||+|.|..+.+
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            3357999999999999999999999999998887   4566899999999999999999999999999999999999877


Q ss_pred             CCC
Q 002823          222 KDN  224 (876)
Q Consensus       222 k~~  224 (876)
                      +-.
T Consensus       174 rV~  176 (376)
T KOG0125|consen  174 RVH  176 (376)
T ss_pred             hhc
Confidence            643

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.03  E-value=4e-10  Score=107.47  Aligned_cols=79  Identities=20%  Similarity=0.279  Sum_probs=71.5

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      .+.||||+||...++||+|.++|+++|+|+.|-+     +..+.|||||+|.+.++|+.|++.++|..+..++|+|.|..
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            4679999999999999999999999999999766     45567999999999999999999999999999999999976


Q ss_pred             Cchh
Q 002823          306 LRGL  309 (876)
Q Consensus       306 ~k~~  309 (876)
                      .=.+
T Consensus       115 GF~e  118 (153)
T KOG0121|consen  115 GFVE  118 (153)
T ss_pred             cchh
Confidence            5443

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.03  E-value=3.5e-09  Score=115.51  Aligned_cols=169  Identities=18%  Similarity=0.207  Sum_probs=132.9

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHc--cccccCCceeeE
Q 002823          139 EHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSL--QNKLTRSGKLDI  216 (876)
Q Consensus       139 e~p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~L--ng~~l~Gr~L~V  216 (876)
                      ..+....++-.|.|++|-..++|.+|.+.++.||+|..+.. ...+..|.|+|++++.|++++..-  +...+.|+.--+
T Consensus        23 ~dphk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~-~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~  101 (494)
T KOG1456|consen   23 ADPHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTC-MPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALF  101 (494)
T ss_pred             CCCCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEe-ccccceeeeeeccccchhhheehhccCcccccCchhhc
Confidence            34556677889999999999999999999999999988875 456678999999999999998532  223467777777


Q ss_pred             eecCCCCCCC---ccccccceeEe--ecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCC
Q 002823          217 HYSIPKDNPS---EKEINQGTLVV--FNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS  291 (876)
Q Consensus       217 ~~A~pk~~~~---ek~~~~~tLfV--~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG  291 (876)
                      .|+..+.-..   +.......|.+  -|--..+|-+-|..++...|+|..|.|-.+..-.|.|||++.+.|++|...|||
T Consensus       102 NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNG  181 (494)
T KOG1456|consen  102 NYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNG  181 (494)
T ss_pred             ccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhccc
Confidence            7774432211   11123334444  444467999999999999999999888666566899999999999999999999


Q ss_pred             ceeC--CeEEEEEeecCch
Q 002823          292 RYIA--GKQIKLEPSHLRG  308 (876)
Q Consensus       292 ~~I~--Gr~IkVs~A~~k~  308 (876)
                      ..|.  -++|+|+|+++..
T Consensus       182 ADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  182 ADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             ccccccceeEEEEecCcce
Confidence            9885  4999999999964

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=99.02  E-value=3.3e-10  Score=129.19  Aligned_cols=166  Identities=23%  Similarity=0.333  Sum_probs=134.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      .+.+.++|+|-|||..|++++|+.+|+.||+|+.|+.+...+|.+||+|+|..+|++|+++|++.++.|+.|+.......
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~~  150 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGARR  150 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCcccc
Confidence            36778999999999999999999999999999999999999999999999999999999999999999998884222111


Q ss_pred             CC------------------CCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHH
Q 002823          223 DN------------------PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEA  284 (876)
Q Consensus       223 ~~------------------~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~k  284 (876)
                      ..                  .....-+...+|.- |++..+..-++.++..+|.++. +.++..+..-|++|.+..++..
T Consensus       151 ~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~~~~~~hq~~~~~~~~~s~a~  228 (549)
T KOG4660|consen  151 AMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RETPLLNHQRFVEFADNRSYAF  228 (549)
T ss_pred             cchhcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-ccccchhhhhhhhhccccchhh
Confidence            10                  00001123344443 9999888888899999999998 8878777789999999999977


Q ss_pred             HHHHhCCceeCCeEEEEEeecCchhHH
Q 002823          285 ALRELNSRYIAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       285 AL~~LnG~~I~Gr~IkVs~A~~k~~Rr  311 (876)
                      +...+ |..+.++...+.++.+.+..+
T Consensus       229 ~~~~~-G~~~s~~~~v~t~S~~~g~~n  254 (549)
T KOG4660|consen  229 SEPRG-GFLISNSSGVITFSGPGGVWN  254 (549)
T ss_pred             cccCC-ceecCCCCceEEecCCCcccC
Confidence            77754 788888888899998866543

>PF13893 RRM_5: RNA recognition motif

Probab=99.01  E-value=1.5e-09  Score=89.53  Aligned_cols=56  Identities=29%  Similarity=0.525  Sum_probs=51.4

Q ss_pred             HHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          249 LHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       249 LreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      |+++|++||+|..|++....+++|||+|.+.++|.+|++.|||..+.|++|+|+|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999996555799999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.01  E-value=7.9e-10  Score=115.35  Aligned_cols=77  Identities=22%  Similarity=0.308  Sum_probs=72.9

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...+|-|.||+.++++++|+++|.+||.|..|.+     ++..||||||.|.++++|.+||+.|||.-+..-.|+|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            4568999999999999999999999999998766     88899999999999999999999999999999999999999


Q ss_pred             Cc
Q 002823          306 LR  307 (876)
Q Consensus       306 ~k  307 (876)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            85

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.00  E-value=5e-09  Score=116.11  Aligned_cols=72  Identities=18%  Similarity=0.226  Sum_probs=64.4

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ++|+|+|||.++|++.|++-|..||.|.+..|....+..+.|.|.++++|++|+..|+|..+.|+.|+|.|.
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            589999999999999999999999999998773333444599999999999999999999999999999873

>smart00362 RRM_2 RNA recognition motif

Probab=99.00  E-value=1.4e-09  Score=90.08  Aligned_cols=69  Identities=20%  Similarity=0.428  Sum_probs=62.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEeC---CCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          149 TLLLRKINSNIEDSELKALFEQYGDVRTFYRA---SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       149 TLFVgNLP~~vTEeeL~elFsqfG~I~sV~~t---gksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      +|||+|||..+++++|+++|++||+|..++..   +..+++|||+|.+.++|++|++.+++..+.|++|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999988732   4468999999999999999999999999999998873

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.99  E-value=4.6e-09  Score=119.12  Aligned_cols=158  Identities=18%  Similarity=0.281  Sum_probs=115.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-------CCCccc---eEeeecCCHHHHHHHHHHccccccCCce
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-------ASKHCG---FVTISYYDIRAARNAMKSLQNKLTRSGK  213 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-------tgksrG---fAFV~F~d~edA~kAl~~Lng~~l~Gr~  213 (876)
                      ..-+++|||++||++++|++|...|..||.+..-..       ....+|   |+|+.|+++...+.-+.+..-   ...+
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~~  332 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEGN  332 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---cccc
Confidence            345799999999999999999999999998865441       122566   999999999998887765432   2233


Q ss_pred             eeEeecCCCCC-------------------CCccccccceeEeecCCCCCcHHHHHHHhh-hcCCeEEEEecC-----Cc
Q 002823          214 LDIHYSIPKDN-------------------PSEKEINQGTLVVFNLDSSVSNDELHHIFG-VYGEIKEIRETP-----QK  268 (876)
Q Consensus       214 L~V~~A~pk~~-------------------~~ek~~~~~tLfV~NLP~svTeedLreiFs-~fG~I~sVritg-----~s  268 (876)
                      +.++.+.+...                   ....-.+.+||||++||.-++.++|..+|+ .||.|..+-|+.     -+
T Consensus       333 ~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYP  412 (520)
T KOG0129|consen  333 YYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYP  412 (520)
T ss_pred             eEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCC
Confidence            33322222211                   111223677999999999999999999999 999999977632     36


Q ss_pred             ccEEEEEecCHHHHHHHHHHh----CCceeCCeEEEEEeec
Q 002823          269 IHQKYIEFYDTRAAEAALREL----NSRYIAGKQIKLEPSH  305 (876)
Q Consensus       269 kG~AFVeF~d~E~A~kAL~~L----nG~~I~Gr~IkVs~A~  305 (876)
                      +|-|-|.|.+..+-.+||.+-    +..+| .|+|+|+...
T Consensus       413 kGaGRVtFsnqqsYi~AIsarFvql~h~d~-~KRVEIkPYv  452 (520)
T KOG0129|consen  413 KGAGRVTFSNQQAYIKAISARFVQLDHTDI-DKRVEIKPYV  452 (520)
T ss_pred             CCcceeeecccHHHHHHHhhheEEEecccc-ceeeeeccee
Confidence            799999999999999998741    22222 3566666654

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.98  E-value=6.1e-10  Score=115.77  Aligned_cols=77  Identities=16%  Similarity=0.297  Sum_probs=66.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .+..-++|||++|+|.+..++|+++|++||+|.+..     .++++|||+||+|+|.++|.+|++.-+ -.|+||+-.|.
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccc
Confidence            344557999999999999999999999999998876     579999999999999999999997543 56899988887


Q ss_pred             ecC
Q 002823          218 YSI  220 (876)
Q Consensus       218 ~A~  220 (876)
                      ++.
T Consensus        87 lA~   89 (247)
T KOG0149|consen   87 LAS   89 (247)
T ss_pred             hhh
Confidence            763

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.97  E-value=1.4e-09  Score=116.13  Aligned_cols=86  Identities=20%  Similarity=0.337  Sum_probs=77.5

Q ss_pred             cCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCC
Q 002823          137 AGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRS  211 (876)
Q Consensus       137 ~ge~p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G  211 (876)
                      ........+|-+||||.-|+.+++|.+|+..|++||+|+.|.     ++++++|||||+|+++.+...|.+..+|..|.|
T Consensus        91 ~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idg  170 (335)
T KOG0113|consen   91 NNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDG  170 (335)
T ss_pred             CCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecC
Confidence            334444568889999999999999999999999999999987     689999999999999999999999999999999


Q ss_pred             ceeeEeecCCC
Q 002823          212 GKLDIHYSIPK  222 (876)
Q Consensus       212 r~L~V~~A~pk  222 (876)
                      +.|.|.+....
T Consensus       171 rri~VDvERgR  181 (335)
T KOG0113|consen  171 RRILVDVERGR  181 (335)
T ss_pred             cEEEEEecccc
Confidence            99999886543

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.96  E-value=8e-10  Score=111.04  Aligned_cols=77  Identities=27%  Similarity=0.384  Sum_probs=70.6

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ..++|||+|||.++.+.||.++|.+||.|.+|.+  .+....||||+|++..+|+.||..-+|..+.|++|+|+|.+..
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            4678999999999999999999999999999887  3334679999999999999999999999999999999999865

>smart00360 RRM RNA recognition motif

Probab=98.95  E-value=2.9e-09  Score=87.76  Aligned_cols=66  Identities=30%  Similarity=0.538  Sum_probs=59.9

Q ss_pred             eecCCCCCcHHHHHHHhhhcCCeEEEEec-----CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 002823          237 VFNLDSSVSNDELHHIFGVYGEIKEIRET-----PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLE  302 (876)
Q Consensus       237 V~NLP~svTeedLreiFs~fG~I~sVrit-----g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs  302 (876)
                      |+|||..+++++|+++|++||.|..+++.     +..+++|||+|.+.++|.+|++.+++..+.|++|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            67999999999999999999999998872     3347899999999999999999999999999999874

>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

Probab=98.94  E-value=5.3e-09  Score=87.12  Aligned_cols=70  Identities=30%  Similarity=0.546  Sum_probs=64.2

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCC----cccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQ----KIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVritg~----skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      +|+|+|||..+++++|+++|+.||.|..+.+...    .+++|||+|.+.++|..|++.+++..+.|+++.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999887433    378999999999999999999999999999999875

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.94  E-value=2.8e-09  Score=113.87  Aligned_cols=92  Identities=27%  Similarity=0.377  Sum_probs=80.1

Q ss_pred             cCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCce
Q 002823          219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRY  293 (876)
Q Consensus       219 A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~  293 (876)
                      ..|..++.....+-.||||+-|+.++++.+|+..|+.||.|+.|++     +++++|||||+|++..+..+|.+..+|.+
T Consensus        88 wdP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~  167 (335)
T KOG0113|consen   88 WDPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIK  167 (335)
T ss_pred             cCCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCce
Confidence            3454444444456779999999999999999999999999999876     88999999999999999999999999999


Q ss_pred             eCCeEEEEEeecCchhH
Q 002823          294 IAGKQIKLEPSHLRGLR  310 (876)
Q Consensus       294 I~Gr~IkVs~A~~k~~R  310 (876)
                      |.|+.|.|.+-+....+
T Consensus       168 Idgrri~VDvERgRTvk  184 (335)
T KOG0113|consen  168 IDGRRILVDVERGRTVK  184 (335)
T ss_pred             ecCcEEEEEeccccccc
Confidence            99999999998765443

>PLN03213 repressor of silencing 3; Provisional

Probab=98.93  E-value=2.9e-09  Score=119.16  Aligned_cols=81  Identities=22%  Similarity=0.295  Sum_probs=71.9

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-cCCcccEEEEEecCH--HHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-TPQKIHQKYIEFYDT--RAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-tg~skG~AFVeF~d~--E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ...+|||+||++.+++++|+.+|..||.|..|.+ ....||||||+|.+.  .++.+||..|||..+.|+.|+|..+++.
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP~   88 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKEH   88 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccHH
Confidence            3458999999999999999999999999999877 222389999999987  7899999999999999999999999987


Q ss_pred             hhHH
Q 002823          308 GLRK  311 (876)
Q Consensus       308 ~~Rr  311 (876)
                      -.-|
T Consensus        89 YLeR   92 (759)
T PLN03213         89 YLAR   92 (759)
T ss_pred             HHHH
Confidence            6444

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.93  E-value=1.3e-09  Score=111.19  Aligned_cols=81  Identities=20%  Similarity=0.381  Sum_probs=74.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      +.+...-.+|.|-||...++.++|+.+|++||.|-+|+     .++.++|||||.|.+..+|+.|+++|+|.+|.|+.|+
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            44555568999999999999999999999999999998     5788999999999999999999999999999999999


Q ss_pred             EeecCC
Q 002823          216 IHYSIP  221 (876)
Q Consensus       216 V~~A~p  221 (876)
                      |+++.-
T Consensus        87 Vq~ary   92 (256)
T KOG4207|consen   87 VQMARY   92 (256)
T ss_pred             ehhhhc
Confidence            998854

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.92  E-value=6.1e-10  Score=114.34  Aligned_cols=80  Identities=19%  Similarity=0.379  Sum_probs=74.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ..|||||++|..+|+|..|...|-+||+|..|.     .+.++||||||+|...|+|..||..|++.+|.||.|+|.+++
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            358999999999999999999999999999998     578999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002823          221 PKDNP  225 (876)
Q Consensus       221 pk~~~  225 (876)
                      |..-.
T Consensus        89 P~kik   93 (298)
T KOG0111|consen   89 PEKIK   93 (298)
T ss_pred             Ccccc
Confidence            86543

>PLN03213 repressor of silencing 3; Provisional

Probab=98.90  E-value=3.1e-09  Score=118.96  Aligned_cols=79  Identities=13%  Similarity=0.211  Sum_probs=70.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-eCCCccceEeeecCCH--HHHHHHHHHccccccCCceeeEeecC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-RASKHCGFVTISYYDI--RAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-~tgksrGfAFV~F~d~--edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      +....+||||||++.+++++|+.+|..||.|.+|. ...+.||||||+|.+.  .++.+||..|+|..+.|+.|+|.-|+
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            34457999999999999999999999999999988 2223499999999987  78999999999999999999998887


Q ss_pred             CC
Q 002823          221 PK  222 (876)
Q Consensus       221 pk  222 (876)
                      |.
T Consensus        87 P~   88 (759)
T PLN03213         87 EH   88 (759)
T ss_pred             HH
Confidence            65

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=98.90  E-value=7.6e-09  Score=115.37  Aligned_cols=74  Identities=27%  Similarity=0.346  Sum_probs=68.7

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEeec
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIA-GKQIKLEPSH  305 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~-Gr~IkVs~A~  305 (876)
                      -..|||+.||.++.|++|.-+|++.|+|-++|+     .+.+||||||.|.+.++|++|++.||+.+|. ||.|.|..+.
T Consensus        83 G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sv  162 (506)
T KOG0117|consen   83 GCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSV  162 (506)
T ss_pred             CceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEee
Confidence            348999999999999999999999999999887     6789999999999999999999999999995 8999988765

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.89  E-value=5.8e-09  Score=109.98  Aligned_cols=73  Identities=21%  Similarity=0.270  Sum_probs=66.8

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .+|||+||++.+|+++|+++|+.||+|.+|++  .+..+++|||+|+++++|+.|+ .|+|..|.+++|.|.....
T Consensus         6 ~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          6 YTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             eEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCcc
Confidence            58999999999999999999999999999988  4455689999999999999999 5999999999999998654

>smart00360 RRM RNA recognition motif

Probab=98.89  E-value=4.9e-09  Score=86.42  Aligned_cols=66  Identities=20%  Similarity=0.438  Sum_probs=59.9

Q ss_pred             EcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          152 LRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       152 VgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      |+|||..+++++|+++|++||.|..+..     +++++++|||+|.+.++|.+|++.+++..+.|++|.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            6899999999999999999999988872     35568999999999999999999999999999998873

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.88  E-value=2.2e-09  Score=109.68  Aligned_cols=75  Identities=27%  Similarity=0.460  Sum_probs=70.5

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      -.+|.|-||-.-++.++|+.+|++||.|-+|.|     +..++|||||.|.+..+|+.|+++|+|..+.|+.|+|++++=
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            458999999999999999999999999999887     777899999999999999999999999999999999998864

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.87  E-value=3.7e-08  Score=107.73  Aligned_cols=162  Identities=21%  Similarity=0.311  Sum_probs=134.5

Q ss_pred             CCCcEEEEcCCCC--CCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccC--CceeeEeecC
Q 002823          145 HPSRTLLLRKINS--NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTR--SGKLDIHYSI  220 (876)
Q Consensus       145 ~pSrTLFVgNLP~--~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~--Gr~L~V~~A~  220 (876)
                      .+...|.+.=|.+  .+|.+.|..+....|+|..|.+-.|.--.|+|+|++.+.|++|..+|||..|.  -..|+|+|++
T Consensus       118 ~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAk  197 (494)
T KOG1456|consen  118 TPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAK  197 (494)
T ss_pred             CCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEEecC
Confidence            4456666666654  58999999999999999999976777778999999999999999999998864  4689999987


Q ss_pred             CCCCCCc---------------------cc--------------------------------------------------
Q 002823          221 PKDNPSE---------------------KE--------------------------------------------------  229 (876)
Q Consensus       221 pk~~~~e---------------------k~--------------------------------------------------  229 (876)
                      |.+-...                     +.                                                  
T Consensus       198 P~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g  277 (494)
T KOG1456|consen  198 PTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRG  277 (494)
T ss_pred             cceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCC
Confidence            6521000                     00                                                  


Q ss_pred             -------cccceeEeecCCCC-CcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 002823          230 -------INQGTLVVFNLDSS-VSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL  301 (876)
Q Consensus       230 -------~~~~tLfV~NLP~s-vTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkV  301 (876)
                             .....+.|.+|+.. ++-+.|..+|..||.|..|++.....+.|.||+.|..+.++|+..||+..+-|.+|.|
T Consensus       278 ~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v  357 (494)
T KOG1456|consen  278 YASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNV  357 (494)
T ss_pred             CCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEE
Confidence                   01226788999874 6778999999999999999997778899999999999999999999999999999999


Q ss_pred             EeecC
Q 002823          302 EPSHL  306 (876)
Q Consensus       302 s~A~~  306 (876)
                      .+++.
T Consensus       358 ~~SkQ  362 (494)
T KOG1456|consen  358 CVSKQ  362 (494)
T ss_pred             eeccc
Confidence            98875

>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

Probab=98.86  E-value=9.5e-09  Score=85.58  Aligned_cols=70  Identities=23%  Similarity=0.481  Sum_probs=63.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCC----CccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          149 TLLLRKINSNIEDSELKALFEQYGDVRTFYRAS----KHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       149 TLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tg----ksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      +|+|+|||..+++++|+++|+.||.|..+....    +.+++|||+|.+.++|..|++.+++..+.|+++.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            589999999999999999999999999988322    3589999999999999999999999999999998864

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.86  E-value=8.8e-09  Score=105.71  Aligned_cols=75  Identities=28%  Similarity=0.511  Sum_probs=70.3

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ..+|||+|||.++++++|+++|..||.|..|++     ++..+|+|||+|.+.++|..|+..+++..+.|++|+|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            579999999999999999999999999988766     467889999999999999999999999999999999999775

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.84  E-value=1.2e-08  Score=107.58  Aligned_cols=73  Identities=12%  Similarity=0.156  Sum_probs=66.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ..||||+||++.+|+++|+++|+.||+|..|+  ..++.++||||+|.++++|+.|+ .|+|..|.+++|.|....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            57999999999999999999999999999998  34567789999999999999999 699999999999996653

>PF13893 RRM_5: RNA recognition motif

Probab=98.83  E-value=8e-09  Score=85.18  Aligned_cols=56  Identities=23%  Similarity=0.492  Sum_probs=50.6

Q ss_pred             HHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          164 LKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       164 L~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      |+++|++||+|..+....+.+++|||+|.+.++|++|++.|+|..+.|++|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999964444799999999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.82  E-value=5.3e-09  Score=100.66  Aligned_cols=76  Identities=24%  Similarity=0.409  Sum_probs=71.1

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      -.|||.++-...++++|.+.|..||+|+.|++     ++--||||+|+|++.++|++|+.++||..+.|..|.|.|+-.+
T Consensus        73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen   73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             EEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            38999999999999999999999999999887     5667899999999999999999999999999999999998765


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      +
T Consensus       153 g  153 (170)
T KOG0130|consen  153 G  153 (170)
T ss_pred             C
Confidence            5

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.82  E-value=2.1e-09  Score=110.40  Aligned_cols=81  Identities=25%  Similarity=0.423  Sum_probs=75.2

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||++|...+++.-|...|-+||.|+.|.+     +.+.|+||||+|...|+|.+||..||+.++.||.|+|.+++
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            3569999999999999999999999999999887     56779999999999999999999999999999999999999


Q ss_pred             CchhHH
Q 002823          306 LRGLRK  311 (876)
Q Consensus       306 ~k~~Rr  311 (876)
                      |...+.
T Consensus        89 P~kike   94 (298)
T KOG0111|consen   89 PEKIKE   94 (298)
T ss_pred             CccccC
Confidence            977554

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.80  E-value=7.2e-09  Score=107.94  Aligned_cols=77  Identities=23%  Similarity=0.316  Sum_probs=67.4

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      .-++|||++|++.+..|+|++.|++||+|++..+     ++++||||||+|.|.++|.+|++.- .-.|+||+..|.++.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccchhh
Confidence            4569999999999999999999999999999544     7889999999999999999998743 456899999999887


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      -..
T Consensus        90 lg~   92 (247)
T KOG0149|consen   90 LGG   92 (247)
T ss_pred             hcC
Confidence            644

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.80  E-value=1e-08  Score=117.09  Aligned_cols=81  Identities=25%  Similarity=0.310  Sum_probs=76.2

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ..+||+|+|+++++++|.++|+..|.|.++++     +++.+||||++|.+.++|.+|++.|||.++.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            78999999999999999999999999999887     7888999999999999999999999999999999999999988


Q ss_pred             hhHHHH
Q 002823          308 GLRKCL  313 (876)
Q Consensus       308 ~~Rr~l  313 (876)
                      ..+.+.
T Consensus        99 ~~~~~~  104 (435)
T KOG0108|consen   99 KNAERS  104 (435)
T ss_pred             chhHHH
Confidence            766644

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.77  E-value=4.4e-09  Score=124.96  Aligned_cols=159  Identities=21%  Similarity=0.318  Sum_probs=140.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeC----CCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA----SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~t----gksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      +...++|||++||+..+++.+|+..|..+|.|.+|.+.    +....||||.|.+...+-+|..++.+..|..-.+++.+
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            34558999999999999999999999999999998732    33556999999999999999999999998877888887


Q ss_pred             cCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCC--
Q 002823          219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAG--  296 (876)
Q Consensus       219 A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G--  296 (876)
                      ..++      ....+.++|++|...+....|.+.|..||.|..|.+ .+..-|++|.|++...|+.|+..|-|..|++  
T Consensus       448 G~~k------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy-~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~  520 (975)
T KOG0112|consen  448 GQPK------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY-RHGQPYAYIQYESPPAAQAATHDMRGAPLGGPP  520 (975)
T ss_pred             cccc------cccceeeccCCCCCCChHHHHHHHhhccCcceeeec-ccCCcceeeecccCccchhhHHHHhcCcCCCCC
Confidence            7653      234678999999999999999999999999999998 5667799999999999999999999999987  


Q ss_pred             eEEEEEeecCch
Q 002823          297 KQIKLEPSHLRG  308 (876)
Q Consensus       297 r~IkVs~A~~k~  308 (876)
                      ++++|.|+.+..
T Consensus       521 ~r~rvdla~~~~  532 (975)
T KOG0112|consen  521 RRLRVDLASPPG  532 (975)
T ss_pred             cccccccccCCC
Confidence            889999998765

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.76  E-value=1.2e-08  Score=116.57  Aligned_cols=77  Identities=22%  Similarity=0.362  Sum_probs=72.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ++|||||||+++++++|.++|+..|.|.+++     .+++.+||||++|.+.++|.+|++.|+|.++.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            8999999999999999999999999999988     68999999999999999999999999999999999999998654


Q ss_pred             CC
Q 002823          223 DN  224 (876)
Q Consensus       223 ~~  224 (876)
                      +.
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            43

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.73  E-value=1.5e-08  Score=106.72  Aligned_cols=107  Identities=17%  Similarity=0.273  Sum_probs=85.8

Q ss_pred             CceeeEeecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHH
Q 002823          211 SGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAAL  286 (876)
Q Consensus       211 Gr~L~V~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL  286 (876)
                      .|.|.|+.+......    ...++|||+-|.+.-.|||++.+|..||.|.+|.+    ++.+|||+||+|.+.-+|..||
T Consensus         2 nrpiqvkpadsesrg----~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI   77 (371)
T KOG0146|consen    2 NRPIQVKPADSESRG----GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAI   77 (371)
T ss_pred             CCCccccccccccCC----ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHH
Confidence            366777665443222    24678999999999999999999999999999877    6778999999999999999999


Q ss_pred             HHhCCce-eCC--eEEEEEeecCchhHH--HHhhcCCchhh
Q 002823          287 RELNSRY-IAG--KQIKLEPSHLRGLRK--CLANQLPPELE  322 (876)
Q Consensus       287 ~~LnG~~-I~G--r~IkVs~A~~k~~Rr--~l~qQ~~~q~~  322 (876)
                      ..|+|.. +-|  ..|.|+|+...++|.  +| ||+.-++.
T Consensus        78 ~aLHgSqTmpGASSSLVVK~ADTdkER~lRRM-QQma~qlG  117 (371)
T KOG0146|consen   78 NALHGSQTMPGASSSLVVKFADTDKERTLRRM-QQMAGQLG  117 (371)
T ss_pred             HHhcccccCCCCccceEEEeccchHHHHHHHH-HHHHHHhc
Confidence            9999955 444  789999999888776  55 55544443

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.71  E-value=1.6e-08  Score=101.84  Aligned_cols=74  Identities=27%  Similarity=0.354  Sum_probs=69.3

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..||||+||+..++++.|+++|-+.|.|+.+++     +...+|||||+|.++|+|+-|++.||..++.||+|+|..+.
T Consensus         9 d~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    9 DATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            459999999999999999999999999999987     44578999999999999999999999999999999999887

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.70  E-value=2.6e-08  Score=117.00  Aligned_cols=77  Identities=25%  Similarity=0.411  Sum_probs=72.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDN  224 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~  224 (876)
                      ++||||+.|+..+++.||..+|+.||+|.+|.. ...++||||++....+|.+|+.+|.+..+.++.|+|.|+..+.-
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~l-i~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~  497 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIIL-IPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGP  497 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEee-ccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCc
Confidence            799999999999999999999999999999996 56899999999999999999999999999999999999976643

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.69  E-value=2.4e-09  Score=107.51  Aligned_cols=75  Identities=17%  Similarity=0.340  Sum_probs=70.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ..+.-|||+|||.+.||.+|...|++||+|..|.     .||+++||||+.|++.++..-|+..|||..|.||.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            4577999999999999999999999999999886     68999999999999999999999999999999999999654

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.67  E-value=3.8e-08  Score=102.23  Aligned_cols=76  Identities=34%  Similarity=0.559  Sum_probs=71.5

Q ss_pred             ceeEeecCCCCCcHHHHHH----HhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          233 GTLVVFNLDSSVSNDELHH----IFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLre----iFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .||||.||...+..++|++    +|++||+|.+|..  +++-+|.|||.|.+.+.|..|++.|+|..+.|++++|.||+.
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s   89 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKS   89 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccC
Confidence            3999999999999999998    9999999999876  777899999999999999999999999999999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      +.
T Consensus        90 ~s   91 (221)
T KOG4206|consen   90 DS   91 (221)
T ss_pred             cc
Confidence            65

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.66  E-value=2.8e-08  Score=106.02  Aligned_cols=72  Identities=28%  Similarity=0.432  Sum_probs=68.9

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      +|||+|||..+++.+|+.+|++||+|.+|.|   -|.||||..++...|+.||+.|+|.+|.|..|.|+-++.|.
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDI---vKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDI---VKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeee---ecccceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            6999999999999999999999999999998   47899999999999999999999999999999999998873

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.64  E-value=4.5e-08  Score=94.38  Aligned_cols=79  Identities=13%  Similarity=0.367  Sum_probs=72.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ...-.|||.++-..+++++|.+.|..||+|+.+.     .++..||||+|+|.+.++|++|+.++||..|-|.+|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            3456899999999999999999999999999987     57889999999999999999999999999999999999998


Q ss_pred             CCCC
Q 002823          220 IPKD  223 (876)
Q Consensus       220 ~pk~  223 (876)
                      --+.
T Consensus       150 Fv~g  153 (170)
T KOG0130|consen  150 FVKG  153 (170)
T ss_pred             EecC
Confidence            5443

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.63  E-value=4.2e-09  Score=105.83  Aligned_cols=74  Identities=22%  Similarity=0.375  Sum_probs=69.4

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      .+.-|||+|||..+|+.||.-+|++||+|+.|.+     |++++||||+.|++..+..-|+..|||..|.||.|+|...
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            4568999999999999999999999999999766     8899999999999999999999999999999999999864

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.61  E-value=6.3e-08  Score=111.60  Aligned_cols=162  Identities=17%  Similarity=0.274  Sum_probs=131.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcc-----------C-CeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCc
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQY-----------G-DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSG  212 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqf-----------G-~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr  212 (876)
                      ...+.++|+++|+.+++++.-.+|..-           | .|..+.. ...+.||||+|.+.++|..|+ .+++..+.|+
T Consensus       173 ~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~-n~~~nfa~ie~~s~~~at~~~-~~~~~~f~g~  250 (500)
T KOG0120|consen  173 RQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQL-NLEKNFAFIEFRSISEATEAM-ALDGIIFEGR  250 (500)
T ss_pred             hhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee-cccccceeEEecCCCchhhhh-cccchhhCCC
Confidence            336899999999999999999888743           2 3666665 678899999999999999998 5788888888


Q ss_pred             eeeEeecCCCCC-------------------CCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCc
Q 002823          213 KLDIHYSIPKDN-------------------PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQK  268 (876)
Q Consensus       213 ~L~V~~A~pk~~-------------------~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~s  268 (876)
                      .+.+.--.....                   ..........+||++||..+++++++++...||.++..++     ++.+
T Consensus       251 ~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~s  330 (500)
T KOG0120|consen  251 PLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNS  330 (500)
T ss_pred             CceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccc
Confidence            777632211100                   0001113458999999999999999999999999988554     5678


Q ss_pred             ccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          269 IHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       269 kG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ++|||.+|.+......|+..|||..+++++|.|..+....
T Consensus       331 kg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  331 KGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             cceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence            9999999999999999999999999999999999998765

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.61  E-value=2.1e-07  Score=102.23  Aligned_cols=165  Identities=11%  Similarity=0.160  Sum_probs=120.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccC-------CeEEEE-eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYG-------DVRTFY-RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG-------~I~sV~-~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      -.|-+++||.++++.++.++|.+--       .|.-|+ ..++..|-|||.|..+++|+.|+.. +...++.|-|.+-.+
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRS  240 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHH
Confidence            4567799999999999999997322       233333 4788999999999999999999964 333344333322100


Q ss_pred             ----------------------C---C--CCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEE---EEe----c
Q 002823          220 ----------------------I---P--KDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKE---IRE----T  265 (876)
Q Consensus       220 ----------------------~---p--k~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~s---Vri----t  265 (876)
                                            .   +  .............|-+++||+..+.++|.++|..|-.-+.   |++    .
T Consensus       241 TaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~q  320 (508)
T KOG1365|consen  241 TAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQ  320 (508)
T ss_pred             hHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCC
Confidence                                  0   0  0000111223568999999999999999999998875333   443    5


Q ss_pred             CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchhHHHH
Q 002823          266 PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCL  313 (876)
Q Consensus       266 g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~Rr~l  313 (876)
                      +++.|-|||+|.+.|+|.+|..+.+.+..+.|-|.|-.+...+..+.+
T Consensus       321 GrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~eeln~vL  368 (508)
T KOG1365|consen  321 GRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEELNEVL  368 (508)
T ss_pred             CCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHHHHHHH
Confidence            667899999999999999999999998889999999988877755533

>smart00361 RRM_1 RNA recognition motif

Probab=98.61  E-value=1.2e-07  Score=82.16  Aligned_cols=57  Identities=30%  Similarity=0.564  Sum_probs=50.5

Q ss_pred             HHHHHHHhh----hcCCeEEEE-e-----c--CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 002823          246 NDELHHIFG----VYGEIKEIR-E-----T--PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLE  302 (876)
Q Consensus       246 eedLreiFs----~fG~I~sVr-i-----t--g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs  302 (876)
                      +++|+++|+    .||.|..|. +     +  +.++|+|||+|.+.++|.+|++.|||..+.|++|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578888888    999999874 2     2  6679999999999999999999999999999999863

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.59  E-value=1e-07  Score=112.05  Aligned_cols=80  Identities=26%  Similarity=0.334  Sum_probs=76.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchhH
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLR  310 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~R  310 (876)
                      .++||||+.|+..+++.||..+|+.||+|.+|.+ -.+++||||.+..+.+|.+|+.+|+...+.++.|+|.|+..++.|
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~l-i~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~k  498 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIIL-IPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPK  498 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEee-ccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcc
Confidence            6789999999999999999999999999999998 457899999999999999999999999999999999999999877


Q ss_pred             H
Q 002823          311 K  311 (876)
Q Consensus       311 r  311 (876)
                      .
T Consensus       499 s  499 (894)
T KOG0132|consen  499 S  499 (894)
T ss_pred             h
Confidence            6

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.53  E-value=2.1e-08  Score=103.42  Aligned_cols=141  Identities=18%  Similarity=0.207  Sum_probs=113.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ...+||||.|+-..|+|+-|.++|-+.|+|..|.    ..++.| ||||.|.++-...-|++.++|..+.++.++|++-.
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            3468999999999999999999999999999988    234455 99999999999999999999999999988886632


Q ss_pred             CCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC
Q 002823          221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG  296 (876)
Q Consensus       221 pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G  296 (876)
                      .....             -|+..++++.+.+.|+.-|.+..+++    ++.++.++|+.+....+.-.|+...++....-
T Consensus        86 G~sha-------------pld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~  152 (267)
T KOG4454|consen   86 GNSHA-------------PLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELFQ  152 (267)
T ss_pred             CCCcc-------------hhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcCC
Confidence            21111             15567889999999999999998887    45577899999988888888887766655544


Q ss_pred             eEE
Q 002823          297 KQI  299 (876)
Q Consensus       297 r~I  299 (876)
                      +++
T Consensus       153 ~~~  155 (267)
T KOG4454|consen  153 KKV  155 (267)
T ss_pred             CCc
Confidence            443

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.53  E-value=2.5e-07  Score=100.98  Aligned_cols=83  Identities=20%  Similarity=0.352  Sum_probs=72.5

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccc-cccCCceeeEe
Q 002823          139 EHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN-KLTRSGKLDIH  217 (876)
Q Consensus       139 e~p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng-~~l~Gr~L~V~  217 (876)
                      ..+..+...+||||++|...++|.+|++.|.+||+|+++.. -..++||||+|.+.++|+.|.++.-+ ..|.|++|.|.
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~-~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRI-LPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEe-ecccccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            55667778899999999999999999999999999999995 34567999999999999999876555 45899999999


Q ss_pred             ecCCC
Q 002823          218 YSIPK  222 (876)
Q Consensus       218 ~A~pk  222 (876)
                      |..++
T Consensus       299 Wg~~~  303 (377)
T KOG0153|consen  299 WGRPK  303 (377)
T ss_pred             eCCCc
Confidence            99884

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.51  E-value=2.3e-07  Score=101.28  Aligned_cols=77  Identities=26%  Similarity=0.349  Sum_probs=68.8

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEEeecC
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALREL-NSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~L-nG~~I~Gr~IkVs~A~~  306 (876)
                      +....+|||++|-..+++.+|+++|.+||+|+.|++. ..+++|||+|.+.++|+.|..++ +...|.|++|+|.|+++
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~-~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRIL-PRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEee-cccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            4456799999999999999999999999999999984 35669999999999999998765 55778999999999998

>smart00361 RRM_1 RNA recognition motif

Probab=98.48  E-value=2.7e-07  Score=79.93  Aligned_cols=56  Identities=18%  Similarity=0.302  Sum_probs=50.1

Q ss_pred             HHHHHHHhh----ccCCeEEEE---e---C--CCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          161 DSELKALFE----QYGDVRTFY---R---A--SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       161 EeeL~elFs----qfG~I~sV~---~---t--gksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      +++|+++|+    +||.|.++.   .   +  ++++|||||+|.+.++|.+|++.|+|..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888888    999998873   1   2  778999999999999999999999999999999876

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.38  E-value=8.2e-08  Score=106.32  Aligned_cols=170  Identities=16%  Similarity=0.293  Sum_probs=131.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcc--CCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccc-cCCceeeEeecCCCCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQY--GDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKL-TRSGKLDIHYSIPKDN  224 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqf--G~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~-l~Gr~L~V~~A~pk~~  224 (876)
                      .++|++||.+.++..+|+.+|...  +--..+   -...||+||.+.+...|.+|++.++|+. +.|+++.|.++.++..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~f---l~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkq   78 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQF---LVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ   78 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcce---eeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH
Confidence            368999999999999999999743  111111   1145899999999999999999999975 9999999999988765


Q ss_pred             CCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCC--cccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 002823          225 PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQ--KIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLE  302 (876)
Q Consensus       225 ~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~--skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs  302 (876)
                      .      .+++-|+|+|+...++.|..+...||.|..|..+..  ..-..-|+|...+.+..||..|+|..+....++|.
T Consensus        79 r------srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~  152 (584)
T KOG2193|consen   79 R------SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVG  152 (584)
T ss_pred             H------hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcc
Confidence            4      345899999999999999999999999998765222  22234578899999999999999999999999999


Q ss_pred             eecCchhHHHHhhcCCchhhhhhcCCCC
Q 002823          303 PSHLRGLRKCLANQLPPELEQEECGSYQ  330 (876)
Q Consensus       303 ~A~~k~~Rr~l~qQ~~~q~~q~~~g~~~  330 (876)
                      |--...    .+|+.+.+..|...++..
T Consensus       153 YiPdeq----~~q~~p~q~~q~hh~~g~  176 (584)
T KOG2193|consen  153 YIPDEQ----NAQHQPGQHQQGHHGSGN  176 (584)
T ss_pred             cCchhh----hhccCccccccccccccc
Confidence            875432    223344444444444444

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.30  E-value=6.4e-07  Score=98.02  Aligned_cols=163  Identities=21%  Similarity=0.260  Sum_probs=130.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ....++|++++...+.+.+...++..+|.+....     ....++++++|.|...+.+..|+.....+.+.++.+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            4568999999999999999999999999665554     45678999999999999999999765555666665554443


Q ss_pred             CCCCCCCc------cccccceeE-eecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHH
Q 002823          220 IPKDNPSE------KEINQGTLV-VFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALR  287 (876)
Q Consensus       220 ~pk~~~~e------k~~~~~tLf-V~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~  287 (876)
                      ........      ......++| |++++.++++++|+..|..+|.|..+++     ++..+++|+|+|.....+..|+.
T Consensus       166 ~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~  245 (285)
T KOG4210|consen  166 TRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALN  245 (285)
T ss_pred             ccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhh
Confidence            33221110      011233555 9999999999999999999999999987     55678999999999999999998


Q ss_pred             HhCCceeCCeEEEEEeecCch
Q 002823          288 ELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       288 ~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      . ....+.++++.+.+..+..
T Consensus       246 ~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  246 D-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             c-ccCcccCcccccccCCCCc
Confidence            8 8899999999999988764

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.23  E-value=2.7e-06  Score=87.56  Aligned_cols=80  Identities=20%  Similarity=0.359  Sum_probs=71.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcc-CCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQY-GDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqf-G~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ......-+||..+|.-+.+.++..+|.+| |.|+.++     .||.++|||||+|++++.|+-|.+.||+..+.++.|.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            44455688999999999999999999998 6777776     58999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 002823          217 HYSIPK  222 (876)
Q Consensus       217 ~~A~pk  222 (876)
                      ++-.|.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            997654

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.23  E-value=1.5e-06  Score=94.83  Aligned_cols=79  Identities=22%  Similarity=0.385  Sum_probs=72.4

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ++.+.|||..|.+-+++++|.-+|+.||+|++|.+     ++.+-.||||+|++.+++++|.-+|++..|.+++|.|.|+
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            46789999999999999999999999999999776     5666789999999999999999999999999999999998


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      ..-.
T Consensus       317 QSVs  320 (479)
T KOG0415|consen  317 QSVS  320 (479)
T ss_pred             hhhh
Confidence            7644

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.19  E-value=1.7e-07  Score=111.38  Aligned_cols=139  Identities=9%  Similarity=0.134  Sum_probs=119.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ..++||+||+..+.+.+|...|..+|.+..+.     ..++.||+|||.|..+++|.+|+.-.. ..+.|          
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d-~~~~g----------  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRD-SCFFG----------  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhh-hhhhh----------
Confidence            35889999999999999999999999887765     467889999999999999999996433 33333          


Q ss_pred             CCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCe
Q 002823          222 KDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK  297 (876)
Q Consensus       222 k~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr  297 (876)
                                ...|+|.|.|...|.++|+.++..+|.++++++    .++++|.++|.|.+..+|.+++...+...+.-+
T Consensus       736 ----------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~  805 (881)
T KOG0128|consen  736 ----------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKREN  805 (881)
T ss_pred             ----------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhc
Confidence                      236899999999999999999999999999765    677899999999999999999999988888877


Q ss_pred             EEEEEeecC
Q 002823          298 QIKLEPSHL  306 (876)
Q Consensus       298 ~IkVs~A~~  306 (876)
                      .+.|..+.+
T Consensus       806 ~~~v~vsnp  814 (881)
T KOG0128|consen  806 NGEVQVSNP  814 (881)
T ss_pred             CccccccCC
Confidence            777777655

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.13  E-value=2.5e-06  Score=93.18  Aligned_cols=79  Identities=16%  Similarity=0.386  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..|...|||-.|.+-+++++|.-+|+.||+|.+|.     .++.+..||||+|.+.+++++|.-.|++..|..+.|.|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            35668999999999999999999999999999886     5788999999999999999999999999999999999999


Q ss_pred             cCCC
Q 002823          219 SIPK  222 (876)
Q Consensus       219 A~pk  222 (876)
                      +..-
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            8543

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.11  E-value=2.5e-06  Score=90.09  Aligned_cols=161  Identities=19%  Similarity=0.242  Sum_probs=118.7

Q ss_pred             cEEEEcCCCCCCCHHH-H--HHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          148 RTLLLRKINSNIEDSE-L--KALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       148 rTLFVgNLP~~vTEee-L--~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ...++.++-..+..+- |  ...|+.|-.+...+    ..++-++++|+.|.....-.++-..-+++++..+.+++.-..
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gt  176 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGT  176 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeecccc
Confidence            4556777766666554 3  56666666544433    456778999999998888888877777777777766664333


Q ss_pred             CCCCCC--ccccccceeEeecCCCCCcHHHHHHHhhhcCCeE---EEEe--cCCcccEEEEEecCHHHHHHHHHHhCCce
Q 002823          221 PKDNPS--EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIK---EIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRY  293 (876)
Q Consensus       221 pk~~~~--ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~---sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~  293 (876)
                      .-.++.  +-+...-+||.+.|.-+++++-|...|.+|-...   .||.  +++++||+||.|.+..++.+|+++|+|+.
T Consensus       177 swedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gky  256 (290)
T KOG0226|consen  177 SWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKY  256 (290)
T ss_pred             ccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccc
Confidence            222221  2223455899999999999999999999886432   2333  78999999999999999999999999999


Q ss_pred             eCCeEEEEEeecCch
Q 002823          294 IAGKQIKLEPSHLRG  308 (876)
Q Consensus       294 I~Gr~IkVs~A~~k~  308 (876)
                      ++.++|++.-+.-++
T Consensus       257 VgsrpiklRkS~wke  271 (290)
T KOG0226|consen  257 VGSRPIKLRKSEWKE  271 (290)
T ss_pred             cccchhHhhhhhHHh
Confidence            999999987665544

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.10  E-value=7.5e-06  Score=95.97  Aligned_cols=85  Identities=13%  Similarity=0.285  Sum_probs=75.6

Q ss_pred             cCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE--------eCCCccceEeeecCCHHHHHHHHHHccccc
Q 002823          137 AGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY--------RASKHCGFVTISYYDIRAARNAMKSLQNKL  208 (876)
Q Consensus       137 ~ge~p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~--------~tgksrGfAFV~F~d~edA~kAl~~Lng~~  208 (876)
                      .|....++.-+++|||+||++.++++.|...|..||+|.+++        ...+.+.|+||.|.+..+|++|++.|+|..
T Consensus       164 ~gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~i  243 (877)
T KOG0151|consen  164 PGSFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGII  243 (877)
T ss_pred             CCcCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhccee
Confidence            345555667789999999999999999999999999999998        245578899999999999999999999999


Q ss_pred             cCCceeeEeecCC
Q 002823          209 TRSGKLDIHYSIP  221 (876)
Q Consensus       209 l~Gr~L~V~~A~p  221 (876)
                      +.+..+++.|+++
T Consensus       244 v~~~e~K~gWgk~  256 (877)
T KOG0151|consen  244 VMEYEMKLGWGKA  256 (877)
T ss_pred             eeeeeeeeccccc
Confidence            9999999999844

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.09  E-value=3.1e-06  Score=87.65  Aligned_cols=151  Identities=13%  Similarity=0.075  Sum_probs=101.4

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ..+||||+|+...++++-|.++|-+-|.|..|.|    +.+.| ||||+|.++....-|++.+||..+.++.++|.+-..
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            3569999999999999999999999999999988    23344 999999999999999999999999999999998765


Q ss_pred             chhH----HHHhhcCCchhhhhhcCC-CCCCCCCCCCCCCCcccceeeeccCchhhhHHH-HHHhhccccccCCcCcccc
Q 002823          307 RGLR----KCLANQLPPELEQEECGS-YQQQNSPPNKPTNESAGMITIVISLPLNVKSLA-IIYLFTGAFAHGSKSSRIT  380 (876)
Q Consensus       307 k~~R----r~l~qQ~~~q~~q~~~g~-~~~gsp~~~sp~~~~~~~~~~~fssP~n~~~~~-l~~l~~~~~~~g~~~s~~~  380 (876)
                      ....    +.-..+...-..+..... ....+..-+-+........++.+.+|.+.+... |+....+...+|++++..+
T Consensus        87 ~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~~~~ggk~Gg~~l  166 (267)
T KOG4454|consen   87 NSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELFQKKVTIGGKQGGKQL  166 (267)
T ss_pred             CCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcCCCCcccccccCCCcC
Confidence            4211    111011000000000000 000000001122233345567789999998877 7777777777777777666


Q ss_pred             cC
Q 002823          381 DT  382 (876)
Q Consensus       381 ~~  382 (876)
                      ++
T Consensus       167 pq  168 (267)
T KOG4454|consen  167 PQ  168 (267)
T ss_pred             Cc
Confidence            54

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.07  E-value=9.6e-06  Score=83.60  Aligned_cols=78  Identities=15%  Similarity=0.223  Sum_probs=71.9

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhc-CCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVY-GEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~f-G~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ...+.+||..+|.-+.+.++...|.+| |.|..+++     ||.++|||||+|++.+.|.-|.+.||+..+.++.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            346789999999999999999999998 77777777     888999999999999999999999999999999999999


Q ss_pred             ecCc
Q 002823          304 SHLR  307 (876)
Q Consensus       304 A~~k  307 (876)
                      -.+.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            9887

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.06  E-value=5e-06  Score=91.80  Aligned_cols=114  Identities=17%  Similarity=0.260  Sum_probs=86.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      .+++|||++||.+++++++++.|++||.|..+.     .+.+.+||+||.|.+++.+++++. ..-..|.++++.|..|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            578999999999999999999999999887765     567899999999999999999984 56677999999999999


Q ss_pred             CCCCCCccccc-cceeEeecCCCCCcHHHHHHHhhhcCCeE
Q 002823          221 PKDNPSEKEIN-QGTLVVFNLDSSVSNDELHHIFGVYGEIK  260 (876)
Q Consensus       221 pk~~~~ek~~~-~~tLfV~NLP~svTeedLreiFs~fG~I~  260 (876)
                      |++........ .......|+....+.-.|...|.-|+.+.
T Consensus       175 pk~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~~~g~~~~~  215 (311)
T KOG4205|consen  175 PKEVMQSTKSSVSTRGKGNNLGNGRTGFFLKKYFKGYGPVG  215 (311)
T ss_pred             chhhccccccccccccccccccccccccccchhccccCccc
Confidence            98765432211 11222334544444555666666666553

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.02  E-value=1.1e-05  Score=92.21  Aligned_cols=77  Identities=17%  Similarity=0.253  Sum_probs=68.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..-+|+|||.+|...+...+|+.+|++||+|...+     .+.-.++|+||++.+.++|.+||..|+.+.|.|+.|.|.-
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            34579999999999999999999999999998776     1233588999999999999999999999999999999976


Q ss_pred             cC
Q 002823          219 SI  220 (876)
Q Consensus       219 A~  220 (876)
                      ++
T Consensus       482 aK  483 (940)
T KOG4661|consen  482 AK  483 (940)
T ss_pred             cc
Confidence            63

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=98.00  E-value=5.6e-06  Score=84.75  Aligned_cols=92  Identities=21%  Similarity=0.370  Sum_probs=60.9

Q ss_pred             CCCceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEec--cc--ccccceeEEEEEecCCccchHHHHHHhcCccccCC
Q 002823          702 EDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLP--ID--FKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKF  777 (876)
Q Consensus       702 ~d~rTTvMirNIPnk~t~~~L~~~ide~~~g~yDF~Ylp--~D--f~~~~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~  777 (876)
                      +..++.|.||++|..+|.+.+++.|+......++|-|.+  .+  --..+-...|||||.+.+++..|.+.|+|+.|..-
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            356889999999999999999998887666675555554  22  22345678899999999999999999999999865


Q ss_pred             CC-ccEEEEEeeccccH
Q 002823          778 NS-EKVASLAYARIQGK  793 (876)
Q Consensus       778 ~s-~Kv~~v~yA~iQG~  793 (876)
                      .. .-.+.|.||-.|-.
T Consensus        84 kg~~~~~~VE~Apyqk~  100 (176)
T PF03467_consen   84 KGNEYPAVVEFAPYQKV  100 (176)
T ss_dssp             TS-EEEEEEEE-SS---
T ss_pred             CCCCcceeEEEcchhcc
Confidence            54 46799999998753

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.94  E-value=1.2e-05  Score=94.29  Aligned_cols=78  Identities=24%  Similarity=0.368  Sum_probs=70.9

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe--------cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE--------TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri--------tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      ++..+.|||+||++.++++.|...|+.||.|..|++        ....+.|+||-|-+..+|++|++.|+|..+.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            456779999999999999999999999999999987        223467999999999999999999999999999999


Q ss_pred             EEeecC
Q 002823          301 LEPSHL  306 (876)
Q Consensus       301 Vs~A~~  306 (876)
                      +.|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999954

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.91  E-value=8.2e-06  Score=85.58  Aligned_cols=71  Identities=21%  Similarity=0.403  Sum_probs=66.8

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      .+||++||..+.+.+|.++|..||.|.++.+   ..+|+||+|.+..+|..|+..||++.|.|.++.|+|++..
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m---k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADM---KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhcccccccee---ecccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            5899999999999999999999999999988   5689999999999999999999999999988999999863

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.89  E-value=3.5e-05  Score=80.24  Aligned_cols=80  Identities=21%  Similarity=0.263  Sum_probs=68.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEE--EEecCCcc----cEEEEEecCHHHHHHHHHHhCCceeC---CeEEEE
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKE--IRETPQKI----HQKYIEFYDTRAAEAALRELNSRYIA---GKQIKL  301 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~s--Vritg~sk----G~AFVeF~d~E~A~kAL~~LnG~~I~---Gr~IkV  301 (876)
                      .-+||||.+||.++...||..+|..|-.-+.  ++.+.+.+    -+|||.|.+.++|.+|+++|||..|.   +..|+|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            3579999999999999999999999877665  45554443    69999999999999999999999985   799999


Q ss_pred             EeecCchhH
Q 002823          302 EPSHLRGLR  310 (876)
Q Consensus       302 s~A~~k~~R  310 (876)
                      ++++....+
T Consensus       113 ElAKSNtK~  121 (284)
T KOG1457|consen  113 ELAKSNTKR  121 (284)
T ss_pred             eehhcCccc
Confidence            999875533

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.87  E-value=3.3e-05  Score=82.56  Aligned_cols=79  Identities=20%  Similarity=0.347  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      .+..+.+|+|.|||..|++++|+++|..||.++.+-    ..+.+.|.|-|.|...++|.+|++.+++..+.|+.|.+..
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            344457999999999999999999999999887775    5788999999999999999999999999999999998877


Q ss_pred             cCC
Q 002823          219 SIP  221 (876)
Q Consensus       219 A~p  221 (876)
                      ..+
T Consensus       159 i~~  161 (243)
T KOG0533|consen  159 ISS  161 (243)
T ss_pred             ecC
Confidence            644

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=97.85  E-value=2.6e-05  Score=89.33  Aligned_cols=75  Identities=19%  Similarity=0.347  Sum_probs=68.1

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .+.|||.+|...+...+|+.+|++||+|+-.++     ++..+.|+||++.+.++|.+||..|+..++.|+.|.|+.++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            348999999999999999999999999998666     455678999999999999999999999999999999998864

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.75  E-value=7.7e-05  Score=79.83  Aligned_cols=77  Identities=22%  Similarity=0.363  Sum_probs=69.5

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ..+|+|.|||..++++||+++|..||.++.+-+    .+.+.|.|-|.|...++|.+|++.++|..+.|+++++....+.
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            468999999999999999999999998877655    5667799999999999999999999999999999999988775


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus       163 ~  163 (243)
T KOG0533|consen  163 S  163 (243)
T ss_pred             c
Confidence            4

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.73  E-value=3.7e-05  Score=88.04  Aligned_cols=74  Identities=18%  Similarity=0.301  Sum_probs=62.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ..+|||+|||.++++++|++.|++||+|+...+     .++..+||||+|.+.++++.|+.+- -..+++++|.|+--++
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCeeEEEEeccc
Confidence            456999999999999999999999999988762     2444599999999999999999764 6678999999976544

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.72  E-value=5.1e-05  Score=86.87  Aligned_cols=75  Identities=23%  Similarity=0.301  Sum_probs=64.2

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---c--CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---T--PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri---t--g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      .+|||+|||.+++.++|+++|..||.|+..+|   .  .+...||||+|.+.++++.||.+- -..|++++|.|+-.++.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCeeEEEEecccc
Confidence            36999999999999999999999999999655   2  223389999999999999999865 78889999999977664


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      -
T Consensus       368 ~  368 (419)
T KOG0116|consen  368 F  368 (419)
T ss_pred             c
Confidence            3

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.69  E-value=8.1e-05  Score=81.77  Aligned_cols=74  Identities=16%  Similarity=0.284  Sum_probs=67.0

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEE--------EEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKE--------IRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQI  299 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~s--------Vri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~I  299 (876)
                      ...|||.|||.++|.+++.++|++||.|..        |++    .+.-||-|.|.|-..+++.-|++.|++..+.|++|
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~  213 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKL  213 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEE
Confidence            446999999999999999999999999876        444    56678999999999999999999999999999999


Q ss_pred             EEEeec
Q 002823          300 KLEPSH  305 (876)
Q Consensus       300 kVs~A~  305 (876)
                      +|+.|+
T Consensus       214 rVerAk  219 (382)
T KOG1548|consen  214 RVERAK  219 (382)
T ss_pred             EEehhh
Confidence            999874

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.69  E-value=0.00037  Score=79.70  Aligned_cols=154  Identities=10%  Similarity=0.152  Sum_probs=105.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEE-EE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRT-FY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~s-V~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .....|-+++||+.||++||.++|+-.-.|.. |.    ..++..|-|||+|++.+.|++|+.. +...|..|-|.|-.+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            34568999999999999999999996654444 21    4566888999999999999999964 444555554444110


Q ss_pred             -----------------------C------------CCCC------------------------C--------Cccc---
Q 002823          220 -----------------------I------------PKDN------------------------P--------SEKE---  229 (876)
Q Consensus       220 -----------------------~------------pk~~------------------------~--------~ek~---  229 (876)
                                             .            .+..                        .        ..++   
T Consensus       180 s~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~  259 (510)
T KOG4211|consen  180 SRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNY  259 (510)
T ss_pred             HHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccccccccccccc
Confidence                                   0            0000                        0        0000   


Q ss_pred             ------------------ccc-ceeEeecCCCCCcHHHHHHHhhhcCCeE-EEEe--cCCcccEEEEEecCHHHHHHHHH
Q 002823          230 ------------------INQ-GTLVVFNLDSSVSNDELHHIFGVYGEIK-EIRE--TPQKIHQKYIEFYDTRAAEAALR  287 (876)
Q Consensus       230 ------------------~~~-~tLfV~NLP~svTeedLreiFs~fG~I~-sVri--tg~skG~AFVeF~d~E~A~kAL~  287 (876)
                                        ... ..+..++||...++.++..+|+..-.+. .|.+  +++..+-|+|+|.+.++|..|+.
T Consensus       260 ~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~~v~i~ig~dGr~TGEAdveF~t~edav~Ams  339 (510)
T KOG4211|consen  260 PVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPYRVHIEIGPDGRATGEADVEFATGEDAVGAMG  339 (510)
T ss_pred             CCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCceeEEEEeCCCCccCCcceeecccchhhHhhhc
Confidence                              011 3567789999999999999999665542 2444  67778999999999999999986


Q ss_pred             HhCCceeCCeEEE
Q 002823          288 ELNSRYIAGKQIK  300 (876)
Q Consensus       288 ~LnG~~I~Gr~Ik  300 (876)
                       -++..+..+-|.
T Consensus       340 -kd~anm~hrYVE  351 (510)
T KOG4211|consen  340 -KDGANMGHRYVE  351 (510)
T ss_pred             -cCCcccCcceee
Confidence             344444444443

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.61  E-value=0.00025  Score=66.03  Aligned_cols=73  Identities=19%  Similarity=0.339  Sum_probs=59.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcc--CCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccC----CceeeE
Q 002823          148 RTLLLRKINSNIEDSELKALFEQY--GDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTR----SGKLDI  216 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqf--G~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~----Gr~L~V  216 (876)
                      +||.|+|||...|.++|.+++...  |...-++     .++.+.|||||.|.+++.|.+..+.++|+.+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            599999999999999999888743  4444444     45678999999999999999999999998875    455677


Q ss_pred             eecC
Q 002823          217 HYSI  220 (876)
Q Consensus       217 ~~A~  220 (876)
                      .||.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            7764

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.60  E-value=0.00064  Score=75.53  Aligned_cols=157  Identities=14%  Similarity=0.162  Sum_probs=110.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhc-----cCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQ-----YGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsq-----fG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ..-+-.++||+..++.+|..+|+-     -|.+......++..|+|.|.|.|.|.-+-|++. +...+.++.|.|--+.+
T Consensus        60 ~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYka~g  138 (508)
T KOG1365|consen   60 NVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYKATG  138 (508)
T ss_pred             ceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeeccCc
Confidence            345667999999999999999973     334444446677889999999999999999864 55667778777743332


Q ss_pred             CCC---------CCc---cccccceeEeecCCCCCcHHHHHHHhhhcC----C---eEEEEe-cCCcccEEEEEecCHHH
Q 002823          222 KDN---------PSE---KEINQGTLVVFNLDSSVSNDELHHIFGVYG----E---IKEIRE-TPQKIHQKYIEFYDTRA  281 (876)
Q Consensus       222 k~~---------~~e---k~~~~~tLfV~NLP~svTeedLreiFs~fG----~---I~sVri-tg~skG~AFVeF~d~E~  281 (876)
                      .+-         ...   .+.+.-.|-.++||.++++.|+.++|..--    .   |.-|+. +++..|-|||.|..+++
T Consensus       139 e~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~  218 (508)
T KOG1365|consen  139 EEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEED  218 (508)
T ss_pred             hhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHH
Confidence            211         100   112344677899999999999999996321    2   222433 67778999999999999


Q ss_pred             HHHHHHHhCCceeCCeEEEEEeec
Q 002823          282 AEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       282 A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      |+.||.+ |...|+-|-|.+-.+.
T Consensus       219 aq~aL~k-hrq~iGqRYIElFRST  241 (508)
T KOG1365|consen  219 AQFALRK-HRQNIGQRYIELFRST  241 (508)
T ss_pred             HHHHHHH-HHHHHhHHHHHHHHHh
Confidence            9999984 4445555555544433

>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

Probab=97.58  E-value=0.0002  Score=64.68  Aligned_cols=70  Identities=19%  Similarity=0.281  Sum_probs=49.3

Q ss_pred             cEEEEcCCCCCCCHHHHH----HHhhccC-CeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          148 RTLLLRKINSNIEDSELK----ALFEQYG-DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~----elFsqfG-~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ..|||.|||.+.+...|+    .+++.|| +|..|.     .+.|+|.|.+.+.|++|.+.|+|..+.|.+|.|.|....
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~-----~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~   77 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS-----GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKN   77 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-----CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCc
Confidence            368999999999987655    6666776 777763     478999999999999999999999999999999997443

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.53  E-value=7.7e-05  Score=79.06  Aligned_cols=76  Identities=17%  Similarity=0.267  Sum_probs=65.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeE-----EEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVR-----TFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~-----sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ....+||.+.|..+++++.|-..|.+|-...     .-+.+++++||+||.|.++.++.+|+++|+|+.++.+.|++.-+
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            3357999999999999999999999987432     22368999999999999999999999999999999999887554


Q ss_pred             C
Q 002823          220 I  220 (876)
Q Consensus       220 ~  220 (876)
                      .
T Consensus       268 ~  268 (290)
T KOG0226|consen  268 E  268 (290)
T ss_pred             h
Confidence            3

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.49  E-value=0.0002  Score=84.17  Aligned_cols=165  Identities=13%  Similarity=0.068  Sum_probs=119.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhh-ccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFE-QYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFs-qfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ....+.+-+++++.+.++.+++++|. .+-.-..+.   ..+...|-++|.|....++++|++. +......|.+.|.-.
T Consensus       308 v~d~~y~~~~gm~fn~~~nd~rkfF~g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~  386 (944)
T KOG4307|consen  308 VSDKYYNNYKGMEFNNDFNDGRKFFPGRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPP  386 (944)
T ss_pred             cchhheeeecccccccccchhhhhcCcccccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCC
Confidence            33445666789999999999999997 333323332   4445589999999999999999853 555566666665221


Q ss_pred             CC------------CCC-------------------CCcc----ccccceeEeecCCCCCcHHHHHHHhhhcCCeEE-EE
Q 002823          220 IP------------KDN-------------------PSEK----EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKE-IR  263 (876)
Q Consensus       220 ~p------------k~~-------------------~~ek----~~~~~tLfV~NLP~svTeedLreiFs~fG~I~s-Vr  263 (876)
                      ..            +..                   ...+    ......|||..||..+++.++.++|..--.|++ |.
T Consensus       387 g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~  466 (944)
T KOG4307|consen  387 GNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIE  466 (944)
T ss_pred             CccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeE
Confidence            00            000                   0000    113458999999999999999999998877777 77


Q ss_pred             e----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchh
Q 002823          264 E----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       264 i----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~  309 (876)
                      +    +.+.++.|||+|..++++.+|...-+...++.+.|+|.-...++.
T Consensus       467 lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~m  516 (944)
T KOG4307|consen  467 LTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYAM  516 (944)
T ss_pred             eccCCcccccchhhheeccccccchhhhcccccccCceEEEeechhhHHH
Confidence            6    344567899999999999999887777778889999987765553

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.49  E-value=0.00012  Score=78.15  Aligned_cols=78  Identities=22%  Similarity=0.287  Sum_probs=69.6

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ......+||+|++..++.+++..+|+.||.|..|.+     .+++|+|+||+|.+.+.++.|++ ||+..|.|+.++|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            345668999999999999999999999999975544     55689999999999999999999 999999999999998


Q ss_pred             ecCc
Q 002823          304 SHLR  307 (876)
Q Consensus       304 A~~k  307 (876)
                      .+..
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            8764

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.43  E-value=7.3e-05  Score=83.02  Aligned_cols=157  Identities=16%  Similarity=0.135  Sum_probs=113.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe--------CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe-e
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYR--------ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH-Y  218 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~--------tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~-~  218 (876)
                      ..|-|.||.+.++.++++.||.-.|+|..+..        .......|||.|.|...+..|.. |.++++-++.|.|- |
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            38999999999999999999999999998872        12346789999999999988874 66666666655552 2


Q ss_pred             cCCCCC----------------------------CC--cc---------------------ccccceeEeecCCCCCcHH
Q 002823          219 SIPKDN----------------------------PS--EK---------------------EINQGTLVVFNLDSSVSND  247 (876)
Q Consensus       219 A~pk~~----------------------------~~--ek---------------------~~~~~tLfV~NLP~svTee  247 (876)
                      ..+...                            +.  ..                     .....+++|++|+..+...
T Consensus        87 ~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~  166 (479)
T KOG4676|consen   87 GDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILP  166 (479)
T ss_pred             CCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcch
Confidence            211000                            00  00                     0022579999999999999


Q ss_pred             HHHHHhhhcCCeEEEEe-cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          248 ELHHIFGVYGEIKEIRE-TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       248 dLreiFs~fG~I~sVri-tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ++.+.|..+|+|.+.++ .+...-+|-|+|........|++ ++|..+.-+...+...+|
T Consensus       167 e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~kP  225 (479)
T KOG4676|consen  167 ESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAIIKP  225 (479)
T ss_pred             hhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhcCc
Confidence            99999999999998766 34445678899999888888887 667666543333333333

>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

Probab=97.40  E-value=0.00063  Score=61.53  Aligned_cols=69  Identities=19%  Similarity=0.235  Sum_probs=48.5

Q ss_pred             ceeEeecCCCCCcHHH----HHHHhhhcC-CeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          233 GTLVVFNLDSSVSNDE----LHHIFGVYG-EIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       233 ~tLfV~NLP~svTeed----LreiFs~fG-~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ..|+|.|||.+.+...    |++++..+| +|.+|.     .+.|+|.|.+.+.|.+|.+.|+|..+.|++|.|.|...
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~-----~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS-----GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-----CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            4699999999887765    667777776 465552     57899999999999999999999999999999999843

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.25  E-value=0.00032  Score=74.88  Aligned_cols=79  Identities=11%  Similarity=0.213  Sum_probs=69.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ..+...+.+||+|+...++.+++...|+.||.|..+.     ..+..+||+||+|.+.+.+++|++ |++..|.++.+.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            3456678999999999999999999999999996444     455689999999999999999997 9999999999999


Q ss_pred             eecCC
Q 002823          217 HYSIP  221 (876)
Q Consensus       217 ~~A~p  221 (876)
                      .+..-
T Consensus       175 t~~r~  179 (231)
T KOG4209|consen  175 TLKRT  179 (231)
T ss_pred             eeeee
Confidence            77543

>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

Probab=97.16  E-value=0.00072  Score=63.81  Aligned_cols=77  Identities=23%  Similarity=0.353  Sum_probs=50.2

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhC-----CceeCCeEEEEEeecCch
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELN-----SRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~Ln-----G~~I~Gr~IkVs~A~~k~  308 (876)
                      .|.|.+++..++.++|++.|+.||.|..|.+. .....|+|.|.+.++|++|+..+.     +..|.+..+.++.-...+
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~-~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vLeGee   81 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFS-RGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVLEGEE   81 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE---TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE---HHH
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEec-CCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEECCCHH
Confidence            57888999999999999999999999999983 355689999999999999998774     346788888888777666


Q ss_pred             hHH
Q 002823          309 LRK  311 (876)
Q Consensus       309 ~Rr  311 (876)
                      +++
T Consensus        82 E~~   84 (105)
T PF08777_consen   82 EEE   84 (105)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            555

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.83  E-value=0.0014  Score=73.90  Aligned_cols=69  Identities=32%  Similarity=0.354  Sum_probs=57.4

Q ss_pred             ccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCC------------------cccEEEEEecCHHHHHHHHHH
Q 002823          227 EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQ------------------KIHQKYIEFYDTRAAEAALRE  288 (876)
Q Consensus       227 ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~------------------skG~AFVeF~d~E~A~kAL~~  288 (876)
                      +.....++|++.|||.+-.-+.|.++|+.+|.|+.|+|...                  .+-+|+|+|+..+.|.+|.+.
T Consensus       226 ~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            33456889999999999999999999999999999998211                  145899999999999999998


Q ss_pred             hCCceeC
Q 002823          289 LNSRYIA  295 (876)
Q Consensus       289 LnG~~I~  295 (876)
                      |+...-.
T Consensus       306 ~~~e~~w  312 (484)
T KOG1855|consen  306 LNPEQNW  312 (484)
T ss_pred             hchhhhh
Confidence            8655443

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.82  E-value=0.0002  Score=86.17  Aligned_cols=155  Identities=14%  Similarity=0.130  Sum_probs=119.6

Q ss_pred             CcEEEEcCCCCCCCHH-HHHHHhhccCCeEEEEeCC-----CccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          147 SRTLLLRKINSNIEDS-ELKALFEQYGDVRTFYRAS-----KHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       147 SrTLFVgNLP~~vTEe-eL~elFsqfG~I~sV~~tg-----ksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      .+...+.++-+...+. ..+..|+.+|.|+.|+...     ....++++.+....+++.|. ...+.-+.++...|..+.
T Consensus       571 ~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat-~pa~~~~a~~~~av~~ad  649 (881)
T KOG0128|consen  571 RREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESAT-VPAGGALANRSAAVGLAD  649 (881)
T ss_pred             hhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcc-cccccccCCccccCCCCC
Confidence            4677888887777766 5678899999999998322     12238899999999999888 467778888988888887


Q ss_pred             CCCCCCccc------cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHh
Q 002823          221 PKDNPSEKE------INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALREL  289 (876)
Q Consensus       221 pk~~~~ek~------~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~L  289 (876)
                      ++.......      ....++||+||+..+.+.+|...|..+|.+..+++     .++.+|+|+|+|...++|.+|+...
T Consensus       650 ~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~  729 (881)
T KOG0128|consen  650 AEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFR  729 (881)
T ss_pred             chhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhh
Confidence            665322111      12348999999999999999999999999887655     5667899999999999999999977


Q ss_pred             CCceeCCeEEEEE
Q 002823          290 NSRYIAGKQIKLE  302 (876)
Q Consensus       290 nG~~I~Gr~IkVs  302 (876)
                      ++..++...+-|.
T Consensus       730 d~~~~gK~~v~i~  742 (881)
T KOG0128|consen  730 DSCFFGKISVAIS  742 (881)
T ss_pred             hhhhhhhhhhhee
Confidence            7666663333333

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.74  E-value=0.0021  Score=70.59  Aligned_cols=75  Identities=21%  Similarity=0.339  Sum_probs=61.8

Q ss_pred             cEEEEcCCCCCCCHHHHH------HHhhccCCeEEEEeCCCc------c--ceEeeecCCHHHHHHHHHHccccccCCce
Q 002823          148 RTLLLRKINSNIEDSELK------ALFEQYGDVRTFYRASKH------C--GFVTISYYDIRAARNAMKSLQNKLTRSGK  213 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~------elFsqfG~I~sV~~tgks------r--GfAFV~F~d~edA~kAl~~Lng~~l~Gr~  213 (876)
                      .-+||-+||+.+-++++.      ++|.+||+|..|.+..+.      .  --.||.|.+.|+|.+||.+.+|..++||.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            468999999998887732      899999999998843331      1  22599999999999999999999999999


Q ss_pred             eeEeecCCC
Q 002823          214 LDIHYSIPK  222 (876)
Q Consensus       214 L~V~~A~pk  222 (876)
                      |+..|...|
T Consensus       195 lkatYGTTK  203 (480)
T COG5175         195 LKATYGTTK  203 (480)
T ss_pred             EeeecCchH
Confidence            999886543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.72  E-value=0.0042  Score=68.25  Aligned_cols=82  Identities=22%  Similarity=0.424  Sum_probs=67.0

Q ss_pred             cceeEeecCCCCCcHHHH------HHHhhhcCCeEEEEecCCc------ccE--EEEEecCHHHHHHHHHHhCCceeCCe
Q 002823          232 QGTLVVFNLDSSVSNDEL------HHIFGVYGEIKEIRETPQK------IHQ--KYIEFYDTRAAEAALRELNSRYIAGK  297 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedL------reiFs~fG~I~sVritg~s------kG~--AFVeF~d~E~A~kAL~~LnG~~I~Gr  297 (876)
                      .+-+||-+|++.+..|++      .++|++||+|+.|.+..+.      .+.  .||.|.+.|+|.+||.+.+|..+.||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            456899999999887772      4789999999998873322      122  39999999999999999999999999


Q ss_pred             EEEEEeecCchhHHHH
Q 002823          298 QIKLEPSHLRGLRKCL  313 (876)
Q Consensus       298 ~IkVs~A~~k~~Rr~l  313 (876)
                      .|+..|...+---..+
T Consensus       194 ~lkatYGTTKYCtsYL  209 (480)
T COG5175         194 VLKATYGTTKYCTSYL  209 (480)
T ss_pred             eEeeecCchHHHHHHH
Confidence            9999999887644444

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.55  E-value=0.0019  Score=71.70  Aligned_cols=77  Identities=25%  Similarity=0.318  Sum_probs=69.1

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEE--------EEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeE
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKE--------IRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQ  298 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~s--------Vri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~  298 (876)
                      ..+|||-+||..+++++|.++|.++|.|+.        |.+     |..+|+-|.|.|.+...|++|+.-++++.+.+.+
T Consensus        66 ~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~  145 (351)
T KOG1995|consen   66 NETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNT  145 (351)
T ss_pred             cccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCCC
Confidence            458999999999999999999999999865        222     6778899999999999999999999999999999


Q ss_pred             EEEEeecCch
Q 002823          299 IKLEPSHLRG  308 (876)
Q Consensus       299 IkVs~A~~k~  308 (876)
                      |+|.++..+.
T Consensus       146 ikvs~a~~r~  155 (351)
T KOG1995|consen  146 IKVSLAERRT  155 (351)
T ss_pred             chhhhhhhcc
Confidence            9999887654

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.54  E-value=0.0042  Score=66.34  Aligned_cols=87  Identities=23%  Similarity=0.376  Sum_probs=73.9

Q ss_pred             HHHHHHHHHccccccCCceeeEeecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEE----EEecCCccc
Q 002823          195 RAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKE----IRETPQKIH  270 (876)
Q Consensus       195 edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~s----Vritg~skG  270 (876)
                      .-|+.|..+|.+....++.++|.|+..           ..|||.||...++.+.|.+.|+.||.|..    +...++..+
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~-----------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~   73 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH-----------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTR   73 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc-----------ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccc
Confidence            346777788999999999999999852           46999999999999999999999999866    333566678


Q ss_pred             EEEEEecCHHHHHHHHHHhCCc
Q 002823          271 QKYIEFYDTRAAEAALRELNSR  292 (876)
Q Consensus       271 ~AFVeF~d~E~A~kAL~~LnG~  292 (876)
                      -++|+|...-.|.+|+..+.-.
T Consensus        74 eg~v~~~~k~~a~~a~rr~~~~   95 (275)
T KOG0115|consen   74 EGIVEFAKKPNARKAARRCREG   95 (275)
T ss_pred             cchhhhhcchhHHHHHHHhccC
Confidence            8999999999999999987543

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.50  E-value=0.0058  Score=50.72  Aligned_cols=52  Identities=23%  Similarity=0.403  Sum_probs=43.3

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHH
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAAL  286 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL  286 (876)
                      +.|-|.+.+.+.. +++...|..||+|..+.++ ......+|+|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            4678888887765 4566688999999999984 55779999999999999985

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.29  E-value=0.0038  Score=70.59  Aligned_cols=78  Identities=19%  Similarity=0.282  Sum_probs=61.4

Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCC----------C--------ccceEeeecCCHHHHHHHH
Q 002823          140 HLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRAS----------K--------HCGFVTISYYDIRAARNAM  201 (876)
Q Consensus       140 ~p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tg----------k--------srGfAFV~F~d~edA~kAl  201 (876)
                      .+..+-++|||.+-|||.+-.-+-|.++|..+|.|+.|++-.          .        .+-||+|+|...+.|.+|.
T Consensus       224 ~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~  303 (484)
T KOG1855|consen  224 FDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAR  303 (484)
T ss_pred             ccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHH
Confidence            334456899999999999999999999999999999998311          1        2568999999999999999


Q ss_pred             HHccccccCCceeeEe
Q 002823          202 KSLQNKLTRSGKLDIH  217 (876)
Q Consensus       202 ~~Lng~~l~Gr~L~V~  217 (876)
                      +.++...-...-|+|.
T Consensus       304 e~~~~e~~wr~glkvk  319 (484)
T KOG1855|consen  304 ELLNPEQNWRMGLKVK  319 (484)
T ss_pred             Hhhchhhhhhhcchhh
Confidence            8876554444444443

>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

Probab=96.26  E-value=0.0098  Score=56.19  Aligned_cols=59  Identities=19%  Similarity=0.239  Sum_probs=39.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcccc
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNK  207 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~  207 (876)
                      ..|.|.+++..++.++|++.|++||+|..|.. .+...-|||.|.+.+.|++|+..+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~-~~G~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDF-SRGDTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE---TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEe-cCCCCEEEEEECCcchHHHHHHHHHhc
Confidence            46889999999999999999999999999885 234558999999999999999877654

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]

Probab=96.08  E-value=0.003  Score=70.81  Aligned_cols=73  Identities=19%  Similarity=0.440  Sum_probs=60.7

Q ss_pred             CCceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEec-cccccc-ceeEEEEEecCCccchHHHHHHhcCccccC
Q 002823          703 DNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLP-IDFKNK-CNVGYAFINMTDPSQIVPFYQSFNGKKWEK  776 (876)
Q Consensus       703 d~rTTvMirNIPnk~t~~~L~~~ide~~~g~yDF~Ylp-~Df~~~-~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~  776 (876)
                      +....|.||++|+++|.+.|++.||- +...+.|-|+- -|+... |-++.|||||..+.++..|...|+|+.+-.
T Consensus         5 ~~~~Kvv~rrlpp~l~~~~~~eqi~p-~~~~v~~~~F~~a~~s~~~~~ysrayinFk~~~dv~ef~~~f~g~ifld   79 (376)
T KOG1295|consen    5 EAKVKVVVRRLPPKLTEEQLLEQINP-FPEHVNWEFFAKADESLRNHKYSRAYINFKNPEDVEEFRRRFDGYIFLD   79 (376)
T ss_pred             ccceeeeeecCCCcccHHHHhhhcCC-CccccchheeccccccchhhhhhhhhhccccHHHHHHHHhhCCceEEec
Confidence            34567999999999999999999999 88888887654 555433 336669999999999999999999998754

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.02  E-value=0.013  Score=48.74  Aligned_cols=52  Identities=12%  Similarity=0.358  Sum_probs=43.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHH
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAM  201 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl  201 (876)
                      +.|-|.+.+++..+. +.+.|..||+|..+..+ ....+.+|+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            578899998776654 55588899999999874 55779999999999999985

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.00  E-value=0.0055  Score=68.17  Aligned_cols=80  Identities=16%  Similarity=0.214  Sum_probs=69.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-------------eCCCccceEeeecCCHHHHHHHHHHccccccC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-------------RASKHCGFVTISYYDIRAARNAMKSLQNKLTR  210 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-------------~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~  210 (876)
                      ..-.-+|||-+||..+++.+|.++|.++|.|..-+             .|.+.|+-|.|.|.|...|+.|+..++++.+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            34457999999999999999999999999886533             56789999999999999999999999999999


Q ss_pred             CceeeEeecCCCC
Q 002823          211 SGKLDIHYSIPKD  223 (876)
Q Consensus       211 Gr~L~V~~A~pk~  223 (876)
                      +.+|+|.++..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999998775443

>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 []

Probab=95.96  E-value=0.02  Score=53.74  Aligned_cols=73  Identities=21%  Similarity=0.320  Sum_probs=53.9

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEE------------ecCCcccEEEEEecCHHHHHHHHHHhCCceeCCe-E
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR------------ETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK-Q  298 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVr------------itg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr-~  298 (876)
                      ...|.|.+.|+. ....|.+.|++||+|.+..            -.+.......|+|.++.+|.+||+ .||..+.|. .
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            456899999988 5567889999999998875            124456799999999999999998 799999885 4


Q ss_pred             EEEEeecC
Q 002823          299 IKLEPSHL  306 (876)
Q Consensus       299 IkVs~A~~  306 (876)
                      +-|.+.++
T Consensus        84 vGV~~~~~   91 (100)
T PF05172_consen   84 VGVKPCDP   91 (100)
T ss_dssp             EEEEE-HH
T ss_pred             EEEEEcHH
Confidence            44777643

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=95.87  E-value=0.018  Score=68.41  Aligned_cols=71  Identities=18%  Similarity=0.215  Sum_probs=62.7

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEE-EEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKE-IRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~s-Vri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      +.|-+.|+|.+++-+||.++|..|-.+.. |++    .+...|-|.|-|++.++|.+|...|+++.|..++|+|..
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            47889999999999999999999987643 333    566789999999999999999999999999999999864

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=95.73  E-value=0.0089  Score=65.89  Aligned_cols=79  Identities=16%  Similarity=0.341  Sum_probs=69.7

Q ss_pred             CCCcEEE-EcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          145 HPSRTLL-LRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       145 ~pSrTLF-VgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      .++.++| |++|+.++++++|+..|..+|.|..++     .++..+|||||.|.....+..++.. +...+.++++.+.+
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  260 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEE  260 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccccc
Confidence            3455666 999999999999999999999999998     4678999999999999999999987 88889999999999


Q ss_pred             cCCCCC
Q 002823          219 SIPKDN  224 (876)
Q Consensus       219 A~pk~~  224 (876)
                      ..+...
T Consensus       261 ~~~~~~  266 (285)
T KOG4210|consen  261 DEPRPK  266 (285)
T ss_pred             CCCCcc
Confidence            876643

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=95.61  E-value=0.0073  Score=64.58  Aligned_cols=68  Identities=25%  Similarity=0.446  Sum_probs=58.8

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCc-------------c----cEEEEEecCHHHHHHHHHHhCCce
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQK-------------I----HQKYIEFYDTRAAEAALRELNSRY  293 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~s-------------k----G~AFVeF~d~E~A~kAL~~LnG~~  293 (876)
                      ..+.||+++||+.+....|+++|+.||+|-.|.+.+..             +    .-|.|+|.+...|.++...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            46799999999999999999999999999998873221             1    138999999999999999999999


Q ss_pred             eCCeE
Q 002823          294 IAGKQ  298 (876)
Q Consensus       294 I~Gr~  298 (876)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99854

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.41  E-value=0.021  Score=64.62  Aligned_cols=88  Identities=24%  Similarity=0.363  Sum_probs=69.0

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhc--CCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCc-eeCCeEEEEEeecCchh
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVY--GEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSR-YIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~f--G~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~-~I~Gr~IkVs~A~~k~~  309 (876)
                      ..+|++||.+.++..+|..+|...  +.-..+.+   ..+|+||.+.+...|.+|++.++|+ ++.|+++.|.++.++.+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~---k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkq   78 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV---KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ   78 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee---ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH
Confidence            368999999999999999999754  11112222   4689999999999999999999995 68999999999999887


Q ss_pred             HH---HHhhcCCchhhhh
Q 002823          310 RK---CLANQLPPELEQE  324 (876)
Q Consensus       310 Rr---~l~qQ~~~q~~q~  324 (876)
                      |.   ++ +.+.+++.++
T Consensus        79 rsrk~Qi-rnippql~we   95 (584)
T KOG2193|consen   79 RSRKIQI-RNIPPQLQWE   95 (584)
T ss_pred             HhhhhhH-hcCCHHHHHH
Confidence            65   33 4455555554

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.25  E-value=0.066  Score=53.43  Aligned_cols=77  Identities=29%  Similarity=0.361  Sum_probs=53.9

Q ss_pred             cccceeEeecCC-----CCCcH----HHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          230 INQGTLVVFNLD-----SSVSN----DELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       230 ~~~~tLfV~NLP-----~svTe----edLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      ++..||.|.=+.     ...-.    .+|.+.|..||+|.=||+..   +.-+|.|.+-+.|.+|+. ++|.+++|+.|+
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~---~~mwVTF~dg~sALaals-~dg~~v~g~~l~  100 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG---DTMWVTFRDGQSALAALS-LDGIQVNGRTLK  100 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET---TCEEEEESSCHHHHHHHH-GCCSEETTEEEE
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC---CeEEEEECccHHHHHHHc-cCCcEECCEEEE
Confidence            345677776555     11222    36888899999999999853   578999999999999997 999999999999


Q ss_pred             EEeecCchhH
Q 002823          301 LEPSHLRGLR  310 (876)
Q Consensus       301 Vs~A~~k~~R  310 (876)
                      |....+.-.+
T Consensus       101 i~LKtpdW~~  110 (146)
T PF08952_consen  101 IRLKTPDWLK  110 (146)
T ss_dssp             EEE-------
T ss_pred             EEeCCccHHH
Confidence            9998886643

; PDB: 1UFW_A 2DNR_A.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.15  E-value=0.01  Score=63.58  Aligned_cols=65  Identities=31%  Similarity=0.546  Sum_probs=54.1

Q ss_pred             HHHHHHhh-hcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchhHH
Q 002823          247 DELHHIFG-VYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       247 edLreiFs-~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~Rr  311 (876)
                      ++|...|+ +||+|+++.+    -.+-+|-++|+|...++|++|+..||+..+.|++|..++.--..-+.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~re  152 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDFRE  152 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCchhh
Confidence            45555566 9999999765    23346889999999999999999999999999999999987766555

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=95.14  E-value=0.017  Score=61.79  Aligned_cols=68  Identities=19%  Similarity=0.300  Sum_probs=58.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeC-------------CCccc----eEeeecCCHHHHHHHHHHccccc
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA-------------SKHCG----FVTISYYDIRAARNAMKSLQNKL  208 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~t-------------gksrG----fAFV~F~d~edA~kAl~~Lng~~  208 (876)
                      ..-.||+++||+.++-.-|+++|.+||.|-.|+..             +..++    -|+|+|.+...|.++...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            56689999999999999999999999999999821             11221    28999999999999999999999


Q ss_pred             cCCce
Q 002823          209 TRSGK  213 (876)
Q Consensus       209 l~Gr~  213 (876)
                      |.|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.97  E-value=0.085  Score=64.66  Aligned_cols=79  Identities=18%  Similarity=0.258  Sum_probs=70.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCC--ceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRS--GKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G--r~L~V~~A~  220 (876)
                      ...+++.+||++|+..+....|...|..||.|+.|.. .+..-||+|.|++...|+.|++.|.|..|.+  +.++|.|+.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy-~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~  529 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY-RHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLAS  529 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeec-ccCCcceeeecccCccchhhHHHHhcCcCCCCCccccccccc
Confidence            4567899999999999999999999999999999875 4566799999999999999999999999875  678998886


Q ss_pred             CC
Q 002823          221 PK  222 (876)
Q Consensus       221 pk  222 (876)
                      +.
T Consensus       530 ~~  531 (975)
T KOG0112|consen  530 PP  531 (975)
T ss_pred             CC
Confidence            54

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=94.96  E-value=0.13  Score=49.22  Aligned_cols=85  Identities=20%  Similarity=0.326  Sum_probs=66.5

Q ss_pred             CceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEecccccccceeEEEEEecCCccchHHHHHHhcCccccCCCCccEE
Q 002823          704 NRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVA  783 (876)
Q Consensus       704 ~rTTvMirNIPnk~t~~~L~~~ide~~~g~yDF~Ylp~Df~~~~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~Kv~  783 (876)
                      .+|+|-+=-+|+.++..+++..+-+.+.....-+.+.-|..  -|.-=+-|-|.++++|..||+.|||+++...-. .+|
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEp-E~C   87 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFNSLEP-ETC   87 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccCCCCC-cee
Confidence            35666666889999888777677777777777666666643  466679999999999999999999999987765 459


Q ss_pred             EEEe-eccc
Q 002823          784 SLAY-ARIQ  791 (876)
Q Consensus       784 ~v~y-A~iQ  791 (876)
                      .|.| .+||
T Consensus        88 hvvfV~~Ve   96 (110)
T PF07576_consen   88 HVVFVKSVE   96 (110)
T ss_pred             EEEEEEEEE
Confidence            9999 4554

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=94.95  E-value=0.053  Score=59.06  Aligned_cols=63  Identities=25%  Similarity=0.404  Sum_probs=52.4

Q ss_pred             HHHHHHHhhhcCCeEEEEe--cC-C---cccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          246 NDELHHIFGVYGEIKEIRE--TP-Q---KIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       246 eedLreiFs~fG~I~sVri--tg-~---skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ++++++.+++||+|..|-+  .+ .   ..--.||+|...++|.+|+-.|||+.|+|+.++..|..-.+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~ek  368 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLEK  368 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHHh
Confidence            5688999999999988665  11 1   12358999999999999999999999999999999887654

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=94.83  E-value=0.035  Score=65.22  Aligned_cols=81  Identities=17%  Similarity=0.198  Sum_probs=68.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhh-hcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCcee---CCeEEEEEeec
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFG-VYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYI---AGKQIKLEPSH  305 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs-~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I---~Gr~IkVs~A~  305 (876)
                      ...+.|+|.||-..+|.-+|+.++. ..|.|.+..| .+-|.+|||.|.+.++|.+.+.+|||..+   +.+.|.+.|..
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm-DkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~  520 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM-DKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVR  520 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHH-HHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecc
Confidence            4567999999999999999999999 5555666644 44577999999999999999999999876   56999999998


Q ss_pred             CchhHH
Q 002823          306 LRGLRK  311 (876)
Q Consensus       306 ~k~~Rr  311 (876)
                      ..+..+
T Consensus       521 ~deld~  526 (718)
T KOG2416|consen  521 ADELDK  526 (718)
T ss_pred             hhHHHH
Confidence            877554

>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 []

Probab=94.62  E-value=0.071  Score=50.11  Aligned_cols=73  Identities=8%  Similarity=0.190  Sum_probs=53.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE------------eCCCccceEeeecCCHHHHHHHHHHccccccCCc-
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY------------RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSG-  212 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~------------~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr-  212 (876)
                      ..+.|.|-+.|+. ....|.+.|++||.|.+..            .......+..|+|.++.+|++||. .||+.+.|. 
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            3567899999988 6677888999999998886            223456789999999999999995 699999875 


Q ss_pred             eeeEeecC
Q 002823          213 KLDIHYSI  220 (876)
Q Consensus       213 ~L~V~~A~  220 (876)
                      .+-|.+..
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence            44577653

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=94.57  E-value=0.058  Score=63.11  Aligned_cols=73  Identities=16%  Similarity=0.219  Sum_probs=56.7

Q ss_pred             ccceeEeecCCCC--Cc----HHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeC-CeEE
Q 002823          231 NQGTLVVFNLDSS--VS----NDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIA-GKQI  299 (876)
Q Consensus       231 ~~~tLfV~NLP~s--vT----eedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~-Gr~I  299 (876)
                      ....|+|.|+|.-  ..    ..-|.++|+++|+|..+.+    .+..+||.|++|.+..+|+.|++.|||+.+. ..+.
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            3457889999852  22    2346788999999998766    4557899999999999999999999999886 4555


Q ss_pred             EEEe
Q 002823          300 KLEP  303 (876)
Q Consensus       300 kVs~  303 (876)
                      .|..
T Consensus       137 ~v~~  140 (698)
T KOG2314|consen  137 FVRL  140 (698)
T ss_pred             Eeeh
Confidence            5543

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.30  E-value=0.13  Score=58.93  Aligned_cols=81  Identities=30%  Similarity=0.381  Sum_probs=70.9

Q ss_pred             ceeEEeecCCCCCCHHHHHHHHHhhCCCcccEEEecccccccceeEEEEEecCCccchHHHHHHhcCccccCCCCccEEE
Q 002823          705 RTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSEKVAS  784 (876)
Q Consensus       705 rTTvMirNIPnk~t~~~L~~~ide~~~g~yDF~Ylp~Df~~~~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~Kv~~  784 (876)
                      -|+|-|=-+|+.+|..+|+..+...+.-=-|+-.++ |  .--|.--+-|-|.+..++..||+.|||+++...-.+ +|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivR-d--~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e-~Ch  149 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVR-D--GMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPE-VCH  149 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEee-c--CCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCcc-cee
Confidence            788999999999999999999998888777888888 3  445666689999999999999999999999887777 999


Q ss_pred             EEeec
Q 002823          785 LAYAR  789 (876)
Q Consensus       785 v~yA~  789 (876)
                      |-|+.
T Consensus       150 ll~V~  154 (493)
T KOG0804|consen  150 LLYVD  154 (493)
T ss_pred             EEEEE
Confidence            99964

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=93.97  E-value=0.12  Score=60.67  Aligned_cols=71  Identities=18%  Similarity=0.279  Sum_probs=56.1

Q ss_pred             CCcEEEEcCCCCCCC--H----HHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccC-Ccee
Q 002823          146 PSRTLLLRKINSNIE--D----SELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTR-SGKL  214 (876)
Q Consensus       146 pSrTLFVgNLP~~vT--E----eeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~-Gr~L  214 (876)
                      -...|+|-|+|---.  .    .-|.++|+++|+|..++    ..+..+||.|++|.+.++|+.|++.|+|+.|. ...+
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            346889999985322  2    23458999999999988    45779999999999999999999999999875 3444


Q ss_pred             eE
Q 002823          215 DI  216 (876)
Q Consensus       215 ~V  216 (876)
                      .|
T Consensus       137 ~v  138 (698)
T KOG2314|consen  137 FV  138 (698)
T ss_pred             Ee
Confidence            44

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=93.87  E-value=0.049  Score=60.36  Aligned_cols=70  Identities=11%  Similarity=0.153  Sum_probs=59.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccC--CeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYG--DVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG--~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ...+||+||-|.+|+++|.+.+...|  .+.+++     ..+.+||||+|..-+....++.++.|-.+.|.|..-.|
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            35899999999999999999888666  344443     67889999999999999999999999989998876544

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=93.52  E-value=0.04  Score=59.13  Aligned_cols=57  Identities=18%  Similarity=0.331  Sum_probs=47.0

Q ss_pred             HHHHHhh-ccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          163 ELKALFE-QYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       163 eL~elFs-qfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      +|...|+ +||+|+.+.+    .-.-+|-+||.|...++|++|+..||+..+.|++|...+.
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            3334444 9999999862    2235788999999999999999999999999999999885

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=93.06  E-value=0.077  Score=62.46  Aligned_cols=79  Identities=20%  Similarity=0.268  Sum_probs=66.1

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhh-ccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcccccc---CCceeeE
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFE-QYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLT---RSGKLDI  216 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFs-qfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l---~Gr~L~V  216 (876)
                      |....++..|+|.||-.-+|.-+|++++. ..|.|...++ .+-|.-|||.|.+.++|.....+|+|..+   +.+.|.+
T Consensus       438 PsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm-DkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  438 PSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM-DKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             CCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH-HHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            44567789999999999999999999999 6667777765 44566799999999999999999999875   4678888


Q ss_pred             eecC
Q 002823          217 HYSI  220 (876)
Q Consensus       217 ~~A~  220 (876)
                      .|..
T Consensus       517 df~~  520 (718)
T KOG2416|consen  517 DFVR  520 (718)
T ss_pred             eecc
Confidence            7763

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=92.69  E-value=0.12  Score=58.19  Aligned_cols=73  Identities=25%  Similarity=0.483  Sum_probs=60.5

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCC--------cccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQ--------KIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~--------skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +.|.|.||.++++.++++.+|.-.|+|.++++.+.        ....|||.|.|...+..|.. |....+-++.|.|-.+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            47999999999999999999999999999988442        23589999999999998855 7777777777776655


Q ss_pred             cC
Q 002823          305 HL  306 (876)
Q Consensus       305 ~~  306 (876)
                      -.
T Consensus        87 ~~   88 (479)
T KOG4676|consen   87 GD   88 (479)
T ss_pred             CC
Confidence            43

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.40  E-value=0.5  Score=47.09  Aligned_cols=77  Identities=16%  Similarity=0.282  Sum_probs=60.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCCH-HHH---HHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          141 LNDEHPSRTLLLRKINSNIED-SEL---KALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTE-eeL---~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ...+.|-.||.|+-|..++.. +||   ...++.||+|.+|...|  +-.|.|.|.|..+|-+|+.+++. ...|..+++
T Consensus        80 ~~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qC  156 (166)
T PF15023_consen   80 NTKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQC  156 (166)
T ss_pred             cCCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEe
Confidence            345677889999988777653 344   45677999999998654  45799999999999999999886 677888888


Q ss_pred             eecC
Q 002823          217 HYSI  220 (876)
Q Consensus       217 ~~A~  220 (876)
                      .|-.
T Consensus       157 sWqq  160 (166)
T PF15023_consen  157 SWQQ  160 (166)
T ss_pred             eccc
Confidence            7753

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.15  E-value=0.53  Score=46.95  Aligned_cols=75  Identities=19%  Similarity=0.198  Sum_probs=58.2

Q ss_pred             ccccceeEeecCCCCCc----HHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          229 EINQGTLVVFNLDSSVS----NDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svT----eedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +++-.||+|+=|..++.    ...+.+.++.||.|.+|...+  +.-|.|.|.|..+|.+|+.++.. ...|..+++.|.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            34567899977766543    234555678999999998754  66899999999999999999876 677888888886


Q ss_pred             cC
Q 002823          305 HL  306 (876)
Q Consensus       305 ~~  306 (876)
                      .+
T Consensus       160 qr  161 (166)
T PF15023_consen  160 QR  161 (166)
T ss_pred             cc
Confidence            54

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=92.09  E-value=0.34  Score=48.51  Aligned_cols=75  Identities=24%  Similarity=0.332  Sum_probs=52.4

Q ss_pred             CCCCcEEEEcCCC-----C-CCCH---HHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCcee
Q 002823          144 EHPSRTLLLRKIN-----S-NIED---SELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKL  214 (876)
Q Consensus       144 e~pSrTLFVgNLP-----~-~vTE---eeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L  214 (876)
                      ..|..||.|.=+.     . ..++   .+|.+.|..||+|.-++..   .+.-+|+|.+-+.|.+|+ .++|..+.|+.|
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv---~~~mwVTF~dg~sALaal-s~dg~~v~g~~l   99 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFV---GDTMWVTFRDGQSALAAL-SLDGIQVNGRTL   99 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEE---TTCEEEEESSCHHHHHHH-HGCCSEETTEEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEe---CCeEEEEECccHHHHHHH-ccCCcEECCEEE
Confidence            3556788887665     1 2332   3667888999998877742   257899999999999999 589999999999


Q ss_pred             eEeecCCC
Q 002823          215 DIHYSIPK  222 (876)
Q Consensus       215 ~V~~A~pk  222 (876)
                      +|+...|.
T Consensus       100 ~i~LKtpd  107 (146)
T PF08952_consen  100 KIRLKTPD  107 (146)
T ss_dssp             EEEE----
T ss_pred             EEEeCCcc
Confidence            99886543

; PDB: 1UFW_A 2DNR_A.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=91.81  E-value=0.31  Score=56.88  Aligned_cols=63  Identities=17%  Similarity=0.223  Sum_probs=54.1

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhh-ccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHH
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFE-QYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKS  203 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFs-qfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~  203 (876)
                      ...-+|.+|||||+||.-++.++|..+|+ -||.|.-+-+     -+-.+|-|=|.|.+..+-.+||.+
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            34557789999999999999999999999 8999987752     244789999999999999999964

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=90.51  E-value=0.43  Score=56.10  Aligned_cols=78  Identities=23%  Similarity=0.234  Sum_probs=61.7

Q ss_pred             cCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhh--ccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccc--cccCCc
Q 002823          137 AGEHLNDEHPSRTLLLRKINSNIEDSELKALFE--QYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN--KLTRSG  212 (876)
Q Consensus       137 ~ge~p~~e~pSrTLFVgNLP~~vTEeeL~elFs--qfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng--~~l~Gr  212 (876)
                      +|++....+.-+.|.++-||..+..++++.||+  .|-++.+|.....  .--||+|++..||+.|.+.|..  +.|.|+
T Consensus       165 kgekVrp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N--~nWyITfesd~DAQqAykylreevk~fqgK  242 (684)
T KOG2591|consen  165 KGEKVRPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN--DNWYITFESDTDAQQAYKYLREEVKTFQGK  242 (684)
T ss_pred             CccccccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec--CceEEEeecchhHHHHHHHHHHHHHhhcCc
Confidence            556665666667888999999999999999998  5788888874222  2468999999999999998876  347787


Q ss_pred             eeeE
Q 002823          213 KLDI  216 (876)
Q Consensus       213 ~L~V  216 (876)
                      +|..
T Consensus       243 pImA  246 (684)
T KOG2591|consen  243 PIMA  246 (684)
T ss_pred             chhh
Confidence            7654

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=90.27  E-value=0.27  Score=56.87  Aligned_cols=62  Identities=19%  Similarity=0.211  Sum_probs=53.2

Q ss_pred             cHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          245 SNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       245 TeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      +-.+|...|.+||+|..|.+. .+.-.|.|+|.+..+|-+|.. ..+..|.++.|+|.|-.+..
T Consensus       386 t~a~ln~hfA~fG~i~n~qv~-~~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  386 TIADLNPHFAQFGEIENIQVD-YSSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hHhhhhhhhhhcCcccccccc-Cchhhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            457899999999999999883 335689999999999977754 78999999999999998854

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=90.23  E-value=0.62  Score=54.82  Aligned_cols=98  Identities=12%  Similarity=0.169  Sum_probs=70.7

Q ss_pred             CHHHHHHHHHHccccccCCceeeEeecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhh--hcCCeEEEEecCCccc
Q 002823          193 DIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFG--VYGEIKEIRETPQKIH  270 (876)
Q Consensus       193 d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs--~fG~I~sVritg~skG  270 (876)
                      |++-..+++++.-+..++.+-.+|.-.          ...+.|.++-||..+-.|+++.+|+  .+-++++|.+. ... 
T Consensus       146 DvdLI~Evlresp~VqvDekgekVrp~----------~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa-~N~-  213 (684)
T KOG2591|consen  146 DVDLIVEVLRESPNVQVDEKGEKVRPN----------HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFA-HND-  213 (684)
T ss_pred             chHHHHHHHhcCCCceeccCccccccC----------cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeee-ecC-
Confidence            344455666666666666665555332          2345788999999999999999998  47788888872 222 


Q ss_pred             EEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEE
Q 002823          271 QKYIEFYDTRAAEAALRELNS--RYIAGKQIKLE  302 (876)
Q Consensus       271 ~AFVeF~d~E~A~kAL~~LnG--~~I~Gr~IkVs  302 (876)
                      -=||+|++..||+.|.+.|..  ++|.||+|...
T Consensus       214 nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  214 NWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            358999999999999998854  56777776543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=88.71  E-value=0.21  Score=55.59  Aligned_cols=75  Identities=15%  Similarity=0.261  Sum_probs=60.1

Q ss_pred             cEEEEcCCCCCCCHHHHH---HHhhccCCeEEEEeCCCc--------cceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          148 RTLLLRKINSNIEDSELK---ALFEQYGDVRTFYRASKH--------CGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~---elFsqfG~I~sV~~tgks--------rGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      .-+||-+|+..+.++++.   +.|.+||.|..|.+.+..        -.-++|+|...++|..||...+|..+.|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            467888998887665554   689999999999843321        223899999999999999999999999999888


Q ss_pred             eecCCC
Q 002823          217 HYSIPK  222 (876)
Q Consensus       217 ~~A~pk  222 (876)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            887654

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=88.62  E-value=0.48  Score=52.88  Aligned_cols=72  Identities=14%  Similarity=0.086  Sum_probs=59.1

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCC--eEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGE--IKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~--I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      -.+||+||-+.+|++||.+.....|.  +.++++     .+.+||||+|...+..+.++.++.|-.++|.|+.-.|...
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            36899999999999999998886663  344443     7889999999999999999999999999999965555443

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=88.49  E-value=0.74  Score=50.52  Aligned_cols=74  Identities=19%  Similarity=0.320  Sum_probs=55.3

Q ss_pred             CcEEEEcCC--CCCCC---HHHHHHHhhccCCeEEEEe---CC---CccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          147 SRTLLLRKI--NSNIE---DSELKALFEQYGDVRTFYR---AS---KHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       147 SrTLFVgNL--P~~vT---EeeL~elFsqfG~I~sV~~---tg---ksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      ++.|.++|+  +-.++   ++++++..++||.|..|.+   .+   ...--.||+|...++|.+|+-.|+|..++||.++
T Consensus       281 tkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~  360 (378)
T KOG1996|consen  281 TKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVS  360 (378)
T ss_pred             hHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeee
Confidence            344556655  33444   3567789999999988762   11   1233589999999999999999999999999998


Q ss_pred             EeecC
Q 002823          216 IHYSI  220 (876)
Q Consensus       216 V~~A~  220 (876)
                      ..|..
T Consensus       361 A~Fyn  365 (378)
T KOG1996|consen  361 ACFYN  365 (378)
T ss_pred             heecc
Confidence            87753

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=87.38  E-value=1.8  Score=39.59  Aligned_cols=54  Identities=15%  Similarity=0.265  Sum_probs=42.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcc
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ  205 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Ln  205 (876)
                      ...+|. .|..+...||.++|+.||.|.--.+   .-..|||...+.+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi---~dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWI---NDTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEE---CTTEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEE---cCCcEEEEeecHHHHHHHHHHhc
Confidence            456666 9999999999999999999987775   33479999999999999998775

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=84.91  E-value=1.6  Score=45.03  Aligned_cols=74  Identities=11%  Similarity=0.149  Sum_probs=50.4

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhh-cCCe---EEEE--e-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC----
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGV-YGEI---KEIR--E-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG----  296 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~-fG~I---~sVr--i-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G----  296 (876)
                      ..+|+|++||+.+|++++++.+.. ++..   ..+.  .     ....-.-|||.|.+.+++..-...++|..+-+    
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            448999999999999999997776 6665   3443  1     11112469999999999999999999988743    


Q ss_pred             -eEEEEEeec
Q 002823          297 -KQIKLEPSH  305 (876)
Q Consensus       297 -r~IkVs~A~  305 (876)
                       .+..|++|-
T Consensus        87 ~~~~~VE~Ap   96 (176)
T PF03467_consen   87 EYPAVVEFAP   96 (176)
T ss_dssp             EEEEEEEE-S
T ss_pred             CcceeEEEcc
Confidence             455566653

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=84.04  E-value=3.9  Score=37.54  Aligned_cols=54  Identities=9%  Similarity=0.234  Sum_probs=41.6

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCC
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS  291 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG  291 (876)
                      ..+|. .|..+...||.++|+.||.|.---+   ...-|||...+.+.|..|+..+.-
T Consensus        11 VFhlt-FPkeWK~~DI~qlFspfG~I~VsWi---~dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   11 VFHLT-FPKEWKTSDIYQLFSPFGQIYVSWI---NDTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             EEEEE---TT--HHHHHHHCCCCCCEEEEEE---CTTEEEEEECCCHHHHHHHHHHTT
T ss_pred             EEEEe-CchHhhhhhHHHHhccCCcEEEEEE---cCCcEEEEeecHHHHHHHHHHhcc
Confidence            34455 9999999999999999999876555   245799999999999999998863

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.99  E-value=1.5  Score=49.98  Aligned_cols=53  Identities=15%  Similarity=0.238  Sum_probs=43.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccC----CeEEEEeCCCccceEeeecCCHHHHHHHHH
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYG----DVRTFYRASKHCGFVTISYYDIRAARNAMK  202 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG----~I~sV~~tgksrGfAFV~F~d~edA~kAl~  202 (876)
                      .-.+.|=|.++|.....+||...|+.|+    +|..|.     ...||-.|.+...|..|+.
T Consensus       389 dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvD-----dthalaVFss~~~AaeaLt  445 (528)
T KOG4483|consen  389 DLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVD-----DTHALAVFSSVNRAAEALT  445 (528)
T ss_pred             cccceeEeccCchhhccHHHHHHHHHhhcCCceeEEee-----cceeEEeecchHHHHHHhh
Confidence            3457889999999999999999999997    444443     3468999999999999984

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=83.91  E-value=0.47  Score=52.98  Aligned_cols=80  Identities=16%  Similarity=0.316  Sum_probs=64.1

Q ss_pred             cceeEeecCCCCCcHHHHH---HHhhhcCCeEEEEecCCc--------ccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          232 QGTLVVFNLDSSVSNDELH---HIFGVYGEIKEIRETPQK--------IHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLr---eiFs~fG~I~sVritg~s--------kG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      ..-+||-+|+..+..+.+.   +.|.+||.|..|.+....        ..-++|.|...++|..||...+|....|+.++
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            3467888888877666554   468899999998873322        12489999999999999999999999999999


Q ss_pred             EEeecCchhHH
Q 002823          301 LEPSHLRGLRK  311 (876)
Q Consensus       301 Vs~A~~k~~Rr  311 (876)
                      ..+...+..-.
T Consensus       157 a~~gttkycs~  167 (327)
T KOG2068|consen  157 ASLGTTKYCSF  167 (327)
T ss_pred             HhhCCCcchhH
Confidence            99998877544

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=83.09  E-value=4.3  Score=35.15  Aligned_cols=53  Identities=21%  Similarity=0.431  Sum_probs=40.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcc----CCeEEEEeCCCccceEeeecCCHHHHHHHHHHc
Q 002823          148 RTLLLRKINSNIEDSELKALFEQY----GDVRTFYRASKHCGFVTISYYDIRAARNAMKSL  204 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqf----G~I~sV~~tgksrGfAFV~F~d~edA~kAl~~L  204 (876)
                      .+|+|+++. +++.++|+.+|..|    ++.+-=.+..   ..|=|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD---tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD---TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC---CcEEEEECCHHHHHHHHHcC
Confidence            489999996 58889999999999    5332222211   24779999999999999764

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=82.87  E-value=5.2  Score=34.69  Aligned_cols=53  Identities=25%  Similarity=0.313  Sum_probs=40.7

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhc----CCeEEEEecCCcccEEEEEecCHHHHHHHHHHh
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVY----GEIKEIRETPQKIHQKYIEFYDTRAAEAALREL  289 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~f----G~I~sVritg~skG~AFVeF~d~E~A~kAL~~L  289 (876)
                      ..|+|++++ +++.++|+.+|..|    +. ..|....  ..-|-|.|.+.+.|.+||.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~-~~IEWId--DtScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGP-FRIEWID--DTSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCC-ceEEEec--CCcEEEEECCHHHHHHHHHcC
Confidence            479999995 68999999999999    43 2333322  235789999999999999865

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=82.86  E-value=2.1  Score=44.64  Aligned_cols=62  Identities=19%  Similarity=0.282  Sum_probs=45.8

Q ss_pred             CHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcc--ccccCCceeeEeecCCC
Q 002823          160 EDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ--NKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       160 TEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Ln--g~~l~Gr~L~V~~A~pk  222 (876)
                      ..+.|+++|..|+.+..+.. -++-+-..|.|.+.++|.+|...|+  +..+.|..++|.|+.+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~-L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSP-LKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEE-ETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEE-cCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            35789999999998888774 3455668999999999999999999  88999999999998543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=82.50  E-value=2.6  Score=43.93  Aligned_cols=63  Identities=16%  Similarity=0.227  Sum_probs=45.5

Q ss_pred             cHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhC--CceeCCeEEEEEeecCch
Q 002823          245 SNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELN--SRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       245 TeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~Ln--G~~I~Gr~IkVs~A~~k~  308 (876)
                      ..+.|+++|..|+.+..+..-+. =+-..|.|.+.++|.+|...|+  +..+.|..++|-|+....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            45789999999999888665332 3358899999999999999999  999999999999996543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=80.91  E-value=1.1  Score=55.19  Aligned_cols=74  Identities=14%  Similarity=0.209  Sum_probs=61.4

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCcee--CCeEEEEEeecCch
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYI--AGKQIKLEPSHLRG  308 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I--~Gr~IkVs~A~~k~  308 (876)
                      +.++.|.+-..+-.-|..+|.+||.|.+.+. -+.-..|.|+|...+.|..|+.+|+|+++  -|-+.+|.+++.-.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wt-lr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWT-LRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhhee-cccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            3445556667778889999999999999875 33456899999999999999999999886  58889999998754

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=80.61  E-value=1.7  Score=47.14  Aligned_cols=59  Identities=14%  Similarity=0.209  Sum_probs=51.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccc
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQN  206 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng  206 (876)
                      ..|||.||...+..+.|...|++||+|....    ..++..+-++|.|...-.|.+|++.+.-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhcc
Confidence            6899999999999999999999999886543    5677888899999999999999987743

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	876
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		4e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-05
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		7e-05
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		6e-04

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 40/162 (24%), Positives = 72/162 (44%), Gaps = 15/162 (9%)
Query: 141 LNDEHPSRT-LLLRKINSNIEDSELKALFEQYGDVRTF-----YRASKHCGFVTISYYDI 194
           +ND   S T L++  +  +  D EL ALF   G + T      Y+     G+  + +   
Sbjct: 7   MNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSE 66
Query: 195 RAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFG 254
             ++ A+K L     R+ +L + Y+     P  + I    L V NL  ++++D+L  IFG
Sbjct: 67  XDSQRAIKVLNGITVRNKRLKVSYA----RPGGESIKDTNLYVTNLPRTITDDQLDTIFG 122
Query: 255 VYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRELNS 291
            YG I +      K+  +     ++ +     A+ A+  LN+
Sbjct: 123 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN 164

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/152 (23%), Positives = 68/152 (44%), Gaps = 14/152 (9%)
Query: 150 LLLRKINSNIEDSELKALFEQYGDVRTF-----YRASKHCGFVTISYYDIRAARNAMKSL 204
           L++  +  ++ D EL ALF   G + T      Y+     G+  + +     ++ A+K L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 205 QNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE 264
                R+ +L + Y+     P  + I    L V NL  ++++D+L  IFG YG I +   
Sbjct: 66  NGITVRNKRLKVSYA----RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 265 TPQKIHQK-----YIEFYDTRAAEAALRELNS 291
              K+  +     ++ +     A+ A+  LN+
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNN 153

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 33/111 (29%), Positives = 49/111 (44%)
Query: 191 YYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELH 250
           Y D  +A +  K+L+    +    +I    PK   S+KE +  TL+  NL   V+ DEL 
Sbjct: 52  YVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELK 111
Query: 251 HIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL 301
            +F    EI+ + +  +     YIEF     AE    E     I G+ I L
Sbjct: 112 EVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 48/175 (27%), Positives = 76/175 (43%), Gaps = 18/175 (10%)
Query: 138 GEHLNDEHPSRT---LLLRKINSNIEDSELK-ALFEQYG-------DVRTFYRASKHCGF 186
           G H+ +   S T   L +  +N N   +ELK A+ E +        DVRT    ++  G+
Sbjct: 1   GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT--GTNRKFGY 58
Query: 187 VTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSN 246
           V     D  +A +  K+L+    +    +I    PK   S+K     TL+  NL  +++ 
Sbjct: 59  V-----DFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITE 113
Query: 247 DELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL 301
           DEL  +F    EI+ + +  +     YIEF     AE  L E     I G+ + L
Sbjct: 114 DELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	876
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-21
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-20
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-19
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-19
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-04
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-19
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-05
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-13
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-10
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-12
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-05
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-12
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-12
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-05
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-07
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	5e-11
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	6e-05
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-11
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-11
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-06
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	9e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-10
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-10
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-04
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-06
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-04
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	6e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-04
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	9e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-06
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-06
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-05
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-04
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-09
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-06
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-09
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-09
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-06
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-09
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-05
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	6e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-04
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-09
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	8e-09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-06
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	8e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	6e-04
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-09
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-08
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	8e-04
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	3e-08
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	3e-08
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-08
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-04
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-08
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-04
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	7e-08
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-08
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	8e-08
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	8e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	9e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-04
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-07
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-06
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-07
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-07
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-07
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	7e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	6e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-06
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	6e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	6e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-07
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	8e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-06
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-06
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-06
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-06
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-06
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-05
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	9e-06
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-06
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-06
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-06
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-06
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	9e-06
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-04
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-06
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-05
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	1e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-05
2div_A	99	TRNA selenocysteine associated protein; structural	2e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-05
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-05
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	4e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-05
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-05
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-05
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-05
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-04
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	7e-04

>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 Length = 205

 Score = 92.8 bits (230), Expect = 1e-21
 Identities = 31/201 (15%), Positives = 58/201 (28%), Gaps = 40/201 (19%)

Query: 146 PSRTLLLRKIN-SNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSL 204
            S  L++  ++ S +    +  +F  YG+V          G   +   D  A   A+  L
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62

Query: 205 QNKLTRSGKLDIHYS------------IPKDNPSEKEINQG------------------- 233
            N      K+++  S            +   + S K+ ++                    
Sbjct: 63  NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122

Query: 234 --TLVVFNLDSSVSNDELHHIFGVYG-----EIKEIRETPQKIHQKYIEFYDTRAAEAAL 286
              L  FN    V+ +    I    G      +K      ++     +E+     A   L
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182

Query: 287 RELNSRYIAGKQIKLEPSHLR 307
             LN   +        P  L+
Sbjct: 183 GFLNHYQMKNPNGPY-PYTLK 202

>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 Length = 205

 Score = 67.8 bits (165), Expect = 5e-13
 Identities = 24/140 (17%), Positives = 56/140 (40%), Gaps = 6/140 (4%)

Query: 234 TLVVFNLD-SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSR 292
            L+V+ LD S ++ D + ++F +YG +++++    K     +E  D  A + A+  LN+ 
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNN 65

Query: 293 YIAGKQIKLEPSHLRGLRKCLANQLP---PELEQEECGSYQQQNSPPNKPTNE--SAGMI 347
           ++ G+++ +  S    +    +  L       +        + ++P     N       +
Sbjct: 66  FMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNV 125

Query: 348 TIVISLPLNVKSLAIIYLFT 367
               + PL V       +  
Sbjct: 126 LHFFNAPLEVTEENFFEICD 145

>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 Length = 175

 Score = 88.4 bits (220), Expect = 2e-20
 Identities = 33/170 (19%), Positives = 65/170 (38%), Gaps = 18/170 (10%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVR---------TFYRASKHCGFVTISYYDIRAA 197
           +  + + ++     + +L+ LFEQYG V               SK C FVT  +Y  +AA
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVT--FYTRKAA 60

Query: 198 RNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYG 257
             A  +L N     G        P D+     +    L +  +    + +++  +F  +G
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG 120

Query: 258 EIKEIR--ETPQKIHQKY--IEFYDTRAAEAALRELNSRYI---AGKQIK 300
           +I+E R    P  + +    + F     A+ A++ ++           + 
Sbjct: 121 QIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170

>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 Length = 175

 Score = 55.3 bits (134), Expect = 6e-09
 Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKY--IEFYDTRAAE 283
           +   + V  +  + S  +L  +F  YG + EI     R       +    + FY  +AA 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 284 AALRELNSRYIAGKQIK 300
            A   L++  +      
Sbjct: 62  EAQNALHNMKVLPGMHH 78

>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 Length = 175

 Score = 85.0 bits (211), Expect = 4e-19
 Identities = 34/176 (19%), Positives = 65/176 (36%), Gaps = 17/176 (9%)

Query: 142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY------RASKHCGFVTISYYDIR 195
           ++      L +  +N N   +ELK    +                ++  G+V   +    
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVD--FESAE 65

Query: 196 AARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGV 255
               A++ L        ++ +     +D+   +     TL+  NL  +++ DEL  +F  
Sbjct: 66  DLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAAR--TLLAKNLSFNITEDELKEVFED 122

Query: 256 YGEIKEIRETPQKIHQK---YIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG 308
             EI+ + +  +    K   YIEF     AE  L E     I G+ + L  +  +G
Sbjct: 123 ALEIRLVSQDGKS---KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>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 Length = 175

 Score = 57.6 bits (140), Expect = 8e-10
 Identities = 20/93 (21%), Positives = 31/93 (33%), Gaps = 7/93 (7%)

Query: 224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYD 278
               +      L + NL+ + S  EL           ++               Y++F  
Sbjct: 5   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFES 63

Query: 279 TRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK 311
               E AL EL    + G +IKLE    R  +K
Sbjct: 64  AEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKK 95

>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 Length = 175

 Score = 43.7 bits (104), Expect = 6e-05
 Identities = 23/139 (16%), Positives = 48/139 (34%), Gaps = 27/139 (19%)

Query: 91  DMDDL-DFFSSVGG------MDLGNDSS----YV-------AQKKSEICIGFSNHELGV- 131
            + +L    S +        +D+   ++    YV        +K     +  +  ++   
Sbjct: 26  SVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK----ALELTGLKVFGN 81

Query: 132 ---CNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVT 188
                     +       +RTLL + ++ NI + ELK +FE   ++R   +  K  G   
Sbjct: 82  EIKLEKPKGRDSKKVR-AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAY 140

Query: 189 ISYYDIRAARNAMKSLQNK 207
           I +     A   ++  Q  
Sbjct: 141 IEFKSEADAEKNLEEKQGA 159

>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 Length = 229

 Score = 86.2 bits (213), Expect = 5e-19
 Identities = 33/190 (17%), Positives = 61/190 (32%), Gaps = 34/190 (17%)

Query: 146 PSRTLLLRKIN-SNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSL 204
            +  LL+  +N   +    L  LF  YGDV+             +   D   A+ AM  L
Sbjct: 33  GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHL 92

Query: 205 QNKLTRSGKLDIHYSIPKDNPSEKEINQG------------------------------- 233
                    + I  S  ++    +E  +                                
Sbjct: 93  NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 152

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEI-KEIRETPQKIHQKYIEFYDTRAAEAALRELNSR 292
           TL + N+  SVS ++L  +F   G + K  +   +      I+      A  AL +L++ 
Sbjct: 153 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 212

Query: 293 YIA-GKQIKL 301
            +     +++
Sbjct: 213 DLGENHHLRV 222

>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 Length = 229

 Score = 69.3 bits (169), Expect = 3e-13
 Identities = 33/147 (22%), Positives = 61/147 (41%), Gaps = 4/147 (2%)

Query: 225 PSEKEINQGTLVVFNLD-SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAE 283
           P         L+V NL+   V+   L  +FGVYG+++ ++    K     ++  D   A+
Sbjct: 27  PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQ 86

Query: 284 AALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNK--PTN 341
            A+  LN   + GK I++  S  + ++     Q    L ++   S   +   P      N
Sbjct: 87  LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 146

Query: 342 ESAGMITIVIS-LPLNVKSLAIIYLFT 367
                 T+ +S +P +V    +  LF+
Sbjct: 147 IFPPSATLHLSNIPPSVSEEDLKVLFS 173

>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 Length = 229

 Score = 43.1 bits (101), Expect = 1e-04
 Identities = 23/110 (20%), Positives = 40/110 (36%), Gaps = 6/110 (5%)

Query: 114 AQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYG- 172
            Q+   +   + N  L       +    N   PS TL L  I  ++ + +LK LF   G 
Sbjct: 118 GQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG 177

Query: 173 --DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN-KLTRSGKLDIHYS 219
                 F++  +    +      +  A  A+  L N  L  +  L + +S
Sbjct: 178 VVKGFKFFQKDRKMALIQ--MGSVEEAVQALIDLHNHDLGENHHLRVSFS 225

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 84.9 bits (210), Expect = 6e-19
 Identities = 33/189 (17%), Positives = 59/189 (31%), Gaps = 34/189 (17%)

Query: 147 SRTLLLRKIN-SNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ 205
           +  LL+  +N   +    L  LF  YGDV+             +   D   A+ AM  L 
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 206 NKLTRSGKLDIHYSIPKDNPSEKEINQG-------------------------------T 234
                   + I  S  ++    +E  +                                T
Sbjct: 63  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 122

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEI-KEIRETPQKIHQKYIEFYDTRAAEAALRELN-SR 292
           L + N+  SVS ++L  +F   G + K  +   +      I+      A  AL +L+   
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 182

Query: 293 YIAGKQIKL 301
                 +++
Sbjct: 183 LGENHHLRV 191

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 66.8 bits (163), Expect = 1e-12
 Identities = 32/142 (22%), Positives = 61/142 (42%), Gaps = 4/142 (2%)

Query: 230 INQGTLVVFNLD-SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRE 288
           +    L+V NL+   V+   L  +FGVYG+++ ++    K     ++  D   A+ A+  
Sbjct: 1   MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH 60

Query: 289 LNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNK--PTNESAGM 346
           LN   + GK I++  S  + ++     Q    L ++   S   +   P      N     
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 347 ITIVIS-LPLNVKSLAIIYLFT 367
            T+ +S +P +V    +  LF+
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFS 142

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 45.3 bits (107), Expect = 2e-05
 Identities = 24/110 (21%), Positives = 41/110 (37%), Gaps = 6/110 (5%)

Query: 114 AQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGD 173
            Q+   +   + N  L       +    N   PS TL L  I  ++ + +LK LF   G 
Sbjct: 87  GQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG 146

Query: 174 V---RTFYRASKHCGFVTISYYDIRAARNAMKSLQN-KLTRSGKLDIHYS 219
           V     F++  +    +      +  A  A+  L N  L  +  L + +S
Sbjct: 147 VVKGFKFFQKDRKMALIQ--MGSVEEAVQALIDLHNHDLGENHHLRVSFS 194

>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: 3h2u_B 3h2v_E Length = 284

 Score = 86.6 bits (215), Expect = 1e-18
 Identities = 30/195 (15%), Positives = 63/195 (32%), Gaps = 24/195 (12%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMK 202
                R +L+R +  ++ + E+  L   Y     F    K   FVT    +   A  A+ 
Sbjct: 18  QFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVT--LLNGEQAEAAIN 75

Query: 203 SLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI 262
           +      R  +L +                  L V NL  S++  +   +   +G ++  
Sbjct: 76  AFHQSRLRERELSVQLQPTDAL----------LCVANLPPSLTQQQFEELVRPFGSLERC 125

Query: 263 RETPQKIHQK-----YIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQ- 316
                +   +     + E+    +A  A  +L  + +  + + +  +    L   L +  
Sbjct: 126 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR 185

Query: 317 ------LPPELEQEE 325
                 LPP     +
Sbjct: 186 CLCVDRLPPGFNDVD 200

>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: 3h2u_B 3h2v_E Length = 284

 Score = 80.0 bits (198), Expect = 2e-16
 Identities = 26/196 (13%), Positives = 56/196 (28%), Gaps = 26/196 (13%)

Query: 155 INSNIEDSELKALFEQYGDVRT-------FYRASKHCGFVTISYYDIRAARNAMKSLQNK 207
           +  ++   + + L   +G +             SK  GF    Y    +A  A   L  K
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFA--EYMKKDSAARAKSDLLGK 160

Query: 208 LTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDE-LHHIFGVYGEIKEIRETP 266
                 L +H++      +   ++   L V  L    ++ + L             +   
Sbjct: 161 PLGPRTLYVHWTDAG-QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLAC 219

Query: 267 QKIHQK----YIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELE 322
            +  Q      +E+     AE A ++ +   + G  +++                 P   
Sbjct: 220 GQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS----------FC-APGPPGR 268

Query: 323 QEECGSYQQQNSPPNK 338
                    Q +  N+
Sbjct: 269 SMLAALIAAQATALNR 284

>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: 3h2u_B 3h2v_E Length = 284

 Score = 60.4 bits (147), Expect = 6e-10
 Identities = 20/107 (18%), Positives = 47/107 (43%), Gaps = 12/107 (11%)

Query: 223 DNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK----YIEFYD 278
           ++   +  N+  +++  L   V+N E+H +   Y  +K        + +     ++   +
Sbjct: 13  EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYC-----FVDKYKGTAFVTLLN 66

Query: 279 TRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEE 325
              AEAA+   +   +  +++ ++         C+AN LPP L Q++
Sbjct: 67  GEQAEAAINAFHQSRLRERELSVQLQP-TDALLCVAN-LPPSLTQQQ 111

>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 Length = 168

 Score = 79.2 bits (196), Expect = 3e-17
 Identities = 38/167 (22%), Positives = 67/167 (40%), Gaps = 18/167 (10%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY-------RASKHCGFVTISYYDIRAARN 199
           +  L++  +  ++ D EL ALF   G + T           S    FV   +     ++ 
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVD--FTSEMDSQR 60

Query: 200 AMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEI 259
           A+K L     R+ +L + Y+     P  + I    L V NL  ++++D+L  IFG YG I
Sbjct: 61  AIKVLNGITVRNKRLKVSYA----RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSI 116

Query: 260 KEIR--ETPQKIHQK---YIEFYDTRAAEAALRELNSRYIAGKQIKL 301
            +            +   ++ +     A+ A+  LN+    G    L
Sbjct: 117 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL 163

>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 Length = 168

 Score = 54.5 bits (132), Expect = 1e-08
 Identities = 19/104 (18%), Positives = 41/104 (39%), Gaps = 9/104 (8%)

Query: 231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAA 285
           +   L+V  L   +++ EL+ +F   G I   R              +++F     ++ A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 286 LRELNSRYIAGKQIKLEPSHLRGLRKCLAN----QLPPELEQEE 325
           ++ LN   +  K++K+  +   G      N     LP  +  ++
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQ 105

>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 Length = 167

 Score = 76.1 bits (188), Expect = 3e-16
 Identities = 36/160 (22%), Positives = 62/160 (38%), Gaps = 18/160 (11%)

Query: 155 INSNIEDSELKALFEQYGDVRTFY-------RASKHCGFVTISYYDIRAARNAMKSLQNK 207
           +  N+   E ++LF   G++ +           S   GFV   Y D + A  A+ +L   
Sbjct: 10  LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVN--YIDPKDAEKAINTLNGL 67

Query: 208 LTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR--ET 265
             ++  + + Y+ P    S   I    L V  L  +++  EL  +F  YG I   R    
Sbjct: 68  RLQTKTIKVSYARP----SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVD 123

Query: 266 PQKIHQK---YIEFYDTRAAEAALRELNSRYIAGKQIKLE 302
                 +   +I F     AE A++ LN +  +G    + 
Sbjct: 124 QVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 163

>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 Length = 167

 Score = 54.1 bits (131), Expect = 1e-08
 Identities = 26/104 (25%), Positives = 46/104 (44%), Gaps = 9/104 (8%)

Query: 231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKE---IRETPQKIHQKY--IEFYDTRAAEAA 285
           ++  L+V  L  +++ +E   +FG  GEI+    +R+        Y  + + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 286 LRELNSRYIAGKQIKLEPSHLRGLRKCLAN----QLPPELEQEE 325
           +  LN   +  K IK+  +         AN     LP  + Q+E
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKE 104

>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 Length = 292

 Score = 77.3 bits (191), Expect = 1e-15
 Identities = 34/237 (14%), Positives = 75/237 (31%), Gaps = 40/237 (16%)

Query: 96  DFFSSVGG-------MDLGNDSSY--VAQKKSEICIGFSNHE-----LGVCNGAVAGEHL 141
            +F   G          L  +  +  +          F+ ++     +   +  V    +
Sbjct: 60  KYFKHCGPIIHVDVADSLKKNFRFARIE---------FARYDGALAAITKTHKVVGQNEI 110

Query: 142 NDEH-PSRTLLLRKINSNIEDSELKALFEQYGDVRT---FYRAS--KHCGFVTISYYDIR 195
              H    TL +     +     ++ L +    V                F  I      
Sbjct: 111 IVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKE 170

Query: 196 AARNAMKSLQNKLTRSGKLDIHYSIP--KDNPSEKEINQG-TLVVFNLDSSVSN-DELHH 251
            AR  ++ L         L    S P  K   ++    +G  +++ NL + + + + L  
Sbjct: 171 DARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRE 230

Query: 252 IFGVYGEIKEIR---ETPQKIHQK---YIEFYDTRAAEAALRELNSRYIAGKQIKLE 302
            F  +G I++I       +        ++ F +  +AE AL ++N   +  ++I + 
Sbjct: 231 SFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVS 286

>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 Length = 292

 Score = 73.9 bits (182), Expect = 2e-14
 Identities = 26/164 (15%), Positives = 52/164 (31%), Gaps = 20/164 (12%)

Query: 149 TLLLRKINSNIEDSELKALFEQYG---DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ 205
           T+L++ +  +   +++   F+  G    V       K+  F  I +     A  A+    
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 102

Query: 206 NKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET 265
             +   G+ +I  S   +          TL + N   S +   +  +      +      
Sbjct: 103 KVV---GQNEIIVSHLTEC---------TLWMTNFPPSYTQRNIRDLLQDINVVALSIRL 150

Query: 266 PQKIHQK-----YIEFYDTRAAEAALRELNSRYIAGKQIKLEPS 304
           P           YI+      A   + +LN   I G  +  + S
Sbjct: 151 PSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS 194

>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 Length = 292

 Score = 56.9 bits (138), Expect = 7e-09
 Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 5/86 (5%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK---YIEFY 277
             +  +       T++V NL  S + ++++  F   G I  +              IEF 
Sbjct: 31  ANEALTRNR-ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFA 89

Query: 278 DTRAAEAALRELNSRYIAGKQIKLEP 303
               A AA+ + + + +   +I +  
Sbjct: 90  RYDGALAAITKTH-KVVGQNEIIVSH 114

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 74.6 bits (184), Expect = 2e-15
 Identities = 35/201 (17%), Positives = 77/201 (38%), Gaps = 14/201 (6%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRT-------FYRASKHCGFVTISYYDIR 195
             +P  +L +  ++ ++ ++ L   F   G + +         R S    +V   +    
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN--FQQPA 68

Query: 196 AARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGV 255
            A  A+ ++   + +   + I +S     PS ++   G + + NLD S+ N  L+  F  
Sbjct: 69  DAERALDTMNFDVIKGKPVRIMWSQRD--PSLRKSGVGNIFIKNLDKSIDNKALYDTFSA 126

Query: 256 YGEIKEIRETPQKIHQK---YIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKC 312
           +G I   +    +   K   ++ F    AAE A+ ++N   +  +++ +     R  R+ 
Sbjct: 127 FGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 186

Query: 313 LANQLPPELEQEECGSYQQQN 333
                  E    +   Y   +
Sbjct: 187 ELGARAKEFYPYDVPDYAGSS 207

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 62.3 bits (152), Expect = 4e-11
 Identities = 25/87 (28%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYD 278
           NPS       +L V +L   V+   L+  F   G I  IR     I ++     Y+ F  
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 279 TRAAEAALRELNSRYIAGKQIKLEPSH 305
              AE AL  +N   I GK +++  S 
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMWSQ 93

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 70.0 bits (172), Expect = 1e-13
 Identities = 25/178 (14%), Positives = 68/178 (38%), Gaps = 21/178 (11%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVR-------TFYRASKHCGFVTISYYDIR 195
                  + +  I   + +  ++  F  +G ++       +     K   FV   Y    
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE--YEVPE 81

Query: 196 AARNAMKSLQNKLTRSGKLDIHYSIPK-------DNPSEKEINQGTLVVFNLDSSVSNDE 248
           AA+ A++ + + +     + +             D  +E+      + V ++   +S+D+
Sbjct: 82  AAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDD 141

Query: 249 LHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRELNSRYIAGKQIKL 301
           +  +F  +G+IK           K     +IE+   ++++ A+  +N   + G+ +++
Sbjct: 142 IKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 59.6 bits (145), Expect = 3e-10
 Identities = 22/108 (20%), Positives = 42/108 (38%), Gaps = 5/108 (4%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIE 275
                         + V ++   +  D +   F  +G IK I  +   +  K     ++E
Sbjct: 17  SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76

Query: 276 FYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQ 323
           +    AA+ AL ++NS  + G+ IK+      G  + + +QL  E   
Sbjct: 77  YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124

>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 Length = 172

 Score = 68.4 bits (168), Expect = 2e-13
 Identities = 26/175 (14%), Positives = 56/175 (32%), Gaps = 32/175 (18%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA------------SKHCGFVTISYYDI 194
           +R L +  I   I +  +   F     +    +A             K+  F+   +  +
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE--FRSV 61

Query: 195 RAARNAMKSLQNKLTRSGK-LDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIF 253
                AM    + +   G+ L I                  L +  L + +++D++  + 
Sbjct: 62  DETTQAMAF--DGIIFQGQSLKIRRPHDYQPLP----GAHKLFIGGLPNYLNDDQVKELL 115

Query: 254 GVYGEIKEIR-----ETPQKIHQK---YIEFYDTRAAEAALRELNSRYIAGKQIK 300
             +G +K         T      K   + E+ D    + A+  LN   +  K++ 
Sbjct: 116 TSFGPLKAFNLVKDSATGLS---KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167

>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} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 64.3 bits (157), Expect = 1e-12
 Identities = 25/108 (23%), Positives = 51/108 (47%), Gaps = 5/108 (4%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIR--ETPQKIHQKYIEFYDTRAAEAALRELNS 291
            L + NL   ++ +E++ IFG YG I++IR   TP+     Y+ + D   A+ A+  L+ 
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69

Query: 292 RYIAGKQIKLEPSHL-RGLRKCLANQLPPELEQEECGSYQQQNSPPNK 338
             ++ + + +   +  R  +K    +   +L+  +       N+ P K
Sbjct: 70  FNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLK--EKYGINTDPPK 115

>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} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 53.1 bits (128), Expect = 1e-08
 Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 6/88 (6%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAM 201
            +R L +R +   I   E+  +F +YG +R         ++   +V   Y DI  A+NA+
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVV--YEDIFDAKNAV 64

Query: 202 KSLQNKLTRSGKLDIHYSIPKDNPSEKE 229
             L      +  L + Y        + +
Sbjct: 65  DHLSGFNVSNRYLVVLYYNANRAFQKMD 92

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 65.6 bits (161), Expect = 1e-12
 Identities = 25/166 (15%), Positives = 66/166 (39%), Gaps = 17/166 (10%)

Query: 148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKS 203
           R L +  ++  I +  LK  F+  G +        + +K+  +  + Y+    A  A+++
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 204 LQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR 263
           L  K   +  + I+++           +   L V +L+ +V ++ L + F  +       
Sbjct: 61  LNGKQIENNIVKINWAFQS--QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118

Query: 264 -----ETPQKIHQK---YIEFYDTRAAEAALRELNSRYIAGKQIKL 301
                +T      +   ++ F     A+ A+  +  + + G+ +++
Sbjct: 119 VMWDMQTGSS---RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161

>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* ... Length = 97

 Score = 63.0 bits (154), Expect = 2e-12
 Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 6/86 (6%)

Query: 143 DEHPSRTLLLRKINSNIEDSELK----ALFEQYGDVR--TFYRASKHCGFVTISYYDIRA 196
           +  P+ T+ +  +N  I+  ELK    A+F ++G +      R+ K  G   + + ++ +
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63

Query: 197 ARNAMKSLQNKLTRSGKLDIHYSIPK 222
           A NA++S+Q        + I Y+   
Sbjct: 64  ATNALRSMQGFPFYDKPMRIQYAKTD 89

>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* ... Length = 97

 Score = 56.5 bits (137), Expect = 4e-10
 Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 12/90 (13%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDEL----HHIFGVYGEIKEIR--ETPQKIHQK 272
           ++P+  P+       T+ + NL+  +  DEL    H IF  +G+I +I    + +   Q 
Sbjct: 1   AVPETRPNH------TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQA 54

Query: 273 YIEFYDTRAAEAALRELNSRYIAGKQIKLE 302
           ++ F +  +A  ALR +       K ++++
Sbjct: 55  FVIFKEVSSATNALRSMQGFPFYDKPMRIQ 84

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 62.7 bits (153), Expect = 3e-12
 Identities = 29/113 (25%), Positives = 49/113 (43%), Gaps = 8/113 (7%)

Query: 201 MKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIK 260
           M S  +    S  L    S    +  E E++   L V      V   EL+ IFG +G +K
Sbjct: 1   MGSSHHHHHHSSGLVPRGS-HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMK 59

Query: 261 EIRETPQKIHQKY--IEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK 311
           E+     KI   +  +EF +  +A  A+ E++ +  A + +++  S L   R 
Sbjct: 60  EV-----KILNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 20/112 (17%), Positives = 41/112 (36%), Gaps = 11/112 (9%)

Query: 114 AQKKSEICIGFSNHELGVCNGAVAGEHLNDEHPSRT-LLLRKINSNIEDSELKALFEQYG 172
           +            H  G+        H  +   S T L +R    ++++SEL  +F  +G
Sbjct: 4   SHHHHH-------HSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFG 56

Query: 173 DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDN 224
            +    +      FV   + +  +A  A++ +  K   +  L++ YS     
Sbjct: 57  PM-KEVKILNGFAFVE--FEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 65.1 bits (159), Expect = 4e-12
 Identities = 27/191 (14%), Positives = 59/191 (30%), Gaps = 40/191 (20%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA------------SKHCGFVTISYYD 193
            +R L +  I   I +  +   F     +    +A             K+  F+   +  
Sbjct: 3   MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE--FRS 60

Query: 194 IRAARNAM---------KSL-----QNKLTRSGKLDIHYSIPKDNPSEKEINQG-TLVVF 238
           +     AM         +SL      +     G  +          S    +    L + 
Sbjct: 61  VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIG 120

Query: 239 NLDSSVSNDELHHIFGVYGEIKEIR-----ETPQKIHQK---YIEFYDTRAAEAALRELN 290
            L + +++D++  +   +G +K         T      K   + E+ D    + A+  LN
Sbjct: 121 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS---KGYAFCEYVDINVTDQAIAGLN 177

Query: 291 SRYIAGKQIKL 301
              +  K++ +
Sbjct: 178 GMQLGDKKLLV 188

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.3 bits (152), Expect = 5e-12
 Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK---YIEFYDTR 280
              E +    TL V NL   V+   +  +F   G  K  +   +        ++EFY+ R
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66

Query: 281 AAEAALRELNSRYIAGKQIKLEPSHLRGLRK 311
            A AAL  +N R I GK++K+  +     +K
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWATTPSSQK 97

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 62.2 bits (151), Expect = 8e-12
 Identities = 15/88 (17%), Positives = 34/88 (38%), Gaps = 7/88 (7%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDEL----HHIFGVYGEIKEIR--ETPQKIHQKYI 274
               P   E +Q  +++ N++  V  ++L    + +    G+I +I    +     + YI
Sbjct: 19  LGSTPPHTEPSQ-VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYI 77

Query: 275 EFYDTRAAEAALRELNSRYIAGKQIKLE 302
            F    +A+A +         G  + + 
Sbjct: 78  VFATQESAQAFVEAFQGYPFQGNPLVIT 105

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 61.1 bits (148), Expect = 2e-11
 Identities = 17/94 (18%), Positives = 37/94 (39%), Gaps = 6/94 (6%)

Query: 142 NDEHPSRTLLLRKINSNIEDSELK----ALFEQYGDVRTFY--RASKHCGFVTISYYDIR 195
               PS+ +L+  IN  +   +L+    AL    GD+       +  + G   I +    
Sbjct: 24  PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQE 83

Query: 196 AARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKE 229
           +A+  +++ Q    +   L I +S    +   ++
Sbjct: 84  SAQAFVEAFQGYPFQGNPLVITFSETPQSQVAED 117

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 61.1 bits (149), Expect = 1e-11
 Identities = 24/88 (27%), Positives = 39/88 (44%)

Query: 224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAE 283
             S+K     TL+  NL  +++ DEL  +F    EI+ + +  +     YIEF     AE
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 284 AALRELNSRYIAGKQIKLEPSHLRGLRK 311
             L E     I G+ + L  +  +G  +
Sbjct: 68  KNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 53.4 bits (129), Expect = 5e-09
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 4/85 (4%)

Query: 144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR--ASKHCGFVTISYYDIRAARNAM 201
              +RTLL + ++ NI + ELK +FE   ++R   +   SK   ++   +     A   +
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIE--FKSEADAEKNL 70

Query: 202 KSLQNKLTRSGKLDIHYSIPKDNPS 226
           +  Q        + ++Y+  K    
Sbjct: 71  EEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 Length = 150

 Score = 62.6 bits (152), Expect = 1e-11
 Identities = 30/134 (22%), Positives = 50/134 (37%), Gaps = 12/134 (8%)

Query: 184 CGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEI------------N 231
            G  T    D   A    K   N     G+     +      +E                
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPL 72

Query: 232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS 291
              + V NL ++ +  EL   FG YG ++ +          ++EF D R A  A+REL+ 
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDG 132

Query: 292 RYIAGKQIKLEPSH 305
           R + G ++++E S+
Sbjct: 133 RTLCGCRVRVELSN 146

>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 Length = 150

 Score = 44.9 bits (106), Expect = 1e-05
 Identities = 16/69 (23%), Positives = 32/69 (46%)

Query: 139 EHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAAR 198
            H +       + +  + +N   +EL+  F  YG +R+ + A    GF  + + D R A 
Sbjct: 65  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAA 124

Query: 199 NAMKSLQNK 207
           +A++ L  +
Sbjct: 125 DAVRELDGR 133

>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 Length = 261

 Score = 64.7 bits (158), Expect = 1e-11
 Identities = 38/196 (19%), Positives = 67/196 (34%), Gaps = 30/196 (15%)

Query: 155 INSNIEDSELKALFEQYGDVRT-FYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGK 213
           + ++I + + K LFE+YG+    F    +  GF+         A  A   L   + +S  
Sbjct: 30  LPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIR--LESRTLAEIAKAELDGTILKSRP 87

Query: 214 LDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR----ETPQKI 269
           L I ++               L V NL   VSN+ L   F  +G +++      +     
Sbjct: 88  LRIRFATHGAA----------LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR--GR 135

Query: 270 HQKY--IEFYDTRAAEAALRELNSRYI----AGKQIKLEPSHLRGLRKCLANQLPPELEQ 323
                 +EF     A  AL              + + +EP         L  +L  + +Q
Sbjct: 136 ATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQ 195

Query: 324 EECGSYQQQNSPPNKP 339
                Y ++   P + 
Sbjct: 196 -----YHKEREQPPRF 206

>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 Length = 261

 Score = 58.2 bits (141), Expect = 2e-09
 Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 221 PKDNPSEKEINQGT-LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK---YIEF 276
               P EK   Q   L V NL + ++ ++   +F  YGE  E+         +   +I  
Sbjct: 10  SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVF----INRDRGFGFIRL 65

Query: 277 YDTRAAEAALRELNSRYIAGKQIK 300
                AE A  EL+   +  + ++
Sbjct: 66  ESRTLAEIAKAELDGTILKSRPLR 89

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 60.0 bits (146), Expect = 3e-11
 Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
           T  + N+    +  +L  +F  +G I + +  P+K    +I++     A   +  L +  
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK-GCCFIKYDTHEQAAVCIVALANFP 87

Query: 294 IAGKQIKL 301
             G+ ++ 
Sbjct: 88  FQGRNLRT 95

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 43.5 bits (103), Expect = 2e-05
 Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 155 INSNIEDSELKALFEQYG---DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNK 207
           I     +++L  LF+ +G   D + +    K C F+   Y     A   + +L N 
Sbjct: 35  IPHFATEADLIPLFQNFGFILDFKHY--PEKGCCFIK--YDTHEQAAVCIVALANF 86

>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 Length = 97

 Score = 59.6 bits (145), Expect = 4e-11
 Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 1/68 (1%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
            L V  L  + S   L   F  +G I+ I          YI++    AA+AA  ++    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD-SFAYIQYESLDAAQAACAKMRGFP 77

Query: 294 IAGKQIKL 301
           + G   +L
Sbjct: 78  LGGPDRRL 85

>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 Length = 97

 Score = 55.7 bits (135), Expect = 7e-10
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 3/82 (3%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTF-YRASKHCGFVTISYYDIRAARNAMKSL 204
           P+  L +  +  N   + L   F+++G +RT  +       ++   Y  + AA+ A   +
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQ--YESLDAAQAACAKM 73

Query: 205 QNKLTRSGKLDIHYSIPKDNPS 226
           +          +     K  PS
Sbjct: 74  RGFPLGGPDRRLRVDFAKSGPS 95

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 59.5 bits (144), Expect = 4e-11
 Identities = 21/104 (20%), Positives = 41/104 (39%), Gaps = 5/104 (4%)

Query: 133 NGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDV-RTFYRASKHCGFVTISY 191
            G+    H     PSR + +RK+  ++ + E+ +L   +G V        K+  F+    
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFI--EM 59

Query: 192 YDIRAARNAMKSLQNK--LTRSGKLDIHYSIPKDNPSEKEINQG 233
               AA   +    +   + R   + I +S  K+  ++   NQ 
Sbjct: 60  NTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 103

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.5 bits (113), Expect = 8e-07
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALREL--NS 291
            + +  L   V+  E+  +   +G++  +     K +Q +IE     AA   +      +
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVT 76

Query: 292 RYIAGKQIKLEPSHLRGLRK 311
             + G+ I ++ S+ + L+ 
Sbjct: 77  PVLRGQPIYIQFSNHKELKT 96

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 60.1 bits (145), Expect = 5e-11
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 221 PKDNPSEKEINQGTLV-VFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDT 279
           P +       N+  L+ + N    ++ D L+ +    G+++ I    +   Q  +EF   
Sbjct: 13  PGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESV 72

Query: 280 RAAEAALRELNSRYIAGKQIKLEPSHLR 307
             A+ A   LN   I      L+  + R
Sbjct: 73  LCAQKAKAALNGADIYAGCCTLKIEYAR 100

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 42.7 bits (100), Expect = 6e-05
 Identities = 14/86 (16%), Positives = 28/86 (32%), Gaps = 4/86 (4%)

Query: 142 NDEHPSRTLLL--RKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARN 199
           +    ++ LLL  +     I    L  +    G V+      ++     + +  +  A+ 
Sbjct: 18  DPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQK 77

Query: 200 AMKSLQNK--LTRSGKLDIHYSIPKD 223
           A  +L           L I Y+ P  
Sbjct: 78  AKAALNGADIYAGCCTLKIEYARPTR 103

>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 Length = 111

 Score = 59.4 bits (144), Expect = 6e-11
 Identities = 17/104 (16%), Positives = 33/104 (31%), Gaps = 5/104 (4%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
            ++  NL +     E+   F  +G +  +      I    +EF +   A  A R L    
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT-AIVEFLEPLEARKAFRHLAYSK 70

Query: 294 IAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPN 337
                + LE                 +  Q E  + + ++ P +
Sbjct: 71  FHHVPLYLE----WAPIGVFGAAPQKKDSQHEQPAEKAESGPSS 110

>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 Length = 111

 Score = 51.0 bits (122), Expect = 5e-08
 Identities = 11/71 (15%), Positives = 25/71 (35%), Gaps = 3/71 (4%)

Query: 138 GEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDV-RTFYRASKHCGFVTISYYDIRA 196
           G   +       +L + + +    +E++  F ++G + R           V   + +   
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVE--FLEPLE 58

Query: 197 ARNAMKSLQNK 207
           AR A + L   
Sbjct: 59  ARKAFRHLAYS 69

>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 Length = 103

 Score = 58.8 bits (143), Expect = 7e-11
 Identities = 23/106 (21%), Positives = 46/106 (43%), Gaps = 18/106 (16%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFYDTRAAEAALRELNS 291
            L V NL ++V+ + L   F  +G+++ +     K  + Y  I F +   A  A+ E+N 
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERV-----KKLKDYAFIHFDERDGAVKAMEEMNG 67

Query: 292 RYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPN 337
           + + G+ I++            A + P +  +E     Q  + P +
Sbjct: 68  KDLEGENIEIV----------FA-KPPDQKRKERKAQRQAASGPSS 102

>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 Length = 103

 Score = 45.3 bits (108), Expect = 4e-06
 Identities = 16/87 (18%), Positives = 37/87 (42%), Gaps = 3/87 (3%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ 205
             + L +R + + + +  L+  F Q+G +    +  K   F+   + +   A  AM+ + 
Sbjct: 10  KVKVLFVRNLANTVTEEILEKAFSQFGKL-ERVKKLKDYAFIH--FDERDGAVKAMEEMN 66

Query: 206 NKLTRSGKLDIHYSIPKDNPSEKEINQ 232
            K      ++I ++ P D   ++   Q
Sbjct: 67  GKDLEGENIEIVFAKPPDQKRKERKAQ 93

>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 Length = 109

 Score = 58.9 bits (143), Expect = 9e-11
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 223 DNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAA 282
           D  ++      T+    + S +++  +   F  +G+I EIR  P+K    ++ F    +A
Sbjct: 16  DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-GYSFVRFSTHESA 74

Query: 283 EAALRELNSRYIAGKQIKL 301
             A+  +N   I G  +K 
Sbjct: 75  AHAIVSVNGTTIEGHVVKC 93

>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 Length = 196

 Score = 61.2 bits (149), Expect = 1e-10
 Identities = 30/172 (17%), Positives = 64/172 (37%), Gaps = 20/172 (11%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHC---GFVTISYYDIR 195
           +    R L +  ++    D  L++ FEQ+G +          +K     GFVT  Y  + 
Sbjct: 9   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT--YATVE 66

Query: 196 AARNAMKSLQNKLTRSGK-LDIHYSIPKDNPSEKEINQGTLVVF--NLDSSVSNDELHHI 252
               AM +  +K+   G+ ++   ++ +++      +     +F   +        L   
Sbjct: 67  EVDAAMNARPHKV--DGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124

Query: 253 FGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQI 299
           F  YG+I+ I     R + +K    ++ F D  + +  +       + G   
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNC 175

>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 Length = 93

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
            L + NL  +V+ D+L  +FG         +   K    ++++ D   A  A+  L+ + 
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRKLPLA-GQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 68

Query: 294 -IAGKQIKLEPSHLRGLRK 311
            + GK ++++ S  + LR 
Sbjct: 69  ELHGKIMEVDYSVSKKLRS 87

>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 Length = 93

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 4/74 (5%)

Query: 155 INSNIEDSELKALFEQYGDVRT-FYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGK 213
           ++  +   +L+ LF                  FV   Y D   A  A+++L  K+   GK
Sbjct: 16  LSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVD--YPDQNWAIRAIETLSGKVELHGK 73

Query: 214 -LDIHYSIPKDNPS 226
            +++ YS+ K   S
Sbjct: 74  IMEVDYSVSKKLRS 87

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 58.1 bits (141), Expect = 1e-10
 Identities = 21/72 (29%), Positives = 34/72 (47%)

Query: 239 NLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQ 298
           NL +     EL   F  YG ++ +          ++EF D R AE A+R L+ + I G +
Sbjct: 7   NLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSR 66

Query: 299 IKLEPSHLRGLR 310
           +++E S     R
Sbjct: 67  VRVELSTGMPRR 78

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 16/53 (30%), Positives = 26/53 (49%)

Query: 155 INSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNK 207
           + +     EL+  F  YG +RT + A    GF  + + D R A +A++ L  K
Sbjct: 8   LGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK 60

>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 Length = 119

 Score = 58.4 bits (141), Expect = 2e-10
 Identities = 21/104 (20%), Positives = 42/104 (40%), Gaps = 5/104 (4%)

Query: 133 NGAVAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTF-YRASKHCGFVTISY 191
            G+  G+  +   PSR + +RK+  ++ + E+ +L   +G V        K+  F+    
Sbjct: 17  RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFI--EM 74

Query: 192 YDIRAARNAMKSLQ-NKLTRSGK-LDIHYSIPKDNPSEKEINQG 233
               AA   +           G+ + I +S  K+  ++   NQ 
Sbjct: 75  NTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 118

>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 Length = 119

 Score = 46.4 bits (110), Expect = 3e-06
 Identities = 13/73 (17%), Positives = 30/73 (41%), Gaps = 3/73 (4%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALR--ELNS 291
            + +  L   V+  E+  +   +G++  +     K +Q +IE     AA   +      +
Sbjct: 33  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVT 91

Query: 292 RYIAGKQIKLEPS 304
             + G+ I ++ S
Sbjct: 92  PVLRGQPIYIQFS 104

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 56.8 bits (138), Expect = 3e-10
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 237 VFNLDS-SVSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFYDTRAAEAALRELNSRY 293
           + NL   +VS ++L  IF  YG I +I      I   +  I+F + ++   A+   +   
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQIN-----IKNAFGFIQFDNPQSVRDAIECESQEM 69

Query: 294 IAGKQIKLEPSH 305
             GK++ LE S 
Sbjct: 70  NFGKKLILEVSS 81

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 158 NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH 217
           N+   +L  +F  YG +          GF+   + + ++ R+A++    ++    KL + 
Sbjct: 22  NVSKEDLFRIFSPYGHIMQI-NIKNAFGFIQ--FDNPQSVRDAIECESQEMNFGKKLILE 78

Query: 218 YSIPKDNPSEKEINQGT 234
            S     P     + GT
Sbjct: 79  VSSSNARPQFDHGDHGT 95

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 57.0 bits (138), Expect = 3e-10
 Identities = 22/107 (20%), Positives = 38/107 (35%), Gaps = 12/107 (11%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALRE 288
            +    L+ +V    L  +   YGE++E+       T + +    + F  TR A+  ++ 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 289 LNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSP 335
           L+   + G  I  +       R           E    GSY  Q  P
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRM-------KYYELIVNGSYTPQTVP 107

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 51.2 bits (123), Expect = 4e-08
 Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 5/67 (7%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNA 200
           P + +   ++N N+ ++ LK +  +YG+V         R  KH G   + +   R A+  
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64

Query: 201 MKSLQNK 207
           +K+L   
Sbjct: 65  VKNLHLT 71

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

 Score = 62.9 bits (152), Expect = 4e-10
 Identities = 96/720 (13%), Positives = 182/720 (25%), Gaps = 241/720 (33%)

Query: 209 TRSGKLDIHYSIPKDNPSEKEINQGTLVVF--NLDSSVSNDELHHIFGVYGEIKEIRETP 266
             +G+    Y         K+I       F  N D     D    I     EI  I  + 
Sbjct: 9   FETGEHQYQY---------KDILSVFEDAFVDNFDCKDVQDMPKSILSK-EEIDHIIMSK 58

Query: 267 QKIHQKYIEF-----YDTRAAEAALREL---NSRYIAGKQIKLEPSHLRGLRKCLANQLP 318
             +      F           +  + E+   N +++    IK E             Q  
Sbjct: 59  DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM-SPIKTEQ-----------RQ-- 104

Query: 319 PELEQEECGSYQ---QQNSPPNKPTN-ESAGMITIVISLPLNVKSLAIIYLFTGAFAHG- 373
           P +        +     ++      N         +    L ++    + +       G 
Sbjct: 105 PSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI------DGV 158

Query: 374 ---SKSSRITDTCIVSVVPSAVKAPPTESAFHLGI--------SSSVPSLVRMESFGTQ- 421
               K+          V      +   +      I        +S    L  ++    Q 
Sbjct: 159 LGSGKTW---------VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209

Query: 422 --SALAEPGH----------LQGQLKFNIRSTPSFHPHSL--------PECHDGLNKGVR 461
             +  +   H          +Q +L+  ++S P  + + L         +  +  N  + 
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP--YENCLLVLLNVQNAKAWNAFN--LS 265

Query: 462 C-------NSSGTKGANINIKPPEIIDSRHFSRVSSNGHSIGFTE-----VFGSASNGSC 509
           C           T          + + +   + +S + HS+  T      +         
Sbjct: 266 CKILLTTRFKQVT----------DFLSAATTTHISLDHHSMTLTPDEVKSLLLK------ 309

Query: 510 PRPGHQYSWNNSYCPQLPGMMWPNSPSLVSGIFNTYSPTRVHGLPRAPSHMVNTVLPIGS 569
                   + +     LP  +   +P  +S I                            
Sbjct: 310 --------YLDCRPQDLPREVLTTNPRRLSII---------------------------- 333

Query: 570 HHVGSAPTVDPSLWER-QHAYVAESPEASGFHLGSHGSMRISNNSLHSVE----FVSHNI 624
                +     + W+  +H    +              +  S N L   E    F   ++
Sbjct: 334 ---AESIRDGLATWDNWKHVNCDKLTTI----------IESSLNVLEPAEYRKMFDRLSV 380

Query: 625 FPCVGGNGMDMPLPSK--------------NSVFQSHHQRSMMFSGRGQ---TIP---LM 664
           FP          +P+                 V    H+ S++     +   +IP   L 
Sbjct: 381 FP------PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLE 434

Query: 665 NSFDPPNERARNRRNEGAVNQ-ADKKQYELDIDRILRGEDNRTTLMIKNIPNKYTSKML- 722
                 NE A +R     V+     K ++ D D I    D             Y    + 
Sbjct: 435 LKVKLENEYALHRS---IVDHYNIPKTFDSD-DLIPPYLDQ------------YFYSHIG 478

Query: 723 --LAAIDERHKGTYDF--IYLPIDF-KNK-CNVGYAFINMTDPSQIVPFYQSFNGKKWEK 776
             L  I+   + T  F  ++L   F + K  +   A+        I+   Q    K ++ 
Sbjct: 479 HHLKNIEHPERMTL-FRMVFLDFRFLEQKIRHDSTAW---NASGSILNTLQQL--KFYKP 532

Query: 777 FNSEKVASLAYARIQGKAALIAHF---QNSSLMNEDKRC--RPILFNTDGP---NAGDQV 828
           +  +      Y R+      I  F      +L+        R  L   D      A  QV
Sbjct: 533 YICDN--DPKYERLVN---AILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587

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

 Score = 46.0 bits (108), Expect = 6e-05
 Identities = 44/318 (13%), Positives = 85/318 (26%), Gaps = 99/318 (31%)

Query: 14  LSELFSRKLRLSSDIASYGHS---VDTVSSHYEEEEPFESLEEIEAQTIGNLLPDDDDLF 70
           L  L   K         Y +    +  V +  +    F     +  +    LL       
Sbjct: 234 LRRLLKSK--------PYENCLLVLLNVQNA-KAWNAFN----LSCKI---LLTTRF--- 274

Query: 71  SGVTDGL-------ECTVHPSGGSGGDDMDDLDFFSSVGGM---DLGNDSSYVAQKKSEI 120
             VTD L           H S     D++  L            DL            E+
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSL--LLKYLDCRPQDL----------PREV 322

Query: 121 CIGFSNHELGVCNGAVAGEHLNDEHPSR-----TLLLRKINSNIEDSELKALFEQYGDVR 175
                 +   +   ++  E + D   +       +   K+ + IE S L  L  +  + R
Sbjct: 323 LTT---NPRRL---SIIAESIRD-GLATWDNWKHVNCDKLTTIIESS-LNVL--EPAEYR 372

Query: 176 TFYRASKHCG-F---VTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEIN 231
             +        F     I                     +  L + +     +     +N
Sbjct: 373 KMFDR---LSVFPPSAHIP--------------------TILLSLIWFDVIKSDVMVVVN 409

Query: 232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAA---EAALRE 288
           +  L  ++L      +    I  +Y E+K   E    +H+  ++ Y+       +  +  
Sbjct: 410 K--LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPP 467

Query: 289 LNSRYIAGKQIKLEPSHL 306
              +Y          SH+
Sbjct: 468 YLDQYFY--------SHI 477

>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 Length = 110

 Score = 56.2 bits (136), Expect = 6e-10
 Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 8/86 (9%)

Query: 223 DNPSEKEINQGTLVVFNLDSS-VSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFYDT 279
            N ++ +     + + NL+++ V   ++  IF  YG +         +H+ Y  +++ + 
Sbjct: 18  TNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGC-----SVHKGYAFVQYSNE 72

Query: 280 RAAEAALRELNSRYIAGKQIKLEPSH 305
           R A AA+   N R +AG+ + +  + 
Sbjct: 73  RHARAAVLGENGRVLAGQTLDINMAG 98

>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 Length = 110

 Score = 39.7 bits (93), Expect = 4e-04
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 157 SNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI 216
           + ++ S+++ +F +YG V       K   FV   Y + R AR A+     ++     LDI
Sbjct: 38  ALVKKSDVETIFSKYGRVAGC-SVHKGYAFVQ--YSNERHARAAVLGENGRVLAGQTLDI 94

Query: 217 HYSIPKDNP 225
           + +      
Sbjct: 95  NMAGEPKPD 103

>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 Length = 156

 Score = 57.1 bits (138), Expect = 9e-10
 Identities = 21/100 (21%), Positives = 42/100 (42%), Gaps = 5/100 (5%)

Query: 210 RSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RE 264
            S   D H+    +   +      TL V NL    + ++++ +F   G+IK+I     + 
Sbjct: 17  LSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM 76

Query: 265 TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS 304
                   ++E+Y    AE A+R +N   +  + I+ +  
Sbjct: 77  KKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD 116

>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 Length = 97

 Score = 55.4 bits (134), Expect = 1e-09
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 237 VFNLDS-SVSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFYDTRAAEAALRELNSRY 293
           + NL   +VS ++L  IF  YG I +I      I   +  I+F + ++   A+   +   
Sbjct: 27  IGNLPLKNVSKEDLFRIFSPYGHIMQI-----NIKNAFGFIQFDNPQSVRDAIEXESQEM 81

Query: 294 IAGKQIKLEPSH 305
             GK++ LE S 
Sbjct: 82  NFGKKLILEVSS 93

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 55.4 bits (134), Expect = 1e-09
 Identities = 28/96 (29%), Positives = 38/96 (39%), Gaps = 7/96 (7%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-RETPQKIHQK---YI 274
           S      S       TLV+ NL  S + + L  +F     IK    +  +    K   +I
Sbjct: 2   SSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKS---KGYAFI 58

Query: 275 EFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLR 310
           EF     A+ AL   N R I G+ I+LE    RG  
Sbjct: 59  EFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP 94

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 11/65 (16%), Positives = 28/65 (43%), Gaps = 5/65 (7%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHC---GFVTISYYDIRAARNAMK 202
            S+TL+L  ++ +  +  L+ +FE+   ++     +       F+   +     A+ A+ 
Sbjct: 14  ESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIE--FASFEDAKEALN 71

Query: 203 SLQNK 207
           S   +
Sbjct: 72  SCNKR 76

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 55.4 bits (134), Expect = 1e-09
 Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 6/85 (7%)

Query: 221 PKDNPSEKEINQGT-LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFY 277
              +  E  ++    L V NL  S S + +   F         R    K  + Y  + F 
Sbjct: 3   SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV---KKIRDYAFVHFS 59

Query: 278 DTRAAEAALRELNSRYIAGKQIKLE 302
           +   A  A++ LN + + G  I++ 
Sbjct: 60  NREDAVEAMKALNGKVLDGSPIEVT 84

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 46.9 bits (112), Expect = 1e-06
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 3/82 (3%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVR-TFYRASKHCGFVTISYYDIRAARNAMKSL 204
             + L +R +  +  +  ++  F           +  +   FV   + +   A  AMK+L
Sbjct: 14  SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVH--FSNREDAVEAMKAL 71

Query: 205 QNKLTRSGKLDIHYSIPKDNPS 226
             K+     +++  + P D  S
Sbjct: 72  NGKVLDGSPIEVTLAKPVDKDS 93

>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} Length = 88

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIR------ETPQKIHQKYIEFYDTRAAEAALR 287
            + +  L  +V+ D +  IF  YG+IK I                Y+EF +   AE AL+
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 288 ELNSRYIAGKQIK 300
            ++   I G++I 
Sbjct: 66  HMDGGQIDGQEIT 78

>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 Length = 99

 Score = 55.0 bits (133), Expect = 1e-09
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 225 PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK---YIEFYDTRA 281
             +    +  L V NL   ++ +E+  +F  YG+  E+         K   +I       
Sbjct: 8   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF----IHKDKGFGFIRLETRTL 63

Query: 282 AEAALRELNSRYIAGKQIKLE 302
           AE A  EL++  + GKQ+++ 
Sbjct: 64  AEIAKVELDNMPLRGKQLRVR 84

>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 Length = 99

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 3/63 (4%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDV-RTFYRASKHCGFVTISYYDIRAARNAMKSL 204
               L +  +  +I + E++ LFE+YG     F    K  GF+         A  A   L
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIR--LETRTLAEIAKVEL 71

Query: 205 QNK 207
            N 
Sbjct: 72  DNM 74

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 55.0 bits (133), Expect = 1e-09
 Identities = 16/87 (18%), Positives = 34/87 (39%), Gaps = 8/87 (9%)

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEA 284
             L + NL+ S + + L  +F   G IK       +     +      ++E+     A+ 
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 285 ALRELNSRYIAGKQIKLEPSHLRGLRK 311
           AL++L    + G ++++  S       
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERATKPA 92

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 12/93 (12%)

Query: 144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRT----------FYRASKHCGFVTISYYD 193
              S  L ++ +N +  +  LK +F + G +++              S   GFV   Y  
Sbjct: 2   SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVE--YKK 59

Query: 194 IRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPS 226
              A+ A+K LQ       KL++  S     P+
Sbjct: 60  PEQAQKALKQLQGHTVDGHKLEVRISERATKPA 92

>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 Length = 109

 Score = 55.0 bits (133), Expect = 2e-09
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFYDTRAAEAALRE 288
           N   + V NL   +   ++  +F  YG I++I    ++    +  +EF D R AE A+  
Sbjct: 21  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 80

Query: 289 LNSRYIAGKQIKLEPSH 305
            +     G ++++E   
Sbjct: 81  RDGYDYDGYRLRVEFPR 97

>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 Length = 109

 Score = 42.7 bits (101), Expect = 4e-05
 Identities = 12/69 (17%), Positives = 26/69 (37%), Gaps = 6/69 (8%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAAR 198
             +    + +  +  +I   +++ +F +YG +R       R      FV   + D R A 
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVE--FEDPRDAE 75

Query: 199 NAMKSLQNK 207
           +A+      
Sbjct: 76  DAVYGRDGY 84

>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 Length = 167

 Score = 56.8 bits (138), Expect = 2e-09
 Identities = 27/168 (16%), Positives = 57/168 (33%), Gaps = 27/168 (16%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHC---GFVTISYYDIRAARN 199
           S  + +  +N +  +  L+  F +YG V         A+      GF++  +    +   
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLS--FEKPSSVDE 60

Query: 200 AMKS---LQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVY 256
            +K+   L  K      +D   +IP+D         G + V  +   V   E    F  +
Sbjct: 61  VVKTQHILDGK-----VIDPKRAIPRDEQD----KTGKIFVGGIGPDVRPKEFEEFFSQW 111

Query: 257 GEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRELNSRYIAGKQI 299
           G I + +    K   +     ++ +    A +    +        ++I
Sbjct: 112 GTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKI 158

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAE-AALRELNSR 292
           TL V  L  +++  +L + F  +GEI+ I    ++    +I+F   +AAE AA +  N  
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ-QCAFIQFATRQAAEVAAEKSFNKL 72

Query: 293 YIAGKQIKL 301
            + G+++ +
Sbjct: 73  IVNGRRLNV 81

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 148 RTLLLRKINSNIEDSELKALFEQYGDVRT-FYRASKHCGFVTISYYDIRAARNAMKSLQN 206
            TL +  +   I +++L+  F Q+G++RT      + C F+   +   +AA  A +   N
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQ--FATRQAAEVAAEKSFN 70

Query: 207 KLTRSGK 213
           KL  +G+
Sbjct: 71  KLIVNGR 77

>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

 Score = 55.0 bits (133), Expect = 2e-09
 Identities = 21/98 (21%), Positives = 42/98 (42%), Gaps = 12/98 (12%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK--- 272
           P DN S +E +  T+    L + +   +L   F   G+++++     R +      K   
Sbjct: 14  PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSR---RSKGIA 70

Query: 273 YIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLR 310
           Y+EF + ++   A+  L  + + G  I ++ S     R
Sbjct: 71  YVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNR 107

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 56.3 bits (135), Expect = 2e-09
 Identities = 28/152 (18%), Positives = 62/152 (40%), Gaps = 4/152 (2%)

Query: 190 SYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLV-VFNLDSSVSNDE 248
            ++   +A+ A++++ +  + +  L    +      +    +    + V NL   V+ D 
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV 62

Query: 249 LHHIFGVYGEIKEIRETPQKIH-QKYIEFYDTRAAEAALRELNSRYI--AGKQIKLEPSH 305
           LH IF  +G + +I    +    Q  +++ D  +A+ A   L+ + I  A   ++++ S 
Sbjct: 63  LHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 122

Query: 306 LRGLRKCLANQLPPELEQEECGSYQQQNSPPN 337
           L  L     N    +  + +  S   Q S   
Sbjct: 123 LTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQ 154

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 237 VFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFYDTRAAEAALRELNSRYI 294
           V N+  + +N EL   F  YG + E       I + Y  +       A  A+R L++   
Sbjct: 15  VGNISPTCTNQELRAKFEEYGPVIEC-----DIVKDYAFVHMERAEDAVEAIRGLDNTEF 69

Query: 295 AGKQIKLEPSHLR 307
            GK++ ++ S  R
Sbjct: 70  QGKRMHVQLSTSR 82

>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} Length = 143

 Score = 54.8 bits (132), Expect = 4e-09
 Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 18/97 (18%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKE----------IRETPQKIHQKYIEFYDTRAAE 283
            + V NL   V   +L +IFG Y +             + +  +   Q +I   + +AA 
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 284 AALRELNSRYIAGKQIKLE--------PSHLRGLRKC 312
            AL+E N   + GK + ++             G RKC
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSARPKQDPKEGKRKC 143

>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} Length = 143

 Score = 47.9 bits (114), Expect = 1e-06
 Identities = 12/96 (12%), Positives = 38/96 (39%), Gaps = 14/96 (14%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA------------SKHCGFVTISYYD 193
           P+  + ++ +  ++++ +LK +F +Y D  +  +              K   F+ +   +
Sbjct: 44  PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLP--N 101

Query: 194 IRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKE 229
            +AA  A+K     +     + + ++       + +
Sbjct: 102 EKAAAKALKEANGYVLFGKPMVVQFARSARPKQDPK 137

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 53.1 bits (128), Expect = 6e-09
 Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 3/68 (4%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
           TL V+  D  ++   L   F  +G I ++   P + +  ++ +    +A+ A+ ELN   
Sbjct: 17  TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESADQAVAELNGTQ 73

Query: 294 IAGKQIKL 301
           +   Q+K+
Sbjct: 74  VESVQLKV 81

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 41.5 bits (98), Expect = 7e-05
 Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 7/55 (12%)

Query: 156 NSNIEDSELKALFEQYG---DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNK 207
             ++  + L+  F  +G   D+       ++C FVT  Y  + +A  A+  L   
Sbjct: 22  GEDMTPTLLRGAFSPFGNIIDLSMD--PPRNCAFVT--YEKMESADQAVAELNGT 72

>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 Length = 115

 Score = 53.4 bits (129), Expect = 7e-09
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALRE 288
            L + NL   V+  +L  +F  + E K         T +   Q +I F +   A  AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 289 LNSRYIAGKQIKLE 302
           +N   + GK + +E
Sbjct: 87  VNGYKLYGKILVIE 100

>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 Length = 115

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 9/88 (10%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-------RASKHCGFVTISYYDIRAAR 198
           P++ L L+ ++  + + +L +LF ++ + +             +   F+T  + +   A 
Sbjct: 24  PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFIT--FPNKEIAW 81

Query: 199 NAMKSLQNKLTRSGKLDIHYSIPKDNPS 226
            A+  +         L I +   K   S
Sbjct: 82  QALHLVNGYKLYGKILVIEFGKNKKQRS 109

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 52.8 bits (127), Expect = 8e-09
 Identities = 18/73 (24%), Positives = 27/73 (36%), Gaps = 3/73 (4%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSR- 292
            + +  L   V   +L      +G I  +   P+K  Q  +EF D   A  A+       
Sbjct: 23  VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK-RQALVEFEDVLGACNAVNYAADNQ 81

Query: 293 -YIAGKQIKLEPS 304
            YIAG    +  S
Sbjct: 82  IYIAGHPAFVNYS 94

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.9 bits (109), Expect = 2e-06
 Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 5/80 (6%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTF-YRASKHCGFVTISYYDIRAARNAMKSL 204
            S  + +R +   + +++L    +++G +        K    V   + D+  A NA+   
Sbjct: 20  ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALV--EFEDVLGACNAVNYA 77

Query: 205 QNK--LTRSGKLDIHYSIPK 222
            +           ++YS  +
Sbjct: 78  ADNQIYIAGHPAFVNYSTSQ 97

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 52.6 bits (127), Expect = 8e-09
 Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 7/69 (10%)

Query: 239 NLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFYDTRAAEAALRELNSRYIAG 296
           NL    +  E+  +F  YG++ E       I + Y  +   D  AAE A+R L+   + G
Sbjct: 15  NLPREATEQEIRSLFEQYGKVLEC-----DIIKNYGFVHIEDKTAAEDAIRNLHHYKLHG 69

Query: 297 KQIKLEPSH 305
             I +E S 
Sbjct: 70  VNINVEASK 78

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 155 INSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNK 207
           +     + E+++LFEQYG V       K+ GFV     D  AA +A+++L + 
Sbjct: 16  LPREATEQEIRSLFEQYGKVLEC-DIIKNYGFVH--IEDKTAAEDAIRNLHHY 65

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 53.6 bits (129), Expect = 9e-09
 Identities = 28/117 (23%), Positives = 51/117 (43%), Gaps = 13/117 (11%)

Query: 196 AARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGV 255
           A    M++  +K+T     +     P     +KEI++ ++ V N+D   +  +L   F  
Sbjct: 1   AIAPCMQTTHSKMTAGAYTEGP-PQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS 59

Query: 256 YGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAALRELNSRYIAGKQIKLEPS 304
            G I  I     + +    H K   YIEF +  + +AA+  ++     G+ IK+ P 
Sbjct: 60  CGSINRITILCDKFSG---HPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK 112

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 237 VFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY--IEFYDTRAAEAALRELNSRYI 294
           V N+ ++ ++ EL  +F   G + E       + + Y  +       A+AA+ +LN + +
Sbjct: 14  VGNVSAACTSQELRSLFERRGRVIEC-----DVVKDYAFVHMEKEADAKAAIAQLNGKEV 68

Query: 295 AGKQIKLEPSHLRGLR 310
            GK+I +E S     +
Sbjct: 69  KGKRINVELSTKGQKK 84

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 38.3 bits (90), Expect = 8e-04
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 3/81 (3%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ 205
            +  + +  +++     EL++LFE+ G V       K   FV         A+ A+  L 
Sbjct: 8   NTWKIFVGNVSAACTSQELRSLFERRGRVIEC-DVVKDYAFVH--MEKEADAKAAIAQLN 64

Query: 206 NKLTRSGKLDIHYSIPKDNPS 226
            K  +  ++++  S      S
Sbjct: 65  GKEVKGKRINVELSTKGQKKS 85

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 52.1 bits (125), Expect = 2e-08
 Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 4/66 (6%)

Query: 142 NDEHPSRTLLLRKINSNIEDSELKALFEQYG--DVRTFYRASKHCGFVTISYYDIRAARN 199
                +  + +  +  +   S+LK    + G   +R  ++  +   F+   Y D  AA+ 
Sbjct: 14  EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLH--YPDSAAAQQ 71

Query: 200 AMKSLQ 205
           A+  LQ
Sbjct: 72  AVSCLQ 77

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 50.6 bits (121), Expect = 5e-08
 Identities = 13/85 (15%), Positives = 28/85 (32%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTR 280
           P   P E       + V NL       +L       G +           + ++ + D+ 
Sbjct: 8   PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSA 67

Query: 281 AAEAALRELNSRYIAGKQIKLEPSH 305
           AA+ A+  L    +    +++  + 
Sbjct: 68  AAQQAVSCLQGLRLGTDTLRVALAR 92

>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 Length = 88

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 2/74 (2%)

Query: 231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELN 290
               ++V NL    +  E+H +   Y    +     +     ++   +   A+ A++  +
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYD--LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFH 61

Query: 291 SRYIAGKQIKLEPS 304
                GK + ++  
Sbjct: 62  QYSFRGKDLIVQLQ 75

>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 Length = 88

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN 206
           S  +L++ +  +    E+  L + Y     +   +K   FVT    +   A+NA++    
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVT--LLNGEQAQNAIQMFHQ 62

Query: 207 KLTRSGKLDIHYS 219
              R   L +   
Sbjct: 63  YSFRGKDLIVQLQ 75

>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 Length = 104

 Score = 51.7 bits (124), Expect = 2e-08
 Identities = 19/73 (26%), Positives = 29/73 (39%), Gaps = 3/73 (4%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSR- 292
            + V  L  SV   +L      +G I  +   P K  Q  +EF +  +A+  +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK-RQALVEFENIDSAKECVTFAADVP 75

Query: 293 -YIAGKQIKLEPS 304
            YIAG+Q     S
Sbjct: 76  VYIAGQQAFFNYS 88

>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 Length = 104

 Score = 49.4 bits (118), Expect = 1e-07
 Identities = 13/80 (16%), Positives = 33/80 (41%), Gaps = 5/80 (6%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-RASKHCGFVTISYYDIRAARNAMKSL 204
            S  + +R +  ++ +++L    E++G +        K    V   + +I +A+  +   
Sbjct: 14  VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALV--EFENIDSAKECVTFA 71

Query: 205 Q-NKLTRSGK-LDIHYSIPK 222
               +  +G+    +YS  K
Sbjct: 72  ADVPVYIAGQQAFFNYSTSK 91

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 52.3 bits (125), Expect = 3e-08
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIH-QKYIEFYDTRAAEAALRELNSRY 293
           ++V NL   V+ D LH IF  +G + +I    +    Q  +++ D  +A+ A   L+ + 
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 90

Query: 294 I--AGKQIKLEPSHLRGL 309
           I  A   ++++ S L  L
Sbjct: 91  IYNACCTLRIDFSKLTSL 108

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 51.2 bits (122), Expect = 3e-08
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 7/86 (8%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN 206
           S  LLL+ + + I+   L+ L  Q+G + +F+      G     Y     A  A  +L N
Sbjct: 7   SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ-GIALCKYTTREEANKAQMALNN 65

Query: 207 KLTRSGKLDIHYSIPKDNPSEKEINQ 232
            +  +       +I  ++PSE E+  
Sbjct: 66  CVLANT------TIFAESPSENEVQS 85

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 51.5 bits (124), Expect = 3e-08
 Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 11/82 (13%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAA 285
           TL V NL    S D L  +F  YG + ++       T      +   ++ F+D R A+ A
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAP---RGFAFVRFHDRRDAQDA 71

Query: 286 LRELNSRYIAGKQIKLEPSHLR 307
              ++   + G++++++ +   
Sbjct: 72  EAAMDGAELDGRELRVQVARYG 93

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 9/72 (12%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-------RASKHCGFVTISYYDIR 195
           D     TL +  +        L+ +FE+YG V   Y       +A +   FV   ++D R
Sbjct: 9   DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR--FHDRR 66

Query: 196 AARNAMKSLQNK 207
            A++A  ++   
Sbjct: 67  DAQDAEAAMDGA 78

>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* Length = 110

 Score = 50.8 bits (122), Expect = 5e-08
 Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 11/86 (12%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAA 285
            L V ++      DE+   F  YGEIK I     R T      K    +E+   + A AA
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS---KGYALVEYETHKQALAA 84

Query: 286 LRELNSRYIAGKQIKLEPSHLRGLRK 311
              LN   I G+ I+++   ++G ++
Sbjct: 85  KEALNGAEIMGQTIQVDWCFVKGPKR 110

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 52.1 bits (125), Expect = 5e-08
 Identities = 27/135 (20%), Positives = 51/135 (37%), Gaps = 20/135 (14%)

Query: 185 GFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQG---------TL 235
           G  T    D   A    K   N     G+     +      +E   +           +L
Sbjct: 14  GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSL 73

Query: 236 VVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAALR 287
            V NL    S D L  +F  YG + ++     R T +    +   ++ F+D R AE A+ 
Sbjct: 74  KVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKES---RGFAFVRFHDKRDAEDAMD 130

Query: 288 ELNSRYIAGKQIKLE 302
            ++   + G++++++
Sbjct: 131 AMDGAVLDGRELRVQ 145

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 21/95 (22%), Positives = 35/95 (36%), Gaps = 7/95 (7%)

Query: 223 DNPSEKEINQGTLVVF--NLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK----YIEF 276
           ++P E   +     +F  NL+ + S  EL           ++     +        Y++F
Sbjct: 6   EDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 65

Query: 277 YDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK 311
                 E AL EL    + G +IKLE    R   +
Sbjct: 66  ESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGTR 99

>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 Length = 99

 Score = 50.3 bits (121), Expect = 6e-08
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 11/83 (13%)

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEA 284
           G L V NL  + S ++L  +F  YG + E+       T +    K   ++ F     A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKP---KGFAFVTFMFPEHAVK 65

Query: 285 ALRELNSRYIAGKQIKLEPSHLR 307
           A  E++ +   G+ + + PS ++
Sbjct: 66  AYAEVDGQVFQGRMLHVLPSTIK 88

>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 Length = 99

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 9/69 (13%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-------RASKHCGFVTISYYDIRAAR 198
            S  L +R ++    + +L+ LF  YG +   +       +  K   FVT  +     A 
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVT--FMFPEHAV 64

Query: 199 NAMKSLQNK 207
            A   +  +
Sbjct: 65  KAYAEVDGQ 73

>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 Length = 105

 Score = 50.3 bits (121), Expect = 7e-08
 Identities = 23/84 (27%), Positives = 35/84 (41%), Gaps = 9/84 (10%)

Query: 224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKY--IEF 276
            P  +     T+ V  LD  VS   L  +F   G +        R T Q  HQ Y  +EF
Sbjct: 7   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQ--HQGYGFVEF 64

Query: 277 YDTRAAEAALRELNSRYIAGKQIK 300
                A+ A++ ++   + GK I+
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIR 88

>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 Length = 165

 Score = 51.8 bits (124), Expect = 7e-08
 Identities = 24/99 (24%), Positives = 42/99 (42%), Gaps = 11/99 (11%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK--- 272
             +   ++ +    L V ++      DE+   F  YGEIK I     R T      K   
Sbjct: 61  ELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS---KGYA 117

Query: 273 YIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK 311
            +E+   + A AA   LN   I G+ I+++   ++G ++
Sbjct: 118 LVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 156

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 50.3 bits (121), Expect = 8e-08
 Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 3/91 (3%)

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK---YIEFYDTRAAEAALREL 289
           G + + NLD S+ N  L+  F  +G I   +    +   K   ++ F    AAE A+ ++
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65

Query: 290 NSRYIAGKQIKLEPSHLRGLRKCLANQLPPE 320
           N   +  +++ +     R  R+        E
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGARAKE 96

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 49.9 bits (120), Expect = 8e-08
 Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 15/88 (17%)

Query: 223 DNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK----- 272
              S     +  L V  L   V +  LH  F  +G+I +I      ET     +K     
Sbjct: 3   SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYET-----EKHRGFA 57

Query: 273 YIEFYDTRAAEAALRELNSRYIAGKQIK 300
           ++EF     A AA+  +N   + G+ I+
Sbjct: 58  FVEFELAEDAAAAIDNMNESELFGRTIR 85

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 49.8 bits (119), Expect = 9e-08
 Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 2/71 (2%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIR--ETPQKIHQKYIEFYDTRAAEAALRELNS 291
            L + N+   +  + L  +   YG ++      T  +     + +     A  AL +LN 
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNG 76

Query: 292 RYIAGKQIKLE 302
             +    +K+ 
Sbjct: 77  FQLENFTLKVA 87

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 40.1 bits (94), Expect = 3e-04
 Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTF----YRASKHCGFVTISYYDIRAARNAMK 202
            R L +R I  +++   L +L  QYG V +       +      VT  Y     AR A+ 
Sbjct: 15  IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVT--YSSKDQARQALD 72

Query: 203 SLQNKLTRSGKLDIHYSIPK 222
            L      +  L + Y   +
Sbjct: 73  KLNGFQLENFTLKVAYIPDE 92

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 49.6 bits (119), Expect = 1e-07
 Identities = 20/92 (21%), Positives = 43/92 (46%), Gaps = 9/92 (9%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK------ 272
           S        K+     ++V N+    +  E+  +F  +GE+K +R  P+K+         
Sbjct: 2   SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVR-LPKKMTGTGAHRGF 60

Query: 273 -YIEFYDTRAAEAALREL-NSRYIAGKQIKLE 302
            +++F   + A+ A   L +S ++ G+++ LE
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLE 92

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 44.6 bits (106), Expect = 7e-06
 Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 11/93 (11%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDV--------RTFYRASKHCGFVTISYYDI 194
            +  +  +L+R I       E++ LF  +G++         T   A +  GFV   +   
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD--FITK 68

Query: 195 RAARNAMKSLQNKLTRSGK-LDIHYSIPKDNPS 226
           + A+ A  +L +     G+ L + ++  +    
Sbjct: 69  QDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 50.2 bits (120), Expect = 2e-07
 Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 9/89 (10%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKY 273
           S            +  L V  L   V +  LH  F  +G+I +I      ET +K H+ +
Sbjct: 50  SGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYET-EK-HRGF 107

Query: 274 --IEFYDTRAAEAALRELNSRYIAGKQIK 300
             +EF     A AA+  +N   + G+ I+
Sbjct: 108 AFVEFELAEDAAAAIDNMNESELFGRTIR 136

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 9/74 (12%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKY--IEFYDTRAAEAAL 286
            L V  L   V +  LH  F  +G+I +I      ET +  H+ +  +EF     A AA+
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEK--HRGFAFVEFELAEDAAAAI 66

Query: 287 RELNSRYIAGKQIK 300
             +N   + G+ I+
Sbjct: 67  DNMNESELFGRTIR 80

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 49.3 bits (118), Expect = 2e-07
 Identities = 20/124 (16%), Positives = 49/124 (39%), Gaps = 16/124 (12%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----Y 273
           S       +   N   + V +L   ++ +++   F  +G I + R        K     +
Sbjct: 2   SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61

Query: 274 IEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQN 333
           + F++   AE A++++  +++ G+QI+   +  +           P   +    S  +Q+
Sbjct: 62  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK-----------PPAPKSTYESNTKQS 110

Query: 334 SPPN 337
            P +
Sbjct: 111 GPSS 114

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 15/77 (19%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK-----YIEFYDTRAAE 283
            L VF L    +  +L  +F  YG I ++     +++     ++     ++ F +   A+
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQS-----RRSRGFAFVYFENVDDAK 71

Query: 284 AALRELNSRYIAGKQIK 300
            A    N   + G++I+
Sbjct: 72  EAKERANGMELDGRRIR 88

>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 Length = 282

 Score = 52.2 bits (124), Expect = 2e-07
 Identities = 20/119 (16%), Positives = 48/119 (40%), Gaps = 9/119 (7%)

Query: 234 TLVVFNLDSSVSNDEL----HHIFGVYGEIKEIR--ETPQKIHQKYIEFYDTRAAEAALR 287
           T+ + NL+  +  DEL    + IF  +G+I +I    + +   Q ++ F +  +A  ALR
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 70

Query: 288 ELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGM 346
            +       K ++++ +           ++     + +    +++      P  + A  
Sbjct: 71  SMQGFPFYDKPMRIQYAKTDSDII---AKMKGTFVERDRKREKRKPKSQETPATKKAVQ 126

>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 Length = 282

 Score = 48.7 bits (115), Expect = 4e-06
 Identities = 21/98 (21%), Positives = 41/98 (41%), Gaps = 10/98 (10%)

Query: 143 DEHPSRTLLLRKINSNIEDSELK----ALFEQYGDVRTFY----RASKHCGFVTISYYDI 194
           +  P+ T+ +  +N  I+  ELK    A+F Q+G +           +   FV   + ++
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVI--FKEV 62

Query: 195 RAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQ 232
            +A NA++S+Q        + I Y+    +   K    
Sbjct: 63  SSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT 100

>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 Length = 282

 Score = 46.0 bits (108), Expect = 2e-05
 Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELN 290
               L + NL    +   L  +F  +   KE+R  P +    ++EF +   A AA   L 
Sbjct: 206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQ 265

Query: 291 SRYI-AGKQIKLE 302
              I     +K+ 
Sbjct: 266 GFKITQNNAMKIS 278

>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 Length = 282

 Score = 45.6 bits (107), Expect = 4e-05
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 139 EHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAAR 198
           + L++  P+  L L  +     +  L  LF Q+   +             + + +   A 
Sbjct: 199 QPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAG 258

Query: 199 NAMKSLQN-KLTRSGKLDIHYS 219
            A  +LQ  K+T++  + I ++
Sbjct: 259 AARDALQGFKITQNNAMKISFA 280

>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 Length = 114

 Score = 49.2 bits (117), Expect = 3e-07
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 234 TLVVFN--LDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS 291
           +LVV N  L + VS ++L  +    G +  +   P K +  +  +  T  ++ A   LN 
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPY-SFARYRTTEESKRAYVTLNG 85

Query: 292 RYIAGKQIKLEPSHLR 307
           + +     +    +L 
Sbjct: 86  KEVVDDLGQKITLYLN 101

>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 Length = 114

 Score = 48.4 bits (115), Expect = 4e-07
 Identities = 11/75 (14%), Positives = 28/75 (37%), Gaps = 5/75 (6%)

Query: 142 NDEHPSRTLLLR--KINSNIEDSELKALFEQYGDVRTFY-RASKHCGFVTISYYDIRAAR 198
              + +++L++    + + +  ++L  + E+ G V       +K   F    Y     ++
Sbjct: 20  TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFAR--YRTTEESK 77

Query: 199 NAMKSLQNKLTRSGK 213
            A  +L  K      
Sbjct: 78  RAYVTLNGKEVVDDL 92

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 48.8 bits (117), Expect = 3e-07
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 11/83 (13%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAA 285
            L V  +    + +++H  F  YGEIK I     R T      K    +E+   + A+AA
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL---KGYTLVEYETYKEAQAA 81

Query: 286 LRELNSRYIAGKQIKLEPSHLRG 308
           +  LN + + G+ I ++   +RG
Sbjct: 82  MEGLNGQDLMGQPISVDWCFVRG 104

>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* Length = 126

 Score = 49.3 bits (118), Expect = 3e-07
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 22/117 (18%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAA 285
            L V  +    + +++H  F  YGEIK I     R T      K    +E+   + A+AA
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL---KGYTLVEYETYKEAQAA 80

Query: 286 LRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNE 342
           +  LN + + G+ I ++   +RG         PP+ ++   G  ++  SP  +   E
Sbjct: 81  MEGLNGQDLMGQPISVDWCFVRG---------PPKGKRR--GGRRRSRSPDRRRRLE 126

>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 Length = 129

 Score = 49.0 bits (117), Expect = 4e-07
 Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 15/79 (18%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK-----YIEFYDTRAAE 283
            L VF L    +  +L  +F  YG I ++     +++     ++     ++ F +   A+
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQS-----RRSRGFAFVYFENVDDAK 102

Query: 284 AALRELNSRYIAGKQIKLE 302
            A    N   + G++I+++
Sbjct: 103 EAKERANGMELDGRRIRVD 121

>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 Length = 129

 Score = 39.7 bits (93), Expect = 7e-04
 Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 9/69 (13%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-------RASKHCGFVTISYYDIRAAR 198
           P+  L +  ++    + +L+ +F +YG +           R S+   FV   + ++  A+
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY--FENVDDAK 102

Query: 199 NAMKSLQNK 207
            A +     
Sbjct: 103 EAKERANGM 111

>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 Length = 101

 Score = 47.5 bits (113), Expect = 6e-07
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 9/88 (10%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA-SKHCGFVTISYYDIRAARNAMKSL 204
           PSR L +RK+   + ++E+ AL   +G V        K+  F+        AA   +   
Sbjct: 14  PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFL--ELATEEAAITMVNYY 71

Query: 205 Q-NKLTRSGK-LDIHYS----IPKDNPS 226
                    + + I YS    +    PS
Sbjct: 72  SAVTPHLRNQPIYIQYSNHKELKTSGPS 99

>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 Length = 101

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 13/73 (17%), Positives = 30/73 (41%), Gaps = 3/73 (4%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALR--ELNS 291
            L +  L   V+  E+  +   +G++  I     K +Q ++E     AA   +      +
Sbjct: 17  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-NQAFLELATEEAAITMVNYYSAVT 75

Query: 292 RYIAGKQIKLEPS 304
            ++  + I ++ S
Sbjct: 76  PHLRNQPIYIQYS 88

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 47.2 bits (113), Expect = 6e-07
 Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 11/75 (14%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAA 285
           T+ V NL  S++N++L+ IF  YG++ ++     ++T +    K   +I F D  +A+  
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKS---KGVAFILFLDKDSAQNC 74

Query: 286 LRELNSRYIAGKQIK 300
            R +N++ + G+ IK
Sbjct: 75  TRAINNKQLFGRVIK 89

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 47.6 bits (114), Expect = 6e-07
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 9/70 (12%)

Query: 237 VFNLDSSVSNDELHHIFGVYGEI---KEIRETPQKIHQK---YIEFYDTRAAEAALRELN 290
           V NLD  + ++ L   F  +G I   K + E  +    K   ++ F     A  A+ E+N
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGR---SKGFGFVCFSSPEEATKAVTEMN 76

Query: 291 SRYIAGKQIK 300
            R +A K + 
Sbjct: 77  GRIVATKPLY 86

>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} Length = 87

 Score = 46.8 bits (112), Expect = 7e-07
 Identities = 13/68 (19%), Positives = 32/68 (47%), Gaps = 5/68 (7%)

Query: 239 NLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRELNSRY 293
           +L   ++   +   F  +G I + R        K     ++ F++   AE A++++  ++
Sbjct: 13  DLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW 72

Query: 294 IAGKQIKL 301
           + G+QI+ 
Sbjct: 73  LGGRQIRT 80

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 47.2 bits (113), Expect = 8e-07
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 11/86 (12%)

Query: 225 PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEF 276
           P+ +  +  T+ V NL       +L  +F  +G I  I     + T Q    K   +I F
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQS---KGFAFISF 64

Query: 277 YDTRAAEAALRELNSRYIAGKQIKLE 302
           +    A  A+  ++        + +E
Sbjct: 65  HRREDAARAIAGVSGFGYDHLILNVE 90

>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 Length = 95

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 20/89 (22%), Positives = 31/89 (34%), Gaps = 5/89 (5%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIE 275
                S  +     + V N+  +VS DE+   F  Y  I                   + 
Sbjct: 4   GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 276 FYDTRAAEAALRELNSRYIAGKQIKLEPS 304
           F     A AA+ +LN R I  +++KL   
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 13/95 (13%)

Query: 222 KDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY-------- 273
             +      +  T+ V  L  +V+ + +   F   G IK  ++T Q +   Y        
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 274 -----IEFYDTRAAEAALRELNSRYIAGKQIKLEP 303
                + F D  +A+AA+   + +  +G  IK+  
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 8/97 (8%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI--RETPQKIHQK---Y 273
           S     P+ +     TL V  L    + + L   F      + +  RET      K   +
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSS---KGFGF 58

Query: 274 IEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLR 310
           ++F     A+AA   +    I G ++ L+ +  +G  
Sbjct: 59  VDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG 95

>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 Length = 111

 Score = 46.6 bits (111), Expect = 2e-06
 Identities = 16/101 (15%), Positives = 42/101 (41%), Gaps = 15/101 (14%)

Query: 142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTF----YRASKH---CGFVTISYYDI 194
           +D    +T+ +R ++ + E+  L  + +Q+GD++      +  ++H   C F    +   
Sbjct: 10  SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQ--FMTQ 67

Query: 195 RAARNAMKSLQNKLTRSGK------LDIHYSIPKDNPSEKE 229
            AA+  + +   +    G       L +  ++ +D  +   
Sbjct: 68  EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGP 108

>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 Length = 111

 Score = 42.7 bits (101), Expect = 4e-05
 Identities = 16/97 (16%), Positives = 35/97 (36%), Gaps = 17/97 (17%)

Query: 222 KDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---Y 273
                       T+ + NL      + L  +   +G++K +      +T    H K   +
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTE---HSKGCAF 61

Query: 274 IEFYDTRAAEAALRELNSR------YIAGKQIKLEPS 304
            +F    AA+  L   +         + G+Q+K++ +
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA 98

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 8/90 (8%), Positives = 33/90 (36%), Gaps = 7/90 (7%)

Query: 227 EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRA 281
           + ++   ++ +    +  + D++       G++  I+   + +H+      ++ F    +
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIES 64

Query: 282 AEAALRELNSRYIAGKQIKLEPSHLRGLRK 311
           A+  + E   +      + +        +K
Sbjct: 65  AKKFV-ETPGQKYKETDLLILFKDDYFAKK 93

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 46.5 bits (111), Expect = 2e-06
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 15/87 (17%)

Query: 224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK-----Y 273
             S    ++G L V  L    +   L  +F  YG+I E+     RET     Q+     +
Sbjct: 4   GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRET-----QRSRGFGF 58

Query: 274 IEFYDTRAAEAALRELNSRYIAGKQIK 300
           + F +   A+ A+  +N + + G+QI+
Sbjct: 59  VTFENIDDAKDAMMAMNGKSVDGRQIR 85

>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 Length = 89

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 12/80 (15%)

Query: 229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTR 280
           E +  ++ V N+D   + +EL   F   G +  +     + +    H K   YIEF D  
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSG---HPKGFAYIEFSDKE 59

Query: 281 AAEAALRELNSRYIAGKQIK 300
           +   +L  L+     G+QIK
Sbjct: 60  SVRTSL-ALDESLFRGRQIK 78

>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 Length = 106

 Score = 46.2 bits (110), Expect = 2e-06
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 9/67 (13%)

Query: 154 KINSNIEDSELKALFEQYGDVRTFY-------RASKHCGFVTISYYDIRAARNAMKSLQN 206
           +I  N+++ +LK LFE++G +              K C F+T  Y +  +A  A  +L  
Sbjct: 20  QIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT--YCERESALKAQSALHE 77

Query: 207 KLTRSGK 213
           + T  G 
Sbjct: 78  QKTLPGM 84

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 45.2 bits (108), Expect = 2e-06
 Identities = 9/73 (12%), Positives = 28/73 (38%), Gaps = 15/73 (20%)

Query: 239 NLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK-----YIEFYDTRAAEAALRE 288
           +L+ +V ++ L + F  +            +T            ++ F     A+ A+  
Sbjct: 8   DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQT-----GSSRGYGFVSFTSQDDAQNAMDS 62

Query: 289 LNSRYIAGKQIKL 301
           +  + + G+ +++
Sbjct: 63  MQGQDLNGRPLRI 75

>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 Length = 98

 Score = 45.7 bits (109), Expect = 3e-06
 Identities = 20/89 (22%), Positives = 31/89 (34%), Gaps = 5/89 (5%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIE 275
                S  +     + V N+  +VS DE+   F  Y  I                   + 
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 276 FYDTRAAEAALRELNSRYIAGKQIKLEPS 304
           F     A AA+ +LN R I  +++KL   
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLVLG 92

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 11/74 (14%), Positives = 31/74 (41%), Gaps = 15/74 (20%)

Query: 237 VFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK-----YIEFYDTRAAEAAL 286
           + ++    + +++  +    G +  +      +T      +     +IEF D  ++ +A+
Sbjct: 7   LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQT-----GRSKGYAFIEFRDLESSASAV 61

Query: 287 RELNSRYIAGKQIK 300
           R LN   +  + +K
Sbjct: 62  RNLNGYQLGSRFLK 75

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 45.3 bits (108), Expect = 4e-06
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 10/74 (13%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKY--IEFYDTRAAEAAL 286
           T+ V NL++ V  + L+ +F   G + ++     RE      + +  + F    +   A+
Sbjct: 18  TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG---KPKSFGFVCFKHPESVSYAI 74

Query: 287 RELNSRYIAGKQIK 300
             LN   + G+ I 
Sbjct: 75  ALLNGIRLYGRPIN 88

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 45.9 bits (109), Expect = 4e-06
 Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 13/88 (14%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY-------------IEFYDTR 280
           T+ V  L  +V+ + +   F   G IK  ++T Q +   Y             + F D  
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 281 AAEAALRELNSRYIAGKQIKLEPSHLRG 308
           +A+AA+   + +  +G  IK+  +  R 
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFATRRA 96

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 12/79 (15%)

Query: 231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI------RETPQKIHQK---YIEFYDTRA 281
               + + NLD  +    L+  F  +G I +        +T      K   +I F    A
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNS---KGYAFINFASFDA 60

Query: 282 AEAALRELNSRYIAGKQIK 300
           ++AA+  +N +Y+  + I 
Sbjct: 61  SDAAIEAMNGQYLCNRPIT 79

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 45.0 bits (107), Expect = 4e-06
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 4/75 (5%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK----YIEFYDTRAAEAALREL 289
            L +  L  S + +EL  I   +G +K++R    +  +     Y+E+ +   A  A+ ++
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78

Query: 290 NSRYIAGKQIKLEPS 304
           +   I    IK+  S
Sbjct: 79  DGMTIKENIIKVAIS 93

>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 Length = 105

 Score = 45.0 bits (107), Expect = 5e-06
 Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 8/77 (10%)

Query: 142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDV------RTFYRASKHCGFVTISYYDIR 195
           +     R L +  +N    + ++  LF+ +G +      R    +SK C FV   +    
Sbjct: 10  SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVK--FSSHT 67

Query: 196 AARNAMKSLQNKLTRSG 212
            A+ A+ +L    T  G
Sbjct: 68  EAQAAIHALHGSQTMPG 84

>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 Length = 105

 Score = 43.4 bits (103), Expect = 2e-05
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 224 NPSEKEINQGT-LVVFNLDSSVSNDELHHIFGVYGEIKEIR--ETPQKIHQKY--IEFYD 278
           + SE    +   L V  L+   S +++  +F  +G I E      P    +    ++F  
Sbjct: 6   SGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSS 65

Query: 279 TRAAEAALRELNSRYI 294
              A+AA+  L+    
Sbjct: 66  HTEAQAAIHALHGSQT 81

>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 Length = 103

 Score = 45.0 bits (107), Expect = 6e-06
 Identities = 18/90 (20%), Positives = 38/90 (42%), Gaps = 13/90 (14%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK- 272
           S      SE +     L V N+     + +L  +FG +G+I ++              K 
Sbjct: 2   SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-----KG 56

Query: 273 --YIEFYDTRAAEAALRELNSRYIAGKQIK 300
             ++ F ++  A+ A  +L+   + G++I+
Sbjct: 57  FGFVTFENSADADRAREKLHGTVVEGRKIE 86

>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 Length = 109

 Score = 45.2 bits (107), Expect = 6e-06
 Identities = 13/98 (13%), Positives = 31/98 (31%), Gaps = 13/98 (13%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDV---------RTFYRASKHCGFVTISYYDIRA 196
            +  L +  I    +  E+     +  +                ++   FV   Y   RA
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVE--YESHRA 64

Query: 197 ARNAMKSLQNKLTRSG--KLDIHYSIPKDNPSEKEINQ 232
           A  A + L     +    ++ + ++ P+ +  E  +  
Sbjct: 65  AAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 102

>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 Length = 109

 Score = 44.4 bits (105), Expect = 9e-06
 Identities = 13/82 (15%), Positives = 26/82 (31%), Gaps = 9/82 (10%)

Query: 230 INQGTLVVFNLDSSVSNDELHHIFGVYGE-------IKEIRETPQKIHQKYIEFYDTRAA 282
                L +  +      +E+        E            +  +     ++E+   RAA
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 283 EAALRELNSR--YIAGKQIKLE 302
             A R+L      + G QI ++
Sbjct: 66  AMARRKLMPGRIQLWGHQIAVD 87

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 44.5 bits (106), Expect = 6e-06
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 11/76 (14%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAA 285
            L V +L  +++ D L  IF  +G+I  I      +T +    K   +I F D+  A  A
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRS---KGYGFITFSDSECARRA 63

Query: 286 LRELNSRYIAGKQIKL 301
           L +LN   +AG+ +++
Sbjct: 64  LEQLNGFELAGRPMRV 79

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 45.1 bits (107), Expect = 6e-06
 Identities = 14/86 (16%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 221 PKDNPSEKEINQGT-LVVFNLDSSVSNDELHHIFGVYGEI---KEIRETPQKIHQKY--I 274
                 + E  +G  L +++L    ++ +L   F  +G +   K   +    + + +  +
Sbjct: 28  AAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFV 87

Query: 275 EFYDTRAAEAALRELNSRYIAGKQIK 300
            F +  +A+ A++ +N   +  K++K
Sbjct: 88  SFDNPDSAQVAIKAMNGFQVGTKRLK 113

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 45.5 bits (108), Expect = 7e-06
 Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 11/78 (14%)

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEA 284
            +L V NL    S D L  +F  YG + ++     R T +    +   ++ F+D R AE 
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKES---RGFAFVRFHDKRDAED 104

Query: 285 ALRELNSRYIAGKQIKLE 302
           A+  ++   + G++++++
Sbjct: 105 AMDAMDGAVLDGRELRVQ 122

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 44.1 bits (105), Expect = 7e-06
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 11/72 (15%)

Query: 237 VFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAALRE 288
           +  L    ++ +L  +   YG+I        + T +    K   +++F    AA+ A+  
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKC---KGYGFVDFDSPSAAQKAVTA 66

Query: 289 LNSRYIAGKQIK 300
           L +  +  +  K
Sbjct: 67  LKASGVQAQMAK 78

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 43.9 bits (104), Expect = 9e-06
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 11/80 (13%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYG--EIKEIRETPQKIHQK-----YIEFYDTRAAEAAL 286
           T+++ N+      D +      Y    +  IR    K  Q+     +++      A   L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 287 RELNSR----YIAGKQIKLE 302
           + L S      I GK I ++
Sbjct: 71  QILQSLHPPLKIDGKTIGVD 90

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 13/75 (17%), Positives = 24/75 (32%), Gaps = 15/75 (20%)

Query: 144 EHPSRTLLLRKINSNIEDSELKALFEQYG-----------DVRTFYRASKHCGFVTISYY 192
            H   T++LR I  +     +      Y            D +T  + ++   FV     
Sbjct: 6   HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQT--QQNRGFAFVQ--LS 61

Query: 193 DIRAARNAMKSLQNK 207
               A   ++ LQ+ 
Sbjct: 62  SAMDASQLLQILQSL 76

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 44.5 bits (105), Expect = 9e-06
 Identities = 16/93 (17%), Positives = 38/93 (40%), Gaps = 12/93 (12%)

Query: 222 KDNPSEKEINQGTLV-VFNLDSSVSNDEL---HHIFGVYGEIKEIRETPQKIHQK----- 272
             + +   + Q  LV V  L   +++ E+      FG +G+I ++       +       
Sbjct: 4   GSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPS 63

Query: 273 ---YIEFYDTRAAEAALRELNSRYIAGKQIKLE 302
              Y+ +  +  A  A++ +N+  + G+ +K  
Sbjct: 64  ASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS 96

>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 Length = 115

 Score = 44.6 bits (106), Expect = 1e-05
 Identities = 17/81 (20%), Positives = 41/81 (50%), Gaps = 6/81 (7%)

Query: 226 SEKEINQGT-LVVFNLDSSVSNDELHHIFGVYGEI---KEIRETPQKIHQKY--IEFYDT 279
           S+KE  +G  L +++L     + +L  +F  +G +   K   +    + + +  + + + 
Sbjct: 18  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77

Query: 280 RAAEAALRELNSRYIAGKQIK 300
            +A+AA++ +N   I  K++K
Sbjct: 78  VSAQAAIQSMNGFQIGMKRLK 98

>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 Length = 104

 Score = 44.1 bits (104), Expect = 1e-05
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 4/60 (6%)

Query: 247 DELHHIFGVYGEIKEIR----ETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLE 302
           +    +   YGE++E+          +   Y++F     AE A+ +LN+R+  G+ I  E
Sbjct: 42  EVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 201 MKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIK 260
           M S  +    S  L    S        +      L V N+     + +L  +FG +G+I 
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMNTENKSQPKR---LHVSNIPFRFRDPDLRQMFGQFGKIL 57

Query: 261 EIRETPQKIHQK---YIEFYDTRAAEAALRELNSRYIAGKQIK 300
           ++     +   K   ++ F ++  A+ A  +L+   + G++I+
Sbjct: 58  DVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 100

>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} Length = 116

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 14/90 (15%)

Query: 231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR----ETPQKIHQK-----YIEFYDTRA 281
           + G L +  L+   +   L  +FG +G I E+      T      K     +I F +   
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT-----SKSRGFAFITFENPAD 60

Query: 282 AEAALRELNSRYIAGKQIKLEPSHLRGLRK 311
           A+ A +++N + + GK IK+E +     + 
Sbjct: 61  AKNAAKDMNGKSLHGKAIKVEQAKKPSFQS 90

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 44.3 bits (105), Expect = 2e-05
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 14/78 (17%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK---------YIEFYDTRAAEA 284
            L+V NLD  VS+ ++  +F  +G +K+       +             + F     A  
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKA-----AVDYDRSGRSLGTADVHFERRADALK 91

Query: 285 ALRELNSRYIAGKQIKLE 302
           A+++     + G+ + ++
Sbjct: 92  AMKQYKGVPLDGRPMDIQ 109

>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* Length = 437

 Score = 47.2 bits (111), Expect = 2e-05
 Identities = 25/113 (22%), Positives = 49/113 (43%), Gaps = 9/113 (7%)

Query: 195 RAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFG 254
           R  R  ++  Q ++    K+      P ++P+ +     TL V  ++   +  +L   F 
Sbjct: 69  RKRREKIERRQQEVETELKMWD----PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFE 124

Query: 255 VYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRELNSRYIAGKQIKLE 302
           VYG IK I     K   K     +IE+   R   +A +  + + I G+++ ++
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 177

>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 Length = 107

 Score = 43.8 bits (104), Expect = 2e-05
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 14/78 (17%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK---------YIEFYDTRAAEA 284
            L+V NLD  VS+ ++  +F  +G +K+       +H            + F     A  
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKA-----AVHYDRSGRSLGTADVHFERKADALK 85

Query: 285 ALRELNSRYIAGKQIKLE 302
           A+++ N   + G+ + ++
Sbjct: 86  AMKQYNGVPLDGRPMNIQ 103

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 43.2 bits (102), Expect = 2e-05
 Identities = 17/91 (18%), Positives = 32/91 (35%), Gaps = 6/91 (6%)

Query: 226 SEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTR 280
           S    N G + +  L    S +E+   F     +      P     +     +++F    
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 281 AAEAALRELNSRYIAGKQIKLEPSHLRGLRK 311
            AE AL + +   I  + I++  S    +R 
Sbjct: 69  IAEKAL-KKHKERIGHRYIEIFKSSRAEVRT 98

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 10/78 (12%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGE----IKEIR--ETPQKIHQKYIEFYDTRAAEAALR 287
           +L + +L+  +  + +   F   GE    +K IR   T       ++EF D   AE  L 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 288 ELNSRYIAG----KQIKL 301
           ++N + + G    K+ KL
Sbjct: 71  KINGKPLPGATPAKRFKL 88

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 43.2 bits (102), Expect = 3e-05
 Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 13/98 (13%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKY----- 273
           S       +++ +   + V  L+ SV+ D+L   F   G +K  + T Q +   Y     
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 274 --------IEFYDTRAAEAALRELNSRYIAGKQIKLEP 303
                   + + D   A+AA+   + +   G ++K+  
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSL 99

>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 Length = 114

 Score = 43.2 bits (102), Expect = 3e-05
 Identities = 11/102 (10%), Positives = 34/102 (33%), Gaps = 6/102 (5%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----Y 273
           S       +    +    + N+  S++  ++          +         + +      
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61

Query: 274 IEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLAN 315
           ++F +   A  + R L+ + + G++  +    L  +R+   N
Sbjct: 62  VQFKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMREIEKN 102

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 44.5 bits (105), Expect = 4e-05
 Identities = 16/96 (16%), Positives = 36/96 (37%), Gaps = 15/96 (15%)

Query: 217 HYSIPKDNPSEKEINQGT-LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK--- 272
           H          + +  G  L+V NLD  VS+ ++  +F  +G +K+       +      
Sbjct: 72  HDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA-----AVDYDRSG 126

Query: 273 ------YIEFYDTRAAEAALRELNSRYIAGKQIKLE 302
                  + F     A  A+++     + G+ + ++
Sbjct: 127 RSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ 162

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 43.6 bits (103), Expect = 4e-05
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 11/74 (14%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAAL 286
           L+V  + ++V   +L  +F  YG I+ +     RET Q    +   +++F    +A+ A+
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQS---RGYGFVKFQSGSSAQQAI 101

Query: 287 RELNSRYIAGKQIK 300
             LN   I  K++K
Sbjct: 102 AGLNGFNILNKRLK 115

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 45.2 bits (106), Expect = 4e-05
 Identities = 20/121 (16%), Positives = 45/121 (37%), Gaps = 11/121 (9%)

Query: 197 ARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSN---------D 247
            + A+++         K   +        S ++ N+ TL V  +D ++++          
Sbjct: 100 GKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNK-TLYVGGIDGALNSKHLKPAQIES 158

Query: 248 ELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR 307
            +  +F   G+I  IR    K +  +++F     AE A   ++++ +     K       
Sbjct: 159 RIRFVFSRLGDIDRIRYVESK-NCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRRE 217

Query: 308 G 308
           G
Sbjct: 218 G 218

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 42.7 bits (101), Expect = 4e-05
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 237 VFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALRELNS 291
           V +L  +++ D L  IF  +G I+ I      ET +     +I F D+  A+ AL +LN 
Sbjct: 31  VGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNG 90

Query: 292 RYIAGKQIK 300
             +AG+ +K
Sbjct: 91  FELAGRPMK 99

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 15/76 (19%), Positives = 26/76 (34%), Gaps = 13/76 (17%)

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK--------YIEFYDTRAAEA 284
             + V NL    +   L   F   G +         I  +         ++F     AE 
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYA-----DIKMENGKSKGCGVVKFESPEVAER 63

Query: 285 ALRELNSRYIAGKQIK 300
           A R +N   ++G++I 
Sbjct: 64  ACRMMNGMKLSGREID 79

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 14/70 (20%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
           ++ V      V + +L   F  +G +  +     K     +E  D  A EA L +     
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHS- 68

Query: 294 IAGKQIKLEP 303
           + G ++++ P
Sbjct: 69  LGGHRLRVRP 78

>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 Length = 104

 Score = 41.9 bits (99), Expect = 7e-05
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 11/75 (14%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK---YIEFYDTRAAEAA 285
           ++ V N+    + ++L  IF   G +        RET +    K   + E+ D   A +A
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKP---KGYGFCEYQDQETALSA 66

Query: 286 LRELNSRYIAGKQIK 300
           +R LN R  +G+ ++
Sbjct: 67  MRNLNGREFSGRALR 81

>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 Length = 124

 Score = 42.1 bits (99), Expect = 7e-05
 Identities = 13/96 (13%), Positives = 34/96 (35%), Gaps = 6/96 (6%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIE 275
            +            + +  L     N  +   F     +++        + K     ++E
Sbjct: 14  KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVE 73

Query: 276 FYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK 311
           F +    +AAL   + +Y+  + I++ P   +G+ +
Sbjct: 74  FRNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLE 108

>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 Length = 114

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 11/77 (14%)

Query: 232 QGT-LVVFNLDSSVSNDELHHIFGVYGEIKEIR----ETPQKIHQK---YIEFYDTRAAE 283
             T L + NL  S+   EL ++   +G++   R     +      +   +     T   E
Sbjct: 24  DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT---SRGVGFARMESTEKCE 80

Query: 284 AALRELNSRYIAGKQIK 300
           A +   N ++I      
Sbjct: 81  AVIGHFNGKFIKTPPGV 97

>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 Length = 126

 Score = 41.4 bits (97), Expect = 1e-04
 Identities = 17/98 (17%), Positives = 34/98 (34%), Gaps = 6/98 (6%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----Y 273
            + + + S    N G + +  L    + +E+   F     +      P     K     +
Sbjct: 29  QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88

Query: 274 IEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK 311
           ++F     AE AL   +   I  + I++  S    +R 
Sbjct: 89  VQFASQELAEKAL-GKHKERIGHRYIEVFKSSQEEVRS 125

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 9/85 (10%)

Query: 222 KDNPSEKEINQGTLVVFNL------DSSVSNDELHHIFGVYGEIKEI---RETPQKIHQK 272
           KD P E +     +VV N+            + +H IF  +G+I       E  +     
Sbjct: 5   KDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYI 64

Query: 273 YIEFYDTRAAEAALRELNSRYIAGK 297
           ++E+     A  A++  +   +  +
Sbjct: 65  FLEYASPAHAVDAVKNADGYKLDKQ 89

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 18/113 (15%), Positives = 39/113 (34%), Gaps = 18/113 (15%)

Query: 221 PKDNPSEKEINQGT-LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK------- 272
              + + +    G+ + V NLD  V   +L  +F + G +         I +        
Sbjct: 3   SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRA-----DILEDKDGKSRG 57

Query: 273 --YIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLANQLPPELEQ 323
              + F  +  A  A+   N + +  + + ++       +    +  PPE  Q
Sbjct: 58  IGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKG---DFFPPERPQ 107

>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 Length = 112

 Score = 40.3 bits (94), Expect = 3e-04
 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 234 TLVVFNL-DSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALR--ELN 290
            + + NL  S  S+  +  +   YG+IK       K  Q +IE      A A +      
Sbjct: 27  VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK-SQAFIEMETREDAMAMVDHCLKK 85

Query: 291 SRYIAGKQIKLEPSH 305
           + +  G+ +K++ S 
Sbjct: 86  ALWFQGRCVKVDLSE 100

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 39.0 bits (91), Expect = 7e-04
 Identities = 10/100 (10%), Positives = 31/100 (31%), Gaps = 8/100 (8%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIE 275
               P     +   + V  +  S   +++   F     +  +    +    +      ++
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVH-LLKDHVGRNNGNGLVK 62

Query: 276 FYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRKCLAN 315
           F   +    AL + N   +  + +++ P+  R       +
Sbjct: 63  FLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQWVAAGGH 101

>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 Length = 114

 Score = 39.2 bits (92), Expect = 7e-04
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 7/49 (14%)

Query: 256 YGEIKEI---RETPQ-KIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK 300
           +G +  I   + + Q  +   Y++     AA AA+  L+ R+ AGK I 
Sbjct: 41  HGGVIHIYVDKNSAQGNV---YVKCPSIAAAIAAVNALHGRWFAGKMIT 86

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	876
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.96
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.96
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.96
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.95
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.95
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.95
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.94
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.93
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.93
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.93
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.92
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.79
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.78
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.75
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.64
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.62
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.62
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.6
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.6
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.59
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.59
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.59
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.58
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.58
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.58
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.58
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.57
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.57
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.56
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.56
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.56
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.56
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.56
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.55
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.55
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.55
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.55
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.55
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.55
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.55
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.55
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.55
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.55
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.55
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.55
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.55
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.55
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.55
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.54
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.54
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.54
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.54
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.54
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.54
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.54
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.54
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.54
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.54
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.54
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.53
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.53
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.53
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.53
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.53
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.53
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.53
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.53
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.53
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.53
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.53
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.53
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.53
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.53
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.53
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.53
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.52
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.52
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.52
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.52
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.52
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.52
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.52
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.52
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.52
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.52
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.51
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.51
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.51
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.51
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.51
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.51
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.51
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.51
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.51
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.51
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.51
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.51
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.51
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.51
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.51
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.51
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.51
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.51
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.51
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.51
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.51
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.51
2div_A	99	TRNA selenocysteine associated protein; structural	99.51
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.51
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.5
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.5
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.5
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.5
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.5
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.5
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.5
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.5
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.5
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.5
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.5
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.5
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.5
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.5
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.5
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.49
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.49
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.49
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.49
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.49
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.49
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.49
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.49
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.49
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.49
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.49
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.49
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.49
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.49
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.49
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.49
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.49
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.49
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.49
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.49
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.49
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.49
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.49
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.49
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.48
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.48
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.48
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.48
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.48
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.48
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.48
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.48
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.48
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.48
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.48
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.48
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.48
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.48
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.48
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.48
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.48
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.48
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.48
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.48
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.48
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.48
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.47
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.47
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.47
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.47
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.47
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.47
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.47
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.47
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.47
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.47
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.47
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.47
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.47
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.47
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.47
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.47
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.46
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.46
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.46
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.46
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.46
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.46
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.46
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.46
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.46
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.46
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.46
1x5p_A	97	Negative elongation factor E; structure genomics,	99.46
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.46
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.46
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.46
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.46
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.46
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.46
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.46
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.46
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.46
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.45
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.45
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.45
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.45
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.45
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.45
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.45
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.45
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.45
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.45
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.45
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.45
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.45
2div_A	99	TRNA selenocysteine associated protein; structural	99.45
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.45
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.44
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.44
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.44
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.44
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.44
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.44
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.44
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.44
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.44
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.44
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.44
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.44
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.43
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.43
1x5p_A	97	Negative elongation factor E; structure genomics,	99.43
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.43
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.43
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.43
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.43
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.43
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.43
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.43
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.43
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.42
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.42
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.42
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.42
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.42
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.42
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.42
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.42
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.42
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.41
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.41
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.41
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.41
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.41
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.41
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.41
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.41
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.41
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.41
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.41
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.41
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.41
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.4
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.4
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.4
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.4
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.4
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.4
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.4
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.39
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.39
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.39
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.39
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.38
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.38
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.38
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.38
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.37
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.37
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.37
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.37
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.37
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.37
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.36
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.36
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.36
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.36
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.36
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.36
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.35
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.35
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.35
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.34
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.34
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.34
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.34
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.33
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.01
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.33
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.33
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.33
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.33
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.33
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.33
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.33
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.32
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.32
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.32
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.32
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.32
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.31
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.31
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.31
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.31
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.31
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.31
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.31
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.3
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.29
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.29
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.29
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.28
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.28
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.27
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.27
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.26
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.26
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.25
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.25
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.25
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.24
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.24
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.24
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.23
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.23
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.22
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.22
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.22
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.21
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.19
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.19
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.18
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.16
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.12
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.1
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.09
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.09
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.07
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.01
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.99
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.99
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.96
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.95
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.93
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.92
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.84
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.76
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.66
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.59
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	98.58
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.43
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.42
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.37
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.27
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.13
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.13
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.69
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.48
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.31
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.78
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.72
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.68
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.32
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.68
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	94.78
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	93.97
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	93.32
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.63
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	92.42
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.41
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	92.38
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	92.2
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	90.65
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	88.27

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.97  E-value=5.3e-30  Score=262.52  Aligned_cols=166  Identities=17%  Similarity=0.320  Sum_probs=148.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..|.+||||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.+++..+.|+.|++.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            46789999999999999999999999999999998     3578899999999999999999999999999999999999


Q ss_pred             cCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeC
Q 002823          219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIA  295 (876)
Q Consensus       219 A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~  295 (876)
                      +......  ......+|||+|||.++++++|+++|++||.|+.|++   ...++|||||+|.+.++|.+|++.|||..|.
T Consensus        92 ~~~~~~~--~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~  169 (213)
T 4f02_A           92 SQRDPSL--RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN  169 (213)
T ss_dssp             CCCCTHH--HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             ccccccc--cccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEEC
Confidence            8654322  2234568999999999999999999999999999887   3446899999999999999999999999999


Q ss_pred             CeEEEEEeecCchhHH
Q 002823          296 GKQIKLEPSHLRGLRK  311 (876)
Q Consensus       296 Gr~IkVs~A~~k~~Rr  311 (876)
                      |++|+|.+++++.+|+
T Consensus       170 g~~i~V~~a~~~~~~~  185 (213)
T 4f02_A          170 DRKVFVGRFKSRKERE  185 (213)
T ss_dssp             TEECEEEECCCHHHHH
T ss_pred             CEEEEEEEcCCCcccc
Confidence            9999999999987665

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.96  E-value=5.8e-29  Score=240.29  Aligned_cols=157  Identities=17%  Similarity=0.285  Sum_probs=143.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      |+|||+|||.++++++|+++|++||+|.+++.    .++++|||||+|.+.++|++|++.+++..+.|+.|.|.++.++.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            69999999999999999999999999999983    46689999999999999999999999999999999999997765


Q ss_pred             CCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeE
Q 002823          224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQ  298 (876)
Q Consensus       224 ~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~  298 (876)
                      ...  .....+|||+|||..+++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.|++
T Consensus        81 ~~~--~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  158 (166)
T 3md3_A           81 QSS--SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP  158 (166)
T ss_dssp             CCC--CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCC--CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE
Confidence            432  345679999999999999999999999999999887     3567899999999999999999999999999999


Q ss_pred             EEEEeecC
Q 002823          299 IKLEPSHL  306 (876)
Q Consensus       299 IkVs~A~~  306 (876)
                      |+|.|+++
T Consensus       159 i~v~~a~~  166 (166)
T 3md3_A          159 LRINWAAK  166 (166)
T ss_dssp             CEEEESCC
T ss_pred             EEEEecCC
Confidence            99999864

>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

Probab=99.96  E-value=2.3e-28  Score=237.37  Aligned_cols=155  Identities=23%  Similarity=0.430  Sum_probs=142.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ++++|||+|||+++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.|++..+.|++|.|.|+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            578999999999999999999999999999998     256688999999999999999999999999999999999998


Q ss_pred             CCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeC
Q 002823          221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIA  295 (876)
Q Consensus       221 pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~  295 (876)
                      ++...    ....+|||+|||..+++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.
T Consensus        82 ~~~~~----~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  157 (168)
T 1b7f_A           82 PGGES----IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE  157 (168)
T ss_dssp             CCSST----TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT
T ss_pred             CCccc----CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEec
Confidence            76543    34679999999999999999999999999999887     4456799999999999999999999999998


Q ss_pred             C--eEEEEEee
Q 002823          296 G--KQIKLEPS  304 (876)
Q Consensus       296 G--r~IkVs~A  304 (876)
                      |  ++|+|.||
T Consensus       158 g~~~~l~V~~A  168 (168)
T 1b7f_A          158 GGSQPLSVRLA  168 (168)
T ss_dssp             TCSSCCEEEEC
T ss_pred             CCCeEEEEEeC
Confidence            7  99999986

>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

Probab=99.96  E-value=3.2e-28  Score=235.30  Aligned_cols=155  Identities=23%  Similarity=0.408  Sum_probs=141.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ++++|||+|||+++++++|+++|++||+|..++.     +++++|||||+|.+.++|++|++.|++..+.|++|+|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            4689999999999999999999999999999882     67788999999999999999999999999999999999998


Q ss_pred             CCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeC
Q 002823          221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIA  295 (876)
Q Consensus       221 pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~  295 (876)
                      ++..    .....+|||+|||..+++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.
T Consensus        81 ~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~  156 (167)
T 1fxl_A           81 PSSA----SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS  156 (167)
T ss_dssp             CCCG----GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT
T ss_pred             CCcc----cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccC
Confidence            6543    234678999999999999999999999999999887     3456899999999999999999999999999


Q ss_pred             Ce--EEEEEee
Q 002823          296 GK--QIKLEPS  304 (876)
Q Consensus       296 Gr--~IkVs~A  304 (876)
                      |+  +|+|.||
T Consensus       157 g~~~~i~v~~A  167 (167)
T 1fxl_A          157 GATEPITVKFA  167 (167)
T ss_dssp             TCSSCCEEEEC
T ss_pred             CCccceEEEeC
Confidence            96  4888885

>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

Probab=99.96  E-value=2.6e-28  Score=243.17  Aligned_cols=169  Identities=14%  Similarity=0.288  Sum_probs=141.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      +....+.++|||+|||+++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++. ++..+.|+.|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~   85 (196)
T 1l3k_A            7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVE   85 (196)
T ss_dssp             -CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEee
Confidence            345567899999999999999999999999999999882     467899999999999999999976 88999999999


Q ss_pred             EeecCCCCCCCc--cccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHH
Q 002823          216 IHYSIPKDNPSE--KEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRE  288 (876)
Q Consensus       216 V~~A~pk~~~~e--k~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~  288 (876)
                      |.++.++.....  ......+|||+|||.++++++|+++|+.||.|..|++     ++.++|||||+|.+.++|.+|++.
T Consensus        86 v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  165 (196)
T 1l3k_A           86 PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ  165 (196)
T ss_dssp             EEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC
T ss_pred             eecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh
Confidence            999877654322  2234579999999999999999999999999999887     455789999999999999999986


Q ss_pred             hCCceeCCeEEEEEeecCchhHH
Q 002823          289 LNSRYIAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       289 LnG~~I~Gr~IkVs~A~~k~~Rr  311 (876)
                       ++..|.|++|+|.|+.++.+.+
T Consensus       166 -~~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          166 -KYHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             -SCCEETTEECEEEECC------
T ss_pred             -CCcEECCEEEEEEecCChhHhc
Confidence             8999999999999999977553

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.95  E-value=5.5e-28  Score=244.39  Aligned_cols=165  Identities=15%  Similarity=0.279  Sum_probs=145.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+.++|||+|||.++|+++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..+.|+.|.|.+
T Consensus        25 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~  104 (216)
T 2qfj_A           25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR  104 (216)
T ss_dssp             HHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEEC
T ss_pred             cCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEec
Confidence            345789999999999999999999999999999984     577899999999999999999999999999999999998


Q ss_pred             cCCCCCCCc-------cccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHH
Q 002823          219 SIPKDNPSE-------KEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAAL  286 (876)
Q Consensus       219 A~pk~~~~e-------k~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL  286 (876)
                      +..+.....       ......+|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|+
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~  184 (216)
T 2qfj_A          105 PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV  184 (216)
T ss_dssp             CSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHH
Confidence            876542211       1234569999999999999999999999999999887     3456899999999999999999


Q ss_pred             HHhCCceeCCeEEEEEeecCch
Q 002823          287 RELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       287 ~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      +.|||..|.|++|+|.|+.++.
T Consensus       185 ~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          185 SSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HHHTTCBCSSSBCEEEECSSCS
T ss_pred             HHccCCEeCCcEEEEEEecCCC
Confidence            9999999999999999998864

>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

Probab=99.95  E-value=1.3e-27  Score=252.93  Aligned_cols=164  Identities=23%  Similarity=0.373  Sum_probs=146.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HHhhccCCeEEEE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          143 DEHPSRTLLLRKINSNIEDSELK----ALFEQYGDVRTFY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~----elFsqfG~I~sV~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      +..++++|||+|||.++++++|+    ++|++||.|.+|+  .+++++|||||+|.+.++|++|++.|+|..+.|+.|+|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            46778999999999999999977    8999999999998  36789999999999999999999999999999999999


Q ss_pred             eecCCCCCCC----------------------------------------------------------------------
Q 002823          217 HYSIPKDNPS----------------------------------------------------------------------  226 (876)
Q Consensus       217 ~~A~pk~~~~----------------------------------------------------------------------  226 (876)
                      .|+..+....                                                                      
T Consensus        85 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  164 (282)
T 3pgw_A           85 QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM  164 (282)
T ss_pred             EEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCC
Confidence            9987654210                                                                      


Q ss_pred             -------------------------------------ccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcc
Q 002823          227 -------------------------------------EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKI  269 (876)
Q Consensus       227 -------------------------------------ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~sk  269 (876)
                                                           .......+|||+|||..+++++|+++|++||.|++|++....+
T Consensus       165 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~  244 (282)
T 3pgw_A          165 PPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH  244 (282)
T ss_pred             CCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCC
Confidence                                                 0111346899999999999999999999999999999976667


Q ss_pred             cEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEeecC
Q 002823          270 HQKYIEFYDTRAAEAALRELNSRYIA-GKQIKLEPSHL  306 (876)
Q Consensus       270 G~AFVeF~d~E~A~kAL~~LnG~~I~-Gr~IkVs~A~~  306 (876)
                      |||||+|.+.++|.+|++.|||..|. |++|+|+|++.
T Consensus       245 g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~akk  282 (282)
T 3pgw_A          245 DIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK  282 (282)
T ss_pred             cEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEecC
Confidence            99999999999999999999999999 99999999863

>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

Probab=99.95  E-value=2.2e-28  Score=240.27  Aligned_cols=162  Identities=20%  Similarity=0.251  Sum_probs=145.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEE----EeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTF----YRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV----~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ...+.++|||+|||.++++++|+++|.+||.|..+    ..+++++|||||+|.+.++|++|+ +|++..+.|++|+|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            45678999999999999999999999999865431    245789999999999999999999 5999999999999999


Q ss_pred             cCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeE
Q 002823          219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQ  298 (876)
Q Consensus       219 A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~  298 (876)
                      +.++....  .....+|||+|||.++++++|+++|++||.|..+..++.++|||||+|.+.++|.+|++.|||..|.|++
T Consensus        88 ~~~~~~~~--~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  165 (175)
T 1fje_B           88 PKGRDSKK--VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS  165 (175)
T ss_dssp             CCCSSCST--TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEE
T ss_pred             CCCccccc--cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            98765432  3456799999999999999999999999999988557788999999999999999999999999999999


Q ss_pred             EEEEeecCc
Q 002823          299 IKLEPSHLR  307 (876)
Q Consensus       299 IkVs~A~~k  307 (876)
                      |+|+|++++
T Consensus       166 i~v~~a~~k  174 (175)
T 1fje_B          166 VSLYYTGEK  174 (175)
T ss_dssp             EEEEECSSC
T ss_pred             EEEEecCCC
Confidence            999999875

>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

Probab=99.95  E-value=1.5e-27  Score=246.94  Aligned_cols=165  Identities=20%  Similarity=0.226  Sum_probs=148.0

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          143 DEHPSRTLLLRKINS-NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~-~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ...++++|||+|||+ ++++++|+++|++||.|..|+.....+|||||+|.+.++|++|++.|++..+.|++|+|.++.+
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  109 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH  109 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            346789999999999 9999999999999999999997556689999999999999999999999999999999999976


Q ss_pred             CCCCCcc-------------------------------ccccceeEeecCCCCCcHHHHHHHhhhcC-CeEEEEecCCcc
Q 002823          222 KDNPSEK-------------------------------EINQGTLVVFNLDSSVSNDELHHIFGVYG-EIKEIRETPQKI  269 (876)
Q Consensus       222 k~~~~ek-------------------------------~~~~~tLfV~NLP~svTeedLreiFs~fG-~I~sVritg~sk  269 (876)
                      +.....+                               ..+..+|||+|||..+++++|+++|++|| .|..|++....+
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~  189 (229)
T 2adc_A          110 QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR  189 (229)
T ss_dssp             CCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSST
T ss_pred             ccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCC
Confidence            5211100                               11356899999999999999999999999 999999977779


Q ss_pred             cEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEeecCc
Q 002823          270 HQKYIEFYDTRAAEAALRELNSRYIA-GKQIKLEPSHLR  307 (876)
Q Consensus       270 G~AFVeF~d~E~A~kAL~~LnG~~I~-Gr~IkVs~A~~k  307 (876)
                      ++|||+|.+.++|.+|++.|+|..+. |++|+|.|++++
T Consensus       190 g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          190 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             TCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             cEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            99999999999999999999999999 999999999874

>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

Probab=99.95  E-value=1.8e-27  Score=232.35  Aligned_cols=155  Identities=15%  Similarity=0.270  Sum_probs=140.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcc----C-------CeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCce
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQY----G-------DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGK  213 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqf----G-------~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~  213 (876)
                      +++++|||+|||+++|+++|+++|++|    |       .|..++. ++++|||||+|.+.++|++|+ .+++..+.|++
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~-~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~   79 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   79 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE-ETTTTEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEe-cCCCCEEEEEeCCHHHHHHHH-HhCCcEecCce
Confidence            357899999999999999999999999    7       7888775 677999999999999999999 89999999999


Q ss_pred             eeEeecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHH
Q 002823          214 LDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRE  288 (876)
Q Consensus       214 L~V~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~  288 (876)
                      |+|.++.+....    ....+|||+|||..+++++|+++|++||.|..|++     ++.++|+|||+|.+.++|.+|++.
T Consensus        80 i~v~~~~~~~~~----~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~  155 (172)
T 2g4b_A           80 LKIRRPHDYQPL----PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG  155 (172)
T ss_dssp             CEEECCSSCCCC----TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHH
T ss_pred             eeecCCcccCCC----CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            999997655432    23679999999999999999999999999999887     455689999999999999999999


Q ss_pred             hCCceeCCeEEEEEeec
Q 002823          289 LNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       289 LnG~~I~Gr~IkVs~A~  305 (876)
                      |||..+.|++|+|+||.
T Consensus       156 l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          156 LNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             HTTCEETTEECEEEECC
T ss_pred             cCCCEECCeEEEEEeCC
Confidence            99999999999999973

>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

Probab=99.95  E-value=2.9e-27  Score=230.65  Aligned_cols=157  Identities=16%  Similarity=0.316  Sum_probs=138.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CC--CccceEeeecCCHHHHHHHHHHccccccC---Cceee
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----AS--KHCGFVTISYYDIRAARNAMKSLQNKLTR---SGKLD  215 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tg--ksrGfAFV~F~d~edA~kAl~~Lng~~l~---Gr~L~  215 (876)
                      .+++|||+|||+++++++|+++|++||+|.+++.     ++  +++|||||+|.+.++|++|++.|++..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            4689999999999999999999999999999882     22  78999999999999999999999998875   67888


Q ss_pred             EeecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCC
Q 002823          216 IHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNS  291 (876)
Q Consensus       216 V~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG  291 (876)
                      +.++.++...   .....+|||+|||.++++++|+++|++||.|..|++    ++.++|||||+|.+.++|.+|++.|||
T Consensus        82 ~~~~~~~~~~---~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g  158 (175)
T 3nmr_A           82 MKPADSEKNN---AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ  158 (175)
T ss_dssp             EEECGGGCCS---CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             Eccccccccc---cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcC
Confidence            8887655433   235679999999999999999999999999999887    445689999999999999999999999


Q ss_pred             ceeC---CeEEEEEeec
Q 002823          292 RYIA---GKQIKLEPSH  305 (876)
Q Consensus       292 ~~I~---Gr~IkVs~A~  305 (876)
                      ..+.   +++|+|.|+.
T Consensus       159 ~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          159 AQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SCCCTTCSSCCEEEECC
T ss_pred             CcccCCCCCCeEEEecC
Confidence            8776   4999999973

>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

Probab=99.95  E-value=5.3e-28  Score=235.01  Aligned_cols=155  Identities=17%  Similarity=0.328  Sum_probs=140.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ++++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.  +..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            578999999999999999999999999999998     2577899999999999999999984  568999999999987


Q ss_pred             CCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeC
Q 002823          221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIA  295 (876)
Q Consensus       221 pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~  295 (876)
                      ++..    .....+|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++ +++..+.
T Consensus        80 ~~~~----~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~  154 (167)
T 2cjk_A           80 PRDE----QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFK  154 (167)
T ss_dssp             CHHH----HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSS
T ss_pred             chhh----ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeC
Confidence            6432    234669999999999999999999999999999987     35568999999999999999998 8999999


Q ss_pred             CeEEEEEeecCc
Q 002823          296 GKQIKLEPSHLR  307 (876)
Q Consensus       296 Gr~IkVs~A~~k  307 (876)
                      |++|+|.|+.++
T Consensus       155 g~~i~V~~a~pk  166 (167)
T 2cjk_A          155 DRKIEIKRAEPR  166 (167)
T ss_dssp             SSCEEEEECCCC
T ss_pred             CeEEEEeecCCC
Confidence            999999999886

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.95  E-value=2.8e-27  Score=236.05  Aligned_cols=161  Identities=15%  Similarity=0.253  Sum_probs=142.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcc----C-------CeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCcee
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQY----G-------DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKL  214 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqf----G-------~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L  214 (876)
                      .+++|||+|||+++++++|+++|++|    |       .|..++. ++++|||||+|.+.++|++|+ .|++..+.|+.|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~-~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i   80 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE-ETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe-cCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceE
Confidence            47899999999999999999999999    5       6777765 678999999999999999999 899999999999


Q ss_pred             eEeecCCCCCCCc----------------cccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEE
Q 002823          215 DIHYSIPKDNPSE----------------KEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKY  273 (876)
Q Consensus       215 ~V~~A~pk~~~~e----------------k~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AF  273 (876)
                      +|.++.++.....                ......+|||+|||..+++++|+++|++||.|..|++     ++.++||||
T Consensus        81 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~af  160 (198)
T 2yh0_A           81 KIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF  160 (198)
T ss_dssp             EEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEE
T ss_pred             EEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEE
Confidence            9999876532210                1134579999999999999999999999999999887     445689999


Q ss_pred             EEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          274 IEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       274 VeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      |+|.+.++|.+|++.|||..|.|++|+|.|++++.
T Consensus       161 V~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          161 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             EEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             EEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            99999999999999999999999999999999865

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.95  E-value=2.3e-27  Score=238.17  Aligned_cols=161  Identities=20%  Similarity=0.238  Sum_probs=145.2

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCCC
Q 002823          147 SRTLLLRKINS-NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNP  225 (876)
Q Consensus       147 SrTLFVgNLP~-~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~~  225 (876)
                      +++|||+|||+ ++++++|+++|++||.|..|+.....+|||||+|.+.++|++|++.|++..+.|++|+|.++.++...
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~   82 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQ   82 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCcC
Confidence            58999999999 99999999999999999999965556899999999999999999999999999999999999765321


Q ss_pred             Ccc-------------------------------ccccceeEeecCCCCCcHHHHHHHhhhcC-CeEEEEecCCcccEEE
Q 002823          226 SEK-------------------------------EINQGTLVVFNLDSSVSNDELHHIFGVYG-EIKEIRETPQKIHQKY  273 (876)
Q Consensus       226 ~ek-------------------------------~~~~~tLfV~NLP~svTeedLreiFs~fG-~I~sVritg~skG~AF  273 (876)
                      ..+                               ..+..+|||+|||..+++++|+++|++|| .|.+|++.+..+|+||
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~af  162 (198)
T 1qm9_A           83 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMAL  162 (198)
T ss_dssp             CSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEE
T ss_pred             CCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEE
Confidence            100                               12366899999999999999999999999 9999999777799999


Q ss_pred             EEecCHHHHHHHHHHhCCceeC-CeEEEEEeecCc
Q 002823          274 IEFYDTRAAEAALRELNSRYIA-GKQIKLEPSHLR  307 (876)
Q Consensus       274 VeF~d~E~A~kAL~~LnG~~I~-Gr~IkVs~A~~k  307 (876)
                      |+|.+.++|.+|++.|||..+. |++|+|.|++++
T Consensus       163 V~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          163 IQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             EECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            9999999999999999999999 999999999874

>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

Probab=99.95  E-value=7e-27  Score=239.89  Aligned_cols=160  Identities=18%  Similarity=0.199  Sum_probs=138.0

Q ss_pred             CCCcEEEEcCCC-CCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          145 HPSRTLLLRKIN-SNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       145 ~pSrTLFVgNLP-~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      .++++|||+||| ..+++++|+++|++||.|.+|+.....+|||||+|.+.++|++|++.|+|..+.|++|+|.++..+.
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCc
Confidence            357899999999 8999999999999999999999766679999999999999999999999999999999999986432


Q ss_pred             CCCc------------c---------------------ccccceeEeecCCCCCcHHHHHHHhhhcCCe--EEEEecC--
Q 002823          224 NPSE------------K---------------------EINQGTLVVFNLDSSVSNDELHHIFGVYGEI--KEIRETP--  266 (876)
Q Consensus       224 ~~~e------------k---------------------~~~~~tLfV~NLP~svTeedLreiFs~fG~I--~sVritg--  266 (876)
                      ....            +                     ..+..+|||+|||.++++++|+++|++||.|  .+|++..  
T Consensus        82 ~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~  161 (205)
T 3tyt_A           82 IMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK  161 (205)
T ss_dssp             CCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC
T ss_pred             cCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC
Confidence            1000            0                     0124579999999999999999999999999  8888732  


Q ss_pred             -CcccEEEEEecCHHHHHHHHHHhCCceeCCe----EEEEEee
Q 002823          267 -QKIHQKYIEFYDTRAAEAALRELNSRYIAGK----QIKLEPS  304 (876)
Q Consensus       267 -~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr----~IkVs~A  304 (876)
                       ..+|+|||+|.+.++|.+||..|||..|.|+    ++.|+++
T Consensus       162 ~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          162 SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence             3468999999999999999999999999885    6666664

>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

Probab=99.94  E-value=6.1e-27  Score=248.16  Aligned_cols=166  Identities=14%  Similarity=0.179  Sum_probs=150.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .+.++|||+|||+++++++|+++|++||.|..++     .+++++|||||+|.+.++|.+|++.|++..+.|++|.|.|+
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            3568999999999999999999999999999887     25778999999999999999999999999999999999999


Q ss_pred             CCCCCCCccccccceeEeecCCCCC-cHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCcee
Q 002823          220 IPKDNPSEKEINQGTLVVFNLDSSV-SNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYI  294 (876)
Q Consensus       220 ~pk~~~~ek~~~~~tLfV~NLP~sv-TeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I  294 (876)
                      .++.... ......+|||+|||.++ ++++|+++|+.||.|..|++    ++.++|+|||+|.+.++|.+|++.|||..+
T Consensus       173 ~~~~~~~-~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~  251 (284)
T 3smz_A          173 DAGQLTP-ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSL  251 (284)
T ss_dssp             CGGGCCT-TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCc-ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCcc
Confidence            8765443 23456799999999995 99999999999999999887    455789999999999999999999999999


Q ss_pred             CCeEEEEEeecCchhHH
Q 002823          295 AGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       295 ~Gr~IkVs~A~~k~~Rr  311 (876)
                      .|++|+|.|+.++..++
T Consensus       252 ~g~~l~v~~a~~~~~~~  268 (284)
T 3smz_A          252 GGSHLRVSFCAPGPPGR  268 (284)
T ss_dssp             TTEECEEEECCSSSCHH
T ss_pred             CCeEEEEEEecCCCccc
Confidence            99999999999998776

>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

Probab=99.93  E-value=1.6e-25  Score=238.10  Aligned_cols=161  Identities=16%  Similarity=0.240  Sum_probs=141.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccC-CeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYG-DVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG-~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ..++|||+|||+++++++|+++|++|| .|..|+.    .++++|||||+|.+.++|++|++.|+|..+.|+.|.|.++.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  195 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN  195 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            578999999999999999999999999 9999982    35689999999999999999999999999999999999998


Q ss_pred             CCCCCCc---cccccceeEeecCCCC-CcHHHHHHHhhhcCCeEEEEec------CCcccEEEEEecCHHHHHHHHHHhC
Q 002823          221 PKDNPSE---KEINQGTLVVFNLDSS-VSNDELHHIFGVYGEIKEIRET------PQKIHQKYIEFYDTRAAEAALRELN  290 (876)
Q Consensus       221 pk~~~~e---k~~~~~tLfV~NLP~s-vTeedLreiFs~fG~I~sVrit------g~skG~AFVeF~d~E~A~kAL~~Ln  290 (876)
                      ++.....   ......+|||+|||.. +++++|+++|++||.|..|++.      +.++|||||+|.+.++|.+|+ .||
T Consensus       196 ~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~  274 (292)
T 2ghp_A          196 PLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMN  274 (292)
T ss_dssp             CC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGT
T ss_pred             CCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-Hhc
Confidence            7765432   2235579999999999 9999999999999999999982      567899999999999999999 999


Q ss_pred             CceeCCeEEEEEeecCc
Q 002823          291 SRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       291 G~~I~Gr~IkVs~A~~k  307 (876)
                      |..|.|++|+|.|++++
T Consensus       275 g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          275 RSLLGNREISVSLADKK  291 (292)
T ss_dssp             TEEETTEEEEEEECCCC
T ss_pred             CCEECCcEEEEEEecCC
Confidence            99999999999999886

>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

Probab=99.93  E-value=3.8e-25  Score=234.41  Aligned_cols=152  Identities=16%  Similarity=0.285  Sum_probs=141.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDN  224 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~  224 (876)
                      .++++|||+|||.++|+++|+++|++|| |..++. ++++|||||+|.+.++|++|++.|++..+.|++|.|.++.    
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~----   93 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP----   93 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC----
Confidence            4578999999999999999999999999 999987 7889999999999999999999999999999999999853    


Q ss_pred             CCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 002823          225 PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQI  299 (876)
Q Consensus       225 ~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~I  299 (876)
                            ...+|||+|||.++++++|+++|+.||.|..+++     ++.++|||||+|.+.++|.+|++.|+|..+.|++|
T Consensus        94 ------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i  167 (284)
T 3smz_A           94 ------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL  167 (284)
T ss_dssp             ------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             ------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence                  2468999999999999999999999999999876     45578999999999999999999999999999999


Q ss_pred             EEEeecCch
Q 002823          300 KLEPSHLRG  308 (876)
Q Consensus       300 kVs~A~~k~  308 (876)
                      +|.|+.++.
T Consensus       168 ~v~~a~~~~  176 (284)
T 3smz_A          168 YVHWTDAGQ  176 (284)
T ss_dssp             EEEECCGGG
T ss_pred             EEEECCCCC
Confidence            999998753

>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

Probab=99.93  E-value=3.2e-25  Score=234.01  Aligned_cols=157  Identities=22%  Similarity=0.352  Sum_probs=142.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      ..+.++|||+|||+++|+++|+++|++||.|..|+. .+++|||||+|.+.++|++|++.+++..+.|+.|+|.++.+  
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i-~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~--   95 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH--   95 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc--
Confidence            355689999999999999999999999999999987 56799999999999999999999999999999999999864  


Q ss_pred             CCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhC-CceeC---
Q 002823          224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELN-SRYIA---  295 (876)
Q Consensus       224 ~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~Ln-G~~I~---  295 (876)
                              ..+|||+|||..+++++|+++|+.||.|..|++    ++.++|||||+|.+.++|.+|++.|+ +..+.   
T Consensus        96 --------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~  167 (261)
T 3sde_A           96 --------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTT  167 (261)
T ss_dssp             --------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSS
T ss_pred             --------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCC
Confidence                    458999999999999999999999999999887    55678999999999999999999995 45554   


Q ss_pred             CeEEEEEeecCchhHH
Q 002823          296 GKQIKLEPSHLRGLRK  311 (876)
Q Consensus       296 Gr~IkVs~A~~k~~Rr  311 (876)
                      +++|.|.++.+...++
T Consensus       168 ~r~i~v~~~~~~~~~~  183 (261)
T 3sde_A          168 PRPVIVEPMEQFDDED  183 (261)
T ss_dssp             CCBCEEEECCCEESSS
T ss_pred             CceEEEeeccccCccC
Confidence            8999999998876433

>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

Probab=99.92  E-value=1.2e-24  Score=231.30  Aligned_cols=192  Identities=16%  Similarity=0.186  Sum_probs=151.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe---CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR---ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~---tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      +..+.+.++|||+|||+++|+++|+++|++||+|..|+.   ...++|||||+|.+.++|++|+ .+++..+.|+.|.|.
T Consensus        35 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           35 LTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVS  113 (292)
T ss_dssp             -------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHH-HhCCcEeCCcEEEEE
Confidence            345677899999999999999999999999999999983   2335899999999999999999 599999999999999


Q ss_pred             ecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcC-CeEEEEec----CCcccEEEEEecCHHHHHHHHHHhCCc
Q 002823          218 YSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYG-EIKEIRET----PQKIHQKYIEFYDTRAAEAALRELNSR  292 (876)
Q Consensus       218 ~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG-~I~sVrit----g~skG~AFVeF~d~E~A~kAL~~LnG~  292 (876)
                      ++           ...+|||+|||..+++++|+++|+.|| .|..|++.    +..+|||||+|.+.++|.+|++.|+|.
T Consensus       114 ~~-----------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~  182 (292)
T 2ghp_A          114 HL-----------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL  182 (292)
T ss_dssp             EC-----------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTC
T ss_pred             EC-----------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            86           256899999999999999999999999 99999872    356899999999999999999999999


Q ss_pred             eeCCeEEEEEeecCchhHHHHhhcCCchhhhhhcCCCCCCCCCCCCCCCCcccceeeeccCchh-hhHHHHHHhhccc
Q 002823          293 YIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLN-VKSLAIIYLFTGA  369 (876)
Q Consensus       293 ~I~Gr~IkVs~A~~k~~Rr~l~qQ~~~q~~q~~~g~~~~gsp~~~sp~~~~~~~~~~~fssP~n-~~~~~l~~l~~~~  369 (876)
                      .+.|++|+|.++.++......                     .....    ....-..-+.|.+ +....|..+|...
T Consensus       183 ~~~g~~l~v~~a~~~~~~~~~---------------------~~~~~----~~~~l~v~nlp~~~~t~~~l~~~F~~~  235 (292)
T 2ghp_A          183 KIEGYTLVTKVSNPLEKSKRT---------------------DSATL----EGREIMIRNLSTELLDENLLRESFEGF  235 (292)
T ss_dssp             EETTEECEEEECCCC------------------------------CC----TTTEEEEEEECTTTCCHHHHHHHHGGG
T ss_pred             EeCCcEEEEEECCCCcccccc---------------------cccCC----CCceEEEECCCcccCCHHHHHHHHhcc
Confidence            999999999999876533211                     00000    1112233466777 7777788888764

>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

Probab=99.79  E-value=3.9e-19  Score=172.46  Aligned_cols=127  Identities=21%  Similarity=0.254  Sum_probs=113.0

Q ss_pred             CCccceEeeecCCHHHHHHHHHHc-cccccCCceeeEeecCCCC------------CCCccccccceeEeecCCCCCcHH
Q 002823          181 SKHCGFVTISYYDIRAARNAMKSL-QNKLTRSGKLDIHYSIPKD------------NPSEKEINQGTLVVFNLDSSVSND  247 (876)
Q Consensus       181 gksrGfAFV~F~d~edA~kAl~~L-ng~~l~Gr~L~V~~A~pk~------------~~~ek~~~~~tLfV~NLP~svTee  247 (876)
                      .+.+|+++|+|.+.++|++|++.+ ++..+.| .+.+.++.++.            .........++|||+|||.+++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            456899999999999999999999 9999999 99999886531            112223356799999999999999


Q ss_pred             HHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          248 ELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       248 dLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      +|+++|++||.|.+|++...++|||||+|.+.++|.+|++.|||..|.|++|+|+|++++.
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            9999999999999999976689999999999999999999999999999999999998753

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.78  E-value=2e-18  Score=168.21  Aligned_cols=131  Identities=19%  Similarity=0.267  Sum_probs=104.6

Q ss_pred             EeCCCccceEeeecCCHHHHHHHHHHccccccCCceee-------EeecCCCCC--CCccccccceeEeecCCCCCcHHH
Q 002823          178 YRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD-------IHYSIPKDN--PSEKEINQGTLVVFNLDSSVSNDE  248 (876)
Q Consensus       178 ~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~-------V~~A~pk~~--~~ek~~~~~tLfV~NLP~svTeed  248 (876)
                      ....+.+|||||+|.+.++|++|++.+++.......+.       .........  .........+|||+|||.++++++
T Consensus         7 ln~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~   86 (158)
T 2kn4_A            7 LNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDT   86 (158)
T ss_dssp             EECSSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCHHH
T ss_pred             ecCccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHH
Confidence            34557899999999999999999998886543222222       222211111  112223467999999999999999


Q ss_pred             HHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          249 LHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       249 LreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      |+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|.|++++.
T Consensus        87 l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           87 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             HHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             HHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            9999999999999987     45678999999999999999999999999999999999998864

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.75  E-value=2e-18  Score=160.92  Aligned_cols=103  Identities=12%  Similarity=0.246  Sum_probs=72.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      .+.+|||+|||+++++++|+++|++||.|.+|+   ..+.+||||||+|.+.++|++|++.|++..|.|++|+|.++.++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            357999999999999999999999999999987   34567999999999999999999999999999999999999877


Q ss_pred             CCCCc----cccccceeEeecCCCCCcHHH
Q 002823          223 DNPSE----KEINQGTLVVFNLDSSVSNDE  248 (876)
Q Consensus       223 ~~~~e----k~~~~~tLfV~NLP~svTeed  248 (876)
                      .....    ......+|||+|||+++|++.
T Consensus        84 ~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           84 KEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CC----------------------------
T ss_pred             cccccccccccCCCCceEeCCCCCCccccc
Confidence            54322    122345899999999998863

>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

Probab=99.64  E-value=2.2e-16  Score=145.96  Aligned_cols=104  Identities=22%  Similarity=0.324  Sum_probs=92.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe--CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR--ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~--tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ...++++|||+|||.++++++|+++|++||.|..|+.  .+.++|||||+|.+.++|++|++.|+|..+.|+.|.|.|+.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            3467899999999999999999999999999999983  56779999999999999999999999999999999999987


Q ss_pred             CCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCC
Q 002823          221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGE  258 (876)
Q Consensus       221 pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~  258 (876)
                      ++...            .+++...++++|.++|++||.
T Consensus        84 ~~~~~------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           84 ANRAF------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHHT------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             CChhh------------hhhhHhHhHHHHHHHHHHhCC
Confidence            64322            466778899999999999985

>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}

Probab=99.62  E-value=6.3e-16  Score=140.80  Aligned_cols=75  Identities=23%  Similarity=0.448  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      +++|||+|||+++|+++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|+|++|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            57999999999999999999999999999987     3578999999999999999999999999999999999999976

>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}

Probab=99.62  E-value=1.1e-15  Score=139.12  Aligned_cols=75  Identities=23%  Similarity=0.398  Sum_probs=70.7

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||.++|+++|+++|++||+|++|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+|++|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            458999999999999999999999999999887     466789999999999999999999999999999999999986

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.60  E-value=6.5e-16  Score=148.35  Aligned_cols=119  Identities=18%  Similarity=0.287  Sum_probs=76.5

Q ss_pred             ceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe
Q 002823          185 GFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE  264 (876)
Q Consensus       185 GfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri  264 (876)
                      -++|++|.+...|..|+..+++....|+. .+.+..+    .......++|||+|||.++++++|+++|++||.|+.|++
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~~----~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i   79 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGRP----PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYI   79 (135)
T ss_dssp             -------------------------------CCSCCS----CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEEC
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCC-CCCcCCC----CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE
Confidence            36888999999999999999887766553 2233333    223345679999999999999999999999999999988


Q ss_pred             -----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          265 -----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       265 -----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                           ++..+|||||+|.+.++|++|++.|||..|.|++|+|+|++++.
T Consensus        80 ~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           80 PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             CCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence                 45678999999999999999999999999999999999998765

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.60  E-value=6.4e-15  Score=136.83  Aligned_cols=83  Identities=19%  Similarity=0.259  Sum_probs=76.7

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      +.++|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            4679999999999999999999999999999887     46788999999999999999999999999999999999999


Q ss_pred             CchhHHHH
Q 002823          306 LRGLRKCL  313 (876)
Q Consensus       306 ~k~~Rr~l  313 (876)
                      .+..|+++
T Consensus        85 ~~~~~~~~   92 (110)
T 3s8s_A           85 KGQQRMKY   92 (110)
T ss_dssp             TTHHHHHH
T ss_pred             CCcHHHHH
Confidence            88776644

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.59  E-value=1.9e-15  Score=136.50  Aligned_cols=94  Identities=21%  Similarity=0.306  Sum_probs=81.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCCCCc
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSE  227 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~~~e  227 (876)
                      ++|||+|||.++++++|+++|++||+|..++....++|||||+|.+.++|++|++.|++..+.|++|+|.++.++.....
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~   80 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSR   80 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCccc
Confidence            48999999999999999999999999999985444899999999999999999999999999999999999987764322


Q ss_pred             c------ccccceeEeecCC
Q 002823          228 K------EINQGTLVVFNLD  241 (876)
Q Consensus       228 k------~~~~~tLfV~NLP  241 (876)
                      .      .....+|||+||+
T Consensus        81 ~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           81 FDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSCCCSCCCCSCCCSCCCC
T ss_pred             CCCCCccccCCCceecCCCC
Confidence            1      1235589999997

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.59  E-value=1.2e-15  Score=136.53  Aligned_cols=80  Identities=20%  Similarity=0.364  Sum_probs=72.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccC-CeEEEE-----eCCCccceEeeecCCHHHHHHHHHHcc-ccccCCceeeEeec
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYG-DVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQ-NKLTRSGKLDIHYS  219 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG-~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Ln-g~~l~Gr~L~V~~A  219 (876)
                      +++|||+|||+++|+++|+++|++|| .|.+|+     .++++||||||+|.+.++|++|++.++ +..+.|++|+|+|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            57999999999999999999999999 798887     357899999999999999999999874 56799999999999


Q ss_pred             CCCCCCC
Q 002823          220 IPKDNPS  226 (876)
Q Consensus       220 ~pk~~~~  226 (876)
                      .|+....
T Consensus        81 ~~~~~~~   87 (91)
T 2lxi_A           81 DPKPKIN   87 (91)
T ss_dssp             CSCCCCS
T ss_pred             CCCCCCC
Confidence            9876554

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=6.2e-15  Score=132.94  Aligned_cols=83  Identities=14%  Similarity=0.221  Sum_probs=75.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ....+.++|||+|||.++++++|+++|++||+|..|+.    +++++|||||+|.+.++|++|++.|++..+.|++|+|.
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            35567899999999999999999999999999999883    46788999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 002823          218 YSIPKDN  224 (876)
Q Consensus       218 ~A~pk~~  224 (876)
                      |+.++..
T Consensus        92 ~a~~~~~   98 (100)
T 2do4_A           92 ISNSGPS   98 (100)
T ss_dssp             ECCCCSC
T ss_pred             ECCCCCC
Confidence            9988754

>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

Probab=99.58  E-value=9.3e-15  Score=131.37  Aligned_cols=83  Identities=20%  Similarity=0.311  Sum_probs=76.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..++++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..+.|++|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456799999999999999999999999999999983     677899999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 002823          219 SIPKDNPS  226 (876)
Q Consensus       219 A~pk~~~~  226 (876)
                      +.++....
T Consensus        85 a~~~~~~~   92 (99)
T 1whw_A           85 STIKKEAS   92 (99)
T ss_dssp             CCCCSTTC
T ss_pred             cCCCcccc
Confidence            98876543

>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

Probab=99.58  E-value=4.2e-15  Score=146.69  Aligned_cols=123  Identities=20%  Similarity=0.263  Sum_probs=73.3

Q ss_pred             eecCCHHHHHHHHHHccccccC--CceeeEeecCCCC----------------CCCccccccceeEeecCCCCCcHHHHH
Q 002823          189 ISYYDIRAARNAMKSLQNKLTR--SGKLDIHYSIPKD----------------NPSEKEINQGTLVVFNLDSSVSNDELH  250 (876)
Q Consensus       189 V~F~d~edA~kAl~~Lng~~l~--Gr~L~V~~A~pk~----------------~~~ek~~~~~tLfV~NLP~svTeedLr  250 (876)
                      .+|.+.++|+.|+..+++....  |+.+...+.....                ..........+|||+|||..+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            6789999999999999887654  6666655432110                011122345689999999999999999


Q ss_pred             HHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchhHH
Q 002823          251 HIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       251 eiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~Rr  311 (876)
                      ++|++||.|..|++     ++..+|||||+|.+.++|.+||+.|||..|.|++|+|.|+.++..++
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC---
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCC
Confidence            99999999999887     44568999999999999999999999999999999999998876554

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.58  E-value=4.1e-15  Score=138.17  Aligned_cols=79  Identities=22%  Similarity=0.433  Sum_probs=73.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      +.|.++|||+|||+++++++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|+.+.|+.|+|.+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            46789999999999999999999999999999988     3588999999999999999999999999999999999999


Q ss_pred             cCCC
Q 002823          219 SIPK  222 (876)
Q Consensus       219 A~pk  222 (876)
                      +..+
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            8654

>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

Probab=99.58  E-value=7.2e-15  Score=135.99  Aligned_cols=86  Identities=16%  Similarity=0.264  Sum_probs=77.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      .....+.++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++|+
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   98 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   98 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            345567799999999999999999999999999988872     677899999999999999999999999999999999


Q ss_pred             EeecCCCCCCC
Q 002823          216 IHYSIPKDNPS  226 (876)
Q Consensus       216 V~~A~pk~~~~  226 (876)
                      |+|+.++....
T Consensus        99 V~~a~~~~~~~  109 (115)
T 2cpz_A           99 VQLKRSKNDSK  109 (115)
T ss_dssp             EECCCCSCCCC
T ss_pred             EEEcCCCCcCC
Confidence            99998876543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.57  E-value=6e-15  Score=135.67  Aligned_cols=80  Identities=13%  Similarity=0.204  Sum_probs=73.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccc--cCCceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKL--TRSGKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~--l~Gr~L~V~~A~  220 (876)
                      ...|+++|||+|||.++|+++|+++|++||.|.+++. .+.||||||+|.+.++|++|++.|++..  +.|++|+|+|+.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i-~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~   95 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVV-MPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST   95 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECS
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEE-EcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecc
Confidence            4568899999999999999999999999999999986 3578999999999999999999999976  789999999998


Q ss_pred             CCC
Q 002823          221 PKD  223 (876)
Q Consensus       221 pk~  223 (876)
                      ++.
T Consensus        96 ~k~   98 (100)
T 3r27_A           96 SQK   98 (100)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            754

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.57  E-value=5.6e-15  Score=137.52  Aligned_cols=80  Identities=23%  Similarity=0.378  Sum_probs=72.3

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      .++|||+|||.++++++|+++|++||.|++|++   ...++|||||+|.+.++|++|++.|+|..|.|++|+|.+++++.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~   84 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   84 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcc
Confidence            468999999999999999999999999999887   34468999999999999999999999999999999999998876


Q ss_pred             hHH
Q 002823          309 LRK  311 (876)
Q Consensus       309 ~Rr  311 (876)
                      .+.
T Consensus        85 ~~~   87 (115)
T 4f25_A           85 ERE   87 (115)
T ss_dssp             C--
T ss_pred             ccc
Confidence            554

>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

Probab=99.56  E-value=1.5e-14  Score=131.31  Aligned_cols=84  Identities=14%  Similarity=0.220  Sum_probs=77.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ....+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..+.|++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            35567899999999999999999999999999999983     6778999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 002823          217 HYSIPKDNP  225 (876)
Q Consensus       217 ~~A~pk~~~  225 (876)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            999887554

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=9.3e-15  Score=132.46  Aligned_cols=85  Identities=20%  Similarity=0.281  Sum_probs=77.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      +....+.++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.|++..+.|++|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            445677899999999999999999999999999999983     477899999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q 002823          216 IHYSIPKDNP  225 (876)
Q Consensus       216 V~~A~pk~~~  225 (876)
                      |.++.++...
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dnm_A           87 VQVARYGRRD   96 (103)
T ss_dssp             EEECSSCCSC
T ss_pred             EEECCcCCCC
Confidence            9999876544

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=1.4e-14  Score=129.04  Aligned_cols=82  Identities=18%  Similarity=0.313  Sum_probs=75.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .++++|||+|||.++++++|+++|++||+|..++.     +++++|||||+|.+.++|++|++.|++..+.|++|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            46789999999999999999999999999999982     4678999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 002823          220 IPKDNPS  226 (876)
Q Consensus       220 ~pk~~~~  226 (876)
                      .++....
T Consensus        83 ~~~~~~~   89 (95)
T 2dnz_A           83 TERLDGG   89 (95)
T ss_dssp             SCCCCCC
T ss_pred             ccccCCC
Confidence            8876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.7e-14  Score=129.82  Aligned_cols=83  Identities=20%  Similarity=0.360  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++ |++..+.|++|+|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            4567899999999999999999999999999999983     46789999999999999999998 99999999999999


Q ss_pred             ecCCCCCCC
Q 002823          218 YSIPKDNPS  226 (876)
Q Consensus       218 ~A~pk~~~~  226 (876)
                      ++.++....
T Consensus        85 ~a~~~~~~~   93 (99)
T 2dgs_A           85 RAEPRDSKS   93 (99)
T ss_dssp             ECCCCCCCC
T ss_pred             ECCCCcccC
Confidence            998876543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.56  E-value=9e-15  Score=131.41  Aligned_cols=81  Identities=15%  Similarity=0.142  Sum_probs=73.5

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchhHH
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~Rr  311 (876)
                      ...|||+||++.+|+++|+++|.+||+|+++++ ..+||||||+|.+.++|++|++.||+.++.|++|+|+++...+..+
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l-~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e~~~~~   85 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHP-YLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSENEVQS   85 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCHHHHHH
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEE-cCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCHHHHHH
Confidence            568999999999999999999999999999998 4489999999999999999999999999999999999996545444


Q ss_pred             HH
Q 002823          312 CL  313 (876)
Q Consensus       312 ~l  313 (876)
                      .+
T Consensus        86 ~~   87 (89)
T 2wbr_A           86 IM   87 (89)
T ss_dssp             HH
T ss_pred             Hh
Confidence            44

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.55  E-value=2e-14  Score=130.77  Aligned_cols=84  Identities=18%  Similarity=0.378  Sum_probs=77.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe------CCCccceEeeecCCHHHHHHHHHHc-cccccCCcee
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR------ASKHCGFVTISYYDIRAARNAMKSL-QNKLTRSGKL  214 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~------tgksrGfAFV~F~d~edA~kAl~~L-ng~~l~Gr~L  214 (876)
                      ..+.+.++|||+|||.++++++|+++|++||.|..|+.      +++++|||||+|.+.++|++|++.| ++..+.|++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            35677899999999999999999999999999999984      5667999999999999999999999 9999999999


Q ss_pred             eEeecCCCCCC
Q 002823          215 DIHYSIPKDNP  225 (876)
Q Consensus       215 ~V~~A~pk~~~  225 (876)
                      +|.|+.++...
T Consensus        90 ~v~~a~~~~~~  100 (107)
T 2cph_A           90 VLEWADSEVTV  100 (107)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999887654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.5e-14  Score=131.13  Aligned_cols=84  Identities=14%  Similarity=0.326  Sum_probs=77.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe---CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR---ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~---tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ...+.++|||+|||+++++++|+++|++||.|..|+.   +++++|||||+|.+.++|++|++.|++..+.|++|+|.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            4567899999999999999999999999999999883   4678999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 002823          220 IPKDNPS  226 (876)
Q Consensus       220 ~pk~~~~  226 (876)
                      .++....
T Consensus        91 ~~~~~~~   97 (103)
T 2d9p_A           91 QRKEERQ   97 (103)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            8876544

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.55  E-value=1.9e-14  Score=132.91  Aligned_cols=85  Identities=15%  Similarity=0.334  Sum_probs=77.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ....+.++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.|++..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            35567899999999999999999999999999999883     5678999999999999999999999999999999999


Q ss_pred             eecCCCCCCC
Q 002823          217 HYSIPKDNPS  226 (876)
Q Consensus       217 ~~A~pk~~~~  226 (876)
                      .|+.++....
T Consensus        90 ~~a~~~~~~~   99 (115)
T 2dgo_A           90 NWATRKPPAP   99 (115)
T ss_dssp             EESSCCCCCS
T ss_pred             EEccCCCCCC
Confidence            9998876543

>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

Probab=99.55  E-value=1.1e-14  Score=126.40  Aligned_cols=77  Identities=21%  Similarity=0.346  Sum_probs=71.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      +.+|||+|||.++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            46899999999999999999999999999987     2577899999999999999999999999999999999999987


Q ss_pred             CC
Q 002823          222 KD  223 (876)
Q Consensus       222 k~  223 (876)
                      ++
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.55  E-value=1.3e-14  Score=128.43  Aligned_cols=83  Identities=14%  Similarity=0.195  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ...+.++|||+|||.++++++|+++|++||+|..++   .+++++|||||+|.+.++|++|++.|++..+.|++|+|+++
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            345679999999999999999999999999999988   35678999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 002823          220 IPKDNP  225 (876)
Q Consensus       220 ~pk~~~  225 (876)
                      .++...
T Consensus        84 ~~~~~~   89 (92)
T 2dgv_A           84 RNASGP   89 (92)
T ss_dssp             SCCSSC
T ss_pred             CCCCCC
Confidence            876543

>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

Probab=99.55  E-value=1.7e-14  Score=133.05  Aligned_cols=84  Identities=12%  Similarity=0.167  Sum_probs=74.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccc--cCCceeeEee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKL--TRSGKLDIHY  218 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~--l~Gr~L~V~~  218 (876)
                      +....|+++|||+|||+++++++|+++|++||.|..|+.. +.||||||+|.+.++|++|++.|++..  +.|++|+|.|
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~   87 (104)
T 1wex_A            9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-CCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            3456788999999999999999999999999999999853 358999999999999999999998754  9999999999


Q ss_pred             cCCCCCC
Q 002823          219 SIPKDNP  225 (876)
Q Consensus       219 A~pk~~~  225 (876)
                      +.++...
T Consensus        88 a~~~~~~   94 (104)
T 1wex_A           88 STSKRIT   94 (104)
T ss_dssp             CSSSSCC
T ss_pred             ccCcccc
Confidence            9876543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1e-14  Score=135.29  Aligned_cols=83  Identities=20%  Similarity=0.261  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccc--cccCCceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN--KLTRSGKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng--~~l~Gr~L~V~~A~  220 (876)
                      ...+.++|||+|||+++++++|+++|++||+|.+|++. +.||||||+|.+.++|++|++.+++  ..+.|++|+|.|+.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~-~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~   90 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN   90 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcC
Confidence            45678999999999999999999999999999999953 3589999999999999999998864  68999999999998


Q ss_pred             CCCCCC
Q 002823          221 PKDNPS  226 (876)
Q Consensus       221 pk~~~~  226 (876)
                      ++....
T Consensus        91 ~~~~~~   96 (105)
T 1sjq_A           91 HKELKT   96 (105)
T ss_dssp             SSSCCC
T ss_pred             CCCCCc
Confidence            876544

>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

Probab=99.55  E-value=1.8e-14  Score=132.04  Aligned_cols=84  Identities=13%  Similarity=0.241  Sum_probs=76.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ....+.++|||+|||.++++++|+++|++||.|..|+  .+++++|||||+|.+.++|++|++.|++..|.|++|+|+|+
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            3556789999999999999999999999999999988  44567899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 002823          220 IPKDNP  225 (876)
Q Consensus       220 ~pk~~~  225 (876)
                      .++...
T Consensus        97 ~~~~~~  102 (109)
T 1x4a_A           97 RSGRGT  102 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            876543

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.55  E-value=1.1e-14  Score=130.45  Aligned_cols=79  Identities=23%  Similarity=0.333  Sum_probs=73.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      |+++|||+|||.++++++|+++|++||.|..++.     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.|+.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            5789999999999999999999999999999983     46789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 002823          221 PKDN  224 (876)
Q Consensus       221 pk~~  224 (876)
                      ++..
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7654

>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}

Probab=99.55  E-value=8.2e-15  Score=128.27  Aligned_cols=78  Identities=14%  Similarity=0.322  Sum_probs=70.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .+.++|||+|||.++++++|+++|++||.|..++.     +++++|||||+|.+.++|++|++.|++..+.|++|+|.|+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            46789999999999999999999999999999883     5678999999999999999999999999999999999999


Q ss_pred             CCC
Q 002823          220 IPK  222 (876)
Q Consensus       220 ~pk  222 (876)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            765

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1.3e-14  Score=131.54  Aligned_cols=83  Identities=18%  Similarity=0.368  Sum_probs=76.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            4567899999999999999999999999999999882     56789999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 002823          218 YSIPKDNP  225 (876)
Q Consensus       218 ~A~pk~~~  225 (876)
                      |+.++...
T Consensus        91 ~a~~~~~~   98 (103)
T 2cq0_A           91 WAKPSTNS   98 (103)
T ss_dssp             ESSCCCCS
T ss_pred             ECCCCCCC
Confidence            99887654

>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

Probab=99.55  E-value=2.9e-14  Score=129.18  Aligned_cols=85  Identities=15%  Similarity=0.311  Sum_probs=76.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe---CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR---ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~---tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ....+.++|||+|||+++++++|+++|++||.|..|+.   ...++|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35567899999999999999999999999999999983   234799999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 002823          219 SIPKDNPS  226 (876)
Q Consensus       219 A~pk~~~~  226 (876)
                      +.++....
T Consensus        90 a~~~~~~~   97 (103)
T 2cq3_A           90 ATARVMTN   97 (103)
T ss_dssp             CCSSCCCC
T ss_pred             cccCCCCC
Confidence            98876543

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=2.3e-14  Score=129.82  Aligned_cols=84  Identities=14%  Similarity=0.356  Sum_probs=75.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe---CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR---ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~---tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+.+.++|||+|||+++++++|+++|++||.|..|+.   ...++|||||+|.+.++|++|++.|++..+.|++|+|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            35577899999999999999999999999999999983   344789999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002823          219 SIPKDNP  225 (876)
Q Consensus       219 A~pk~~~  225 (876)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9886544

>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

Probab=99.55  E-value=1.5e-14  Score=136.90  Aligned_cols=90  Identities=20%  Similarity=0.256  Sum_probs=77.3

Q ss_pred             ccCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccc--cccCCce
Q 002823          136 VAGEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN--KLTRSGK  213 (876)
Q Consensus       136 ~~ge~p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng--~~l~Gr~  213 (876)
                      .+++......++++|||+|||+++++++|+++|++||.|.+|++. +.||||||+|.+.++|++|++.+++  ..+.|++
T Consensus        20 ~~~~~~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~-~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~   98 (119)
T 2ad9_A           20 HMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQP   98 (119)
T ss_dssp             --CCTTSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEE-GGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBC
T ss_pred             ccccccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEECCHHHHHHHHHHhccCCceECCeE
Confidence            344445566789999999999999999999999999999999853 3589999999999999999999885  5799999


Q ss_pred             eeEeecCCCCCCC
Q 002823          214 LDIHYSIPKDNPS  226 (876)
Q Consensus       214 L~V~~A~pk~~~~  226 (876)
                      |+|.|+.++....
T Consensus        99 l~V~~a~~k~~~~  111 (119)
T 2ad9_A           99 IYIQFSNHKELKT  111 (119)
T ss_dssp             CEEEECSSSSCCC
T ss_pred             EEEEEccCCCCCc
Confidence            9999998876554

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.55  E-value=3.4e-15  Score=133.68  Aligned_cols=77  Identities=17%  Similarity=0.256  Sum_probs=69.9

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcC-CeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhC-CceeCCeEEEEEee
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYG-EIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELN-SRYIAGKQIKLEPS  304 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG-~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~Ln-G~~I~Gr~IkVs~A  304 (876)
                      +++|||+|||.++|+++|+++|++|| +|++|++     ++.++|||||+|.+.++|++|++.++ +..+.|++|+|+|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 8999887     46788999999999999999999875 56899999999999


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      .++.
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8864

>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}

Probab=99.54  E-value=2.2e-14  Score=125.60  Aligned_cols=77  Identities=18%  Similarity=0.409  Sum_probs=70.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      +..+|||+|||.++++++|+++|++||.|.+|++     ++..+|||||+|.+.++|++|++.|||..+.|++|+|+|++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            4569999999999999999999999999999887     44568999999999999999999999999999999999998


Q ss_pred             Cc
Q 002823          306 LR  307 (876)
Q Consensus       306 ~k  307 (876)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            75

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.7e-14  Score=128.22  Aligned_cols=78  Identities=19%  Similarity=0.306  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||.++++++|+++|++||+|..++.     +++++|||||+|.+.++|++|++.|++..+.|++|+|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            4466799999999999999999999999999999983     36789999999999999999999999999999999999


Q ss_pred             ecC
Q 002823          218 YSI  220 (876)
Q Consensus       218 ~A~  220 (876)
                      |++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

>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

Probab=99.54  E-value=3.1e-14  Score=127.78  Aligned_cols=81  Identities=19%  Similarity=0.333  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccC--CceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTR--SGKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~--Gr~L~V~~A~  220 (876)
                      ...++++|||+|||.++++++|+++|++||+|..|+... .+|||||+|.+.++|++|++.|++..+.  |++|+|.|+.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~   91 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeC-CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECC
Confidence            346679999999999999999999999999999998643 4899999999999999999999999999  9999999998


Q ss_pred             CCCC
Q 002823          221 PKDN  224 (876)
Q Consensus       221 pk~~  224 (876)
                      ++..
T Consensus        92 ~~~~   95 (97)
T 1why_A           92 SGPS   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8653

>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

Probab=99.54  E-value=2.9e-14  Score=130.56  Aligned_cols=85  Identities=15%  Similarity=0.344  Sum_probs=77.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHcc------ccccC
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQ------NKLTR  210 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Ln------g~~l~  210 (876)
                      ....+.++|||+|||+++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|+      +..+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            35567899999999999999999999999999999983     46789999999999999999999999      99999


Q ss_pred             CceeeEeecCCCCCCC
Q 002823          211 SGKLDIHYSIPKDNPS  226 (876)
Q Consensus       211 Gr~L~V~~A~pk~~~~  226 (876)
                      |+.|+|.|+.++....
T Consensus        90 g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             SCEEEEECCCCCCCCC
T ss_pred             CEEEEEEECCCCccCC
Confidence            9999999998876543

>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

Probab=99.54  E-value=2.7e-14  Score=129.62  Aligned_cols=83  Identities=14%  Similarity=0.279  Sum_probs=75.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCC---ceee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRS---GKLD  215 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G---r~L~  215 (876)
                      ...+.++|||+|||.++++++|+++|++||.|..|+    .+++++|||||+|.+.++|++|++.|++..+.|   ++|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            345689999999999999999999999999999988    346679999999999999999999999999998   9999


Q ss_pred             EeecCCCCCC
Q 002823          216 IHYSIPKDNP  225 (876)
Q Consensus       216 V~~A~pk~~~  225 (876)
                      |.|+.++...
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9999887654

>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

Probab=99.54  E-value=2.2e-14  Score=124.47  Aligned_cols=76  Identities=14%  Similarity=0.214  Sum_probs=71.0

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      .+|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|.|++++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            47999999999999999999999999999887     3556899999999999999999999999999999999999986


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.6e-14  Score=130.44  Aligned_cols=83  Identities=18%  Similarity=0.323  Sum_probs=76.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..+.|++|+|.|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            457799999999999999999999999999999983     466899999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 002823          219 SIPKDNPS  226 (876)
Q Consensus       219 A~pk~~~~  226 (876)
                      +.++....
T Consensus        89 a~~~~~~~   96 (102)
T 2cqb_A           89 AKPMRIKE   96 (102)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCCCC
Confidence            98876543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.4e-14  Score=131.79  Aligned_cols=82  Identities=12%  Similarity=0.330  Sum_probs=75.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ....++++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..+.|++|.|
T Consensus        18 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   97 (106)
T 1p27_B           18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   97 (106)
T ss_dssp             CCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            34566789999999999999999999999999999983     4778999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 002823          217 HYSIPKD  223 (876)
Q Consensus       217 ~~A~pk~  223 (876)
                      .|+.++.
T Consensus        98 ~~a~~~~  104 (106)
T 1p27_B           98 DWCFVRG  104 (106)
T ss_dssp             EESEESS
T ss_pred             EeecCCC
Confidence            9998764

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=2.4e-14  Score=129.03  Aligned_cols=79  Identities=22%  Similarity=0.308  Sum_probs=73.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...++|||+|||.++++++|+++|++||.|..|++    ++..++||||+|.+.++|++|++.|||..+.|++|+|.|++
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   94 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISN   94 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            45679999999999999999999999999999887    35567999999999999999999999999999999999999


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      ++.
T Consensus        95 ~~~   97 (100)
T 2do4_A           95 SGP   97 (100)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            865

>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*

Probab=99.54  E-value=1.7e-14  Score=125.66  Aligned_cols=77  Identities=18%  Similarity=0.348  Sum_probs=71.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+.++|||+|||+++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|+|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45779999999999999999999999999999998     3566899999999999999999999999999999999999


Q ss_pred             cC
Q 002823          219 SI  220 (876)
Q Consensus       219 A~  220 (876)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.9e-14  Score=129.99  Aligned_cols=83  Identities=14%  Similarity=0.329  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||+++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..+.|++|+|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3456799999999999999999999999999999983     45689999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 002823          218 YSIPKDNP  225 (876)
Q Consensus       218 ~A~pk~~~  225 (876)
                      |+.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99877654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.8e-14  Score=128.14  Aligned_cols=79  Identities=13%  Similarity=0.274  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...++++|||+|||.++++++|+++|++||+|..++.     +++++|||||+|.+.++|++|++.|++..+.|++|+|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4567899999999999999999999999999999983     46789999999999999999999999999999999999


Q ss_pred             ecCC
Q 002823          218 YSIP  221 (876)
Q Consensus       218 ~A~p  221 (876)
                      |+..
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9864

>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

Probab=99.53  E-value=2.6e-14  Score=128.47  Aligned_cols=80  Identities=24%  Similarity=0.420  Sum_probs=74.1

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++.|||..|.|++|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34679999999999999999999999999999998     4557899999999999999999999999999999999999


Q ss_pred             cCchh
Q 002823          305 HLRGL  309 (876)
Q Consensus       305 ~~k~~  309 (876)
                      +++..
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            98754

>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

Probab=99.53  E-value=3.3e-14  Score=130.30  Aligned_cols=79  Identities=23%  Similarity=0.315  Sum_probs=72.9

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ...++|||+|||.++++++|+++|++||.|+.|++  ++..++||||+|.+.++|++|++.||+..|.|++|+|+|++++
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   99 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   99 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccC
Confidence            45679999999999999999999999999999888  4456899999999999999999999999999999999999885


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus       100 ~  100 (109)
T 1x4a_A          100 R  100 (109)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=3.9e-14  Score=128.36  Aligned_cols=81  Identities=28%  Similarity=0.359  Sum_probs=73.7

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEec---CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET---PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVrit---g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...++|||+|||..+++++|+++|++||.|+.|++.   ...++||||+|.+.++|++|++.|++..|.|++|+|.|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   92 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   92 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCC
Confidence            456799999999999999999999999999999882   33679999999999999999999999999999999999998


Q ss_pred             chhH
Q 002823          307 RGLR  310 (876)
Q Consensus       307 k~~R  310 (876)
                      +..+
T Consensus        93 ~~~~   96 (103)
T 2cqi_A           93 PSSQ   96 (103)
T ss_dssp             TTCC
T ss_pred             Cccc
Confidence            6543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.53  E-value=2e-14  Score=128.88  Aligned_cols=81  Identities=23%  Similarity=0.379  Sum_probs=74.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe--------CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR--------ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~--------tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      .+.++|||+|||.++++++|+++|++||+|..|+.        +++++|||||+|.+.++|++|++.|++..+.|++|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            56789999999999999999999999999999882        3378999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 002823          217 HYSIPKDNP  225 (876)
Q Consensus       217 ~~A~pk~~~  225 (876)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999877654

>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

Probab=99.53  E-value=2.9e-14  Score=130.85  Aligned_cols=84  Identities=24%  Similarity=0.249  Sum_probs=74.1

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcc--ccccCCceeeEee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ--NKLTRSGKLDIHY  218 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Ln--g~~l~Gr~L~V~~  218 (876)
                      +....|+++|||+|||+++++++|+++|++||.|..|+.. +.||||||+|.+.++|++|++.|+  +..+.|++|+|.|
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~   87 (101)
T 2cq1_A            9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML-KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQY   87 (101)
T ss_dssp             CCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-CCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEE
Confidence            3455788999999999999999999999999999999853 359999999999999999999875  5679999999999


Q ss_pred             cCCCCCC
Q 002823          219 SIPKDNP  225 (876)
Q Consensus       219 A~pk~~~  225 (876)
                      +.++...
T Consensus        88 a~~~~~~   94 (101)
T 2cq1_A           88 SNHKELK   94 (101)
T ss_dssp             CSCSSCC
T ss_pred             cCcccCc
Confidence            9876544

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.3e-14  Score=129.43  Aligned_cols=82  Identities=15%  Similarity=0.344  Sum_probs=74.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEE-E-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTF-Y-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV-~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      .++++|||+|||.++++++|+++|++||.|..+ +     .+++++|||||+|.+.++|++|++.|++..+.|++|+|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            467899999999999999999999999999877 5     3566899999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 002823          219 SIPKDNPS  226 (876)
Q Consensus       219 A~pk~~~~  226 (876)
                      +.++....
T Consensus        83 a~~~~~~~   90 (96)
T 1x5t_A           83 AFKKDSKG   90 (96)
T ss_dssp             SCCCCCCC
T ss_pred             ecccCCCC
Confidence            98876543

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.53  E-value=2e-14  Score=132.57  Aligned_cols=82  Identities=16%  Similarity=0.316  Sum_probs=75.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ....++++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|+|..+.|++|+|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            35567899999999999999999999999999999882     4678999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 002823          217 HYSIPKD  223 (876)
Q Consensus       217 ~~A~pk~  223 (876)
                      .++.++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9998764

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=5.1e-14  Score=125.21  Aligned_cols=77  Identities=19%  Similarity=0.318  Sum_probs=71.7

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||..+++++|+++|++||.|..|++     ++..++||||+|.+.++|.+|++.|||..+.|++|+|+|+
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP   92 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            45679999999999999999999999999999887     3567899999999999999999999999999999999998


Q ss_pred             cC
Q 002823          305 HL  306 (876)
Q Consensus       305 ~~  306 (876)
                      ++
T Consensus        93 ~~   94 (95)
T 2cqc_A           93 SS   94 (95)
T ss_dssp             SC
T ss_pred             CC
Confidence            75

>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

Probab=99.53  E-value=1.8e-14  Score=137.43  Aligned_cols=83  Identities=16%  Similarity=0.330  Sum_probs=76.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      +....++++|||+|||.++++++|+++|++||+|..|+.     +++.+|||||+|.+.++|++|++.|++..|.|++|+
T Consensus        40 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~  119 (129)
T 2kxn_B           40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR  119 (129)
T ss_dssp             SSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            345677899999999999999999999999999999983     467899999999999999999999999999999999


Q ss_pred             EeecCCCC
Q 002823          216 IHYSIPKD  223 (876)
Q Consensus       216 V~~A~pk~  223 (876)
                      |+|+.++.
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99998764

>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

Probab=99.53  E-value=2.5e-14  Score=130.06  Aligned_cols=84  Identities=20%  Similarity=0.394  Sum_probs=76.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHcccccc---CCce
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLT---RSGK  213 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l---~Gr~  213 (876)
                      ..+.+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..+   .|++
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            35667899999999999999999999999999999982     467899999999999999999999999987   8999


Q ss_pred             eeEeecCCCCCC
Q 002823          214 LDIHYSIPKDNP  225 (876)
Q Consensus       214 L~V~~A~pk~~~  225 (876)
                      |+|.|+.++...
T Consensus        88 l~v~~a~~~~~~   99 (106)
T 2dgp_A           88 IQVKPADSESRG   99 (106)
T ss_dssp             CEEEECCCCSCC
T ss_pred             EEEEECCccccc
Confidence            999999877543

>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

Probab=99.53  E-value=1.8e-14  Score=132.83  Aligned_cols=81  Identities=12%  Similarity=0.094  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccc--cCCceeeEeec
Q 002823          143 DEHPSRTLLLRKINS-NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKL--TRSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~-~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~--l~Gr~L~V~~A  219 (876)
                      ...|+++|||+|||+ ++++++|+++|++||.|.+|++ .+.+|||||+|.+.++|++|++.|++..  |.|++|+|.|+
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i-~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   89 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLS   89 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEE-CSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEE
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEE-EcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEEC
Confidence            345789999999999 9999999999999999999996 3567999999999999999999999754  99999999999


Q ss_pred             CCCCC
Q 002823          220 IPKDN  224 (876)
Q Consensus       220 ~pk~~  224 (876)
                      .++..
T Consensus        90 ~~~~~   94 (102)
T 1x4d_A           90 QKYKR   94 (102)
T ss_dssp             CCCTT
T ss_pred             CCCCC
Confidence            86543

>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*

Probab=99.53  E-value=3.3e-14  Score=123.86  Aligned_cols=75  Identities=25%  Similarity=0.391  Sum_probs=70.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++..++||||+|.+.++|.+|++.|||..+.|++|+|+|++
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            4679999999999999999999999999999887     34578999999999999999999999999999999999985

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.53  E-value=2.2e-14  Score=131.91  Aligned_cols=78  Identities=21%  Similarity=0.172  Sum_probs=71.5

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCce--eCCeEEEEEeecCc
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY--IAGKQIKLEPSHLR  307 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~--I~Gr~IkVs~A~~k  307 (876)
                      .+.++|||+|||.++++++|+++|++||.|++|++. +.||+|||+|.+.++|.+|++.|++..  +.|++|+|+|++.+
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~-~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM-PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecccc
Confidence            357799999999999999999999999999999984 468999999999999999999999875  78999999999875


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      +
T Consensus        98 ~   98 (100)
T 3r27_A           98 K   98 (100)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=3.9e-14  Score=131.27  Aligned_cols=83  Identities=18%  Similarity=0.311  Sum_probs=75.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ..+.+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.+++ .+.|++|+|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            35677899999999999999999999999999999983     467899999999999999999999998 899999999


Q ss_pred             eecCCCCCC
Q 002823          217 HYSIPKDNP  225 (876)
Q Consensus       217 ~~A~pk~~~  225 (876)
                      +++.++..+
T Consensus        91 ~~a~~~~~~   99 (116)
T 2cqd_A           91 NLAYLGAKP   99 (116)
T ss_dssp             EESTTTCCC
T ss_pred             EEcccCCCc
Confidence            999776544

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=3.6e-14  Score=126.17  Aligned_cols=83  Identities=19%  Similarity=0.266  Sum_probs=75.4

Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          140 HLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       140 ~p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .+....+.++|||+|||.++++++|+++|++||.|..++..   ++||||+|.+.++|++|++.|++..+.|++|+|+++
T Consensus         3 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            3 SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CSCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            34456778999999999999999999999999999999873   569999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 002823          220 IPKDNP  225 (876)
Q Consensus       220 ~pk~~~  225 (876)
                      .++...
T Consensus        80 ~~~~~~   85 (92)
T 2dgt_A           80 TSRLRT   85 (92)
T ss_dssp             SCCCSC
T ss_pred             cCCCCC
Confidence            887654

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.52  E-value=1.6e-14  Score=128.58  Aligned_cols=80  Identities=15%  Similarity=0.191  Sum_probs=72.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      +..+.+.++|||+|||+++++++|+++|++||+|..|+.    .++++|||||+|.+.++|++|++.|++..+.|++|+|
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV   89 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEE
Confidence            345667899999999999999999999999999999882    3667999999999999999999999999999999999


Q ss_pred             eecC
Q 002823          217 HYSI  220 (876)
Q Consensus       217 ~~A~  220 (876)
                      +|+.
T Consensus        90 ~~a~   93 (95)
T 2ywk_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             EEcC
Confidence            9975

>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

Probab=99.52  E-value=1.8e-14  Score=135.07  Aligned_cols=82  Identities=13%  Similarity=0.139  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEcCCCCC-CCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccc--cccCCceeeEeec
Q 002823          143 DEHPSRTLLLRKINSN-IEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN--KLTRSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~-vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng--~~l~Gr~L~V~~A  219 (876)
                      ...|+++|||+|||++ +++++|+++|++||+|.+|++ .+.||||||+|.+.++|++|++.|++  ..+.|++|+|.|+
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i-~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a   99 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   99 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEE-ecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEC
Confidence            4678999999999998 999999999999999999996 46799999999999999999999875  4599999999999


Q ss_pred             CCCCCC
Q 002823          220 IPKDNP  225 (876)
Q Consensus       220 ~pk~~~  225 (876)
                      .++...
T Consensus       100 ~~~~~~  105 (112)
T 1x4f_A          100 EKYKKL  105 (112)
T ss_dssp             CSCSSS
T ss_pred             cccccc
Confidence            876543

>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

Probab=99.52  E-value=2.4e-14  Score=132.41  Aligned_cols=80  Identities=16%  Similarity=0.313  Sum_probs=73.6

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|++||.|++|++     ++..++||||+|.+.++|++|++.||+..|.|++|+|+|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            35679999999999999999999999999999887     4566799999999999999999999999999999999999


Q ss_pred             cCchh
Q 002823          305 HLRGL  309 (876)
Q Consensus       305 ~~k~~  309 (876)
                      +++..
T Consensus       103 ~~~~~  107 (115)
T 2cpz_A          103 RSKND  107 (115)
T ss_dssp             CCSCC
T ss_pred             CCCCc
Confidence            98653

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=2.5e-14  Score=129.62  Aligned_cols=82  Identities=22%  Similarity=0.336  Sum_probs=74.9

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ....++|||+|||.++++++|+++|++||.|..|++   ++..++||||+|.+.++|++|++.|||..|.|++|+|.|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ   91 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEec
Confidence            345679999999999999999999999999999887   34678999999999999999999999999999999999999


Q ss_pred             CchhH
Q 002823          306 LRGLR  310 (876)
Q Consensus       306 ~k~~R  310 (876)
                      ++..+
T Consensus        92 ~~~~~   96 (103)
T 2d9p_A           92 RKEER   96 (103)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87644

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.52  E-value=4e-14  Score=126.84  Aligned_cols=79  Identities=15%  Similarity=0.245  Sum_probs=73.4

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||..+++++|+++|++||.|.+|++     ++..+|||||+|.+.++|.+|++.|+|..+.|++|+|.++++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            568999999999999999999999999999988     355689999999999999999999999999999999999998


Q ss_pred             chhH
Q 002823          307 RGLR  310 (876)
Q Consensus       307 k~~R  310 (876)
                      +...
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            7644

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=4e-14  Score=125.40  Aligned_cols=79  Identities=20%  Similarity=0.296  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      ..+.++|||+|||.++++++|+++|++||+|..++..   +|||||+|.+.++|++|++.|++..+.|++|+|+|+.++.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   81 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKS   81 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCC
Confidence            4567999999999999999999999999999999874   8999999999999999999999999999999999998876


Q ss_pred             CC
Q 002823          224 NP  225 (876)
Q Consensus       224 ~~  225 (876)
                      ..
T Consensus        82 ~~   83 (90)
T 2dnq_A           82 KA   83 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.52  E-value=3.5e-14  Score=131.74  Aligned_cols=80  Identities=16%  Similarity=0.237  Sum_probs=73.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      +....+.++|||+|||+++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..+.|++|+
T Consensus        34 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  113 (118)
T 2khc_A           34 QIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK  113 (118)
T ss_dssp             SCCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            345667899999999999999999999999999999983     467899999999999999999999999999999999


Q ss_pred             EeecC
Q 002823          216 IHYSI  220 (876)
Q Consensus       216 V~~A~  220 (876)
                      |+|++
T Consensus       114 V~~ak  118 (118)
T 2khc_A          114 VQLKK  118 (118)
T ss_dssp             EEEC-
T ss_pred             EEecC
Confidence            99873

>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

Probab=99.52  E-value=4.5e-14  Score=128.35  Aligned_cols=83  Identities=13%  Similarity=0.248  Sum_probs=75.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----C-CCccceEeeecCCHHHHHHHHHHccccccCCcee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----A-SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKL  214 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----t-gksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L  214 (876)
                      +....+.++|||+|||.++++++|+++|++|| |..|+.     + ++++|||||+|.+.++|++|+ .|++..+.|++|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   86 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEE
Confidence            34556789999999999999999999999999 999983     2 778999999999999999999 999999999999


Q ss_pred             eEeecCCCCCC
Q 002823          215 DIHYSIPKDNP  225 (876)
Q Consensus       215 ~V~~A~pk~~~  225 (876)
                      +|.++.++...
T Consensus        87 ~V~~a~~~~~~   97 (104)
T 1wi8_A           87 RVDVADQAQDK   97 (104)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999887654

>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*

Probab=99.52  E-value=3.6e-14  Score=130.06  Aligned_cols=81  Identities=27%  Similarity=0.370  Sum_probs=74.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||..+++++|+++|++||.|..|++     ++..+|||||+|.+.++|.+|++.|+|..|.|++|+|.|+
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            35679999999999999999999999999999988     3456899999999999999999999999999999999999


Q ss_pred             cCchhH
Q 002823          305 HLRGLR  310 (876)
Q Consensus       305 ~~k~~R  310 (876)
                      +++..+
T Consensus       104 ~~~~~~  109 (110)
T 1oo0_B          104 FVKGPK  109 (110)
T ss_dssp             EESSCC
T ss_pred             ccCCCC
Confidence            887654

>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

Probab=99.52  E-value=3.2e-14  Score=129.21  Aligned_cols=79  Identities=23%  Similarity=0.293  Sum_probs=73.5

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||.++++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++.|++..|.|++|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   92 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   92 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            45679999999999999999999999999999988     4557899999999999999999999999999999999999


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      +++.
T Consensus        93 ~~~~   96 (105)
T 1x5u_A           93 SAHN   96 (105)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8865

>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*

Probab=99.51  E-value=2.9e-14  Score=130.69  Aligned_cols=83  Identities=14%  Similarity=0.300  Sum_probs=75.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ....++++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.|+|..+.|++|+|
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  100 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  100 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34566799999999999999999999999999999983     4678999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 002823          217 HYSIPKDN  224 (876)
Q Consensus       217 ~~A~pk~~  224 (876)
                      .|+.++..
T Consensus       101 ~~a~~~~~  108 (110)
T 1oo0_B          101 DWCFVKGP  108 (110)
T ss_dssp             EESEESSC
T ss_pred             EEcccCCC
Confidence            99987643

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.51  E-value=4.3e-14  Score=128.58  Aligned_cols=81  Identities=20%  Similarity=0.358  Sum_probs=73.8

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEec------CCcccEEEEEecCHHHHHHHHHHh-CCceeCCeEEEE
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET------PQKIHQKYIEFYDTRAAEAALREL-NSRYIAGKQIKL  301 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVrit------g~skG~AFVeF~d~E~A~kAL~~L-nG~~I~Gr~IkV  301 (876)
                      .....+|||+|||..+++++|+++|++||.|..|++.      +..++||||+|.+.++|++|++.| |+..|.|++|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            3456799999999999999999999999999999883      335899999999999999999999 999999999999


Q ss_pred             EeecCchh
Q 002823          302 EPSHLRGL  309 (876)
Q Consensus       302 s~A~~k~~  309 (876)
                      +|++++..
T Consensus        92 ~~a~~~~~   99 (107)
T 2cph_A           92 EWADSEVT   99 (107)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99998653

>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*

Probab=99.51  E-value=9.7e-15  Score=165.99  Aligned_cols=145  Identities=19%  Similarity=0.281  Sum_probs=103.9

Q ss_pred             HHHHhhccCCeEEEEe-------CCCccceE-----eeecCCHHHHHHHHHHccccccCCc-----------e--eeEee
Q 002823          164 LKALFEQYGDVRTFYR-------ASKHCGFV-----TISYYDIRAARNAMKSLQNKLTRSG-----------K--LDIHY  218 (876)
Q Consensus       164 L~elFsqfG~I~sV~~-------tgksrGfA-----FV~F~d~edA~kAl~~Lng~~l~Gr-----------~--L~V~~  218 (876)
                      |.++|.++|+|..|..       ..+..+|+     |+.|....++..++..++......+           .  ..+..
T Consensus         9 L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~~   88 (437)
T 3pgw_S            9 LLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKM   88 (437)
T ss_pred             HHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            7889999999988731       11233444     7788776555444433222211111           0  01111


Q ss_pred             cCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCce
Q 002823          219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRY  293 (876)
Q Consensus       219 A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~  293 (876)
                      ..+............+|||+|||..+|+++|+++|++||.|+.|++     ++..+|||||+|.+.++|.+||..|||..
T Consensus        89 ~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~  168 (437)
T 3pgw_S           89 WDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKK  168 (437)
T ss_pred             cCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCE
Confidence            1222222222334579999999999999999999999999999887     45678999999999999999999999999


Q ss_pred             eCCeEEEEEeecCch
Q 002823          294 IAGKQIKLEPSHLRG  308 (876)
Q Consensus       294 I~Gr~IkVs~A~~k~  308 (876)
                      |.|++|+|.|+.++.
T Consensus       169 i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          169 IDGRRVLVDVERGRT  183 (437)
T ss_pred             ECCEEEEEEEeCCCC
Confidence            999999999998754

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=7.2e-14  Score=124.20  Aligned_cols=76  Identities=28%  Similarity=0.425  Sum_probs=70.5

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++.||+..|.|++|+|+|+
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            45679999999999999999999999999999988     2456799999999999999999999999999999999998


Q ss_pred             c
Q 002823          305 H  305 (876)
Q Consensus       305 ~  305 (876)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=3.6e-14  Score=128.66  Aligned_cols=83  Identities=18%  Similarity=0.312  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhc-cCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccc-cCCceeeE
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQ-YGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKL-TRSGKLDI  216 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsq-fG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~-l~Gr~L~V  216 (876)
                      ...+.++|||+|||+++++++|+++|++ ||.|..|+.    +++++|||||+|.+.++|++|++.|++.. +.|++|+|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            4567899999999999999999999999 999999883    56789999999999999999999999999 99999999


Q ss_pred             eecCCCCCC
Q 002823          217 HYSIPKDNP  225 (876)
Q Consensus       217 ~~A~pk~~~  225 (876)
                      .++.++...
T Consensus        85 ~~a~~~~~~   93 (104)
T 2dhg_A           85 SVAIPKASR   93 (104)
T ss_dssp             CBCCCCCSC
T ss_pred             EEccCCCcC
Confidence            999877654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.51  E-value=2.2e-14  Score=128.21  Aligned_cols=82  Identities=23%  Similarity=0.332  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      .+.+.++|||+|||.++++++|+++|++||.|..+..+++++|||||+|.+.++|++|++.|++..+.|++|+|.++.++
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            45678999999999999999999999999999888778889999999999999999999999999999999999999876


Q ss_pred             CC
Q 002823          223 DN  224 (876)
Q Consensus       223 ~~  224 (876)
                      ..
T Consensus        92 ~~   93 (96)
T 1fjc_A           92 GG   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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

Probab=99.51  E-value=4.1e-14  Score=127.50  Aligned_cols=81  Identities=22%  Similarity=0.340  Sum_probs=74.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ...+.++|||+|||+++++++|+++|++||+|..|+. .+.+|||||+|.+.++|++|++.|++..+.|++|+|.|+.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~-~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   89 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEE-ETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEE-ecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCC
Confidence            3466789999999999999999999999999999986 356899999999999999999999999999999999999876


Q ss_pred             CC
Q 002823          223 DN  224 (876)
Q Consensus       223 ~~  224 (876)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpj_A           90 AS   91 (99)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=3.7e-14  Score=126.30  Aligned_cols=78  Identities=28%  Similarity=0.376  Sum_probs=72.4

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++.|||..+.|++|+|++++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            4579999999999999999999999999999888     35568999999999999999999999999999999999998


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      ++.
T Consensus        84 ~~~   86 (95)
T 2dnz_A           84 ERL   86 (95)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            864

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.51  E-value=5.9e-14  Score=129.63  Aligned_cols=81  Identities=19%  Similarity=0.404  Sum_probs=74.0

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||..+++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++.|+|..|.|++|+|.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   92 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            35679999999999999999999999999999887     4456899999999999999999999999999999999999


Q ss_pred             cCchhH
Q 002823          305 HLRGLR  310 (876)
Q Consensus       305 ~~k~~R  310 (876)
                      +++..+
T Consensus        93 ~~~~~~   98 (115)
T 2dgo_A           93 TRKPPA   98 (115)
T ss_dssp             SCCCCC
T ss_pred             cCCCCC
Confidence            986543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=3.6e-14  Score=128.11  Aligned_cols=83  Identities=18%  Similarity=0.326  Sum_probs=75.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ...+.++|||+|||.++++++|+++|++||.|.-++ .+++.+|||||+|.+.++|++|++.|++..+.|+.|+|.|+.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   90 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGP   90 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCC
Confidence            456789999999999999999999999999995554 4678899999999999999999999999999999999999988


Q ss_pred             CCCC
Q 002823          222 KDNP  225 (876)
Q Consensus       222 k~~~  225 (876)
                      +...
T Consensus        91 ~~~~   94 (101)
T 2fc9_A           91 RGSP   94 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=4.4e-14  Score=127.99  Aligned_cols=80  Identities=20%  Similarity=0.210  Sum_probs=73.7

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++.|||..|.|++|+|.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   92 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEC
Confidence            45679999999999999999999999999999887     4566899999999999999999999999999999999999


Q ss_pred             cCchh
Q 002823          305 HLRGL  309 (876)
Q Consensus       305 ~~k~~  309 (876)
                      +++..
T Consensus        93 ~~~~~   97 (103)
T 2cq0_A           93 KPSTN   97 (103)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            88653

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=2.9e-14  Score=129.70  Aligned_cols=84  Identities=15%  Similarity=0.286  Sum_probs=76.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ....+.++|||+|||+++++++|+++|++||+|..|+     .+++++|||||+|.+.++|++|++. ++..|.|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            3566789999999999999999999999999999988     2567899999999999999999998 999999999999


Q ss_pred             eecCCCCCCC
Q 002823          217 HYSIPKDNPS  226 (876)
Q Consensus       217 ~~A~pk~~~~  226 (876)
                      .++.++....
T Consensus        90 ~~a~~~~~~~   99 (105)
T 2dh8_A           90 KPCTPRGMQP   99 (105)
T ss_dssp             CCSCCSSCCT
T ss_pred             EEccCCCCCC
Confidence            9998876543

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=4.2e-14  Score=123.39  Aligned_cols=78  Identities=18%  Similarity=0.350  Sum_probs=71.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHc-cccccCCceeeEeecC
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSL-QNKLTRSGKLDIHYSI  220 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~L-ng~~l~Gr~L~V~~A~  220 (876)
                      ..+.+.++|||+|||.++++++|+++|++||.|..++.. +++|||||+|.+.++|++|++.| ++..+.|++|+|+|++
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~-~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEE-CCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            355678999999999999999999999999999999863 46899999999999999999999 9999999999999974

>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

Probab=99.51  E-value=4.6e-14  Score=128.14  Aligned_cols=81  Identities=16%  Similarity=0.199  Sum_probs=73.7

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC---eEEEEE
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG---KQIKLE  302 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G---r~IkVs  302 (876)
                      ...++|||+|||..+++++|+++|++||.|..|++    ++..++||||+|.+.++|++|++.|||..+.|   ++|+|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            35679999999999999999999999999999887    34458999999999999999999999999998   999999


Q ss_pred             eecCchhH
Q 002823          303 PSHLRGLR  310 (876)
Q Consensus       303 ~A~~k~~R  310 (876)
                      |++++..+
T Consensus        93 ~a~~~~~~  100 (105)
T 2dnh_A           93 FADTDKES  100 (105)
T ss_dssp             ESCSSCCC
T ss_pred             ECccCccc
Confidence            99987644

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=3.7e-14  Score=129.01  Aligned_cols=79  Identities=27%  Similarity=0.431  Sum_probs=73.0

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||..+++++|+++|++||.|..|++     ++..+|||||+|.+.++|++|++.|||..|.|++|+|.|+
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            35679999999999999999999999999999887     3566899999999999999999999999999999999999


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      +++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            8764

>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

Probab=99.51  E-value=1.2e-14  Score=129.08  Aligned_cols=78  Identities=13%  Similarity=0.147  Sum_probs=66.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccC--CeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYG--DVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG--~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      .+|||+|||+++++++|+++|++||  .|.+++     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4899999999999999999999999  888887     367899999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 002823          221 PKDNP  225 (876)
Q Consensus       221 pk~~~  225 (876)
                      ++...
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            76543

>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}

Probab=99.51  E-value=3.7e-14  Score=124.16  Aligned_cols=77  Identities=27%  Similarity=0.424  Sum_probs=71.1

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEec-----CC-cccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET-----PQ-KIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVrit-----g~-skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      .++|||+|||.++++++|+++|++||.|..|++.     +. .+|||||+|.+.++|.+|++.|||..+.|++|+|+++.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   83 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL   83 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECC
Confidence            5689999999999999999999999999998872     12 78999999999999999999999999999999999998


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      +..
T Consensus        84 ~~~   86 (88)
T 4a8x_A           84 APW   86 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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

Probab=99.51  E-value=6.1e-14  Score=128.38  Aligned_cols=81  Identities=19%  Similarity=0.314  Sum_probs=74.4

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEec-----CCcccEEEEEecCHHHHHHHHHHhC------CceeCCeE
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET-----PQKIHQKYIEFYDTRAAEAALRELN------SRYIAGKQ  298 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVrit-----g~skG~AFVeF~d~E~A~kAL~~Ln------G~~I~Gr~  298 (876)
                      ...++|||+|||.++++++|+++|++||.|..|++.     +..++||||+|.+.++|.+|++.|+      +..|.|++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            356799999999999999999999999999999883     4678999999999999999999999      99999999


Q ss_pred             EEEEeecCchhH
Q 002823          299 IKLEPSHLRGLR  310 (876)
Q Consensus       299 IkVs~A~~k~~R  310 (876)
                      |+|.|++++..+
T Consensus        93 l~v~~a~~~~~~  104 (111)
T 1x4h_A           93 LKVDLAVTRDEA  104 (111)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEEECCCCccC
Confidence            999999987543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.1e-14  Score=133.10  Aligned_cols=79  Identities=18%  Similarity=0.246  Sum_probs=71.7

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEEeecCch
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS--RYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG--~~I~Gr~IkVs~A~~k~  308 (876)
                      ...+|||+|||+++++++|+++|++||+|++|++.. .||||||+|.+.++|++|++.|++  ..|.|++|+|.|++++.
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~-~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~   93 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE   93 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCC
Confidence            467999999999999999999999999999999843 489999999999999999999864  78999999999998865


Q ss_pred             hH
Q 002823          309 LR  310 (876)
Q Consensus       309 ~R  310 (876)
                      .+
T Consensus        94 ~~   95 (105)
T 1sjq_A           94 LK   95 (105)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.51  E-value=4.2e-14  Score=135.08  Aligned_cols=82  Identities=21%  Similarity=0.325  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HHhhccCCeEEEEe--CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          143 DEHPSRTLLLRKINSNIEDSELK----ALFEQYGDVRTFYR--ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~----elFsqfG~I~sV~~--tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ...++++|||+|||+.+++++|+    ++|++||+|.+|..  +++++|||||+|.+.++|++|++.|+|..+.|++|+|
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            45678999999999999999876    69999999999884  5688999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 002823          217 HYSIPKDN  224 (876)
Q Consensus       217 ~~A~pk~~  224 (876)
                      .|+.++..
T Consensus       105 ~~a~~~~~  112 (127)
T 2a3j_A          105 TFSETPQS  112 (127)
T ss_dssp             EECCCCCH
T ss_pred             EEccCcch
Confidence            99987643

>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

Probab=99.51  E-value=9.9e-14  Score=125.69  Aligned_cols=80  Identities=19%  Similarity=0.355  Sum_probs=73.3

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEec---CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET---PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVrit---g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ....++|||+|||.++++++|+++|++||.|..|++.   ...++||||+|.+.++|++|++.|++..|.|++|+|.+++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   91 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            3456799999999999999999999999999999883   2358999999999999999999999999999999999999


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      ++.
T Consensus        92 ~~~   94 (103)
T 2cq3_A           92 ARV   94 (103)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            865

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.51  E-value=1.8e-14  Score=130.76  Aligned_cols=75  Identities=21%  Similarity=0.294  Sum_probs=68.1

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCC--eEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCc----eeCCeEEE
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGE--IKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSR----YIAGKQIK  300 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~--I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~----~I~Gr~Ik  300 (876)
                      -.+|||+|||+++|+++|+++|++||.  |.+|++     ++.+||||||+|.+.++|++|++.|||.    .|.||+|+
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~   88 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIG   88 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEE
Confidence            458999999999999999999999995  567776     4677899999999999999999999996    58999999


Q ss_pred             EEeecC
Q 002823          301 LEPSHL  306 (876)
Q Consensus       301 Vs~A~~  306 (876)
                      |+|++.
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999975

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=4e-14  Score=127.22  Aligned_cols=80  Identities=10%  Similarity=0.288  Sum_probs=73.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeE-EEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCce----
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVR-TFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGK----  213 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~-sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~----  213 (876)
                      ..++++|||+|||+++++++|+++|++||+|. .++     .+++++|||||+|.+.++|++|++.|++..+.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            45689999999999999999999999999998 887     25678999999999999999999999999999999    


Q ss_pred             eeEeecCCCC
Q 002823          214 LDIHYSIPKD  223 (876)
Q Consensus       214 L~V~~A~pk~  223 (876)
                      |+|.|+.+..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999998754

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.5e-14  Score=129.27  Aligned_cols=80  Identities=24%  Similarity=0.355  Sum_probs=73.6

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++.||+..|.|++|+|.|+
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            35679999999999999999999999999999988     3457899999999999999999999999999999999999


Q ss_pred             cCchh
Q 002823          305 HLRGL  309 (876)
Q Consensus       305 ~~k~~  309 (876)
                      +++..
T Consensus        90 ~~~~~   94 (102)
T 2cqb_A           90 KPMRI   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98653

>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* ...

Probab=99.50  E-value=2.5e-14  Score=127.84  Aligned_cols=82  Identities=23%  Similarity=0.461  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HHhhccCCeEEEEe--CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          143 DEHPSRTLLLRKINSNIEDSELK----ALFEQYGDVRTFYR--ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~----elFsqfG~I~sV~~--tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      +..++++|||+|||.++++++|+    ++|++||.|..|+.  +++++|||||+|.+.++|++|++.|+|..+.|+.|+|
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            45678999999999999999999    99999999999984  3568899999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 002823          217 HYSIPKDN  224 (876)
Q Consensus       217 ~~A~pk~~  224 (876)
                      .|+.++..
T Consensus        84 ~~a~~~~~   91 (97)
T 1nu4_A           84 QYAKTDSD   91 (97)
T ss_dssp             EECSSCCT
T ss_pred             EEccCCCc
Confidence            99987653

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.50  E-value=6.4e-14  Score=127.09  Aligned_cols=83  Identities=14%  Similarity=0.298  Sum_probs=74.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      +....+.++|||+|||.++++++|+++|++|| |..|+.     +++++|||||+|.+.++|++|+ .|++..|.|++|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   86 (103)
T 2dng_A            9 ELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLR   86 (103)
T ss_dssp             CCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEE
Confidence            34556789999999999999999999999997 988872     4778999999999999999999 8999999999999


Q ss_pred             EeecCCCCCC
Q 002823          216 IHYSIPKDNP  225 (876)
Q Consensus       216 V~~A~pk~~~  225 (876)
                      |.++.++...
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dng_A           87 VDIAEGRKQD   96 (103)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEecCCCCC
Confidence            9999887654

>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}

Probab=99.50  E-value=4.8e-14  Score=123.47  Aligned_cols=78  Identities=10%  Similarity=0.267  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe------CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR------ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~------tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .+++|||+|||.++++++|+++|++||.|..++.      .++.+|||||+|.+.++|++|++.|+|..+.|+.|+|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            4579999999999999999999999999999983      1238999999999999999999999999999999999999


Q ss_pred             CCCC
Q 002823          220 IPKD  223 (876)
Q Consensus       220 ~pk~  223 (876)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=2.7e-14  Score=128.98  Aligned_cols=79  Identities=23%  Similarity=0.422  Sum_probs=73.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++.||+..|.|++|+|+|++
T Consensus        11 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   90 (102)
T 1x5s_A           11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   90 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            4679999999999999999999999999999988     33468999999999999999999999999999999999998


Q ss_pred             Cchh
Q 002823          306 LRGL  309 (876)
Q Consensus       306 ~k~~  309 (876)
                      ++..
T Consensus        91 ~~~~   94 (102)
T 1x5s_A           91 KSSD   94 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=5.7e-14  Score=126.24  Aligned_cols=81  Identities=16%  Similarity=0.146  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ....+++|||+|||+++++++|+++|++||.|.....+++++|||||+|.+.++|++|++.|++..+.|++|+|.++.++
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            34557899999999999999999999999999633355788999999999999999999999999999999999999876


Q ss_pred             C
Q 002823          223 D  223 (876)
Q Consensus       223 ~  223 (876)
                      .
T Consensus        95 ~   95 (97)
T 2e5j_A           95 R   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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

Probab=99.50  E-value=3.4e-14  Score=130.59  Aligned_cols=95  Identities=18%  Similarity=0.295  Sum_probs=81.6

Q ss_pred             CCceeeEeecCCCCCCCccccccceeEeecCCCC-CcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHH
Q 002823          210 RSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSS-VSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRE  288 (876)
Q Consensus       210 ~Gr~L~V~~A~pk~~~~ek~~~~~tLfV~NLP~s-vTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~  288 (876)
                      .|.+|.|..+.+..... .....++|||+|||.. +++++|+++|++||.|..|++   .++||||+|.+.++|++|++.
T Consensus         6 ~g~~~~~~~s~~~~~~~-~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~   81 (110)
T 1wf1_A            6 SGMSLKLQASNVTNKND-PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLG   81 (110)
T ss_dssp             CSCCCCCCCCCSCCSCC-CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHH
T ss_pred             CCcccccccCCCCCCCC-CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHH
Confidence            46677777665543332 2234579999999999 999999999999999999998   789999999999999999999


Q ss_pred             hCCceeCCeEEEEEeecCch
Q 002823          289 LNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       289 LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      |++..|.|++|+|+|++++.
T Consensus        82 l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           82 ENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             HTTCEETTEECCEEESCCCC
T ss_pred             cCCCEECCeEEEEEECCCCC
Confidence            99999999999999998643

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.50  E-value=6.3e-14  Score=133.71  Aligned_cols=83  Identities=17%  Similarity=0.346  Sum_probs=76.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .+.+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..+.|++|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            4567899999999999999999999999999999883     46789999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 002823          218 YSIPKDNP  225 (876)
Q Consensus       218 ~A~pk~~~  225 (876)
                      ++.++...
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99887654

>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}

Probab=99.50  E-value=5.8e-14  Score=131.10  Aligned_cols=83  Identities=20%  Similarity=0.320  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      +..+.++|||+|||.++++++|+++|++||.|..|+.    +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.+
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999883    567899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002823          219 SIPKDNP  225 (876)
Q Consensus       219 A~pk~~~  225 (876)
                      +.++...
T Consensus        83 a~~~~~~   89 (116)
T 2fy1_A           83 AKKPSFQ   89 (116)
T ss_dssp             CCCSSCS
T ss_pred             CCCCCCC
Confidence            9876543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=5e-14  Score=129.75  Aligned_cols=83  Identities=22%  Similarity=0.321  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeE--------EEE-----eCCCccceEeeecCCHHHHHHHHHHcccccc
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVR--------TFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLT  209 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~--------sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l  209 (876)
                      .+.+.++|||+|||.++++++|+++|++||.|.        .|+     .+++++|||||+|.+.++|++|++.|++..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            556789999999999999999999999999998        466     3467899999999999999999999999999


Q ss_pred             CCceeeEeecCCCCCC
Q 002823          210 RSGKLDIHYSIPKDNP  225 (876)
Q Consensus       210 ~Gr~L~V~~A~pk~~~  225 (876)
                      .|++|+|.++.++...
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999887654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=5.6e-14  Score=126.41  Aligned_cols=79  Identities=18%  Similarity=0.322  Sum_probs=72.7

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||..+++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++ |++..|.|++|+|.++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            35679999999999999999999999999999988     34578999999999999999998 9999999999999999


Q ss_pred             cCchh
Q 002823          305 HLRGL  309 (876)
Q Consensus       305 ~~k~~  309 (876)
                      +++..
T Consensus        87 ~~~~~   91 (99)
T 2dgs_A           87 EPRDS   91 (99)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            98653

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.50  E-value=5.2e-14  Score=126.83  Aligned_cols=79  Identities=18%  Similarity=0.322  Sum_probs=72.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEE--------EE-----eCCCccceEeeecCCHHHHHHHHHHccccc
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRT--------FY-----RASKHCGFVTISYYDIRAARNAMKSLQNKL  208 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~s--------V~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~  208 (876)
                      ....+.++|||+|||.++++++|+++|++||.|..        ++     .+++++|||||+|.+.++|++|++.|+|..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34567899999999999999999999999999988        66     246789999999999999999999999999


Q ss_pred             cCCceeeEeecC
Q 002823          209 TRSGKLDIHYSI  220 (876)
Q Consensus       209 l~Gr~L~V~~A~  220 (876)
                      +.|++|+|+++.
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999873

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=5.5e-14  Score=127.00  Aligned_cols=83  Identities=18%  Similarity=0.357  Sum_probs=76.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ...+.++|||+|||.++++++|+++|++|+.|..++  .+++++|||||+|.+.++|++|++.|++..|.|++|+|.|+.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   90 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK   90 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            456789999999999999999999999998887776  467889999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002823          221 PKDNP  225 (876)
Q Consensus       221 pk~~~  225 (876)
                      ++...
T Consensus        91 ~~~~~   95 (102)
T 2fc8_A           91 PKGEG   95 (102)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            87654

>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

Probab=99.50  E-value=9.7e-14  Score=127.54  Aligned_cols=79  Identities=20%  Similarity=0.389  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEcCCCCC-CCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          143 DEHPSRTLLLRKINSN-IEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~-vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ...+.++|||+|||++ +++++|+++|++||+|..|+.   .+|||||+|.+.++|++|++.|++..+.|++|+|.|+.+
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   99 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE   99 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCC
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            4456689999999999 999999999999999999988   789999999999999999999999999999999999975


Q ss_pred             CCC
Q 002823          222 KDN  224 (876)
Q Consensus       222 k~~  224 (876)
                      +..
T Consensus       100 ~~~  102 (110)
T 1wf1_A          100 PKP  102 (110)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            443

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=9.2e-14  Score=127.98  Aligned_cols=81  Identities=15%  Similarity=0.174  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ...++++|||+|||.++++++|+++|++||.|..|+    .+++++|||||+|.+.++|++|++.|++..+.|++|+|++
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            456689999999999999999999999999999887    2466799999999999999999999999999999999999


Q ss_pred             cCCCC
Q 002823          219 SIPKD  223 (876)
Q Consensus       219 A~pk~  223 (876)
                      +.+..
T Consensus        91 a~~~~   95 (114)
T 2do0_A           91 DERAL   95 (114)
T ss_dssp             CSCCC
T ss_pred             cccCC
Confidence            87543

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.50  E-value=7.7e-14  Score=124.22  Aligned_cols=77  Identities=18%  Similarity=0.225  Sum_probs=71.1

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...++|||+|||..+++++|+++|++||+|..|++    .+..++||||+|.+.++|++|++.||+..+.|++|+|+|++
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            35679999999999999999999999999999887    34458999999999999999999999999999999999987


Q ss_pred             C
Q 002823          306 L  306 (876)
Q Consensus       306 ~  306 (876)
                      .
T Consensus        94 ~   94 (95)
T 2ywk_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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

Probab=99.49  E-value=7.7e-14  Score=125.24  Aligned_cols=78  Identities=19%  Similarity=0.227  Sum_probs=72.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeC--CeEEEEEeecCc
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIA--GKQIKLEPSHLR  307 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~--Gr~IkVs~A~~k  307 (876)
                      .+.++|||+|||.++++++|+++|++||.|+.|++.. .++||||+|.+.++|++|++.||+..+.  |++|+|+|++++
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~   93 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeC-CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCC
Confidence            3467999999999999999999999999999999843 4899999999999999999999999999  999999999986


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus        94 ~   94 (97)
T 1why_A           94 P   94 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=3.8e-14  Score=130.67  Aligned_cols=80  Identities=16%  Similarity=0.350  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe---CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR---ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~---tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ...+.++|||+|||.++++++|+++|++||+|..++.   .++++|||||+|.+.++|++|++.|+|..+.|++|+|+++
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  104 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA  104 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4567899999999999999999999999999998883   3457999999999999999999999999999999999999


Q ss_pred             CCC
Q 002823          220 IPK  222 (876)
Q Consensus       220 ~pk  222 (876)
                      .++
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            875

>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

Probab=99.49  E-value=5.2e-14  Score=129.83  Aligned_cols=84  Identities=18%  Similarity=0.308  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCe----EEEE-eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDV----RTFY-RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I----~sV~-~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...++++|||+|||.++++++|+++|++||.|    ..++ .+++++|||||+|.+.++|++|++.|++..+.|++|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            45678999999999999999999999999988    4444 578899999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 002823          218 YSIPKDNPS  226 (876)
Q Consensus       218 ~A~pk~~~~  226 (876)
                      |+.++....
T Consensus       101 ~a~~~~~~~  109 (115)
T 2cpx_A          101 FGKNKKQRS  109 (115)
T ss_dssp             ECCCCSCCC
T ss_pred             EccCCCCCC
Confidence            998876543

>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

Probab=99.49  E-value=7.2e-14  Score=125.66  Aligned_cols=78  Identities=21%  Similarity=0.261  Sum_probs=71.5

Q ss_pred             ccceeEeecCCCCCcHHHHH----HHhhhcCCeEEEEec--CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          231 NQGTLVVFNLDSSVSNDELH----HIFGVYGEIKEIRET--PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLr----eiFs~fG~I~sVrit--g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...+|||+|||.++++++|+    ++|++||+|++|++.  ...++||||+|.+.++|++|++.|||..+.|++|+|+++
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   87 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   87 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            45689999999999999999    999999999999983  223899999999999999999999999999999999999


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      +++.
T Consensus        88 ~~~~   91 (96)
T 2dgx_A           88 TGAS   91 (96)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            8754

>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

Probab=99.49  E-value=1.7e-14  Score=130.64  Aligned_cols=82  Identities=22%  Similarity=0.351  Sum_probs=74.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .+.+.++|||+|||.++++++|+++|++||.|..++.     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.
T Consensus         4 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   83 (104)
T 1p1t_A            4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             SHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             cCCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            3456789999999999999999999999999988872     56789999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 002823          218 YSIPKDN  224 (876)
Q Consensus       218 ~A~pk~~  224 (876)
                      |+.++..
T Consensus        84 ~a~~~~~   90 (104)
T 1p1t_A           84 NAASEKN   90 (104)
T ss_dssp             ETTCTTH
T ss_pred             eCCCccc
Confidence            9987653

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.49  E-value=6.3e-14  Score=133.70  Aligned_cols=82  Identities=23%  Similarity=0.311  Sum_probs=74.5

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ....++|||+|||.++++++|+++|+.||+|++|++     ++..+|||||+|.+.++|.+|++.|||..|.|++|+|++
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345679999999999999999999999999999887     345689999999999999999999999999999999999


Q ss_pred             ecCchhH
Q 002823          304 SHLRGLR  310 (876)
Q Consensus       304 A~~k~~R  310 (876)
                      ++++..+
T Consensus       119 a~~~~~~  125 (139)
T 1u6f_A          119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9987543

>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*

Probab=99.49  E-value=6.6e-14  Score=131.35  Aligned_cols=84  Identities=13%  Similarity=0.349  Sum_probs=76.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ....+.++|||+|||.++++++|+++|++||.|..|..     +++++|||||+|.+.++|++|++.|++..|.|+.|.|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            34566789999999999999999999999999999983     6778999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 002823          217 HYSIPKDNP  225 (876)
Q Consensus       217 ~~A~pk~~~  225 (876)
                      .|+.++...
T Consensus        97 ~~a~~~~~~  105 (126)
T 3ex7_B           97 DWCFVRGPP  105 (126)
T ss_dssp             EESEESSSC
T ss_pred             EEecCCCCC
Confidence            999876544

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=3.4e-14  Score=126.76  Aligned_cols=79  Identities=20%  Similarity=0.365  Sum_probs=72.5

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEE-Ee-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-RE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sV-ri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ..++|||+|||.++++++|+++|++||.|..| ++     ++..++||||+|.+.++|++|++.|||..+.|++|+|+|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45799999999999999999999999999888 77     3446899999999999999999999999999999999999


Q ss_pred             cCchh
Q 002823          305 HLRGL  309 (876)
Q Consensus       305 ~~k~~  309 (876)
                      +++..
T Consensus        84 ~~~~~   88 (96)
T 1x5t_A           84 FKKDS   88 (96)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            88653

>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

Probab=99.49  E-value=9e-14  Score=127.61  Aligned_cols=80  Identities=16%  Similarity=0.191  Sum_probs=71.9

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHh--CCceeCCeEEEEEeecCc
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALREL--NSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~L--nG~~I~Gr~IkVs~A~~k  307 (876)
                      .+.++|||+|||.++++++|+++|++||.|++|++.. .||||||+|.+.++|.+|++.|  ++..+.|++|+|.|++++
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   91 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   91 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcc
Confidence            4567999999999999999999999999999998843 4899999999999999999987  568899999999999986


Q ss_pred             hhH
Q 002823          308 GLR  310 (876)
Q Consensus       308 ~~R  310 (876)
                      ..+
T Consensus        92 ~~~   94 (101)
T 2cq1_A           92 ELK   94 (101)
T ss_dssp             SCC
T ss_pred             cCc
Confidence            533

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=4.9e-14  Score=127.70  Aligned_cols=79  Identities=23%  Similarity=0.337  Sum_probs=73.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||.++++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++.|||..|.|++|+|.++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            34679999999999999999999999999999988     3567899999999999999999999999999999999999


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      +++.
T Consensus        91 ~~~~   94 (103)
T 2dnm_A           91 RYGR   94 (103)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            8754

>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

Probab=99.49  E-value=4.7e-14  Score=130.31  Aligned_cols=80  Identities=19%  Similarity=0.378  Sum_probs=73.6

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEec-----CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET-----PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVrit-----g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|+.||.|..|++.     +..+|||||+|.+.++|++|+ .|||..|.|++|+|.++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            356699999999999999999999999999999983     567899999999999999999 99999999999999999


Q ss_pred             cCchhH
Q 002823          305 HLRGLR  310 (876)
Q Consensus       305 ~~k~~R  310 (876)
                      +++..+
T Consensus       102 ~~~~~~  107 (114)
T 2cq4_A          102 QAEKNR  107 (114)
T ss_dssp             HHHHHH
T ss_pred             CCCccC
Confidence            887654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.49  E-value=2.8e-14  Score=129.54  Aligned_cols=78  Identities=15%  Similarity=0.289  Sum_probs=69.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCC--eEEEE-----eCCCccceEeeecCCHHHHHHHHHHcccc----ccCCc
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGD--VRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNK----LTRSG  212 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~--I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~----~l~Gr  212 (876)
                      +..=.||||+|||+++|+++|+++|++||.  |.+|+     .++++||||||+|.+.++|++|++.|++.    .+.||
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            344579999999999999999999999995  55666     46889999999999999999999999997    48999


Q ss_pred             eeeEeecCC
Q 002823          213 KLDIHYSIP  221 (876)
Q Consensus       213 ~L~V~~A~p  221 (876)
                      +|.|+||+.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999864

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.49  E-value=4.1e-14  Score=127.77  Aligned_cols=78  Identities=18%  Similarity=0.216  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ....++|||+|||.++++++|+++|++||.|..++.. +++|||||+|.+.++|++|++.|++..+.|++|+|.|+.++
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            3456899999999999999999999999999999863 78999999999999999999999999999999999998764

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=4.6e-14  Score=126.57  Aligned_cols=78  Identities=21%  Similarity=0.354  Sum_probs=71.8

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEec------C--CcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET------P--QKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLE  302 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVrit------g--~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs  302 (876)
                      ..++|||+|||.++++++|+++|++||.|..|++.      +  ..++||||+|.+.++|++|++.|||..|.|++|+|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            45789999999999999999999999999998872      1  567999999999999999999999999999999999


Q ss_pred             eecCch
Q 002823          303 PSHLRG  308 (876)
Q Consensus       303 ~A~~k~  308 (876)
                      +++++.
T Consensus        84 ~a~~~~   89 (98)
T 2cpf_A           84 ISERAT   89 (98)
T ss_dssp             CSSCSS
T ss_pred             EccCCC
Confidence            998864

>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

Probab=99.49  E-value=1.4e-13  Score=126.39  Aligned_cols=81  Identities=15%  Similarity=0.178  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCC-----ceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRS-----GKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G-----r~L~V~  217 (876)
                      .....++|||+|||+++++++|+++|++||+|..|++...  |||||+|.+.++|++|++.|+++.|.|     ++|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~   88 (108)
T 1x4c_A           11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   88 (108)
T ss_dssp             CCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEE
Confidence            3456799999999999999999999999999999986333  999999999999999999999999999     999999


Q ss_pred             ecCCCCCC
Q 002823          218 YSIPKDNP  225 (876)
Q Consensus       218 ~A~pk~~~  225 (876)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (108)
T 1x4c_A           89 VDGPRSPS   96 (108)
T ss_dssp             ESSCCSCC
T ss_pred             eCCCCCCC
Confidence            99887654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.49  E-value=1.5e-14  Score=131.34  Aligned_cols=79  Identities=16%  Similarity=0.195  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCC------CCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCC-
Q 002823          144 EHPSRTLLLRKINS------NIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRS-  211 (876)
Q Consensus       144 e~pSrTLFVgNLP~------~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G-  211 (876)
                      +..+++|||+|||.      ++++++|+++|++||.|.+|+     .+++++|||||+|.+.++|++|++.|+|..+.| 
T Consensus         3 ~~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~   82 (100)
T 3ns6_A            3 LGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK   82 (100)
T ss_dssp             SCGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            34568999999999      999999999999999999998     248899999999999999999999999999999 


Q ss_pred             ceeeEeecCCC
Q 002823          212 GKLDIHYSIPK  222 (876)
Q Consensus       212 r~L~V~~A~pk  222 (876)
                      +.|+|.++.++
T Consensus        83 r~l~V~~a~~~   93 (100)
T 3ns6_A           83 HRLFLYTMKDV   93 (100)
T ss_dssp             CBCEEEESHHH
T ss_pred             eEEEEEECchh
Confidence            99999998764

>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

Probab=99.49  E-value=1.1e-13  Score=125.70  Aligned_cols=81  Identities=17%  Similarity=0.363  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ...+.++|||+|||+++++++|+++|++||.|..|+..   ++||||+|.+.++|++|++.|++..|.|++|+|.|+.++
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   83 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP   83 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCC
Confidence            34567999999999999999999999999999999863   779999999999999999999999999999999999887


Q ss_pred             CCCC
Q 002823          223 DNPS  226 (876)
Q Consensus       223 ~~~~  226 (876)
                      ....
T Consensus        84 ~~~~   87 (103)
T 2dgu_A           84 DQKR   87 (103)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            6543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=6.4e-14  Score=124.05  Aligned_cols=76  Identities=25%  Similarity=0.376  Sum_probs=71.7

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ...++|||+|||.++++++|+++|++||.|+.|++.   ++||||+|.+.++|++|++.||+..+.|++|+|+|++++.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   81 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKS   81 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCC
Confidence            346799999999999999999999999999999984   8999999999999999999999999999999999998865

>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

Probab=99.49  E-value=6.3e-14  Score=127.46  Aligned_cols=81  Identities=15%  Similarity=0.292  Sum_probs=73.7

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCcee---CCeEEE
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYI---AGKQIK  300 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I---~Gr~Ik  300 (876)
                      .....+|||+|||.++++++|+++|++||.|.+|++     ++..++||||+|.+.++|.+|++.||+..+   .|++|+
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            345679999999999999999999999999999988     355789999999999999999999999998   899999


Q ss_pred             EEeecCchh
Q 002823          301 LEPSHLRGL  309 (876)
Q Consensus       301 Vs~A~~k~~  309 (876)
                      |.+++++..
T Consensus        90 v~~a~~~~~   98 (106)
T 2dgp_A           90 VKPADSESR   98 (106)
T ss_dssp             EEECCCCSC
T ss_pred             EEECCcccc
Confidence            999998653

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.49  E-value=3.2e-14  Score=136.56  Aligned_cols=88  Identities=20%  Similarity=0.363  Sum_probs=78.8

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCce
Q 002823          139 EHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGK  213 (876)
Q Consensus       139 e~p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~  213 (876)
                      ..+....+.++|||+|||+++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++.|++..|.|++
T Consensus        39 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~  118 (135)
T 2lea_A           39 RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE  118 (135)
T ss_dssp             CSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSC
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            34455667899999999999999999999999999999983     5778999999999999999999999999999999


Q ss_pred             eeEeecCCCCCCC
Q 002823          214 LDIHYSIPKDNPS  226 (876)
Q Consensus       214 L~V~~A~pk~~~~  226 (876)
                      |+|.|+.++....
T Consensus       119 l~V~~a~~~~~~~  131 (135)
T 2lea_A          119 LRVQMARYGRPPD  131 (135)
T ss_dssp             CEEEECCCCCCCT
T ss_pred             EEEEECCCCCCCc
Confidence            9999998765543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.49  E-value=4.4e-14  Score=126.97  Aligned_cols=73  Identities=22%  Similarity=0.254  Sum_probs=69.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .+.-|||+||++.+|+++|+++|.+||+|.+++. ..+||||||+|.++++|++|++.||+..+.|++|+|+++
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l-~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHP-YLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEE-cCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            4678999999999999999999999999999996 458999999999999999999999999999999999987

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=8.7e-14  Score=121.40  Aligned_cols=75  Identities=25%  Similarity=0.391  Sum_probs=70.0

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEEeec
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALREL-NSRYIAGKQIKLEPSH  305 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~L-nG~~I~Gr~IkVs~A~  305 (876)
                      ...++|||+|||..+++++|+++|++||.|..|++. ..++||||+|.+.++|.+|++.| ++..+.|++|+|+|++
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~-~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEE-CCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            456799999999999999999999999999999984 46899999999999999999999 9999999999999985

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.49  E-value=5e-14  Score=124.70  Aligned_cols=78  Identities=18%  Similarity=0.187  Sum_probs=72.6

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ...+|||+|||.++++++|+++|++||.|..|++   ++..++||||+|.+.++|++|++.|++..+.|++|+|++++++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   86 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA   86 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            4679999999999999999999999999999887   4557899999999999999999999999999999999999886


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus        87 ~   87 (92)
T 2dgv_A           87 S   87 (92)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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

Probab=99.49  E-value=5.1e-14  Score=129.74  Aligned_cols=76  Identities=18%  Similarity=0.288  Sum_probs=69.8

Q ss_pred             ccceeEeecCCC-CCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDS-SVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS--RYIAGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~-svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG--~~I~Gr~IkVs~A~~k  307 (876)
                      +..+|||+|||. ++++++|+++|++||+|.+|++. ..++||||+|.+.++|.+|++.|++  ..|.|++|+|.|++..
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   92 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   92 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCC
Confidence            567999999999 99999999999999999999984 4579999999999999999999986  4599999999999864

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1e-13  Score=123.26  Aligned_cols=76  Identities=24%  Similarity=0.311  Sum_probs=71.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ...++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..+.|++|+|++++++.
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            456799999999999999999999999999999984   6699999999999999999999999999999999998864

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1e-13  Score=122.69  Aligned_cols=80  Identities=15%  Similarity=0.264  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ...+.++|||+|||.++++++|+++|++||.|..++..   ++||||+|.+.++|++|++.|++..+.|++|+|.++.++
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   81 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG   81 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCC
Confidence            34667999999999999999999999999999999973   569999999999999999999999999999999999877


Q ss_pred             CCC
Q 002823          223 DNP  225 (876)
Q Consensus       223 ~~~  225 (876)
                      ...
T Consensus        82 ~~~   84 (90)
T 2dnp_A           82 QKK   84 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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

Probab=99.48  E-value=7.2e-14  Score=127.29  Aligned_cols=78  Identities=17%  Similarity=0.341  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ...+.++|||+|||+++++++|+++|++||.|..|+    .+++++|||||+|.+.++|++|++.|++..+.|++|+|++
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            456789999999999999999999999999999987    3567899999999999999999999999999999999999


Q ss_pred             cC
Q 002823          219 SI  220 (876)
Q Consensus       219 A~  220 (876)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            74

>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

Probab=99.48  E-value=4.1e-14  Score=128.08  Aligned_cols=84  Identities=21%  Similarity=0.343  Sum_probs=76.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||..+++++|+++|++||.|..|++     ++..+|||||+|.+.++|++|++.|||..+.|++|+|.|+
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            34679999999999999999999999999999887     3456899999999999999999999999999999999999


Q ss_pred             cCchhHHHH
Q 002823          305 HLRGLRKCL  313 (876)
Q Consensus       305 ~~k~~Rr~l  313 (876)
                      .++..++..
T Consensus        86 ~~~~~~~~~   94 (104)
T 1p1t_A           86 ASEKNKEEL   94 (104)
T ss_dssp             TCTTHHHHH
T ss_pred             CCccchhhh
Confidence            998766533

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=1.8e-13  Score=123.22  Aligned_cols=80  Identities=16%  Similarity=0.308  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcc--CCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQY--GDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqf--G~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ...+.++|||+|||+++++++|+++|++|  |.|..++.   .+|||||+|.+.++|++|++.|++..+.|++|+|.|+.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK---IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   87 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE---CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE---eCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            44667999999999999999999999999  99999876   47899999999999999999999999999999999998


Q ss_pred             CCCCC
Q 002823          221 PKDNP  225 (876)
Q Consensus       221 pk~~~  225 (876)
                      ++...
T Consensus        88 ~~~~~   92 (99)
T 2cpd_A           88 PVDKD   92 (99)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87643

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.48  E-value=4.9e-14  Score=125.92  Aligned_cols=80  Identities=28%  Similarity=0.327  Sum_probs=74.5

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchh
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~  309 (876)
                      ....+|||+|||..+++++|+++|++||.|..+..++..+|||||+|.+.++|.+|++.|+|..+.|++|+|.+++++..
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            45679999999999999999999999999988866788899999999999999999999999999999999999988653

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=7.5e-14  Score=128.68  Aligned_cols=79  Identities=19%  Similarity=0.374  Sum_probs=72.7

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEec---CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET---PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVrit---g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ....++|||+|||.++++++|+++|++||+|..|++.   ...+|||||+|.+.++|++|++.|+|..+.|++|+|++++
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  105 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT  105 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            3456799999999999999999999999999999883   3458999999999999999999999999999999999998


Q ss_pred             Cc
Q 002823          306 LR  307 (876)
Q Consensus       306 ~k  307 (876)
                      ++
T Consensus       106 ~~  107 (109)
T 2err_A          106 AR  107 (109)
T ss_dssp             CS
T ss_pred             CC
Confidence            75

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.48  E-value=8.1e-14  Score=128.52  Aligned_cols=80  Identities=29%  Similarity=0.381  Sum_probs=73.3

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ....++|||+|||..+++++|+++|++||.|..|++     ++..+|||||+|.+.++|++|++.|+|..|.|++|+|++
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345679999999999999999999999999999887     345689999999999999999999999999999999999


Q ss_pred             ecCch
Q 002823          304 SHLRG  308 (876)
Q Consensus       304 A~~k~  308 (876)
                      ++++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            98864

>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

Probab=99.48  E-value=5.6e-14  Score=129.59  Aligned_cols=78  Identities=23%  Similarity=0.230  Sum_probs=70.7

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCc--eeCCeEEEEEeecCc
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSR--YIAGKQIKLEPSHLR  307 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~--~I~Gr~IkVs~A~~k  307 (876)
                      .+.++|||+|||.++++++|+++|++||.|.+|++.. .|+||||+|.+.++|.+|++.|++.  .|.|++|+|.|++.+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            3567999999999999999999999999999999843 5899999999999999999998764  599999999999876


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus        92 ~   92 (104)
T 1wex_A           92 R   92 (104)
T ss_dssp             S
T ss_pred             c
Confidence            5

>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

Probab=99.48  E-value=5.6e-14  Score=125.02  Aligned_cols=81  Identities=17%  Similarity=0.263  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCC-eEEEEeCCCccceEeeecCCHHHHHHHHHHccc-cccCCceeeEeecCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGD-VRTFYRASKHCGFVTISYYDIRAARNAMKSLQN-KLTRSGKLDIHYSIP  221 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~-I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng-~~l~Gr~L~V~~A~p  221 (876)
                      ..+.++|||+|||.++++++|+++|++||. |..+..  .++|||||+|.+.++|++|++.|++ ..+.|++|+|.|+.+
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~   82 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL--LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   82 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE--EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE--cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccC
Confidence            356789999999999999999999999999 665554  4689999999999999999999999 999999999999988


Q ss_pred             CCCCC
Q 002823          222 KDNPS  226 (876)
Q Consensus       222 k~~~~  226 (876)
                      +....
T Consensus        83 ~~~~~   87 (93)
T 2cqh_A           83 KKLRS   87 (93)
T ss_dssp             CCCCC
T ss_pred             ccccC
Confidence            76543

>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

Probab=99.48  E-value=2.2e-14  Score=127.40  Aligned_cols=76  Identities=18%  Similarity=0.177  Sum_probs=66.0

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcC--CeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYG--EIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG--~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      .+|||+|||.++++++|+++|++||  .|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            3799999999999999999999999  8988876     56778999999999999999999999999999999999998


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            864

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.48  E-value=9.7e-14  Score=128.78  Aligned_cols=76  Identities=16%  Similarity=0.334  Sum_probs=69.9

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|++||+|++|++     ++..+|||||+|.+.++|++|++.|||..|.|++|+|+|+
T Consensus        38 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            35679999999999999999999999999999988     3456899999999999999999999999999999999997


Q ss_pred             c
Q 002823          305 H  305 (876)
Q Consensus       305 ~  305 (876)
                      +
T Consensus       118 k  118 (118)
T 2khc_A          118 K  118 (118)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=1.7e-13  Score=123.51  Aligned_cols=76  Identities=20%  Similarity=0.311  Sum_probs=71.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhc--CCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVY--GEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~f--G~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ...++|||+|||..+++++|+++|++|  |.|..|++   .++||||+|.+.++|.+|++.|||..|.|++|+|.|++++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK---IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   89 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE---CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE---eCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            456799999999999999999999999  99999987   4789999999999999999999999999999999999886


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus        90 ~   90 (99)
T 2cpd_A           90 D   90 (99)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.48  E-value=7.5e-14  Score=128.89  Aligned_cols=79  Identities=27%  Similarity=0.449  Sum_probs=72.8

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ....++|||+|||.++++++|+++|++||.|+.|++.   +|||||+|.+.++|++|++.|||..+.|++|+|+|++++.
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  104 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA  104 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCC
Confidence            4467799999999999999999999999999999985   8999999999999999999999999999999999999876


Q ss_pred             hH
Q 002823          309 LR  310 (876)
Q Consensus       309 ~R  310 (876)
                      .|
T Consensus       105 ~r  106 (108)
T 2jvo_A          105 KR  106 (108)
T ss_dssp             --
T ss_pred             CC
Confidence            44

>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

Probab=99.48  E-value=1.8e-13  Score=126.17  Aligned_cols=80  Identities=14%  Similarity=0.252  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHcccccc--------C
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLT--------R  210 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l--------~  210 (876)
                      .+.+.++|||+|||+++++++|+++|++||.|..++.    +++++|||||+|.+.++|++|++.|+|..+        .
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            4566799999999999999999999999999999883    567899999999999999999999999998        5


Q ss_pred             CceeeEeecCCC
Q 002823          211 SGKLDIHYSIPK  222 (876)
Q Consensus       211 Gr~L~V~~A~pk  222 (876)
                      +++|.|.|+.|+
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            788999998764

>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

Probab=99.48  E-value=4.7e-14  Score=133.53  Aligned_cols=80  Identities=18%  Similarity=0.264  Sum_probs=72.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEEeecCc
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS--RYIAGKQIKLEPSHLR  307 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG--~~I~Gr~IkVs~A~~k  307 (876)
                      .+.++|||+|||+++++++|+++|++||+|++|++. ..||||||+|.+.++|.+|++.|++  ..|.|++|+|.|++++
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~-~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k  107 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK  107 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEE-GGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCC
Confidence            356799999999999999999999999999999984 3589999999999999999999984  6899999999999986


Q ss_pred             hhH
Q 002823          308 GLR  310 (876)
Q Consensus       308 ~~R  310 (876)
                      ..+
T Consensus       108 ~~~  110 (119)
T 2ad9_A          108 ELK  110 (119)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            644

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.48  E-value=9.6e-14  Score=126.99  Aligned_cols=81  Identities=11%  Similarity=0.226  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCCCC------CHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCc-
Q 002823          143 DEHPSRTLLLRKINSNI------EDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSG-  212 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~v------TEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr-  212 (876)
                      .+..+++|||+|||+.+      ++++|+++|++||.|..|+   .+++++|||||+|.+.++|++|++.|+|..+.|+ 
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            45567999999999999      7899999999999999998   3567899999999999999999999999999999 


Q ss_pred             eeeEeecCCCC
Q 002823          213 KLDIHYSIPKD  223 (876)
Q Consensus       213 ~L~V~~A~pk~  223 (876)
                      +|+|.++...+
T Consensus        91 ~l~V~~a~~~~  101 (105)
T 2nlw_A           91 TFRVNLFTDFD  101 (105)
T ss_dssp             EEEEECSCCCC
T ss_pred             eEEEEEcchHh
Confidence            99999987543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1.2e-13  Score=122.39  Aligned_cols=76  Identities=24%  Similarity=0.322  Sum_probs=71.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ...++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..+.|++|+|.+++++.
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            356799999999999999999999999999999984   6699999999999999999999999999999999998864

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.48  E-value=3.5e-14  Score=128.96  Aligned_cols=77  Identities=13%  Similarity=0.137  Sum_probs=72.2

Q ss_pred             cceeEeecCCC------CCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC-eEE
Q 002823          232 QGTLVVFNLDS------SVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG-KQI  299 (876)
Q Consensus       232 ~~tLfV~NLP~------svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G-r~I  299 (876)
                      .++|||+|||.      ++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|.+|++.|||..|.| ++|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            56899999999      9999999999999999999987     36788999999999999999999999999999 999


Q ss_pred             EEEeecCch
Q 002823          300 KLEPSHLRG  308 (876)
Q Consensus       300 kVs~A~~k~  308 (876)
                      +|.++.+++
T Consensus        86 ~V~~a~~~~   94 (100)
T 3ns6_A           86 FLYTMKDVE   94 (100)
T ss_dssp             EEEESHHHH
T ss_pred             EEEECchhh
Confidence            999998754

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.48  E-value=8.4e-14  Score=130.06  Aligned_cols=77  Identities=19%  Similarity=0.104  Sum_probs=71.1

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcC-CeEEEEe-cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYG-EIKEIRE-TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG-~I~sVri-tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..+|||+|||.++++++|+++|++|| +|..+++ ...++|||||+|.+.++|++|++.|||..|.|++|+|++++.+.
T Consensus        28 ~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           28 RYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             CEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC--
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            56899999999999999999999999 9999998 45689999999999999999999999999999999999997654

>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

Probab=99.48  E-value=1.2e-13  Score=124.27  Aligned_cols=81  Identities=16%  Similarity=0.204  Sum_probs=72.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHH----HHhhccCCeEEEEeC--CCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          145 HPSRTLLLRKINSNIEDSELK----ALFEQYGDVRTFYRA--SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~----elFsqfG~I~sV~~t--gksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ...++|||+|||+++++++|+    ++|++||+|.+|+..  ...+|||||+|.+.++|++|++.|+|..+.|++|+|.+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   86 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL   86 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345799999999999999999    999999999999842  22289999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002823          219 SIPKDNP  225 (876)
Q Consensus       219 A~pk~~~  225 (876)
                      +.++...
T Consensus        87 a~~~~~~   93 (96)
T 2dgx_A           87 ATGASGP   93 (96)
T ss_dssp             CCCSSCC
T ss_pred             cCCCCCC
Confidence            9876543

>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

Probab=99.48  E-value=7.6e-14  Score=125.71  Aligned_cols=78  Identities=23%  Similarity=0.333  Sum_probs=72.6

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ...++|||+|||..+++++|+++|++||+|..|++. ..++||||+|.+.++|++|++.|+|..|.|++|+|.|++++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            356799999999999999999999999999999984 458999999999999999999999999999999999998854

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.47  E-value=6e-14  Score=126.69  Aligned_cols=76  Identities=14%  Similarity=0.197  Sum_probs=71.5

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ..++|||+|||.++++++|+++|++||.|.+|++. ..++||||+|.+.++|.+|++.|||..+.|++|+|.|++++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            35699999999999999999999999999999984 67899999999999999999999999999999999999874

>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

Probab=99.47  E-value=9.5e-14  Score=126.14  Aligned_cols=77  Identities=21%  Similarity=0.405  Sum_probs=72.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchhH
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGLR  310 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~R  310 (876)
                      +.++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.||+..|.|++|+|.|++++..+
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            46799999999999999999999999999999984   779999999999999999999999999999999999987644

>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

Probab=99.47  E-value=1.7e-13  Score=123.85  Aligned_cols=76  Identities=28%  Similarity=0.378  Sum_probs=71.5

Q ss_pred             cccceeEeecCCC-CCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          230 INQGTLVVFNLDS-SVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       230 ~~~~tLfV~NLP~-svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ...++|||+|||. ++++++|+++|++||.|..|++   .+|||||+|.+.++|.+|++.|||..+.|++|+|++++++.
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA   96 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE---CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCCC
Confidence            4567999999998 9999999999999999999999   48999999999999999999999999999999999998753

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.47  E-value=4e-14  Score=134.56  Aligned_cols=84  Identities=15%  Similarity=0.273  Sum_probs=75.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEE--EE-----eCCCccceEeeecCCHHHHHHHHHHcccc----cc
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRT--FY-----RASKHCGFVTISYYDIRAARNAMKSLQNK----LT  209 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~s--V~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~----~l  209 (876)
                      +..+.+.++|||+|||+++|+++|+++|++||.|..  |+     .++++||||||+|.+. +|++|++.|++.    .+
T Consensus        17 ~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~   95 (131)
T 2m2b_A           17 PSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTI   95 (131)
T ss_dssp             CCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccC
Confidence            345577899999999999999999999999999966  66     3688999999999999 999999999999    99


Q ss_pred             CCceeeEeecCCCCCC
Q 002823          210 RSGKLDIHYSIPKDNP  225 (876)
Q Consensus       210 ~Gr~L~V~~A~pk~~~  225 (876)
                      .|++|+|+++.++...
T Consensus        96 ~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           96 DGKTINVEFAKGSKRD  111 (131)
T ss_dssp             GGCCCCCEECCCSCCC
T ss_pred             CCEEEEEEECCCCCCC
Confidence            9999999999887543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.47  E-value=8.7e-14  Score=128.43  Aligned_cols=81  Identities=20%  Similarity=0.382  Sum_probs=72.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ...+.++++|||+|||.++++++|+++|++||.|..++..   +|||||+|.+.++|++|++.|+|..+.|+.|+|.|+.
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  101 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK  101 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCS
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            3456778999999999999999999999999999999864   8999999999999999999999999999999999998


Q ss_pred             CCCC
Q 002823          221 PKDN  224 (876)
Q Consensus       221 pk~~  224 (876)
                      ++..
T Consensus       102 ~~~~  105 (108)
T 2jvo_A          102 LPAK  105 (108)
T ss_dssp             CCC-
T ss_pred             CCCC
Confidence            7643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.47  E-value=1.3e-13  Score=124.15  Aligned_cols=76  Identities=24%  Similarity=0.311  Sum_probs=70.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEE--------EEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKE--------IRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG  296 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~s--------Vri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G  296 (876)
                      ....+|||+|||.++++++|+++|++||.|..        |++     ++..+|||||+|.+.++|++|++.|||..+.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            45679999999999999999999999999998        776     35668999999999999999999999999999


Q ss_pred             eEEEEEeec
Q 002823          297 KQIKLEPSH  305 (876)
Q Consensus       297 r~IkVs~A~  305 (876)
                      ++|+|++++
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999974

>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

Probab=99.47  E-value=1.5e-13  Score=124.17  Aligned_cols=77  Identities=18%  Similarity=0.325  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          143 DEHPSRTLLLRKINS-NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~-~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ...++++|||+|||. ++++++|+++|++||.|..++.   .+|||||+|.+.++|++|++.|+|..+.|++|+|+|+.+
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE---CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            456789999999998 9999999999999999999988   489999999999999999999999999999999999876


Q ss_pred             C
Q 002823          222 K  222 (876)
Q Consensus       222 k  222 (876)
                      +
T Consensus        95 ~   95 (97)
T 2xnq_A           95 N   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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

Probab=99.47  E-value=1.2e-13  Score=126.83  Aligned_cols=78  Identities=21%  Similarity=0.290  Sum_probs=72.6

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchh
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~  309 (876)
                      ..++|||+|||..+++++|+++|++||.|..|++... ++||||+|.+.++|.+|++.|+|..|.|++|+|.|++++..
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            4669999999999999999999999999999998443 89999999999999999999999999999999999998653

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=4e-14  Score=123.72  Aligned_cols=76  Identities=18%  Similarity=0.247  Sum_probs=70.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .++++|||+|||+++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.|+|..+.|+.|++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            5678999999999999999999999999999998     35678999999999999999999999999999999998875


Q ss_pred             C
Q 002823          220 I  220 (876)
Q Consensus       220 ~  220 (876)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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

Probab=99.47  E-value=1.3e-13  Score=126.49  Aligned_cols=82  Identities=12%  Similarity=0.199  Sum_probs=74.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ...+.++|||+|||.++++++|+++|++||.|..|+... .+|||||+|.+.++|++|++.|++..+.|++|+|.|+.++
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   99 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   99 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCC
Confidence            345678999999999999999999999999999998633 3899999999999999999999999999999999999887


Q ss_pred             CCC
Q 002823          223 DNP  225 (876)
Q Consensus       223 ~~~  225 (876)
                      ...
T Consensus       100 ~~~  102 (109)
T 1x4g_A          100 PDM  102 (109)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            654

>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

Probab=99.47  E-value=1e-13  Score=121.74  Aligned_cols=76  Identities=20%  Similarity=0.350  Sum_probs=70.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ..++|||+|||.++++++|+++|++||.|..++     .+++++|||||+|.+.++|++|+ .+++..+.|++|+|.++.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            358999999999999999999999999999987     26778999999999999999999 999999999999999987


Q ss_pred             CC
Q 002823          221 PK  222 (876)
Q Consensus       221 pk  222 (876)
                      ++
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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

Probab=99.47  E-value=2.4e-13  Score=123.17  Aligned_cols=82  Identities=15%  Similarity=0.251  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||.++++++|+++|++||+|..|+.     +++++|||||+|.+.++|++|++  ++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            4567799999999999999999999999999999872     47789999999999999999998  4678999999999


Q ss_pred             ecCCCCCCC
Q 002823          218 YSIPKDNPS  226 (876)
Q Consensus       218 ~A~pk~~~~  226 (876)
                      ++.++....
T Consensus        89 ~a~~~~~~~   97 (103)
T 2cqg_A           89 LPNSKQSQD   97 (103)
T ss_dssp             CCCTTCCCC
T ss_pred             ecCCCCcCC
Confidence            998876543

>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

Probab=99.47  E-value=1.1e-13  Score=121.52  Aligned_cols=76  Identities=25%  Similarity=0.407  Sum_probs=70.4

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++.+++||||+|.+.++|++|+ .|||..+.|++|+|.+++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            4579999999999999999999999999999887     4556899999999999999999 999999999999999998


Q ss_pred             Cc
Q 002823          306 LR  307 (876)
Q Consensus       306 ~k  307 (876)
                      ++
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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

Probab=99.47  E-value=6.5e-14  Score=129.77  Aligned_cols=78  Identities=12%  Similarity=0.197  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      +...++|||+|||.++++++|+++|++||.|..|+.. +.+|||||+|.+.++|++|++.|+|..+.|+.|+|.|+...
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            3456899999999999999999999999999999863 58899999999999999999999999999999999998654

>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

Probab=99.47  E-value=1.1e-13  Score=128.23  Aligned_cols=77  Identities=18%  Similarity=0.254  Sum_probs=71.9

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..++|||+|||..+++++|+++|++||.|..|++ ...++||||+|.+.++|++|++.|||..+.|++|+|+|+....
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            4569999999999999999999999999999998 4578999999999999999999999999999999999997643

>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

Probab=99.47  E-value=9.2e-14  Score=132.46  Aligned_cols=79  Identities=20%  Similarity=0.321  Sum_probs=73.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|++||+|+.|++     ++..+|||||+|.+.++|++|++.|||..|.|++|+|+|+
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a  123 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS  123 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            35679999999999999999999999999999988     3567899999999999999999999999999999999999


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      +++.
T Consensus       124 ~~~~  127 (129)
T 2kxn_B          124 ITKR  127 (129)
T ss_dssp             SSSS
T ss_pred             cCCC
Confidence            8864

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.46  E-value=8e-14  Score=125.22  Aligned_cols=80  Identities=19%  Similarity=0.351  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          143 DEHPSRTLLLRKINS-NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~-~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ...++++|||+|||+ ++++++|+++|++||+|..++.   .+|||||+|.+.++|++|++.|++..+.|++|+|+++.+
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   82 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSS   82 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE---ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEEC
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCc
Confidence            456789999999998 9999999999999999999987   489999999999999999999999999999999999987


Q ss_pred             CCCC
Q 002823          222 KDNP  225 (876)
Q Consensus       222 k~~~  225 (876)
                      +...
T Consensus        83 ~~~~   86 (96)
T 2kvi_A           83 NARP   86 (96)
T ss_dssp             CCC-
T ss_pred             CCCC
Confidence            6544

>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

Probab=99.46  E-value=1.9e-13  Score=124.48  Aligned_cols=76  Identities=21%  Similarity=0.390  Sum_probs=70.6

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ....+|||+|||..+++++|+++|++||.|+.|++    ++..++||||+|.+.++|++|++.|+|..|.|++|+|+++.
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            35679999999999999999999999999999887    44568999999999999999999999999999999999986

>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* ...

Probab=99.46  E-value=1e-13  Score=123.89  Aligned_cols=80  Identities=23%  Similarity=0.341  Sum_probs=73.5

Q ss_pred             ccceeEeecCCCCCcHHHHH----HHhhhcCCeEEEEec--CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          231 NQGTLVVFNLDSSVSNDELH----HIFGVYGEIKEIRET--PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLr----eiFs~fG~I~sVrit--g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +.++|||+|||.++++++|+    ++|++||.|..|++.  +..+|||||+|.+.++|.+|++.|||..+.|++|+|.|+
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   86 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   86 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            46799999999999999999    999999999999883  356899999999999999999999999999999999999


Q ss_pred             cCchhH
Q 002823          305 HLRGLR  310 (876)
Q Consensus       305 ~~k~~R  310 (876)
                      +++..+
T Consensus        87 ~~~~~~   92 (97)
T 1nu4_A           87 KTDSDI   92 (97)
T ss_dssp             SSCCTH
T ss_pred             cCCCcc
Confidence            987543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=9.3e-14  Score=124.85  Aligned_cols=79  Identities=13%  Similarity=0.145  Sum_probs=70.9

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ....+|||+|||.++++++|+++|++||.|....+++..++||||+|.+.++|++|++.|||..|.|++|+|++++++.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            3467999999999999999999999999996322356789999999999999999999999999999999999998864

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.46  E-value=1.3e-13  Score=131.62  Aligned_cols=81  Identities=16%  Similarity=0.263  Sum_probs=73.6

Q ss_pred             ccceeEeecCCCCCcHHHHH----HHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          231 NQGTLVVFNLDSSVSNDELH----HIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLr----eiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +..+|||+|||..+++++|+    ++|++||.|.+|.+  ++..+|||||+|.+.++|.+|++.|||..|.|++|+|.|+
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a  107 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS  107 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEc
Confidence            46799999999999999876    69999999999887  4678999999999999999999999999999999999999


Q ss_pred             cCchhHH
Q 002823          305 HLRGLRK  311 (876)
Q Consensus       305 ~~k~~Rr  311 (876)
                      +.+..+.
T Consensus       108 ~~~~~~~  114 (127)
T 2a3j_A          108 ETPQSQV  114 (127)
T ss_dssp             CCCCHHH
T ss_pred             cCcchhc
Confidence            9876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=1.7e-13  Score=126.14  Aligned_cols=79  Identities=16%  Similarity=0.170  Sum_probs=72.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...++|||+|||.++++++|+++|++||.|+.|++    ++..++||||+|.+.++|++|++.||+..|.|++|+|++++
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   92 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDE   92 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcc
Confidence            34679999999999999999999999999999887    34467999999999999999999999999999999999998


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      ...
T Consensus        93 ~~~   95 (114)
T 2do0_A           93 RAL   95 (114)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=1.2e-13  Score=127.30  Aligned_cols=80  Identities=21%  Similarity=0.308  Sum_probs=72.9

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeE--------EEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIK--------EIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG  296 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~--------sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G  296 (876)
                      ...++|||+|||.++++++|+++|++||.|.        .|++     ++..++||||+|.+.++|++|++.|||..|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   92 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCC
Confidence            4567999999999999999999999999998        5776     35568999999999999999999999999999


Q ss_pred             eEEEEEeecCchh
Q 002823          297 KQIKLEPSHLRGL  309 (876)
Q Consensus       297 r~IkVs~A~~k~~  309 (876)
                      ++|+|.+++++..
T Consensus        93 ~~l~V~~a~~~~~  105 (113)
T 2cpe_A           93 SKLKVSLARKKPP  105 (113)
T ss_dssp             EECEEECSSCCCC
T ss_pred             CEEEEEECCCCCC
Confidence            9999999998653

>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

Probab=99.46  E-value=6e-14  Score=125.84  Aligned_cols=80  Identities=11%  Similarity=0.130  Sum_probs=71.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .....++|||+|||+++++++|+++|++||.|..++     .+++++|||||+|.+.++|++|++.|++..+.|++|+|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            345568999999999999999999999999885432     457789999999999999999999999999999999999


Q ss_pred             ecCCC
Q 002823          218 YSIPK  222 (876)
Q Consensus       218 ~A~pk  222 (876)
                      ++..+
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98653

>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

Probab=99.46  E-value=1.4e-13  Score=125.83  Aligned_cols=82  Identities=17%  Similarity=0.193  Sum_probs=74.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCC-eEEEEe------CCCccceEeeecCCHHHHHHHHHHcc--ccccCCceee
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGD-VRTFYR------ASKHCGFVTISYYDIRAARNAMKSLQ--NKLTRSGKLD  215 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~-I~sV~~------tgksrGfAFV~F~d~edA~kAl~~Ln--g~~l~Gr~L~  215 (876)
                      .+.++|||+|||.++++++|+++|++||. |..+..      +++++|||||+|.+.++|++|++.|+  +..+.|++|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            46789999999999999999999999998 999984      34789999999999999999999996  5899999999


Q ss_pred             EeecCCCCCCC
Q 002823          216 IHYSIPKDNPS  226 (876)
Q Consensus       216 V~~A~pk~~~~  226 (876)
                      |.|+.++....
T Consensus        86 V~~a~~~~~~~   96 (109)
T 2dis_A           86 VDWAEPEIDVD   96 (109)
T ss_dssp             EEESCSSCSTT
T ss_pred             EEEcCCCCCcC
Confidence            99998876543

>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

Probab=99.46  E-value=1.2e-13  Score=121.18  Aligned_cols=76  Identities=14%  Similarity=0.286  Sum_probs=69.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .+.+.++|||+|||+++++++|+++|++||.|..++.     +++++|||||+|.+.++|++|++ +++..+.|+.|+|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            4567899999999999999999999999999999982     47789999999999999999995 57888999999998


Q ss_pred             ec
Q 002823          218 YS  219 (876)
Q Consensus       218 ~A  219 (876)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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

Probab=99.46  E-value=2e-13  Score=133.07  Aligned_cols=82  Identities=20%  Similarity=0.344  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            4457899999999999999999999999999999984     57789999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 002823          218 YSIPKDN  224 (876)
Q Consensus       218 ~A~pk~~  224 (876)
                      |+.++..
T Consensus       115 ~a~~~~~  121 (156)
T 1h2v_Z          115 WDAGFKE  121 (156)
T ss_dssp             EESCCCT
T ss_pred             ECCCCCC
Confidence            9987654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=3.3e-13  Score=121.29  Aligned_cols=80  Identities=14%  Similarity=0.223  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ...+.++|||+||  ++++++|+++|++||+|..|+. .+.+|||||+|.+.++|++|++.|++..+.|++|+|.|+.++
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~   87 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   87 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSC
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEe-cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCC
Confidence            4467799999996  8999999999999999999997 578999999999999999999999999999999999999887


Q ss_pred             CCC
Q 002823          223 DNP  225 (876)
Q Consensus       223 ~~~  225 (876)
                      ...
T Consensus        88 ~~~   90 (97)
T 1x5p_A           88 PML   90 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.46  E-value=1.8e-13  Score=124.07  Aligned_cols=78  Identities=19%  Similarity=0.234  Sum_probs=71.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||.++++++|+++|++|| |..|++     ++..+|||||+|.+.++|++|+ .||+..|.|++|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEe
Confidence            3567999999999999999999999997 999887     3567899999999999999999 89999999999999999


Q ss_pred             cCchh
Q 002823          305 HLRGL  309 (876)
Q Consensus       305 ~~k~~  309 (876)
                      +++..
T Consensus        91 ~~~~~   95 (103)
T 2dng_A           91 EGRKQ   95 (103)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            88653

>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

Probab=99.46  E-value=1.4e-13  Score=125.04  Aligned_cols=79  Identities=22%  Similarity=0.248  Sum_probs=72.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEec------CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET------PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVrit------g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ....+|||+|||.++++++|+++|+.|| |..|++.      +..++||||+|.+.++|++|+ .|++..|.|++|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            3567999999999999999999999999 9999882      567899999999999999999 9999999999999999


Q ss_pred             ecCchhH
Q 002823          304 SHLRGLR  310 (876)
Q Consensus       304 A~~k~~R  310 (876)
                      ++++..+
T Consensus        91 a~~~~~~   97 (104)
T 1wi8_A           91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9986543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.8e-13  Score=121.20  Aligned_cols=79  Identities=9%  Similarity=0.203  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      .....++|||+|||+++++++|+++|++| .|..|+    .+++++|||||+|.+.++|++|++ |++..+.|+.|.|.+
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            34567899999999999999999999999 888887    357789999999999999999999 999999999999999


Q ss_pred             cCCCC
Q 002823          219 SIPKD  223 (876)
Q Consensus       219 A~pk~  223 (876)
                      +.++.
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98764

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.46  E-value=7e-14  Score=126.68  Aligned_cols=79  Identities=14%  Similarity=0.279  Sum_probs=69.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe------CCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR------ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~------tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ...+.++|||+|||.++++++|+++|++|| |..|+.      +++++|||||+|.+.++|++|+ .|++..+.|+.|+|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            446679999999999999999999999999 999983      5678999999999999999999 89999999999999


Q ss_pred             eecCCCC
Q 002823          217 HYSIPKD  223 (876)
Q Consensus       217 ~~A~pk~  223 (876)
                      +++.++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9998764

>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

Probab=99.46  E-value=1.8e-13  Score=125.68  Aligned_cols=76  Identities=18%  Similarity=0.197  Sum_probs=71.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCC-----eEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAG-----KQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G-----r~IkVs~A~  305 (876)
                      ...+|||+|||.++++++|+++|++||+|+.|++...  +||||+|.+.++|++||+.|||..|.|     ++|+|++++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~   91 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   91 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCC
Confidence            4679999999999999999999999999999998443  999999999999999999999999999     999999999


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      ++.
T Consensus        92 ~~~   94 (108)
T 1x4c_A           92 PRS   94 (108)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            865

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.46  E-value=8.5e-14  Score=128.59  Aligned_cols=81  Identities=12%  Similarity=0.224  Sum_probs=73.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH---HHhhccCCeEEEEe--------CCCccceEeeecCCHHHHHHHHHHccccccCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELK---ALFEQYGDVRTFYR--------ASKHCGFVTISYYDIRAARNAMKSLQNKLTRS  211 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~---elFsqfG~I~sV~~--------tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G  211 (876)
                      .....++|||+|||+++++++|+   ++|++||+|..|+.        .++++|||||+|.+.++|++|++.|++..|.|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            34567899999999999999999   99999999999983        12566999999999999999999999999999


Q ss_pred             ceeeEeecCCCC
Q 002823          212 GKLDIHYSIPKD  223 (876)
Q Consensus       212 r~L~V~~A~pk~  223 (876)
                      ++|+|.|+.++.
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999998875

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.46  E-value=2.1e-13  Score=132.68  Aligned_cols=84  Identities=21%  Similarity=0.396  Sum_probs=76.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||+++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.
T Consensus        66 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  145 (158)
T 2kn4_A           66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  145 (158)
T ss_dssp             CCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3456789999999999999999999999999999982     67899999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 002823          218 YSIPKDNPS  226 (876)
Q Consensus       218 ~A~pk~~~~  226 (876)
                      |+.++....
T Consensus       146 ~a~~~~~~~  154 (158)
T 2kn4_A          146 MARYGRPPD  154 (158)
T ss_dssp             EECCSSCCC
T ss_pred             ECCCCCCCC
Confidence            998775443

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.46  E-value=2.3e-13  Score=129.18  Aligned_cols=77  Identities=18%  Similarity=0.347  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||.++++++|+++|++||+|..++.     +++++|||||+|.+.++|++|++.|++..+.|++|+|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4457899999999999999999999999999999983     46789999999999999999999999999999999998


Q ss_pred             ec
Q 002823          218 YS  219 (876)
Q Consensus       218 ~A  219 (876)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            85

>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

Probab=99.46  E-value=2e-13  Score=132.97  Aligned_cols=81  Identities=22%  Similarity=0.260  Sum_probs=74.4

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||..+++++|+++|++||+|+.|++     ++..++||||+|.+.++|++|++.||+..|.|++|+|+|+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            35679999999999999999999999999999988     4567899999999999999999999999999999999999


Q ss_pred             cCchhH
Q 002823          305 HLRGLR  310 (876)
Q Consensus       305 ~~k~~R  310 (876)
                      ++...+
T Consensus       117 ~~~~~~  122 (156)
T 1h2v_Z          117 AGFKEG  122 (156)
T ss_dssp             SCCCTT
T ss_pred             CCCCCc
Confidence            986543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.8e-13  Score=126.80  Aligned_cols=79  Identities=22%  Similarity=0.302  Sum_probs=72.2

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      +...++|||+|||.++++++|+++|++||.|+.|++     ++..++||||+|.+.++|++|++.+++ .|.|++|+|++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            345779999999999999999999999999999988     345689999999999999999999998 89999999999


Q ss_pred             ecCch
Q 002823          304 SHLRG  308 (876)
Q Consensus       304 A~~k~  308 (876)
                      ++++.
T Consensus        93 a~~~~   97 (116)
T 2cqd_A           93 AYLGA   97 (116)
T ss_dssp             STTTC
T ss_pred             cccCC
Confidence            98754

>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}

Probab=99.45  E-value=1.2e-13  Score=128.99  Aligned_cols=78  Identities=26%  Similarity=0.421  Sum_probs=72.4

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ..++|||+|||.++++++|+++|++||.|+.|++    ++..+|||||+|.+.++|++|++.|||..|.|++|+|+++++
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   85 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK   85 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4579999999999999999999999999999888    455679999999999999999999999999999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      +.
T Consensus        86 ~~   87 (116)
T 2fy1_A           86 PS   87 (116)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.45  E-value=1.1e-13  Score=129.38  Aligned_cols=79  Identities=10%  Similarity=0.073  Sum_probs=72.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccC-CeEEEEe-CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYG-DVRTFYR-ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG-~I~sV~~-tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ....++|||+|||+++++++|+++|++|| +|..+.+ ..+++|||||+|.+.++|++|++.|+|..+.|+.|+|.++..
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            34568999999999999999999999999 8999986 467899999999999999999999999999999999999865


Q ss_pred             C
Q 002823          222 K  222 (876)
Q Consensus       222 k  222 (876)
                      .
T Consensus       105 ~  105 (111)
T 2jvr_A          105 P  105 (111)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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

Probab=99.45  E-value=1e-13  Score=127.81  Aligned_cols=81  Identities=25%  Similarity=0.275  Sum_probs=73.1

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCe----EEEEe-cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEI----KEIRE-TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I----~sVri-tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||.++++++|+++|++||.|    ..+++ ++..+|||||+|.+.++|++|++.|+|..|.|++|+|.|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            356799999999999999999999999998    45554 6788999999999999999999999999999999999999


Q ss_pred             cCchhH
Q 002823          305 HLRGLR  310 (876)
Q Consensus       305 ~~k~~R  310 (876)
                      +++..+
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            986543

>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

Probab=99.45  E-value=2.3e-13  Score=131.81  Aligned_cols=81  Identities=20%  Similarity=0.330  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ...+.++|||+|||+++++++|+++|++||.|.+|+....++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.++
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            45667999999999999999999999999999999976668999999999999999999999999999999999999876


Q ss_pred             C
Q 002823          223 D  223 (876)
Q Consensus       223 ~  223 (876)
                      .
T Consensus       149 ~  149 (150)
T 2i2y_A          149 K  149 (150)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.45  E-value=2.2e-13  Score=127.84  Aligned_cols=83  Identities=16%  Similarity=0.299  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ...++++|||+|||.++++++|+++|++||+|..|+.    +++++|||||+|.+.++|++|++.|++..+.|++|+|++
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4467799999999999999999999999999998883    466899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002823          219 SIPKDNP  225 (876)
Q Consensus       219 A~pk~~~  225 (876)
                      +.++...
T Consensus       111 a~~~~~~  117 (124)
T 2kt5_A          111 VASQIDL  117 (124)
T ss_dssp             ECCTTCC
T ss_pred             eCCCCCC
Confidence            9876543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=2e-13  Score=123.31  Aligned_cols=81  Identities=19%  Similarity=0.258  Sum_probs=72.7

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ....++|||+|||.++++++|+++|+.|+.|.-++.  ++..++||||+|.+.++|++|++.||+..|.|++|+|+|+++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   91 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP   91 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            445779999999999999999999999987766654  566789999999999999999999999999999999999998


Q ss_pred             chh
Q 002823          307 RGL  309 (876)
Q Consensus       307 k~~  309 (876)
                      +..
T Consensus        92 ~~~   94 (102)
T 2fc8_A           92 KGE   94 (102)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=9.1e-14  Score=125.96  Aligned_cols=80  Identities=20%  Similarity=0.235  Sum_probs=73.8

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhh-cCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCce-eCCeEEEEEee
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGV-YGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRY-IAGKQIKLEPS  304 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~-fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~-I~Gr~IkVs~A  304 (876)
                      ...+|||+|||.++++++|+++|++ ||.|..|++    ++..++||||+|.+.++|.+|++.|++.. +.|++|+|.++
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a   87 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVA   87 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEc
Confidence            4679999999999999999999999 999999887    45578999999999999999999999999 99999999999


Q ss_pred             cCchhH
Q 002823          305 HLRGLR  310 (876)
Q Consensus       305 ~~k~~R  310 (876)
                      .++..+
T Consensus        88 ~~~~~~   93 (104)
T 2dhg_A           88 IPKASR   93 (104)
T ss_dssp             CCCCSC
T ss_pred             cCCCcC
Confidence            887644

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.45  E-value=1.7e-13  Score=125.34  Aligned_cols=78  Identities=14%  Similarity=0.150  Sum_probs=71.4

Q ss_pred             cccceeEeecCCCCC------cHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCe-EE
Q 002823          230 INQGTLVVFNLDSSV------SNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK-QI  299 (876)
Q Consensus       230 ~~~~tLfV~NLP~sv------TeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr-~I  299 (876)
                      ...++|||+|||..+      ++++|+++|++||.|..|++   ++.++|||||+|.+.++|.+|++.|||..|.|+ +|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            346799999999999      78999999999999999988   456789999999999999999999999999998 99


Q ss_pred             EEEeecCc
Q 002823          300 KLEPSHLR  307 (876)
Q Consensus       300 kVs~A~~k  307 (876)
                      +|.++...
T Consensus        93 ~V~~a~~~  100 (105)
T 2nlw_A           93 RVNLFTDF  100 (105)
T ss_dssp             EEECSCCC
T ss_pred             EEEEcchH
Confidence            99999764

>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

Probab=99.45  E-value=1.4e-13  Score=123.44  Aligned_cols=78  Identities=24%  Similarity=0.210  Sum_probs=69.8

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||.++++++|+++|++||.|..+++     ++..++||||+|.+.++|++|++.|||..|.|++|+|+++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            34579999999999999999999999999875332     4567899999999999999999999999999999999998


Q ss_pred             cCc
Q 002823          305 HLR  307 (876)
Q Consensus       305 ~~k  307 (876)
                      +.+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            764

>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

Probab=99.45  E-value=4.5e-14  Score=125.75  Aligned_cols=77  Identities=12%  Similarity=0.137  Sum_probs=68.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+.++|||+|||+++++++|+++|++||.|..++     .+++++|||||+|.+.++|++|++.|++..+.|++|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            34568999999999999999999999999886443     3567899999999999999999999999999999999998


Q ss_pred             cC
Q 002823          219 SI  220 (876)
Q Consensus       219 A~  220 (876)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.45  E-value=1.1e-13  Score=124.23  Aligned_cols=77  Identities=27%  Similarity=0.352  Sum_probs=71.6

Q ss_pred             cccceeEeecCCC-CCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          230 INQGTLVVFNLDS-SVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       230 ~~~~tLfV~NLP~-svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      .+..+|||+|||. .+++++|+++|++||.|..|++   .++||||+|.+.++|.+|++.|+|..+.|++|+|++++++.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE---ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            4567999999998 9999999999999999999998   48999999999999999999999999999999999998765


Q ss_pred             h
Q 002823          309 L  309 (876)
Q Consensus       309 ~  309 (876)
                      .
T Consensus        85 ~   85 (96)
T 2kvi_A           85 R   85 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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*

Probab=99.45  E-value=1.4e-13  Score=129.16  Aligned_cols=81  Identities=26%  Similarity=0.408  Sum_probs=74.0

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||..+++++|+++|++||.|..|++     ++..++||||+|.+.++|++|++.|||..|.|++|+|+|+
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            34669999999999999999999999999999988     4556899999999999999999999999999999999999


Q ss_pred             cCchhH
Q 002823          305 HLRGLR  310 (876)
Q Consensus       305 ~~k~~R  310 (876)
                      .++..+
T Consensus       100 ~~~~~~  105 (126)
T 3ex7_B          100 FVRGPP  105 (126)
T ss_dssp             EESSSC
T ss_pred             cCCCCC
Confidence            876543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=1.3e-13  Score=123.83  Aligned_cols=78  Identities=22%  Similarity=0.342  Sum_probs=71.8

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeE-EEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeE----EE
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIK-EIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQ----IK  300 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~-sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~----Ik  300 (876)
                      ..++|||+|||.++++++|+++|++||.|. .|++     ++..++||||+|.+.++|++|++.|||..+.|+.    |+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~   87 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFK   87 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEE
Confidence            467999999999999999999999999999 8877     4567799999999999999999999999999999    99


Q ss_pred             EEeecCch
Q 002823          301 LEPSHLRG  308 (876)
Q Consensus       301 Vs~A~~k~  308 (876)
                      |.|+++..
T Consensus        88 v~~a~~~~   95 (99)
T 2div_A           88 LNYATYSG   95 (99)
T ss_dssp             EEETTCCS
T ss_pred             EeecCCCC
Confidence            99998753

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.45  E-value=1.8e-13  Score=126.32  Aligned_cols=79  Identities=16%  Similarity=0.345  Sum_probs=71.8

Q ss_pred             cccceeEeecCCCCCcHHHHH---HHhhhcCCeEEEEecC--------CcccEEEEEecCHHHHHHHHHHhCCceeCCeE
Q 002823          230 INQGTLVVFNLDSSVSNDELH---HIFGVYGEIKEIRETP--------QKIHQKYIEFYDTRAAEAALRELNSRYIAGKQ  298 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLr---eiFs~fG~I~sVritg--------~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~  298 (876)
                      ...++|||+|||.++++++|+   ++|++||+|..|++..        .++|||||+|.+.++|++|++.|||..|.|++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            346799999999999999999   9999999999988822        34589999999999999999999999999999


Q ss_pred             EEEEeecCch
Q 002823          299 IKLEPSHLRG  308 (876)
Q Consensus       299 IkVs~A~~k~  308 (876)
                      |+|+|++++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998864

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.44  E-value=2.1e-13  Score=134.34  Aligned_cols=80  Identities=13%  Similarity=0.234  Sum_probs=73.6

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcC--CeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYG--EIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG--~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ..+|||+|||.++++++|+++|+.||  .|.+|++     ++..+|||||+|.+.++|++||+.|||..|.|++|+|.++
T Consensus        55 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a  134 (156)
T 3n9u_C           55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA  134 (156)
T ss_dssp             -CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEc
Confidence            46999999999999999999999999  9999887     5677899999999999999999999999999999999999


Q ss_pred             cCchhHH
Q 002823          305 HLRGLRK  311 (876)
Q Consensus       305 ~~k~~Rr  311 (876)
                      .++..++
T Consensus       135 ~~~~~~~  141 (156)
T 3n9u_C          135 TRQNLSQ  141 (156)
T ss_dssp             CHHHHHH
T ss_pred             CCCcchh
Confidence            8866544

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.44  E-value=1.1e-13  Score=120.35  Aligned_cols=70  Identities=11%  Similarity=0.276  Sum_probs=65.2

Q ss_pred             CcEEEEcCCCCCC------CHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCc-eeeE
Q 002823          147 SRTLLLRKINSNI------EDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSG-KLDI  216 (876)
Q Consensus       147 SrTLFVgNLP~~v------TEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr-~L~V  216 (876)
                      +++|||+|||..+      ++++|+++|++||+|..++   .+++++|||||+|.+.++|++|++.|+|..+.|+ +|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            4799999999999      7799999999999999998   4567899999999999999999999999999999 8877

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.44  E-value=1.8e-13  Score=126.27  Aligned_cols=82  Identities=13%  Similarity=0.287  Sum_probs=70.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|++.+ +..+.|+.|+|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            4566799999999999999999999999999999983     4778999999999999999999876 589999999999


Q ss_pred             ecCCCCCC
Q 002823          218 YSIPKDNP  225 (876)
Q Consensus       218 ~A~pk~~~  225 (876)
                      ++.++...
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99887543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=1.3e-13  Score=124.44  Aligned_cols=79  Identities=32%  Similarity=0.372  Sum_probs=71.4

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ...++|||+|||.++++++|+++|++||.|.-++. ++..++||||+|.+.++|++|++.||+..|.|++|+|+|++++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRG   92 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCC
Confidence            45679999999999999999999999999854433 56678999999999999999999999999999999999998864

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=1.1e-13  Score=128.24  Aligned_cols=81  Identities=12%  Similarity=0.318  Sum_probs=73.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+.++|||+|||.++++++|+++|++||.|..|+     .+++++|||||+|.+.++|++|++. ++..|.|+.|+|.+
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEE
Confidence            34468999999999999999999999999998887     2467899999999999999999987 99999999999999


Q ss_pred             cCCCCCC
Q 002823          219 SIPKDNP  225 (876)
Q Consensus       219 A~pk~~~  225 (876)
                      +.++...
T Consensus       103 a~~~~~~  109 (116)
T 1x4b_A          103 AVAREES  109 (116)
T ss_dssp             CSSCCCC
T ss_pred             CCCCccC
Confidence            9987654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.44  E-value=4.8e-14  Score=131.95  Aligned_cols=76  Identities=24%  Similarity=0.403  Sum_probs=70.6

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||+|||.++++++|+++|++||.|.+|++     ++..+|||||+|.+.++|++|+ .|||..|.|++|+|++++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4569999999999999999999999999999887     4567899999999999999999 799999999999999998


Q ss_pred             Cc
Q 002823          306 LR  307 (876)
Q Consensus       306 ~k  307 (876)
                      +.
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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

Probab=99.44  E-value=1.9e-13  Score=126.22  Aligned_cols=80  Identities=24%  Similarity=0.356  Sum_probs=73.7

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..++|||+|||..+++++|+++|+.||.|..|++  ++..+|||||+|.+.++|.+|++.|||..+.|++|+|.|+.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANR   86 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCh
Confidence            3569999999999999999999999999999888  56678999999999999999999999999999999999998755


Q ss_pred             hH
Q 002823          309 LR  310 (876)
Q Consensus       309 ~R  310 (876)
                      .+
T Consensus        87 ~~   88 (115)
T 3lqv_A           87 AF   88 (115)
T ss_dssp             HT
T ss_pred             hh
Confidence            43

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.44  E-value=7.7e-14  Score=125.97  Aligned_cols=76  Identities=28%  Similarity=0.417  Sum_probs=71.5

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ++|||+|||.++++++|+++|++||+|..|++...+++||||+|.+.++|++|++.|+|..+.|++|+|++++++.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            3799999999999999999999999999999855479999999999999999999999999999999999998865

>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

Probab=99.44  E-value=1.2e-13  Score=122.91  Aligned_cols=77  Identities=22%  Similarity=0.285  Sum_probs=69.9

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCC-eEEEEecCCcccEEEEEecCHHHHHHHHHHhCC-ceeCCeEEEEEeecCch
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGE-IKEIRETPQKIHQKYIEFYDTRAAEAALRELNS-RYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~-I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG-~~I~Gr~IkVs~A~~k~  308 (876)
                      ..++|||+|||.++++++|+++|++||. |..+.+  .+++||||+|.+.++|++|++.||| ..+.|++|+|+|++++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~   84 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL--LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   84 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE--EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE--cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcc
Confidence            4579999999999999999999999999 665555  3689999999999999999999999 99999999999999865


Q ss_pred             h
Q 002823          309 L  309 (876)
Q Consensus       309 ~  309 (876)
                      .
T Consensus        85 ~   85 (93)
T 2cqh_A           85 L   85 (93)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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

Probab=99.44  E-value=7.5e-14  Score=128.94  Aligned_cols=78  Identities=18%  Similarity=0.312  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      +...++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|+ .|++..|.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEe
Confidence            345689999999999999999999999999999984     3778999999999999999999 9999999999999999


Q ss_pred             cCCC
Q 002823          219 SIPK  222 (876)
Q Consensus       219 A~pk  222 (876)
                      +.++
T Consensus       101 a~~~  104 (114)
T 2cq4_A          101 SQAE  104 (114)
T ss_dssp             HHHH
T ss_pred             cCCC
Confidence            8764

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=1.5e-13  Score=127.24  Aligned_cols=80  Identities=13%  Similarity=0.232  Sum_probs=72.6

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ....++|||+|||.++++++|+++|++||.|..|++     ++..+|||||+|.+.++|++|++. ++..|.|++|+|.+
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEE
Confidence            345679999999999999999999999999999887     355689999999999999999998 99999999999999


Q ss_pred             ecCchh
Q 002823          304 SHLRGL  309 (876)
Q Consensus       304 A~~k~~  309 (876)
                      ++++..
T Consensus       103 a~~~~~  108 (116)
T 1x4b_A          103 AVAREE  108 (116)
T ss_dssp             CSSCCC
T ss_pred             CCCCcc
Confidence            998753

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=3e-13  Score=123.54  Aligned_cols=80  Identities=15%  Similarity=0.164  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEE-EE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRT-FY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~s-V~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .....++|||+|||+++++++|+++|++||.|.. |+    .+++++|||||+|.+.++|++|++. ++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            3456789999999999999999999999999987 65    3678999999999999999999987 9999999999999


Q ss_pred             ecCCCC
Q 002823          218 YSIPKD  223 (876)
Q Consensus       218 ~A~pk~  223 (876)
                      ++.+++
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            987654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.43  E-value=5.7e-13  Score=124.94  Aligned_cols=79  Identities=18%  Similarity=0.311  Sum_probs=72.6

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ....+|||+|||..+++++|+++|++||.|+.|++    ++..+|||||+|.+.++|.+|++.|||..+.|++|+|+++.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  112 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  112 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeC
Confidence            35569999999999999999999999999999888    34578999999999999999999999999999999999998


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      +..
T Consensus       113 ~~~  115 (124)
T 2kt5_A          113 SQI  115 (124)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            753

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=1.7e-13  Score=124.62  Aligned_cols=79  Identities=27%  Similarity=0.414  Sum_probs=72.4

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||..+++++|+++|++||+|..|++     ++..++||||+|.+.++|++|++. ++..|.|++|+|.++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a   92 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPC   92 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEc
Confidence            45679999999999999999999999999999887     345679999999999999999998 999999999999999


Q ss_pred             cCchh
Q 002823          305 HLRGL  309 (876)
Q Consensus       305 ~~k~~  309 (876)
                      +++..
T Consensus        93 ~~~~~   97 (105)
T 2dh8_A           93 TPRGM   97 (105)
T ss_dssp             CCSSC
T ss_pred             cCCCC
Confidence            98653

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=4.7e-13  Score=120.21  Aligned_cols=77  Identities=18%  Similarity=0.316  Sum_probs=71.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchh
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~  309 (876)
                      ...++|||+|+  ++++++|+++|++||+|..|++ ...++||||+|.+.++|.+|++.|+|..|.|++|+|.|++++..
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEe-cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            35679999996  8999999999999999999998 57899999999999999999999999999999999999988653

>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

Probab=99.43  E-value=1.3e-13  Score=122.77  Aligned_cols=76  Identities=25%  Similarity=0.256  Sum_probs=68.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...+|||+|||.++++++|+++|++||.|..+++     ++..++||||+|.+.++|++|++.||+..|.|++|+|+++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            4579999999999999999999999999876443     45678999999999999999999999999999999999986


Q ss_pred             C
Q 002823          306 L  306 (876)
Q Consensus       306 ~  306 (876)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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

Probab=99.43  E-value=4e-13  Score=117.82  Aligned_cols=74  Identities=22%  Similarity=0.320  Sum_probs=67.5

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++ +++..+.|++|+|++|
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            45679999999999999999999999999999887     35678999999999999999996 5888999999999975

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.43  E-value=3e-13  Score=134.72  Aligned_cols=77  Identities=25%  Similarity=0.323  Sum_probs=70.4

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEec-CCcccEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEeecCch
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRET-PQKIHQKYIEFYDTRAAEAALRELNSRYIAG--KQIKLEPSHLRG  308 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVrit-g~skG~AFVeF~d~E~A~kAL~~LnG~~I~G--r~IkVs~A~~k~  308 (876)
                      ..+|||+||+..+++++|+++|++||+|++|++. ..+++||||+|.+.++|++|++.|||..|.|  ++|+|+|++++.
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            4579999999999999999999999999999883 4457899999999999999999999999965  999999999864

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.43  E-value=1.4e-13  Score=135.60  Aligned_cols=78  Identities=13%  Similarity=0.203  Sum_probs=71.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccC--CeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYG--DVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG--~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...++|||+|||+++++++|+++|++||  .|.+|+.     +++++|||||+|.+.++|++|++.|+|..|.|+.|+|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            3568999999999999999999999999  9999883     68899999999999999999999999999999999999


Q ss_pred             ecCCC
Q 002823          218 YSIPK  222 (876)
Q Consensus       218 ~A~pk  222 (876)
                      ++.++
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98754

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=1.8e-13  Score=125.69  Aligned_cols=78  Identities=13%  Similarity=0.229  Sum_probs=70.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      .+.+.++|||+|||+++|+++|+++|++||+|.+|+.    .++++|||||+|.+.++|++|++ +++..+.|+.|.|.+
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999982    37789999999999999999998 899999999999998


Q ss_pred             cCC
Q 002823          219 SIP  221 (876)
Q Consensus       219 A~p  221 (876)
                      +..
T Consensus        86 ~~~   88 (103)
T 1s79_A           86 KDD   88 (103)
T ss_dssp             HHH
T ss_pred             chH
Confidence            643

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.43  E-value=3.1e-13  Score=129.80  Aligned_cols=76  Identities=24%  Similarity=0.319  Sum_probs=70.6

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccE-EEEEecCHHHHHHHHHHhCCceeCC--eEEEEEeecCch
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQ-KYIEFYDTRAAEAALRELNSRYIAG--KQIKLEPSHLRG  308 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~-AFVeF~d~E~A~kAL~~LnG~~I~G--r~IkVs~A~~k~  308 (876)
                      -.|||+||+..+|+++|+++|++||+|.+|++..+.+++ |||+|.+.++|++|++.|||..|.|  ++|+|+|++++.
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSS
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCc
Confidence            478999999999999999999999999999886566787 9999999999999999999999988  999999999864

>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

Probab=99.43  E-value=2e-13  Score=120.63  Aligned_cols=76  Identities=16%  Similarity=0.269  Sum_probs=70.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ...++|||+|||+++++++|+++|++| .|..++.. +++|||||+|.+.++|++|++.|++..+.|++|+|+++..+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            456899999999999999999999999 99998863 88999999999999999999999999999999999998654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.43  E-value=8.6e-14  Score=125.66  Aligned_cols=81  Identities=14%  Similarity=0.185  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ..+.++|||+|||.++++++|+++|++||.|..+.    .+++++|||||+|.+.++|++|++ |++..+.|+.|+|.++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            34678999999999999999999999999776511    457899999999999999999998 9999999999999999


Q ss_pred             CCCCCC
Q 002823          220 IPKDNP  225 (876)
Q Consensus       220 ~pk~~~  225 (876)
                      .++...
T Consensus        93 ~~~~~~   98 (101)
T 1fj7_A           93 KGRDGT   98 (101)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            887543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.42  E-value=2.7e-13  Score=125.05  Aligned_cols=79  Identities=19%  Similarity=0.284  Sum_probs=70.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|+.||.|.+|++     ++..+|||||+|.+.++|.+|++.+ +..+.|++|+|.++
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVA  101 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEc
Confidence            45679999999999999999999999999999988     3566899999999999999999976 59999999999999


Q ss_pred             cCchh
Q 002823          305 HLRGL  309 (876)
Q Consensus       305 ~~k~~  309 (876)
                      .++..
T Consensus       102 ~~~~~  106 (109)
T 2rs2_A          102 FPRRA  106 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98754

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=2.3e-13  Score=124.96  Aligned_cols=80  Identities=6%  Similarity=0.073  Sum_probs=72.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...++|||+|||.++|+++|+++|++||.|.+|++    .+.++|||||+|.+.++|.+|+. +++..+.|++|+|.++.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            35679999999999999999999999999999988    25578999999999999999999 99999999999999987


Q ss_pred             CchhH
Q 002823          306 LRGLR  310 (876)
Q Consensus       306 ~k~~R  310 (876)
                      .-..+
T Consensus        88 ~~~~~   92 (103)
T 1s79_A           88 DYFAK   92 (103)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            74433

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=5.4e-13  Score=119.16  Aligned_cols=80  Identities=23%  Similarity=0.306  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ....++|||+|||+++++++|+++|++||.|..++  ...+..+.|||+|.+.++|++|++.|+|..+.|++|+|.++.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            34578999999999999999999999999999994  4444556699999999999999999999999999999999988


Q ss_pred             CC
Q 002823          222 KD  223 (876)
Q Consensus       222 k~  223 (876)
                      ++
T Consensus        92 ~~   93 (96)
T 2e44_A           92 EM   93 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            74

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.42  E-value=1.5e-13  Score=117.21  Aligned_cols=70  Identities=14%  Similarity=0.286  Sum_probs=65.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          149 TLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       149 TLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      +|||+|||+++++++|+++|++||+|..++.     +++++|||||+|.+.++|++|++ +++..+.|++|+|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            5999999999999999999999999999882     57789999999999999999997 9999999999999875

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.42  E-value=6.8e-13  Score=125.93  Aligned_cols=75  Identities=25%  Similarity=0.385  Sum_probs=69.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||..+++++|+++|++||+|..|++     ++..+|||||+|.+.++|++|++.|||..|.|++|+|+||
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            35679999999999999999999999999999988     3457899999999999999999999999999999999986

>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

Probab=99.42  E-value=2.7e-13  Score=125.85  Aligned_cols=83  Identities=12%  Similarity=0.145  Sum_probs=74.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCe-EEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEI-KEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I-~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||.++++++|+++|+.||.| ..|++    ++..+|||||+|.+.++|++||+. |+..|.|++|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVV   91 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEEC
Confidence            346799999999999999999999999999 67776    456789999999999999999987 999999999999999


Q ss_pred             cCchhHHHH
Q 002823          305 HLRGLRKCL  313 (876)
Q Consensus       305 ~~k~~Rr~l  313 (876)
                      .++..++..
T Consensus        92 ~~~~~~~~~  100 (114)
T 2cpy_A           92 TLEDMREIE  100 (114)
T ss_dssp             CHHHHHHHH
T ss_pred             CHHHHHHHH
Confidence            988766544

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.42  E-value=6e-14  Score=123.91  Aligned_cols=77  Identities=19%  Similarity=0.279  Sum_probs=67.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ++|||+|||.++++++|+++|++||+|..++.     +++++|||||+|.+.+ |++|++.|+|..+.|++|+|+++.++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            68999999999999999999999999999883     4778999999999999 99999999999999999999999876


Q ss_pred             CCC
Q 002823          223 DNP  225 (876)
Q Consensus       223 ~~~  225 (876)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>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

Probab=99.42  E-value=9.5e-14  Score=130.59  Aligned_cols=79  Identities=11%  Similarity=0.138  Sum_probs=70.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEE---EE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRT---FY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~s---V~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||+++++++|+++|++||.|..   +.  .+++++|||||+|.+.++|++|++ |++..|.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            3456689999999999999999999999998854   22  467889999999999999999998 99999999999999


Q ss_pred             ecCCC
Q 002823          218 YSIPK  222 (876)
Q Consensus       218 ~A~pk  222 (876)
                      ++.++
T Consensus       100 ~a~~~  104 (124)
T 1wel_A          100 PITKK  104 (124)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.42  E-value=1.8e-13  Score=116.84  Aligned_cols=70  Identities=14%  Similarity=0.274  Sum_probs=65.4

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++ |++..+.|++|+|.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            5899999999999999999999999999887     45568999999999999999998 9999999999999985

>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

Probab=99.41  E-value=1.3e-13  Score=129.12  Aligned_cols=78  Identities=21%  Similarity=0.197  Sum_probs=70.7

Q ss_pred             cccceeEeecCCCC-CcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEEeecC
Q 002823          230 INQGTLVVFNLDSS-VSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS--RYIAGKQIKLEPSHL  306 (876)
Q Consensus       230 ~~~~tLfV~NLP~s-vTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG--~~I~Gr~IkVs~A~~  306 (876)
                      .+..+|||+|||.+ +++++|+++|++||+|.+|++ ...|+||||+|.+.++|.+|++.|++  ..|.|++|+|.|++.
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i-~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  101 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK  101 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEE-ecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcc
Confidence            35679999999998 999999999999999999998 45689999999999999999998864  569999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      +.
T Consensus       102 ~~  103 (112)
T 1x4f_A          102 YK  103 (112)
T ss_dssp             CS
T ss_pred             cc
Confidence            54

>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

Probab=99.41  E-value=3.2e-13  Score=119.39  Aligned_cols=75  Identities=15%  Similarity=0.284  Sum_probs=70.3

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ..++|||+|||.++++++|+++|++| +|.++++. ..+|||||+|.+.++|++|++.|||..+.|++|+|+|+..+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            35689999999999999999999999 99999884 78999999999999999999999999999999999998764

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.41  E-value=1.5e-13  Score=128.48  Aligned_cols=79  Identities=11%  Similarity=0.242  Sum_probs=72.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .+.++|||+|||.++++++|+++|++||.|..|+.     +++++|||||+|.+.++|++|+ .|++..|.|+.|+|.++
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            34689999999999999999999999999999873     6778999999999999999999 89999999999999999


Q ss_pred             CCCCC
Q 002823          220 IPKDN  224 (876)
Q Consensus       220 ~pk~~  224 (876)
                      .+...
T Consensus       113 ~~~~~  117 (124)
T 2jwn_A          113 RTNMP  117 (124)
T ss_dssp             SCCCS
T ss_pred             CCCCC
Confidence            76543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.41  E-value=5.6e-13  Score=119.05  Aligned_cols=78  Identities=15%  Similarity=0.152  Sum_probs=70.4

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEE-e-cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR-E-TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVr-i-tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ...+|||+|||.++++++|+++|++||.|..|+ + .....+.|||+|.+.++|.+|++.|||..|.|++|+|+++.+++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            457999999999999999999999999999995 5 33344569999999999999999999999999999999999874

>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

Probab=99.41  E-value=3.6e-13  Score=123.06  Aligned_cols=79  Identities=16%  Similarity=0.132  Sum_probs=72.2

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCC-eEEEEec------CCcccEEEEEecCHHHHHHHHHHhC--CceeCCeEEEE
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGE-IKEIRET------PQKIHQKYIEFYDTRAAEAALRELN--SRYIAGKQIKL  301 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~-I~sVrit------g~skG~AFVeF~d~E~A~kAL~~Ln--G~~I~Gr~IkV  301 (876)
                      ..++|||+|||.++++++|+++|++||. |.+|++.      +..+|||||+|.+.++|.+|++.|+  +..+.|++|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            4679999999999999999999999998 9999873      3678999999999999999999996  58999999999


Q ss_pred             EeecCchh
Q 002823          302 EPSHLRGL  309 (876)
Q Consensus       302 s~A~~k~~  309 (876)
                      .|++++..
T Consensus        87 ~~a~~~~~   94 (109)
T 2dis_A           87 DWAEPEID   94 (109)
T ss_dssp             EESCSSCS
T ss_pred             EEcCCCCC
Confidence            99998654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=7.1e-13  Score=120.42  Aligned_cols=78  Identities=15%  Similarity=0.259  Sum_probs=69.5

Q ss_pred             CCCcE-EEEcCCCCCCCHHH----HHHHhhcc-CCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          145 HPSRT-LLLRKINSNIEDSE----LKALFEQY-GDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       145 ~pSrT-LFVgNLP~~vTEee----L~elFsqf-G~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      .|+.| |||+|||.++++++    |+++|++| |+|.+|  ++   |+|||.|.+.++|++|++.|+|..+.||+|+|+|
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            46777 99999999999988    55899999 599998  33   9999999999999999999999999999999999


Q ss_pred             cCCCCCCCc
Q 002823          219 SIPKDNPSE  227 (876)
Q Consensus       219 A~pk~~~~e  227 (876)
                      +..+.+..+
T Consensus        81 A~~~sd~~~   89 (96)
T 2diu_A           81 TPKNRELCE   89 (96)
T ss_dssp             SCCSCCCCC
T ss_pred             cCCCcceeE
Confidence            988776543

>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}

Probab=99.41  E-value=4.8e-13  Score=128.49  Aligned_cols=83  Identities=14%  Similarity=0.302  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEE--------E--EeCCCccceEeeecCCHHHHHHHHHHccccccCCc
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRT--------F--YRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSG  212 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~s--------V--~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr  212 (876)
                      ...++++|||+|||+++++++|+++|++||.|..        +  ..+++++|||||+|.+.++|++|++.|+|..+.|+
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            3567899999999999999999999999998865        2  25789999999999999999999999999999999


Q ss_pred             eeeEeecCCCCCC
Q 002823          213 KLDIHYSIPKDNP  225 (876)
Q Consensus       213 ~L~V~~A~pk~~~  225 (876)
                      .|.|.|+.+....
T Consensus       121 ~l~V~~a~~~~~~  133 (143)
T 3egn_A          121 PMVVQFARSARPK  133 (143)
T ss_dssp             ECEEEECCCSCC-
T ss_pred             EEEEEECCCCCCc
Confidence            9999999776543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=6.6e-13  Score=117.60  Aligned_cols=76  Identities=16%  Similarity=0.227  Sum_probs=70.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...+|||+|||.++++++|+++|+.| .|..|++    ++..+|||||+|.+.++|.+|++ |||..|.|++|+|.++.+
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~   86 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKS   86 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESS
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCc
Confidence            45799999999999999999999999 9999877    45568999999999999999999 999999999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      +.
T Consensus        87 ~~   88 (91)
T 2dgw_A           87 GP   88 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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

Probab=99.41  E-value=4e-13  Score=132.55  Aligned_cols=85  Identities=14%  Similarity=0.282  Sum_probs=75.1

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      +....+.++|||+|||+.+++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|+|..|.|++|.
T Consensus        66 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  145 (165)
T 1rk8_A           66 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ  145 (165)
T ss_dssp             CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            344567889999999999999999999999999999883     566899999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q 002823          216 IHYSIPKDNP  225 (876)
Q Consensus       216 V~~A~pk~~~  225 (876)
                      |.|+.++...
T Consensus       146 V~~a~~~~~~  155 (165)
T 1rk8_A          146 VDWCFVKGPK  155 (165)
T ss_dssp             EEESEECC--
T ss_pred             EEEecCCCCC
Confidence            9999876543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.41  E-value=1.5e-13  Score=117.46  Aligned_cols=71  Identities=14%  Similarity=0.302  Sum_probs=66.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ++|||+|||+++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.++ ..+.|++|+|+++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            4899999999999999999999999998887     257789999999999999999999999 9999999999986

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.41  E-value=6.9e-13  Score=132.09  Aligned_cols=83  Identities=17%  Similarity=0.216  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-CCCccceEeeecCCHHHHHHHHHHccccccCC--ceeeEeec
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-ASKHCGFVTISYYDIRAARNAMKSLQNKLTRS--GKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G--r~L~V~~A  219 (876)
                      ......+|||+||++.+|+++|+++|++||+|++|++ +.+.+|||||+|.+.++|++|++.|+|..|.|  ++|+|+|+
T Consensus        42 ~ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           42 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             CCCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             CCCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            3444578999999999999999999999999999995 34568899999999999999999999999965  99999999


Q ss_pred             CCCCCC
Q 002823          220 IPKDNP  225 (876)
Q Consensus       220 ~pk~~~  225 (876)
                      +++...
T Consensus       122 k~~~l~  127 (164)
T 1sjr_A          122 KLTSLN  127 (164)
T ss_dssp             SSSSCC
T ss_pred             cCCccc
Confidence            987543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=8.8e-14  Score=121.53  Aligned_cols=76  Identities=17%  Similarity=0.268  Sum_probs=69.6

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++..+|||||+|.+.++|.+|++.|||..+.|+.|++.+.+
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            4579999999999999999999999999999887     35568999999999999999999999999999999988765


Q ss_pred             C
Q 002823          306 L  306 (876)
Q Consensus       306 ~  306 (876)
                      +
T Consensus        84 s   84 (85)
T 1x4e_A           84 S   84 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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

Probab=99.41  E-value=6.5e-13  Score=122.46  Aligned_cols=78  Identities=18%  Similarity=0.270  Sum_probs=71.0

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCcee--------CCe
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYI--------AGK  297 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I--------~Gr  297 (876)
                      ....+|||+|||.++++++|+++|++||.|..|++    ++..++||||+|.+.++|++|++.|||..|        .++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~  102 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE  102 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCC
Confidence            35679999999999999999999999999999887    345689999999999999999999999999        578


Q ss_pred             EEEEEeecCc
Q 002823          298 QIKLEPSHLR  307 (876)
Q Consensus       298 ~IkVs~A~~k  307 (876)
                      +|+|.|+.++
T Consensus       103 ~l~v~~a~p~  112 (114)
T 1x5o_A          103 PLLCKFSGPS  112 (114)
T ss_dssp             CBEEEECCCS
T ss_pred             ceeEEccCCC
Confidence            8999999875

>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

Probab=99.40  E-value=3.1e-13  Score=130.55  Aligned_cols=82  Identities=12%  Similarity=0.123  Sum_probs=72.9

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCC---eEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGE---IKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~---I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ...+|||+|||.++|+++|+++|++||.   |..|++    .++++|||||+|.+.++|++|++ ||+..|.|++|+|.+
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~  121 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFK  121 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            4568999999999999999999999999   777776    35678999999999999999999 999999999999999


Q ss_pred             ecCchhHHHH
Q 002823          304 SHLRGLRKCL  313 (876)
Q Consensus       304 A~~k~~Rr~l  313 (876)
                      +.+++..+.+
T Consensus       122 a~~~e~~~~~  131 (136)
T 2hgl_A          122 SHRTEMDWVL  131 (136)
T ss_dssp             CCHHHHHHHH
T ss_pred             CChHHHHHHH
Confidence            9877655443

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.40  E-value=2.1e-13  Score=118.50  Aligned_cols=69  Identities=16%  Similarity=0.257  Sum_probs=64.2

Q ss_pred             ceeEeecCCCCC------cHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCe-EEEE
Q 002823          233 GTLVVFNLDSSV------SNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK-QIKL  301 (876)
Q Consensus       233 ~tLfV~NLP~sv------TeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr-~IkV  301 (876)
                      ++|||+|||..+      ++++|+++|++||+|.+|++   ++.++|||||+|.+.++|.+|++.|||..+.|+ +|+|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            589999999999      78999999999999999987   446789999999999999999999999999999 8876

>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

Probab=99.40  E-value=5.1e-13  Score=125.59  Aligned_cols=80  Identities=13%  Similarity=0.210  Sum_probs=71.8

Q ss_pred             CCCCCcEEEE--cCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcccccc-----CCceee
Q 002823          143 DEHPSRTLLL--RKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLT-----RSGKLD  215 (876)
Q Consensus       143 ~e~pSrTLFV--gNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l-----~Gr~L~  215 (876)
                      ...|+++|||  +||++++++++|+++|++||.|..|++. ..||||||+|.+.++|++|++.|+|+.+     .|++|.
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~-~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~   99 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   99 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEE
Confidence            4567899999  7799999999999999999999999863 4689999999999999999999999988     689999


Q ss_pred             EeecCCCC
Q 002823          216 IHYSIPKD  223 (876)
Q Consensus       216 V~~A~pk~  223 (876)
                      |.|+....
T Consensus       100 v~~a~~~p  107 (114)
T 2cq2_A          100 LNFVEKVQ  107 (114)
T ss_dssp             EEEESCCC
T ss_pred             EEecccCc
Confidence            99986543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.40  E-value=4.2e-13  Score=125.63  Aligned_cols=81  Identities=11%  Similarity=0.130  Sum_probs=72.3

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCC---eEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGE---IKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~---I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ...+|||+|||.++++++|+++|+.||.   |..|++    .++++|||||+|.+.++|++||+ +|+..|.|+.|+|.+
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~   94 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFK   94 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEE
Confidence            4568999999999999999999999999   777776    45678999999999999999999 999999999999999


Q ss_pred             ecCchhHHH
Q 002823          304 SHLRGLRKC  312 (876)
Q Consensus       304 A~~k~~Rr~  312 (876)
                      +.+++..+.
T Consensus        95 a~~~~~~~~  103 (118)
T 2db1_A           95 SHRTEMDWV  103 (118)
T ss_dssp             ECHHHHHHH
T ss_pred             CCHHHHHHH
Confidence            987664443

>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

Probab=99.40  E-value=1.2e-12  Score=118.50  Aligned_cols=77  Identities=14%  Similarity=0.291  Sum_probs=70.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|++||.|+.|++     ++.++|||||+|.+.++|.+|++  ++..|.|++|+|.++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a   90 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLP   90 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEec
Confidence            35679999999999999999999999999999887     35678999999999999999998  578999999999999


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      .++.
T Consensus        91 ~~~~   94 (103)
T 2cqg_A           91 NSKQ   94 (103)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            9865

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.40  E-value=1.2e-13  Score=122.02  Aligned_cols=75  Identities=16%  Similarity=0.351  Sum_probs=67.3

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ++|||+|||.++++++|+++|++||+|.+|++     ++.++|||||+|.+.+ |.+|++.|||..+.|++|+|+++.++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            57999999999999999999999999999988     3566899999999999 99999999999999999999999885


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.40  E-value=1.5e-13  Score=130.53  Aligned_cols=78  Identities=21%  Similarity=0.255  Sum_probs=71.6

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEE--EEe-----cCCcccEEEEEecCHHHHHHHHHHhCCc----eeCCeE
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKE--IRE-----TPQKIHQKYIEFYDTRAAEAALRELNSR----YIAGKQ  298 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~s--Vri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~----~I~Gr~  298 (876)
                      ...++|||+|||.++++++|+++|++||.|..  |++     ++.++|||||+|.+. +|.+|++.|||.    .+.|++
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            45679999999999999999999999999966  776     566789999999999 999999999999    999999


Q ss_pred             EEEEeecCch
Q 002823          299 IKLEPSHLRG  308 (876)
Q Consensus       299 IkVs~A~~k~  308 (876)
                      |+|++++++.
T Consensus       100 l~V~~a~~~~  109 (131)
T 2m2b_A          100 INVEFAKGSK  109 (131)
T ss_dssp             CCCEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999998854

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.39  E-value=6.8e-13  Score=127.47  Aligned_cols=81  Identities=20%  Similarity=0.276  Sum_probs=72.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccce-EeeecCCHHHHHHHHHHccccccCC--ceeeEeecCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGF-VTISYYDIRAARNAMKSLQNKLTRS--GKLDIHYSIP  221 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGf-AFV~F~d~edA~kAl~~Lng~~l~G--r~L~V~~A~p  221 (876)
                      .+-..|||+||++.+|+++|+++|++||+|.+|++..+.+|| |||+|.+.++|++|++.|+|..|.|  +.|+|+|+++
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~  105 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  105 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSC
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCC
Confidence            444677899999999999999999999999999965567888 9999999999999999999999988  8999999988


Q ss_pred             CCCC
Q 002823          222 KDNP  225 (876)
Q Consensus       222 k~~~  225 (876)
                      +.-.
T Consensus       106 ~~l~  109 (130)
T 3zzy_A          106 TSLN  109 (130)
T ss_dssp             SSCC
T ss_pred             Ccee
Confidence            7543

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.39  E-value=1.9e-13  Score=123.73  Aligned_cols=77  Identities=21%  Similarity=0.258  Sum_probs=68.9

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe------cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE------TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri------tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ...++|||+|||.++++++|+++|+.|| |.+|++      ++..+|||||+|.+.++|.+|+ .|+|..|.|++|+|++
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEe
Confidence            3567999999999999999999999999 999998      2445899999999999999999 8999999999999999


Q ss_pred             ecCch
Q 002823          304 SHLRG  308 (876)
Q Consensus       304 A~~k~  308 (876)
                      ++++.
T Consensus        95 a~~~~   99 (100)
T 2j76_E           95 ADQAQ   99 (100)
T ss_dssp             CCCSC
T ss_pred             ccCCC
Confidence            98753

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.39  E-value=1.3e-12  Score=116.72  Aligned_cols=80  Identities=13%  Similarity=0.213  Sum_probs=70.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDN  224 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~  224 (876)
                      ...++|||+|||+++++++|+++|++||.|..|........||||+|.+.++|++|++ |++..+.|+.|.|.++.++..
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCC
Confidence            4568999999999999999999999999999986432222299999999999999999 999999999999999877654


Q ss_pred             C
Q 002823          225 P  225 (876)
Q Consensus       225 ~  225 (876)
                      .
T Consensus        85 ~   85 (94)
T 2e5g_A           85 Q   85 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.39  E-value=1.5e-13  Score=124.00  Aligned_cols=79  Identities=24%  Similarity=0.239  Sum_probs=70.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEE----ecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR----ETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVr----itg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...+|||+|||.++++++|+++|++||.|..+.    .++.++|||||+|.+.++|++|++ |||..|.|++|+|.++++
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~   94 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   94 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCC
Confidence            467999999999999999999999999876611    246789999999999999999998 999999999999999988


Q ss_pred             chhH
Q 002823          307 RGLR  310 (876)
Q Consensus       307 k~~R  310 (876)
                      +..+
T Consensus        95 ~~~~   98 (101)
T 1fj7_A           95 RDGT   98 (101)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6543

>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}

Probab=99.38  E-value=6.5e-13  Score=118.44  Aligned_cols=78  Identities=21%  Similarity=0.388  Sum_probs=63.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccc--cCCceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKL--TRSGKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~--l~Gr~L~V~~A~  220 (876)
                      ...+..+|||+|||+++|+++|+++|++||+|.+|+....+||||||+|.+.++|++    +++..  +.|++|.|.++.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~   82 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAE   82 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcC
Confidence            456789999999999999999999999999999999766799999999999999984    34444  569999999998


Q ss_pred             CCCC
Q 002823          221 PKDN  224 (876)
Q Consensus       221 pk~~  224 (876)
                      ++..
T Consensus        83 ~k~~   86 (89)
T 3d2w_A           83 PKHN   86 (89)
T ss_dssp             ----
T ss_pred             CCCc
Confidence            7654

>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

Probab=99.38  E-value=3e-13  Score=125.50  Aligned_cols=80  Identities=11%  Similarity=0.089  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCe-EEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDV-RTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I-~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .+.+.++|||+|||+++++++|+++|++||.| ..|+    .+++++|||||+|.+.++|++|++. ++..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            34567999999999999999999999999999 5565    3577899999999999999999977 9999999999999


Q ss_pred             ecCCCC
Q 002823          218 YSIPKD  223 (876)
Q Consensus       218 ~A~pk~  223 (876)
                      ++.++.
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            986543

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.38  E-value=9.1e-13  Score=120.28  Aligned_cols=78  Identities=18%  Similarity=0.257  Sum_probs=71.0

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEE-EEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKE-IRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~s-Vri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ....+|||+|||.++++++|+++|++||.|.. |++    +++++|||||+|.+.++|++|++. ++..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEEC
Confidence            34679999999999999999999999999987 776    566789999999999999999997 999999999999998


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      .+++
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7754

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.38  E-value=2.9e-13  Score=115.70  Aligned_cols=71  Identities=20%  Similarity=0.326  Sum_probs=66.1

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ++|||+|||.++++++|+++|++||+|..|++     ++.++|||||+|.+.++|++|++.++ ..+.|++|+|+++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            37999999999999999999999999999887     35568999999999999999999999 9999999999987

>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}

Probab=99.37  E-value=1.7e-12  Score=115.77  Aligned_cols=77  Identities=17%  Similarity=0.293  Sum_probs=63.9

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCce--eCCeEEEEEeecCc
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY--IAGKQIKLEPSHLR  307 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~--I~Gr~IkVs~A~~k  307 (876)
                      ....+|||+|||.++++++|+++|++||.|.+|++..++||||||+|.+.++|++    +++..  +.|++|+|.++.++
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCC
Confidence            4567999999999999999999999999999999977789999999999999983    56655  45999999999987


Q ss_pred             hhH
Q 002823          308 GLR  310 (876)
Q Consensus       308 ~~R  310 (876)
                      ..+
T Consensus        85 ~~~   87 (89)
T 3d2w_A           85 HNK   87 (89)
T ss_dssp             ---
T ss_pred             CcC
Confidence            643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.37  E-value=4.1e-13  Score=125.70  Aligned_cols=78  Identities=10%  Similarity=0.078  Sum_probs=69.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCC---eEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGD---VRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~---I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ....++|||+|||+++|+++|+++|++||.   |..|+    ..++++|||||+|.+.++|++|++ +++..|.|+.|+|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            455789999999999999999999999998   66665    347789999999999999999998 9999999999999


Q ss_pred             eecCCC
Q 002823          217 HYSIPK  222 (876)
Q Consensus       217 ~~A~pk  222 (876)
                      .++.++
T Consensus        93 ~~a~~~   98 (118)
T 2db1_A           93 FKSHRT   98 (118)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            987543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.07  E-value=4.6e-14  Score=130.90  Aligned_cols=83  Identities=18%  Similarity=0.320  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEE--------EE-----eCCCccceEeeecCCHHHHHHHHHHcccccc
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRT--------FY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLT  209 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~s--------V~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l  209 (876)
                      +..+.++|||+|||.++++++|+++|++||.|..        |+     .+++++|||||+|.+.++|++|++.|++..+
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            4567899999999999999999999999999987        54     3467899999999999999999999999999


Q ss_pred             CCceeeEeecCCCCCC
Q 002823          210 RSGKLDIHYSIPKDNP  225 (876)
Q Consensus       210 ~Gr~L~V~~A~pk~~~  225 (876)
                      .|++|+|.++.++...
T Consensus        83 ~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           83 SGNPIKVSFATRRADF   98 (116)
Confidence            9999999999887654

>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}

Probab=99.37  E-value=7e-13  Score=127.36  Aligned_cols=80  Identities=26%  Similarity=0.361  Sum_probs=71.7

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEE--------EE--ecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKE--------IR--ETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~s--------Vr--itg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      ...+|||+|||..+++++|+++|+.||.|..        |+  .++..+|||||+|.+.++|.+|++.|||..|.|++|+
T Consensus        44 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~  123 (143)
T 3egn_A           44 PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMV  123 (143)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            4679999999999999999999999998865        33  3678899999999999999999999999999999999


Q ss_pred             EEeecCchhH
Q 002823          301 LEPSHLRGLR  310 (876)
Q Consensus       301 Vs~A~~k~~R  310 (876)
                      |.|+++...+
T Consensus       124 V~~a~~~~~~  133 (143)
T 3egn_A          124 VQFARSARPK  133 (143)
T ss_dssp             EEECCCSCC-
T ss_pred             EEECCCCCCc
Confidence            9999876544

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.37  E-value=2.1e-13  Score=123.36  Aligned_cols=81  Identities=19%  Similarity=0.355  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      .+.++++|||+|||.++++++|+++|++||.|..++.    +++++|||||+|.+.++|++|++  ++..+.|+.|.|.+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             CEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            4556799999999999999999999999999999883    56789999999999999999997  88999999999999


Q ss_pred             cCCCCCC
Q 002823          219 SIPKDNP  225 (876)
Q Consensus       219 A~pk~~~  225 (876)
                      +.++...
T Consensus        83 a~~~~~~   89 (102)
T 2xs2_A           83 AIRKQNL   89 (102)
T ss_dssp             EEECC--
T ss_pred             CCcCcch
Confidence            9876543

>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

Probab=99.37  E-value=8.5e-13  Score=120.69  Aligned_cols=79  Identities=8%  Similarity=0.154  Sum_probs=69.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ...+.++|||+|||+++|+++|+++|++||.| .|+    .+++++|||||+|.+.++|++|+ .+++..|.++.|.|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEE
Confidence            34566899999999999999999999999965 665    36788999999999999999999 5799999999999999


Q ss_pred             cCCCC
Q 002823          219 SIPKD  223 (876)
Q Consensus       219 A~pk~  223 (876)
                      +.+..
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87654

>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

Probab=99.37  E-value=3.2e-13  Score=127.00  Aligned_cols=80  Identities=16%  Similarity=0.268  Sum_probs=71.4

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEE-EEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKE-IRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~s-Vri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...+|||+|||.++++++|+++|+.||.|.. +.+    ++..+|||||+|.+.++|++||+ ||+..|.|++|+|.++.
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            4569999999999999999999999999865 222    56778999999999999999999 99999999999999999


Q ss_pred             CchhHH
Q 002823          306 LRGLRK  311 (876)
Q Consensus       306 ~k~~Rr  311 (876)
                      +++..+
T Consensus       103 ~~~~~~  108 (124)
T 1wel_A          103 KKGMLE  108 (124)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877554

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.36  E-value=1.4e-12  Score=124.30  Aligned_cols=74  Identities=20%  Similarity=0.154  Sum_probs=67.7

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccE-EEEEecCHHHHHHHHHHhCCceeCC--eEEEEEeecCch
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQ-KYIEFYDTRAAEAALRELNSRYIAG--KQIKLEPSHLRG  308 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~-AFVeF~d~E~A~kAL~~LnG~~I~G--r~IkVs~A~~k~  308 (876)
                      .|||+||+..+++++|+++|++||+|++|++..+ .|+ |||+|.+.++|.+|++.|||..|.|  ++|+|.|++++.
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            5789999999999999999999999999988443 586 9999999999999999999999987  699999999864

>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

Probab=99.36  E-value=7.3e-13  Score=116.76  Aligned_cols=79  Identities=20%  Similarity=0.394  Sum_probs=68.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDN  224 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~  224 (876)
                      .++++|||+|||+++++++|+++|++||+|..|+....++|||||+|.+.++|++|+..  ...+.|++|+|.++.++..
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~~   80 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCCC
Confidence            45789999999999999999999999999999997667899999999999999865432  3456899999999988765


Q ss_pred             C
Q 002823          225 P  225 (876)
Q Consensus       225 ~  225 (876)
                      .
T Consensus        81 ~   81 (88)
T 1wf0_A           81 S   81 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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

Probab=99.36  E-value=7e-13  Score=138.31  Aligned_cols=80  Identities=18%  Similarity=0.181  Sum_probs=73.5

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcC--CeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYG--EIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG--~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ..+|||+||+.++++++|+++|++||  +|++|++     ++++||||||+|.+.++|++||+.||+..|.|++|+|.++
T Consensus        68 ~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a  147 (229)
T 3q2s_C           68 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPV  147 (229)
T ss_dssp             -CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEEC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEEC
Confidence            55899999999999999999999999  9999887     5668899999999999999999999999999999999999


Q ss_pred             cCchhHH
Q 002823          305 HLRGLRK  311 (876)
Q Consensus       305 ~~k~~Rr  311 (876)
                      ++....+
T Consensus       148 ~~~~~~~  154 (229)
T 3q2s_C          148 NKQFLSQ  154 (229)
T ss_dssp             CHHHHHH
T ss_pred             CCCccch
Confidence            8876544

>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

Probab=99.36  E-value=1.2e-12  Score=123.01  Aligned_cols=75  Identities=17%  Similarity=0.208  Sum_probs=69.1

Q ss_pred             ccceeEe--ecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCcee-----CCeEEEEEe
Q 002823          231 NQGTLVV--FNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYI-----AGKQIKLEP  303 (876)
Q Consensus       231 ~~~tLfV--~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I-----~Gr~IkVs~  303 (876)
                      +..+|||  +||+.++++++|+++|++||+|.+|.+. ..||||||+|.+.++|++|++.|||.++     .|++|.|.|
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~-~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~  102 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEe
Confidence            4678999  6699999999999999999999999984 4689999999999999999999999998     689999999


Q ss_pred             ecC
Q 002823          304 SHL  306 (876)
Q Consensus       304 A~~  306 (876)
                      ++.
T Consensus       103 a~~  105 (114)
T 2cq2_A          103 VEK  105 (114)
T ss_dssp             ESC
T ss_pred             ccc
Confidence            875

>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}

Probab=99.36  E-value=5.2e-13  Score=122.50  Aligned_cols=82  Identities=11%  Similarity=0.108  Sum_probs=73.6

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCC---eEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGE---IKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~---I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ...+|||+|||.++++++|+++|+.||.   |..|++    .+.++|||||+|.+.++|++|++ +++..++|+.|+|.+
T Consensus        10 ~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYE   88 (107)
T ss_dssp             SCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEE
Confidence            4568999999999999999999999998   888887    35578999999999999999999 999999999999999


Q ss_pred             ecCchhHHHH
Q 002823          304 SHLRGLRKCL  313 (876)
Q Consensus       304 A~~k~~Rr~l  313 (876)
                      +.+++.++.+
T Consensus        89 a~~~~~~~~~   98 (107)
T 2lmi_A           89 INNEDVDALM   98 (107)
T ss_dssp             CCHHHHHHHH
T ss_pred             CCHHHHHHHH
Confidence            9887765544

>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

Probab=99.36  E-value=1.8e-12  Score=132.75  Aligned_cols=76  Identities=24%  Similarity=0.476  Sum_probs=71.8

Q ss_pred             ccceeEeecCC-CCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLD-SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP-~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...+|||+||| ..+++++|+++|++||.|.+|++....+|||||+|.+.++|++|++.|||..+.|++|+|.+++.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            35689999999 89999999999999999999999777799999999999999999999999999999999999875

>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

Probab=99.35  E-value=4.6e-13  Score=114.08  Aligned_cols=70  Identities=14%  Similarity=0.389  Sum_probs=64.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          149 TLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       149 TLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      +|||+|||+++++++|+++|++||+|..+.     .+++++|||||+|.+.++|++|++. ++..+.|++|.|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            699999999999999999999999999987     2477899999999999999999974 889999999999875

>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

Probab=99.35  E-value=1.3e-12  Score=114.16  Aligned_cols=72  Identities=17%  Similarity=0.300  Sum_probs=67.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcc----C-------CeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCce
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQY----G-------DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGK  213 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqf----G-------~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~  213 (876)
                      .+.++|||+|||+++++++|+++|++|    |       .|.+++. .+.+|||||+|.+.++|++|+ .|++..+.|++
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~-~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~   81 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   81 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE-CSSSSEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEe-cCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeE
Confidence            567899999999999999999999999    8       9999986 456999999999999999999 99999999999


Q ss_pred             eeEee
Q 002823          214 LDIHY  218 (876)
Q Consensus       214 L~V~~  218 (876)
                      |+|+.
T Consensus        82 l~V~r   86 (87)
T 2hzc_A           82 LKIRR   86 (87)
T ss_dssp             CEEEC
T ss_pred             EEEeC
Confidence            99974

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=1.5e-12  Score=116.19  Aligned_cols=77  Identities=18%  Similarity=0.297  Sum_probs=67.7

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..++|||+|||.++++++|+++|++||.|.+|........||||+|.+.++|.+|++ |+|..|.|++|+|.++.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~   83 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCC
Confidence            356999999999999999999999999999985433222299999999999999999 99999999999999887654

>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

Probab=99.34  E-value=1.4e-12  Score=127.45  Aligned_cols=80  Identities=24%  Similarity=0.338  Sum_probs=75.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ...+.++|||+|||.++++++|+++|++||.|+.+..+++++|||||+|.+.++|.+|++.|+|..+.|++|+|.|+.++
T Consensus        95 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B           95 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            44567999999999999999999999999999998667889999999999999999999999999999999999999876

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.34  E-value=4.6e-12  Score=120.68  Aligned_cols=79  Identities=16%  Similarity=0.206  Sum_probs=69.4

Q ss_pred             CCCcE--EEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccce-EeeecCCHHHHHHHHHHccccccCC--ceeeEeec
Q 002823          145 HPSRT--LLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGF-VTISYYDIRAARNAMKSLQNKLTRS--GKLDIHYS  219 (876)
Q Consensus       145 ~pSrT--LFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGf-AFV~F~d~edA~kAl~~Lng~~l~G--r~L~V~~A  219 (876)
                      .|+++  |||+||++.+++++|+++|++||.|.+|++..+ .|| |||+|.+.++|++|++.|+|..|.|  +.|+|.|+
T Consensus        21 ~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           21 GGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             CCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             CCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            34544  679999999999999999999999999985334 486 9999999999999999999999987  69999999


Q ss_pred             CCCCC
Q 002823          220 IPKDN  224 (876)
Q Consensus       220 ~pk~~  224 (876)
                      +++..
T Consensus       100 k~~~l  104 (124)
T 2e5i_A          100 RPTRL  104 (124)
T ss_dssp             SCSCC
T ss_pred             cCCcc
Confidence            88764

>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

Probab=99.34  E-value=1.4e-12  Score=121.37  Aligned_cols=75  Identities=19%  Similarity=0.217  Sum_probs=65.5

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeE-----EEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQ-----IKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~-----IkVs~A~  305 (876)
                      ...+|||+|||.++++++|+++|++||+|+.|++...  +||||+|.+.++|++||+.|||..|.|++     |+|..+.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~   92 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   92 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCC
Confidence            3569999999999999999999999999999998543  99999999999999999999999999998     6666655


Q ss_pred             Cc
Q 002823          306 LR  307 (876)
Q Consensus       306 ~k  307 (876)
                      ++
T Consensus        93 ~~   94 (115)
T 3beg_B           93 PR   94 (115)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>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

Probab=99.34  E-value=3.5e-12  Score=111.46  Aligned_cols=71  Identities=15%  Similarity=0.329  Sum_probs=66.2

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhc----C-------CeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVY----G-------EIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQI  299 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~f----G-------~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~I  299 (876)
                      ..++|||+|||.++++++|+++|++|    |       .|.++++ ...++||||+|.+.++|.+|+ .|||..+.|++|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~-~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l   82 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   82 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE-CSSSSEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEe-cCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEE
Confidence            46799999999999999999999999    8       9999998 455899999999999999999 999999999999


Q ss_pred             EEEe
Q 002823          300 KLEP  303 (876)
Q Consensus       300 kVs~  303 (876)
                      +|+.
T Consensus        83 ~V~r   86 (87)
T 2hzc_A           83 KIRR   86 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9974

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.33  E-value=3.1e-12  Score=122.87  Aligned_cols=79  Identities=20%  Similarity=0.322  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...+.++|||+|||.++++++|+++|++||.|..++.     +++++|||||+|.+.++|.+|++.|+|..+.|++|+|.
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            4566899999999999999999999999999999872     56789999999999999999999999999999999999


Q ss_pred             ecCC
Q 002823          218 YSIP  221 (876)
Q Consensus       218 ~A~p  221 (876)
                      |+.+
T Consensus       163 ~a~~  166 (166)
T 3md3_A          163 WAAK  166 (166)
T ss_dssp             ESCC
T ss_pred             ecCC
Confidence            9853

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.01  E-value=1.1e-13  Score=128.29  Aligned_cols=81  Identities=23%  Similarity=0.275  Sum_probs=72.9

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEE--------EEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKE--------IRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG  296 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~s--------Vri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G  296 (876)
                      ...++|||+|||.++++++|+++|++||.|..        |++     ++..++||||+|.+.++|.+|++.|||..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            34679999999999999999999999999988        665     34568999999999999999999999999999


Q ss_pred             eEEEEEeecCchhH
Q 002823          297 KQIKLEPSHLRGLR  310 (876)
Q Consensus       297 r~IkVs~A~~k~~R  310 (876)
                      ++|+|.+++++..+
T Consensus        85 ~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           85 NPIKVSFATRRADF   98 (116)
Confidence            99999999886543

>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

Probab=99.33  E-value=1.8e-12  Score=120.62  Aligned_cols=77  Identities=16%  Similarity=0.192  Sum_probs=65.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCce-----eeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGK-----LDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~-----L~V~~A  219 (876)
                      ...++|||+|||+++++++|+++|++||+|..|.+...  |||||+|.+.++|++|++.|+++.|.|++     |+|..+
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~   91 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   91 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccC
Confidence            45689999999999999999999999999999996433  99999999999999999999999999998     667666


Q ss_pred             CCCC
Q 002823          220 IPKD  223 (876)
Q Consensus       220 ~pk~  223 (876)
                      .++.
T Consensus        92 ~~~~   95 (115)
T 3beg_B           92 GPRS   95 (115)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            5543

>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

Probab=99.33  E-value=4.2e-12  Score=122.11  Aligned_cols=77  Identities=26%  Similarity=0.440  Sum_probs=71.5

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||.++++++|+++|+.||.|.+|++     ++.++|||||+|.+.++|.+|++.|+|..+.|++|+|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            468999999999999999999999999999887     455679999999999999999999999999999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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

Probab=99.33  E-value=8.7e-13  Score=127.43  Aligned_cols=78  Identities=9%  Similarity=0.071  Sum_probs=69.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCC---eEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGD---VRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~---I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      .....++|||+|||+++|+++|+++|++||.   |..|+    ..++++|||||+|.+.++|++|++ +++..|.|+.|+
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            3456789999999999999999999999998   66655    347889999999999999999998 999999999999


Q ss_pred             EeecCC
Q 002823          216 IHYSIP  221 (876)
Q Consensus       216 V~~A~p  221 (876)
                      |.++.+
T Consensus       119 V~~a~~  124 (136)
T 2hgl_A          119 VFKSHR  124 (136)
T ss_dssp             EEECCH
T ss_pred             EEECCh
Confidence            998754

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.33  E-value=3.8e-12  Score=118.34  Aligned_cols=76  Identities=12%  Similarity=0.216  Sum_probs=68.6

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...+|||+|||.++++++|+++|+.| .|..|++    .++++|||||+|.+.++|++|| .+|+..|.|+.|+|..+.+
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            34699999999999999999999999 8999887    4567899999999999999999 6999999999999998876


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      ++
T Consensus        93 ~~   94 (109)
T 2dnn_A           93 RQ   94 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            43

>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

Probab=99.33  E-value=6.5e-13  Score=113.11  Aligned_cols=70  Identities=14%  Similarity=0.308  Sum_probs=64.7

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++ +++..+.|++|+|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            5899999999999999999999999999887     35568999999999999999999 4899999999999875

>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

Probab=99.33  E-value=6.4e-12  Score=127.69  Aligned_cols=115  Identities=10%  Similarity=0.092  Sum_probs=89.8

Q ss_pred             CHHHHHHHHHHc--cccccCCceeeEeecCCCCCCCc-----cccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-
Q 002823          193 DIRAARNAMKSL--QNKLTRSGKLDIHYSIPKDNPSE-----KEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-  264 (876)
Q Consensus       193 d~edA~kAl~~L--ng~~l~Gr~L~V~~A~pk~~~~e-----k~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-  264 (876)
                      +.+.+..|++..  ....+.+...+|.....+..+..     .....++|||+|||.++++++|+++|++||.|..|++ 
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~  142 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR  142 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEE
Confidence            677888888877  55566666666655532222111     2234579999999999999999999999999999987 


Q ss_pred             ---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          265 ---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       265 ---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                         ++..+|||||+|.+.++|.+|++.++ ..+.|++|+|.+++.-.
T Consensus       143 ~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          143 RTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDDYF  188 (193)
T ss_dssp             ECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTTC-
T ss_pred             ECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHHHH
Confidence               35678999999999999999998654 59999999999987643

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.33  E-value=2e-12  Score=129.77  Aligned_cols=80  Identities=16%  Similarity=0.326  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ...++++|||+|||+++++++|+++|++||+|..|.+    +++++|||||+|.+.++|++|++.|++..|.|++|+|+|
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999884    367899999999999999999999999999999999999


Q ss_pred             cCCC
Q 002823          219 SIPK  222 (876)
Q Consensus       219 A~pk  222 (876)
                      +.+.
T Consensus       164 a~~~  167 (177)
T 2f3j_A          164 VASQ  167 (177)
T ss_dssp             ESSG
T ss_pred             ecCC
Confidence            8764

>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

Probab=99.32  E-value=4e-12  Score=122.81  Aligned_cols=77  Identities=22%  Similarity=0.342  Sum_probs=71.3

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||.++++++|+++|+.||.|.+|++     ++.++|||||+|.+.++|.+|++.|+|..+.|++|+|.|+.+
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   82 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   82 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCC
Confidence            568999999999999999999999999999887     345679999999999999999999999999999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      +.
T Consensus        83 ~~   84 (168)
T 1b7f_A           83 GG   84 (168)
T ss_dssp             CS
T ss_pred             Cc
Confidence            53

>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

Probab=99.32  E-value=1.2e-12  Score=136.62  Aligned_cols=76  Identities=12%  Similarity=0.130  Sum_probs=70.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccC--CeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYG--DVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG--~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..++|||+|||+++|+++|+++|++||  +|+.|+     .++++||||||+|.+.++|++||+.|+++.|.|++|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567999999999999999999999999  999988     3678999999999999999999999999999999999999


Q ss_pred             cCC
Q 002823          219 SIP  221 (876)
Q Consensus       219 A~p  221 (876)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>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

Probab=99.32  E-value=1.2e-12  Score=119.78  Aligned_cols=76  Identities=12%  Similarity=0.169  Sum_probs=68.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...+|||+|||.++++++|+++|++||.| +|++    +++++|||||+|.+.++|++||+ +|+..|.|+.|+|.++.+
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~   91 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNST   91 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCC
Confidence            45699999999999999999999999955 7776    55678999999999999999995 799999999999999876


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      .+
T Consensus        92 ~~   93 (102)
T 1wez_A           92 AG   93 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.32  E-value=4.6e-13  Score=129.83  Aligned_cols=120  Identities=10%  Similarity=0.046  Sum_probs=69.5

Q ss_pred             ceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe
Q 002823          185 GFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE  264 (876)
Q Consensus       185 GfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri  264 (876)
                      ++||..|..++.+..++..+... ..|....-.+...  ..........+|||+|||.++++++|+++|++|| |++|++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~--~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i   77 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDS--EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHI   77 (139)
T ss_dssp             ----------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEEC
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCCc--ccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEE
Confidence            67788888877777776655433 2332221111111  1111223456999999999999999999999999 668887


Q ss_pred             ----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchh
Q 002823          265 ----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       265 ----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~  309 (876)
                          .++++|||||+|.+.++|++|| .+|+..|.|+.|+|.++.+++.
T Consensus        78 ~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           78 EIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             EECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence                3457899999999999999999 7999999999999999987653

>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}

Probab=99.31  E-value=8.3e-13  Score=121.15  Aligned_cols=79  Identities=8%  Similarity=0.009  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCC---eEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGD---VRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~---I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      .....++|||+|||+++|+++|+++|++||.   |..|+    ..++++|||||+|.+.++|++|++ +++..+.|+.|+
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            3456789999999999999999999999998   77777    237789999999999999999998 999999999999


Q ss_pred             EeecCCC
Q 002823          216 IHYSIPK  222 (876)
Q Consensus       216 V~~A~pk  222 (876)
                      |.++.++
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9998653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.31  E-value=2e-12  Score=116.91  Aligned_cols=78  Identities=23%  Similarity=0.408  Sum_probs=70.8

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...++|||+|||.++++++|+++|++||.|..|++    ++..+|||||+|.+.++|++|++  ++..+.|++|.|.++.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            45679999999999999999999999999999887    45578999999999999999999  9999999999999998


Q ss_pred             Cchh
Q 002823          306 LRGL  309 (876)
Q Consensus       306 ~k~~  309 (876)
                      ++..
T Consensus        85 ~~~~   88 (102)
T 2xs2_A           85 RKQN   88 (102)
T ss_dssp             ECC-
T ss_pred             cCcc
Confidence            7653

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.31  E-value=4.4e-12  Score=127.72  Aligned_cols=81  Identities=17%  Similarity=0.365  Sum_probs=74.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .+.++|||+|||.++++++|+++|++||.|..++.     +++++|||||+|.+.++|.+|++.|++..|.|+.|.|.|+
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            45689999999999999999999999999999883     5678999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 002823          220 IPKDNP  225 (876)
Q Consensus       220 ~pk~~~  225 (876)
                      .++...
T Consensus       203 ~~~~~~  208 (216)
T 2qfj_A          203 VTPPMP  208 (216)
T ss_dssp             SSCSST
T ss_pred             cCCCCC
Confidence            887544

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.31  E-value=6.2e-12  Score=128.41  Aligned_cols=109  Identities=23%  Similarity=0.236  Sum_probs=89.2

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      +.++|||+|||.++++++|+++|++||+|++|++     ++.++|||||+|.+.++|.+|++.+++..+.|+.|++.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            4679999999999999999999999999999887     46678999999999999999999999999999999999998


Q ss_pred             CchhHHHHhhcCCchhhhhhcCCCCCCCCCCCCCCCCcccceeeeccCchhhhHHHHHHhhccc
Q 002823          306 LRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLAIIYLFTGA  369 (876)
Q Consensus       306 ~k~~Rr~l~qQ~~~q~~q~~~g~~~~gsp~~~sp~~~~~~~~~~~fssP~n~~~~~l~~l~~~~  369 (876)
                      ........  .        .                    .....-+.|.++....|..+|...
T Consensus        94 ~~~~~~~~--~--------~--------------------~~l~v~nl~~~~t~~~l~~~F~~~  127 (213)
T 4f02_A           94 RDPSLRKS--G--------V--------------------GNIFIKNLDKSIDNKALYDTFSAF  127 (213)
T ss_dssp             CCTHHHHH--C--------T--------------------TEEEEESCCTTCCHHHHHHHHGGG
T ss_pred             cccccccc--c--------c--------------------ccceECCcccccHHHHHHHHHhhc
Confidence            76533211  0        0                    012334677777788888888764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.31  E-value=3.1e-12  Score=116.23  Aligned_cols=71  Identities=20%  Similarity=0.301  Sum_probs=64.4

Q ss_pred             ceeEeecCCCCCcHHH----HHHHhhhc-CCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          233 GTLVVFNLDSSVSNDE----LHHIFGVY-GEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       233 ~tLfV~NLP~svTeed----LreiFs~f-G~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      +.|||+|||..+++++    |+++|++| |+|.+|  ++   |+|||+|.+.++|.+|++.|+|..+.||+|+|.|++.+
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~   84 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKN   84 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCS
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCC
Confidence            3499999999999988    55899999 599998  33   99999999999999999999999999999999999875


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus        85 s   85 (96)
T 2diu_A           85 R   85 (96)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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

Probab=99.31  E-value=1.1e-12  Score=115.60  Aligned_cols=77  Identities=17%  Similarity=0.283  Sum_probs=66.5

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchh
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~  309 (876)
                      ..++|||+|||.++++++|+++|++||.|.+|++...++|||||+|.+.++|++|+..  ...+.|++|+|.+++++..
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~~   80 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCCC
Confidence            3579999999999999999999999999999999767899999999999999864321  3445899999999988653

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.30  E-value=1.7e-12  Score=120.62  Aligned_cols=75  Identities=7%  Similarity=0.103  Sum_probs=67.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ...++|||+|||+++++++|+++|++| .|..|++    .++++|||||+|.+.++|++|+ .+++..|.||.|.|..+.
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            345899999999999999999999999 8888873    4778999999999999999999 699999999999998775


Q ss_pred             C
Q 002823          221 P  221 (876)
Q Consensus       221 p  221 (876)
                      +
T Consensus        92 ~   92 (109)
T 2dnn_A           92 E   92 (109)
T ss_dssp             H
T ss_pred             c
Confidence            3

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.29  E-value=5.1e-12  Score=126.86  Aligned_cols=78  Identities=18%  Similarity=0.326  Sum_probs=72.5

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...+|||+|||..+++++|+++|++||.|+.|++    ++..++||||+|.+.++|++|++.|||..|.|++|+|+|+..
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~  166 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS  166 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            4579999999999999999999999999999988    355789999999999999999999999999999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      ..
T Consensus       167 ~~  168 (177)
T 2f3j_A          167 QI  168 (177)
T ss_dssp             GG
T ss_pred             CC
Confidence            54

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.29  E-value=1.9e-12  Score=122.99  Aligned_cols=82  Identities=21%  Similarity=0.230  Sum_probs=71.9

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCe----EEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEI----KEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLE  302 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I----~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs  302 (876)
                      ...+|||+|||+++|+++|+++|++||.|    ..|++    +++++|||||+|.+.++|++||+. |+..|.|+.|+|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~  100 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEE
Confidence            35689999999999999999999999976    45655    566789999999999999999996 9999999999999


Q ss_pred             eecCchhHHHH
Q 002823          303 PSHLRGLRKCL  313 (876)
Q Consensus       303 ~A~~k~~Rr~l  313 (876)
                      .+.+++.++.+
T Consensus       101 ~a~~~e~~~~~  111 (123)
T 2dha_A          101 RSTAAEVQQVL  111 (123)
T ss_dssp             EECHHHHHHHH
T ss_pred             ECCHHHHHHHH
Confidence            99887766544

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.29  E-value=6e-12  Score=125.07  Aligned_cols=81  Identities=17%  Similarity=0.329  Sum_probs=74.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+.++|||+|||.++++++|+++|++||.|..++.     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.|
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            366799999999999999999999999999999882     667799999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 002823          219 SIPKDN  224 (876)
Q Consensus       219 A~pk~~  224 (876)
                      +.++..
T Consensus       191 a~~~~~  196 (198)
T 2yh0_A          191 ASVGAK  196 (198)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            988654

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.28  E-value=1.7e-12  Score=125.85  Aligned_cols=80  Identities=9%  Similarity=0.143  Sum_probs=69.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      .....++|||+|||+++|+++|+++|++|| |..|+    ..++++|||||+|.+.++|++|+ .+++..|.|+.|.|.+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            445678999999999999999999999999 55777    34778999999999999999999 8999999999999999


Q ss_pred             cCCCCC
Q 002823          219 SIPKDN  224 (876)
Q Consensus       219 A~pk~~  224 (876)
                      +.++..
T Consensus       120 a~~~~~  125 (139)
T 2hgn_A          120 NSTTGA  125 (139)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            876543

>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

Probab=99.28  E-value=3.9e-12  Score=123.04  Aligned_cols=78  Identities=15%  Similarity=0.304  Sum_probs=72.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .+.++|||+|||.++++++|+++|++||.|..++     .+++++|||||+|.+.++|++|++ +++..+.|++|.|.|+
T Consensus        85 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a  163 (167)
T 2cjk_A           85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRA  163 (167)
T ss_dssp             HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEEC
T ss_pred             cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeec
Confidence            4568999999999999999999999999999998     257789999999999999999997 8999999999999999


Q ss_pred             CCCC
Q 002823          220 IPKD  223 (876)
Q Consensus       220 ~pk~  223 (876)
                      .|+.
T Consensus       164 ~pk~  167 (167)
T 2cjk_A          164 EPRH  167 (167)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8863

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.27  E-value=9.9e-12  Score=115.21  Aligned_cols=74  Identities=12%  Similarity=0.206  Sum_probs=62.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eC---CCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RA---SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~t---gksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      ...+++|||+|||+++++++|+++|++||+|. +.     .+   ++++|||||+|.+.++|++|++.|++  +.|+.+.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCCcEEE
Confidence            35578999999999999999999999999999 55     12   58899999999999999999999843  6777776


Q ss_pred             EeecC
Q 002823          216 IHYSI  220 (876)
Q Consensus       216 V~~A~  220 (876)
                      +..+.
T Consensus        82 ~~~~~   86 (114)
T 2dnl_A           82 CVSSP   86 (114)
T ss_dssp             EECCS
T ss_pred             eccCC
Confidence            66543

>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

Probab=99.27  E-value=1.8e-11  Score=113.24  Aligned_cols=83  Identities=11%  Similarity=0.253  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEcCCCCCCC-----------HHHHHHHhhccCCeEEEEe-CCCccceEeeecCCHHHHHHHHHHccccccC
Q 002823          143 DEHPSRTLLLRKINSNIE-----------DSELKALFEQYGDVRTFYR-ASKHCGFVTISYYDIRAARNAMKSLQNKLTR  210 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vT-----------EeeL~elFsqfG~I~sV~~-tgksrGfAFV~F~d~edA~kAl~~Lng~~l~  210 (876)
                      ...++++|+|+||....+           +++|+++|++||.|..|.+ ...++|||||+|.+.++|++|++.|+|..+.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            557899999999944332           5899999999999999874 4557999999999999999999999999999


Q ss_pred             CceeeEeecCCCCCC
Q 002823          211 SGKLDIHYSIPKDNP  225 (876)
Q Consensus       211 Gr~L~V~~A~pk~~~  225 (876)
                      |++|+|.|+.++...
T Consensus        91 gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           91 GRQITAQAWDGTTDY  105 (112)
T ss_dssp             TEECEEEECCSCCCS
T ss_pred             CcEEEEEEeCCCCCc
Confidence            999999999886543

>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

Probab=99.26  E-value=9.1e-12  Score=121.02  Aligned_cols=76  Identities=18%  Similarity=0.343  Sum_probs=70.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ....++|||+|||.++++++|+++|++||+|..++.     +++++|||||+|.+.++|++|++.|+|..+.|++|.|.|
T Consensus        91 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  170 (172)
T 2g4b_A           91 LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  170 (172)
T ss_dssp             CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            345789999999999999999999999999999883     677899999999999999999999999999999999998


Q ss_pred             c
Q 002823          219 S  219 (876)
Q Consensus       219 A  219 (876)
                      |
T Consensus       171 A  171 (172)
T 2g4b_A          171 A  171 (172)
T ss_dssp             C
T ss_pred             C
Confidence            7

>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

Probab=99.26  E-value=4.4e-12  Score=121.11  Aligned_cols=77  Identities=13%  Similarity=0.159  Sum_probs=67.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeE--EEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVR--TFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~--sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      .....++|||+|||+++|+++|+++|++| .|.  .|+    ..++++|||||+|.+.++|++|++. ++..|.||.|+|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V  115 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            34567899999999999999999999999 566  777    3478899999999999999999974 779999999999


Q ss_pred             eecCC
Q 002823          217 HYSIP  221 (876)
Q Consensus       217 ~~A~p  221 (876)
                      ..+.+
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88754

>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

Probab=99.25  E-value=1.2e-11  Score=120.02  Aligned_cols=78  Identities=14%  Similarity=0.339  Sum_probs=70.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccC---Cceee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTR---SGKLD  215 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~---Gr~L~  215 (876)
                      ...+.++|||+|||.++++++|+++|++||.|..++    .+++++|||||+|.+.++|++|++.|+|..+.   +++|.
T Consensus        91 ~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~  170 (175)
T 3nmr_A           91 NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV  170 (175)
T ss_dssp             SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCE
T ss_pred             ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeE
Confidence            445678999999999999999999999999999988    34667999999999999999999999998776   49999


Q ss_pred             EeecC
Q 002823          216 IHYSI  220 (876)
Q Consensus       216 V~~A~  220 (876)
                      |.|+.
T Consensus       171 V~~ad  175 (175)
T 3nmr_A          171 VKFAD  175 (175)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99973

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.25  E-value=3.2e-12  Score=121.44  Aligned_cols=76  Identities=14%  Similarity=0.173  Sum_probs=66.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCe----EEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDV----RTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I----~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      ...++|||+|||+++|+++|+++|++||.|    ..|+    .+++++|||||+|.+.++|++|++. ++..+.+|.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            456899999999999999999999999975    3443    4678999999999999999999986 999999999999


Q ss_pred             eecCC
Q 002823          217 HYSIP  221 (876)
Q Consensus       217 ~~A~p  221 (876)
                      ..+.+
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            87643

>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

Probab=99.25  E-value=2e-11  Score=121.15  Aligned_cols=113  Identities=11%  Similarity=0.124  Sum_probs=86.2

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|+.||.|.+|++     ++.++|||||+|.+.++|.+|++. ++..+.|+.|+|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            45679999999999999999999999999999887     355789999999999999999985 999999999999999


Q ss_pred             cCchhHHHHhhcCCchhhhhhcCCCCCCCCCCCCCCCCcccceeeeccCchhhhHHHHHHhhccc
Q 002823          305 HLRGLRKCLANQLPPELEQEECGSYQQQNSPPNKPTNESAGMITIVISLPLNVKSLAIIYLFTGA  369 (876)
Q Consensus       305 ~~k~~Rr~l~qQ~~~q~~q~~~g~~~~gsp~~~sp~~~~~~~~~~~fssP~n~~~~~l~~l~~~~  369 (876)
                      ..+.....-                     ...     .....-..-+.|.++....|..+|...
T Consensus        90 ~~~~~~~~~---------------------~~~-----~~~~~l~V~nLp~~~t~~~l~~~F~~~  128 (196)
T 1l3k_A           90 VSREDSQRP---------------------GAH-----LTVKKIFVGGIKEDTEEHHLRDYFEQY  128 (196)
T ss_dssp             CC-------------------------------------CCSEEEEECCTTTCCHHHHHHHHTTT
T ss_pred             cCccccccc---------------------ccC-----CCcceEEEeCCCCCCCHHHHHHHHhcC
Confidence            875422100                     000     001122345678888888888888654

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.24  E-value=1.2e-11  Score=130.25  Aligned_cols=80  Identities=18%  Similarity=0.264  Sum_probs=70.7

Q ss_pred             ccccceeEeecCCCCC---------cHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCcee-----
Q 002823          229 EINQGTLVVFNLDSSV---------SNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYI-----  294 (876)
Q Consensus       229 ~~~~~tLfV~NLP~sv---------TeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I-----  294 (876)
                      ....++|||+||+..+         ++++|+++|++||+|++|++. ..+|||||+|.+.++|++|+++|+|..|     
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~-~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEE-CCCCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            3456799999999998         799999999999999999984 5799999999999999999999999999     


Q ss_pred             -------CCeEEEEEeecCchh
Q 002823          295 -------AGKQIKLEPSHLRGL  309 (876)
Q Consensus       295 -------~Gr~IkVs~A~~k~~  309 (876)
                             .|++|.|.|++....
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC----
T ss_pred             ccccccCCCCEEEEEEccCCCC
Confidence                   899999999987653

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.24  E-value=8.4e-12  Score=131.42  Aligned_cols=81  Identities=15%  Similarity=0.254  Sum_probs=71.3

Q ss_pred             CCCCcEEEEcCCCCCC---------CHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcccccc-----
Q 002823          144 EHPSRTLLLRKINSNI---------EDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLT-----  209 (876)
Q Consensus       144 e~pSrTLFVgNLP~~v---------TEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l-----  209 (876)
                      ....++|||+||+..+         ++++|+++|++||+|.+|++ ..++|||||+|.+.++|+.|+++|+|+.|     
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v-~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRY-VESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEE-EGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEE-ECCCCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            5678999999999998         79999999999999999986 35799999999999999999999999999     


Q ss_pred             -------CCceeeEeecCCCCCC
Q 002823          210 -------RSGKLDIHYSIPKDNP  225 (876)
Q Consensus       210 -------~Gr~L~V~~A~pk~~~  225 (876)
                             .|+.|.|.|+..+.++
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC-----
T ss_pred             ccccccCCCCEEEEEEccCCCCH
Confidence                   8999999999876554

>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*

Probab=99.24  E-value=1.6e-11  Score=139.70  Aligned_cols=81  Identities=21%  Similarity=0.336  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+.++|||+|||..+|+++|+++|++||.|..|.+     +++++|||||+|.+.++|++||+.|+|..|.|+.|.|.|
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456789999999999999999999999999999873     677899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 002823          219 SIPKDN  224 (876)
Q Consensus       219 A~pk~~  224 (876)
                      +.++..
T Consensus       179 a~~~~~  184 (437)
T 3pgw_S          179 ERGRTV  184 (437)
T ss_pred             eCCCCC
Confidence            987643

>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

Probab=99.23  E-value=6.3e-12  Score=120.04  Aligned_cols=76  Identities=21%  Similarity=0.253  Sum_probs=67.5

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeE--EEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIK--EIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~--sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...+|||+|||+++++++|+++|+.| .|+  .|++    .++++|||||+|.+.++|++||+ +++..|.|+.|+|.++
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~a  118 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKS  118 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            45689999999999999999999999 666  7877    35678999999999999999998 4789999999999998


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      .+++
T Consensus       119 ~~~e  122 (126)
T 2hgm_A          119 SQEE  122 (126)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.23  E-value=3.5e-11  Score=120.34  Aligned_cols=79  Identities=27%  Similarity=0.328  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccC-CeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccC-CceeeEeecCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYG-DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTR-SGKLDIHYSIP  221 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG-~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~-Gr~L~V~~A~p  221 (876)
                      ..++++|||+|||.++++++|+++|++|| .|..++.....+|||||+|.+.++|.+|++.|+|..+. |++|+|.|+.+
T Consensus       117 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             CCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence            35689999999999999999999999999 99999976667999999999999999999999999999 99999999876


Q ss_pred             C
Q 002823          222 K  222 (876)
Q Consensus       222 k  222 (876)
                      +
T Consensus       197 ~  197 (198)
T 1qm9_A          197 T  197 (198)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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

Probab=99.22  E-value=2.6e-11  Score=127.94  Aligned_cols=79  Identities=23%  Similarity=0.365  Sum_probs=72.8

Q ss_pred             cccceeEeecCCCCCcHHHHH----HHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          230 INQGTLVVFNLDSSVSNDELH----HIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLr----eiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      ...++|||+|||.++++++|+    ++|++||.|.+|++  ++..+|||||+|.+.++|.+|++.|||..|.|++|+|.|
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   86 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   86 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEE
Confidence            357799999999999999977    89999999999987  567889999999999999999999999999999999999


Q ss_pred             ecCch
Q 002823          304 SHLRG  308 (876)
Q Consensus       304 A~~k~  308 (876)
                      ++.+.
T Consensus        87 a~~~~   91 (282)
T 3pgw_A           87 AKTDS   91 (282)
T ss_pred             eccCc
Confidence            97654

>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

Probab=99.22  E-value=3e-11  Score=127.17  Aligned_cols=76  Identities=20%  Similarity=0.321  Sum_probs=71.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...++|||+|||.++|+++|+++|+.||.|..|++ ...+|||||+|.+.++|.+|+..|+|..+.|++|+|.++.+
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i-~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~   95 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH   95 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc
Confidence            45679999999999999999999999999999998 55689999999999999999999999999999999999874

>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

Probab=99.22  E-value=2.7e-11  Score=124.98  Aligned_cols=79  Identities=27%  Similarity=0.328  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccC-CeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccC-CceeeEeecCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYG-DVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTR-SGKLDIHYSIP  221 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG-~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~-Gr~L~V~~A~p  221 (876)
                      ..++++|||+|||.++++++|+++|++|| .|..++...+.+|||||+|.+.++|++|++.|+|..+. |++|+|.|+.+
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            35679999999999999999999999999 99999976667999999999999999999999999999 99999999976


Q ss_pred             C
Q 002823          222 K  222 (876)
Q Consensus       222 k  222 (876)
                      +
T Consensus       228 ~  228 (229)
T 2adc_A          228 T  228 (229)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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

Probab=99.21  E-value=5.1e-11  Score=110.22  Aligned_cols=79  Identities=15%  Similarity=0.290  Sum_probs=69.4

Q ss_pred             cccceeEeecCCCCCc-----------HHHHHHHhhhcCCeEEEEe-cCCcccEEEEEecCHHHHHHHHHHhCCceeCCe
Q 002823          230 INQGTLVVFNLDSSVS-----------NDELHHIFGVYGEIKEIRE-TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK  297 (876)
Q Consensus       230 ~~~~tLfV~NLP~svT-----------eedLreiFs~fG~I~sVri-tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr  297 (876)
                      ...++|+|.||.....           +++|+++|++||.|.+|.+ +..++|||||+|.+.++|.+|++.|||..+.|+
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   92 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   92 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            4577999999954432           5899999999999999876 445789999999999999999999999999999


Q ss_pred             EEEEEeecCch
Q 002823          298 QIKLEPSHLRG  308 (876)
Q Consensus       298 ~IkVs~A~~k~  308 (876)
                      +|+|.|+.++.
T Consensus        93 ~l~v~~a~~~~  103 (112)
T 2dit_A           93 QITAQAWDGTT  103 (112)
T ss_dssp             ECEEEECCSCC
T ss_pred             EEEEEEeCCCC
Confidence            99999998754

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.19  E-value=5.7e-11  Score=109.62  Aligned_cols=78  Identities=19%  Similarity=0.237  Sum_probs=68.0

Q ss_pred             ccceeEeecCCC-----CCcHHHHHHHhhhcCCeEEEEec------CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 002823          231 NQGTLVVFNLDS-----SVSNDELHHIFGVYGEIKEIRET------PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQI  299 (876)
Q Consensus       231 ~~~tLfV~NLP~-----svTeedLreiFs~fG~I~sVrit------g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~I  299 (876)
                      ++++|+|.|+..     +-++++|+++|++||+|.+|++.      +.++|+|||+|.+.++|.+|++.|||+.+.||+|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            467999999963     23789999999999999998872      3568999999999999999999999999999999


Q ss_pred             EEEeecCch
Q 002823          300 KLEPSHLRG  308 (876)
Q Consensus       300 kVs~A~~k~  308 (876)
                      +|.++....
T Consensus        87 ~v~~a~~~~   95 (105)
T 2pe8_A           87 KACFYNLDK   95 (105)
T ss_dssp             EEEECCHHH
T ss_pred             EEEEcCHHH
Confidence            999997643

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.19  E-value=3.4e-11  Score=111.15  Aligned_cols=78  Identities=17%  Similarity=0.234  Sum_probs=68.4

Q ss_pred             CCCCcEEEEcCCCC-----CCCHHHHHHHhhccCCeEEEEe------CCCccceEeeecCCHHHHHHHHHHccccccCCc
Q 002823          144 EHPSRTLLLRKINS-----NIEDSELKALFEQYGDVRTFYR------ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSG  212 (876)
Q Consensus       144 e~pSrTLFVgNLP~-----~vTEeeL~elFsqfG~I~sV~~------tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr  212 (876)
                      ..++++|+|+||..     +-++++|+++|++||+|.+|++      +++++|||||+|.+.++|++|++.|+|+.+.||
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            36789999999963     2368999999999999999983      246799999999999999999999999999999


Q ss_pred             eeeEeecCC
Q 002823          213 KLDIHYSIP  221 (876)
Q Consensus       213 ~L~V~~A~p  221 (876)
                      .|.|.|+.+
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999854

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.18  E-value=3.4e-11  Score=111.57  Aligned_cols=75  Identities=15%  Similarity=0.140  Sum_probs=64.2

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----c---CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----T---PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLE  302 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----t---g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs  302 (876)
                      ..++|||+|||.++++++|+++|++||+|. +++     +   +.++|||||+|.+.++|++|++.|+  .+.|+.|.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            457899999999999999999999999999 665     1   4678999999999999999999994  4778888877


Q ss_pred             eecCch
Q 002823          303 PSHLRG  308 (876)
Q Consensus       303 ~A~~k~  308 (876)
                      .+.+..
T Consensus        84 ~~~~~~   89 (114)
T 2dnl_A           84 SSPTIK   89 (114)
T ss_dssp             CCSSSC
T ss_pred             cCCCcC
Confidence            665543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.16  E-value=3.1e-11  Score=115.63  Aligned_cols=79  Identities=20%  Similarity=0.343  Sum_probs=69.1

Q ss_pred             ceeEeecC----CCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecC----HHH----HHHHHH--HhCCce
Q 002823          233 GTLVVFNL----DSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYD----TRA----AEAALR--ELNSRY  293 (876)
Q Consensus       233 ~tLfV~NL----P~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d----~E~----A~kAL~--~LnG~~  293 (876)
                      .+|||+||    |+.+++++|+++|+.||+|.++++     ++.++|||||+|.+    +++    |.+|++  .|+|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    999999999999999999999887     77889999999996    333    889988  789999


Q ss_pred             eCCeEEEEEeecCchhHH
Q 002823          294 IAGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       294 I~Gr~IkVs~A~~k~~Rr  311 (876)
                      |.|++|+|.+-+.....+
T Consensus        83 I~Gr~irV~ln~~g~~~~  100 (136)
T 2j8a_A           83 IMGFKFEVILNKHSILNN  100 (136)
T ss_dssp             ETTEEEEEEECCTTHHHH
T ss_pred             ecCcEEEEEECcccHHHH
Confidence            999999999988766544

>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

Probab=99.12  E-value=9.8e-11  Score=118.96  Aligned_cols=75  Identities=13%  Similarity=0.228  Sum_probs=67.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ..++|||+|||+++++++|+++|++||.|..|+.    +++++|||||+|.+.++|++|++.+ +..+.|+.|.|.++..
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            3589999999999999999999999999999983    4678999999999999999999765 4589999999998654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.10  E-value=5.7e-11  Score=113.84  Aligned_cols=72  Identities=19%  Similarity=0.328  Sum_probs=64.7

Q ss_pred             cEEEEcCC----CCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCC----HHH----HHHHHH--Hccccc
Q 002823          148 RTLLLRKI----NSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYD----IRA----ARNAMK--SLQNKL  208 (876)
Q Consensus       148 rTLFVgNL----P~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d----~ed----A~kAl~--~Lng~~  208 (876)
                      .+|||+||    |+.+++++|+++|++||+|.++.     .+++++|||||+|.+    +++    |.+|++  .++|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    99999999999999999999988     588999999999996    333    889988  789999


Q ss_pred             cCCceeeEeec
Q 002823          209 TRSGKLDIHYS  219 (876)
Q Consensus       209 l~Gr~L~V~~A  219 (876)
                      |.|++|+|.+-
T Consensus        83 I~Gr~irV~ln   93 (136)
T 2j8a_A           83 IMGFKFEVILN   93 (136)
T ss_dssp             ETTEEEEEEEC
T ss_pred             ecCcEEEEEEC
Confidence            99999999884

>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

Probab=99.09  E-value=1.7e-10  Score=106.31  Aligned_cols=78  Identities=18%  Similarity=0.348  Sum_probs=67.9

Q ss_pred             CCCCcEEEEcCC--CCCCC--------HHHHHHHhhccCCeEEEEeC-------CCccceEeeecCCHHHHHHHHHHccc
Q 002823          144 EHPSRTLLLRKI--NSNIE--------DSELKALFEQYGDVRTFYRA-------SKHCGFVTISYYDIRAARNAMKSLQN  206 (876)
Q Consensus       144 e~pSrTLFVgNL--P~~vT--------EeeL~elFsqfG~I~sV~~t-------gksrGfAFV~F~d~edA~kAl~~Lng  206 (876)
                      ..|++.|.|+|+  |.++.        +++|++.|++||+|.+|++.       ++++|+|||+|.+.++|++|++.|||
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            468999999999  44544        36899999999999999932       25789999999999999999999999


Q ss_pred             cccCCceeeEeecCC
Q 002823          207 KLTRSGKLDIHYSIP  221 (876)
Q Consensus       207 ~~l~Gr~L~V~~A~p  221 (876)
                      +.+.||.|+|.|+.+
T Consensus        82 ~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           82 RKFANRVVVTKYCDP   96 (105)
T ss_dssp             CEETTEECEEEEECH
T ss_pred             CEeCCCEEEEEEeCH
Confidence            999999999999753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.09  E-value=2.1e-10  Score=105.22  Aligned_cols=65  Identities=22%  Similarity=0.279  Sum_probs=59.3

Q ss_pred             CCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          242 SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       242 ~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..+++++|+++|++||+|.+|++.+.++|||||+|.+.++|++|++.+++  +.|++|+|.|++++.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            57899999999999999999999888999999999999999999998544  689999999998764

>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

Probab=99.07  E-value=2.8e-10  Score=104.89  Aligned_cols=78  Identities=15%  Similarity=0.247  Sum_probs=66.6

Q ss_pred             ccceeEeecC--CCCC--------cHHHHHHHhhhcCCeEEEEec-------CCcccEEEEEecCHHHHHHHHHHhCCce
Q 002823          231 NQGTLVVFNL--DSSV--------SNDELHHIFGVYGEIKEIRET-------PQKIHQKYIEFYDTRAAEAALRELNSRY  293 (876)
Q Consensus       231 ~~~tLfV~NL--P~sv--------TeedLreiFs~fG~I~sVrit-------g~skG~AFVeF~d~E~A~kAL~~LnG~~  293 (876)
                      +++.|+|.|+  |..+        .+++|++.|++||+|.+|++.       +.++|++||+|.+.++|.+|++.|||+.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4678899998  3333        247899999999999999982       2458999999999999999999999999


Q ss_pred             eCCeEEEEEeecCch
Q 002823          294 IAGKQIKLEPSHLRG  308 (876)
Q Consensus       294 I~Gr~IkVs~A~~k~  308 (876)
                      +.||+|+|.|+....
T Consensus        84 f~GR~i~v~~~~~~~   98 (105)
T 3v4m_A           84 FANRVVVTKYCDPDS   98 (105)
T ss_dssp             ETTEECEEEEECHHH
T ss_pred             eCCCEEEEEEeCHHH
Confidence            999999999987643

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.04  E-value=1.2e-09  Score=100.19  Aligned_cols=76  Identities=20%  Similarity=0.260  Sum_probs=64.4

Q ss_pred             CcEEEEcCCC-------CCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          147 SRTLLLRKIN-------SNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       147 SrTLFVgNLP-------~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .++|.|.-..       .++++++|+++|++||+|..|++.++++|||||+|.+.++|++|++.+++  +.+++|+|.|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEc
Confidence            3455555443       46899999999999999999997789999999999999999999998554  67999999999


Q ss_pred             CCCCC
Q 002823          220 IPKDN  224 (876)
Q Consensus       220 ~pk~~  224 (876)
                      .++..
T Consensus        88 ~~~~~   92 (100)
T 2d9o_A           88 EGQPQ   92 (100)
T ss_dssp             SCCCC
T ss_pred             cCCCC
Confidence            87654

>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

Probab=99.01  E-value=1.7e-10  Score=106.04  Aligned_cols=68  Identities=31%  Similarity=0.500  Sum_probs=58.7

Q ss_pred             eecCCCCCcHHHHHHHh------------hhcCCeEEEEec----CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          237 VFNLDSSVSNDELHHIF------------GVYGEIKEIRET----PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       237 V~NLP~svTeedLreiF------------s~fG~I~sVrit----g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      +.+|+..+++++|++.|            ++||+|.+|++.    ++++|||||+|.+.++|.+|++.|||+.+.||+|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            55677777777776666            999999999983    34689999999999999999999999999999999


Q ss_pred             EEee
Q 002823          301 LEPS  304 (876)
Q Consensus       301 Vs~A  304 (876)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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

Probab=98.99  E-value=6.7e-10  Score=104.74  Aligned_cols=76  Identities=13%  Similarity=0.182  Sum_probs=65.9

Q ss_pred             CCCcEEEEcCCC--CCC---CHHHHHHHhhccCCeEEEEe---------CCCccceEeeecCCHHHHHHHHHHccccccC
Q 002823          145 HPSRTLLLRKIN--SNI---EDSELKALFEQYGDVRTFYR---------ASKHCGFVTISYYDIRAARNAMKSLQNKLTR  210 (876)
Q Consensus       145 ~pSrTLFVgNLP--~~v---TEeeL~elFsqfG~I~sV~~---------tgksrGfAFV~F~d~edA~kAl~~Lng~~l~  210 (876)
                      .|+++|+|+|+-  .++   -+++|++.|++||+|.+|++         +++++|+|||+|.+.++|.+|++.|+|+.+.
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            479999999993  222   26899999999999999882         2356799999999999999999999999999


Q ss_pred             CceeeEeecC
Q 002823          211 SGKLDIHYSI  220 (876)
Q Consensus       211 Gr~L~V~~A~  220 (876)
                      ||.|+|.|+.
T Consensus        98 GR~i~v~~~~  107 (118)
T 3ue2_A           98 GRKVVAEVYD  107 (118)
T ss_dssp             TEECEEEEEC
T ss_pred             CcEEEEEEcC
Confidence            9999999974

>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*

Probab=98.99  E-value=5.2e-10  Score=123.50  Aligned_cols=76  Identities=13%  Similarity=0.250  Sum_probs=66.7

Q ss_pred             CCCCCcEEEEcC--CCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccC---Cc--eee
Q 002823          143 DEHPSRTLLLRK--INSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTR---SG--KLD  215 (876)
Q Consensus       143 ~e~pSrTLFVgN--LP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~---Gr--~L~  215 (876)
                      ...|+++|||+|  |+..+|+++|+++|++||+|.+|++. .+||||||+|.+.++|++|++.|||+.+.   |+  .|+
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~-~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly   92 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   92 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECC-TTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEE
Confidence            357899999999  57899999999999999999999863 47899999999999999999999999873   44  577


Q ss_pred             Eeec
Q 002823          216 IHYS  219 (876)
Q Consensus       216 V~~A  219 (876)
                      |.|+
T Consensus        93 ~~~~   96 (345)
T 3tht_A           93 LNFV   96 (345)
T ss_dssp             EEEC
T ss_pred             EEEe
Confidence            7776

>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*

Probab=98.96  E-value=1e-09  Score=121.22  Aligned_cols=75  Identities=20%  Similarity=0.293  Sum_probs=66.4

Q ss_pred             cccceeEeec--CCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeC---Ce--EEEEE
Q 002823          230 INQGTLVVFN--LDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIA---GK--QIKLE  302 (876)
Q Consensus       230 ~~~~tLfV~N--LP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~---Gr--~IkVs  302 (876)
                      .++.+|||+|  |+..+|+++|+++|++||+|++|++. ..||||||+|.+.++|++|++.|||+.+.   |+  .|.|.
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~-~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~   94 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN   94 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECC-TTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEE
Confidence            4577999999  57899999999999999999999884 47899999999999999999999999883   44  68888


Q ss_pred             eec
Q 002823          303 PSH  305 (876)
Q Consensus       303 ~A~  305 (876)
                      |..
T Consensus        95 ~~~   97 (345)
T 3tht_A           95 FVE   97 (345)
T ss_dssp             ECS
T ss_pred             Eee
Confidence            874

>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

Probab=98.95  E-value=2.4e-10  Score=105.11  Aligned_cols=68  Identities=21%  Similarity=0.351  Sum_probs=59.2

Q ss_pred             EcCCCCCCCHHHHHHHh------------hccCCeEEEEe----CCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          152 LRKINSNIEDSELKALF------------EQYGDVRTFYR----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       152 VgNLP~~vTEeeL~elF------------sqfG~I~sV~~----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      +.+||..+++++|++.|            ++||+|.+|++    .++++|||||+|.+.++|++|++.|+|+.+.||+|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56677777888777666            99999999994    345799999999999999999999999999999999


Q ss_pred             Eeec
Q 002823          216 IHYS  219 (876)
Q Consensus       216 V~~A  219 (876)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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

Probab=98.93  E-value=2.9e-09  Score=99.87  Aligned_cols=81  Identities=20%  Similarity=0.190  Sum_probs=67.0

Q ss_pred             ccceeEeecCCCCC----------cHHHHHHHhhhcCCeEEEEecC-CcccEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 002823          231 NQGTLVVFNLDSSV----------SNDELHHIFGVYGEIKEIRETP-QKIHQKYIEFYDTRAAEAALRELNSRYIAGKQI  299 (876)
Q Consensus       231 ~~~tLfV~NLP~sv----------TeedLreiFs~fG~I~sVritg-~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~I  299 (876)
                      +++.|.+.|+=..-          -++||++.|++||.|.+|.+.. ..+|++||+|.+.++|.+|++.|||+.+.||+|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i   85 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI   85 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            45678888874321          2368999999999999999833 358999999999999999999999999999999


Q ss_pred             EEEeecCchhHH
Q 002823          300 KLEPSHLRGLRK  311 (876)
Q Consensus       300 kVs~A~~k~~Rr  311 (876)
                      +|.|+....-.+
T Consensus        86 ~v~~~~~~~y~~   97 (114)
T 3s6e_A           86 TAAYVPLPTYHN   97 (114)
T ss_dssp             EEEEECHHHHHH
T ss_pred             EEEEEcHHHHHH
Confidence            999997655433

>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

Probab=98.92  E-value=2.7e-09  Score=100.63  Aligned_cols=77  Identities=19%  Similarity=0.335  Sum_probs=65.6

Q ss_pred             ccceeEeecCCC--C---CcHHHHHHHhhhcCCeEEEEec---------CCcccEEEEEecCHHHHHHHHHHhCCceeCC
Q 002823          231 NQGTLVVFNLDS--S---VSNDELHHIFGVYGEIKEIRET---------PQKIHQKYIEFYDTRAAEAALRELNSRYIAG  296 (876)
Q Consensus       231 ~~~tLfV~NLP~--s---vTeedLreiFs~fG~I~sVrit---------g~skG~AFVeF~d~E~A~kAL~~LnG~~I~G  296 (876)
                      ++++|+|.|+-.  +   --++||++.|++||+|.+|++.         +..+|++||+|.+.++|.+|++.|||+.+.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            467899999842  1   2468999999999999998872         1346999999999999999999999999999


Q ss_pred             eEEEEEeecCc
Q 002823          297 KQIKLEPSHLR  307 (876)
Q Consensus       297 r~IkVs~A~~k  307 (876)
                      |+|+|.|+...
T Consensus        99 R~i~v~~~~~~  109 (118)
T 3ue2_A           99 RKVVAEVYDQE  109 (118)
T ss_dssp             EECEEEEECHH
T ss_pred             cEEEEEEcChH
Confidence            99999998753

>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

Probab=98.84  E-value=6.7e-09  Score=97.36  Aligned_cols=77  Identities=16%  Similarity=0.168  Sum_probs=65.5

Q ss_pred             CCCCcEEEEcCCCCCCC----------HHHHHHHhhccCCeEEEEeCC-CccceEeeecCCHHHHHHHHHHccccccCCc
Q 002823          144 EHPSRTLLLRKINSNIE----------DSELKALFEQYGDVRTFYRAS-KHCGFVTISYYDIRAARNAMKSLQNKLTRSG  212 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vT----------EeeL~elFsqfG~I~sV~~tg-ksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr  212 (876)
                      ..|++.|.+.|+=..-.          +++|++.|++||.|.+|++.. ..+|+|||+|.+.++|++|++.|+|+.+.||
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR   83 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGK   83 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            46789999999833221          357889999999999998533 3589999999999999999999999999999


Q ss_pred             eeeEeecC
Q 002823          213 KLDIHYSI  220 (876)
Q Consensus       213 ~L~V~~A~  220 (876)
                      .|+|.|+.
T Consensus        84 ~i~v~~~~   91 (114)
T 3s6e_A           84 MITAAYVP   91 (114)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEEc
Confidence            99999974

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=98.76  E-value=1.6e-08  Score=91.43  Aligned_cols=84  Identities=20%  Similarity=0.339  Sum_probs=72.3

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcccEE-Eeccccccc-ceeEEEEEecCCccchHHHHHHhcCccccCCC-CccE
Q 002823          706 TTLMIKNIPNKYTSKMLLAAIDERHKGTYDFI-YLPIDFKNK-CNVGYAFINMTDPSQIVPFYQSFNGKKWEKFN-SEKV  782 (876)
Q Consensus       706 TTvMirNIPnk~t~~~L~~~ide~~~g~yDF~-Ylp~Df~~~-~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~-s~Kv  782 (876)
                      |.|.||++|..+|++.+++.|...  .++||+ |.|-+...+ +-.+.|||||.+++++..|.+.|+|+.|...+ .+-.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~--~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~   79 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPM--PEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYP   79 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSC--CCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCc--ccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEee
Confidence            789999999999999999999975  378988 568777654 45688999999999999999999999998764 3455


Q ss_pred             EEEEeeccc
Q 002823          783 ASLAYARIQ  791 (876)
Q Consensus       783 ~~v~yA~iQ  791 (876)
                      +.|.||-.|
T Consensus        80 a~VE~AP~q   88 (91)
T 1uw4_A           80 AIVEFAPFQ   88 (91)
T ss_dssp             CEEEECSSC
T ss_pred             eEEEEcCCC
Confidence            899999887

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.66  E-value=6e-08  Score=87.43  Aligned_cols=75  Identities=25%  Similarity=0.381  Sum_probs=62.8

Q ss_pred             cccceeEeecCCC----CCcH----HHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 002823          230 INQGTLVVFNLDS----SVSN----DELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL  301 (876)
Q Consensus       230 ~~~~tLfV~NLP~----svTe----edLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkV  301 (876)
                      ++..||+|.-.+.    .+-.    .+|.+.|.+||+|..+|+..   +.+||+|.+.++|.+|++ |||..+.||.|+|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~---d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV   80 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE---DKMWVTFLEGSSALNVLS-LNGKELLNRTITI   80 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS---SSEEEEESSHHHHHHGGG-GTTCEETTEEEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec---CCEEEEECChHHHHHHHh-cCCeEeCCeEEEE
Confidence            3456888887762    3333    67999999999999999943   339999999999999999 9999999999999


Q ss_pred             EeecCch
Q 002823          302 EPSHLRG  308 (876)
Q Consensus       302 s~A~~k~  308 (876)
                      .++++.-
T Consensus        81 ~lkt~dW   87 (91)
T 2dnr_A           81 ALKSPSG   87 (91)
T ss_dssp             EECCCSS
T ss_pred             EeCCCCc
Confidence            9998753

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.59  E-value=1.1e-07  Score=90.31  Aligned_cols=80  Identities=19%  Similarity=0.150  Sum_probs=70.8

Q ss_pred             ccceeEeecCCCC-CcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecC-HHHHHHHHHHhC--CceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSS-VSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYD-TRAAEAALRELN--SRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~s-vTeedLreiFs~fG~I~sVritg~skG~AFVeF~d-~E~A~kAL~~Ln--G~~I~Gr~IkVs~A~~  306 (876)
                      ....|||+||+.. ++.++|+++|++||+|.+|.+.. ....|||+|.+ .++|.+|++.|+  +..|.|..++++....
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~-g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~G   95 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEG   95 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT-TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCH
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEec-CCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECCC
Confidence            3458999999999 99999999999999999999843 34479999999 899999999995  7889999999999887


Q ss_pred             chhHH
Q 002823          307 RGLRK  311 (876)
Q Consensus       307 k~~Rr  311 (876)
                      .++++
T Consensus        96 eeE~~  100 (121)
T 1owx_A           96 EVEKE  100 (121)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77776

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=98.58  E-value=2e-08  Score=91.48  Aligned_cols=85  Identities=21%  Similarity=0.354  Sum_probs=70.9

Q ss_pred             ceeEEeecCCCCCCHHHHHHHHHhhCCCcccEE-Eecccccccc-eeEEEEEecCCccchHHHHHHhcCccccCCCC-cc
Q 002823          705 RTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFI-YLPIDFKNKC-NVGYAFINMTDPSQIVPFYQSFNGKKWEKFNS-EK  781 (876)
Q Consensus       705 rTTvMirNIPnk~t~~~L~~~ide~~~g~yDF~-Ylp~Df~~~~-N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s-~K  781 (876)
                      --.|+||++|+.+|++.+++.|+....  .||+ |.|-|...+- -...|||||++++++..|.+.|+|+.|...+. +-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~--~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~   86 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPA--HDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEY   86 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSS--EEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCc--cceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEe
Confidence            347999999999999999999987543  5777 6788877644 44789999999999999999999999997654 44


Q ss_pred             EEEEEeeccc
Q 002823          782 VASLAYARIQ  791 (876)
Q Consensus       782 v~~v~yA~iQ  791 (876)
                      .+.|.||-.|
T Consensus        87 ~a~VE~APyq   96 (97)
T 2l08_A           87 PAVVEFAPFQ   96 (97)
T ss_dssp             EEEEEECCCC
T ss_pred             eeEEEecCCC
Confidence            5889999887

>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

Probab=98.43  E-value=3.3e-07  Score=83.13  Aligned_cols=73  Identities=22%  Similarity=0.308  Sum_probs=61.6

Q ss_pred             cccceeEeecCCCC-----CcH----HHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          230 INQGTLVVFNLDSS-----VSN----DELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       230 ~~~~tLfV~NLP~s-----vTe----edLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      ++..||+|.-++.+     +-.    .+|.+.|..||+|..+|+....   +||+|.+.++|.+||+ |||.++.||.|+
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~   88 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---MLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---EEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---EEEEEcChHHHHHHHh-cCCeeeCCeEEE
Confidence            45679999988743     222    5699999999999999984333   9999999999999998 999999999999


Q ss_pred             EEeecC
Q 002823          301 LEPSHL  306 (876)
Q Consensus       301 Vs~A~~  306 (876)
                      |.+..+
T Consensus        89 V~~k~~   94 (95)
T 1ufw_A           89 ISGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EeccCC
Confidence            998754

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.42  E-value=3.5e-07  Score=82.43  Aligned_cols=74  Identities=22%  Similarity=0.274  Sum_probs=62.1

Q ss_pred             CCCcEEEEcCCCC----CCCH----HHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          145 HPSRTLLLRKINS----NIED----SELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       145 ~pSrTLFVgNLP~----~vTE----eeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      .|..||+|.-.+.    ++-+    .+|.+.|.+||+|..++...   +.+||+|.+.++|.+|++ |+|..+.||.|+|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~---d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV   80 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE---DKMWVTFLEGSSALNVLS-LNGKELLNRTITI   80 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS---SSEEEEESSHHHHHHGGG-GTTCEETTEEEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec---CCEEEEECChHHHHHHHh-cCCeEeCCeEEEE
Confidence            5667999988772    3434    67889999999999999532   339999999999999997 9999999999999


Q ss_pred             eecCCC
Q 002823          217 HYSIPK  222 (876)
Q Consensus       217 ~~A~pk  222 (876)
                      +++.|.
T Consensus        81 ~lkt~d   86 (91)
T 2dnr_A           81 ALKSPS   86 (91)
T ss_dssp             EECCCS
T ss_pred             EeCCCC
Confidence            998764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.37  E-value=9.4e-07  Score=83.82  Aligned_cols=76  Identities=14%  Similarity=0.110  Sum_probs=64.4

Q ss_pred             CCCCCcEEEEcCCCCC-CCHHHHHHHhhccCCeEEEEeCCCccceEeeecCC-HHHHHHHHHHcc--ccccCCceeeEee
Q 002823          143 DEHPSRTLLLRKINSN-IEDSELKALFEQYGDVRTFYRASKHCGFVTISYYD-IRAARNAMKSLQ--NKLTRSGKLDIHY  218 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~-vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d-~edA~kAl~~Ln--g~~l~Gr~L~V~~  218 (876)
                      .-.+...|||+||+.+ +++++|+++|++||+|..|.. .+....|||.|.+ .++|.+|++.++  +..|.+..+.++.
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~-~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDF-VRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEEC-CTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEE-ecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            3466789999999999 999999999999999999985 2333479999999 899999999995  6778888777765


Q ss_pred             c
Q 002823          219 S  219 (876)
Q Consensus       219 A  219 (876)
                      .
T Consensus        93 L   93 (121)
T 1owx_A           93 L   93 (121)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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}

Probab=98.27  E-value=1.2e-06  Score=89.85  Aligned_cols=65  Identities=20%  Similarity=0.351  Sum_probs=58.1

Q ss_pred             CCcHHHHHHHhhhcCCeEEEEec---------CCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          243 SVSNDELHHIFGVYGEIKEIRET---------PQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       243 svTeedLreiFs~fG~I~sVrit---------g~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      .-.+++|++.|++||+|.+|++.         +..+|++||+|.+.++|.+|++.|||+.+.||+|++.|+...
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~  213 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQE  213 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHH
Confidence            34678999999999999998872         267899999999999999999999999999999999998654

>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

Probab=98.13  E-value=2.9e-06  Score=76.95  Aligned_cols=73  Identities=11%  Similarity=0.126  Sum_probs=60.0

Q ss_pred             CCCCcEEEEcCCCCC-----CCH----HHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCcee
Q 002823          144 EHPSRTLLLRKINSN-----IED----SELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKL  214 (876)
Q Consensus       144 e~pSrTLFVgNLP~~-----vTE----eeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L  214 (876)
                      ..|..||+|.-++..     +-+    .+|.+.|.+||.|..++....   -+||+|.+.++|.+|++ |+|+.+.||.|
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d---~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L   87 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG---QMLVTFADSHSALSVLD-VDGMKVKGRAV   87 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT---EEEEECSCSHHHHHHHH-GGGSEETTEEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC---cEEEEEcChHHHHHHHh-cCCeeeCCeEE
Confidence            356789999998753     222    568899999999999884222   29999999999999998 99999999999


Q ss_pred             eEeecC
Q 002823          215 DIHYSI  220 (876)
Q Consensus       215 ~V~~A~  220 (876)
                      +|++..
T Consensus        88 ~V~~k~   93 (95)
T 1ufw_A           88 KISGPS   93 (95)
T ss_dssp             EEECCC
T ss_pred             EEeccC
Confidence            998753

>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}

Probab=98.13  E-value=2.9e-06  Score=86.84  Aligned_cols=62  Identities=10%  Similarity=0.077  Sum_probs=55.9

Q ss_pred             CCHHHHHHHhhccCCeEEEEe---------CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          159 IEDSELKALFEQYGDVRTFYR---------ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       159 vTEeeL~elFsqfG~I~sV~~---------tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      -.+++|++.|++||.|.++++         +++++|++||+|.+.++|++|++.|+|+.+.||.|.+.|+.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            346889999999999999983         23789999999999999999999999999999999999974

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.69  E-value=0.00012  Score=67.90  Aligned_cols=71  Identities=23%  Similarity=0.287  Sum_probs=64.6

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhc-----CCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVY-----GEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~f-----G~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      .++|-+-|||..+++..|+.+.++|     |.|+.|.+.+. -+-|+|+|.|...|.+|.-+|+|.+|.|++|+|.-
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-CCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            5689999999999999999999999     99999888554 34699999999999999999999999999999864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.48  E-value=0.00027  Score=65.69  Aligned_cols=72  Identities=11%  Similarity=0.111  Sum_probs=65.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcc-----CCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQY-----GDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqf-----G~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ...++|-+-|||..+++..|+.+.++|     |+|+.+.. ....+-|+|+|.|...|-+|.-+|+|..|.||+|+|.
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L-~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILL-VSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEE-ETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEE-ecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            346899999999999999999999999     99999985 3345679999999999999999999999999999983

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.31  E-value=0.0017  Score=59.75  Aligned_cols=88  Identities=16%  Similarity=0.244  Sum_probs=72.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhc-c----CCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQ-Y----GDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsq-f----G~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ..++|.|.|||++++++.|.-+|+. -    |+|..+....   +-|+|+|.+.+.|++.++. ....|.+..|.|.-..
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~   82 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAP   82 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECC
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCC
Confidence            3579999999999999999999996 2    5999998644   7899999999999999853 3567889999997655


Q ss_pred             CCCCCCccccccceeEeecCCCCCc
Q 002823          221 PKDNPSEKEINQGTLVVFNLDSSVS  245 (876)
Q Consensus       221 pk~~~~ek~~~~~tLfV~NLP~svT  245 (876)
                      +++        ..+|++.+|++.++
T Consensus        83 ~~~--------~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           83 PRA--------PARLLLQGLPPGTS   99 (104)
T ss_dssp             CCC--------CCCCCCCSCCCCCC
T ss_pred             CCC--------cceEeeecCCCCCC
Confidence            443        45799999998765

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.78  E-value=0.0048  Score=56.72  Aligned_cols=78  Identities=21%  Similarity=0.236  Sum_probs=66.2

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhh-----cCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGV-----YGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~-----fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ..+|.|.|||+.+.++.|.-+|+.     =|+|..|+..+   +-|+|+|.+.+.|++.|+ -....+.+.+|.|....+
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLA-QADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEEEECCC
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhc-CCcceecCeEEEEEcCCC
Confidence            468999999999999999999986     26788898755   789999999999999987 236788899999999888


Q ss_pred             chhHHHH
Q 002823          307 RGLRKCL  313 (876)
Q Consensus       307 k~~Rr~l  313 (876)
                      +..+|.+
T Consensus        84 ~~~~r~l   90 (104)
T 2dhx_A           84 RAPARLL   90 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCcceEe
Confidence            8766644

>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

Probab=96.72  E-value=0.0021  Score=59.27  Aligned_cols=76  Identities=18%  Similarity=0.251  Sum_probs=63.4

Q ss_pred             CcEEEEcCCCCCC-CH----HHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNI-ED----SELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~v-TE----eeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ..+|+|.||+.+| ..    +.++++|..|+++.+... -++-.-..|.|.++++|.+|...|++..+.|++|+|-|+.+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~-lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY-FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEE-ETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceee-cCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            3689999999876 32    567899999999888663 34444679999999999999999999999999999999875


Q ss_pred             CC
Q 002823          222 KD  223 (876)
Q Consensus       222 k~  223 (876)
                      ..
T Consensus        84 ~~   85 (104)
T 1wey_A           84 LH   85 (104)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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

Probab=96.68  E-value=0.0022  Score=59.16  Aligned_cols=76  Identities=18%  Similarity=0.197  Sum_probs=62.9

Q ss_pred             cceeEeecCCCCC-c----HHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSV-S----NDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~sv-T----eedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|+|.||+.++ .    .+.++++|..|+++.....-+.-| -..|.|.+.++|.+|...|++..+.|++++|-|+.+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK-RVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT-EEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce-EEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            4589999998765 2    257789999999988866533223 578999999999999999999999999999999985


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      ..
T Consensus        84 ~~   85 (104)
T 1wey_A           84 LH   85 (104)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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

Probab=96.32  E-value=0.017  Score=54.49  Aligned_cols=76  Identities=17%  Similarity=0.208  Sum_probs=63.9

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCC-eEEEEEeecCch
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAG-KQIKLEPSHLRG  308 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G-r~IkVs~A~~k~  308 (876)
                      .....|.|.+.|+.. ...|.+.|++||+|.+... .....+-.|+|.++.+|++||. .||..|.| -.|-|.+...+.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~d~~   98 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDKN   98 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCHH
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECCCHH
Confidence            346689999999885 6778889999999999887 5567899999999999999998 69999985 777788776554

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=95.68  E-value=0.043  Score=49.37  Aligned_cols=64  Identities=11%  Similarity=0.154  Sum_probs=53.3

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-cCC------cccEEEEEecCHHHHHHHHHHhCCceeCC
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-TPQ------KIHQKYIEFYDTRAAEAALRELNSRYIAG  296 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri-tg~------skG~AFVeF~d~E~A~kAL~~LnG~~I~G  296 (876)
                      .+|.|++||+.+|++++.+.++...++..... .++      .-.-|+|.|.+.+++..-.+.++|..+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            36999999999999999999999988766554 121      22469999999999999999999998854

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=94.78  E-value=0.088  Score=48.02  Aligned_cols=55  Identities=15%  Similarity=0.230  Sum_probs=44.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcc
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ  205 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Ln  205 (876)
                      .+.++| ++|+.+...||.++|+.||.|.--.+   .-..|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEE---ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            356677 99999999999999999985433222   23479999999999999998764

>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

Probab=93.97  E-value=0.14  Score=48.28  Aligned_cols=71  Identities=15%  Similarity=0.182  Sum_probs=57.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCC-ceeeEeec
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRS-GKLDIHYS  219 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G-r~L~V~~A  219 (876)
                      ..+-|.|-+.|+.. ...|...|++||.|.+... .....+..|.|.++.+|++||. .||+.+.+ -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            35789999999884 6778889999999999886 3456899999999999999995 59988874 45555543

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=93.32  E-value=0.19  Score=45.87  Aligned_cols=53  Identities=13%  Similarity=0.261  Sum_probs=43.3

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhC
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELN  290 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~Ln  290 (876)
                      .++| +.|+.+...||.++|+.||.|.--.+   ....|||.|.+++.|..|++.+.
T Consensus        18 Vf~l-~FP~ewKt~DI~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           18 VLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             EEEE-ECCTTCCHHHHHHHHTTTCSCCCEEE---ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             EEEE-eCChhhhhHHHHHHhhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            4555 99999999999999999996543333   24589999999999999999763

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.63  E-value=0.051  Score=62.19  Aligned_cols=56  Identities=13%  Similarity=0.147  Sum_probs=43.9

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHH
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALR  287 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~  287 (876)
                      ..++|+|. .|..+++.+|.+.|++||.|..+........||.|||.+.+++.+++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            45689997 799999999999999999999988877777899999999999997765

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=92.42  E-value=0.21  Score=45.53  Aligned_cols=73  Identities=10%  Similarity=0.093  Sum_probs=54.1

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-cCC------cccEEEEEecCHHHHHHHHHHhCCceeCC-----eEE
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-TPQ------KIHQKYIEFYDTRAAEAALRELNSRYIAG-----KQI  299 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-tg~------skG~AFVeF~d~E~A~kAL~~LnG~~I~G-----r~I  299 (876)
                      .-+|+|+.||+.+|++++.+.++..-++..... .++      .-.-|+|.|.+.++...-.+..+|..+-+     -+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            347999999999999999988887655433222 111      12459999999999999999999988854     344


Q ss_pred             EEEee
Q 002823          300 KLEPS  304 (876)
Q Consensus       300 kVs~A  304 (876)
                      .|++|
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            46655

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.41  E-value=0.05  Score=62.22  Aligned_cols=58  Identities=10%  Similarity=0.291  Sum_probs=44.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHH
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKS  203 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~  203 (876)
                      ...|+|||. .|..+++++|.++|++||+|.++.......-||.|+|.+.+++..++..
T Consensus        51 qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           51 QAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHSS
T ss_pred             HhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHhc
Confidence            446899998 7999999999999999999999986555567999999999999977643

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=92.38  E-value=0.13  Score=46.95  Aligned_cols=53  Identities=13%  Similarity=0.258  Sum_probs=43.4

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhC
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELN  290 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~Ln  290 (876)
                      .++| +.|+.+...||.++|+.||.|.--.+   ....|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEEEEEEE---ETTEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            4555 99999999999999999995543233   24589999999999999999875

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=92.20  E-value=0.18  Score=48.21  Aligned_cols=73  Identities=19%  Similarity=0.269  Sum_probs=57.3

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEE-EEec----------------C--CcccEEEEEecCHHHHHHHHHHhCCc
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKE-IRET----------------P--QKIHQKYIEFYDTRAAEAALRELNSR  292 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~s-Vrit----------------g--~skG~AFVeF~d~E~A~kAL~~LnG~  292 (876)
                      ...|.|.+.|++.+ ..+.+.|++||.|.+ +...                +  ...++..|+|.+..+|.+||. .||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            34688899977654 567788999999977 2211                1  145788999999999999998 7999


Q ss_pred             eeCCeEEEEEeecC
Q 002823          293 YIAGKQIKLEPSHL  306 (876)
Q Consensus       293 ~I~Gr~IkVs~A~~  306 (876)
                      .|.|.-|-|.+..+
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999888998853

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=90.65  E-value=0.13  Score=46.99  Aligned_cols=54  Identities=15%  Similarity=0.238  Sum_probs=43.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcc
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ  205 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Ln  205 (876)
                      +.++| ++|+++...||.++|+.||.|.--.+   .-..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEE---ETTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            35566 99999999999999999994433333   34579999999999999998764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=88.27  E-value=0.4  Score=45.88  Aligned_cols=70  Identities=13%  Similarity=0.189  Sum_probs=53.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-eC-------------C-----CccceEeeecCCHHHHHHHHHHccccc
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY-RA-------------S-----KHCGFVTISYYDIRAARNAMKSLQNKL  208 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-~t-------------g-----ksrGfAFV~F~d~edA~kAl~~Lng~~  208 (876)
                      ..|.|-+.|+.. ...+.+.|++||.|.+-. ..             .     ....+..|+|.+..+|++|+. .+|+.
T Consensus         8 ~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            467888887654 556778999999997732 10             0     135688999999999999995 69999


Q ss_pred             cCCceeeEeec
Q 002823          209 TRSGKLDIHYS  219 (876)
Q Consensus       209 l~Gr~L~V~~A  219 (876)
                      +.|..|-|...
T Consensus        86 i~G~mIGV~Py   96 (132)
T 3p3d_A           86 FNGVLLGVIPY   96 (132)
T ss_dssp             ETTEECEEEEC
T ss_pred             eCcEEEEEEEC
Confidence            99987777664

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	876
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	0.003
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-05
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-09
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	7e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	7e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	0.001
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-04
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-05
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-09
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-07
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-04
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-09
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	8e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-04
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-08
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-08
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	9e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-05
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 8e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	7e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	7e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	0.004
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-05
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	7e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	7e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	7e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	0.002
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-04
d1uw4a_	91	d.58.7.4 (A:) RNA processing protein UPF3x, RRM do	0.001
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.002
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.002
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	0.004
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.004

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

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]

 Score = 59.9 bits (145), Expect = 6e-12
 Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIR-----ETPQKIHQKYIEFYDTRAAEAALRE 288
           +L V +L   V+   L+  F   G I  IR      T + +   Y+ F     AE AL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 289 LNSRYIAGKQIKLEPSH 305
           +N   I GK +++  S 
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

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]

 Score = 42.6 bits (100), Expect = 8e-06
 Identities = 9/76 (11%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 149 TLLLRKINSNIEDSELKALFEQYGDVR-----TFYRASKHCGFVTISYYDIRAARNAMKS 203
           +L +  ++ ++ ++ L   F   G +            +  G+  +++     A  A+ +
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 204 LQNKLTRSGKLDIHYS 219
           +   + +   + I +S
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.2 bits (143), Expect = 1e-11
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 4/74 (5%)

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIR----ETPQKIHQKYIEFYDTRAAEAALRE 288
           G L+V NLD  VS+ ++  +F  +G +K+       + + +    + F     A  A+++
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 289 LNSRYIAGKQIKLE 302
            N   + G+ + ++
Sbjct: 61  YNGVPLDGRPMNIQ 74

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 13/76 (17%), Positives = 26/76 (34%), Gaps = 8/76 (10%)

Query: 150 LLLRKINSNIEDSELKALFEQYGD------VRTFYRASKHCGFVTISYYDIRAARNAMKS 203
           LL+  ++  + D++++ LF ++G              S     V   +     A  AMK 
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVH--FERKADALKAMKQ 60

Query: 204 LQNKLTRSGKLDIHYS 219
                     ++I   
Sbjct: 61  YNGVPLDGRPMNIQLV 76

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 58.5 bits (141), Expect = 3e-11
 Identities = 24/84 (28%), Positives = 38/84 (45%)

Query: 225 PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEA 284
            S+K     TL+  NL  +++ DEL  +F    EI+ + +  +     YIEF     AE 
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 285 ALRELNSRYIAGKQIKLEPSHLRG 308
            L E     I G+ + L  +  +G
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTGEKG 92

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 48.5 bits (115), Expect = 1e-07
 Identities = 19/81 (23%), Positives = 35/81 (43%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ 205
            +RTLL + ++ NI + ELK +FE   ++R   +  K  G   I +     A   ++  Q
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 74

Query: 206 NKLTRSGKLDIHYSIPKDNPS 226
                   + ++Y+  K    
Sbjct: 75  GAEIDGRSVSLYYTGEKGGTR 95

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

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]

 Score = 57.7 bits (139), Expect = 4e-11
 Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 3/89 (3%)

Query: 225 PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYG---EIKEIRETPQKIHQKYIEFYDTRA 281
           PS ++   G + + NLD S+ N  L+  F  +G     K + +        ++ F    A
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 60

Query: 282 AEAALRELNSRYIAGKQIKLEPSHLRGLR 310
           AE A+ ++N   +  +++ +     R  R
Sbjct: 61  AERAIEKMNGMLLNDRKVFVGRFKSRKER 89

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

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]

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 10/79 (12%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYG---DVRTFYRASKHCGFVTISYYDIRAARNAMKS 203
              + ++ ++ +I++  L   F  +G     +     +   G+  + +    AA  A++ 
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 204 LQNKLTRSGKLDIHYSIPK 222
           +   L    K+ +     +
Sbjct: 68  MNGMLLNDRKVFVGRFKSR 86

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 5e-11
 Identities = 21/105 (20%), Positives = 42/105 (40%), Gaps = 2/105 (1%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIH--QKYIEFYDTRAAEAALRELNS 291
            L + NL   ++ +E++ IFG YG I++IR           Y+ + D   A+ A   L+ 
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSG 68

Query: 292 RYIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPP 336
             +  + + +   +     + +  +   E  +     Y     PP
Sbjct: 69  FNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPP 113

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 2e-09
 Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 2/86 (2%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHC--GFVTISYYDIRAARNAMKS 203
            +R L +R +   I   E+  +F +YG +R     +     G   + Y DI  A+NA   
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 204 LQNKLTRSGKLDIHYSIPKDNPSEKE 229
           L      +  L + Y        + +
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMD 91

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 7e-11
 Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 6/82 (7%)

Query: 227 EKEINQG-TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTR 280
           EK + +  TL V NL    + ++++ +F   G+IK+I     K+ +      ++E+Y   
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 60

Query: 281 AAEAALRELNSRYIAGKQIKLE 302
            AE A+R +N   +  + I+ +
Sbjct: 61  DAENAMRYINGTRLDDRIIRTD 82

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (109), Expect = 7e-07
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNA 200
            S TL +  ++    + ++  LF + GD++             CGF  + YY    A NA
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 201 MKSLQNKLTRSGKLDIHYSIPK 222
           M+ +         +   +    
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGF 87

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.2 bits (142), Expect = 1e-10
 Identities = 22/173 (12%), Positives = 54/173 (31%), Gaps = 12/173 (6%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVR----TFYRASKHCGFVTISYYDIRAAR 198
           +    R L +  ++    D  L++ FEQ+G +          +K         Y      
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 199 NAMKSLQNKLTRSGKLDIHYSIPK--DNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVY 256
           +A  + +        ++   ++ +         +    + V  +        L   F  Y
Sbjct: 62  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 121

Query: 257 GEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRELNSRYIAGKQIKLEPS 304
           G+I+ I     +   K     ++ F D  + +  +       + G   ++  +
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA 173

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 2e-10
 Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 6/89 (6%)

Query: 221 PKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR-----ETPQKIHQKYIE 275
           P DN S +E +  T+    L + +   +L   F   G+++++R      + +     Y+E
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 276 FYDTRAAEAALRELNSRYIAGKQIKLEPS 304
           F + ++   A+  L  + + G  I ++ S
Sbjct: 67  FCEIQSVPLAI-GLTGQRLLGVPIIVQAS 94

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 17/89 (19%), Positives = 35/89 (39%), Gaps = 10/89 (11%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA-------SKHCGFVTISYYDIR 195
           +E  +RT+   ++ + I   +L+  F   G VR            SK   +V   + +I+
Sbjct: 14  EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE--FCEIQ 71

Query: 196 AARNAMKSLQNKLTRSGKLDIHYSIPKDN 224
           +   A+  L  +      + +  S  + N
Sbjct: 72  SVPLAIG-LTGQRLLGVPIIVQASQAEKN 99

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.1 bits (135), Expect = 2e-10
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 223 DNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAA 282
           D  ++      T+    + S +++  +   F  +G+I EIR    +    ++ F    +A
Sbjct: 9   DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR-VFPEKGYSFVRFSTHESA 67

Query: 283 EAALRELNSRYIAGKQIKLE 302
             A+  +N   I G  +K  
Sbjct: 68  AHAIVSVNGTTIEGHVVKCY 87

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.4 bits (102), Expect = 5e-06
 Identities = 11/81 (13%), Positives = 30/81 (37%), Gaps = 1/81 (1%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ 205
            + T+    I S + D  ++  F  +G +    R     G+  + +    +A +A+ S+ 
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEI-RVFPEKGYSFVRFSTHESAAHAIVSVN 75

Query: 206 NKLTRSGKLDIHYSIPKDNPS 226
                   +  ++     + +
Sbjct: 76  GTTIEGHVVKCYWGKESPDMT 96

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 5/85 (5%)

Query: 225 PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKE-----IRETPQKIHQKYIEFYDT 279
           P+ +  +  T+ V NL       +L  +F  +G I        + T Q     +I F+  
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 280 RAAEAALRELNSRYIAGKQIKLEPS 304
             A  A+  ++        + +E +
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWA 85

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 16/84 (19%), Positives = 37/84 (44%), Gaps = 5/84 (5%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA-----SKHCGFVTISYYDIRAARNA 200
            + T+ +  ++ +  +++L+ LF  +G +   Y A      +  GF  IS++    A  A
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 201 MKSLQNKLTRSGKLDIHYSIPKDN 224
           +  +         L++ ++ P  N
Sbjct: 67  IAGVSGFGYDHLILNVEWAKPSTN 90

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 3e-10
 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 5/72 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALRE 288
            L VF L    +  +L  +F  YG I ++     +++ +     ++ F +   A+ A   
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 289 LNSRYIAGKQIK 300
            N   + G++I+
Sbjct: 71  ANGMELDGRRIR 82

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 10/67 (14%), Positives = 29/67 (43%), Gaps = 5/67 (7%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTF-----YRASKHCGFVTISYYDIRAARNA 200
           P+  L +  ++    + +L+ +F +YG +         ++ +  GF  + + ++  A+ A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 201 MKSLQNK 207
            +     
Sbjct: 68  KERANGM 74

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.0 bits (132), Expect = 5e-10
 Identities = 25/88 (28%), Positives = 40/88 (45%), Gaps = 3/88 (3%)

Query: 227 EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQK---IHQKYIEFYDTRAAE 283
           E +    TL V NL   V+   +  +F   G  K  +   +        ++EFY+ R A 
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 284 AALRELNSRYIAGKQIKLEPSHLRGLRK 311
           AAL  +N R I GK++K+  +     +K
Sbjct: 63  AALAAMNGRKILGKEVKVNWATTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 5e-07
 Identities = 12/85 (14%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYG---DVRTFYRASKHCGFVTISYYDIRAARN 199
           D+   RTL +  ++ ++ +  +  LF Q G     +     + +  +  + +Y+ R A  
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query: 200 AMKSLQNKLTRSGKLDIHYSIPKDN 224
           A+ ++  +     ++ ++++    +
Sbjct: 64  ALAAMNGRKILGKEVKVNWATTPSS 88

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 9e-10
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 225 PSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR-----ETPQKIHQKYIEFYDT 279
           P  +     T+ V  LD  VS   L  +F   G +          T Q     ++EF   
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 280 RAAEAALRELNSRYIAGKQIKLEPS 304
             A+ A++ ++   + GK I++  +
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKA 86

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 3e-06
 Identities = 11/87 (12%), Positives = 31/87 (35%), Gaps = 5/87 (5%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGD-----VRTFYRASKHCGFVTISYYDIRAA 197
           + +   T+ +  ++  + +  L  LF Q G      +       +H G+  + +     A
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 64

Query: 198 RNAMKSLQNKLTRSGKLDIHYSIPKDN 224
             A+K +         + ++ +   + 
Sbjct: 65  DYAIKIMDMIKLYGKPIRVNKASAHNK 91

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 53.5 bits (128), Expect = 1e-09
 Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIR-----ETPQKIHQKYIEFYDTRAAEAALRE 288
            L+V  L   +++ EL+ +F   G I   R     +T       +++F     ++ A++ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 289 LNSRYIAGKQIKLEPS 304
           LN   +  K++K+  +
Sbjct: 64  LNGITVRNKRLKVSYA 79

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVR-----TFYRASKHCGFVTISYYDIRAARNAM 201
           +  L++  +  ++ D EL ALF   G +        Y+     G+  + +     ++ A+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 202 KSLQNKLTRSGKLDIHYSIP 221
           K L     R+ +L + Y+ P
Sbjct: 62  KVLNGITVRNKRLKVSYARP 81

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.8 bits (129), Expect = 1e-09
 Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 13/90 (14%)

Query: 220 IPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGE------IKEIRETPQKIHQKY 273
           +PK   + K      ++V N+    +  E+  +F  +GE       K++  T       +
Sbjct: 2   VPKKQTTSK------ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 55

Query: 274 IEFYDTRAAEAALREL-NSRYIAGKQIKLE 302
           ++F   + A+ A   L +S ++ G+++ LE
Sbjct: 56  VDFITKQDAKKAFNALCHSTHLYGRRLVLE 85

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.4 bits (115), Expect = 1e-07
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 7/87 (8%)

Query: 144 EHPSRTLLLRKINSNIEDSELKALFEQYGD------VRTFYRASKHCGFVTISYYDIRAA 197
           +  +  +L+R I       E++ LF  +G+       +       H GF  + +   + A
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 198 RNAMKSLQNKLTRSGK-LDIHYSIPKD 223
           + A  +L +     G+ L + ++  + 
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEV 91

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.4 bits (128), Expect = 1e-09
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 227 EKEINQGT-LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAA 285
           EK   Q + L V NL   ++ +E+  +F  YG+  E+    +     +I       AE A
Sbjct: 2   EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEIA 60

Query: 286 LRELNSRYIAGKQIKLE 302
             EL++  + GKQ+++ 
Sbjct: 61  KVELDNMPLRGKQLRVR 77

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.5 bits (128), Expect = 1e-09
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 8/79 (10%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK--------YIEFYDTRAAEAAL 286
           L + NL+ S + + L  +F   G IK    + +K            ++E+     A+ AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 287 RELNSRYIAGKQIKLEPSH 305
           ++L    + G ++++  S 
Sbjct: 61  KQLQGHTVDGHKLEVRISE 79

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.9 bits (111), Expect = 3e-07
 Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 8/85 (9%)

Query: 150 LLLRKINSNIEDSELKALFEQYGDV--------RTFYRASKHCGFVTISYYDIRAARNAM 201
           L ++ +N +  +  LK +F + G +        +         GF  + Y     A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 202 KSLQNKLTRSGKLDIHYSIPKDNPS 226
           K LQ       KL++  S     P+
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKPA 85

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 53.6 bits (128), Expect = 1e-09
 Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 227 EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIK-----EIRETPQKIHQKYIEFYDTRA 281
           ++ +    L V ++      DE+   F  YGEIK       R T        +E+   + 
Sbjct: 2   QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 61

Query: 282 AEAALRELNSRYIAGKQIKLEPSHLRG 308
           A AA   LN   I G+ I+++   ++G
Sbjct: 62  ALAAKEALNGAEIMGQTIQVDWCFVKG 88

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 39.3 bits (91), Expect = 1e-04
 Identities = 12/82 (14%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASK-----HCGFVTISYYDIRAARNA 200
               L +  I+   ++ E++  F  YG+++  +           G+  + Y   + A  A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 201 MKSLQNKLTRSGKLDIHYSIPK 222
            ++L         + + +   K
Sbjct: 66  KEALNGAEIMGQTIQVDWCFVK 87

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.7 bits (126), Expect = 2e-09
 Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALRE 288
            L V  L   V +  LH  F  +G+I +I      ET +     ++EF     A AA+  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 289 LNSRYIAGKQIKLEPS 304
           +N   + G+ I++  +
Sbjct: 67  MNESELFGRTIRVNLA 82

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 4e-06
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRAS-----KHCGFVTISYYDIRAARNA 200
             R L +  +   ++D  L A F  +GD+            KH GF  + +     A  A
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 201 MKSLQNKLTRSGKLDIHYSIPK 222
           + ++         + ++ + P 
Sbjct: 64  IDNMNESELFGRTIRVNLAKPM 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 52.3 bits (125), Expect = 3e-09
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 5/74 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIK-----EIRETPQKIHQKYIEFYDTRAAEAALRE 288
            L V NL  ++++D+L  IFG YG I        + T +     ++ +     A+ A+  
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 289 LNSRYIAGKQIKLE 302
           LN+    G    L 
Sbjct: 68  LNNVIPEGGSQPLS 81

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 43.0 bits (101), Expect = 5e-06
 Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 13/78 (16%)

Query: 138 GEHLNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA-------SKHCGFVTIS 190
           GE + D      L +  +   I D +L  +F +YG +              +   FV   
Sbjct: 1   GESIKD----TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR-- 54

Query: 191 YYDIRAARNAMKSLQNKL 208
           Y     A+ A+ +L N +
Sbjct: 55  YNKREEAQEAISALNNVI 72

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 8e-09
 Identities = 17/82 (20%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 226 SEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK---YIEFYDTRAA 282
           SE +     L V N+     + +L  +FG +G+I ++     +   K   ++ F ++  A
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 64

Query: 283 EAALRELNSRYIAGKQIKLEPS 304
           + A  +L+   + G++I++  +
Sbjct: 65  DRAREKLHGTVVEGRKIEVNNA 86

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 1e-04
 Identities = 13/87 (14%), Positives = 34/87 (39%), Gaps = 3/87 (3%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHC---GFVTISYYDIRAARN 199
            +   + L +  I     D +L+ +F Q+G +             GF  +++ +   A  
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 66

Query: 200 AMKSLQNKLTRSGKLDIHYSIPKDNPS 226
           A + L   +    K++++ +  +   +
Sbjct: 67  AREKLHGTVVEGRKIEVNNATARVMTN 93

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 1e-08
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEI-----KEIRETPQKIHQKYIEFYDTRAAEAALRE 288
            L+V  L  +++ +E   +FG  GEI        + T Q +   ++ + D + AE A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 289 LNSRYIAGKQIKLEPS 304
           LN   +  K IK+  +
Sbjct: 64  LNGLRLQTKTIKVSYA 79

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.6 bits (121), Expect = 2e-08
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 4/72 (5%)

Query: 234 TLVVFNLDS-SVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSR 292
            + + NL++  V   ++  IF  YG+I             ++++ + R A AA+   + R
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS---VHKGFAFVQYVNERNARAAVAGEDGR 73

Query: 293 YIAGKQIKLEPS 304
            IAG+ + +  +
Sbjct: 74  MIAGQVLDINLA 85

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (108), Expect = 1e-06
 Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 4/81 (4%)

Query: 146 PSRTLLLRKINS-NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSL 204
            +  + +  +N+  ++ S+++A+F +YG +      S H GF  + Y + R AR A+   
Sbjct: 14  MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIV---GCSVHKGFAFVQYVNERNARAAVAGE 70

Query: 205 QNKLTRSGKLDIHYSIPKDNP 225
             ++     LDI+ +      
Sbjct: 71  DGRMIAGQVLDINLAAEPKVN 91

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.2 bits (119), Expect = 3e-08
 Identities = 20/95 (21%), Positives = 38/95 (40%), Gaps = 14/95 (14%)

Query: 224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-------------RETPQKIH 270
           +P E   N   + V  L+ SV+ D+L   F   G +K               +ET +   
Sbjct: 1   DPDEDSDN-SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG 59

Query: 271 QKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH 305
              + + D   A+AA+   + +   G ++K+  + 
Sbjct: 60  DATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 94

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 3e-08
 Identities = 12/71 (16%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
            + V      ++ DEL   F  YG++ ++          ++ F D + A++         
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLI 64

Query: 294 IAGKQIKLEPS 304
           I G  + +  +
Sbjct: 65  IKGISVHISNA 75

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 5e-05
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 4/82 (4%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ 205
            S  + + +   ++ + EL+  F QYGDV   +       F  +++ D + A++      
Sbjct: 4   GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--- 60

Query: 206 NKLTRSGK-LDIHYSIPKDNPS 226
             L   G  + I  + PK N +
Sbjct: 61  EDLIIKGISVHISNAEPKHNSN 82

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.7 bits (118), Expect = 4e-08
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQK-----IHQKYIEFYDTRAAEAALR 287
           G L V NL  + S ++L  +F  YG + E+               ++ F     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 288 ELNSRYIAGKQIKLEPSHLR 307
           E++ +   G+ + + PS ++
Sbjct: 69  EVDGQVFQGRMLHVLPSTIK 88

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 6e-08
 Identities = 11/79 (13%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALREL 289
           L +  L + +++D++  +   +G +K                 + E+ D    + A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 290 NSRYIAGKQIKLEPSHLRG 308
           N   +  K++ ++ + +  
Sbjct: 64  NGMQLGDKKLLVQRASVGA 82

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 9/87 (10%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA-------SKHCGFVTISYYDIRAARN 199
           +  L +  + + + D ++K L   +G ++ F          SK   F    Y DI     
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE--YVDINVTDQ 58

Query: 200 AMKSLQNKLTRSGKLDIHYSIPKDNPS 226
           A+  L        KL +  +      +
Sbjct: 59  AIAGLNGMQLGDKKLLVQRASVGAKNA 85

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 7e-08
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKE------IRETPQKIHQKYIEFYDTRAAEAALRE 288
           + + NLD  +    L+  F  +G I +        +T       +I F    A++AA+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 289 LNSRYIAGKQIKLEPSHLRGLR 310
           +N +Y+  + I +  +  +  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 5e-06
 Identities = 11/81 (13%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 150 LLLRKINSNIEDSELKALFEQYGDVRTFYR------ASKHCGFVTISYYDIRAARNAMKS 203
           + +  ++  I++  L   F  +G +    +           G+  I++    A+  A+++
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 204 LQNKLTRSGKLDIHYSIPKDN 224
           +  +   +  + + Y+  KD+
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 9e-08
 Identities = 28/106 (26%), Positives = 53/106 (50%), Gaps = 7/106 (6%)

Query: 234 TLVVFNLD-SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSR 292
            L+V NL+   V+   L  +FGVYG+++ ++    K     ++  D   A+ A+  LN  
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 63

Query: 293 YIAGKQIKLEPSHLRGLRKCLANQLPPELEQEECGSYQQQNSPPNK 338
            + GK I++  S  + +      QLP E ++++  +    NSP ++
Sbjct: 64  KLHGKPIRITLSKHQNV------QLPREGQEDQGLTKDYGNSPLHR 103

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 1e-07
 Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQ-----KYIEFYDTRAAEAALRE 288
            L V  L  +++  EL  +F  YG I   R    ++        +I F     AE A++ 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 289 LNSRYIAGKQIKLE 302
           LN +  +G    + 
Sbjct: 68  LNGQKPSGATEPIT 81

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 15/65 (23%), Positives = 23/65 (35%), Gaps = 5/65 (7%)

Query: 148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYRASK-----HCGFVTISYYDIRAARNAMK 202
             L +  +   +   EL+ LF QYG + T             G   I +     A  A+K
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 203 SLQNK 207
            L  +
Sbjct: 67  GLNGQ 71

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 1e-07
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
            L V NL  S S + +   F         R   +     ++ F +   A  A++ LN + 
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER-VKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 294 IAGKQIKLEPS 304
           + G  I++  +
Sbjct: 69  LDGSPIEVTLA 79

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 1/80 (1%)

Query: 147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN 206
            + L +R +  +  +  ++  F          R  K   +  + + +   A  AMK+L  
Sbjct: 8   VKILYVRNLMLSTSEEMIEKEFNNIKPGA-VERVKKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 207 KLTRSGKLDIHYSIPKDNPS 226
           K+     +++  + P D  S
Sbjct: 67  KVLDGSPIEVTLAKPVDKDS 86

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 1e-07
 Identities = 13/93 (13%), Positives = 29/93 (31%), Gaps = 9/93 (9%)

Query: 149 TLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHC-------GFVTISYYDIRAARNAM 201
            L +  I    +  E+     +  +                  GF  + Y   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 202 KSLQNKLTRSG--KLDIHYSIPKDNPSEKEINQ 232
           + L     +    ++ + ++ P+ +  E  +  
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.2 bits (96), Expect = 3e-05
 Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 9/78 (11%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-------YIEFYDTRAAEAAL 286
            L +  +      +E+        E             K       ++E+   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 287 RELNSRYI--AGKQIKLE 302
           R+L    I   G QI ++
Sbjct: 63  RKLMPGRIQLWGHQIAVD 80

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 10/91 (10%), Positives = 35/91 (38%), Gaps = 6/91 (6%)

Query: 219 SIPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----Y 273
           ++P +    ++     L +  L    + + L + +  +G++ +         ++     +
Sbjct: 7   TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 66

Query: 274 IEFYDTRAAEAALRELNSRYIAGKQIKLEPS 304
           + F      +AA+       I G+ ++ + +
Sbjct: 67  VTFSSMAEVDAAM-AARPHSIDGRVVEPKRA 96

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 10/87 (11%), Positives = 31/87 (35%), Gaps = 6/87 (6%)

Query: 142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHC-----GFVTISYYDIRA 196
            ++   R L +  ++    +  L+  +EQ+G +               GF  +++  +  
Sbjct: 15  REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 74

Query: 197 ARNAMKSLQNKLTRSGKLDIHYSIPKD 223
              AM   +        ++   ++ ++
Sbjct: 75  VDAAMA-ARPHSIDGRVVEPKRAVARE 100

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.6 bits (110), Expect = 2e-07
 Identities = 11/71 (15%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIR-----ETPQKIHQKYIEFYDTRAAEAALREL 289
           + V  L  + + +++ H F  +G++ +        T +     ++ F      E    E+
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 290 NSRYIAGKQIK 300
           +   I  K ++
Sbjct: 61  HFHEINNKMVE 71

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 46.7 bits (110), Expect = 2e-07
 Identities = 13/76 (17%), Positives = 23/76 (30%), Gaps = 5/76 (6%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRE 288
           TL + N   S +   +  +      +      P           YI+      A   + +
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 289 LNSRYIAGKQIKLEPS 304
           LN   I G  +  + S
Sbjct: 63  LNGLKIEGYTLVTKVS 78

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 3e-07
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI--RETPQKIHQKYIEFYDTRAAEAALRE 288
           N   + V NL   +   ++  +F  YG I++I  +         ++EF D R AE A+  
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 72

Query: 289 LNSRYIAGKQIKLEPSH 305
            +     G ++++E   
Sbjct: 73  RDGYDYDGYRLRVEFPR 89

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.1 bits (109), Expect = 4e-07
 Identities = 13/71 (18%), Positives = 27/71 (38%), Gaps = 6/71 (8%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALREL 289
           + +  L    + + L   FG +GE+KE       + ++     ++ F D    +  L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 290 NSRYIAGKQIK 300
           +   +  K I 
Sbjct: 62  SRHELDSKTID 72

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (111), Expect = 5e-07
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIH-QKYIEFYDTRAAEAALRELNSR- 292
           ++V NL   V+ D LH IF  +G + +I    +    Q  +++ D  +A+ A   L+ + 
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 69

Query: 293 -YIAGKQIKLEPSHLRGLRKCLANQ 316
            Y A   ++++ S L  L     N 
Sbjct: 70  IYNACCTLRIDFSKLTSLNVKYNND 94

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 8e-07
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 7/94 (7%)

Query: 218 YSIPKDNPSEKE---INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIR----ETPQKIH 270
           Y  P+++    +        + +         +    +   YGE++E+          + 
Sbjct: 10  YRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVG 69

Query: 271 QKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS 304
             Y++F     AE A+ +LN+R+  G+ I  E S
Sbjct: 70  NVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.3 bits (107), Expect = 1e-06
 Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 7/76 (9%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALRE 288
            L+V  L    +  +L   F  +GE+  +      +T       ++ F +       + +
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 289 LNSRYIAGKQIKLEPS 304
            +   I G+    +  
Sbjct: 70  RH--MIDGRWCDCKLP 83

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 12/85 (14%), Positives = 24/85 (28%), Gaps = 7/85 (8%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRAS-----KHCGFVTISYYDIRAARNA 200
            +  L++  +     + +LK  F  +G+V               GF  + + +       
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

Query: 201 MKSLQNKLTRSGKLDIHYSIPKDNP 225
           M        R    D      K + 
Sbjct: 67  MSQRHMIDGR--WCDCKLPNSKQSQ 89

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 2e-06
 Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 5/71 (7%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKE-----IRETPQKIHQKYIEFYDTRAAEAALREL 289
           L +  L    ++ +L  +   YG+I        + T +     +++F    AA+ A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 290 NSRYIAGKQIK 300
            +  +  +  K
Sbjct: 61  KASGVQAQMAK 71

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 45.3 bits (106), Expect = 3e-06
 Identities = 24/127 (18%), Positives = 52/127 (40%), Gaps = 13/127 (10%)

Query: 189 ISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDNPSEKEINQGTLVVFNLDSSVSNDE 248
           +S YD       ++ LQ +  +         IP    + +      L+V  + ++V   +
Sbjct: 7   VSQYDPYGQTAQLQQLQQQQQQH--------IPPTQMNPEPDVLRNLMVNYIPTTVDEVQ 58

Query: 249 LHHIFGVYGEIKEIRETPQKIHQ-----KYIEFYDTRAAEAALRELNSRYIAGKQIKLEP 303
           L  +F  YG I+ ++    +  +      +++F    +A+ A+  LN   I  K++K+  
Sbjct: 59  LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118

Query: 304 SHLRGLR 310
           +     R
Sbjct: 119 AASGHQR 125

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.4 bits (102), Expect = 3e-06
 Identities = 10/71 (14%), Positives = 27/71 (38%), Gaps = 6/71 (8%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYIEFYDTRAAEAALREL 289
           + +  L    +  +L   F  +GE+ +        T +     ++ F ++ + +  + + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 290 NSRYIAGKQIK 300
               + GK I 
Sbjct: 61  KEHKLNGKVID 71

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 7e-06
 Identities = 17/86 (19%), Positives = 40/86 (46%), Gaps = 6/86 (6%)

Query: 224 NPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQ-----KYIEFYD 278
           +P+  + +  ++ V N+    + ++L  IF   G +   R    +         + E+ D
Sbjct: 1   DPA-VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 279 TRAAEAALRELNSRYIAGKQIKLEPS 304
              A +A+R LN R  +G+ ++++ +
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNA 85

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.6 bits (100), Expect = 7e-06
 Identities = 11/71 (15%), Positives = 25/71 (35%), Gaps = 6/71 (8%)

Query: 235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALREL 289
           + V  L      +++   FG +GE++ I         K     +I F +    +  + E 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 290 NSRYIAGKQIK 300
               +   + +
Sbjct: 61  KYHNVGLSKCE 71

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.5 bits (99), Expect = 1e-05
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 4/82 (4%)

Query: 227 EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQ----KYIEFYDTRAA 282
           ++E +   L + NL  S+   EL ++   +G++   R             +     T   
Sbjct: 13  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 72

Query: 283 EAALRELNSRYIAGKQIKLEPS 304
           EA +   N ++I        P+
Sbjct: 73  EAVIGHFNGKFIKTPPGVSAPT 94

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.1 bits (98), Expect = 2e-05
 Identities = 22/92 (23%), Positives = 35/92 (38%), Gaps = 9/92 (9%)

Query: 222 KDNPSEKEINQG----TLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQK 272
           +  P     N G     L + NL   V+  +L  +F  + E K         T +   Q 
Sbjct: 4   RKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 63

Query: 273 YIEFYDTRAAEAALRELNSRYIAGKQIKLEPS 304
           +I F +   A  AL  +N   + GK + +E  
Sbjct: 64  FITFPNKEIAWQALHLVNGYKLYGKILVIEFG 95

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 0.004
 Identities = 14/86 (16%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASK-----HCGFVTISYYDIRAARNA 200
           P++ L L+ ++  + + +L +LF ++ + +      +       G   I++ +   A  A
Sbjct: 17  PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 76

Query: 201 MKSLQNKLTRSGKLDIHYSIPKDNPS 226
           +  +         L I +   K   S
Sbjct: 77  LHLVNGYKLYGKILVIEFGKNKKQRS 102

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.2 bits (96), Expect = 3e-05
 Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
           TL V+  D  ++   L   F  +G I ++       +  ++ +    +A+ A+ ELN   
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLS-MDPPRNCAFVTYEKMESADQAVAELNGTQ 63

Query: 294 IAGKQIKLEPS 304
           +   Q+K+  +
Sbjct: 64  VESVQLKVNIA 74

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
            L + NL  +V+ D+L  +FG        +   +     ++++ D   A  A+  L+ + 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-GYAFVDYPDQNWAIRAIETLSGKV 61

Query: 294 -IAGKQIKLEPSHLRGLR 310
            + GK ++++ S  + LR
Sbjct: 62  ELHGKIMEVDYSVSKKLR 79

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 6e-05
 Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAA 285
           ++G L V  L    +   L  +F  YG+I E+     +  Q+     ++ F +   A+ A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 286 LRELNSRYIAGKQIKLEPS 304
           +  +N + + G+QI+++ +
Sbjct: 64  MMAMNGKSVDGRQIRVDQA 82

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 7e-05
 Identities = 10/71 (14%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
            ++V NL    +  E+H +   Y    +     +     ++   +   A+ A++  +   
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYD--LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64

Query: 294 IAGKQIKLEPS 304
             GK + ++  
Sbjct: 65  FRGKDLIVQLQ 75

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.6 bits (94), Expect = 7e-05
 Identities = 17/96 (17%), Positives = 37/96 (38%), Gaps = 16/96 (16%)

Query: 220 IPKDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-----RETPQKIHQKYI 274
           +P D    K     T+ + NL      + L  +   +G++K +      +T       + 
Sbjct: 1   LPSDVTEGK-----TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 55

Query: 275 EFYDTRAAEAALRELNSRY------IAGKQIKLEPS 304
           +F    AA+  L   +         + G+Q+K++ +
Sbjct: 56  QFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA 91

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.4 bits (94), Expect = 7e-05
 Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 1/81 (1%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ 205
           P+  L +  +  N   + L   F+++G +RT     K   F  I Y  + AA+ A   ++
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMR 74

Query: 206 NKLTRSGKLDIHYSIPKDNPS 226
                     +     K  PS
Sbjct: 75  GFPLGGPDRRLRVDFAKSGPS 95

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 1/68 (1%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRY 293
            L V  L  + S   L   F  +G I+ I             +    AA+AA  ++    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQ-YESLDAAQAACAKMRGFP 77

Query: 294 IAGKQIKL 301
           + G   +L
Sbjct: 78  LGGPDRRL 85

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 7e-05
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 234 TLVVF--NLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS 291
           +LVV    L + VS ++L  +    G +  +   P      +  +  T  ++ A   LN 
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALL-MPPNKPYSFARYRTTEESKRAYVTLNG 78

Query: 292 RYI---AGKQIKLEPSHLRGLR 310
           + +    G++I L  + +  ++
Sbjct: 79  KEVVDDLGQKITLYLNFVEKVQ 100

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 10/72 (13%), Positives = 28/72 (38%), Gaps = 5/72 (6%)

Query: 145 HPSRTLLLRK--INSNIEDSELKALFEQYGDVRT-FYRASKHCGFVTISYYDIRAARNAM 201
           + +++L++    + + +  ++L  + E+ G V       +K   F      +   ++ A 
Sbjct: 16  YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTE--ESKRAY 73

Query: 202 KSLQNKLTRSGK 213
            +L  K      
Sbjct: 74  VTLNGKEVVDDL 85

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 8/72 (11%), Positives = 26/72 (36%), Gaps = 6/72 (8%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQK-----YIEFYDTRAAEAALRE 288
            L +  L    +++ L   F  +G + +         ++     ++ +      +AA+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-N 66

Query: 289 LNSRYIAGKQIK 300
                + G+ ++
Sbjct: 67  ARPHKVDGRVVE 78

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 9/73 (12%)

Query: 143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRA-------SKHCGFVTISYYDIR 195
           +    R L +  ++    D  L++ FEQ+G +             S+  GFVT  Y  + 
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT--YATVE 59

Query: 196 AARNAMKSLQNKL 208
               AM +  +K+
Sbjct: 60  EVDAAMNARPHKV 72

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.3 bits (91), Expect = 1e-04
 Identities = 15/78 (19%), Positives = 37/78 (47%), Gaps = 8/78 (10%)

Query: 234 TLVVFNLDSSVSN-DELHHIFGVYGEIKEI------RETPQKIHQKYIEFYDTRAAEAAL 286
            +++ NL + + + + L   F  +G I++I      +E        ++ F +  +AE AL
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 287 RELNSRYIAGKQIKLEPS 304
            ++N   +  ++I +  +
Sbjct: 66  -QMNRSLLGNREISVSLA 82

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.6 bits (87), Expect = 6e-04
 Identities = 12/62 (19%), Positives = 27/62 (43%), Gaps = 5/62 (8%)

Query: 247 DELHHIFGVYGEIKEIRETPQKIHQK---YIEFYDTRAAEAALRELNSRYIAGKQIKLEP 303
           ++L      +G+I+++       H      + F D   A+  ++ L+ R+  G+QI  + 
Sbjct: 34  EDLRVECSKFGQIRKLL--LFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 91

Query: 304 SH 305
             
Sbjct: 92  WD 93

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 706 TTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNV-GYAFINMTDPSQIVP 764
           + ++I+ +P   T + L   +    +  Y F +   D     ++   A+IN  +   I+ 
Sbjct: 2   SKVVIRRLPPTLTKEQLQEHLQPMPEHDY-FEFFSNDTSLYPHMYARAYINFKNQEDIIL 60

Query: 765 FYQSFNGKKWE-KFNSEKVASLAYA 788
           F   F+G  +      E  A + +A
Sbjct: 61  FRDRFDGYVFLDNKGQEYPAIVEFA 85

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 14/84 (16%), Positives = 32/84 (38%), Gaps = 5/84 (5%)

Query: 146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRAS-----KHCGFVTISYYDIRAARNA 200
               L +  +     D +L  +F  +G+V +              F  +SY +  +A+ A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 201 MKSLQNKLTRSGKLDIHYSIPKDN 224
           ++S+        +L +     K++
Sbjct: 77  IQSMNGFQIGMKRLKVQLKRSKND 100

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 8/74 (10%), Positives = 19/74 (25%), Gaps = 2/74 (2%)

Query: 701 GEDNRTTLMIKNIPNKYTSKMLLAAIDERHKGTYDFIYLPIDFKNKCNVGYAFINMTDPS 760
           G+   T + ++N+P   +   +L                    +     G A +      
Sbjct: 5   GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVC--LKYNEKGMPTGEAMVAFESRD 62

Query: 761 QIVPFYQSFNGKKW 774
           +        N +  
Sbjct: 63  EATAAVIDLNDRPI 76

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.9 bits (82), Expect = 0.003
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 3/80 (3%)

Query: 234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNS-- 291
            + V  L  SV   +L      +G I  +        Q  +EF +  +A+  +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVM-MMPFKRQALVEFENIDSAKECVTFAADVP 75

Query: 292 RYIAGKQIKLEPSHLRGLRK 311
            YIAG+Q     S  + + +
Sbjct: 76  VYIAGQQAFFNYSTSKRITR 95

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 4/75 (5%)

Query: 234 TLVVFNLDSS-VSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALR--ELN 290
            + + +         +L  +   +G I        KI++ +IE   T  A+AA+      
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHL-ILNKINEAFIEMATTEDAQAAVDYYTTT 68

Query: 291 SRYIAGKQIKLEPSH 305
              + GK +++  S 
Sbjct: 69  PALVFGKPVRVHLSQ 83

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 6/30 (20%), Positives = 14/30 (46%)

Query: 273 YIEFYDTRAAEAALRELNSRYIAGKQIKLE 302
           ++EF      + A++ L  R  A + +  +
Sbjct: 62  FVEFTSVFDCQKAMQGLTGRKFANRVVVTK 91

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	876
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.94
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.63
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.63
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.63
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.62
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.62
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.62
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.62
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.61
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.61
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.61
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.61
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.61
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.61
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.61
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.61
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.6
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.6
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.6
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.59
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.59
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.59
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.59
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.59
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.59
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.58
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.58
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.58
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.58
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.58
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.58
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.58
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.57
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.57
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.57
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.57
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.57
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.57
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.57
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.57
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.57
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.56
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.56
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.56
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.56
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.56
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.55
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.55
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.55
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.55
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.55
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.55
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.55
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.55
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.55
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.55
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.55
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.55
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.55
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.55
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.54
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.54
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.54
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.54
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.54
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.54
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.54
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.54
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.54
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.54
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.53
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.53
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.53
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.53
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.53
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.53
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.52
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.52
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.52
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.52
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.52
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.52
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.52
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.51
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.51
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.51
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.51
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.51
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.51
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.51
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.51
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.51
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.51
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.5
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.5
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.5
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.5
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.5
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.5
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.5
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.49
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.49
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.48
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.48
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.48
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.47
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.47
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.47
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.47
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.47
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.47
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.47
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.47
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.47
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.46
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.46
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.46
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.45
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.44
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.44
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.44
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.44
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.43
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.43
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.43
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.43
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.43
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.42
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.42
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.42
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.41
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.41
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.41
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.4
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.4
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.39
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.39
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.39
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.39
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.38
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.38
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.37
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.37
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.36
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.35
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.34
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.34
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.34
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.3
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.29
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.26
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.25
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.24
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.19
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.19
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	99.17
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.16
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.16
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.16
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.11
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.1
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	99.09
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.08
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.96
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.89
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.88
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.86
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.88
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.52
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	95.61
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	94.96
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	94.91
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	86.75
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	81.98

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=3.9e-26  Score=225.08  Aligned_cols=163  Identities=15%  Similarity=0.292  Sum_probs=141.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      .|+|||+|||+++|+++|+++|++||.|.++.     .+++++|||||+|.+.++|++|+.. .+..+.++.+.+....+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhh
Confidence            48999999999999999999999999999887     3678899999999999999999975 55667788888877665


Q ss_pred             CCCCC--ccccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCcee
Q 002823          222 KDNPS--EKEINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYI  294 (876)
Q Consensus       222 k~~~~--ek~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I  294 (876)
                      +....  ......++|||+|||..+++++|+++|+.||.|..+.+     ++.++|||||+|.+.++|.+|++ +++..+
T Consensus        85 ~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~  163 (183)
T d1u1qa_          85 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTV  163 (183)
T ss_dssp             TTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEE
T ss_pred             cccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeE
Confidence            54322  22335679999999999999999999999999999876     35678999999999999999997 799999


Q ss_pred             CCeEEEEEeecCchhHH
Q 002823          295 AGKQIKLEPSHLRGLRK  311 (876)
Q Consensus       295 ~Gr~IkVs~A~~k~~Rr  311 (876)
                      .|++|+|.++.++.+++
T Consensus       164 ~G~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         164 NGHNCEVRKALSKQEMA  180 (183)
T ss_dssp             TTEEEEEEECCCHHHHH
T ss_pred             CCEEEEEEecCCccccc
Confidence            99999999999987553

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.63  E-value=3.7e-16  Score=135.06  Aligned_cols=76  Identities=21%  Similarity=0.318  Sum_probs=70.9

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||.++++++|+++|++||.|+++++     ++..++||||+|.+.++|++|++.|||..+.|++|+|+|++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            357999999999999999999999999999887     456789999999999999999999999999999999999987


Q ss_pred             c
Q 002823          307 R  307 (876)
Q Consensus       307 k  307 (876)
                      +
T Consensus        82 g   82 (82)
T d1b7fa1          82 G   82 (82)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.63  E-value=2.7e-16  Score=135.97  Aligned_cols=75  Identities=23%  Similarity=0.447  Sum_probs=70.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      +++|||+|||+++++++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|+|++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999988     3577899999999999999999999999999999999999976

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=5.1e-16  Score=138.00  Aligned_cols=81  Identities=15%  Similarity=0.215  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+.++|||+|||.++|+++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|++..+.|++|+|+|
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999997     3578999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 002823          219 SIPKDN  224 (876)
Q Consensus       219 A~pk~~  224 (876)
                      |.++..
T Consensus        86 A~~~~~   91 (93)
T d1x5ua1          86 ASAHNK   91 (93)
T ss_dssp             TTTTSC
T ss_pred             cCCCCC
Confidence            988653

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=6.2e-16  Score=133.47  Aligned_cols=75  Identities=27%  Similarity=0.451  Sum_probs=70.3

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||.++++++|+++|++||.|.+|++     .+..+|||||+|.+.++|++|++.|||..+.|++|+|+|++|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            357999999999999999999999999999887     456789999999999999999999999999999999999987

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.62  E-value=3.5e-16  Score=137.65  Aligned_cols=80  Identities=16%  Similarity=0.340  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .....++|||+|||.++|+++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|+
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345678999999999999999999999999999987     357789999999999999999999999999999999999


Q ss_pred             ecCCC
Q 002823          218 YSIPK  222 (876)
Q Consensus       218 ~A~pk  222 (876)
                      |+.+|
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99875

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.62  E-value=7.2e-16  Score=135.58  Aligned_cols=78  Identities=28%  Similarity=0.369  Sum_probs=72.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...+|||+|||.++++++|+++|++||+|++|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+|+.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            4568999999999999999999999999999887     45678999999999999999999999999999999999998


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      +++
T Consensus        86 ~kG   88 (88)
T d1rk8a_          86 VKG   88 (88)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            764

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4.4e-16  Score=137.39  Aligned_cols=80  Identities=18%  Similarity=0.373  Sum_probs=74.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+..+|||+|||.++++++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|+|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45668999999999999999999999999999987     3577899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 002823          219 SIPKD  223 (876)
Q Consensus       219 A~pk~  223 (876)
                      ++|+.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            99875

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=7.1e-16  Score=139.32  Aligned_cols=81  Identities=17%  Similarity=0.289  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .++++|||+|||+++++++|+++|++||.|.+++     .+++++|||||+|.+.++|++|++.|+|..|.|++|+|+|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            4567899999999999999999999999998877     35788999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 002823          220 IPKDNP  225 (876)
Q Consensus       220 ~pk~~~  225 (876)
                      .++.+.
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            987653

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=9.7e-16  Score=135.18  Aligned_cols=81  Identities=28%  Similarity=0.360  Sum_probs=73.5

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...++|||+|||.++++++|+++|+.||.|..|++   ....++||||+|.+.++|.+|++.|+|..+.|++|+|.|+++
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            34569999999999999999999999999999887   234578999999999999999999999999999999999998


Q ss_pred             chhH
Q 002823          307 RGLR  310 (876)
Q Consensus       307 k~~R  310 (876)
                      +..+
T Consensus        86 ~~~~   89 (90)
T d2cqia1          86 PSSQ   89 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            7644

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=4.7e-16  Score=136.95  Aligned_cols=78  Identities=19%  Similarity=0.370  Sum_probs=73.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ..++|||+|||+++++++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|++..+.|++|+|.|+.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            458999999999999999999999999999998     357899999999999999999999999999999999999998


Q ss_pred             CCC
Q 002823          221 PKD  223 (876)
Q Consensus       221 pk~  223 (876)
                      |+.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=3.9e-16  Score=137.49  Aligned_cols=79  Identities=24%  Similarity=0.371  Sum_probs=73.4

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||.++++++|+++|++||+|++|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+|+++
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            569999999999999999999999999999987     466789999999999999999999999999999999999998


Q ss_pred             chhH
Q 002823          307 RGLR  310 (876)
Q Consensus       307 k~~R  310 (876)
                      +..|
T Consensus        85 ~~~k   88 (89)
T d2cqba1          85 MRIK   88 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=3.6e-16  Score=143.28  Aligned_cols=103  Identities=22%  Similarity=0.332  Sum_probs=86.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ...+++|||+|||.++++++|+++|++||.|.+|+  .+++++|||||+|.+.++|.+|++.|+|..|.|+.|+|.|+.+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            35679999999999999999999999999999998  4677899999999999999999999999999999999999865


Q ss_pred             CCCCCccccccceeEeecCCCCCcHHHHHHHhhhcCC
Q 002823          222 KDNPSEKEINQGTLVVFNLDSSVSNDELHHIFGVYGE  258 (876)
Q Consensus       222 k~~~~ek~~~~~tLfV~NLP~svTeedLreiFs~fG~  258 (876)
                      +....            .......++++..+.++||.
T Consensus        84 ~~~~~------------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          84 NRAFQ------------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             HHHTT------------TSCHHHHHHHHHHHHHHHCC
T ss_pred             Cchhh------------hhHHHHHHHHHHHHHHHhCC
Confidence            32211            11122346778888888875

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=1.3e-15  Score=136.56  Aligned_cols=82  Identities=21%  Similarity=0.312  Sum_probs=75.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ..+++|||+|||+++++++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|+++.|.|++|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4567899999999999999999999999999998     35788999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 002823          220 IPKDNPS  226 (876)
Q Consensus       220 ~pk~~~~  226 (876)
                      .++....
T Consensus        86 ~~~~~~~   92 (99)
T d1whwa_          86 TIKKEAS   92 (99)
T ss_dssp             CCCSTTC
T ss_pred             CCCCccC
Confidence            9876544

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=5.7e-16  Score=133.69  Aligned_cols=74  Identities=19%  Similarity=0.450  Sum_probs=70.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ++|||+|||+++++++|+++|++||+|.+++     ..++.+|||||+|.+.++|++|++.|+|..+.|++|+|.|++|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5799999999999999999999999999987     3568899999999999999999999999999999999999986

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=7.5e-16  Score=135.88  Aligned_cols=78  Identities=21%  Similarity=0.244  Sum_probs=72.8

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...+|||+|||.++++++|+++|++||+|.+|++     ++..+|||||+|.+.++|.+|++.|||..+.|++|+|+|++
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            4678999999999999999999999999999887     45678999999999999999999999999999999999999


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      |+.
T Consensus        87 p~~   89 (90)
T d2cq0a1          87 PST   89 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.1e-15  Score=135.74  Aligned_cols=79  Identities=20%  Similarity=0.382  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ..++||||+|||+++|+++|+++|++||+|.+|.     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            4678999999999999999999999999999998     35778999999999999999999999999999999999998


Q ss_pred             CCCC
Q 002823          220 IPKD  223 (876)
Q Consensus       220 ~pk~  223 (876)
                      .+..
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7543

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.4e-15  Score=134.12  Aligned_cols=82  Identities=15%  Similarity=0.362  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe---CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR---ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~---tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ++.+.+||||+|||.++|+++|+++|++||+|..|+.   ....+|||||+|.+.++|++|++.|+|..+.|+.|+|.|+
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            4566789999999999999999999999999999873   3446899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002823          220 IPKDN  224 (876)
Q Consensus       220 ~pk~~  224 (876)
                      .++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            76543

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=1.5e-15  Score=135.12  Aligned_cols=81  Identities=19%  Similarity=0.401  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe------CCCccceEeeecCCHHHHHHHHHHc-cccccCCceee
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYR------ASKHCGFVTISYYDIRAARNAMKSL-QNKLTRSGKLD  215 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~------tgksrGfAFV~F~d~edA~kAl~~L-ng~~l~Gr~L~  215 (876)
                      ...++++|||+|||.++++++|+++|++||.|..|+.      +++++|||||+|.+.++|++|++.| ++..+.|++|+
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~   83 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   83 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEE
Confidence            3456789999999999999999999999999999982      5678999999999999999999998 88999999999


Q ss_pred             EeecCCCC
Q 002823          216 IHYSIPKD  223 (876)
Q Consensus       216 V~~A~pk~  223 (876)
                      |+|+.++.
T Consensus        84 V~~A~~~~   91 (94)
T d2cpha1          84 LEWADSEV   91 (94)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99997754

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=9.8e-16  Score=138.41  Aligned_cols=80  Identities=16%  Similarity=0.323  Sum_probs=74.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      +..+|||+|||.++++++|+++|+.||.|.++++     ++..+|||||+|.+.++|++||+.|||..|.|++|+|+|++
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            4568999999999999999999999999999776     45678999999999999999999999999999999999999


Q ss_pred             CchhH
Q 002823          306 LRGLR  310 (876)
Q Consensus       306 ~k~~R  310 (876)
                      ++..+
T Consensus        97 ~k~~~  101 (102)
T d2cpza1          97 SKNDS  101 (102)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            98755

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.59  E-value=1.5e-15  Score=143.89  Aligned_cols=82  Identities=17%  Similarity=0.350  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ....++|||+|||+++|+++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|+|..|.|++|+|+|
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999987     2578899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002823          219 SIPKDNP  225 (876)
Q Consensus       219 A~pk~~~  225 (876)
                      +.++...
T Consensus       119 a~~~~~~  125 (139)
T d1u6fa1         119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             cCCCCCC
Confidence            9876654

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

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=99.59  E-value=5.4e-16  Score=136.54  Aligned_cols=79  Identities=23%  Similarity=0.370  Sum_probs=72.5

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      .++|||+|||.++++++|+++|++||.|.++++   ...++|||||+|.+.++|++|++.|||..|.|++|+|++++++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            458999999999999999999999999999988   23357999999999999999999999999999999999999876


Q ss_pred             hH
Q 002823          309 LR  310 (876)
Q Consensus       309 ~R  310 (876)
                      +|
T Consensus        88 ~R   89 (89)
T d1cvja2          88 ER   89 (89)
T ss_dssp             TC
T ss_pred             CC
Confidence            54

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=2.4e-15  Score=129.32  Aligned_cols=74  Identities=22%  Similarity=0.405  Sum_probs=69.3

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ++|||+|||+++++++|+++|++||.|.++++    +++.+|||||+|.+.++|.+|++.|||..+.|++|+|+++.+
T Consensus         1 grl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           1 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            47999999999999999999999999999988    556788999999999999999999999999999999999863

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=2.1e-15  Score=134.05  Aligned_cols=79  Identities=23%  Similarity=0.279  Sum_probs=72.8

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...+|||+|||.++++++|+++|++||+|.+|++     ++..+|||||+|.+.++|.+|++.|||..+.|++|+|+|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3569999999999999999999999999999887     45678899999999999999999999999999999999998


Q ss_pred             Cchh
Q 002823          306 LRGL  309 (876)
Q Consensus       306 ~k~~  309 (876)
                      ....
T Consensus        86 ~~~~   89 (93)
T d1h2vz_          86 GFKE   89 (93)
T ss_dssp             CCCT
T ss_pred             CCCC
Confidence            6543

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.7e-15  Score=134.60  Aligned_cols=77  Identities=23%  Similarity=0.310  Sum_probs=72.4

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||..+++++|+++|++||.|++|++     ++..+|||||+|.+.++|++|++.|||..+.|++|+|.|+++
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~   88 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASA   88 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTT
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            468999999999999999999999999999987     467889999999999999999999999999999999999988


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      +.
T Consensus        89 ~~   90 (93)
T d1x5ua1          89 HN   90 (93)
T ss_dssp             TS
T ss_pred             CC
Confidence            64

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=3.3e-15  Score=132.56  Aligned_cols=82  Identities=16%  Similarity=0.326  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .....++|||+|||+++++++|+++|++||+|.+|+   ....++|||||+|.+.++|++|++.|++..+.|++|+|+|+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            344567999999999999999999999999999988   34457899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002823          220 IPKDN  224 (876)
Q Consensus       220 ~pk~~  224 (876)
                      .++..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            88653

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.7e-15  Score=132.26  Aligned_cols=78  Identities=15%  Similarity=0.240  Sum_probs=72.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDN  224 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~  224 (876)
                      ..++|||+|||+++++++|+++|++||.|..+.. .+++|||||+|.+.++|.+|+..|+|..|.|++|+|+|++|++.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~-~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE-EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE-ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            4589999999999999999999999999887765 67899999999999999999999999999999999999998764

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=3e-15  Score=133.07  Aligned_cols=82  Identities=16%  Similarity=0.354  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHcc------ccccCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQ------NKLTRS  211 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Ln------g~~l~G  211 (876)
                      +....++|||+|||+++|+++|+++|++||+|.++.     .+++++|||||+|.+.++|++|++.++      |..+.|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            455678999999999999999999999999999988     356689999999999999999999886      567899


Q ss_pred             ceeeEeecCCCCC
Q 002823          212 GKLDIHYSIPKDN  224 (876)
Q Consensus       212 r~L~V~~A~pk~~  224 (876)
                      ++|+|+|+.++.+
T Consensus        84 r~l~v~~a~~k~~   96 (98)
T d1x4ha1          84 RQLKVDLAVTRDE   96 (98)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCCc
Confidence            9999999988764

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.6e-15  Score=133.37  Aligned_cols=79  Identities=15%  Similarity=0.373  Sum_probs=73.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      ..++|||+|||+++++++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|+++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999999887     457789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 002823          221 PKDN  224 (876)
Q Consensus       221 pk~~  224 (876)
                      ++.+
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.58  E-value=1.1e-15  Score=131.82  Aligned_cols=74  Identities=18%  Similarity=0.165  Sum_probs=66.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      +||||+|||+++|+++|+++|++||.|..++     ..++++|||||+|.+.++|++|++.|+|+.+.|++|+|+++.|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999997665     4678999999999999999999999999999999999999987

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.58  E-value=2.9e-15  Score=130.14  Aligned_cols=78  Identities=14%  Similarity=0.270  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcccccc-CCceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLT-RSGKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l-~Gr~L~V~~A~  220 (876)
                      ...|+++|||+|||.++++++|+++|++||+|..++.....+|||||+|.+.++|.+|++.|+|..+ .|++|+|.|++
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            4567899999999999999999999999999999997677789999999999999999999999988 46899999985

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

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=99.58  E-value=2.1e-15  Score=130.19  Aligned_cols=73  Identities=30%  Similarity=0.374  Sum_probs=68.8

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .|||+|||+.+|+++|+++|++||+|.+|++     ++.++|||||+|.+.++|.+|++.|+|..+.|++|+|.|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            5999999999999999999999999999887     456789999999999999999999999999999999999964

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=4.9e-15  Score=131.48  Aligned_cols=79  Identities=19%  Similarity=0.356  Sum_probs=72.4

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...++|||+|||.++++++|+++|++||+|++|++   ...+++||||+|.+.++|.+|++.|||..+.|++|+|+|+++
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~   88 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   88 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCc
Confidence            34668999999999999999999999999999887   334689999999999999999999999999999999999998


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      +.
T Consensus        89 r~   90 (93)
T d2cq3a1          89 RV   90 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.58  E-value=1.3e-15  Score=135.80  Aligned_cols=81  Identities=23%  Similarity=0.334  Sum_probs=76.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      ..++++|||+|||.++|+++|+++|++||.|..++.++++++||||+|.+.++|++|++.|++..|.|++|+|.|+.++.
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            45578999999999999999999999999999999889999999999999999999999999999999999999999876


Q ss_pred             C
Q 002823          224 N  224 (876)
Q Consensus       224 ~  224 (876)
                      .
T Consensus        93 ~   93 (96)
T d1fjca_          93 G   93 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3e-15  Score=131.24  Aligned_cols=77  Identities=26%  Similarity=0.335  Sum_probs=71.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-eCCCccceEeeecCCHHHHHHHHHHcccccc-CCceeeEeecCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-RASKHCGFVTISYYDIRAARNAMKSLQNKLT-RSGKLDIHYSIP  221 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-~tgksrGfAFV~F~d~edA~kAl~~Lng~~l-~Gr~L~V~~A~p  221 (876)
                      .|+++|||+|||.++++++|+++|++||.|..+. ...+.+|||||+|.+.++|.+|+..|+|..+ .|++|+|.|+++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            5789999999999999999999999999997776 5677899999999999999999999999988 589999999875

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=2.5e-15  Score=133.77  Aligned_cols=78  Identities=22%  Similarity=0.391  Sum_probs=72.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe------cCCcccEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEEe
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE------TPQKIHQKYIEFYDTRAAEAALREL-NSRYIAGKQIKLEP  303 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri------tg~skG~AFVeF~d~E~A~kAL~~L-nG~~I~Gr~IkVs~  303 (876)
                      ...+|||+|||.++++++|+++|++||.|.+|++      ++..+|||||+|.+.++|.+|++.| ||..+.|++|+|+|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            4568999999999999999999999999999987      3457899999999999999999998 89999999999999


Q ss_pred             ecCch
Q 002823          304 SHLRG  308 (876)
Q Consensus       304 A~~k~  308 (876)
                      +..+.
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98764

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.5e-15  Score=133.65  Aligned_cols=78  Identities=23%  Similarity=0.418  Sum_probs=72.4

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||+++++++|+++|++||.|..+.+     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+++.+
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            567999999999999999999999999999876     566789999999999999999999999999999999999988


Q ss_pred             chh
Q 002823          307 RGL  309 (876)
Q Consensus       307 k~~  309 (876)
                      +..
T Consensus        85 ~~~   87 (90)
T d1x5sa1          85 SSD   87 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.57  E-value=1.5e-15  Score=135.48  Aligned_cols=81  Identities=27%  Similarity=0.322  Sum_probs=76.1

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCchh
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~  309 (876)
                      ...++|||+|||.++++++|+++|++||.|..++.++..++||||+|.+.++|++|++.|||..|.|++|+|.|+.++..
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            34679999999999999999999999999999998889999999999999999999999999999999999999998764


Q ss_pred             H
Q 002823          310 R  310 (876)
Q Consensus       310 R  310 (876)
                      +
T Consensus        94 ~   94 (96)
T d1fjca_          94 T   94 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=6.8e-16  Score=139.46  Aligned_cols=81  Identities=21%  Similarity=0.350  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .++..+||||+|||+++++++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|++.|++..+.|++|+|+
T Consensus         4 ~~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~   83 (104)
T d1p1ta_           4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             SHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345568999999999999999999999999999887     357789999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 002823          218 YSIPKD  223 (876)
Q Consensus       218 ~A~pk~  223 (876)
                      |+.++.
T Consensus        84 ~a~~~~   89 (104)
T d1p1ta_          84 NAASEK   89 (104)
T ss_dssp             ETTCTT
T ss_pred             ECCCCC
Confidence            987654

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.57  E-value=3.5e-15  Score=129.63  Aligned_cols=76  Identities=21%  Similarity=0.294  Sum_probs=71.3

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEeec
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIA-GKQIKLEPSH  305 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~-Gr~IkVs~A~  305 (876)
                      ++.++|||+|||..+++++|+++|++||.|++|++....++||||+|.+.++|.+|++.|+|..|. |++|+|+|++
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            456799999999999999999999999999999997778899999999999999999999999884 6999999997

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

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=99.57  E-value=2.2e-15  Score=132.63  Aligned_cols=78  Identities=13%  Similarity=0.294  Sum_probs=71.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      ..+|||+|||+++++++|+++|++||.|..++   ....++|||||+|.+.++|++|++.|+|+.+.|++|.|.++.++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            45899999999999999999999999999988   334578999999999999999999999999999999999998775


Q ss_pred             C
Q 002823          224 N  224 (876)
Q Consensus       224 ~  224 (876)
                      +
T Consensus        88 ~   88 (89)
T d1cvja2          88 E   88 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2e-15  Score=130.88  Aligned_cols=73  Identities=14%  Similarity=0.327  Sum_probs=68.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeE
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDI  216 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V  216 (876)
                      +.|+++|||+|||+++|+++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|++..+.|++|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            45678999999999999999999999999999987     35788999999999999999999999999999999987

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=3.8e-15  Score=133.45  Aligned_cols=78  Identities=24%  Similarity=0.451  Sum_probs=72.6

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||+|||..+++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|.+++
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            3568999999999999999999999999999987     45678999999999999999999999999999999999999


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      ++.
T Consensus        87 ~~~   89 (99)
T d1whwa_          87 IKK   89 (99)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            864

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.1e-15  Score=131.81  Aligned_cols=76  Identities=18%  Similarity=0.347  Sum_probs=71.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      .+|||+|||+++|+++|+++|++||+|.+++     .+++++|||||+|.++++|++|++.|++..+.|++|.|.|+.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            4799999999999999999999999999987     35789999999999999999999999999999999999999765


Q ss_pred             C
Q 002823          223 D  223 (876)
Q Consensus       223 ~  223 (876)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=5e-15  Score=131.79  Aligned_cols=79  Identities=14%  Similarity=0.260  Sum_probs=72.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      ..+.++|||+|||+++|+++|+++|++||.|..++  .....++||||+|.+.++|++|++.|+++.|.|++|+|+|+++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            35567999999999999999999999999999988  3466899999999999999999999999999999999999876


Q ss_pred             C
Q 002823          222 K  222 (876)
Q Consensus       222 k  222 (876)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

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=99.56  E-value=2.2e-15  Score=130.00  Aligned_cols=72  Identities=13%  Similarity=0.309  Sum_probs=68.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          149 TLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       149 TLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      +|||+|||+++|+++|+++|++||+|.+++     .+++++|||||+|.++++|++|++.|+|..+.|++|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            799999999999999999999999999998     357789999999999999999999999999999999999984

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=4.1e-15  Score=136.16  Aligned_cols=77  Identities=25%  Similarity=0.382  Sum_probs=72.0

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      .++|||+|||.++++++|+++|++||.|++|++  ++..+|||||+|.+.++|.+|++.|||..|.|++|+|.|+.+..
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   85 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANR   85 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            568999999999999999999999999999988  56678999999999999999999999999999999999987643

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.56  E-value=3.7e-15  Score=141.24  Aligned_cols=77  Identities=23%  Similarity=0.346  Sum_probs=71.8

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||.++++++|+++|++||+|++|++     ++.++|||||+|.+.++|.+||+.|||..|.|++|+|+|+++
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~  121 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS  121 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            458999999999999999999999999999887     456789999999999999999999999999999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      +.
T Consensus       122 ~~  123 (139)
T d1u6fa1         122 GH  123 (139)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.56  E-value=3.3e-15  Score=128.79  Aligned_cols=74  Identities=16%  Similarity=0.147  Sum_probs=66.5

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .+|||+|||.++|+++|+++|++||.|..+.+     .+.++|||||+|.+.++|.+|++.|||..+.|++|+|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            58999999999999999999999999987654     466789999999999999999999999999999999999987

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=2.9e-15  Score=135.42  Aligned_cols=79  Identities=18%  Similarity=0.371  Sum_probs=72.0

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...++|||+|||.++++++|+++|+.||+|.+|++     ++.++|||||+|.+.++|.+|++ |||..|.|++|+|.++
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            34568999999999999999999999999999988     46789999999999999999995 9999999999999998


Q ss_pred             cCchh
Q 002823          305 HLRGL  309 (876)
Q Consensus       305 ~~k~~  309 (876)
                      .++..
T Consensus        95 ~~~~n   99 (101)
T d2cq4a1          95 QAEKN   99 (101)
T ss_dssp             HHHHH
T ss_pred             CCCCC
Confidence            76543

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=3.3e-15  Score=129.99  Aligned_cols=74  Identities=23%  Similarity=0.378  Sum_probs=67.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----C---CCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          150 LLLRKINSNIEDSELKALFEQYGDVRTFYR-----A---SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       150 LFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----t---gksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      |||+|||+++|+++|+++|++||+|.+++.     +   +++||||||+|.+.++|++|++.|+|..+.|++|+|+|+.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            899999999999999999999999999872     1   24689999999999999999999999999999999999865


Q ss_pred             CC
Q 002823          222 KD  223 (876)
Q Consensus       222 k~  223 (876)
                      +.
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=2e-15  Score=132.63  Aligned_cols=80  Identities=20%  Similarity=0.399  Sum_probs=73.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDN  224 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~  224 (876)
                      ..+++|||+|||+++|+++|+++|++||+|.+|+....+++||||+|.+.++|++|+.  ++..|.|++|+|.++.++..
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            4678999999999999999999999999999999888899999999999999999985  77889999999999988765


Q ss_pred             CC
Q 002823          225 PS  226 (876)
Q Consensus       225 ~~  226 (876)
                      ..
T Consensus        81 ~~   82 (88)
T d1wf0a_          81 SN   82 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=2.5e-15  Score=135.71  Aligned_cols=82  Identities=21%  Similarity=0.345  Sum_probs=74.7

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||+|||.++++++|+++|++||+|.+|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+|+.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            4568999999999999999999999999999887     45678999999999999999999999999999999999998


Q ss_pred             CchhHHH
Q 002823          306 LRGLRKC  312 (876)
Q Consensus       306 ~k~~Rr~  312 (876)
                      ++..++.
T Consensus        87 ~~~~~~~   93 (104)
T d1p1ta_          87 SEKNKEE   93 (104)
T ss_dssp             CTTHHHH
T ss_pred             CCCCccc
Confidence            8765543

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=5.5e-15  Score=130.82  Aligned_cols=79  Identities=14%  Similarity=0.259  Sum_probs=71.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ...+++|||+|||+++|+++|+++|++||+|..|+     .++++||||||+|.+.++|++|++.+  ..|.|+.|.|++
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~v~~   82 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEEe
Confidence            45678999999999999999999999999999987     36889999999999999999999854  479999999999


Q ss_pred             cCCCCC
Q 002823          219 SIPKDN  224 (876)
Q Consensus       219 A~pk~~  224 (876)
                      +.++..
T Consensus        83 a~~k~~   88 (90)
T d2cqga1          83 PNSKQS   88 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            988764

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=3.8e-15  Score=128.04  Aligned_cols=72  Identities=18%  Similarity=0.378  Sum_probs=68.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          149 TLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       149 TLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      +|||+|||+++++++|+++|++||+|.+++    .+++++|||||+|.+.++|++|++.|+|+.+.|++|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            699999999999999999999999999998    467789999999999999999999999999999999999974

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.2e-15  Score=131.88  Aligned_cols=77  Identities=23%  Similarity=0.299  Sum_probs=70.0

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCc-eeCCeEEEEEeecCchhH
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSR-YIAGKQIKLEPSHLRGLR  310 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~-~I~Gr~IkVs~A~~k~~R  310 (876)
                      .+|||+|||.++++++|+++|++||.|..+++ ...+|||||+|.+.++|.+|++.|||. .+.|++|+|+|+.++.+|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~-~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCE-EEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEE-ecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            36999999999999999999999999987665 346899999999999999999999996 699999999999997654

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.5e-15  Score=136.33  Aligned_cols=82  Identities=16%  Similarity=0.277  Sum_probs=74.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..|+++|||+|||.++++++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++.|+|..|.|++|+|.|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            35789999999999999999999999999876654     4688999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002823          219 SIPKDNP  225 (876)
Q Consensus       219 A~pk~~~  225 (876)
                      +.+++++
T Consensus        95 ak~k~~r  101 (102)
T d2cpxa1          95 GKNKKQR  101 (102)
T ss_dssp             CCCCSCC
T ss_pred             CCCcccC
Confidence            9987653

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=5.3e-15  Score=132.28  Aligned_cols=76  Identities=20%  Similarity=0.286  Sum_probs=71.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ...+|||+|||..+++++|+++|++||.|++|++. ..+|||||+|.+.++|.+|+..|||..|.|++|+|.|++++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~-~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF-PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEE-ecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            34689999999999999999999999999999994 45899999999999999999999999999999999999874

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.55  E-value=4.8e-15  Score=129.19  Aligned_cols=75  Identities=19%  Similarity=0.375  Sum_probs=69.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCC--ceeeEe
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRS--GKLDIH  217 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G--r~L~V~  217 (876)
                      ...++|||+|||+++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.|++..+.|  ++|+|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            3457899999999999999999999999999987     357899999999999999999999999999876  889999


Q ss_pred             ec
Q 002823          218 YS  219 (876)
Q Consensus       218 ~A  219 (876)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=3.3e-15  Score=133.61  Aligned_cols=84  Identities=21%  Similarity=0.310  Sum_probs=74.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-------------eCCCccceEeeecCCHHHHHHHHHHcccc
Q 002823          141 LNDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-------------RASKHCGFVTISYYDIRAARNAMKSLQNK  207 (876)
Q Consensus       141 p~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-------------~tgksrGfAFV~F~d~edA~kAl~~Lng~  207 (876)
                      |.++...++|||+|||.++|+++|+++|++||+|..+.             .+++.+|||||+|.+.++|++|++.|+|.
T Consensus         2 p~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           2 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC
Confidence            33556678999999999999999999999999885432             24678999999999999999999999999


Q ss_pred             ccCCceeeEeecCCCCC
Q 002823          208 LTRSGKLDIHYSIPKDN  224 (876)
Q Consensus       208 ~l~Gr~L~V~~A~pk~~  224 (876)
                      .|.|++|+|+++.++..
T Consensus        82 ~~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          82 DFQGSKLKVSLARKKPP   98 (101)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             EECCEEEEEEEcCCCCC
Confidence            99999999999987654

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=5.5e-15  Score=132.15  Aligned_cols=77  Identities=13%  Similarity=0.208  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      +.++|||+|||.++++++|+++|++||+|.+|+. .+.||||||+|.+.++|++|+..|+|+.|.|++|+|.|++++.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i-~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEE-EecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            4579999999999999999999999999999996 3569999999999999999999999999999999999997654

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=3.2e-15  Score=132.05  Aligned_cols=80  Identities=23%  Similarity=0.450  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHH----HhhccCCeEEEEe--CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          145 HPSRTLLLRKINSNIEDSELKA----LFEQYGDVRTFYR--ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~e----lFsqfG~I~sV~~--tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      +|++||||+|||+++++++|++    +|++||+|.+|+.  +++++|||||+|.+.++|.+|++.++|..+.|+.|+|.|
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4789999999999999999864    6899999999983  456899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 002823          219 SIPKDN  224 (876)
Q Consensus       219 A~pk~~  224 (876)
                      +.++.+
T Consensus        81 ak~~~~   86 (91)
T d1nu4a_          81 AKTDSD   86 (91)
T ss_dssp             CSSCCT
T ss_pred             eCCCch
Confidence            987653

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=9.8e-15  Score=129.88  Aligned_cols=77  Identities=23%  Similarity=0.340  Sum_probs=71.4

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ...+|||+|||.++++++|+++|++||.|+.+++  +...++||||+|.+.++|++|++.|||..|.|++|+|+|+++.
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            3558999999999999999999999999999887  4567899999999999999999999999999999999999864

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=3.8e-15  Score=135.30  Aligned_cols=77  Identities=12%  Similarity=0.203  Sum_probs=71.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      +..++|||+|||+++++++|+++|++||+|..|.+ .+.+|||||+|.+.++|++|++.|||..|.|++|.|+|+...
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l-~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEe-eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            45589999999999999999999999999999987 568899999999999999999999999999999999998654

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=7.2e-15  Score=133.43  Aligned_cols=77  Identities=18%  Similarity=0.254  Sum_probs=72.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..++|||+|||..+++++|+++|++||+|..|++ +..++||||+|.+.++|.+|++.|||..|.|++|+|+|+....
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l-~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEe-eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            4569999999999999999999999999999998 6678999999999999999999999999999999999997643

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=5.1e-15  Score=133.29  Aligned_cols=78  Identities=12%  Similarity=0.205  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      +...++|||+|||+++++++|+++|++||+|..+.    .+++++|||||+|.+.++|++|++.|||+.|.|+++.|.++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            44568999999999999999999999999998876    45678999999999999999999999999999999999887


Q ss_pred             CC
Q 002823          220 IP  221 (876)
Q Consensus       220 ~p  221 (876)
                      .|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=3.4e-15  Score=129.35  Aligned_cols=75  Identities=21%  Similarity=0.384  Sum_probs=68.5

Q ss_pred             eEeecCCCCCcHHHHHHHhhhcCCeEEE-Ee-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          235 LVVFNLDSSVSNDELHHIFGVYGEIKEI-RE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       235 LfV~NLP~svTeedLreiFs~fG~I~sV-ri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      |||+|||.++++++|+++|++||.|..+ ++     +++++|||||+|.+.++|.+|++.|+|..+.|++|+|+|+.+++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998653 44     45678999999999999999999999999999999999999876


Q ss_pred             h
Q 002823          309 L  309 (876)
Q Consensus       309 ~  309 (876)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=2.7e-15  Score=129.97  Aligned_cols=75  Identities=15%  Similarity=0.380  Sum_probs=68.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEE-E-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          150 LLLRKINSNIEDSELKALFEQYGDVRTF-Y-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       150 LFVgNLP~~vTEeeL~elFsqfG~I~sV-~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      |||+|||+++|+++|+++|++||.|..+ +     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|+|+.+++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            8999999999999999999999998553 2     357889999999999999999999999999999999999998875


Q ss_pred             C
Q 002823          224 N  224 (876)
Q Consensus       224 ~  224 (876)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=1.1e-14  Score=126.17  Aligned_cols=71  Identities=21%  Similarity=0.378  Sum_probs=66.5

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKL  301 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkV  301 (876)
                      +.++|||+|||.++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4679999999999999999999999999999887     4567899999999999999999999999999999987

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=6e-15  Score=128.31  Aligned_cols=73  Identities=22%  Similarity=0.393  Sum_probs=67.1

Q ss_pred             eEeecCCCCCcHHHHHHHhhhcCCeEEEEec-----C---CcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRET-----P---QKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       235 LfV~NLP~svTeedLreiFs~fG~I~sVrit-----g---~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      |||+|||.++++++|+++|++||.|++|++.     +   .++|||||+|.+.++|.+|++.|||..+.|++|+|+|+++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999998771     1   2478999999999999999999999999999999999875


Q ss_pred             c
Q 002823          307 R  307 (876)
Q Consensus       307 k  307 (876)
                      +
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=6.2e-15  Score=128.70  Aligned_cols=73  Identities=21%  Similarity=0.331  Sum_probs=67.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCC--ceeeEeec
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRS--GKLDIHYS  219 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G--r~L~V~~A  219 (876)
                      .++|||+|||+++|+++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.|+|..+.|  ++|+|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            46899999999999999999999999999987     257799999999999999999999999999987  56899886

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=2.3e-15  Score=130.06  Aligned_cols=77  Identities=18%  Similarity=0.264  Sum_probs=69.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcccc-ccCCceeeEeecCCCCCC
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNK-LTRSGKLDIHYSIPKDNP  225 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~-~l~Gr~L~V~~A~pk~~~  225 (876)
                      .+|||+|||.++|+++|+++|++||.|.+++. .+.+|||||+|.+.++|++|++.|+|. .+.|++|+|+|+.|+...
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~-~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCE-EEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEE-ecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            37999999999999999999999999877654 457899999999999999999999996 599999999999987653

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=8.5e-15  Score=128.28  Aligned_cols=77  Identities=19%  Similarity=0.247  Sum_probs=70.2

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-cCCcccEEEEEecCHHHHHHHHHHhCCcee-CCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-TPQKIHQKYIEFYDTRAAEAALRELNSRYI-AGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-tg~skG~AFVeF~d~E~A~kAL~~LnG~~I-~Gr~IkVs~A~~k  307 (876)
                      ++++|||+|||.++++++|+++|++||.|..+++ .++.++||||+|.+.++|.+|+..|+|..+ .|++|+|+|+++.
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            4679999999999999999999999999987654 667789999999999999999999999998 5899999999863

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=1.1e-14  Score=131.70  Aligned_cols=80  Identities=18%  Similarity=0.301  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      +...++|||+|||+.+++++|+++|++||+|.+++     .+++++|||||+|.+.++|++|++.+++ .|.|++|+|++
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEE
Confidence            34457899999999999999999999999999998     3578999999999999999999998875 69999999999


Q ss_pred             cCCCCC
Q 002823          219 SIPKDN  224 (876)
Q Consensus       219 A~pk~~  224 (876)
                      +.++..
T Consensus        86 a~~~~~   91 (103)
T d2cqda1          86 AYLGAK   91 (103)
T ss_dssp             STTTCC
T ss_pred             cCCCCC
Confidence            976644

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=9e-15  Score=127.56  Aligned_cols=76  Identities=20%  Similarity=0.202  Sum_probs=71.3

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      .++|||+|||.++++++|+++|++||.|..+++ ...+|||||+|.+.++|.+|+..|||..|.|++|+|+|++|++
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~-~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE-EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE-ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            468999999999999999999999999888776 5678999999999999999999999999999999999999865

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=4.1e-15  Score=129.93  Aligned_cols=75  Identities=16%  Similarity=0.324  Sum_probs=70.6

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      +|||+|||..+++++|+++|++||+|++|++     ++.++|||||+|.+.++|.+|++.|||..+.|++|+|+|+.+..
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            6999999999999999999999999999887     46778999999999999999999999999999999999998753

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=7e-15  Score=133.25  Aligned_cols=77  Identities=27%  Similarity=0.483  Sum_probs=71.2

Q ss_pred             cceeEeecCCC-CCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          232 QGTLVVFNLDS-SVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       232 ~~tLfV~NLP~-svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..+|||+||++ .+++++|+++|+.||+|+.|++....+|||||+|+++++|.+|++.|||..|.|++|+|+|++.+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            46899999965 599999999999999999999977789999999999999999999999999999999999987543

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=9.6e-15  Score=127.45  Aligned_cols=73  Identities=27%  Similarity=0.392  Sum_probs=67.3

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEee
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG--KQIKLEPS  304 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G--r~IkVs~A  304 (876)
                      ..+|||+|||..+++++|+++|++||+|+++++     ++.++|||||+|.+.++|++|++.|||..+.|  ++|+|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            457999999999999999999999999999887     45678999999999999999999999999987  66999986

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.53  E-value=4.7e-15  Score=129.77  Aligned_cols=76  Identities=14%  Similarity=0.332  Sum_probs=67.3

Q ss_pred             CCcEEEEcCCCCCCC-HHHHHHHhhccCCeEEEE------eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          146 PSRTLLLRKINSNIE-DSELKALFEQYGDVRTFY------RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       146 pSrTLFVgNLP~~vT-EeeL~elFsqfG~I~sV~------~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..++|||+|||++++ +++|+++|++||+|.+++      .+++++|||||+|.+.++|++|++ |++..+.|++|+|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            368999999999986 566999999999999997      256789999999999999999995 999999999999999


Q ss_pred             cCCC
Q 002823          219 SIPK  222 (876)
Q Consensus       219 A~pk  222 (876)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9876

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.53  E-value=1.1e-14  Score=126.81  Aligned_cols=73  Identities=25%  Similarity=0.428  Sum_probs=67.7

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEee
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG--KQIKLEPS  304 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G--r~IkVs~A  304 (876)
                      .++|||+|||.++++++|+++|++||+|.++++     ++.++|||||+|.+.++|.+|++.|||..+.|  ++|+|+||
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            457999999999999999999999999999886     45678999999999999999999999999976  89999986

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=7.8e-15  Score=126.33  Aligned_cols=75  Identities=15%  Similarity=0.264  Sum_probs=69.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ..++||||+||+  +|+++|+++|++||+|.+++. .+.++||||+|.+.++|.+|++.|+|..+.|++|+|.|++++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~-~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeee-ccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            456899999996  999999999999999999986 567899999999999999999999999999999999999765

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=8.2e-15  Score=128.92  Aligned_cols=78  Identities=14%  Similarity=0.232  Sum_probs=68.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCCC
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKDN  224 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~~  224 (876)
                      ..+++|||+|||++++++||+++|++|| ++.+.. .+.+|||||+|.+.++|++|++.|+++.+.|++|+|+|+..+..
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~-~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~~   80 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDAL   80 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            3467999999999999999999999999 222332 56899999999999999999999999999999999999966543

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.5e-14  Score=131.12  Aligned_cols=77  Identities=22%  Similarity=0.252  Sum_probs=71.0

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          147 SRTLLLRKINS-NIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       147 SrTLFVgNLP~-~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      +++|||+|||+ .+|+++|+++|++||+|..|++....+|||||+|.+.++|++|++.|+|..|.|+.|+|+|+..+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            57999999965 599999999999999999999766778999999999999999999999999999999999986543

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=2.5e-14  Score=127.79  Aligned_cols=79  Identities=20%  Similarity=0.344  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCC--ceeeEeecCC
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRS--GKLDIHYSIP  221 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~G--r~L~V~~A~p  221 (876)
                      ..|+++|||+|||+++++++|+++|++||+|..++. .+.++||||+|.+.++|++|++.|++..|.|  ++|+|+|+++
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~-~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~   92 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEE-CSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEee-eccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCC
Confidence            357899999999999999999999999999999986 4568999999999999999999999999976  5899999976


Q ss_pred             CC
Q 002823          222 KD  223 (876)
Q Consensus       222 k~  223 (876)
                      ..
T Consensus        93 ~~   94 (97)
T d1whya_          93 GP   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.1e-14  Score=131.71  Aligned_cols=79  Identities=22%  Similarity=0.302  Sum_probs=71.2

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEP  303 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~  303 (876)
                      +...++|||+|||..+++++|+++|++||+|++|++     ++.++|||||+|.+.++|++|++.+++ .|.|++|+|.+
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEE
Confidence            344568999999999999999999999999999988     456789999999999999999998876 79999999999


Q ss_pred             ecCch
Q 002823          304 SHLRG  308 (876)
Q Consensus       304 A~~k~  308 (876)
                      +..+.
T Consensus        86 a~~~~   90 (103)
T d2cqda1          86 AYLGA   90 (103)
T ss_dssp             STTTC
T ss_pred             cCCCC
Confidence            98754

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=9e-15  Score=132.63  Aligned_cols=77  Identities=13%  Similarity=0.239  Sum_probs=71.2

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      .++|||+|||.++++++|+++|++||+|..+++     ++..+|||||+|.+.++|.+|++ +++..|.|++|.|.++.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            468999999999999999999999999999887     45678999999999999999996 799999999999999998


Q ss_pred             chh
Q 002823          307 RGL  309 (876)
Q Consensus       307 k~~  309 (876)
                      +++
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=1.1e-14  Score=127.53  Aligned_cols=76  Identities=24%  Similarity=0.377  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      .++|||+|||.++++++|+++|++||+|.+|+. .+.++||||+|.+.++|++|++.|+|..+.|++|+|+|+.++.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~-~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEE-ETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeee-ecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            457999999999999999999999999999986 4678999999999999999999999999999999999998764

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=3.8e-15  Score=133.60  Aligned_cols=80  Identities=25%  Similarity=0.260  Sum_probs=73.4

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      +.++|||+|||.++++++|+++|++||.|..+++     ++..++||||+|.+.++|.+|++.|||..|.|++|+|+|++
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            4679999999999999999999999999877543     57789999999999999999999999999999999999999


Q ss_pred             CchhH
Q 002823          306 LRGLR  310 (876)
Q Consensus       306 ~k~~R  310 (876)
                      ++++|
T Consensus        97 ~k~~r  101 (102)
T d2cpxa1          97 NKKQR  101 (102)
T ss_dssp             CCSCC
T ss_pred             CcccC
Confidence            97654

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.51  E-value=1.1e-14  Score=127.41  Aligned_cols=75  Identities=19%  Similarity=0.340  Sum_probs=66.8

Q ss_pred             cceeEeecCCCCCc-HHHHHHHhhhcCCeEEEEe------cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          232 QGTLVVFNLDSSVS-NDELHHIFGVYGEIKEIRE------TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       232 ~~tLfV~NLP~svT-eedLreiFs~fG~I~sVri------tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      .++|||+|||.+++ +++|+++|++||.|.+|++      ++..+|||||+|.+.++|++|++ |||..+.|++|+|+++
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEc
Confidence            56899999999986 5669999999999999987      34568899999999999999996 9999999999999999


Q ss_pred             cCc
Q 002823          305 HLR  307 (876)
Q Consensus       305 ~~k  307 (876)
                      +++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=8.2e-15  Score=128.38  Aligned_cols=76  Identities=24%  Similarity=0.341  Sum_probs=70.8

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..+|||+|||.++++++|+++|++||+|.+|++. ..++||||+|.+.++|.+|++.|||..|.|++|+|+|+..+.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~-~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeee-cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            3579999999999999999999999999999984 468999999999999999999999999999999999998753

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.2e-14  Score=130.51  Aligned_cols=74  Identities=22%  Similarity=0.357  Sum_probs=68.5

Q ss_pred             ccceeEeecCC-CCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLD-SSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP-~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      ...+|||+||| ..+++++|+++|++||.|++|++   .++||||+|.+.++|++|++.|||..|.|++|+|+|++++
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            45589999997 56888999999999999999998   6899999999999999999999999999999999999764

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=2.2e-14  Score=129.26  Aligned_cols=80  Identities=14%  Similarity=0.295  Sum_probs=70.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE------eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY------RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~------~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      ..|.++|||+|||+++|+++|+++|++|| |..++      .+++.+|||||+|.+.++|++|+ .|++..|.|++|+|.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEE
Confidence            45779999999999999999999999999 55555      35678999999999999998776 699999999999999


Q ss_pred             ecCCCCCC
Q 002823          218 YSIPKDNP  225 (876)
Q Consensus       218 ~A~pk~~~  225 (876)
                      ++.++...
T Consensus        90 ~a~~~~~~   97 (104)
T d1wi8a_          90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99887654

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.4e-14  Score=131.79  Aligned_cols=83  Identities=17%  Similarity=0.205  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-eCCCccceEeeecCCHHHHHHHHHHcccccc--CCceeeEeec
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-RASKHCGFVTISYYDIRAARNAMKSLQNKLT--RSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-~tgksrGfAFV~F~d~edA~kAl~~Lng~~l--~Gr~L~V~~A  219 (876)
                      .+.+..+|||+|||.++|+++|+++|++||.|..++ ...+.+|||||+|.+.++|++|++.|+|..|  .+++|+|.|+
T Consensus         3 ~~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           3 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             CCCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             CCCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            456788999999999999999999999999999987 3456789999999999999999999999998  5789999999


Q ss_pred             CCCCCC
Q 002823          220 IPKDNP  225 (876)
Q Consensus       220 ~pk~~~  225 (876)
                      .++...
T Consensus        83 ~~~~~~   88 (108)
T d2adba1          83 KLTSLN   88 (108)
T ss_dssp             SSCSCC
T ss_pred             CCcccc
Confidence            876543

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=2.5e-14  Score=125.31  Aligned_cols=81  Identities=25%  Similarity=0.278  Sum_probs=72.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcc--ccccCCceeeEeec
Q 002823          142 NDEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ--NKLTRSGKLDIHYS  219 (876)
Q Consensus       142 ~~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Ln--g~~l~Gr~L~V~~A  219 (876)
                      .+..|+++|||+|||.++++++|+++|++||.|.+++. .+.++||||+|.+.++|++|++.++  +..+.|++|+|.|+
T Consensus         3 ~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~-~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~s   81 (88)
T d2cq1a1           3 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS   81 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccc-cccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEEC
Confidence            35679999999999999999999999999999999986 4678999999999999999998765  56799999999999


Q ss_pred             CCCC
Q 002823          220 IPKD  223 (876)
Q Consensus       220 ~pk~  223 (876)
                      ..+.
T Consensus        82 k~~~   85 (88)
T d2cq1a1          82 NHKE   85 (88)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            7654

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1e-14  Score=130.39  Aligned_cols=79  Identities=22%  Similarity=0.322  Sum_probs=70.5

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEE--------EEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCC
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKE--------IRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAG  296 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~s--------Vri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G  296 (876)
                      ....+|||+|||..+++++|+++|+.||.|..        +++     ++..++||||+|.+.++|.+|++.|||..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            34679999999999999999999999999854        222     35678999999999999999999999999999


Q ss_pred             eEEEEEeecCch
Q 002823          297 KQIKLEPSHLRG  308 (876)
Q Consensus       297 r~IkVs~A~~k~  308 (876)
                      ++|+|++++++.
T Consensus        86 r~i~V~~a~~~~   97 (101)
T d2cpea1          86 SKLKVSLARKKP   97 (101)
T ss_dssp             EECEEECSSCCC
T ss_pred             EEEEEEEcCCCC
Confidence            999999998864

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.1e-14  Score=125.34  Aligned_cols=73  Identities=21%  Similarity=0.354  Sum_probs=68.4

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      .++|||+|++  +|+++|+++|++||+|.+|++ .+.++||||+|.+.++|.+|++.|||..+.|++|+|+|++++
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~-~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeee-ccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            4689999996  899999999999999999998 456889999999999999999999999999999999999875

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.4e-14  Score=127.90  Aligned_cols=80  Identities=23%  Similarity=0.347  Sum_probs=71.7

Q ss_pred             ccceeEeecCCCCCcHHHHHH----HhhhcCCeEEEEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          231 NQGTLVVFNLDSSVSNDELHH----IFGVYGEIKEIRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLre----iFs~fG~I~sVri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +.++|||+|||..++++||++    +|++||+|.+|++  ++..+|||||+|.+.++|.+|++.|||..+.|++|+|.|+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            357999999999999999864    6899999999988  3456899999999999999999999999999999999999


Q ss_pred             cCchhH
Q 002823          305 HLRGLR  310 (876)
Q Consensus       305 ~~k~~R  310 (876)
                      +++...
T Consensus        82 k~~~~~   87 (91)
T d1nu4a_          82 KTDSDI   87 (91)
T ss_dssp             SSCCTH
T ss_pred             CCCchh
Confidence            987543

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=2.8e-14  Score=126.68  Aligned_cols=77  Identities=21%  Similarity=0.354  Sum_probs=70.3

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhC------CceeCCeEEE
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELN------SRYIAGKQIK  300 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~Ln------G~~I~Gr~Ik  300 (876)
                      .++|||+|||.++++++|+++|++||.|.++++     .+.++|||||+|.+.++|.+|++.|+      |..+.|++|+
T Consensus         8 ~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~   87 (98)
T d1x4ha1           8 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLK   87 (98)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEE
Confidence            568999999999999999999999999999887     44578999999999999999999986      6788999999


Q ss_pred             EEeecCch
Q 002823          301 LEPSHLRG  308 (876)
Q Consensus       301 Vs~A~~k~  308 (876)
                      |+|+.++.
T Consensus        88 v~~a~~k~   95 (98)
T d1x4ha1          88 VDLAVTRD   95 (98)
T ss_dssp             EECCCCCC
T ss_pred             EEECCCCC
Confidence            99999865

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.50  E-value=3.6e-15  Score=132.13  Aligned_cols=78  Identities=13%  Similarity=0.170  Sum_probs=70.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      +...++|||+|||+++++++|+++|++||.|..++    .+++++|||||+|.+.++|++|++ |++..+.|++|+|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            45568999999999999999999999999876654    568899999999999999999995 9999999999999998


Q ss_pred             CCC
Q 002823          220 IPK  222 (876)
Q Consensus       220 ~pk  222 (876)
                      .+|
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            764

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=6.4e-15  Score=129.43  Aligned_cols=76  Identities=16%  Similarity=0.288  Sum_probs=71.2

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ..++|||+|||.++++++|+++|++||+|.+|++...+++||||+|.+.++|++|+.  ++..|.|++|+|++++++.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~   79 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCC
Confidence            356999999999999999999999999999999988889999999999999999985  8899999999999998765

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=2e-14  Score=125.40  Aligned_cols=75  Identities=17%  Similarity=0.338  Sum_probs=68.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ...++|||+|||+++|+++|+++|++||+|..++     .+++++|||||+|.+.++|++|++ +++..|.|+.|+|+.|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            3458999999999999999999999999999987     358899999999999999999996 6889999999999887


Q ss_pred             C
Q 002823          220 I  220 (876)
Q Consensus       220 ~  220 (876)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=1.8e-14  Score=130.67  Aligned_cols=78  Identities=13%  Similarity=0.308  Sum_probs=71.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEe-----CCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYR-----ASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~-----tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~p  221 (876)
                      .++|||+|||+++++++|+++|++||.|..+..     +++++|||||+|.+.++|++|++ +++..|.|+.|.|+++.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            479999999999999999999999999999883     56789999999999999999995 799999999999999998


Q ss_pred             CCCC
Q 002823          222 KDNP  225 (876)
Q Consensus       222 k~~~  225 (876)
                      +++.
T Consensus        99 ke~~  102 (103)
T d1x4ba1          99 REES  102 (103)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7653

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=5.1e-15  Score=133.73  Aligned_cols=77  Identities=17%  Similarity=0.312  Sum_probs=70.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ...+||||+|||.++++++|+++|++||+|.+|+     .+++++|||||+|.+.++|++|+ .|+|..|.|+.|+|+++
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEEC
Confidence            3458999999999999999999999999999998     35889999999999999999999 59999999999999997


Q ss_pred             CCC
Q 002823          220 IPK  222 (876)
Q Consensus       220 ~pk  222 (876)
                      .++
T Consensus        95 ~~~   97 (101)
T d2cq4a1          95 QAE   97 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            543

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=1.5e-14  Score=127.27  Aligned_cols=74  Identities=15%  Similarity=0.271  Sum_probs=66.5

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      .++|||+|||.+++++||+++|++|| ++.+.+ ...++||||+|.+.++|++|++.||+..+.|++|+|+|++.+
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~-~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            46899999999999999999999999 333443 557899999999999999999999999999999999999764

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=2e-14  Score=129.09  Aligned_cols=77  Identities=22%  Similarity=0.422  Sum_probs=69.9

Q ss_pred             CCCCcEEEEcCCC-CCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          144 EHPSRTLLLRKIN-SNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       144 e~pSrTLFVgNLP-~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ....++|||+||| ..+++++|+++|++||+|..+++   .||||||+|.+.++|++|++.|+|+.|.|++|+|+|+.++
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            3445789999997 56889999999999999999987   6899999999999999999999999999999999999765


Q ss_pred             C
Q 002823          223 D  223 (876)
Q Consensus       223 ~  223 (876)
                      .
T Consensus        89 ~   89 (98)
T d1wf2a_          89 K   89 (98)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=3.8e-14  Score=125.34  Aligned_cols=77  Identities=14%  Similarity=0.295  Sum_probs=69.6

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...+|||+|||+++|+++|+++|+.||.|.+|++     ++.++|||||+|.+.++|++||+.  ...|.|+.|.|.++.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            3568999999999999999999999999999887     577889999999999999999984  558999999999998


Q ss_pred             Cchh
Q 002823          306 LRGL  309 (876)
Q Consensus       306 ~k~~  309 (876)
                      +++.
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            8653

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=5.6e-14  Score=122.44  Aligned_cols=73  Identities=12%  Similarity=0.251  Sum_probs=67.9

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      .++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++ +++..|.|++|+|..|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            468999999999999999999999999999887     57789999999999999999997 69999999999998875

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=2.9e-14  Score=122.06  Aligned_cols=72  Identities=17%  Similarity=0.375  Sum_probs=66.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .|+|||+|||+++|+++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++ +++..|.|++|.|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            47999999999999999999999999999887     367789999999999999999994 8999999999999876

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.48  E-value=4.5e-14  Score=120.57  Aligned_cols=71  Identities=15%  Similarity=0.310  Sum_probs=66.0

Q ss_pred             eEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCc
Q 002823          235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       235 LfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k  307 (876)
                      |||+|||.++++++|+++|++|| ++.+++ ...++||||+|.+.++|++|++.|||..+.|++|+|+|++.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 666665 668999999999999999999999999999999999999764

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=2.9e-14  Score=121.58  Aligned_cols=70  Identities=13%  Similarity=0.283  Sum_probs=64.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          149 TLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       149 TLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      +|||+|||+++++++|+++|++||+|..+.     .+++++|||||+|.+.++|++|++ +++..|.|+.|+|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            589999999999999999999999999998     457899999999999999999996 7889999999999654

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=2.2e-14  Score=129.05  Aligned_cols=76  Identities=18%  Similarity=0.291  Sum_probs=69.7

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ..++|||+|||.++++++|+++|++||.|..+++    ++.++|||||+|.+.++|.+|++.|||..|.|+++.|.+++|
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            3568999999999999999999999999998776    455688999999999999999999999999999999988876

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=5.5e-14  Score=125.51  Aligned_cols=77  Identities=21%  Similarity=0.273  Sum_probs=70.8

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEeecCc
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAG--KQIKLEPSHLR  307 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~G--r~IkVs~A~~k  307 (876)
                      .+.++|||+|||.++++++|+++|++||+|+.|++. ..++||||+|.+.++|++|++.||+..|.|  ++|+|+|++++
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~-~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEEC-SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeee-ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            356799999999999999999999999999999984 468899999999999999999999999976  68999999874

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=5.5e-14  Score=120.06  Aligned_cols=71  Identities=15%  Similarity=0.347  Sum_probs=65.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          150 LLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       150 LFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      |||+|||+++++++|+++|++|| +..++. .+.+|||||+|.+.++|++|++.|||..+.|++|+|+|+...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 555554 678999999999999999999999999999999999998643

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=4.4e-14  Score=125.68  Aligned_cols=80  Identities=19%  Similarity=0.215  Sum_probs=70.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCC-eEEEEe------CCCccceEeeecCCHHHHHHHHHHcccc--ccCCceeeEee
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGD-VRTFYR------ASKHCGFVTISYYDIRAARNAMKSLQNK--LTRSGKLDIHY  218 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~-I~sV~~------tgksrGfAFV~F~d~edA~kAl~~Lng~--~l~Gr~L~V~~  218 (876)
                      ++|||+|||.++++++|+++|++||+ |..++.      +++++|||||+|.+.++|.+|++.|++.  .+.|+.|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            58999999999999999999999996 888882      4678999999999999999999999754  46799999999


Q ss_pred             cCCCCCCCc
Q 002823          219 SIPKDNPSE  227 (876)
Q Consensus       219 A~pk~~~~e  227 (876)
                      +.|+.++.+
T Consensus        82 A~p~~~~~~   90 (96)
T d2disa1          82 AEPEIDVDE   90 (96)
T ss_dssp             SCSSCSTTT
T ss_pred             cCCCCCCCh
Confidence            998876643

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=1.4e-14  Score=124.47  Aligned_cols=71  Identities=14%  Similarity=0.299  Sum_probs=66.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ++|||+|||+++|+++|+++|++||+|.+++     .++++||||||+|.+.++|++|++ +++..+.|++|.|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            4799999999999999999999999998877     468899999999999999999996 7999999999999876

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.47  E-value=1.1e-14  Score=128.97  Aligned_cols=76  Identities=25%  Similarity=0.258  Sum_probs=69.3

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...+|||+|||.++++++|+++|+.||.|..+++    ++.++|||||+|.+.++|++||+ |||..+.|++|+|++++.
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            3558999999999999999999999999877554    67789999999999999999996 999999999999999986


Q ss_pred             c
Q 002823          307 R  307 (876)
Q Consensus       307 k  307 (876)
                      +
T Consensus        91 k   91 (91)
T d1fjeb1          91 R   91 (91)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=4.1e-14  Score=120.62  Aligned_cols=70  Identities=14%  Similarity=0.297  Sum_probs=64.7

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +|||+|||+++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++ +++..|.|++|+|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            5899999999999999999999999999987     46678999999999999999997 7999999999998653

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=7e-14  Score=119.67  Aligned_cols=71  Identities=15%  Similarity=0.292  Sum_probs=65.7

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ++|||+|||+++|+++|+++|++||.|..+++     ++..+|||||+|.+.++|.+|++ ++|..|.|++|+|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            58999999999999999999999999999877     55678999999999999999985 8999999999999876

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=4.9e-14  Score=126.46  Aligned_cols=81  Identities=16%  Similarity=0.149  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      .....++|||+|||+++++++|+++|++||+|+.+..  ..+|||||+|.+.++|++|++.||+..+.|+.|+|.|..++
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i--~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~   88 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADV--QKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVY   88 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEE--ETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccc--cccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecC
Confidence            3456789999999999999999999999999999986  35799999999999999999999999999999999998765


Q ss_pred             CCC
Q 002823          223 DNP  225 (876)
Q Consensus       223 ~~~  225 (876)
                      .+.
T Consensus        89 ~~~   91 (98)
T d1wg4a_          89 PER   91 (98)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=1.2e-13  Score=124.72  Aligned_cols=81  Identities=12%  Similarity=0.182  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccc--cccCCceeeEeecC
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQN--KLTRSGKLDIHYSI  220 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng--~~l~Gr~L~V~~A~  220 (876)
                      ...|+++|||+|||.++++++|+++|++||.|..++. .+.|+||||+|.+.++|++|++.+++  ..+.|++|+|.|+.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~-~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~   89 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEE-EecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcC
Confidence            4568999999999999999999999999999999986 56799999999999999999998854  56889999999997


Q ss_pred             CCCC
Q 002823          221 PKDN  224 (876)
Q Consensus       221 pk~~  224 (876)
                      .+..
T Consensus        90 ~~~~   93 (104)
T d1wexa_          90 SKRI   93 (104)
T ss_dssp             SSSC
T ss_pred             CCcc
Confidence            6543

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=3e-14  Score=120.52  Aligned_cols=70  Identities=14%  Similarity=0.296  Sum_probs=65.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          149 TLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       149 TLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      +|||+|||+++|+++|+++|++||.|..+.     .+++.++||||+|.+.++|++|++ +++..|.|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            599999999999999999999999999887     357789999999999999999996 9999999999999875

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=3.6e-14  Score=120.02  Aligned_cols=70  Identities=14%  Similarity=0.274  Sum_probs=65.2

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +|||+|||.++|+++|+++|++||.|..+.+     ++..++||||+|.+.++|.+|++ +||..|.|++|+|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            5899999999999999999999999999776     45678999999999999999996 9999999999999875

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=8.4e-14  Score=121.93  Aligned_cols=79  Identities=15%  Similarity=0.167  Sum_probs=71.5

Q ss_pred             ccccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHh--CCceeCCeEEEEEeecC
Q 002823          229 EINQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALREL--NSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       229 ~~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~L--nG~~I~Gr~IkVs~A~~  306 (876)
                      ..+.++|||+|||.++++++|+++|++||.|.++++ ...+++|||+|.+.++|++|++.+  ++..+.|++|+|.|++.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~-~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccc-cccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            346789999999999999999999999999999998 456789999999999999999865  67899999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      +.
T Consensus        84 ~~   85 (88)
T d2cq1a1          84 KE   85 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=2e-14  Score=125.95  Aligned_cols=74  Identities=16%  Similarity=0.127  Sum_probs=68.5

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ++|||+|||+++++++|+++|++||+|.++++.  .+|||||+|.+.++|++||+.|||..|.|+.|+|.+++.+.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY--RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEEC--TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccc--ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            369999999999999999999999999999984  35899999999999999999999999999999999887654

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=9.1e-14  Score=121.34  Aligned_cols=73  Identities=14%  Similarity=0.250  Sum_probs=67.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          146 PSRTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       146 pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ..++|||+|||.++|+++|+++|++||+|..|+    .+++++|||||+|.+.++|++|++ +++..+.|+.|.|.|.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEc
Confidence            458999999999999999999999999999998    357789999999999999999995 7999999999999985

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=1.3e-13  Score=124.18  Aligned_cols=76  Identities=22%  Similarity=0.271  Sum_probs=67.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe------cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE------TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri------tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +..+|||+|||.++++++|+++|+.|| |+++++      ++..+|||||+|.+.++|++|+ .||+..|.|++|+|.++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            457999999999999999999999999 666655      3456789999999999998777 59999999999999999


Q ss_pred             cCch
Q 002823          305 HLRG  308 (876)
Q Consensus       305 ~~k~  308 (876)
                      .++.
T Consensus        92 ~~~~   95 (104)
T d1wi8a_          92 DQAQ   95 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.44  E-value=3.3e-14  Score=122.09  Aligned_cols=70  Identities=20%  Similarity=0.337  Sum_probs=65.7

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +|||+|||.++++++|+++|++||.|+++++     ++.+||||||+|.+.++|.+|++ +++..+.|++|+|..|
T Consensus         2 klfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            6999999999999999999999999998876     56789999999999999999997 7999999999999876

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=7.9e-14  Score=126.76  Aligned_cols=78  Identities=27%  Similarity=0.344  Sum_probs=70.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-cCCcccEEEEEecCHHHHHHHHHHhCCcee--CCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-TPQKIHQKYIEFYDTRAAEAALRELNSRYI--AGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri-tg~skG~AFVeF~d~E~A~kAL~~LnG~~I--~Gr~IkVs~A~~k  307 (876)
                      +..+|||+|||..+|+++|+++|++||.|+.|++ ..+.+|+|||+|.+.++|++|++.|||..|  .+++|+|.|++++
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~   85 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT   85 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCc
Confidence            3558999999999999999999999999999877 344689999999999999999999999998  5799999999875


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus        86 ~   86 (108)
T d2adba1          86 S   86 (108)
T ss_dssp             S
T ss_pred             c
Confidence            3

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=1.7e-13  Score=119.61  Aligned_cols=74  Identities=7%  Similarity=0.108  Sum_probs=68.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ..++|||+|||.++|+++|+++|+.||.|..|++    ++..+|||||+|.+.++|.+|++ +++..+.|++|+|.|..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4579999999999999999999999999999887    45668999999999999999996 79999999999999864

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.43  E-value=1.8e-13  Score=116.80  Aligned_cols=71  Identities=21%  Similarity=0.240  Sum_probs=64.6

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe---cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE---TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri---tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      .+|||+|||.++++++|+++|+.||.|+.|++   ....++||||+|.+.++|.+|+. +++..|+|++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            37999999999999999999999999999887   33456799999999999999985 8999999999999865

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=4.3e-14  Score=123.79  Aligned_cols=73  Identities=18%  Similarity=0.123  Sum_probs=67.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeecCCCC
Q 002823          149 TLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSIPKD  223 (876)
Q Consensus       149 TLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~pk~  223 (876)
                      +|||+|||+++++++|+++|++||+|..++..  .+|||||+|.+.++|++|++.|+|..|.|+.|+|.++.++.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY--RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEEC--TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccc--ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            69999999999999999999999999999863  45999999999999999999999999999999998876554

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=9.8e-14  Score=123.41  Aligned_cols=78  Identities=17%  Similarity=0.131  Sum_probs=68.7

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCC-eEEEEe------cCCcccEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEEe
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGE-IKEIRE------TPQKIHQKYIEFYDTRAAEAALRELNS--RYIAGKQIKLEP  303 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~-I~sVri------tg~skG~AFVeF~d~E~A~kAL~~LnG--~~I~Gr~IkVs~  303 (876)
                      .+|||+|||.++++++|+++|+.||+ |.+|++      .+.++|||||+|.+.++|.+|++.|++  ..+.|++|+|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            47999999999999999999999996 888887      245679999999999999999999965  456799999999


Q ss_pred             ecCchhH
Q 002823          304 SHLRGLR  310 (876)
Q Consensus       304 A~~k~~R  310 (876)
                      ++++.+.
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9986543

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.43  E-value=1.2e-13  Score=123.96  Aligned_cols=76  Identities=17%  Similarity=0.119  Sum_probs=70.5

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecCch
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHLRG  308 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~  308 (876)
                      ...+|||+|||.++++++|+++|++||+|+.+++.  .+|||||+|.+.++|++||+.|||..|.|+.|+|.+++.+.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ--KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE--TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccc--ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            35589999999999999999999999999999884  46899999999999999999999999999999999997754

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=1.4e-13  Score=123.64  Aligned_cols=80  Identities=14%  Similarity=0.146  Sum_probs=71.1

Q ss_pred             CCCCCcEEEEcCCCCC-CCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHH--HccccccCCceeeEeec
Q 002823          143 DEHPSRTLLLRKINSN-IEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMK--SLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~-vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~--~Lng~~l~Gr~L~V~~A  219 (876)
                      ...++++|||+|||.+ +|+++|+++|++||.|..++. .+.+|||||+|.+.++|.+|++  .+++..+.|+.|+|.|+
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~-~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s   92 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   92 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEE-eecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEc
Confidence            4467899999999986 899999999999999999986 4678999999999999999998  46777899999999999


Q ss_pred             CCCC
Q 002823          220 IPKD  223 (876)
Q Consensus       220 ~pk~  223 (876)
                      ..+.
T Consensus        93 ~~~~   96 (99)
T d1x4fa1          93 EKYK   96 (99)
T ss_dssp             CSCS
T ss_pred             CCcc
Confidence            7654

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=7.4e-14  Score=119.44  Aligned_cols=70  Identities=14%  Similarity=0.378  Sum_probs=64.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          149 TLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       149 TLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      +|||+|||+++|+++|+++|++||+|..++     .+++++|||||+|.+.++|++|++ .++..+.|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            599999999999999999999999999998     467899999999999999999995 5778899999999764

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=2.4e-13  Score=122.84  Aligned_cols=78  Identities=22%  Similarity=0.181  Sum_probs=70.8

Q ss_pred             cccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHh--CCceeCCeEEEEEeecCc
Q 002823          230 INQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALREL--NSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       230 ~~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~L--nG~~I~Gr~IkVs~A~~k  307 (876)
                      .+..+|||+|||..+++++|+++|++||.|+.|++ .+.|++|||+|.+.++|++|++.|  ++..+.|++|+|.|++.+
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~-~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEE-EecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCC
Confidence            45779999999999999999999999999999998 456899999999999999999988  566789999999999875


Q ss_pred             h
Q 002823          308 G  308 (876)
Q Consensus       308 ~  308 (876)
                      .
T Consensus        92 ~   92 (104)
T d1wexa_          92 R   92 (104)
T ss_dssp             S
T ss_pred             c
Confidence            4

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=1.2e-13  Score=121.60  Aligned_cols=71  Identities=18%  Similarity=0.397  Sum_probs=63.6

Q ss_pred             cceeEeecCCCCCcHHHH---HHHhhhcCCeEEEEec-----CC---cccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          232 QGTLVVFNLDSSVSNDEL---HHIFGVYGEIKEIRET-----PQ---KIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedL---reiFs~fG~I~sVrit-----g~---skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      .++|||+|||+++++++|   +++|++||+|..|++.     +.   .++||||+|.+.++|.+|++.|||..+.|++|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            457999999999999999   6789999999999872     12   248999999999999999999999999999999


Q ss_pred             EE
Q 002823          301 LE  302 (876)
Q Consensus       301 Vs  302 (876)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=6.4e-14  Score=117.98  Aligned_cols=66  Identities=20%  Similarity=0.326  Sum_probs=62.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          150 LLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       150 LFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      |||+|||+++|+++|+++|++||+|..++     .+++++|||||+|.+.++|++|++.|+|+.+.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999987     3577999999999999999999999999999999874

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=8.7e-14  Score=119.00  Aligned_cols=70  Identities=14%  Similarity=0.308  Sum_probs=64.4

Q ss_pred             eeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          234 TLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       234 tLfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      +|||+|||+++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++||+ +++..|.|+.|+|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            5899999999999999999999999999987     46678999999999999999997 5778899999999865

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.40  E-value=2.8e-13  Score=119.40  Aligned_cols=79  Identities=14%  Similarity=0.110  Sum_probs=70.6

Q ss_pred             CCCCCcEEEEcCCCCC-CCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHc--cccccCCceeeEeec
Q 002823          143 DEHPSRTLLLRKINSN-IEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSL--QNKLTRSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~-vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~L--ng~~l~Gr~L~V~~A  219 (876)
                      ...++++|||+|||.. +|++||.++|++||.|..++. .+.+++|||+|.+.++|.+|++.+  ++..+.|++|+|.|+
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i-~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s   82 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLS   82 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEE-CSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEe-eccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEEC
Confidence            4678999999999986 889999999999999999997 456789999999999999999976  456799999999999


Q ss_pred             CCC
Q 002823          220 IPK  222 (876)
Q Consensus       220 ~pk  222 (876)
                      ...
T Consensus        83 ~~~   85 (89)
T d1x4da1          83 QKY   85 (89)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            754

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.40  E-value=2.5e-13  Score=118.15  Aligned_cols=74  Identities=26%  Similarity=0.280  Sum_probs=66.5

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEE-EEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKE-IRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~s-Vri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ...+|||+|||.+++++||+++|+.||.|.. +.+    ++.++|+|||+|.+.++|.+|++.||+..+.|++|+|+++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3557999999999999999999999999865 333    5677899999999999999999999999999999999875

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=1e-13  Score=120.57  Aligned_cols=75  Identities=12%  Similarity=0.167  Sum_probs=66.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEE---EE--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRT---FY--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~s---V~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ....+|||+|||.++++++|+++|+.||.|..   +.  .+++++|||||+|.+.++|++|++.|+++.+.||+|+|.++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34567999999999999999999999998743   22  56788999999999999999999999999999999999874

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=2.1e-13  Score=122.33  Aligned_cols=77  Identities=21%  Similarity=0.209  Sum_probs=69.3

Q ss_pred             cccceeEeecCCCC-CcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHH--HhCCceeCCeEEEEEeecC
Q 002823          230 INQGTLVVFNLDSS-VSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALR--ELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       230 ~~~~tLfV~NLP~s-vTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~--~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...++|||+|||.+ +|+++|+++|++||.|.+|++ ...+++|||+|.+.++|.+|++  .+++..+.|++|+|.|++.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~-~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEE-eecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            34568999999985 899999999999999999998 4468999999999999999998  5788899999999999976


Q ss_pred             c
Q 002823          307 R  307 (876)
Q Consensus       307 k  307 (876)
                      +
T Consensus        95 ~   95 (99)
T d1x4fa1          95 Y   95 (99)
T ss_dssp             C
T ss_pred             c
Confidence            5

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=5.4e-13  Score=120.31  Aligned_cols=81  Identities=15%  Similarity=0.123  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      +.....+|||+|||+++|+++|+++|..||.|..+.     .+++.+|||||+|.++++|++|++ +++..|.||.|+|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            344556899999999999999999999999887754     467789999999999999999995 89999999999999


Q ss_pred             ecCCCCC
Q 002823          218 YSIPKDN  224 (876)
Q Consensus       218 ~A~pk~~  224 (876)
                      ++.+++.
T Consensus        90 ~~~~~~~   96 (104)
T d1wg5a_          90 KSSRAEV   96 (104)
T ss_dssp             EECTTTS
T ss_pred             ECCHHHh
Confidence            9987653

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=8.7e-14  Score=117.14  Aligned_cols=66  Identities=20%  Similarity=0.334  Sum_probs=61.8

Q ss_pred             eEeecCCCCCcHHHHHHHhhhcCCeEEEEe-----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          235 LVVFNLDSSVSNDELHHIFGVYGEIKEIRE-----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       235 LfV~NLP~svTeedLreiFs~fG~I~sVri-----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      |||+|||.++++++|+++|++||.|..+++     ++..+|+|||+|.+.++|++|++.|||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            799999999999999999999999999876     456789999999999999999999999999998874

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=3.3e-13  Score=121.42  Aligned_cols=82  Identities=9%  Similarity=0.171  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ......+|||+|||+++|+++|+++|+.||.+....   .+++.+|||||+|.+.++|++|++ ++++.|.||.|+|.++
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCcceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            445568999999999999999999999999653322   467789999999999999999985 8999999999999998


Q ss_pred             CCCCCC
Q 002823          220 IPKDNP  225 (876)
Q Consensus       220 ~pk~~~  225 (876)
                      .++...
T Consensus        90 ~~~~~~   95 (102)
T d1weza_          90 STAGTS   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.38  E-value=3.9e-13  Score=114.65  Aligned_cols=71  Identities=14%  Similarity=0.258  Sum_probs=64.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE---eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY---RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~---~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      .||||+|||+++++++|+++|++||+|..++   .....++||||+|.+.++|++|+ .++++.|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            4899999999999999999999999999888   34456789999999999999999 58999999999999764

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.37  E-value=8.1e-13  Score=116.34  Aligned_cols=76  Identities=18%  Similarity=0.280  Sum_probs=68.9

Q ss_pred             ccceeEeecCCCC-CcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHh--CCceeCCeEEEEEeecCc
Q 002823          231 NQGTLVVFNLDSS-VSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALREL--NSRYIAGKQIKLEPSHLR  307 (876)
Q Consensus       231 ~~~tLfV~NLP~s-vTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~L--nG~~I~Gr~IkVs~A~~k  307 (876)
                      ..++|||+|||.. +|++||+++|++||+|.+|++ ...+++|||+|++.++|.+|++.|  ++..+.|++|+|.|+++.
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i-~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~   85 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   85 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEE-CSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEe-eccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCc
Confidence            4678999999986 899999999999999999998 446789999999999999999966  678999999999999864

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=7.3e-13  Score=119.47  Aligned_cols=77  Identities=18%  Similarity=0.219  Sum_probs=69.0

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEE-Ee----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEI-RE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sV-ri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...+|||+|||+++|++||+++|+.||.|..+ .+    ++.++|+|||+|.+.++|++|++ +|+..|.||.|+|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            45589999999999999999999999998873 33    55678999999999999999996 99999999999999998


Q ss_pred             Cch
Q 002823          306 LRG  308 (876)
Q Consensus       306 ~k~  308 (876)
                      +++
T Consensus        93 ~~~   95 (104)
T d1wg5a_          93 RAE   95 (104)
T ss_dssp             TTT
T ss_pred             HHH
Confidence            765

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.36  E-value=2e-13  Score=120.19  Aligned_cols=71  Identities=13%  Similarity=0.266  Sum_probs=63.2

Q ss_pred             CcEEEEcCCCCCCCHHHH---HHHhhccCCeEEEEe-----C---CCccceEeeecCCHHHHHHHHHHccccccCCceee
Q 002823          147 SRTLLLRKINSNIEDSEL---KALFEQYGDVRTFYR-----A---SKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLD  215 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL---~elFsqfG~I~sV~~-----t---gksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~  215 (876)
                      .++|||+|||+++++++|   +++|++||+|..|..     +   +..+|||||+|.+.++|++|++.|||..+.|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            468999999999999999   678999999999982     1   22458999999999999999999999999999999


Q ss_pred             Ee
Q 002823          216 IH  217 (876)
Q Consensus       216 V~  217 (876)
                      |.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            73

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=1.8e-13  Score=133.45  Aligned_cols=80  Identities=16%  Similarity=0.361  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          143 DEHPSRTLLLRKINSNIEDSELKALFEQYGDVRTFY-----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       143 ~e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~-----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      .....++|||+|||..+|+++|+++|+.||.|..+.     .+++++|||||+|.+.++|++|++ +++..+.|++|.|.
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVR  171 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEE
Confidence            456678999999999999999999999999999987     347889999999999999999996 78889999999999


Q ss_pred             ecCCCC
Q 002823          218 YSIPKD  223 (876)
Q Consensus       218 ~A~pk~  223 (876)
                      ++.+|.
T Consensus       172 ~A~~k~  177 (183)
T d1u1qa_         172 KALSKQ  177 (183)
T ss_dssp             ECCCHH
T ss_pred             ecCCcc
Confidence            998763

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.34  E-value=3.2e-13  Score=122.51  Aligned_cols=79  Identities=18%  Similarity=0.222  Sum_probs=70.8

Q ss_pred             CCCcEEEEcCCCCCC-CH----HHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNI-ED----SELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~v-TE----eeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ..+.+|||+||+.++ ++    ++|+++|++||+|.+++. .++++||||+|.+.++|.+|++.|||+.|.|++|+|.|+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~-~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   81 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY-FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFA   81 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEE-ETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEE-ecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeec
Confidence            456899999999986 33    568999999999999986 578999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002823          220 IPKDN  224 (876)
Q Consensus       220 ~pk~~  224 (876)
                      .++..
T Consensus        82 ~~~~~   86 (104)
T d1weya_          82 QTLHI   86 (104)
T ss_dssp             CCSSC
T ss_pred             ccCCC
Confidence            77654

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=4e-13  Score=120.93  Aligned_cols=76  Identities=12%  Similarity=0.169  Sum_probs=67.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ...+|||+|||+++|++||+++|+.||.+ .|++    ++..+|||||+|.+.++|++|++ +|+..|.||.|+|.++.+
T Consensus        14 ~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~   91 (102)
T d1weza_          14 TGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNST   91 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCC
Confidence            44589999999999999999999999854 4443    55678999999999999999986 899999999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      +.
T Consensus        92 ~~   93 (102)
T d1weza_          92 AG   93 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=9.8e-13  Score=118.17  Aligned_cols=79  Identities=14%  Similarity=0.212  Sum_probs=69.8

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEE-EEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKE-IRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~s-Vri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ..+|||+|||.++++++|+++|+.||.|.. +.+    ++..+|+|||+|.+.++|++|++ ||+..|.|++|+|.++..
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECH
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCH
Confidence            458999999999999999999999998865 444    56679999999999999999996 999999999999999876


Q ss_pred             chhHH
Q 002823          307 RGLRK  311 (876)
Q Consensus       307 k~~Rr  311 (876)
                      +..++
T Consensus        87 ~~~~~   91 (103)
T d2cpya1          87 EDMRE   91 (103)
T ss_dssp             HHHHH
T ss_pred             HHhhh
Confidence            65544

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.30  E-value=6.1e-13  Score=120.65  Aligned_cols=76  Identities=18%  Similarity=0.230  Sum_probs=68.4

Q ss_pred             cceeEeecCCCCC-c----HHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          232 QGTLVVFNLDSSV-S----NDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       232 ~~tLfV~NLP~sv-T----eedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      ..+|||+||+.++ +    .++|+++|++||.|+++++ .+.++||||+|.+.++|.+|++.|||..|.|++|+|.|+++
T Consensus         5 ~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~-~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   83 (104)
T d1weya_           5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY-FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEE-ETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEE-ecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeeccc
Confidence            5689999999876 3    3579999999999999998 45788999999999999999999999999999999999987


Q ss_pred             ch
Q 002823          307 RG  308 (876)
Q Consensus       307 k~  308 (876)
                      ..
T Consensus        84 ~~   85 (104)
T d1weya_          84 LH   85 (104)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=8e-13  Score=118.78  Aligned_cols=75  Identities=12%  Similarity=0.115  Sum_probs=66.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhccCCeEE-EE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          145 HPSRTLLLRKINSNIEDSELKALFEQYGDVRT-FY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       145 ~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~s-V~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ....+|||+|||+++|+++|+++|..||.|.. +.    .+++++|||||+|.+.++|++|++ ++++.|.|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            44578999999999999999999999998754 22    467899999999999999999995 9999999999999886


Q ss_pred             C
Q 002823          220 I  220 (876)
Q Consensus       220 ~  220 (876)
                      .
T Consensus        85 ~   85 (103)
T d2cpya1          85 T   85 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=1.4e-12  Score=119.32  Aligned_cols=77  Identities=10%  Similarity=0.115  Sum_probs=67.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhccCCeEEE---E--eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEee
Q 002823          144 EHPSRTLLLRKINSNIEDSELKALFEQYGDVRTF---Y--RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHY  218 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTEeeL~elFsqfG~I~sV---~--~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~  218 (876)
                      ..+.++|||+|||+++|+++|+++|+.||.|..+   .  .+++.+|||||+|.+.++|++|++ +++..|.|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            4456799999999999999999999999977432   2  568899999999999999999995 999999999999987


Q ss_pred             cCC
Q 002823          219 SIP  221 (876)
Q Consensus       219 A~p  221 (876)
                      +.+
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            643

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=1.6e-13  Score=120.57  Aligned_cols=71  Identities=14%  Similarity=0.272  Sum_probs=63.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----------eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEe
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY----------RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIH  217 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----------~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~  217 (876)
                      |+|||+|||.++|+++|+++|++||.|..+.          .+++++|||||+|.+.++|++|+ +|+|..+.|++|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            7899999999999999999999999775443          34678999999999999999998 599999999999997


Q ss_pred             ec
Q 002823          218 YS  219 (876)
Q Consensus       218 ~A  219 (876)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            53

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=2.5e-12  Score=117.53  Aligned_cols=80  Identities=16%  Similarity=0.273  Sum_probs=70.1

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEE---EEe--cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeec
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKE---IRE--TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSH  305 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~s---Vri--tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~  305 (876)
                      ...+|||+|||+++|+++|+++|+.||.|..   +..  ++..+|+|||+|.+.++|++|++ |||..|+|+.|+|..+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            3458999999999999999999999998854   222  67788999999999999999996 99999999999999998


Q ss_pred             CchhHH
Q 002823          306 LRGLRK  311 (876)
Q Consensus       306 ~k~~Rr  311 (876)
                      +++..+
T Consensus        96 ~~~~~~  101 (112)
T d1wela1          96 KKGMLE  101 (112)
T ss_dssp             HHHHHH
T ss_pred             hHHHHH
Confidence            877554

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=1.6e-11  Score=110.02  Aligned_cols=83  Identities=12%  Similarity=0.280  Sum_probs=72.1

Q ss_pred             CCCCCCcEEEEcCC--CCCCC---------HHHHHHHhhccCCeEEEE-eCCCccceEeeecCCHHHHHHHHHHcccccc
Q 002823          142 NDEHPSRTLLLRKI--NSNIE---------DSELKALFEQYGDVRTFY-RASKHCGFVTISYYDIRAARNAMKSLQNKLT  209 (876)
Q Consensus       142 ~~e~pSrTLFVgNL--P~~vT---------EeeL~elFsqfG~I~sV~-~tgksrGfAFV~F~d~edA~kAl~~Lng~~l  209 (876)
                      .....+++|+|+||  |.++.         +++|++.|++||.|..|+ ...+.+|||||+|.+.++|.+|++.|+|..+
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            35577899999999  65532         267889999999999998 5667799999999999999999999999999


Q ss_pred             CCceeeEeecCCCCC
Q 002823          210 RSGKLDIHYSIPKDN  224 (876)
Q Consensus       210 ~Gr~L~V~~A~pk~~  224 (876)
                      .||+|.|+|+.++.+
T Consensus        83 ~gr~i~v~~~~g~~~   97 (99)
T d2dita1          83 GGRQITAQAWDGTTD   97 (99)
T ss_dssp             TTEECEEEECCSCCC
T ss_pred             CCEEEEEEEeCCcCC
Confidence            999999999877643

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=1.4e-11  Score=110.84  Aligned_cols=66  Identities=14%  Similarity=0.254  Sum_probs=60.0

Q ss_pred             CCCCCcEEEEcC--CCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcccccc
Q 002823          143 DEHPSRTLLLRK--INSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLT  209 (876)
Q Consensus       143 ~e~pSrTLFVgN--LP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l  209 (876)
                      ...|+++|||.|  ||.++|+++|+++|++||.|+.++. .+.++||||+|.+.++|.+|++.|+|+.+
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~-~~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEEC-CTTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEee-ccCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            356788999955  9999999999999999999999986 45789999999999999999999999886

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.17  E-value=4e-12  Score=115.14  Aligned_cols=72  Identities=22%  Similarity=0.364  Sum_probs=67.5

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEee
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPS  304 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri----tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A  304 (876)
                      ..++|.+++.++++++|+++|++||+|++|++    ++..+|+|||+|.+.++|.+|++.|||+.+.||+|+|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            46889999999999999999999999999998    4567899999999999999999999999999999999985

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=2.9e-11  Score=108.76  Aligned_cols=63  Identities=22%  Similarity=0.342  Sum_probs=57.7

Q ss_pred             ccceeEeec--CCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCcee
Q 002823          231 NQGTLVVFN--LDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYI  294 (876)
Q Consensus       231 ~~~tLfV~N--LP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I  294 (876)
                      +..+|+|.|  ||.++|+++|+++|++||.|+.|++ ...++||||+|.+.++|.+|++.|||+.+
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~-~~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEEC-CTTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEee-ccCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            456788855  9999999999999999999999998 45688999999999999999999999987

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=4.1e-13  Score=117.82  Aligned_cols=70  Identities=14%  Similarity=0.291  Sum_probs=62.1

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe----------cCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE----------TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIKLE  302 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri----------tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs  302 (876)
                      ++|||+|||.++++++|+++|+.||.|..+.+          +...+|||||+|.+.++|++|++ |||..+.|++|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            57999999999999999999999998765433          34568999999999999999985 99999999999996


Q ss_pred             e
Q 002823          303 P  303 (876)
Q Consensus       303 ~  303 (876)
                      .
T Consensus        81 r   81 (90)
T d1u2fa_          81 R   81 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=2e-11  Score=111.76  Aligned_cols=77  Identities=21%  Similarity=0.202  Sum_probs=67.2

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCH-HHHHHHHHHhCCceeCCeEEEEEeecCchh
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDT-RAAEAALRELNSRYIAGKQIKLEPSHLRGL  309 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~-E~A~kAL~~LnG~~I~Gr~IkVs~A~~k~~  309 (876)
                      ...+||+|||..+|+++|+++|++||+|.+|++ ...++||||+|.+. ++|.+|+..|++..+.++.+.|.|...+..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i-~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~~~   88 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDF-VRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGE   88 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEEC-CTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCHH
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEE-ecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeeccch
Confidence            346799999999999999999999999999999 45789999999985 789999999999998887777777765543

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=7.2e-11  Score=105.68  Aligned_cols=79  Identities=15%  Similarity=0.286  Sum_probs=68.4

Q ss_pred             cccceeEeecC--CCCC---------cHHHHHHHhhhcCCeEEEEe-cCCcccEEEEEecCHHHHHHHHHHhCCceeCCe
Q 002823          230 INQGTLVVFNL--DSSV---------SNDELHHIFGVYGEIKEIRE-TPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK  297 (876)
Q Consensus       230 ~~~~tLfV~NL--P~sv---------TeedLreiFs~fG~I~sVri-tg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr  297 (876)
                      ...++|+|.|+  |.++         ..+||++.|++||.|..|++ .+..+|+|||+|.+.++|.+|+..|||..+.|+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr   85 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   85 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCE
Confidence            35679999999  5432         23689999999999999987 566789999999999999999999999999999


Q ss_pred             EEEEEeecCch
Q 002823          298 QIKLEPSHLRG  308 (876)
Q Consensus       298 ~IkVs~A~~k~  308 (876)
                      +|+|+|+.++.
T Consensus        86 ~i~v~~~~g~~   96 (99)
T d2dita1          86 QITAQAWDGTT   96 (99)
T ss_dssp             ECEEEECCSCC
T ss_pred             EEEEEEeCCcC
Confidence            99999987653

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.10  E-value=9.1e-11  Score=101.62  Aligned_cols=74  Identities=19%  Similarity=0.211  Sum_probs=64.6

Q ss_pred             cceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCe-EEEEEeecCch
Q 002823          232 QGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGK-QIKLEPSHLRG  308 (876)
Q Consensus       232 ~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr-~IkVs~A~~k~  308 (876)
                      ...|+|+++|++.+++.| +.|++||+|.++++ +..++||||+|.++++|++||+ +||..|+|+ .|.|..+..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~-~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k~   78 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDKN   78 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCHH
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEe-cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCChh
Confidence            567999999999986555 57999999999998 6678999999999999999996 999999997 56798887754

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=6.5e-12  Score=113.76  Aligned_cols=72  Identities=15%  Similarity=0.242  Sum_probs=67.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEE----eCCCccceEeeecCCHHHHHHHHHHccccccCCceeeEeec
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFY----RASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYS  219 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~----~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A  219 (876)
                      ..++|++++.++++++|+++|++||+|.+|+    .+++++|||||+|.+.++|.+|++.|+|+.+.||+|.|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4688899999999999999999999999998    35788999999999999999999999999999999999986

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=9.5e-11  Score=107.22  Aligned_cols=75  Identities=11%  Similarity=0.132  Sum_probs=66.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCH-HHHHHHHHHccccccCCceeeEeecCCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDI-RAARNAMKSLQNKLTRSGKLDIHYSIPK  222 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~-edA~kAl~~Lng~~l~Gr~L~V~~A~pk  222 (876)
                      ...+||+|||..+|+++|+++|++||+|..|.. -+.+|||||.|.++ ++|.+|+..+++..+.++.+.|.++..+
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i-~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDF-VRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEEC-CTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEE-ecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence            456799999999999999999999999999996 36799999999995 7899999999999998888888776543

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.96  E-value=4.1e-10  Score=97.39  Aligned_cols=72  Identities=17%  Similarity=0.217  Sum_probs=62.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCce-eeEeecCC
Q 002823          147 SRTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGK-LDIHYSIP  221 (876)
Q Consensus       147 SrTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~-L~V~~A~p  221 (876)
                      .+.|+|.++|++++++.| ++|++||+|.+++. .+.++||||+|.++++|++|++ +||+.+.|+. |.|.....
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~-~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEe-cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            467999999999987655 57999999999986 5778999999999999999995 9999999984 56876644

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=7.6e-10  Score=99.62  Aligned_cols=78  Identities=15%  Similarity=0.247  Sum_probs=65.7

Q ss_pred             ccceeEeecC--CCCC--------cHHHHHHHhhhcCCeEEEEec-------CCcccEEEEEecCHHHHHHHHHHhCCce
Q 002823          231 NQGTLVVFNL--DSSV--------SNDELHHIFGVYGEIKEIRET-------PQKIHQKYIEFYDTRAAEAALRELNSRY  293 (876)
Q Consensus       231 ~~~tLfV~NL--P~sv--------TeedLreiFs~fG~I~sVrit-------g~skG~AFVeF~d~E~A~kAL~~LnG~~  293 (876)
                      +++.|+|.|+  +..+        ..+||++.|++||.|++|.+.       ....|++||+|.+.++|.+|++.|||+.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4678999999  4443        235799999999999999982       2235899999999999999999999999


Q ss_pred             eCCeEEEEEeecCch
Q 002823          294 IAGKQIKLEPSHLRG  308 (876)
Q Consensus       294 I~Gr~IkVs~A~~k~  308 (876)
                      ++||+|+|.|.....
T Consensus        83 f~gR~v~v~f~~~~~   97 (104)
T d1o0pa_          83 FANRVVVTKYCDPDS   97 (104)
T ss_dssp             SSSSCCEEEEECHHH
T ss_pred             ECCeEEEEEEcCHHH
Confidence            999999999987543

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=7.1e-10  Score=99.83  Aligned_cols=77  Identities=18%  Similarity=0.356  Sum_probs=66.1

Q ss_pred             CCCcEEEEcCC--CCCCC--------HHHHHHHhhccCCeEEEEeC-------CCccceEeeecCCHHHHHHHHHHcccc
Q 002823          145 HPSRTLLLRKI--NSNIE--------DSELKALFEQYGDVRTFYRA-------SKHCGFVTISYYDIRAARNAMKSLQNK  207 (876)
Q Consensus       145 ~pSrTLFVgNL--P~~vT--------EeeL~elFsqfG~I~sV~~t-------gksrGfAFV~F~d~edA~kAl~~Lng~  207 (876)
                      .|++.|.|+||  |.++.        .++|++.|++||.|.+|++.       ....|++||+|.+.++|.+|++.|+|+
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            57999999999  65543        35688999999999999831       234689999999999999999999999


Q ss_pred             ccCCceeeEeecCC
Q 002823          208 LTRSGKLDIHYSIP  221 (876)
Q Consensus       208 ~l~Gr~L~V~~A~p  221 (876)
                      .+.||+|.|.|..+
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999753

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=2.5e-09  Score=94.37  Aligned_cols=84  Identities=19%  Similarity=0.324  Sum_probs=73.2

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcccEE-Eecccccccc-eeEEEEEecCCccchHHHHHHhcCccccCCCCc-cE
Q 002823          706 TTLMIKNIPNKYTSKMLLAAIDERHKGTYDFI-YLPIDFKNKC-NVGYAFINMTDPSQIVPFYQSFNGKKWEKFNSE-KV  782 (876)
Q Consensus       706 TTvMirNIPnk~t~~~L~~~ide~~~g~yDF~-Ylp~Df~~~~-N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~-Kv  782 (876)
                      |.|.||++|+.+|++.+++.|+  ..+++||+ |.|-|...+- -...|||||.+++++..|.+.|+|+.+-.-+.. -.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~--~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~   79 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQ--PMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYP   79 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHC--SCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhC--CcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEee
Confidence            8999999999999999999997  57899998 6888877664 458899999999999999999999999875544 46


Q ss_pred             EEEEeeccc
Q 002823          783 ASLAYARIQ  791 (876)
Q Consensus       783 ~~v~yA~iQ  791 (876)
                      +.|.||-.|
T Consensus        80 a~VE~AP~q   88 (91)
T d1uw4a_          80 AIVEFAPFQ   88 (91)
T ss_dssp             CEEEECSSC
T ss_pred             eEEEEcCcc
Confidence            899999877

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.88  E-value=0.0019  Score=53.31  Aligned_cols=59  Identities=19%  Similarity=0.253  Sum_probs=51.9

Q ss_pred             HHHHHhhhcCCeEEEEecCCcc--cEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeecC
Q 002823          248 ELHHIFGVYGEIKEIRETPQKI--HQKYIEFYDTRAAEAALRELNSRYIAGKQIKLEPSHL  306 (876)
Q Consensus       248 dLreiFs~fG~I~sVritg~sk--G~AFVeF~d~E~A~kAL~~LnG~~I~Gr~IkVs~A~~  306 (876)
                      -|...|.++|.|..+.+.+...  -.|-|...+.++|.-|+..|+..+|++|+|.|.++..
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            3556799999999999955555  3799999999999999999999999999999999853

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.52  E-value=0.0026  Score=54.98  Aligned_cols=73  Identities=23%  Similarity=0.340  Sum_probs=57.9

Q ss_pred             cccceeEeecCCCCCc---------HHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 002823          230 INQGTLVVFNLDSSVS---------NDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELNSRYIAGKQIK  300 (876)
Q Consensus       230 ~~~~tLfV~NLP~svT---------eedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~LnG~~I~Gr~Ik  300 (876)
                      ++..||.|.=..++..         -.+|.+.|..||+|.-||+.   .+...|+|.+-+.|.+|++ ++|.++.|+.|+
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv---~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~   88 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRIN---QGQMLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEE---TTEEEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEe---CCeEEEEECCcHHHHHHhc-cCCeEEcceEEE
Confidence            3456777754443322         24688999999999999984   4579999999999999998 999999999999


Q ss_pred             EEeecC
Q 002823          301 LEPSHL  306 (876)
Q Consensus       301 Vs~A~~  306 (876)
                      |....+
T Consensus        89 It~~~~   94 (95)
T d1ufwa_          89 ISGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            986543

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.61  E-value=0.023  Score=49.07  Aligned_cols=72  Identities=11%  Similarity=0.126  Sum_probs=58.0

Q ss_pred             ceeEeecCCCCCcHHHHHHHhhhcCCeEEEEe-cCC------cccEEEEEecCHHHHHHHHHHhCCceeCC-----eEEE
Q 002823          233 GTLVVFNLDSSVSNDELHHIFGVYGEIKEIRE-TPQ------KIHQKYIEFYDTRAAEAALRELNSRYIAG-----KQIK  300 (876)
Q Consensus       233 ~tLfV~NLP~svTeedLreiFs~fG~I~sVri-tg~------skG~AFVeF~d~E~A~kAL~~LnG~~I~G-----r~Ik  300 (876)
                      ++|+|+.||+.+|++++.+.++..|++..... .++      .-.-|+|.|.+.++...-.+..+|..+-+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            47999999999999999999999999887655 111      12469999999999999999999998854     2445


Q ss_pred             EEee
Q 002823          301 LEPS  304 (876)
Q Consensus       301 Vs~A  304 (876)
                      |++|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            5655

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.96  E-value=0.035  Score=45.62  Aligned_cols=63  Identities=17%  Similarity=0.209  Sum_probs=52.2

Q ss_pred             CCCHHHH----HHHhhccCCeEEEEeCCCc--cceEeeecCCHHHHHHHHHHccccccCCceeeEeecC
Q 002823          158 NIEDSEL----KALFEQYGDVRTFYRASKH--CGFVTISYYDIRAARNAMKSLQNKLTRSGKLDIHYSI  220 (876)
Q Consensus       158 ~vTEeeL----~elFsqfG~I~sV~~tgks--rGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L~V~~A~  220 (876)
                      .+++.+|    .+.|.++|+|.++.....+  .-.|-|...+..+|..|+..|+..+|++++|.|.|+.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3455554    4789999999999953333  3479999999999999999999999999999999874

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.91  E-value=0.021  Score=49.19  Aligned_cols=72  Identities=14%  Similarity=0.242  Sum_probs=57.0

Q ss_pred             CCCCcEEEEcCCCCCCCH---------HHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHccccccCCcee
Q 002823          144 EHPSRTLLLRKINSNIED---------SELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQNKLTRSGKL  214 (876)
Q Consensus       144 e~pSrTLFVgNLP~~vTE---------eeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Lng~~l~Gr~L  214 (876)
                      ..|.-||.|.=..++.++         .+|.+.|..||+|.-++.   -.+-..|+|.+-+.|.+|+ .++++++.|+.|
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRF---v~d~mwVTF~dG~SAL~al-~l~g~~v~G~~l   87 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRI---NQGQMLVTFADSHSALSVL-DVDGMKVKGRAV   87 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEE---ETTEEEEECSCSHHHHHHH-HGGGSEETTEEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEE---eCCeEEEEECCcHHHHHHh-ccCCeEEcceEE
Confidence            356678888766544433         467788999999988884   2356899999999999999 589999999999


Q ss_pred             eEeec
Q 002823          215 DIHYS  219 (876)
Q Consensus       215 ~V~~A  219 (876)
                      +|...
T Consensus        88 ~It~~   92 (95)
T d1ufwa_          88 KISGP   92 (95)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99653

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.75  E-value=0.74  Score=39.80  Aligned_cols=55  Identities=15%  Similarity=0.207  Sum_probs=45.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhccCCeEEEEeCCCccceEeeecCCHHHHHHHHHHcc
Q 002823          148 RTLLLRKINSNIEDSELKALFEQYGDVRTFYRASKHCGFVTISYYDIRAARNAMKSLQ  205 (876)
Q Consensus       148 rTLFVgNLP~~vTEeeL~elFsqfG~I~sV~~tgksrGfAFV~F~d~edA~kAl~~Ln  205 (876)
                      ..||.-..|..+...||.++|+.||.|.--.+   .--.|||...+.++|+.+++.+.
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI---ddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE---ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCceEEEEe---cCceEEEEecCHHHHHHHHHHhc
Confidence            47899999999999999999999998765554   22379999999999999887544

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.98  E-value=1.6  Score=37.56  Aligned_cols=57  Identities=9%  Similarity=0.231  Sum_probs=47.7

Q ss_pred             ccceeEeecCCCCCcHHHHHHHhhhcCCeEEEEecCCcccEEEEEecCHHHHHHHHHHhC
Q 002823          231 NQGTLVVFNLDSSVSNDELHHIFGVYGEIKEIRETPQKIHQKYIEFYDTRAAEAALRELN  290 (876)
Q Consensus       231 ~~~tLfV~NLP~svTeedLreiFs~fG~I~sVritg~skG~AFVeF~d~E~A~kAL~~Ln  290 (876)
                      ...-||.-..|..+...||.++|+.||.|.---++   ..-|||.-.+.++|..+++.+.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswId---dTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEE---TTEEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEec---CceEEEEecCHHHHHHHHHHhc
Confidence            35579999999999999999999999998654442   3379999999999999987654