Citrus Sinensis ID: 003400

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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---
Protein Sequence
MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVMQLTFP
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEEccccccccccccccEEEEEEcccccccHHHHHHHHcccccEEEcccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcHHHHHcccccccHHHHHcccccHHHHHHHHHHHHcccccccEEEEccccccccccEEEEEEccccccHHHHHHHHccccccccccccEEEEEEHHHHcHHHHHHHHccccccccccccccEEEccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccEEEEEEccccccccccccEEEcccccccHHHHHHccHHHcccccHEccccccHHHHHcccccEEEccccccccHHHHHHHccccccEEEEEccccccccEEEEEEcccHHHHccHHHcccccEccccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEcccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEccccccccHcccccEEEEEEcccccccHHHHHHHHcccccEEEEEEcccccccEEEEcccHHHHHHHHHHHcccHccccEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccEEEEcHHHHHcccccccEEEEEcccccHHHHHHHHHHHHHccccEEEEEEEcccccccccEEEEEEcccHHHHHHHHHHHcccccEcccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEccccccccccEEEcccc
Coil and Loop (DISEMBL)
mkqffdhssgppkipqlnipkevgggscgriagsdsylasddaslfssslpvlpheklnlnamglgrqsvddissglskvhhgvasddplegvmnpaignslpddeDELLAGimddfdlrglpssledledydifgsgggmelegepqeslsmsmskisisdsasgngllhysvpngagtvagehpygehpsrtLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQnkplrrrkldihfsipkdnpsdkdlnqgtlvvfnldpsvsnedLRQIFGAYGevkeiretphkrhhkFIEFYDVRAAEAALKSLnrsdiagkriklepsrpggarRNLMLQLNQELEQDESRILqhqvgspitnsppgnwvqfsspiehnplqtiskspnfrnmspttsnhmpglasilhpqvstlekiapigkdqgrgslMEHALTntisangasfqqsnsfsepkiglyrgtvssfgpspsngsgvetlsgpqflwgspsrysehssspawqtssmghpfssngkihglpysgrqgsflgssqhhhvgsapsgvplerrfgflpespetsfmnpvafcgmgigqndgsfmvnmgsrasvnpgitvprnlsdngssfrvmssprlspvflgngpypgltpanieGLYERGrsrriennngnqldsKKQFQLELEKIrsgedtrtTLMIKNIPNKYTSKMLLAAIDEnhkgtydflylpidfknkcnVGYAFINmlsplhiipfyeafngkkwekfNSEKVASLAYARIQGRAALVAHFqnsslmnedkrcrpilfhsegpeagdqVMQLTFP
Flexible Loop (DISEMBL)
mkqffdhssgppkipqlniPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRalqnkplrrrKLDIhfsipkdnpsdkdlnQGTLVVFNldpsvsneDLRQIFGAYGEvkeiretphkrhhKFIEFYDVRAAEAALKslnrsdiagkriklepsrpggarrNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRriennngnqldskkqFQLELEkirsgedtrttlmiknipnkYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFhsegpeagdqVMQLTFP
Low Complexity Region (SEG)
MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIagsdsylasddaslfssslPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQEslsmsmskisisdsasGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMlqlnqeleqdeSRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVssfgpspsngsgVETLSGPQFLWGspsrysehsssPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVMQLTFP
Disordered region (IsUnstruct)
************************************************************************************************************LLAGIMDDFDLRGL********DYDIF**********************************LHYSV******************RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK*LR*RKLDIHF*************QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK**********************************************************************************************************************************************************************************************************************************************************FMNPVAFCGMGIGQNDGSFMVN**********************************VFLGNGPYPGLT***I****************************************TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSL******CRPILF*****************
Disordered Region (DISOPRED)
***************************************SDDASLFSSSLPVLPHEKLN*************************************AIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQES***************************************H**RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI******************LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG*************************************WVQFSSPI*******************************************************************************************************************************************************************************************************************************************************************************************QLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGP************
Disordered Region (DISEMBL)
**********PPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMEL**********SMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGS*******************HPFSSNGKIHGLPYSGRQGSFLG************GVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVMQLTFP
Disordered Region (DISPRO)
**************************SCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPI*****************************SFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSR*********LDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVMQ**F*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVMQLTFP
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	823	2.2.26 [Sep-21-2011]
Q6ZI17	848	Protein MEI2-like 2 OS=Or	yes	no	0.911	0.884	0.620	0.0
Q8VWF5	800	Protein MEI2-like 5 OS=Ar	yes	no	0.930	0.957	0.619	0.0
Q9SVV9	759	Protein MEI2-like 3 OS=Ar	no	no	0.871	0.944	0.577	0.0
Q6EQX3	811	Protein MEI2-like 5 OS=Or	no	no	0.930	0.944	0.510	0.0
Q9SJG8	843	Protein MEI2-like 2 OS=Ar	no	no	0.900	0.879	0.486	0.0
Q75M35	955	Protein MEI2-like 3 OS=Or	no	no	0.844	0.727	0.414	1e-134
Q64M78	1001	Protein MEI2-like 4 OS=Or	no	no	0.402	0.330	0.540	1e-79
Q9LYN7	907	Protein MEI2-like 4 OS=Ar	no	no	0.309	0.281	0.569	5e-72
Q8W4I9	915	Protein MEI2-like 1 OS=Ar	no	no	0.291	0.262	0.494	1e-58
P08965	750	Meiosis protein mei2 OS=S	yes	no	0.168	0.185	0.535	5e-37

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

 Score =  928 bits (2398), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 487/785 (62%), Positives = 578/785 (73%), Gaps = 35/785 (4%)

Query: 42  DASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNS 101
           +ASLFS+SLPVLPHEK+N      G   +DD S+ L ++       D         I + 
Sbjct: 47  NASLFSTSLPVLPHEKINFLDSARGTPLMDDASAKLKELDDDPEGKDYKFDFDLRQIDDL 106

Query: 102 LPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISIS 161
           LP+ ED+L AGI ++ +  G  +S+E+LE++D+FGSGGGMEL+ +P ES++  +   SI+
Sbjct: 107 LPN-EDDLFAGITNEIEPAGQTNSMEELEEFDVFGSGGGMELDTDPVESITAGLGNTSIA 165

Query: 162 DSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT 221
           D   GNG+ H+   N A TVAGEHPYGEHPSRTLFVRNINSNV+D+ELR+LFEQYGDIRT
Sbjct: 166 DGLRGNGVNHFGPSNSASTVAGEHPYGEHPSRTLFVRNINSNVDDTELRSLFEQYGDIRT 225

Query: 222 LYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLV 281
           LYTA KHRGFVMISY+DIRAAR AMR LQNKPLRRRKLDIHFSIPK+NPSDKDLNQGTLV
Sbjct: 226 LYTATKHRGFVMISYFDIRAARGAMRGLQNKPLRRRKLDIHFSIPKENPSDKDLNQGTLV 285

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           +FNLDPSVSNE++RQIFG YGEVKEIRETP+K+HHKFIEFYDVRAAEAAL+SLN+S+IAG
Sbjct: 286 IFNLDPSVSNEEVRQIFGTYGEVKEIRETPNKKHHKFIEFYDVRAAEAALRSLNKSEIAG 345

Query: 342 KRIKLEPSRPGGARRNLMLQLNQELEQDESRILQ-HQVGSPITNSPPGNWVQFSSPIEHN 400
           KRIKLEPSRPGG RRNLM QL  +++QDE R  +   VGSPI +SPPG W Q+SSP ++N
Sbjct: 346 KRIKLEPSRPGGTRRNLMQQLGHDIDQDEPRSYRIPHVGSPIASSPPGAWAQYSSPTDNN 405

Query: 401 PLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTI 460
            LQ  + SP    MSP       G+   L   +S   KIAPIGKD    S  +   +N  
Sbjct: 406 LLQAFNASPTGNGMSPI------GMPPSL---ISNAVKIAPIGKDS-NWSKYDKVFSNNN 455

Query: 461 SANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSS 520
             +GA+FQ S+S+ + K             S    S   TL+GP+FLWGSP  YSEH+ S
Sbjct: 456 QPHGAAFQHSHSYQDHK-------------SEHMSSSPGTLTGPEFLWGSPKPYSEHAQS 502

Query: 521 PAWQTSSMGHPFSSNGKI--HGLPYSGRQGSFLGSS---QHHHVGSAPSGVPLERRFGFL 575
           P W+  ++GH   SN +    GL Y GRQ S  GS     HHHVGSAPSG P E  FGFL
Sbjct: 503 PIWRPPAIGHAIPSNTRSQGQGLLYGGRQASLFGSQDQLHHHHVGSAPSGAPFESHFGFL 562

Query: 576 PESPETSFMNPVAF---CGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNG-SSFRVM 631
           PESPETS+MN V F     +G G+N    M+NM +RASVNP   +  N+SDN  SSFR +
Sbjct: 563 PESPETSYMNQVRFGNIGNIGSGRNGTGLMLNMAARASVNPVSALSGNMSDNNSSSFRPI 622

Query: 632 SSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGE 691
            SPRL   F GN  Y G     ++   ERGR+RR++++   Q DSKKQ+QL+LEKIR G+
Sbjct: 623 LSPRLGQSFYGNPTYQGPGSFGLDNSIERGRNRRVDSSVF-QADSKKQYQLDLEKIRKGD 681

Query: 692 DTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHI 751
           DTRTTLMIKNIPNKYTSKMLLAAIDE HKGTYDF YLPIDFKNKCNVGYAFINM+SP+HI
Sbjct: 682 DTRTTLMIKNIPNKYTSKMLLAAIDEFHKGTYDFFYLPIDFKNKCNVGYAFINMISPVHI 741

Query: 752 IPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGP 811
           + FY+AFNGKKWEKFNSEKVASLAYARIQGR AL++HFQNSSLMNEDKRCRPILFHS GP
Sbjct: 742 VSFYQAFNGKKWEKFNSEKVASLAYARIQGRTALISHFQNSSLMNEDKRCRPILFHSNGP 801

Query: 812 EAGDQ 816
           +AG+Q
Sbjct: 802 DAGNQ 806

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 =  899 bits (2324), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 504/813 (61%), Positives = 613/813 (75%), Gaps = 47/813 (5%)

Query: 17  LNIPKEVGGGSCGRIAG-SDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISS 75
           ++IP E   G+ G + G    +  S DA+LFSSSLPV P  KL L+    G   +DD  +
Sbjct: 1   MDIPHEAEAGAWGILPGFGRHHHPSSDATLFSSSLPVFPRGKLQLSDNRDGFSLIDD--T 58

Query: 76  GLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIF 135
            +S+ +    S D  E   + +IGN LPD+ED LL G+MDD DL  LP    D +DYD+F
Sbjct: 59  AVSRTNKFNESADDFE---SHSIGNLLPDEED-LLTGMMDDLDLGELP----DADDYDLF 110

Query: 136 GSGGGMELEGEPQESLSMSMS-KISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRT 194
           GSGGGMEL+ + +++LSMS   ++S+S S  GN +  +++PNGAGTVAGEHPYGEHPSRT
Sbjct: 111 GSGGGMELDADFRDNLSMSGPPRLSLS-SLGGNAIPQFNIPNGAGTVAGEHPYGEHPSRT 169

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFVRNINSNVEDSEL ALFEQYGDIRTLYT CKHRGFVMISYYDIR+AR AMR+LQNKPL
Sbjct: 170 LFVRNINSNVEDSELTALFEQYGDIRTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPL 229

Query: 255 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR 314
           RRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLDPS+SN+DL  IFGA+GE+KEIRETPHKR
Sbjct: 230 RRRKLDIHFSIPKDNPSEKDMNQGTLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKR 289

Query: 315 HHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRIL 374
           HHKF+EFYDVR AEAALK+LNR +IAGKRIK+EPSRPGGARR+LMLQLNQ+LE D+   L
Sbjct: 290 HHKFVEFYDVRGAEAALKALNRCEIAGKRIKVEPSRPGGARRSLMLQLNQDLENDDLHYL 349

Query: 375 QHQVGSPITNSPP--GNWVQFSSPIEHNPLQTI-SKSPNFRNMSPTTSNHMPGLASILHP 431
              +GSP+ NSPP  GNW   +SP+E +PLQ++ S+SP F  +SPT + H+ GLAS L+ 
Sbjct: 350 P-MIGSPMANSPPMQGNW-PLNSPVEGSPLQSVLSRSPVF-GLSPTRNGHLSGLASALNS 406

Query: 432 QVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNS-FSEPKI-GLYRGTVSSFG 489
           Q  +  K+APIG+ Q             I +NG  FQQS+  F EPK+   Y G +S  G
Sbjct: 407 QGPS-SKLAPIGRGQ-------------IGSNG--FQQSSHLFQEPKMDNKYTGNLSPSG 450

Query: 490 PSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGS 549
           P  SNG G+ETLSG +FLWGSP+  SE SSS  W TSS G+P  S      +P+  +  +
Sbjct: 451 PLISNGGGIETLSGSEFLWGSPNARSEPSSSSVWSTSSTGNPLFSTRVDRSVPFPHQHQN 510

Query: 550 FLGSSQHHHVGSAPSGVPLERRFGFLPESPETS-FMNPVAFCGM-GIGQNDGSFMVNMGS 607
              S  H HVGSAPSGVPLE+ FGF+PES + + FMN V   GM G+G N GSF   M +
Sbjct: 511 QSRSHHHFHVGSAPSGVPLEKHFGFVPESSKDALFMNTVGLQGMSGMGLNGGSFSSKMAN 570

Query: 608 RASVNPGITVPRNLSDNG-SSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRI 666
              +N G     ++++NG SS+R+MSSPR SP+FL +G  PG   +  + LYE GR RR+
Sbjct: 571 NGIINSG-----SMAENGFSSYRMMSSPRFSPMFLSSGLNPGRFASGFDSLYENGRPRRV 625

Query: 667 ENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFL 726
           ENN+ NQ++S+KQFQL+LEKI +GED+RTTLMIKNIPNKYTSKMLLAAIDE ++GTY+FL
Sbjct: 626 ENNS-NQVESRKQFQLDLEKILNGEDSRTTLMIKNIPNKYTSKMLLAAIDEKNQGTYNFL 684

Query: 727 YLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALV 786
           YLPIDFKNKCNVGYAFINML+P  IIPFYEAFNGKKWEKFNSEKVASLAYARIQG++AL+
Sbjct: 685 YLPIDFKNKCNVGYAFINMLNPELIIPFYEAFNGKKWEKFNSEKVASLAYARIQGKSALI 744

Query: 787 AHFQNSSLMNEDKRCRPILFHS-EGPEAGDQVM 818
           AHFQNSSLMNED RCRPI+F +   PE+ +QV+
Sbjct: 745 AHFQNSSLMNEDMRCRPIIFDTPNNPESVEQVV 777

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  799 bits (2063), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 460/797 (57%), Positives = 561/797 (70%), Gaps = 80/797 (10%)

Query: 17  LNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSG 76
           +NIP        G  + SD + AS DASLFSSSLP++ H+  N+N      QSVD+++SG
Sbjct: 1   MNIP-------SGTFSRSDHFHASSDASLFSSSLPLIQHQ--NINPRDSYHQSVDEMASG 51

Query: 77  LSKVHHGVAS--DDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDI 134
           L     G+ +  DD   G  +P IGN LPDDE+EL +G+MDD +L  LP++L+DLEDYD+
Sbjct: 52  LDHFSGGIGNMLDD---GDSHP-IGNMLPDDEEELFSGLMDDLNLSSLPATLDDLEDYDL 107

Query: 135 FGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRT 194
           FGSGGG+ELE +P +SL+   S++  +DS   N +      NG G++AGEHPYGEHPSRT
Sbjct: 108 FGSGGGLELETDPYDSLNKGFSRMGFADSNVDNVMPQNIFQNGVGSIAGEHPYGEHPSRT 167

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFVRNINSNVEDSEL+ALFEQYG IRTLYTACK RGFVM+SY DIRA+R AMRALQ K L
Sbjct: 168 LFVRNINSNVEDSELQALFEQYGHIRTLYTACKQRGFVMVSYNDIRASRAAMRALQGKLL 227

Query: 255 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR 314
           ++RKLDIHFSIPKDNPS+KD+NQGTLVVFNL PSVSN DL  IFG YGE+KEIRETP+KR
Sbjct: 228 KKRKLDIHFSIPKDNPSEKDVNQGTLVVFNLAPSVSNRDLENIFGVYGEIKEIRETPNKR 287

Query: 315 HHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRIL 374
           HHKF+EF+DVR+A+AALK+LNR++IAGKRIKLE SRPGGARRN+MLQ+N ELEQD+S   
Sbjct: 288 HHKFVEFFDVRSADAALKALNRTEIAGKRIKLEHSRPGGARRNMMLQMNPELEQDDSYSY 347

Query: 375 QHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVS 434
            + V SP+ +SP GNW   +SPI+H PLQ+ SKSP F N+SPT         +I +P+ S
Sbjct: 348 LNHVESPLASSPIGNWR--NSPIDH-PLQSFSKSPIFGNLSPTK--------NIRYPEFS 396

Query: 435 TLEKIAPIGKDQG--RGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSP 492
              K A +  DQ   R S ++H  +++ S N AS + S +F +P+      +  S    P
Sbjct: 397 M--KTASVNNDQEGRRFSHLDHLFSSS-SYNNASHKAS-TFQQPQSFGSVSSFGSLNSHP 452

Query: 493 SNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLG 552
           S+   VETLSG +FLWGSP       SS AW  +    PFSSN + H  PYS + GS   
Sbjct: 453 SH---VETLSGSEFLWGSP-------SSSAWPVN----PFSSNRENHRFPYSAQNGSL-- 496

Query: 553 SSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVN 612
             Q HH+GSAPS        GF P SPETS M  VAF G                 AS N
Sbjct: 497 -HQLHHIGSAPS--------GFFPRSPETSSMGSVAFRG-----------------ASGN 530

Query: 613 PGITVPRNLSDNGS-SFRVMSSPRLSPVFLGNGPY--PGLTPANIEGLYERGRSRRIENN 669
             +   RNL +  S +F+++S+PR S +F GNG Y  P  T  +I+   E G +++ + +
Sbjct: 531 --MNAQRNLRETSSPNFKMLSAPRRSQLFTGNGSYLWPAATMVSIDDPLEDGSNQQFD-S 587

Query: 670 NGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLP 729
           NGNQ D K QFQL+L KI  GED RTTLMIKNIPNKYT  MLLAAIDE + GTYDFLYLP
Sbjct: 588 NGNQADIKIQFQLDLSKIMRGEDPRTTLMIKNIPNKYTRNMLLAAIDEKNSGTYDFLYLP 647

Query: 730 IDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHF 789
           IDFKNKCNVGYAFINM+SP   I  YEAFNGKKW+KFNSEKVASLAYARIQG+AAL+AHF
Sbjct: 648 IDFKNKCNVGYAFINMVSPKFTIALYEAFNGKKWDKFNSEKVASLAYARIQGKAALIAHF 707

Query: 790 QNSSLMNEDKRCRPILF 806
           QNSSLMNED+RC+PI+F
Sbjct: 708 QNSSLMNEDRRCQPIVF 724

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 =  751 bits (1939), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 425/833 (51%), Positives = 537/833 (64%), Gaps = 67/833 (8%)

Query: 1   MKQFFDH--SSGPPKIP-----QLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLP-V 52
           M+Q  DH  SS P  IP     Q+      GG S   + GS       DA LFSSSLP V
Sbjct: 1   MEQREDHTKSSEPAFIPSKRTHQMRNIWAWGGPSSTTVNGSS------DAVLFSSSLPSV 54

Query: 53  LPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAG 112
           L   KL         Q  DD+   + +        DP++ V    IGN LPDDE ELLAG
Sbjct: 55  LQFGKLPGKEREYNAQPKDDMFPMMKQPGTNARVADPMDDVAQHLIGNLLPDDE-ELLAG 113

Query: 113 IMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHY 172
           +++DFD   L + +E+ E+YD+F + GGMEL+ +P ES++   +K S+ +  +G+    Y
Sbjct: 114 VIEDFDHVKLRTQVEESEEYDVFRNSGGMELDIDPLESITFGTAKASLVN-GTGSSTNQY 172

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFV 232
           S+ NGAGTV GEHPYGEHPSRTLFVRNINSNVEDSELR+LFE +GDIR++YTA KHRGFV
Sbjct: 173 SIQNGAGTVTGEHPYGEHPSRTLFVRNINSNVEDSELRSLFEPFGDIRSMYTATKHRGFV 232

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNE 292
           MISYYDIR AR A  ALQ+KPLRRRKLDIH+SIPK+NPSDKD+NQGTLV+FNL+P+VSNE
Sbjct: 233 MISYYDIRHARNAKTALQSKPLRRRKLDIHYSIPKENPSDKDMNQGTLVIFNLEPAVSNE 292

Query: 293 DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 352
           +L QIFGA+GEV+EIRETPHKRHH+FIEFYDVRAAE+AL+SLN+SDIAGKR+KLEPSRPG
Sbjct: 293 ELLQIFGAFGEVREIRETPHKRHHRFIEFYDVRAAESALRSLNKSDIAGKRVKLEPSRPG 352

Query: 353 GARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFR 412
           GARR+ +   N E EQDE++    Q+GSP  NSPP  W Q  SP + N L  ++++    
Sbjct: 353 GARRSFIQHFNHEFEQDETKHNSFQIGSPSANSPPSLWSQLGSPTDENKLNALNETAFNG 412

Query: 413 NMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNS 472
            MSP  SNH+ G +S   P  S      P+GK     S   +   + I     +   S+S
Sbjct: 413 GMSPLGSNHLSGFSSGYPPMKS------PVGK-----SSYWNNRADNIFHGSPTLHNSHS 461

Query: 473 FSEPKIGLYRGTVSSFGPSPSNGS--GVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGH 530
           F E   G+   +      + S  +  G   L+G  FLWG+ +   +H    + Q+ ++ +
Sbjct: 462 FPEHHGGIISASPLVSSAASSASTASGFTALTGTSFLWGNNNNLRDHGQPSSIQSQALSN 521

Query: 531 PFSSNGKIHGLP--YSGRQGSFLGSSQHH---HVGSAPSGVPLERRFGFLPESPETSFMN 585
               N +       Y   +GSF G+S+H    +VGSAPS  P E  FG+  +SP+TS+M 
Sbjct: 522 SLFPNNQPQRQSNLYQNLRGSF-GASEHFSQFNVGSAPSVFPFESNFGYFSDSPDTSYMR 580

Query: 586 PVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGP 645
              F G G  +  GS M N G+                          PR++   + NG 
Sbjct: 581 QGKFGGTGPTRVSGSLMTNFGAY-------------------------PRINVASMQNGS 615

Query: 646 YPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNK 705
                    EGL +RGR++ +  N+G Q DS+ Q+QL+LEKI +G+DTRTTLMIKNIPNK
Sbjct: 616 ------VGFEGLLDRGRNQTV-GNSGCQEDSRVQYQLDLEKIIAGKDTRTTLMIKNIPNK 668

Query: 706 YTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEK 765
           YTS MLL  IDE H+GTYDF YLPIDFKNKCNVGYAFINM SP +I+ F++AF G+KWEK
Sbjct: 669 YTSNMLLEVIDETHEGTYDFFYLPIDFKNKCNVGYAFINMASPGYIVSFFKAFAGRKWEK 728

Query: 766 FNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVM 818
           FNSEKV SLAYARIQG+AALV HFQNSSLMNEDKRCRP+LF  +  E  +Q++
Sbjct: 729 FNSEKVVSLAYARIQGKAALVNHFQNSSLMNEDKRCRPMLFDPKHTENNNQIL 781

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 =  667 bits (1720), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 376/773 (48%), Positives = 494/773 (63%), Gaps = 32/773 (4%)

Query: 50  LPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDEL 109
           LP L HEKLN+        S D+ S  L+K+  G +  D LE V   A+   LP+DE+EL
Sbjct: 56  LPTLFHEKLNMTDSD-SWLSFDESSPNLNKLVIGNSEKDSLEDVEPDALEILLPEDENEL 114

Query: 110 LAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGL 169
           L G++D+ +  GLP  L+DLE+ D+F +GGGMEL+ E Q++ ++  S + ISD  + N  
Sbjct: 115 LPGLIDELNFTGLPDELDDLEECDVFCTGGGMELDVESQDNHAVDASGMQISDRGAANAF 174

Query: 170 LHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR 229
           +    PN AG V+ EHP GEHPSRTLFVRNINS+VEDSEL ALFE +G+IR+LYTACK R
Sbjct: 175 VPRKRPNTAGRVSVEHPNGEHPSRTLFVRNINSSVEDSELSALFEPFGEIRSLYTACKSR 234

Query: 230 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSV 289
           GFVMISYYDIRAA  AMRALQN  LR+R LDIHFSIPK+NPS+KD+NQGTLV+FN+D +V
Sbjct: 235 GFVMISYYDIRAAHAAMRALQNTLLRKRTLDIHFSIPKENPSEKDMNQGTLVIFNVDTTV 294

Query: 290 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS 349
           SN++L Q+FGAYGE++EIRETP++R H+FIE+YDVR AE ALK+LNRS+I GK IKLE S
Sbjct: 295 SNDELLQLFGAYGEIREIRETPNRRFHRFIEYYDVRDAETALKALNRSEIGGKCIKLELS 354

Query: 350 RPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSP 409
           RPGGARR  +   +Q+LE+ E     +QVGS + NSPPGNW    SP++ +P    ++  
Sbjct: 355 RPGGARRLSVPSQSQDLERTEVTNFYNQVGSHVANSPPGNW-PIGSPVKGSPSHAFTRPH 413

Query: 410 NFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQ 469
               + P  S++MPGLASIL    S+    +P+  DQG  +     + N    +  S+ Q
Sbjct: 414 GLGMVRPVNSDNMPGLASILPAHPSSFHGFSPVSNDQGLLNHSNQTILNKGLMHNISYGQ 473

Query: 470 SNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQ----- 524
            +S  E   G    ++    P   + SG  T S  ++ WGSP    +H + P +      
Sbjct: 474 PHSLPEHITGGISNSMRFIAP---HSSGFGTSSDHRYRWGSP---PQHMNYPGYTGVSSS 527

Query: 525 TSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFM 584
           +SS   PF+     HG P++ RQ S LG  Q HHVGSAPS +    +      SPE    
Sbjct: 528 SSSTERPFTVR---HGFPFAERQASLLGKYQ-HHVGSAPSSIHFNTQMNCYTGSPEI--- 580

Query: 585 NPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNG 644
            P+ F  MGI +N  S      +    N G+++P N S+   +   MSS    P     G
Sbjct: 581 -PLGFSDMGINRNYNS------AHGKANLGVSLPGNSSEQDFTGFGMSSMPTVPF----G 629

Query: 645 PYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPN 704
              GL     E   E+GR    E++N NQ     ++ ++L++I SG++ RTTL+IKNIPN
Sbjct: 630 GSRGLQSVRPEPFAEQGRIHNHESHNQNQFIDGGRYHIDLDRIASGDEIRTTLIIKNIPN 689

Query: 705 KYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWE 764
           KYT KML+A IDE HKG YDFL LP DFKNKCN+G+AFINM+SPLHI+PF + FNGK WE
Sbjct: 690 KYTYKMLVAEIDEKHKGDYDFLCLPTDFKNKCNMGHAFINMVSPLHIVPFQQTFNGKIWE 749

Query: 765 KFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRP-ILFHSEGPEAGDQ 816
           KFNS KVASLAYA IQG++AL ++ Q  S M E K+  P + +H +G +A D 
Sbjct: 750 KFNSGKVASLAYAEIQGKSALASYMQTPSSMKEQKQLFPEVSYHDDGQDANDH 802

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 =  479 bits (1233), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 333/804 (41%), Positives = 437/804 (54%), Gaps = 109/804 (13%)

Query: 64  GLGRQSVDDISSGLSKVHHGVA-SDDPLE---GVMNPAIGNSLPDDEDELLAGIMDDFDL 119
           G  R+ V  +    +  H  +  SD+PLE    +    IG+ LPDD+D+L++GI D F+ 
Sbjct: 156 GKSREIVSGVLCQSTGTHTSIYDSDEPLESMEAIEAQTIGDLLPDDDDDLISGIADGFEF 215

Query: 120 RGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAG 179
            G+ S+ +D  D DIF +GGGMELE                +DS  G+ +   S  +   
Sbjct: 216 TGM-STNQDDADEDIFCTGGGMELEN---------------NDSVKGDKVQDGSFKS--- 256

Query: 180 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 239
            ++  H   + PSRTL VRNI +N+EDS+L  LF+QYGDIR LYT+ KH GFV +SYYDI
Sbjct: 257 QISSGHSINKQPSRTLVVRNITANIEDSDLTVLFQQYGDIRMLYTSFKHHGFVTVSYYDI 316

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 299
           RAA+ AMRAL +KPL   KLD+ FS PK+N   KD+++G LVV N+D S+SN+DL Q+  
Sbjct: 317 RAAQNAMRALHSKPLGLMKLDVQFSFPKENVPGKDIDKGMLVVSNIDSSISNDDLLQMLS 376

Query: 300 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 359
            YG+VKEI  +P     KF+EFYDVRAAE AL  LN+  I+G + K+E S+ G A   L 
Sbjct: 377 VYGDVKEISSSPISCTKKFVEFYDVRAAEEALHDLNKGGISGPKFKVELSQHGEAGSCLR 436

Query: 360 LQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHN-PLQTISKSPNFRNMSPTT 418
            Q ++E +QD    L HQ      NS PG   +  +  + N  +  +    N +  SPT 
Sbjct: 437 QQHSREWKQDS---LPHQP----KNSSPGTIGKLGTKCQDNSTVHNLFSPVNQQLESPTQ 489

Query: 419 SNHMPGLASILHP-----------QVSTLEKIAPIGKDQ-GRG-------SLMEHALTNT 459
                G   +  P           Q S  +   P+G+   GRG       SL EH   N 
Sbjct: 490 CISTTGPQILSSPIRIKSTLQHNNQASVGDLSGPLGQGNFGRGIQTLHPRSLPEHH--NR 547

Query: 460 ISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVET--------------LSGPQ 505
           I  N  S   S   +  +       +   GP+   G   +               L G  
Sbjct: 548 ICNNSKSMTVSGRNASSRQDGVDHNIQKVGPAGFCGHSFDQNNEAFGFTEIGSCPLHGYH 607

Query: 506 FLWGSPSRYSEHSSSPA-WQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPS 564
           + W   + + +  S+P  W  S++ HP   +      P+    GS+      HH+GSAP 
Sbjct: 608 YTWNHTNVFPQSPSAPILW--SNLQHPMHVHSYPGVPPHMLNTGSY--PMDQHHLGSAPD 663

Query: 565 GVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDN 624
                            SF N  +F    +G        ++G   S  P +  P  LS  
Sbjct: 664 N--------------GGSFGNVHSFHPGSLG--------SIGLHGS--PQL-YPSELSAF 698

Query: 625 GSSFRVMSSPRLSPVFLG-----------NGPYPGL-TPANIEGLYERGRSRRIENNNGN 672
            SS         SPV  G           NG  P +    + +   +R RSRR  + N  
Sbjct: 699 ASSRGNFREALFSPVGGGFQSLQQMCNAINGRNPMIHVSTSYDATNDRMRSRR-HDGNPA 757

Query: 673 QLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDF 732
           Q ++K+QF+L++++I  GED+RTTLMIKNIPNKY  K+LLA IDENH+GTYDF+YLPIDF
Sbjct: 758 QSENKRQFELDIDRIAKGEDSRTTLMIKNIPNKYNCKLLLAVIDENHRGTYDFIYLPIDF 817

Query: 733 KNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNS 792
           KNKCNVGYAFINM  P HIIPFY+ FNGKKWEKFNSEKVASLAYARIQGR+AL+AHFQNS
Sbjct: 818 KNKCNVGYAFINMTDPQHIIPFYKTFNGKKWEKFNSEKVASLAYARIQGRSALIAHFQNS 877

Query: 793 SLMNEDKRCRPILFHSEGPEAGDQ 816
           SLMNEDK CRP+LFH +GP AGDQ
Sbjct: 878 SLMNEDKWCRPMLFHKDGPNAGDQ 901

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  298 bits (762), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 199/368 (54%), Positives = 254/368 (69%), Gaps = 37/368 (10%)

Query: 27  SCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAM-GLGRQSVDDISSGLSKVHHGVA 85
           S GRI  + +Y   ++  LFSSS+  +  +KL L +  GL  QS++       KV     
Sbjct: 129 SDGRINPNGAY---NENGLFSSSVSDIFDKKLRLTSKNGLVGQSIE-------KVDLNHV 178

Query: 86  SDDPLE---GVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYD--IFGSGGG 140
            D+P E    +    IGN L  D+D+LL+G++D+    G P++  + +D D  IF +GGG
Sbjct: 179 DDEPFELTEEIEAQIIGNLL-PDDDDLLSGVVDEV---GYPTNANNRDDADDDIFYTGGG 234

Query: 141 MELEGEPQESLSMSMSKISISDSAS-GNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRN 199
           MELE +  + L         + SA+ G GLL+       G + GEH Y E PSRTLFVRN
Sbjct: 235 MELETDENKKLQ------EFNGSANDGIGLLN-------GVLNGEHLYREQPSRTLFVRN 281

Query: 200 INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL 259
           INSNVEDSEL+ LFE +GDIR LYTACKHRGFVMISYYDIR+A  A   LQNK LRRRKL
Sbjct: 282 INSNVEDSELKLLFEHFGDIRALYTACKHRGFVMISYYDIRSALNAKMELQNKALRRRKL 341

Query: 260 DIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFI 319
           DIH+SIPKDNPS+KD+NQGT+V+FN+D S++N+DL +IFG YGE+KEIR+TP K HHK I
Sbjct: 342 DIHYSIPKDNPSEKDINQGTIVLFNVDLSLTNDDLHKIFGDYGEIKEIRDTPQKGHHKII 401

Query: 320 EFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVG 379
           EFYDVRAAEAAL++LNR+DIAGK+IKLE SR G ARR L   ++ EL Q+E  +   ++G
Sbjct: 402 EFYDVRAAEAALRALNRNDIAGKKIKLETSRLGAARR-LSQHMSSELCQEEFGVC--KLG 458

Query: 380 SPITNSPP 387
           SP T+SPP
Sbjct: 459 SPSTSSPP 466

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  273 bits (697), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 152/267 (56%), Positives = 189/267 (70%), Gaps = 12/267 (4%)

Query: 556 HHHVGSAPS-GVPL-ERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNP 613
           HHH+GSAP    P  +RR  ++ ESPE+S  +  +   MG   +  S  ++ GS    + 
Sbjct: 603 HHHIGSAPVLNSPFWDRRQAYVAESPESSGFHLGSPGSMGFPGSSPSHPMDFGSHKVFS- 661

Query: 614 GITVPRNLSDNGSSFRVMSSPRLSP-VFLGNGPYPGLTPANIEGLYERGRS---RRIENN 669
              V  N  +  S   V+ S R  P +F G  P   ++  + +   ER R+   RR E+N
Sbjct: 662 --HVGGNRMEANSKNAVLRSSRQMPHLFTGRSPMLSVS-GSFDLPNERYRNLSHRRSESN 718

Query: 670 NGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLP 729
           + N    KK ++L++++I  GED+RTTLMIKNIPNKYTSKMLLAAIDE  KGTYDFLYLP
Sbjct: 719 SSNA--EKKLYELDVDRILRGEDSRTTLMIKNIPNKYTSKMLLAAIDEYCKGTYDFLYLP 776

Query: 730 IDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHF 789
           IDFKNKCNVGYAFIN++ P +I+PFY+AFNGKKWEKFNSEKVASLAY RIQG++AL+AHF
Sbjct: 777 IDFKNKCNVGYAFINLIEPENIVPFYKAFNGKKWEKFNSEKVASLAYGRIQGKSALIAHF 836

Query: 790 QNSSLMNEDKRCRPILFHSEGPEAGDQ 816
           QNSSLMNEDKRCRPILFH+ GP AGDQ
Sbjct: 837 QNSSLMNEDKRCRPILFHTAGPNAGDQ 863

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  228 bits (582), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 128/259 (49%), Positives = 172/259 (66%), Gaps = 19/259 (7%)

Query: 97  AIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMS 156
            IGN LPD ED+L A +  +   +   ++ ++L+++D+F S GGMEL+G+   S+S    
Sbjct: 140 TIGNLLPD-EDDLFAEVTGEVGRKSRANTGDELDEFDLFSSVGGMELDGDIFSSVS---- 194

Query: 157 KISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQY 216
                         H +   G     GE   GE PSRTL V NI+SNVED EL+ LFEQ+
Sbjct: 195 --------------HRNGERGGNNSVGELNRGEIPSRTLLVGNISSNVEDYELKVLFEQF 240

Query: 217 GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLN 276
           GDI+ L+TACK+RGF+M+SY DIRAA+ A RALQNK LR  KLDI +SI K+NPS KD +
Sbjct: 241 GDIQALHTACKNRGFIMVSYCDIRAAQNAARALQNKLLRGTKLDIRYSISKENPSQKDTS 300

Query: 277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           +G L+V NLD S+SN++L ++  +YGEVKEIR T H     +IEF+DVRAA AAL  LN 
Sbjct: 301 KGALLVNNLDSSISNQELNRLVKSYGEVKEIRRTMHDNSQIYIEFFDVRAAAAALGGLNG 360

Query: 337 SDIAGKRIKLEPSRPGGAR 355
            ++AGK+++L P+ P G R
Sbjct: 361 LEVAGKKLQLVPTYPEGTR 379

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

 Score =  156 bits (395), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 76/142 (53%), Positives = 98/142 (69%), Gaps = 3/142 (2%)

Query: 682 LELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYA 741
           ++  +I SG DTRTT+MIKNIPNK+T +ML   ID  +KGTYDFLYL IDF NKCNVGYA
Sbjct: 584 VDYAQIASGIDTRTTVMIKNIPNKFTQQMLRDYIDVTNKGTYDFLYLRIDFVNKCNVGYA 643

Query: 742 FINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRC 801
           FIN + P  II F +A  G +W  F+SEK+  ++YA IQG+  L+  F+NS +M+E+   
Sbjct: 644 FINFIEPQSIITFGKARVGTQWNVFHSEKICDISYANIQGKDRLIEKFRNSCVMDENPAY 703

Query: 802 RPILFHSEGPEAGDQVMQLTFP 823
           RP +F S GP  G   M+  FP
Sbjct: 704 RPKIFVSHGPNRG---MEEPFP 722

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	823
47834701	858	AML1 [Citrus unshiu]	0.995	0.954	0.991	0.0
225463378	860	PREDICTED: protein MEI2-like 2-like [Vit	0.981	0.939	0.776	0.0
356556525	862	PREDICTED: protein MEI2-like 2-like [Gly	0.990	0.945	0.762	0.0
356530557	862	PREDICTED: protein MEI2-like 2-like [Gly	0.990	0.945	0.753	0.0
359485142	842	PREDICTED: protein MEI2-like 2-like [Vit	0.970	0.948	0.726	0.0
357450609	865	Polyadenylate-binding protein [Medicago	0.995	0.946	0.716	0.0
297740630	787	unnamed protein product [Vitis vinifera]	0.867	0.907	0.695	0.0
356567420	857	PREDICTED: protein MEI2-like 2-like [Gly	0.976	0.938	0.692	0.0
357450611	764	Polyadenylate-binding protein [Medicago	0.872	0.939	0.742	0.0
449444985	846	PREDICTED: protein MEI2-like 2-like [Cuc	0.978	0.951	0.682	0.0

>gi|47834701|gb|AAT39004.1| AML1 [Citrus unshiu]

 Score = 1669 bits (4323), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 812/819 (99%), Positives = 817/819 (99%)

Query: 1   MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNL 60
           MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNL
Sbjct: 1   MKQFFDHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNL 60

Query: 61  NAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLR 120
           NAMGLGRQSVD+ISSGLSKVHHGV+SDDPLEG+MNPAIGNSLPDDEDELLAGIMDDFDLR
Sbjct: 61  NAMGLGRQSVDNISSGLSKVHHGVSSDDPLEGIMNPAIGNSLPDDEDELLAGIMDDFDLR 120

Query: 121 GLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGT 180
           GLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGT
Sbjct: 121 GLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGT 180

Query: 181 VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIR 240
           VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIR
Sbjct: 181 VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIR 240

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA 300
           AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA
Sbjct: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA 300

Query: 301 YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML 360
           YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML
Sbjct: 301 YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML 360

Query: 361 QLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSN 420
           QLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSN
Sbjct: 361 QLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSN 420

Query: 421 HMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGL 480
           HMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGL
Sbjct: 421 HMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGL 480

Query: 481 YRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHG 540
           YRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHG
Sbjct: 481 YRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHG 540

Query: 541 LPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGS 600
           LPYSGRQGSFLGSSQHHH+GSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGS
Sbjct: 541 LPYSGRQGSFLGSSQHHHIGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGS 600

Query: 601 FMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYER 660
           FMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPAN EGLYER
Sbjct: 601 FMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANSEGLYER 660

Query: 661 GRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHK 720
           GRSRRIENNNGNQ+DSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHK
Sbjct: 661 GRSRRIENNNGNQIDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHK 720

Query: 721 GTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQ 780
           GTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQ
Sbjct: 721 GTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQ 780

Query: 781 GRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVMQ 819
           GRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQV Q
Sbjct: 781 GRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVTQ 819

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225463378|ref|XP_002271605.1| PREDICTED: protein MEI2-like 2-like [Vitis vinifera]

 Score = 1280 bits (3312), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 633/815 (77%), Positives = 710/815 (87%), Gaps = 7/815 (0%)

Query: 13  KIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDD 72
           KIP ++IPK VG G+ G   GSD Y AS+DA+LFS SLPVLPHEKLNLN      QS+DD
Sbjct: 14  KIPYVSIPKAVGSGAWGMRPGSDGYNASNDATLFSCSLPVLPHEKLNLNDTEHCCQSIDD 73

Query: 73  ISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDY 132
             +GL K+   V + + LE     AIG+ LPDDEDELLAGIMDDFDL GL + +ED+E+Y
Sbjct: 74  --AGLDKLQQDVEAGESLEDDGIHAIGSLLPDDEDELLAGIMDDFDLSGLSNPMEDVEEY 131

Query: 133 DIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPS 192
           D+FGSGGGMELE +PQESL+M M+K+S+SD   GNGL  Y +PNG+GTVAGEHPYGEHPS
Sbjct: 132 DLFGSGGGMELEIDPQESLNMGMAKVSLSDGVVGNGLAQYGLPNGSGTVAGEHPYGEHPS 191

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 252
           RTLFVRNINSNVEDSELR LFEQYG IRTLYTACKHRGFVMISYYDIRAARTAMRALQNK
Sbjct: 192 RTLFVRNINSNVEDSELRTLFEQYGAIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 251

Query: 253 PLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH 312
           PLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVSN+DLRQIFGAYGEVKEIRETPH
Sbjct: 252 PLRRRKLDIHFSIPKDNPSDKDVNQGTLVVFNLDPSVSNDDLRQIFGAYGEVKEIRETPH 311

Query: 313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 372
           KRHHKFIEFYDVRAAEAAL+SLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR
Sbjct: 312 KRHHKFIEFYDVRAAEAALRSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 371

Query: 373 ILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQ 432
             +H VGSP+ NSPPG+W QFSSPIEH+PLQ++SKSP FR +SPTTSNH+PGLASIL+ Q
Sbjct: 372 SFRHHVGSPMANSPPGSWAQFSSPIEHSPLQSLSKSPGFRTVSPTTSNHLPGLASILNSQ 431

Query: 433 VSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSP 492
           +S   K+APIGKDQGRG  +E+   NT S +G +FQQS+SFSEP +G Y G  SSFG S 
Sbjct: 432 ISNSVKVAPIGKDQGRGIHVENIFNNTNSNHGTAFQQSHSFSEPNLGPYPGNGSSFGAST 491

Query: 493 SNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLG 552
           SNGSG+ETLSGPQFLWGSP+ YSEH++S AWQ  SMGHPF+SNG+  G PYSGR GSFLG
Sbjct: 492 SNGSGIETLSGPQFLWGSPAPYSEHTNSSAWQPPSMGHPFASNGQGRGFPYSGRHGSFLG 551

Query: 553 SSQ---HHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRA 609
           SS+   HHHVGSAPSGVPLER FG+ PESPE SFM PVAF GMG+  NDGSFM+NM +RA
Sbjct: 552 SSRHHHHHHVGSAPSGVPLERHFGYFPESPEASFMTPVAFGGMGLAHNDGSFMLNMSARA 611

Query: 610 SVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIEN 668
            +N GI++P N+S++GS+ FR++SSPRLSP+F GNGP+PGL P+NIEGL +RGRSR +E 
Sbjct: 612 GMNAGISIPANMSESGSANFRMISSPRLSPMFPGNGPFPGLAPSNIEGLADRGRSRWVE- 670

Query: 669 NNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYL 728
           NNGNQ+DSKKQFQL+L+KI +GEDTRTTLMIKNIPNKYTSKMLLAAIDE H+GTYDFLYL
Sbjct: 671 NNGNQIDSKKQFQLDLDKILNGEDTRTTLMIKNIPNKYTSKMLLAAIDEYHRGTYDFLYL 730

Query: 729 PIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAH 788
           PIDFKNKCNVGYAFINMLSP HIIPFY+AFNGKKWEKFNSEKVASLAYARIQG+AALV H
Sbjct: 731 PIDFKNKCNVGYAFINMLSPSHIIPFYQAFNGKKWEKFNSEKVASLAYARIQGKAALVTH 790

Query: 789 FQNSSLMNEDKRCRPILFHSEGPEAGDQVMQLTFP 823
           FQNSSLMNEDKRCRPILFHSEGPEAGDQ++Q   P
Sbjct: 791 FQNSSLMNEDKRCRPILFHSEGPEAGDQIIQEHLP 825

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556525|ref|XP_003546575.1| PREDICTED: protein MEI2-like 2-like [Glycine max]

 Score = 1234 bits (3193), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 628/824 (76%), Positives = 693/824 (84%), Gaps = 9/824 (1%)

Query: 1   MKQFFDHSS-GPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLN 59
           M+Q FD S  GP KIP + +P + G G+   ++GSDSY AS DASLFSSSLPVLPHEKLN
Sbjct: 1   MRQSFDPSFLGPSKIPSIKVPGKAGNGAWEALSGSDSYHASSDASLFSSSLPVLPHEKLN 60

Query: 60  LNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDL 119
           LN    G QS+DDISSG  K+H     +  LE     AIG +LPDDE+ELLAGI DDFDL
Sbjct: 61  LNETANGYQSIDDISSGFKKLHQDADGNGSLEDGDTHAIGPALPDDEEELLAGITDDFDL 120

Query: 120 RGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAG 179
            GLP SLEDLE+YD+FGSGGGMELE +PQE L++ +SK+S +DS  GNGL  YS PNG G
Sbjct: 121 SGLPGSLEDLEEYDLFGSGGGMELETDPQEGLTVGLSKLSFADSTVGNGLPPYSFPNGVG 180

Query: 180 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 239
           TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI
Sbjct: 181 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 240

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 299
           RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVSNEDLRQIFG
Sbjct: 241 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDINQGTLVVFNLDPSVSNEDLRQIFG 300

Query: 300 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 359
           AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM
Sbjct: 301 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 360

Query: 360 LQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTS 419
           LQLNQEL+QDESR  ++QVGSP+ NSPPGNW+QF+SP+E N +QTI+ SP  R +SPTT 
Sbjct: 361 LQLNQELDQDESRSFRYQVGSPVANSPPGNWLQFNSPVEQNSMQTINYSPGSRIISPTTG 420

Query: 420 NHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIG 479
           NH+PGLASIL PQVS   K A IG D  R S  EH  T   S++GA+F QS+S  EPK  
Sbjct: 421 NHLPGLASILQPQVSNTVKAAAIGNDLERSSQGEHIFTGMNSSHGATF-QSHSLPEPKFS 479

Query: 480 LYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIH 539
            YRG +SS GPS SNGS VETLSGPQFLWGSP+ YSEH+   AW  SS+GHPF+SNGK H
Sbjct: 480 QYRGALSSIGPSTSNGSSVETLSGPQFLWGSPTLYSEHTKPSAWPRSSVGHPFASNGKSH 539

Query: 540 GLPYSGRQGSFLGSSQ---HHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQ 596
             PYS +  SF+GSSQ   HHHVGSAPSG+P ER FGF PES ETSFMN V + G+G G 
Sbjct: 540 AFPYSTQNSSFVGSSQHLHHHHVGSAPSGLPFERHFGFHPESSETSFMNNVGYGGIGPGH 599

Query: 597 NDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANIE 655
           NDG+ MVN+G   SVNP IT+PRN+SDNGSS FR+ SSPRLSPVFLGNGP+PGL P  +E
Sbjct: 600 NDGNHMVNVG--GSVNPNITIPRNISDNGSSNFRMRSSPRLSPVFLGNGPFPGLPPTTLE 657

Query: 656 GLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAI 715
           GL +R RSR IE NNG+Q+DSKKQFQL L+KI+SGEDTRTTLMIKNIPNKYTSKMLLAAI
Sbjct: 658 GLADRARSRWIE-NNGSQVDSKKQFQLNLDKIKSGEDTRTTLMIKNIPNKYTSKMLLAAI 716

Query: 716 DENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLA 775
           DENH+GTYDFLYLPIDFKNKCNVGYAFINMLSP  IIPF+E FNGKKWEKFNSEKVASLA
Sbjct: 717 DENHRGTYDFLYLPIDFKNKCNVGYAFINMLSPSLIIPFFETFNGKKWEKFNSEKVASLA 776

Query: 776 YARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVMQ 819
           YARIQG++ALV+HFQNSSLMNEDKRCRPILFHSEG E  D ++Q
Sbjct: 777 YARIQGKSALVSHFQNSSLMNEDKRCRPILFHSEGSEVCDLIVQ 820

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530557|ref|XP_003533847.1| PREDICTED: protein MEI2-like 2-like [Glycine max]

 Score = 1214 bits (3141), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 622/825 (75%), Positives = 689/825 (83%), Gaps = 10/825 (1%)

Query: 1   MKQFFDHSS-GPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLN 59
           M+Q FD SS GP KIP + IP + G G+   ++GSDSY AS DASLFSSSLPVLPHEKLN
Sbjct: 1   MRQSFDPSSLGPSKIPSIKIPGKAGNGAWEALSGSDSYHASSDASLFSSSLPVLPHEKLN 60

Query: 60  LNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDL 119
           LN      QS+DDISSG  K+H     +  LE     AIG +LPDDE+ELLAGIMDDFDL
Sbjct: 61  LNETANAYQSIDDISSGFKKLHQDAEGNGSLEDGDTHAIGPALPDDEEELLAGIMDDFDL 120

Query: 120 RGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAG 179
            GLP SLEDLE+YD+FG GGGMELE +PQESL++ +SK+S +DS  G+ L  YS PNG G
Sbjct: 121 SGLPGSLEDLEEYDLFGCGGGMELETDPQESLTVGISKLSFADSTVGSVLPPYSFPNGVG 180

Query: 180 TVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 239
            VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI
Sbjct: 181 AVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI 240

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 299
           RAARTAMR+LQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVSNEDLRQIFG
Sbjct: 241 RAARTAMRSLQNKPLRRRKLDIHFSIPKDNPSDKDINQGTLVVFNLDPSVSNEDLRQIFG 300

Query: 300 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 359
           AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM
Sbjct: 301 AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 360

Query: 360 LQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTS 419
           LQLNQEL+Q+ESR  ++QV SP+ NSPPGNW+QF+SP+E N +QTI+ SP  R +SPTT 
Sbjct: 361 LQLNQELDQEESRSFRYQVSSPVANSPPGNWLQFNSPVEQNSMQTINHSPGSRIISPTTG 420

Query: 420 NHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIG 479
           NH+PGLASIL PQVS   K A IG D GR S  EH  +   S++GA+F QS+S  EPK  
Sbjct: 421 NHLPGLASILQPQVSNAVKAAAIGNDLGRSSQGEHIFSGMNSSHGATF-QSHSLPEPKFS 479

Query: 480 LYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPF-SSNGKI 538
            YRG +SS GPS SNGS VETLSGPQFLWGSP+ YSEH+    W  SS+GHPF +SNGK 
Sbjct: 480 QYRGALSSIGPSTSNGSSVETLSGPQFLWGSPTLYSEHTKPSVWPRSSVGHPFAASNGKS 539

Query: 539 HGLPYSGRQGSFLGSSQ---HHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIG 595
           H  PYS +  SF+GSSQ   HHHVGSAPSG+P ER FGF PES ETSFMN V + G+G+G
Sbjct: 540 HAFPYSTQNSSFVGSSQHHHHHHVGSAPSGLPFERHFGFHPESSETSFMNNVGYGGIGLG 599

Query: 596 QNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANI 654
            NDG++MVN G   SVNP  T+PRN+SDNGSS  R+ SSPRLSPVFLGNGPYPGL P  +
Sbjct: 600 HNDGNYMVNAG--GSVNPNTTIPRNISDNGSSNLRMRSSPRLSPVFLGNGPYPGLPPTTL 657

Query: 655 EGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAA 714
           E L +R RSR IE NNG+Q+DSKKQFQL+L+KIRSGEDTRTTLMIKNIPNKYTSKMLLAA
Sbjct: 658 ESLADRARSRWIE-NNGSQVDSKKQFQLDLDKIRSGEDTRTTLMIKNIPNKYTSKMLLAA 716

Query: 715 IDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASL 774
           IDENH+G YDFLYLPIDFK KCNVGYAFINMLSP  IIPFYE FNGKKWEKFNSEKVASL
Sbjct: 717 IDENHRGAYDFLYLPIDFKKKCNVGYAFINMLSPFLIIPFYETFNGKKWEKFNSEKVASL 776

Query: 775 AYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVMQ 819
           AYARIQG++ALV+HFQNSSLMNEDKRCRPILFHSEG E GD ++Q
Sbjct: 777 AYARIQGKSALVSHFQNSSLMNEDKRCRPILFHSEGSEVGDLIVQ 821

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485142|ref|XP_002279792.2| PREDICTED: protein MEI2-like 2-like [Vitis vinifera]

 Score = 1147 bits (2966), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 588/809 (72%), Positives = 668/809 (82%), Gaps = 10/809 (1%)

Query: 9   SGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQ 68
           SGP KIP LN+PK++G G+ G   G+D+Y  S D SLFSSSLPVLPHEKL+ N       
Sbjct: 10  SGPFKIPSLNVPKKIGSGAWGIPHGTDAYHTSSDVSLFSSSLPVLPHEKLHFNDSEHCGH 69

Query: 69  SVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLED 128
           SVDD S  L+K+     S DPLE V   AIG+ LPDDEDELLAGIMDDFDL GLP+ +ED
Sbjct: 70  SVDDGSPSLNKLQQDEESKDPLEDVDLNAIGSLLPDDEDELLAGIMDDFDLSGLPTQVED 129

Query: 129 LEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYG 188
           LED D+FGSGGGMEL+        + +SK+S+SD  +GNG+ HY +PNG  TVAGEHPYG
Sbjct: 130 LED-DLFGSGGGMELD------FDIGISKLSLSDGVAGNGIGHYGLPNGVATVAGEHPYG 182

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA 248
           EHPSRTLFVRNINSNVEDSEL+ LFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA
Sbjct: 183 EHPSRTLFVRNINSNVEDSELKTLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA 242

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
           LQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLD SVSN+DLRQIFGAYGEVKEIR
Sbjct: 243 LQNKPLRRRKLDIHFSIPKDNPSEKDINQGTLVVFNLDASVSNDDLRQIFGAYGEVKEIR 302

Query: 309 ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQ 368
           ETPHKRHHKFIEFYDVRAAEAAL++LNRSDIAGKRIKLEPSRPGGARRNLM QL+QELEQ
Sbjct: 303 ETPHKRHHKFIEFYDVRAAEAALRALNRSDIAGKRIKLEPSRPGGARRNLMQQLSQELEQ 362

Query: 369 DESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASI 428
           DE+R  +H VGSP+TNSPPGNW  F SP+EHNPLQ  S SP   N+SP  SNH+PGLASI
Sbjct: 363 DEARSFRHHVGSPVTNSPPGNWAAF-SPVEHNPLQAYSHSPGLGNISPINSNHLPGLASI 421

Query: 429 LHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSF 488
           L P +S   KIAPIGKDQGR + +    TN     GA++Q S+S  E K+    G +SS 
Sbjct: 422 LPPHISNSVKIAPIGKDQGRVNHVNQVFTNAKPTQGAAYQISHSVPEQKLSASPGPISSL 481

Query: 489 GPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQG 548
           G S SN SG+ TLSGPQFLWGSP+ YSE  +S AW TSS+GHPF S+G+  G PYS + G
Sbjct: 482 GESNSNSSGIGTLSGPQFLWGSPTPYSERPNSSAWPTSSVGHPFVSSGQGQGFPYSNQHG 541

Query: 549 SFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSR 608
           SFLGS QHHHVGSAPSGVPL+R FG+ PESPETSFM+PV F GMG+ +++G+F +N+G+R
Sbjct: 542 SFLGSHQHHHVGSAPSGVPLDRHFGYFPESPETSFMSPVTFGGMGLSRSNGNFAMNVGAR 601

Query: 609 ASVNPGITVPRNLSDNG-SSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIE 667
           A++N G+ +P N+++NG  SFR++S PR  P FLGNG YP     + E L ERGR+RR+E
Sbjct: 602 AAINTGVALPGNMTENGLPSFRMLSLPRHGPPFLGNGTYPVSGVTSNEVLAERGRTRRVE 661

Query: 668 NNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLY 727
            N+GNQ+DSKKQ+QL+L+KI SGEDTRTTLMIKNIPNKYTSKMLLAAIDENH+GTYDFLY
Sbjct: 662 -NSGNQIDSKKQYQLDLDKIISGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGTYDFLY 720

Query: 728 LPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVA 787
           LPIDFKNKCNVGYAFINM+SP HIIPFYEAFNGKKWEKFNSEKVASLAYARIQG+AALV 
Sbjct: 721 LPIDFKNKCNVGYAFINMVSPSHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGKAALVT 780

Query: 788 HFQNSSLMNEDKRCRPILFHSEGPEAGDQ 816
           HFQNSSLMNEDKRCRPILFHSEG E  DQ
Sbjct: 781 HFQNSSLMNEDKRCRPILFHSEGQETVDQ 809

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357450609|ref|XP_003595581.1| Polyadenylate-binding protein [Medicago truncatula] gi|47834691|gb|AAT38999.1| AML5 [Medicago truncatula] gi|87241360|gb|ABD33218.1| RNA-binding region RNP-1 (RNA recognition motif); RNA recognition motif 2 [Medicago truncatula] gi|355484629|gb|AES65832.1| Polyadenylate-binding protein [Medicago truncatula]

 Score = 1128 bits (2918), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 596/832 (71%), Positives = 670/832 (80%), Gaps = 13/832 (1%)

Query: 1   MKQFFDHS-SGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLN 59
           MKQ FD S   P KIP +N   ++  G+    +GSDSY AS DASLFSSSLPVLPHEKLN
Sbjct: 1   MKQSFDPSFIAPSKIPPINTAGKLRHGALEVSSGSDSYHASSDASLFSSSLPVLPHEKLN 60

Query: 60  LNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDL 119
           LN    G QSVDDIS+   K H     +  L+   N AIG  LPDD++ELLAGIMDDFDL
Sbjct: 61  LNETENGFQSVDDISTNFKKHHQEAELNGSLDNGNNHAIGTMLPDDDEELLAGIMDDFDL 120

Query: 120 RGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAG 179
           RGLP SLEDLE+YD+F S GG+ELE +PQESLS+ +SK+S+SDS+ GN +  YS+PNG G
Sbjct: 121 RGLPGSLEDLEEYDLFDSSGGLELETDPQESLSVGISKLSLSDSSVGNSMPPYSLPNGVG 180

Query: 180 TVAG--EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYY 237
             A   EHPYGEHPSRTLFVRNINSNVED+ELR LFEQYGDIRTLYTACKHRGFVMISYY
Sbjct: 181 GGAVAGEHPYGEHPSRTLFVRNINSNVEDTELRTLFEQYGDIRTLYTACKHRGFVMISYY 240

Query: 238 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQI 297
           DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVSNEDLRQI
Sbjct: 241 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDINQGTLVVFNLDPSVSNEDLRQI 300

Query: 298 FGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           FGAYGEVKEIRETPHKRHHKFIE+YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN
Sbjct: 301 FGAYGEVKEIRETPHKRHHKFIEYYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 360

Query: 358 LMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPT 417
           LMLQLNQEL+QDESR  ++QVGSP+  SPPGNW+QF+SPIE + L  ++ SP  + MSPT
Sbjct: 361 LMLQLNQELDQDESRSFRYQVGSPLAGSPPGNWLQFNSPIEQSSLPNLNHSPGSKIMSPT 420

Query: 418 TSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPK 477
           TSNH+PGLASIL PQ+S   K A IG+D GR S  +H   N IS+ G++F  S+S  EPK
Sbjct: 421 TSNHLPGLASILQPQLSNTVKAATIGQDIGRSSHGDHIFPNKISSAGSNF-NSHSLPEPK 479

Query: 478 IGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFS-SNG 536
              YRG +SSFG S SNGS VETL+ PQFLWGSP+  SE +   AW   S+GH  S SNG
Sbjct: 480 FSPYRGALSSFGASTSNGSSVETLTAPQFLWGSPNLSSEPTKPSAWPRPSVGHQLSTSNG 539

Query: 537 KIHGLPYSGRQGSFL----GSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGM 592
             H  PYS +  SF+        HHHVGSAPSG+P ER FGF P+S ETS MN V + GM
Sbjct: 540 TSHAFPYSSQNNSFVSSSQQQHHHHHVGSAPSGLPFERHFGFFPKSSETSLMNNVGYRGM 599

Query: 593 GIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTP 651
           G+G NDG++M+N G   S N GI++PRN+ DNGSS FR+ SSP LSPVFLGNGPYPGL P
Sbjct: 600 GLGHNDGNYMLNSG--ISGNVGISIPRNMPDNGSSNFRMRSSPILSPVFLGNGPYPGLLP 657

Query: 652 ANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKML 711
             +E   +R RSR I+ NNG+Q+D+KK FQL+L+KIRSGEDTRTTLMIKNIPNKYTSKML
Sbjct: 658 TAMESFTDRVRSRWID-NNGSQVDNKKLFQLDLDKIRSGEDTRTTLMIKNIPNKYTSKML 716

Query: 712 LAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKV 771
           LAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSP  IIPFYE F+GKKWEKFNSEKV
Sbjct: 717 LAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPSLIIPFYETFHGKKWEKFNSEKV 776

Query: 772 ASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVMQLTFP 823
           ASLAYARIQG+ ALV HFQNSSLMNEDKRCRPI+FHS+G E  DQ++Q   P
Sbjct: 777 ASLAYARIQGKNALVNHFQNSSLMNEDKRCRPIVFHSDGSEVADQIVQEHLP 828

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297740630|emb|CBI30812.3| unnamed protein product [Vitis vinifera]

 Score = 1110 bits (2871), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 565/812 (69%), Positives = 631/812 (77%), Gaps = 98/812 (12%)

Query: 13  KIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDD 72
           KIP ++IPK VG G+ G   GSD Y AS+DA+LFS SLPVLPHEKLNLN      QS+DD
Sbjct: 38  KIPYVSIPKAVGSGAWGMRPGSDGYNASNDATLFSCSLPVLPHEKLNLNDTEHCCQSIDD 97

Query: 73  ISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDY 132
             +GL K+   V + + LE     AIG+ LPDDEDELLAGIMDDFDL GL + +ED+E+Y
Sbjct: 98  --AGLDKLQQDVEAGESLEDDGIHAIGSLLPDDEDELLAGIMDDFDLSGLSNPMEDVEEY 155

Query: 133 DIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPS 192
           D+FGSGGGMELE +PQESL+M M+K+S+SD   GNGL  Y +PNG+GTVAGEHPYGEHPS
Sbjct: 156 DLFGSGGGMELEIDPQESLNMGMAKVSLSDGVVGNGLAQYGLPNGSGTVAGEHPYGEHPS 215

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 252
           RTLFVRNINSNVEDSELR LFEQYG IRTLYTACKHRGFVMISYYDIRAARTAMRALQNK
Sbjct: 216 RTLFVRNINSNVEDSELRTLFEQYGAIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 275

Query: 253 PLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH 312
           PLRRRKLDIHFSIPKDNPSDKD+NQGTLVVFNLDPSVSN+DLRQIFGAYGEVKEIRETPH
Sbjct: 276 PLRRRKLDIHFSIPKDNPSDKDVNQGTLVVFNLDPSVSNDDLRQIFGAYGEVKEIRETPH 335

Query: 313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 372
           KRHHKFIEFYDVRAAEAAL+SLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR
Sbjct: 336 KRHHKFIEFYDVRAAEAALRSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 395

Query: 373 ILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQ 432
             +H VGSP+ NSPPG+W QFSSPIEH+PLQ++SKSP FR +SPTTSNH+PGLASIL+ Q
Sbjct: 396 SFRHHVGSPMANSPPGSWAQFSSPIEHSPLQSLSKSPGFRTVSPTTSNHLPGLASILNSQ 455

Query: 433 VSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSP 492
           +S   K+APIGKDQGR                                     + FGP  
Sbjct: 456 ISNSVKVAPIGKDQGR-------------------------------------AKFGP-- 476

Query: 493 SNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLG 552
                             P+ YSEH++S AWQ  SMGHPF+SNG+  G PYSGR      
Sbjct: 477 ---------------ISCPAPYSEHTNSSAWQPPSMGHPFASNGQGRGFPYSGRH----- 516

Query: 553 SSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVN 612
                           ER FG+ PESPE SFM PVAF GMG+  NDG+            
Sbjct: 517 ----------------ERHFGYFPESPEASFMTPVAFGGMGLAHNDGT------------ 548

Query: 613 PGITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNG 671
                  N+S++GS+ FR++SSPRLSP+F GNGP+PGL P+NIEGL +RGRSR +E NNG
Sbjct: 549 -------NMSESGSANFRMISSPRLSPMFPGNGPFPGLAPSNIEGLADRGRSRWVE-NNG 600

Query: 672 NQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPID 731
           NQ+DSKKQFQL+L+KI +GEDTRTTLMIKNIPNKYTSKMLLAAIDE H+GTYDFLYLPID
Sbjct: 601 NQIDSKKQFQLDLDKILNGEDTRTTLMIKNIPNKYTSKMLLAAIDEYHRGTYDFLYLPID 660

Query: 732 FKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQN 791
           FKNKCNVGYAFINMLSP HIIPFY+AFNGKKWEKFNSEKVASLAYARIQG+AALV HFQN
Sbjct: 661 FKNKCNVGYAFINMLSPSHIIPFYQAFNGKKWEKFNSEKVASLAYARIQGKAALVTHFQN 720

Query: 792 SSLMNEDKRCRPILFHSEGPEAGDQVMQLTFP 823
           SSLMNEDKRCRPILFHSEGPEAGDQ++Q   P
Sbjct: 721 SSLMNEDKRCRPILFHSEGPEAGDQIIQEHLP 752

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356567420|ref|XP_003551918.1| PREDICTED: protein MEI2-like 2-like [Glycine max]

 Score = 1076 bits (2783), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 562/811 (69%), Positives = 641/811 (79%), Gaps = 7/811 (0%)

Query: 8   SSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGR 67
           ++GP  I   N+PK+ G  + G    SD +  S D SLFSSSLPVLPHEKL+L       
Sbjct: 14  AAGPSGISPHNVPKKAGSSAWGIPRASDVFHDSSDVSLFSSSLPVLPHEKLDLTDSENYG 73

Query: 68  QSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLE 127
           Q VDD    L KVH      DP +     AIGN LPDDE++LLAGIMDDFDL  LPS LE
Sbjct: 74  QPVDDNLLTLDKVHKEDEGHDPFDDFETNAIGNMLPDDEEDLLAGIMDDFDLSKLPSQLE 133

Query: 128 DLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPY 187
           DL++ D+F +GGG E++ EPQESL++SMSKI ISD  + NG+  Y++PNG GTVAGEHPY
Sbjct: 134 DLDENDLFVNGGGFEMDFEPQESLNISMSKIGISDGIASNGIGQYAIPNGVGTVAGEHPY 193

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           GEHPSRTLFVRNINSNVEDSELR LFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR
Sbjct: 194 GEHPSRTLFVRNINSNVEDSELRTLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 253

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI 307
           ALQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLDPSVSN+DLRQIFGAYGEVKEI
Sbjct: 254 ALQNKPLRRRKLDIHFSIPKDNPSEKDINQGTLVVFNLDPSVSNDDLRQIFGAYGEVKEI 313

Query: 308 RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELE 367
           RETPHKRHHKFIEFYDVRAAEAALK+LNRSDIAGKRIKLEPSRPGGARRNLM QL+QELE
Sbjct: 314 RETPHKRHHKFIEFYDVRAAEAALKALNRSDIAGKRIKLEPSRPGGARRNLMQQLSQELE 373

Query: 368 QDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLAS 427
           QDE+R  +HQV SP+ NSPPG+W QF SP+E NPL + SKSP     SP  +NH+ GLA+
Sbjct: 374 QDEARTFRHQVVSPVANSPPGSWAQFGSPVEQNPLASFSKSPGLGPASPINTNHLSGLAA 433

Query: 428 ILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSS 487
           IL PQ +T  KIAPIGKD GR +      +N+ S  GA+FQ S SF E  +      +S+
Sbjct: 434 ILSPQATTSTKIAPIGKDPGRAA--NQMFSNSGSTQGAAFQHSISFPEQNVKASPRPIST 491

Query: 488 FGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQ 547
           FG S S+ S + TLSGPQFLWGSP+ YSEHS++ AW +SS+G PF+S+ +  G PY+   
Sbjct: 492 FGESSSSASSIGTLSGPQFLWGSPTPYSEHSNTSAWSSSSVGLPFTSSVQRQGFPYTSNH 551

Query: 548 GSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMV-NMG 606
             FLGS  HHHVGSAPSG+PL+R F + PESPE S M+PVAF  +  G  DG+FM+ N+ 
Sbjct: 552 SPFLGSHSHHHVGSAPSGLPLDRHFSYFPESPEASLMSPVAFGNLNHG--DGNFMMNNIS 609

Query: 607 SRASVNPGITVPRNLSDNGS-SFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRR 665
           +RASV  G+ +  N  +  S +FR+MS PR   +F GN  Y G    NIEGL ERGRSRR
Sbjct: 610 ARASVGAGVGLSGNTPEISSPNFRMMSLPRHGSLFHGNSLYSGPGATNIEGLAERGRSRR 669

Query: 666 IENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDF 725
            E N GNQ+DSKK +QL+L+KI  GEDTRTTLMIKNIPNKYTSKMLLAAIDENH+GTYDF
Sbjct: 670 PE-NGGNQIDSKKLYQLDLDKIVCGEDTRTTLMIKNIPNKYTSKMLLAAIDENHQGTYDF 728

Query: 726 LYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAAL 785
           LYLPIDFKNKCNVGYAFINM+SP HII FY+AFNGKKWEKFNSEKVASLAYARIQG+AAL
Sbjct: 729 LYLPIDFKNKCNVGYAFINMVSPSHIIAFYKAFNGKKWEKFNSEKVASLAYARIQGKAAL 788

Query: 786 VAHFQNSSLMNEDKRCRPILFHSEGPEAGDQ 816
           V HFQNSSLMNEDKRCRPILFHSEG + GDQ
Sbjct: 789 VMHFQNSSLMNEDKRCRPILFHSEGQDTGDQ 819

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357450611|ref|XP_003595582.1| Polyadenylate-binding protein [Medicago truncatula] gi|355484630|gb|AES65833.1| Polyadenylate-binding protein [Medicago truncatula]

 Score = 1069 bits (2764), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 542/730 (74%), Positives = 608/730 (83%), Gaps = 12/730 (1%)

Query: 102 LPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISIS 161
           LPDD++ELLAGIMDDFDLRGLP SLEDLE+YD+F S GG+ELE +PQESLS+ +SK+S+S
Sbjct: 2   LPDDDEELLAGIMDDFDLRGLPGSLEDLEEYDLFDSSGGLELETDPQESLSVGISKLSLS 61

Query: 162 DSASGNGLLHYSVPNGAGTVAG--EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI 219
           DS+ GN +  YS+PNG G  A   EHPYGEHPSRTLFVRNINSNVED+ELR LFEQYGDI
Sbjct: 62  DSSVGNSMPPYSLPNGVGGGAVAGEHPYGEHPSRTLFVRNINSNVEDTELRTLFEQYGDI 121

Query: 220 RTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT 279
           RTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD+NQGT
Sbjct: 122 RTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDINQGT 181

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIE+YDVRAAEAALKSLNRSDI
Sbjct: 182 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEYYDVRAAEAALKSLNRSDI 241

Query: 340 AGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEH 399
           AGKRIKLEPSRPGGARRNLMLQLNQEL+QDESR  ++QVGSP+  SPPGNW+QF+SPIE 
Sbjct: 242 AGKRIKLEPSRPGGARRNLMLQLNQELDQDESRSFRYQVGSPLAGSPPGNWLQFNSPIEQ 301

Query: 400 NPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNT 459
           + L  ++ SP  + MSPTTSNH+PGLASIL PQ+S   K A IG+D GR S  +H   N 
Sbjct: 302 SSLPNLNHSPGSKIMSPTTSNHLPGLASILQPQLSNTVKAATIGQDIGRSSHGDHIFPNK 361

Query: 460 ISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSS 519
           IS+ G++F  S+S  EPK   YRG +SSFG S SNGS VETL+ PQFLWGSP+  SE + 
Sbjct: 362 ISSAGSNF-NSHSLPEPKFSPYRGALSSFGASTSNGSSVETLTAPQFLWGSPNLSSEPTK 420

Query: 520 SPAWQTSSMGHPFS-SNGKIHGLPYSGRQGSFL----GSSQHHHVGSAPSGVPLERRFGF 574
             AW   S+GH  S SNG  H  PYS +  SF+        HHHVGSAPSG+P ER FGF
Sbjct: 421 PSAWPRPSVGHQLSTSNGTSHAFPYSSQNNSFVSSSQQQHHHHHVGSAPSGLPFERHFGF 480

Query: 575 LPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNGSS-FRVMSS 633
            P+S ETS MN V + GMG+G NDG++M+N G   S N GI++PRN+ DNGSS FR+ SS
Sbjct: 481 FPKSSETSLMNNVGYRGMGLGHNDGNYMLNSG--ISGNVGISIPRNMPDNGSSNFRMRSS 538

Query: 634 PRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIENNNGNQLDSKKQFQLELEKIRSGEDT 693
           P LSPVFLGNGPYPGL P  +E   +R RSR I+ NNG+Q+D+KK FQL+L+KIRSGEDT
Sbjct: 539 PILSPVFLGNGPYPGLLPTAMESFTDRVRSRWID-NNGSQVDNKKLFQLDLDKIRSGEDT 597

Query: 694 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIP 753
           RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSP  IIP
Sbjct: 598 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPSLIIP 657

Query: 754 FYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHSEGPEA 813
           FYE F+GKKWEKFNSEKVASLAYARIQG+ ALV HFQNSSLMNEDKRCRPI+FHS+G E 
Sbjct: 658 FYETFHGKKWEKFNSEKVASLAYARIQGKNALVNHFQNSSLMNEDKRCRPIVFHSDGSEV 717

Query: 814 GDQVMQLTFP 823
            DQ++Q   P
Sbjct: 718 ADQIVQEHLP 727

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449444985|ref|XP_004140254.1| PREDICTED: protein MEI2-like 2-like [Cucumis sativus]

 Score = 1068 bits (2762), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 559/819 (68%), Positives = 650/819 (79%), Gaps = 14/819 (1%)

Query: 6   DHSSGPPKIPQLNIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGL 65
           D  SG  K   +N+P++ G  + G    SDS+ AS D SLFSSSLPVLPHEKL+ ++  L
Sbjct: 7   DSMSGQAKNLLVNVPRKAGSSAWGIPCASDSFHASSDVSLFSSSLPVLPHEKLDFDSE-L 65

Query: 66  GRQSVDDISSGLSKVHHGVASDDPLEGVMNP--AIGNSLPDDEDELLAGIMDDFDLRGLP 123
            +    D+S+ L          DPLE V     AIGN LPDD DEL +G+MDDFDL GLP
Sbjct: 66  CQSDGADLSNELDP---KTDIKDPLEEVEVEVDAIGNLLPDD-DELFSGLMDDFDLSGLP 121

Query: 124 SSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAG 183
           S LEDLE+YD+FGSGGGMEL+ EPQE+LSM MSK+++SDS +G+ + HY++PNG GTVAG
Sbjct: 122 SQLEDLEEYDLFGSGGGMELDFEPQENLSMGMSKLNLSDSVTGSMVSHYALPNGVGTVAG 181

Query: 184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR 243
           EHPYGEHPSRTLFVRNINSNVED+ELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR
Sbjct: 182 EHPYGEHPSRTLFVRNINSNVEDAELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR 241

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
           TAMRALQNKPLRRRKLDIHFSIPKDNPS+KD+NQGTLVVFNLD SVSN+DLR+IFGAYGE
Sbjct: 242 TAMRALQNKPLRRRKLDIHFSIPKDNPSEKDINQGTLVVFNLDASVSNDDLRRIFGAYGE 301

Query: 304 VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLN 363
           VKEIRETPHKRHHKFIEFYDVRAAEAAL++LNRSDIAGKRIKLEPSRPGGARRNLM QL+
Sbjct: 302 VKEIRETPHKRHHKFIEFYDVRAAEAALRALNRSDIAGKRIKLEPSRPGGARRNLMQQLS 361

Query: 364 QELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMP 423
           QELEQD++R  +HQVGSP TNSPPGNW    SP+EHN   + SKSP   ++SP  S+H+ 
Sbjct: 362 QELEQDDARTFRHQVGSPATNSPPGNWSHIGSPVEHN---SFSKSPGLGSLSPINSSHLS 418

Query: 424 GLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNSFSEPKIGLYRG 483
           GLASIL P +S   +IAPIGKDQGR +     LTN+    G ++    SF + K     G
Sbjct: 419 GLASILPPNLSNSPRIAPIGKDQGRANHASQVLTNSALMQGTTYHHHQSFPDNKFSSNGG 478

Query: 484 TVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPY 543
           + SS     SN S + TLSGPQFLWGSP+ Y+E  +S AW T S G PF+SNG+  G PY
Sbjct: 479 STSSVADLNSNSSSIGTLSGPQFLWGSPTPYAERPNSSAWPTPSAGQPFTSNGQGQGFPY 538

Query: 544 SGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMV 603
               GS LG S HHHVGSAPSGVPL+R FG+ PESPETSFM+P       + +++G+FM 
Sbjct: 539 VRHHGSLLG-SHHHHVGSAPSGVPLDRPFGYFPESPETSFMSPGTLGSTSLSRHNGNFM- 596

Query: 604 NMGSRASVNPGITVPRNLSDNGS-SFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGR 662
           N+ +RA++  G+ +P N+++NGS +FR+MS PR   ++ GNG +PG    + +GL ERGR
Sbjct: 597 NLSTRAAMTGGLGLPTNMAENGSPNFRLMSLPRQGSIYYGNGSFPGSGVVSADGLLERGR 656

Query: 663 SRRIENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGT 722
           SRR+E N GNQ++SKKQ+QL+LEKI SGEDTRTTLMIKNIPNKYTSKMLLAAIDENH+G 
Sbjct: 657 SRRVE-NVGNQIESKKQYQLDLEKIVSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHRGA 715

Query: 723 YDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGR 782
           YDFLYLPIDFKNKCNVGYAFINM+SP  IIPFYEAFNGKKWEKFNSEKVASLAYARIQG+
Sbjct: 716 YDFLYLPIDFKNKCNVGYAFINMVSPTQIIPFYEAFNGKKWEKFNSEKVASLAYARIQGK 775

Query: 783 AALVAHFQNSSLMNEDKRCRPILFHSEGPEAGDQVMQLT 821
            ALV HFQNSSLMNEDKRCRPILF SEG E GDQ + L+
Sbjct: 776 TALVTHFQNSSLMNEDKRCRPILFRSEGQEIGDQDILLS 814

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	823
TAIR|locus:2013583	800	ML5 "MEI2-like protein 5" [Ara	0.770	0.792	0.514	1.7e-162
TAIR|locus:2156166	915	ML1 "MEI2-like protein 1" [Ara	0.312	0.280	0.566	4.5e-139
TAIR|locus:2182885	907	ML4 "MEI2-like 4" [Arabidopsis	0.313	0.284	0.566	9.3e-131
TAIR|locus:2117706	759	ML3 "MEI2-like 3" [Arabidopsis	0.726	0.787	0.457	7.8e-126
TAIR|locus:2045605	843	ML2 "MEI2-like 2" [Arabidopsis	0.686	0.670	0.448	7.7e-119
TAIR|locus:2090350	615	TEL1 "terminal EAR1-like 1" [A	0.113	0.151	0.526	6.9e-52
TAIR|locus:2008530	527	TEL2 "terminal EAR1-like 2" [A	0.139	0.218	0.446	6.1e-45
POMBASE|SPAC27D7.03c	750	mei2 "RNA-binding protein invo	0.168	0.185	0.535	1.9e-39
DICTYBASE|DDB_G0279255	1698	DDB_G0279255 [Dictyostelium di	0.123	0.060	0.470	3.2e-34
GENEDB_PFALCIPARUM|PFF1125c	427	PFF1125c "RNA-binding protein	0.138	0.266	0.495	3.4e-25

TAIR|locus:2013583 ML5 "MEI2-like protein 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 1582 (562.0 bits), Expect = 1.7e-162, P = 1.7e-162
 Identities = 348/676 (51%), Positives = 429/676 (63%)

Query:    17 LNIPKEVGGGSCGRIXXXXXXXX-XXXXXXXXXXXPVLPHEKLNLNAMGLGRQSVDDISS 75
             ++IP E   G+ G +                    PV P  KL L+    G   +DD  +
Sbjct:     1 MDIPHEAEAGAWGILPGFGRHHHPSSDATLFSSSLPVFPRGKLQLSDNRDGFSLIDD--T 58

Query:    76 GLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIF 135
              +S+ +    S D  E   + +IGN LPD+ED LL G+MDD DL  LP    D +DYD+F
Sbjct:    59 AVSRTNKFNESADDFE---SHSIGNLLPDEED-LLTGMMDDLDLGELP----DADDYDLF 110

Query:   136 GSGGGMELEGEPQEXXXXXXXXXXXXXXXXGNGLLHYSVPNGAGTVAGEHPYGEHPSRTL 195
             GSGGGMEL+ + ++                GN +  +++PNGAGTVAGEHPYGEHPSRTL
Sbjct:   111 GSGGGMELDADFRDNLSMSGPPRLSLSSLGGNAIPQFNIPNGAGTVAGEHPYGEHPSRTL 170

Query:   196 FVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR 255
             FVRNINSNVEDSEL ALFEQYGDIRTLYT CKHRGFVMISYYDIR+AR AMR+LQNKPLR
Sbjct:   171 FVRNINSNVEDSELTALFEQYGDIRTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPLR 230

Query:   256 RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH 315
             RRKLDIHFSIPKDNPS+KD+NQGTLVVFNLDPS+SN+DL  IFGA+GE+KEIRETPHKRH
Sbjct:   231 RRKLDIHFSIPKDNPSEKDMNQGTLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRH 290

Query:   316 HKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMXXXXXXXXXXXSRILQ 375
             HKF+EFYDVR AEAALK+LNR +IAGKRIK+EPSRPGGARR+LM              L 
Sbjct:   291 HKFVEFYDVRGAEAALKALNRCEIAGKRIKVEPSRPGGARRSLMLQLNQDLENDDLHYLP 350

Query:   376 HQVGSPITNSPP--GNWVQFSSPIEHNPLQTI-SKSPNFRNMSPTTSNHMPGLASILHPQ 432
               +GSP+ NSPP  GNW   +SP+E +PLQ++ S+SP F  +SPT + H+ GLAS L+ Q
Sbjct:   351 -MIGSPMANSPPMQGNW-PLNSPVEGSPLQSVLSRSPVF-GLSPTRNGHLSGLASALNSQ 407

Query:   433 VSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQSNS-FSEPKI-GLYRGTVXXXXX 490
               +  K+APIG+ Q             I +NG  FQQS+  F EPK+   Y G +     
Sbjct:   408 GPS-SKLAPIGRGQ-------------IGSNG--FQQSSHLFQEPKMDNKYTGNLSPSGP 451

Query:   491 XXXXXXXVETLSGPQFLWGXXXXXXXXXXXPAWQTSSMGHPFSSNGKIHGLPYSGRQGSF 550
                    +ETLSG +FLWG             W TSS G+P  S      +P+  +  + 
Sbjct:   452 LISNGGGIETLSGSEFLWGSPNARSEPSSSSVWSTSSTGNPLFSTRVDRSVPFPHQHQNQ 511

Query:   551 LGSSQHHHVGSAPSGVPLERRFGFLPESPETS-FMNPVAFCGM-GIGQNDGSFMVNMGSR 608
               S  H HVGSAPSGVPLE+ FGF+PES + + FMN V   GM G+G N GSF   M + 
Sbjct:   512 SRSHHHFHVGSAPSGVPLEKHFGFVPESSKDALFMNTVGLQGMSGMGLNGGSFSSKMANN 571

Query:   609 ASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPANIEGLYERGRSRRIEN 668
               +N G ++  N     SS+R+MSSPR SP+FL +G  PG   +  + LYE GR RR+EN
Sbjct:   572 GIINSG-SMAEN---GFSSYRMMSSPRFSPMFLSSGLNPGRFASGFDSLYENGRPRRVEN 627

Query:   669 NNGNQLDSKK-QFQLE 683
             N+      K+ Q  LE
Sbjct:   628 NSNQVESRKQFQLDLE 643

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

TAIR|locus:2156166 ML1 "MEI2-like protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 722 (259.2 bits), Expect = 4.5e-139, Sum P(4) = 4.5e-139
 Identities = 153/270 (56%), Positives = 193/270 (71%)

Query:   553 SSQHHHVGSAPS-GVPL-ERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRAS 610
             S  HHH+GSAP    P  +RR  ++ ES E+S  +  +   MGI  +  S  +++GS  +
Sbjct:   603 SPVHHHIGSAPVLNSPFWDRRQAYVAESLESSGFHIGSHGSMGIPGSSPSHPMDIGSHKT 662

Query:   611 VNPGITVPRNLSDNGSSFRVMSSPR-LSPVFLGNGPYPGLTPANIEGLYERGRS---RRI 666
              + G     N  D  S   V+ SP+ LS +F G  P  G  P + +   ER R+   RR 
Sbjct:   663 FSVG----GNRMDVNSQNAVLRSPQQLSHLFPGRSPM-GSMPGSFDSPNERYRNLSHRRS 717

Query:   667 ENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFL 726
             E+++ N    KK ++L++++I  GED RTTLMIKNIPNKYTSKMLL+AIDE+ KGTYDFL
Sbjct:   718 ESSSSNA--DKKLYELDVDRILRGEDRRTTLMIKNIPNKYTSKMLLSAIDEHCKGTYDFL 775

Query:   727 YLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALV 786
             YLPIDFKNKCNVGYAFIN++ P  I+PF++AFNGKKWEKFNSEKVA+L YARIQG+ AL+
Sbjct:   776 YLPIDFKNKCNVGYAFINLIEPEKIVPFFKAFNGKKWEKFNSEKVATLTYARIQGKTALI 835

Query:   787 AHFQNSSLMNEDKRCRPILFHSEGPEAGDQ 816
             AHFQNSSLMNEDKRCRPILFH++GP AGDQ
Sbjct:   836 AHFQNSSLMNEDKRCRPILFHTDGPNAGDQ 865

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0048507 "meristem development" evidence=IGI

GO:0045836 "positive regulation of meiosis" evidence=IGI

TAIR|locus:2182885 ML4 "MEI2-like 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 711 (255.3 bits), Expect = 9.3e-131, Sum P(3) = 9.3e-131
 Identities = 153/270 (56%), Positives = 190/270 (70%)

Query:   553 SSQHHHVGSAPS-GVPL-ERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRAS 610
             S  HHH+GSAP    P  +RR  ++ ESPE+S  +  +   MG   +  S  ++ GS   
Sbjct:   600 SPVHHHIGSAPVLNSPFWDRRQAYVAESPESSGFHLGSPGSMGFPGSSPSHPMDFGSHKV 659

Query:   611 VNPGITVPRNLSDNGSSFRVMSSPRLSP-VFLGNGPYPGLTPANIEGLYERGRS---RRI 666
              +    V  N  +  S   V+ S R  P +F G  P   ++  + +   ER R+   RR 
Sbjct:   660 FSH---VGGNRMEANSKNAVLRSSRQMPHLFTGRSPMLSVS-GSFDLPNERYRNLSHRRS 715

Query:   667 ENNNGNQLDSKKQFQLELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFL 726
             E+N+ N    KK ++L++++I  GED+RTTLMIKNIPNKYTSKMLLAAIDE  KGTYDFL
Sbjct:   716 ESNSSNA--EKKLYELDVDRILRGEDSRTTLMIKNIPNKYTSKMLLAAIDEYCKGTYDFL 773

Query:   727 YLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALV 786
             YLPIDFKNKCNVGYAFIN++ P +I+PFY+AFNGKKWEKFNSEKVASLAY RIQG++AL+
Sbjct:   774 YLPIDFKNKCNVGYAFINLIEPENIVPFYKAFNGKKWEKFNSEKVASLAYGRIQGKSALI 833

Query:   787 AHFQNSSLMNEDKRCRPILFHSEGPEAGDQ 816
             AHFQNSSLMNEDKRCRPILFH+ GP AGDQ
Sbjct:   834 AHFQNSSLMNEDKRCRPILFHTAGPNAGDQ 863

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

GO:0048507 "meristem development" evidence=IGI

TAIR|locus:2117706 ML3 "MEI2-like 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 1236 (440.2 bits), Expect = 7.8e-126, P = 7.8e-126
 Identities = 294/642 (45%), Positives = 382/642 (59%)

Query:    51 PVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVAS--DDPLEGVMNPAIGNSLPDDEDE 108
             P++ H+  N+N      QSVD+++SGL     G+ +  DD   G  +P IGN LPDDE+E
Sbjct:    28 PLIQHQ--NINPRDSYHQSVDEMASGLDHFSGGIGNMLDD---GDSHP-IGNMLPDDEEE 81

Query:   109 LLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQEXXXXXXXXXXXXXXXXGNG 168
             L +G+MDD +L  LP++L+DLEDYD+FGSGGG+ELE +P +                 N 
Sbjct:    82 LFSGLMDDLNLSSLPATLDDLEDYDLFGSGGGLELETDPYDSLNKGFSRMGFADSNVDNV 141

Query:   169 LLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH 228
             +      NG G++AGEHPYGEHPSRTLFVRNINSNVEDSEL+ALFEQYG IRTLYTACK 
Sbjct:   142 MPQNIFQNGVGSIAGEHPYGEHPSRTLFVRNINSNVEDSELQALFEQYGHIRTLYTACKQ 201

Query:   229 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS 288
             RGFVM+SY DIRA+R AMRALQ K L++RKLDIHFSIPKDNPS+KD+NQGTLVVFNL PS
Sbjct:   202 RGFVMVSYNDIRASRAAMRALQGKLLKKRKLDIHFSIPKDNPSEKDVNQGTLVVFNLAPS 261

Query:   289 VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 348
             VSN DL  IFG YGE+KEIRETP+KRHHKF+EF+DVR+A+AALK+LNR++IAGKRIKLE 
Sbjct:   262 VSNRDLENIFGVYGEIKEIRETPNKRHHKFVEFFDVRSADAALKALNRTEIAGKRIKLEH 321

Query:   349 SRPGGARRNLMXXXXXXXXXXXSRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKS 408
             SRPGGARRN+M           S    + V SP+ +SP GNW   +SPI+H PLQ+ SKS
Sbjct:   322 SRPGGARRNMMLQMNPELEQDDSYSYLNHVESPLASSPIGNWR--NSPIDH-PLQSFSKS 378

Query:   409 PNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQ-GRG-SLMEHALTNTISANGAS 466
             P F N+SPT +        I +P+ S   K A +  DQ GR  S ++H  +++ S N AS
Sbjct:   379 PIFGNLSPTKN--------IRYPEFSM--KTASVNNDQEGRRFSHLDHLFSSS-SYNNAS 427

Query:   467 FQQSNSFSEPKIGLYRGTVXXXXXXXXXXXXVETLSGPQFLWGXXXXXXXXXXXPAWQTS 526
              + S +F +P+     G+V            VETLSG +FLWG            +    
Sbjct:   428 HKAS-TFQQPQSF---GSVSSFGSLNSHPSHVETLSGSEFLWGSPSSSAWPVNPFSSNRE 483

Query:   527 SMGHPFSS-NGKIHGLPYSGR--QGSFLGSSQHHHVGS-----APSGVPLERRFGFLPES 578
             +   P+S+ NG +H L + G    G F  S +   +GS     A   +  +R    L E+
Sbjct:   484 NHRFPYSAQNGSLHQLHHIGSAPSGFFPRSPETSSMGSVAFRGASGNMNAQRN---LRET 540

Query:   579 PETSFMNPVAFCGMGIGQNDGSFMVNMGSRASVNPGITVPRN--LSDNGSS--FRVMSSP 634
                +F    A     +   +GS++    +  S++  +    N     NG+    ++    
Sbjct:   541 SSPNFKMLSAPRRSQLFTGNGSYLWPAATMVSIDDPLEDGSNQQFDSNGNQADIKIQFQL 600

Query:   635 RLSPVFLGNGPYPGLTPANIEGLYERGRS-RRIENNNGNQLD 675
              LS +  G  P   L   NI   Y R      I+  N    D
Sbjct:   601 DLSKIMRGEDPRTTLMIKNIPNKYTRNMLLAAIDEKNSGTYD 642

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

TAIR|locus:2045605 ML2 "MEI2-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 1170 (416.9 bits), Expect = 7.7e-119, P = 7.7e-119
 Identities = 263/587 (44%), Positives = 342/587 (58%)

Query:    51 PVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPDDEDELL 110
             P L HEKLN+        S D+ S  L+K+  G +  D LE V   A+   LP+DE+ELL
Sbjct:    57 PTLFHEKLNMTDSD-SWLSFDESSPNLNKLVIGNSEKDSLEDVEPDALEILLPEDENELL 115

Query:   111 AGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQEXXXXXXXXXXXXXXXXGNGLL 170
              G++D+ +  GLP  L+DLE+ D+F +GGGMEL+ E Q+                 N  +
Sbjct:   116 PGLIDELNFTGLPDELDDLEECDVFCTGGGMELDVESQDNHAVDASGMQISDRGAANAFV 175

Query:   171 HYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG 230
                 PN AG V+ EHP GEHPSRTLFVRNINS+VEDSEL ALFE +G+IR+LYTACK RG
Sbjct:   176 PRKRPNTAGRVSVEHPNGEHPSRTLFVRNINSSVEDSELSALFEPFGEIRSLYTACKSRG 235

Query:   231 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVS 290
             FVMISYYDIRAA  AMRALQN  LR+R LDIHFSIPK+NPS+KD+NQGTLV+FN+D +VS
Sbjct:   236 FVMISYYDIRAAHAAMRALQNTLLRKRTLDIHFSIPKENPSEKDMNQGTLVIFNVDTTVS 295

Query:   291 NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
             N++L Q+FGAYGE++EIRETP++R H+FIE+YDVR AE ALK+LNRS+I GK IKLE SR
Sbjct:   296 NDELLQLFGAYGEIREIRETPNRRFHRFIEYYDVRDAETALKALNRSEIGGKCIKLELSR 355

Query:   351 PGGARRNLMXXXXXXXXXXXSRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPN 410
             PGGARR  +                +QVGS + NSPPGNW    SP++ +P    ++   
Sbjct:   356 PGGARRLSVPSQSQDLERTEVTNFYNQVGSHVANSPPGNW-PIGSPVKGSPSHAFTRPHG 414

Query:   411 FRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRGSLMEHALTNTISANGASFQQS 470
                + P  S++MPGLASIL    S+    +P+  DQG  +     + N    +  S+ Q 
Sbjct:   415 LGMVRPVNSDNMPGLASILPAHPSSFHGFSPVSNDQGLLNHSNQTILNKGLMHNISYGQP 474

Query:   471 NSFSEPKIGLYRGTVXXXXXXXXXXXXVETLSGPQFLWGX--XXXXXXXXXXPAWQTSSM 528
             +S  E   G   G                T S  ++ WG              +  +SS 
Sbjct:   475 HSLPEHITG---GISNSMRFIAPHSSGFGTSSDHRYRWGSPPQHMNYPGYTGVSSSSSST 531

Query:   529 GHPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVA 588
               PF+     HG P++ RQ S LG  QHH VGSAPS +    +      SPE     P+ 
Sbjct:   532 ERPFTVR---HGFPFAERQASLLGKYQHH-VGSAPSSIHFNTQMNCYTGSPEI----PLG 583

Query:   589 FCGMGIGQNDGSFMVNMGSRASVNPGITVPRNLSDNG-SSFRVMSSP 634
             F  MGI +N  S      +    N G+++P N S+   + F + S P
Sbjct:   584 FSDMGINRNYNS------AHGKANLGVSLPGNSSEQDFTGFGMSSMP 624

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

TAIR|locus:2090350 TEL1 "terminal EAR1-like 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 263 (97.6 bits), Expect = 6.9e-52, Sum P(4) = 6.9e-52
 Identities = 49/93 (52%), Positives = 65/93 (69%)

Query:   263 FSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFY 322
             F +P  +      NQGTLV+FNLDP VS+  LRQIF  YG +KE+RETP+K+H +F+EFY
Sbjct:   198 FVVPATSAVPGGCNQGTLVIFNLDPEVSSITLRQIFQVYGPIKELRETPYKKHQRFVEFY 257

Query:   323 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR 355
             DVR A  A   +N  +I GK++ +E SRPGG +
Sbjct:   258 DVRDAARAFDRMNGKEIGGKQVVIEFSRPGGIK 290

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

TAIR|locus:2008530 TEL2 "terminal EAR1-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 262 (97.3 bits), Expect = 6.1e-45, Sum P(3) = 6.1e-45
 Identities = 59/132 (44%), Positives = 78/132 (59%)

Query:   692 DTRTTLMIKNIPNKYTSKMLLAAID------------ENHK---GTYDFLYLPIDFKNKC 736
             D RTT+MIKNIPNKYT K+LL  +D            E +K    +YDF+YLPIDF NK 
Sbjct:   334 DGRTTVMIKNIPNKYTQKLLLKMLDTHCKDCNQSVIKEGNKTPMSSYDFVYLPIDFSNKS 393

Query:   737 NVGYAFINMLSPLHIIPFYEAFNGKKWEKFNS-EKVASLAYARIQGRAALVAHFQNSSLM 795
             NVGY F+NM SP  +   Y++F+ + W  F +  K+  + YARIQG  +L  HF+N  L 
Sbjct:   394 NVGYGFVNMTSPEAVWRLYKSFHNQHWRDFTTTRKICEVTYARIQGLESLREHFKNVRLA 453

Query:   796 N-EDKRCRPILF 806
               E     P++F
Sbjct:   454 GVEIDEYMPVVF 465

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

POMBASE|SPAC27D7.03c mei2 "RNA-binding protein involved in meiosis Mei2" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 378 (138.1 bits), Expect = 1.9e-39, Sum P(3) = 1.9e-39
 Identities = 76/142 (53%), Positives = 98/142 (69%)

Query:   682 LELEKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYA 741
             ++  +I SG DTRTT+MIKNIPNK+T +ML   ID  +KGTYDFLYL IDF NKCNVGYA
Sbjct:   584 VDYAQIASGIDTRTTVMIKNIPNKFTQQMLRDYIDVTNKGTYDFLYLRIDFVNKCNVGYA 643

Query:   742 FINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRC 801
             FIN + P  II F +A  G +W  F+SEK+  ++YA IQG+  L+  F+NS +M+E+   
Sbjct:   644 FINFIEPQSIITFGKARVGTQWNVFHSEKICDISYANIQGKDRLIEKFRNSCVMDENPAY 703

Query:   802 RPILFHSEGPEAGDQVMQLTFP 823
             RP +F S GP  G   M+  FP
Sbjct:   704 RPKIFVSHGPNRG---MEEPFP 722

GO:0003723 "RNA binding" evidence=IDA

GO:0004860 "protein kinase inhibitor activity" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0007127 "meiosis I" evidence=TAS

GO:0033620 "Mei2 nuclear dot" evidence=IDA

GO:0034064 "Tor2-Mei2-Ste11 complex" evidence=IDA

GO:0045836 "positive regulation of meiosis" evidence=IMP

DICTYBASE|DDB_G0279255 DDB_G0279255 [Dictyostelium discoideum (taxid:44689)]

 Score = 248 (92.4 bits), Expect = 3.2e-34, Sum P(3) = 3.2e-34
 Identities = 48/102 (47%), Positives = 67/102 (65%)

Query:   685 EKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFIN 744
             E I SG DTRT+LMI+NIPN+ T + L A IDE  K TYDFL +P+D   K + GYAFIN
Sbjct:  1564 ENIISGVDTRTSLMIRNIPNRLTQQTLTALIDEEFKDTYDFLNMPLDPHTKVSRGYAFIN 1623

Query:   745 MLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQGRAALV 786
                 +++  F++ F   +W+ +N +K+  + YA IQG  AL+
Sbjct:  1624 FKDHMNVYRFHQKFFHTRWKNYNHDKICEINYAIIQGEEALL 1665

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GENEDB_PFALCIPARUM|PFF1125c PFF1125c "RNA-binding protein mei2 homologue, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 306 (112.8 bits), Expect = 3.4e-25, P = 3.4e-25
 Identities = 57/115 (49%), Positives = 79/115 (68%)

Query:   695 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPF 754
             TT+M++NIPNKYT  ML+  ++E+ KG YDF YLPIDF+NKCNVGYAFIN + P +   F
Sbjct:   290 TTVMLRNIPNKYTQNMLMDVMNEHFKGLYDFFYLPIDFRNKCNVGYAFINFIHPYYAELF 349

Query:   755 YEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQNSSLMNED-KRCRPILFHS 808
              + FN  K   F S KV S+ + R+QG  A + H++NS++M     + +PILF +
Sbjct:   350 IKFFNNYKLNAFKSNKVCSVTWGRVQGLKANIEHYRNSAIMTIPIPQYKPILFQN 404

GO:0003723 "RNA binding" evidence=ISS

GO:0045836 "positive regulation of meiosis" evidence=ISS

---

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)
Q8VWF5	AML5_ARATH	No assigned EC number	0.6199	0.9307	0.9575	yes	no
Q6ZI17	OML2_ORYSJ	No assigned EC number	0.6203	0.9113	0.8844	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	823
pfam04059	97	pfam04059, RRM_2, RNA recognition motif 2	6e-65
cd12531	86	cd12531, RRM3_MEI2_like, RNA recognition motif 3 i	9e-63
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-49
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	6e-44
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	4e-43
cd12530	101	cd12530, RRM3_EAR1_like, RNA recognition motif 3 i	3e-38
cd12532	90	cd12532, RRM3_MEI2_fungi, RNA recognition motif 3	6e-37
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	9e-32
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	3e-31
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	2e-28
smart00360	73	smart00360, RRM, RNA recognition motif	9e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	9e-14
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	4e-12
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	4e-12
smart00360	73	smart00360, RRM, RNA recognition motif	5e-12
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	8e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	9e-11
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-10
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	9e-10
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	9e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-09
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-09
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	6e-09
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-08
cd12526	71	cd12526, RRM1_EAR1_like, RNA recognition motif 1 i	2e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-08
cd12525	72	cd12525, RRM1_MEI2_fungi, RNA recognition motif 1	3e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-08
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	5e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	6e-08
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	6e-08
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-07
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-07
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-07
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-07
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-07
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	3e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-07
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	3e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-07
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	6e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	7e-07
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	8e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	8e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	9e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	9e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-06
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-06
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-06
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	2e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	3e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-06
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	3e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	3e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	3e-06
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	4e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	5e-06
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	5e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-06
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	6e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	7e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	7e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	7e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	8e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	9e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	9e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-05
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	1e-05
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	1e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-05
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	3e-05
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	3e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	3e-05
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	4e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	4e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	5e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	5e-05
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	5e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	5e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	5e-05
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	6e-05
cd12288	93	cd12288, RRM_La_like_plant, RNA recognition motif	7e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	8e-05
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	9e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	9e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	9e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	9e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	9e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	9e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-04
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	1e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-04
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	1e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	2e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	2e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-04
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	2e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-04
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	2e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-04
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	3e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-04
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	3e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	3e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	3e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	3e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	4e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	4e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	5e-04
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	5e-04
cd12695	93	cd12695, RRM3_PTBP1, RNA recognition motif 3 in ve	5e-04
cd12697	76	cd12697, RRM3_ROD1, RNA recognition motif 3 in ver	6e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	6e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	6e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	6e-04
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	6e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	6e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	7e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	7e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	7e-04
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	7e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	8e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	8e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	8e-04
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	8e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	8e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	8e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	8e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	9e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	9e-04
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	0.001
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	0.001
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.001
cd12256	89	cd12256, RRM2_LKAP, RNA recognition motif 2 in Lim	0.001
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	0.001
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.001
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.001
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	0.001
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.001
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.001
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.001
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	0.001
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.002
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.002
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.002
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	0.002
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.002
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	0.002
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.002
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.002
cd12419	80	cd12419, RRM_Ssp2_like, RNA recognition motif in y	0.002
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	0.002
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.002
cd12696	107	cd12696, RRM3_PTBP2, RNA recognition motif 3 in ve	0.002
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	0.002
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.003
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.003
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.003
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	0.003
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	0.003
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	0.003
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	0.003
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.003
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	0.003
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	0.003
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.003
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	0.004
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	0.004
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.004
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.004
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.004
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.004
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.004
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	0.004
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.004

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

 Score =  211 bits (538), Expect = 6e-65
 Identities = 85/97 (87%), Positives = 90/97 (92%)

Query: 694 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIP 753
           RTTLMIKNIPNKYT KMLLAAIDE +KGTYDFLYLPIDFKNKCNVGYAFINM+ P  IIP
Sbjct: 1   RTTLMIKNIPNKYTQKMLLAAIDEKNKGTYDFLYLPIDFKNKCNVGYAFINMIEPQSIIP 60

Query: 754 FYEAFNGKKWEKFNSEKVASLAYARIQGRAALVAHFQ 790
           F +AFNGKKWEKFNSEKVASLAYARIQG+ AL+AHFQ
Sbjct: 61  FGKAFNGKKWEKFNSEKVASLAYARIQGKDALIAHFQ 97

Length = 97

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

 Score =  204 bits (522), Expect = 9e-63
 Identities = 75/86 (87%), Positives = 80/86 (93%)

Query: 697 LMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYE 756
           LMIKNIPNKYT KMLLAAIDE H+GTYDF YLPIDFKNKCNVGYAFINM+SP  I+PFY+
Sbjct: 1   LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYK 60

Query: 757 AFNGKKWEKFNSEKVASLAYARIQGR 782
           AFNGKKWEKFNSEKV SLAYARIQG+
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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score =  167 bits (426), Expect = 2e-49
 Identities = 66/77 (85%), Positives = 69/77 (89%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           SRTLFVRNINSNVED ELRALFEQ+GDIRTLYTACKHRGF+M+SYYDIRAAR A RALQ 
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 252 KPLRRRKLDIHFSIPKD 268
             L  RKLDIHFSIPKD
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 =  152 bits (385), Expect = 6e-44
 Identities = 64/71 (90%), Positives = 70/71 (98%)

Query: 277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           QGTLVVFNLDPSVSN+DL QIFGAYGE+KEIRETP+KRHHKFIEFYDVR+AEAALK+LNR
Sbjct: 1   QGTLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNR 60

Query: 337 SDIAGKRIKLE 347
           S+IAGKRIKLE
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|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like proteins and terminal EAR1-like proteins

 Score =  150 bits (381), Expect = 4e-43
 Identities = 58/86 (67%), Positives = 70/86 (81%), Gaps = 1/86 (1%)

Query: 697 LMIKNIPNKYTSKMLLAAIDENHKG-TYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFY 755
           +MI+NIPNKYT +MLL  +DE+ KG  YDFLYLPIDFKNKCNVGYAFIN ++P +   FY
Sbjct: 1   VMIRNIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFY 60

Query: 756 EAFNGKKWEKFNSEKVASLAYARIQG 781
           +AFNGKKW+ 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|240974 cd12530, RRM3_EAR1_like, RNA recognition motif 3 in terminal EAR1-like proteins

 Score =  137 bits (346), Expect = 3e-38
 Identities = 53/101 (52%), Positives = 70/101 (69%), Gaps = 13/101 (12%)

Query: 694 RTTLMIKNIPNKYTSKMLL-----------AAIDENH--KGTYDFLYLPIDFKNKCNVGY 740
           RTTLMIKNIPNKY+ K+LL             I+++     +YDF+YLPIDFKNKCN+GY
Sbjct: 1   RTTLMIKNIPNKYSQKLLLDMLDTHCIQCNQHIEDSSQPVSSYDFVYLPIDFKNKCNLGY 60

Query: 741 AFINMLSPLHIIPFYEAFNGKKWEKFNSEKVASLAYARIQG 781
           AF+N  SP     FY+AF+ ++WE+FNS K+  + YAR+QG
Sbjct: 61  AFVNFTSPEATWRFYKAFHNQQWEEFNSRKICQITYARVQG 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|240976 cd12532, RRM3_MEI2_fungi, RNA recognition motif 3 in fungal Mei2-like proteins

 Score =  133 bits (336), Expect = 6e-37
 Identities = 53/89 (59%), Positives = 67/89 (75%)

Query: 694 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIP 753
           RTT+M+KNIPNK+T +ML   IDE + GTYDF+YL IDF N CNVGYAF+N + P+ II 
Sbjct: 1   RTTVMLKNIPNKFTQQMLRKYIDETNPGTYDFMYLRIDFNNSCNVGYAFVNFIEPISIIT 60

Query: 754 FYEAFNGKKWEKFNSEKVASLAYARIQGR 782
           F +A  G KW  F+SEKV  ++YA IQG+
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|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score =  117 bits (296), Expect = 9e-32
 Identities = 40/71 (56%), Positives = 55/71 (77%)

Query: 277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           QGTL+VFNLD  +S+++LR +F  +GEVK+IRETP +   KF+EFYD+RAAEAAL +LN 
Sbjct: 1   QGTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 337 SDIAGKRIKLE 347
               G R+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 =  116 bits (292), Expect = 3e-31
 Identities = 42/71 (59%), Positives = 57/71 (80%)

Query: 277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           QGTLV+FNLDP+VS+E LR IF  YG+VKE+RETP KR  +F+EF+DVR A  AL+++N 
Sbjct: 1   QGTLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNG 60

Query: 337 SDIAGKRIKLE 347
            +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 =  108 bits (271), Expect = 2e-28
 Identities = 29/71 (40%), Positives = 44/71 (61%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           SR+LFV N+  +V +S LR LFE YGD+R + T     G V + +YDIR A+ A+R L  
Sbjct: 1   SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCG 60

Query: 252 KPLRRRKLDIH 262
           + ++++ 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 = 72.2 bits (178), Expect = 9e-16
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 5/73 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
           TL V NL P  + E+LR++F  +G+V+ +R    K   K     F+EF     AE AL++
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 334 LNRSDIAGKRIKL 346
           LN  ++ G+ +K+
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 71.6 bits (176), Expect = 2e-15
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 4/72 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLN 335
           L V NL P  + EDLR++F  +GE++ +R    +    +   F+EF     AE AL++LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 336 RSDIAGKRIKLE 347
             ++ 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 66.5 bits (163), Expect = 9e-14
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 4/70 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLN 335
           L V NL P  + EDL+ +F  +G ++ IR    ET   +   F+EF D   AE AL++LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 336 RSDIAGKRIK 345
             ++ 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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 61.9 bits (151), Expect = 4e-12
 Identities = 21/73 (28%), Positives = 44/73 (60%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           TL V N++ +V +E+LR +F  +G+++ +      R    + +YD+RAA  A ++L  ++
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTE 62

Query: 339 IAGKRIKLEPSRP 351
           + G+++ +  S P
Sbjct: 63  LGGRKLDIHFSIP 75

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 = 61.8 bits (151), Expect = 4e-12
 Identities = 24/68 (35%), Positives = 39/68 (57%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 253
           TL V N++S + D ELR+LF Q+G+++ +           + +YDIRAA  A+ AL  +P
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGRP 62

Query: 254 LRRRKLDI 261
               +L +
Sbjct: 63  FLGGRLKV 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|214636 smart00360, RRM, RNA recognition motif

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRA 248
           TLFV N+  +  + ELR LF ++G + ++         K +GF  + +     A  A+ A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 249 LQNKPLRRRKLDI 261
           L  K L  R L +
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 61.4 bits (150), Expect = 8e-12
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 8/78 (10%)

Query: 194 TLFVRNINSNVEDSELR----ALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAM 246
           TL++ N+N  ++  EL+    ALF Q+G   DI    T  K RG   + + D+ +A  A+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTL-KMRGQAFVVFKDVESATNAL 59

Query: 247 RALQNKPLRRRKLDIHFS 264
           RALQ  P   + + I ++
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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 60.0 bits (146), Expect = 2e-11
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQ 250
           LFV N+  +  + +LR LF ++G+I ++        K +GF  + +     A  A+ AL 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 251 NKPLRRRKLDIH 262
            K L  RKL + 
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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 60.3 bits (147), Expect = 2e-11
 Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V NL  +V+ EDL+ +FG +GEV        RET   R   F+E      A AA++ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 334 LNRSDIAGKRIKLEPSRP 351
           LN +D  G+ + +  +RP
Sbjct: 61  LNGTDFGGRTLTVNEARP 78

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|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 = 58.4 bits (142), Expect = 9e-11
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALK 332
             L V  L    + ++L  +F  +G V+E+      ET   R   F+ F  V  A+AA++
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 333 SLNRSDIAGKRIKLEPSR 350
            LN  ++ G+ IK+E ++
Sbjct: 62  DLNGKELEGRVIKVEKAK 79

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

 Score = 57.7 bits (140), Expect = 1e-10
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE-AALKSLNRS 337
           TL V  L   V+ +DLR  F  +GE++ I   P ++   F+ F    AAE AA +  N+ 
Sbjct: 3   TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVP-RQQCAFVTFTTREAAEKAAERLFNKL 61

Query: 338 DIAGKRIKL 346
            I G+R+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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 55.6 bits (135), Expect = 5e-10
 Identities = 14/56 (25%), Positives = 24/56 (42%)

Query: 209 LRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 264
           L  LF  +G++  +    K  GF  + +    AA  A++ L       R L + +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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 55.5 bits (134), Expect = 9e-10
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVMISYYDIRAARTAMRA 248
           +L+VRN+       +LR LF +YG I  +Y          RGF  + + D+R A  A+  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 249 LQNKPLRRRKLDIHFS 264
           L       R+++I F+
Sbjct: 62  LDRTRFLGREIEIQFA 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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 55.3 bits (134), Expect = 9e-10
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI---RETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           V NL P  +  +L   F  YG ++ +   R  P      F+EF D R AE A+++L+   
Sbjct: 4   VGNLGPRATKRELEDEFEKYGPLRSVWVARNPPG---FAFVEFEDPRDAEDAVRALDGRR 60

Query: 339 IAGKRIKLEPSRP 351
           I G R+++E SR 
Sbjct: 61  ICGNRVRVELSRG 73

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 29/69 (42%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNR 336
           L V NL PSV+ EDLR+ F  YG+V+ +R   +K   +   F+EF     AEAALK LN 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 337 SDIAGKRIK 345
             + G+ ++
Sbjct: 61  LVLDGRTLR 69

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

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAMRALQ 250
           LFV N+  +  + +L+ LF ++G I ++        + +GF  + + D   A  A+ AL 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 251 NKPLRRRKL 259
            K L  R+L
Sbjct: 61  GKELGGREL 69

(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 = 54.5 bits (132), Expect = 2e-09
 Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 6/76 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH--HK---FIEFYDVRAAEAALKS 333
            L+V N+    + ++LR++F  +G+VK +R  P K    H+   F+EF   + A+ A+++
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 334 LNRSDIAGKRIKLEPS 349
           L  + + 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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 54.6 bits (132), Expect = 2e-09
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLN 335
           ++ V  L P V+ E+L + F  +G++ E   I+   H     FI+F   +AA  A++S N
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64

Query: 336 RSDIAGKRIKLE 347
            S +  K + ++
Sbjct: 65  HSMLKNKTMHVQ 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 52.9 bits (128), Expect = 3e-09
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 294 LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS 349
           L ++F  +G V++I+    K    F+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|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 = 52.7 bits (127), Expect = 6e-09
 Identities = 26/68 (38%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           T+ V  LDP+V+ ++LR +FG +GE+  ++  P  +   F++F    AAEAA++ L  + 
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVK-IPPGKGCGFVQFVHRAAAEAAIQQLQGTI 61

Query: 339 IAGKRIKL 346
           I G RI+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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 52.8 bits (127), Expect = 1e-08
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           +L V N+  +   +DLR++FG YG + ++       T   R   +++F DVR AE AL  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 334 LNRSDIAGKRIKLE 347
           L+R+   G+ I+++
Sbjct: 62  LDRTRFLGREIEIQ 75

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

 Score = 58.3 bits (141), Expect = 1e-08
 Identities = 52/216 (24%), Positives = 92/216 (42%), Gaps = 35/216 (16%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVMISYYDIRAARTAMRAL 249
           L+V+N++ +V + +LR LF ++G+I +     K      RGF  +++     A  A+  +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSA-AVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 250 -------------------QNKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSV 289
                              Q +  R  +L   F   +     K   QG  L V NLD +V
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFE--ELQQERKMKAQGVNLYVKNLDDTV 297

Query: 290 SNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
           ++E LR++F   GE+   +    E    R   F+ F +   A  A+  ++   + GK + 
Sbjct: 298 TDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLY 357

Query: 346 LEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSP 381
           +  ++    RR     L  +  Q + R+ Q  +GSP
Sbjct: 358 VALAQRKEQRRA---HLQDQFMQLQPRMRQLPMGSP 390

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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 57.6 bits (139), Expect = 2e-08
 Identities = 45/176 (25%), Positives = 87/176 (49%), Gaps = 19/176 (10%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAAR 243
           E   RT+FV  +     + +L   F + G +R +       + + +G   + +YD+ +  
Sbjct: 86  ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVI 145

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLN--QGT------LVVFNLDPSVSNEDLR 295
            A+ AL  + L  R + +  S  + N + K      G       L V NL  +++ ++LR
Sbjct: 146 KAL-ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELR 204

Query: 296 QIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           QIF  +G++++++     ET   +   FI+F+D   A+ AL+ +N  ++AG+ IK+
Sbjct: 205 QIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKV 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|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal EAR1-like proteins

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 17/59 (28%), Positives = 33/59 (55%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           SR L +  +  ++ +++LR   EQ+G +R +       G V + +YD+R A  A+R ++
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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 57.1 bits (138), Expect = 3e-08
 Identities = 47/197 (23%), Positives = 94/197 (47%), Gaps = 15/197 (7%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAMRALQ 250
           +FV+N++ +V++  L   F ++G+I +   A     K RG+  + +    +A+ A++ + 
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 251 NKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR- 308
              L  +++ +   I K       L + T L V NLDPSV+ + LR++F  +GE+     
Sbjct: 151 GMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAV 210

Query: 309 ---ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI----AGKRIKLEPSRPGGARRNLMLQ 361
               +   R   F+ F     A  A++ +N   I     GK++ +  ++    R   + +
Sbjct: 211 MKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRR 270

Query: 362 LNQELEQDESRILQHQV 378
             +EL+Q+  R ++ Q 
Sbjct: 271 KFEELQQE--RKMKAQG 285

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

 Score = 50.8 bits (122), Expect = 3e-08
 Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-RGFVMISYYDIRAARTAMRALQ 250
           +R L V  +  +V  S L+ +FE+ GD++ ++      +G V++S++D+R A  A + LQ
Sbjct: 1   TRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLLSKGIVIVSFHDLRQAIKAYKDLQ 60

Query: 251 NKPL 254
           +K  
Sbjct: 61  SKRA 64

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

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSL 334
           L+V NL    +  DL+++F  +G V E+   P K   K     F++F     AE A+K +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEV-TIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 335 NRSDIAGKRI 344
           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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 50.6 bits (122), Expect = 4e-08
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V  L  +V+ + L++IF  YG VK++     RE    R + ++EF     AE A+K +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 335 NRSDIAGKRIKLE 347
           +   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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 9/75 (12%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHK---FIEFYDVRAAEAALKS 333
           V NLD  +  +DLR IF  +GEV+ IR     +    R +    F+ F D  +AE AL+ 
Sbjct: 5   VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ- 63

Query: 334 LNRSDIAGKRIKLEP 348
           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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRT----------LYTACKHRGFVMISYYDIRAA 242
            TLFV+N+N    +  L+  FE+ G +R+                  G+  + +    AA
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 243 RTAMRALQNKPLRRRKLDIHFS 264
           + A++ LQ   L    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|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 50.2 bits (120), Expect = 6e-08
 Identities = 25/69 (36%), Positives = 40/69 (57%), Gaps = 9/69 (13%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR----HHKFIEFYDVRAAEAALKSLN 335
           L V NLDP V+ + L+QIF   G V+ ++  P K     ++ F+E++    AE AL++LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 336 RSDIAGKRI 344
                G++I
Sbjct: 61  -----GRQI 64

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

 Score = 50.4 bits (121), Expect = 6e-08
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           T+ V NLDP+ + + L + F   GEVK +R    ET   R + F+EF +  +   ALK L
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTR-YAFVEFAEQTSVINALK-L 63

Query: 335 NRSDIAGKRIKLEPSR 350
           N +   G+ +K+  S 
Sbjct: 64  NGAMFGGRPLKVNHSN 79

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|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 49.5 bits (119), Expect = 9e-08
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V N+    + E L +IF   G V   R     +T   + + F EF D+  A +A+++LN 
Sbjct: 3   VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG 62

Query: 337 SDIAGKRIKLEPS 349
            +  G+ ++++ +
Sbjct: 63  YEFNGRALRVDFA 75

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

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

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 18/77 (23%), Positives = 41/77 (53%), Gaps = 9/77 (11%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDIRAART 244
           R ++VRN++  +++ +LR +F ++G++ ++    K        + GF  +++ D  +A  
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 245 AMRALQNKPLRRRKLDI 261
           A+  L    L  RK+ +
Sbjct: 61  AL-QLNGTELGGRKISV 76

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

 Score = 49.5 bits (119), Expect = 1e-07
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRA 248
           TLFVRN+  +  D +L   F + G I+  +        K RGF  +++     A+ A+  
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 249 LQNKPLRRRKLDIHFSIPK 267
            +      RK+ + F+  K
Sbjct: 61  KKKTKFGGRKIHVEFAKKK 79

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

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKE--IRETPHK--RHHKFIEFYDVRAAEAALKSLN 335
           L+V NL   +  + LR++F A+G + +  ++ T     R   F+ +     A+ ALK  N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 336 RSDIAGKRIKLEP 348
            S 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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 27/69 (39%), Positives = 41/69 (59%), Gaps = 4/69 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           L V NLD +V+ + L ++F   G +   K IRE      + F+E+YD R+A AAL+++N 
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE-HGNDPYAFVEYYDHRSAAAALQTMNG 59

Query: 337 SDIAGKRIK 345
             I G+ IK
Sbjct: 60  RLILGQEIK 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|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQ----IFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALK 332
           TL + NL+  +  ++L++    +F  +G V +I   +T   R   F+ F DV +A  AL+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 333 SLNRSDIAGKRIKLEPSR 350
           +L       K ++++ ++
Sbjct: 61  ALQGFPFYDKPMRIQYAK 78

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

 Score = 49.1 bits (118), Expect = 2e-07
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVK--EIRETPHKRHHKFIEFYDVRAAEAALK----S 333
           L V  L PSV+  DL + F  +G V   EI +       +   + D+R +EA LK    +
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 334 LNRSDIAGKRIKLEPSR 350
           LN +   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|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 49.2 bits (118), Expect = 2e-07
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           T+ V NL  S++N DL +IF  YG+V ++     +ET   +   FI F D   A   +K+
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 334 LNRSDIAGKRIK 345
           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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
           TL V N  PS    D+R +F  YGE+  IR  P  R +K     +++F    +A AA+  
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIR-FPSLRFNKTRRFCYVQFTSPESAAAAVAL 60

Query: 334 LNRSDIAGKRIKLEPSRP 351
           LN     G ++ ++ S P
Sbjct: 61  LNGKLGEGYKLVVKISDP 78

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

 Score = 48.3 bits (115), Expect = 3e-07
 Identities = 19/68 (27%), Positives = 38/68 (55%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 253
           TL V N++ +V + +L  +F  YG+I+ +      R    I +YD+R+A  A++AL    
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSE 62

Query: 254 LRRRKLDI 261
           +  +++ +
Sbjct: 63  IAGKRIKL 70

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|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 = 48.0 bits (115), Expect = 3e-07
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           T+ V NL   ++ E+L++ F  +G ++E+R    K  + F+ F    AA  A+ ++N + 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK-GYAFVRFDTHEAAATAIVAVNGTS 60

Query: 339 IAGKRIK 345
           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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 5/72 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V NL  +++ +DLR IF  +GE++ ++     ET   + + FI+F D   A+ AL+ L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 335 NRSDIAGKRIKL 346
           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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 18/70 (25%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE--IRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           TL + NL+ + +  DLR+ F  +GE+ +  I++      + FI++ D+ +   A++ ++ 
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63

Query: 337 SDIAGKRIKL 346
             +   R+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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 52.6 bits (125), Expect = 3e-07
 Identities = 32/128 (25%), Positives = 56/128 (43%), Gaps = 5/128 (3%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 321
             +         TL V NL   V+ EDLR++F  +G VK +     RET   R   F+EF
Sbjct: 105 PKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEF 164

Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSP 381
               +AE A++ LN  ++ G+ ++++ ++P    R+ +          +    +  +   
Sbjct: 165 ESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEK 224

Query: 382 ITNSPPGN 389
             N   GN
Sbjct: 225 SDNLYVGN 232

Length = 306

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

 Score = 47.5 bits (114), Expect = 4e-07
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI---RTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           L+VRN+  +V + +LR  F  YG +   R +    + RGF  + +     A  A++ L  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 252 KPLRRRKL 259
             L  R L
Sbjct: 61  LVLDGRTL 68

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

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 47.1 bits (112), Expect = 6e-07
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 279 TLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           TL V   DP +   ED+ ++F  +G +        ++   F+EF D   A  AL++L+ S
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCD---IRKTFAFVEFEDSEDATKALEALHGS 57

Query: 338 DIAGKRIKLE 347
            I G  + +E
Sbjct: 58  RIDGSVLTVE 67

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

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

 Score = 47.2 bits (113), Expect = 7e-07
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKF--IEFYDVRAAEAALKS 333
           TL V NL    ++E L + F   G +K    +++   K+   F  + F     A+ AL+ 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 334 LNRSDIAGKRIKLE 347
             ++   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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 46.9 bits (112), Expect = 7e-07
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
            L       D+ + F  YG ++EI     K    F+EF D R A+ A+  LN  ++ G+R
Sbjct: 6   RLPYRARERDVERFFKGYGRIREIN---LKNGFGFVEFEDPRDADDAVYELNGKELCGER 62

Query: 344 IKLEPSRP 351
           + +E +R 
Sbjct: 63  VIVEHARG 70

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|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 52.1 bits (125), Expect = 8e-07
 Identities = 40/161 (24%), Positives = 72/161 (44%), Gaps = 14/161 (8%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           PS  + VRN+  +V +++L      +G + +       +   ++ + D  +A+  +    
Sbjct: 1   PSPVVHVRNLPQDVVEADLVEALIPFGPV-SYVMMLPGKRQALVEFEDEESAKACVNFAT 59

Query: 251 NKP--LRRRKLDIHFS----IPKDNPSDKDLNQGTLV----VFNLDPSVSNEDLRQIFGA 300
           + P  +R +    ++S    I +D  SD D      V    V N    ++ + L QIF  
Sbjct: 60  SVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNP 119

Query: 301 YGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRSDI 339
           YG+V  I  T  K +     +EF  V +A+ A  +LN +DI
Sbjct: 120 YGKVLRI-VTFTKNNVFQALVEFESVNSAQHAKAALNGADI 159

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). Length = 481

>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 = 47.3 bits (113), Expect = 8e-07
 Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           TL V  L    + E LR++F  YG+++ +R      T   + + F+E+   R A  A + 
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 334 LNRSDIAGKRI 344
            ++  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|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 = 46.8 bits (112), Expect = 9e-07
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACK----HRGFVMISYYDIRAARTAMRAL 249
            L VRN+       ELR LF  +G ++++    K    HRGF  + +   + A+ AM AL
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 250 QNKPLRRRKLDIHFS 264
           ++  L  R L + ++
Sbjct: 62  KSTHLYGRHLVLEYA 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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 46.5 bits (111), Expect = 9e-07
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V NL    + +DLR++F  YGEV ++     R T   R   F+ FYD R AE A+ ++
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 335 NRSDIAGKRIK 345
           +  ++ 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 51.7 bits (124), Expect = 1e-06
 Identities = 39/173 (22%), Positives = 80/173 (46%), Gaps = 11/173 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHR--GFVMISYYDIRAARTAMRA 248
           +L+V +++ +V +++L  LF+ +G    +R    +   R  G+  +++ +   A  A+  
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
           +  K L  + + I +S  + +PS +    G + V NLD SV N+ L   F  +G +   +
Sbjct: 62  MNFKRLGGKPIRIMWS--QRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCK 119

Query: 309 ----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
               E    R + F+ F    +A+AA++ +N   +  K + +        R  
Sbjct: 120 VATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREA 172

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

 Score = 47.0 bits (112), Expect = 1e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L+V  L   ++ E+LR +F A G ++       R T     + F+++ D   A+ A+ +L
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 335 NRSDIAGKRIK 345
           N  +I  KR+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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 46.8 bits (112), Expect = 1e-06
 Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V +L P V+   L +IF   G V  IR      T     + ++ F +   AE AL +L
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 335 NRSDIAGKRIKLEPS 349
           N   I GK I++  S
Sbjct: 62  NFDVIKGKPIRIMWS 76

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|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L VF L    +  DLR++F  YG ++++     ++T   R   F+ F  V  A+ A + L
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 335 NRSDIAGKRIKLEPS 349
           N  +I G+RI+++ S
Sbjct: 62  NGMEIDGRRIRVDYS 76

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

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

 Score = 46.5 bits (110), Expect = 1e-06
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRA 248
           +LFVRNI  +    +LR  F +YG I  +Y        + RGF  + + D+R A  A+  
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 249 LQNKPLRRRKLDIHFS 264
           L  K +  R+++I F+
Sbjct: 62  LDRKWICGRQIEIQFA 77

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

 Score = 50.3 bits (119), Expect = 2e-06
 Identities = 40/188 (21%), Positives = 70/188 (37%), Gaps = 26/188 (13%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAAR 243
           +  + TLFV N+  +V + +LR LF+++G ++ +         K RGF  + +    +A 
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNP--------------------SDKDLNQGTLVVF 283
            A+  L  K L  R L +  + P   P                    +        L V 
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
           NL    + E+L  +F + G++      P K   K  +       EA+  +L  +    K+
Sbjct: 232 NLPLKTAEEELADLFKSRGDIVRASLPPSKD-GKIPKSRSFVGNEASKDALESNSRGNKK 290

Query: 344 IKLEPSRP 351
             L     
Sbjct: 291 KILGRGPR 298

Length = 306

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 46.2 bits (110), Expect = 2e-06
 Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 5/80 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH-----HKFIEFYDVRAAEAALKS 333
            L++  L  ++++E+ R +F A G VK  +    KR        F+++     A+ A+++
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 334 LNRSDIAGKRIKLEPSRPGG 353
           LN   +  KRIK+  +RPGG
Sbjct: 62  LNGLQLQNKRIKVAYARPGG 81

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. 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 also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

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

 Score = 46.2 bits (109), Expect = 2e-06
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           +L V N+  +   EDLR+ FG YG + ++       T   R   +I+F DVR AE AL +
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 334 LNRSDIAGKRIKLE 347
           LNR  + G++I+++
Sbjct: 62  LNRKWVCGRQIEIQ 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|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 = 45.8 bits (109), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 4/75 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLN 335
           T+ V  +D S+S +DL++ F   GEV  +R    ++H     F+EF D  +A +AL +L+
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSAL-NLS 60

Query: 336 RSDIAGKRIKLEPSR 350
            + + G  +++ PS+
Sbjct: 61  GTLLGGHPLRVSPSK 75

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

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 6/75 (8%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-----RHHKFIEFYDVRAAEAALK 332
             ++V NL    + +D+R +F +YG++K +R  P K     R   F+EF   + A  A+ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMN 59

Query: 333 SLNRSDIAGKRIKLE 347
           +L  + + G+R+ 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|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 = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-FIEFYDVRAAEAALKSLNRSD 338
           + + NL   V+ + L Q+F  YG V++I         +  ++F  V +AE A K+LN  +
Sbjct: 4   VTISNLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRN 63

Query: 339 I 339
           I
Sbjct: 64  I 64

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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           T+ V NL      +DLR++F  +G +  +     +ET   R   F+ F+    AE A++ 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 334 LNR 336
           LN 
Sbjct: 61  LNG 63

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

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

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 20/70 (28%), Positives = 36/70 (51%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           ++V N+       EL   FE+YG +R+++ A    GF  + + D R A  A+RAL  + +
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRI 61

Query: 255 RRRKLDIHFS 264
              ++ +  S
Sbjct: 62  CGNRVRVELS 71

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

 Score = 45.7 bits (108), Expect = 3e-06
 Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           +L V N+     +EDLR+ FG YG + ++       T   R   +++F DVR AE AL +
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 334 LNRSDIAGKRIKLE 347
           L+R  I G++I+++
Sbjct: 62  LDRKWICGRQIEIQ 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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 9/75 (12%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGE---VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           L V NL  S + E LR++F  YGE   VK+I++      + F+ F +   A  A++ +N 
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD------YAFVHFEERDDAVKAMEEMNG 57

Query: 337 SDIAGKRIKLEPSRP 351
            ++ G  I++  ++P
Sbjct: 58  KELEGSPIEVSLAKP 72

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 45.3 bits (107), Expect = 3e-06
 Identities = 22/69 (31%), Positives = 37/69 (53%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            LVV NL  S S + L+++F     ++  +     + + F+EF     A+ AL S N ++
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTE 62

Query: 339 IAGKRIKLE 347
           I G+ I+LE
Sbjct: 63  IEGRSIRLE 71

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>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 = 45.4 bits (108), Expect = 3e-06
 Identities = 20/76 (26%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           S TL++ +++  V + +L+ LFE+YG+I+++      RG   +     + A  A++ L+N
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSI-DMIPPRGCAYVCMETRQDAHRALQKLRN 60

Query: 252 KPLRRRKLDIHFSIPK 267
             L  +K+ + ++  K
Sbjct: 61  VKLAGKKIKVAWAPNK 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|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 50.5 bits (120), Expect = 3e-06
 Identities = 38/169 (22%), Positives = 87/169 (51%), Gaps = 17/169 (10%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRAL 249
           ++V +I+  + +  +R  F+ +G I+++  +      KH+GF  + Y    AA+ A+  +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 250 QNKPLRRRKLDIHF--SIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 302
             + L  R + +    ++P+  P    + +       + V ++ P +S  D++ +F A+G
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFG 229

Query: 303 EVK--EIRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           E+   ++   P  R HK   FIE+ ++++   A+ S+N  D+ G+ +++
Sbjct: 230 EIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. 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. Length = 612

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

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH--RGFVMISYYDIRAARTAMRAL 249
           +R L+VRN+   +   EL  LF +YG IR +        RG   + Y DI  A+ A   L
Sbjct: 2   NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

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

 Score = 44.9 bits (106), Expect = 4e-06
 Identities = 23/62 (37%), Positives = 38/62 (61%), Gaps = 3/62 (4%)

Query: 289 VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 348
           V  +D+++ FG YG++ EI     K  + F+EF D R A+ A+  LN  D+ G+R+ +E 
Sbjct: 11  VREKDIQRFFGGYGKLLEI---DLKNGYGFVEFEDSRDADDAVYELNGKDLCGERVIVEH 67

Query: 349 SR 350
           +R
Sbjct: 68  AR 69

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|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 = 44.8 bits (107), Expect = 4e-06
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRAL 249
           LFV  +     + ++RALFE+YG+I  +         + +G   + +     A+ A+ AL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 250 QNK 252
             K
Sbjct: 62  HGK 64

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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 9/61 (14%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAARTAMRALQN 251
           LFV N+       ELRALFE+YG +    T C   K+ GFV +   +   A  A++AL  
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTV----TECDVVKNYGFVHME--EEEDAEDAIKALNG 55

Query: 252 K 252
            
Sbjct: 56  Y 56

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is 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. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           TL+V +L P +S +D   +   +G   V+ +      ++  F  F + +AA  AL  L++
Sbjct: 1   TLLVRHLPPELSEDDKEDLLKHFGASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQ 60

Query: 337 SDIAGKRIKLE 347
             I GKR+ +E
Sbjct: 61  LKILGKRLVVE 71

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

>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 = 44.5 bits (106), Expect = 6e-06
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRA 248
            LFV  +++   + EL ALF ++G +  +         + RGF  +++  +  A  A+R 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 249 LQNKPLRRRKLDI 261
           L  K L  R + +
Sbjct: 63  LNGKELEGRVIKV 75

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|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 = 26/105 (24%), Positives = 47/105 (44%), Gaps = 13/105 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYD-----VRAAE 328
            +VV+   PS S + ++  F ++GE+ EIR      T        I++Y       RAA+
Sbjct: 4   EIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDRAAK 63

Query: 329 AALKSLNR---SDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDE 370
           AALK++ +     I G   K+E +        +  +L ++  +  
Sbjct: 64  AALKAVRKAQDCRIGGAEFKVELNPNERKLEKIKDKLIKQNRKKS 108

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|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 44.6 bits (106), Expect = 6e-06
 Identities = 18/69 (26%), Positives = 43/69 (62%), Gaps = 5/69 (7%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRH--HKFIEFYDVRAAEAALKSLNR 336
           V ++ P +S +D++ +F A+G++K      +    +H  + FIE+ + ++A+ A+ S+N 
Sbjct: 5   VASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNL 64

Query: 337 SDIAGKRIK 345
            D+ G++++
Sbjct: 65  FDLGGQQLR 73

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

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

 Score = 44.2 bits (105), Expect = 7e-06
 Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMRA 248
           L V N+       +LR +FE+YG++      R  YT  + RGF  + +YD R A  AM A
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTR-ESRGFAFVRFYDKRDAEDAMDA 59

Query: 249 LQNKPLRRRKL 259
           +  K L  R+L
Sbjct: 60  MDGKELDGREL 70

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

 Score = 44.1 bits (105), Expect = 7e-06
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           L+V  +      +EL   F+++G IR +      R +  I Y  I AA+ A  AL+  PL
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI-DYDPGRNYAYIEYESIEAAQAAKEALRGFPL 59

Query: 255 RR--RKLDIHFS 264
               R+L + F+
Sbjct: 60  GGPGRRLRVDFA 71

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

 Score = 44.5 bits (106), Expect = 7e-06
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMR 247
           +TLFV  +N +  +S+LR  FE+YG I+ +         K RG+  I +   R  + A +
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 248 ALQNKPL--RRRKLDI 261
               K +  RR  +D+
Sbjct: 62  YADGKKIDGRRVLVDV 77

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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 44.5 bits (106), Expect = 8e-06
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 10/76 (13%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEIR-----ETPHKRHHKFIEFYDVRAAEAAL 331
           TL++  LD   + ED+ Q   A     +K++R      T   R   F+EF  +  A   +
Sbjct: 4   TLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWM 63

Query: 332 KSLNRSD---IAGKRI 344
            +LN  D   I G+ +
Sbjct: 64  DALNNLDPFVIDGRVV 79

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

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

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRA-ARTAMRALQNKP 253
           LFV N+ +++ + E + LF +YG++  ++   K +GF  I   D R  A  A   L    
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVF-LNKEKGFGFIR-LDTRTNAEKAKAELDGIM 61

Query: 254 LRRRKLDIHF 263
            + R+L + F
Sbjct: 62  RKGRQLRVRF 71

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|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 44.2 bits (105), Expect = 9e-06
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--------RHHKFIEFYDVRAAEAA 330
            L + NLD  ++   L ++F  YG++K+     HK        R + F+ F     AE A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 331 LKSLNRSDIAGKRIKLEPSR 350
           LKSLN     GK++ +  + 
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

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

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRA 248
           +LFVRN+       +LR  F +YG I  +Y        + RGF  I + D+R A  A+  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 249 LQNKPLRRRKLDIHFS 264
           L  K +  R+++I F+
Sbjct: 62  LNRKWVCGRQIEIQFA 77

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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 252
           + L+VRN+  +  + +LR LF +YG++  +    K + +  + + +   A  AM  +  K
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVK---KIKDYAFVHFEERDDAVKAMEEMNGK 58

Query: 253 PLRRRKLDIHFSIP 266
            L    +++  + P
Sbjct: 59  ELEGSPIEVSLAKP 72

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK----RHHKFIEFYDVRAAEAALKSL 334
            L V  L  SV+ E+L ++F  +G VK +R   ++    +   ++E+ +  +A  A+  +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 335 NRSDIAGKRIKLEPSRPG 352
           + ++I  K I +  S P 
Sbjct: 64  DGTEIKEKTISVAISNPP 81

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is 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 = 81

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 285 LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI 344
           L+P+   +D+ + F  YG    IR+   KR   F+EF D R A+ A+  L+  ++  +R+
Sbjct: 7   LNPAAREKDVERFFKGYGR---IRDIDLKRGFGFVEFDDPRDADDAVYELDGKELCNERV 63

Query: 345 KLEPSR 350
            +E +R
Sbjct: 64  TIEHAR 69

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that 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 it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains 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. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 8/78 (10%)

Query: 194 TLFVRNINSNVEDSELR----ALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAM 246
           T+++ N+N  V+  EL+    A+F Q+G   DI  L T  K RG   + + DI +A  A+
Sbjct: 1   TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKT-LKMRGQAFVVFKDISSATNAL 59

Query: 247 RALQNKPLRRRKLDIHFS 264
           R++Q  P   + + I +S
Sbjct: 60  RSMQGFPFYDKPMRIAYS 77

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila 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). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

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

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKF-----IEFYDVRAAEAALKSL 334
           L V NL      + + + FG YGE+  +R        +      +EF    AA+AAL +L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 335 NRSDIAGKRIKLE 347
             +D+ 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|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 5/74 (6%)

Query: 196 FVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQ 250
           FV NI  +  + +L  +F + G + +          K +G+    + DI  A +A+R L 
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 251 NKPLRRRKLDIHFS 264
                 R L + F+
Sbjct: 62  GYEFNGRALRVDFA 75

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 9/71 (12%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           L V NL  + ++E+LR +F  YG V E   +      +++ F+   +   AE A+K+LN 
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV------KNYGFVHMEEEEDAEDAIKALNG 55

Query: 337 SDIAGKRIKLE 347
            +  GKRI +E
Sbjct: 56  YEFMGKRINVE 66

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is 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. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V NL  + + E+LR++F A+GE+ E+     +ET   +   F+ F     A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 335 NRSDIAGK 342
           + S   G+
Sbjct: 62  DGSIFQGR 69

This subfamily corresponds to the RRM3 of RBM19 and RRM2 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). 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 = 74

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 43.4 bits (103), Expect = 2e-05
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 14/84 (16%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIR----TLYTACKH---RGFVMISYYDIRAARTA 245
           RT+F+RN+  +  + EL+ LF Q+G+++           H     FV   +    +A+  
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFV--KFKTKESAQKC 58

Query: 246 MRALQNKP-----LRRRKLDIHFS 264
           + A  N       L  R+L +  +
Sbjct: 59  LEAADNAEDSGLSLDGRRLIVTLA 82

This subfamily corresponds to the RRM3 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 = 82

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           L +++L    +++DL Q+F  +G V   +      T   +   F+ + +  +A+AA+K++
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 335 NRSDIAGKRIKLE 347
           N   + GKR+K++
Sbjct: 61  NGFQVGGKRLKVQ 73

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed 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. . Length = 73

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

 Score = 42.5 bits (100), Expect = 3e-05
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 4/61 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLY-TACK-HRGFVMISYYDIRAARTAMRALQN 251
           TL + N++  V    LR++F+ YGD++ L  T CK  + FV   ++D+R A  A+RA+  
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFV--EFFDVRDAAKALRAMNG 60

Query: 252 K 252
           K
Sbjct: 61  K 61

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 = 42.5 bits (100), Expect = 3e-05
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL 334
           +L V N+   V+   LR++F  YG+V+ ++          + FYD+R A+ A++ L
Sbjct: 3   SLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVREL 58

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 = 42.4 bits (100), Expect = 3e-05
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAMR 247
           +RTLF+ N+      S+LR  FE++G+I  +    K +G    +  I Y DI +   AMR
Sbjct: 2   TRTLFIGNLEKTTTYSDLREAFERFGEI--IDIDIKKQGGNPAYAFIQYADIASVVKAMR 59

Query: 248 ALQNKPLRRRKL 259
            +  + L   ++
Sbjct: 60  KMDGEYLGNNRV 71

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

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           TL V  L+   +   LR+ F  YG +K IR     +T   R + FIEF   R  +AA K 
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62

Query: 334 LNRSDIAGKRIKLEPSR 350
            +   I G+R+ ++  R
Sbjct: 63  ADGKKIDGRRVLVDVER 79

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|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 42.7 bits (101), Expect = 3e-05
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRAL 249
           LFVRN+     + ELR LFE +G+I  ++        + +GF  +S+     A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 250 QNKPLRRRKLDI 261
                + R L +
Sbjct: 62  DGSIFQGRLLHV 73

This subfamily corresponds to the RRM3 of RBM19 and RRM2 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). 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 = 74

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

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 192 SRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRAL 249
           SR +FV N+N++ V   +L  +F +YG I         H+G+  + + +   AR A+   
Sbjct: 1   SR-VFVGNLNTDKVSKEDLEEIFSKYGKI----LGISLHKGYGFVQFDNEEDARAAVAGE 55

Query: 250 QNKPLRRRKLDI 261
             + +  +KLDI
Sbjct: 56  NGREIAGQKLDI 67

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

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 24/68 (35%), Positives = 40/68 (58%), Gaps = 5/68 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRHHK---FIEFYDVRAAEAALKSL 334
           T+ V NLD SV  ++LR++F   GE+ ++R    +K   K   ++EF +  + + ALK L
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALK-L 59

Query: 335 NRSDIAGK 342
           +R  I G+
Sbjct: 60  DRELIKGR 67

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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 12/73 (16%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC--------KHRGFVMISYYDIRAARTAM 246
           ++V+N+  +++D +L+ LF +YG I    T+         K +GF  +++ +  AA+ A+
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKI----TSAKVMKDDEGKSKGFGFVNFENHEAAQKAV 59

Query: 247 RALQNKPLRRRKL 259
             L  K +  +KL
Sbjct: 60  EELNGKEVNGKKL 72

This subfamily corresponds to the RRM3 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 an 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. 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 mammalian, 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 the 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|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 = 21/65 (32%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           L V NL   +S+E+L  +FG YG +++IR   T   R   F+ + D+  A+ A   L+  
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGF 64

Query: 338 DIAGK 342
           ++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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHK---FIEFYDVRAAEAALKSL 334
           L V  L   V  + L   F  +G++K+I+       + H+   F+EF +   A AA+ ++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 335 NRSDIAGKRIK 345
           N S++ G+ I+
Sbjct: 61  NESELFGRTIR 71

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 42.2 bits (99), Expect = 4e-05
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A  A   L N PL
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFIH-KDKGFGFIRLETRTLAEIAKAELDNMPL 62

Query: 255 RRRKLDIHF 263
           R ++L + F
Sbjct: 63  RGKQLRVRF 71

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional 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. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 42.3 bits (100), Expect = 4e-05
 Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 5/65 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVK--EIRETPHKRHHK---FIEFYDVRAAEAALKS 333
           T+ V  L  + ++E L+ +F  YG V    +    H    K   FIEF     A+ A K 
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 334 LNRSD 338
           LN   
Sbjct: 61  LNNPP 65

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

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

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTL-YTACKHRGFVMISYYDIRAARTAMRALQN 251
            TL+V  +   V + +LR  F Q+G+IR++     +   FV  ++    AA  A   L N
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFV--TFTTREAAEKAAERLFN 59

Query: 252 K 252
           K
Sbjct: 60  K 60

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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 5/57 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAM 246
           L+V  +   V++  L A F  +GDI+ +     Y   KHRGF  + + +   A  A+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

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

 Score = 42.0 bits (98), Expect = 5e-05
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLN 335
           TL V NL   V+   + Q+F   G  K    I +T     + F+EF++ R A A+L ++N
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60

Query: 336 RSDIAGKRIKL 346
              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|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 42.3 bits (99), Expect = 5e-05
 Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYTA--CKHRGFVMISYYDIRAART 244
           P+ T+++ N+N  ++  EL+    A+F ++G I  +  +   K RG   + + ++ +A  
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 245 AMRALQNKPLRRRKLDIHFS 264
           A+R++Q  P   + + I ++
Sbjct: 62  ALRSMQGFPFYDKPMRIQYA 81

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), 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 and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

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

 Score = 42.3 bits (100), Expect = 5e-05
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--------ETPHKRHHKFIEFYDVRAAEAAL 331
           L V NL+P V+ E L Q FG +G +  ++        E    R+  F+ F +   AE AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 332 KSLNRSDIAGKRIKL 346
             L+  D+ 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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 42.0 bits (99), Expect = 5e-05
 Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 4/72 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE--IRETPHKRHHK--FIEFYDVRAAEAALKSL 334
           TL V NL+ +++ E+LR+ F  YG V++  I+  P  + +   F++F ++  A  A  ++
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 335 NRSDIAGKRIKL 346
           +   I   +IK+
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|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 41.5 bits (98), Expect = 6e-05
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 280 LVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L+V NL+   V+ + L  +FG YG+V  ++   +K+    I+  D + A+ AL  LN   
Sbjct: 2   LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIR 61

Query: 339 IAGKRIKLEPSR 350
           + GK++++  S+
Sbjct: 62  LHGKKLRVTLSK 73

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|240734 cd12288, RRM_La_like_plant, RNA recognition motif in plant proteins related to the La autoantigen

 Score = 42.1 bits (99), Expect = 7e-05
 Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 20/77 (25%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----------ETPHKRH----------HKF 318
           T+V  NL    S E+L +IFG  G VK +R           T  K            H  
Sbjct: 2   TVVAENLPEDHSIENLEEIFGTVGSVKNVRICDPGRVGSGSTASKAKKPDTLVSNKLHAL 61

Query: 319 IEFYDVRAAEAALKSLN 335
           +E+  V AAE A+  L+
Sbjct: 62  VEYETVEAAEKAVTELS 78

This subfamily corresponds to the RRM of plant La-like proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Members in this family contain an LAM domain followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

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

 Score = 41.0 bits (97), Expect = 8e-05
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 7/64 (10%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQY-G--DIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           P++ LF++N+        L  LF Q+ G  ++R +      RG   + +     A  A++
Sbjct: 1   PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV----PRRGIAFVEFETEEQATVALQ 56

Query: 248 ALQN 251
           ALQ 
Sbjct: 57  ALQG 60

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|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 = 41.2 bits (97), Expect = 9e-05
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           TL + +L   V+ EDL+ +F  YGE++ I   P  R   ++     + A  AL+ L    
Sbjct: 4   TLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-PRGCAYVCMETRQDAHRALQKLRNVK 62

Query: 339 IAGKRIKL 346
           +AGK+IK+
Sbjct: 63  LAGKKIKV 70

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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 41.4 bits (98), Expect = 9e-05
 Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 10/81 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHK---FIEFYDVRAAEAALKS 333
           T+ + NL    + E+L+++F  +GEVK  R    K   H K   F++F    +A+  L++
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 334 LNRSD-----IAGKRIKLEPS 349
            + ++     + G+R+ +  +
Sbjct: 62  ADNAEDSGLSLDGRRLIVTLA 82

This subfamily corresponds to the RRM3 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 = 82

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 41.4 bits (98), Expect = 9e-05
 Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 9/66 (13%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRETPHKRHHK--------FIEFYDVRAAEA 329
            L V NL   V+ EDL  IFG + +   E +     R           F+ F     A  
Sbjct: 3   RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATK 62

Query: 330 ALKSLN 335
           AL  +N
Sbjct: 63  ALNLVN 68

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 41.2 bits (97), Expect = 9e-05
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEI--RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V  L  +    DL+Q+F  YG+V   K +    +P  R   F+    V  A   ++ L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 335 NRSDIAGKRIKLE 347
           +R+++ G+ I +E
Sbjct: 62  HRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 40.8 bits (96), Expect = 9e-05
 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 6/70 (8%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK----FIEFYDVRAAEAALKSLNRS 337
           V NL   +   D+  +F  YG +K I      R       F+EF D R AE A++  +  
Sbjct: 4   VGNLPGDIRERDIEDLFYKYGPIKAI--DLKNRRRGPPFAFVEFEDPRDAEDAVRGRDGY 61

Query: 338 DIAGKRIKLE 347
           D  G R+++E
Sbjct: 62  DFDGYRLRVE 71

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

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

 Score = 41.2 bits (97), Expect = 9e-05
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRAL 249
           LFVRN+  + ++ +L  LF ++G++  ++ A      K +GF  + + D   A  A + L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 250 QNKPLRRRKLDI 261
             K  + R + I
Sbjct: 65  DGKVFQGRLIHI 76

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|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 = 40.7 bits (96), Expect = 1e-04
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 7/64 (10%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQ 250
           T+FV  ++  V + ELR+LF  +G+I  +Y      K  GFV   +    AA  A++ LQ
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEI--VYVKIPPGKGCGFV--QFVHRAAAEAAIQQLQ 58

Query: 251 NKPL 254
              +
Sbjct: 59  GTII 62

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|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVK--EI---RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V  L+P  ++EDL  IF  +G++K  E+   ++T     + FIEF      E A   
Sbjct: 5   VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFK 64

Query: 334 LNRSDIAGKRIK 345
           ++   I  +RI 
Sbjct: 65  MDNVLIDDRRIH 76

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           TL V NL  SV +E L+  F  +G V        RET   R   +++F     A+ A+++
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 334 LNRSDIAGKRIKLEPS 349
           ++  ++ G+ I ++ S
Sbjct: 61  MDGKELDGRPINVDFS 76

This subfamily corresponds to the RRM1 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 = 76

>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 25/80 (31%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 192 SRTLFVRNINSNVED-SELRALFEQYGDIRTLYTACKH----RGFVMISYYDIRAARTAM 246
           SR LFV  +     D S LR LF Q G       A       RGF  + Y     A  A 
Sbjct: 2   SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61

Query: 247 RALQNKPLRRRKLDIHFSIP 266
           +AL    L+   + + F  P
Sbjct: 62  QALNGHSLQGSPIRVSFGNP 81

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

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

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 18/72 (25%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           SR +++ NI+ ++ + +LR  F QYG+I ++    + +    +++ +I  A  A+  +++
Sbjct: 3   SRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNY-LREKNCAFVNFTNISNAIKAIDGVKS 61

Query: 252 KPLRRRKLDIHF 263
            PL  +K  I +
Sbjct: 62  HPL-FKKFKISY 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|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMRA 248
           TLFVRN+  +V   +L   F     I+     T     + RG+  +++  +  A+ A+  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 249 LQNKPL--RRRKLDI 261
           L+NK L  R  +LDI
Sbjct: 61  LKNKKLHGRILRLDI 75

This subgroup corresponds to the RRM1 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           TL V NL  SV+ EDL   F     +K        ET   R + F+ F  +  A+ AL  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 334 LNRSDIAGKRIKLEPSRP 351
           L    + G+ ++L+ +  
Sbjct: 61  LKNKKLHGRILRLDIAER 78

This subgroup corresponds to the RRM1 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 40.9 bits (95), Expect = 1e-04
 Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAAEAALKSLN 335
           TL V NL   V+   + Q+F   G  K    I E      + F+EFY+ R A AAL ++N
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 336 RSDIAGKRIKL 346
              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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK----RHHKFIEFYDVRAAEAALKSLN 335
           ++V NL   V+ + LR+ F + GEV +++    +    R   F+ F     A+ A+K  N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 336 RSDIAGKRIKLE 347
           ++ I   +I +E
Sbjct: 63  KTFIDTSKISVE 74

This subgroup corresponds to the RRM1 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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN--RS 337
           L V  L P  S  +L + F  +G ++ I   P +  + +IE+  + AA+AA ++L     
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRN-YAYIEYESIEAAQAAKEALRGFPL 59

Query: 338 DIAGKRIKLE 347
              G+R++++
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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 40.6 bits (96), Expect = 2e-04
 Identities = 17/65 (26%), Positives = 36/65 (55%), Gaps = 4/65 (6%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           NL   + +E L+++FG YG++   +    +    +   F+ F +  AA+ A++ LN  ++
Sbjct: 8   NLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEV 67

Query: 340 AGKRI 344
            GK++
Sbjct: 68  NGKKL 72

This subfamily corresponds to the RRM3 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 an 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. 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 mammalian, 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 the 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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN 335
            L + NL    + E L  +F  +   KE+R  P +R   F+EF     A  AL++L 
Sbjct: 4   ILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVP-RRGIAFVEFETEEQATVALQALQ 59

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

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALK 332
           G L V NL  S   +DL ++F  +GE+ E+     K+  K     ++ F D   A  A K
Sbjct: 3   GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

Query: 333 SLNRSDIAGKRIKLEP 348
            L+     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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 5/59 (8%)

Query: 292 EDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
           ++L++ F  +G VK +R     +T + +H+ FI+F +   A  A KS+N   + GK ++
Sbjct: 14  KELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQ 72

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 24/81 (29%), Positives = 46/81 (56%), Gaps = 5/81 (6%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAA 330
           ++  L+V  L  +++ E+L+ +FG+ GE+   K +R+  T     + F+ + D + AE A
Sbjct: 3   SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

Query: 331 LKSLNRSDIAGKRIKLEPSRP 351
           + +LN   +  K IK+  +RP
Sbjct: 63  INTLNGLRLQTKTIKVSYARP 83

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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L + NL   V+  DLRQ+F  +   V  +     K  + F++  D   A+ A++ LN   
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSV--LVKKGGYAFVDCPDQSWADKAIEKLNGKI 58

Query: 339 IAGKRIKLEPSRPG 352
           + GK I++E S P 
Sbjct: 59  LQGKVIEVEHSVPK 72

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 18/70 (25%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           T+       S    D++++F   G V+++   +   + H FI F ++ AA+ A+++LN +
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 338 DIAGKRIKLE 347
            + G  IK++
Sbjct: 61  SVDGNCIKVQ 70

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 8/80 (10%)

Query: 192 SRTLFVRNINSNVEDSELR----ALFEQYG---DIRTLYTACKHRGFVMISYYDIRAART 244
           + T+++ N+N  ++  EL+    ALF Q+G   DI  L T  K RG   + + ++ +A  
Sbjct: 1   NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTM-KMRGQAFVIFKELSSATN 59

Query: 245 AMRALQNKPLRRRKLDIHFS 264
           A+R LQ  P   + + I ++
Sbjct: 60  ALRQLQGFPFYGKPMRIQYA 79

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. 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. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

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

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 10/81 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRHHK------FIEFYDVRAAE 328
           TL V NL+   + E L++ F   G V+ +    ++ P            F+EF    AA+
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 329 AALKSLNRSDIAGKRIKLEPS 349
            ALK L  + + G  ++L+ S
Sbjct: 62  KALKRLQGTVLDGHALELKLS 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|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKH----RGFVMISYYDIRAARTAMRALQ 250
           + V+N+       ++R LF  YG ++++    K     RGF  + +   + A  AM AL+
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 251 NKPLRRRKLDIHFS 264
           +  L  R+L + ++
Sbjct: 63  DTHLLGRRLVLQYA 76

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|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 280 LVVFNLDPSVSNED-LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L+V+ LD    N D L  +F  YG V  I+    K     ++  D +AAE A++ LN   
Sbjct: 2   LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVV 61

Query: 339 IAGKRIKLEP 348
           + G+++++  
Sbjct: 62  LFGQKLEVNF 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. 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 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. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The 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 polypyrimidine tract binding protein (PTB) that 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. Like PTB, PTBPH3 contains four RRMs. Length = 71

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

 Score = 43.9 bits (103), Expect = 3e-04
 Identities = 48/186 (25%), Positives = 82/186 (44%), Gaps = 20/186 (10%)

Query: 160 ISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI 219
           +++ AS N L      N  G+   +     +    L V  +  ++ D EL ALF   G I
Sbjct: 81  MANMASTNSL------NSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPI 134

Query: 220 RTL-----YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD 274
            T      Y      G+  + +     ++ A++ L    +R ++L + ++ P    S KD
Sbjct: 135 NTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP-GGESIKD 193

Query: 275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEV--KEI---RETPHKRHHKFIEFYDVRAAEA 329
            N   L V NL  +++++ L  IFG YG++  K I   + T   R   F+ F     A+ 
Sbjct: 194 TN---LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQE 250

Query: 330 ALKSLN 335
           A+ +LN
Sbjct: 251 AISALN 256

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

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           ++V N+ +N   +EL   F  YG +R+++ A    GF  + + D R A  A+R L  + L
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 66

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|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           T+ V NL   +   ++  +F  YG + +I  +  P    + FIEF D R AE A++  + 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 337 SDIAGKRIKLE 347
            D  G+R+++E
Sbjct: 61  YDFDGQRLRVE 71

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFV N+ +++ + E + LF +YG+   ++   K +GF  I       A  A   L + P+
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEPGEVFIN-KGKGFGFIKLESRALAEIAKAELDDTPM 62

Query: 255 RRRKLDIHF 263
           R R+L + F
Sbjct: 63  RGRQLRVRF 71

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 19/72 (26%), Positives = 42/72 (58%), Gaps = 3/72 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           L V NL  +V+ E L + FG +G+++ +++    + + FI F +   A  A++ +N  ++
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKEL 60

Query: 340 AGKRIKLEPSRP 351
            G+ I++  ++P
Sbjct: 61  EGENIEIVFAKP 72

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           + V  +      ED+   F  +GE+K +     R T   + +  IE+   + A+AA++ L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 335 NRSDIAGKRIK 345
           N  ++ G+ I 
Sbjct: 69  NGKELLGQTIS 79

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 5/62 (8%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRA 248
           T+ V N++ + ++ +LR LF  +G I  +Y A      + RGF  ++++    A  A+  
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 249 LQ 250
           L 
Sbjct: 61  LN 62

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 39.6 bits (93), Expect = 4e-04
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 9/77 (11%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGD------IRTLYT-ACKHRGFVMISYYDIRAARTAM 246
            +FV N+  + ++S L  LF  +G       IR L T  CK  GFV ++ Y+   A +A+
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE--EAYSAI 60

Query: 247 RALQNKPLRRRKLDIHF 263
            +L    L  R L + F
Sbjct: 61  ASLNGYRLGGRVLQVSF 77

This subfamily corresponds to the RRM3 of the Hu proteins family which represent 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 the 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. . Length = 78

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
            L V NL   V+ EDL ++FG  GEVK+++   + R  +      + F     AE A+K 
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVK-INYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 334 LNRSDIAGKRIKLE 347
            N   + G+ +++E
Sbjct: 61  FNGVLLDGQPMQVE 74

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

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

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 10/67 (14%)

Query: 282 VFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNRS 337
           V NL+   VS EDL +IF  YG++  I        HK   F++F +   A AA+   N  
Sbjct: 5   VGNLNTDKVSKEDLEEIFSKYGKILGI------SLHKGYGFVQFDNEEDARAAVAGENGR 58

Query: 338 DIAGKRI 344
           +IAG+++
Sbjct: 59  EIAGQKL 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|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 39.0 bits (91), Expect = 5e-04
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 288 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
            VS EDL +IF  YGE+ +I     K  + F++F    +   A+       I G+++ LE
Sbjct: 11  RVSKEDLFRIFSTYGELAQIV---LKNAYGFVQFDSPESCANAINCEQGKMIRGRKLHLE 67

Query: 348 PSRP 351
            S+P
Sbjct: 68  VSKP 71

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 1 (PTB)

 Score = 39.6 bits (92), Expect = 5e-04
 Identities = 25/92 (27%), Positives = 52/92 (56%), Gaps = 7/92 (7%)

Query: 280 LVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+ A+  LN   
Sbjct: 2   LLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQK 61

Query: 339 IAGKRIKLEPSRPGGARRNLMLQLNQELEQDE 370
           + GK +++  S      ++  +QL +E ++D+
Sbjct: 62  LHGKPLRITLS------KHQTVQLPREGQEDQ 87

This subgroup corresponds to the RRM3 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence show that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution. . Length = 93

>gnl|CDD|241141 cd12697, RRM3_ROD1, RNA recognition motif 3 in vertebrate regulator of differentiation 1 (Rod1)

 Score = 39.2 bits (91), Expect = 6e-04
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 280 LVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L+V NL+P +++   L  +FG YG+V  ++   +K+ +  ++  D   A+ A+  LN   
Sbjct: 3   LLVSNLNPDAITPHGLFILFGVYGDVHRVKIMFNKKENALVQMADATQAQLAMSHLNGQR 62

Query: 339 IAGKRIKLEPSR 350
           + GK I+   S+
Sbjct: 63  LYGKVIRATLSK 74

This subgroup corresponds to the RRM3 of ROD1 coding protein Rod1, 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. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. . Length = 76

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 39.5 bits (93), Expect = 6e-04
 Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 8/52 (15%)

Query: 292 EDLRQIFGAYGEVKEIR-ETPHKRHHK-------FIEFYDVRAAEAALKSLN 335
           ED+++  G YG+V  +    P             F+EF DV  A+ A  +L 
Sbjct: 26  EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALA 77

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 39.3 bits (92), Expect = 6e-04
 Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL------YTACKHRGFVMISYYDIRA 241
            +  +  LFV  I  N+E+ +LR LFEQ+G I  L      YT   H+G   ++Y    +
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTG-MHKGCAFLTYCARES 59

Query: 242 ARTAMRALQNK 252
           A  A  AL  +
Sbjct: 60  ALKAQSALHEQ 70

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains 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 effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 39.0 bits (91), Expect = 6e-04
 Identities = 24/72 (33%), Positives = 30/72 (41%), Gaps = 12/72 (16%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTA-------CKHRGFVMISYYDIRAARTAMR 247
           LFV N++    + ELRA F + G IR +          CK   FV     D      A  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFV-----DFEEIEFATN 55

Query: 248 ALQNKPLRRRKL 259
           AL+ K L  R L
Sbjct: 56  ALKGKHLNGRAL 67

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 38.9 bits (91), Expect = 6e-04
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIR--ETPHKRHHKFIEFYDVRAAEAALKSL 334
           L+V  L  +++ +++R +F + GE+   K IR   T     + F+ + D   AE A+ +L
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 335 NRSDIAGKRIK 345
           N   +  K IK
Sbjct: 64  NGLRLQNKTIK 74

This subfamily corresponds to the RRM1 of the Hu proteins family which 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 the 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. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. 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. . Length = 78

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 38.8 bits (90), Expect = 6e-04
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 195 LFVRNINSN-VEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNK 252
           +F+ N+N+  V+ S++ A+F +YG I      C  H+GF  + Y + R AR A+     +
Sbjct: 4   VFIGNLNTLVVKKSDVEAIFSKYGKI----VGCSVHKGFAFVQYVNERNARAAVAGEDGR 59

Query: 253 PLRRRKLDIHFS 264
            +  + LDI+ +
Sbjct: 60  MIAGQVLDINLA 71

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, 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 hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V N+D   + E+L++ F + G +  I     + T   +   +IEF D  + E AL  LN 
Sbjct: 4   VGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LNE 62

Query: 337 SDIAGKRIK 345
           S+  G++IK
Sbjct: 63  SEFRGRQIK 71

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are 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. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 38.6 bits (90), Expect = 7e-04
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRSDI 339
           V NL P +  +D+  +F  YG +++I +  ++R     F+EF D R AE A+   +  D 
Sbjct: 4   VGNLPPDIRTKDIEDLFYKYGAIRDI-DLKNRRGPPFAFVEFEDPRDAEDAVYGRDGYDY 62

Query: 340 AGKRIKLEPSR 350
            G R+++E  R
Sbjct: 63  DGYRLRVEFPR 73

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           V N+  + ++++LR +F  +G V E  +    + + F+       A AA+++LN  ++ G
Sbjct: 5   VGNVSATCTSDELRGLFEEFGRVVECDKV---KDYAFVHMEREEEALAAIEALNGKEVKG 61

Query: 342 KRIKLE 347
           +RI +E
Sbjct: 62  RRINVE 67

This subgroup corresponds to the RRM2 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 = 68

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 39.1 bits (91), Expect = 7e-04
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 7/74 (9%)

Query: 280 LVVFNLDPSVSN-EDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
           L++ NL  S+     L++IFG YG+V+E    P KR  K     F+     + AE AL++
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREA-TIPRKRGGKLCGFAFVTMKKRKNAEIALEN 61

Query: 334 LNRSDIAGKRIKLE 347
            N  +I G+ + ++
Sbjct: 62  TNGLEIDGRPVAVD 75

This subgroup corresponds to the RRM2 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 38.7 bits (91), Expect = 7e-04
 Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSL 334
           TL V NL P+ + E+LRQ+F      + ++   H +      F+EF DV  A  AL SL
Sbjct: 4   TLFVANLGPNTTEEELRQLFSRQPGFRRLKM--HNKGGGPVCFVEFEDVSFATQALNSL 60

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>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 = 39.2 bits (92), Expect = 8e-04
 Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTA 245
           P  TLFV  ++    +  LR +F +YGDIR L           +G+  + Y   R A  A
Sbjct: 2   PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61

Query: 246 MRALQN 251
            R    
Sbjct: 62  YRDAHK 67

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

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRA-AEAALKSLNRSD 338
           L V NL   ++ E+ +++F  YGEV E+     ++   FI   D R  AE A   L+   
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVF-LNKEKGFGFIR-LDTRTNAEKAKAELDGIM 61

Query: 339 IAGKRIK 345
             G++++
Sbjct: 62  RKGRQLR 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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAMR 247
           +RTLFV N+   + + ELR  FE+YG +  +      RG    +  + + ++  A  A  
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61

Query: 248 ALQNKPLRRRKLDI 261
           A+  + + R ++ I
Sbjct: 62  AMSGQYIGRNQIKI 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|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           T+ +FN+  +V+ E ++  F   G +V++I   P       +EF     A  A  SLN S
Sbjct: 2   TIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDH-EGALVEFESPSDAGKASLSLNGS 60

Query: 338 DIAGKRIKL 346
              GK IK+
Sbjct: 61  QFGGKTIKI 69

This subfamily corresponds to the RRM4 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 = 71

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V +L P +  E LR  F  +GE+ + R     +T   + + F+ F     AE A++S+N 
Sbjct: 4   VGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNG 63

Query: 337 SDIAGKRIK 345
             + G+ I+
Sbjct: 64  QWLGGRAIR 72

This subfamily corresponds to the RRM2 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 = 75

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 7/66 (10%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEI---RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA 340
            LD SV+ + L + F  YG V  +   R    +R    + F  V AA+AA+  +    + 
Sbjct: 14  GLDESVTEQYLTRHFSRYGPVVHVVIDR----QRGQALVFFDKVEAAQAAVNEMKGRKLG 69

Query: 341 GKRIKL 346
           G+++++
Sbjct: 70  GRKLQV 75

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is 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 = 77

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 38.6 bits (89), Expect = 8e-04
 Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 5/81 (6%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAA 330
           ++  L+V  L  +++ E+ R +FG+ GE+   K +R+  T     + F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 331 LKSLNRSDIAGKRIKLEPSRP 351
           + +LN   +  K IK+  +RP
Sbjct: 61  INTLNGLRLQTKTIKVSYARP 81

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD 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. . Length = 83

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 42.3 bits (99), Expect = 9e-04
 Identities = 33/134 (24%), Positives = 63/134 (47%), Gaps = 16/134 (11%)

Query: 227 KHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPKDNPSDKDLNQGTLVVF- 283
           K+RGF  + Y   RAA  A R L    ++     + + ++ P++   D+D+     +++ 
Sbjct: 180 KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEV-DEDVMAKVKILYV 238

Query: 284 -NLDPSVSNEDLRQIF-----GAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
            NL  + + E + + F     G    VK+IR+      + F+ F D   A  A+  LN  
Sbjct: 239 RNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD------YAFVHFEDREDAVKAMDELNGK 292

Query: 338 DIAGKRIKLEPSRP 351
           ++ G  I++  ++P
Sbjct: 293 ELEGSEIEVTLAKP 306

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. Length = 578

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 38.4 bits (90), Expect = 9e-04
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            + V  L    +++ LR+ F  +GE++E      R+T   R + F+ F D  +AE A K 
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 334 LNRSDIAGKRIKLE 347
            N   I G++  + 
Sbjct: 62  PNPI-IDGRKANVN 74

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 7/72 (9%)

Query: 194 TLFVRNINSNVEDSELRALFEQYG---DIRTLY---TACKHRGFVMISYYDIRAARTAMR 247
            L+V N+  NV + +L+ LF Q+G     R +    T  + RGF  +       A  A+ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETG-RSRGFGFVEMETAEEANAAIE 59

Query: 248 ALQNKPLRRRKL 259
            L       R L
Sbjct: 60  KLNGTDFGGRTL 71

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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKF--IEFYDVRAAEAALKSL 334
           TL V NL  S   +DL + F   GEV ++R  +    R   F  +EF     A+ AL+  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-K 59

Query: 335 NRSDIAGKRIKLE 347
           +  ++ G+ I+++
Sbjct: 60  SGEELLGREIRVD 72

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

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

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           + V N+D   S E+LR +F AYG V         R   F+      AA+ A++ LN  ++
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM---RQFAFVHLRGEAAADRAIEELNGREL 59

Query: 340 AGKRIKLEPS 349
            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|240702 cd12256, RRM2_LKAP, RNA recognition motif 2 in Limkain-b1 (LKAP) and similar proteins

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 6/81 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQI----FGAYGEVKEIRETPHKRHHKF--IEFYDVRAAEAALK 332
            L V NLD  +S ++L+Q     F  +G+V  +   P         +   +++ A+ A+ 
Sbjct: 6   DLQVSNLDYRLSRKELQQTLTNQFKRHGKVLSVSLRPQTDGSLVASVRVPNLQDAQYAIS 65

Query: 333 SLNRSDIAGKRIKLEPSRPGG 353
            L+R  I  KRI +  ++   
Sbjct: 66  QLHRRKIGSKRILVSYAQGSS 86

This subfamily corresponds to the RRM2 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes. Length = 89

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 14/31 (45%), Positives = 20/31 (64%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
             LVV NL PSV+ +D+ ++F A G +K  R
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGALKRAR 31

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
           + L V NI     D +LR +F Q+G   D+  ++     +GF  +++ +   A  A   L
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKL 60

Query: 250 QNKPLRRRKLDIH 262
               +  RK++++
Sbjct: 61  HGTVVEGRKIEVN 73

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 7/68 (10%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKF--IEFYDVRAAEAAL----K 332
           T+ V NL    +   +RQ F   GE++E+ +           IEF     A AAL    K
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREV-KIVESEGGLVAVIEFETEDEALAALTKDHK 60

Query: 333 SLNRSDIA 340
            L  ++I+
Sbjct: 61  RLGGNEIS 68

This subfamily corresponds to the RRM1 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 = 71

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIR-TLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           +RTLFV+N+  N+   EL+ +FE   DIR         +G   I+Y + +    A +AL+
Sbjct: 3   ARTLFVKNLPYNITVDELKEVFEDAVDIRLPSGKDGSSKG---IAYIEFKTEAEAEKALE 59

Query: 251 NK 252
            K
Sbjct: 60  EK 61

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 9/63 (14%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAARTAMRALQN 251
           LFV N+     + E+R+LFEQYG +      C   K+ GFV +   D  AA  A+R L +
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKV----LECDIIKNYGFVHMD--DKTAADEAIRNLHH 56

Query: 252 KPL 254
             L
Sbjct: 57  YKL 59

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 10/77 (12%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG---DIRTLYT---ACKHRGFVMISYYDIRAART 244
           P+R +FV  I  +  + ELR  F ++G   D++ +       K  GFV  ++     A  
Sbjct: 2   PNR-IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFV--TFETQEDAEK 58

Query: 245 AMRALQNKPLRRRKLDI 261
              A+ N   R +KL+I
Sbjct: 59  I-LAMGNLNFRGKKLNI 74

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 10/80 (12%)

Query: 279 TLVVFNLDPSVSNED----LRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEA 329
           T+ V   D S+  +D    L + F + GE+  +     RET   +   +IEF  V   E 
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 330 ALKSLNRSDIAGKRIKLEPS 349
           AL+ L+ SD+ G  + ++ +
Sbjct: 61  ALE-LDGSDLGGGNLVVDEA 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMI-----SYYDIRAARTAMRAL 249
           LFV N+ +++ + + + LFE+YG+   ++   + RGF  I     +  +I  A      L
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTIL 62

Query: 250 QNKPLRRR 257
           +N+PLR R
Sbjct: 63  KNRPLRIR 70

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 41.4 bits (97), Expect = 0.002
 Identities = 33/157 (21%), Positives = 62/157 (39%), Gaps = 15/157 (9%)

Query: 235 SYYDIRAARTAMRALQNKPLR------RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS 288
            YY  R  R+  R+             RR         K+  ++ + +  T+ V  L   
Sbjct: 41  DYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALK 100

Query: 289 VSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSLNRSDIAGKR 343
               DL + F   G+V++++    +   +     ++EFYDV +   AL +L    + G+ 
Sbjct: 101 ARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRP 159

Query: 344 IKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGS 380
           I ++ S+   A +N   +       D    L+  VG+
Sbjct: 160 IIVQSSQ---AEKNRAAKAATHQPGDIPNFLKLYVGN 193

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

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMR 247
             L V  +  ++   ELR+LFE  G I +          +  G+  + Y D   A+ A+ 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 248 ALQNKPLRRRKLDIHF 263
            L    +R ++L + +
Sbjct: 61  TLNGFEIRNKRLKVSY 76

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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTL----YTACKHRGFVMISYYDIRAARTAMRAL 249
            LFV  +  +V   EL  LF+++G ++++      + K +G   + Y +  +A  A+  +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 250 QNKPLRRRKLDIHFSIP 266
               ++ + + +  S P
Sbjct: 64  DGTEIKEKTISVAISNP 80

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is 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 = 81

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 10/65 (15%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIR------TLYTACKHRGFVMISYYDIRAARTAM 246
             +FV  +  +  D  LR  F Q+G+I          T  K RG+  +++ D  +   A 
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTG-KSRGYGFVTFKDKES---AE 56

Query: 247 RALQN 251
           RA ++
Sbjct: 57  RACKD 61

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 39.6 bits (92), Expect = 0.002
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L +  L     +  LR  F  +G+V +      RET   R   F+ F D  AA AA+  +
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 335 NRSDIAGKRIKLEPS--RPGGAR 355
           +  ++ G+ I++ P+  RP   R
Sbjct: 97  DGKELNGRHIRVNPANDRPSAPR 119

Length = 144

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 294 LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
           +RQ F  +G++ EIR  P K  + FI F    +A  A+ S+N + I G  +K
Sbjct: 17  MRQTFSPFGQIMEIRVFPEK-GYSFIRFSTHESAAHAIVSVNGTTIEGHVVK 67

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, 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 = 73

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 5/65 (7%)

Query: 293 DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 352
           D+ + F  YG++ E+     K  + F+EF D+R A+ A+  LN  D+ G+R+ +E +R  
Sbjct: 15  DVERFFKGYGKILEV---DLKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHAR-- 69

Query: 353 GARRN 357
           G RR+
Sbjct: 70  GPRRD 74

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSL 334
           L V NL   ++ ++L++ F  +G V E+R        +     F+ F D  A +  L + 
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 335 NRSDIAGKRIKLEPSR 350
                   R+ +E  +
Sbjct: 66  PIYFRGDHRLNVEEKK 81

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|240865 cd12419, RRM_Ssp2_like, RNA recognition motif in yeast sporulation-specific protein 2 (Ssp2) and similar protein

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 287 PSVSN-EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKR 343
           PS  + E+L+  F  +GE+ +I     ++    I F D+R+A  A ++L    S +  K 
Sbjct: 3   PSDFDVEELKDDFTVFGEIVDISPIISRKLCVSIFFADIRSAIRAKETLEDKGSSLNNKY 62

Query: 344 IK 345
           IK
Sbjct: 63  IK 64

This subfamily corresponds to the RRM of the lineage specific yeast sporulation-specific protein 2 (Ssp2) and similar proteins. Ssp2 is encoded by a sporulation-specific gene necessary for outer spore wall assembly in the yeast Saccharomyces cerevisiae. It localizes to the spore wall and may play an important role after meiosis II and during spore wall formation. Ssp2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 80

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 15/79 (18%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYG-----DIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           R +F  N   +   SE+  LF +YG     D+++        GF  +   D R A  A+R
Sbjct: 1   RPVFCGNFEYDARQSEIERLFGKYGRVDRVDMKS--------GFAFVYMEDERDAEDAIR 52

Query: 248 ALQNKPL--RRRKLDIHFS 264
            L N     +RR+L + ++
Sbjct: 53  GLDNFEFGRQRRRLRVEWA 71

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK------HRGFVMISYYDIRAARTAMRA 248
           + VRNI       ELR LF  +G+++T+    K      HRGF  + +   + A+ A +A
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 249 LQ 250
           L 
Sbjct: 63  LC 64

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is 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 = 79

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

 Score = 38.1 bits (88), Expect = 0.002
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 278 GTLVVFNL-DPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
             L+V NL +  V+ + L  +FG YG+V+ ++   +K+    I+  D   ++ A+  LN 
Sbjct: 14  TVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNG 73

Query: 337 SDIAGKRIKLEPSR 350
             + GK I++  S+
Sbjct: 74  QKMYGKIIRVTLSK 87

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|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 279 TLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           TL V N DP +    DL + F  YG++  +R    +R+  F+++     A  AL+S N S
Sbjct: 1   TLFVINFDPINTRTRDLERHFEPYGKLVNVRI---RRNFAFVQYETQEDATKALESTNMS 57

Query: 338 DIAGKRIKLE 347
            +  + I +E
Sbjct: 58  KVLDRVISVE 67

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>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 = 36.8 bits (86), Expect = 0.003
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 7/64 (10%)

Query: 194 TLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           T++V N+   + + EL+  F  +G   ++R      K +G+  + +    AA TA+ A+ 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVF----KDKGYAFVRFDTHEAAATAIVAVN 57

Query: 251 NKPL 254
              +
Sbjct: 58  GTSI 61

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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMRA 248
           +FV +++  ++   LRA F  +G+I      + + T  K +G+  +S+     A  A+++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTG-KSKGYGFVSFVKKEDAENAIQS 60

Query: 249 LQNKPLRRRKL 259
           +  + L  R +
Sbjct: 61  MNGQWLGGRAI 71

This subfamily corresponds to the RRM2 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 = 75

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

 Score = 37.3 bits (86), Expect = 0.003
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           V NL       +L + F  YG ++ +    +     F+EF D R AE A++ L+   I G
Sbjct: 4   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 63

Query: 342 KRIKLEPSRPGGARR 356
            R+++E S  G  RR
Sbjct: 64  SRVRVELS-TGMPRR 77

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|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 37.4 bits (87), Expect = 0.003
 Identities = 11/62 (17%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           +  +F ++  +    +R  F  +G+ K +    H+    F+ F    AAE    +++ + 
Sbjct: 4   SFFLFGVEDDLPEYKIRDYFEQFGKSKSVI-VNHRAKCGFVRFETREAAEKFAAAISENG 62

Query: 339 IA 340
           + 
Sbjct: 63  LN 64

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK----FIEFYDVRAAEAALKSLN 335
           L V NL  +V  E + + F  YG V+ ++  P +        F++F D+++A+ A  ++N
Sbjct: 2   LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAVN 61

Query: 336 RSD 338
           +  
Sbjct: 62  KMG 64

This subfamily corresponds to the RRM1 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 = 75

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 5/70 (7%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V NLD  V+ E L ++F   G V  +     R T   + + F+EF     A+ A+K +N 
Sbjct: 3   VGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNM 62

Query: 337 SDIAGKRIKL 346
             + GK I++
Sbjct: 63  IKLYGKPIRV 72

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), 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 is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 12/46 (26%), Positives = 25/46 (54%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYD 238
           R +FV  +  ++ + +LR  F Q+G++  +Y     R F  +++ D
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFAD 46

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH-RGFVMISYYDIRAARTAMRALQ 250
           +FV  I  ++ + EL  LFE+ G   ++R +       RG+  ++Y +  AA+ A++ L 
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 251 NKPLRRRKL 259
           N  +R  K 
Sbjct: 64  NYEIRPGKR 72

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V N+    + E L+ IF   G V        RET   + + F E+ D   A +A+++LN 
Sbjct: 3   VGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNG 62

Query: 337 SDIAGKRIKLE 347
            ++ G++++++
Sbjct: 63  YELNGRQLRVD 73

This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. . Length = 75

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 22/61 (36%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR----HHKFIEFYDVRAAEAALKSL 334
            L V NL P VSNE L Q F  +GEV+        R        +EF     A+AA+K  
Sbjct: 1   ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRC 60

Query: 335 N 335
           +
Sbjct: 61  S 61

This subfamily corresponds to the RRM2 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. The family 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 contains 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 = 80

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 11/27 (40%), Positives = 18/27 (66%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDI 219
           RT+FV N+    +  +L+ LF+Q+G I
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPI 27

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

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

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRA 248
             ++FV  ++ +V   EL   F ++G   ++  +  A     F  I +   +AA  A+ +
Sbjct: 3   KYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVES 62

Query: 249 -----LQNKPLR 255
                L+NK + 
Sbjct: 63  ENHSMLKNKTMH 74

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|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 = 36.4 bits (85), Expect = 0.004
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 10/69 (14%)

Query: 288 SVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK 342
           + + ED+R +F  YG ++E+     ++T   +   F++F     A+ A+++L+     GK
Sbjct: 10  TATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH-----GK 64

Query: 343 RIKLEPSRP 351
                 SRP
Sbjct: 65  VTMPGASRP 73

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

 Score = 36.9 bits (85), Expect = 0.004
 Identities = 20/68 (29%), Positives = 36/68 (52%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           V NL  + +  +L + FG YG ++ +    +     F+EF D R A  A++ L+   + G
Sbjct: 9   VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCG 68

Query: 342 KRIKLEPS 349
            R+++E S
Sbjct: 69  CRVRVELS 76

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

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           +FV N++ +    ELRALFE YG    + +    R F  +      AA  A+  L  + L
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYG---AVLSCAVMRQFAFVHLRGEAAADRAIEELNGREL 59

Query: 255 RRRKLDIHFS 264
             RKL +  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|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           ++V N+ +     EL   F  YG +RT++ A    GF  + + D R A  A+R L  K +
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 61

Query: 255 --RRRKLDIHFSIPK 267
              R ++++   +P+
Sbjct: 62  CGSRVRVELSTGMPR 76

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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 37.0 bits (85), Expect = 0.004
 Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 5/77 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAALKSL 334
           L+V  L  +++ ++LR +F + GEV   K IR+    H   + F+ + + + AE A+ +L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 335 NRSDIAGKRIKLEPSRP 351
           N   +  K IK+  +RP
Sbjct: 64  NGLRLQSKTIKVSYARP 80

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a 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. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR 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 = 81

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 21/84 (25%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMIS--------Y----YDIRA 241
            L V N+     D + R L   +G +         R F++ S        Y    Y  +A
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAV--------ERCFLVYSESTGESKGYGFVEYASKA 52

Query: 242 -ARTAMRALQNKPLRRRKLDIHFS 264
            A  A   L  K +  RKL + ++
Sbjct: 53  SALKAKNQLDGKQIGGRKLQVDWA 76

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|240867 cd12421, RRM1_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 = 36.4 bits (85), Expect = 0.004
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI-RTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 253
           L +RN+  +V +S+L AL   +G +   L    K++  V      + +A++ +      P
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALV--EMDSVESAKSMVDYYLTVP 59

Query: 254 LRRRKLDIHF 263
              R   ++ 
Sbjct: 60  ALIRGRRVYI 69

This subfamily corresponds to the RRM1 of the majority of family members that include 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. 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. The 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. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 24/69 (34%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRE--TPHKRHHKFIEFYDVRAAEAALKS 333
           TL + +L+P +    +   F   GE   VK IR   T     + F+EF    AAE AL+S
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 334 LNRSDIAGK 342
           LN   I   
Sbjct: 61  LNGKPIPNT 69

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 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. NAM8 also contains three RRMs. . Length = 81

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	823
KOG4660	549	consensus Protein Mei2, essential for commitment t	100.0
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.98
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.96
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.95
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.95
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.95
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.95
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.92
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.92
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.9
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.9
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.9
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.88
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.88
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.87
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.86
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.85
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.85
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.83
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.83
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.82
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.8
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.76
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.74
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.74
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.73
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.72
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.7
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.67
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.65
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.64
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.63
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.62
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.59
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.49
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.47
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.46
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.45
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.42
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.41
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.36
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.35
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.31
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.28
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.26
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.25
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.23
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.21
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.19
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.17
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.16
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.16
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.16
KOG0122	270	consensus Translation initiation factor 3, subunit	99.13
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.13
KOG0122	270	consensus Translation initiation factor 3, subunit	99.13
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.12
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.12
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.12
PLN03120	260	nucleic acid binding protein; Provisional	99.12
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.12
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.1
PLN03120	260	nucleic acid binding protein; Provisional	99.08
smart00362	72	RRM_2 RNA recognition motif.	99.07
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.06
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.05
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.04
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.03
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.0
smart00362	72	RRM_2 RNA recognition motif.	99.0
PLN03213	759	repressor of silencing 3; Provisional	98.99
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.98
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.97
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.97
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.97
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.95
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.92
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.92
PLN03121	243	nucleic acid binding protein; Provisional	98.91
PLN03213	759	repressor of silencing 3; Provisional	98.9
smart00360	71	RRM RNA recognition motif.	98.9
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.89
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.88
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.87
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.86
PLN03121	243	nucleic acid binding protein; Provisional	98.86
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.85
smart00360	71	RRM RNA recognition motif.	98.84
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.83
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.83
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.8
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.77
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.75
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.74
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.7
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.69
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.68
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.68
smart00361	70	RRM_1 RNA recognition motif.	98.65
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.63
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.63
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.62
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.6
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.53
smart00361	70	RRM_1 RNA recognition motif.	98.46
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.44
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.41
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.38
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.37
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.32
KOG4210	285	consensus Nuclear localization sequence binding pr	98.26
KOG0226	290	consensus RNA-binding proteins [General function p	98.21
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.19
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.18
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.16
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.15
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.1
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.02
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.99
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	97.98
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.98
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	97.94
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	97.9
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.86
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.86
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.84
KOG0151	877	consensus Predicted splicing regulator, contains R	97.82
KOG0151	877	consensus Predicted splicing regulator, contains R	97.79
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.71
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.68
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.67
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.66
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.64
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.63
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.56
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.49
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.37
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.25
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.2
KOG0226	290	consensus RNA-binding proteins [General function p	97.18
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.15
KOG4210	285	consensus Nuclear localization sequence binding pr	97.03
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.79
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.78
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.42
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.38
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.36
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.23
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.21
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.21
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.19
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.14
KOG3152	278	consensus TBP-binding protein, activator of basal	95.95
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.93
KOG1855	484	consensus Predicted RNA-binding protein [General f	95.93
KOG1295	376	consensus Nonsense-mediated decay protein Upf3 [RN	95.83
KOG1995	351	consensus Conserved Zn-finger protein [General fun	95.66
KOG2314	698	consensus Translation initiation factor 3, subunit	95.53
KOG3152	278	consensus TBP-binding protein, activator of basal	95.49
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	95.38
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.89
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.8
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.75
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	94.74
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.34
KOG1996	378	consensus mRNA splicing factor [RNA processing and	94.3
KOG2314	698	consensus Translation initiation factor 3, subunit	94.24
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	93.65
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.83
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	91.95
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.82
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	91.68
KOG1996	378	consensus mRNA splicing factor [RNA processing and	91.55
KOG2135	526	consensus Proteins containing the RNA recognition	91.45
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	91.11
KOG2591	684	consensus c-Mpl binding protein, contains La domai	91.02
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	90.93
KOG2591	684	consensus c-Mpl binding protein, contains La domai	90.62
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	89.3
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	89.15
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	89.08
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	89.01
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	88.77
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	88.68
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	88.28
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	87.97
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	86.14
KOG2068	327	consensus MOT2 transcription factor [Transcription	83.62
KOG2068	327	consensus MOT2 transcription factor [Transcription	82.41

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

Probab=100.00  E-value=1.4e-74  Score=637.33  Aligned_cols=495  Identities=53%  Similarity=0.807  Sum_probs=374.6

Q ss_pred             HHHHhhcCCCcEEEeccCccCcccceeEeeecCccccccccccccCCCCccccCCCCCCCCCCcEEEEcCCCCCCCHHHH
Q 003400          130 EDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSEL  209 (823)
Q Consensus       130 el~dlFs~~G~v~V~~d~~es~~~g~~~v~~~e~~~a~~~~~~~l~n~~~~~~~~~~~~e~~srtLfV~NLP~~vteeeL  209 (823)
                      +++++|...|++++..+.......   +              -...+..+.+..++|..+  +++ +|         .+|
T Consensus         2 ~d~~lf~~~G~~el~~~~~~~~~~---~--------------~~~~n~~~~~~~~~P~~~--s~~-~~---------~~l   52 (549)
T KOG4660|consen    2 EDCDLFSSGGGMELDADSFDNLSV---R--------------NSDRNSAGFVFPEHPPGE--SRT-FV---------SEL   52 (549)
T ss_pred             CccccccCCCCCCcccccccchhh---c--------------ccccCCCccccCCCCCCC--CCC-Ch---------hhH
Confidence            457889999999776664433221   1              122255667788888877  666 77         788


Q ss_pred             HHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCCCCCCCCCccceeeecCCCCC
Q 003400          210 RALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSV  289 (823)
Q Consensus       210 r~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~~v  289 (823)
                      ..+|+.|                                       ++++.      .+.+.+++.++++|+|.|||.++
T Consensus        53 ~a~f~~~---------------------------------------~~p~~------~~np~~~~~~~~~L~v~nl~~~V   87 (549)
T KOG4660|consen   53 SALFEPF---------------------------------------NKPLR------PDNPSEKDMNQGTLVVFNLPRSV   87 (549)
T ss_pred             Hhhhhcc---------------------------------------CCCCC------cCCCCcccCccceEEEEecCCcC
Confidence            8899888                                       11111      15566677889999999999999


Q ss_pred             CHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcccchhhhccccccCHH
Q 003400          290 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQD  369 (823)
Q Consensus       290 teedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~r~~~~~ql~~~~~~~  369 (823)
                      ++++|+++|+.||+|+.|+.+...+|..||+|+|+.+|++|+++||+.+|.|++|+    ++++.++..+-+..      
T Consensus        88 sn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k----~~~~~~~~~~~~~~------  157 (549)
T KOG4660|consen   88 SNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK----RPGGARRAMGLQSG------  157 (549)
T ss_pred             CHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc----CCCcccccchhccc------
Confidence            99999999999999999999999999999999999999999999999999999998    77777776665554      


Q ss_pred             HHHHHHhhcCCCCCCCCCCCCccCCCCCCCCccccccCCCCCCCCCCCcCCCCCCCcccCCCCCCcccccccCCCCcCcc
Q 003400          370 ESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRG  449 (823)
Q Consensus       370 ~l~~~f~~~GsP~a~spP~~~~~~~~p~~~~~~q~~~~~p~~~~~sP~~~~~~~g~~s~~p~~~s~~~~~~~~~~~~~~~  449 (823)
                        ..+..++++|.++++|+.|.+               .+.++.++|......       +...++ +-....+...+.-
T Consensus       158 --~~~~~~~~~p~a~s~pgg~~~---------------~~~~g~l~P~~s~~~-------~~~~~~-~~~~~~~~~~~~~  212 (549)
T KOG4660|consen  158 --TSFLNHFGSPLANSPPGGWPR---------------GQLFGMLSPTRSSIL-------LEHISS-VDGSSPGRETPLL  212 (549)
T ss_pred             --chhhhhccchhhcCCCCCCcC---------------Ccceeeeccchhhhh-------hhcchh-ccCccccccccch
Confidence              567789999999999999951               123444666544322       222111 1111111233333


Q ss_pred             cchhhhcccccccCCCcccccCCCCCCCCCccCCcccCCCCCCCCCCCCccCCCCcccCCCCCCCCCCCCCCcccCCCCC
Q 003400          450 SLMEHALTNTISANGASFQQSNSFSEPKIGLYRGTVSSFGPSPSNGSGVETLSGPQFLWGSPSRYSEHSSSPAWQTSSMG  529 (823)
Q Consensus       450 ~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~w~~~~~~  529 (823)
                      .|  |.|.+      ....-+|+++++..          |..+++..++.+++++--+|                     
T Consensus       213 ~h--q~~~~------~~~~~s~a~~~~~~----------G~~~s~~~~v~t~S~~~g~~---------------------  253 (549)
T KOG4660|consen  213 NH--QRFVE------FADNRSYAFSEPRG----------GFLISNSSGVITFSGPGGVW---------------------  253 (549)
T ss_pred             hh--hhhhh------hccccchhhcccCC----------ceecCCCCceEEecCCCccc---------------------
Confidence            33  33332      11224567777632          66667777888888874444                     


Q ss_pred             CCCCCCCccCCCCCCCCCCCCCCCccccCcCCCCCCCccccccCCCCCCCCCcCCCCccccCCCCCCCCCccccccCCCc
Q 003400          530 HPFSSNGKIHGLPYSGRQGSFLGSSQHHHVGSAPSGVPLERRFGFLPESPETSFMNPVAFCGMGIGQNDGSFMVNMGSRA  609 (823)
Q Consensus       530 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gsap~~~~~~~~~~~~~~s~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  609 (823)
                      +++...         ......+..+++||||+||+                  ..+....+++++.+.++++.++.+.  
T Consensus       254 n~~~~~---------r~~~~~~~~~~~~hi~~~Ps------------------~~~l~~~~~~~f~~~s~~~~~~~~~--  304 (549)
T KOG4660|consen  254 NPFPSR---------RQRQNSSSSHYEHHIGSAPS------------------MHHLLSRISVGFNGGSGALEMNSNG--  304 (549)
T ss_pred             CCcccc---------ccccccCcccccCccCCCcc------------------cccccccCccccCCCCCCccccccc--
Confidence            112111         11122344567999999996                  1222335566777777776554222  


Q ss_pred             cCCCC-ccCCCCCCCCCCc-ccccCCCCCCCcccCCCCCCCCCCCccccccc---cccccccccCCCCccccccccccch
Q 003400          610 SVNPG-ITVPRNLSDNGSS-FRVMSSPRLSPVFLGNGPYPGLTPANIEGLYE---RGRSRRIENNNGNQLDSKKQFQLEL  684 (823)
Q Consensus       610 ~~~~~-~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---r~r~rr~~~~~~~~~~~~~~~~~~~  684 (823)
                      ..|-| .+..+++.+..+. +++.+.++..+.|-+++.+.    ...+...+   ..+.||.+. ...+ ...+++.+|+
T Consensus       305 ~~n~g~~~~t~~~~e~~s~n~~~e~~~rv~~~f~~~~~~~----~~~~~~~~~~~~~~~~Rtt~-~i~n-i~n~~~~~dl  378 (549)
T KOG4660|consen  305 QANQGFLTKTGNVTEFNSKNVGMESSPRVPKNFEGRRSYT----SQNDYPVELILNYRDRRTTV-MIKN-IPNKYGQLDL  378 (549)
T ss_pred             cCCCCccccCcccccccCCCccccccCCCCcccccccccc----cccccccccccccccchhhh-hhhc-cccchhHHHH
Confidence            23444 4578899888886 99999999999999888653    33444444   777788886 3333 3489999999


Q ss_pred             hhHhcCCCcceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEeeecccccceeEEEEEecCCcccHHHHHHHhcCCccc
Q 003400          685 EKIRSGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWE  764 (823)
Q Consensus       685 ~~i~~g~d~rTt~MirNIPnk~~~~~l~~~id~~~~~~ydf~Ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~g~~w~  764 (823)
                      .+|.+|+|.|||+||||||||||++||++. ||.++|+|||+||||||+|+||||||||||++|++|++||++|||++|+
T Consensus       379 ~~Ildge~~rtt~~iknipNK~T~~ml~~~-d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~  457 (549)
T KOG4660|consen  379 LRILDGECPRTTLMIKNIPNKYTSKMLLAA-DEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWE  457 (549)
T ss_pred             HHHHhCcCchhhhHhhccCchhhHHhhhhh-hccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchh
Confidence            999999999999999999999999999999 9999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccEEEEEeeecccHHHHHHHhccCccCCCCCCccceEEcC
Q 003400          765 KFNSEKVASLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHS  808 (823)
Q Consensus       765 ~~~s~k~~~~~~A~iQg~~~l~~~~~~s~~~~~~~~~~p~~f~~  808 (823)
                      +|+|+|||+|+|||||||++|++|||||++|||++.|+|++|++
T Consensus       458 ~FnS~Kia~itYArIQGk~~Li~hFqnS~lm~E~e~y~Pvvf~p  501 (549)
T KOG4660|consen  458 KFNSEKIASITYARIQGKEALIEHFQNSSLMCEDEAYRPVVFSP  501 (549)
T ss_pred             hhcceeeeeeehhhhhchHHHHHHhhcccccccchhcCceEecC
Confidence            99999999999999999999999999999999999999999997

>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=2.2e-46  Score=337.58  Aligned_cols=97  Identities=67%  Similarity=1.202  Sum_probs=96.4

Q ss_pred             ceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEeeecccccceeEEEEEecCCcccHHHHHHHhcCCcccCCCCccEEE
Q 003400          694 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVAS  773 (823)
Q Consensus       694 rTt~MirNIPnk~~~~~l~~~id~~~~~~ydf~Ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~g~~w~~~~s~k~~~  773 (823)
                      |||||||||||||||+||+++||+.++|+||||||||||+++||+|||||||++++++.+|+++|+|++|+.++|+|||+
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             EEeeecccHHHHHHHhc
Q 003400          774 LAYARIQGRAALVAHFQ  790 (823)
Q Consensus       774 ~~~A~iQg~~~l~~~~~  790 (823)
                      |+||||||++|||+|||
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).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.98  E-value=1.9e-31  Score=295.35  Aligned_cols=241  Identities=18%  Similarity=0.291  Sum_probs=199.3

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP  186 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~  186 (823)
                      .++++|++||.+++|.++.++|+.+|.|   .|..|..++..+|++++.|.+.+.|.    .+++..+.+....+....+
T Consensus         3 ~~~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~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            3689999999999999999999999986   67778888889999999999876664    4566666666555544333


Q ss_pred             CC-CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccc--cc
Q 003400          187 YG-EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RK  258 (823)
Q Consensus       187 ~~-e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g--r~  258 (823)
                      .. ....++|||+|||.++++++|+++|++||.|..+++     .+.++|||||+|.+.++|++|++.|+|..+.|  .+
T Consensus        83 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~  162 (352)
T TIGR01661        83 SSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEP  162 (352)
T ss_pred             cccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCcee
Confidence            32 235679999999999999999999999999988874     35678999999999999999999999998876  56


Q ss_pred             ccccccCCCCCCCC----------------C-------------------------------------------------
Q 003400          259 LDIHFSIPKDNPSD----------------K-------------------------------------------------  273 (823)
Q Consensus       259 L~V~~a~pk~~~~~----------------~-------------------------------------------------  273 (823)
                      |.|.|+........                .                                                 
T Consensus       163 i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (352)
T TIGR01661       163 ITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQ  242 (352)
T ss_pred             EEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccc
Confidence            77777643220000                0                                                 


Q ss_pred             -----------------------CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHH
Q 003400          274 -----------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVR  325 (823)
Q Consensus       274 -----------------------~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e  325 (823)
                                             .....+|||+|||.++++++|+++|++||.|.++++     ++.++|||||+|.+.+
T Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~  322 (352)
T TIGR01661       243 RASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYD  322 (352)
T ss_pred             cCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHH
Confidence                                   000125999999999999999999999999999986     5678999999999999


Q ss_pred             HHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          326 AAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       326 ~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      +|.+|+..|||..|+|+.|+|.|..++..
T Consensus       323 ~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       323 EAAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            99999999999999999999999987753

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.97  E-value=1.2e-29  Score=273.84  Aligned_cols=244  Identities=20%  Similarity=0.313  Sum_probs=208.6

Q ss_pred             hhHhhhcCccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCC
Q 003400          106 EDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGA  178 (823)
Q Consensus       106 ~d~l~~~v~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~  178 (823)
                      ++......-+|+||++||.++.|++|+.||+..|.|   +|++|+.++.++|++||+|.....|+    .++++.+..+.
T Consensus        75 weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK  154 (506)
T KOG0117|consen   75 WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGK  154 (506)
T ss_pred             ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCC
Confidence            455555678999999999999999999999999987   89999999999999999999987665    56777776552


Q ss_pred             ccccCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCC-EEEEE------eCCCcccEEEEEeCCHHHHHHHHHHhcC
Q 003400          179 GTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLY------TACKHRGFVMISYYDIRAARTAMRALQN  251 (823)
Q Consensus       179 ~~~~~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~-I~~v~------~~~ksrG~AFV~F~~~e~A~~Ai~~Lng  251 (823)
                      ..-    ......+++|||+|||.+.++++|++.|++.++ |..|.      -..++||||||+|++...|..|.++|-.
T Consensus       155 ~ig----vc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~  230 (506)
T KOG0117|consen  155 LLG----VCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMP  230 (506)
T ss_pred             EeE----EEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccC
Confidence            111    112346799999999999999999999999985 55554      2567999999999999999999998854


Q ss_pred             --CccccccccccccCCCCCCCCCCC-CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHH
Q 003400          252 --KPLRRRKLDIHFSIPKDNPSDKDL-NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE  328 (823)
Q Consensus       252 --~~l~gr~L~V~~a~pk~~~~~~~~-~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~  328 (823)
                        ..+.|..+.|.||.|...+..+.. .-+.|||+||+.++|+|.|+++|+.||.|..|+..   +.||||.|.++++|.
T Consensus       231 g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~---rDYaFVHf~eR~dav  307 (506)
T KOG0117|consen  231 GKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP---RDYAFVHFAEREDAV  307 (506)
T ss_pred             CceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecc---cceeEEeecchHHHH
Confidence              446799999999999887655433 23689999999999999999999999999999864   679999999999999


Q ss_pred             HHHHHhCCCccCCceEEEEecCCCcccc
Q 003400          329 AALKSLNRSDIAGKRIKLEPSRPGGARR  356 (823)
Q Consensus       329 kAl~~LnG~~i~Gr~I~V~~s~~~~~r~  356 (823)
                      +|++.+||++|+|..|.|.+++|..+++
T Consensus       308 kAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  308 KAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             HHHHHhcCceecCceEEEEecCChhhhc
Confidence            9999999999999999999999987654

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

Probab=99.97  E-value=3.4e-30  Score=303.25  Aligned_cols=292  Identities=18%  Similarity=0.274  Sum_probs=227.5

Q ss_pred             CCCCcccccceeecCCcccccccCCCceeeccCCccccccccccccCCCCCcccccCCCccccCCCCCCCCCcccccCCC
Q 003400           18 NIPKEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPA   97 (823)
Q Consensus        18 ~~~~~~~~~t~~~p~~a~~~~~~~d~~~fs~~l~~l~~~k~~~~~~~~~~~~~d~~~~~~kk~~~eee~~k~~ee~e~~~   97 (823)
                      ...++.++.+|.-+++|.+|+..+++..+.|+-+.|.-.+.             +..  ..+                  
T Consensus        39 ~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~-------------~~~--~~~------------------   85 (562)
T TIGR01628        39 RRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR-------------DPS--LRR------------------   85 (562)
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc-------------ccc--ccc------------------
Confidence            34556888999999999999999998877776554433110             000  000                  


Q ss_pred             CCCCCCcchhHhhhcCccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----ccc
Q 003400           98 IGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLL  170 (823)
Q Consensus        98 i~n~LP~d~d~l~~~v~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~  170 (823)
                            ..        ...++|++|+.++++.+++++|+.+|.|   .|..+ ..+..++++++.|.+.+.+.    .++
T Consensus        86 ------~~--------~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~-~~g~skg~afV~F~~~e~A~~Ai~~ln  150 (562)
T TIGR01628        86 ------SG--------VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVN  150 (562)
T ss_pred             ------cC--------CCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeec-CCCCcccEEEEEECCHHHHHHHHHHhc
Confidence                  01        2468999999999999999999999987   33333 35667899999999886665    333


Q ss_pred             ccccCCCCccccCCC------CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHH
Q 003400          171 HYSVPNGAGTVAGEH------PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIR  240 (823)
Q Consensus       171 ~~~l~n~~~~~~~~~------~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e  240 (823)
                      +..+.+....+....      .......++|||+|||.++|+++|+++|++||+|.++.+    .++++|||||+|.+.+
T Consensus       151 g~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e  230 (562)
T TIGR01628       151 GMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHE  230 (562)
T ss_pred             ccEecCceEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHH
Confidence            333333322221111      112334578999999999999999999999999999874    4567899999999999


Q ss_pred             HHHHHHHHhcCCccc----cccccccccCCCCCCC--------------CCCCCccceeeecCCCCCCHHHHHHHhcccC
Q 003400          241 AARTAMRALQNKPLR----RRKLDIHFSIPKDNPS--------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG  302 (823)
Q Consensus       241 ~A~~Ai~~Lng~~l~----gr~L~V~~a~pk~~~~--------------~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG  302 (823)
                      +|.+|++.|++..+.    |+.|.|.++..+....              .......+|||+||+.++|+++|+++|++||
T Consensus       231 ~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G  310 (562)
T TIGR01628       231 DAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECG  310 (562)
T ss_pred             HHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcC
Confidence            999999999999999    9999998876554321              0122345899999999999999999999999


Q ss_pred             ceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcccch
Q 003400          303 EVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN  357 (823)
Q Consensus       303 ~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~r~~  357 (823)
                      .|++|++    ++.++|||||+|.+.++|.+|++.|||..+.|++|.|.++.++..++.
T Consensus       311 ~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~~~  369 (562)
T TIGR01628       311 EITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRA  369 (562)
T ss_pred             CeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHHHHH
Confidence            9999976    467899999999999999999999999999999999999998876654

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

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

Probab=99.97  E-value=1e-29  Score=299.25  Aligned_cols=265  Identities=19%  Similarity=0.338  Sum_probs=217.9

Q ss_pred             ccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCcccccc----ccccccCCCCccccCC--CC
Q 003400          116 DFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGE--HP  186 (823)
Q Consensus       116 el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~~----~~~~~l~n~~~~~~~~--~~  186 (823)
                      .++|++|+.+++|.+|+++|+.+|.|   .|..|..+..++|++++.|.+...|..    ++...+.+...++...  .+
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            58999999999999999999999986   667777778889999999999876652    3333343333333211  11


Q ss_pred             -CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 -YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 -~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                       ......++|||+|||.++++++|+++|++||.|.+|++    .++++|||||+|.+.++|++|++.|+|..+.++.|.|
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v  161 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYV  161 (562)
T ss_pred             cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEE
Confidence             12223568999999999999999999999999999874    4568999999999999999999999999999999999


Q ss_pred             cccCCCCCCC-CCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCC
Q 003400          262 HFSIPKDNPS-DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNR  336 (823)
Q Consensus       262 ~~a~pk~~~~-~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG  336 (823)
                      ....++.... ......++|||+||+.++|+++|+++|+.||.|.++++    .++++|||||+|.+.++|.+|++.|||
T Consensus       162 ~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g  241 (562)
T TIGR01628       162 GRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNG  241 (562)
T ss_pred             eccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCC
Confidence            8765544331 22334568999999999999999999999999999876    345789999999999999999999999


Q ss_pred             CccC----CceEEEEecCCCccc----------------------chhhhccccccCHHHHHHHHhhcCC
Q 003400          337 SDIA----GKRIKLEPSRPGGAR----------------------RNLMLQLNQELEQDESRILQHQVGS  380 (823)
Q Consensus       337 ~~i~----Gr~I~V~~s~~~~~r----------------------~~~~~ql~~~~~~~~l~~~f~~~Gs  380 (823)
                      ..+.    |+.|.|.+++.+..+                      ..++.++...++.++++.+|.+||.
T Consensus       242 ~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~  311 (562)
T TIGR01628       242 KKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGE  311 (562)
T ss_pred             cEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCC
Confidence            9999    999999988766544                      1356778888999999999999984

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.96  E-value=1.1e-29  Score=257.57  Aligned_cols=213  Identities=25%  Similarity=0.420  Sum_probs=177.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ++..++|+|..||.++|++|||.+|...|+|++|+     +++.+.||+||.|.+++||++|+..|+|.+++.+.|+|.|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            44568899999999999999999999999999998     5889999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 003400          264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (823)
Q Consensus       264 a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~  338 (823)
                      ++|..    ..+...+|||++||+.+|..||+++|++||.|+..|+     ++.+||.|||+|+.+.+|++||+.|||..
T Consensus       118 ARPSs----~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  118 ARPSS----DSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             ccCCh----hhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence            98754    4566789999999999999999999999999988764     67899999999999999999999999998


Q ss_pred             cCC--ceEEEEecCCCcccchhhhccccccCHHHHHHHHhhcCCCCCCCCCCCCccCCCCCCCCcccccc------CCCC
Q 003400          339 IAG--KRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPIEHNPLQTIS------KSPN  410 (823)
Q Consensus       339 i~G--r~I~V~~s~~~~~r~~~~~ql~~~~~~~~l~~~f~~~GsP~a~spP~~~~~~~~p~~~~~~q~~~------~~p~  410 (823)
                      ..|  .+|.|+|+....++.....          +.   +-|++|.        +++++|++| +.|++.      +...
T Consensus       194 P~g~tepItVKFannPsq~t~~a~----------ls---~ly~sp~--------rr~~Gp~hh-~~~r~r~~~~~~~~~~  251 (360)
T KOG0145|consen  194 PSGCTEPITVKFANNPSQKTNQAL----------LS---QLYQSPA--------RRYGGPMHH-QAQRFRLDNLLNPHAA  251 (360)
T ss_pred             CCCCCCCeEEEecCCcccccchhh----------hH---HhhcCcc--------ccCCCcccc-hhhhhccccccchhhh
Confidence            887  6899999988755443211          11   1233332        567889888 555542      2223


Q ss_pred             CCCCCCCcCCCCCCCcc
Q 003400          411 FRNMSPTTSNHMPGLAS  427 (823)
Q Consensus       411 ~~~~sP~~~~~~~g~~s  427 (823)
                      ..+|||++.+++.|+++
T Consensus       252 ~~rfsP~~~d~m~~l~~  268 (360)
T KOG0145|consen  252 QARFSPMTIDGMSGLAG  268 (360)
T ss_pred             hccCCCccccccceeee
Confidence            45888888888777643

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=3e-27  Score=261.87  Aligned_cols=159  Identities=21%  Similarity=0.406  Sum_probs=143.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      +.++|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|+|+.
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            5789999999999999999999999999999874     46789999999999999999999999999999999999997


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 003400          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (823)
Q Consensus       266 pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~  340 (823)
                      +...    .....+|||+|||..+++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++.|||..+.
T Consensus        82 ~~~~----~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~  157 (352)
T TIGR01661        82 PSSD----SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPS  157 (352)
T ss_pred             cccc----ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccC
Confidence            6543    234568999999999999999999999999988865     3457899999999999999999999999998


Q ss_pred             C--ceEEEEecCCCc
Q 003400          341 G--KRIKLEPSRPGG  353 (823)
Q Consensus       341 G--r~I~V~~s~~~~  353 (823)
                      |  .+|.|.++....
T Consensus       158 g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       158 GCTEPITVKFANNPS  172 (352)
T ss_pred             CCceeEEEEECCCCC
Confidence            7  678888887654

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.96  E-value=1.6e-28  Score=284.33  Aligned_cols=235  Identities=21%  Similarity=0.316  Sum_probs=193.2

Q ss_pred             hcCccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCc-ccc
Q 003400          111 AGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAG-TVA  182 (823)
Q Consensus       111 ~~v~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~-~~~  182 (823)
                      ....+++||++||.+++|.+|+++|+.+|.|   .|..| .++.+++++++.|.+.+.+.    .++.+.+.++.. .+.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            3356899999999999999999999999976   67677 77889999999999887665    344455543311 111


Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCC-EEEEEe------CCCcccEEEEEeCCHHHHHHHHHHhcC--Cc
Q 003400          183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLYT------ACKHRGFVMISYYDIRAARTAMRALQN--KP  253 (823)
Q Consensus       183 ~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~-I~~v~~------~~ksrG~AFV~F~~~e~A~~Ai~~Lng--~~  253 (823)
                           .....++|||+|||.++++++|++.|++++. |..+.+      ..+++|||||+|.+.++|.+|++.|..  ..
T Consensus       134 -----~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~  208 (578)
T TIGR01648       134 -----ISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQ  208 (578)
T ss_pred             -----ccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceE
Confidence                 1234689999999999999999999999964 333322      346899999999999999999998864  35


Q ss_pred             cccccccccccCCCCCCCCCC-CCccceeeecCCCCCCHHHHHHHhccc--CceEEEEeCCCcccEEEEEEcCHHHHHHH
Q 003400          254 LRRRKLDIHFSIPKDNPSDKD-LNQGTLVVFNLDPSVSNEDLRQIFGAY--GEVKEIRETPHKRHHKFIEFYDVRAAEAA  330 (823)
Q Consensus       254 l~gr~L~V~~a~pk~~~~~~~-~~~~tLfV~NLp~~vteedL~~~Fs~f--G~I~~iri~~~srG~aFVeF~d~e~A~kA  330 (823)
                      +.|+.|.|.|+.++....... ...++|||+||+.++++++|+++|++|  |+|++|++.   ++||||+|.+.++|++|
T Consensus       209 l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~---rgfAFVeF~s~e~A~kA  285 (578)
T TIGR01648       209 LWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI---RDYAFVHFEDREDAVKA  285 (578)
T ss_pred             ecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee---cCeEEEEeCCHHHHHHH
Confidence            789999999998765443322 234689999999999999999999999  999999764   67999999999999999


Q ss_pred             HHHhCCCccCCceEEEEecCCCcc
Q 003400          331 LKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       331 l~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      ++.|||.+|.|+.|+|+|+++...
T Consensus       286 i~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       286 MDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HHHhCCCEECCEEEEEEEccCCCc
Confidence            999999999999999999988653

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.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.95  E-value=1.1e-27  Score=276.78  Aligned_cols=262  Identities=18%  Similarity=0.233  Sum_probs=197.5

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcEE-EeccCccCcccceeEeeecCcccccccc------ccccCCCCccccCC---
Q 003400          115 DDFDLRGLPSSLEDLEDYDIFGSGGGME-LEGEPQESLSMSMSKISISDSASGNGLL------HYSVPNGAGTVAGE---  184 (823)
Q Consensus       115 ~el~V~~Lp~~~~E~el~dlFs~~G~v~-V~~d~~es~~~g~~~v~~~e~~~a~~~~------~~~l~n~~~~~~~~---  184 (823)
                      ..++|++||.+++|.+++++|+.||.|. +.+-    ..++++++.|.+.+.|....      ...+.+....+...   
T Consensus         3 ~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~----~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~   78 (481)
T TIGR01649         3 PVVHVRNLPQDVVEADLVEALIPFGPVSYVMML----PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQ   78 (481)
T ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEE----CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCc
Confidence            5689999999999999999999999982 2111    13578888888876665322      22333332222111   


Q ss_pred             ---CCC-------CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCC-cccEEEEEeCCHHHHHHHHHHhcCCc
Q 003400          185 ---HPY-------GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNKP  253 (823)
Q Consensus       185 ---~~~-------~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~k-srG~AFV~F~~~e~A~~Ai~~Lng~~  253 (823)
                         .+.       ......+|||+||+..+|+++|+++|+.||+|.+|.+..+ .+++|||+|.+.++|.+|++.|+|..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~  158 (481)
T TIGR01649        79 EIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGAD  158 (481)
T ss_pred             ccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCc
Confidence               000       0112247999999999999999999999999999986433 34799999999999999999999999


Q ss_pred             ccc--ccccccccCCCCC-------CC----------C------------------------------------------
Q 003400          254 LRR--RKLDIHFSIPKDN-------PS----------D------------------------------------------  272 (823)
Q Consensus       254 l~g--r~L~V~~a~pk~~-------~~----------~------------------------------------------  272 (823)
                      |.+  +.|+|.|+.+...       ..          +                                          
T Consensus       159 i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  238 (481)
T TIGR01649       159 IYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGG  238 (481)
T ss_pred             ccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCccccc
Confidence            965  4777777654210       00          0                                          


Q ss_pred             --------------------------------CCCCccceeeecCCC-CCCHHHHHHHhcccCceEEEEeCCCcccEEEE
Q 003400          273 --------------------------------KDLNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFI  319 (823)
Q Consensus       273 --------------------------------~~~~~~tLfV~NLp~-~vteedL~~~Fs~fG~I~~iri~~~srG~aFV  319 (823)
                                                      ......+|||+||+. .+|+++|+++|+.||.|.+|++...++|+|||
T Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV  318 (481)
T TIGR01649       239 DRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALI  318 (481)
T ss_pred             ccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEE
Confidence                                            001235899999998 69999999999999999999987667899999


Q ss_pred             EEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc-----------------------------------------cchh
Q 003400          320 EFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA-----------------------------------------RRNL  358 (823)
Q Consensus       320 eF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~-----------------------------------------r~~~  358 (823)
                      +|.+.++|.+|++.|||..|.|++|+|.+++....                                         +..+
T Consensus       319 ~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~  398 (481)
T TIGR01649       319 EMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLH  398 (481)
T ss_pred             EECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEE
Confidence            99999999999999999999999999998854210                                         1123


Q ss_pred             hhccccccCHHHHHHHHhhcCC
Q 003400          359 MLQLNQELEQDESRILQHQVGS  380 (823)
Q Consensus       359 ~~ql~~~~~~~~l~~~f~~~Gs  380 (823)
                      +.++...+++++++.+|..+|.
T Consensus       399 v~NLp~~~tee~L~~lF~~~G~  420 (481)
T TIGR01649       399 LSNIPLSVSEEDLKELFAENGV  420 (481)
T ss_pred             EecCCCCCCHHHHHHHHHhcCC
Confidence            5566667788888888888773

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).

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

Probab=99.95  E-value=4.9e-27  Score=240.20  Aligned_cols=215  Identities=18%  Similarity=0.346  Sum_probs=177.8

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccccccccccCCCCccccCCCCC-CC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPY-GE  189 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~~~~~~~l~n~~~~~~~~~~~-~e  189 (823)
                      .+.|||++|...++|+-+..||.+.|.|   .|.+|..        ++     .++..             .+.+.. ..
T Consensus         6 prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~--------~v-----~wa~~-------------p~nQsk~t~   59 (321)
T KOG0148|consen    6 PRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDEL--------KV-----NWATA-------------PGNQSKPTS   59 (321)
T ss_pred             CceEEeeccChhhHHHHHHHHHHhccccccceeehhhh--------cc-----ccccC-------------cccCCCCcc
Confidence            4679999999999999999999999987   4555510        01     00000             011110 11


Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...-.+||+.|...++-++||+.|.+||+|.++++     +.++|||+||.|.+.++|++||..|+|..|.+|.|+-.|+
T Consensus        60 ~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWA  139 (321)
T KOG0148|consen   60 NQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWA  139 (321)
T ss_pred             ccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccc
Confidence            12457999999999999999999999999998873     7899999999999999999999999999999999999999


Q ss_pred             CCCCCCCC------------CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHH
Q 003400          265 IPKDNPSD------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK  332 (823)
Q Consensus       265 ~pk~~~~~------------~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~  332 (823)
                      ..|.....            .....++|||+|++.-+||++|++.|++||.|.+||+.+ -+||+||+|++.|+|.+||.
T Consensus       140 TRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk-~qGYaFVrF~tkEaAahAIv  218 (321)
T KOG0148|consen  140 TRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFK-DQGYAFVRFETKEAAAHAIV  218 (321)
T ss_pred             ccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEec-ccceEEEEecchhhHHHHHH
Confidence            76542211            123457999999999999999999999999999999974 57999999999999999999


Q ss_pred             HhCCCccCCceEEEEecCCCccc
Q 003400          333 SLNRSDIAGKRIKLEPSRPGGAR  355 (823)
Q Consensus       333 ~LnG~~i~Gr~I~V~~s~~~~~r  355 (823)
                      .+|+.+|.|+.+++.|.+.....
T Consensus       219 ~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  219 QMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             HhcCceeCceEEEEeccccCCCC
Confidence            99999999999999999876543

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=9.3e-28  Score=243.59  Aligned_cols=246  Identities=19%  Similarity=0.305  Sum_probs=204.5

Q ss_pred             cccccCCCCCCCCCcchhHhhhcCccccccccCCCCCChHHHHHhhcCCCcEEEeccCccCcccceeEeeecCccccc--
Q 003400           90 LEGVMNPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN--  167 (823)
Q Consensus        90 ~ee~e~~~i~n~LP~d~d~l~~~v~~el~V~~Lp~~~~E~el~dlFs~~G~v~V~~d~~es~~~g~~~v~~~e~~~a~--  167 (823)
                      .++.+...|.|+||..        |++..++.||.+++|+|.+++.+         |..++.+.|+.|+.+.+..++.  
T Consensus        37 t~~skTNLIvNYLPQ~--------MTqdE~rSLF~SiGeiEScKLvR---------DKitGqSLGYGFVNYv~p~DAe~A   99 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQN--------MTQDELRSLFGSIGEIESCKLVR---------DKITGQSLGYGFVNYVRPKDAEKA   99 (360)
T ss_pred             cCcccceeeeeecccc--------cCHHHHHHHhhcccceeeeeeee---------ccccccccccceeeecChHHHHHH
Confidence            3456678899999988        78878888888888888766654         5678888899999998876554  


Q ss_pred             --cccccccCCCCccccCCCCCCC-CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCH
Q 003400          168 --GLLHYSVPNGAGTVAGEHPYGE-HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDI  239 (823)
Q Consensus       168 --~~~~~~l~n~~~~~~~~~~~~e-~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~  239 (823)
                        .+++..+.++.++++..+|..+ ....+|||.+||..+|..||+.+|++||.|..-+     +++.+||.+||.|...
T Consensus       100 intlNGLrLQ~KTIKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr  179 (360)
T KOG0145|consen  100 INTLNGLRLQNKTIKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKR  179 (360)
T ss_pred             HhhhcceeeccceEEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecch
Confidence              6788889999999999888754 4567999999999999999999999999987654     5788999999999999


Q ss_pred             HHHHHHHHHhcCCcccc--ccccccccCCCCCCCC------------------------C--------------------
Q 003400          240 RAARTAMRALQNKPLRR--RKLDIHFSIPKDNPSD------------------------K--------------------  273 (823)
Q Consensus       240 e~A~~Ai~~Lng~~l~g--r~L~V~~a~pk~~~~~------------------------~--------------------  273 (823)
                      ++|+.||+.|+|..-.|  .+|.|+|+........                        +                    
T Consensus       180 ~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~  259 (360)
T KOG0145|consen  180 IEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMT  259 (360)
T ss_pred             hHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCcc
Confidence            99999999999988665  4788888643211100                        0                    


Q ss_pred             ---------------CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHH
Q 003400          274 ---------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  333 (823)
Q Consensus       274 ---------------~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~  333 (823)
                                     .....+|||.||.++.+|.-|+++|++||.|..|++     +.+.+|||||.+.+.++|..||..
T Consensus       260 ~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~s  339 (360)
T KOG0145|consen  260 IDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIAS  339 (360)
T ss_pred             ccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHH
Confidence                           001148999999999999999999999999999875     467899999999999999999999


Q ss_pred             hCCCccCCceEEEEecCCC
Q 003400          334 LNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       334 LnG~~i~Gr~I~V~~s~~~  352 (823)
                      |||..+++|.|.|.|...+
T Consensus       340 LNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  340 LNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             hcCccccceEEEEEEecCC
Confidence            9999999999999997554

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.95  E-value=1.1e-26  Score=256.65  Aligned_cols=163  Identities=23%  Similarity=0.419  Sum_probs=145.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      .....++|||+|||+++|+++|+++|+.||+|++|++     +++++|||||+|.++++|++|++.|++..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            3446799999999999999999999999999999874     56788999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCC
Q 003400          263 FSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRS  337 (823)
Q Consensus       263 ~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~  337 (823)
                      |+.+...    .....+|||.|||.++|+++|+++|++||.|+.|++     ++++++||||+|.+.++|++||+.||+.
T Consensus       183 ~a~p~~~----~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  258 (346)
T TIGR01659       183 YARPGGE----SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNV  258 (346)
T ss_pred             ccccccc----ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            9876432    234568999999999999999999999999999875     4567899999999999999999999999


Q ss_pred             ccCC--ceEEEEecCCCcc
Q 003400          338 DIAG--KRIKLEPSRPGGA  354 (823)
Q Consensus       338 ~i~G--r~I~V~~s~~~~~  354 (823)
                      .+.|  ++|+|++++....
T Consensus       259 ~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       259 IPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             ccCCCceeEEEEECCcccc
Confidence            8876  7899999886543

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).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.94  E-value=8.1e-26  Score=261.31  Aligned_cols=163  Identities=25%  Similarity=0.330  Sum_probs=140.8

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          190 HPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       190 ~~srtLfV~NLP~-~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      .++++|||+|||. .+|+++|+++|+.||+|.+|++....+|||||+|.+.++|++|++.|+|..|.|++|+|.++..+.
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~  352 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQN  352 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccccc
Confidence            3668999999998 699999999999999999999766678999999999999999999999999999999999875431


Q ss_pred             CCCC------------C---------------------CCCccceeeecCCCCCCHHHHHHHhcccCc--eEEEEeCCC-
Q 003400          269 NPSD------------K---------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGE--VKEIRETPH-  312 (823)
Q Consensus       269 ~~~~------------~---------------------~~~~~tLfV~NLp~~vteedL~~~Fs~fG~--I~~iri~~~-  312 (823)
                      ....            +                     .....+|||+|||.++++++|+++|+.||.  |+.|++... 
T Consensus       353 ~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~  432 (481)
T TIGR01649       353 VQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD  432 (481)
T ss_pred             ccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC
Confidence            1000            0                     012358999999999999999999999998  888877433 


Q ss_pred             --cccEEEEEEcCHHHHHHHHHHhCCCccCCce------EEEEecCCC
Q 003400          313 --KRHHKFIEFYDVRAAEAALKSLNRSDIAGKR------IKLEPSRPG  352 (823)
Q Consensus       313 --srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~------I~V~~s~~~  352 (823)
                        ++++|||+|.+.++|.+||..|||+.|.|+.      |+|.|++++
T Consensus       433 ~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       433 NERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             CCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence              3789999999999999999999999999985      999999764

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).

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.94  E-value=3.3e-27  Score=267.46  Aligned_cols=326  Identities=18%  Similarity=0.184  Sum_probs=252.0

Q ss_pred             CcccccceeecCCcccccccCCCceeeccCCccccccccccccCCCCCcccccCCCccccCCCCCCCCCcccccCCCCCC
Q 003400           21 KEVGGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGN  100 (823)
Q Consensus        21 ~~~~~~t~~~p~~a~~~~~~~d~~~fs~~l~~l~~~k~~~~~~~~~~~~~d~~~~~~kk~~~eee~~k~~ee~e~~~i~n  100 (823)
                      +.+++.+|++|++|+++|.++|+.+|+|||+|+++.+.+.+..    ...+.....||+    +++.+.+.....-..||
T Consensus       246 ~lfa~v~~~~~~~avka~~~~D~k~fqgrmlhvlp~~~k~~~~----~~~~~~~~~~k~----~ke~~rk~~~~~~~~wn  317 (725)
T KOG0110|consen  246 KLFAFVTFMFPEHAVKAYSELDGKVFQGRMLHVLPSKEKSTAK----EDASELGSDYKK----EKELKRKAASASFHSWN  317 (725)
T ss_pred             HhhHHHhhhhhHHHHhhhhhccccccccceeeecCcchhhhhh----hhHhhcCCcHHH----HHHhccccchhcceecc
Confidence            3448899999999999999999999999999999998765433    223333344766    67777777777778999


Q ss_pred             CCCcchhHhhhcCccccccccCCCCCChHHHHHhhcCCCcEEEeccCccCcccceeEeeecCccccccccccccCCCCcc
Q 003400          101 SLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGT  180 (823)
Q Consensus       101 ~LP~d~d~l~~~v~~el~V~~Lp~~~~E~el~dlFs~~G~v~V~~d~~es~~~g~~~v~~~e~~~a~~~~~~~l~n~~~~  180 (823)
                      .|..++++++..++.++.|.+.              +       +.+.+.... .+++.+.+......+..+...+++..
T Consensus       318 ~l~~~~~ava~~~a~k~~v~k~--------------~-------i~d~~~~gs-avr~al~etr~~~e~~~~~ee~gV~l  375 (725)
T KOG0110|consen  318 TLFMGANAVAGILAQKLGVEKS--------------R-------ILDGSLSGS-AVRLALGETRVVQEVRRFFEENGVKL  375 (725)
T ss_pred             cccccccHHHHHHHHHhCCeee--------------e-------eechhhcch-HHHHHHHHhhhchhhhhhHHhhCccc
Confidence            9999999999988888888661              0       111111111 34555556666666666667776655


Q ss_pred             ccCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          181 VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       181 ~~~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      .....  .++..+.|+|+|||..+..++|..+|..||+|..|.+ ....-.++|+|.+..+|++|++.|.+..+...+++
T Consensus       376 ~~F~~--~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvll-p~~G~~aiv~fl~p~eAr~Afrklaysr~k~~ply  452 (725)
T KOG0110|consen  376 DAFSQ--AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLL-PPGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLY  452 (725)
T ss_pred             ccchh--hhhhcceeeeccCccccccHHHHHHhhcccccceeec-CcccceeeeeecCccchHHHHHHhchhhhccCccc
Confidence            55544  6678899999999999999999999999999999944 44444599999999999999999999999999999


Q ss_pred             ccccCCCCCC--------------------CC------------CC-------------CCc-cceeeecCCCCCCHHHH
Q 003400          261 IHFSIPKDNP--------------------SD------------KD-------------LNQ-GTLVVFNLDPSVSNEDL  294 (823)
Q Consensus       261 V~~a~pk~~~--------------------~~------------~~-------------~~~-~tLfV~NLp~~vteedL  294 (823)
                      +.|+....-.                    ..            .+             ... ++|||.||++++|.++|
T Consensus       453 le~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l  532 (725)
T KOG0110|consen  453 LEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDL  532 (725)
T ss_pred             cccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHH
Confidence            8885211000                    00            00             011 24999999999999999


Q ss_pred             HHHhcccCceEEEEeCCC--------cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC--------CCc---c-
Q 003400          295 RQIFGAYGEVKEIRETPH--------KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR--------PGG---A-  354 (823)
Q Consensus       295 ~~~Fs~fG~I~~iri~~~--------srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~--------~~~---~-  354 (823)
                      ..+|...|.|.++.|..+        ++|||||+|.+.++|+.|++.|+|+.|+|+.|.|+++.        ++.   . 
T Consensus       533 ~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~  612 (725)
T KOG0110|consen  533 EDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKK  612 (725)
T ss_pred             HHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccc
Confidence            999999999999976322        45999999999999999999999999999999999998        111   1 


Q ss_pred             -cchhhhccccccCHHHHHHHHhhcC
Q 003400          355 -RRNLMLQLNQELEQDESRILQHQVG  379 (823)
Q Consensus       355 -r~~~~~ql~~~~~~~~l~~~f~~~G  379 (823)
                       .+.+++++.-+.+..+++..|..||
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFG  638 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFG  638 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhccc
Confidence             1346777877888899999999987

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.93  E-value=6e-25  Score=252.24  Aligned_cols=238  Identities=21%  Similarity=0.279  Sum_probs=188.1

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc---cccccccCCCCccccC----
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAGTVAG----  183 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~---~~~~~~l~n~~~~~~~----  183 (823)
                      ...++|++||..+++.+|.++|+.+|.|   .|..+..++..+|+++|.|.+...+.   .+.+..+.+....+..    
T Consensus        89 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~  168 (457)
T TIGR01622        89 DRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAE  168 (457)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecchh
Confidence            4679999999999999999999999987   66677777888999999999876554   2333333322211110    


Q ss_pred             ---------CCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHh
Q 003400          184 ---------EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRAL  249 (823)
Q Consensus       184 ---------~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~L  249 (823)
                               .........++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|.+|+..|
T Consensus       169 ~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l  248 (457)
T TIGR01622       169 KNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM  248 (457)
T ss_pred             hhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhc
Confidence                     00111123689999999999999999999999999999874     3478899999999999999999999


Q ss_pred             cCCccccccccccccCCCCCCC----------------------------------------------------------
Q 003400          250 QNKPLRRRKLDIHFSIPKDNPS----------------------------------------------------------  271 (823)
Q Consensus       250 ng~~l~gr~L~V~~a~pk~~~~----------------------------------------------------------  271 (823)
                      +|..|.|++|.|.|+.......                                                          
T Consensus       249 ~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  328 (457)
T TIGR01622       249 NGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRD  328 (457)
T ss_pred             CCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccc
Confidence            9999999999999953110000                                                          


Q ss_pred             -------C---------------------CCCCccceeeecCCCCCC----------HHHHHHHhcccCceEEEEeC-CC
Q 003400          272 -------D---------------------KDLNQGTLVVFNLDPSVS----------NEDLRQIFGAYGEVKEIRET-PH  312 (823)
Q Consensus       272 -------~---------------------~~~~~~tLfV~NLp~~vt----------eedL~~~Fs~fG~I~~iri~-~~  312 (823)
                             .                     ......+|+|.||....+          .+||++.|++||.|+.|.+. +.
T Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~  408 (457)
T TIGR01622       329 GIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKN  408 (457)
T ss_pred             ccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCC
Confidence                   0                     002235788888855443          36899999999999999875 67


Q ss_pred             cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       313 srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ..|++||+|.++++|.+|++.|||..++|+.|.|.+...
T Consensus       409 ~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       409 SAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             CceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcH
Confidence            789999999999999999999999999999999999754

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.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.93  E-value=1.2e-24  Score=252.99  Aligned_cols=237  Identities=16%  Similarity=0.211  Sum_probs=175.8

Q ss_pred             CccccccccCCCCCChHHHHHhhcCCC-----------cEEEeccCccCcccceeEeeecCcccccc---ccccccCCCC
Q 003400          113 IMDDFDLRGLPSSLEDLEDYDIFGSGG-----------GMELEGEPQESLSMSMSKISISDSASGNG---LLHYSVPNGA  178 (823)
Q Consensus       113 v~~el~V~~Lp~~~~E~el~dlFs~~G-----------~v~V~~d~~es~~~g~~~v~~~e~~~a~~---~~~~~l~n~~  178 (823)
                      .+.+|||++||.++++.+|.++|.+++           .+.+  +......++|+||.|.+.+.|..   +++..+.+..
T Consensus       174 ~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~--~~~~~~~kg~afVeF~~~e~A~~Al~l~g~~~~g~~  251 (509)
T TIGR01642       174 QARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVS--SVNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVF  251 (509)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceE--EEEECCCCCEEEEEeCCHHHHhhhhcCCCeEeeCce
Confidence            357899999999999999999999752           1111  11123346788888877655542   2222222221


Q ss_pred             ccccCC------------------------------CCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----
Q 003400          179 GTVAGE------------------------------HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----  224 (823)
Q Consensus       179 ~~~~~~------------------------------~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----  224 (823)
                      .++...                              ........++|||+|||..+++++|+++|+.||.|..+.+    
T Consensus       252 l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~  331 (509)
T TIGR01642       252 LKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDI  331 (509)
T ss_pred             eEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC
Confidence            111000                              0001234589999999999999999999999999998863    


Q ss_pred             -CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCCCCC------------------------CCCCccc
Q 003400          225 -ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD------------------------KDLNQGT  279 (823)
Q Consensus       225 -~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~~~~------------------------~~~~~~t  279 (823)
                       +++++|||||+|.+.++|..|+..|+|..|.|++|.|.++........                        ......+
T Consensus       332 ~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v  411 (509)
T TIGR01642       332 ATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKV  411 (509)
T ss_pred             CCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccCCCceE
Confidence             467899999999999999999999999999999999999754321110                        0113457


Q ss_pred             eeeecCCCC--C--------CHHHHHHHhcccCceEEEEeCC--------CcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 003400          280 LVVFNLDPS--V--------SNEDLRQIFGAYGEVKEIRETP--------HKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (823)
Q Consensus       280 LfV~NLp~~--v--------teedL~~~Fs~fG~I~~iri~~--------~srG~aFVeF~d~e~A~kAl~~LnG~~i~G  341 (823)
                      |+|.|+...  +        ..++|+++|++||.|+.|++..        ...|++||+|.+.++|++|+..|||..|.|
T Consensus       412 ~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~g  491 (509)
T TIGR01642       412 VQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFND  491 (509)
T ss_pred             EEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECC
Confidence            899998532  1        2367999999999999998742        236899999999999999999999999999


Q ss_pred             ceEEEEecCC
Q 003400          342 KRIKLEPSRP  351 (823)
Q Consensus       342 r~I~V~~s~~  351 (823)
                      +.|.|.|...
T Consensus       492 r~v~~~~~~~  501 (509)
T TIGR01642       492 RVVVAAFYGE  501 (509)
T ss_pred             eEEEEEEeCH
Confidence            9999999754

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.92  E-value=2.1e-24  Score=250.49  Aligned_cols=163  Identities=20%  Similarity=0.402  Sum_probs=143.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..++|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            4589999999999999999999999999999984     57899999999999999999999999999999999998654


Q ss_pred             CCCCCC-------CCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHH
Q 003400          266 PKDNPS-------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  333 (823)
Q Consensus       266 pk~~~~-------~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~  333 (823)
                      ......       .......+|||+||+.++++++|+++|+.||.|++|++     ++.++|||||+|.+.++|.+||..
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH
Confidence            221110       11123468999999999999999999999999999976     345799999999999999999999


Q ss_pred             hCCCccCCceEEEEecCCCc
Q 003400          334 LNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       334 LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      |||..|+|+.|+|.++.++.
T Consensus       266 mNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             hCCCeeCCeEEEEEecCCCc
Confidence            99999999999999987653

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.

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=1.7e-23  Score=225.40  Aligned_cols=164  Identities=23%  Similarity=0.437  Sum_probs=143.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCc-ccc--ccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKP-LRR--RKLDI  261 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~-l~g--r~L~V  261 (823)
                      .+.-+|||+-||..++|+|||++|++||.|.+|.     .++.++|||||.|++.++|.+|+.+|++.. |.|  .+|.|
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            4557899999999999999999999999999986     477899999999999999999999998855 444  68888


Q ss_pred             cccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCC
Q 003400          262 HFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRS  337 (823)
Q Consensus       262 ~~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~  337 (823)
                      +|+.......   ..+.+|||+-|++.+||.|++++|++||.|++|++    .+.+||||||+|.+.+.|..||++|||.
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            8886543322   34678999999999999999999999999999976    4678999999999999999999999996


Q ss_pred             -ccCC--ceEEEEecCCCcccc
Q 003400          338 -DIAG--KRIKLEPSRPGGARR  356 (823)
Q Consensus       338 -~i~G--r~I~V~~s~~~~~r~  356 (823)
                       .+.|  .+|.|+|+++++.|.
T Consensus       189 ~tmeGcs~PLVVkFADtqkdk~  210 (510)
T KOG0144|consen  189 QTMEGCSQPLVVKFADTQKDKD  210 (510)
T ss_pred             eeeccCCCceEEEecccCCCch
Confidence             6777  689999999887654

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=3.7e-23  Score=227.85  Aligned_cols=242  Identities=19%  Similarity=0.294  Sum_probs=190.1

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCccc------
Q 003400          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTV------  181 (823)
Q Consensus       115 ~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~------  181 (823)
                      ..|+|++||.++...++-++|+.+|+|   +|..+...+..+||.+++|.-.+.++    +..+..+.+....+      
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            569999999999999999999999997   78788888888999999887554433    11111111110000      


Q ss_pred             -------cC-----CCCC---------CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEe
Q 003400          182 -------AG-----EHPY---------GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISY  236 (823)
Q Consensus       182 -------~~-----~~~~---------~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F  236 (823)
                             .+     +.+.         ...+.-+|+|+|||+.+.+.+|+.+|+.||.|..|.+    .++-+|||||+|
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                   00     0111         1223678999999999999999999999999999985    345569999999


Q ss_pred             CCHHHHHHHHHHhcCCccccccccccccCCCCCCCC-----------------------------------------C--
Q 003400          237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD-----------------------------------------K--  273 (823)
Q Consensus       237 ~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~~~~-----------------------------------------~--  273 (823)
                      ....+|..|++.+++..|.|++|-|.||.++..-..                                         +  
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~  245 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEET  245 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccc
Confidence            999999999999999999999999999865532100                                         0  


Q ss_pred             CC-------------------------------------------CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-
Q 003400          274 DL-------------------------------------------NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-  309 (823)
Q Consensus       274 ~~-------------------------------------------~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-  309 (823)
                      +.                                           ...+|||+|||+++|+++|.++|++||.|.++.+ 
T Consensus       246 D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV  325 (678)
T KOG0127|consen  246 DGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIV  325 (678)
T ss_pred             cccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEE
Confidence            00                                           0148999999999999999999999999999864 


Q ss_pred             ----CCCcccEEEEEEcCHHHHHHHHHHh-----CC-CccCCceEEEEecCCCcccc
Q 003400          310 ----TPHKRHHKFIEFYDVRAAEAALKSL-----NR-SDIAGKRIKLEPSRPGGARR  356 (823)
Q Consensus       310 ----~~~srG~aFVeF~d~e~A~kAl~~L-----nG-~~i~Gr~I~V~~s~~~~~r~  356 (823)
                          ++.++|.|||.|.+..+|..||...     .| ..+.||.|+|..+-.+....
T Consensus       326 ~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~RkeA~  382 (678)
T KOG0127|consen  326 KDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKEAA  382 (678)
T ss_pred             eccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHHHH
Confidence                7889999999999999999999976     24 67899999999987765443

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.90  E-value=8.2e-23  Score=234.59  Aligned_cols=163  Identities=25%  Similarity=0.450  Sum_probs=143.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      .+.+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|+. |+|..+.|++|.|.
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            3567899999999999999999999999999999984     46789999999999999999997 89999999999998


Q ss_pred             ccCCCCCCCC--------CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHH
Q 003400          263 FSIPKDNPSD--------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEA  329 (823)
Q Consensus       263 ~a~pk~~~~~--------~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~k  329 (823)
                      ++........        ......+|||+|||..+++++|+++|++||.|..|++.     +.++|||||+|.+.++|.+
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            8654322110        11224789999999999999999999999999999763     4678999999999999999


Q ss_pred             HHHHhCCCccCCceEEEEecCC
Q 003400          330 ALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       330 Al~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      |++.|||..|.|+.|+|.|+..
T Consensus       244 A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       244 ALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HHHhcCCcEECCEEEEEEEccC
Confidence            9999999999999999999873

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.

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=1.5e-23  Score=225.92  Aligned_cols=241  Identities=18%  Similarity=0.318  Sum_probs=194.0

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccccc-----cccccCCC--CccccC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGL-----LHYSVPNG--AGTVAG  183 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~~~-----~~~~l~n~--~~~~~~  183 (823)
                      +-++||+.+|+.+.|.+++.+|+.||.|   -|..|..+...+|++|+.+.....+.+.     +...+++.  ...+..
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            4679999999999999999999999987   5678888999999999999987655421     12223322  122222


Q ss_pred             CCCCCC--CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCc-ccc
Q 003400          184 EHPYGE--HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKP-LRR  256 (823)
Q Consensus       184 ~~~~~e--~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~-l~g  256 (823)
                      .....+  ...++|||+-|++.+||.|++++|++||.|++|++    .+.+||||||.|.+.|.|..||++|+|.. ++|
T Consensus       114 Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeG  193 (510)
T KOG0144|consen  114 ADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEG  193 (510)
T ss_pred             cchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeecc
Confidence            222222  24789999999999999999999999999999984    56799999999999999999999999964 554


Q ss_pred             --ccccccccCCCCCCCCCC------------------------------------------------------------
Q 003400          257 --RKLDIHFSIPKDNPSDKD------------------------------------------------------------  274 (823)
Q Consensus       257 --r~L~V~~a~pk~~~~~~~------------------------------------------------------------  274 (823)
                        .+|.|+|+.+++++..+.                                                            
T Consensus       194 cs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~  273 (510)
T KOG0144|consen  194 CSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQ  273 (510)
T ss_pred             CCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhH
Confidence              588888876654321000                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q 003400          275 --------------------------------------------------------------------------------  274 (823)
Q Consensus       275 --------------------------------------------------------------------------------  274 (823)
                                                                                                      
T Consensus       274 ~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~  353 (510)
T KOG0144|consen  274 LQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAG  353 (510)
T ss_pred             HHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhccccccccc
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------CCccceeeecCC
Q 003400          275 --------------------------------------------------------------------LNQGTLVVFNLD  286 (823)
Q Consensus       275 --------------------------------------------------------------------~~~~tLfV~NLp  286 (823)
                                                                                          ....+|||.+||
T Consensus       354 a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlP  433 (510)
T KOG0144|consen  354 AGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLP  433 (510)
T ss_pred             ccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCc
Confidence                                                                                000379999999


Q ss_pred             CCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          287 PSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       287 ~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      .+.-+.+|-..|..||.|++.++     ++-++.|+||.|++..+|..||..|||..|+.++++|...+.+.+
T Consensus       434 qefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~n  506 (510)
T KOG0144|consen  434 QEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRNN  506 (510)
T ss_pred             hhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccCC
Confidence            99999999999999999998753     667899999999999999999999999999999999998876543

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.88  E-value=3.6e-22  Score=231.63  Aligned_cols=178  Identities=22%  Similarity=0.321  Sum_probs=153.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccc-cccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~-gr~L~V~~a~  265 (823)
                      ..++|||+|||.+++|++|+++|++||.|.+|++    +++++|||||+|.+.++|++||+.|++..+. ++.|.|.++.
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            4589999999999999999999999999999874    5789999999999999999999999999986 7788777653


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCc-eEEEEe------CCCcccEEEEEEcCHHHHHHHHHHhCC--
Q 003400          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNR--  336 (823)
Q Consensus       266 pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~-I~~iri------~~~srG~aFVeF~d~e~A~kAl~~LnG--  336 (823)
                                ..++|||+|||.++++++|.+.|++++. ++++.+      ..+++|||||+|.+.++|++|++.|+.  
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                      3468999999999999999999999863 443322      235689999999999999999998864  


Q ss_pred             CccCCceEEEEecCCCcc---------cchhhhccccccCHHHHHHHHhhc
Q 003400          337 SDIAGKRIKLEPSRPGGA---------RRNLMLQLNQELEQDESRILQHQV  378 (823)
Q Consensus       337 ~~i~Gr~I~V~~s~~~~~---------r~~~~~ql~~~~~~~~l~~~f~~~  378 (823)
                      ..+.|+.|.|+|+.+...         +..++.++...++++++..+|.++
T Consensus       207 i~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f  257 (578)
T TIGR01648       207 IQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEF  257 (578)
T ss_pred             eEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhc
Confidence            367899999999987532         345788999999999999999999

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.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.88  E-value=2.8e-21  Score=224.58  Aligned_cols=154  Identities=13%  Similarity=0.246  Sum_probs=126.4

Q ss_pred             cCccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCC
Q 003400          112 GIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGE  184 (823)
Q Consensus       112 ~v~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~  184 (823)
                      ..++++||++|+.+++|.+++++|+.||.|   .+..|..++..+||+|+.|.+...+.    .+++..+.+...++...
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            357899999999999999999999999997   67778888899999999999886665    34455555443333211


Q ss_pred             C------C------CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHH
Q 003400          185 H------P------YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMR  247 (823)
Q Consensus       185 ~------~------~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~  247 (823)
                      .      +      ......++|||+|||.++++++|+++|+.||+|.+|++     +++++|||||+|.+.++|.+|++
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            1      0      11124579999999999999999999999999999874     45789999999999999999999


Q ss_pred             HhcCCccccccccccccC
Q 003400          248 ALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       248 ~Lng~~l~gr~L~V~~a~  265 (823)
                      .||+..+.|+.|+|.++.
T Consensus       265 amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       265 SMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             HhCCCeeCCeEEEEEecC
Confidence            999999999999987754

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.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.87  E-value=1.3e-21  Score=227.56  Aligned_cols=164  Identities=16%  Similarity=0.277  Sum_probs=136.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcC------------CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQY------------GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~f------------G~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l  254 (823)
                      ......++|||+|||.++|+++|+++|.+|            +.|..+. ..+.+|||||+|.+.++|..||. |+|..|
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~-~~~~kg~afVeF~~~e~A~~Al~-l~g~~~  247 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVN-INKEKNFAFLEFRTVEEATFAMA-LDSIIY  247 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEE-ECCCCCEEEEEeCCHHHHhhhhc-CCCeEe
Confidence            345677999999999999999999999975            3445443 46789999999999999999995 999999


Q ss_pred             ccccccccccCCCCCC------------C-------------CCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe
Q 003400          255 RRRKLDIHFSIPKDNP------------S-------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE  309 (823)
Q Consensus       255 ~gr~L~V~~a~pk~~~------------~-------------~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri  309 (823)
                      .|+.|+|.........            .             .......+|||+|||..+++++|+++|+.||.|..+.+
T Consensus       248 ~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~  327 (509)
T TIGR01642       248 SNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNL  327 (509)
T ss_pred             eCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE
Confidence            9999998743211100            0             00112358999999999999999999999999998865


Q ss_pred             -----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          310 -----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       310 -----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                           ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++...
T Consensus       328 ~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       328 IKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             EecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence                 4668999999999999999999999999999999999998654

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.86  E-value=3e-21  Score=209.23  Aligned_cols=180  Identities=22%  Similarity=0.351  Sum_probs=158.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccc-ccccccccc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFS  264 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~-gr~L~V~~a  264 (823)
                      -.+-|||+.||.++.|+||.-+|++.|+|-.+++     ++.+||||||.|.+.++|++|++.||+.+|+ |+.|.|..+
T Consensus        82 ~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~S  161 (506)
T KOG0117|consen   82 RGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVS  161 (506)
T ss_pred             CCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEe
Confidence            4589999999999999999999999999999983     6789999999999999999999999999996 899999876


Q ss_pred             CCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCc-eEEEEe------CCCcccEEEEEEcCHHHHHHHHHHhC-C
Q 003400          265 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLN-R  336 (823)
Q Consensus       265 ~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~-I~~iri------~~~srG~aFVeF~d~e~A~kAl~~Ln-G  336 (823)
                      .          ..++|||+|||++.++++|.+.+++.++ |.+|.+      ..++||||||+|+++..|..|.+.|- |
T Consensus       162 v----------an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g  231 (506)
T KOG0117|consen  162 V----------ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPG  231 (506)
T ss_pred             e----------ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCC
Confidence            4          4578999999999999999999999863 455533      34689999999999999999998774 4


Q ss_pred             -CccCCceEEEEecCCCcc---------cchhhhccccccCHHHHHHHHhhcCC
Q 003400          337 -SDIAGKRIKLEPSRPGGA---------RRNLMLQLNQELEQDESRILQHQVGS  380 (823)
Q Consensus       337 -~~i~Gr~I~V~~s~~~~~---------r~~~~~ql~~~~~~~~l~~~f~~~Gs  380 (823)
                       .++.|+.+.|+|+.+...         +..|++++...++++.+...|.++|.
T Consensus       232 ~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~  285 (506)
T KOG0117|consen  232 KIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGK  285 (506)
T ss_pred             ceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccc
Confidence             378899999999998653         24589999999999999999999873

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.85  E-value=1.5e-20  Score=209.15  Aligned_cols=229  Identities=15%  Similarity=0.320  Sum_probs=187.2

Q ss_pred             ccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCCCCC
Q 003400          116 DFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYG  188 (823)
Q Consensus       116 el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~~~  188 (823)
                      .++|+   .+++|..++++|+..|.+   .|..|. +  +.|++++.|.+...+.    .++...+.+...++.-.    
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s----   72 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWS----   72 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehh----
Confidence            36777   899999999999999986   787777 5  7889999999887665    34444444443333222    


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      .++.+.|||+||+++++.++|.++|+.||+|.+|++   ..-++|| ||+|.+.++|++|+..++|..+.+++|.|....
T Consensus        73 ~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~  151 (369)
T KOG0123|consen   73 QRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFE  151 (369)
T ss_pred             ccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeecc
Confidence            223334999999999999999999999999999994   2338899 999999999999999999999999999998776


Q ss_pred             CCCCCCCC----CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCC
Q 003400          266 PKDNPSDK----DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRS  337 (823)
Q Consensus       266 pk~~~~~~----~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~  337 (823)
                      .+......    ...-.+++|.|++.+++++.|.+.|..||.|..+.+    .+++++|+||+|.+.++|..|++.|++.
T Consensus       152 ~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~  231 (369)
T KOG0123|consen  152 RKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGK  231 (369)
T ss_pred             chhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCC
Confidence            55433221    122468999999999999999999999999999865    4557999999999999999999999999


Q ss_pred             ccCCceEEEEecCCCccc
Q 003400          338 DIAGKRIKLEPSRPGGAR  355 (823)
Q Consensus       338 ~i~Gr~I~V~~s~~~~~r  355 (823)
                      .+.++.+.|..+..+..+
T Consensus       232 ~~~~~~~~V~~aqkk~e~  249 (369)
T KOG0123|consen  232 IFGDKELYVGRAQKKSER  249 (369)
T ss_pred             cCCccceeecccccchhh
Confidence            999999999988775444

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.85  E-value=5e-21  Score=186.77  Aligned_cols=162  Identities=24%  Similarity=0.334  Sum_probs=143.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ...||||+||+..++++.|+++|-+.|+|..++     ++..++|||||+|.++|+|+-|++-|+...+.|++|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            457999999999999999999999999999997     466799999999999999999999999999999999998875


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEE------EeCCCcccEEEEEEcCHHHHHHHHHHhCCCcc
Q 003400          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI------RETPHKRHHKFIEFYDVRAAEAALKSLNRSDI  339 (823)
Q Consensus       266 pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~i------ri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i  339 (823)
                      .   .........+|||+||++.+++..|.++|+.||.+...      ..++.++++|||.|.+.+.+.+|+..+||..+
T Consensus        88 ~---~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l  164 (203)
T KOG0131|consen   88 A---HQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYL  164 (203)
T ss_pred             c---ccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchh
Confidence            1   11222234799999999999999999999999988763      24678899999999999999999999999999


Q ss_pred             CCceEEEEecCCCccc
Q 003400          340 AGKRIKLEPSRPGGAR  355 (823)
Q Consensus       340 ~Gr~I~V~~s~~~~~r  355 (823)
                      ..++|+|.++..++.+
T Consensus       165 ~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  165 CNRPITVSYAFKKDTK  180 (203)
T ss_pred             cCCceEEEEEEecCCC
Confidence            9999999999876644

>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=7e-21  Score=196.92  Aligned_cols=148  Identities=28%  Similarity=0.462  Sum_probs=137.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCCCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD  272 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~~~~  272 (823)
                      -+|||+|||.++++.+|+.+|++||+|.+|.+   -|.||||..++...|+.|++.|++..|.|..|.|+-++.+.    
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   45799999999999999999999999999999999886553    


Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       273 ~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                        ....+|+|+||.+.++.+||+..|++||.|++|+|.   ++|+||.|+-.++|..|++.|++.++.|++++|..+..+
T Consensus        76 --k~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv---kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen   76 --KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV---KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             --CCccccccCCCCccccCHHHhhhhcccCCceeeeee---cceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence              245689999999999999999999999999999986   689999999999999999999999999999999998764

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.83  E-value=2.5e-20  Score=207.42  Aligned_cols=276  Identities=22%  Similarity=0.348  Sum_probs=215.4

Q ss_pred             cccceeecCCcccccccCCCceeeccCCccccccccccccCCCCCcccccCCCccccCCCCCCCCCcccccCCCCCCCCC
Q 003400           24 GGGSCGRIAGSDSYLASDDASLFSSSLPVLPHEKLNLNAMGLGRQSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLP  103 (823)
Q Consensus        24 ~~~t~~~p~~a~~~~~~~d~~~fs~~l~~l~~~k~~~~~~~~~~~~~d~~~~~~kk~~~eee~~k~~ee~e~~~i~n~LP  103 (823)
                      |-..|.-|++|-+|+.+++-.++.|+..-|..+...             .+  +                          
T Consensus        40 ~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd-------------~~--~--------------------------   78 (369)
T KOG0123|consen   40 AYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD-------------PS--L--------------------------   78 (369)
T ss_pred             EEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC-------------Cc--e--------------------------
Confidence            446677788888888888888777776655552211             01  0                          


Q ss_pred             cchhHhhhcCccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCC
Q 003400          104 DDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPN  176 (823)
Q Consensus       104 ~d~d~l~~~v~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n  176 (823)
                                   ++|.+|+.+++...++|+|+.+|.|   .|..+..-  .+|+ +|.|.+...|.    .+++..+.+
T Consensus        79 -------------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g--~kg~-FV~f~~e~~a~~ai~~~ng~ll~~  142 (369)
T KOG0123|consen   79 -------------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG--SKGY-FVQFESEESAKKAIEKLNGMLLNG  142 (369)
T ss_pred             -------------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC--ceee-EEEeCCHHHHHHHHHHhcCcccCC
Confidence                         8999999999999999999999997   66555433  7888 99999887665    333333333


Q ss_pred             CCccc-------cCCCCCCC--CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHH
Q 003400          177 GAGTV-------AGEHPYGE--HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAAR  243 (823)
Q Consensus       177 ~~~~~-------~~~~~~~e--~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~  243 (823)
                      ....+       ....+..+  ...+.++|+|++.++++++|.++|..||.|.++.+    .+++++|+||.|.+.++|.
T Consensus       143 kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~  222 (369)
T KOG0123|consen  143 KKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAK  222 (369)
T ss_pred             CeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHH
Confidence            21111       11111222  23468999999999999999999999999999873    5668999999999999999


Q ss_pred             HHHHHhcCCccccccccccccCCCCCCC--------------CCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe
Q 003400          244 TAMRALQNKPLRRRKLDIHFSIPKDNPS--------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE  309 (823)
Q Consensus       244 ~Ai~~Lng~~l~gr~L~V~~a~pk~~~~--------------~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri  309 (823)
                      .|+..|++..+.+..+.|..+..+....              .......+|||.||+..++.+.|+++|+.||+|..+++
T Consensus       223 ~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv  302 (369)
T KOG0123|consen  223 KAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKV  302 (369)
T ss_pred             HHHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEE
Confidence            9999999999999999988775532111              11234569999999999999999999999999999876


Q ss_pred             ----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcccc
Q 003400          310 ----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR  356 (823)
Q Consensus       310 ----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~r~  356 (823)
                          .+.++|++||+|...++|.+|+..+|+..+.++.|.|.++.....++
T Consensus       303 ~~~~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~r~  353 (369)
T KOG0123|consen  303 MVDENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKEDRR  353 (369)
T ss_pred             EeccCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhccch
Confidence                46789999999999999999999999999999999999988655444

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.82  E-value=8.9e-20  Score=201.41  Aligned_cols=161  Identities=22%  Similarity=0.368  Sum_probs=143.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      .||||++||++++.++|.++|+.+|+|..|.+     ...++||+||.|.-.+++++|+..+.+..|.|+.|.|.++.++
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            79999999999999999999999999999873     3468999999999999999999999999999999999998665


Q ss_pred             CCCCC--------------------C--CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC----CCcccEEEEEE
Q 003400          268 DNPSD--------------------K--DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEF  321 (823)
Q Consensus       268 ~~~~~--------------------~--~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~----~~srG~aFVeF  321 (823)
                      .....                    .  +.....|.|+|||+.+...+|+.+|+.||.|.+|.|.    ++-+|||||+|
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            43220                    0  1124589999999999999999999999999999873    44579999999


Q ss_pred             cCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       322 ~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      .+..+|.+|++.+||..|+||+|-|.||-++.
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            99999999999999999999999999998765

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.80  E-value=1.8e-19  Score=204.99  Aligned_cols=161  Identities=25%  Similarity=0.459  Sum_probs=139.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCC--------CcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC--------KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       194 tLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~--------ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      +|||+||+.++|.++|..+|...|.|.++.+..        .+.|||||+|.+.++|+.|++.|+|+.|.|+.|.|+++.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            499999999999999999999999999996421        245999999999999999999999999999999999986


Q ss_pred             CCCCC-----CCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCC-----cccEEEEEEcCHHHHHHHHHHhC
Q 003400          266 PKDNP-----SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH-----KRHHKFIEFYDVRAAEAALKSLN  335 (823)
Q Consensus       266 pk~~~-----~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~-----srG~aFVeF~d~e~A~kAl~~Ln  335 (823)
                      .+...     .......+.|.|+|||+..+-.+++++|..||.|++||+..+     .+|||||+|-++++|..|+++|.
T Consensus       597 ~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~  676 (725)
T KOG0110|consen  597 NKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALG  676 (725)
T ss_pred             CccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhc
Confidence            11110     011112358999999999999999999999999999998543     48999999999999999999999


Q ss_pred             CCccCCceEEEEecCCCcc
Q 003400          336 RSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       336 G~~i~Gr~I~V~~s~~~~~  354 (823)
                      .+.+.||+|.++|+.....
T Consensus       677 STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  677 STHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             ccceechhhheehhccchH
Confidence            9999999999999987654

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

Probab=99.76  E-value=3e-18  Score=176.12  Aligned_cols=161  Identities=24%  Similarity=0.371  Sum_probs=130.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      +..-|||||+||..+|||+-|..||.+.|.|..+++...                              .|+|.|+....
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~------------------------------e~~v~wa~~p~   52 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD------------------------------ELKVNWATAPG   52 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh------------------------------hhccccccCcc
Confidence            345699999999999999999999999999999875322                              55677765443


Q ss_pred             CCCCCCCC-ccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCc
Q 003400          269 NPSDKDLN-QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  342 (823)
Q Consensus       269 ~~~~~~~~-~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr  342 (823)
                      ..+..... .--+||+.|...++.|+|++.|.+||+|.++|+     ++++||||||.|.+.++|+.||..|||.+|++|
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            33332222 346999999999999999999999999999876     678999999999999999999999999999999


Q ss_pred             eEEEEecCCCccc--------------------chhhhccccccCHHHHHHHHhhcC
Q 003400          343 RIKLEPSRPGGAR--------------------RNLMLQLNQELEQDESRILQHQVG  379 (823)
Q Consensus       343 ~I~V~~s~~~~~r--------------------~~~~~ql~~~~~~~~l~~~f~~~G  379 (823)
                      .|+-.|+.++...                    ..|+..++..++++.+++.|.+||
T Consensus       133 ~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG  189 (321)
T KOG0148|consen  133 TIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFG  189 (321)
T ss_pred             eeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCC
Confidence            9999999876532                    124455555677778888777776

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.74  E-value=6e-18  Score=179.01  Aligned_cols=156  Identities=22%  Similarity=0.473  Sum_probs=137.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      -++|||+.|...+.|+.||..|..||+|++|.     ++.+++|||||+|+-+|.|+.|++.+||..+.||.|+|..  |
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr--P  190 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR--P  190 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC--C
Confidence            47999999999999999999999999999997     5899999999999999999999999999999999999984  3


Q ss_pred             CCCCCCC---------CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHH
Q 003400          267 KDNPSDK---------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALK  332 (823)
Q Consensus       267 k~~~~~~---------~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~  332 (823)
                      ...+...         ...-.+|||..+.++++++||+.+|+.||+|.+|.+     ....+||+||||.+...-.+||.
T Consensus       191 sNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAia  270 (544)
T KOG0124|consen  191 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA  270 (544)
T ss_pred             CCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhh
Confidence            3222111         112358999999999999999999999999999976     34568999999999999999999


Q ss_pred             HhCCCccCCceEEEEec
Q 003400          333 SLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       333 ~LnG~~i~Gr~I~V~~s  349 (823)
                      .||-..++|.-|+|..+
T Consensus       271 sMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  271 SMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             hcchhhcccceEecccc
Confidence            99999999999998655

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.74  E-value=1.3e-17  Score=184.58  Aligned_cols=153  Identities=20%  Similarity=0.311  Sum_probs=127.3

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP  186 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~  186 (823)
                      .++|+|++||.+++|.+|+++|+.+|.|   .|..|..+...+++++|.|.+.+.|.    .++...+.+...++....+
T Consensus       107 ~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p  186 (346)
T TIGR01659       107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP  186 (346)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccc
Confidence            5889999999999999999999999987   66677788889999999999876654    4555556555555544333


Q ss_pred             C-CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccc--cc
Q 003400          187 Y-GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RK  258 (823)
Q Consensus       187 ~-~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g--r~  258 (823)
                      . .....++|||+|||.++|+++|+++|++||+|+.|++     +++++|||||+|.+.++|++|++.|++..+.+  ++
T Consensus       187 ~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~  266 (346)
T TIGR01659       187 GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQP  266 (346)
T ss_pred             cccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCcee
Confidence            2 2234678999999999999999999999999998873     56778999999999999999999999998865  68


Q ss_pred             ccccccCC
Q 003400          259 LDIHFSIP  266 (823)
Q Consensus       259 L~V~~a~p  266 (823)
                      |.|.++..
T Consensus       267 l~V~~a~~  274 (346)
T TIGR01659       267 LTVRLAEE  274 (346)
T ss_pred             EEEEECCc
Confidence            88888764

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).

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.73  E-value=5.7e-17  Score=164.27  Aligned_cols=162  Identities=27%  Similarity=0.457  Sum_probs=142.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHH----HhhcCCCEEEEE--eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRA----LFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~----lFs~fG~I~~v~--~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ..+..||||+||+..+..++|+.    +|++||.|..|.  .+.+.+|-|||.|.+.+.|-.|+++|+|..+.|++++|+
T Consensus         6 ~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    6 VNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             cCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            34667999999999999999988    999999999987  377899999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCC----------------------------------------------CCCccceeeecCCCCCCHHHHHH
Q 003400          263 FSIPKDNPSDK----------------------------------------------DLNQGTLVVFNLDPSVSNEDLRQ  296 (823)
Q Consensus       263 ~a~pk~~~~~~----------------------------------------------~~~~~tLfV~NLp~~vteedL~~  296 (823)
                      ||..+.+...+                                              ......|++.|||.+++.+.|..
T Consensus        86 yA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~  165 (221)
T KOG4206|consen   86 YAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSD  165 (221)
T ss_pred             cccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHH
Confidence            98654321100                                              12335799999999999999999


Q ss_pred             HhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccC-CceEEEEecC
Q 003400          297 IFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSR  350 (823)
Q Consensus       297 ~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~-Gr~I~V~~s~  350 (823)
                      +|.+|...++||......+.|||+|.+...|..|...|+|..|. ...++|.+++
T Consensus       166 lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  166 LFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            99999999999988778899999999999999999999999887 7888888875

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.72  E-value=6.7e-18  Score=172.74  Aligned_cols=166  Identities=23%  Similarity=0.430  Sum_probs=138.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcc-cc--ccccccc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPL-RR--RKLDIHF  263 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l-~g--r~L~V~~  263 (823)
                      +.|+|||+-|.+.-.|||++.+|..||.|.+|.+    .+.+||||||.|.+.-+|..||..|+|... .|  ..|.|+|
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            5689999999999999999999999999999974    577999999999999999999999998653 22  2344444


Q ss_pred             cCCCCCCC------------------------------------------------------------------------
Q 003400          264 SIPKDNPS------------------------------------------------------------------------  271 (823)
Q Consensus       264 a~pk~~~~------------------------------------------------------------------------  271 (823)
                      +...+++.                                                                        
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            32111000                                                                        


Q ss_pred             --------------------------------------------------------------------------------
Q 003400          272 --------------------------------------------------------------------------------  271 (823)
Q Consensus       272 --------------------------------------------------------------------------------  271 (823)
                                                                                                      
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             ----------------------CCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCH
Q 003400          272 ----------------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDV  324 (823)
Q Consensus       272 ----------------------~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~  324 (823)
                                            .+..+.++|||..||.+..+.||.++|-+||.|++.++     +..+|.|+||.|+++
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence                                  00012268999999999999999999999999998754     678999999999999


Q ss_pred             HHHHHHHHHhCCCccCCceEEEEecCCCcccc
Q 003400          325 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARR  356 (823)
Q Consensus       325 e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~r~  356 (823)
                      .+|+.||.+|||..|+-|+|+|...+|++..|
T Consensus       338 ~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanR  369 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIGMKRLKVQLKRPKDANR  369 (371)
T ss_pred             hhHHHHHHHhcchhhhhhhhhhhhcCccccCC
Confidence            99999999999999999999999999987655

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.70  E-value=1.1e-16  Score=178.56  Aligned_cols=237  Identities=19%  Similarity=0.239  Sum_probs=179.1

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc---cccccccCCCCcccc-----
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAGTVA-----  182 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~---~~~~~~l~n~~~~~~-----  182 (823)
                      ...+++-.|......-+++++|+..|.|   .+..|..+.+.+|++++.|.+...+.   .+.+-.+..-...+.     
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEae  258 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAE  258 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHHH
Confidence            4567777777888899999999999986   67788889999999999999875443   222222221111110     


Q ss_pred             ----------CCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHH
Q 003400          183 ----------GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMR  247 (823)
Q Consensus       183 ----------~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~  247 (823)
                                ........|-+.|||+||-.++++++|+.+|+.||.|..|.+     ++.++||+||+|.+.++|++|+.
T Consensus       259 knr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e  338 (549)
T KOG0147|consen  259 KNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALE  338 (549)
T ss_pred             HHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHH
Confidence                      000111334455999999999999999999999999999872     78899999999999999999999


Q ss_pred             HhcCCccccccccccccCCCCCCCC-------------------------------------------------------
Q 003400          248 ALQNKPLRRRKLDIHFSIPKDNPSD-------------------------------------------------------  272 (823)
Q Consensus       248 ~Lng~~l~gr~L~V~~a~pk~~~~~-------------------------------------------------------  272 (823)
                      .|||..|.|+.|+|.....+-....                                                       
T Consensus       339 ~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~  418 (549)
T KOG0147|consen  339 QLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASA  418 (549)
T ss_pred             HhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchH
Confidence            9999999999998765321100000                                                       


Q ss_pred             -------------CC-------CCccceeeecCC--CCCC--------HHHHHHHhcccCceEEEEeCCCcccEEEEEEc
Q 003400          273 -------------KD-------LNQGTLVVFNLD--PSVS--------NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFY  322 (823)
Q Consensus       273 -------------~~-------~~~~tLfV~NLp--~~vt--------eedL~~~Fs~fG~I~~iri~~~srG~aFVeF~  322 (823)
                                   ..       +...++.++|+=  .+.|        .+|+.+.+.+||.|..|.+...+-|+.||.|.
T Consensus       419 ~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~  498 (549)
T KOG0147|consen  419 AQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCP  498 (549)
T ss_pred             HhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecC
Confidence                         00       111245555552  2222        27788999999999999998888899999999


Q ss_pred             CHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          323 DVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       323 d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      +.++|..|+++|||.+|.|+.|+..|-.
T Consensus       499 s~~~A~~a~~alhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  499 SAEAAGTAVKALHGRWFAGRMITAKYLP  526 (549)
T ss_pred             cHHHHHHHHHHHhhhhhccceeEEEEee
Confidence            9999999999999999999999998854

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.67  E-value=4.7e-14  Score=152.81  Aligned_cols=159  Identities=23%  Similarity=0.379  Sum_probs=131.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhh-cCCCEEEEE----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFE-QYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs-~fG~I~~v~----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      .|.+||.|||+++...+|++||. +.|+|+.|.    ..++.+|||.|+|+++|.+++|++.|+...+.|++|.|+--..
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            46799999999999999999997 789999997    3789999999999999999999999999999999998864211


Q ss_pred             CCC------------------------------------------CCCC-------------------------------
Q 003400          267 KDN------------------------------------------PSDK-------------------------------  273 (823)
Q Consensus       267 k~~------------------------------------------~~~~-------------------------------  273 (823)
                      ...                                          +.++                               
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                                          0000                               


Q ss_pred             --------CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 003400          274 --------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (823)
Q Consensus       274 --------~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G  341 (823)
                              ......+||.||.+.+....|++.|.--|.|..|.+    .+.++|++.|+|+.+-+|..||..|++.-+..
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                    001147899999999999999999999999988853    46789999999999999999999999877777


Q ss_pred             ceEEEEecC
Q 003400          342 KRIKLEPSR  350 (823)
Q Consensus       342 r~I~V~~s~  350 (823)
                      ++..+...+
T Consensus       284 ~~~~~Rl~~  292 (608)
T KOG4212|consen  284 RRMTVRLDR  292 (608)
T ss_pred             ccceeeccc
Confidence            887777643

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=9.6e-16  Score=162.46  Aligned_cols=239  Identities=14%  Similarity=0.262  Sum_probs=179.9

Q ss_pred             hcCccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccC
Q 003400          111 AGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAG  183 (823)
Q Consensus       111 ~~v~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~  183 (823)
                      -.+|+++||+.+..++.|+.++..|..||.|   ...-|+.+...++|+|+.+.-.+.+.    .+++..+.++..++..
T Consensus       110 LaiMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  110 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             HHHhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            3569999999999999999999999999997   45678889999999999887655443    3444444333333321


Q ss_pred             CC------C------CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHH
Q 003400          184 EH------P------YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAM  246 (823)
Q Consensus       184 ~~------~------~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai  246 (823)
                      ..      +      ...+.-.+|||..+.++.+|+||+.+|+.||+|..|.+     ...++||+||+|.+..+...|+
T Consensus       190 PsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAi  269 (544)
T KOG0124|consen  190 PSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAI  269 (544)
T ss_pred             CCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHh
Confidence            11      1      01223579999999999999999999999999999983     5679999999999999999999


Q ss_pred             HHhcCCccccccccccccCCCCCC--------------------------------------------------------
Q 003400          247 RALQNKPLRRRKLDIHFSIPKDNP--------------------------------------------------------  270 (823)
Q Consensus       247 ~~Lng~~l~gr~L~V~~a~pk~~~--------------------------------------------------------  270 (823)
                      ..+|-..+.|+-|+|..+......                                                        
T Consensus       270 asMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~  349 (544)
T KOG0124|consen  270 ASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPL  349 (544)
T ss_pred             hhcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCC
Confidence            999988888887776542110000                                                        


Q ss_pred             ---------------------------C-------------------------CC-------------------------
Q 003400          271 ---------------------------S-------------------------DK-------------------------  273 (823)
Q Consensus       271 ---------------------------~-------------------------~~-------------------------  273 (823)
                                                 .                         .+                         
T Consensus       350 ~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G  429 (544)
T KOG0124|consen  350 GTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISG  429 (544)
T ss_pred             CCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccC
Confidence                                       0                         00                         


Q ss_pred             -------------CCCccceeeecC--CCCCC---HHHHHHHhcccCceEEEEeCCCccc---------EEEEEEcCHHH
Q 003400          274 -------------DLNQGTLVVFNL--DPSVS---NEDLRQIFGAYGEVKEIRETPHKRH---------HKFIEFYDVRA  326 (823)
Q Consensus       274 -------------~~~~~tLfV~NL--p~~vt---eedL~~~Fs~fG~I~~iri~~~srG---------~aFVeF~d~e~  326 (823)
                                   ....+.+.++|+  |.+++   +.+|.+.+++||.|.+|.+.....+         .-||+|....+
T Consensus       430 ~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e  509 (544)
T KOG0124|consen  430 SSARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASE  509 (544)
T ss_pred             ccHHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhH
Confidence                         001135677787  45554   4688999999999999876433222         36999999999


Q ss_pred             HHHHHHHhCCCccCCceEEEEec
Q 003400          327 AEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       327 A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      +.+|+.+|+|+.++|+++..+..
T Consensus       510 ~~rak~ALdGRfFgGr~VvAE~Y  532 (544)
T KOG0124|consen  510 THRAKQALDGRFFGGRKVVAEVY  532 (544)
T ss_pred             HHHHHHhhccceecCceeehhhh
Confidence            99999999999999999986653

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.64  E-value=3.8e-15  Score=160.52  Aligned_cols=239  Identities=23%  Similarity=0.310  Sum_probs=169.8

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE------------EEeccCccCcccceeEeeecCccccc--ccccc--------
Q 003400          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM------------ELEGEPQESLSMSMSKISISDSASGN--GLLHY--------  172 (823)
Q Consensus       115 ~el~V~~Lp~~~~E~el~dlFs~~G~v------------~V~~d~~es~~~g~~~v~~~e~~~a~--~~~~~--------  172 (823)
                      .-+.+++||++++|.|+++++..||.|            +|++.+.+++..-...++-.......  -+..|        
T Consensus        29 kV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGknQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~sn~~~lkt  108 (492)
T KOG1190|consen   29 KVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQYSNHSELKT  108 (492)
T ss_pred             ceeEeccCCccccHHHHHHhcccccceeeeeeeccchhhhhhhcchhhhhheeecccccCccccCcceeehhhhHHHHhc
Confidence            568899999999999999999999987            66666666554311111100000000  00000        


Q ss_pred             -ccCC-------------C---CccccC--CCC-CCCCCC--cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCccc
Q 003400          173 -SVPN-------------G---AGTVAG--EHP-YGEHPS--RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG  230 (823)
Q Consensus       173 -~l~n-------------~---~~~~~~--~~~-~~e~~s--rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG  230 (823)
                       ...+             .   +.....  ... ....++  -+++|.|+-.-|+-+-|..+|++||.|..|.+..|..+
T Consensus       109 ~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~  188 (492)
T KOG1190|consen  109 DSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNG  188 (492)
T ss_pred             cCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccc
Confidence             0000             0   000000  000 111223  35688999999999999999999999999988888888


Q ss_pred             E-EEEEeCCHHHHHHHHHHhcCCcccc--ccccccccC----------CCCCC-------CC------------------
Q 003400          231 F-VMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSI----------PKDNP-------SD------------------  272 (823)
Q Consensus       231 ~-AFV~F~~~e~A~~Ai~~Lng~~l~g--r~L~V~~a~----------pk~~~-------~~------------------  272 (823)
                      | |+|+|.|.+.|..|..+|+|..|.+  +.|+|.|+.          .+.+.       ..                  
T Consensus       189 FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~  268 (492)
T KOG1190|consen  189 FQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVP  268 (492)
T ss_pred             hhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccc
Confidence            7 9999999999999999999988753  456665542          11100       00                  


Q ss_pred             ----------------------CCC--CccceeeecCCC-CCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHH
Q 003400          273 ----------------------KDL--NQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAA  327 (823)
Q Consensus       273 ----------------------~~~--~~~tLfV~NLp~-~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A  327 (823)
                                            -..  ....|.|.||.. .+|.+.|..+|+.||+|.+|++.-+++..|.|+|.|...|
T Consensus       269 ~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qA  348 (492)
T KOG1190|consen  269 AVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQA  348 (492)
T ss_pred             cccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHH
Confidence                                  000  024678888865 5899999999999999999998777778999999999999


Q ss_pred             HHHHHHhCCCccCCceEEEEecCCCc
Q 003400          328 EAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       328 ~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      +-|+..|+|..+.||+|+|.+++...
T Consensus       349 qLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  349 QLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             HHHHHHhhcceecCceEEEeeccCcc
Confidence            99999999999999999999998754

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.63  E-value=2.1e-15  Score=147.54  Aligned_cols=149  Identities=22%  Similarity=0.329  Sum_probs=127.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCC--cccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~k--srG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      +.+++|||+|||.++-+.||+++|-+||.|..|.+..+  ...||||+|++..+|+.||..-+|..+.|..|+|+|+..-
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            46799999999999999999999999999999986444  3479999999999999999999999999999999997543


Q ss_pred             CCCCC----------------------CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHH
Q 003400          268 DNPSD----------------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR  325 (823)
Q Consensus       268 ~~~~~----------------------~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e  325 (823)
                      .....                      ....+..+.|.+||.+-+++||+++..+-|.|....+..  .|++.|+|...+
T Consensus        84 r~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~r--Dg~GvV~~~r~e  161 (241)
T KOG0105|consen   84 RSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQR--DGVGVVEYLRKE  161 (241)
T ss_pred             CcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeec--ccceeeeeeehh
Confidence            21110                      111234899999999999999999999999999888753  568999999999


Q ss_pred             HHHHHHHHhCCCccC
Q 003400          326 AAEAALKSLNRSDIA  340 (823)
Q Consensus       326 ~A~kAl~~LnG~~i~  340 (823)
                      +.+-|++.|....+.
T Consensus       162 DMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  162 DMKYAVRKLDDQKFR  176 (241)
T ss_pred             hHHHHHHhhcccccc
Confidence            999999999877654

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.62  E-value=2.8e-16  Score=175.22  Aligned_cols=163  Identities=23%  Similarity=0.357  Sum_probs=139.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ..++..||+|+--|+..++..+|.++|+.+|.|..|.+     +.+++|.|||+|.|.+....|+. |.|..+.|.+|.|
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~v  252 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIV  252 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEe
Confidence            35667799999999999999999999999999999873     56799999999999999999996 9999999999999


Q ss_pred             cccCCCCCCCC----------CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHH
Q 003400          262 HFSIPKDNPSD----------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRA  326 (823)
Q Consensus       262 ~~a~pk~~~~~----------~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~  326 (823)
                      +.....++...          -..+-..|||+||...+++++|+.+|++||.|..|..     ++.++|||||+|.+.++
T Consensus       253 q~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~  332 (549)
T KOG0147|consen  253 QLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKED  332 (549)
T ss_pred             cccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHH
Confidence            87543322110          0111123999999999999999999999999999853     78899999999999999


Q ss_pred             HHHHHHHhCCCccCCceEEEEecC
Q 003400          327 AEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       327 A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      |.+|+..|||.+|.|+.|+|....
T Consensus       333 ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  333 ARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             HHHHHHHhccceecCceEEEEEee
Confidence            999999999999999999987653

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.59  E-value=2.4e-15  Score=162.80  Aligned_cols=161  Identities=19%  Similarity=0.402  Sum_probs=140.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..++|||++|+++++++.|++.|.+||+|..|.+     +++++||+||+|.+.+...+++.. ....|.|+.|.+..+.
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            6789999999999999999999999999999873     678999999999999999998873 5677999999999998


Q ss_pred             CCCCCCCCCC--CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 003400          266 PKDNPSDKDL--NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (823)
Q Consensus       266 pk~~~~~~~~--~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~  338 (823)
                      +.........  ...++||++|+.+++++++++.|.+||.|..+.+     +...++|+||.|++++.+.+++. ..-+.
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            8765443222  3568999999999999999999999998877743     45679999999999999999887 56789


Q ss_pred             cCCceEEEEecCCCc
Q 003400          339 IAGKRIKLEPSRPGG  353 (823)
Q Consensus       339 i~Gr~I~V~~s~~~~  353 (823)
                      |.|+.+.|..|.++.
T Consensus       163 ~~gk~vevkrA~pk~  177 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKE  177 (311)
T ss_pred             ecCceeeEeeccchh
Confidence            999999999998875

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.49  E-value=8.4e-13  Score=142.63  Aligned_cols=161  Identities=25%  Similarity=0.336  Sum_probs=137.4

Q ss_pred             CcEEEEcCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCCC
Q 003400          192 SRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP  270 (823)
Q Consensus       192 srtLfV~NLP~~-vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~~  270 (823)
                      +..|.|.||... +|.+.|..+|.-||+|.+|++....+--|+|+|.|...|+.|++.|+|..+.|++|+|.+++.....
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            578899999755 8999999999999999999987777789999999999999999999999999999999998643211


Q ss_pred             CCC-------------------------------CCCccceeeecCCCCCCHHHHHHHhcccCce-EEEEeCCCcccEEE
Q 003400          271 SDK-------------------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV-KEIRETPHKRHHKF  318 (823)
Q Consensus       271 ~~~-------------------------------~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I-~~iri~~~srG~aF  318 (823)
                      ..+                               .....+|.+.|+|.+++||+|+..|..-|.. +-.+..++.+.+|.
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            100                               0123589999999999999999999988755 55677777888999


Q ss_pred             EEEcCHHHHHHHHHHhCCCccCC-ceEEEEecCCC
Q 003400          319 IEFYDVRAAEAALKSLNRSDIAG-KRIKLEPSRPG  352 (823)
Q Consensus       319 VeF~d~e~A~kAl~~LnG~~i~G-r~I~V~~s~~~  352 (823)
                      +++.++|+|..|+..++.+.+++ ..|+|.|++..
T Consensus       457 ~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks~  491 (492)
T KOG1190|consen  457 PQLESVEEAIQALIDLHNHYLGENHHLRVSFSKST  491 (492)
T ss_pred             cccCChhHhhhhccccccccCCCCceEEEEeeccc
Confidence            99999999999999999999886 59999998753

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.47  E-value=5.7e-14  Score=146.09  Aligned_cols=145  Identities=21%  Similarity=0.339  Sum_probs=118.2

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE-EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYG  188 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v-~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~~~  188 (823)
                      +.++||++||...++.+++.||+++|.| +..      ..+.+.||++.+...+.    .+.+|.+.+..+++...+. +
T Consensus         2 ~~KLFIGNLp~~~~~~elr~lFe~ygkVlECD------IvKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSks-K   74 (346)
T KOG0109|consen    2 PVKLFIGNLPREATEQELRSLFEQYGKVLECD------IVKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKS-K   74 (346)
T ss_pred             ccchhccCCCcccchHHHHHHHHhhCceEeee------eecccceEEeecccccHHHHhhcccceecceEEEEEeccc-c
Confidence            4689999999999999999999999987 221      12345666666554433    3567777666655554433 3


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      ...+++|+|+||.+.++.+||+..|++||.|..|++   -++|+||.|.-.++|..|++.|++++|+|++++|+.+..+-
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdi---vkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDI---VKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL  151 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeee---ecceeEEEEeeccchHHHHhcccccccccceeeeeeecccc
Confidence            567899999999999999999999999999999976   56899999999999999999999999999999999986543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.46  E-value=3.6e-13  Score=135.51  Aligned_cols=150  Identities=20%  Similarity=0.335  Sum_probs=116.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE--eCCCc----ccEEEEEeCCHHHHHHHHHHhcCCccc---cccccc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY--TACKH----RGFVMISYYDIRAARTAMRALQNKPLR---RRKLDI  261 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~--~~~ks----rG~AFV~F~~~e~A~~Ai~~Lng~~l~---gr~L~V  261 (823)
                      .-|||||.+||.++...||..+|..|--.+.+.  .+.+.    +.+|||.|.+.++|..|+.+|||.+|.   +..|+|
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            359999999999999999999999986655543  33333    379999999999999999999999985   677888


Q ss_pred             cccCCCCCCCC----------------------C-C-------------------------C------------------
Q 003400          262 HFSIPKDNPSD----------------------K-D-------------------------L------------------  275 (823)
Q Consensus       262 ~~a~pk~~~~~----------------------~-~-------------------------~------------------  275 (823)
                      ++++......+                      . .                         .                  
T Consensus       113 ElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~  192 (284)
T KOG1457|consen  113 ELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPS  192 (284)
T ss_pred             eehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCc
Confidence            77642110000                      0 0                         0                  


Q ss_pred             ----------------CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCC-CcccEEEEEEcCHHHHHHHHHHhCCCc
Q 003400          276 ----------------NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP-HKRHHKFIEFYDVRAAEAALKSLNRSD  338 (823)
Q Consensus       276 ----------------~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~-~srG~aFVeF~d~e~A~kAl~~LnG~~  338 (823)
                                      .-.||||-||..+++|++|+++|+.|-....+++.. .....||++|++.+.|..|+..|+|..
T Consensus       193 a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~  272 (284)
T KOG1457|consen  193 ANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNL  272 (284)
T ss_pred             ccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcce
Confidence                            003899999999999999999999997655555532 234589999999999999999999887


Q ss_pred             cC
Q 003400          339 IA  340 (823)
Q Consensus       339 i~  340 (823)
                      |.
T Consensus       273 ~s  274 (284)
T KOG1457|consen  273 LS  274 (284)
T ss_pred             ec
Confidence            63

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.45  E-value=8.4e-14  Score=142.60  Aligned_cols=150  Identities=26%  Similarity=0.431  Sum_probs=129.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCC---
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN---  269 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~---  269 (823)
                      ..+||++||+.+.+.+|..+|..||.|..|.+   ..||+||+|.+..+|..|+..|++..|.+..+.|+|+.....   
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            46899999999999999999999999999865   357899999999999999999999999998899999874210   


Q ss_pred             ---CC----------CCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC
Q 003400          270 ---PS----------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR  336 (823)
Q Consensus       270 ---~~----------~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG  336 (823)
                         ..          .-......|+|.|+...+.+.+|.++|.++|.+.....   ..+++||+|...++|.+|+..|+|
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               00          00123457899999999999999999999999955544   578999999999999999999999


Q ss_pred             CccCCceEEEEe
Q 003400          337 SDIAGKRIKLEP  348 (823)
Q Consensus       337 ~~i~Gr~I~V~~  348 (823)
                      ..+.++.|++..
T Consensus       156 ~~~~~~~l~~~~  167 (216)
T KOG0106|consen  156 KKLNGRRISVEK  167 (216)
T ss_pred             hhhcCceeeecc
Confidence            999999999943

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.42  E-value=7.3e-13  Score=129.57  Aligned_cols=78  Identities=24%  Similarity=0.453  Sum_probs=71.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+||+.++++++|+++|++||.|++|++     +++++|||||+|.+.++|++|++.||+..|.|+.|+|++++
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            4568999999999999999999999999999876     45679999999999999999999999999999999999987


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      ++.
T Consensus       113 ~~~  115 (144)
T PLN03134        113 DRP  115 (144)
T ss_pred             cCC
Confidence            643

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.41  E-value=9.4e-13  Score=128.79  Aligned_cols=81  Identities=23%  Similarity=0.437  Sum_probs=73.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ...+++|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
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            446789999999999999999999999999999874     567899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 003400          264 SIPKDN  269 (823)
Q Consensus       264 a~pk~~  269 (823)
                      +.++..
T Consensus       111 a~~~~~  116 (144)
T PLN03134        111 ANDRPS  116 (144)
T ss_pred             CCcCCC
Confidence            876543

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.36  E-value=2.2e-11  Score=130.33  Aligned_cols=232  Identities=19%  Similarity=0.279  Sum_probs=170.2

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE------------EEeccCccCcccceeEeeecCcc---ccc--cccccccCCC
Q 003400          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM------------ELEGEPQESLSMSMSKISISDSA---SGN--GLLHYSVPNG  177 (823)
Q Consensus       115 ~el~V~~Lp~~~~E~el~dlFs~~G~v------------~V~~d~~es~~~g~~~v~~~e~~---~a~--~~~~~~l~n~  177 (823)
                      --+.|++|-..+.|.++.+..+.||.|            .|+|++.+++...   ++|....   .+.  .+.+|.... 
T Consensus        32 pvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r~alvefedi~~akn~---Vnfaa~n~i~i~gq~Al~NyStsq-  107 (494)
T KOG1456|consen   32 PVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKRQALVEFEDIEGAKNC---VNFAADNQIYIAGQQALFNYSTSQ-  107 (494)
T ss_pred             ceEEEeccccccchhHHHHHHhcCCceEEEEeccccceeeeeeccccchhhh---eehhccCcccccCchhhcccchhh-
Confidence            457899999999999999999999987            3444444433211   1111110   000  111111111 


Q ss_pred             CccccCCCCCCCCCCcEEEEcCCC--CCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccc
Q 003400          178 AGTVAGEHPYGEHPSRTLFVRNIN--SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (823)
Q Consensus       178 ~~~~~~~~~~~e~~srtLfV~NLP--~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~  255 (823)
                        .+.........++..|.+.=|.  ..+|.+-|..+....|+|.+|.+..+..-.|+|+|++.+.|++|..+|||..|.
T Consensus       108 --~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIY  185 (494)
T KOG1456|consen  108 --CIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIY  185 (494)
T ss_pred             --hhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhccccccc
Confidence              1111122334456677666554  568999999999999999999988887778999999999999999999999885


Q ss_pred             --cccccccccCCCCCCCC-------------------------------------------------------------
Q 003400          256 --RRKLDIHFSIPKDNPSD-------------------------------------------------------------  272 (823)
Q Consensus       256 --gr~L~V~~a~pk~~~~~-------------------------------------------------------------  272 (823)
                        -.+|+|+|++|.+....                                                             
T Consensus       186 sGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P  265 (494)
T KOG1456|consen  186 SGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPP  265 (494)
T ss_pred             ccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCC
Confidence              46899999876421000                                                             


Q ss_pred             -------CC----------CCccceeeecCCCC-CCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHh
Q 003400          273 -------KD----------LNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL  334 (823)
Q Consensus       273 -------~~----------~~~~tLfV~NLp~~-vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~L  334 (823)
                             .+          .....+.|.+|+.. +.-+.|..+|..||.|.+|++...+.|-|.||+.|..+.++|+..|
T Consensus       266 ~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hL  345 (494)
T KOG1456|consen  266 SRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHL  345 (494)
T ss_pred             CCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHh
Confidence                   00          00136888999864 6788999999999999999998888899999999999999999999


Q ss_pred             CCCccCCceEEEEecCCC
Q 003400          335 NRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       335 nG~~i~Gr~I~V~~s~~~  352 (823)
                      |+..+-|.+|.|.+++..
T Consensus       346 nn~~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  346 NNIPLFGGKLNVCVSKQN  363 (494)
T ss_pred             ccCccccceEEEeecccc
Confidence            999999999999998643

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.35  E-value=1.3e-11  Score=131.59  Aligned_cols=163  Identities=15%  Similarity=0.252  Sum_probs=132.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEE--------EE----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRT--------LY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRR  257 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~--------v~----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr  257 (823)
                      .-++.|||.|||.++|.+++.++|++||-|..        |+    ..++-+|=|.+.|...+++..|+..|++..|+|+
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            34567999999999999999999999998765        22    2567889999999999999999999999999999


Q ss_pred             cccccccCCCCCC----------------------------------CCCCCCccceeeecCCC----CCC-------HH
Q 003400          258 KLDIHFSIPKDNP----------------------------------SDKDLNQGTLVVFNLDP----SVS-------NE  292 (823)
Q Consensus       258 ~L~V~~a~pk~~~----------------------------------~~~~~~~~tLfV~NLp~----~vt-------ee  292 (823)
                      .|+|+.|.-....                                  ..+....++|.|+|+=.    ..+       ++
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            9999876421100                                  00111236899998832    222       46


Q ss_pred             HHHHHhcccCceEEEEe-CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          293 DLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       293 dL~~~Fs~fG~I~~iri-~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      +|++-+.+||.|.+|.+ ..++.|.+-|.|.+.++|..||+.|+|+.++||+|..+...-+
T Consensus       292 dl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  292 DLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            77888999999999976 4567899999999999999999999999999999998876554

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.31  E-value=5.1e-11  Score=129.56  Aligned_cols=70  Identities=23%  Similarity=0.292  Sum_probs=64.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri--~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ++|+|+|||.+.|++.|++-|..||.|..+.|  .++++  +.|+|.++++|++|+..|||..+.|+.|+|.|.
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~Gksk--GVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSK--GVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhhccCCcc--ceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            48999999999999999999999999999887  55555  499999999999999999999999999999873

>PF00076 RRM_1: RNA recognition motif

Probab=99.28  E-value=1.1e-11  Score=104.44  Aligned_cols=66  Identities=36%  Similarity=0.634  Sum_probs=61.5

Q ss_pred             eeeecCCCCCCHHHHHHHhcccCceEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 003400          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       280 LfV~NLp~~vteedL~~~Fs~fG~I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      |||+|||.++|+++|+++|++||.|..+++.    +..+++|||+|.+.++|++|++.|+|..+.|++|+
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            7999999999999999999999999988653    45789999999999999999999999999999985

(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 ....

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.26  E-value=7.1e-12  Score=122.50  Aligned_cols=77  Identities=30%  Similarity=0.475  Sum_probs=72.8

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      .++|||+||+..+++.||+.+|..||.|..|.+.....|||||||+|+.+|+.|+..|+|+.|.|..|+|+++.-..
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            56899999999999999999999999999999887889999999999999999999999999999999999987543

>PF00076 RRM_1: RNA recognition motif

Probab=99.25  E-value=1.2e-11  Score=104.15  Aligned_cols=66  Identities=29%  Similarity=0.603  Sum_probs=61.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          195 LFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       195 LfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      |||+|||.++|+++|+++|++||.|..+.+    .++.+++|||+|.+.++|++|++.|+|..+.|++|+
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            799999999999999999999999998874    356889999999999999999999999999998874

(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 ....

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.23  E-value=1.1e-11  Score=121.32  Aligned_cols=77  Identities=26%  Similarity=0.512  Sum_probs=72.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      -.++|||+||+..+++.||+.+|..||.|.+|++.....|||||+|+++.+|+.|+..|+|+.|.|..|.|+.+.-.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~   85 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGR   85 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCC
Confidence            36899999999999999999999999999999999899999999999999999999999999999999999987543

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.21  E-value=1.3e-10  Score=131.93  Aligned_cols=162  Identities=17%  Similarity=0.355  Sum_probs=126.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .....+||++||..+++.+++++.+.||.+....     .++-++||||.+|.+......|+..|+|..+.+++|.|+.+
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            3457899999999999999999999999988765     24679999999999999999999999999999999999887


Q ss_pred             CCCCCCCCC--------------------CCCccceeeecCC--CCC-CH-------HHHHHHhcccCceEEEEeCC---
Q 003400          265 IPKDNPSDK--------------------DLNQGTLVVFNLD--PSV-SN-------EDLRQIFGAYGEVKEIRETP---  311 (823)
Q Consensus       265 ~pk~~~~~~--------------------~~~~~tLfV~NLp--~~v-te-------edL~~~Fs~fG~I~~iri~~---  311 (823)
                      .........                    ......|.+.|+-  .++ .+       |+++..+.+||.|..|.+..   
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            543221110                    1111233333331  111 11       55677788999999997632   


Q ss_pred             -----CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          312 -----HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       312 -----~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                           ...|..||+|.+.+++++|..+|+|.++.|+.|...|...
T Consensus       447 ~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  447 DENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             CCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence                 1357799999999999999999999999999999988754

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.19  E-value=6e-11  Score=128.79  Aligned_cols=157  Identities=13%  Similarity=0.231  Sum_probs=123.1

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc---cccccccCCCCccccCCC--
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAGTVAGEH--  185 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~---~~~~~~l~n~~~~~~~~~--  185 (823)
                      .++++|++|.++.+++.|.+.|+++|.|   .|+.|....+.+++.+++|.+.....   ......+.........+.  
T Consensus         6 ~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r   85 (311)
T KOG4205|consen    6 SGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSR   85 (311)
T ss_pred             CcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccCc
Confidence            4789999999999999999999999987   78888889999999999999554332   112222333322211111  


Q ss_pred             -----CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccc
Q 003400          186 -----PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (823)
Q Consensus       186 -----~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~  255 (823)
                           ........+|||++||.+++++++++.|++||.|..+.     .+.+.+||+||.|.+.+.+++++. ...+.|.
T Consensus        86 ~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~  164 (311)
T KOG4205|consen   86 EDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFN  164 (311)
T ss_pred             ccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeec
Confidence                 11222356999999999999999999999999888775     367789999999999999999988 5778899


Q ss_pred             cccccccccCCCCCCC
Q 003400          256 RRKLDIHFSIPKDNPS  271 (823)
Q Consensus       256 gr~L~V~~a~pk~~~~  271 (823)
                      ++.+.|..|.|++...
T Consensus       165 gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  165 GKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             CceeeEeeccchhhcc
Confidence            9999999999876543

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.17  E-value=1.4e-10  Score=120.54  Aligned_cols=119  Identities=27%  Similarity=0.444  Sum_probs=101.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      .++|||+|||.++++++|+++|.+||.|..+.+     +++++|||||+|.+.++|..|+..+++..|.|++|.|.++.+
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            699999999999999999999999999987762     578999999999999999999999999999999999999542


Q ss_pred             ----CCCCC----------------CCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC
Q 003400          267 ----KDNPS----------------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET  310 (823)
Q Consensus       267 ----k~~~~----------------~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~  310 (823)
                          .....                ........+++.+++..++..++...|..+|.+..+.+.
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  258 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLP  258 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeecc
Confidence                22111                011223589999999999999999999999999777653

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.16  E-value=3.5e-11  Score=118.38  Aligned_cols=155  Identities=16%  Similarity=0.260  Sum_probs=124.7

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccC--CC
Q 003400          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAG--EH  185 (823)
Q Consensus       115 ~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~--~~  185 (823)
                      .++||++|+..+.+..++++|-+.|.|   .+..|.......|++|+.|...+.+.    -++...+-+..+++..  ..
T Consensus        10 ~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~   89 (203)
T KOG0131|consen   10 ATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAH   89 (203)
T ss_pred             ceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecccc
Confidence            579999999999999999999999986   55666677778899999998877665    3333444455443322  22


Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEE---E---eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccc
Q 003400          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL---Y---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  259 (823)
Q Consensus       186 ~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v---~---~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L  259 (823)
                      ...-....+|||+||.+.++|..|.++|+.||.+...   -   .++..+|||||.|.+.+.+.+|+..++|..+..+++
T Consensus        90 ~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~i  169 (203)
T KOG0131|consen   90 QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPI  169 (203)
T ss_pred             cccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCce
Confidence            2233455899999999999999999999999987652   1   367889999999999999999999999999999999


Q ss_pred             cccccCCCCC
Q 003400          260 DIHFSIPKDN  269 (823)
Q Consensus       260 ~V~~a~pk~~  269 (823)
                      .|.|+..+..
T Consensus       170 tv~ya~k~~~  179 (203)
T KOG0131|consen  170 TVSYAFKKDT  179 (203)
T ss_pred             EEEEEEecCC
Confidence            9999875543

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.16  E-value=2.4e-10  Score=126.85  Aligned_cols=157  Identities=18%  Similarity=0.279  Sum_probs=121.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE---eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~---~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      .-.|-+++||+++|++||.++|+.++ |+.+.   .+++..|-|||+|.+.+++++|++ .+...+..+-|.|--+.+++
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~e   87 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGAE   87 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCcc
Confidence            35677899999999999999999986 55554   467889999999999999999999 47777777777776554332


Q ss_pred             CC-------CCCCCCccceeeecCCCCCCHHHHHHHhcccCceEE-EEe----CCCcccEEEEEEcCHHHHHHHHHHhCC
Q 003400          269 NP-------SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRE----TPHKRHHKFIEFYDVRAAEAALKSLNR  336 (823)
Q Consensus       269 ~~-------~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~-iri----~~~srG~aFVeF~d~e~A~kAl~~LnG  336 (823)
                      ..       .........|.+++||+.+|++||.++|+..-.|.. |-+    .+++.|-|||+|++.+.|++|+.. |.
T Consensus        88 ~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hr  166 (510)
T KOG4211|consen   88 ADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HR  166 (510)
T ss_pred             ccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HH
Confidence            21       111235568999999999999999999997654444 211    345678899999999999999984 56


Q ss_pred             CccCCceEEEEecCC
Q 003400          337 SDIAGKRIKLEPSRP  351 (823)
Q Consensus       337 ~~i~Gr~I~V~~s~~  351 (823)
                      ..|.-+-|.|-.+..
T Consensus       167 e~iGhRYIEvF~Ss~  181 (510)
T KOG4211|consen  167 ENIGHRYIEVFRSSR  181 (510)
T ss_pred             HhhccceEEeehhHH
Confidence            677777788766543

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.16  E-value=7.9e-11  Score=124.78  Aligned_cols=99  Identities=18%  Similarity=0.295  Sum_probs=80.3

Q ss_pred             cCCccccccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe---CCCcccEEEEEEcCHHH
Q 003400          250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRA  326 (823)
Q Consensus       250 ng~~l~gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri---~~~srG~aFVeF~d~e~  326 (823)
                      ++....|..+.+..+..    +......++|+|+|||+...+-||+.+|++||+|.+|.|   ...+||||||+|++.+|
T Consensus        73 ~~~~t~g~~~~~~~st~----s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~d  148 (376)
T KOG0125|consen   73 NGAPTDGQPIQTQPSTN----SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPAD  148 (376)
T ss_pred             CCCCCCCCccccCCCCc----CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhh
Confidence            44455566655543321    112223468999999999999999999999999999976   34589999999999999


Q ss_pred             HHHHHHHhCCCccCCceEEEEecCCC
Q 003400          327 AEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       327 A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      |++|..+|||..|.||+|+|..+..+
T Consensus       149 adRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  149 ADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHHHHHhhcceeeceEEEEeccchh
Confidence            99999999999999999999988764

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.13  E-value=1.2e-10  Score=119.34  Aligned_cols=77  Identities=25%  Similarity=0.428  Sum_probs=72.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir-----i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|.|.||+.++++++|+++|.+||.|..|.     .++.++|||||.|.++++|++||..|||.-++.-.|+|+|++
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            457899999999999999999999999999884     488899999999999999999999999999999999999999


Q ss_pred             CC
Q 003400          351 PG  352 (823)
Q Consensus       351 ~~  352 (823)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            86

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

Probab=99.13  E-value=5.5e-11  Score=133.73  Aligned_cols=163  Identities=27%  Similarity=0.403  Sum_probs=132.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      ...+.++|+|-|||..|++++|+.+|+.||+|+.|+.+...+|.+||+|+|+++|++|+++|++.++.|+.|+.......
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            35678999999999999999999999999999999988889999999999999999999999999999998883322110


Q ss_pred             CC------------------CCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHH
Q 003400          268 DN------------------PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEA  329 (823)
Q Consensus       268 ~~------------------~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~k  329 (823)
                      ..                  .....-.+..+++- |++..+...++.+|..+|.+.. +.++.....-|++|.+..++..
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            00                  00111123455555 9999999889999999999988 8888777789999999999977


Q ss_pred             HHHHhCCCccCCceEEEEecCCCc
Q 003400          330 ALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       330 Al~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ++... |..+.++...+.++.+.+
T Consensus       229 ~~~~~-G~~~s~~~~v~t~S~~~g  251 (549)
T KOG4660|consen  229 SEPRG-GFLISNSSGVITFSGPGG  251 (549)
T ss_pred             cccCC-ceecCCCCceEEecCCCc
Confidence            77744 778888887788887744

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.13  E-value=1.6e-10  Score=118.48  Aligned_cols=78  Identities=22%  Similarity=0.434  Sum_probs=73.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +++.+|-|.||+.+++|++|++||.+||.|.+|+     .++.++|||||.|++.++|.+||+.|+|.-+..--|+|+|+
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            4678999999999999999999999999999998     37899999999999999999999999999999999999999


Q ss_pred             CCC
Q 003400          265 IPK  267 (823)
Q Consensus       265 ~pk  267 (823)
                      +|+
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            875

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.12  E-value=8e-10  Score=118.56  Aligned_cols=171  Identities=19%  Similarity=0.293  Sum_probs=134.9

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHh--cCCcccccccc
Q 003400          183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL--QNKPLRRRKLD  260 (823)
Q Consensus       183 ~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~L--ng~~l~gr~L~  260 (823)
                      ...+....++-.|.|++|-..++|.+|.+-++.||.|..|.. ...+..|.|+|+|++.|+.|+.--  +...+.|+.--
T Consensus        22 ~~dphk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~-~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al  100 (494)
T KOG1456|consen   22 NADPHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTC-MPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQAL  100 (494)
T ss_pred             CCCCCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEe-ccccceeeeeeccccchhhheehhccCcccccCchhh
Confidence            344555667889999999999999999999999999998854 446678999999999999998733  33445677777


Q ss_pred             ccccCCCCCCCC--C-CCCcccee--eecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhC
Q 003400          261 IHFSIPKDNPSD--K-DLNQGTLV--VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  335 (823)
Q Consensus       261 V~~a~pk~~~~~--~-~~~~~tLf--V~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~Ln  335 (823)
                      +.|+..+.....  + ....+.|.  |-|--+.+|.+-|..++.+.|+|.+|.|..+..-.|.|||++.+.|++|..+||
T Consensus       101 ~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alN  180 (494)
T KOG1456|consen  101 FNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALN  180 (494)
T ss_pred             cccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcc
Confidence            777754332211  1 11223343  445557899999999999999999999887765679999999999999999999


Q ss_pred             CCccCC--ceEEEEecCCCcc
Q 003400          336 RSDIAG--KRIKLEPSRPGGA  354 (823)
Q Consensus       336 G~~i~G--r~I~V~~s~~~~~  354 (823)
                      |..|..  ++|+|+|++|..-
T Consensus       181 GADIYsGCCTLKIeyAkP~rl  201 (494)
T KOG1456|consen  181 GADIYSGCCTLKIEYAKPTRL  201 (494)
T ss_pred             cccccccceeEEEEecCccee
Confidence            998874  8899999998753

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.12  E-value=7.7e-11  Score=109.82  Aligned_cols=76  Identities=26%  Similarity=0.475  Sum_probs=70.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      .+.++||||+||...++|++|.+||+++|+|+.|.+     +....|||||+|.+.++|+.|++.+++..+..++|.+.|
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            357899999999999999999999999999999863     455779999999999999999999999999999999988


Q ss_pred             c
Q 003400          264 S  264 (823)
Q Consensus       264 a  264 (823)
                      -
T Consensus       113 D  113 (153)
T KOG0121|consen  113 D  113 (153)
T ss_pred             c
Confidence            5

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.12  E-value=1.9e-10  Score=103.60  Aligned_cols=78  Identities=28%  Similarity=0.485  Sum_probs=72.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      ..++.|||+|||.++|.++..++|.+||.|+.|++  +...+|.|||.|+++.+|++|++.|+|..+.++.|.|.|..+.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            45789999999999999999999999999999985  5668999999999999999999999999999999999987654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.12  E-value=2e-10  Score=120.90  Aligned_cols=74  Identities=20%  Similarity=0.413  Sum_probs=67.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCC--CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP--HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~--~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      .++|||+||++.+|+++|+++|+.||+|++|++..  ..+|||||+|.+.++|+.||. |||..|.|+.|+|.+++.
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            46899999999999999999999999999998743  357999999999999999996 999999999999999764

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.12  E-value=2.4e-10  Score=102.90  Aligned_cols=81  Identities=23%  Similarity=0.404  Sum_probs=74.0

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri--~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      ..-|||+|||+++|.|+..++|++||.|..||+  +...+|-|||.|+|..+|.+|++.|+|..+.++-|.|-+-.+...
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~~   97 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPEDA   97 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHHH
Confidence            457999999999999999999999999999997  556789999999999999999999999999999999999888765


Q ss_pred             cch
Q 003400          355 RRN  357 (823)
Q Consensus       355 r~~  357 (823)
                      .+.
T Consensus        98 ~~~  100 (124)
T KOG0114|consen   98 FKL  100 (124)
T ss_pred             HHH
Confidence            443

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.10  E-value=1.2e-10  Score=108.63  Aligned_cols=76  Identities=21%  Similarity=0.345  Sum_probs=69.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir-----i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..+||||+||...++||+|.++|+++|+|+.|.     .+....|||||+|...++|+.|++.++|..++.+.|+|.|..
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            457999999999999999999999999999984     355678999999999999999999999999999999999864


Q ss_pred             C
Q 003400          351 P  351 (823)
Q Consensus       351 ~  351 (823)
                      -
T Consensus       115 G  115 (153)
T KOG0121|consen  115 G  115 (153)
T ss_pred             c
Confidence            3

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.08  E-value=3.1e-10  Score=119.45  Aligned_cols=76  Identities=18%  Similarity=0.292  Sum_probs=68.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC--CCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA--CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~--~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      .++|||+|||+.+|+++|+++|+.||+|.+|++.  ...+|||||+|.+.++|+.|+. |+|..|.|+.|.|.++....
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            5899999999999999999999999999999853  3367999999999999999996 99999999999999886443

>smart00362 RRM_2 RNA recognition motif

Probab=99.07  E-value=5.3e-10  Score=92.87  Aligned_cols=69  Identities=32%  Similarity=0.643  Sum_probs=63.0

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEeCCC---cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH---KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~---srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~  347 (823)
                      +|+|+|||..+++++|+++|++||.|..+++...   .+++|||+|.+.++|++|++.++|..+.|++|+|+
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            5899999999999999999999999999876433   47999999999999999999999999999999874

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.06  E-value=4.3e-10  Score=95.50  Aligned_cols=66  Identities=35%  Similarity=0.644  Sum_probs=58.8

Q ss_pred             eeeecCCCCCCHHHHHHHhcccCceEEEEeCC----CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 003400          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP----HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       280 LfV~NLp~~vteedL~~~Fs~fG~I~~iri~~----~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      |||+|||.++++++|+++|+.||.|..+++..    ..+++|||+|.+.++|.+|++.++|..+.|+.|+
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            79999999999999999999999999997643    3579999999999999999999999999999885

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 ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.05  E-value=3.9e-10  Score=119.58  Aligned_cols=79  Identities=23%  Similarity=0.418  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..--++|+|.|||...-|-||+.+|++||.|.+|.+   ..-+|||+||+|++++||++|.++|+|..+.||+|.|..+.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            334579999999999999999999999999999884   45689999999999999999999999999999999999886


Q ss_pred             CC
Q 003400          266 PK  267 (823)
Q Consensus       266 pk  267 (823)
                      ++
T Consensus       173 ar  174 (376)
T KOG0125|consen  173 AR  174 (376)
T ss_pred             hh
Confidence            54

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.04  E-value=4.5e-10  Score=95.36  Aligned_cols=66  Identities=23%  Similarity=0.545  Sum_probs=58.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC----CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          195 LFVRNINSNVEDSELRALFEQYGDIRTLYTA----CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       195 LfV~NLP~~vteeeLr~lFs~fG~I~~v~~~----~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      |||+|||+++++++|+++|+.||.|..+.+.    ++.+++|||+|.+.++|++|++.+++..+.|+.|+
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            7999999999999999999999999998742    34689999999999999999999988999998764

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 ....

>PF13893 RRM_5: RNA recognition motif

Probab=99.03  E-value=8.1e-10  Score=90.14  Aligned_cols=56  Identities=34%  Similarity=0.594  Sum_probs=51.6

Q ss_pred             HHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          294 LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       294 L~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      |+++|++||+|.++++....+++|||+|.+.++|++|++.|||..+.|++|+|+||
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            68999999999999987666799999999999999999999999999999999986

(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 ....

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.00  E-value=1.9e-09  Score=116.05  Aligned_cols=160  Identities=13%  Similarity=0.206  Sum_probs=112.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcC-----CC--EEEEE-eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQY-----GD--IRTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~f-----G~--I~~v~-~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      .-.|-+++||.++++.|+.++|..-     |.  |.-|. ..++..|-|||.|..+++|+.|+.+ +...+..|-|.+-.
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFR  239 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFR  239 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHH
Confidence            3466789999999999999999622     22  22333 2677889999999999999999985 33333333222211


Q ss_pred             cC-----------------C-----C-----CCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCc-eEE--EEe----
Q 003400          264 SI-----------------P-----K-----DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKE--IRE----  309 (823)
Q Consensus       264 a~-----------------p-----k-----~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~-I~~--iri----  309 (823)
                      +.                 +     -     ...........+|.+++||++.+.|+|-++|..|-. |+.  |.+    
T Consensus       240 STaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~  319 (508)
T KOG1365|consen  240 STAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG  319 (508)
T ss_pred             HhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC
Confidence            10                 0     0     000111223568999999999999999999998863 222  322    


Q ss_pred             CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          310 TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       310 ~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      .++..|-|||+|.+.++|..|....+.+...++-|+|-.+.-.
T Consensus       320 qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~e  362 (508)
T KOG1365|consen  320 QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVE  362 (508)
T ss_pred             CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHH
Confidence            3566789999999999999999988888888888888766443

>smart00362 RRM_2 RNA recognition motif

Probab=99.00  E-value=1.3e-09  Score=90.58  Aligned_cols=69  Identities=30%  Similarity=0.580  Sum_probs=62.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC---CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTA---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       194 tLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~---~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      +|||+|||..+++++|+++|++||+|..+.+.   +..+|+|||+|.+.++|++|++.+++..+.|++|.|+
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            58999999999999999999999999998753   3357999999999999999999999999999888763

>PLN03213 repressor of silencing 3; Provisional

Probab=98.99  E-value=7.7e-10  Score=121.92  Aligned_cols=77  Identities=25%  Similarity=0.352  Sum_probs=69.0

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCC-CcccEEEEEEcCH--HHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP-HKRHHKFIEFYDV--RAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~-~srG~aFVeF~d~--e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ...+|||+||.+++++++|+.+|..||.|.+|.+.. ..||||||+|.+.  .++.+||..|||.++.|+.|+|..+++.
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP~   88 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKEH   88 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccHH
Confidence            446899999999999999999999999999986531 2389999999987  7899999999999999999999999874

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.98  E-value=1.6e-09  Score=113.72  Aligned_cols=92  Identities=30%  Similarity=0.413  Sum_probs=79.9

Q ss_pred             ccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCC
Q 003400          263 FSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRS  337 (823)
Q Consensus       263 ~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir-----i~~~srG~aFVeF~d~e~A~kAl~~LnG~  337 (823)
                      ...|..++......-+||||.-|+++++|.+|+..|+.||.|+.|+     ++++++|||||+|++..+...|.+..+|.
T Consensus        87 ~wdP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~  166 (335)
T KOG0113|consen   87 LWDPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGI  166 (335)
T ss_pred             hcCCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCc
Confidence            3455555544455668999999999999999999999999999996     47899999999999999999999999999


Q ss_pred             ccCCceEEEEecCCCcc
Q 003400          338 DIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       338 ~i~Gr~I~V~~s~~~~~  354 (823)
                      .|+|+.|.|.+-+-...
T Consensus       167 ~Idgrri~VDvERgRTv  183 (335)
T KOG0113|consen  167 KIDGRRILVDVERGRTV  183 (335)
T ss_pred             eecCcEEEEEecccccc
Confidence            99999999999766543

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.97  E-value=6.5e-10  Score=109.46  Aligned_cols=78  Identities=31%  Similarity=0.492  Sum_probs=70.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeC--CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~--~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ..++|||+|||.++.+.||+++|-+||.|..|.+.  .....||||+|++..+|+.||..-+|..++|++|+|+|.+...
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr   84 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGR   84 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCC
Confidence            46789999999999999999999999999999763  3345799999999999999999999999999999999998664

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.97  E-value=7.5e-10  Score=110.84  Aligned_cols=80  Identities=26%  Similarity=0.465  Sum_probs=73.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      .......+|.|-||..-++.++|+.+|++||.|.+|++     +..++|||||.|.+..+|+.|+++|+|..|.|+.|.|
T Consensus         8 Pdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrV   87 (256)
T KOG4207|consen    8 PDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRV   87 (256)
T ss_pred             CCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeee
Confidence            34445689999999999999999999999999999984     7889999999999999999999999999999999999


Q ss_pred             cccCC
Q 003400          262 HFSIP  266 (823)
Q Consensus       262 ~~a~p  266 (823)
                      ++|.-
T Consensus        88 q~ary   92 (256)
T KOG4207|consen   88 QMARY   92 (256)
T ss_pred             hhhhc
Confidence            98853

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.97  E-value=9.6e-10  Score=112.44  Aligned_cols=77  Identities=23%  Similarity=0.444  Sum_probs=66.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      .+..-++|||++|++.+..++|++.|++||+|.+..     .++++|||+||+|.|.++|.+|++. ..-.|.||+..+.
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccc
Confidence            344558999999999999999999999999998875     3789999999999999999999985 4456888888777


Q ss_pred             ccC
Q 003400          263 FSI  265 (823)
Q Consensus       263 ~a~  265 (823)
                      .+.
T Consensus        87 lA~   89 (247)
T KOG0149|consen   87 LAS   89 (247)
T ss_pred             hhh
Confidence            653

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.95  E-value=7.3e-10  Score=110.92  Aligned_cols=76  Identities=33%  Similarity=0.543  Sum_probs=70.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ..+|.|-||-+-++.++|+.+|++||.|-+|.|     +..++|||||.|.+..+|+.|+.+|+|..++|+.|+|++++-
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            458999999999999999999999999999865     778999999999999999999999999999999999998865


Q ss_pred             C
Q 003400          352 G  352 (823)
Q Consensus       352 ~  352 (823)
                      +
T Consensus        93 g   93 (256)
T KOG4207|consen   93 G   93 (256)
T ss_pred             C
Confidence            4

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.92  E-value=9e-09  Score=114.62  Aligned_cols=229  Identities=14%  Similarity=0.162  Sum_probs=150.7

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcEEEeccCccCcccceeEeeecCccccc---cccccccCCCCc----------cc
Q 003400          115 DDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAG----------TV  181 (823)
Q Consensus       115 ~el~V~~Lp~~~~E~el~dlFs~~G~v~V~~d~~es~~~g~~~v~~~e~~~a~---~~~~~~l~n~~~----------~~  181 (823)
                      -.+-+++|||++++.|+.++|++++--.|.+-..+++..|-++|.+...+.++   +...-.+.+.-+          +.
T Consensus        11 ~~vr~rGLPwsat~~ei~~Ff~~~~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~e~d~   90 (510)
T KOG4211|consen   11 FEVRLRGLPWSATEKEILDFFSNCGIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGAEADW   90 (510)
T ss_pred             eEEEecCCCccccHHHHHHHHhcCceeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCccccc
Confidence            44667999999999999999999987666666677888898999888776554   111111222200          00


Q ss_pred             cC--CCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEE-EE----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcc
Q 003400          182 AG--EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT-LY----TACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (823)
Q Consensus       182 ~~--~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~-v~----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l  254 (823)
                      ..  ..+......-+|-+++||..||++||.++|+-.-.|.. +.    ...+..|=|||+|.+.+.|++|+.. +...|
T Consensus        91 ~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~i  169 (510)
T KOG4211|consen   91 VMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENI  169 (510)
T ss_pred             cccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhh
Confidence            00  01112235578999999999999999999996644433 11    2355778899999999999999974 43444


Q ss_pred             cccccccccc-----------------------CCCCCCC---------------C------------------------
Q 003400          255 RRRKLDIHFS-----------------------IPKDNPS---------------D------------------------  272 (823)
Q Consensus       255 ~gr~L~V~~a-----------------------~pk~~~~---------------~------------------------  272 (823)
                      ..+-|.|-.+                       .+.....               .                        
T Consensus       170 GhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~g  249 (510)
T KOG4211|consen  170 GHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFG  249 (510)
T ss_pred             ccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccc
Confidence            3333322110                       0000000               0                        


Q ss_pred             -----CC---------------------CCc-cceeeecCCCCCCHHHHHHHhcccCce---EEEEeCCCcccEEEEEEc
Q 003400          273 -----KD---------------------LNQ-GTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFY  322 (823)
Q Consensus       273 -----~~---------------------~~~-~tLfV~NLp~~vteedL~~~Fs~fG~I---~~iri~~~srG~aFVeF~  322 (823)
                           ++                     ... ..++.++||+..++.++...|+..-.+   ..|..+++..|-|+|+|.
T Consensus       250 s~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~~v~i~ig~dGr~TGEAdveF~  329 (510)
T KOG4211|consen  250 SYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPYRVHIEIGPDGRATGEADVEFA  329 (510)
T ss_pred             ccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCceeEEEEeCCCCccCCcceeecc
Confidence                 00                     000 257778999999999999999976433   223336677889999999


Q ss_pred             CHHHHHHHHHHhCCCccCCceEE
Q 003400          323 DVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       323 d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      +.++|..|+-. ++..+..+-|.
T Consensus       330 t~edav~Amsk-d~anm~hrYVE  351 (510)
T KOG4211|consen  330 TGEDAVGAMGK-DGANMGHRYVE  351 (510)
T ss_pred             cchhhHhhhcc-CCcccCcceee
Confidence            99999999873 55555554444

>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=98.92  E-value=5.5e-09  Score=87.17  Aligned_cols=70  Identities=39%  Similarity=0.672  Sum_probs=64.0

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEeCCC----cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH----KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~----srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      +|+|+|||..+++++|+++|+.||.|..+.+...    .+++|||+|.+.++|..|++.+++..+.|+.|.|.+
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            5899999999999999999999999999876443    378999999999999999999999999999999864

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).

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.91  E-value=3.9e-09  Score=109.65  Aligned_cols=73  Identities=22%  Similarity=0.322  Sum_probs=66.3

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeC--CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~--~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..+|||+||++.+|+++|+++|+.||+|.+|++.  +..+++|||+|.++++|+.|+. |+|..|.+++|.|....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            4589999999999999999999999999999874  3456899999999999999995 99999999999998764

>PLN03213 repressor of silencing 3; Provisional

Probab=98.90  E-value=2.9e-09  Score=117.51  Aligned_cols=78  Identities=14%  Similarity=0.217  Sum_probs=69.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-CCCcccEEEEEeCCH--HHHHHHHHHhcCCccccccccccccCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-ACKHRGFVMISYYDI--RAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-~~ksrG~AFV~F~~~--e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ....+|||+||++++++++|+.+|..||.|.+|.+ ....||||||+|.+.  .++.+||..|+|..+.|+.|+|..|+|
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            34579999999999999999999999999999984 223489999999987  789999999999999999999998865


Q ss_pred             C
Q 003400          267 K  267 (823)
Q Consensus       267 k  267 (823)
                      .
T Consensus        88 ~   88 (759)
T PLN03213         88 H   88 (759)
T ss_pred             H
Confidence            3

>smart00360 RRM RNA recognition motif

Probab=98.90  E-value=4.5e-09  Score=86.78  Aligned_cols=66  Identities=33%  Similarity=0.649  Sum_probs=59.7

Q ss_pred             eecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 003400          282 VFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (823)
Q Consensus       282 V~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~  347 (823)
                      |+|||..+++++|+++|++||.|..+++.     +.++++|||+|.+.++|.+|++.|++..+.|+.|+|+
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            67999999999999999999999998763     3447899999999999999999999999999999874

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.89  E-value=1.1e-09  Score=110.38  Aligned_cols=80  Identities=28%  Similarity=0.509  Sum_probs=74.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||++|..++++.-|...|-+||.|+.|.+     +.+.||||||+|.-.|+|..||..||+.++.||.|+|.+++
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            4579999999999999999999999999999975     56789999999999999999999999999999999999999


Q ss_pred             CCccc
Q 003400          351 PGGAR  355 (823)
Q Consensus       351 ~~~~r  355 (823)
                      |...+
T Consensus        89 P~kik   93 (298)
T KOG0111|consen   89 PEKIK   93 (298)
T ss_pred             Ccccc
Confidence            97644

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.88  E-value=4.3e-09  Score=110.67  Aligned_cols=78  Identities=27%  Similarity=0.491  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ..+|-+||||.-|+.+++|.+|+..|+.||+|+.|.     ++++++|||||+|++..+...|.+..+|..|.|+.|.|.
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            447889999999999999999999999999999986     589999999999999999999999999999999999998


Q ss_pred             ccC
Q 003400          263 FSI  265 (823)
Q Consensus       263 ~a~  265 (823)
                      +-.
T Consensus       177 vER  179 (335)
T KOG0113|consen  177 VER  179 (335)
T ss_pred             ecc
Confidence            754

>PF13893 RRM_5: RNA recognition motif

Probab=98.87  E-value=3.4e-09  Score=86.49  Aligned_cols=56  Identities=23%  Similarity=0.591  Sum_probs=50.9

Q ss_pred             HHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          209 LRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       209 Lr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      |+++|++||+|..+.+..+.+++|||+|.+.++|++|++.|+|..+.|++|+|.||
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            68999999999999876555799999999999999999999999999999999885

(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 ....

>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=7.4e-09  Score=86.36  Aligned_cols=70  Identities=34%  Similarity=0.652  Sum_probs=63.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCC----CcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       194 tLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~----ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      +|+|+|||..+++++|+++|+.||.|..+.+..    ..+++|||+|.+.++|..|++.+++..+.++.+.|.+
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            589999999999999999999999999987533    2479999999999999999999999999999888764

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).

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.86  E-value=6e-09  Score=108.30  Aligned_cols=73  Identities=16%  Similarity=0.189  Sum_probs=66.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..+|||+||++.+|+++|+++|+.||+|.+|++  .++.+++|||+|+++++|+.|+. |+|..|.+++|.|....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            479999999999999999999999999999985  45567899999999999999996 99999999999887643

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.85  E-value=3.5e-09  Score=108.41  Aligned_cols=77  Identities=27%  Similarity=0.350  Sum_probs=67.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      .-++|||++|+++++.|+|++.|++||+|.+..+     ++++||||||+|.|.++|.+|++.- .-.|+||+..|.++.
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            4468999999999999999999999999998743     7889999999999999999999953 468999999998876


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      -+.
T Consensus        90 lg~   92 (247)
T KOG0149|consen   90 LGG   92 (247)
T ss_pred             hcC
Confidence            643

>smart00360 RRM RNA recognition motif

Probab=98.84  E-value=7e-09  Score=85.63  Aligned_cols=66  Identities=32%  Similarity=0.584  Sum_probs=59.1

Q ss_pred             EcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          197 VRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       197 V~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      |+|||..+++++|+++|++||.|..+.+     +++++|+|||+|.+.++|.+|++.+++..+.|+.|.|+
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            5799999999999999999999998874     34557999999999999999999999999999888763

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.83  E-value=5e-09  Score=98.57  Aligned_cols=80  Identities=23%  Similarity=0.417  Sum_probs=72.1

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ......|||.++....++++|.+.|..||+|+.+.+     ++-.+|||+|+|.+.++|++|+.+|||..+.|..|.|.|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            345568999999999999999999999999999964     667799999999999999999999999999999999998


Q ss_pred             cCCCc
Q 003400          349 SRPGG  353 (823)
Q Consensus       349 s~~~~  353 (823)
                      +--++
T Consensus       149 ~Fv~g  153 (170)
T KOG0130|consen  149 CFVKG  153 (170)
T ss_pred             EEecC
Confidence            75443

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.83  E-value=2.1e-09  Score=108.34  Aligned_cols=81  Identities=26%  Similarity=0.507  Sum_probs=75.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...|+|||++|..+|+|.-|...|-.||+|..|.+     +.++||||||+|...|+|..||..|++.++.|+.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            35799999999999999999999999999999973     6789999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 003400          265 IPKDNP  270 (823)
Q Consensus       265 ~pk~~~  270 (823)
                      .|.+..
T Consensus        88 kP~kik   93 (298)
T KOG0111|consen   88 KPEKIK   93 (298)
T ss_pred             CCcccc
Confidence            986543

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.80  E-value=1.3e-08  Score=105.74  Aligned_cols=75  Identities=36%  Similarity=0.625  Sum_probs=70.0

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ..+|||+|||.++++++|+++|..||.|..+++     ++..+|+|||+|.+.++|..|+..++|..+.|++|.|.++..
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            589999999999999999999999999988754     567899999999999999999999999999999999999764

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.77  E-value=5.2e-08  Score=109.33  Aligned_cols=157  Identities=20%  Similarity=0.346  Sum_probs=112.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-------CCCccc---EEEEEeCCHHHHHHHHHHhcCCcccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-------ACKHRG---FVMISYYDIRAARTAMRALQNKPLRRRK  258 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-------~~ksrG---~AFV~F~~~e~A~~Ai~~Lng~~l~gr~  258 (823)
                      ..-+++|||++||++++|++|...|..||.+..=+-       ....+|   |+|+.|+++..++.-+.+..-   ....
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            345789999999999999999999999998764331       122455   999999999999887775432   2223


Q ss_pred             ccccccCCCCC-------------------CCCCCCCccceeeecCCCCCCHHHHHHHhc-ccCceEEEEeC-----CCc
Q 003400          259 LDIHFSIPKDN-------------------PSDKDLNQGTLVVFNLDPSVSNEDLRQIFG-AYGEVKEIRET-----PHK  313 (823)
Q Consensus       259 L~V~~a~pk~~-------------------~~~~~~~~~tLfV~NLp~~vteedL~~~Fs-~fG~I~~iri~-----~~s  313 (823)
                      ++++.+.+...                   ....-...+||||++||..++.++|..+|. -||.|..+-|.     +..
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            33322222111                   111122457999999999999999999999 79999998653     346


Q ss_pred             ccEEEEEEcCHHHHHHHHHH----hCCCccCCceEEEEec
Q 003400          314 RHHKFIEFYDVRAAEAALKS----LNRSDIAGKRIKLEPS  349 (823)
Q Consensus       314 rG~aFVeF~d~e~A~kAl~~----LnG~~i~Gr~I~V~~s  349 (823)
                      +|-|-|.|.+..+-.+||.+    |+..+| .|+|+|+..
T Consensus       413 kGaGRVtFsnqqsYi~AIsarFvql~h~d~-~KRVEIkPY  451 (520)
T KOG0129|consen  413 KGAGRVTFSNQQAYIKAISARFVQLDHTDI-DKRVEIKPY  451 (520)
T ss_pred             CCcceeeecccHHHHHHHhhheEEEecccc-ceeeeecce
Confidence            88899999999999999873    222233 246666543

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.75  E-value=5.2e-09  Score=122.96  Aligned_cols=159  Identities=21%  Similarity=0.365  Sum_probs=138.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC----CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA----CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~----~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...++|||++||+..+++.+|+..|..+|.|..|.+.    +....|+||.|.+...+-+|...+.+..|....+++.+.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            3467899999999999999999999999999998753    334459999999999999999999999998778788777


Q ss_pred             CCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCC--c
Q 003400          265 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--K  342 (823)
Q Consensus       265 ~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G--r  342 (823)
                      .++      ....+.++|++|...+....|...|..||.|..|.+. +..-||+|.|.+...|+.|...|.|..|+|  +
T Consensus       449 ~~k------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~-hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~  521 (975)
T KOG0112|consen  449 QPK------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR-HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPR  521 (975)
T ss_pred             ccc------cccceeeccCCCCCCChHHHHHHHhhccCcceeeecc-cCCcceeeecccCccchhhHHHHhcCcCCCCCc
Confidence            552      2345689999999999999999999999999999874 345699999999999999999999999987  8


Q ss_pred             eEEEEecCCCcc
Q 003400          343 RIKLEPSRPGGA  354 (823)
Q Consensus       343 ~I~V~~s~~~~~  354 (823)
                      +|.|.|+.....
T Consensus       522 r~rvdla~~~~~  533 (975)
T KOG0112|consen  522 RLRVDLASPPGA  533 (975)
T ss_pred             ccccccccCCCC
Confidence            899999887653

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.74  E-value=1.8e-08  Score=114.20  Aligned_cols=79  Identities=27%  Similarity=0.389  Sum_probs=73.6

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ..+||+|+|+++++++|..+|+..|.|.++++     +++.+||||++|.+.++|++|++.|||.++.|++|+|.|+...
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            78999999999999999999999999999964     7889999999999999999999999999999999999999876


Q ss_pred             cccc
Q 003400          353 GARR  356 (823)
Q Consensus       353 ~~r~  356 (823)
                      ..+.
T Consensus        99 ~~~~  102 (435)
T KOG0108|consen   99 KNAE  102 (435)
T ss_pred             chhH
Confidence            6543

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.70  E-value=2.5e-08  Score=103.25  Aligned_cols=97  Identities=20%  Similarity=0.348  Sum_probs=81.9

Q ss_pred             cccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHH
Q 003400          256 RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAAL  331 (823)
Q Consensus       256 gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl  331 (823)
                      +|+|.|+.+......    .++++|||+-|.+.-.|||++.+|.+||.|.+|.+    .+.+||+|||.|.+..+|..||
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            467788877544332    25679999999999999999999999999999976    4668999999999999999999


Q ss_pred             HHhCCC-ccCC--ceEEEEecCCCcccc
Q 003400          332 KSLNRS-DIAG--KRIKLEPSRPGGARR  356 (823)
Q Consensus       332 ~~LnG~-~i~G--r~I~V~~s~~~~~r~  356 (823)
                      ..|+|. .+.|  ..|.|+|+...++|.
T Consensus        78 ~aLHgSqTmpGASSSLVVK~ADTdkER~  105 (371)
T KOG0146|consen   78 NALHGSQTMPGASSSLVVKFADTDKERT  105 (371)
T ss_pred             HHhcccccCCCCccceEEEeccchHHHH
Confidence            999996 5655  789999998877654

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.69  E-value=2.2e-08  Score=113.40  Aligned_cols=76  Identities=24%  Similarity=0.438  Sum_probs=71.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      +.|||+|||.+++|++|.++|+..|.|.+++     .+++.+||||++|.+.++|.+|++.|+|..+.|++|+|.|+...
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            8999999999999999999999999999987     47899999999999999999999999999999999999998544


Q ss_pred             C
Q 003400          268 D  268 (823)
Q Consensus       268 ~  268 (823)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            3

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.68  E-value=2.9e-09  Score=104.81  Aligned_cols=76  Identities=22%  Similarity=0.390  Sum_probs=69.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ....-|||+|||+++||.||.-+|++||+|..|.+     +|+++||||+.|+|.++..-|+..|||..|.||.|+|...
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            34568999999999999999999999999999853     8899999999999999999999999999999999999854


Q ss_pred             C
Q 003400          350 R  350 (823)
Q Consensus       350 ~  350 (823)
                      .
T Consensus       113 ~  113 (219)
T KOG0126|consen  113 S  113 (219)
T ss_pred             c
Confidence            3

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.68  E-value=3.3e-08  Score=101.08  Aligned_cols=76  Identities=29%  Similarity=0.597  Sum_probs=71.1

Q ss_pred             cceeeecCCCCCCHHHHHH----HhcccCceEEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          278 GTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~----~Fs~fG~I~~iri--~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      .||||.||+..+..++|+.    +|++||+|.+|..  +++.+|.|||.|++.+.|..|+++|+|..+.|+.++|.||+.
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    9999999999975  567899999999999999999999999999999999999987


Q ss_pred             Cc
Q 003400          352 GG  353 (823)
Q Consensus       352 ~~  353 (823)
                      +.
T Consensus        90 ~s   91 (221)
T KOG4206|consen   90 DS   91 (221)
T ss_pred             cc
Confidence            65

>smart00361 RRM_1 RNA recognition motif

Probab=98.65  E-value=6.7e-08  Score=82.78  Aligned_cols=56  Identities=32%  Similarity=0.500  Sum_probs=50.0

Q ss_pred             HHHHHHHhc----ccCceEEEE---e---C--CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEE
Q 003400          291 NEDLRQIFG----AYGEVKEIR---E---T--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL  346 (823)
Q Consensus       291 eedL~~~Fs----~fG~I~~ir---i---~--~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V  346 (823)
                      +++|+++|+    +||.|.+|.   +   +  +.++|+|||+|.+.++|.+|++.|||+.+.|+.|++
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    999999884   2   2  667999999999999999999999999999999986

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.63  E-value=3.8e-08  Score=92.71  Aligned_cols=78  Identities=18%  Similarity=0.467  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...-.|||.++...++|++|.+.|..||+|+.+.+     ++-.+|||+|+|++.++|++|+.++||..|.+++|.|.|+
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            34468999999999999999999999999999873     6678999999999999999999999999999999999997


Q ss_pred             CCC
Q 003400          265 IPK  267 (823)
Q Consensus       265 ~pk  267 (823)
                      .-+
T Consensus       150 Fv~  152 (170)
T KOG0130|consen  150 FVK  152 (170)
T ss_pred             Eec
Confidence            543

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.63  E-value=4.1e-09  Score=103.79  Aligned_cols=76  Identities=20%  Similarity=0.432  Sum_probs=70.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .++.-|||+|||.+.||.||.-+|++||+|..|.     .+++++||||+.|+|.++...|+..|+|..|.||.|+|...
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            3578899999999999999999999999999986     38999999999999999999999999999999999999765


Q ss_pred             C
Q 003400          265 I  265 (823)
Q Consensus       265 ~  265 (823)
                      .
T Consensus       113 ~  113 (219)
T KOG0126|consen  113 S  113 (219)
T ss_pred             c
Confidence            3

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.62  E-value=7.6e-08  Score=109.75  Aligned_cols=165  Identities=19%  Similarity=0.349  Sum_probs=131.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcC-----------C-CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQY-----------G-DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR  256 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~f-----------G-~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g  256 (823)
                      ....+.++|+++|..++++....+|..-           | .|..+.+ +..+.||||+|.+.++|..|+. +++..+.|
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~-n~~~nfa~ie~~s~~~at~~~~-~~~~~f~g  249 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQL-NLEKNFAFIEFRSISEATEAMA-LDGIIFEG  249 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee-cccccceeEEecCCCchhhhhc-ccchhhCC
Confidence            3456899999999999999999999753           3 3666644 6678999999999999999998 78888888


Q ss_pred             ccccccccCCCC-------------------CCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCC
Q 003400          257 RKLDIHFSIPKD-------------------NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPH  312 (823)
Q Consensus       257 r~L~V~~a~pk~-------------------~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~  312 (823)
                      .++++.--....                   ...........++|++||..+++.+++++...||.++..+.     ++.
T Consensus       250 ~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~  329 (500)
T KOG0120|consen  250 RPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGN  329 (500)
T ss_pred             CCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccccccc
Confidence            877654311100                   00011122358999999999999999999999998877643     467


Q ss_pred             cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCccc
Q 003400          313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  355 (823)
Q Consensus       313 srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~r  355 (823)
                      ++||||.+|.+......|+..|||..+.+++|.|..+..+...
T Consensus       330 skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~  372 (500)
T KOG0120|consen  330 SKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASN  372 (500)
T ss_pred             ccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchh
Confidence            8999999999999999999999999999999999998876543

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.60  E-value=6.1e-08  Score=112.52  Aligned_cols=77  Identities=30%  Similarity=0.528  Sum_probs=71.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~  269 (823)
                      +|||||+.|+.+++|.||.++|+.||+|.+|.+ ...+|||||.+....+|.+|+.+|.+..+.++.|+|.|+.-+..
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            689999999999999999999999999999975 45799999999999999999999999999999999999976543

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.53  E-value=1.7e-07  Score=109.01  Aligned_cols=80  Identities=29%  Similarity=0.397  Sum_probs=74.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCccc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  355 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~r  355 (823)
                      ..+||||+.|+..+++.||..+|+.||.|.+|.+. .++++|||.+..+.+|.+|+.+|+...+.++.|+|.|+..++-+
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li-~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~k  498 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI-PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPK  498 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeec-cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcc
Confidence            34799999999999999999999999999999886 46899999999999999999999999999999999999998877


Q ss_pred             c
Q 003400          356 R  356 (823)
Q Consensus       356 ~  356 (823)
                      .
T Consensus       499 s  499 (894)
T KOG0132|consen  499 S  499 (894)
T ss_pred             h
Confidence            5

>smart00361 RRM_1 RNA recognition motif

Probab=98.46  E-value=2.9e-07  Score=78.87  Aligned_cols=56  Identities=20%  Similarity=0.374  Sum_probs=49.9

Q ss_pred             HHHHHHHhh----cCCCEEEEE---e---C--CCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          206 DSELRALFE----QYGDIRTLY---T---A--CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       206 eeeLr~lFs----~fG~I~~v~---~---~--~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      +++|+++|+    +||.|.+|.   +   +  +.++|||||+|.+.++|.+|++.|+|..+.|+.|.+
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            678899998    999999884   2   2  668999999999999999999999999999999875

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.44  E-value=3.1e-07  Score=98.72  Aligned_cols=83  Identities=23%  Similarity=0.430  Sum_probs=72.1

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHh-cCCccccccccc
Q 003400          183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDI  261 (823)
Q Consensus       183 ~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~L-ng~~l~gr~L~V  261 (823)
                      -..+..+...++|||++|-..++|.+|++.|.+||+|+++.+.. .+++|||+|.+.++|+.|.+++ +...|.|++|.|
T Consensus       219 ~lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~-~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  219 TLEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP-RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             ccCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec-ccccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            35566677789999999999999999999999999999997543 5679999999999999998875 445578999999


Q ss_pred             cccCC
Q 003400          262 HFSIP  266 (823)
Q Consensus       262 ~~a~p  266 (823)
                      .|..+
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99987

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.41  E-value=2.4e-07  Score=93.97  Aligned_cols=143  Identities=20%  Similarity=0.309  Sum_probs=115.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ...+||||.|+-..|+|+-|.++|-+-|+|..|.+    ..+.+ ||||.|.++-...-|++.++|..+.++.+.+.+-.
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            35699999999999999999999999999999974    23334 99999999999999999999999999998887532


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 003400          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (823)
Q Consensus       266 pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G  341 (823)
                      -..        ..-     |+..++++.+...|+.-|.+..+|+    .+.++.++|+.+....+.-.|+....+....-
T Consensus        86 G~s--------hap-----ld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~  152 (267)
T KOG4454|consen   86 GNS--------HAP-----LDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELFQ  152 (267)
T ss_pred             CCC--------cch-----hhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcCC
Confidence            110        111     5667899999999999999988875    35578899999998888888888777666554


Q ss_pred             ceEEE
Q 003400          342 KRIKL  346 (823)
Q Consensus       342 r~I~V  346 (823)
                      +++.+
T Consensus       153 ~~~~~  157 (267)
T KOG4454|consen  153 KKVTI  157 (267)
T ss_pred             CCccc
Confidence            44443

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.38  E-value=7.1e-08  Score=113.34  Aligned_cols=140  Identities=14%  Similarity=0.222  Sum_probs=120.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ..++||+||+..+.+.+|...|..+|.+..+.     ..++-+|+|||.|..+++|.+|+....+..+.           
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g-----------  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG-----------  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh-----------
Confidence            35889999999999999999999999887765     35778899999999999999999854444333           


Q ss_pred             CCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCc
Q 003400          267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  342 (823)
Q Consensus       267 k~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr  342 (823)
                                ...|+|.|.|+..|.++|+.++..+|.+.+.++    .++.+|.|+|.|.+..+|.+++...++..+.-+
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                      236999999999999999999999999999864    467789999999999999999998888888777


Q ss_pred             eEEEEecCCC
Q 003400          343 RIKLEPSRPG  352 (823)
Q Consensus       343 ~I~V~~s~~~  352 (823)
                      .+.|..+.+.
T Consensus       806 ~~~v~vsnp~  815 (881)
T KOG0128|consen  806 NGEVQVSNPE  815 (881)
T ss_pred             CccccccCCc
Confidence            8888776653

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.37  E-value=6.9e-07  Score=96.05  Aligned_cols=78  Identities=35%  Similarity=0.526  Sum_probs=68.5

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHH-hCCCccCCceEEEEecCC
Q 003400          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS-LNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       273 ~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~-LnG~~i~Gr~I~V~~s~~  351 (823)
                      ++..-.+|||++|...+++.+|+++|.+||+|++|++... +++|||+|.++++|+.|..+ +|...|+|++|+|.|+++
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            3445579999999999999999999999999999998754 56999999999999998764 455689999999999988

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.32  E-value=6.3e-07  Score=96.16  Aligned_cols=77  Identities=27%  Similarity=0.426  Sum_probs=70.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      +.+.|||--|.+-+++++|.-||+.||.|.+|.+     ++.+-.||||+|++.+++++|.-.|++..|++++|.|.|+.
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            4578999999999999999999999999999864     56677899999999999999999999999999999999986


Q ss_pred             CC
Q 003400          351 PG  352 (823)
Q Consensus       351 ~~  352 (823)
                      .-
T Consensus       318 SV  319 (479)
T KOG0415|consen  318 SV  319 (479)
T ss_pred             hh
Confidence            53

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.26  E-value=1.2e-06  Score=95.04  Aligned_cols=164  Identities=20%  Similarity=0.276  Sum_probs=128.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...+++|++++...+.+.++..++..+|.+..+.     -...++|++.|.|...+.+..|+.......+.++.+.....
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            4578999999999999999999999999766554     24568999999999999999999954434555554444333


Q ss_pred             CCCCCCC------CCCCCcccee-eecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHH
Q 003400          265 IPKDNPS------DKDLNQGTLV-VFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALK  332 (823)
Q Consensus       265 ~pk~~~~------~~~~~~~tLf-V~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~  332 (823)
                      .......      .......+++ |.+|+..+++++|+..|..+|.|..+++     ++..+++|+|+|.+...+..|+.
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            2221100      0111223555 9999999999999999999999999976     45678999999999999999999


Q ss_pred             HhCCCccCCceEEEEecCCCcc
Q 003400          333 SLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       333 ~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      . +...+.++.+.|.+..+...
T Consensus       246 ~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  246 D-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             c-ccCcccCcccccccCCCCcc
Confidence            7 88899999999999887643

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.21  E-value=1e-06  Score=91.21  Aligned_cols=129  Identities=17%  Similarity=0.181  Sum_probs=100.9

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCCCC--CCCCCccceeeecCCCCCCHHHHHHHhcccC
Q 003400          225 ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS--DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG  302 (823)
Q Consensus       225 ~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~~~--~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG  302 (823)
                      ...-++++|+.|.....-.++-..-+++.+.-.++++.-.....++.  +.+.++.+||++.|..+++++.|...|.+|-
T Consensus       136 p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfp  215 (290)
T KOG0226|consen  136 PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFP  215 (290)
T ss_pred             CCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCcccccCccccceeecccccccccHHHHHHHHHhcc
Confidence            45677899999999888888877667777766666554433333332  3345667999999999999999999999985


Q ss_pred             ce-----EEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          303 EV-----KEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       303 ~I-----~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ..     ..-.-+++++||+||.|.+..++..|+++|+|+.++.+.|++.-+..+.
T Consensus       216 sf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  216 SFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             chhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHh
Confidence            33     2223478999999999999999999999999999999999987665543

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.19  E-value=1.5e-06  Score=93.36  Aligned_cols=78  Identities=21%  Similarity=0.419  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..|...|||..|.+-+|+++|.-+|+.||.|.+|.+     ++.+..||||+|++.+++++|.-+|++..|..+.|.|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            357899999999999999999999999999999873     677888999999999999999999999999999999999


Q ss_pred             cCC
Q 003400          264 SIP  266 (823)
Q Consensus       264 a~p  266 (823)
                      +..
T Consensus       316 SQS  318 (479)
T KOG0415|consen  316 SQS  318 (479)
T ss_pred             hhh
Confidence            853

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.18  E-value=2.2e-06  Score=88.55  Aligned_cols=148  Identities=16%  Similarity=0.203  Sum_probs=96.3

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE----------EEeccCccCcccceeEeeecCcc---ccccccc---cccCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM----------ELEGEPQESLSMSMSKISISDSA---SGNGLLH---YSVPNG  177 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v----------~V~~d~~es~~~g~~~v~~~e~~---~a~~~~~---~~l~n~  177 (823)
                      |.+++|++|++...+.++..+|..+|.+          +|++++.-.+..++-.+.-.+..   .+.+...   ......
T Consensus         1 m~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~~   80 (216)
T KOG0106|consen    1 MPRVYIGRLPYRARERDVERFFKGYGKIPDADMKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRGRP   80 (216)
T ss_pred             CCceeecccCCccchhHHHHHHhhccccccceeecccceeccCchhhhhcccchhcCceecceeeeeecccccccccCCC
Confidence            4578999999999999999999999986          34444332222221111100000   0000000   000000


Q ss_pred             -Ccc---ccCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 003400          178 -AGT---VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP  253 (823)
Q Consensus       178 -~~~---~~~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~  253 (823)
                       .+.   ............+.|+|.+++..+.+.+|.+.|.++|.+.....   ..+++||+|.+.++|.+|+..|++..
T Consensus        81 ~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~~~  157 (216)
T KOG0106|consen   81 RGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEKLDGKK  157 (216)
T ss_pred             CCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchhccchh
Confidence             000   00000111334578999999999999999999999999954432   67899999999999999999999999


Q ss_pred             ccccccccccc
Q 003400          254 LRRRKLDIHFS  264 (823)
Q Consensus       254 l~gr~L~V~~a  264 (823)
                      +.++.|.+...
T Consensus       158 ~~~~~l~~~~~  168 (216)
T KOG0106|consen  158 LNGRRISVEKN  168 (216)
T ss_pred             hcCceeeeccc
Confidence            99999998543

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.16  E-value=1.5e-05  Score=85.84  Aligned_cols=153  Identities=14%  Similarity=0.201  Sum_probs=103.0

Q ss_pred             hcCccccccccCCCCCChHHHHHhhcCCCcE-----------EEeccCccCcccceeEeeecCccccc----cccccccC
Q 003400          111 AGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM-----------ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVP  175 (823)
Q Consensus       111 ~~v~~el~V~~Lp~~~~E~el~dlFs~~G~v-----------~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~  175 (823)
                      ..+-+.+||.+||.+++..+..++|+.||.|           .|=.+ ..+.-+|-+...+...+.+.    -+....+.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd-~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRD-NQGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEec-CCCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            3456789999999999999999999999987           22111 22444555555554443222    11111111


Q ss_pred             CCC-----------------cccc-----------------C-----CCCCCCCCCcEEEEcCCCC----CCC-------
Q 003400          176 NGA-----------------GTVA-----------------G-----EHPYGEHPSRTLFVRNINS----NVE-------  205 (823)
Q Consensus       176 n~~-----------------~~~~-----------------~-----~~~~~e~~srtLfV~NLP~----~vt-------  205 (823)
                      +..                 .+..                 +     ..+...+..++|.++|+=.    ..+       
T Consensus       210 g~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dl  289 (382)
T KOG1548|consen  210 GKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDL  289 (382)
T ss_pred             CcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHH
Confidence            110                 0000                 0     1123344568999999832    122       


Q ss_pred             HHHHHHHhhcCCCEEEEEeC-CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          206 DSELRALFEQYGDIRTLYTA-CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       206 eeeLr~lFs~fG~I~~v~~~-~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +++|++-.++||.|.+|.+. ....|.+-|.|.+.++|..||+.|+|+.|.||.|.....
T Consensus       290 kedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~  349 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIW  349 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEe
Confidence            45677778999999999864 456799999999999999999999999999999987765

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.15  E-value=5.2e-06  Score=84.03  Aligned_cols=78  Identities=18%  Similarity=0.264  Sum_probs=71.3

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhccc-CceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAY-GEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~f-G~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ...+.++|..+|.-+.+.++...|.+| |.|..+|+     +|.++|||||+|++.+.|.-|-+.||++.+.++.|.|.+
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            345689999999999999999999999 77777765     788999999999999999999999999999999999999


Q ss_pred             cCCC
Q 003400          349 SRPG  352 (823)
Q Consensus       349 s~~~  352 (823)
                      -.+.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            8776

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.10  E-value=7e-06  Score=83.09  Aligned_cols=79  Identities=18%  Similarity=0.369  Sum_probs=70.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcC-CCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQY-GDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~f-G~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      .......+||..+|.-+.+.+|..+|.+| |.|+.++     .++.++|||||+|++.+.|+-|-+.||+..+.++-|.|
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            34456789999999999999999999999 6777776     37889999999999999999999999999999999999


Q ss_pred             cccCC
Q 003400          262 HFSIP  266 (823)
Q Consensus       262 ~~a~p  266 (823)
                      ++-.|
T Consensus       125 ~vmpp  129 (214)
T KOG4208|consen  125 HVMPP  129 (214)
T ss_pred             EEeCc
Confidence            98754

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.02  E-value=1.5e-05  Score=81.27  Aligned_cols=79  Identities=22%  Similarity=0.304  Sum_probs=66.3

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEE--EeCCCc----ccEEEEEEcCHHHHHHHHHHhCCCccC---CceEEEE
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHK----RHHKFIEFYDVRAAEAALKSLNRSDIA---GKRIKLE  347 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~i--ri~~~s----rG~aFVeF~d~e~A~kAl~~LnG~~i~---Gr~I~V~  347 (823)
                      -+||||.+||.++...||..+|..|-.-+.+  +.+.+.    +-+|||.|.+.++|..|+++|||..++   +..|+|+
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            4799999999999999999999998544443  444433    368999999999999999999999887   6899999


Q ss_pred             ecCCCccc
Q 003400          348 PSRPGGAR  355 (823)
Q Consensus       348 ~s~~~~~r  355 (823)
                      +++....+
T Consensus       114 lAKSNtK~  121 (284)
T KOG1457|consen  114 LAKSNTKR  121 (284)
T ss_pred             ehhcCccc
Confidence            99876543

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.99  E-value=4.6e-05  Score=86.16  Aligned_cols=150  Identities=19%  Similarity=0.204  Sum_probs=105.8

Q ss_pred             CCCCCCcchhHhhhcCccccccccCCCCCChHHHHHhhcCCCcEEEeccC-cc----Ccccc---eeEeeecCccccccc
Q 003400           98 IGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEP-QE----SLSMS---MSKISISDSASGNGL  169 (823)
Q Consensus        98 i~n~LP~d~d~l~~~v~~el~V~~Lp~~~~E~el~dlFs~~G~v~V~~d~-~e----s~~~g---~~~v~~~e~~~a~~~  169 (823)
                      ..+.+|.. ..-...+..++||++||++++|.++...|..||.+.|+-.. .+    ...+|   ++++-|.++..+..+
T Consensus       244 ~~~~~~~~-~~~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~L  322 (520)
T KOG0129|consen  244 WSGSLPPR-GYRSPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSL  322 (520)
T ss_pred             hccccCCC-CCCccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHH
Confidence            33455544 34445567999999999999999999999999999876552 11    12345   999988877544311


Q ss_pred             cccc----------cCCCCccc---------------cCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhh-cCCCEEEEE
Q 003400          170 LHYS----------VPNGAGTV---------------AGEHPYGEHPSRTLFVRNINSNVEDSELRALFE-QYGDIRTLY  223 (823)
Q Consensus       170 ~~~~----------l~n~~~~~---------------~~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs-~fG~I~~v~  223 (823)
                      ..-.          +.....+.               ..+....-++.+||||++||.-++.+||..+|+ -||.|..+-
T Consensus       323 l~aC~~~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaG  402 (520)
T KOG0129|consen  323 LSACSEGEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVG  402 (520)
T ss_pred             HHHHhhcccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEE
Confidence            1100          11110000               112223456889999999999999999999999 899998876


Q ss_pred             e--C---CCcccEEEEEeCCHHHHHHHHHH
Q 003400          224 T--A---CKHRGFVMISYYDIRAARTAMRA  248 (823)
Q Consensus       224 ~--~---~ksrG~AFV~F~~~e~A~~Ai~~  248 (823)
                      +  .   +-.+|-|-|.|.+..+=.+||.+
T Consensus       403 IDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  403 IDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             eccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            4  2   23679999999999999999984

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=97.98  E-value=1.1e-05  Score=91.05  Aligned_cols=75  Identities=24%  Similarity=0.457  Sum_probs=68.2

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      .+|+|.+|...+...+|+.+|++||+|+-.++     ++..+.|+||++.+.++|.++|..|+.+++.|+.|.|+.+++.
T Consensus       406 RNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNE  485 (940)
T KOG4661|consen  406 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNE  485 (940)
T ss_pred             cceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccC
Confidence            58999999999999999999999999988765     3446789999999999999999999999999999999988763

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.98  E-value=6.5e-07  Score=97.85  Aligned_cols=149  Identities=18%  Similarity=0.352  Sum_probs=121.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcC--CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCC-ccccccccccccCCCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQY--GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK-PLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~f--G~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~-~l~gr~L~V~~a~pk~~  269 (823)
                      .+||++||.+.++.++|+.+|..-  +--..+   --..||+||.+.+...|.+|++.++|+ .+.|+++.+.++.++..
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            468999999999999999999753  111111   124589999999999999999999985 58899999999887654


Q ss_pred             CCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCC--cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 003400          270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH--KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (823)
Q Consensus       270 ~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~--srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~  347 (823)
                      .      .+.+-|.|+|+...++-|..+...||.|..|..+..  ..-..-|+|...+.+..||..|+|..+....++|.
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            3      345899999999999999999999999999864322  12234578899999999999999999999999888


Q ss_pred             ecC
Q 003400          348 PSR  350 (823)
Q Consensus       348 ~s~  350 (823)
                      |--
T Consensus       153 YiP  155 (584)
T KOG2193|consen  153 YIP  155 (584)
T ss_pred             cCc
Confidence            753

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=97.94  E-value=2e-05  Score=89.03  Aligned_cols=76  Identities=18%  Similarity=0.340  Sum_probs=67.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .-.|+|||.+|...+-..+|+.||++||.|.-.++     +.-.+.|+||++.+.++|.+||..|+.+.|.|+.|.|+.+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34589999999999999999999999999987662     3345679999999999999999999999999999999876


Q ss_pred             C
Q 003400          265 I  265 (823)
Q Consensus       265 ~  265 (823)
                      +
T Consensus       483 K  483 (940)
T KOG4661|consen  483 K  483 (940)
T ss_pred             c
Confidence            4

>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=97.90  E-value=8.6e-06  Score=82.50  Aligned_cols=90  Identities=21%  Similarity=0.368  Sum_probs=60.2

Q ss_pred             CcceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEee--eccc--ccceeEEEEEecCCcccHHHHHHHhcCCcccCCC
Q 003400          692 DTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLP--IDFK--NKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFN  767 (823)
Q Consensus       692 d~rTt~MirNIPnk~~~~~l~~~id~~~~~~ydf~Ylp--~d~~--~~~n~gyafin~~~~~~~~~f~~~f~g~~w~~~~  767 (823)
                      ..++.|.||++|..+|++.+++.|+......++|-|.+  .+..  ..+-...|||||.+.+++..|.+.|+|+.|..-.
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            45789999999999999999998887666665555554  2222  3345677999999999999999999999998654


Q ss_pred             C-ccEEEEEeeeccc
Q 003400          768 S-EKVASLAYARIQG  781 (823)
Q Consensus       768 s-~k~~~~~~A~iQg  781 (823)
                      . .-++.|.||--|-
T Consensus        85 g~~~~~~VE~Apyqk   99 (176)
T PF03467_consen   85 GNEYPAVVEFAPYQK   99 (176)
T ss_dssp             S-EEEEEEEE-SS--
T ss_pred             CCCcceeEEEcchhc
Confidence            3 4889999998764

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.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.86  E-value=3.1e-05  Score=92.08  Aligned_cols=152  Identities=20%  Similarity=0.265  Sum_probs=116.0

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE-EEeccCc-cCcccceeEeeecCccccc----cccccccCCCCccccCCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM-ELEGEPQ-ESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPY  187 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v-~V~~d~~-es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~~  187 (823)
                      .+.+++++|...+++.++...|..+|.+ .|.++.. -....++.|+.+.....+.    ......+.++..+..-..+ 
T Consensus       372 trTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~-  450 (975)
T KOG0112|consen  372 TRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQP-  450 (975)
T ss_pred             hhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccccc-
Confidence            5889999999999999999999999988 6777764 4445566666666553332    2223333333222222222 


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccc--ccccccccC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSI  265 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g--r~L~V~~a~  265 (823)
                      ...+++.++|++|+..+....|...|..||.|+.|.. .....||+|.|.+...|+.|++.+.|..|.+  +.|.|.|+.
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            4467899999999999999999999999999999854 3456799999999999999999999999974  678888876


Q ss_pred             CC
Q 003400          266 PK  267 (823)
Q Consensus       266 pk  267 (823)
                      +.
T Consensus       530 ~~  531 (975)
T KOG0112|consen  530 PP  531 (975)
T ss_pred             CC
Confidence            54

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.86  E-value=3.1e-05  Score=81.70  Aligned_cols=77  Identities=22%  Similarity=0.364  Sum_probs=68.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      .-..+|+|.|||..|+++||+++|+.||.+..+-+    .+++.|.|-|.|...++|.+|++.+++..+.|++|++....
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            34478999999999999999999999998887763    67788999999999999999999999999999998888764


Q ss_pred             C
Q 003400          266 P  266 (823)
Q Consensus       266 p  266 (823)
                      +
T Consensus       161 ~  161 (243)
T KOG0533|consen  161 S  161 (243)
T ss_pred             C
Confidence            3

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.84  E-value=4.4e-05  Score=80.54  Aligned_cols=78  Identities=24%  Similarity=0.350  Sum_probs=69.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ...+|+|.|||+.++++||+++|..||.++.+-+    .+.+.|.|-|.|...++|.+|++.+||..++|+.+++....+
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            3468999999999999999999999998887744    567789999999999999999999999999999999988765


Q ss_pred             Cc
Q 003400          352 GG  353 (823)
Q Consensus       352 ~~  353 (823)
                      ..
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            44

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.82  E-value=3.9e-05  Score=88.95  Aligned_cols=81  Identities=17%  Similarity=0.361  Sum_probs=71.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe--------CCCcccEEEEEeCCHHHHHHHHHHhcCCccccc
Q 003400          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRR  257 (823)
Q Consensus       186 ~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~--------~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr  257 (823)
                      ..++..+++|||+||++.++++.|...|..||+|.+|++        ..+.+.|+||.|-+..+|++|++.|+|..+.+.
T Consensus       168 DdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~  247 (877)
T KOG0151|consen  168 DDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEY  247 (877)
T ss_pred             CCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeee
Confidence            344566789999999999999999999999999999984        234567999999999999999999999999999


Q ss_pred             cccccccCC
Q 003400          258 KLDIHFSIP  266 (823)
Q Consensus       258 ~L~V~~a~p  266 (823)
                      .+++.|+++
T Consensus       248 e~K~gWgk~  256 (877)
T KOG0151|consen  248 EMKLGWGKA  256 (877)
T ss_pred             eeeeccccc
Confidence            999999843

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.79  E-value=2.7e-05  Score=90.22  Aligned_cols=78  Identities=29%  Similarity=0.414  Sum_probs=70.1

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC--------CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET--------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~--------~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      +...++|||+||++.++++.|...|+.||.|..+++.        ...+.+|||-|-+..+|++|++.|+|..+.+..++
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            3456799999999999999999999999999999762        23467899999999999999999999999999999


Q ss_pred             EEecCC
Q 003400          346 LEPSRP  351 (823)
Q Consensus       346 V~~s~~  351 (823)
                      +.|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999864

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.71  E-value=3.7e-05  Score=87.13  Aligned_cols=73  Identities=23%  Similarity=0.387  Sum_probs=61.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---C--CCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---A--CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~--~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..+|||+|||.++++++|+++|..||+|+...+   .  .+...||||+|++.++++.|+.+ +-..+.+++|.|+--+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            356999999999999999999999999988653   2  34448999999999999999996 5667788888887543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.68  E-value=0.00039  Score=75.93  Aligned_cols=143  Identities=15%  Similarity=0.192  Sum_probs=103.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhc-----CCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQ-----YGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~-----fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +++..+-.++||+..++.+|..+|.-     -|.+......++..|.|.|.|.|.|.-+.|++. +...+.++.|.|--+
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYka  136 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYKA  136 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeecc
Confidence            35567778999999999999999973     233333334677789999999999999999984 556667777766544


Q ss_pred             CCCCC---------C---CCCCCCccceeeecCCCCCCHHHHHHHhccc-----C--ceEEEEe-CCCcccEEEEEEcCH
Q 003400          265 IPKDN---------P---SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY-----G--EVKEIRE-TPHKRHHKFIEFYDV  324 (823)
Q Consensus       265 ~pk~~---------~---~~~~~~~~tLfV~NLp~~vteedL~~~Fs~f-----G--~I~~iri-~~~srG~aFVeF~d~  324 (823)
                      ...+-         .   -....++--|.+++||++.++.|+.++|.+-     |  .|..|+- .++..|-|||.|..+
T Consensus       137 ~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~e  216 (508)
T KOG1365|consen  137 TGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACE  216 (508)
T ss_pred             CchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCH
Confidence            32210         0   0011234467789999999999999999632     2  2333433 667789999999999


Q ss_pred             HHHHHHHHH
Q 003400          325 RAAEAALKS  333 (823)
Q Consensus       325 e~A~kAl~~  333 (823)
                      ++|+.||..
T Consensus       217 e~aq~aL~k  225 (508)
T KOG1365|consen  217 EDAQFALRK  225 (508)
T ss_pred             HHHHHHHHH
Confidence            999999984

>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=97.67  E-value=0.00016  Score=63.69  Aligned_cols=68  Identities=22%  Similarity=0.406  Sum_probs=49.2

Q ss_pred             cEEEEcCCCCCCCHHH----HHHHhhcCC-CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          193 RTLFVRNINSNVEDSE----LRALFEQYG-DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       193 rtLfV~NLP~~vteee----Lr~lFs~fG-~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..|+|.|||.+.+...    |+.+++.+| .|..|     ..+.|+|.|.+.+.|++|.+.|+|..+.|.+|.|.|..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            4699999999998765    556777786 67776     45899999999999999999999999999999999973

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=97.66  E-value=0.00015  Score=66.21  Aligned_cols=73  Identities=18%  Similarity=0.352  Sum_probs=58.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcC--CCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccc----cccccc
Q 003400          193 RTLFVRNINSNVEDSELRALFEQY--GDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLR----RRKLDI  261 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~f--G~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~----gr~L~V  261 (823)
                      +||.|+|||...|.++|.+++...  |...-++     .+..+.|||||.|.+++.|.+..+.++|..+.    .+...|
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            699999999999999999988753  3433333     25668999999999999999999999998875    344556


Q ss_pred             cccC
Q 003400          262 HFSI  265 (823)
Q Consensus       262 ~~a~  265 (823)
                      .||+
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            6654

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

>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=97.64  E-value=0.0002  Score=63.09  Aligned_cols=70  Identities=26%  Similarity=0.321  Sum_probs=48.2

Q ss_pred             cceeeecCCCCCCHHH----HHHHhccc-CceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          278 GTLVVFNLDPSVSNED----LRQIFGAY-GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       278 ~tLfV~NLp~~vteed----L~~~Fs~f-G~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ..|+|.|||.+.+...    |++++.-+ |+|..|.     .+.|+|.|.+.+.|++|.+.|+|..+.|++|.|.|....
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            4699999999888655    56777778 4676662     467999999999999999999999999999999998543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.63  E-value=8.2e-05  Score=84.35  Aligned_cols=75  Identities=27%  Similarity=0.493  Sum_probs=64.3

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      .+|||.|||.+++.++|+++|..||.|+..+|.     ++...||||+|.+.++++.||.+ +-..|++++|.|+--++.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            469999999999999999999999999987652     22337999999999999999996 477899999999987664


Q ss_pred             c
Q 003400          353 G  353 (823)
Q Consensus       353 ~  353 (823)
                      .
T Consensus       368 ~  368 (419)
T KOG0116|consen  368 F  368 (419)
T ss_pred             c
Confidence            3

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.56  E-value=9.4e-05  Score=78.04  Aligned_cols=79  Identities=24%  Similarity=0.372  Sum_probs=69.1

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 003400          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (823)
Q Consensus       273 ~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir-----i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~  347 (823)
                      .......+||+|+++.+|.+++..+|+.||.|..+.     ..++.+||+||+|.+.+.+++|++ |||..|.|+.|.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            344567899999999999999999999999997553     356689999999999999999999 99999999999998


Q ss_pred             ecCCC
Q 003400          348 PSRPG  352 (823)
Q Consensus       348 ~s~~~  352 (823)
                      +.+-.
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            86543

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.49  E-value=3.7e-05  Score=83.89  Aligned_cols=157  Identities=17%  Similarity=0.178  Sum_probs=114.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC--------CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTA--------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~--------~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ..|-|.||.+.+|.++++.||.-.|+|..+.+.        ......|||.|.|...+..|.. |.++.|-++.|.|-..
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            489999999999999999999999999988742        2345689999999999998877 6777666655544321


Q ss_pred             CCCC-------------------CCCC------C---CC------------------------CccceeeecCCCCCCHH
Q 003400          265 IPKD-------------------NPSD------K---DL------------------------NQGTLVVFNLDPSVSNE  292 (823)
Q Consensus       265 ~pk~-------------------~~~~------~---~~------------------------~~~tLfV~NLp~~vtee  292 (823)
                      ....                   .+..      .   .+                        -..|++|.+|...+...
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            1000                   0000      0   00                        01479999999999999


Q ss_pred             HHHHHhcccCceEEEEeC-CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          293 DLRQIFGAYGEVKEIRET-PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       293 dL~~~Fs~fG~I~~iri~-~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ++-+.|..+|+|...+.. +....+|.|+|........|++ ++|.++.-....+..-+|
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            999999999999988763 3345578899999999999998 567777644444444444

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.37  E-value=0.00026  Score=82.04  Aligned_cols=161  Identities=15%  Similarity=0.064  Sum_probs=113.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhc-CCCEEEEE---eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQ-YGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~-fG~I~~v~---~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      +++.+-+++.+.+.++.|++++|.. +-.-..+.   +.....|-++|.|....++++|++. +...+..|.+.+..+..
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g~  388 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPGRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPGN  388 (944)
T ss_pred             hhheeeecccccccccchhhhhcCcccccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCCc
Confidence            4455667889999999999999863 22222222   3444578999999999999999884 55555555555433210


Q ss_pred             C------------CCCC-------------------C----CCCCccceeeecCCCCCCHHHHHHHhcccCceEE-EEeC
Q 003400          267 K------------DNPS-------------------D----KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRET  310 (823)
Q Consensus       267 k------------~~~~-------------------~----~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~-iri~  310 (823)
                      .            ....                   .    -.....+|||..||..+++.++.+.|..--.|++ |.++
T Consensus       389 ~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt  468 (944)
T KOG4307|consen  389 LGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELT  468 (944)
T ss_pred             cccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEec
Confidence            0            0000                   0    0011258999999999999999999998777776 6553


Q ss_pred             ----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          311 ----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       311 ----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                          ++.++.|||+|..++++.+|+..-..+.++-+.|+|.-....
T Consensus       469 ~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~  514 (944)
T KOG4307|consen  469 RLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADY  514 (944)
T ss_pred             cCCcccccchhhheeccccccchhhhcccccccCceEEEeechhhH
Confidence                345778999999999999999876777777899999765443

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.25  E-value=0.00018  Score=73.56  Aligned_cols=75  Identities=20%  Similarity=0.198  Sum_probs=66.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ...||||.|+...++++-|.++|-+-|.|..|.|.    ++.+ ||||+|.++-...-|++.|||..+.+..|+|++-.-
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            45799999999999999999999999999999773    2233 999999999999999999999999999999887543

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.20  E-value=0.00038  Score=73.54  Aligned_cols=77  Identities=16%  Similarity=0.304  Sum_probs=68.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      .+.+.+.+||+|+...+|.+++...|+.||.|..+.     ..+..+||+||+|.+.+.++.|+. |+|..|.++.+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            455779999999999999999999999999997554     245689999999999999999999 99999999999988


Q ss_pred             ccC
Q 003400          263 FSI  265 (823)
Q Consensus       263 ~a~  265 (823)
                      +.+
T Consensus       176 ~~r  178 (231)
T KOG4209|consen  176 LKR  178 (231)
T ss_pred             eee
Confidence            754

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.18  E-value=0.00055  Score=71.50  Aligned_cols=75  Identities=20%  Similarity=0.345  Sum_probs=65.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEE-----EEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRT-----LYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~-----v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...-+||.+.|..+++++.|-..|.+|-....     -+.+++++||+||.|.++.++..|+++++|..+..++|++.-+
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            34568999999999999999999999875332     2358999999999999999999999999999999999988754

>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=97.15  E-value=0.00089  Score=62.25  Aligned_cols=71  Identities=28%  Similarity=0.427  Sum_probs=45.1

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC-----CccCCceEEEEecC
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR-----SDIAGKRIKLEPSR  350 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG-----~~i~Gr~I~V~~s~  350 (823)
                      .|.|.+++..++.++|++.|+.||.|..|.+... ...|+|+|.+.++|++|+..+.-     ..|.+..++++.-.
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vLe   78 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVLE   78 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT--SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE---
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEECC
Confidence            5789999999999999999999999999998643 34799999999999999987753     36667776666543

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.03  E-value=0.00077  Score=73.42  Aligned_cols=170  Identities=15%  Similarity=0.196  Sum_probs=110.3

Q ss_pred             CCCCCCCCCcchhHhhhcCccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc---c
Q 003400           95 NPAIGNSLPDDEDELLAGIMDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN---G  168 (823)
Q Consensus        95 ~~~i~n~LP~d~d~l~~~v~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~---~  168 (823)
                      ...++++....+.   .+....++++++-..+++.++..++...|..   .+.+.......+++..+.|.......   .
T Consensus        72 ~~~~~~~s~~~~~---~~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~  148 (285)
T KOG4210|consen   72 LSEEDSLSSKEEL---RGSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALE  148 (285)
T ss_pred             hhhcccccCCccc---ccccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHH
Confidence            3445555553322   2456789999999999999888888888854   22222223334455555544332111   1


Q ss_pred             ccc-ccc---------CCCCcccc-CCC-CCCCCCCcEEE-EcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCccc
Q 003400          169 LLH-YSV---------PNGAGTVA-GEH-PYGEHPSRTLF-VRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRG  230 (823)
Q Consensus       169 ~~~-~~l---------~n~~~~~~-~~~-~~~e~~srtLf-V~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG  230 (823)
                      +.. +.+         ....+... ... .....+..++| |++|+.++++++|+..|..+|.|..+++     ++..+|
T Consensus       149 ~s~~~~~~~~~~~~dl~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg  228 (285)
T KOG4210|consen  149 ESGSKVLDGNKGEKDLNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKG  228 (285)
T ss_pred             hhhccccccccccCcccccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhh
Confidence            111 011         00011000 000 11122344555 9999999999999999999999999983     567899


Q ss_pred             EEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          231 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       231 ~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      ||+|.|.+...+..++.. +...+.++++.+.+..+..
T Consensus       229 ~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  229 FAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             hhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCc
Confidence            999999999999999987 8888999999999886643

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.79  E-value=0.0038  Score=67.35  Aligned_cols=76  Identities=21%  Similarity=0.441  Sum_probs=62.5

Q ss_pred             ccceeeecCCCCCCHHHH------HHHhcccCceEEEEeCCCc------ccE--EEEEEcCHHHHHHHHHHhCCCccCCc
Q 003400          277 QGTLVVFNLDPSVSNEDL------RQIFGAYGEVKEIRETPHK------RHH--KFIEFYDVRAAEAALKSLNRSDIAGK  342 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL------~~~Fs~fG~I~~iri~~~s------rG~--aFVeF~d~e~A~kAl~~LnG~~i~Gr  342 (823)
                      ..-+||-+|++.+-.|++      .++|++||+|+.|.+..+.      .+.  .+|+|.+.++|.+||.+.+|..++||
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            346899999999877762      4899999999999764331      122  39999999999999999999999999


Q ss_pred             eEEEEecCCC
Q 003400          343 RIKLEPSRPG  352 (823)
Q Consensus       343 ~I~V~~s~~~  352 (823)
                      .|+..|...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999987543

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.78  E-value=0.00049  Score=81.92  Aligned_cols=141  Identities=13%  Similarity=0.165  Sum_probs=109.2

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcEEE---eccCccCcccceeEeeecCccccccccccccCCCCccccCCCCCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGMEL---EGEPQESLSMSMSKISISDSASGNGLLHYSVPNGAGTVAGEHPYGEH  190 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v~V---~~d~~es~~~g~~~v~~~e~~~a~~~~~~~l~n~~~~~~~~~~~~e~  190 (823)
                      ..+.|+++|+..+.+.++...|..+|.+.+   ..-..+..-+|++++.|.+...+.....+...    ..        -
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~----~~--------~  734 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDS----CF--------F  734 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhh----hh--------h
Confidence            345899999999999999999999998722   12234556678888877776554433222211    01        1


Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      .+..|+|+|.|...|.++|+.++..+|.+.++.    ..++.+|.|+|.|.+..+|.+++...+...+..+.+.|..+.|
T Consensus       735 gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  735 GKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            257899999999999999999999999999886    3678899999999999999999998888777777777777665

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.42  E-value=0.0028  Score=70.12  Aligned_cols=101  Identities=26%  Similarity=0.349  Sum_probs=79.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhccc--CceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC-ccCCceEEEEecCCCcc
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAY--GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS-DIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~f--G~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~-~i~Gr~I~V~~s~~~~~  354 (823)
                      ..||++||.+.++..||+.+|...  +.-..+-   ...||+||.+.|..-|.+|++.++|+ ++.|+++.|+.+-++..
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFL---VKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ   78 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCccee---eecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH
Confidence            368999999999999999999754  1111111   24689999999999999999999997 89999999999988776


Q ss_pred             cc--hhhhccccccCHHHHHHHHhhcCCC
Q 003400          355 RR--NLMLQLNQELEQDESRILQHQVGSP  381 (823)
Q Consensus       355 r~--~~~~ql~~~~~~~~l~~~f~~~GsP  381 (823)
                      +.  ..+++..+++..+-+..+..+||.+
T Consensus        79 rsrk~Qirnippql~wevld~Ll~qyg~v  107 (584)
T KOG2193|consen   79 RSRKIQIRNIPPQLQWEVLDSLLAQYGTV  107 (584)
T ss_pred             HhhhhhHhcCCHHHHHHHHHHHHhccCCH
Confidence            53  3566777777777777777777755

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.38  E-value=0.0078  Score=48.95  Aligned_cols=53  Identities=17%  Similarity=0.387  Sum_probs=43.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHH
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAM  246 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai  246 (823)
                      ++.|-|.+.+++..+.- +..|..||+|..+... ....+.+|.|.+..+|++|+
T Consensus         1 ~~wI~V~Gf~~~~~~~v-l~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    1 STWISVSGFPPDLAEEV-LEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             CcEEEEEeECchHHHHH-HHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            36788999987776554 5588899999998765 45679999999999999985

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.36  E-value=0.0048  Score=66.58  Aligned_cols=75  Identities=25%  Similarity=0.407  Sum_probs=61.7

Q ss_pred             CCcEEEEcCCCCCCCHHH----H--HHHhhcCCCEEEEEeCCCc------ccE--EEEEeCCHHHHHHHHHHhcCCcccc
Q 003400          191 PSRTLFVRNINSNVEDSE----L--RALFEQYGDIRTLYTACKH------RGF--VMISYYDIRAARTAMRALQNKPLRR  256 (823)
Q Consensus       191 ~srtLfV~NLP~~vteee----L--r~lFs~fG~I~~v~~~~ks------rG~--AFV~F~~~e~A~~Ai~~Lng~~l~g  256 (823)
                      ...-+||-+||+.+..++    |  .++|.+||.|..|.+..+.      .+.  +||.|.+.++|.+||.+.+|..+.|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            346789999999988777    3  3799999999998753331      122  4999999999999999999999999


Q ss_pred             ccccccccC
Q 003400          257 RKLDIHFSI  265 (823)
Q Consensus       257 r~L~V~~a~  265 (823)
                      +-|+..|..
T Consensus       193 r~lkatYGT  201 (480)
T COG5175         193 RVLKATYGT  201 (480)
T ss_pred             ceEeeecCc
Confidence            999998864

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.23  E-value=0.006  Score=67.97  Aligned_cols=66  Identities=33%  Similarity=0.473  Sum_probs=55.6

Q ss_pred             CCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCC------------------cccEEEEEEcCHHHHHHHHHH
Q 003400          272 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH------------------KRHHKFIEFYDVRAAEAALKS  333 (823)
Q Consensus       272 ~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~------------------srG~aFVeF~d~e~A~kAl~~  333 (823)
                      .+....++|.+.|||.+-.-+-|.+||+.+|.|+.|||-..                  .+-+|+|+|+..+.|.+|.+.
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            34457789999999999999999999999999999987221                  145799999999999999998


Q ss_pred             hCCC
Q 003400          334 LNRS  337 (823)
Q Consensus       334 LnG~  337 (823)
                      |+..
T Consensus       306 ~~~e  309 (484)
T KOG1855|consen  306 LNPE  309 (484)
T ss_pred             hchh
Confidence            8644

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.21  E-value=0.0071  Score=63.53  Aligned_cols=86  Identities=24%  Similarity=0.354  Sum_probs=73.4

Q ss_pred             HHHHHHHHHhcCCccccccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEE----EeCCCccc
Q 003400          240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRH  315 (823)
Q Consensus       240 e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~i----ri~~~srG  315 (823)
                      .-|+.|.++|++....++.|+|.|+..           +.|||.||..-++.+.|.+.|+.||.|...    ...++..+
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            357788888999999999999999842           579999999999999999999999987653    33456667


Q ss_pred             EEEEEEcCHHHHHHHHHHhCC
Q 003400          316 HKFIEFYDVRAAEAALKSLNR  336 (823)
Q Consensus       316 ~aFVeF~d~e~A~kAl~~LnG  336 (823)
                      -++|+|...-.|.+|++.++-
T Consensus        74 eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   74 EGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             cchhhhhcchhHHHHHHHhcc
Confidence            899999999999999998753

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.21  E-value=0.0087  Score=48.68  Aligned_cols=52  Identities=21%  Similarity=0.429  Sum_probs=42.7

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHH
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAAL  331 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl  331 (823)
                      +.|.|.+.+.+..+. +...|..||+|..+.+. ......+|+|.++.+|++|+
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            357888888776644 55588899999999986 34678999999999999995

>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=96.19  E-value=0.012  Score=54.77  Aligned_cols=59  Identities=14%  Similarity=0.253  Sum_probs=39.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK  252 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~  252 (823)
                      ..|.|.+++..++-++|++.|++||+|..|... +....|+|.|.+.++|++|+.++.-.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~-~G~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFS-RGDTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE---TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEec-CCCCEEEEEECCcchHHHHHHHHHhc
Confidence            468899999999999999999999999998743 34558999999999999999987544

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.14  E-value=0.0048  Score=67.63  Aligned_cols=78  Identities=24%  Similarity=0.329  Sum_probs=69.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEE-------------EeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  342 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~i-------------ri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr  342 (823)
                      ...++||.+|+..+++.+|.++|.++|.|+.=             +++...++-|.|.|+|...|+.|+.-++++.+.|.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            34699999999999999999999999988653             23566789999999999999999999999999999


Q ss_pred             eEEEEecCCCc
Q 003400          343 RIKLEPSRPGG  353 (823)
Q Consensus       343 ~I~V~~s~~~~  353 (823)
                      .|+|.++..+.
T Consensus       145 ~ikvs~a~~r~  155 (351)
T KOG1995|consen  145 TIKVSLAERRT  155 (351)
T ss_pred             Cchhhhhhhcc
Confidence            99999887654

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=95.95  E-value=0.0047  Score=64.81  Aligned_cols=68  Identities=21%  Similarity=0.408  Sum_probs=58.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCC-------------Cccc----EEEEEeCCHHHHHHHHHHhcCCc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-------------KHRG----FVMISYYDIRAARTAMRALQNKP  253 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~-------------ksrG----~AFV~F~~~e~A~~Ai~~Lng~~  253 (823)
                      ..-.||+.+||+.+...-|+++|+.||.|-+|++..             .++.    =|.|+|.+...|.++...||+..
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            567899999999999999999999999999998422             1111    28899999999999999999999


Q ss_pred             ccccc
Q 003400          254 LRRRK  258 (823)
Q Consensus       254 l~gr~  258 (823)
                      |.|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

>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=95.93  E-value=0.019  Score=53.01  Aligned_cols=72  Identities=21%  Similarity=0.369  Sum_probs=52.5

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEE------------eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce-
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR------------ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR-  343 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir------------i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~-  343 (823)
                      ..-|.|.+.|+. ....|.+.|++||+|.+..            -.......--|+|+++.+|.+||+ -||..+.|.. 
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            456889999988 4567889999999998875            122346789999999999999998 5999999854 


Q ss_pred             EEEEecC
Q 003400          344 IKLEPSR  350 (823)
Q Consensus       344 I~V~~s~  350 (823)
                      +-|.+.+
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            4467764

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.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=95.93  E-value=0.0077  Score=67.17  Aligned_cols=75  Identities=24%  Similarity=0.383  Sum_probs=60.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCC------------------cccEEEEEeCCHHHHHHHHHHh
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK------------------HRGFVMISYYDIRAARTAMRAL  249 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~k------------------srG~AFV~F~~~e~A~~Ai~~L  249 (823)
                      .+-++++|.+-|||.+-.-+-|.++|..+|.|..|++...                  .+-+|+|+|...+.|.+|.+.|
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            3458999999999999999999999999999999984211                  2568999999999999999987


Q ss_pred             cCCcccccccccc
Q 003400          250 QNKPLRRRKLDIH  262 (823)
Q Consensus       250 ng~~l~gr~L~V~  262 (823)
                      +...-+..-|+|.
T Consensus       307 ~~e~~wr~glkvk  319 (484)
T KOG1855|consen  307 NPEQNWRMGLKVK  319 (484)
T ss_pred             chhhhhhhcchhh
Confidence            6554444444443

>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]

Probab=95.83  E-value=0.0046  Score=68.44  Aligned_cols=73  Identities=19%  Similarity=0.402  Sum_probs=60.4

Q ss_pred             CcceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEee-eccccc-ceeEEEEEecCCcccHHHHHHHhcCCcccC
Q 003400          692 DTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLP-IDFKNK-CNVGYAFINMLSPLHIIPFYEAFNGKKWEK  765 (823)
Q Consensus       692 d~rTt~MirNIPnk~~~~~l~~~id~~~~~~ydf~Ylp-~d~~~~-~n~gyafin~~~~~~~~~f~~~f~g~~w~~  765 (823)
                      +....|.||++|+++|...|+..||- +...+.|.|+- -|+... |-.+.|||||..+.++..|...|+|+..=.
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 88888888765 555432 235669999999999999999999987754

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=95.66  E-value=0.011  Score=64.84  Aligned_cols=77  Identities=21%  Similarity=0.286  Sum_probs=68.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-------------eCCCcccEEEEEeCCHHHHHHHHHHhcCCccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------------TACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-------------~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~  255 (823)
                      .....+|||-+||..+++.+|.++|.++|.|..=+             .+.+.|+-|.|.|.|...|+.|+.-++++.+.
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            34557999999999999999999999999886532             36678999999999999999999999999999


Q ss_pred             cccccccccC
Q 003400          256 RRKLDIHFSI  265 (823)
Q Consensus       256 gr~L~V~~a~  265 (823)
                      +.+|+|..+.
T Consensus       143 gn~ikvs~a~  152 (351)
T KOG1995|consen  143 GNTIKVSLAE  152 (351)
T ss_pred             CCCchhhhhh
Confidence            9999988774

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=95.53  E-value=0.025  Score=65.05  Aligned_cols=73  Identities=19%  Similarity=0.243  Sum_probs=57.8

Q ss_pred             CccceeeecCCCCCC------HHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC-CceE
Q 003400          276 NQGTLVVFNLDPSVS------NEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKRI  344 (823)
Q Consensus       276 ~~~tLfV~NLp~~vt------eedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~-Gr~I  344 (823)
                      -...|+|.|+|.--.      ..-|..+|+++|+|....+    .+..+||.|++|.+.++|+.|++.|||+.++ .++.
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            456889999885321      2346789999999988754    4568999999999999999999999999886 4677


Q ss_pred             EEEe
Q 003400          345 KLEP  348 (823)
Q Consensus       345 ~V~~  348 (823)
                      .|..
T Consensus       137 ~v~~  140 (698)
T KOG2314|consen  137 FVRL  140 (698)
T ss_pred             Eeeh
Confidence            6653

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=95.49  E-value=0.0072  Score=63.44  Aligned_cols=68  Identities=29%  Similarity=0.523  Sum_probs=58.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCC-------------ccc----EEEEEEcCHHHHHHHHHHhCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH-------------KRH----HKFIEFYDVRAAEAALKSLNRSD  338 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~-------------srG----~aFVeF~d~e~A~kAl~~LnG~~  338 (823)
                      ..+.||+++||+.+....|+++|+.||.|-.|.+.+.             +..    -|.|+|.+...|.+....||+..
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            4578999999999999999999999999999865321             111    28999999999999999999999


Q ss_pred             cCCce
Q 003400          339 IAGKR  343 (823)
Q Consensus       339 i~Gr~  343 (823)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99965

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=95.38  E-value=0.034  Score=65.24  Aligned_cols=70  Identities=21%  Similarity=0.260  Sum_probs=60.2

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceE-EE--E--eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVK-EI--R--ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~-~i--r--i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      .|-+.|+|++++-+||.++|..|-.+- +|  |  ..+...|-|.|-|++.++|.+|...|+++.|..++|+|.+
T Consensus       869 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  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            688999999999999999999995331 22  2  2566788999999999999999999999999999998864

>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=94.89  E-value=0.051  Score=50.13  Aligned_cols=72  Identities=11%  Similarity=0.184  Sum_probs=52.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE------------eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccc-
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY------------TACKHRGFVMISYYDIRAARTAMRALQNKPLRRR-  257 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~------------~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr-  257 (823)
                      ..+-|.|-+.|+. ....|.+.|++||+|.+..            ..........|.|.++.+|++|++ .||..+.|. 
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            4567888899987 6677888999999998875            123455689999999999999999 499998875 


Q ss_pred             ccccccc
Q 003400          258 KLDIHFS  264 (823)
Q Consensus       258 ~L~V~~a  264 (823)
                      -+-|.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            3445555

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.

>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=94.80  E-value=0.18  Score=47.36  Aligned_cols=85  Identities=19%  Similarity=0.285  Sum_probs=66.6

Q ss_pred             cceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEeeecccccceeEEEEEecCCcccHHHHHHHhcCCcccCCCCccEE
Q 003400          693 TRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVA  772 (823)
Q Consensus       693 ~rTt~MirNIPnk~~~~~l~~~id~~~~~~ydf~Ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~g~~w~~~~s~k~~  772 (823)
                      .+|+|-+=-+|+.++..+++..+-+.+.....-+.+--|..  -|.-=+-|-|.+..+|..||+.|||++.+.... -+|
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            44666666899999988777777777777777666666644  465569999999999999999999999988765 459


Q ss_pred             EEEe-eecc
Q 003400          773 SLAY-ARIQ  780 (823)
Q Consensus       773 ~~~~-A~iQ  780 (823)
                      .|.| .+||
T Consensus        88 hvvfV~~Ve   96 (110)
T PF07576_consen   88 HVVFVKSVE   96 (110)
T ss_pred             EEEEEEEEE
Confidence            9999 4555

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=94.75  E-value=0.084  Score=51.73  Aligned_cols=75  Identities=31%  Similarity=0.414  Sum_probs=53.8

Q ss_pred             CCccceeeecCCC-----CCCH----HHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 003400          275 LNQGTLVVFNLDP-----SVSN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       275 ~~~~tLfV~NLp~-----~vte----edL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      ...+|+.|.=+.+     ..-.    .+|-+.|..||+|.-+|+.+   +.-+|+|.+-+.|.+|+. |+|.++.|+.|+
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            3556777775551     1222    36788999999999999875   457999999999999998 899999999999


Q ss_pred             EEecCCCc
Q 003400          346 LEPSRPGG  353 (823)
Q Consensus       346 V~~s~~~~  353 (823)
                      |+...+.-
T Consensus       101 i~LKtpdW  108 (146)
T PF08952_consen  101 IRLKTPDW  108 (146)
T ss_dssp             EEE-----
T ss_pred             EEeCCccH
Confidence            99876653

; PDB: 1UFW_A 2DNR_A.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=94.74  E-value=0.015  Score=61.35  Aligned_cols=61  Identities=31%  Similarity=0.405  Sum_probs=49.5

Q ss_pred             HHHHHHhc-ccCceEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          292 EDLRQIFG-AYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       292 edL~~~Fs-~fG~I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ++|...|+ +||+|+++.+-    ..-.|-++|.|...++|++|+..||+..+.|++|..+++.-.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            44555555 89999988542    234678999999999999999999999999999999987543

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.34  E-value=0.14  Score=57.91  Aligned_cols=81  Identities=30%  Similarity=0.349  Sum_probs=70.5

Q ss_pred             ceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEeeecccccceeEEEEEecCCcccHHHHHHHhcCCcccCCCCccEEE
Q 003400          694 RTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAFNGKKWEKFNSEKVAS  773 (823)
Q Consensus       694 rTt~MirNIPnk~~~~~l~~~id~~~~~~ydf~Ylp~d~~~~~n~gyafin~~~~~~~~~f~~~f~g~~w~~~~s~k~~~  773 (823)
                      -|+|-|=-||+.+|..+|+..+.....---|+--++ |  .--|.--+-|-|.+..+|..||+.|||+.++....+ +|.
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            589999999999999999999998888888888888 3  344545599999999999999999999999887766 999


Q ss_pred             EEeee
Q 003400          774 LAYAR  778 (823)
Q Consensus       774 ~~~A~  778 (823)
                      |-|+.
T Consensus       150 ll~V~  154 (493)
T KOG0804|consen  150 LLYVD  154 (493)
T ss_pred             EEEEE
Confidence            99964

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=94.30  E-value=0.08  Score=56.67  Aligned_cols=61  Identities=20%  Similarity=0.243  Sum_probs=49.5

Q ss_pred             HHHHHHHhcccCceEEEEeCC---Cc---ccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          291 NEDLRQIFGAYGEVKEIRETP---HK---RHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       291 eedL~~~Fs~fG~I~~iri~~---~s---rG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ++++++.+++||+|..|-|..   ..   .--.||+|...++|.+|+-.|||+.|+|+.++..|..-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            467889999999998885421   11   11379999999999999999999999999999887643

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=94.24  E-value=0.083  Score=60.91  Aligned_cols=70  Identities=20%  Similarity=0.392  Sum_probs=54.8

Q ss_pred             CcEEEEcCCCCCCC------HHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccc-ccccc
Q 003400          192 SRTLFVRNINSNVE------DSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLD  260 (823)
Q Consensus       192 srtLfV~NLP~~vt------eeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~-gr~L~  260 (823)
                      ...|+|.|+|.--.      ..-|..+|+++|+|..++.    .+..+||.|++|.+.++|+.|++.|+|..|. .+++.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            46788888885322      2236689999999998873    4668999999999999999999999998875 44444


Q ss_pred             c
Q 003400          261 I  261 (823)
Q Consensus       261 V  261 (823)
                      |
T Consensus       138 v  138 (698)
T KOG2314|consen  138 V  138 (698)
T ss_pred             e
Confidence            4

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=93.65  E-value=0.031  Score=58.97  Aligned_cols=58  Identities=22%  Similarity=0.351  Sum_probs=47.6

Q ss_pred             HHHHHHhh-cCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          207 SELRALFE-QYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       207 eeLr~lFs-~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ++|...|+ +||+|+.+++    ...-.|-++|.|...++|++|+..|++..+.|++|...++
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            34444445 9999998853    2235678999999999999999999999999999998876

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.83  E-value=0.31  Score=47.38  Aligned_cols=75  Identities=21%  Similarity=0.352  Sum_probs=57.6

Q ss_pred             CCCCCCcEEEEcCCCCCCC-HHHHH---HHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVE-DSELR---ALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vt-eeeLr---~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ..+.+-.||.|+=|..++. .+||+   ..++.||+|.+|...  .+-.|.|.|+|..+|-+|+.+++. ...|..+++.
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c--GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCs  157 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC--GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCS  157 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec--CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEee
Confidence            4566889999988877764 34444   556789999998544  456899999999999999999876 5567777777


Q ss_pred             cc
Q 003400          263 FS  264 (823)
Q Consensus       263 ~a  264 (823)
                      |.
T Consensus       158 Wq  159 (166)
T PF15023_consen  158 WQ  159 (166)
T ss_pred             cc
Confidence            65

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=91.95  E-value=0.14  Score=55.86  Aligned_cols=70  Identities=16%  Similarity=0.284  Sum_probs=57.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCC--CEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYG--DIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG--~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      .-.+||+||-+.+|++||.+.....|  .+.+++     ..+++||||+|...+..+.++.++.|-.+.|.|+.-.|
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            45799999999999999998887666  233332     57899999999999999999999999888888875444

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.82  E-value=0.6  Score=45.48  Aligned_cols=75  Identities=20%  Similarity=0.297  Sum_probs=57.3

Q ss_pred             CCCccceeeecCCCCC-CHHHH---HHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          274 DLNQGTLVVFNLDPSV-SNEDL---RQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~v-teedL---~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      +..-.||.|+=|...+ ..+||   .+..+.||.|.+|...|  +.-|.|.|.|..+|.+|+.+++. ...|..+.+.|.
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            3455689998766665 23444   45567899999998876  45799999999999999999865 667888888886


Q ss_pred             CC
Q 003400          350 RP  351 (823)
Q Consensus       350 ~~  351 (823)
                      .+
T Consensus       160 qr  161 (166)
T PF15023_consen  160 QR  161 (166)
T ss_pred             cc
Confidence            43

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=91.68  E-value=0.12  Score=60.09  Aligned_cols=67  Identities=21%  Similarity=0.344  Sum_probs=56.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhh-cCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFE-QYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs-~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l  254 (823)
                      .....+..|+|.||-.-.|.-+|+.++. ..|.|...++ .+-+..|||.|.+.++|..-..+|+|..+
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm-DkIKShCyV~yss~eEA~atr~AlhnV~W  506 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM-DKIKSHCYVSYSSVEEAAATREALHNVQW  506 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH-HHhhcceeEecccHHHHHHHHHHHhcccc
Confidence            3456789999999999999999999999 5667777654 34567899999999999999999998554

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=91.55  E-value=0.31  Score=52.30  Aligned_cols=75  Identities=19%  Similarity=0.362  Sum_probs=56.2

Q ss_pred             CCcEEEEcCC--CCCCC---HHHHHHHhhcCCCEEEEEeC-----CCc-ccEEEEEeCCHHHHHHHHHHhcCCccccccc
Q 003400          191 PSRTLFVRNI--NSNVE---DSELRALFEQYGDIRTLYTA-----CKH-RGFVMISYYDIRAARTAMRALQNKPLRRRKL  259 (823)
Q Consensus       191 ~srtLfV~NL--P~~vt---eeeLr~lFs~fG~I~~v~~~-----~ks-rG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L  259 (823)
                      +++.|.++|.  +-.++   ++++++.+++||.|..|.+.     ... .--.||+|...++|.+|+-.|+|+.|.|+.+
T Consensus       280 ptkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v  359 (378)
T KOG1996|consen  280 PTKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVV  359 (378)
T ss_pred             chHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceee
Confidence            3445666654  23344   45788999999999988642     111 2348999999999999999999999999998


Q ss_pred             cccccC
Q 003400          260 DIHFSI  265 (823)
Q Consensus       260 ~V~~a~  265 (823)
                      ...|..
T Consensus       360 ~A~Fyn  365 (378)
T KOG1996|consen  360 SACFYN  365 (378)
T ss_pred             eheecc
Confidence            887753

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=91.45  E-value=0.25  Score=56.23  Aligned_cols=73  Identities=21%  Similarity=0.239  Sum_probs=58.6

Q ss_pred             ceeeecCCCCC-CHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          279 TLVVFNLDPSV-SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       279 tLfV~NLp~~v-teedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      .|-+.-.+..+ +.++|...|.+||+|..|.+.-. .-.|.|+|.+..+|-+|-. ..+..|+++.|+|.|-.+..
T Consensus       374 ~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  374 PLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hhhhhccCCCCchHhhhhhhhhhcCccccccccCc-hhhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            34444445554 56899999999999999987432 4569999999999988876 58999999999999998865

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=91.11  E-value=0.75  Score=40.97  Aligned_cols=54  Identities=13%  Similarity=0.278  Sum_probs=41.8

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  335 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~Ln  335 (823)
                      ...+|. .|.++...||.++|++||.|.-.-+..   .-|||...+.+.|..|++.+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~d---TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIND---TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEECT---TEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcC---CcEEEEeecHHHHHHHHHHhc
Confidence            345565 899999999999999999987666643   459999999999999999885

; 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.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=91.02  E-value=0.35  Score=55.94  Aligned_cols=78  Identities=18%  Similarity=0.213  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhc--CCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcC--Ccccccc
Q 003400          183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQ--YGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRK  258 (823)
Q Consensus       183 ~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~--fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng--~~l~gr~  258 (823)
                      +++....+..+.|+++-||..+.+|+++.||+.  +-++.+|...-  ..--||+|++..||+.|.+.|..  +.|.|++
T Consensus       166 gekVrp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~--N~nWyITfesd~DAQqAykylreevk~fqgKp  243 (684)
T KOG2591|consen  166 GEKVRPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAH--NDNWYITFESDTDAQQAYKYLREEVKTFQGKP  243 (684)
T ss_pred             ccccccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeee--cCceEEEeecchhHHHHHHHHHHHHHhhcCcc
Confidence            333333445578899999999999999999984  77888886322  22378999999999999998865  4577887


Q ss_pred             cccc
Q 003400          259 LDIH  262 (823)
Q Consensus       259 L~V~  262 (823)
                      |...
T Consensus       244 ImAR  247 (684)
T KOG2591|consen  244 IMAR  247 (684)
T ss_pred             hhhh
Confidence            7644

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=90.93  E-value=0.98  Score=40.25  Aligned_cols=55  Identities=15%  Similarity=0.298  Sum_probs=43.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN  251 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng  251 (823)
                      ...+|. .|..+...||.++|+.||.|.--.+..   ..|||...+.+.|..|+..+..
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~d---TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIND---TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEECT---TEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcC---CcEEEEeecHHHHHHHHHHhcc
Confidence            456676 999999999999999999998766644   4699999999999999998754

; 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.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=90.62  E-value=0.52  Score=54.60  Aligned_cols=70  Identities=17%  Similarity=0.231  Sum_probs=55.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcc--cCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC--CccCCceEEEE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGA--YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR--SDIAGKRIKLE  347 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~--fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG--~~i~Gr~I~V~  347 (823)
                      +.+.+.|+-|+..+..|+++.+|+.  +-++++|.+.-.  .--||+|++..||+.|.+.|..  ++|.||.|...
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N--~nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN--DNWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec--CceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            4567888999999999999999985  678888876422  2369999999999999988863  46777776543

>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=89.30  E-value=0.66  Score=47.59  Aligned_cols=63  Identities=17%  Similarity=0.276  Sum_probs=45.8

Q ss_pred             CHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhC--CCccCCceEEEEecCCCc
Q 003400          290 SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN--RSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       290 teedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~Ln--G~~i~Gr~I~V~~s~~~~  353 (823)
                      ..+.|+++|..|+.+......+. -+-..|.|.+.++|.+|...|+  +..+.|..++|-|+....
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            35789999999998888765433 3348999999999999999999  999999999999986543

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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=89.15  E-value=1.5  Score=36.95  Aligned_cols=53  Identities=25%  Similarity=0.352  Sum_probs=40.6

Q ss_pred             cceeeecCCCCCCHHHHHHHhccc----CceEEEEeCCCcccEEEEEEcCHHHHHHHHHHh
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAY----GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL  334 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~f----G~I~~iri~~~srG~aFVeF~d~e~A~kAl~~L  334 (823)
                      ..|+|.+++ +++.++|+.+|..|    +. ..|.-...  .-|-|.|.+.+.|.+||.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~-~~IEWIdD--tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGP-FRIEWIDD--TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCC-ceEEEecC--CcEEEEECCHHHHHHHHHcC
Confidence            479999986 58889999999998    42 33432222  24889999999999999875

>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=89.08  E-value=0.41  Score=48.74  Aligned_cols=77  Identities=8%  Similarity=0.056  Sum_probs=50.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhc-CCCE---EEEE--e-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccc-
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQ-YGDI---RTLY--T-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRR-  257 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~-fG~I---~~v~--~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr-  257 (823)
                      ....+|.||+||+++|++++.+.+.. +++-   ..+.  .     ......-|||.|.+.+++......++|..|.+. 
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34569999999999999999998887 6765   3332  1     111234699999999999999999999877543 


Q ss_pred             ----cccccccCC
Q 003400          258 ----KLDIHFSIP  266 (823)
Q Consensus       258 ----~L~V~~a~p  266 (823)
                          ...|++|.-
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence                334566543

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.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=89.01  E-value=0.38  Score=52.68  Aligned_cols=73  Identities=15%  Similarity=0.154  Sum_probs=59.6

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccC--ceEEE-----EeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG--~I~~i-----ri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      .-++||+||-+.+|++||.+.....|  .+.++     |..++++|||+|-..+..+..+-++.|-.++|.|..-.|...
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            34799999999999999998887666  23333     457889999999999999999999999999999976665543

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=88.77  E-value=0.31  Score=56.74  Aligned_cols=77  Identities=19%  Similarity=0.286  Sum_probs=63.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhc-ccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCcc---CCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFG-AYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI---AGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs-~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i---~Gr~I~V~~s~~  351 (823)
                      ..+.|+|.||-...|.-+|+.++. ..|.|.+..+. +-+.+|||.|.+.++|...+.+|||...   +++.|.+.|...
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmD-kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~~  521 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMD-KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVRA  521 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHHHHH-HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecch
Confidence            346899999999999999999999 45666666443 3456899999999999999999999854   358999999865


Q ss_pred             Cc
Q 003400          352 GG  353 (823)
Q Consensus       352 ~~  353 (823)
                      ..
T Consensus       522 de  523 (718)
T KOG2416|consen  522 DE  523 (718)
T ss_pred             hH
Confidence            43

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=88.68  E-value=0.75  Score=45.20  Aligned_cols=72  Identities=25%  Similarity=0.373  Sum_probs=51.5

Q ss_pred             CCcEEEEcCCC-----CCCCH----HHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          191 PSRTLFVRNIN-----SNVED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       191 ~srtLfV~NLP-----~~vte----eeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      +..||.|.=+.     ...-+    .+|.+.|..||+|.-++..   .+.-+|.|.+-+.|-+|+. ++|..+.|+.|+|
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv---~~~mwVTF~dg~sALaals-~dg~~v~g~~l~i  101 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFV---GDTMWVTFRDGQSALAALS-LDGIQVNGRTLKI  101 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEE---TTCEEEEESSCHHHHHHHH-GCCSEETTEEEEE
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEe---CCeEEEEECccHHHHHHHc-cCCcEECCEEEEE
Confidence            55677776554     11223    3677889999998877642   3568999999999999999 8999999999999


Q ss_pred             cccCC
Q 003400          262 HFSIP  266 (823)
Q Consensus       262 ~~a~p  266 (823)
                      ....|
T Consensus       102 ~LKtp  106 (146)
T PF08952_consen  102 RLKTP  106 (146)
T ss_dssp             EE---
T ss_pred             EeCCc
Confidence            87654

; PDB: 1UFW_A 2DNR_A.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=88.28  E-value=0.46  Score=52.88  Aligned_cols=71  Identities=23%  Similarity=0.529  Sum_probs=57.6

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEeCCC--------cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH--------KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~--------srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      +.|.|.||.+.+|.++++.+|.-.|+|.++++.+.        ..-.|||.|.|...+..|.. |..+.+=++.|.|-..
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            47899999999999999999999999999987552        23479999999999888876 5666666666666554

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=87.97  E-value=2.2  Score=35.99  Aligned_cols=53  Identities=21%  Similarity=0.438  Sum_probs=41.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcC----CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHh
Q 003400          193 RTLFVRNINSNVEDSELRALFEQY----GDIRTLYTACKHRGFVMISYYDIRAARTAMRAL  249 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~f----G~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~L  249 (823)
                      .+|+|+++. +++.++|+.+|..|    +...-=++...   -|=|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt---ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT---SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC---cEEEEECCHHHHHHHHHcC
Confidence            579999995 69999999999999    54332224332   4789999999999999864

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=86.14  E-value=2.5  Score=45.85  Aligned_cols=73  Identities=22%  Similarity=0.289  Sum_probs=55.6

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce-EEEEecCCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR-IKLEPSRPG  352 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~-I~V~~s~~~  352 (823)
                      +.=|.|.+.++.-. .-|..+|++||.|.+.... .+..+-.|+|.++-+|.+||. -||+.|+|.. |-|+.+..+
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~-~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP-SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecC-CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCCH
Confidence            44577778876544 4577899999999887654 566799999999999999998 4899999844 446654443

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=83.62  E-value=0.66  Score=51.00  Aligned_cols=77  Identities=16%  Similarity=0.320  Sum_probs=60.2

Q ss_pred             ccceeeecCCCCCCHHHH-H--HHhcccCceEEEEeCCCc--------ccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 003400          277 QGTLVVFNLDPSVSNEDL-R--QIFGAYGEVKEIRETPHK--------RHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL-~--~~Fs~fG~I~~iri~~~s--------rG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      ..-+||-+|+..+..+.+ +  +.|.+||.|..|......        ..-++|+|...++|..||...+|...+|+.|+
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            346788888887755444 3  688999999999764321        11389999999999999999999999999988


Q ss_pred             EEecCCCc
Q 003400          346 LEPSRPGG  353 (823)
Q Consensus       346 V~~s~~~~  353 (823)
                      ..+...+-
T Consensus       157 a~~gttky  164 (327)
T KOG2068|consen  157 ASLGTTKY  164 (327)
T ss_pred             HhhCCCcc
Confidence            88776654

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=82.41  E-value=0.79  Score=50.44  Aligned_cols=75  Identities=19%  Similarity=0.295  Sum_probs=58.8

Q ss_pred             CcEEEEcCCCCCCCHHHHH---HHhhcCCCEEEEEeCCCc------cc--EEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          192 SRTLFVRNINSNVEDSELR---ALFEQYGDIRTLYTACKH------RG--FVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr---~lFs~fG~I~~v~~~~ks------rG--~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      .+-+||-+|+..+.++++.   +.|.+||.|..|.+....      .+  -++|.|...++|..||...+|..+.|+.|+
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            3567888898887655544   588899999998743311      11  389999999999999999999999999988


Q ss_pred             ccccCC
Q 003400          261 IHFSIP  266 (823)
Q Consensus       261 V~~a~p  266 (823)
                      ..+...
T Consensus       157 a~~gtt  162 (327)
T KOG2068|consen  157 ASLGTT  162 (327)
T ss_pred             HhhCCC
Confidence            887654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	823
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-07
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-06
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-06
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		8e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-05
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		3e-05
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		5e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		6e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-05
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		7e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		8e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-04
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		2e-04
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		2e-04
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		3e-04
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-04
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		6e-04
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		6e-04

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/111 (32%), Positives = 55/111 (49%), Gaps = 11/111 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A  A   L N PL
Sbjct: 25  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 83
Query: 255 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
           R ++L + F+           +  +L V NL   VSNE L + F  +G+V+
Sbjct: 84  RGKQLRVRFAC----------HSASLTVRNLPQYVSNELLEEAFSVFGQVE 124

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 37/169 (21%), Positives = 83/169 (49%), Gaps = 17/169 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
           ++V +I   + +  +R  F  +G I+++         KH+GF  + Y    AA+ A+  +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 250 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 302
            +  L  R + +    +I +  P    L +       + V ++   +S++D++ +F A+G
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 303 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           ++K   +   P    HK   FIE+   ++++ A+ S+N  D+ G+ +++
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 43/146 (29%), Positives = 65/146 (44%), Gaps = 18/146 (12%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           LFV N+ +++ + + + LFE+YG+   ++   + RGF  I       A  A   L    L
Sbjct: 25  LFVGNLPTDITEEDFKRLFERYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 255 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE----IRET 310
           + R L I F+           +   L V NL P VSNE L Q F  +G V++    + + 
Sbjct: 84  KSRPLRIRFAT----------HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR 133
Query: 311 PHKRHHKFIEFYDVRAAEAALKSLNR 336
                  F+EF    A   A K+L R
Sbjct: 134 GRATGKGFVEF---AAKPPARKALER 156

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 37/169 (21%), Positives = 83/169 (49%), Gaps = 17/169 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
           ++V +I   + +  +R  F  +G I+++         KH+GF  + Y    AA+ A+  +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 250 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 302
            +  L  R + +    +I +  P    L +       + V ++   +S++D++ +F A+G
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 303 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           ++K   +   P    HK   FIE+   ++++ A+ S+N  D+ G+ +++
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 40/151 (26%), Positives = 70/151 (46%), Gaps = 14/151 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
           L V  +  ++ D EL ALF   G I T      Y      G+  + +     ++ A++ L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--- 306
               +R ++L + ++ P    S KD N   L V NL  +++++ L  IFG YG + +   
Sbjct: 66  NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 307 IRE--TPHKRHHKFIEFYDVRAAEAALKSLN 335
           +R+  T   R   F+ +     A+ A+ +LN
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 73/157 (46%), Gaps = 17/157 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 247
           +FV  +     + +LR LFEQYG   +I  L    ++    +G   +++Y  +AA  A  
Sbjct: 18  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 248 ALQNKPLRRRKLDIHFSI---PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           AL N  +      +H  I   P D+  +  +    L +  +    +  D+R +F ++G++
Sbjct: 78  ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 134
Query: 305 KEIR--ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 337
           +E R    P    R   F+ F     A+ A+K+++++
Sbjct: 135 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 171

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 73/157 (46%), Gaps = 17/157 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 247
           +FV  +     + +LR LFEQYG   +I  L    ++    +G   +++Y  +AA  A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 248 ALQNKPLRRRKLDIHFSI---PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           AL N  +      +H  I   P D+  +  +    L +  +    +  D+R +F ++G++
Sbjct: 66  ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122
Query: 305 KEIR--ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 337
           +E R    P    R   F+ F     A+ A+K+++++
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 41/161 (25%), Positives = 67/161 (41%), Gaps = 22/161 (13%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRAARTA 245
           L V  +  N+   E R+LF   G+I +    CK           G+  ++Y D + A  A
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIES----CKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
           +  L    L+ + + + ++     PS   +    L V  L  +++ ++L Q+F  YG + 
Sbjct: 61  INTLNGLRLQTKTIKVSYA----RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 306 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
             R      T   R   FI F     AE A+K LN    +G
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 40/155 (25%), Positives = 64/155 (41%), Gaps = 22/155 (14%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRAARTA 245
           L V  +  N+   E ++LF   GDI +    CK           G+  ++Y D   A  A
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIES----CKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
           +  L    L+ + + + ++     PS   +    L V  L  ++S +++ Q+F  YG + 
Sbjct: 63  INTLNGLKLQTKTIKVSYA----RPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRII 118
Query: 306 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLN 335
             R      T   R   FI F     AE A+K LN
Sbjct: 119 TSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 40/151 (26%), Positives = 69/151 (45%), Gaps = 14/151 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
           L V  +  +  D EL ALF   G I T      Y      G+  + +     ++ A++ L
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--- 306
               +R ++L + ++ P    S KD N   L V NL  +++++ L  IFG YG + +   
Sbjct: 77  NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 307 IRE--TPHKRHHKFIEFYDVRAAEAALKSLN 335
           +R+  T   R   F+ +     A+ A+ +LN
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 163

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 46.2 bits (108), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 41/186 (22%), Positives = 85/186 (45%), Gaps = 28/186 (15%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
           ++V +I   + +  +R  F  +G I+++         KH+GF  + Y    AA+ A+   
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 250 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQ-----GTLVVFNLDPSVSNEDLRQIFGAYG 302
            +  L  R + +    +I +  P    L +       + V ++   +S++D++ +F A+G
Sbjct: 75  NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 303 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIK-----------L 346
           ++K   +   P    HK   FIE+   ++++ A+ S N  D+ G+ ++           L
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXPLL 194
Query: 347 EPSRPG 352
            P+ PG
Sbjct: 195 TPATPG 200

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 5/79 (6%)
Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAA 330
           ++G L V  L    + + L Q+F  YG++ E+     RET   R   F+ F ++  A+ A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 331 LKSLNRSDIAGKRIKLEPS 349
           + ++N   + G++I+++ +
Sbjct: 71  MMAMNGKSVDGRQIRVDQA 89

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 45/170 (26%), Positives = 74/170 (43%), Gaps = 19/170 (11%)
Query: 195 LFVRNINSNVEDSELRA----LFEQYG----DIRTLYTACKHRGFVMISYYDIRAARTAM 246
           LFV N+N N    EL+     +F +      D+R   T    R F    Y D  +A    
Sbjct: 10  LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMT----RKF---GYVDFESAEDLE 62
Query: 247 RALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE 306
           +AL+   L+    +I    PK   S K+ +  TL+  NL   V+ ++L+++F    E++ 
Sbjct: 63  KALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRL 122
Query: 307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL----EPSRPG 352
           + +    +   +IEF     AE   +    ++I G+ I L    EP   G
Sbjct: 123 VSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGEPKGEG 172

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/81 (24%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 190 HPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAAR 243
            P+ T+++ N+N  ++  EL+    A+F Q+G I  +    + K RG   + + ++ +A 
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 244 TAMRALQNKPLRRRKLDIHFS 264
            A+R++Q  P   + + I ++
Sbjct: 67  NALRSMQGFPFYDKPMRIQYA 87

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/160 (25%), Positives = 74/160 (46%), Gaps = 15/160 (9%)
Query: 195 LFVRNINSNVEDSELR-ALFEQYG-------DIRTLYTACKHRGFVMISYYDIRAARTAM 246
           LF+ N+N N   +EL+ A+ E +        D+RT      +R F    Y D  +A    
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT----GTNRKF---GYVDFESAEDLE 68
Query: 247 RALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE 306
           +AL+   L+    +I    PK   S K     TL+  NL  +++ ++L+++F    E++ 
Sbjct: 69  KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL 128
Query: 307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           + +    +   +IEF     AE  L+    ++I G+ + L
Sbjct: 129 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/155 (21%), Positives = 74/155 (47%), Gaps = 12/155 (7%)
Query: 190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR------GFVMISYYDIRAAR 243
           +P  +L+V +++ +V ++ L   F   G I ++   C+        G+  +++     A 
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
            A+  +    ++ + + I +S  + +PS +    G + + NLD S+ N+ L   F A+G 
Sbjct: 72  RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129
Query: 304 V---KEIRETPHKRHHKFIEFYDVRAAEAALKSLN 335
           +   K + +    + + F+ F    AAE A++ +N
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 36/153 (23%), Positives = 67/153 (43%), Gaps = 11/153 (7%)
Query: 196 FVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMRA 248
           FV  +     + +LR LFEQYG   +I  L    ++    +G   +++Y  +AA  A  A
Sbjct: 7   FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
           L N  +           P D+  +  +    L +  +    +  D+R  F ++G+++E R
Sbjct: 67  LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECR 126
Query: 309 --ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 337
               P    R   F+ F     A+ A+K+ +++
Sbjct: 127 ILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQA 159

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-RHHKFIEFYDVRAAEAALKSLNRS 337
           TLV+ NL  S + E L+++F     +K  +    K + + FIEF     A+ AL S N+ 
Sbjct: 17  TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76
Query: 338 DIAGKRIKLEPSRPGGA 354
           +I G+ I+LE   P G+
Sbjct: 77  EIEGRAIRLELQGPRGS 93

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	823
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-32
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-32
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-30
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-29
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-26
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-28
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-26
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-24
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-25
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-24
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-04
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-06
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-13
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	9e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-12
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-22
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-21
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	8e-12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-06
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-21
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-04
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-20
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	6e-20
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	9e-20
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-19
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-15
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-19
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-17
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-16
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-16
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-16
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-12
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-15
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	6e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-15
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-11
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-15
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-10
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-15
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-10
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-13
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-15
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-15
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-09
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-09
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-15
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-11
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	7e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-14
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-14
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-14
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-14
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-10
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-14
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	9e-14
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	9e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	9e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-13
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	7e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-08
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	6e-11
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-13
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-13
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-13
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-09
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-13
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-13
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-10
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	5e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	7e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-12
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-13
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-11
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	7e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	8e-13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-10
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	9e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-13
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-08
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	9e-13
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	9e-13
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-11
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-07
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	8e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	8e-08
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-12
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-11
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-12
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	9e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	4e-12
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	4e-10
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-12
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-06
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-12
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	5e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-09
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-12
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-12
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	9e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-11
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-08
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-11
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-06
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-07
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	8e-10
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-11
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	5e-08
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-11
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	8e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	7e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-11
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	7e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-10
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-10
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-08
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-10
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-06
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	7e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	7e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	8e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	8e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-08
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	8e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	3e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	7e-08
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-09
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-07
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-09
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	7e-09
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
2div_A	99	TRNA selenocysteine associated protein; structural	9e-09
2div_A	99	TRNA selenocysteine associated protein; structural	2e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	7e-05
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-08
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-06
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-04
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	9e-08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	8e-06
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-06
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-04
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-08
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	9e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	9e-08
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	8e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-06
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	6e-04
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-06
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	9e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	6e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	5e-04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	6e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	5e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	5e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-04
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	3e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-04
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	8e-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 =  124 bits (311), Expect = 2e-32
 Identities = 33/196 (16%), Positives = 59/196 (30%), Gaps = 39/196 (19%)

Query: 191 PSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
            S  L V  ++ S +    +  +F  YG++  +       G  M+   D  A   A+  L
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62

Query: 250 QNKPLRRRKLDIHFS------------IPKDNPSDKDLNQG------------------- 278
            N  +  +K+++  S            +   + S KD ++                    
Sbjct: 63  NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122

Query: 279 --TLVVFNLDPSVSNEDLRQIFGAYG-----EVKEIRETPHKRHHKFIEFYDVRAAEAAL 331
              L  FN    V+ E+  +I    G      VK       +     +E+     A   L
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182

Query: 332 KSLNRSDIAGKRIKLE 347
             LN   +        
Sbjct: 183 GFLNHYQMKNPNGPYP 198

>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 = 69.7 bits (170), Expect = 1e-13
 Identities = 25/122 (20%), Positives = 46/122 (37%), Gaps = 1/122 (0%)

Query: 279 TLVVFNLDPSVSNED-LRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
            L+V+ LD S  N D +  +F  YG V++++    K     +E  D  A + A+  LN +
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNN 65

Query: 338 DIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQFSSPI 397
            + G+++ +  S+           L       +                  N +Q  S +
Sbjct: 66  FMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNV 125

Query: 398 EH 399
            H
Sbjct: 126 LH 127

>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 = 51.2 bits (122), Expect = 3e-07
 Identities = 9/82 (10%), Positives = 27/82 (32%), Gaps = 5/82 (6%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYG-----DIRTLYTACKHRGFVMISYYDIRAAR 243
           +HPS  L   N    V +     + ++ G      ++      +     ++ +     A 
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 244 TAMRALQNKPLRRRKLDIHFSI 265
             +  L +  ++       +++
Sbjct: 180 ETLGFLNHYQMKNPNGPYPYTL 201

>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 =  123 bits (309), Expect = 6e-32
 Identities = 49/226 (21%), Positives = 81/226 (35%), Gaps = 40/226 (17%)

Query: 166 GNGLLHYSVPNGAGTVAGEHPYGEHP------SRTLFVRNIN-SNVEDSELRALFEQYGD 218
           G+   H+   +G             P      +  L V N+N   V    L  LF  YGD
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD 61

Query: 219 IRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS------IPKDNPSD 272
           ++ +      +   ++   D   A+ AM  L    L  + + I  S      +P++   D
Sbjct: 62  VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQED 121

Query: 273 KDLNQG-------------------------TLVVFNLDPSVSNEDLRQIFGAYGE-VKE 306
           + L +                          TL + N+ PSVS EDL+ +F + G  VK 
Sbjct: 122 QGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKG 181

Query: 307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRP 351
            +     R    I+   V  A  AL  L+  D+     +++  S+ 
Sbjct: 182 FKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 227

>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 = 66.9 bits (163), Expect = 2e-12
 Identities = 31/131 (23%), Positives = 57/131 (43%), Gaps = 6/131 (4%)

Query: 270 PSDKDLNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE 328
           P         L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+
Sbjct: 27  PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQ 86

Query: 329 AALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDES-----RILQHQVGSPIT 383
            A+  LN   + GK I++  S+    +     Q +Q L +D       R  +    +   
Sbjct: 87  LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 146

Query: 384 NSPPGNWVQFS 394
             PP   +  S
Sbjct: 147 IFPPSATLHLS 157

>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 =  116 bits (291), Expect = 8e-30
 Identities = 44/189 (23%), Positives = 72/189 (38%), Gaps = 34/189 (17%)

Query: 192 SRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           +  L V N+N   V    L  LF  YGD++ +      +   ++   D   A+ AM  L 
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 251 NKPLRRRKLDIHFS------IPKDNPSDKDLNQG-------------------------T 279
              L  + + I  S      +P++   D+ L +                          T
Sbjct: 63  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 122

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGE-VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           L + N+ PSVS EDL+ +F + G  VK  +     R    I+   V  A  AL  L+  D
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 182

Query: 339 IA-GKRIKL 346
           +     +++
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 = 71.1 bits (174), Expect = 3e-14
 Identities = 44/215 (20%), Positives = 82/215 (38%), Gaps = 28/215 (13%)

Query: 275 LNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS 333
           +    L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+ A+  
Sbjct: 1   MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH 60

Query: 334 LNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQF 393
           LN   + GK I++  S+    +     Q +Q L +D      H               +F
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLH---------------RF 105

Query: 394 SSPIEHNPLQTISKSPN--FRNMSPTTSNHMPGLASILHPQVSTLEKIAPIGKDQGRG-- 449
             P   N       S      N+ P+ S     L  +       ++      KD+     
Sbjct: 106 KKPGSKNFQNIFPPSATLHLSNIPPSVSEED--LKVLFSSNGGVVKGFKFFQKDRKMALI 163

Query: 450 --SLMEHALTNTISANGASFQQSN----SFSEPKI 478
               +E A+   I  +     +++    SFS+  I
Sbjct: 164 QMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 198

>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 = 55.7 bits (134), Expect = 6e-09
 Identities = 28/101 (27%), Positives = 40/101 (39%), Gaps = 6/101 (5%)

Query: 166 GNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYT 224
           GN  LH     G+       P    PS TL + NI  +V + +L+ LF   G + +    
Sbjct: 98  GNSPLHRFKKPGSKNFQNIFP----PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF 153

Query: 225 ACKHRGFVMISYYDIRAARTAMRALQNKPLRR-RKLDIHFS 264
             K R   +I    +  A  A+  L N  L     L + FS
Sbjct: 154 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 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 =  117 bits (294), Expect = 3e-29
 Identities = 35/192 (18%), Positives = 68/192 (35%), Gaps = 11/192 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
               L V N+  ++   +   L   +G +   +        + +G+    Y    +A  A
Sbjct: 94  TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNED-LRQIFGAYGEV 304
              L  KPL  R L +H++      +   L+   L V  L P  ++ D L +   A    
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAG-QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSP 212

Query: 305 KEIRETPHKR-HHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML 360
              +    +    K    +E+     AE A +  +   + G  +++    PG   R+++ 
Sbjct: 213 TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLA 272

Query: 361 QLNQELEQDESR 372
            L        +R
Sbjct: 273 ALIAAQATALNR 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 =  108 bits (273), Expect = 2e-26
 Identities = 29/169 (17%), Positives = 62/169 (36%), Gaps = 17/169 (10%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
            R + +R +  +V + E+  L   Y  ++  +   K++G   ++  +   A  A+ A   
Sbjct: 22  RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-KYKGTAFVTLLNGEQAEAAINAFHQ 79

Query: 252 KPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--E 309
             LR R+L +                  L V NL PS++ +   ++   +G ++      
Sbjct: 80  SRLRERELSVQLQPTDAL----------LCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129

Query: 310 TPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR 355
           +      K   F E+    +A  A   L    +  + + +  +  G   
Sbjct: 130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLT 178

>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 = 64.6 bits (158), Expect = 2e-11
 Identities = 15/104 (14%), Positives = 42/104 (40%), Gaps = 11/104 (10%)

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
           L  + +R+R         +    ++      +++  L   V+N+++  +   Y  +K   
Sbjct: 3   LDPEEIRKR-----LEHTERQFRNR----RKILIRGLPGDVTNQEVHDLLSDYE-LKYCF 52

Query: 309 ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 352
              +K    F+   +   AEAA+ + ++S +  + + ++     
Sbjct: 53  VDKYKG-TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95

>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 = 53.1 bits (128), Expect = 1e-07
 Identities = 17/90 (18%), Positives = 25/90 (27%), Gaps = 13/90 (14%)

Query: 189 EHPSRTLFVRNINSNVEDSE-LRALFEQYGDIRTLYTACK--------HRGFVMISYYDI 239
              SR L V  +     D + L              T C+         +GF ++ Y   
Sbjct: 181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSP----TFCQLACGQDGQLKGFAVLEYETA 236

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
             A  A +      L    L + F  P   
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266

>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 =  109 bits (275), Expect = 8e-28
 Identities = 30/169 (17%), Positives = 67/169 (39%), Gaps = 7/169 (4%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAART 244
                 LF+ N+N N   +EL+    +      L         +R F  + +        
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           A+  L    +   ++ +     +D+   +     TL+  NL  +++ ++L+++F    E+
Sbjct: 70  AL-ELTGLKVFGNEIKLEKPKGRDSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEI 126

Query: 305 KEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG 353
           + + +    +   +IEF     AE  L+    ++I G+ + L  +   G
Sbjct: 127 RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 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 = 69.6 bits (171), Expect = 7e-14
 Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 5/92 (5%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHK---FIEFYDV 324
               +      L + NL+P+ S  +L+          ++         ++   +++F   
Sbjct: 5   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 64

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
              E AL+ L    + G  IKLE  +   +++
Sbjct: 65  EDLEKALE-LTGLKVFGNEIKLEKPKGRDSKK 95

>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 =  108 bits (272), Expect = 3e-26
 Identities = 37/175 (21%), Positives = 67/175 (38%), Gaps = 16/175 (9%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT---LYTAC--KHRGFVMISYYDIRAA 242
                 TL++ N   +     +R L +    +     L +      R F  I       A
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172

Query: 243 RTAMRALQNKPLRRRKLDIHFSIP--KDNPSDKDLNQG-TLVVFNLDPSVSNED-LRQIF 298
           R  +  L    +    L    S P  K   +D    +G  +++ NL   + +E+ LR+ F
Sbjct: 173 RYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESF 232

Query: 299 GAYGEVKEIR------ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
             +G +++I       E        F+ F +  +AE AL+ +NRS +  + I + 
Sbjct: 233 EGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS 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 =  101 bits (254), Expect = 7e-24
 Identities = 31/182 (17%), Positives = 61/182 (33%), Gaps = 20/182 (10%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAARTAMRALQ 250
           T+ V+N+  +   +++   F+  G I  +  A    K+  F  I +     A  A+    
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 102

Query: 251 NKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET 310
               +   +  H +            + TL + N  PS +  ++R +      V      
Sbjct: 103 KVVGQNEIIVSHLT------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRL 150

Query: 311 PHKRHHK-----FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQE 365
           P  R +      +I+      A   ++ LN   I G  +  + S P    +       + 
Sbjct: 151 PSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEG 210

Query: 366 LE 367
            E
Sbjct: 211 RE 212

>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 = 63.5 bits (155), Expect = 5e-11
 Identities = 14/85 (16%), Positives = 31/85 (36%), Gaps = 4/85 (4%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYD 323
            +    ++    T++V NL  S +   + + F   G +  +      + +     IEF  
Sbjct: 31  ANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFAR 90

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEP 348
              A AA+   ++  +    I +  
Sbjct: 91  YDGALAAITKTHKV-VGQNEIIVSH 114

>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 =  101 bits (255), Expect = 4e-25
 Identities = 35/171 (20%), Positives = 69/171 (40%), Gaps = 16/171 (9%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------TACKHRGFVMISYYDIRAART 244
           +  +FV  +     + +LR LFEQYG +  +           + +G   +++Y  +AA  
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           A  AL N  +           P D+  +  +    L +  +    +  D+R +F ++G++
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122

Query: 305 KEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           +E R         R   F+ F     A+ A+K+++       +     S P
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH-----QAQTMEGCSSP 168

>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 = 63.0 bits (154), Expect = 1e-11
 Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 7/89 (7%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHK---FIEFYDVRAAE 328
           +   + V  +  + S +DLR++F  YG V EI      + +    K   F+ FY  +AA 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 329 AALKSLNRSDIAGKRIKLEPSRPGGARRN 357
            A  +L+   +          +P  + +N
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKN 90

>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 = 99.6 bits (249), Expect = 2e-24
 Identities = 36/166 (21%), Positives = 68/166 (40%), Gaps = 16/166 (9%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGFVMISYYDIRAARTA 245
           +  L V  +  ++ D EL ALF   G       +R   T     G+  + +     ++ A
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTG-YSYGYAFVDFTSEMDSQRA 61

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
           ++ L    +R ++L + ++     P  + +    L V NL  +++++ L  IFG YG + 
Sbjct: 62  IKVLNGITVRNKRLKVSYA----RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIV 117

Query: 306 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
           +        T   R   F+ +     A+ A+ +LN     G    L
Sbjct: 118 QKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL 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 = 67.2 bits (165), Expect = 4e-13
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 5/87 (5%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHK---FIEFYDVRAAEAA 330
           +   L+V  L   +++ +L  +F A G +   R        +     F++F     ++ A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 331 LKSLNRSDIAGKRIKLEPSRPGGARRN 357
           +K LN   +  KR+K+  +RPGG    
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIK 88

>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 = 41.4 bits (98), Expect = 3e-04
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
               L+V N+   + D +L  +F +YG I            + RG   + Y     A+ A
Sbjct: 88  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147

Query: 246 MRALQNKPL 254
           + AL N   
Sbjct: 148 ISALNNVIP 156

>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 = 99.2 bits (248), Expect = 3e-24
 Identities = 26/169 (15%), Positives = 60/169 (35%), Gaps = 20/169 (11%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----------KHRGFVMISYYDIRA 241
           +R L+V NI   + +  +   F     +  L  A           + + F  + +  +  
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 242 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY 301
              AM A      + + L I                  L +  L   ++++ ++++  ++
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLP----GAHKLFIGGLPNYLNDDQVKELLTSF 118

Query: 302 GEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
           G +K         T   + + F E+ D+   + A+  LN   +  K++ 
Sbjct: 119 GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167

>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 = 46.8 bits (112), Expect = 4e-06
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 185 HPYGEHPS-RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYD 238
           H Y   P    LF+  + + + D +++ L   +G ++             +G+    Y D
Sbjct: 86  HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145

Query: 239 IRAARTAMRALQNKPLRRRKLDI 261
           I     A+  L    L  +KL +
Sbjct: 146 INVTDQAIAGLNGMQLGDKKLLV 168

>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 = 97.0 bits (242), Expect = 4e-23
 Identities = 28/194 (14%), Positives = 65/194 (33%), Gaps = 32/194 (16%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----------KHRGFVMISYYDIR 240
            +R L+V NI   + +  +   F     +  L  A           + + F  + +  + 
Sbjct: 3   MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG----------------TLVVFN 284
               AM A      + + L I              N                   L +  
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121

Query: 285 LDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           L   ++++ ++++  ++G +K         T   + + F E+ D+   + A+  LN   +
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181

Query: 340 AGKRIKLEPSRPGG 353
             K++ ++ +  G 
Sbjct: 182 GDKKLLVQRASVGA 195

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 97.4 bits (243), Expect = 4e-23
 Identities = 33/176 (18%), Positives = 81/176 (46%), Gaps = 17/176 (9%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAA 242
                  ++V +I   + +  +R  F  +G I+++  +      KH+GF  + Y    AA
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPK-------DNPSDKDLNQGTLVVFNLDPSVSNEDLR 295
           + A+  + +  L  R + +             D  +++      + V ++   +S++D++
Sbjct: 84  QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIK 143

Query: 296 QIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
            +F A+G++K         T   + + FIE+   ++++ A+ S+N  D+ G+ +++
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 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 = 67.7 bits (166), Expect = 7e-13
 Identities = 25/130 (19%), Positives = 48/130 (36%), Gaps = 12/130 (9%)

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
           + M ++       R                      + V ++   +  + +RQ F  +G 
Sbjct: 2   SHMASMTGGQQMGRG-------SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGP 54

Query: 304 VKEIR--ETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
           +K I          HK   F+E+    AA+ AL+ +N   + G+ IK+      G  + +
Sbjct: 55  IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPI 114

Query: 359 MLQLNQELEQ 368
           + QL +E   
Sbjct: 115 IDQLAEEARA 124

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 52.7 bits (127), Expect = 9e-08
 Identities = 16/86 (18%), Positives = 44/86 (51%), Gaps = 5/86 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
               ++V +++ ++ D +++++FE +G I++   A      KH+G+  I Y   ++++ A
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA 183

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPS 271
           + ++    L  + L +  ++    P 
Sbjct: 184 VSSMNLFDLGGQYLRVGKAVTPPMPL 209

>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 = 96.6 bits (241), Expect = 7e-23
 Identities = 36/204 (17%), Positives = 85/204 (41%), Gaps = 10/204 (4%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAAR 243
            +P  +L+V +++ +V ++ L   F   G I ++         +  G+  +++     A 
Sbjct: 12  SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
            A+  +    ++ + + I +S     PS +    G + + NLD S+ N+ L   F A+G 
Sbjct: 72  RALDTMNFDVIKGKPVRIMWSQRD--PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129

Query: 304 VKEIR---ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLML 360
           +   +   +    + + F+ F    AAE A++ +N   +  +++ +   +    R   + 
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 189

Query: 361 QLNQELEQDESRILQHQVGSPITN 384
              +E    +        G  +T+
Sbjct: 190 ARAKEFYPYDVPDYAGSSGRIVTD 213

>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 = 65.8 bits (161), Expect = 3e-12
 Identities = 25/93 (26%), Positives = 40/93 (43%), Gaps = 5/93 (5%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYD 323
           NPS       +L V +L P V+   L + F   G +  IR      T     + ++ F  
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
              AE AL ++N   I GK +++  S+   + R
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMWSQRDPSLR 99

>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 = 94.9 bits (237), Expect = 1e-22
 Identities = 39/167 (23%), Positives = 67/167 (40%), Gaps = 16/167 (9%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK------HRGFVMISYYDIRAARTA 245
              L V  +  N+   E R+LF   G+I +     +        G+  ++Y D + A  A
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESC-KLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
           +  L    L+ + + + ++ P    S   +    L V  L  +++ ++L Q+F  YG + 
Sbjct: 61  INTLNGLRLQTKTIKVSYARP----SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116

Query: 306 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
             R      T   R   FI F     AE A+K LN    +G    + 
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 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 = 67.6 bits (166), Expect = 2e-13
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK--RHHK---FIEFYDVRAAEAA 330
           ++  L+V  L  +++ E+ R +FG+ GE++  +    K         F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 331 LKSLNRSDIAGKRIKLEPSRPGGAR 355
           + +LN   +  K IK+  +RP  A 
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSAS 85

>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 = 88.4 bits (220), Expect = 2e-21
 Identities = 19/85 (22%), Positives = 44/85 (51%), Gaps = 6/85 (7%)

Query: 189 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISYYDIRAA 242
             P+ T+++ N+N  ++  EL+    A+F ++G I    +  + K RG   + + ++ +A
Sbjct: 5   TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPK 267
             A+R++Q  P   + + I ++   
Sbjct: 65  TNALRSMQGFPFYDKPMRIQYAKTD 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 = 61.1 bits (149), Expect = 8e-12
 Identities = 19/94 (20%), Positives = 47/94 (50%), Gaps = 12/94 (12%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIR--ETPHKRHHK 317
           ++P+  P+       T+ + NL+  +  ++L++    IF  +G++ +I    +   R   
Sbjct: 1   AVPETRPNH------TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQA 54

Query: 318 FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           F+ F +V +A  AL+S+       K ++++ ++ 
Sbjct: 55  FVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 88

>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 = 93.6 bits (233), Expect = 3e-21
 Identities = 48/196 (24%), Positives = 75/196 (38%), Gaps = 19/196 (9%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 253
            LFV N+ +++ + + + LFE+YG+   ++   + RGF  I       A  A   L    
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTI 82

Query: 254 LRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----E 309
           L+ R L I F+               L V NL P VSNE L Q F  +G V++      +
Sbjct: 83  LKSRPLRIRFATHGAA----------LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD 132

Query: 310 TPHKRHHKFIEFYDVRAAEAALKSLNRSDI----AGKRIKLEPSRPGGARRNLMLQLNQE 365
                   F+EF     A  AL+             + + +EP         L  +L Q+
Sbjct: 133 RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQK 192

Query: 366 LEQDESRILQHQVGSP 381
            +Q      Q    + 
Sbjct: 193 TQQYHKEREQPPRFAQ 208

>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 = 68.2 bits (167), Expect = 9e-13
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 2/88 (2%)

Query: 266 PKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV 324
               P +K   Q   L V NL   ++ ED +++F  YGE  E+      R   FI     
Sbjct: 10  SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVF-INRDRGFGFIRLESR 68

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRPG 352
             AE A   L+ + +  + +++  +  G
Sbjct: 69  TLAEIAKAELDGTILKSRPLRIRFATHG 96

>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 = 47.4 bits (113), Expect = 7e-06
 Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 4/67 (5%)

Query: 190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTA 245
                L V+N++  V +  L   F Q+G +           +  G   + +     AR A
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKA 153

Query: 246 MRALQNK 252
           +    + 
Sbjct: 154 LERCGDG 160

>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 = 90.7 bits (226), Expect = 3e-21
 Identities = 34/167 (20%), Positives = 70/167 (41%), Gaps = 19/167 (11%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDIRAART 244
           R L+V N++  + +  L+  F+  G I        +      K+  +  + Y+    A  
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN----NKNVNYAFVEYHQSHDANI 56

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           A++ L  K +    + I+++      S  D +   L V +L+ +V +E LR  F  +   
Sbjct: 57  ALQTLNGKQIENNIVKINWAFQ-SQQSSSD-DTFNLFVGDLNVNVDDETLRNAFKDFPSY 114

Query: 305 KEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
                    +T   R + F+ F     A+ A+ S+   D+ G+ +++
Sbjct: 115 LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161

>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 = 64.5 bits (158), Expect = 3e-12
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
            L V NLD +++ + L+Q F   G +  I+    +     ++ F+E++    A  AL++L
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 335 NRSDIAGKRIKLEPSRPGGARRN 357
           N   I    +K+  +       +
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSS 84

>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 = 41.7 bits (99), Expect = 2e-04
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 13/78 (16%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRA 241
            +  LFV ++N NV+D  LR  F+ +    +                RG+  +S+     
Sbjct: 86  DTFNLFVGDLNVNVDDETLRNAFKDFPSYLS----GHVMWDMQTGSSRGYGFVSFTSQDD 141

Query: 242 ARTAMRALQNKPLRRRKL 259
           A+ AM ++Q + L  R L
Sbjct: 142 AQNAMDSMQGQDLNGRPL 159

>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 = 87.6 bits (218), Expect = 3e-20
 Identities = 31/174 (17%), Positives = 68/174 (39%), Gaps = 25/174 (14%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAA 242
           S  +F+  +N +  +  LR  F +YG +    T           + RGF  +S+    + 
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTV----TDLKIMKDPATGRSRGFGFLSFEKPSSV 58

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG 302
              ++      L  + +D   +IP+D         G + V  + P V  ++  + F  +G
Sbjct: 59  DEVVKTQHI--LDGKVIDPKRAIPRDEQD----KTGKIFVGGIGPDVRPKEFEEFFSQWG 112

Query: 303 EVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
            + +      ++T   R   F+ +    A +   +     D   ++I+++ + P
Sbjct: 113 TIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEP 165

>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 = 48.3 bits (116), Expect = 1e-06
 Identities = 18/87 (20%), Positives = 31/87 (35%), Gaps = 14/87 (16%)

Query: 190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIR 240
             +  +FV  I  +V   E    F Q+G I                + RGF  ++Y    
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTI----IDAQLMLDKDTGQSRGFGFVTYDSAD 140

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPK 267
           A        +    + RK++I  + P+
Sbjct: 141 AVDRVC-QNKFIDFKDRKIEIKRAEPR 166

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 84.5 bits (209), Expect = 6e-20
 Identities = 25/103 (24%), Positives = 42/103 (40%), Gaps = 3/103 (2%)

Query: 178 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYY 237
            G+    H     PSR + +R +  +V + E+ +L   +G + T     K +    I   
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKV-TNLLMLKGKNQAFIEMN 60

Query: 238 DIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKDLNQG 278
              AA T +    +    LR + + I FS  K+  +D   NQ 
Sbjct: 61  TEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 103

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 54.5 bits (131), Expect = 2e-09
 Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 3/75 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLNR 336
            + +  L   V+  ++  +   +G+V  +     K +  FIE     AA   +   +   
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVT 76

Query: 337 SDIAGKRIKLEPSRP 351
             + G+ I ++ S  
Sbjct: 77  PVLRGQPIYIQFSNH 91

>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 = 87.0 bits (216), Expect = 9e-20
 Identities = 39/196 (19%), Positives = 73/196 (37%), Gaps = 29/196 (14%)

Query: 184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMI 234
           E P      R LF+  ++    D  LR+ FEQ+G +    T C         + RGF  +
Sbjct: 5   ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60

Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVF--NLDPSVSNE 292
           +Y  +     AM A +   +  R ++   ++ +++      +     +F   +       
Sbjct: 61  TYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119

Query: 293 DLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI--- 344
            LR  F  YG+++ I     R +  KR   F+ F D  + +  +       + G      
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 178

Query: 345 ----KLEPSRPGGARR 356
               K E +    ++R
Sbjct: 179 KALSKQEMASASSSQR 194

>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 = 51.5 bits (124), Expect = 2e-07
 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 6/94 (6%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYY 237
            + P      + +FV  I  + E+  LR  FEQYG I  +         K RGF  +++ 
Sbjct: 95  SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154

Query: 238 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
           D  +    +   +   +     ++  ++ K   +
Sbjct: 155 DHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMA 187

>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 = 48.8 bits (117), Expect = 1e-06
 Identities = 19/98 (19%), Positives = 35/98 (35%), Gaps = 8/98 (8%)

Query: 265 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFI 319
           + K     +      L +  L    ++E LR  F  +G + +        T   R   F+
Sbjct: 1   MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 320 EFYDVRAAEAALKSLNRSDIAGKRI--KLEPSRPGGAR 355
            +  V   +AA+ +     + G+ +  K   SR    R
Sbjct: 61  TYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQR 97

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 83.4 bits (206), Expect = 4e-19
 Identities = 25/98 (25%), Positives = 40/98 (40%), Gaps = 6/98 (6%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISY 236
           G  P    PS+ + + NIN  V   +L+    AL    GDI    +  +  + G   I +
Sbjct: 20  GSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVF 79

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD 274
               +A+  + A Q  P +   L I FS    +   +D
Sbjct: 80  ATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAED 117

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 71.1 bits (174), Expect = 6e-15
 Identities = 15/92 (16%), Positives = 37/92 (40%), Gaps = 7/92 (7%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIR--ETPHKRHHKFI 319
               P   + +Q  +++ N++P V  E L+     +  + G++ +I    +       +I
Sbjct: 19  LGSTPPHTEPSQ-VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYI 77

Query: 320 EFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
            F    +A+A +++       G  + +  S  
Sbjct: 78  VFATQESAQAFVEAFQGYPFQGNPLVITFSET 109

>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 = 83.0 bits (205), Expect = 4e-19
 Identities = 26/113 (23%), Positives = 46/113 (40%), Gaps = 6/113 (5%)

Query: 171 HYSVPNGA---GTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 227
           H+   +G    G+  G+      PSR + +R +  +V + E+ +L   +G +       K
Sbjct: 7   HHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN-LLMLK 65

Query: 228 HRGFVMISYYDIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKDLNQG 278
            +    I      AA T +    +    LR + + I FS  K+  +D   NQ 
Sbjct: 66  GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 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 = 54.5 bits (131), Expect = 4e-09
 Identities = 18/112 (16%), Positives = 37/112 (33%), Gaps = 9/112 (8%)

Query: 242 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY 301
             +      +  L  R   +  S     PS        + +  L   V+  ++  +   +
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGDSRSAGVPSR------VIHIRKLPIDVTEGEVISLGLPF 55

Query: 302 GEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLNRSDIAGKRIKLEPSRP 351
           G+V  +     K +  FIE     AA   +   +     + G+ I ++ S  
Sbjct: 56  GKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106

>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 = 77.4 bits (191), Expect = 3e-17
 Identities = 20/89 (22%), Positives = 45/89 (50%), Gaps = 2/89 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNR 336
            L + NL   ++ E++  IFG YG +++IR   TP  R   ++ + D+  A+ A+  L+ 
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69

Query: 337 SDIAGKRIKLEPSRPGGARRNLMLQLNQE 365
            +++ + + +       A + +  +  +E
Sbjct: 70  FNVSNRYLVVLYYNANRAFQKMDTKKKEE 98

>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 = 74.3 bits (183), Expect = 3e-16
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 4/88 (4%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMR 247
            +R L++RN+   +   E+  +F +YG    IR   T  + RG   + Y DI  A+ A+ 
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP-ETRGTAYVVYEDIFDAKNAVD 65

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDKDL 275
            L    +  R L + +          D 
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQKMDT 93

>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 = 76.5 bits (189), Expect = 3e-17
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 2/91 (2%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR 325
           P  +   +     TL+  NL  +++ ++L+++F    E++ + +    +   +IEF    
Sbjct: 7   PCTSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEA 64

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
            AE  L+    ++I G+ + L  +   G  R
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 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 = 75.0 bits (185), Expect = 1e-16
 Identities = 18/83 (21%), Positives = 37/83 (44%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA 248
              +RTL  +N++ N+ + EL+ +FE   +IR +    K +G   I +     A   +  
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 249 LQNKPLRRRKLDIHFSIPKDNPS 271
            Q   +  R + ++++  K    
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 75.0 bits (185), Expect = 1e-16
 Identities = 21/79 (26%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN-RS 337
            L + NL P+V+ +DLRQ+FG         +   K  + F+++ D   A  A+++L+ + 
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRKLPLA-GQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 68

Query: 338 DIAGKRIKLEPSRPGGARR 356
           ++ GK ++++ S     R 
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 = 59.2 bits (144), Expect = 4e-11
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 2/88 (2%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTA 245
             G      L++ N++  V   +LR LF                G+  + Y D   A  A
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRA 60

Query: 246 MRALQNKP-LRRRKLDIHFSIPKDNPSD 272
           +  L  K  L  + +++ +S+ K   S 
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKLRSS 88

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 73.1 bits (180), Expect = 6e-16
 Identities = 11/81 (13%), Positives = 28/81 (34%), Gaps = 1/81 (1%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR 325
                        T  + N+    +  DL  +F  +G + + +    ++   FI++    
Sbjct: 16  VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFK-HYPEKGCCFIKYDTHE 74

Query: 326 AAEAALKSLNRSDIAGKRIKL 346
            A   + +L      G+ ++ 
Sbjct: 75  QAAVCIVALANFPFQGRNLRT 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 = 57.3 bits (139), Expect = 2e-10
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
             T ++ NI     +++L  LF+ +G I         +G   I Y     A   + AL N
Sbjct: 27  VTTAYIGNIPHFATEADLIPLFQNFGFILDFKH-YPEKGCCFIKYDTHEQAAVCIVALAN 85

Query: 252 KPLRRRKL 259
            P + R L
Sbjct: 86  FPFQGRNL 93

>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 = 74.9 bits (184), Expect = 6e-16
 Identities = 31/154 (20%), Positives = 53/154 (34%), Gaps = 17/154 (11%)

Query: 215 QYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN----------KPLRRRKLDIHFS 264
           QY  I    T     G       D   A    +   N              +       S
Sbjct: 2   QYKLILNGKTLK---GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGS 58

Query: 265 IPKDNPSDKD--LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFY 322
               +   +D       + V NL  + +  +L + FG YG ++ +    +     F+EF 
Sbjct: 59  HHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFE 118

Query: 323 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
           D R A  A++ L+   + G R+++E S     +R
Sbjct: 119 DPRDAADAVRELDGRTLCGCRVRVELSNGE--KR 150

>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 = 64.9 bits (158), Expect = 2e-12
 Identities = 21/84 (25%), Positives = 38/84 (45%)

Query: 184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR 243
            H         ++V N+ +N   +EL   F  YG +R+++ A    GF  + + D R A 
Sbjct: 65  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAA 124

Query: 244 TAMRALQNKPLRRRKLDIHFSIPK 267
            A+R L  + L   ++ +  S  +
Sbjct: 125 DAVRELDGRTLCGCRVRVELSNGE 148

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 73.5 bits (181), Expect = 6e-16
 Identities = 21/107 (19%), Positives = 44/107 (41%), Gaps = 4/107 (3%)

Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE 309
            +       L    S    +  + +L+   L V      V   +L +IFG +G +KE++ 
Sbjct: 5   HHHHHHSSGLVPRGS-HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63

Query: 310 TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
                   F+EF +  +A  A++ ++    A + +++  S+    R 
Sbjct: 64  ---LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 61.9 bits (151), Expect = 7e-12
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           GE  +  LFVR    +V++SEL  +F  +G ++         GF  + + +  +A  A+ 
Sbjct: 27  GELSNTRLFVRPFPLDVQESELNEIFGPFGPMK---EVKILNGFAFVEFEEAESAAKAIE 83

Query: 248 ALQNKPLRRRKLDIHFSIPKDN 269
            +  K    + L++ +S     
Sbjct: 84  EVHGKSFANQPLEVVYSKLPAK 105

>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 = 71.8 bits (177), Expect = 1e-15
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR------ETPHKRHHKFIEFYDVRAAEAALK 332
            + +  L  +V+ + + +IF  YG++K I            + + ++EF +   AE ALK
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 333 SLNRSDIAGKRIKLEPSRP 351
            ++   I G+ I       
Sbjct: 66  HMDGGQIDGQEITATAVLA 84

>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 = 49.8 bits (120), Expect = 6e-08
 Identities = 9/85 (10%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTL------YTACKHRGFVMISYYDIRAART 244
               + +  +  NV    +  +F  YG I+ +            +G+  + + +   A  
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDN 269
           A++ +    +  +++     +    
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWP 87

>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 = 71.9 bits (177), Expect = 2e-15
 Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 1/95 (1%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-RETPHKRHHKFIEFY 322
           S      S       TLV+ NL  S + E L+++F     +K    +    + + FIEF 
Sbjct: 2   SSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFA 61

Query: 323 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
               A+ AL S N+ +I G+ I+LE   P G+  +
Sbjct: 62  SFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNS 96

>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 = 61.1 bits (149), Expect = 1e-11
 Identities = 18/97 (18%), Positives = 44/97 (45%), Gaps = 4/97 (4%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIR--TLYTACKHRGFVMI 234
           G+   +G   +    S+TL + N++ +  +  L+ +FE+   I+        K +G+  I
Sbjct: 1   GSSGSSGNSTWSG-ESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNG-KSKGYAFI 58

Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
            +     A+ A+ +   + +  R + +    P+ +P+
Sbjct: 59  EFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPN 95

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 71.9 bits (177), Expect = 2e-15
 Identities = 21/74 (28%), Positives = 34/74 (45%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
           NL       +L + F  YG ++ +    +     F+EF D R AE A++ L+   I G R
Sbjct: 7   NLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSR 66

Query: 344 IKLEPSRPGGARRN 357
           +++E S     R  
Sbjct: 67  VRVELSTGMPRRSR 80

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 58.8 bits (143), Expect = 6e-11
 Identities = 22/80 (27%), Positives = 36/80 (45%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           ++V N+ +     EL   F  YG +RT++ A    GF  + + D R A  A+R L  K +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

Query: 255 RRRKLDIHFSIPKDNPSDKD 274
              ++ +  S      S  D
Sbjct: 63  CGSRVRVELSTGMPRRSRFD 82

>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 = 72.4 bits (178), Expect = 2e-15
 Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALK 332
           N   + V NL P +  +D+  +F  YG +++I +  ++R      F+EF D R AE A+ 
Sbjct: 21  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI-DLKNRRGGPPFAFVEFEDPRDAEDAVY 79

Query: 333 SLNRSDIAGKRIKLEPSRPGGARR 356
             +  D  G R+++E  R G    
Sbjct: 80  GRDGYDYDGYRLRVEFPRSGRGTG 103

>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 = 56.2 bits (136), Expect = 6e-10
 Identities = 16/94 (17%), Positives = 34/94 (36%), Gaps = 2/94 (2%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH--RG 230
           S  +G            +    ++V N+  ++   ++  +F +YG IR +    +     
Sbjct: 3   SGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP 62

Query: 231 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 264
           F  + + D R A  A+           +L + F 
Sbjct: 63  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP 96

>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 = 71.5 bits (176), Expect = 3e-15
 Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 5/84 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           TL V NL    S + LR++F  YG V ++       T   R   F+ F+D R A+ A  +
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
           ++ +++ G+ ++++ +R G    +
Sbjct: 75  MDGAELDGRELRVQVARYGRRDLS 98

>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 = 57.2 bits (139), Expect = 2e-10
 Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 5/91 (5%)

Query: 182 AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISY 236
           +G          TL V N+        LR +FE+YG +  +Y          RGF  + +
Sbjct: 3   SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
           +D R A+ A  A+    L  R+L +  +   
Sbjct: 63  HDRRDAQDAEAAMDGAELDGRELRVQVARYG 93

>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 = 71.2 bits (175), Expect = 3e-15
 Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V NL  S S E + + F        +      R + F+ F +   A  A+K+LN   
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGA-VERVKKIRDYAFVHFSNREDAVEAMKALNGKV 75

Query: 339 IAGKRIKLEPSRP 351
           + G  I++  ++P
Sbjct: 76  LDGSPIEVTLAKP 88

>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 = 65.0 bits (159), Expect = 4e-13
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
             + L+VRN+  +  +  +   F             K R +  + + +   A  AM+AL 
Sbjct: 14  SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-KIRDYAFVHFSNREDAVEAMKALN 72

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
            K L    +++  + P D  S
Sbjct: 73  GKVLDGSPIEVTLAKPVDKDS 93

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 71.7 bits (176), Expect = 3e-15
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 5/83 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHK---FIEFYDVRAAEAALKS 333
            +    L+ +V    L+ +   YGEV+E+     P  R H     + F   R A+  +K+
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           L+ + + G  I  +    G  R 
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRM 90

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.3 bits (170), Expect = 2e-14
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAA 242
           G+ P + +    +N NV ++ L+ +  +YG++  +         KH G   + +   R A
Sbjct: 2   GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDN 269
           +  ++ L    +    +     I    
Sbjct: 62  KETVKNLHLTSVMGNIIHAQLDIKGQQ 88

>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 = 71.1 bits (175), Expect = 3e-15
 Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 3/92 (3%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVR 325
              + D    TL V NL   V+   + Q+F   G  K  +       +    F+EFY+ R
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
            A AAL ++N   I GK +K+  +    ++++
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98

>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 = 49.6 bits (119), Expect = 1e-07
 Identities = 17/96 (17%), Positives = 45/96 (46%), Gaps = 4/96 (4%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLYTACKHRGFVM 233
           G+   +G     +   RTL+V N++ +V +  +  LF Q G     + +     +  +  
Sbjct: 1   GSSGSSGMME-DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF 59

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
           + +Y+ R A  A+ A+  + +  +++ ++++    +
Sbjct: 60  VEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS 95

>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 = 70.7 bits (174), Expect = 4e-15
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 1/87 (1%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEA 329
                  +  L V NL P ++ E++R++F  YG+  E+      +   FI       AE 
Sbjct: 8   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEI 66

Query: 330 ALKSLNRSDIAGKRIKLEPSRPGGARR 356
           A   L+   + GK++++  +    +  
Sbjct: 67  AKVELDNMPLRGKQLRVRFACHSASLT 93

>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 = 60.3 bits (147), Expect = 1e-11
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
               LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A  A   L 
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEIAKVELD 72

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
           N PLR ++L + F+    + +
Sbjct: 73  NMPLRGKQLRVRFACHSASLT 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 = 71.2 bits (175), Expect = 4e-15
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 1/90 (1%)

Query: 268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAA 327
           D  +       T+    +   ++++ +RQ F  +G++ EIR  P K  + F+ F    +A
Sbjct: 16  DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-YSFVRFSTHESA 74

Query: 328 EAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
             A+ S+N + I G  +K    +      +
Sbjct: 75  AHAIVSVNGTTIEGHVVKCYWGKESPDMTS 104

>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 = 54.3 bits (131), Expect = 3e-09
 Identities = 11/81 (13%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           + T++   I S + D  +R  F  +G I  +      +G+  + +    +A  A+ ++  
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEI-RVFPEKGYSFVRFSTHESAAHAIVSVNG 83

Query: 252 KPLRRRKLDIHFSIPKDNPSD 272
             +    +  ++     + + 
Sbjct: 84  TTIEGHVVKCYWGKESPDMTS 104

>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 = 72.6 bits (178), Expect = 5e-15
 Identities = 28/143 (19%), Positives = 56/143 (39%), Gaps = 14/143 (9%)

Query: 229 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG---------T 279
           +G       D   A    +   N      +     +      ++   +           +
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTS 72

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           L V NL    S + LR++F  YG V ++     R T   R   F+ F+D R AE A+ ++
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132

Query: 335 NRSDIAGKRIKLEPSRPGGARRN 357
           + + + G+ ++++ +R G    +
Sbjct: 133 DGAVLDGRELRVQMARYGRPPDS 155

>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 = 56.0 bits (135), Expect = 2e-09
 Identities = 25/101 (24%), Positives = 40/101 (39%), Gaps = 5/101 (4%)

Query: 175 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHR 229
               G+    H        +L V N+        LR +FE+YG +  +Y        + R
Sbjct: 53  TVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR 112

Query: 230 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 270
           GF  + ++D R A  AM A+    L  R+L +  +     P
Sbjct: 113 GFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 153

>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 = 70.4 bits (173), Expect = 5e-15
 Identities = 20/79 (25%), Positives = 43/79 (54%), Gaps = 3/79 (3%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V NL  +V+ E L + F  +G+++ +++    + + FI F +   A  A++ +N  D
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKK---LKDYAFIHFDERDGAVKAMEEMNGKD 69

Query: 339 IAGKRIKLEPSRPGGARRN 357
           + G+ I++  ++P   +R 
Sbjct: 70  LEGENIEIVFAKPPDQKRK 88

>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 = 60.8 bits (148), Expect = 1e-11
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRAL 249
             + LFVRN+ + V +  L   F Q+G +       K  + +  I + +   A  AM  +
Sbjct: 10  KVKVLFVRNLANTVTEEILEKAFSQFGKL----ERVKKLKDYAFIHFDERDGAVKAMEEM 65

Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQ 277
             K L    ++I F+ P D    +   Q
Sbjct: 66  NGKDLEGENIEIVFAKPPDQKRKERKAQ 93

>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 = 71.8 bits (176), Expect = 7e-15
 Identities = 25/118 (21%), Positives = 48/118 (40%), Gaps = 6/118 (5%)

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
           A+R+     L + + D HF    +          TL V NL    + E + ++F   G++
Sbjct: 8   ALRSDSYVELSQYR-DQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI 66

Query: 305 KEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           K+I     +         F+E+Y    AE A++ +N + +  + I+ +        R 
Sbjct: 67  KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 124

>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 = 56.4 bits (136), Expect = 1e-09
 Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
            S TL+V N++    + ++  LF + GDI+ +            GF  + YY    A  A
Sbjct: 38  KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           MR +    L  R +   +      
Sbjct: 98  MRYINGTRLDDRIIRTDWDAGFKE 121

>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 = 69.7 bits (171), Expect = 1e-14
 Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 4/91 (4%)

Query: 268 DNPSDKDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRA 326
            N +D       + + NL+ + V   D+  IF  YG V         + + F+++ + R 
Sbjct: 18  TNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS---VHKGYAFVQYSNERH 74

Query: 327 AEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           A AA+   N   +AG+ + +  +      R+
Sbjct: 75  ARAAVLGENGRVLAGQTLDINMAGEPKPDRS 105

>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 = 7e-10
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 6/82 (7%)

Query: 191 PSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRA 248
            +  +F+ N+N+  V+ S++  +F +YG +      C  H+G+  + Y + R AR A+  
Sbjct: 26  INSRVFIGNLNTALVKKSDVETIFSKYGRVA----GCSVHKGYAFVQYSNERHARAAVLG 81

Query: 249 LQNKPLRRRKLDIHFSIPKDNP 270
              + L  + LDI+ +      
Sbjct: 82  ENGRVLAGQTLDINMAGEPKPD 103

>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 = 68.8 bits (169), Expect = 1e-14
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE- 328
            S +D    TL V  L  +++  DLR  F  +GE++ I     ++   FI+F   +AAE 
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTIT-VVQRQQCAFIQFATRQAAEV 63

Query: 329 AALKSLNRSDIAGKRIKL 346
           AA KS N+  + G+R+ +
Sbjct: 64  AAEKSFNKLIVNGRRLNV 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 = 52.7 bits (127), Expect = 6e-09
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 236
           G+   +GE         TL+V  +   + +++LR  F Q+G+IRT+ T  + +    I +
Sbjct: 1   GSSGSSGEDK----TITTLYVGGLGDTITETDLRNHFYQFGEIRTI-TVVQRQQCAFIQF 55

Query: 237 YDIRAARTAMRALQNK 252
              +AA  A     NK
Sbjct: 56  ATRQAAEVAAEKSFNK 71

>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 = 68.8 bits (169), Expect = 2e-14
 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V  L P+ S   L + F  +G ++ I          +I++  + AA+AA   +    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTID-HVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 339 IAG--KRIKLEPSRPGGAR 355
           + G  +R++++ ++ G + 
Sbjct: 78  LGGPDRRLRVDFAKSGPSS 96

>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 = 67.3 bits (165), Expect = 6e-14
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           P+  L+V  +  N   + L   F+++G IRT+    K   F  I Y  + AA+ A   ++
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMR 74

Query: 251 NKPLRRRKLDIHFSIPKDNPSD 272
             PL      +     K  PS 
Sbjct: 75  GFPLGGPDRRLRVDFAKSGPSS 96

>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 = 67.2 bits (165), Expect = 4e-14
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           V N+  + ++++LR +F   G V E       + + F+       A+AA+  LN  ++ G
Sbjct: 14  VGNVSAACTSQELRSLFERRGRVIECD---VVKDYAFVHMEKEADAKAAIAQLNGKEVKG 70

Query: 342 KRIKLEPSRPGGARR 356
           KRI +E S  G  + 
Sbjct: 71  KRINVELSTKGQKKS 85

>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 = 58.8 bits (143), Expect = 5e-11
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            +  +FV N+++     ELR+LFE+ G +         + +  +       A+ A+  L 
Sbjct: 8   NTWKIFVGNVSAACTSQELRSLFERRGRVI---ECDVVKDYAFVHMEKEADAKAAIAQLN 64

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
            K ++ +++++  S      S
Sbjct: 65  GKEVKGKRINVELSTKGQKKS 85

>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 = 67.2 bits (165), Expect = 5e-14
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
           NL    + +++R +F  YG+V E       +++ F+   D  AAE A+++L+   + G  
Sbjct: 15  NLPREATEQEIRSLFEQYGKVLECD---IIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVN 71

Query: 344 IKLEPSRPGGARRN 357
           I +E S+      +
Sbjct: 72  INVEASKNKSKASS 85

>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 = 55.7 bits (135), Expect = 5e-10
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G      LF+ N+     + E+R+LFEQYG +         + +  +   D  AA  A+R
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVL---ECDIIKNYGFVHIEDKTAAEDAIR 60

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPS 271
            L +  L    +++  S  K   S
Sbjct: 61  NLHHYKLHGVNINVEASKNKSKAS 84

>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 = 67.2 bits (165), Expect = 6e-14
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L VF L    +  DLR++F  YG + ++     +++   R   F+ F +V  A+ A + 
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 334 LNRSDIAGKRIKLEPSRPG 352
            N  ++ G+RI++     G
Sbjct: 77  ANGMELDGRRIRVSGPSSG 95

>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 = 51.8 bits (125), Expect = 2e-08
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGF 231
           G+   +G     + P+  L V  ++    + +LR +F +YG I  +         + RGF
Sbjct: 1   GSSGSSGNRANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 59

Query: 232 VMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 264
             + + ++  A+ A        L  R++ +   
Sbjct: 60  AFVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>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 = 66.5 bits (163), Expect = 9e-14
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
           V N+ P+ +N++LR  F  YG V E       + + F+       A  A++ L+ ++  G
Sbjct: 15  VGNISPTCTNQELRAKFEEYGPVIECDI---VKDYAFVHMERAEDAVEAIRGLDNTEFQG 71

Query: 342 KRIKLEPSRPGGARRN 357
           KR+ ++ S       +
Sbjct: 72  KRMHVQLSTSRLRTAS 87

>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 = 58.0 bits (141), Expect = 9e-11
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            S  L V NI+    + ELRA FE+YG +         + +  +       A  A+R L 
Sbjct: 9   ASTKLHVGNISPTCTNQELRAKFEEYGPVI---ECDIVKDYAFVHMERAEDAVEAIRGLD 65

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
           N   + +++ +  S  +   +
Sbjct: 66  NTEFQGKRMHVQLSTSRLRTA 86

>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 = 67.3 bits (165), Expect = 9e-14
 Identities = 21/96 (21%), Positives = 43/96 (44%), Gaps = 6/96 (6%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIE 320
           P DN S ++ +  T+    L   +   DL   F A G+V+++     R +   +   ++E
Sbjct: 14  PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 73

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
           F ++++   A+  L    + G  I ++ S+    R 
Sbjct: 74  FCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRL 108

>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 = 48.1 bits (115), Expect = 5e-07
 Identities = 16/102 (15%), Positives = 37/102 (36%), Gaps = 6/102 (5%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----K 227
           S  +            E  +RT+F   + + +   +L   F   G +R +         +
Sbjct: 6   SGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRR 65

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
            +G   + + +I++   A+  L  + L    + +  S  + N
Sbjct: 66  SKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKN 106

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 66.5 bits (163), Expect = 1e-13
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 282 VFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA 340
           + NL   +VS EDL +IF  YG + +I     K    FI+F + ++   A++  ++    
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIECESQEMNF 71

Query: 341 GKRIKLEPSRPGGARR 356
           GK++ LE S      +
Sbjct: 72  GKKLILEVSSSNARPQ 87

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 58.4 bits (142), Expect = 7e-11
 Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 6/91 (6%)

Query: 191 PSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRA 248
           P   LF+ N+   NV   +L  +F  YG I            F  I + + ++ R A+  
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM----QINIKNAFGFIQFDNPQSVRDAIEC 64

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT 279
              +    +KL +  S     P     + GT
Sbjct: 65  ESQEMNFGKKLILEVSSSNARPQFDHGDHGT 95

>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 = 66.8 bits (163), Expect = 1e-13
 Identities = 22/102 (21%), Positives = 42/102 (41%), Gaps = 4/102 (3%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 236
           G+   +G+   G  PSR L +R +   V ++E+ AL   +G +  +    K +    +  
Sbjct: 1   GSSGSSGDKMDGA-PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLEL 58

Query: 237 YDIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKDLN 276
               AA T +         LR + + I +S  K+  +    +
Sbjct: 59  ATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTSGPSS 100

>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 = 52.5 bits (126), Expect = 1e-08
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 5/88 (5%)

Query: 267 KDNPSDKDLNQGTLVVF--NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV 324
             +  DK     + V+    L   V+  ++  +   +G+V  I     K +  F+E    
Sbjct: 3   SGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-NQAFLELATE 61

Query: 325 RAAEAALK--SLNRSDIAGKRIKLEPSR 350
            AA   +   S     +  + I ++ S 
Sbjct: 62  EAAITMVNYYSAVTPHLRNQPIYIQYSN 89

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 67.8 bits (166), Expect = 1e-13
 Identities = 27/129 (20%), Positives = 54/129 (41%), Gaps = 6/129 (4%)

Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNED 293
           S++    +   +    +         +            D+   T L V NL    S + 
Sbjct: 4   SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDT 63

Query: 294 LRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 348
           LR++F  YG V ++     R T   R   F+ F+D R AE A+ +++ + + G+ ++++ 
Sbjct: 64  LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123

Query: 349 SRPGGARRN 357
           +R G    +
Sbjct: 124 ARYGRPPDS 132

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 55.9 bits (135), Expect = 2e-09
 Identities = 24/110 (21%), Positives = 40/110 (36%), Gaps = 5/110 (4%)

Query: 163 SASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL 222
            +    +             G  P       +L V N+        LR +FE+YG +  +
Sbjct: 18  GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 77

Query: 223 YTAC-----KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
           Y        + RGF  + ++D R A  AM A+    L  R+L +  +   
Sbjct: 78  YIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 127

>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 = 67.5 bits (165), Expect = 2e-13
 Identities = 16/93 (17%), Positives = 39/93 (41%), Gaps = 10/93 (10%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----------KHRGFVMISYYDIR 240
           P+  ++V+N+  +V++ +L+ +F +Y D  +               + +G   I   + +
Sbjct: 44  PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 103

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 273
           AA  A++      L  + + + F+       D 
Sbjct: 104 AAAKALKEANGYVLFGKPMVVQFARSARPKQDP 136

>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 = 60.2 bits (146), Expect = 6e-11
 Identities = 22/99 (22%), Positives = 38/99 (38%), Gaps = 14/99 (14%)

Query: 267 KDNPSDKDLNQG----TLVVFNLDPSVSNEDLRQIFGAYGEVKE----------IRETPH 312
           +     +    G     + V NL   V  +DL+ IFG Y +             + +   
Sbjct: 31  ETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGR 90

Query: 313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
            +   FI   + +AA  ALK  N   + GK + ++ +R 
Sbjct: 91  MKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 129

>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 = 66.5 bits (163), Expect = 2e-13
 Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L + NL P V+  DL  +F  + E K         T   R   FI F +   A  AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 334 LNRSDIAGKRIKLEPSRPGGAR 355
           +N   + GK + +E  +    R
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQR 108

>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 = 65.0 bits (159), Expect = 7e-13
 Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG------DIRTLYTACKHRGFVMISYYDIRAART 244
           P++ L+++N++  V + +L +LF ++           + T  + RG   I++ +   A  
Sbjct: 24  PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTG-RMRGQAFITFPNKEIAWQ 82

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSD 272
           A+  +    L  + L I F   K   S 
Sbjct: 83  ALHLVNGYKLYGKILVIEFGKNKKQRSS 110

>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 = 66.2 bits (162), Expect = 2e-13
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V ++      +++++ F  YGE+K I     R T   + +  +E+   + A AA ++
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           LN ++I G+ I+++     G +R
Sbjct: 88  LNGAEIMGQTIQVDWCFVKGPKR 110

>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 = 56.5 bits (137), Expect = 5e-10
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 5/103 (4%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----K 227
            V N         P        LFV +I+   ++ E++  F  YG+I+ ++         
Sbjct: 7   RVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGF 66

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 270
            +G+ ++ Y   + A  A  AL    +  + + + +   K   
Sbjct: 67  SKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 65.9 bits (161), Expect = 2e-13
 Identities = 10/79 (12%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            S  + +R +   V +++L    +++G I  +      +   ++ + D+  A  A+    
Sbjct: 20  ASPVVHIRGLIDGVVEADLVEALQEFGPISYV-VVMPKKRQALVEFEDVLGACNAVNYAA 78

Query: 251 NKP--LRRRKLDIHFSIPK 267
           +    +      +++S  +
Sbjct: 79  DNQIYIAGHPAFVNYSTSQ 97

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 59.0 bits (143), Expect = 5e-11
 Identities = 20/100 (20%), Positives = 33/100 (33%), Gaps = 9/100 (9%)

Query: 253 PLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPH 312
                 ++ +    K   S        + +  L   V   DL +    +G +  +   P 
Sbjct: 3   HHHHHHMENYDDPHKTPASP------VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56

Query: 313 KRHHKFIEFYDVRAAEAALKSLNRSD--IAGKRIKLEPSR 350
           KR    +EF DV  A  A+     +   IAG    +  S 
Sbjct: 57  KR-QALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95

>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 = 66.7 bits (163), Expect = 2e-13
 Identities = 26/125 (20%), Positives = 57/125 (45%), Gaps = 10/125 (8%)

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGA 300
           A    M+   +K +           P      K++++ ++ V N+D   + +DL   F +
Sbjct: 1   AIAPCMQTTHSK-MTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS 59

Query: 301 YGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR---PG 352
            G +  I     + + H + + +IEF +  + +AA+ +++ +   G+ IK+ P R   PG
Sbjct: 60  CGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPG 118

Query: 353 GARRN 357
            +  +
Sbjct: 119 ISSTD 123

>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 = 45.5 bits (108), Expect = 5e-06
 Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 6/92 (6%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----K 227
           +   G           E   R+++V N++      +L A F   G I  +   C      
Sbjct: 17  AYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGH 76

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKL 259
            +G+  I + +  +   A+ A+     R R +
Sbjct: 77  PKGYAYIEFAERNSVDAAV-AMDETVFRGRTI 107

>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 = 66.3 bits (162), Expect = 3e-13
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L VF L    +  DLR++F  YG + ++     +++   R   F+ F +V  A+ A + 
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107

Query: 334 LNRSDIAGKRIKLEPSRP 351
            N  ++ G+RI+++ S  
Sbjct: 108 ANGMELDGRRIRVDFSIT 125

>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 = 55.5 bits (134), Expect = 2e-09
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
           P+  L V  ++    + +LR +F +YG I  +         + RGF  + + ++  A+ A
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
                   L  R++ + FSI K
Sbjct: 105 KERANGMELDGRRIRVDFSITK 126

>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 = 67.2 bits (164), Expect = 4e-13
 Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 5/84 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V ++      +++++ F  YGE+K I     R T   + +  +E+   + A AA ++
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
           LN ++I G+ I+++     G +R 
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKRV 157

>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 = 61.0 bits (148), Expect = 5e-11
 Identities = 20/108 (18%), Positives = 41/108 (37%), Gaps = 5/108 (4%)

Query: 171 HYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---- 226
           +  V N         P        LFV +I+   ++ E++  F  YG+I+ ++       
Sbjct: 51  YERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 110

Query: 227 -KHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 273
              +G+ ++ Y   + A  A  AL    +  + + + +   K     K
Sbjct: 111 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVK 158

>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 = 65.2 bits (159), Expect = 4e-13
 Identities = 13/89 (14%), Positives = 37/89 (41%), Gaps = 3/89 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            S  + VR +  +V +++L    E++G I  +      +   ++ + +I +A+  +    
Sbjct: 14  VSPVVHVRGLCESVVEADLVEALEKFGTICYV-MMMPFKRQALVEFENIDSAKECVTFAA 72

Query: 251 NKP--LRRRKLDIHFSIPKDNPSDKDLNQ 277
           + P  +  ++   ++S  K      +   
Sbjct: 73  DVPVYIAGQQAFFNYSTSKRITRPGNSGP 101

>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 = 58.3 bits (141), Expect = 1e-10
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            + V  L  SV   DL +    +G +  +   P KR    +EF ++ +A+  +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-QALVEFENIDSAKECVTFAADVP 75

Query: 339 --IAGKRIKLEPSR 350
             IAG++     S 
Sbjct: 76  VYIAGQQAFFNYST 89

>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 = 65.0 bits (159), Expect = 4e-13
 Identities = 23/96 (23%), Positives = 48/96 (50%), Gaps = 15/96 (15%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH----HK-- 317
            +PK   + K      ++V N+    +  ++R++F  +GE+K +R  P K      H+  
Sbjct: 8   QVPKKQTTSK------ILVRNIPFQANQREIRELFSTFGELKTVR-LPKKMTGTGAHRGF 60

Query: 318 -FIEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSRP 351
            F++F   + A+ A  +L + + + G+R+ LE +  
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>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 = 61.6 bits (150), Expect = 8e-12
 Identities = 24/102 (23%), Positives = 46/102 (45%), Gaps = 8/102 (7%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY------TACKHRG 230
           G+   +G+ P  +  +  + VRNI       E+R LF  +G+++T+           HRG
Sbjct: 1   GSSGSSGQVPKKQ-TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59

Query: 231 FVMISYYDIRAARTAMRALQN-KPLRRRKLDIHFSIPKDNPS 271
           F  + +   + A+ A  AL +   L  R+L + ++  +    
Sbjct: 60  FGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>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 = 64.6 bits (158), Expect = 5e-13
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 8/88 (9%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHK---FIEFYDVRAAEA 329
             L + NL+ S + E L+ +F   G +K       +            F+E+     A+ 
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 330 ALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           ALK L    + G ++++  S       +
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERATKPAS 93

>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 = 55.7 bits (135), Expect = 7e-10
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 8/92 (8%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDI 239
           G   S  LF++N+N +  +  L+ +F + G I        +         GF  + Y   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
             A+ A++ LQ   +   KL++  S     P+
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRISERATKPA 92

>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 = 65.2 bits (159), Expect = 5e-13
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           G           +  +N+ +    +E++  F ++G +  +          ++ + +   A
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-GITAIVEFLEPLEA 59

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 273
           R A R L         L + ++ P       
Sbjct: 60  RKAFRHLAYSKFHHVPLYLEWA-PIGVFGAA 89

>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 = 62.9 bits (153), Expect = 3e-12
 Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            ++  NL       ++++ F  +G +  +   P       +EF +   A  A + L  S 
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVL-LPEGGITAIVEFLEPLEARKAFRHLAYSK 70

Query: 339 IAGKRIKLE 347
                + LE
Sbjct: 71  FHHVPLYLE 79

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 64.5 bits (157), Expect = 6e-13
 Identities = 17/87 (19%), Positives = 30/87 (34%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVR 325
           P   P +       + V NL       DL++     G V         R   F+ + D  
Sbjct: 8   PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSA 67

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPG 352
           AA+ A+  L    +    +++  +R  
Sbjct: 68  AAQQAVSCLQGLRLGTDTLRVALARQQ 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 60.6 bits (147), Expect = 2e-11
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 177 GAGTVAGEHP--YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMI 234
            +G+     P   G   +  ++V N+  +   S+L+    + G +    T    R    +
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFL 61

Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
            Y D  AA+ A+  LQ   L    L +  +  + +
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 96

>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 = 64.6 bits (158), Expect = 7e-13
 Identities = 18/92 (19%), Positives = 37/92 (40%), Gaps = 5/92 (5%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 324
           P+ +  +  T+ V NL       DL+++F  +G +  I     + T   +   FI F+  
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
             A  A+  ++        + +E ++P     
Sbjct: 68  EDAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99

>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 = 53.8 bits (130), Expect = 4e-09
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
            + T+ V N++ +  +++L+ LF  +G I  +Y A      + +GF  IS++    A  A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           +  +         L++ ++ P  N
Sbjct: 74  IAGVSGFGYDHLILNVEWAKPSTN 97

>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 = 64.3 bits (157), Expect = 8e-13
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 282 VFNLD-PSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA 340
           + NL   +VS EDL +IF  YG + +I     K    FI+F + ++   A++  ++    
Sbjct: 27  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIEXESQEMNF 83

Query: 341 GKRIKLEPSRPG 352
           GK++ LE S   
Sbjct: 84  GKKLILEVSSSN 95

>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 = 56.9 bits (138), Expect = 2e-10
 Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 182 AGEHPYGEHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDI 239
           +G  P G H    LF+ N+   NV   +L  +F  YG I            F  I + + 
Sbjct: 12  SGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM----QINIKNAFGFIQFDNP 67

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPK 267
           ++ R A+     +    +KL +  S   
Sbjct: 68  QSVRDAIEXESQEMNFGKKLILEVSSSN 95

>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 = 64.2 bits (157), Expect = 9e-13
 Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 5/95 (5%)

Query: 268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFY 322
              S     +  L V  L   V ++ L   F  +G++ +I      ET   R   F+EF 
Sbjct: 3   SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62

Query: 323 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
               A AA+ ++N S++ G+ I++  ++P   + +
Sbjct: 63  LAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES 97

>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 = 53.0 bits (128), Expect = 7e-09
 Identities = 22/87 (25%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTA 245
             R L+V  +   V+D  L A F  +GDI        Y   KHRGF  + +     A  A
Sbjct: 11  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSD 272
           +  +    L  R + ++ + P      
Sbjct: 71  IDNMNESELFGRTIRVNLAKPMRIKES 97

>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 = 64.2 bits (157), Expect = 9e-13
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
            P  +     T+ V  LD  VS   L ++F   G V        R T   + + F+EF  
Sbjct: 7   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRP 351
              A+ A+K ++   + GK I++  +  
Sbjct: 67  EEDADYAIKIMDMIKLYGKPIRVNKASA 94

>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 = 50.7 bits (122), Expect = 5e-08
 Identities = 15/98 (15%), Positives = 39/98 (39%), Gaps = 6/98 (6%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGF 231
           G+   +G      +   T++V  ++  V +  L  LF Q G +   +        +H+G+
Sbjct: 1   GSSGSSG-PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY 59

Query: 232 VMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
             + +     A  A++ +    L  + + ++ +   + 
Sbjct: 60  GFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK 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 = 64.2 bits (157), Expect = 9e-13
 Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 2/96 (2%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEF 321
           S     P+ +     TL V  L    + E L++ F      + +  RET   +   F++F
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDF 61

Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
                A+AA +++   +I G ++ L+ ++P G   +
Sbjct: 62  NSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGS 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 = 54.2 bits (131), Expect = 3e-09
 Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 4/84 (4%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMR 247
           PS+TLFV+ ++ +  +  L+  F+     R +    T    +GF  + +     A+ A  
Sbjct: 14  PSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETG-SSKGFGFVDFNSEEDAKAAKE 72

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPS 271
           A+++  +   K+ + ++ PK    
Sbjct: 73  AMEDGEIDGNKVTLDWAKPKGEGG 96

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 63.8 bits (156), Expect = 9e-13
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 4/86 (4%)

Query: 274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEA 329
            L +  L +  L  S + E+L +I  A+G VK++R         +   ++E+ +   A  
Sbjct: 14  SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQ 73

Query: 330 ALKSLNRSDIAGKRIKLEPSRPGGAR 355
           A+  ++   I    IK+  S  G + 
Sbjct: 74  AVMKMDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAARTAM 246
               LF+  +  +    EL  + + +G ++ L        K +G   + Y +   A  A+
Sbjct: 16  EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV 75

Query: 247 RALQNKPLRRRKLDIHFSIPKDN 269
             +    ++   + +  S    +
Sbjct: 76  MKMDGMTIKENIIKVAISNSGPS 98

>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 = 63.8 bits (156), Expect = 1e-12
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALK 332
           G L V NL  + S EDL ++F AYG + E+       T   +   F+ F     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 333 SLNRSDIAGKRIKLEPSRPGGARRN 357
            ++     G+ + + PS        
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 59.9 bits (146), Expect = 3e-11
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
            S  LFVRN++    + +L  LF  YG +  L+        K +GF  +++     A  A
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSD 272
              +  +  + R L +  S  K   S 
Sbjct: 67  YAEVDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 63.5 bits (155), Expect = 1e-12
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 271 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAA 330
                   TL V+  D  ++   LR  F  +G + ++   P +    F+ +  + +A+ A
Sbjct: 9   RRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNC-AFVTYEKMESADQA 65

Query: 331 LKSLNRSDIAGKRIKLEPSRP 351
           +  LN + +   ++K+  +R 
Sbjct: 66  VAELNGTQVESVQLKVNIARK 86

>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 = 47.7 bits (114), Expect = 5e-07
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 4/94 (4%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 236
           G+   +GE         TL+V   +  +  + LR  F  +G+I  L      R    ++Y
Sbjct: 1   GSSGSSGERR-APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTY 56

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 270
             + +A  A+  L    +   +L ++ +  +   
Sbjct: 57  EKMESADQAVAELNGTQVESVQLKVNIARKQPML 90

>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 = 63.8 bits (156), Expect = 1e-12
 Identities = 21/97 (21%), Positives = 45/97 (46%), Gaps = 3/97 (3%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIE 320
           S      S+       L V N+     + DLRQ+FG +G++ ++    ++R  K   F+ 
Sbjct: 2   SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 61

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           F +   A+ A + L+ + + G++I++  +       +
Sbjct: 62  FENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98

>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 = 48.8 bits (117), Expect = 2e-07
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 3/86 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDI---RTLYTACKHRGFVMISYYDIRAARTAMR 247
             + L V NI     D +LR +F Q+G I     ++     +GF  +++ +   A  A  
Sbjct: 14  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 73

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDK 273
            L    +  RK++++ +  +   +  
Sbjct: 74  KLHGTVVEGRKIEVNNATARVMTNSG 99

>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 = 64.3 bits (157), Expect = 1e-12
 Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V  +    + ED+   F  YGE+K I     R T + + +  +E+   + A+AA++ 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
           LN  D+ G+ I ++     G  + 
Sbjct: 84  LNGQDLMGQPISVDWCFVRGPPKG 107

>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 = 57.8 bits (140), Expect = 3e-10
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 5/88 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
               LFV  ++    + ++   F +YG+I+ ++          +G+ ++ Y   + A+ A
Sbjct: 21  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDK 273
           M  L  + L  + + + +   +  P  K
Sbjct: 81  MEGLNGQDLMGQPISVDWCFVRGPPKGK 108

>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 = 63.0 bits (154), Expect = 2e-12
 Identities = 23/94 (24%), Positives = 46/94 (48%), Gaps = 5/94 (5%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
             S    ++G L V  L    + + L Q+F  YG++ E+     RET   R   F+ F +
Sbjct: 4   GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           +  A+ A+ ++N   + G++I+++ +      R+
Sbjct: 64  IDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 97

>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 = 49.9 bits (120), Expect = 8e-08
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 13/88 (14%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRA 241
               LFV  ++ +  +  L  +F +YG I    +             RGF  +++ +I  
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQI----SEVVVVKDRETQRSRGFGFVTFENIDD 66

Query: 242 ARTAMRALQNKPLRRRKLDIHFSIPKDN 269
           A+ AM A+  K +  R++ +  +    +
Sbjct: 67  AKDAMMAMNGKSVDGRQIRVDQAGKSSD 94

>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 = 63.0 bits (154), Expect = 3e-12
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSL 334
           G + + NLD S+ N+ L   F A+G +   K + +    + + F+ F    AAE A++ +
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65

Query: 335 NRSDIAGKRIKLEPSRPGGARR 356
           N   +  +++ +   +    R 
Sbjct: 66  NGMLLNDRKVFVGRFKSRKERE 87

>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 = 52.6 bits (127), Expect = 1e-08
 Identities = 18/112 (16%), Positives = 43/112 (38%), Gaps = 15/112 (13%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-------HRGFVMISYYDIRAART 244
           S  +F++N++ ++++  L   F  +G+I     +CK        +G+  + +    AA  
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAFGNI----LSCKVVCDENGSKGYGFVHFETQEAAER 60

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDN----PSDKDLNQGTLVVFNLDPSVSNE 292
           A+  +    L  RK+ +     +         +      + + N  P  +  
Sbjct: 61  AIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112

>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 = 62.0 bits (151), Expect = 3e-12
 Identities = 9/75 (12%), Positives = 28/75 (37%), Gaps = 2/75 (2%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN 335
               ++V NL    + +++  +   Y    +       +   F+   +   A+ A++  +
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYD--LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFH 61

Query: 336 RSDIAGKRIKLEPSR 350
           +    GK + ++   
Sbjct: 62  QYSFRGKDLIVQLQP 76

>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 = 58.2 bits (141), Expect = 7e-11
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G   S  + V+N+  +    E+  L + Y  ++  Y   +++    ++  +   A+ A++
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-RNKRTAFVTLLNGEQAQNAIQ 58

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG 278
                  R + L +        P+D  L  G
Sbjct: 59  MFHQYSFRGKDLIVQLQ-----PTDALLCSG 84

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 63.2 bits (153), Expect = 3e-12
 Identities = 24/114 (21%), Positives = 43/114 (37%), Gaps = 11/114 (9%)

Query: 262 HFSIPKDNPSDKDLNQGTLV-VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIE 320
             + P +       N+  L+ + N    ++ + L  +    G+V+ I           +E
Sbjct: 9   RITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVE 68

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKL--EPSRPGGARRNLMLQLNQELEQDESR 372
           F  V  A+ A  +LN +DI      L  E +RP         +LN     ++S 
Sbjct: 69  FESVLCAQKAKAALNGADIYAGCCTLKIEYARPT--------RLNVIRNDNDSW 114

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 50.5 bits (120), Expect = 9e-08
 Identities = 12/84 (14%), Positives = 30/84 (35%), Gaps = 4/84 (4%)

Query: 189 EHPSRTLF--VRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAM 246
              ++ L   ++N    +    L  +    G ++ +    ++    M+ +  +  A+ A 
Sbjct: 20  SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAK 79

Query: 247 RALQNKPL--RRRKLDIHFSIPKD 268
            AL    +      L I ++ P  
Sbjct: 80  AALNGADIYAGCCTLKIEYARPTR 103

>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 = 64.4 bits (156), Expect = 4e-12
 Identities = 29/144 (20%), Positives = 60/144 (41%), Gaps = 12/144 (8%)

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLV-VFNLDPSVSN 291
           M  ++   +A+ A++A+ +       L    +      +    +    + V NL   V+ 
Sbjct: 1   MHHHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTL 60

Query: 292 EDLRQIFGAYGEVKEIRETPHKRHHK-FIEFYDVRAAEAALKSLNRSDI--AGKRIKLEP 348
           + L QIF  +G V +I         +  +++ D  +A+ A  SL+  +I  A   ++++ 
Sbjct: 61  DVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120

Query: 349 SRPGGARRNLMLQLNQELEQDESR 372
           S+           LN +   D+SR
Sbjct: 121 SKLT--------SLNVKYNNDKSR 136

>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 = 58.6 bits (141), Expect = 4e-10
 Identities = 28/129 (21%), Positives = 49/129 (37%), Gaps = 9/129 (6%)

Query: 172 YSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGF 231
               + A   AG    G+ P   + V N+   V    L  +F ++G +  + T  K+  F
Sbjct: 26  ALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF 85

Query: 232 -VMISYYDIRAARTAMRALQNKPL--RRRKLDIHFSIPKD------NPSDKDLNQGTLVV 282
             ++ Y D  +A+ A  +L  + +      L I FS          N   +D  +  L  
Sbjct: 86  QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPS 145

Query: 283 FNLDPSVSN 291
            +  PS+  
Sbjct: 146 GDSQPSLDQ 154

>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 = 61.8 bits (151), Expect = 4e-12
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V  L   V ++ L   F  +G++ +I      ET   R   F+EF     A AA+ +
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 334 LNRSDIAGKRIK 345
           +N S++ G+ I+
Sbjct: 69  MNESELFGRTIR 80

>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 = 51.4 bits (124), Expect = 2e-08
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
             R L+V  +   V+D  L A F  +GDI  +         KHRGF  + +     A  A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 246 MRALQNKPLRRRKL 259
           +  +    L  R +
Sbjct: 66  IDNMNESELFGRTI 79

>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 = 61.4 bits (150), Expect = 5e-12
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           +  L P  +++DL ++   YG++        + T   + + F++F    AA+ A+ +L  
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69

Query: 337 SDIAGKRIKLEPSRPG 352
           S +  +  K      G
Sbjct: 70  SGVQAQMAKQSGPSSG 85

>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 = 48.7 bits (117), Expect = 1e-07
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 13/81 (16%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYD 238
           G   S  L++R +     D +L  L + YG I     + K          +G+  + +  
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKI----VSTKAILDKTTNKCKGYGFVDFDS 56

Query: 239 IRAARTAMRALQNKPLRRRKL 259
             AA+ A+ AL+   ++ +  
Sbjct: 57  PSAAQKAVTALKASGVQAQMA 77

>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 = 63.2 bits (154), Expect = 5e-12
 Identities = 32/130 (24%), Positives = 57/130 (43%), Gaps = 13/130 (10%)

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNE 292
           ++S YD       ++ LQ +  +         IP    + +      L+V  +  +V   
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQH--------IPPTQMNPEPDVLRNLMVNYIPTTVDEV 57

Query: 293 DLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
            LRQ+F  YG ++ +     RET   R + F++F    +A+ A+  LN  +I  KR+K+ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 348 PSRPGGARRN 357
            +  G  R  
Sbjct: 118 LAASGHQRPG 127

>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 = 46.7 bits (111), Expect = 3e-06
 Identities = 21/115 (18%), Positives = 39/115 (33%), Gaps = 13/115 (11%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK----- 227
                      +        R L V  I + V++ +LR LFE+YG I     + K     
Sbjct: 23  QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI----ESVKIVCDR 78

Query: 228 ----HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG 278
                RG+  + +    +A+ A+  L    +  ++L +  +             G
Sbjct: 79  ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVG 133

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 63.3 bits (154), Expect = 5e-12
 Identities = 22/103 (21%), Positives = 40/103 (38%), Gaps = 6/103 (5%)

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQG-TLVVFNLDPSVSNEDLRQIFGAYGEVKEI 307
           +    +   +  +         S         L V  L   V ++ L   F  +G++ +I
Sbjct: 34  VAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI 93

Query: 308 -----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
                 ET   R   F+EF     A AA+ ++N S++ G+ I+
Sbjct: 94  QIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR 136

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 55.2 bits (133), Expect = 3e-09
 Identities = 22/90 (24%), Positives = 34/90 (37%), Gaps = 5/90 (5%)

Query: 175 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHR 229
            +G    +G         R L+V  +   V+D  L A F  +GDI  +         KHR
Sbjct: 46  VDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105

Query: 230 GFVMISYYDIRAARTAMRALQNKPLRRRKL 259
           GF  + +     A  A+  +    L  R +
Sbjct: 106 GFAFVEFELAEDAAAAIDNMNESELFGRTI 135

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 61.9 bits (151), Expect = 5e-12
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V  +    + ED+   F  YGE+K I     R T + + +  +E+   + A+AA++ 
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 334 LNRSDIAGKRIKLEPSRP 351
           LN  D+ G+ I ++    
Sbjct: 85  LNGQDLMGQPISVDWCFV 102

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 55.0 bits (133), Expect = 2e-09
 Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
               LFV  ++    + ++   F +YG+I+ ++          +G+ ++ Y   + A+ A
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNP 270
           M  L  + L  + + + +   +  P
Sbjct: 82  MEGLNGQDLMGQPISVDWCFVRGPP 106

>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 = 61.5 bits (150), Expect = 5e-12
 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 5/85 (5%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIE 320
                     ++ T+ V NL  S++N DL +IF  YG+V ++     ++T   +   FI 
Sbjct: 5   SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIK 345
           F D  +A+   +++N   + G+ IK
Sbjct: 65  FLDKDSAQNCTRAINNKQLFGRVIK 89

>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 = 50.7 bits (122), Expect = 4e-08
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 8/89 (8%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL------YTACKHRG 230
            +G+             T++V N+  ++ +++L  +F +YG +  +       T  K +G
Sbjct: 2   SSGSSGMSGGLAP-SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTR-KSKG 59

Query: 231 FVMISYYDIRAARTAMRALQNKPLRRRKL 259
              I + D  +A+   RA+ NK L  R +
Sbjct: 60  VAFILFLDKDSAQNCTRAINNKQLFGRVI 88

>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 = 61.4 bits (150), Expect = 6e-12
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAE 328
           + +  ++ V N+D   + E+L   F   G V  +     + + H +   +IEF D  +  
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 329 AALKSLNRSDIAGKRIKLEPSRP 351
            +L  L+ S   G++IK+ P R 
Sbjct: 63  TSLA-LDESLFRGRQIKVIPKRT 84

>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 = 44.8 bits (107), Expect = 4e-06
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAAR 243
           E  +R+++V N++      EL A F   G +  +   C       +GF  I + D  + R
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 244 TAMRALQNKPLRRRKL 259
           T++ AL     R R++
Sbjct: 63  TSL-ALDESLFRGRQI 77

>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 = 61.1 bits (149), Expect = 8e-12
 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
           PSR +++ +I  +  + ++  L    G +  L         + +G+  I + D+ ++ +A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSD 272
           +R L    L  R L   +S   D    
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISGV 87

>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 = 61.1 bits (149), Expect = 9e-12
 Identities = 14/89 (15%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           + ++    + E +  +    G V  +      +T   + + FIEF D+ ++ +A+++LN 
Sbjct: 7   LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 66

Query: 337 SDIAGKRIKLEPSRPGGARRNLMLQLNQE 365
             +  + +K   S         +   +  
Sbjct: 67  YQLGSRFLKCGYSSNSDISGVSLEHHHHH 95

>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 = 61.1 bits (149), Expect = 1e-11
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 5/91 (5%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRHHKFIEFYDVR 325
              +      L + NL+P+ S  +L+          ++      T   R   +++F    
Sbjct: 10  EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 69

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
             E AL+ L    + G  IKLE  +     R
Sbjct: 70  DLEKALE-LTGLKVFGNEIKLEKPKGRDGTR 99

>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 = 42.2 bits (100), Expect = 5e-05
 Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 7/84 (8%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD-----IRTLYTACKHRGFVMISYYDIRAARTA 245
               LF+ N+N N   +EL+    +        +  + T   +R F  + +        A
Sbjct: 16  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTG-TNRKFGYVDFESAEDLEKA 74

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           +  L    +   ++ +     +D 
Sbjct: 75  L-ELTGLKVFGNEIKLEKPKGRDG 97

>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 = 60.6 bits (148), Expect = 1e-11
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V +L  +++ + LR IF  +G++  I      +T   + + FI F D   A  AL+ 
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
           LN  ++AG+ +++          +
Sbjct: 67  LNGFELAGRPMRVGHVTERLDGGS 90

>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 = 52.2 bits (126), Expect = 1e-08
 Identities = 20/90 (22%), Positives = 39/90 (43%), Gaps = 5/90 (5%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAA 242
           G   S  L+V +++ N+ +  LR +FE +G I  +         + +G+  I++ D   A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPSD 272
           R A+  L    L  R + +     + +   
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVTERLDGGS 90

>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 = 60.8 bits (148), Expect = 1e-11
 Identities = 20/106 (18%), Positives = 42/106 (39%), Gaps = 12/106 (11%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 318
           S     PSD      T+ + NL      E L ++   +G++K +      +T H +   F
Sbjct: 3   SGSSGLPSDVT-EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61

Query: 319 IEFYDVRAAEAALKSLNRS------DIAGKRIKLEPSRPGGARRNL 358
            +F    AA+  L + +         + G+++K++ +       + 
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107

>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 = 54.7 bits (132), Expect = 3e-09
 Identities = 17/99 (17%), Positives = 41/99 (41%), Gaps = 11/99 (11%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIR 240
           P      +T+F+RN++ + E+  L  + +Q+GD++ +           +G     +    
Sbjct: 9   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68

Query: 241 AARTAMRALQNKPLRR------RKLDIHFSIPKDNPSDK 273
           AA+  + A   +          R+L +  ++ +D  +  
Sbjct: 69  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107

>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 = 60.4 bits (147), Expect = 2e-11
 Identities = 23/93 (24%), Positives = 48/93 (51%), Gaps = 6/93 (6%)

Query: 271 SDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 324
           S K+  +G  L +++L     ++DL Q+F  +G V        ++T   +   F+ + + 
Sbjct: 18  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
            +A+AA++S+N   I  KR+K++  R     ++
Sbjct: 78  VSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>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 = 45.8 bits (109), Expect = 4e-06
 Identities = 19/116 (16%), Positives = 46/116 (39%), Gaps = 19/116 (16%)

Query: 163 SASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL 222
           S+  +GL   S+        G           LF+ ++     D +L  +F  +G++   
Sbjct: 2   SSGSSGLTQQSIGAAGSQKEGP------EGANLFIYHLPQEFGDQDLLQMFMPFGNV--- 52

Query: 223 YTACK---------HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
             + K          + F  +SY +  +A+ A++++    +  ++L +     K++
Sbjct: 53  -VSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 60.0 bits (146), Expect = 3e-11
 Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNRSD 338
           V N+     + DLRQ+FG +G++ ++    ++R  K   F+ F +   A+ A + L+ + 
Sbjct: 34  VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTV 93

Query: 339 IAGKRIKLEPSRP 351
           + G++I++  +  
Sbjct: 94  VEGRKIEVNNATA 106

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 46.9 bits (112), Expect = 1e-06
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDI---RTLYTACKHRGFVMISYYDIRAART 244
            +   + L V NI     D +LR +F Q+G I     ++     +GF  +++ +   A  
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 84

Query: 245 AMRALQNKPLRRRKLDIHFSIPK 267
           A   L    +  RK++++ +  +
Sbjct: 85  AREKLHGTVVEGRKIEVNNATAR 107

>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 = 64.1 bits (155), Expect = 3e-11
 Identities = 21/93 (22%), Positives = 46/93 (49%), Gaps = 6/93 (6%)

Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISYYDIRAART 244
           P+ T+++ N+N  ++  EL+    A+F Q+G I    +  + K RG   + + ++ +A  
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 277
           A+R++Q  P   + + I ++    +   K    
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT 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 = 59.9 bits (144), Expect = 6e-10
 Identities = 27/160 (16%), Positives = 58/160 (36%), Gaps = 9/160 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALK 332
           T+ + NL+  +  ++L++    IF  +G++ +I    +   R   F+ F +V +A  AL+
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 70

Query: 333 SLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWVQ 392
           S+       K ++++ ++        M     E ++   +       +P T         
Sbjct: 71  SMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGA 130

Query: 393 FSSPIEHNPLQTISKSPNFRNMSPTTSNHMPGLASILHPQ 432
                                 +P   +HMPG    + P 
Sbjct: 131 TPVVGAVQGPVP---GMPPMTQAPRIMHHMPGQPPYMPPP 167

>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 = 54.5 bits (130), Expect = 5e-08
 Identities = 14/91 (15%), Positives = 28/91 (30%)

Query: 168 GLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK 227
           G +             +      P+  LF+ N+     +  L  LF Q+   + +     
Sbjct: 183 GAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG 242

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRK 258
                 + + +   A  A  ALQ   + +  
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQNN 273

>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 = 18/73 (24%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L + NL    +   L  +F  +   KE+R  P +    F+EF +   A AA  +L    
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFK 268

Query: 339 I-AGKRIKLEPSR 350
           I     +K+  ++
Sbjct: 269 ITQNNAMKISFAK 281

>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 = 59.8 bits (145), Expect = 3e-11
 Identities = 16/96 (16%), Positives = 36/96 (37%), Gaps = 9/96 (9%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD-------IRTLYTACKHRGFVMISYYDIRAAR 243
            +  LF+  I    +  E+     +  +         +     K+RGF  + Y   RAA 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 244 TAMRALQNKPLRR--RKLDIHFSIPKDNPSDKDLNQ 277
            A R L    ++    ++ + ++ P+ +  +  +  
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 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 = 56.0 bits (135), Expect = 8e-10
 Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 9/85 (10%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV-------KEIRETPHKRHHKFIEFYDVRAAE 328
               L +  +      E++ +      E            +    R   F+E+   RAA 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 329 AALKSLNRSD--IAGKRIKLEPSRP 351
            A + L      + G +I ++ + P
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEP 91

>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 = 60.0 bits (146), Expect = 4e-11
 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 4/86 (4%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAAL 331
           + G L +  L+   + + L+ +FG +G + E+      T   R   FI F +   A+ A 
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65

Query: 332 KSLNRSDIAGKRIKLEPSRPGGARRN 357
           K +N   + GK IK+E ++    +  
Sbjct: 66  KDMNGKSLHGKAIKVEQAKKPSFQSG 91

>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 = 50.8 bits (122), Expect = 5e-08
 Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 12/89 (13%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDIRAA 242
               LF+  +N    +  L+A+F ++G I        RT     K RGF  I++ +   A
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT----SKSRGFAFITFENPADA 61

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
           + A + +  K L  + + +  +      S
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQS 90

>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 = 59.6 bits (145), Expect = 4e-11
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           V +L  +++ + LR IF  +G ++ I      ET   + + FI F D   A+ AL+ LN 
Sbjct: 31  VGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNG 90

Query: 337 SDIAGKRIKLEPSRP 351
            ++AG+ +K+     
Sbjct: 91  FELAGRPMKVGHVTE 105

>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 = 52.3 bits (126), Expect = 1e-08
 Identities = 20/99 (20%), Positives = 43/99 (43%), Gaps = 5/99 (5%)

Query: 176 NGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRG 230
           + A  +A     G      L+V +++ N+ +  LR +FE +G I ++         + +G
Sbjct: 10  HMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKG 69

Query: 231 FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
           +  I++ D   A+ A+  L    L  R + +     + +
Sbjct: 70  YGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 59.7 bits (145), Expect = 4e-11
 Identities = 23/107 (21%), Positives = 45/107 (42%), Gaps = 8/107 (7%)

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGE 303
           +  AL   PL    L    +       +    +G  L +++L    ++ DL   F  +G 
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGKQIEG--PEGCNLFIYHLPQEFTDTDLASTFLPFGN 66

Query: 304 VKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK 345
           V        ++T   +   F+ F +  +A+ A+K++N   +  KR+K
Sbjct: 67  VISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK 113

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 44.7 bits (106), Expect = 8e-06
 Identities = 19/108 (17%), Positives = 47/108 (43%), Gaps = 14/108 (12%)

Query: 161 SDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIR 220
           + + S + L   ++   A   AG+   G      LF+ ++     D++L + F  +G++ 
Sbjct: 10  ASALSTSPLASVALSAAAAAAAGKQIEGPEGCN-LFIYHLPQEFTDTDLASTFLPFGNV- 67

Query: 221 TLYTACK---------HRGFVMISYYDIRAARTAMRALQNKPLRRRKL 259
               + K          + F  +S+ +  +A+ A++A+    +  ++L
Sbjct: 68  ---ISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL 112

>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 = 59.1 bits (144), Expect = 4e-11
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 282 VFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           V NLD  + +E LR+ F  +G +   K + E    +   F+ F     A  A+  +N   
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRI 79

Query: 339 IAGKRIKLEPSRPGGARRN 357
           +A K + +  ++    R++
Sbjct: 80  VATKPLYVALAQRKEERQS 98

>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 = 47.2 bits (113), Expect = 7e-07
 Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 11/81 (13%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK-------HRGFVMISYYDIRAARTAMR 247
           L+V+N++  ++D  LR  F  +G I    T+ K        +GF  + +     A  A+ 
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTI----TSAKVMMEGGRSKGFGFVCFSSPEEATKAVT 73

Query: 248 ALQNKPLRRRKLDIHFSIPKD 268
            +  + +  + L +  +  K+
Sbjct: 74  EMNGRIVATKPLYVALAQRKE 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 58.9 bits (143), Expect = 5e-11
 Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 11/85 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRETPHKRHHK-----FIEFYDVRAAEAAL 331
           T+++ N+ P    + +      Y    V  IR    K+  +     F++      A   L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 332 KSLNRSD----IAGKRIKLEPSRPG 352
           + L        I GK I ++ ++  
Sbjct: 71  QILQSLHPPLKIDGKTIGVDFAKSA 95

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 17/94 (18%), Positives = 32/94 (34%), Gaps = 15/94 (15%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD--------IRTLYTACKHRGFVMI 234
           G H    H   T+ +RNI  +     +      Y          I+   T  ++RGF  +
Sbjct: 2   GHHH--HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQ-QNRGFAFV 58

Query: 235 SYYDIRAARTAMRALQNKPLRR----RKLDIHFS 264
                  A   ++ LQ+         + + + F+
Sbjct: 59  QLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 58.6 bits (142), Expect = 6e-11
 Identities = 14/71 (19%), Positives = 25/71 (35%), Gaps = 2/71 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK--FIEFYDVRAAEAALKSLNR 336
            L + N+ P +  E L  +   YG V+   +           + +     A  AL  LN 
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNG 76

Query: 337 SDIAGKRIKLE 347
             +    +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 = 52.1 bits (125), Expect = 1e-08
 Identities = 21/93 (22%), Positives = 37/93 (39%), Gaps = 3/93 (3%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR--GFVMI 234
           G+   +G  P  +   R L +RNI  +++   L +L  QYG + +            V +
Sbjct: 1   GSSGSSGSVPKRQ-RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNV 59

Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
           +Y     AR A+  L    L    L + +   +
Sbjct: 60  TYSSKDQARQALDKLNGFQLENFTLKVAYIPDE 92

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.5 bits (142), Expect = 7e-11
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           ++ V      V +  L + F A+G V  +     K     +E  DV A EA L   ++  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHS 68

Query: 339 IAGKRIKLEPSRP 351
           + G R+++ P   
Sbjct: 69  LGGHRLRVRPREQ 81

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 47.7 bits (114), Expect = 4e-07
 Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 1/86 (1%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G    R++FV      V+ ++L   F  +G + ++        F ++   D+ A    + 
Sbjct: 4   GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVL- 62

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDK 273
           +     L   +L +     K+  S  
Sbjct: 63  SQSQHSLGGHRLRVRPREQKEFQSPA 88

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 57.2 bits (139), Expect = 2e-10
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 3/83 (3%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAALKSL 334
             + V NL    + + L+  F   G V       E    +    ++F     AE A + +
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 68

Query: 335 NRSDIAGKRIKLEPSRPGGARRN 357
           N   ++G+ I +   R      +
Sbjct: 69  NGMKLSGREIDVRIDRNASGPSS 91

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 17/91 (18%), Positives = 32/91 (35%), Gaps = 11/91 (12%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-------HRGFVMISYYDIR 240
           G   +  +FVRN+  +     L+  F + G +                +G  ++ +    
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHV----LYADIKMENGKSKGCGVVKFESPE 59

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
            A  A R +    L  R++D+        PS
Sbjct: 60  VAERACRMMNGMKLSGREIDVRIDRNASGPS 90

>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 = 57.4 bits (139), Expect = 3e-10
 Identities = 17/99 (17%), Positives = 39/99 (39%), Gaps = 5/99 (5%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 318
           S           N   + V +L P ++ ED++  F  +G + +        T   + + F
Sbjct: 2   SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           + F++   AE A++ +    + G++I+   +        
Sbjct: 62  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPK 100

>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 = 47.7 bits (114), Expect = 7e-07
 Identities = 15/108 (13%), Positives = 44/108 (40%), Gaps = 7/108 (6%)

Query: 178 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGF 231
             + +            +FV +++  +   +++A F  +G       ++ + T  K +G+
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATG-KSKGY 59

Query: 232 VMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGT 279
             +S+++   A  A++ +  + L  R++  +++  K           T
Sbjct: 60  GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNT 107

>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 = 56.4 bits (137), Expect = 3e-10
 Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 5/73 (6%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           +L+ +V +E LR  F  +            +T   R + F+ F     A+ A+ S+   D
Sbjct: 8   DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD 67

Query: 339 IAGKRIKLEPSRP 351
           + G+ +++  +  
Sbjct: 68  LNGRPLRINWAAK 80

>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 = 50.2 bits (121), Expect = 4e-08
 Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 7/84 (8%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGFVMISYYDIRAARTA 245
           +  LFV ++N NV+D  LR  F+ +        +  + T    RG+  +S+     A+ A
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTG-SSRGYGFVSFTSQDDAQNA 59

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           M ++Q + L  R L I+++   ++
Sbjct: 60  MDSMQGQDLNGRPLRINWAAKLEH 83

>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 = 56.9 bits (138), Expect = 3e-10
 Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 5/83 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
           ++ V N+    + E L+ IF   G V        RET   + + F E+ D   A +A+++
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           LN  + +G+ ++++ +     + 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKE 92

>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 = 56.1 bits (136), Expect = 7e-10
 Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 6/99 (6%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIR 240
           P  +   R++FV NI     + +L+ +F + G + +          K +G+    Y D  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDN-PSDKDLNQG 278
            A +AMR L  +    R L +  +  + N    K L  G
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>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 = 56.5 bits (137), Expect = 3e-10
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 6/72 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR--HHK---FIEFYDVRAAEAALKS 333
           T+ V NL+  V  E L ++F   G + ++      R    K   F+ F    +   A+  
Sbjct: 18  TVFVGNLEARVREEILYELFLQAGPLTKVT-ICKDREGKPKSFGFVCFKHPESVSYAIAL 76

Query: 334 LNRSDIAGKRIK 345
           LN   + G+ I 
Sbjct: 77  LNGIRLYGRPIN 88

>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 = 55.7 bits (135), Expect = 7e-10
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 4/87 (4%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFV 232
           G+   +G  P  E   RT+FV N+ + V +  L  LF Q G +  +        K + F 
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKL 259
            + +    +   A+  L    L  R +
Sbjct: 61  FVCFKHPESVSYAIALLNGIRLYGRPI 87

>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 = 56.0 bits (136), Expect = 4e-10
 Identities = 13/73 (17%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           +L P ++   +   F  +G + + R      T   + + F+ F++   AE A++ +    
Sbjct: 13  DLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW 72

Query: 339 IAGKRIKLEPSRP 351
           + G++I+   +  
Sbjct: 73  LGGRQIRTNWATR 85

>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 = 46.0 bits (110), Expect = 1e-06
 Identities = 14/83 (16%), Positives = 40/83 (48%), Gaps = 7/83 (8%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD------IRTLYTACKHRGFVMISYYDIRAART 244
               +FV +++  +  + + A F  +G       ++ + T  K +G+  +S+++   A  
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATG-KSKGYGFVSFFNKWDAEN 63

Query: 245 AMRALQNKPLRRRKLDIHFSIPK 267
           A++ +  + L  R++  +++  K
Sbjct: 64  AIQQMGGQWLGGRQIRTNWATRK 86

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 57.0 bits (138), Expect = 4e-10
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 13/86 (15%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RETPHKRHHKFIEFYDVR 325
           T+ V  L  +V+ E +   F   G +K               RET   +    + F D  
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRP 351
           +A+AA+   +  + +G  IK+  +  
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFATR 94

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 56.3 bits (136), Expect = 7e-10
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 13/96 (13%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRT----------LYT---ACKHRGFVMISYY 237
            + T+FV+ +  NV    +   F+Q G I+T          LYT     K +G   +S+ 
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 238 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDK 273
           D  +A+ A+     K      + + F+  + + +  
Sbjct: 66  DPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRG 101

>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 = 56.5 bits (137), Expect = 6e-10
 Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 5/80 (6%)

Query: 277 QGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAAL 331
             T L + NL  S+  ++L  +   +G+V   R     +   R   F         EA +
Sbjct: 24  DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVI 83

Query: 332 KSLNRSDIAGKRIKLEPSRP 351
              N   I        P+ P
Sbjct: 84  GHFNGKFIKTPPGVSAPTEP 103

>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 = 44.9 bits (107), Expect = 7e-06
 Identities = 10/90 (11%), Positives = 27/90 (30%), Gaps = 17/90 (18%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDIRAARTAM 246
           L++ N+  ++++ EL  + + +G +     + +         RG               +
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQV----ISTRILRDSSGTSRGVGFARMESTEKCEAVI 83

Query: 247 RALQNKPLRRRKLDIHFSIPK-----DNPS 271
                K ++        + P         S
Sbjct: 84  GHFNGKFIKTPPGVSAPTEPLLCKFSGPSS 113

>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 = 56.3 bits (136), Expect = 8e-10
 Identities = 23/101 (22%), Positives = 41/101 (40%), Gaps = 13/101 (12%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RET 310
           S       D+D +   + V  L+ SV+ +DL   F   G VK               +ET
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 311 PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
              +    + + D   A+AA++  +  D  G ++K+  +R 
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 102

>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 = 49.3 bits (118), Expect = 2e-07
 Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 13/93 (13%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-------------RGFVMISYYD 238
           +  ++V+ +N +V   +L   F+Q G ++      +              +G   +SY D
Sbjct: 15  NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74

Query: 239 IRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
              A+ A+     K  +  KL +  +  K   +
Sbjct: 75  PPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.9 bits (135), Expect = 8e-10
 Identities = 11/89 (12%), Positives = 33/89 (37%), Gaps = 5/89 (5%)

Query: 273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHK---FIEFYDVRAAE 328
            D+   ++ +       + +D+++     G+V  I+      +  K   F+ F  + +A+
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66

Query: 329 AALKSLNRSDIAGKRIKLEPSRPGGARRN 357
             ++           + +       A++N
Sbjct: 67  KFVE-TPGQKYKETDLLILFKDDYFAKKN 94

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.3 bits (105), Expect = 7e-06
 Identities = 8/77 (10%), Positives = 31/77 (40%), Gaps = 5/77 (6%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL----YTACKHRGFVMISYYDIRAART 244
           +  +R+++++   ++    +++   E  G +  +          +G + + +  I +A+ 
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 245 AMRALQNKPLRRRKLDI 261
            +     +  +   L I
Sbjct: 68  FV-ETPGQKYKETDLLI 83

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 6/84 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            + V NL  S ++E ++++F  +G+V  +     RET   +   F+E  +  +   A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
           L+ +D  G+ I++  + P  +  +
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEH 85

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMR 247
           R ++V N+  +    +++ LF Q+G +  +         K +GF  +   +  +   A+ 
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPSDKD 274
            L N     R + +  + PK +     
Sbjct: 61  KLDNTDFMGRTIRVTEANPKKSLEHHH 87

>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 = 54.9 bits (133), Expect = 1e-09
 Identities = 17/88 (19%), Positives = 41/88 (46%), Gaps = 6/88 (6%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI------RETPHKRHHKFIEFYDVRAAEA 329
               + + NLDP +  + L   F A+G + +        +T + + + FI F    A++A
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 330 ALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           A++++N   +  + I +  +    ++ +
Sbjct: 64  AIEAMNGQYLCNRPITVSYAFKKDSKGS 91

>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 = 46.8 bits (112), Expect = 1e-06
 Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 14/92 (15%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH----------RGFVMISYY 237
           G   S  +F+ N++  +++  L   F  +G I                   +G+  I++ 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVI----LQTPKIMRDPDTGNSKGYAFINFA 56

Query: 238 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
              A+  A+ A+  + L  R + + ++  KD+
Sbjct: 57  SFDASDAAIEAMNGQYLCNRPITVSYAFKKDS 88

>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 = 54.6 bits (132), Expect = 2e-09
 Identities = 16/91 (17%), Positives = 29/91 (31%), Gaps = 5/91 (5%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 320
                S        + V N+  +VS +++   F  Y  +       +           + 
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           F     A AA+  LN   I  +++KL     
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>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 = 48.8 bits (117), Expect = 2e-07
 Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 5/94 (5%)

Query: 179 GTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVM 233
            + +     G+     + V+N+   V   E+   F  Y  I        +      G  M
Sbjct: 2   SSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
           +++     A  A+  L ++P+  RK+ +      
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP 95

>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 = 54.6 bits (132), Expect = 2e-09
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 13/95 (13%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH---------- 316
             +      +  T+ V  L  +V+ E +   F   G +K  ++T     +          
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 317 K---FIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 348
           K    + F D  +A+AA+   +  + +G  IK+  
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>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 = 52.3 bits (126), Expect = 1e-08
 Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 13/82 (15%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-------------RGFVMISYY 237
            + T+FV+ +  NV    +   F+Q G I+T     +              +G   +S+ 
Sbjct: 12  DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71

Query: 238 DIRAARTAMRALQNKPLRRRKL 259
           D  +A+ A+     K      +
Sbjct: 72  DPPSAKAAIDWFDGKEFSGNPI 93

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 54.3 bits (130), Expect = 2e-09
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
           S  L ++N+ + ++   LR L  Q+G + + +      G  +  Y     A  A  AL N
Sbjct: 7   SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ-GIALCKYTTREEANKAQMALNN 65

Query: 252 KPLRRRKLDIHFSIPKDNPSDKDLNQ 277
             L    +          PS+ ++  
Sbjct: 66  CVLANTTIFAES------PSENEVQS 85

>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 = 54.2 bits (131), Expect = 2e-09
 Identities = 17/92 (18%), Positives = 30/92 (32%), Gaps = 5/92 (5%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 320
                S        + V N+  +VS +++   F  Y  +       +           + 
Sbjct: 4   GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG 352
           F     A AA+  LN   I  +++KL     G
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95

>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 = 50.4 bits (121), Expect = 5e-08
 Identities = 16/92 (17%), Positives = 33/92 (35%), Gaps = 5/92 (5%)

Query: 178 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFV 232
             + +     G+     + V+N+   V   E+   F  Y  I        +      G  
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFS 264
           M+++     A  A+  L ++P+  RK+ +   
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>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 = 54.5 bits (131), Expect = 3e-09
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 3/69 (4%)

Query: 279 TLVVFN--LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           +LVV N  L   VS   L  +    G V  +   P+K  + F  +     ++ A  +LN 
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESKRAYVTLNG 85

Query: 337 SDIAGKRIK 345
            ++     +
Sbjct: 86  KEVVDDLGQ 94

>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 = 53.4 bits (128), Expect = 8e-09
 Identities = 13/90 (14%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 189 EHPSRTLFVRN--INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAM 246
            + +++L V N  + + V  ++L  + E+ G +  L     ++ +    Y     ++ A 
Sbjct: 22  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAY 80

Query: 247 RALQNK---PLRRRKLDIHFSIPKDNPSDK 273
             L  K       +K+ ++ +  +      
Sbjct: 81  VTLNGKEVVDDLGQKITLYLNFVEKVQWSG 110

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 54.6 bits (131), Expect = 3e-09
 Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-FIEFYDVRAAEAALKSLNRSD 338
           ++V NL   V+ + L QIF  +G V +I         +  +++ D  +A+ A  SL+  +
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 90

Query: 339 I--AGKRIKLEPSRP 351
           I  A   ++++ S+ 
Sbjct: 91  IYNACCTLRIDFSKL 105

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 51.2 bits (122), Expect = 7e-08
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 7/102 (6%)

Query: 172 YSVPNGAGTVAGEHPYGEHPSRTLF--VRNINSNVEDSELRALFEQYGDIRTLYTACKHR 229
               + A   AG        S  L   V N+   V    L  +F ++G +  + T  K+ 
Sbjct: 8   ALAASAAAVDAGMAM--AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN 65

Query: 230 GF-VMISYYDIRAARTAMRALQNKPL--RRRKLDIHFSIPKD 268
            F  ++ Y D  +A+ A  +L  + +      L I FS    
Sbjct: 66  QFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 107

>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 Length = 90

 Score = 53.4 bits (129), Expect = 4e-09
 Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 284 NLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           NL    ++EDL +   + G  ++ EI     R     +    +      +++  +  L +
Sbjct: 8   NLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK 67

Query: 337 SDIAGKRIKLEPSRPGGARRN 357
            ++ G+   + PS       +
Sbjct: 68  RELHGQNPVVTPSNKLEHHHH 88

>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 Length = 90

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 9/82 (10%)

Query: 195 LFVRNINSNVEDSELRALFEQYG-----DIRTLY---TACKHRGFVMISYYDIRAARTAM 246
           L++ N+     D +L       G     +I+         + +GF ++      +++  M
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANG-QSKGFALVGVGSEASSKKLM 62

Query: 247 RALQNKPLRRRKLDIHFSIPKD 268
             L  + L  +   +  S   +
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLE 84

>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 = 53.9 bits (130), Expect = 5e-09
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
            L+V NLD  VS+ D++++F  +G +K+       +        + F     A  A+K  
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96

Query: 335 NRSDIAGKRIKLEPSRPGGARR 356
               + G+ + ++         
Sbjct: 97  KGVPLDGRPMDIQLVASQIDLE 118

>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 = 48.1 bits (115), Expect = 7e-07
 Identities = 18/98 (18%), Positives = 35/98 (35%), Gaps = 12/98 (12%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDI 239
           G      L V N++  V D++++ LF ++G +                  G   + +   
Sbjct: 31  GVETGAKLLVSNLDFGVSDADIQELFAEFGTL----KKAAVDYDRSGRSLGTADVHFERR 86

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 277
             A  AM+  +  PL  R +DI     + +      + 
Sbjct: 87  ADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 55.2 bits (133), Expect = 5e-09
 Identities = 20/122 (16%), Positives = 41/122 (33%), Gaps = 5/122 (4%)

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 299
                     + KPL  +     F          +     L+V NLD  VS+ D++++F 
Sbjct: 52  GGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVE-TGAKLLVSNLDFGVSDADIQELFA 110

Query: 300 AYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR 355
            +G +K+       +        + F     A  A+K      + G+ + ++        
Sbjct: 111 EFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 170

Query: 356 RN 357
            +
Sbjct: 171 EH 172

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 4/96 (4%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT---LYTAC-KHRGFVMISYYDIRA 241
             G      L V N++  V D++++ LF ++G ++     Y    +  G   + +     
Sbjct: 82  GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD 141

Query: 242 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 277
           A  AM+  +  PL  R +DI     + +      + 
Sbjct: 142 ALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 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 = 53.4 bits (129), Expect = 6e-09
 Identities = 20/102 (19%), Positives = 41/102 (40%), Gaps = 5/102 (4%)

Query: 251 NKPLRRRKLDIHFSIPKDNPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR- 308
           ++P +      H            +  G  L+V NLD  VS+ D++++F  +G +K+   
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

Query: 309 ---ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
               +        + F     A  A+K  N   + G+ + ++
Sbjct: 62  HYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 103

>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 = 44.6 bits (106), Expect = 7e-06
 Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------HRGFVMISYYDI 239
           G      L V N++  V D++++ LF ++G +                  G   + +   
Sbjct: 25  GVETGGKLLVSNLDFGVSDADIQELFAEFGTL----KKAAVHYDRSGRSLGTADVHFERK 80

Query: 240 RAARTAMRALQNKPLRRRKLDIHF 263
             A  AM+     PL  R ++I  
Sbjct: 81  ADALKAMKQYNGVPLDGRPMNIQL 104

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 56.3 bits (135), Expect = 7e-09
 Identities = 21/113 (18%), Positives = 43/113 (38%), Gaps = 11/113 (9%)

Query: 256 RRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSN---------EDLRQIFGAYGEVKE 306
           R K   +        S +  N+ TL V  +D ++++           +R +F   G++  
Sbjct: 114 REKFADYREDMGGIGSFRKKNK-TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDR 172

Query: 307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 359
           IR     ++  F++F     AE A ++++   +     K    R  G    + 
Sbjct: 173 IR-YVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVK 224

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 49.8 bits (118), Expect = 1e-06
 Identities = 21/98 (21%), Positives = 36/98 (36%), Gaps = 12/98 (12%)

Query: 183 GEHPYGEHPSRTLFVRNINSNV---------EDSELRALFEQYGDIRTL-YTACKHRGFV 232
           G        ++TL+V  I+  +          +S +R +F + GDI  + Y   K+ GFV
Sbjct: 125 GGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFV 184

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNP 270
              +     A  A  A+ N+ L            +   
Sbjct: 185 --KFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220

>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 = 58.3 bits (140), Expect = 9e-09
 Identities = 56/517 (10%), Positives = 131/517 (25%), Gaps = 181/517 (35%)

Query: 9   SGPPKIPQLNIPKE---------------------VGGGSCGRIAGSDSYLASDDASLFS 47
           +      + N+ +                       G    G+     +++A D     S
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK-----TWVALD--VCLS 173

Query: 48  SSLPVLPHEKLNLNA--MGLGR-QSVDDISSGLSKVHHGVASDDPLEGVMNPAIGNSLPD 104
             +      K++     + L    S + +   L K+ + +   DP          +++  
Sbjct: 174 YKV----QCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI---DP-NWTSRSDHSSNIKL 225

Query: 105 DEDELLAGIMDDFDLRGLPSSLEDLED------YDIFGSGGGMELEGEPQESLSMSMSKI 158
               + A +      +   + L  L +      ++ F                     KI
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS-----------------CKI 268

Query: 159 -------SISDSASGNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRA 211
                   ++D  S     H S+                  ++L ++ ++   +D     
Sbjct: 269 LLTTRFKQVTDFLSAATTTHISL------DHHSMTLTPDEVKSLLLKYLDCRPQD----- 317

Query: 212 LFEQYGDIRTLYTACKHRGFV--MIS--------------YYDIRAARTAMRA-LQN-KP 253
           L  +                   +I+              + +     T + + L   +P
Sbjct: 318 LPRE---------VLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP 368

Query: 254 LRRRKLDIHFSI-PKDN--PSDKDLNQGTLVVF--NLDPSV-----------------SN 291
              RK+    S+ P     P+        L +   ++  S                    
Sbjct: 369 AEYRKMFDRLSVFPPSAHIPTI------LLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK 422

Query: 292 EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV--------------------------R 325
           E    I   Y E+K   E  +  H   ++ Y++                          +
Sbjct: 423 ESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLK 482

Query: 326 AAEAALKS-------LNRSDIAGK-RIKLEPSRPGGARRNLMLQLN------QELEQDES 371
             E   +        L+   +  K R         G+  N + QL        + +    
Sbjct: 483 NIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYE 542

Query: 372 RILQ------HQVGSPITNSPPGNWVQFSSPIEHNPL 402
           R++        ++   +  S   + ++ +   E   +
Sbjct: 543 RLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAI 579

>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 = 49.9 bits (118), Expect = 3e-06
 Identities = 47/396 (11%), Positives = 96/396 (24%), Gaps = 133/396 (33%)

Query: 498 VETLSGP--QFLWGSPSRYSEHSSSPAWQTSSMGHPFSSNGKIHGLPYSGRQGSFLGSSQ 555
           VE +     +FL    S        P+  T                 Y  ++      +Q
Sbjct: 83  VEEVLRINYKFLM---SPIKTEQRQPSMMTRM---------------YIEQRDRLYNDNQ 124

Query: 556 ---HHHVGSAPSGVPLER-RFGFLPESPETSFMNPVAFCGM-GIG--------------- 595
               ++V       P  + R   L   P  +    V   G+ G G               
Sbjct: 125 VFAKYNV---SRLQPYLKLRQALLELRPAKN----VLIDGVLGSGKTWVALDVCLSYKVQ 177

Query: 596 --QNDGSFMVNMGSRASVNPGITVPRNLSDNGSSFRVMSSPRLSPVFLGNGPYPGLTPAN 653
              +   F +N+ +  S    + + + L             ++ P +     +       
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLY-----------QIDPNWTSRSDHSSNIKLR 226

Query: 654 IEGLYERGR----SRRIEN------------------------------NNGNQLDSKKQ 679
           I  +    R    S+  EN                                 + L +   
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT 286

Query: 680 FQLELEKIRSGEDTRTTLMI---------KNIPN--KYTSKMLLAAIDE---NHKGTYDF 725
             + L+             +         +++P     T+   L+ I E   +   T+D 
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN 346

Query: 726 LYLPIDFKNKCNVGYAFINMLSPLHIIPFYEAF----NGKK---------WEKFNSEKVA 772
            +  ++      +  + +N+L P      ++                   W       V 
Sbjct: 347 -WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVM 405

Query: 773 SLAYARIQGRAALVAHFQNSSLMNEDKRCRPILFHS 808
            +           V      SL+ +  +   I   S
Sbjct: 406 VV-----------VNKLHKYSLVEKQPKESTISIPS 430

>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 = 52.7 bits (127), Expect = 9e-09
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 10/78 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGE----VKEIR--ETPHKRHHKFIEFYDVRAAEAALK 332
           +L + +L+P +    + + F   GE    VK IR   T     + F+EF D+  AE  L 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 333 SLNRSDIAG----KRIKL 346
            +N   + G    KR KL
Sbjct: 71  KINGKPLPGATPAKRFKL 88

>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 = 13/82 (15%), Positives = 32/82 (39%), Gaps = 8/82 (9%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD-------IRTLYTACKHRGFVMISYYDIRAAR 243
            + +L++ ++   ++++ +   F   G+       IR   T     G+  + + D+  A 
Sbjct: 8   MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTG-IPAGYCFVEFADLATAE 66

Query: 244 TAMRALQNKPLRRRKLDIHFSI 265
             +  +  KPL        F +
Sbjct: 67  KCLHKINGKPLPGATPAKRFKL 88

>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 = 52.9 bits (127), Expect = 9e-09
 Identities = 13/83 (15%), Positives = 34/83 (40%), Gaps = 12/83 (14%)

Query: 277 QGTLV-VFNLDPSVSNEDL---RQIFGAYGEVKEI-----RETPHKRHHK---FIEFYDV 324
           Q  LV V  L   +++ ++    + FG +G++ ++           +      ++ +   
Sbjct: 14  QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 325 RAAEAALKSLNRSDIAGKRIKLE 347
             A  A++ +N   + G+ +K  
Sbjct: 74  EDALRAIQCVNNVVVDGRTLKAS 96

>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 = 39.5 bits (92), Expect = 5e-04
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 11/85 (12%)

Query: 194 TLFVRNINSNVEDSEL---RALFEQYGDI-------RTLYTACK-HRGFVMISYYDIRAA 242
            +FV  ++  + D E+      F ++G I        T Y   +       ++Y     A
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPK 267
             A++ + N  +  R L       K
Sbjct: 77  LRAIQCVNNVVVDGRTLKASLGTTK 101

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.8 bits (127), Expect = 1e-08
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 11/88 (12%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNE-------DLRQIFGAYGEVKEI---RETPHKRHH 316
           KD P + D     +VV N+ P V  +        + +IF  +G++       E    + +
Sbjct: 5   KDRPQEADGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGY 63

Query: 317 KFIEFYDVRAAEAALKSLNRSDIAGKRI 344
            F+E+     A  A+K+ +   +  +  
Sbjct: 64  IFLEYASPAHAVDAVKNADGYKLDKQHT 91

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 41.6 bits (98), Expect = 7e-05
 Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 9/75 (12%)

Query: 189 EHPSRTLFVRNINSNVEDSE------LRALFEQYGDIRTLYTAC---KHRGFVMISYYDI 239
           +     + V N+     D        +  +F ++G I   +      K +G++ + Y   
Sbjct: 12  DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASP 71

Query: 240 RAARTAMRALQNKPL 254
             A  A++      L
Sbjct: 72  AHAVDAVKNADGYKL 86

>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 = 52.3 bits (126), Expect = 2e-08
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           T+ V NLD  V  + L+++F   G V        +    R    + F     A  A+   
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76

Query: 335 NRSDIAGKRIKLEPSRPGGARRN 357
           N   +  + + ++       + +
Sbjct: 77  NGQLLFDRPMHVKMDERALPKGD 99

>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 = 45.4 bits (108), Expect = 5e-06
 Identities = 17/100 (17%), Positives = 33/100 (33%), Gaps = 13/100 (13%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--------H 228
           G+   +G    G     T+FV N++  V   +L+ +F   G +                 
Sbjct: 1   GSSGSSGALQAGR-LGSTVFVANLDYKVGWKKLKEVFSMAGVV----VRADILEDKDGKS 55

Query: 229 RGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 268
           RG   +++     A  A+     + L  R + +       
Sbjct: 56  RGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERAL 95

>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 = 52.4 bits (126), Expect = 2e-08
 Identities = 11/93 (11%), Positives = 30/93 (32%), Gaps = 6/93 (6%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----F 318
           S       D +  +    + N+  S++  D+ Q        +         + +      
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           ++F +   A  + + L+R  + G+   +     
Sbjct: 62  VQFKNEDDARKSER-LHRKKLNGREAFVHVVTL 93

>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 = 41.3 bits (97), Expect = 1e-04
 Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 6/86 (6%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYG----DIRTLYTAC-KHRGFVMISYYDIRAA 242
                    + NI  ++   ++    E        +  L     +  G  ++ + +   A
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKD 268
           R + R L  K L  R+  +H    +D
Sbjct: 71  RKSER-LHRKKLNGREAFVHVVTLED 95

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 51.8 bits (125), Expect = 2e-08
 Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
            +D  +   ++R  F  YG VKE++     T   + + F+ FY+    +  ++  ++ + 
Sbjct: 16  GIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINF 73

Query: 340 AGKRIKLEPSRP 351
            GK++KL P+  
Sbjct: 74  HGKKLKLGPAIR 85

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 49.9 bits (120), Expect = 9e-08
 Identities = 23/103 (22%), Positives = 48/103 (46%), Gaps = 7/103 (6%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRA 241
           P G+    T+FV  I+  ++++E+R+ F +YG ++ +          +G+  +S+Y+   
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62

Query: 242 ARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFN 284
            +  +          +KL +  +I K N S     Q   ++FN
Sbjct: 63  VQKIVE--SQINFHGKKLKLGPAIRKQNLSTYH-VQPRPLIFN 102

>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 = 51.8 bits (124), Expect = 3e-08
 Identities = 14/98 (14%), Positives = 33/98 (33%), Gaps = 6/98 (6%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 320
            +            + +  L     N+ +   F     V++     +  + K     F+E
Sbjct: 14  KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVE 73

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
           F +    +AAL   ++  +  + I++ P    G    +
Sbjct: 74  FRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKI 110

>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 = 55.6 bits (133), Expect = 4e-08
 Identities = 25/113 (22%), Positives = 47/113 (41%), Gaps = 7/113 (6%)

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFG 299
              +   +  + +     +L +    P ++P+ +     TL V  ++   +   LR+ F 
Sbjct: 67  MERKRREKIERRQQEVETELKMW--DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFE 124

Query: 300 AYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
            YG +K I     KR  K     FIE+   R   +A K  +   I G+R+ ++
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 177

>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 = 48.3 bits (114), Expect = 8e-06
 Identities = 28/133 (21%), Positives = 48/133 (36%), Gaps = 7/133 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
             +TLFV  +N +  +S+LR  FE YG I+ ++        K RG+  I Y   R   +A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160

Query: 246 MRALQNKPL--RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
            +    K +  RR  +D+           + L  G          V+     +   +  +
Sbjct: 161 YKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYD 220

Query: 304 VKEIRETPHKRHH 316
            +        R  
Sbjct: 221 ERPGPSPLPHRDR 233

>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 = 51.2 bits (123), Expect = 4e-08
 Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 8/94 (8%)

Query: 182 AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISY 236
           +G     +H +  LF+  I  N+++ +L+ LFE++G I  L          H+G   ++Y
Sbjct: 3   SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62

Query: 237 YDIRAARTAMRALQNK---PLRRRKLDIHFSIPK 267
            +  +A  A  AL  +   P   R + +  +  +
Sbjct: 63  CERESALKAQSALHEQKTLPGMNRPIQVKPADSE 96

>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 = 14/71 (19%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 324
              KD +   L +  +  ++  +DL+ +F  +G++ E+     R T   +   F+ + + 
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65

Query: 325 RAAEAALKSLN 335
            +A  A  +L+
Sbjct: 66  ESALKAQSALH 76

>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 Length = 104

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 8/85 (9%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK------FIEFYDVRAAEAALK 332
           T  + NL   V+ E +++ F     +  +R      + +      + EF D+ +  +AL 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 333 SLNRSDIAGKRIKLEPSRPGGARRN 357
            LN   +  KRI+++ +     + +
Sbjct: 76  -LNEESLGNKRIRVDVADQAQDKDS 99

>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 Length = 104

 Score = 46.9 bits (112), Expect = 1e-06
 Identities = 13/97 (13%), Positives = 37/97 (38%), Gaps = 6/97 (6%)

Query: 178 AGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYG-----DIRTLYTACKHRGFV 232
             + +      + P  T F+ N+  +V +  ++  F           R      + +GF 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
              + D+ +  +A+ +L  + L  +++ +  +    +
Sbjct: 61  YAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD 96

>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 = 51.1 bits (122), Expect = 5e-08
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 4/79 (5%)

Query: 189 EHPSRTLFVRNI-NSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           +   R + + N+ +S   DS +  L E YG I+      + +    I       A   + 
Sbjct: 22  QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVD 80

Query: 248 ALQNKP--LRRRKLDIHFS 264
               K    + R + +  S
Sbjct: 81  HCLKKALWFQGRCVKVDLS 99

>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 = 41.5 bits (97), Expect = 1e-04
 Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 4/75 (5%)

Query: 279 TLVVFNL-DPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLN 335
            + + NL     S+  + ++   YG++K       K    FIE      A A +      
Sbjct: 27  VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS-QAFIEMETREDAMAMVDHCLKK 85

Query: 336 RSDIAGKRIKLEPSR 350
                G+ +K++ S 
Sbjct: 86  ALWFQGRCVKVDLSE 100

>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 = 50.7 bits (122), Expect = 5e-08
 Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 10/88 (11%)

Query: 269 NPSDKDLNQGT-LVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYD 323
           + S+    +   L V  L+   S ED+ ++F  +G + E           +   F++F  
Sbjct: 6   SGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSS 65

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRP 351
              A+AA+ +L+     G +     S  
Sbjct: 66  HTEAQAAIHALH-----GSQTMPGASSS 88

>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 = 50.4 bits (121), Expect = 7e-08
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 10/97 (10%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC----KHRGFVMISYYDIRAART 244
               R LFV  +N    + ++  LF+ +G I             +G   + +     A+ 
Sbjct: 12  GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQA 71

Query: 245 AMRALQNK---PLRRRKLDIHFSIPKDNPSDKDLNQG 278
           A+ AL      P     L + F+   D   +   + G
Sbjct: 72  AIHALHGSQTMPGASSSLVVKFA---DTDKESGPSSG 105

>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 = 51.0 bits (122), Expect = 6e-08
 Identities = 19/93 (20%), Positives = 34/93 (36%), Gaps = 6/93 (6%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----F 318
            + + + S    N G + +  L    + E++ Q F     V      P     K     F
Sbjct: 29  QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           ++F     AE AL   ++  I  + I++  S  
Sbjct: 89  VQFASQELAEKALG-KHKERIGHRYIEVFKSSQ 120

>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 = 41.0 bits (96), Expect = 2e-04
 Identities = 12/101 (11%), Positives = 30/101 (29%), Gaps = 6/101 (5%)

Query: 173 SVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT-----LYTACK 227
           S+  G     G +         + +R +       E+   F     +       +    K
Sbjct: 23  SMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK 82

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 268
             G   + +     A  A+     + +  R +++  S  ++
Sbjct: 83  ITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKSSQEE 122

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 51.4 bits (123), Expect = 6e-08
 Identities = 17/97 (17%), Positives = 33/97 (34%), Gaps = 4/97 (4%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRETPHKRHHK--FIEFY 322
                + +      + +  L    +  D+   F     V+  I   P  R      +EF 
Sbjct: 35  GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFA 94

Query: 323 DVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLM 359
               A AA+   +R+++  + I+L  +   GA     
Sbjct: 95  THEEAVAAMS-KDRANMQHRYIELFLNSTTGASNGAY 130

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 50.4 bits (121), Expect = 8e-08
 Identities = 25/97 (25%), Positives = 42/97 (43%), Gaps = 6/97 (6%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIE 320
              + S KD     + V  L    ++  LR+ F  +G+++E      R+T   R + F+ 
Sbjct: 6   SGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
             D  AAE A K  N   I G++  +  +  G   R+
Sbjct: 66  MADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPRS 101

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 50.4 bits (121), Expect = 9e-08
 Identities = 25/121 (20%), Positives = 43/121 (35%), Gaps = 17/121 (14%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------K 227
            +G+        +     +FV  +  +  D+ LR  FE +GDI                K
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDI----EEAVVITDRQTGK 57

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDP 287
            RG+  ++  D  AA  A +   N  +  RK +++ +     P      Q    +    P
Sbjct: 58  SRGYGFVTMADRAAAERACKDP-NPIIDGRKANVNLAYLGAKPRS---LQTGFAIGVSGP 113

Query: 288 S 288
           S
Sbjct: 114 S 114

>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 = 50.1 bits (120), Expect = 9e-08
 Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 6/91 (6%)

Query: 271 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVR 325
           S    N G + +  L    S E++ Q F     V      P     +     F++F    
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
            AE ALK  ++  I  + I++  S     R 
Sbjct: 69  IAEKALK-KHKERIGHRYIEIFKSSRAEVRT 98

>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 Length = 96

 Score = 49.6 bits (118), Expect = 9e-08
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 6/83 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQI----FGAYGEVKEIRETPHKRHHK--FIEFYDVRAAEAALK 332
            + V N+D  +S ++L+Q+    F  +G+VK +  +PH  +     ++  +++ A  A+ 
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVN 70

Query: 333 SLNRSDIAGKRIKLEPSRPGGAR 355
           SL+R  I  K+I +  +      
Sbjct: 71  SLHRYKIGSKKILVSLATGASGP 93

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 51.5 bits (123), Expect = 1e-07
 Identities = 11/80 (13%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAAL 331
            + V +     +++ L Q+  + G  +V E+     R     + +  +      +    L
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 332 KSLNRSDIAGKRIKLEPSRP 351
           + L    + G+++ + P+  
Sbjct: 117 ELLPGKVLNGEKVDVRPATR 136

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 46.5 bits (110), Expect = 5e-06
 Identities = 11/104 (10%), Positives = 32/104 (30%), Gaps = 7/104 (6%)

Query: 175 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-------K 227
            N    +   +    +    ++V + +    D +L  +    G    +           +
Sbjct: 38  NNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQ 97

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
            +G+  +      +    +  L  K L   K+D+  +  ++   
Sbjct: 98  SKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQ 141

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 5/72 (6%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALK 332
           G  V+ +    V  + L  +F   G+V  +       T   +   F+E   +  A+  +K
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 333 SLNRSDIAGKRI 344
           S +   +  K  
Sbjct: 73  SFHGKRLDLKHR 84

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 38.6 bits (90), Expect = 8e-04
 Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 196 FVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRALQ 250
            + +    V    L +LF + G +  +         K +GF+ +    +  A+  +++  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 251 NKPL 254
            K L
Sbjct: 76  GKRL 79

>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 Length = 108

 Score = 48.6 bits (116), Expect = 3e-07
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            +VV  L PS S +DL+      G+V       ++     +EF        A++ L+ + 
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYADV--YRDGTGVVEFVRKEDMTYAVRKLDNTK 74

Query: 339 IAGKRIKLEPSRP 351
                 +    R 
Sbjct: 75  FRSHEGETAYIRV 87

>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 Length = 108

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 5/82 (6%)

Query: 185 HPYGEHPSRT---LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRA 241
              G    R+   + V  +  +    +L+    + GD+   Y      G  ++ +     
Sbjct: 5   SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEFVRKED 62

Query: 242 ARTAMRALQNKPLRRRKLDIHF 263
              A+R L N   R  + +  +
Sbjct: 63  MTYAVRKLDNTKFRSHEGETAY 84

>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 Length = 115

 Score = 48.3 bits (115), Expect = 4e-07
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            +VV  L PS S +DL+      G+V       ++     +EF        A++ L+ + 
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYAD--VYRDGTGVVEFVRKEDMTYAVRKLDNTK 75

Query: 339 IAGKRIKLEPSRP 351
                 +    R 
Sbjct: 76  FRSHEGETAYIRV 88

>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 Length = 115

 Score = 46.4 bits (110), Expect = 2e-06
 Identities = 13/87 (14%), Positives = 27/87 (31%), Gaps = 2/87 (2%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 236
           G        P        + V  +  +    +L+    + GD+   Y      G  ++ +
Sbjct: 1   GGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEF 58

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHF 263
                   A+R L N   R  + +  +
Sbjct: 59  VRKEDMTYAVRKLDNTKFRSHEGETAY 85

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 48.0 bits (115), Expect = 4e-07
 Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 11/85 (12%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK------FIEFYDVRAAEAALK 332
           T  + NL   V+ E +++ F     +  +R      + +      + EF D+ +  +AL 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 333 SLNRSDIAGKRIKLEPSRPGGARRN 357
            LN   +  +RI+++ +      ++
Sbjct: 80  -LNEESLGNRRIRVDVADQ---AQD 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 47.2 bits (113), Expect = 6e-07
 Identities = 14/92 (15%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYG--DIRTLY---TACKHRGFVMISYY 237
                 + P  T F+ N+  +V +  ++  F       +R         + +GF    + 
Sbjct: 10  HRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFE 69

Query: 238 DIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
           D+ +  +A+ +L  + L  R++ +  +    +
Sbjct: 70  DLDSLLSAL-SLNEESLGNRRIRVDVADQAQD 100

>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 Length = 229

 Score = 50.1 bits (119), Expect = 7e-07
 Identities = 18/152 (11%), Positives = 43/152 (28%), Gaps = 13/152 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYG--EVKEI-----RETPHKRHHKFIEFYDVRAAEAAL 331
            L + NL    ++EDL +   + G  ++ EI     R     +    +      +++  +
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 332 KSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPPGNWV 391
             L + ++ G+   + P       +       +   +  ++  Q             +  
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQ------FEMQSRKTTQSGQMSGEGKAGPPGGSSRA 183

Query: 392 QFSSPIEHNPLQTISKSPNFRNMSPTTSNHMP 423
            F            +     R   P      P
Sbjct: 184 AFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPP 215

>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 Length = 229

 Score = 47.0 bits (111), Expect = 7e-06
 Identities = 14/111 (12%), Positives = 33/111 (29%), Gaps = 7/111 (6%)

Query: 175 PNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYG--DIRTLYTAC-----K 227
             G G               L++ N+     D +L       G  DI  +         +
Sbjct: 51  DVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQ 110

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQG 278
            +GF ++      +++  M  L  + L  +   +     +     +  ++ 
Sbjct: 111 SKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 161

>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 = 46.7 bits (111), Expect = 1e-06
 Identities = 15/90 (16%), Positives = 33/90 (36%), Gaps = 6/90 (6%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHK--FIEF 321
               P   + +   + V  +  S    D+R  F     V  +   +    R++    ++F
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKF 63

Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
              +    ALK  NR  +  + +++ P+  
Sbjct: 64  LSPQDTFEALK-RNRMLMIQRYVEVSPATE 92

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 11/76 (14%)

Query: 279 TLVVFNLDPSVSNE-------DLRQIFGAYGEVKEI---RETPHKRHHKFIEFYDVRAAE 328
            +VV N+ P V  +        + +IF  +G++       E    + + F+E+     A 
Sbjct: 3   VIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61

Query: 329 AALKSLNRSDIAGKRI 344
            A+K+ +   +  +  
Sbjct: 62  DAVKNADGYKLDKQHT 77

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 9/70 (12%)

Query: 194 TLFVRNINSNVED------SELRALFEQYGDIRTLYTAC---KHRGFVMISYYDIRAART 244
            + V N+     D      + +  +F ++G I   +      K +G++ + Y     A  
Sbjct: 3   VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62

Query: 245 AMRALQNKPL 254
           A++      L
Sbjct: 63  AVKNADGYKL 72

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 7/84 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           T  V NL  +    D+  IF     ++ +R     +T   +   ++EF +V + + AL  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74

Query: 334 LNRSDIAGKRIKLEPSRPGGARRN 357
            + + +  + ++++ +      ++
Sbjct: 75  YDGALLGDRSLRVDIAEGRKQDKS 98

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG--DIRTLY---TACKHRGFVMISYYDIRAARTA 245
           P  T +V N+  N    ++ A+F+      +R +    T  K +GF  + + ++ + + A
Sbjct: 14  PPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTD-KFKGFCYVEFDEVDSLKEA 72

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           +       L  R L +  +  +  
Sbjct: 73  L-TYDGALLGDRSLRVDIAEGRKQ 95

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 46.0 bits (110), Expect = 2e-06
 Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 6/66 (9%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            +  +    +LR+ F  +G V E+      E    R   FI F D ++ + A+ +++  D
Sbjct: 17  GIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHFHD 75

Query: 339 IAGKRI 344
           I GK++
Sbjct: 76  IMGKKV 81

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 22/98 (22%), Positives = 44/98 (44%), Gaps = 14/98 (14%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVM 233
           G        S  +FV  I  N  ++ELR  F+++G +    T           + RGF  
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVV----TEVVMIYDAEKQRPRGFGF 56

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
           I++ D ++   A+  +    +  +K+++  + P+D+ S
Sbjct: 57  ITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEPRDSKS 93

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 4/77 (5%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRETPHKRHHK--FIEFYDVRAAEAALKSLN 335
           T+ +     +V+ +++ +       V   I    H       F++F +    + ALK  N
Sbjct: 12  TVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CN 70

Query: 336 RSDIAGKRIKLEPSRPG 352
           R  + G+ I++   + G
Sbjct: 71  REYMGGRYIEVFREKSG 87

>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 Length = 102

 Score = 45.5 bits (108), Expect = 3e-06
 Identities = 14/93 (15%), Positives = 32/93 (34%), Gaps = 4/93 (4%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRETPHKRHHK--FIEFYD 323
               S +      + +  L    +  D+   F     ++  I   P  R      +EF  
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFAT 64

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
              A AA+   +++++  + ++L  +   G   
Sbjct: 65  HEDAVAAMA-KDKANMQHRYVELFLNSTAGTSG 96

>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 Length = 88

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G   S  +FV     ++ + ELR  F QYGD+  ++     R F  +++ D + A++   
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPS 271
             ++  ++   + I  + PK N +
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSN 82

>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 Length = 88

 Score = 40.7 bits (96), Expect = 9e-05
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
                ++ ++LR+ F  YG+V ++      R   F+ F D + A++         I G  
Sbjct: 12  RCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGIS 69

Query: 344 IKLEPSRP 351
           + +  + P
Sbjct: 70  VHISNAEP 77

>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 Length = 87

 Score = 44.3 bits (105), Expect = 6e-06
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 13/78 (16%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHK-------RHHK---FIEFYDVRAAEAALKS 333
           N+   ++ E +   F A   +  + + P            K   F+EF  V     A+ +
Sbjct: 13  NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-A 71

Query: 334 LNRSDIAGKRIKLEPSRP 351
            +     G+ +K+   RP
Sbjct: 72  FDGIIFQGQSLKI--RRP 87

>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 Length = 87

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 11/80 (13%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA----------CKHRGFVMISYYDIRA 241
           +R L+V NI   + +  +   F     +  L  A           + + F  + +  +  
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65

Query: 242 ARTAMRALQNKPLRRRKLDI 261
              AM A      + + L I
Sbjct: 66  TTQAM-AFDGIIFQGQSLKI 84

>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 Length = 87

 Score = 44.1 bits (105), Expect = 7e-06
 Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
           N S  + + G + V  L    S +DL+  F  +GEV +        T   R   FI F D
Sbjct: 3   NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62

Query: 324 VRAAEAALKSLNRSDIAGKRI 344
             + E  L       + G+ I
Sbjct: 63  AASVEKVLDQKEH-RLDGRVI 82

>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 Length = 87

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 13/72 (18%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISY 236
              E  +  +FV  ++ +    +L+  F ++G++      C         + RGF  I +
Sbjct: 5   SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEV----VDCTIKMDPNTGRSRGFGFILF 60

Query: 237 YDIRAARTAMRA 248
            D  +    +  
Sbjct: 61  KDAASVEKVLDQ 72

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 44.0 bits (104), Expect = 1e-05
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 2/79 (2%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRS 337
           + + NL    S +DL+ +               +       +EF        AL+ LN  
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90

Query: 338 DIAGKRIKLEPSRPGGARR 356
           +  G  I +E        R
Sbjct: 91  EFRGSVITVERDDNPPPIR 109

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 39.4 bits (92), Expect = 5e-04
 Identities = 11/98 (11%), Positives = 27/98 (27%), Gaps = 2/98 (2%)

Query: 166 GNGLLHYSVPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGD--IRTLY 223
           G+   H+   +G                 + ++N+       +L+ L  +       +  
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV 61

Query: 224 TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI 261
                 G   + +        A+  L N   R   + +
Sbjct: 62  NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>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 Length = 75

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 6/65 (9%)

Query: 285 LDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           L P    E +R+ FG +GEV+ I      +T  +R   FI F +    +  ++     ++
Sbjct: 7   LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNV 65

Query: 340 AGKRI 344
              + 
Sbjct: 66  GLSKC 70

>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 Length = 75

 Score = 40.9 bits (97), Expect = 6e-05
 Identities = 11/63 (17%), Positives = 26/63 (41%), Gaps = 13/63 (20%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAARTA 245
           +FV  ++ +  + ++R  F  +G++     +          K RGF  I++ +    +  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEV----ESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57

Query: 246 MRA 248
           M  
Sbjct: 58  MEK 60

>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 Length = 103

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 321
                        L+V  L    + +DL++ F  +GEV  +      +T H +   F+ F
Sbjct: 5   SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

Query: 322 YDVRAAEAALKSLNRSDIAGKRI 344
            +       +   +   I G+  
Sbjct: 65  TEYETQVKVMSQRH--MIDGRWC 85

>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 Length = 103

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 11/95 (11%), Positives = 25/95 (26%), Gaps = 15/95 (15%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISY 236
                 +  L V  +     + +L+  F  +G++                  +GF  + +
Sbjct: 9   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEV----LMVQVKKDLKTGHSKGFGFVRF 64

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
            +       M       +  R  D      K +  
Sbjct: 65  TEYETQVKVMSQRHM--IDGRWCDCKLPNSKQSQD 97

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 44.1 bits (104), Expect = 2e-05
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 9/91 (9%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK--------FIEFYDVRAA 327
           NQ  + +  L  + + E++   FG +  +   +E      +         F+ F     A
Sbjct: 22  NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYA 81

Query: 328 EAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
           + AL+  ++  +  + I+L  S     ++ L
Sbjct: 82  QNALR-KHKDLLGKRYIELFRSTAAEVQQVL 111

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 43.4 bits (103), Expect = 2e-05
 Identities = 17/103 (16%), Positives = 38/103 (36%), Gaps = 12/103 (11%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 318
           ++P +    +      L +  L    + E LR  +  +G++ +        +   R   F
Sbjct: 14  TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKL------EPSRPGGAR 355
           + F  +   +AA+ +     I G+ ++       E S  G + 
Sbjct: 74  VTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESGSGPSS 115

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 39.6 bits (93), Expect = 5e-04
 Identities = 17/98 (17%), Positives = 38/98 (38%), Gaps = 14/98 (14%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVM 233
                 +   R LF+  ++    +  LR  +EQ+G +    T C         + RGF  
Sbjct: 18  ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKL----TDCVVMRDPASKRSRGFGF 73

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
           +++  +     AM A +   +  R ++   ++ ++   
Sbjct: 74  VTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESG 110

>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 Length = 102

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 12/80 (15%), Positives = 23/80 (28%), Gaps = 4/80 (5%)

Query: 191 PSRTLFVRNI-NSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
             R + + +         +L  L E +G I              I       A+ A+   
Sbjct: 14  TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYY 72

Query: 250 QNKP--LRRRKLDIHFSIPK 267
              P  +  + + +H S   
Sbjct: 73  TTTPALVFGKPVRVHLSQKY 92

>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} Length = 89

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR 343
                ++ E+L+Q F  YGEV ++      R   F+ F D + A++         I G  
Sbjct: 18  RCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCG--EDLIIKGIS 75

Query: 344 IKLEPSRPGGARRN 357
           + +  + P   + N
Sbjct: 76  VHISNAEPKHNKLN 89

>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} Length = 89

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 20/87 (22%), Positives = 42/87 (48%), Gaps = 3/87 (3%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           G H +  H S+ +FV     ++   EL+  F QYG++  ++     R F  +++ D + A
Sbjct: 3   GSHHHHHHGSK-VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVA 61

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDN 269
           ++     ++  ++   + I  + PK N
Sbjct: 62  QSLCG--EDLIIKGISVHISNAEPKHN 86

>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 Length = 193

 Score = 44.4 bits (104), Expect = 3e-05
 Identities = 8/75 (10%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHK---FIEFYDVRAAEAALKSL 334
           ++ +       + +D+++     G+V  I+      +  K   F+ F  + +A+  +++ 
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 170

Query: 335 NRSDIAGKRIKLEPS 349
            +       + +   
Sbjct: 171 GQK-YKETDLLILFK 184

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 43.0 bits (101), Expect = 4e-05
 Identities = 14/93 (15%), Positives = 29/93 (31%), Gaps = 8/93 (8%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY---GEVKEIRETPHKRHHK----F 318
                  +      + +  L  S S ED++           V  +     +   +    F
Sbjct: 6   SGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAF 65

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           +E       + ALK  +R  +  + I++  S  
Sbjct: 66  VELESEDDVKLALK-KDRESMGHRYIEVFKSHR 97

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 41.5 bits (97), Expect = 1e-04
 Identities = 11/68 (16%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------TACKHRGFVMISYYDIR 240
           G   SR +FV  +  ++++ E+ A F ++G +   +       +    +G+  + + +  
Sbjct: 4   GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

Query: 241 AARTAMRA 248
           + +  + A
Sbjct: 64  SVQALIDA 71

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.7 bits (95), Expect = 2e-04
 Identities = 13/85 (15%), Positives = 32/85 (37%), Gaps = 15/85 (17%)

Query: 282 VF--NLDPSVSNEDLRQIFGAYGEVKEI-------RETPHKRHHKFIEFYDVRAAEAALK 332
           VF   L P +  +++   F  +G +          +     + + F+ F +  + +A + 
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 333 SLNRSD------IAGKRIKLEPSRP 351
           +    D      ++   IK +P + 
Sbjct: 71  ACLEEDGKLYLCVSSPTIKDKPVQI 95

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 40.1 bits (95), Expect = 1e-04
 Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 285 LDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           L  + + ED++  F  +G+V +      + T   R   F+ F      E   +  +  +I
Sbjct: 7   LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHEI 65

Query: 340 AGKRI 344
             K +
Sbjct: 66  NNKMV 70

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 40.1 bits (95), Expect = 1e-04
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 13/63 (20%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAARTA 245
           +FV  ++ N    +++  FEQ+G +                +HRGF  +++         
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKV----DDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57

Query: 246 MRA 248
              
Sbjct: 58  CEI 60

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           + +  L    + E LR+ FG +GEVKE        T   R   F+ F D    +  L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 335 NRSDIAGKRIKLEPSR 350
           +R ++  K I  +P  
Sbjct: 62  SRHELDSKTI--DPKV 75

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 38.6 bits (91), Expect = 5e-04
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 13/63 (20%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAARTA 245
           +F+  ++       LR  F Q+G++      C         + RGF  +++ D       
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEV----KECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

Query: 246 MRA 248
           +  
Sbjct: 59  LAQ 61

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 22/92 (23%), Positives = 36/92 (39%), Gaps = 10/92 (10%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKF 318
            +P+ +          + +  L    + E LR+ FG +GEVKE        T   R   F
Sbjct: 14  LVPRGSHMGSS--GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
           + F D    +  L   +R ++  K I  +P  
Sbjct: 72  VTFMDQAGVDKVLAQ-SRHELDSKTI--DPKV 100

>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} Length = 107

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 11/89 (12%), Positives = 29/89 (32%), Gaps = 8/89 (8%)

Query: 268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAY---GEVKEIRETPHKRHHK----FIE 320
               ++  +   +    L  S + ED+   F           I    ++   +     IE
Sbjct: 2   SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIE 61

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPS 349
               +  + AL+  +R  +  + +++   
Sbjct: 62  MESEQDVQKALE-KHRMYMGQRYVEVYEI 89

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 22/101 (21%), Positives = 39/101 (38%), Gaps = 14/101 (13%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------K 227
           G+   +G +  G      LFV  ++ +     LR+ F QYG++      C         +
Sbjct: 1   GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEV----VDCVIMKDKTTNQ 56

Query: 228 HRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 268
            RGF  + + D     T + + +   L  R +D     P+ 
Sbjct: 57  SRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRG 96

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 24/89 (26%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 321
               +      G L V  LD S + E LR  F  YGEV +      + T   R   F++F
Sbjct: 6   SGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65

Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
            D       L S     + G+ I  +P  
Sbjct: 66  KDPNCVGTVLAS-RPHTLDGRNI--DPKP 91

>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 Length = 104

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 6/86 (6%)

Query: 188 GEHPSRTLFVRNINSNV-----EDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           G   S  L     N +V       ++  +LF  Y    T +   K    V I++ +  +A
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTT-FQYFKSFKRVRINFSNPLSA 59

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKD 268
             A   L       +++ ++F+    
Sbjct: 60  ADARLRLHKTEFLGKEMKLYFAQTLH 85

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.2 bits (92), Expect = 6e-04
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 284 NLDPSVSNEDLRQIFGA-YGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLN-RS 337
           +L P V +  L + F   Y   +  +    +T   + + F++F D    + AL       
Sbjct: 16  DLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAV 75

Query: 338 DIAGKRIKLEPSRPGGARR 356
            +  K ++L  + P  +R 
Sbjct: 76  GLGSKPVRLSVAIPKASRV 94

>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* Length = 345

 Score = 41.7 bits (97), Expect = 8e-04
 Identities = 28/140 (20%), Positives = 43/140 (30%), Gaps = 28/140 (20%)

Query: 256 RRKLDIHFSI-PKDNPSDKDLNQGTLVVFNLDPS--VSNEDLRQIFGAYGEVKEIRETPH 312
           +  L  H  I      +        LVV N      VS   L  +    G V  +   P+
Sbjct: 2   KHTLLRHEGIETVSYATQS------LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN 55

Query: 313 KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 372
           K  + F  +     ++ A  +LN           E     G +  L L   ++++  E R
Sbjct: 56  KP-YSFARYRTTEESKRAYVTLNGK---------EVVDDLGQKITLYLNFVEKVQWKELR 105

Query: 373 ILQHQVGSPITNSPPGNWVQ 392
                        PPG  V 
Sbjct: 106 ---------PQALPPGLMVV 116

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	823
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.98
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.96
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
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.95
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	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
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.95
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	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	99.94
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.94
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.93
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.78
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.78
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.77
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.77
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.76
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.75
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.75
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.75
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.75
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.74
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.73
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.7
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.7
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.7
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.69
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.68
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.63
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.62
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.61
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.61
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.61
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.59
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.59
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.59
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.58
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.57
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.56
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.56
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.55
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.55
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.55
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.55
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.55
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.54
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.54
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.54
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.54
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.54
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.54
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.53
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.53
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.53
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.53
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.53
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.53
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.53
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.53
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.53
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.53
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.53
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.53
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.53
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.52
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.52
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.52
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.52
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.52
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.52
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.52
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.52
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.52
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.52
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.52
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.52
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.52
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.52
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.52
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.52
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.52
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.52
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.51
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.51
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.51
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.51
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.51
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.51
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.51
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.51
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.51
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	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
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.51
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.51
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.51
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.51
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.51
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.51
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.51
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.51
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.5
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.5
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.5
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.5
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.5
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.5
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.5
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.5
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.5
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.5
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.5
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.5
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.5
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.5
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.5
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.5
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.5
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.49
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.49
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.49
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.49
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.49
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.49
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.49
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.49
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.49
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.49
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.49
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.49
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.49
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.49
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.49
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.49
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.49
2div_A	99	TRNA selenocysteine associated protein; structural	99.49
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.48
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.48
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.48
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.48
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.48
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.48
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.48
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.48
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.48
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.48
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.48
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.48
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.48
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.48
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.48
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.48
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.48
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.47
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.47
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.47
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.47
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.47
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.47
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.47
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.47
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.47
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.47
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.47
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.47
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.47
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.47
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.47
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.47
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.47
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.47
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.47
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.47
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.47
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.47
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.47
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.46
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.46
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.46
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.46
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.46
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.46
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.46
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.46
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.46
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.46
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.46
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.46
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.46
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.46
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.46
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.46
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.46
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.46
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.46
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.46
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.46
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.46
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.46
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.46
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.46
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.46
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.45
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.45
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.45
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.45
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.45
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.45
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.45
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.45
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.45
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.45
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.45
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.45
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.45
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.45
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.45
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.45
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.45
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.45
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.45
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.45
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.44
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.44
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.44
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.44
2div_A	99	TRNA selenocysteine associated protein; structural	99.44
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.44
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.44
1x5p_A	97	Negative elongation factor E; structure genomics,	99.44
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.44
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.44
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.44
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.44
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.44
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.43
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.43
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.43
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.43
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.43
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.43
1x5p_A	97	Negative elongation factor E; structure genomics,	99.43
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.43
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.43
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.43
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.43
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.43
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.42
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.42
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.42
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.42
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.42
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.42
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.42
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.42
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.42
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.41
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.41
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.41
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.41
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.41
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.41
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.41
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.41
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.41
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.41
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.41
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.41
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.41
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.4
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.4
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.4
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.4
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.4
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.4
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.4
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.4
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.39
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.39
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.39
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	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
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.39
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.38
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.38
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.38
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.38
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.37
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.37
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.37
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.37
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.37
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.36
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.36
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.36
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.36
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.36
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.35
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.35
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.35
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.34
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.34
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.33
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.33
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.33
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.33
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.33
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.33
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.32
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.32
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.0
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.0
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.32
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.32
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.31
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.31
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.31
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.31
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.3
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.3
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.3
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.3
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.3
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.3
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.29
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.29
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.29
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.29
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.28
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.28
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.28
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.27
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.24
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.24
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.24
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.23
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.22
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.22
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.21
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.21
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.21
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.21
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.2
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.2
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.19
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.18
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.15
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.09
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.09
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.08
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.08
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.06
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.06
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.02
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.99
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.98
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.93
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.93
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.9
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.9
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.84
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.71
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.61
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.59
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.43
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	98.42
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.41
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.31
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.29
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.1
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.1
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.98
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.73
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.54
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.49
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.81
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.46
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.13
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.03
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	94.72
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	94.31
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	94.11
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	93.76
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	93.63
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	93.12
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.67
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	92.14
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	91.41
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	86.92

>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=99.98  E-value=1.3e-31  Score=285.74  Aligned_cols=237  Identities=16%  Similarity=0.231  Sum_probs=198.8

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcEEEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCCCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYGE  189 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~~~e  189 (823)
                      .++++|++||.++++.++.++|+.+|-+.+.+    ...+|++++.|.+...+.    .+++..+.+....+..     .
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~Gi~~~~~----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~-----~   92 (284)
T 3smz_A           22 RRKILIRGLPGDVTNQEVHDLLSDYELKYCFV----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL-----Q   92 (284)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHTTTSCEEEEEE----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE-----C
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCEEEEE----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEe-----c
Confidence            47899999999999999999999999334433    456789999999887664    2344444443333322     2


Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|.+|++.|+|..+.|++|.|.++
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            35689999999999999999999999999999873     5668999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCccceeeecCCCCC-CHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCcc
Q 003400          265 IPKDNPSDKDLNQGTLVVFNLDPSV-SNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI  339 (823)
Q Consensus       265 ~pk~~~~~~~~~~~tLfV~NLp~~v-teedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i  339 (823)
                      .++.... ......+|||+|||.++ ++++|+++|++||.|..+++    ++.++|+|||+|.+.++|.+|++.|||..+
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            8765432 33456799999999995 99999999999999999875    355789999999999999999999999999


Q ss_pred             CCceEEEEecCCCcccchhhh
Q 003400          340 AGKRIKLEPSRPGGARRNLML  360 (823)
Q Consensus       340 ~Gr~I~V~~s~~~~~r~~~~~  360 (823)
                      .|++|+|.|++++..++..+.
T Consensus       252 ~g~~l~v~~a~~~~~~~~~~~  272 (284)
T 3smz_A          252 GGSHLRVSFCAPGPPGRSMLA  272 (284)
T ss_dssp             TTEECEEEECCSSSCHHHHHH
T ss_pred             CCeEEEEEEecCCCcccchhh
Confidence            999999999999887665433

>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=99.97  E-value=4.3e-31  Score=282.76  Aligned_cols=230  Identities=18%  Similarity=0.284  Sum_probs=188.3

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccccc---cccccCCCCccccCCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGL---LHYSVPNGAGTVAGEHPY  187 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~~~---~~~~l~n~~~~~~~~~~~  187 (823)
                      .++++|++||.++++.++.++|+.+|.|   .|..+...  .++++++.|.+...|...   ++..+.+....+.     
T Consensus        41 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~-----  113 (292)
T 2ghp_A           41 LTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVS-----  113 (292)
T ss_dssp             -CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEE-----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEE-----
Confidence            5889999999999999999999999987   44444322  479999999988766533   2233332222222     


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCC-CEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG-~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                       ....++|||+|||.++++++|+++|++|| .|..|++    .++++|||||+|.+.++|.+|++.|+|..+.|++|.|.
T Consensus       114 -~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  192 (292)
T 2ghp_A          114 -HLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTK  192 (292)
T ss_dssp             -ECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             -ECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence             13579999999999999999999999999 9999984    24689999999999999999999999999999999999


Q ss_pred             ccCCCCCCCC---CCCCccceeeecCCCC-CCHHHHHHHhcccCceEEEEeC------CCcccEEEEEEcCHHHHHHHHH
Q 003400          263 FSIPKDNPSD---KDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALK  332 (823)
Q Consensus       263 ~a~pk~~~~~---~~~~~~tLfV~NLp~~-vteedL~~~Fs~fG~I~~iri~------~~srG~aFVeF~d~e~A~kAl~  332 (823)
                      ++.+......   ......+|||+|||.+ +++++|+++|++||.|..|++.      +.++|||||+|.+.++|.+|+ 
T Consensus       193 ~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-  271 (292)
T 2ghp_A          193 VSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-  271 (292)
T ss_dssp             ECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-
T ss_pred             ECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-
Confidence            9987654322   2334579999999999 9999999999999999999873      667899999999999999999 


Q ss_pred             HhCCCccCCceEEEEecCCC
Q 003400          333 SLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       333 ~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      .|||..|.|++|+|.|++++
T Consensus       272 ~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          272 QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             GGTTEEETTEEEEEEECCCC
T ss_pred             HhcCCEECCcEEEEEEecCC
Confidence            99999999999999999875

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.96  E-value=1.1e-29  Score=260.71  Aligned_cols=166  Identities=19%  Similarity=0.349  Sum_probs=146.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.+++..+.|+.|++.+
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            357899999999999999999999999999999984     467899999999999999999999999999999999998


Q ss_pred             cCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 003400          264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (823)
Q Consensus       264 a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri---~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~  340 (823)
                      +......  ......+|||+|||.++|+++|+++|++||.|..|++   .+.++|||||+|.+.++|++|++.|||..|.
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            8643321  1223468999999999999999999999999999976   3446899999999999999999999999999


Q ss_pred             CceEEEEecCCCcccc
Q 003400          341 GKRIKLEPSRPGGARR  356 (823)
Q Consensus       341 Gr~I~V~~s~~~~~r~  356 (823)
                      |++|+|++++++..+.
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            9999999998865443

>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=1.8e-28  Score=238.46  Aligned_cols=157  Identities=20%  Similarity=0.361  Sum_probs=142.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      |+|||+|||.++|+++|+++|++||+|.+|++    .++++|||||+|.+.++|++|++.|++..+.|+.|.|.++.+..
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            68999999999999999999999999999985    35678999999999999999999999999999999999987654


Q ss_pred             CCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce
Q 003400          269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR  343 (823)
Q Consensus       269 ~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~  343 (823)
                      ..  ......+|||+|||.++++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.|++
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 QS--SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP  158 (166)
T ss_dssp             CC--CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CC--CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE
Confidence            32  3345679999999999999999999999999999976     3567899999999999999999999999999999


Q ss_pred             EEEEecCC
Q 003400          344 IKLEPSRP  351 (823)
Q Consensus       344 I~V~~s~~  351 (823)
                      |+|+|+++
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=5e-28  Score=236.40  Aligned_cols=155  Identities=23%  Similarity=0.429  Sum_probs=141.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ++++|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.|+.
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            5799999999999999999999999999999984     45678999999999999999999999999999999999997


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 003400          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (823)
Q Consensus       266 pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~  340 (823)
                      ++..    .....+|||+|||.++++++|+++|++||.|..+++     ++.++|+|||+|.+.++|.+|++.|||..+.
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 PGGE----SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE  157 (168)
T ss_dssp             CCSS----TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT
T ss_pred             CCcc----cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEec
Confidence            6543    235679999999999999999999999999999976     4556899999999999999999999999998


Q ss_pred             C--ceEEEEec
Q 003400          341 G--KRIKLEPS  349 (823)
Q Consensus       341 G--r~I~V~~s  349 (823)
                      |  ++|+|+||
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            8  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=5.4e-28  Score=235.27  Aligned_cols=155  Identities=25%  Similarity=0.441  Sum_probs=140.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ++++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.++.
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            4689999999999999999999999999999874     56678999999999999999999999999999999999997


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 003400          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (823)
Q Consensus       266 pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~  340 (823)
                      +...    .....+|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++.|||..+.
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            6432    335678999999999999999999999999999976     3456899999999999999999999999999


Q ss_pred             Cce--EEEEec
Q 003400          341 GKR--IKLEPS  349 (823)
Q Consensus       341 Gr~--I~V~~s  349 (823)
                      |+.  |+|+||
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            964  888875

>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=1.2e-27  Score=243.56  Aligned_cols=163  Identities=20%  Similarity=0.387  Sum_probs=143.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      +.++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            4689999999999999999999999999999985     46689999999999999999999999999999999999876


Q ss_pred             CCCCCC-------CCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHH
Q 003400          266 PKDNPS-------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  333 (823)
Q Consensus       266 pk~~~~-------~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~  333 (823)
                      ......       .......+|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++.
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  186 (216)
T 2qfj_A          107 NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS  186 (216)
T ss_dssp             CCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHH
Confidence            543211       01224479999999999999999999999999999976     345689999999999999999999


Q ss_pred             hCCCccCCceEEEEecCCCc
Q 003400          334 LNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       334 LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      |||..|.|+.|+|.+++++.
T Consensus       187 l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          187 MNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HTTCBCSSSBCEEEECSSCS
T ss_pred             ccCCEeCCcEEEEEEecCCC
Confidence            99999999999999998764

>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=2.5e-27  Score=245.95  Aligned_cols=164  Identities=26%  Similarity=0.355  Sum_probs=147.2

Q ss_pred             CCCCcEEEEcCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          189 EHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       189 e~~srtLfV~NLP~-~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      ..++++|||+|||. ++++++|+++|++||.|..|++....+|||||+|.+.++|++|++.|++..+.|++|.|.++.++
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  110 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ  110 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCc
Confidence            35789999999999 99999999999999999999976666899999999999999999999999999999999998754


Q ss_pred             CCCCCC-------------------------------CCCccceeeecCCCCCCHHHHHHHhcccC-ceEEEEeCCCccc
Q 003400          268 DNPSDK-------------------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRH  315 (823)
Q Consensus       268 ~~~~~~-------------------------------~~~~~tLfV~NLp~~vteedL~~~Fs~fG-~I~~iri~~~srG  315 (823)
                      .....+                               .....+|||+|||.++++++|+++|++|| .|..|++....+|
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g  190 (229)
T 2adc_A          111 NVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK  190 (229)
T ss_dssp             CCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTT
T ss_pred             cccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCc
Confidence            211100                               11246899999999999999999999999 9999999777799


Q ss_pred             EEEEEEcCHHHHHHHHHHhCCCccC-CceEEEEecCCC
Q 003400          316 HKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRPG  352 (823)
Q Consensus       316 ~aFVeF~d~e~A~kAl~~LnG~~i~-Gr~I~V~~s~~~  352 (823)
                      +|||+|.+.++|.+|++.|||..+. |++|+|.|++++
T Consensus       191 ~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          191 MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9999999999999999999999999 999999999864

>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=99.95  E-value=2.3e-27  Score=237.84  Aligned_cols=167  Identities=19%  Similarity=0.367  Sum_probs=140.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....+.++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++. ++..+.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v   86 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   86 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeee
Confidence            34457799999999999999999999999999999874     456899999999999999999985 899999999999


Q ss_pred             cccCCCCCCCC--CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHh
Q 003400          262 HFSIPKDNPSD--KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSL  334 (823)
Q Consensus       262 ~~a~pk~~~~~--~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~L  334 (823)
                      .++.+......  ......+|||+|||.++|+++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|+.. 
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-  165 (196)
T 1l3k_A           87 KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-  165 (196)
T ss_dssp             EECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-
T ss_pred             ecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-
Confidence            99876543221  2234579999999999999999999999999999976     456789999999999999999986 


Q ss_pred             CCCccCCceEEEEecCCCccc
Q 003400          335 NRSDIAGKRIKLEPSRPGGAR  355 (823)
Q Consensus       335 nG~~i~Gr~I~V~~s~~~~~r  355 (823)
                      +|..|.|+.|.|.++.++...
T Consensus       166 ~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          166 KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             SCCEETTEECEEEECC-----
T ss_pred             CCcEECCEEEEEEecCChhHh
Confidence            799999999999999887644

>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=3.6e-27  Score=251.05  Aligned_cols=164  Identities=23%  Similarity=0.444  Sum_probs=146.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr----~lFs~fG~I~~v~~--~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ...++++|||+|||.++|+++|+    ++|++||.|.+|++  +++++|||||+|.+.++|++|++.|+|..|.|+.|+|
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            34678999999999999999977    89999999999985  6678999999999999999999999999999999999


Q ss_pred             cccCCCCCC-----------------------------------------------------------------------
Q 003400          262 HFSIPKDNP-----------------------------------------------------------------------  270 (823)
Q Consensus       262 ~~a~pk~~~-----------------------------------------------------------------------  270 (823)
                      .|+..+...                                                                       
T Consensus        85 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  164 (282)
T 3pgw_A           85 QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM  164 (282)
T ss_pred             EEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCC
Confidence            998654420                                                                       


Q ss_pred             ------------------------------------CCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcc
Q 003400          271 ------------------------------------SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKR  314 (823)
Q Consensus       271 ------------------------------------~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~sr  314 (823)
                                                          .......++|||+|||.++++++|+++|++||.|.+|++....+
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                                                00112346799999999999999999999999999999876667


Q ss_pred             cEEEEEEcCHHHHHHHHHHhCCCccC-CceEEEEecCC
Q 003400          315 HHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRP  351 (823)
Q Consensus       315 G~aFVeF~d~e~A~kAl~~LnG~~i~-Gr~I~V~~s~~  351 (823)
                      |||||+|.+.++|.+|++.|||..|. |+.|+|+|++.
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=5e-28  Score=238.89  Aligned_cols=162  Identities=19%  Similarity=0.276  Sum_probs=144.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEE----EeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL----YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v----~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ...+.++|||+|||.++|+++|+++|++||.|..+    ..+++++|||||+|.+.++|++|++ |++..+.|++|.|.+
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 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            34578999999999999999999999999865431    1457789999999999999999995 999999999999999


Q ss_pred             cCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce
Q 003400          264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR  343 (823)
Q Consensus       264 a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~  343 (823)
                      +.++...  ......+|||+|||.++++++|+++|++||.|..+..++.++|||||+|.+.++|.+|++.|||..|.|+.
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 PKGRDSK--KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS  165 (175)
T ss_dssp             CCCSSCS--TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEE
T ss_pred             CCCcccc--ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            9765432  23456799999999999999999999999999998667788999999999999999999999999999999


Q ss_pred             EEEEecCCC
Q 003400          344 IKLEPSRPG  352 (823)
Q Consensus       344 I~V~~s~~~  352 (823)
                      |+|+|++++
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

>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=2.8e-27  Score=232.25  Aligned_cols=154  Identities=16%  Similarity=0.340  Sum_probs=139.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcC----C-------CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQY----G-------DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  258 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~f----G-------~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~  258 (823)
                      +++++|||+|||.++|+++|+++|++|    |       .|.++++ .+++|||||+|.+.++|++|+ .|++..+.|++
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            357999999999999999999999999    7       7888864 567999999999999999999 79999999999


Q ss_pred             ccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHH
Q 003400          259 LDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKS  333 (823)
Q Consensus       259 L~V~~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~  333 (823)
                      |.|.++.+....    ....+|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++.
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            999997654332    23679999999999999999999999999999976     455689999999999999999999


Q ss_pred             hCCCccCCceEEEEec
Q 003400          334 LNRSDIAGKRIKLEPS  349 (823)
Q Consensus       334 LnG~~i~Gr~I~V~~s  349 (823)
                      |||..+.|++|+|++|
T Consensus       156 l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          156 LNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HTTCEETTEECEEEEC
T ss_pred             cCCCEECCeEEEEEeC
Confidence            9999999999999997

>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=3.5e-27  Score=241.78  Aligned_cols=159  Identities=18%  Similarity=0.228  Sum_probs=137.9

Q ss_pred             CCcEEEEcCCC-CCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCC
Q 003400          191 PSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       191 ~srtLfV~NLP-~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~  269 (823)
                      ++++|||+||| .++|+++|+++|++||+|.+|++....+|||||+|.+.++|++|++.|+|..+.|++|+|.++..+..
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~   82 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAI   82 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCcc
Confidence            57899999999 89999999999999999999998777899999999999999999999999999999999999864321


Q ss_pred             CCC---------------------C------------CCCccceeeecCCCCCCHHHHHHHhcccCce--EEEEeCC---
Q 003400          270 PSD---------------------K------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV--KEIRETP---  311 (823)
Q Consensus       270 ~~~---------------------~------------~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I--~~iri~~---  311 (823)
                      ...                     .            .....+|||+|||.++|+++|+++|++||.|  .++++..   
T Consensus        83 ~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~  162 (205)
T 3tyt_A           83 MPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKS  162 (205)
T ss_dssp             CCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCS
T ss_pred             CCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCC
Confidence            000                     0            0123579999999999999999999999999  8887643   


Q ss_pred             CcccEEEEEEcCHHHHHHHHHHhCCCccCCc----eEEEEec
Q 003400          312 HKRHHKFIEFYDVRAAEAALKSLNRSDIAGK----RIKLEPS  349 (823)
Q Consensus       312 ~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr----~I~V~~s  349 (823)
                      .++|+|||+|.+.++|.+||..|||..|.|+    ++.|+++
T Consensus       163 ~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          163 ERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            3469999999999999999999999999885    5777664

>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=99.95  E-value=5.6e-27  Score=249.81  Aligned_cols=178  Identities=19%  Similarity=0.317  Sum_probs=162.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~  269 (823)
                      .++++|||+|||.++|+++|+++|++|| |..|++ ++++|||||+|.+.++|++|++.|++..+.|++|.|.++.    
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            3679999999999999999999999999 999977 7889999999999999999999999999999999999864    


Q ss_pred             CCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 003400          270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (823)
Q Consensus       270 ~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I  344 (823)
                            ...+|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++.|+|..+.|+.|
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                  2468999999999999999999999999999875     45578999999999999999999999999999999


Q ss_pred             EEEecCCCcc-------cchhhhcccccc-CHHHHHHHHhhcC
Q 003400          345 KLEPSRPGGA-------RRNLMLQLNQEL-EQDESRILQHQVG  379 (823)
Q Consensus       345 ~V~~s~~~~~-------r~~~~~ql~~~~-~~~~l~~~f~~~G  379 (823)
                      .|.++.++..       +..++.++...+ +++++..+|.++|
T Consensus       168 ~v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G  210 (284)
T 3smz_A          168 YVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVH  210 (284)
T ss_dssp             EEEECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSS
T ss_pred             EEEECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCC
Confidence            9999987652       245788999896 8999999999887

>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=2.1e-27  Score=239.51  Aligned_cols=162  Identities=26%  Similarity=0.363  Sum_probs=145.5

Q ss_pred             CCcEEEEcCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCC
Q 003400          191 PSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       191 ~srtLfV~NLP~-~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~  269 (823)
                      .+++|||+|||. ++++++|+++|++||.|..|++....+|||||+|.+.++|++|++.|+|..+.|++|.|.++.+...
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~   81 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV   81 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCc
Confidence            368999999999 9999999999999999999987666689999999999999999999999999999999999875421


Q ss_pred             CCCC-------------------------------CCCccceeeecCCCCCCHHHHHHHhcccC-ceEEEEeCCCcccEE
Q 003400          270 PSDK-------------------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKRHHK  317 (823)
Q Consensus       270 ~~~~-------------------------------~~~~~tLfV~NLp~~vteedL~~~Fs~fG-~I~~iri~~~srG~a  317 (823)
                      ...+                               .....+|||+|||..+++++|+++|++|| .|..|++....+|+|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~a  161 (198)
T 1qm9_A           82 QLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA  161 (198)
T ss_dssp             CCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCE
T ss_pred             CCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEE
Confidence            1100                               12256899999999999999999999999 999999977779999


Q ss_pred             EEEEcCHHHHHHHHHHhCCCccC-CceEEEEecCCC
Q 003400          318 FIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRPG  352 (823)
Q Consensus       318 FVeF~d~e~A~kAl~~LnG~~i~-Gr~I~V~~s~~~  352 (823)
                      ||+|.+.++|.+|++.|||..+. |++|+|.|++++
T Consensus       162 fV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          162 LIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             EEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            99999999999999999999999 999999999864

>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=5.9e-27  Score=229.99  Aligned_cols=157  Identities=20%  Similarity=0.405  Sum_probs=137.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CC--CcccEEEEEeCCHHHHHHHHHHhcCCccc---ccccc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----AC--KHRGFVMISYYDIRAARTAMRALQNKPLR---RRKLD  260 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~--ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~---gr~L~  260 (823)
                      ++++|||+|||.++|+++|+++|++||+|.+|++     .+  +++|||||+|.+.++|++|++.|++..+.   ++.+.
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            4689999999999999999999999999999874     22  68999999999999999999999998876   56777


Q ss_pred             ccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCC
Q 003400          261 IHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNR  336 (823)
Q Consensus       261 V~~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG  336 (823)
                      +.++.+...   ......+|||+|||.++|+++|+++|++||.|.++++    .+.++|||||+|.+.++|.+|++.|||
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 MKPADSEKN---NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ  158 (175)
T ss_dssp             EEECGGGCC---SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             Ecccccccc---ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcC
Confidence            777655432   2335679999999999999999999999999999976    345689999999999999999999999


Q ss_pred             CccC---CceEEEEecC
Q 003400          337 SDIA---GKRIKLEPSR  350 (823)
Q Consensus       337 ~~i~---Gr~I~V~~s~  350 (823)
                      ..+.   |++|+|+|+.
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   4999999974

>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=1.3e-27  Score=233.51  Aligned_cols=155  Identities=20%  Similarity=0.432  Sum_probs=139.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ++++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.  +..+.|+.|.|.++.
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            5789999999999999999999999999999984     467889999999999999999994  678899999999886


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 003400          266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (823)
Q Consensus       266 pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~  340 (823)
                      ++.    .....++|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++ ++|..+.
T Consensus        80 ~~~----~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~  154 (167)
T 2cjk_A           80 PRD----EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFK  154 (167)
T ss_dssp             CHH----HHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSS
T ss_pred             chh----hccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeC
Confidence            542    1234569999999999999999999999999999976     35678999999999999999998 8999999


Q ss_pred             CceEEEEecCCC
Q 003400          341 GKRIKLEPSRPG  352 (823)
Q Consensus       341 Gr~I~V~~s~~~  352 (823)
                      |++|+|.++.++
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            999999999875

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.94  E-value=7.2e-27  Score=234.57  Aligned_cols=162  Identities=16%  Similarity=0.324  Sum_probs=142.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcC----C-------CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQY----G-------DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  259 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~f----G-------~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L  259 (823)
                      .+++|||+|||.++|+++|+++|++|    |       .|..+++ ++++|||||+|.+.++|++|+ .|+|..+.|++|
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            57999999999999999999999999    5       6777754 678999999999999999999 799999999999


Q ss_pred             cccccCCCCCCCC----------------CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEE
Q 003400          260 DIHFSIPKDNPSD----------------KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKF  318 (823)
Q Consensus       260 ~V~~a~pk~~~~~----------------~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aF  318 (823)
                      .|.++.+......                ......+|||+|||.++++++|+++|++||.|..|++     ++.++||||
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            9999865432110                1134579999999999999999999999999999976     455689999


Q ss_pred             EEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       319 VeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      |+|.+.++|.+|++.|||..+.|+.|+|++++++..
T Consensus       161 V~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          161 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             EEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999999988753

>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=99.94  E-value=2.5e-26  Score=245.72  Aligned_cols=182  Identities=20%  Similarity=0.267  Sum_probs=156.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC---CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       186 ~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~---~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      +..+++.++|||+|||.++|+++|+++|+.||+|..|++.   ..++|||||+|.+.++|++|++ +++..+.|++|.|.
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 LTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVS  113 (292)
T ss_dssp             -------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEE
Confidence            3456678999999999999999999999999999999852   2258999999999999999995 99999999999999


Q ss_pred             ccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccC-ceEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCC
Q 003400          263 FSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRS  337 (823)
Q Consensus       263 ~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG-~I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~  337 (823)
                      ++           ...+|||+|||.++++++|+++|+.|| .|..|++.    +.++|||||+|.+.++|.+|++.|||.
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           356899999999999999999999999 99999863    357899999999999999999999999


Q ss_pred             ccCCceEEEEecCCCcc-----------cchhhhccccc-cCHHHHHHHHhhcC
Q 003400          338 DIAGKRIKLEPSRPGGA-----------RRNLMLQLNQE-LEQDESRILQHQVG  379 (823)
Q Consensus       338 ~i~Gr~I~V~~s~~~~~-----------r~~~~~ql~~~-~~~~~l~~~f~~~G  379 (823)
                      .+.|+.|.|.++.+...           +..++.++... ++.+++..+|.+||
T Consensus       183 ~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G  236 (292)
T 2ghp_A          183 KIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFG  236 (292)
T ss_dssp             EETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGS
T ss_pred             EeCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccC
Confidence            99999999999876543           23468889899 99999999999997

>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=5.5e-25  Score=232.81  Aligned_cols=156  Identities=28%  Similarity=0.418  Sum_probs=141.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~  269 (823)
                      .+.++|||+|||.++|+++|+++|++||.|..|++ .+++|||||+|.+.++|++|+..|+|..+.|+.|.|.++.+   
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            45689999999999999999999999999999976 56799999999999999999999999999999999999863   


Q ss_pred             CCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhC-CCccC---C
Q 003400          270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLN-RSDIA---G  341 (823)
Q Consensus       270 ~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~Ln-G~~i~---G  341 (823)
                             ..+|||+|||..+|+++|+++|+.||.|..|++    ++.++|||||+|.+.++|.+|+..|| |..+.   +
T Consensus        96 -------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~  168 (261)
T 3sde_A           96 -------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTP  168 (261)
T ss_dssp             -------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSC
T ss_pred             -------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCC
Confidence                   458999999999999999999999999999976    45678999999999999999999995 44444   8


Q ss_pred             ceEEEEecCCCcccc
Q 003400          342 KRIKLEPSRPGGARR  356 (823)
Q Consensus       342 r~I~V~~s~~~~~r~  356 (823)
                      ++|.|+++.+...+.
T Consensus       169 r~i~v~~~~~~~~~~  183 (261)
T 3sde_A          169 RPVIVEPMEQFDDED  183 (261)
T ss_dssp             CBCEEEECCCEESSS
T ss_pred             ceEEEeeccccCccC
Confidence            999999998865443

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.78  E-value=3e-19  Score=182.97  Aligned_cols=154  Identities=13%  Similarity=0.239  Sum_probs=125.0

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCcccccc----ccccccCCCCccccCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEHP  186 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~~----~~~~~l~n~~~~~~~~~~  186 (823)
                      .+.+||++||.+++|.+|+++|+.+|.|   .|..|..++..+|++++.|.+...+..    +++..+.+....+.....
T Consensus        15 ~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~   94 (213)
T 4f02_A           15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   94 (213)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccc
Confidence            4689999999999999999999999987   667777888899999999998866552    233333333222221111


Q ss_pred             C---CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          187 Y---GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       187 ~---~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      .   .....++|||+|||.++|+++|+++|++||.|..|++   ...++|||||+|.+.++|++|++.|+|..|.|++|.
T Consensus        95 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~  174 (213)
T 4f02_A           95 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF  174 (213)
T ss_dssp             CTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            1   1224579999999999999999999999999999874   345789999999999999999999999999999999


Q ss_pred             ccccCCC
Q 003400          261 IHFSIPK  267 (823)
Q Consensus       261 V~~a~pk  267 (823)
                      |.++.++
T Consensus       175 V~~a~~~  181 (213)
T 4f02_A          175 VGRFKSR  181 (213)
T ss_dssp             EEECCCH
T ss_pred             EEEcCCC
Confidence            9999764

>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=99.78  E-value=4.6e-19  Score=171.88  Aligned_cols=127  Identities=19%  Similarity=0.244  Sum_probs=112.6

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHh-cCCccccccccccccCCCC------------CCCCCCCCccceeeecCCCCCCHH
Q 003400          226 CKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDIHFSIPKD------------NPSDKDLNQGTLVVFNLDPSVSNE  292 (823)
Q Consensus       226 ~ksrG~AFV~F~~~e~A~~Ai~~L-ng~~l~gr~L~V~~a~pk~------------~~~~~~~~~~tLfV~NLp~~vtee  292 (823)
                      .+.+|+++|+|.+.++|++|++.+ +|..+.| .+.+.++..+.            .........++|||+|||++++++
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            356899999999999999999999 9999999 99999876421            112223456799999999999999


Q ss_pred             HHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          293 DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       293 dL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      +|+++|++||.|.+|++...++|||||+|.+.++|.+|++.|||..|.|++|+|++++++.
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            9999999999999999977789999999999999999999999999999999999998763

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.77  E-value=2.2e-18  Score=174.99  Aligned_cols=157  Identities=13%  Similarity=0.231  Sum_probs=126.4

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP  186 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~  186 (823)
                      .++++|++||.++++.+++++|+.+|.|   .|..+..++..++++++.|.+...+.    .+++..+.+....+.....
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            6789999999999999999999999987   55556667788999999999887665    2444444444433322211


Q ss_pred             C------------CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHh
Q 003400          187 Y------------GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRAL  249 (823)
Q Consensus       187 ~------------~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~L  249 (823)
                      .            ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|.+|++.|
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l  187 (216)
T 2qfj_A          108 IGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM  187 (216)
T ss_dssp             CGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             ccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHc
Confidence            1            1245689999999999999999999999999999984     4567999999999999999999999


Q ss_pred             cCCccccccccccccCCCCCC
Q 003400          250 QNKPLRRRKLDIHFSIPKDNP  270 (823)
Q Consensus       250 ng~~l~gr~L~V~~a~pk~~~  270 (823)
                      +|..|.|+.|.|.|+.++..+
T Consensus       188 ~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          188 NLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             TTCBCSSSBCEEEECSSCSST
T ss_pred             cCCEeCCcEEEEEEecCCCCC
Confidence            999999999999999876543

>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=99.77  E-value=3.2e-18  Score=166.94  Aligned_cols=130  Identities=21%  Similarity=0.281  Sum_probs=102.6

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhcCCccc-------cccccccccCCCC--CCCCCCCCccceeeecCCCCCCHHHHH
Q 003400          225 ACKHRGFVMISYYDIRAARTAMRALQNKPLR-------RRKLDIHFSIPKD--NPSDKDLNQGTLVVFNLDPSVSNEDLR  295 (823)
Q Consensus       225 ~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~-------gr~L~V~~a~pk~--~~~~~~~~~~tLfV~NLp~~vteedL~  295 (823)
                      ..+++|||||+|.+.++|++|++.+++....       +............  ..........+|||+|||.++++++|+
T Consensus         9 ~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~   88 (158)
T 2kn4_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLR   88 (158)
T ss_dssp             CSSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCHHHHH
T ss_pred             CccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHH
Confidence            3468999999999999999999887753221       2222211111111  111223346799999999999999999


Q ss_pred             HHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          296 QIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       296 ~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      ++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|+.|+|++++++..
T Consensus        89 ~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           89 RVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             HHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             HHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            99999999999986     456899999999999999999999999999999999999987653

>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=99.76  E-value=2.3e-18  Score=167.73  Aligned_cols=151  Identities=21%  Similarity=0.319  Sum_probs=123.3

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP  186 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~  186 (823)
                      .++++|++||.++++.++.++|+.+|.|   .+..+..++..+|++++.|.+...+.    .+++..+.+....+....+
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            3679999999999999999999999987   44445567778899999999887665    2344444444333333222


Q ss_pred             C-CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccc--cc
Q 003400          187 Y-GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RK  258 (823)
Q Consensus       187 ~-~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g--r~  258 (823)
                      . ...+.++|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|.+|++.|+|..+.|  ++
T Consensus        83 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~  162 (168)
T 1b7f_A           83 GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQP  162 (168)
T ss_dssp             CSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSC
T ss_pred             CcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeE
Confidence            2 3456789999999999999999999999999999874     45678999999999999999999999999987  99


Q ss_pred             cccccc
Q 003400          259 LDIHFS  264 (823)
Q Consensus       259 L~V~~a  264 (823)
                      |+|.||
T Consensus       163 l~V~~A  168 (168)
T 1b7f_A          163 LSVRLA  168 (168)
T ss_dssp             CEEEEC
T ss_pred             EEEEeC
Confidence            999875

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.76  E-value=3.6e-18  Score=165.58  Aligned_cols=150  Identities=19%  Similarity=0.283  Sum_probs=121.3

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccC---C
Q 003400          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAG---E  184 (823)
Q Consensus       115 ~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~---~  184 (823)
                      ++++|++||.++++.++.++|+.+|.|   .+..+. .+..++++++.|.+...+.    .+++..+.+....+..   .
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            368999999999999999999999997   444443 4667899999999886654    3344444444332221   2


Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccc
Q 003400          185 HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  259 (823)
Q Consensus       185 ~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L  259 (823)
                      ......+.++|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|.+|++.|+|..+.|++|
T Consensus        80 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  159 (166)
T 3md3_A           80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL  159 (166)
T ss_dssp             CCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Confidence            2234556789999999999999999999999999999874     45788999999999999999999999999999999


Q ss_pred             cccccC
Q 003400          260 DIHFSI  265 (823)
Q Consensus       260 ~V~~a~  265 (823)
                      .|.|+.
T Consensus       160 ~v~~a~  165 (166)
T 3md3_A          160 RINWAA  165 (166)
T ss_dssp             EEEESC
T ss_pred             EEEecC
Confidence            999985

>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=99.75  E-value=3.8e-18  Score=165.55  Aligned_cols=150  Identities=21%  Similarity=0.297  Sum_probs=122.2

Q ss_pred             cccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCcccccc----ccccccCCCCccccCCCCC
Q 003400          115 DDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNG----LLHYSVPNGAGTVAGEHPY  187 (823)
Q Consensus       115 ~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~~----~~~~~l~n~~~~~~~~~~~  187 (823)
                      ++++|++||.++++.++.++|+.+|.|   .+..+..++..++++++.|.+...+..    +++..+.+....+....+.
T Consensus         3 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   82 (167)
T 1fxl_A            3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS   82 (167)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             ceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCC
Confidence            679999999999999999999999987   555666677888999999998876652    3444454444333333322


Q ss_pred             -CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccc--c
Q 003400          188 -GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK--L  259 (823)
Q Consensus       188 -~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~--L  259 (823)
                       ...+.++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|+|..+.|+.  |
T Consensus        83 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i  162 (167)
T 1fxl_A           83 SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPI  162 (167)
T ss_dssp             CGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             cccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccce
Confidence             2346689999999999999999999999999999874     4557899999999999999999999999999975  6


Q ss_pred             ccccc
Q 003400          260 DIHFS  264 (823)
Q Consensus       260 ~V~~a  264 (823)
                      .|.||
T Consensus       163 ~v~~A  167 (167)
T 1fxl_A          163 TVKFA  167 (167)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            67664

>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=99.75  E-value=4.3e-18  Score=170.25  Aligned_cols=156  Identities=17%  Similarity=0.277  Sum_probs=120.1

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccccc---cccccCCCCccccC----
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGL---LHYSVPNGAGTVAG----  183 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~~~---~~~~l~n~~~~~~~----  183 (823)
                      .++++|++||.++++.++.++|+.+|.|   .|..+..++..+|++++.|.+...|...   .+..+.+....+..    
T Consensus        13 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~   92 (196)
T 1l3k_A           13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   92 (196)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC-
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCc
Confidence            5789999999999999999999999987   5666767778899999999988665522   22223222222211    


Q ss_pred             ---CCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccc
Q 003400          184 ---EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (823)
Q Consensus       184 ---~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~  255 (823)
                         ..+....+.++|||+|||.++|+++|+++|++||.|..|.+     +++++|||||+|.+.++|.+|++. ++..+.
T Consensus        93 ~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~  171 (196)
T 1l3k_A           93 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVN  171 (196)
T ss_dssp             ----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEET
T ss_pred             ccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEEC
Confidence               11122335689999999999999999999999999999874     466899999999999999999986 799999


Q ss_pred             cccccccccCCCCCC
Q 003400          256 RRKLDIHFSIPKDNP  270 (823)
Q Consensus       256 gr~L~V~~a~pk~~~  270 (823)
                      |+.|.|.++.++...
T Consensus       172 G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          172 GHNCEVRKALSKQEM  186 (196)
T ss_dssp             TEECEEEECC-----
T ss_pred             CEEEEEEecCChhHh
Confidence            999999999887654

>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=99.75  E-value=7.7e-18  Score=164.87  Aligned_cols=151  Identities=15%  Similarity=0.269  Sum_probs=119.0

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccC--cccceeEeeecCccccc----cccccccCCC---Cccc
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQES--LSMSMSKISISDSASGN----GLLHYSVPNG---AGTV  181 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es--~~~g~~~v~~~e~~~a~----~~~~~~l~n~---~~~~  181 (823)
                      .++++|++||.++++.+++++|+.+|.|   .|..+...+  ..++++++.|.+...+.    .+++..+..+   ...+
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~   82 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM   82 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEE
Confidence            4789999999999999999999999987   555555554  78899999999886654    2333333222   1111


Q ss_pred             c--CCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccc
Q 003400          182 A--GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (823)
Q Consensus       182 ~--~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~  255 (823)
                      .  ........+.++|||+|||.++|+++|+++|++||.|..|++    .++++|||||+|.+.++|++|++.|+|..+.
T Consensus        83 ~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~  162 (175)
T 3nmr_A           83 KPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTM  162 (175)
T ss_dssp             EECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCC
T ss_pred             ccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCccc
Confidence            1  111223346789999999999999999999999999999884    4567899999999999999999999998776


Q ss_pred             ---ccccccccc
Q 003400          256 ---RRKLDIHFS  264 (823)
Q Consensus       256 ---gr~L~V~~a  264 (823)
                         +++|.|.|+
T Consensus       163 ~g~~~~l~V~~a  174 (175)
T 3nmr_A          163 EGCSSPMVVKFA  174 (175)
T ss_dssp             TTCSSCCEEEEC
T ss_pred             CCCCCCeEEEec
Confidence               499999987

>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=99.75  E-value=9.6e-19  Score=170.48  Aligned_cols=153  Identities=18%  Similarity=0.275  Sum_probs=121.5

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccccccc--cccCCCCccccCCCCC-
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGLLH--YSVPNGAGTVAGEHPY-  187 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~~~~~--~~l~n~~~~~~~~~~~-  187 (823)
                      .++++|++||.++++.+++++|+.+|.|   .|..+..++..+|++++.|.+...+.....  ..+.+....+....+. 
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~~   82 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRD   82 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCHH
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccchh
Confidence            4689999999999999999999999987   445555677889999999998866642211  1122222222111111 


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++ +++..+.|++|.|.
T Consensus        83 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~  161 (167)
T 2cjk_A           83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIK  161 (167)
T ss_dssp             HHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEE
T ss_pred             hccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEe
Confidence            1234679999999999999999999999999999984     46788999999999999999998 89999999999999


Q ss_pred             ccCCC
Q 003400          263 FSIPK  267 (823)
Q Consensus       263 ~a~pk  267 (823)
                      |+.|+
T Consensus       162 ~a~pk  166 (167)
T 2cjk_A          162 RAEPR  166 (167)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            99875

>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=99.74  E-value=1e-18  Score=172.04  Aligned_cols=154  Identities=14%  Similarity=0.133  Sum_probs=125.8

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE--EEeccCccCcccceeEeeecCccccc---cccccccCCCCccccCCC---
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM--ELEGEPQESLSMSMSKISISDSASGN---GLLHYSVPNGAGTVAGEH---  185 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v--~V~~d~~es~~~g~~~v~~~e~~~a~---~~~~~~l~n~~~~~~~~~---  185 (823)
                      .++++|++||.++++.+++++|+.+|.+  .+..+...+..+|++++.|.+...+.   .+++..+.+....+....   
T Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~~   92 (175)
T 1fje_B           13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRD   92 (175)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCSS
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCCcc
Confidence            5789999999999999999999999875  13345556778899999999886654   344444444433332222   


Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       186 ~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      .....+.++|||+|||.++++++|+++|++||+|..+..+++++|||||+|.+.++|.+|++.|+|..+.|++|.|.|+.
T Consensus        93 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  172 (175)
T 1fje_B           93 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG  172 (175)
T ss_dssp             CSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECS
T ss_pred             ccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecC
Confidence            22344678999999999999999999999999999885567899999999999999999999999999999999999997


Q ss_pred             CC
Q 003400          266 PK  267 (823)
Q Consensus       266 pk  267 (823)
                      ++
T Consensus       173 ~k  174 (175)
T 1fje_B          173 EK  174 (175)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.73  E-value=4.3e-18  Score=158.07  Aligned_cols=103  Identities=16%  Similarity=0.317  Sum_probs=71.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      .+++|||+|||.++|+++|+++|++||.|.+|++   ...++|||||+|.+.++|++|++.|++..|.|++|.|.++.++
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            3679999999999999999999999999999874   3457899999999999999999999999999999999999775


Q ss_pred             CCCCC----CCCCccceeeecCCCCCCHHH
Q 003400          268 DNPSD----KDLNQGTLVVFNLDPSVSNED  293 (823)
Q Consensus       268 ~~~~~----~~~~~~tLfV~NLp~~vteed  293 (823)
                      .....    ......+|||+|||+++|++.
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            53321    122345899999999999864

>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=99.70  E-value=2.3e-17  Score=161.43  Aligned_cols=148  Identities=14%  Similarity=0.266  Sum_probs=116.8

Q ss_pred             ccccccccCCCCCChHHHHHhhcCC----C-------cEEEeccCccCcccceeEeeecCcccccc---ccccccCCCCc
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSG----G-------GMELEGEPQESLSMSMSKISISDSASGNG---LLHYSVPNGAG  179 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~----G-------~v~V~~d~~es~~~g~~~v~~~e~~~a~~---~~~~~l~n~~~  179 (823)
                      .++++|++||.++++.++.++|+.+    |       .|   .+......++++++.|.+.+.|..   +++..+.+...
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v---~~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i   80 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPV---LAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   80 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSE---EEEEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEEC
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCce---eeeEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCcee
Confidence            4789999999999999999999999    5       33   111223457899999988766553   33333443333


Q ss_pred             cccCCCCC-CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 003400          180 TVAGEHPY-GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKP  253 (823)
Q Consensus       180 ~~~~~~~~-~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~  253 (823)
                      .+...... .....++|||+|||.++++++|+++|++||+|..|.+     +++++|||||+|.+.++|++|++.|+|..
T Consensus        81 ~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~  160 (172)
T 2g4b_A           81 KIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ  160 (172)
T ss_dssp             EEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCE
T ss_pred             eecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCE
Confidence            33222221 2234689999999999999999999999999999884     56679999999999999999999999999


Q ss_pred             ccccccccccc
Q 003400          254 LRRRKLDIHFS  264 (823)
Q Consensus       254 l~gr~L~V~~a  264 (823)
                      +.|++|.|.||
T Consensus       161 ~~g~~l~V~~A  171 (172)
T 2g4b_A          161 LGDKKLLVQRA  171 (172)
T ss_dssp             ETTEECEEEEC
T ss_pred             ECCeEEEEEeC
Confidence            99999999987

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.70  E-value=3.6e-17  Score=163.74  Aligned_cols=157  Identities=12%  Similarity=0.213  Sum_probs=118.5

Q ss_pred             CccccccccCCCCCChHHHHHhhcCCCcE---E-----EeccCccCcccceeEeeecCcccccc---ccccccCCCCccc
Q 003400          113 IMDDFDLRGLPSSLEDLEDYDIFGSGGGM---E-----LEGEPQESLSMSMSKISISDSASGNG---LLHYSVPNGAGTV  181 (823)
Q Consensus       113 v~~el~V~~Lp~~~~E~el~dlFs~~G~v---~-----V~~d~~es~~~g~~~v~~~e~~~a~~---~~~~~l~n~~~~~  181 (823)
                      ..++++|++||.++++.++.++|+.+|.+   .     ...+......++++++.|.+...+..   +++..+.+....+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~v   82 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI   82 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEEE
Confidence            35789999999999999999999999521   0     01122234567899999988765542   2333333222111


Q ss_pred             cCCC---------------------CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEE
Q 003400          182 AGEH---------------------PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMIS  235 (823)
Q Consensus       182 ~~~~---------------------~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~  235 (823)
                      ....                     .....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~  162 (198)
T 2yh0_A           83 RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE  162 (198)
T ss_dssp             ECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEE
T ss_pred             eCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEE
Confidence            1110                     011246799999999999999999999999999999884     45679999999


Q ss_pred             eCCHHHHHHHHHHhcCCccccccccccccCCCCC
Q 003400          236 YYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       236 F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~  269 (823)
                      |.+.++|++|++.|+|..+.|+.|.|.|+.++..
T Consensus       163 f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          163 YVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             ESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             ECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            9999999999999999999999999999987543

>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=99.70  E-value=8.4e-17  Score=166.63  Aligned_cols=151  Identities=19%  Similarity=0.216  Sum_probs=118.9

Q ss_pred             ccccccccCCC-CCChHHHHHhhcCCCcE-EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCCC-
Q 003400          114 MDDFDLRGLPS-SLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP-  186 (823)
Q Consensus       114 ~~el~V~~Lp~-~~~E~el~dlFs~~G~v-~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~-  186 (823)
                      ...++|++||. ++++.+++++|+.+|.| .|.+....   ++++++.|.+...|.    .+++..+.+....+....+ 
T Consensus        34 ~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~---~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  110 (229)
T 2adc_A           34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK---KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ  110 (229)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT---SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC---CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCc
Confidence            57899999999 99999999999999987 22222211   678889988876554    2344444443222211100 


Q ss_pred             -----------------------------------CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCC-CEEEEEeCCCccc
Q 003400          187 -----------------------------------YGEHPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYTACKHRG  230 (823)
Q Consensus       187 -----------------------------------~~e~~srtLfV~NLP~~vteeeLr~lFs~fG-~I~~v~~~~ksrG  230 (823)
                                                         ....++++|||+|||.++++++|+++|++|| .|..|++..+.+|
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g  190 (229)
T 2adc_A          111 NVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK  190 (229)
T ss_dssp             CCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTT
T ss_pred             cccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCc
Confidence                                               0123478999999999999999999999999 9999998677899


Q ss_pred             EEEEEeCCHHHHHHHHHHhcCCccc-cccccccccCCC
Q 003400          231 FVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSIPK  267 (823)
Q Consensus       231 ~AFV~F~~~e~A~~Ai~~Lng~~l~-gr~L~V~~a~pk  267 (823)
                      ||||+|.+.++|.+|++.|+|..+. |++|+|.|+.++
T Consensus       191 ~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          191 MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9999999999999999999999999 999999999763

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.69  E-value=9.7e-17  Score=161.39  Aligned_cols=151  Identities=19%  Similarity=0.216  Sum_probs=117.7

Q ss_pred             ccccccccCCC-CCChHHHHHhhcCCCcE-EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCCC-
Q 003400          114 MDDFDLRGLPS-SLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHP-  186 (823)
Q Consensus       114 ~~el~V~~Lp~-~~~E~el~dlFs~~G~v-~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~-  186 (823)
                      .+.++|++||. ++++.++.++|+.+|.| .|.+-...   ++++++.|.+...+.    .+++..+.+....+..... 
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~---~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~   79 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK---KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   79 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC---SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCC
Confidence            36899999999 99999999999999987 33222211   578888888776554    2334344333222210000 


Q ss_pred             -----------------------------------CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCC-CEEEEEeCCCccc
Q 003400          187 -----------------------------------YGEHPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYTACKHRG  230 (823)
Q Consensus       187 -----------------------------------~~e~~srtLfV~NLP~~vteeeLr~lFs~fG-~I~~v~~~~ksrG  230 (823)
                                                         ....++++|||+|||.++++++|+++|++|| .|..|++....+|
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g  159 (198)
T 1qm9_A           80 NVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK  159 (198)
T ss_dssp             SCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSS
T ss_pred             CcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCc
Confidence                                               1123578999999999999999999999999 9999998677799


Q ss_pred             EEEEEeCCHHHHHHHHHHhcCCccc-cccccccccCCC
Q 003400          231 FVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSIPK  267 (823)
Q Consensus       231 ~AFV~F~~~e~A~~Ai~~Lng~~l~-gr~L~V~~a~pk  267 (823)
                      ||||+|.+.++|.+|++.|+|..+. |++|+|.|+.++
T Consensus       160 ~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          160 MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            9999999999999999999999999 999999998753

>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=99.68  E-value=1e-16  Score=170.24  Aligned_cols=75  Identities=20%  Similarity=0.347  Sum_probs=70.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccc-cccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~-gr~L~V~~a~  265 (823)
                      ++++|||+|||.++++++|+++|++||.|.+|++....+|||||+|.+.++|.+|++.|+|..+. |+.|+|.|++
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            56899999999999999999999999999999876656799999999999999999999999999 9999999985

>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=99.63  E-value=6.3e-16  Score=139.92  Aligned_cols=76  Identities=28%  Similarity=0.485  Sum_probs=71.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++|+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            3468999999999999999999999999999976     46788999999999999999999999999999999999998


Q ss_pred             C
Q 003400          351 P  351 (823)
Q Consensus       351 ~  351 (823)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            6

>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=99.62  E-value=6.6e-16  Score=157.95  Aligned_cols=148  Identities=12%  Similarity=0.140  Sum_probs=108.8

Q ss_pred             ccccccccCC-CCCChHHHHHhhcCCCcE-EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCC--
Q 003400          114 MDDFDLRGLP-SSLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEH--  185 (823)
Q Consensus       114 ~~el~V~~Lp-~~~~E~el~dlFs~~G~v-~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~--  185 (823)
                      .+.++|++|+ .++++.+|+++|+.||.| .|.+-. .  .+|++++.|.+...|.    .+++..+.+....+....  
T Consensus         4 ~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~-~--~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~   80 (205)
T 3tyt_A            4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMK-S--KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQP   80 (205)
T ss_dssp             CSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECT-T--STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEec-C--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCC
Confidence            3679999999 899999999999999998 232221 1  3688899988876554    233333333211111000  


Q ss_pred             ---C---------------------------------CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCE--EEEEeC--
Q 003400          186 ---P---------------------------------YGEHPSRTLFVRNINSNVEDSELRALFEQYGDI--RTLYTA--  225 (823)
Q Consensus       186 ---~---------------------------------~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I--~~v~~~--  225 (823)
                         +                                 ....++++|||+|||.++|+++|+++|++||.|  .+|++.  
T Consensus        81 ~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~  160 (205)
T 3tyt_A           81 AIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSG  160 (205)
T ss_dssp             CCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSC
T ss_pred             ccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcC
Confidence               0                                 011356799999999999999999999999998  787743  


Q ss_pred             -CCcccEEEEEeCCHHHHHHHHHHhcCCccccc----ccccccc
Q 003400          226 -CKHRGFVMISYYDIRAARTAMRALQNKPLRRR----KLDIHFS  264 (823)
Q Consensus       226 -~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr----~L~V~~a  264 (823)
                       +..+|||||+|.+.++|.+|+..|+|..|.|.    ++.|+++
T Consensus       161 ~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          161 KSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence             24569999999999999999999999999876    4555543

>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=99.61  E-value=9e-16  Score=138.92  Aligned_cols=76  Identities=22%  Similarity=0.472  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.||+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            4579999999999999999999999999999974     46789999999999999999999999999999999999997


Q ss_pred             C
Q 003400          266 P  266 (823)
Q Consensus       266 p  266 (823)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            6

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.61  E-value=4.7e-16  Score=148.68  Aligned_cols=121  Identities=21%  Similarity=0.330  Sum_probs=77.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe
Q 003400          230 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE  309 (823)
Q Consensus       230 G~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri  309 (823)
                      -++|++|.+...|..|+..++|....|+. .+.+..+    .......++|||+|||.++|+++|+++|++||.|..|++
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            36889999999999999999887666553 2334433    233445679999999999999999999999999999976


Q ss_pred             -----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCccc
Q 003400          310 -----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  355 (823)
Q Consensus       310 -----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~r  355 (823)
                           ++.++|||||+|.+.++|++|++.|||..|.|++|+|++++++..+
T Consensus        80 ~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           80 PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             CCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence                 4567899999999999999999999999999999999999876543

>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=99.61  E-value=4.5e-16  Score=143.74  Aligned_cols=103  Identities=24%  Similarity=0.400  Sum_probs=91.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ..++++|||+|||.++++++|+++|++||.|..|.+  .+.++|||||+|.+.++|++|++.|+|..+.|+.|.|.|+.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   84 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA   84 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            346799999999999999999999999999999985  566789999999999999999999999999999999999975


Q ss_pred             CCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCc
Q 003400          267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE  303 (823)
Q Consensus       267 k~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~  303 (823)
                      +...            .+++...++++|+++|++||.
T Consensus        85 ~~~~------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           85 NRAF------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHT------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             Chhh------------hhhhHhHhHHHHHHHHHHhCC
Confidence            4321            467778899999999999984

>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=99.59  E-value=2.3e-15  Score=139.67  Aligned_cols=80  Identities=23%  Similarity=0.390  Sum_probs=71.8

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~---~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      .++|||+|||+++|+++|+++|++||.|.+|++.   +.++|||||+|.+.++|++||+.|||..|.|++|+|++++++.
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            4689999999999999999999999999999763   3468999999999999999999999999999999999998765


Q ss_pred             ccc
Q 003400          354 ARR  356 (823)
Q Consensus       354 ~r~  356 (823)
                      .+.
T Consensus        85 ~~~   87 (115)
T 4f25_A           85 ERE   87 (115)
T ss_dssp             C--
T ss_pred             ccc
Confidence            543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.59  E-value=2.5e-15  Score=138.70  Aligned_cols=83  Identities=22%  Similarity=0.298  Sum_probs=75.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+||++++++++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|||..+.|+.|+|++++
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            4568999999999999999999999999999976     46789999999999999999999999999999999999998


Q ss_pred             CCcccchh
Q 003400          351 PGGARRNL  358 (823)
Q Consensus       351 ~~~~r~~~  358 (823)
                      .+..++.+
T Consensus        85 ~~~~~~~~   92 (110)
T 3s8s_A           85 KGQQRMKY   92 (110)
T ss_dssp             TTHHHHHH
T ss_pred             CCcHHHHH
Confidence            77655443

>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=99.59  E-value=2.7e-15  Score=158.37  Aligned_cols=146  Identities=15%  Similarity=0.126  Sum_probs=116.3

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE-EEeccCccCcccceeEeeecCccccc----cccccccCCCCccccCCCCCC
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM-ELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYG  188 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v-~V~~d~~es~~~g~~~v~~~e~~~a~----~~~~~~l~n~~~~~~~~~~~~  188 (823)
                      .+.++|++||.++++.++.++|+.+|.| .|.+    ...++++++.|.+...|.    .+++..+.+....+...    
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i----~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a----   93 (261)
T 3sde_A           22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI----NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA----   93 (261)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC----
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE----eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec----
Confidence            4689999999999999999999999997 3322    234689999999876655    24444444443333322    


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCC-ccc---ccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNK-PLR---RRKLD  260 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~-~l~---gr~L~  260 (823)
                       .+.++|||+|||..+|+++|+++|++||.|..|.+    +++++|||||+|.+.++|.+|++.|++. .+.   +++|.
T Consensus        94 -~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           94 -THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             -CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             -ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence             35789999999999999999999999999999874    5668999999999999999999999554 443   89999


Q ss_pred             ccccCCCC
Q 003400          261 IHFSIPKD  268 (823)
Q Consensus       261 V~~a~pk~  268 (823)
                      |.++.+..
T Consensus       173 v~~~~~~~  180 (261)
T 3sde_A          173 VEPMEQFD  180 (261)
T ss_dssp             EEECCCEE
T ss_pred             EeeccccC
Confidence            99987653

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=2.5e-15  Score=135.54  Aligned_cols=94  Identities=24%  Similarity=0.364  Sum_probs=81.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCCCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSD  272 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~~~~  272 (823)
                      ++|||+|||.++|+++|+++|++||+|..|++...++|||||+|.+.++|++|++.|++..+.|++|.|.++.++.....
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            58999999999999999999999999999986544899999999999999999999999999999999999987653221


Q ss_pred             C------CCCccceeeecCC
Q 003400          273 K------DLNQGTLVVFNLD  286 (823)
Q Consensus       273 ~------~~~~~tLfV~NLp  286 (823)
                      .      .....+|||+||+
T Consensus        81 ~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           81 FDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSCCCSCCCCSCCCSCCCC
T ss_pred             CCCCCccccCCCceecCCCC
Confidence            1      1224689999997

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=7.4e-15  Score=134.56  Aligned_cols=82  Identities=23%  Similarity=0.309  Sum_probs=73.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcC--CccccccccccccCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIHFSIP  266 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng--~~l~gr~L~V~~a~p  266 (823)
                      ..+.++|||+|||+++|+++|+++|++||+|.+|++.. .+|||||+|.+.++|++|++.|++  ..|.|++|+|.|+.+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~-~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~   91 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH   91 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCC
Confidence            45789999999999999999999999999999998643 489999999999999999998864  789999999999987


Q ss_pred             CCCCC
Q 003400          267 KDNPS  271 (823)
Q Consensus       267 k~~~~  271 (823)
                      +....
T Consensus        92 ~~~~~   96 (105)
T 1sjq_A           92 KELKT   96 (105)
T ss_dssp             SSCCC
T ss_pred             CCCCc
Confidence            66543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.56  E-value=6.7e-15  Score=133.66  Aligned_cols=80  Identities=13%  Similarity=0.269  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCc--cccccccccccC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP--LRRRKLDIHFSI  265 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~--l~gr~L~V~~a~  265 (823)
                      ...|+++|||+|||.++|+++|+++|++||.|.+|++. +.||||||+|.+.++|++|++.|++..  +.|++|+|+|+.
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 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM-PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST   95 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECS
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecc
Confidence            34588999999999999999999999999999999764 478999999999999999999999876  779999999997


Q ss_pred             CCC
Q 003400          266 PKD  268 (823)
Q Consensus       266 pk~  268 (823)
                      +++
T Consensus        96 ~k~   98 (100)
T 3r27_A           96 SQK   98 (100)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            654

>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=99.56  E-value=6.5e-15  Score=145.13  Aligned_cols=123  Identities=19%  Similarity=0.285  Sum_probs=73.0

Q ss_pred             EEeCCHHHHHHHHHHhcCCccc--cccccccccCCCC----------------CCCCCCCCccceeeecCCCCCCHHHHH
Q 003400          234 ISYYDIRAARTAMRALQNKPLR--RRKLDIHFSIPKD----------------NPSDKDLNQGTLVVFNLDPSVSNEDLR  295 (823)
Q Consensus       234 V~F~~~e~A~~Ai~~Lng~~l~--gr~L~V~~a~pk~----------------~~~~~~~~~~tLfV~NLp~~vteedL~  295 (823)
                      .+|.+.++|+.|+..|++....  |+.+...++....                .........++|||+|||..+++++|+
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            6899999999999999887665  5555554421100                011122345689999999999999999


Q ss_pred             HHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcccc
Q 003400          296 QIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR  356 (823)
Q Consensus       296 ~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~r~  356 (823)
                      ++|++||.|..|++     ++.++|||||+|.+.++|++||+.|||..|.|+.|.|.|+.++..++
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            99999999999976     34568999999999999999999999999999999999998766443

>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=99.55  E-value=1.3e-14  Score=134.00  Aligned_cols=102  Identities=21%  Similarity=0.405  Sum_probs=89.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri--~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++  .+.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++++..
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            3569999999999999999999999999999987  45678999999999999999999999999999999999998765


Q ss_pred             ccchhhhccccccCHHHHHHHHhhcCCC
Q 003400          354 ARRNLMLQLNQELEQDESRILQHQVGSP  381 (823)
Q Consensus       354 ~r~~~~~ql~~~~~~~~l~~~f~~~GsP  381 (823)
                      ..    .++.....++++..++.++|..
T Consensus        87 ~~----~~~~~~~~~~~l~~~~~~~g~~  110 (115)
T 3lqv_A           87 AF----QKMDTKKKEEQLKLLKEKYGIN  110 (115)
T ss_dssp             HT----TTSCHHHHHHHHHHHHHHHCCC
T ss_pred             hh----hhhhHhHhHHHHHHHHHHhCCC
Confidence            33    4455667788899999999854

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.55  E-value=2.4e-15  Score=133.86  Aligned_cols=79  Identities=22%  Similarity=0.409  Sum_probs=70.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCC-CEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhc-CCcccccccccccc
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYG-DIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQ-NKPLRRRKLDIHFS  264 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG-~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Ln-g~~l~gr~L~V~~a  264 (823)
                      +++|||+|||.++|+++|+++|++|| +|.+|++     +++++|||||+|.+.++|++|++.++ +..+.|++|.|+|+
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 7988873     46789999999999999999999874 56799999999999


Q ss_pred             CCCCCC
Q 003400          265 IPKDNP  270 (823)
Q Consensus       265 ~pk~~~  270 (823)
                      .|+...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            887654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.55  E-value=1.1e-14  Score=134.44  Aligned_cols=78  Identities=18%  Similarity=0.395  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.+
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            357899999999999999999999999999999984     478899999999999999999999999999999999999


Q ss_pred             cCC
Q 003400          264 SIP  266 (823)
Q Consensus       264 a~p  266 (823)
                      +..
T Consensus        83 a~~   85 (110)
T 3s8s_A           83 DIK   85 (110)
T ss_dssp             CST
T ss_pred             CCC
Confidence            854

>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=99.55  E-value=1.8e-14  Score=129.30  Aligned_cols=82  Identities=26%  Similarity=0.395  Sum_probs=75.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.+
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            457899999999999999999999999999999985     566889999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003400          264 SIPKDNP  270 (823)
Q Consensus       264 a~pk~~~  270 (823)
                      +.++...
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9876543

>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=99.55  E-value=1.9e-14  Score=129.09  Aligned_cols=80  Identities=28%  Similarity=0.401  Sum_probs=74.1

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+++
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            35679999999999999999999999999999987     4567899999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003400          350 RPGGA  354 (823)
Q Consensus       350 ~~~~~  354 (823)
                      +++..
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            88754

>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=2.8e-14  Score=128.34  Aligned_cols=81  Identities=25%  Similarity=0.354  Sum_probs=73.9

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++.    +.++|||||+|.+.++|++|++.|||..+.|+.|+|+++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            3456799999999999999999999999999999763    556899999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003400          350 RPGGA  354 (823)
Q Consensus       350 ~~~~~  354 (823)
                      +++..
T Consensus        94 ~~~~~   98 (100)
T 2do4_A           94 NSGPS   98 (100)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            88753

>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=99.54  E-value=1.8e-14  Score=135.00  Aligned_cols=87  Identities=23%  Similarity=0.300  Sum_probs=75.7

Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcC--Ccccccccccc
Q 003400          185 HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIH  262 (823)
Q Consensus       185 ~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng--~~l~gr~L~V~  262 (823)
                      ......++++|||+|||+++|+++|+++|++||.|.+|++.. .+|||||+|.+.++|++|++.|++  ..|.|++|+|.
T Consensus        24 ~~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~-~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           24 SRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             TTSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEG-GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            334456789999999999999999999999999999998643 589999999999999999998874  68999999999


Q ss_pred             ccCCCCCCCC
Q 003400          263 FSIPKDNPSD  272 (823)
Q Consensus       263 ~a~pk~~~~~  272 (823)
                      |+.++.....
T Consensus       103 ~a~~k~~~~~  112 (119)
T 2ad9_A          103 FSNHKELKTD  112 (119)
T ss_dssp             ECSSSSCCCC
T ss_pred             EccCCCCCcc
Confidence            9987665443

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.54  E-value=3.1e-14  Score=125.78  Aligned_cols=81  Identities=19%  Similarity=0.282  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..+.++|||+|||.++++++|+++|++||+|..|++   +++++|||||+|.+.++|++|++.|++..+.|++|+|.++.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            456799999999999999999999999999999875   45688999999999999999999999999999999999998


Q ss_pred             CCCC
Q 003400          266 PKDN  269 (823)
Q Consensus       266 pk~~  269 (823)
                      +...
T Consensus        85 ~~~~   88 (92)
T 2dgv_A           85 NASG   88 (92)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.54  E-value=4.3e-15  Score=132.24  Aligned_cols=77  Identities=19%  Similarity=0.383  Sum_probs=69.7

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccC-ceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhC-CCccCCceEEEEecC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLN-RSDIAGKRIKLEPSR  350 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG-~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~Ln-G~~i~Gr~I~V~~s~  350 (823)
                      ++|||+|||+++|+++|+++|++|| .|.+|++     ++.++|||||+|.+.++|++|++.|+ +..+.|++|+|++++
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            5899999999999999999999999 7999875     46789999999999999999999875 568999999999998


Q ss_pred             CCcc
Q 003400          351 PGGA  354 (823)
Q Consensus       351 ~~~~  354 (823)
                      ++..
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8653

>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=99.54  E-value=2.7e-14  Score=129.48  Aligned_cols=82  Identities=24%  Similarity=0.300  Sum_probs=74.8

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      .....+|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345679999999999999999999999999999976     456789999999999999999999999999999999999


Q ss_pred             cCCCccc
Q 003400          349 SRPGGAR  355 (823)
Q Consensus       349 s~~~~~r  355 (823)
                      ++++..+
T Consensus        92 a~~~~~~   98 (105)
T 1x5u_A           92 ASAHNKN   98 (105)
T ss_dssp             TTTTSCC
T ss_pred             CCCCCcC
Confidence            9887543

>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=99.54  E-value=3.1e-14  Score=130.23  Aligned_cols=83  Identities=14%  Similarity=0.215  Sum_probs=73.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCC--ccccccccccc
Q 003400          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK--PLRRRKLDIHF  263 (823)
Q Consensus       186 ~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~--~l~gr~L~V~~  263 (823)
                      +....++++|||+|||.++++++|+++|++||.|..|.+.. .||||||+|.+.++|++|++.|++.  .+.|++|+|.|
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 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            33456789999999999999999999999999999998643 5899999999999999999998765  48999999999


Q ss_pred             cCCCCC
Q 003400          264 SIPKDN  269 (823)
Q Consensus       264 a~pk~~  269 (823)
                      +.++..
T Consensus        88 a~~~~~   93 (104)
T 1wex_A           88 STSKRI   93 (104)
T ss_dssp             CSSSSC
T ss_pred             ccCccc
Confidence            987553

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.53  E-value=3.9e-14  Score=128.71  Aligned_cols=82  Identities=23%  Similarity=0.455  Sum_probs=74.4

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC------CCcccEEEEEEcCHHHHHHHHHHh-CCCccCCceEE
Q 003400          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIK  345 (823)
Q Consensus       273 ~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~------~~srG~aFVeF~d~e~A~kAl~~L-nG~~i~Gr~I~  345 (823)
                      .....++|||+|||..+++++|+++|++||.|..|++.      +.++|||||+|.+.++|++|++.| ||..|.|+.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            34456899999999999999999999999999999873      446899999999999999999999 99999999999


Q ss_pred             EEecCCCcc
Q 003400          346 LEPSRPGGA  354 (823)
Q Consensus       346 V~~s~~~~~  354 (823)
                      |++++++..
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999988754

>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=99.53  E-value=3.7e-14  Score=128.55  Aligned_cols=83  Identities=16%  Similarity=0.302  Sum_probs=75.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|
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            34567899999999999999999999999999999984     5668899999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 003400          262 HFSIPKDN  269 (823)
Q Consensus       262 ~~a~pk~~  269 (823)
                      .++.++..
T Consensus        90 ~~a~~~~~   97 (105)
T 1x5u_A           90 NKASAHNK   97 (105)
T ss_dssp             EETTTTSC
T ss_pred             EECCCCCc
Confidence            99987654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.53  E-value=3.7e-14  Score=128.84  Aligned_cols=83  Identities=25%  Similarity=0.484  Sum_probs=75.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHh-cCCccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKL  259 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~------~~ksrG~AFV~F~~~e~A~~Ai~~L-ng~~l~gr~L  259 (823)
                      ....+.++|||+|||.++++++|+++|++||.|..|++      +++++|||||+|.+.++|++|++.| ++..|.|++|
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            34567899999999999999999999999999999985      4457899999999999999999999 9999999999


Q ss_pred             cccccCCCCC
Q 003400          260 DIHFSIPKDN  269 (823)
Q Consensus       260 ~V~~a~pk~~  269 (823)
                      +|.|+.++..
T Consensus        90 ~v~~a~~~~~   99 (107)
T 2cph_A           90 VLEWADSEVT   99 (107)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEeCCCCCC
Confidence            9999987654

>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=3.6e-14  Score=129.80  Aligned_cols=81  Identities=30%  Similarity=0.469  Sum_probs=73.4

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri--~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++  ++.+++||||+|.+.++|++|++.||+..|.|+.|+|+++++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   98 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   98 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEccc
Confidence            345679999999999999999999999999999887  344689999999999999999999999999999999999987


Q ss_pred             Ccc
Q 003400          352 GGA  354 (823)
Q Consensus       352 ~~~  354 (823)
                      +..
T Consensus        99 ~~~  101 (109)
T 1x4a_A           99 GRG  101 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.53  E-value=2.1e-14  Score=125.48  Aligned_cols=77  Identities=18%  Similarity=0.390  Sum_probs=69.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...+|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|++++
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            4568999999999999999999999999999976     45578999999999999999999999999999999999998


Q ss_pred             CC
Q 003400          351 PG  352 (823)
Q Consensus       351 ~~  352 (823)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            65

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=4.3e-14  Score=126.86  Aligned_cols=82  Identities=23%  Similarity=0.470  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++ |++..+.|++|.|.
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            3457899999999999999999999999999999985     35689999999999999999999 99999999999999


Q ss_pred             ccCCCCCC
Q 003400          263 FSIPKDNP  270 (823)
Q Consensus       263 ~a~pk~~~  270 (823)
                      ++.++...
T Consensus        85 ~a~~~~~~   92 (99)
T 2dgs_A           85 RAEPRDSK   92 (99)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCccc
Confidence            99876543

>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=4.3e-14  Score=129.28  Aligned_cols=83  Identities=17%  Similarity=0.315  Sum_probs=75.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++  ..+++|||||+|.+.++|++|++.|++..|.|++|.|+|+
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            34557799999999999999999999999999999885  4557899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 003400          265 IPKDN  269 (823)
Q Consensus       265 ~pk~~  269 (823)
                      .++..
T Consensus        97 ~~~~~  101 (109)
T 1x4a_A           97 RSGRG  101 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            87654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=3.4e-14  Score=128.50  Aligned_cols=82  Identities=22%  Similarity=0.334  Sum_probs=74.9

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~---~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++.   +.+++||||+|.+.++|++|++.|||..|.|+.|+|++++
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            4466799999999999999999999999999999763   4678999999999999999999999999999999999998


Q ss_pred             CCccc
Q 003400          351 PGGAR  355 (823)
Q Consensus       351 ~~~~r  355 (823)
                      ++..+
T Consensus        92 ~~~~~   96 (103)
T 2d9p_A           92 RKEER   96 (103)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87644

>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=130.29  Aligned_cols=77  Identities=21%  Similarity=0.248  Sum_probs=70.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCc--cCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD--IAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~--i~Gr~I~V~~s~~~~  353 (823)
                      +.++|||+|||.++|+++|+++|++||.|.+|++. +.||+|||+|.+.++|.+|++.|++..  +.|++|+|+||+++.
T Consensus        20 ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~-~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           20 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM-PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            46799999999999999999999999999999986 468999999999999999999999875  789999999998753

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.53  E-value=1.5e-14  Score=127.78  Aligned_cols=72  Identities=18%  Similarity=0.195  Sum_probs=68.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ..-|||+||++.+|+++|+++|.+||+|.++++. .++|||||+|.+.++|++|++.||+..+.|++|+|+++
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~-~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPY-LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEc-CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            4579999999999999999999999999999985 47999999999999999999999999999999999998

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.2e-14  Score=133.11  Aligned_cols=79  Identities=15%  Similarity=0.212  Sum_probs=71.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC--CccCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR--SDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG--~~i~Gr~I~V~~s~~~~  353 (823)
                      ..++|||+|||+++|+++|+++|++||.|.+|++.. .+|||||+|.+.++|++|++.|++  ..|.|++|+|++++++.
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            457999999999999999999999999999999864 489999999999999999998874  78999999999998765


Q ss_pred             cc
Q 003400          354 AR  355 (823)
Q Consensus       354 ~r  355 (823)
                      .+
T Consensus        94 ~~   95 (105)
T 1sjq_A           94 LK   95 (105)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=4.1e-14  Score=125.81  Aligned_cols=81  Identities=23%  Similarity=0.444  Sum_probs=74.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .++++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|+|.++
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            46799999999999999999999999999999984     3567899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 003400          265 IPKDNP  270 (823)
Q Consensus       265 ~pk~~~  270 (823)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876543

>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=99.53  E-value=1.8e-14  Score=125.91  Aligned_cols=78  Identities=18%  Similarity=0.403  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|+|.|+
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            35789999999999999999999999999999884     4567899999999999999999999999999999999999


Q ss_pred             CCC
Q 003400          265 IPK  267 (823)
Q Consensus       265 ~pk  267 (823)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            764

>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=99.52  E-value=2.9e-14  Score=123.40  Aligned_cols=76  Identities=22%  Similarity=0.297  Sum_probs=70.8

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      .+|||+|||.++++++|+++|++||.|.++++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++++++
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            47999999999999999999999999999976     3566899999999999999999999999999999999999876


Q ss_pred             c
Q 003400          353 G  353 (823)
Q Consensus       353 ~  353 (823)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=4e-14  Score=127.33  Aligned_cols=81  Identities=16%  Similarity=0.295  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..+.|++|+|.+
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4457799999999999999999999999999999884    356789999999999999999999999999999999999


Q ss_pred             cCCCC
Q 003400          264 SIPKD  268 (823)
Q Consensus       264 a~pk~  268 (823)
                      +.++.
T Consensus        93 a~~~~   97 (100)
T 2do4_A           93 SNSGP   97 (100)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98754

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=3.7e-14  Score=128.21  Aligned_cols=82  Identities=21%  Similarity=0.321  Sum_probs=74.6

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            445689999999999999999999999999999976     456789999999999999999999999999999999999


Q ss_pred             cCCCccc
Q 003400          349 SRPGGAR  355 (823)
Q Consensus       349 s~~~~~r  355 (823)
                      ++++..+
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9887543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.52  E-value=7.9e-15  Score=132.01  Aligned_cols=76  Identities=22%  Similarity=0.396  Sum_probs=68.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCc--eEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCC----ccCCceE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGE--VKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRS----DIAGKRI  344 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~--I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~----~i~Gr~I  344 (823)
                      .-.||||+|||+++|+++|+++|++||.  |.+|++     ++.++|||||+|.+.++|++|++.|||.    .|+||+|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            3469999999999999999999999995  567764     4678999999999999999999999997    4899999


Q ss_pred             EEEecCC
Q 003400          345 KLEPSRP  351 (823)
Q Consensus       345 ~V~~s~~  351 (823)
                      +|+||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999975

>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=99.52  E-value=2.8e-14  Score=123.53  Aligned_cols=77  Identities=27%  Similarity=0.458  Sum_probs=71.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      +.+|||+|||.++++++|+++|++||+|..|.+     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.+
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            468999999999999999999999999999874     466799999999999999999999999999999999999986


Q ss_pred             CC
Q 003400          267 KD  268 (823)
Q Consensus       267 k~  268 (823)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.52  E-value=4.1e-14  Score=128.80  Aligned_cols=82  Identities=22%  Similarity=0.303  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhc--CCccccccccccccC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ--NKPLRRRKLDIHFSI  265 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Ln--g~~l~gr~L~V~~a~  265 (823)
                      ...++++|||+|||.++++++|+++|++||.|..|.+.. .+|||||+|.+.++|++|++.|+  +..+.|++|+|.|+.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~   89 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   89 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcC
Confidence            345789999999999999999999999999999997643 58999999999999999999875  567999999999998


Q ss_pred             CCCCC
Q 003400          266 PKDNP  270 (823)
Q Consensus       266 pk~~~  270 (823)
                      ++...
T Consensus        90 ~~~~~   94 (101)
T 2cq1_A           90 HKELK   94 (101)
T ss_dssp             CSSCC
T ss_pred             cccCc
Confidence            76543

>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=2.5e-14  Score=127.78  Aligned_cols=78  Identities=23%  Similarity=0.444  Sum_probs=72.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      |+++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.
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            5789999999999999999999999999999985     35679999999999999999999999999999999999998


Q ss_pred             CCC
Q 003400          266 PKD  268 (823)
Q Consensus       266 pk~  268 (823)
                      ++.
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=4.3e-14  Score=125.48  Aligned_cols=78  Identities=26%  Similarity=0.442  Sum_probs=71.9

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++.|||..+.|++|+|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456799999999999999999999999999999763     56789999999999999999999999999999999999


Q ss_pred             cCC
Q 003400          349 SRP  351 (823)
Q Consensus       349 s~~  351 (823)
                      ++.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            875

>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=99.52  E-value=4.7e-14  Score=127.57  Aligned_cols=83  Identities=30%  Similarity=0.403  Sum_probs=74.5

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCC---CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~---~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++..   .++|||||+|.+.++|++|++.|||..|.|+.|+|++++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECC
Confidence            34567999999999999999999999999999998732   367999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 003400          351 PGGARR  356 (823)
Q Consensus       351 ~~~~r~  356 (823)
                      ++..++
T Consensus        92 ~~~~~~   97 (103)
T 2cqi_A           92 TPSSQK   97 (103)
T ss_dssp             CTTCCC
T ss_pred             CCcccc
Confidence            876443

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=3e-14  Score=128.81  Aligned_cols=83  Identities=27%  Similarity=0.397  Sum_probs=75.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....+.++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|++..+.|++|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34567899999999999999999999999999999984     3668899999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 003400          262 HFSIPKDN  269 (823)
Q Consensus       262 ~~a~pk~~  269 (823)
                      .++.+...
T Consensus        88 ~~a~~~~~   95 (103)
T 2dnm_A           88 QVARYGRR   95 (103)
T ss_dssp             EECSSCCS
T ss_pred             EECCcCCC
Confidence            99986554

>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=5e-14  Score=124.37  Aligned_cols=79  Identities=25%  Similarity=0.407  Sum_probs=73.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      ..+.++|||+|||.++++++|+++|++||+|..|++.   +|||||+|.+.++|++|++.|++..+.|++|+|.|+.++.
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            3567999999999999999999999999999999875   7999999999999999999999999999999999998765


Q ss_pred             CC
Q 003400          269 NP  270 (823)
Q Consensus       269 ~~  270 (823)
                      ..
T Consensus        82 ~~   83 (90)
T 2dnq_A           82 KA   83 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.52  E-value=1.9e-14  Score=133.20  Aligned_cols=90  Identities=19%  Similarity=0.128  Sum_probs=71.7

Q ss_pred             ccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccC-ceEEEEeC-CCcccEEEEEEcCHHHHHHHHHHh
Q 003400          257 RKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRET-PHKRHHKFIEFYDVRAAEAALKSL  334 (823)
Q Consensus       257 r~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG-~I~~iri~-~~srG~aFVeF~d~e~A~kAl~~L  334 (823)
                      .++.+.|..+..       ...+|||+|||+++++++|+++|++|| .|..+++. ..++|||||+|.+.++|++||+.|
T Consensus        15 ~~~~~~~~~~p~-------~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~l   87 (111)
T 2jvr_A           15 VPRGSHMSKLPA-------KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERL   87 (111)
T ss_dssp             ----------CC-------CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHT
T ss_pred             eecchhcCCCCC-------CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHc
Confidence            355666664321       356999999999999999999999999 99999884 568999999999999999999999


Q ss_pred             CCCccCCceEEEEecCCCc
Q 003400          335 NRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       335 nG~~i~Gr~I~V~~s~~~~  353 (823)
                      ||..+.|+.|+|++++.+.
T Consensus        88 ng~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           88 NNIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             TTEEETTEEEEEEESCC--
T ss_pred             CCCEECCeEEEEEECCCCC
Confidence            9999999999999997653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.52  E-value=5.4e-14  Score=129.74  Aligned_cols=82  Identities=21%  Similarity=0.410  Sum_probs=74.5

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      .....+|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345679999999999999999999999999999976     455689999999999999999999999999999999999


Q ss_pred             cCCCccc
Q 003400          349 SRPGGAR  355 (823)
Q Consensus       349 s~~~~~r  355 (823)
                      ++++..+
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            9887543

>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=5e-14  Score=127.39  Aligned_cols=83  Identities=18%  Similarity=0.408  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...+.++|||+|||.++|+++|+++|++||+|..|++   +++++|||||+|.+.++|++|++.|++..+.|++|.|.|+
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            4457899999999999999999999999999999885   3578999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 003400          265 IPKDNP  270 (823)
Q Consensus       265 ~pk~~~  270 (823)
                      .++...
T Consensus        91 ~~~~~~   96 (103)
T 2d9p_A           91 QRKEER   96 (103)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            876654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.52  E-value=6.3e-14  Score=129.27  Aligned_cols=83  Identities=17%  Similarity=0.394  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4457899999999999999999999999999999884     45678999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 003400          263 FSIPKDNP  270 (823)
Q Consensus       263 ~a~pk~~~  270 (823)
                      |+.++...
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            99876543

>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=3e-14  Score=131.60  Aligned_cols=81  Identities=25%  Similarity=0.417  Sum_probs=74.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...++|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+++
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            35579999999999999999999999999999876     4567899999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003400          350 RPGGAR  355 (823)
Q Consensus       350 ~~~~~r  355 (823)
                      +++..+
T Consensus       103 ~~~~~~  108 (115)
T 2cpz_A          103 RSKNDS  108 (115)
T ss_dssp             CCSCCC
T ss_pred             CCCCcC
Confidence            887643

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=3.5e-14  Score=128.43  Aligned_cols=82  Identities=22%  Similarity=0.454  Sum_probs=75.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|.
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            3457899999999999999999999999999999984     45788999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 003400          263 FSIPKDN  269 (823)
Q Consensus       263 ~a~pk~~  269 (823)
                      |+.++..
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9987654

>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=99.52  E-value=3.6e-14  Score=123.43  Aligned_cols=75  Identities=27%  Similarity=0.462  Sum_probs=69.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++++
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            4579999999999999999999999999999976     34578999999999999999999999999999999999985

>2dgs_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=6.3e-14  Score=125.77  Aligned_cols=80  Identities=23%  Similarity=0.446  Sum_probs=73.1

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++ ||+..|.|+.|+|+++
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            356799999999999999999999999999999873     4578999999999999999998 9999999999999999


Q ss_pred             CCCccc
Q 003400          350 RPGGAR  355 (823)
Q Consensus       350 ~~~~~r  355 (823)
                      +++..+
T Consensus        87 ~~~~~~   92 (99)
T 2dgs_A           87 EPRDSK   92 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            887643

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=3e-14  Score=129.38  Aligned_cols=81  Identities=17%  Similarity=0.448  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|+|..+.|++|.|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            3456789999999999999999999999999999984     36779999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 003400          263 FSIPKD  268 (823)
Q Consensus       263 ~a~pk~  268 (823)
                      |+.++.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            997654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.51  E-value=3e-14  Score=127.49  Aligned_cols=81  Identities=25%  Similarity=0.456  Sum_probs=73.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC--------CCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA--------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~--------~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      .+.++|||+|||.++++++|+++|++||+|..|++.        ++++|||||+|.+.++|++|++.|++..|.|++|.|
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            467999999999999999999999999999998742        267899999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 003400          262 HFSIPKDNP  270 (823)
Q Consensus       262 ~~a~pk~~~  270 (823)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>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=5.2e-14  Score=125.11  Aligned_cols=79  Identities=27%  Similarity=0.388  Sum_probs=72.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|++++
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            3569999999999999999999999999999976     35578999999999999999999999999999999999998


Q ss_pred             CCcc
Q 003400          351 PGGA  354 (823)
Q Consensus       351 ~~~~  354 (823)
                      ++..
T Consensus        84 ~~~~   87 (95)
T 2dnz_A           84 ERLD   87 (95)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            7654

>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=7.7e-14  Score=126.15  Aligned_cols=84  Identities=21%  Similarity=0.366  Sum_probs=75.5

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC---CCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~---~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ....+.++|||+|||.++++++|+++|++||.|..|++.   ..++|||||+|.+.++|++|++.|++..|.|++|.|.+
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            345678999999999999999999999999999999852   34689999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003400          264 SIPKDNP  270 (823)
Q Consensus       264 a~pk~~~  270 (823)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
Confidence            9876543

>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=7.8e-14  Score=126.43  Aligned_cols=82  Identities=20%  Similarity=0.340  Sum_probs=74.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccc---ccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR---RKLDI  261 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g---r~L~V  261 (823)
                      ..+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..+.+   ++|.|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            346899999999999999999999999999999884    45668999999999999999999999999998   99999


Q ss_pred             cccCCCCCC
Q 003400          262 HFSIPKDNP  270 (823)
Q Consensus       262 ~~a~pk~~~  270 (823)
                      .|+.++...
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999876543

>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=99.51  E-value=4.7e-14  Score=126.01  Aligned_cols=78  Identities=17%  Similarity=0.267  Sum_probs=72.6

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      .++|||+|||.++++++|+++|++||.|.+|++.     +.++|||||+|.+.++|++|++.|||..+.|+.|+|+++++
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            4689999999999999999999999999999873     56689999999999999999999999999999999999998


Q ss_pred             Ccc
Q 003400          352 GGA  354 (823)
Q Consensus       352 ~~~  354 (823)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            764

>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=99.51  E-value=5.8e-14  Score=126.95  Aligned_cols=83  Identities=18%  Similarity=0.419  Sum_probs=74.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC---CCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~---~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ....+.++|||+|||.++++++|+++|++||.|..|++.   ..++|||||+|.+.++|++|++.|++..|.|++|+|.|
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            345678999999999999999999999999999999852   34689999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 003400          264 SIPKDN  269 (823)
Q Consensus       264 a~pk~~  269 (823)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2cqi_A           90 ATTPSS   95 (103)
T ss_dssp             CCCTTC
T ss_pred             CCCCcc
Confidence            987654

>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=99.51  E-value=6.5e-14  Score=125.34  Aligned_cols=78  Identities=21%  Similarity=0.374  Sum_probs=72.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccC--CceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA--GKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~--Gr~I~V~~s~~~~  353 (823)
                      ..++|||+|||.++++++|+++|++||.|.+|++... ++||||+|.+.++|++|++.|||..+.  |++|+|++++++.
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            4579999999999999999999999999999998643 899999999999999999999999999  9999999998865


Q ss_pred             c
Q 003400          354 A  354 (823)
Q Consensus       354 ~  354 (823)
                      .
T Consensus        95 ~   95 (97)
T 1why_A           95 S   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.51  E-value=3.3e-14  Score=123.67  Aligned_cols=77  Identities=26%  Similarity=0.480  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|+|..+.|++|+|+|
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            357799999999999999999999999999999984     456899999999999999999999999999999999998


Q ss_pred             cC
Q 003400          264 SI  265 (823)
Q Consensus       264 a~  265 (823)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>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=7.1e-14  Score=126.70  Aligned_cols=81  Identities=20%  Similarity=0.273  Sum_probs=73.6

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC---ceEEEE
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG---KRIKLE  347 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G---r~I~V~  347 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++.|||..+.|   +.|+|+
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            34679999999999999999999999999999976    34558999999999999999999999999998   999999


Q ss_pred             ecCCCccc
Q 003400          348 PSRPGGAR  355 (823)
Q Consensus       348 ~s~~~~~r  355 (823)
                      +++++..+
T Consensus        93 ~a~~~~~~  100 (105)
T 2dnh_A           93 FADTDKES  100 (105)
T ss_dssp             ESCSSCCC
T ss_pred             ECccCccc
Confidence            99987654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=3.6e-14  Score=128.88  Aligned_cols=80  Identities=25%  Similarity=0.409  Sum_probs=73.2

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++.|||..+.|+.|+|++
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            3456799999999999999999999999999999763     56689999999999999999999999999999999999


Q ss_pred             cCCCc
Q 003400          349 SRPGG  353 (823)
Q Consensus       349 s~~~~  353 (823)
                      ++++.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            98764

>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=99.51  E-value=3.5e-14  Score=131.07  Aligned_cols=83  Identities=16%  Similarity=0.360  Sum_probs=75.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456799999999999999999999999999998874     56788999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 003400          263 FSIPKDNP  270 (823)
Q Consensus       263 ~a~pk~~~  270 (823)
                      |+.++...
T Consensus       101 ~a~~~~~~  108 (115)
T 2cpz_A          101 LKRSKNDS  108 (115)
T ss_dssp             CCCCSCCC
T ss_pred             EcCCCCcC
Confidence            99876543

>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=123.97  Aligned_cols=79  Identities=24%  Similarity=0.396  Sum_probs=71.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCC-----C-cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP-----H-KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~-----~-srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ..++|||+|||.++++++|+++|++||.|..+++..     . ++|||||+|.+.++|++|++.|||..+.|+.|+|+++
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            356899999999999999999999999999998631     2 7899999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003400          350 RPGGA  354 (823)
Q Consensus       350 ~~~~~  354 (823)
                      ++...
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.51  E-value=7.4e-14  Score=127.06  Aligned_cols=80  Identities=15%  Similarity=0.176  Sum_probs=71.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHh--CCCccCCceEEEEecCCC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~L--nG~~i~Gr~I~V~~s~~~  352 (823)
                      ...++|||+|||.++++++|+++|++||.|.+|++.. .+|||||+|.+.++|++|++.|  ++..+.|++|+|.|++++
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            3567999999999999999999999999999998864 4899999999999999999987  467899999999999876


Q ss_pred             ccc
Q 003400          353 GAR  355 (823)
Q Consensus       353 ~~r  355 (823)
                      ..+
T Consensus        92 ~~~   94 (101)
T 2cq1_A           92 ELK   94 (101)
T ss_dssp             SCC
T ss_pred             cCc
Confidence            543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=5.4e-14  Score=124.10  Aligned_cols=76  Identities=26%  Similarity=0.430  Sum_probs=71.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..+.|++|+|++++++..
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            46799999999999999999999999999999986   79999999999999999999999999999999999988654

>2dnm_A SRP46 splicing factor; 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=127.89  Aligned_cols=80  Identities=28%  Similarity=0.432  Sum_probs=73.5

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++.|||..|.|+.|+|+++
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            356799999999999999999999999999999863     567899999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003400          350 RPGGA  354 (823)
Q Consensus       350 ~~~~~  354 (823)
                      ++...
T Consensus        91 ~~~~~   95 (103)
T 2dnm_A           91 RYGRR   95 (103)
T ss_dssp             SSCCS
T ss_pred             CcCCC
Confidence            87653

>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=123.95  Aligned_cols=76  Identities=29%  Similarity=0.430  Sum_probs=70.4

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++.|||..+.|++|+|+++
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            356799999999999999999999999999999873     456899999999999999999999999999999999998


Q ss_pred             C
Q 003400          350 R  350 (823)
Q Consensus       350 ~  350 (823)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.51  E-value=5.7e-14  Score=128.89  Aligned_cols=82  Identities=22%  Similarity=0.457  Sum_probs=74.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|
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            34557799999999999999999999999999999874     3567899999999999999999999999999999999


Q ss_pred             cccCCCC
Q 003400          262 HFSIPKD  268 (823)
Q Consensus       262 ~~a~pk~  268 (823)
                      .++.++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9997654

>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=99.51  E-value=3.2e-14  Score=129.76  Aligned_cols=79  Identities=14%  Similarity=0.158  Sum_probs=71.3

Q ss_pred             CCCCcEEEEcCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCC--ccccccccccccC
Q 003400          189 EHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK--PLRRRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~-~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~--~l~gr~L~V~~a~  265 (823)
                      ..++++|||+|||. ++|+++|+++|++||.|.+|++. +.+|||||+|.+.++|++|++.|++.  .|.|++|+|.|+.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~   90 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   90 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECC
Confidence            35789999999999 99999999999999999999864 46799999999999999999999875  4899999999997


Q ss_pred             CCC
Q 003400          266 PKD  268 (823)
Q Consensus       266 pk~  268 (823)
                      ...
T Consensus        91 ~~~   93 (102)
T 1x4d_A           91 KYK   93 (102)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.50  E-value=3.6e-14  Score=127.05  Aligned_cols=79  Identities=23%  Similarity=0.359  Sum_probs=72.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeC--------CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET--------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~--------~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~  347 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++.        +.++|||||+|.+.++|++|++.|||..|.|++|+|+
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            45699999999999999999999999999999763        2568999999999999999999999999999999999


Q ss_pred             ecCCCcc
Q 003400          348 PSRPGGA  354 (823)
Q Consensus       348 ~s~~~~~  354 (823)
                      +++++..
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9988653

>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=99.50  E-value=6.3e-14  Score=128.17  Aligned_cols=84  Identities=20%  Similarity=0.447  Sum_probs=76.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhc------CCccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQ------NKPLR  255 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Ln------g~~l~  255 (823)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+      +..|.
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            34567899999999999999999999999999999985     35689999999999999999999999      99999


Q ss_pred             cccccccccCCCCCC
Q 003400          256 RRKLDIHFSIPKDNP  270 (823)
Q Consensus       256 gr~L~V~~a~pk~~~  270 (823)
                      |++|.|.|+.++...
T Consensus        90 g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCEEEEECCCCCCCC
T ss_pred             CEEEEEEECCCCccC
Confidence            999999999876543

>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=99.50  E-value=4.7e-14  Score=129.12  Aligned_cols=81  Identities=23%  Similarity=0.390  Sum_probs=74.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++
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            45679999999999999999999999999999986     3456899999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003400          350 RPGGAR  355 (823)
Q Consensus       350 ~~~~~r  355 (823)
                      +++..+
T Consensus       104 ~~~~~~  109 (110)
T 1oo0_B          104 FVKGPK  109 (110)
T ss_dssp             EESSCC
T ss_pred             ccCCCC
Confidence            877644

>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=3.6e-14  Score=130.07  Aligned_cols=95  Identities=20%  Similarity=0.298  Sum_probs=81.4

Q ss_pred             ccccccccccCCCCCCCCCCCCccceeeecCCCC-CCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHH
Q 003400          255 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS  333 (823)
Q Consensus       255 ~gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~~-vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~  333 (823)
                      .|.+|.+..+.+..... .....++|||+|||.+ +++++|+++|++||.|..|++   +++||||+|.+.++|++|++.
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            46677777765543322 2234579999999999 999999999999999999998   689999999999999999999


Q ss_pred             hCCCccCCceEEEEecCCCc
Q 003400          334 LNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       334 LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      |||..|.|+.|+|+++++..
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            99999999999999998654

>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=99.50  E-value=9.1e-14  Score=127.12  Aligned_cols=81  Identities=20%  Similarity=0.363  Sum_probs=74.3

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhC------CCccCCce
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLN------RSDIAGKR  343 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~Ln------G~~i~Gr~  343 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++.||      |..|.|+.
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            356799999999999999999999999999999873     5679999999999999999999999      99999999


Q ss_pred             EEEEecCCCccc
Q 003400          344 IKLEPSRPGGAR  355 (823)
Q Consensus       344 I~V~~s~~~~~r  355 (823)
                      |+|++++++..+
T Consensus        93 l~v~~a~~~~~~  104 (111)
T 1x4h_A           93 LKVDLAVTRDEA  104 (111)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEEECCCCccC
Confidence            999999887644

>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=99.50  E-value=8.9e-14  Score=124.47  Aligned_cols=79  Identities=27%  Similarity=0.477  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccc--cccccccccCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR--RRKLDIHFSIP  266 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~--gr~L~V~~a~p  266 (823)
                      ..++++|||+|||.++++++|+++|++||.|..|++.. .+|||||+|.+.++|++|++.|++..+.  |++|.|.|+.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~   92 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeC-CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCC
Confidence            35679999999999999999999999999999998654 3899999999999999999999999999  99999999987


Q ss_pred             CC
Q 003400          267 KD  268 (823)
Q Consensus       267 k~  268 (823)
                      +.
T Consensus        93 ~~   94 (97)
T 1why_A           93 GP   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.50  E-value=1.1e-14  Score=165.16  Aligned_cols=145  Identities=24%  Similarity=0.349  Sum_probs=103.9

Q ss_pred             HHHHhhcCCCEEEEEe-------CCCcccEE-----EEEeCCHHHHHHHHHHhcCCccccc-----------c--ccccc
Q 003400          209 LRALFEQYGDIRTLYT-------ACKHRGFV-----MISYYDIRAARTAMRALQNKPLRRR-----------K--LDIHF  263 (823)
Q Consensus       209 Lr~lFs~fG~I~~v~~-------~~ksrG~A-----FV~F~~~e~A~~Ai~~Lng~~l~gr-----------~--L~V~~  263 (823)
                      |..+|.++|+|..|..       ..+..+|+     |+.|....++..++..++......+           .  ..+..
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     7788776655544433322221111           0  01111


Q ss_pred             cCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCc
Q 003400          264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSD  338 (823)
Q Consensus       264 a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~  338 (823)
                      ..+...+.......++|||+|||..+|+++|+++|++||.|+.|++     ++.++|||||+|.+.++|.+||..|||..
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            1222222223334579999999999999999999999999999976     45679999999999999999999999999


Q ss_pred             cCCceEEEEecCCCc
Q 003400          339 IAGKRIKLEPSRPGG  353 (823)
Q Consensus       339 i~Gr~I~V~~s~~~~  353 (823)
                      |.|+.|.|.++.+..
T Consensus       169 i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          169 IDGRRVLVDVERGRT  183 (437)
T ss_pred             ECCEEEEEEEeCCCC
Confidence            999999999998754

>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=5e-14  Score=127.03  Aligned_cols=81  Identities=22%  Similarity=0.464  Sum_probs=74.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
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 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            457799999999999999999999999999999985     345789999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 003400          264 SIPKDN  269 (823)
Q Consensus       264 a~pk~~  269 (823)
                      +.++..
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            987654

>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=7.9e-14  Score=129.61  Aligned_cols=78  Identities=28%  Similarity=0.464  Sum_probs=72.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++.|||..|.|+.|+|+++++
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            4579999999999999999999999999999976    455789999999999999999999999999999999999987


Q ss_pred             Cc
Q 003400          352 GG  353 (823)
Q Consensus       352 ~~  353 (823)
                      +.
T Consensus        86 ~~   87 (116)
T 2fy1_A           86 PS   87 (116)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=4e-14  Score=127.67  Aligned_cols=81  Identities=26%  Similarity=0.443  Sum_probs=74.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+++
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            35679999999999999999999999999999986     3457899999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003400          350 RPGGAR  355 (823)
Q Consensus       350 ~~~~~r  355 (823)
                      +++..+
T Consensus        90 ~~~~~~   95 (102)
T 2cqb_A           90 KPMRIK   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            887543

>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=99.50  E-value=5.9e-14  Score=125.70  Aligned_cols=79  Identities=25%  Similarity=0.413  Sum_probs=72.1

Q ss_pred             CccceeeecCCCCCCHHHHH----HHhcccCceEEEEeCCC--cccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          276 NQGTLVVFNLDPSVSNEDLR----QIFGAYGEVKEIRETPH--KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~----~~Fs~fG~I~~iri~~~--srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      +..+|||+|||.++++++|+    ++|++||.|.+|++...  .++||||+|.+.++|++|++.|||..+.|++|+|+++
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            45799999999999999999    99999999999988522  2899999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003400          350 RPGGA  354 (823)
Q Consensus       350 ~~~~~  354 (823)
                      +++..
T Consensus        88 ~~~~~   92 (96)
T 2dgx_A           88 TGASG   92 (96)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87653

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.50  E-value=5.4e-14  Score=124.27  Aligned_cols=79  Identities=19%  Similarity=0.245  Sum_probs=73.0

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe---CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri---~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ...+|||+|||.++++++|+++|++||.|..|++   ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++++.
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            4579999999999999999999999999999976   4557899999999999999999999999999999999999886


Q ss_pred             cc
Q 003400          353 GA  354 (823)
Q Consensus       353 ~~  354 (823)
                      ..
T Consensus        87 ~~   88 (92)
T 2dgv_A           87 SG   88 (92)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.50  E-value=6.5e-14  Score=128.10  Aligned_cols=78  Identities=19%  Similarity=0.238  Sum_probs=70.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC--ccCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS--DIAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~--~i~Gr~I~V~~s~~~~  353 (823)
                      ..++|||+|||.++++++|+++|++||.|.+|++.. .+|||||+|.+.++|.+|++.|++.  .|.|++|+|+|++++.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~   92 (104)
T 1wex_A           14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCcc
Confidence            457999999999999999999999999999998864 4899999999999999999998764  5999999999998765


Q ss_pred             c
Q 003400          354 A  354 (823)
Q Consensus       354 ~  354 (823)
                      .
T Consensus        93 ~   93 (104)
T 1wex_A           93 I   93 (104)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=4e-14  Score=127.67  Aligned_cols=80  Identities=23%  Similarity=0.495  Sum_probs=73.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++.|||..|.|++|+|++++
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            46799999999999999999999999999999873     4468999999999999999999999999999999999998


Q ss_pred             CCccc
Q 003400          351 PGGAR  355 (823)
Q Consensus       351 ~~~~r  355 (823)
                      ++...
T Consensus        91 ~~~~~   95 (102)
T 1x5s_A           91 KSSDN   95 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=1e-13  Score=125.35  Aligned_cols=81  Identities=22%  Similarity=0.406  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhc-CCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCc-ccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQ-YGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKP-LRRRKLDIH  262 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~-fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~-l~gr~L~V~  262 (823)
                      ..+.++|||+|||.++|+++|+++|++ ||.|..|++    +++++|||||+|.+.++|++|++.|++.. +.|++|.|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            456799999999999999999999999 999999885    56689999999999999999999999999 999999999


Q ss_pred             ccCCCCC
Q 003400          263 FSIPKDN  269 (823)
Q Consensus       263 ~a~pk~~  269 (823)
                      ++.++..
T Consensus        86 ~a~~~~~   92 (104)
T 2dhg_A           86 VAIPKAS   92 (104)
T ss_dssp             BCCCCCS
T ss_pred             EccCCCc
Confidence            9977654

>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=99.50  E-value=1.1e-13  Score=125.14  Aligned_cols=81  Identities=21%  Similarity=0.368  Sum_probs=73.6

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCC---CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETP---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~---~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++..   .++|||||+|.+.++|++|++.|||..|.|+.|+|++++
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            34567999999999999999999999999999998742   358999999999999999999999999999999999998


Q ss_pred             CCcc
Q 003400          351 PGGA  354 (823)
Q Consensus       351 ~~~~  354 (823)
                      ++..
T Consensus        92 ~~~~   95 (103)
T 2cq3_A           92 ARVM   95 (103)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            8754

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.50  E-value=3.5e-14  Score=126.63  Aligned_cols=82  Identities=21%  Similarity=0.335  Sum_probs=75.3

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      .....+|||+|||.++++++|+++|++||.|..+..++.++|||||+|.+.++|++|++.|||..+.|+.|+|++++++.
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            34567999999999999999999999999998887778889999999999999999999999999999999999998876


Q ss_pred             cc
Q 003400          354 AR  355 (823)
Q Consensus       354 ~r  355 (823)
                      .+
T Consensus        93 ~~   94 (96)
T 1fjc_A           93 GT   94 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=5.9e-14  Score=124.39  Aligned_cols=81  Identities=23%  Similarity=0.409  Sum_probs=73.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ....+.++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|++..+.|++|+|.++.+
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   81 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTS   81 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccC
Confidence            345678999999999999999999999999999999874   56999999999999999999999999999999999987


Q ss_pred             CCCC
Q 003400          267 KDNP  270 (823)
Q Consensus       267 k~~~  270 (823)
                      +...
T Consensus        82 ~~~~   85 (92)
T 2dgt_A           82 RLRT   85 (92)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            6543

>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=3.5e-14  Score=126.49  Aligned_cols=81  Identities=20%  Similarity=0.437  Sum_probs=73.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEE-Ee-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTL-YT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v-~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      .+.++|||+|||.++++++|+++|++||.|..| ++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.|
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            467999999999999999999999999999887 64     456789999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003400          264 SIPKDNP  270 (823)
Q Consensus       264 a~pk~~~  270 (823)
                      +.++...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9876543

>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=99.49  E-value=1.5e-14  Score=128.02  Aligned_cols=76  Identities=17%  Similarity=0.232  Sum_probs=65.9

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccC--ceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG--~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      .+|||+|||.++|+++|+++|++||  .|.++++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++.
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            4799999999999999999999999  8988875     56789999999999999999999999999999999999998


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            764

>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=4.4e-14  Score=127.32  Aligned_cols=76  Identities=24%  Similarity=0.362  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ...++|||+|||.++++++|+++|++||.|.+|++. +++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            356899999999999999999999999999999864 6899999999999999999999999999999999999875

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.9e-14  Score=125.15  Aligned_cols=79  Identities=20%  Similarity=0.378  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|+|+
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            3456799999999999999999999999999999984     36788999999999999999999999999999999999


Q ss_pred             ccCC
Q 003400          263 FSIP  266 (823)
Q Consensus       263 ~a~p  266 (823)
                      |+.+
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9853

>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=7.5e-14  Score=126.76  Aligned_cols=82  Identities=17%  Similarity=0.359  Sum_probs=74.0

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCcc---CCceEE
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI---AGKRIK  345 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i---~Gr~I~  345 (823)
                      .....+|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+   .|++|+
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            345679999999999999999999999999999986     355789999999999999999999999987   899999


Q ss_pred             EEecCCCccc
Q 003400          346 LEPSRPGGAR  355 (823)
Q Consensus       346 V~~s~~~~~r  355 (823)
                      |++++++..+
T Consensus        90 v~~a~~~~~~   99 (106)
T 2dgp_A           90 VKPADSESRG   99 (106)
T ss_dssp             EEECCCCSCC
T ss_pred             EEECCccccc
Confidence            9999887543

>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=7e-14  Score=126.94  Aligned_cols=83  Identities=24%  Similarity=0.475  Sum_probs=74.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcc---cccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPL---RRRK  258 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l---~gr~  258 (823)
                      ..+.+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+   .+++
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            34567899999999999999999999999999999984     356889999999999999999999999987   8999


Q ss_pred             ccccccCCCCC
Q 003400          259 LDIHFSIPKDN  269 (823)
Q Consensus       259 L~V~~a~pk~~  269 (823)
                      |+|.++.++..
T Consensus        88 l~v~~a~~~~~   98 (106)
T 2dgp_A           88 IQVKPADSESR   98 (106)
T ss_dssp             CEEEECCCCSC
T ss_pred             EEEEECCcccc
Confidence            99999987654

>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=99.49  E-value=6.6e-14  Score=124.46  Aligned_cols=77  Identities=21%  Similarity=0.269  Sum_probs=71.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++.    +.++|||||+|.+.++|++|++.|||..+.|+.|+|++++
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            356799999999999999999999999999999763    4568999999999999999999999999999999999987


Q ss_pred             C
Q 003400          351 P  351 (823)
Q Consensus       351 ~  351 (823)
                      .
T Consensus        94 ~   94 (95)
T 2ywk_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=7.1e-14  Score=121.66  Aligned_cols=79  Identities=22%  Similarity=0.410  Sum_probs=71.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHh-cCCcccccccccccc
Q 003400          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDIHFS  264 (823)
Q Consensus       186 ~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~L-ng~~l~gr~L~V~~a  264 (823)
                      +..+.+.++|||+|||.++++++|+++|++||.|..|++. +++|||||+|.+.++|++|++.| ++..+.|++|+|+|+
T Consensus         6 ~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~-~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A            6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             CCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEE-CCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            3345678999999999999999999999999999999864 46899999999999999999999 999999999999987


Q ss_pred             C
Q 003400          265 I  265 (823)
Q Consensus       265 ~  265 (823)
                      +
T Consensus        85 k   85 (85)
T 2ytc_A           85 R   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=9.2e-14  Score=123.13  Aligned_cols=78  Identities=26%  Similarity=0.410  Sum_probs=72.2

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..+.|+.|+|++++++.
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            3456799999999999999999999999999999986   5699999999999999999999999999999999998765


Q ss_pred             c
Q 003400          354 A  354 (823)
Q Consensus       354 ~  354 (823)
                      .
T Consensus        84 ~   84 (92)
T 2dgt_A           84 R   84 (92)
T ss_dssp             S
T ss_pred             C
Confidence            3

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=6.5e-14  Score=124.25  Aligned_cols=78  Identities=24%  Similarity=0.441  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|+|+
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            3456799999999999999999999999999999985     35678999999999999999999999999999999999


Q ss_pred             ccC
Q 003400          263 FSI  265 (823)
Q Consensus       263 ~a~  265 (823)
                      |++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            873

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.4e-14  Score=127.41  Aligned_cols=82  Identities=26%  Similarity=0.461  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|.|.|
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            457899999999999999999999999999999984     356899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003400          264 SIPKDNP  270 (823)
Q Consensus       264 a~pk~~~  270 (823)
                      +.++...
T Consensus        89 a~~~~~~   95 (102)
T 2cqb_A           89 AKPMRIK   95 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.49  E-value=8.5e-14  Score=127.75  Aligned_cols=80  Identities=28%  Similarity=0.398  Sum_probs=73.1

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|++
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            345679999999999999999999999999999976     355689999999999999999999999999999999999


Q ss_pred             cCCCc
Q 003400          349 SRPGG  353 (823)
Q Consensus       349 s~~~~  353 (823)
                      ++++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            98764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=5.3e-14  Score=126.05  Aligned_cols=79  Identities=19%  Similarity=0.221  Sum_probs=71.1

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ...++|||+|||.++++++|+++|++||.|....+++.++|||||+|.+.++|++|++.|||..|.|++|+|++++++.
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            3457999999999999999999999999996333456789999999999999999999999999999999999998864

>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=1.2e-13  Score=131.80  Aligned_cols=82  Identities=28%  Similarity=0.425  Sum_probs=74.6

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||.++++++|+++|+.||.|.+|++     ++.++|||||+|.+.++|++|++.|||..|.|+.|+|++
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            345679999999999999999999999999999976     355689999999999999999999999999999999999


Q ss_pred             cCCCccc
Q 003400          349 SRPGGAR  355 (823)
Q Consensus       349 s~~~~~r  355 (823)
                      ++++..+
T Consensus       119 a~~~~~~  125 (139)
T 1u6f_A          119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9987644

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.49  E-value=2.2e-14  Score=129.02  Aligned_cols=78  Identities=17%  Similarity=0.353  Sum_probs=69.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCC--EEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCc----cccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGD--IRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKP----LRRR  257 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~--I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~----l~gr  257 (823)
                      +..-.||||+|||+++|+++|+++|++||.  |.+|++     +++++|||||+|.+.++|++|++.|++..    +.|+
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            456689999999999999999999999995  456663     57899999999999999999999999974    8899


Q ss_pred             cccccccCC
Q 003400          258 KLDIHFSIP  266 (823)
Q Consensus       258 ~L~V~~a~p  266 (823)
                      +|.|+||+.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999863

>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=4.3e-14  Score=128.92  Aligned_cols=76  Identities=17%  Similarity=0.235  Sum_probs=69.6

Q ss_pred             CccceeeecCCC-CCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC--ccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS--DIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~-~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~--~i~Gr~I~V~~s~~~  352 (823)
                      ..++|||+|||+ ++|+++|+++|++||.|.+|++.. .++||||+|.+.++|++|++.||+.  .|.|++|+|.+++..
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 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN-KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   92 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS-SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCC
Confidence            467999999999 999999999999999999999863 5799999999999999999999864  599999999999864

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=6.8e-14  Score=125.44  Aligned_cols=80  Identities=11%  Similarity=0.352  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEE-EEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccc----
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIR-TLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK----  258 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~-~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~----  258 (823)
                      ..++++|||+|||.++++++|+++|++||+|. .|++     +++++|||||+|.+.++|++|++.|++..+.|+.    
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            45789999999999999999999999999999 8874     4578899999999999999999999999999999    


Q ss_pred             ccccccCCCC
Q 003400          259 LDIHFSIPKD  268 (823)
Q Consensus       259 L~V~~a~pk~  268 (823)
                      |+|.|+.+..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999997654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=4.3e-14  Score=125.90  Aligned_cols=80  Identities=21%  Similarity=0.387  Sum_probs=72.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEE-Ee-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-RE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~i-ri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ..++|||+|||.++++++|+++|++||.|..+ ++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++
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 65     3456899999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003400          350 RPGGAR  355 (823)
Q Consensus       350 ~~~~~r  355 (823)
                      +++..+
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            887643

>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=4.9e-14  Score=132.01  Aligned_cols=79  Identities=15%  Similarity=0.212  Sum_probs=71.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhC--CCccCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN--RSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~Ln--G~~i~Gr~I~V~~s~~~~  353 (823)
                      ..++|||+|||+++|+++|+++|++||.|.+|++.. .+|||||+|.+.++|++|++.|+  +..|.|++|+|++++++.
T Consensus        30 ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~-~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~  108 (119)
T 2ad9_A           30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE  108 (119)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEG-GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCC
Confidence            457899999999999999999999999999998854 48999999999999999999998  468999999999998876


Q ss_pred             cc
Q 003400          354 AR  355 (823)
Q Consensus       354 ~r  355 (823)
                      .+
T Consensus       109 ~~  110 (119)
T 2ad9_A          109 LK  110 (119)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.48  E-value=5.6e-14  Score=124.90  Aligned_cols=80  Identities=24%  Similarity=0.348  Sum_probs=72.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       186 ~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      +..+.+.++|||+|||.++++++|+++|++||+|..|++    .++++|||||+|.+.++|++|++.|++..+.|++|+|
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            344567799999999999999999999999999999884    3567899999999999999999999999999999999


Q ss_pred             cccC
Q 003400          262 HFSI  265 (823)
Q Consensus       262 ~~a~  265 (823)
                      .++.
T Consensus        90 ~~a~   93 (95)
T 2ywk_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             EEcC
Confidence            9985

>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=99.48  E-value=8.8e-14  Score=126.10  Aligned_cols=82  Identities=16%  Similarity=0.372  Sum_probs=74.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC------CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~------~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      ....+.++|||+|||.++++++|+++|++|| |..|++.      ++++|||||+|.+.++|++|+ .|++..|.|++|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   87 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIR   87 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEE
Confidence            3445779999999999999999999999999 9999852      677999999999999999999 8999999999999


Q ss_pred             ccccCCCCCC
Q 003400          261 IHFSIPKDNP  270 (823)
Q Consensus       261 V~~a~pk~~~  270 (823)
                      |.++.++...
T Consensus        88 V~~a~~~~~~   97 (104)
T 1wi8_A           88 VDVADQAQDK   97 (104)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEccCCCCC
Confidence            9999876543

>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=5.3e-14  Score=129.21  Aligned_cols=80  Identities=24%  Similarity=0.436  Sum_probs=72.7

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       273 ~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      .....++|||+|||.++++++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|||..+.|+.|+|++++++
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            34456899999999999999999999999999999986   899999999999999999999999999999999999887


Q ss_pred             ccc
Q 003400          353 GAR  355 (823)
Q Consensus       353 ~~r  355 (823)
                      ..+
T Consensus       104 ~~r  106 (108)
T 2jvo_A          104 AKR  106 (108)
T ss_dssp             C--
T ss_pred             CCC
Confidence            543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.48  E-value=3.7e-14  Score=125.23  Aligned_cols=73  Identities=22%  Similarity=0.289  Sum_probs=69.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .+.-|||+||++.+||++|+++|.+||+|.++++ ..++|||||+|.+.++|++|++.||+..+.|++|+|+++
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            4678999999999999999999999999999986 348999999999999999999999999999999999987

>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=125.37  Aligned_cols=79  Identities=30%  Similarity=0.526  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      ..+.++|||+|||.++++++|+++|++||+|..|++. +.+|||||+|.+.++|++|++.|++..+.|++|.|.|+.++.
T Consensus        12 ~~~~~~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           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            4567999999999999999999999999999999764 568999999999999999999999999999999999998654

>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=122.38  Aligned_cols=77  Identities=29%  Similarity=0.412  Sum_probs=71.7

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..+.|++|+|+++++...
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence            356799999999999999999999999999999986   56999999999999999999999999999999999987643

>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=99.48  E-value=1.1e-13  Score=125.44  Aligned_cols=79  Identities=23%  Similarity=0.357  Sum_probs=72.3

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC------CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~------~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....+|||+|||.++++++|+++|++|| |..|++.      +.++|||||+|.+.++|++|+ .|||..|.|+.|+|++
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            3457999999999999999999999999 9999863      567899999999999999999 9999999999999999


Q ss_pred             cCCCccc
Q 003400          349 SRPGGAR  355 (823)
Q Consensus       349 s~~~~~r  355 (823)
                      ++++..+
T Consensus        91 a~~~~~~   97 (104)
T 1wi8_A           91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9887644

>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=99.48  E-value=1.2e-13  Score=124.20  Aligned_cols=76  Identities=29%  Similarity=0.410  Sum_probs=71.1

Q ss_pred             CCccceeeecCCC-CCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          275 LNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       275 ~~~~tLfV~NLp~-~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ...++|||+|||. ++++++|+++|++||.|..|++.   +|||||+|.+.++|.+|++.|||..+.|++|+|++++++.
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 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA   96 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC---SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCCC
Confidence            3567999999998 99999999999999999999983   8999999999999999999999999999999999998753

>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=99.48  E-value=9.2e-14  Score=131.77  Aligned_cols=82  Identities=24%  Similarity=0.448  Sum_probs=75.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567899999999999999999999999999999985     3578999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 003400          262 HFSIPKD  268 (823)
Q Consensus       262 ~~a~pk~  268 (823)
                      .|+.++.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9997654

>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=2.8e-14  Score=126.17  Aligned_cols=77  Identities=17%  Similarity=0.259  Sum_probs=65.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCC--CEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYG--DIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG--~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      .+|||+|||.++|+++|+++|++||  .|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.++.
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            5799999999999999999999999  8888873     56789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 003400          266 PKDN  269 (823)
Q Consensus       266 pk~~  269 (823)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7543

>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=99.48  E-value=1.1e-13  Score=131.20  Aligned_cols=79  Identities=27%  Similarity=0.435  Sum_probs=73.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+++
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            34579999999999999999999999999999986     3567899999999999999999999999999999999999


Q ss_pred             CCCc
Q 003400          350 RPGG  353 (823)
Q Consensus       350 ~~~~  353 (823)
                      +++.
T Consensus       124 ~~~~  127 (129)
T 2kxn_B          124 ITKR  127 (129)
T ss_dssp             SSSS
T ss_pred             cCCC
Confidence            8765

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.48  E-value=1e-13  Score=124.49  Aligned_cols=76  Identities=24%  Similarity=0.330  Sum_probs=69.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEE--------EEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--------IRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~--------iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G  341 (823)
                      ....+|||+|||.++++++|+++|++||.|..        |++     ++.++|||||+|.+.++|++|++.|||..+.|
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            35679999999999999999999999999998        765     35678999999999999999999999999999


Q ss_pred             ceEEEEecC
Q 003400          342 KRIKLEPSR  350 (823)
Q Consensus       342 r~I~V~~s~  350 (823)
                      +.|+|++|+
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

>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=99.48  E-value=7.4e-14  Score=127.77  Aligned_cols=82  Identities=20%  Similarity=0.403  Sum_probs=74.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|++|.|
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            34456799999999999999999999999999999985     4567899999999999999999999999999999999


Q ss_pred             cccCCCC
Q 003400          262 HFSIPKD  268 (823)
Q Consensus       262 ~~a~pk~  268 (823)
                      .|+.++.
T Consensus       101 ~~a~~~~  107 (110)
T 1oo0_B          101 DWCFVKG  107 (110)
T ss_dssp             EESEESS
T ss_pred             EEcccCC
Confidence            9997654

>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=99.48  E-value=9.5e-14  Score=127.08  Aligned_cols=78  Identities=23%  Similarity=0.378  Sum_probs=72.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++... +|||||+|.+.++|++|++.|||..|.|+.|+|++++++..
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            4579999999999999999999999999999998654 89999999999999999999999999999999999988754

>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=3.8e-14  Score=126.35  Aligned_cols=82  Identities=22%  Similarity=0.376  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      .+.+.++|||+|||.++++++|+++|++||.|..+..+++++|||||+|.+.++|++|++.|++..+.|++|.|.++.++
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            44577999999999999999999999999999888667889999999999999999999999999999999999999775


Q ss_pred             CC
Q 003400          268 DN  269 (823)
Q Consensus       268 ~~  269 (823)
                      ..
T Consensus        92 ~~   93 (96)
T 1fjc_A           92 GG   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.47  E-value=8.1e-14  Score=135.63  Aligned_cols=82  Identities=28%  Similarity=0.478  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|.|.|
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            355789999999999999999999999999999984     567899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003400          264 SIPKDNP  270 (823)
Q Consensus       264 a~pk~~~  270 (823)
                      +.++...
T Consensus       147 a~~~~~~  153 (158)
T 2kn4_A          147 ARYGRPP  153 (158)
T ss_dssp             ECCSSCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.47  E-value=1.1e-13  Score=120.43  Aligned_cols=76  Identities=30%  Similarity=0.464  Sum_probs=70.4

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHh-CCCccCCceEEEEecC
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSR  350 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~L-nG~~i~Gr~I~V~~s~  350 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++.. ++|||||+|.+.++|++|++.| +|..+.|++|+|+|++
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~-~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG-GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC-CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            34567999999999999999999999999999998863 5899999999999999999999 9999999999999985

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=8.9e-14  Score=131.79  Aligned_cols=80  Identities=28%  Similarity=0.411  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHH----HHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr----~lFs~fG~I~~v~~--~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ..++++|||+|||.++++++|+    ++|++||+|.+|.+  +++++|||||+|.+.++|++|++.|+|..|.|++|+|.
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~  105 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT  105 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEE
Confidence            4568999999999999999876    69999999999885  46789999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 003400          263 FSIPKD  268 (823)
Q Consensus       263 ~a~pk~  268 (823)
                      |+.++.
T Consensus       106 ~a~~~~  111 (127)
T 2a3j_A          106 FSETPQ  111 (127)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            997653

>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=99.47  E-value=1.1e-13  Score=128.58  Aligned_cols=81  Identities=21%  Similarity=0.415  Sum_probs=74.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ..+.++|||+|||.++++++|+++|++||.|..|.+    +++++|||||+|.+.++|++|++.|+|..|.|++|.|.++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            356799999999999999999999999999999885    4567899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 003400          265 IPKDN  269 (823)
Q Consensus       265 ~pk~~  269 (823)
                      .++..
T Consensus        84 ~~~~~   88 (116)
T 2fy1_A           84 KKPSF   88 (116)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            86653

>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=99.47  E-value=8.9e-14  Score=121.54  Aligned_cols=78  Identities=12%  Similarity=0.325  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC------CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~------~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ..++|||+|||.++++++|+++|++||.|..|.+.      ++++|||||+|.+.++|++|++.|+|..+.|+.|.|.++
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            46899999999999999999999999999999842      228899999999999999999999999999999999999


Q ss_pred             CCCC
Q 003400          265 IPKD  268 (823)
Q Consensus       265 ~pk~  268 (823)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=1.1e-13  Score=123.97  Aligned_cols=80  Identities=20%  Similarity=0.262  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      ....++|||+|||.++++++|+++|++||.|....+..+++|||||+|.+.++|++|++.|+|..+.|++|.|.++.++.
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            34578999999999999999999999999996222467889999999999999999999999999999999999997654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=9.4e-14  Score=131.61  Aligned_cols=80  Identities=16%  Similarity=0.321  Sum_probs=72.7

Q ss_pred             CccceeeecCCCCCCHHHHH----HHhcccCceEEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          276 NQGTLVVFNLDPSVSNEDLR----QIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~----~~Fs~fG~I~~iri--~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ..++|||+|||+.+++++|+    ++|++||.|.+|.+  ++.++|||||+|.+.++|.+|++.|||..|.|++|+|+|+
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            45789999999999999876    69999999999977  4578999999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003400          350 RPGGAR  355 (823)
Q Consensus       350 ~~~~~r  355 (823)
                      +++...
T Consensus       108 ~~~~~~  113 (127)
T 2a3j_A          108 ETPQSQ  113 (127)
T ss_dssp             CCCCHH
T ss_pred             cCcchh
Confidence            987643

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.47  E-value=1e-13  Score=128.46  Aligned_cols=77  Identities=21%  Similarity=0.397  Sum_probs=70.2

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||.++++++|+++|++||.|.+|++.     +.++|||||+|.+.++|++|++.|||..|.|++|+|++
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3456799999999999999999999999999999863     45689999999999999999999999999999999999


Q ss_pred             cC
Q 003400          349 SR  350 (823)
Q Consensus       349 s~  350 (823)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            75

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.47  E-value=4e-14  Score=134.50  Aligned_cols=77  Identities=23%  Similarity=0.292  Sum_probs=71.2

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccE-EEEEEcCHHHHHHHHHHhCCCccCC--ceEEEEecCCCcc
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-KFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGGA  354 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~-aFVeF~d~e~A~kAl~~LnG~~i~G--r~I~V~~s~~~~~  354 (823)
                      -.|||+||++.+|+++|+++|++||.|.+|++..+++|+ |||+|.+.++|++|++.|||..|.|  ++|+|+|+++..-
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            468899999999999999999999999999886666787 9999999999999999999999998  9999999998753

>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=1.4e-13  Score=124.71  Aligned_cols=78  Identities=26%  Similarity=0.492  Sum_probs=72.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCccc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGAR  355 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~r  355 (823)
                      ..++|||+|||.++|+++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..|.|+.|+|++++++..+
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            45799999999999999999999999999999985   679999999999999999999999999999999999887654


Q ss_pred             c
Q 003400          356 R  356 (823)
Q Consensus       356 ~  356 (823)
                      +
T Consensus        87 ~   87 (103)
T 2dgu_A           87 R   87 (103)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.47  E-value=1.2e-13  Score=127.23  Aligned_cols=80  Identities=13%  Similarity=0.303  Sum_probs=72.4

Q ss_pred             CCCccceeeecCCCCCCHHHHH---HHhcccCceEEEEeCC--------CcccEEEEEEcCHHHHHHHHHHhCCCccCCc
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLR---QIFGAYGEVKEIRETP--------HKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  342 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~---~~Fs~fG~I~~iri~~--------~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr  342 (823)
                      ....++|||+|||+++++++|+   ++|++||.|..|++..        .++|||||+|.+.++|++|++.|||..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3456799999999999999999   9999999999998632        3458999999999999999999999999999


Q ss_pred             eEEEEecCCCc
Q 003400          343 RIKLEPSRPGG  353 (823)
Q Consensus       343 ~I~V~~s~~~~  353 (823)
                      +|+|++++++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999998764

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=7.2e-14  Score=128.29  Aligned_cols=80  Identities=21%  Similarity=0.405  Sum_probs=73.0

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       273 ~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~---~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      .....++|||+|||.++++++|+++|++||.|..|++.   +.++|||||+|.+.++|++|++.|||..+.|+.|+|+++
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            34456799999999999999999999999999999874   345899999999999999999999999999999999999


Q ss_pred             CCC
Q 003400          350 RPG  352 (823)
Q Consensus       350 ~~~  352 (823)
                      +++
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            875

>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=99.47  E-value=1.1e-13  Score=124.40  Aligned_cols=78  Identities=24%  Similarity=0.412  Sum_probs=72.6

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++. ..+|||||+|.+.++|++|++.|||..+.|++|+|++++++.
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            356799999999999999999999999999999986 458999999999999999999999999999999999998764

>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=5.5e-14  Score=126.67  Aligned_cols=76  Identities=14%  Similarity=0.242  Sum_probs=71.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ..++|||+|||.++++++|+++|++||.|.+|++. .++|||||+|.+.++|++|++.|||..+.|+.|+|++++++
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            35799999999999999999999999999999986 57899999999999999999999999999999999999863

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=2.3e-13  Score=122.25  Aligned_cols=77  Identities=27%  Similarity=0.376  Sum_probs=71.5

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhccc--CceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAY--GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~f--G~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ...++|||+|||.++++++|+++|++|  |.|..|++.   +|||||+|.+.++|++|++.|||..|.|++|+|++++++
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 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   89 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            346799999999999999999999999  999999874   789999999999999999999999999999999999886


Q ss_pred             cc
Q 003400          353 GA  354 (823)
Q Consensus       353 ~~  354 (823)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpd_A           90 DK   91 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=8.7e-14  Score=121.22  Aligned_cols=76  Identities=21%  Similarity=0.338  Sum_probs=70.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|++.++
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            46799999999999999999999999999999984     4667999999999999999999999999999999999876


Q ss_pred             C
Q 003400          265 I  265 (823)
Q Consensus       265 ~  265 (823)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=1.2e-13  Score=125.05  Aligned_cols=79  Identities=25%  Similarity=0.487  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      ..+.++|||+|||.++|+++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|++..|.|++|.|.|+.++.
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   84 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPD   84 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCc
Confidence            4567999999999999999999999999999999864   6799999999999999999999999999999999998765


Q ss_pred             CC
Q 003400          269 NP  270 (823)
Q Consensus       269 ~~  270 (823)
                      ..
T Consensus        85 ~~   86 (103)
T 2dgu_A           85 QK   86 (103)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.47  E-value=8.6e-14  Score=124.53  Aligned_cols=79  Identities=24%  Similarity=0.394  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          189 EHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       189 e~~srtLfV~NLP~-~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      ..++++|||+|||. ++++++|+++|++||.|..|.+   .+|||||+|.+.++|++|++.|++..+.|++|.|.++.++
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   83 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSN   83 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE---ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcC
Confidence            45789999999998 9999999999999999999987   4899999999999999999999999999999999999766


Q ss_pred             CCC
Q 003400          268 DNP  270 (823)
Q Consensus       268 ~~~  270 (823)
                      ..+
T Consensus        84 ~~~   86 (96)
T 2kvi_A           84 ARP   86 (96)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=1.9e-13  Score=126.36  Aligned_cols=83  Identities=24%  Similarity=0.397  Sum_probs=74.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ..+.+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.+++ .|.|++|.|
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            44567899999999999999999999999999999985     356889999999999999999999998 899999999


Q ss_pred             cccCCCCCC
Q 003400          262 HFSIPKDNP  270 (823)
Q Consensus       262 ~~a~pk~~~  270 (823)
                      +++.++..+
T Consensus        91 ~~a~~~~~~   99 (116)
T 2cqd_A           91 NLAYLGAKP   99 (116)
T ss_dssp             EESTTTCCC
T ss_pred             EEcccCCCc
Confidence            999765443

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=9.1e-14  Score=125.76  Aligned_cols=81  Identities=22%  Similarity=0.295  Sum_probs=74.0

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcc-cCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCc-cCCceEEEEec
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGA-YGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSD-IAGKRIKLEPS  349 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~-fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~-i~Gr~I~V~~s  349 (823)
                      ...+|||+|||.++|+++|+++|++ ||.|..|++    ++.++|||||+|.+.++|++|++.|||.. +.|+.|+|+++
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            4579999999999999999999999 999999976    45679999999999999999999999999 99999999999


Q ss_pred             CCCcccc
Q 003400          350 RPGGARR  356 (823)
Q Consensus       350 ~~~~~r~  356 (823)
                      +++..++
T Consensus        88 ~~~~~~~   94 (104)
T 2dhg_A           88 IPKASRV   94 (104)
T ss_dssp             CCCCSCC
T ss_pred             cCCCcCC
Confidence            8776443

>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=99.47  E-value=5.4e-14  Score=130.37  Aligned_cols=80  Identities=16%  Similarity=0.209  Sum_probs=71.8

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcC--CccccccccccccC
Q 003400          189 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~~-vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng--~~l~gr~L~V~~a~  265 (823)
                      ..++++|||+|||.+ +++++|+++|++||+|.+|++ .+++|||||+|.+.++|++|++.|++  ..|.|++|+|.|+.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i-~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~  100 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE  100 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEE-ecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECc
Confidence            457899999999998 999999999999999999986 35799999999999999999998865  55999999999997


Q ss_pred             CCCC
Q 003400          266 PKDN  269 (823)
Q Consensus       266 pk~~  269 (823)
                      .+..
T Consensus       101 ~~~~  104 (112)
T 1x4f_A          101 KYKK  104 (112)
T ss_dssp             SCSS
T ss_pred             cccc
Confidence            6543

>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=99.47  E-value=1.1e-13  Score=129.75  Aligned_cols=84  Identities=18%  Similarity=0.452  Sum_probs=75.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....+.++|||+|||.++|+++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|++..|.|+.|.|
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            34456789999999999999999999999999999985     5667999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 003400          262 HFSIPKDNP  270 (823)
Q Consensus       262 ~~a~pk~~~  270 (823)
                      .|+.++...
T Consensus        97 ~~a~~~~~~  105 (126)
T 3ex7_B           97 DWCFVRGPP  105 (126)
T ss_dssp             EESEESSSC
T ss_pred             EEecCCCCC
Confidence            999766543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=8.2e-14  Score=125.49  Aligned_cols=83  Identities=19%  Similarity=0.399  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ...+.++|||+|||.++++++|+++|++||.|.-+. .+++++|||||+|.+.++|++|++.|++..|.|+.|+|.|+.+
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            445789999999999999999999999999995443 2567899999999999999999999999999999999999987


Q ss_pred             CCCC
Q 003400          267 KDNP  270 (823)
Q Consensus       267 k~~~  270 (823)
                      +...
T Consensus        91 ~~~~   94 (101)
T 2fc9_A           91 RGSP   94 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.46  E-value=1.5e-13  Score=125.66  Aligned_cols=81  Identities=14%  Similarity=0.291  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      ..+.++|||+|||.++++++|+++|++||.|..|++... +|||||+|.+.++|++|++.|++..+.|++|.|.|+.++.
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  100 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP  100 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCC
Confidence            346789999999999999999999999999999986443 8999999999999999999999999999999999998765


Q ss_pred             CC
Q 003400          269 NP  270 (823)
Q Consensus       269 ~~  270 (823)
                      ..
T Consensus       101 ~~  102 (109)
T 1x4g_A          101 DM  102 (109)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=1.9e-13  Score=125.13  Aligned_cols=80  Identities=14%  Similarity=0.215  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccc-----cccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR-----RKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g-----r~L~V~  262 (823)
                      .....++|||+|||.++++++|+++|++||+|..|++...  |||||+|.+.++|++|++.|++..|.|     ++|+|.
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            3456799999999999999999999999999999986444  999999999999999999999999999     999999


Q ss_pred             ccCCCCC
Q 003400          263 FSIPKDN  269 (823)
Q Consensus       263 ~a~pk~~  269 (823)
                      ++.++..
T Consensus        89 ~a~~~~~   95 (108)
T 1x4c_A           89 VDGPRSP   95 (108)
T ss_dssp             ESSCCSC
T ss_pred             eCCCCCC
Confidence            9987654

>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=1.7e-13  Score=125.44  Aligned_cols=77  Identities=21%  Similarity=0.275  Sum_probs=71.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCC-----ceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG-----KRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G-----r~I~V~~s~  350 (823)
                      ...+|||+|||.++++++|+++|++||.|..|++...  |||||+|.+.++|++||+.|||..|.|     +.|+|++++
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            4579999999999999999999999999999998644  999999999999999999999999999     999999998


Q ss_pred             CCcc
Q 003400          351 PGGA  354 (823)
Q Consensus       351 ~~~~  354 (823)
                      ++..
T Consensus        92 ~~~~   95 (108)
T 1x4c_A           92 PRSP   95 (108)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            8653

>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=99.46  E-value=1.5e-13  Score=123.62  Aligned_cols=77  Identities=25%  Similarity=0.396  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          188 GEHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       188 ~e~~srtLfV~NLP~-~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ...++++|||+|||. ++++++|+++|++||.|..|++   .+|||||+|.+.++|++|++.|+|..+.|++|+|+++.+
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            345789999999998 9999999999999999999987   489999999999999999999999999999999999875


Q ss_pred             C
Q 003400          267 K  267 (823)
Q Consensus       267 k  267 (823)
                      +
T Consensus        95 ~   95 (97)
T 2xnq_A           95 N   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.4e-13  Score=124.84  Aligned_cols=83  Identities=23%  Similarity=0.416  Sum_probs=75.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++. ++..|.|+.|.|
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            34567899999999999999999999999999999874     456789999999999999999998 999999999999


Q ss_pred             cccCCCCCC
Q 003400          262 HFSIPKDNP  270 (823)
Q Consensus       262 ~~a~pk~~~  270 (823)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 2dh8_A           90 KPCTPRGMQ   98 (105)
T ss_dssp             CCSCCSSCC
T ss_pred             EEccCCCCC
Confidence            999877644

>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=2.5e-13  Score=124.87  Aligned_cols=80  Identities=19%  Similarity=0.253  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..|.|++|.|.+
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            3456899999999999999999999999999999874    355789999999999999999999999999999999999


Q ss_pred             cCCC
Q 003400          264 SIPK  267 (823)
Q Consensus       264 a~pk  267 (823)
                      +...
T Consensus        91 a~~~   94 (114)
T 2do0_A           91 DERA   94 (114)
T ss_dssp             CSCC
T ss_pred             cccC
Confidence            8654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.5e-13  Score=121.29  Aligned_cols=78  Identities=19%  Similarity=0.406  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      ..+.++|||+|||.++|+++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|++..+.|++|+|.++.++.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            4567999999999999999999999999999999874   5699999999999999999999999999999999998764


Q ss_pred             C
Q 003400          269 N  269 (823)
Q Consensus       269 ~  269 (823)
                      .
T Consensus        83 ~   83 (90)
T 2dnp_A           83 K   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.46  E-value=1.2e-13  Score=128.03  Aligned_cols=79  Identities=15%  Similarity=0.346  Sum_probs=71.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34556799999999999999999999999999999985     3567999999999999999999999999999999999


Q ss_pred             cccC
Q 003400          262 HFSI  265 (823)
Q Consensus       262 ~~a~  265 (823)
                      +|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9873

>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=99.46  E-value=1.2e-13  Score=129.40  Aligned_cols=81  Identities=26%  Similarity=0.407  Sum_probs=73.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ....+|||+|||.++|+++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..|.|+.|+|+++
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            34679999999999999999999999999999987     4556999999999999999999999999999999999999


Q ss_pred             CCCccc
Q 003400          350 RPGGAR  355 (823)
Q Consensus       350 ~~~~~r  355 (823)
                      +++..+
T Consensus       100 ~~~~~~  105 (126)
T 3ex7_B          100 FVRGPP  105 (126)
T ss_dssp             EESSSC
T ss_pred             cCCCCC
Confidence            876543

>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=99.46  E-value=3.8e-14  Score=128.10  Aligned_cols=80  Identities=24%  Similarity=0.451  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      +.+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            446789999999999999999999999999998874     456799999999999999999999999999999999999


Q ss_pred             cCCCC
Q 003400          264 SIPKD  268 (823)
Q Consensus       264 a~pk~  268 (823)
                      +.++.
T Consensus        85 a~~~~   89 (104)
T 1p1t_A           85 AASEK   89 (104)
T ss_dssp             TTCTT
T ss_pred             CCCcc
Confidence            97654

>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=9e-14  Score=124.03  Aligned_cols=80  Identities=24%  Similarity=0.597  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHH----HHhhcCCCEEEEEeC--CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYTA--CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr----~lFs~fG~I~~v~~~--~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ..++++|||+|||.++++++|+    ++|++||.|..|.+.  ++++|||||+|.+.++|++|++.|+|..+.|++|+|.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   84 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4578999999999999999999    999999999999853  4678999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 003400          263 FSIPKD  268 (823)
Q Consensus       263 ~a~pk~  268 (823)
                      |+.++.
T Consensus        85 ~a~~~~   90 (97)
T 1nu4_A           85 YAKTDS   90 (97)
T ss_dssp             ECSSCC
T ss_pred             EccCCC
Confidence            997654

>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=2.3e-13  Score=125.11  Aligned_cols=79  Identities=19%  Similarity=0.178  Sum_probs=71.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++.|||..|.|+.|+|++++.
T Consensus        14 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   93 (114)
T 2do0_A           14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDER   93 (114)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEccc
Confidence            4679999999999999999999999999999876    344689999999999999999999999999999999999986


Q ss_pred             Ccc
Q 003400          352 GGA  354 (823)
Q Consensus       352 ~~~  354 (823)
                      ...
T Consensus        94 ~~~   96 (114)
T 2do0_A           94 ALP   96 (114)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=1.7e-13  Score=125.06  Aligned_cols=82  Identities=21%  Similarity=0.313  Sum_probs=74.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCC-EEEEEeC------CCcccEEEEEeCCHHHHHHHHHHhc--CCcccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLYTA------CKHRGFVMISYYDIRAARTAMRALQ--NKPLRRRKLD  260 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~-I~~v~~~------~ksrG~AFV~F~~~e~A~~Ai~~Ln--g~~l~gr~L~  260 (823)
                      .+.++|||+|||.++++++|+++|++||. |..|.+.      ++++|||||+|.+.++|++|++.|+  +..+.|++|+
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            46799999999999999999999999998 9999853      3789999999999999999999996  5899999999


Q ss_pred             ccccCCCCCCC
Q 003400          261 IHFSIPKDNPS  271 (823)
Q Consensus       261 V~~a~pk~~~~  271 (823)
                      |.|+.++..+.
T Consensus        86 V~~a~~~~~~~   96 (109)
T 2dis_A           86 VDWAEPEIDVD   96 (109)
T ss_dssp             EEESCSSCSTT
T ss_pred             EEEcCCCCCcC
Confidence            99998876543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.46  E-value=9.5e-14  Score=127.50  Aligned_cols=79  Identities=24%  Similarity=0.494  Sum_probs=72.5

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ..+.+.++|||+|||.++++++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|+|..+.|++|.|.|+.+
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  102 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL  102 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            345678999999999999999999999999999999865   89999999999999999999999999999999999976


Q ss_pred             CC
Q 003400          267 KD  268 (823)
Q Consensus       267 k~  268 (823)
                      +.
T Consensus       103 ~~  104 (108)
T 2jvo_A          103 PA  104 (108)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.2e-13  Score=124.32  Aligned_cols=81  Identities=32%  Similarity=0.448  Sum_probs=72.2

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ....++|||+|||.++++++|+++|++||.|.-++. ++.++|||||+|.+.++|++|++.|||..|.|+.|+|++++++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   91 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPR   91 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCC
Confidence            345679999999999999999999999999854443 5668999999999999999999999999999999999999887


Q ss_pred             cc
Q 003400          353 GA  354 (823)
Q Consensus       353 ~~  354 (823)
                      ..
T Consensus        92 ~~   93 (101)
T 2fc9_A           92 GS   93 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.46  E-value=4.8e-14  Score=127.44  Aligned_cols=78  Identities=17%  Similarity=0.267  Sum_probs=72.2

Q ss_pred             CCCcEEEEcCCCC------CCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccc-c
Q 003400          190 HPSRTLFVRNINS------NVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR-R  257 (823)
Q Consensus       190 ~~srtLfV~NLP~------~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g-r  257 (823)
                      ..+++|||+|||.      ++++++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|+|..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      9999999999999999999984     37789999999999999999999999999999 9


Q ss_pred             cccccccCCC
Q 003400          258 KLDIHFSIPK  267 (823)
Q Consensus       258 ~L~V~~a~pk  267 (823)
                      +|+|.++.++
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998653

>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=99.46  E-value=1.1e-13  Score=123.86  Aligned_cols=80  Identities=15%  Similarity=0.269  Sum_probs=72.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHH----HHhhcCCCEEEEEeC--CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYTA--CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr----~lFs~fG~I~~v~~~--~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +.++|||+|||.++++++|+    ++|++||+|.+|++.  ...+|||||+|.+.++|++|++.|+|..+.|++|+|.++
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            56899999999999999999    999999999999863  223899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 003400          265 IPKDNP  270 (823)
Q Consensus       265 ~pk~~~  270 (823)
                      .+...+
T Consensus        88 ~~~~~~   93 (96)
T 2dgx_A           88 TGASGP   93 (96)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            876543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=2e-13  Score=126.16  Aligned_cols=80  Identities=26%  Similarity=0.345  Sum_probs=72.4

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 003400          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (823)
Q Consensus       273 ~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~  347 (823)
                      .+...++|||+|||.++++++|+++|++||.|..|++.     +.++|||||+|.+.++|++|++.|++ .|.|++|+|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            34456899999999999999999999999999999873     45789999999999999999999998 8999999999


Q ss_pred             ecCCCc
Q 003400          348 PSRPGG  353 (823)
Q Consensus       348 ~s~~~~  353 (823)
                      +++++.
T Consensus        92 ~a~~~~   97 (116)
T 2cqd_A           92 LAYLGA   97 (116)
T ss_dssp             ESTTTC
T ss_pred             EcccCC
Confidence            998754

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.46  E-value=2.3e-13  Score=123.06  Aligned_cols=79  Identities=18%  Similarity=0.250  Sum_probs=71.4

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ....+|||+|||.++++++|+++|++|| |..|++     ++.++|||||+|.+.++|++|+ .|||..|.|+.|+|+++
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 999876     3567899999999999999999 89999999999999999


Q ss_pred             CCCccc
Q 003400          350 RPGGAR  355 (823)
Q Consensus       350 ~~~~~r  355 (823)
                      +++..+
T Consensus        91 ~~~~~~   96 (103)
T 2dng_A           91 EGRKQD   96 (103)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            886543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.46  E-value=2e-13  Score=123.55  Aligned_cols=82  Identities=20%  Similarity=0.403  Sum_probs=73.5

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....+.++|||+|||.++++++|+++|++|| |..|++     +++++|||||+|.+.++|++|+ .|++..|.|++|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   87 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV   87 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEE
Confidence            3455789999999999999999999999997 999874     4678999999999999999999 89999999999999


Q ss_pred             cccCCCCCC
Q 003400          262 HFSIPKDNP  270 (823)
Q Consensus       262 ~~a~pk~~~  270 (823)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2dng_A           88 DIAEGRKQD   96 (103)
T ss_dssp             EECCCCCCC
T ss_pred             EEecCCCCC
Confidence            999876543

>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=1.3e-13  Score=126.85  Aligned_cols=81  Identities=26%  Similarity=0.377  Sum_probs=73.1

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceE--------EEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccC
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK--------EIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA  340 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~--------~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~  340 (823)
                      ....++|||+|||.++++++|+++|++||.|.        .|++     ++.++|||||+|.+.++|++|++.|||..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            34567999999999999999999999999998        4665     3567899999999999999999999999999


Q ss_pred             CceEEEEecCCCcc
Q 003400          341 GKRIKLEPSRPGGA  354 (823)
Q Consensus       341 Gr~I~V~~s~~~~~  354 (823)
                      |+.|+|++++++..
T Consensus        92 g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           92 GSKLKVSLARKKPP  105 (113)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CCEEEEEECCCCCC
Confidence            99999999988754

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.46  E-value=1.5e-13  Score=123.41  Aligned_cols=77  Identities=23%  Similarity=0.396  Sum_probs=70.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEE--------EEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--------LYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~--------v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l  254 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..        |++     +++++|||||+|.+.++|++|++.|+|..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3456799999999999999999999999999988        763     457799999999999999999999999999


Q ss_pred             cccccccccc
Q 003400          255 RRRKLDIHFS  264 (823)
Q Consensus       255 ~gr~L~V~~a  264 (823)
                      .|++|+|+++
T Consensus        89 ~g~~l~V~~A   98 (99)
T 2la6_A           89 SGNPIKVSFA   98 (99)
T ss_dssp             SSSBCEEEEC
T ss_pred             CCcEEEEEec
Confidence            9999999987

>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=99.46  E-value=4e-14  Score=130.48  Aligned_cols=78  Identities=21%  Similarity=0.422  Sum_probs=71.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...++|||+|||.++++++|+++|+.||.|..|++.     +.++|||||+|.+.++|++|+ .|||..|.|+.|+|+++
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            345799999999999999999999999999999874     567899999999999999999 99999999999999999


Q ss_pred             CCCc
Q 003400          350 RPGG  353 (823)
Q Consensus       350 ~~~~  353 (823)
                      +++.
T Consensus       102 ~~~~  105 (114)
T 2cq4_A          102 QAEK  105 (114)
T ss_dssp             HHHH
T ss_pred             CCCc
Confidence            7654

>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=99.46  E-value=1.1e-13  Score=127.76  Aligned_cols=76  Identities=17%  Similarity=0.267  Sum_probs=71.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++. ..++||||+|.+.++|++|++.|||..+.|+.|+|+|++..
T Consensus         9 ~~~~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            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            45799999999999999999999999999999986 47899999999999999999999999999999999998764

>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=99.46  E-value=1.5e-13  Score=120.54  Aligned_cols=76  Identities=28%  Similarity=0.473  Sum_probs=70.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|+ .|||..+.|+.|+|++++
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            3568999999999999999999999999999975     4567899999999999999999 899999999999999997


Q ss_pred             CC
Q 003400          351 PG  352 (823)
Q Consensus       351 ~~  352 (823)
                      +.
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=99.46  E-value=6.6e-14  Score=129.11  Aligned_cols=77  Identities=13%  Similarity=0.284  Sum_probs=71.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      +++.++|||+|||.++++++|+++|++||.|..|.+. +++|||||+|.+.++|++|++.|+|..+.|++|+|.|+..
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            3456899999999999999999999999999999764 5889999999999999999999999999999999999864

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.45  E-value=5.1e-14  Score=127.29  Aligned_cols=76  Identities=20%  Similarity=0.228  Sum_probs=71.2

Q ss_pred             ccceeeecCCC------CCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC-ceE
Q 003400          277 QGTLVVFNLDP------SVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG-KRI  344 (823)
Q Consensus       277 ~~tLfV~NLp~------~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G-r~I  344 (823)
                      .++|||+|||.      ++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.| +.|
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      9999999999999999999986     36789999999999999999999999999999 999


Q ss_pred             EEEecCCC
Q 003400          345 KLEPSRPG  352 (823)
Q Consensus       345 ~V~~s~~~  352 (823)
                      +|.++++.
T Consensus        86 ~V~~a~~~   93 (100)
T 3ns6_A           86 FLYTMKDV   93 (100)
T ss_dssp             EEEESHHH
T ss_pred             EEEECchh
Confidence            99999764

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.45  E-value=5.8e-14  Score=126.48  Aligned_cols=76  Identities=28%  Similarity=0.408  Sum_probs=71.6

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ++|||+|||.++|+++|+++|++||.|..|++...++|||||+|.+.++|++|++.|||..+.|+.|+|++++++.
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            3799999999999999999999999999998865578999999999999999999999999999999999998865

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=9.1e-14  Score=127.60  Aligned_cols=81  Identities=22%  Similarity=0.398  Sum_probs=73.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC---CCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~---~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ....+.++|||+|||.++++++|+++|++||+|..|++.   ..++|||||+|.+.++|++|++.|+|..+.|++|+|.+
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345578999999999999999999999999999998852   44789999999999999999999999999999999999


Q ss_pred             cCCC
Q 003400          264 SIPK  267 (823)
Q Consensus       264 a~pk  267 (823)
                      +.++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.45  E-value=1.8e-13  Score=130.50  Aligned_cols=83  Identities=23%  Similarity=0.437  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.
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            4557799999999999999999999999999999984     35679999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 003400          263 FSIPKDNP  270 (823)
Q Consensus       263 ~a~pk~~~  270 (823)
                      ++.++...
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.4e-13  Score=126.53  Aligned_cols=82  Identities=22%  Similarity=0.385  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEE--------EEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIR--------TLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPL  254 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~--------~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l  254 (823)
                      .+.+.++|||+|||.++++++|+++|++||.|.        .|++     +++++|||||+|.+.++|++|++.|++..|
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            456789999999999999999999999999998        4663     356789999999999999999999999999


Q ss_pred             ccccccccccCCCCC
Q 003400          255 RRRKLDIHFSIPKDN  269 (823)
Q Consensus       255 ~gr~L~V~~a~pk~~  269 (823)
                      .|++|+|.++.++..
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999987654

>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=2.1e-13  Score=122.88  Aligned_cols=83  Identities=23%  Similarity=0.407  Sum_probs=73.6

Q ss_pred             CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEE--eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       273 ~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir--i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      .....++|||+|||.++++++|+++|+.|+.|.-++  .++.++|||||+|.+.++|++|++.|||..|.|+.|+|++++
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            344668999999999999999999999998776665  356778999999999999999999999999999999999999


Q ss_pred             CCccc
Q 003400          351 PGGAR  355 (823)
Q Consensus       351 ~~~~r  355 (823)
                      ++..+
T Consensus        91 ~~~~~   95 (102)
T 2fc8_A           91 PKGEG   95 (102)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            87643

>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=99.45  E-value=8.6e-14  Score=125.78  Aligned_cols=81  Identities=22%  Similarity=0.393  Sum_probs=73.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|++++
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            4579999999999999999999999999999876     35568999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 003400          351 PGGARR  356 (823)
Q Consensus       351 ~~~~r~  356 (823)
                      +...+.
T Consensus        87 ~~~~~~   92 (104)
T 1p1t_A           87 SEKNKE   92 (104)
T ss_dssp             CTTHHH
T ss_pred             Cccchh
Confidence            876543

>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=99.45  E-value=2.1e-13  Score=132.78  Aligned_cols=80  Identities=23%  Similarity=0.298  Sum_probs=73.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++|+++|+++|++||.|..|++     ++.+++||||+|.+.++|++||+.|||..|.|+.|+|++++
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  117 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA  117 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            4579999999999999999999999999999987     45678999999999999999999999999999999999998


Q ss_pred             CCccc
Q 003400          351 PGGAR  355 (823)
Q Consensus       351 ~~~~r  355 (823)
                      +...+
T Consensus       118 ~~~~~  122 (156)
T 1h2v_Z          118 GFKEG  122 (156)
T ss_dssp             CCCTT
T ss_pred             CCCCc
Confidence            76543

>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=123.87  Aligned_cols=77  Identities=29%  Similarity=0.404  Sum_probs=71.1

Q ss_pred             CCccceeeecCCC-CCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          275 LNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       275 ~~~~tLfV~NLp~-~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ...++|||+|||. ++++++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|||..+.|++|+|++++++.
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 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE---TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            3567999999998 99999999999999999999983   8999999999999999999999999999999999998764


Q ss_pred             c
Q 003400          354 A  354 (823)
Q Consensus       354 ~  354 (823)
                      .
T Consensus        85 ~   85 (96)
T 2kvi_A           85 R   85 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=2.1e-13  Score=125.67  Aligned_cols=83  Identities=20%  Similarity=0.384  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCE----EEEE-eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDI----RTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I----~~v~-~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...++++|||+|||.++|+++|+++|++||.|    ..++ .+++++|||||+|.+.++|++|++.|++..+.|++|.|.
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            34577999999999999999999999999998    4444 478899999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 003400          263 FSIPKDNP  270 (823)
Q Consensus       263 ~a~pk~~~  270 (823)
                      |+.++...
T Consensus       101 ~a~~~~~~  108 (115)
T 2cpx_A          101 FGKNKKQR  108 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EccCCCCC
Confidence            99876543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=2.9e-13  Score=121.51  Aligned_cols=78  Identities=21%  Similarity=0.406  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcC--CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQY--GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~f--G~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ..+.++|||+|||.++++++|+++|++|  |.|..|++   .+|||||+|.+.++|++|++.|++..|.|++|+|.|+.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK---IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   88 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE---CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE---eCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCC
Confidence            3567999999999999999999999999  99999875   478999999999999999999999999999999999987


Q ss_pred             CCC
Q 003400          267 KDN  269 (823)
Q Consensus       267 k~~  269 (823)
                      +..
T Consensus        89 ~~~   91 (99)
T 2cpd_A           89 VDK   91 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.45  E-value=1.2e-13  Score=130.99  Aligned_cols=83  Identities=19%  Similarity=0.381  Sum_probs=74.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEE--EEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCC----cc
Q 003400          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--LYT-----ACKHRGFVMISYYDIRAARTAMRALQNK----PL  254 (823)
Q Consensus       186 ~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~--v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~----~l  254 (823)
                      +..+.+.++|||+|||.++|+++|+++|++||.|..  |++     +++++|||||+|.+. +|.+|++.|++.    .+
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            345567899999999999999999999999999966  663     677899999999999 999999999999    99


Q ss_pred             ccccccccccCCCCC
Q 003400          255 RRRKLDIHFSIPKDN  269 (823)
Q Consensus       255 ~gr~L~V~~a~pk~~  269 (823)
                      .|++|+|.++.++..
T Consensus        96 ~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           96 DGKTINVEFAKGSKR  110 (131)
T ss_dssp             GGCCCCCEECCCSCC
T ss_pred             CCEEEEEEECCCCCC
Confidence            999999999987654

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.45  E-value=6.8e-14  Score=133.65  Aligned_cols=85  Identities=28%  Similarity=0.479  Sum_probs=76.5

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       186 ~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      +....+.++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+
T Consensus        41 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~  120 (135)
T 2lea_A           41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR  120 (135)
T ss_dssp             CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            334556799999999999999999999999999999984     467899999999999999999999999999999999


Q ss_pred             ccccCCCCCC
Q 003400          261 IHFSIPKDNP  270 (823)
Q Consensus       261 V~~a~pk~~~  270 (823)
                      |.|+.++..+
T Consensus       121 V~~a~~~~~~  130 (135)
T 2lea_A          121 VQMARYGRPP  130 (135)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876543

>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=1.3e-13  Score=123.39  Aligned_cols=78  Identities=21%  Similarity=0.223  Sum_probs=69.8

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEE-----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir-----i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...++|||+|||.++++++|+++|++||.|..++     .++.++|||||+|.+.++|++|++.|||..|.|+.|+|+++
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            3457899999999999999999999999986543     24567899999999999999999999999999999999998


Q ss_pred             CCC
Q 003400          350 RPG  352 (823)
Q Consensus       350 ~~~  352 (823)
                      +.+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            764

>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=99.45  E-value=1.9e-13  Score=124.30  Aligned_cols=78  Identities=22%  Similarity=0.429  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..+.|++|.|++
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            4457899999999999999999999999999999874    456899999999999999999999999999999999998


Q ss_pred             cC
Q 003400          264 SI  265 (823)
Q Consensus       264 a~  265 (823)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            74

>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=1.8e-13  Score=124.73  Aligned_cols=77  Identities=14%  Similarity=0.169  Sum_probs=70.6

Q ss_pred             CccceeeecCCCCC------CHHHHHHHhcccCceEEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCc-eEE
Q 003400          276 NQGTLVVFNLDPSV------SNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK-RIK  345 (823)
Q Consensus       276 ~~~tLfV~NLp~~v------teedL~~~Fs~fG~I~~iri~---~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr-~I~  345 (823)
                      ..++|||+|||..+      ++++|+++|++||.|..|++.   +.++|||||+|.+.++|.+|++.|||..+.|+ +|+
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~   93 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   93 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEE
Confidence            45799999999999      789999999999999999864   56789999999999999999999999999998 999


Q ss_pred             EEecCCC
Q 003400          346 LEPSRPG  352 (823)
Q Consensus       346 V~~s~~~  352 (823)
                      |+++...
T Consensus        94 V~~a~~~  100 (105)
T 2nlw_A           94 VNLFTDF  100 (105)
T ss_dssp             EECSCCC
T ss_pred             EEEcchH
Confidence            9998754

>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=99.45  E-value=8.9e-14  Score=123.35  Aligned_cols=80  Identities=20%  Similarity=0.350  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCC-EEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcC-CccccccccccccCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGD-IRTLYTACKHRGFVMISYYDIRAARTAMRALQN-KPLRRRKLDIHFSIP  266 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~-I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng-~~l~gr~L~V~~a~p  266 (823)
                      ..+.++|||+|||.++|+++|+++|++||. |..+.+  .++|||||+|.+.++|++|++.|++ ..+.|++|+|.|+.+
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            346799999999999999999999999999 665544  4689999999999999999999999 999999999999987


Q ss_pred             CCCC
Q 003400          267 KDNP  270 (823)
Q Consensus       267 k~~~  270 (823)
                      +...
T Consensus        83 ~~~~   86 (93)
T 2cqh_A           83 KKLR   86 (93)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            6543

>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=99.45  E-value=9.1e-14  Score=125.41  Aligned_cols=77  Identities=22%  Similarity=0.354  Sum_probs=69.1

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe------CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri------~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ...++|||+|||.++++++|+++|+.|| |.+|++      +++++|||||+|.+.++|++|+ .|||..|.|+.|+|++
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 999986      3456899999999999999999 8999999999999999


Q ss_pred             cCCCc
Q 003400          349 SRPGG  353 (823)
Q Consensus       349 s~~~~  353 (823)
                      ++++.
T Consensus        95 a~~~~   99 (100)
T 2j76_E           95 ADQAQ   99 (100)
T ss_dssp             CCCSC
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=99.45  E-value=1.1e-13  Score=124.81  Aligned_cols=79  Identities=18%  Similarity=0.387  Sum_probs=69.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~------~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      .....++|||+|||.++++++|+++|++|| |..|++      +++++|||||+|.+.++|++|+ .|+|..|.|+.|.|
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            345679999999999999999999999999 999984      4567999999999999999999 89999999999999


Q ss_pred             cccCCCC
Q 003400          262 HFSIPKD  268 (823)
Q Consensus       262 ~~a~pk~  268 (823)
                      .++.++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9997653

>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=99.45  E-value=1.1e-13  Score=123.39  Aligned_cols=79  Identities=22%  Similarity=0.431  Sum_probs=72.9

Q ss_pred             CccceeeecCCCCCCHHHHH----HHhcccCceEEEEeC--CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          276 NQGTLVVFNLDPSVSNEDLR----QIFGAYGEVKEIRET--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~----~~Fs~fG~I~~iri~--~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ..++|||+|||.++++++|+    ++|++||.|..|++.  +.++|||||+|.+.++|++|++.|||..+.|+.|+|+++
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            45799999999999999999    999999999999874  356899999999999999999999999999999999999


Q ss_pred             CCCcc
Q 003400          350 RPGGA  354 (823)
Q Consensus       350 ~~~~~  354 (823)
                      +++..
T Consensus        87 ~~~~~   91 (97)
T 1nu4_A           87 KTDSD   91 (97)
T ss_dssp             SSCCT
T ss_pred             cCCCc
Confidence            98754

>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=99.44  E-value=1.7e-13  Score=126.27  Aligned_cols=80  Identities=29%  Similarity=0.373  Sum_probs=72.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCce----EEEE-eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV----KEIR-ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I----~~ir-i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++|+++|+++|++||.|    ..++ .++.++|||||+|.+.++|++|++.|||..|.|+.|+|++++
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~  103 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK  103 (115)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEcc
Confidence            45799999999999999999999999998    4554 367789999999999999999999999999999999999998


Q ss_pred             CCccc
Q 003400          351 PGGAR  355 (823)
Q Consensus       351 ~~~~r  355 (823)
                      ++..+
T Consensus       104 ~~~~~  108 (115)
T 2cpx_A          104 NKKQR  108 (115)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87643

>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=99.44  E-value=2.5e-13  Score=131.36  Aligned_cols=81  Identities=25%  Similarity=0.434  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      ...+.++|||+|||.++|+++|+++|++||.|.+|++...++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.++
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            34567999999999999999999999999999999987778999999999999999999999999999999999999765


Q ss_pred             C
Q 003400          268 D  268 (823)
Q Consensus       268 ~  268 (823)
                      .
T Consensus       149 ~  149 (150)
T 2i2y_A          149 K  149 (150)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=8.3e-14  Score=123.55  Aligned_cols=78  Identities=27%  Similarity=0.370  Sum_probs=70.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCc-eEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC-CccCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR-SDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~-I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG-~~i~Gr~I~V~~s~~~~  353 (823)
                      ..++|||+|||.++|+++|+++|++||. |..+.+  .++|||||+|.+.++|++|++.||| ..+.|++|+|++++++.
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 666655  3689999999999999999999999 99999999999998875


Q ss_pred             cc
Q 003400          354 AR  355 (823)
Q Consensus       354 ~r  355 (823)
                      .+
T Consensus        85 ~~   86 (93)
T 2cqh_A           85 LR   86 (93)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=3.9e-14  Score=132.42  Aligned_cols=77  Identities=25%  Similarity=0.446  Sum_probs=70.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|+ .|||..|.|+.|+|++++
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            3579999999999999999999999999999876     4667999999999999999999 799999999999999998


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=1.4e-13  Score=123.44  Aligned_cols=78  Identities=24%  Similarity=0.370  Sum_probs=71.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceE-EEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce----EE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVK-EIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR----IK  345 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~-~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~----I~  345 (823)
                      ..++|||+|||.++++++|+++|++||.|. .|++     ++.++|||||+|.+.++|++|++.|||..+.|+.    |+
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            457999999999999999999999999999 8875     4567899999999999999999999999999999    99


Q ss_pred             EEecCCCc
Q 003400          346 LEPSRPGG  353 (823)
Q Consensus       346 V~~s~~~~  353 (823)
                      |+++++..
T Consensus        88 v~~a~~~~   95 (99)
T 2div_A           88 LNYATYSG   95 (99)
T ss_dssp             EEETTCCS
T ss_pred             EeecCCCC
Confidence            99998764

>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=99.44  E-value=2.6e-13  Score=123.39  Aligned_cols=75  Identities=24%  Similarity=0.383  Sum_probs=69.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...+|||+|||..+++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++.|||..|.|+.|+|+++.
T Consensus        28 ~~~~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           28 TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            4679999999999999999999999999999876    35678999999999999999999999999999999999985

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.44  E-value=1.9e-13  Score=118.25  Aligned_cols=71  Identities=15%  Similarity=0.362  Sum_probs=65.5

Q ss_pred             CcEEEEcCCCCCC------CHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCccccc-cccc
Q 003400          192 SRTLFVRNINSNV------EDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRR-KLDI  261 (823)
Q Consensus       192 srtLfV~NLP~~v------teeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr-~L~V  261 (823)
                      +++|||+|||..+      ++++|+++|++||+|..|++   +++++|||||+|.+.++|++|++.|+|..+.|+ +|+|
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      78999999999999999985   457899999999999999999999999999999 8887


Q ss_pred             c
Q 003400          262 H  262 (823)
Q Consensus       262 ~  262 (823)
                      .
T Consensus        81 ~   81 (81)
T 2krb_A           81 N   81 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=4.2e-13  Score=120.13  Aligned_cols=76  Identities=20%  Similarity=0.392  Sum_probs=70.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      ..++|||+||  ++++++|+++|++||.|..|++ +.++|||||+|.+.++|++|++.|||..|.|++|+|++++++..
T Consensus        14 ~~~~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           14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEe-cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            4579999996  8999999999999999999998 46789999999999999999999999999999999999988653

>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=99.44  E-value=1.2e-13  Score=128.07  Aligned_cols=77  Identities=19%  Similarity=0.201  Sum_probs=70.2

Q ss_pred             CccceeeecCCCC-CCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCC--CccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR--SDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~-vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG--~~i~Gr~I~V~~s~~~  352 (823)
                      ..++|||+|||++ +++++|+++|++||.|.+|++. .++|||||+|.+.++|++|++.|++  ..|.|++|+|.+++.+
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~  102 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY  102 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccc
Confidence            4679999999998 9999999999999999999985 5689999999999999999998864  5699999999999875


Q ss_pred             c
Q 003400          353 G  353 (823)
Q Consensus       353 ~  353 (823)
                      .
T Consensus       103 ~  103 (112)
T 1x4f_A          103 K  103 (112)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=2.4e-13  Score=124.86  Aligned_cols=81  Identities=26%  Similarity=0.388  Sum_probs=70.7

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||.++++++|+++|+.||.|.+|++.     +.++|||||+|.+.++|++|++.+ +..+.|+.|+|++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            3456799999999999999999999999999999873     567899999999999999999986 5999999999999


Q ss_pred             cCCCccc
Q 003400          349 SRPGGAR  355 (823)
Q Consensus       349 s~~~~~r  355 (823)
                      +.++..+
T Consensus       101 a~~~~~~  107 (109)
T 2rs2_A          101 AFPRRAQ  107 (109)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9887643

>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=99.44  E-value=2.4e-13  Score=124.62  Aligned_cols=77  Identities=25%  Similarity=0.508  Sum_probs=71.5

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          189 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       189 e~~srtLfV~NLP~~-vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      ....++|||+|||.+ +++++|+++|++||+|..|.+   ++|||||+|.+.++|++|++.|++..+.|++|+|.++.+.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            345689999999999 999999999999999999987   7899999999999999999999999999999999999754


Q ss_pred             C
Q 003400          268 D  268 (823)
Q Consensus       268 ~  268 (823)
                      .
T Consensus       101 ~  101 (110)
T 1wf1_A          101 K  101 (110)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=2e-13  Score=123.03  Aligned_cols=83  Identities=20%  Similarity=0.436  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE--eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~--~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ...+.++|||+|||.++++++|+++|+.|+.|..+.  .+++++|||||+|.+.++|++|++.|++..|.|+.|+|.|+.
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            345789999999999999999999999998877765  356789999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 003400          266 PKDNP  270 (823)
Q Consensus       266 pk~~~  270 (823)
                      ++...
T Consensus        91 ~~~~~   95 (102)
T 2fc8_A           91 PKGEG   95 (102)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            76543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=2e-13  Score=123.90  Aligned_cols=80  Identities=33%  Similarity=0.473  Sum_probs=72.8

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++. ++..|.|+.|+|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            345679999999999999999999999999999876     355689999999999999999998 99999999999999


Q ss_pred             cCCCcc
Q 003400          349 SRPGGA  354 (823)
Q Consensus       349 s~~~~~  354 (823)
                      ++++..
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            988754

>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=6e-13  Score=124.54  Aligned_cols=79  Identities=20%  Similarity=0.288  Sum_probs=72.4

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++.
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            34579999999999999999999999999999976    34578999999999999999999999999999999999998


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      +..
T Consensus       113 ~~~  115 (124)
T 2kt5_A          113 SQI  115 (124)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            753

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.43  E-value=1e-13  Score=128.35  Aligned_cols=77  Identities=10%  Similarity=0.097  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCC-CEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG-~I~~v~~-~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ...++|||+|||+++++++|+++|++|| +|..+.+ ..+++|||||+|.+.++|++|++.|+|..+.|++|+|.++..
T Consensus        26 ~~~~~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           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            3468999999999999999999999999 8999986 467899999999999999999999999999999999999864

>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=99.43  E-value=2.1e-13  Score=119.60  Aligned_cols=76  Identities=24%  Similarity=0.452  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|+ .|++..+.|++|.|.++.
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            4689999999999999999999999999999874     5667999999999999999999 899999999999999987


Q ss_pred             CC
Q 003400          266 PK  267 (823)
Q Consensus       266 pk  267 (823)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>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=2.1e-13  Score=134.24  Aligned_cols=77  Identities=23%  Similarity=0.295  Sum_probs=70.5

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-CCcccEEEEEEcCHHHHHHHHHHhCCCccCC--ceEEEEecCCCc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-PHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGG  353 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G--r~I~V~~s~~~~  353 (823)
                      ..+|||+||++.+|+++|+++|++||+|++|++. ..+++||||+|.+.++|++|++.|||..|.|  ++|+|+|++++.
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            3579999999999999999999999999999874 4457899999999999999999999999965  999999999874

>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=99.43  E-value=3.5e-13  Score=131.25  Aligned_cols=81  Identities=25%  Similarity=0.410  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|.|.|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            356799999999999999999999999999999985     466889999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 003400          264 SIPKDN  269 (823)
Q Consensus       264 a~pk~~  269 (823)
                      +.+...
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            976543

>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=2.3e-13  Score=124.11  Aligned_cols=77  Identities=10%  Similarity=0.185  Sum_probs=70.5

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ....++|||+|||.++|+++|+++|++||.|.+|++.    +.++|||||+|.+.++|.+|+. ++|..+.|+.|.|.++
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3456799999999999999999999999999999763    5679999999999999999999 9999999999999987


Q ss_pred             CC
Q 003400          350 RP  351 (823)
Q Consensus       350 ~~  351 (823)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            65

>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=5.9e-13  Score=119.18  Aligned_cols=79  Identities=19%  Similarity=0.335  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      ...+.++|||+||  ++++++|+++|++||+|..|.+ .+++|||||+|.+.++|++|++.|++..+.|++|+|.|+.++
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            3457799999996  8999999999999999999987 578999999999999999999999999999999999999876


Q ss_pred             CC
Q 003400          268 DN  269 (823)
Q Consensus       268 ~~  269 (823)
                      ..
T Consensus        88 ~~   89 (97)
T 1x5p_A           88 PM   89 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.43  E-value=1.4e-13  Score=117.04  Aligned_cols=70  Identities=20%  Similarity=0.340  Sum_probs=65.3

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      +|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++ |||..+.|++|+|++|
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            5899999999999999999999999999976     45678999999999999999998 9999999999999875

>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=99.43  E-value=6e-13  Score=122.47  Aligned_cols=80  Identities=16%  Similarity=0.314  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcc--------c
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPL--------R  255 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l--------~  255 (823)
                      .+.+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|+|..+        .
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            3456799999999999999999999999999999884    456789999999999999999999999999        4


Q ss_pred             cccccccccCCC
Q 003400          256 RRKLDIHFSIPK  267 (823)
Q Consensus       256 gr~L~V~~a~pk  267 (823)
                      +++|.|.|+.|+
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            677888888653

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.43  E-value=2.9e-13  Score=123.31  Aligned_cols=80  Identities=14%  Similarity=0.296  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEcCCCCCC------CHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCccccc-
Q 003400          188 GEHPSRTLFVRNINSNV------EDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRR-  257 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~v------teeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr-  257 (823)
                      .....++|||+|||..+      ++++|+++|++||.|..|++   +++++|||||+|.+.++|++|++.|+|..+.|+ 
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            34457899999999999      78999999999999999985   457889999999999999999999999999998 


Q ss_pred             cccccccCCC
Q 003400          258 KLDIHFSIPK  267 (823)
Q Consensus       258 ~L~V~~a~pk  267 (823)
                      +|.|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999998643

>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=99.43  E-value=2.9e-13  Score=123.44  Aligned_cols=79  Identities=20%  Similarity=0.245  Sum_probs=72.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCc-eEEEEeC------CCcccEEEEEEcCHHHHHHHHHHhC--CCccCCceEEE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRET------PHKRHHKFIEFYDVRAAEAALKSLN--RSDIAGKRIKL  346 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~-I~~iri~------~~srG~aFVeF~d~e~A~kAl~~Ln--G~~i~Gr~I~V  346 (823)
                      ..++|||+|||.++++++|+++|++||. |..|++.      +.++|||||+|.+.++|++|++.|+  +..+.|+.|+|
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            4579999999999999999999999998 9999874      3678999999999999999999996  58999999999


Q ss_pred             EecCCCcc
Q 003400          347 EPSRPGGA  354 (823)
Q Consensus       347 ~~s~~~~~  354 (823)
                      ++++++..
T Consensus        87 ~~a~~~~~   94 (109)
T 2dis_A           87 DWAEPEID   94 (109)
T ss_dssp             EESCSSCS
T ss_pred             EEcCCCCC
Confidence            99988654

>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=1.2e-13  Score=122.79  Aligned_cols=76  Identities=20%  Similarity=0.241  Sum_probs=67.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...+|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+++.
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            3479999999999999999999999999875543     45678999999999999999999999999999999999986


Q ss_pred             C
Q 003400          351 P  351 (823)
Q Consensus       351 ~  351 (823)
                      +
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=99.42  E-value=3.7e-13  Score=117.75  Aligned_cols=75  Identities=27%  Similarity=0.401  Sum_probs=67.8

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++ +++..+.|+.|+|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            345679999999999999999999999999999976     36678999999999999999996 588899999999987


Q ss_pred             c
Q 003400          349 S  349 (823)
Q Consensus       349 s  349 (823)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.42  E-value=1.6e-13  Score=134.43  Aligned_cols=78  Identities=13%  Similarity=0.209  Sum_probs=71.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccC--ceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG--~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ...+|||+|||+++|+++|+++|++||  .|.+|++     ++.++|||||+|.+.++|++||+.|||..|.|+.|+|++
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            346999999999999999999999999  9999976     567899999999999999999999999999999999999


Q ss_pred             cCCCc
Q 003400          349 SRPGG  353 (823)
Q Consensus       349 s~~~~  353 (823)
                      +.++.
T Consensus       134 a~~~~  138 (156)
T 3n9u_C          134 ATRQN  138 (156)
T ss_dssp             CCHHH
T ss_pred             cCCCc
Confidence            98754

>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=99.42  E-value=5.5e-13  Score=122.71  Aligned_cols=78  Identities=21%  Similarity=0.284  Sum_probs=70.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCcc--------CCc
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI--------AGK  342 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i--------~Gr  342 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++.|||..|        .++
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            35679999999999999999999999999999976    355789999999999999999999999999        578


Q ss_pred             eEEEEecCCC
Q 003400          343 RIKLEPSRPG  352 (823)
Q Consensus       343 ~I~V~~s~~~  352 (823)
                      +|+|+|++++
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            8999999865

>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=99.42  E-value=2.9e-13  Score=118.44  Aligned_cols=76  Identities=18%  Similarity=0.390  Sum_probs=68.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      .+.+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++ +++..+.|++|.|+
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            4457899999999999999999999999999999984     46789999999999999999997 58888999999998


Q ss_pred             cc
Q 003400          263 FS  264 (823)
Q Consensus       263 ~a  264 (823)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.42  E-value=1.3e-13  Score=130.72  Aligned_cols=79  Identities=23%  Similarity=0.381  Sum_probs=71.6

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEE--EEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCC----ccCCc
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--IRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRS----DIAGK  342 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~--iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~----~i~Gr  342 (823)
                      ....++|||+|||+++|+++|+++|++||.|..  |++     ++.++|||||+|.+. +|.+|++.|||.    .+.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            345679999999999999999999999999966  654     567899999999999 999999999999    99999


Q ss_pred             eEEEEecCCCc
Q 003400          343 RIKLEPSRPGG  353 (823)
Q Consensus       343 ~I~V~~s~~~~  353 (823)
                      .|+|+++++..
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999998764

>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=2.1e-13  Score=124.32  Aligned_cols=77  Identities=12%  Similarity=0.314  Sum_probs=70.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +.+.++|||+|||.++|+++|+++|++||+|.+|.+    .++++|||||+|.+.++|++|+. +++..+.|+.|.|.++
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            345799999999999999999999999999999984    26789999999999999999999 8999999999999986


Q ss_pred             CC
Q 003400          265 IP  266 (823)
Q Consensus       265 ~p  266 (823)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            43

>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=99.42  E-value=1.4e-13  Score=123.09  Aligned_cols=79  Identities=20%  Similarity=0.270  Sum_probs=70.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      .....++|||+|||.++++++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++.|++..|.|++|+|+
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            345678999999999999999999999999986433     256689999999999999999999999999999999999


Q ss_pred             ccCC
Q 003400          263 FSIP  266 (823)
Q Consensus       263 ~a~p  266 (823)
                      ++..
T Consensus        91 ~a~~   94 (98)
T 2cqp_A           91 LGSG   94 (98)
T ss_dssp             ESSC
T ss_pred             EcCC
Confidence            9864

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=1.8e-13  Score=126.53  Aligned_cols=78  Identities=17%  Similarity=0.315  Sum_probs=71.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++||+. ++..|.|+.|+|++++
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            4579999999999999999999999999999976     345689999999999999999997 9999999999999998


Q ss_pred             CCcc
Q 003400          351 PGGA  354 (823)
Q Consensus       351 ~~~~  354 (823)
                      ++..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            8754

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=9.3e-14  Score=121.03  Aligned_cols=76  Identities=21%  Similarity=0.371  Sum_probs=69.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|.+++
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            3569999999999999999999999999999976     35568999999999999999999999999999999888765


Q ss_pred             C
Q 003400          351 P  351 (823)
Q Consensus       351 ~  351 (823)
                      .
T Consensus        84 s   84 (85)
T 1x4e_A           84 S   84 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.41  E-value=2.1e-13  Score=133.64  Aligned_cols=78  Identities=15%  Similarity=0.254  Sum_probs=70.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCC--CEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYG--DIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG--~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...++|||+|||.++|+++|+++|++||  .|.+|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|.|.
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  9999884     57889999999999999999999999999999999999


Q ss_pred             ccCCC
Q 003400          263 FSIPK  267 (823)
Q Consensus       263 ~a~pk  267 (823)
                      ++.++
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98653

>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=99.41  E-value=1.2e-13  Score=122.86  Aligned_cols=77  Identities=19%  Similarity=0.235  Sum_probs=67.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++++++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++.|++..|.|++|+|.+
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            34569999999999999999999999999986543     2457889999999999999999999999999999999998


Q ss_pred             cC
Q 003400          264 SI  265 (823)
Q Consensus       264 a~  265 (823)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.41  E-value=4.4e-13  Score=127.31  Aligned_cols=77  Identities=23%  Similarity=0.333  Sum_probs=70.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccE-EEEEeCCHHHHHHHHHHhcCCcccc--ccccccccCCCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGF-VMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPKDN  269 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~-AFV~F~~~e~A~~Ai~~Lng~~l~g--r~L~V~~a~pk~~  269 (823)
                      -.|||+||+..+|+++|+++|++||+|.+|++..+.+|| |||+|.+.++|++|++.|+|..|.+  ++|+|+|++++..
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            467799999999999999999999999999876677888 9999999999999999999999988  8999999987654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.41  E-value=1.5e-13  Score=118.96  Aligned_cols=69  Identities=16%  Similarity=0.248  Sum_probs=63.8

Q ss_pred             cceeeecCCCCC------CHHHHHHHhcccCceEEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCc-eEEE
Q 003400          278 GTLVVFNLDPSV------SNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK-RIKL  346 (823)
Q Consensus       278 ~tLfV~NLp~~v------teedL~~~Fs~fG~I~~iri~---~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr-~I~V  346 (823)
                      ++|||+|||..+      ++++|+++|++||.|.+|++.   +.++|||||+|.+.++|++|++.|||..+.|+ +|+|
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      679999999999999999763   46789999999999999999999999999999 8876

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.41  E-value=5.1e-13  Score=125.02  Aligned_cols=82  Identities=22%  Similarity=0.422  Sum_probs=74.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ...+.++|||+|||.++++++|+++|++||+|..|++    +++++|||||+|.+.++|++|++.|++..+.|++|+|.+
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            3456799999999999999999999999999999885    456889999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 003400          264 SIPKDN  269 (823)
Q Consensus       264 a~pk~~  269 (823)
                      +.+...
T Consensus       111 a~~~~~  116 (124)
T 2kt5_A          111 VASQID  116 (124)
T ss_dssp             ECCTTC
T ss_pred             eCCCCC
Confidence            976543

>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=7.6e-13  Score=117.90  Aligned_cols=78  Identities=18%  Similarity=0.177  Sum_probs=70.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEE-eC-CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ET-PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir-i~-~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ..++|||+|||.++++++|+++|++||.|..|+ +. ....+.|||+|.+.++|++|++.|||..+.|++|+|+++.++.
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 43 3345669999999999999999999999999999999998874

>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=2.5e-13  Score=119.53  Aligned_cols=75  Identities=13%  Similarity=0.304  Sum_probs=70.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ...+|||+|||.++++++|+++|++| .|.++++. .++|||||+|.+.++|++|++.|||..+.|++|+|+++..+
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 99999885 78999999999999999999999999999999999998664

>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=99.41  E-value=7.6e-13  Score=119.56  Aligned_cols=81  Identities=15%  Similarity=0.318  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++  ++..+.|+.|.|.
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            4457799999999999999999999999999999874     46789999999999999999999  4778999999999


Q ss_pred             ccCCCCCC
Q 003400          263 FSIPKDNP  270 (823)
Q Consensus       263 ~a~pk~~~  270 (823)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99876543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.41  E-value=5.1e-13  Score=126.01  Aligned_cols=74  Identities=26%  Similarity=0.280  Sum_probs=67.9

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccE-EEEEEcCHHHHHHHHHHhCCCccCC--ceEEEEecCCCc
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-KFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGG  353 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~-aFVeF~d~e~A~kAl~~LnG~~i~G--r~I~V~~s~~~~  353 (823)
                      .|||+||++.+++++|+++|++||.|.+|++..+ .|+ |||+|.+.++|.+|++.|||..|.|  +.|+|++++++.
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            4789999999999999999999999999988544 486 9999999999999999999999988  699999999875

>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=99.41  E-value=2.4e-13  Score=125.05  Aligned_cols=80  Identities=18%  Similarity=0.283  Sum_probs=72.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHH---HHhhcCCCEEEEEeC--------CCcccEEEEEeCCHHHHHHHHHHhcCCccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELR---ALFEQYGDIRTLYTA--------CKHRGFVMISYYDIRAARTAMRALQNKPLRRR  257 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr---~lFs~fG~I~~v~~~--------~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr  257 (823)
                      ....++|||+|||.++++++|+   ++|++||+|..|++.        .+++|||||+|.+.++|++|++.|++..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3467899999999999999999   999999999999852        24569999999999999999999999999999


Q ss_pred             cccccccCCCC
Q 003400          258 KLDIHFSIPKD  268 (823)
Q Consensus       258 ~L~V~~a~pk~  268 (823)
                      +|+|.|+.++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999998764

>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=1.8e-13  Score=120.46  Aligned_cols=75  Identities=16%  Similarity=0.374  Sum_probs=70.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      +..++|||+|||.++++++|+++|++| +|..|++. +++|||||+|.+.++|++|++.|+|..+.|++|+|.++..
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            467899999999999999999999999 99998874 7899999999999999999999999999999999999854

>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=99.41  E-value=1.1e-13  Score=122.00  Aligned_cols=75  Identities=21%  Similarity=0.439  Sum_probs=67.2

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEeC-----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ++|||+|||.++++++|+++|++||.|.+|++.     +.++|||||+|.+.+ |++|++.|||..+.|+.|+|+++.+.
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            479999999999999999999999999999863     567899999999999 99999999999999999999999875


Q ss_pred             c
Q 003400          353 G  353 (823)
Q Consensus       353 ~  353 (823)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=5.8e-13  Score=117.59  Aligned_cols=77  Identities=19%  Similarity=0.270  Sum_probs=70.4

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ....+|||+|||.++++++|+++|+.| .|..|++    ++.++|||||+|.+.++|++|++ |||..|.|+.|+|.+++
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEES
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECC
Confidence            346799999999999999999999999 8988876    45678999999999999999999 99999999999999998


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      ++.
T Consensus        86 ~~~   88 (91)
T 2dgw_A           86 SGP   88 (91)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            764

>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=1.1e-13  Score=121.94  Aligned_cols=76  Identities=21%  Similarity=0.414  Sum_probs=67.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      ++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.+ |++|++.|+|..+.|++|+|.++.+.
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            68999999999999999999999999999985     3677999999999999 99999999999999999999999765


Q ss_pred             CC
Q 003400          268 DN  269 (823)
Q Consensus       268 ~~  269 (823)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.40  E-value=3.8e-13  Score=123.52  Aligned_cols=81  Identities=16%  Similarity=0.401  Sum_probs=69.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.+ +..+.|+.|.|.
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            3456799999999999999999999999999999985     3677999999999999999999976 588999999999


Q ss_pred             ccCCCCC
Q 003400          263 FSIPKDN  269 (823)
Q Consensus       263 ~a~pk~~  269 (823)
                      ++.++..
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9987653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.40  E-value=2.2e-13  Score=115.76  Aligned_cols=70  Identities=16%  Similarity=0.401  Sum_probs=65.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       194 tLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +|||+|||.++++++|+++|++||+|..|.+     +++++|||||+|.+.++|++|++ +++..+.|++|.|++|
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            5899999999999999999999999999874     46678999999999999999998 9999999999999875

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.40  E-value=8.5e-13  Score=125.41  Aligned_cols=76  Identities=26%  Similarity=0.437  Sum_probs=69.4

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|++
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345679999999999999999999999999999986     345789999999999999999999999999999999998


Q ss_pred             c
Q 003400          349 S  349 (823)
Q Consensus       349 s  349 (823)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=5.2e-13  Score=117.88  Aligned_cols=78  Identities=9%  Similarity=0.215  Sum_probs=71.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ....++|||+|||.++++++|+++|++| .|..|++    +++++|||||+|.+.++|++|++ |++..|.|+.|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            4567999999999999999999999999 8988874    46679999999999999999999 9999999999999999


Q ss_pred             CCCC
Q 003400          265 IPKD  268 (823)
Q Consensus       265 ~pk~  268 (823)
                      .++.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7653

>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=4.5e-13  Score=124.45  Aligned_cols=78  Identities=17%  Similarity=0.313  Sum_probs=70.3

Q ss_pred             CCCCCcEEEE--cCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcc-----cccccc
Q 003400          188 GEHPSRTLFV--RNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL-----RRRKLD  260 (823)
Q Consensus       188 ~e~~srtLfV--~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l-----~gr~L~  260 (823)
                      ...++++|||  +||+.++++++|+++|++||+|..|.+. ..+|||||+|.+.++|++|++.|+|..+     .+++|+
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            3457899999  6699999999999999999999999764 4689999999999999999999999988     689999


Q ss_pred             ccccCC
Q 003400          261 IHFSIP  266 (823)
Q Consensus       261 V~~a~p  266 (823)
                      |.|+..
T Consensus       100 v~~a~~  105 (114)
T 2cq2_A          100 LNFVEK  105 (114)
T ss_dssp             EEEESC
T ss_pred             EEeccc
Confidence            999863

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.40  E-value=6.8e-13  Score=126.07  Aligned_cols=77  Identities=26%  Similarity=0.490  Sum_probs=70.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.
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            4457899999999999999999999999999999985     35689999999999999999999999999999999998


Q ss_pred             cc
Q 003400          263 FS  264 (823)
Q Consensus       263 ~a  264 (823)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>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=118.31  Aligned_cols=79  Identities=20%  Similarity=0.365  Sum_probs=70.8

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ....++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++  ++..|.|+.|+|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            345679999999999999999999999999999976     35678999999999999999999  57899999999999


Q ss_pred             cCCCcc
Q 003400          349 SRPGGA  354 (823)
Q Consensus       349 s~~~~~  354 (823)
                      ++++..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            988653

>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=1.9e-13  Score=123.08  Aligned_cols=79  Identities=23%  Similarity=0.328  Sum_probs=70.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEE----EeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~i----ri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ...+|||+|||.++++++|+++|++||.|..+    +.++.++|||||+|.+.++|++|++ |||..|.|+.|+|+++++
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            46799999999999999999999999987652    2346789999999999999999999 999999999999999988


Q ss_pred             Cccc
Q 003400          352 GGAR  355 (823)
Q Consensus       352 ~~~r  355 (823)
                      +..+
T Consensus        95 ~~~~   98 (101)
T 1fj7_A           95 RDGT   98 (101)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7654

>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=99.39  E-value=1.3e-13  Score=126.98  Aligned_cols=77  Identities=17%  Similarity=0.381  Sum_probs=71.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC-----CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~-----~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++.     ++++|||||+|.+.++|++|+ .|++..|.|+.|.|.++
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            456899999999999999999999999999999853     678999999999999999999 89999999999999998


Q ss_pred             CCC
Q 003400          265 IPK  267 (823)
Q Consensus       265 ~pk  267 (823)
                      .++
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            654

>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=99.39  E-value=8.5e-13  Score=119.98  Aligned_cols=79  Identities=11%  Similarity=0.196  Sum_probs=71.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEE-EEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT-LYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~-v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++|+++|+++|++||.|.. |.+    +++++|||||+|.+.++|++|++. ++..+.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            346789999999999999999999999999987 653    577899999999999999999997 99999999999998


Q ss_pred             cCCCC
Q 003400          264 SIPKD  268 (823)
Q Consensus       264 a~pk~  268 (823)
                      +.++.
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            86543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.39  E-value=9.6e-13  Score=117.23  Aligned_cols=79  Identities=23%  Similarity=0.294  Sum_probs=71.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-e-CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-T-ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-~-~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      ...++|||+|||.++++++|+++|++||.|..|+ + ..+..+.|||+|.+.++|++|++.|+|..+.|++|+|.++.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcc
Confidence            4578999999999999999999999999999994 3 4445566999999999999999999999999999999999876


Q ss_pred             C
Q 003400          268 D  268 (823)
Q Consensus       268 ~  268 (823)
                      .
T Consensus        93 ~   93 (96)
T 2e44_A           93 M   93 (96)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.39  E-value=1.8e-12  Score=115.36  Aligned_cols=79  Identities=16%  Similarity=0.301  Sum_probs=69.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~  269 (823)
                      ...++|||+|||.++++++|+++|++||.|..|........||||+|.+.++|++|++ |++..|.|+.|.|.++.++..
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            4568999999999999999999999999999985433222299999999999999999 999999999999999876544

>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=3e-13  Score=121.82  Aligned_cols=80  Identities=16%  Similarity=0.230  Sum_probs=70.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ..+.++|||+|||.++++++|+++|++||.|..+.    .+++++|||||+|.+.++|++|++ |++..+.|+.|+|.++
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            34678999999999999999999999999775521    356789999999999999999999 9999999999999999


Q ss_pred             CCCCC
Q 003400          265 IPKDN  269 (823)
Q Consensus       265 ~pk~~  269 (823)
                      .++..
T Consensus        93 ~~~~~   97 (101)
T 1fj7_A           93 KGRDG   97 (101)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87553

>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=99.39  E-value=1.3e-12  Score=118.82  Aligned_cols=78  Identities=23%  Similarity=0.293  Sum_probs=70.4

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEE-EEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~-iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ....+|||+|||+++|+++|+++|++||.|.. |++    +++++|||||+|.+.++|++||+. ++..+.|+.|+|.++
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            34579999999999999999999999999987 765    567899999999999999999997 999999999999998


Q ss_pred             CCCc
Q 003400          350 RPGG  353 (823)
Q Consensus       350 ~~~~  353 (823)
                      .+..
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.38  E-value=2.7e-13  Score=115.58  Aligned_cols=71  Identities=27%  Similarity=0.417  Sum_probs=66.0

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ++|||+|||.++++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++.++ ..+.|++|+|+++
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            47999999999999999999999999999876     35568999999999999999999999 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=99.38  E-value=1.2e-12  Score=128.90  Aligned_cols=79  Identities=20%  Similarity=0.244  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC-CCcccEEEEEeCCHHHHHHHHHHhcCCcccc--ccccccccCCCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-CKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPKD  268 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~-~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g--r~L~V~~a~pk~  268 (823)
                      ..+|||+||+..+|+++|+++|++||+|++|++. .+.+|||||+|.+.++|++|++.|+|..|.+  ++|+|+|++++.
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            4578999999999999999999999999999864 4467899999999999999999999999965  999999998875


Q ss_pred             CC
Q 003400          269 NP  270 (823)
Q Consensus       269 ~~  270 (823)
                      ..
T Consensus       126 l~  127 (164)
T 1sjr_A          126 LN  127 (164)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=1e-12  Score=117.25  Aligned_cols=75  Identities=17%  Similarity=0.344  Sum_probs=66.9

Q ss_pred             CCCcE-EEEcCCCCCCCHHH----HHHHhhcC-CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          190 HPSRT-LFVRNINSNVEDSE----LRALFEQY-GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       190 ~~srt-LfV~NLP~~vteee----Lr~lFs~f-G~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      .|+.| |||+|||.++++++    |+++|++| |+|.+|  ++   |+|||.|.+.++|++|++.|+|..+.|++|+|.|
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            35666 99999999999988    55899999 599998  23   9999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 003400          264 SIPKDN  269 (823)
Q Consensus       264 a~pk~~  269 (823)
                      +..+.+
T Consensus        81 A~~~sd   86 (96)
T 2diu_A           81 TPKNRE   86 (96)
T ss_dssp             SCCSCC
T ss_pred             cCCCcc
Confidence            987654

>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=1.1e-12  Score=116.22  Aligned_cols=76  Identities=25%  Similarity=0.394  Sum_probs=63.7

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCc--cCCceEEEEecCCC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD--IAGKRIKLEPSRPG  352 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~--i~Gr~I~V~~s~~~  352 (823)
                      ....+|||+|||+++|+++|+++|++||.|.+|++...++|||||+|.+.++|++    |+|..  +.|++|.|.+++++
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            3457999999999999999999999999999999987789999999999999983    56664  45999999999886


Q ss_pred             cc
Q 003400          353 GA  354 (823)
Q Consensus       353 ~~  354 (823)
                      ..
T Consensus        85 ~~   86 (89)
T 3d2w_A           85 HN   86 (89)
T ss_dssp             --
T ss_pred             Cc
Confidence            54

>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=99.37  E-value=9.4e-13  Score=122.04  Aligned_cols=75  Identities=21%  Similarity=0.294  Sum_probs=66.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce-----EEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR-----IKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~-----I~V~~s~  350 (823)
                      ...+|||+|||.++++++|+++|++||.|..|++...  |||||+|.+.++|++||+.|||..|.|+.     |+|+.+.
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            3568999999999999999999999999999998644  99999999999999999999999999998     7777665


Q ss_pred             CC
Q 003400          351 PG  352 (823)
Q Consensus       351 ~~  352 (823)
                      +.
T Consensus        93 ~~   94 (115)
T 3beg_B           93 PR   94 (115)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.37  E-value=9.3e-13  Score=123.03  Aligned_cols=77  Identities=18%  Similarity=0.371  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      +.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|+ .|+|..|.|+.|.|.++.
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            4689999999999999999999999999999874     5678999999999999999999 799999999999999987


Q ss_pred             CCC
Q 003400          266 PKD  268 (823)
Q Consensus       266 pk~  268 (823)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.37  E-value=2.4e-13  Score=115.88  Aligned_cols=71  Identities=17%  Similarity=0.430  Sum_probs=66.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ++|||+|||.++++++|+++|++||+|..|.+     +++++|||||+|.+.++|++|++.++ ..+.|++|.|+++
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            57999999999999999999999999998874     46679999999999999999999998 9999999999886

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.37  E-value=1.2e-12  Score=116.75  Aligned_cols=73  Identities=26%  Similarity=0.383  Sum_probs=65.4

Q ss_pred             ccceeeecCCCCCCHHH----HHHHhccc-CceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNED----LRQIFGAY-GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteed----L~~~Fs~f-G~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      .++|||.|||.++++++    |+++|++| |+|.+|  ++   |+|||+|.+.++|.+|++.|||..+.||+|+|.+++.
T Consensus         9 ~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCC
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCC
Confidence            33499999999999988    55899999 599988  33   9999999999999999999999999999999999987


Q ss_pred             Ccc
Q 003400          352 GGA  354 (823)
Q Consensus       352 ~~~  354 (823)
                      +..
T Consensus        84 ~sd   86 (96)
T 2diu_A           84 NRE   86 (96)
T ss_dssp             SCC
T ss_pred             Ccc
Confidence            653

>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=99.37  E-value=1e-12  Score=129.37  Aligned_cols=84  Identities=20%  Similarity=0.420  Sum_probs=74.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       186 ~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      +....+.++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|+|..|.|++|.
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            334567789999999999999999999999999999884     456789999999999999999999999999999999


Q ss_pred             ccccCCCCC
Q 003400          261 IHFSIPKDN  269 (823)
Q Consensus       261 V~~a~pk~~  269 (823)
                      |.|+.++..
T Consensus       146 V~~a~~~~~  154 (165)
T 1rk8_A          146 VDWCFVKGP  154 (165)
T ss_dssp             EEESEECC-
T ss_pred             EEEecCCCC
Confidence            999976553

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=7.2e-13  Score=122.46  Aligned_cols=80  Identities=19%  Similarity=0.437  Sum_probs=72.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++. ++..|.|+.|.|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            34589999999999999999999999999999874     356789999999999999999997 999999999999999


Q ss_pred             CCCCCC
Q 003400          265 IPKDNP  270 (823)
Q Consensus       265 ~pk~~~  270 (823)
                      .++...
T Consensus       104 ~~~~~~  109 (116)
T 1x4b_A          104 VAREES  109 (116)
T ss_dssp             SSCCCC
T ss_pred             CCCccC
Confidence            877543

>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=99.36  E-value=1.1e-12  Score=116.07  Aligned_cols=76  Identities=24%  Similarity=0.475  Sum_probs=63.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcc--ccccccccccCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL--RRRKLDIHFSIP  266 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l--~gr~L~V~~a~p  266 (823)
                      ..+..+|||+|||.++|+++|+++|++||+|.+|++...++|||||+|.+.++|++    +++..+  .|++|.|.++.+
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~   83 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEP   83 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC-
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCC
Confidence            45779999999999999999999999999999999877799999999999999984    455554  589999999987


Q ss_pred             CC
Q 003400          267 KD  268 (823)
Q Consensus       267 k~  268 (823)
                      +.
T Consensus        84 k~   85 (89)
T 3d2w_A           84 KH   85 (89)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>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=1e-12  Score=122.11  Aligned_cols=76  Identities=20%  Similarity=0.253  Sum_probs=68.9

Q ss_pred             Cccceee--ecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCcc-----CCceEEEEe
Q 003400          276 NQGTLVV--FNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI-----AGKRIKLEP  348 (823)
Q Consensus       276 ~~~tLfV--~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i-----~Gr~I~V~~  348 (823)
                      ...+|||  +||+.++++++|+++|++||.|.+|.+.. .+|||||+|.+.++|++|++.|||+++     .|+.|.|.|
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 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEe
Confidence            4568999  66999999999999999999999998853 589999999999999999999999988     689999999


Q ss_pred             cCCC
Q 003400          349 SRPG  352 (823)
Q Consensus       349 s~~~  352 (823)
                      ++.-
T Consensus       103 a~~~  106 (114)
T 2cq2_A          103 VEKV  106 (114)
T ss_dssp             ESCC
T ss_pred             cccC
Confidence            8754

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.36  E-value=1.5e-12  Score=115.85  Aligned_cols=77  Identities=23%  Similarity=0.372  Sum_probs=67.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ...+|||+|||.++++++|+++|++||.|.+|........||||+|.+.++|++|+. |||..|.|+.|+|+++.++.
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            346999999999999999999999999999985433222299999999999999999 99999999999999887654

>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=99.36  E-value=1.2e-12  Score=125.62  Aligned_cols=81  Identities=19%  Similarity=0.378  Sum_probs=72.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEE----------EeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL----------YTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  258 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v----------~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~  258 (823)
                      ..++++|||+|||.++|+++|+++|++||.|..|          ..+++++|||||+|.+.++|.+|++.|+|..|.|++
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3577999999999999999999999999987652          246889999999999999999999999999999999


Q ss_pred             ccccccCCCCC
Q 003400          259 LDIHFSIPKDN  269 (823)
Q Consensus       259 L~V~~a~pk~~  269 (823)
                      |.|.|+.+...
T Consensus       122 l~V~~a~~~~~  132 (143)
T 3egn_A          122 MVVQFARSARP  132 (143)
T ss_dssp             CEEEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999976543

>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=99.35  E-value=1.3e-12  Score=125.40  Aligned_cols=80  Identities=28%  Similarity=0.380  Sum_probs=71.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEE--------E--EeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--------I--RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~--------i--ri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      ...+|||+|||.++|+++|+++|++||.|..        +  ..++.++|||||+|.+.++|.+|+..|||..|.|+.|+
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            4579999999999999999999999998865        3  24678899999999999999999999999999999999


Q ss_pred             EEecCCCccc
Q 003400          346 LEPSRPGGAR  355 (823)
Q Consensus       346 V~~s~~~~~r  355 (823)
                      |.++++...+
T Consensus       124 V~~a~~~~~~  133 (143)
T 3egn_A          124 VQFARSARPK  133 (143)
T ss_dssp             EEECCCSCC-
T ss_pred             EEECCCCCCc
Confidence            9999876543

>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=99.35  E-value=5.6e-13  Score=127.74  Aligned_cols=77  Identities=17%  Similarity=0.146  Sum_probs=69.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCc---eEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~---I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ...+|||+|||+++|+++|+++|++||.   |..|++    .++++|||||+|.+.++|++||+ |||..|.|+.|+|.+
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            4578999999999999999999999999   777765    35678999999999999999999 999999999999999


Q ss_pred             cCCCc
Q 003400          349 SRPGG  353 (823)
Q Consensus       349 s~~~~  353 (823)
                      +.++.
T Consensus       122 a~~~e  126 (136)
T 2hgl_A          122 SHRTE  126 (136)
T ss_dssp             CCHHH
T ss_pred             CChHH
Confidence            86543

>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=99.35  E-value=5.8e-13  Score=123.09  Aligned_cols=78  Identities=10%  Similarity=0.112  Sum_probs=70.3

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCce-EEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEV-KEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I-~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ....+|||+|||+++|+++|+++|+.||.| ..|++    ++.++|||||+|.+.++|++||+. |+..|.|+.|+|.++
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            356799999999999999999999999999 66765    356799999999999999999997 999999999999999


Q ss_pred             CCCc
Q 003400          350 RPGG  353 (823)
Q Consensus       350 ~~~~  353 (823)
                      .++.
T Consensus        92 ~~~~   95 (114)
T 2cpy_A           92 TLED   95 (114)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.34  E-value=2.9e-12  Score=120.82  Aligned_cols=78  Identities=17%  Similarity=0.265  Sum_probs=69.2

Q ss_pred             CCcE--EEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccE-EEEEeCCHHHHHHHHHHhcCCcccc--ccccccccC
Q 003400          191 PSRT--LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGF-VMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSI  265 (823)
Q Consensus       191 ~srt--LfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~-AFV~F~~~e~A~~Ai~~Lng~~l~g--r~L~V~~a~  265 (823)
                      ++++  |||+||+..+|+++|+++|++||+|.+|++..+ .|| |||+|.+.++|++|++.|+|..|.|  ++|+|.|++
T Consensus        22 ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           22 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             CCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            4554  679999999999999999999999999986544 486 9999999999999999999999987  689999998


Q ss_pred             CCCC
Q 003400          266 PKDN  269 (823)
Q Consensus       266 pk~~  269 (823)
                      ++..
T Consensus       101 ~~~l  104 (124)
T 2e5i_A          101 PTRL  104 (124)
T ss_dssp             CSCC
T ss_pred             CCcc
Confidence            7653

>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=99.34  E-value=6.3e-13  Score=116.75  Aligned_cols=78  Identities=24%  Similarity=0.456  Sum_probs=67.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~  269 (823)
                      .++++|||+|||.++++++|+++|++||+|..|++...++|||||+|.+.++|++|+..  ...+.+++|.|.++.++..
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            46799999999999999999999999999999998777899999999999999865432  3445899999999987654

>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=99.33  E-value=1.4e-12  Score=118.54  Aligned_cols=76  Identities=13%  Similarity=0.195  Sum_probs=67.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ...+|||+|||+++|+++|+++|++||.| +|++    +++++|||||+|.+.++|++||+ +|+..|.|+.|+|.++.+
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            45799999999999999999999999955 7765    46678999999999999999995 899999999999999876


Q ss_pred             Cc
Q 003400          352 GG  353 (823)
Q Consensus       352 ~~  353 (823)
                      ..
T Consensus        92 ~~   93 (102)
T 1wez_A           92 AG   93 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.33  E-value=1.8e-12  Score=117.78  Aligned_cols=78  Identities=9%  Similarity=0.212  Sum_probs=69.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ....++|||+|||.++|+++|+++|++||.| .|++    +++++|||||+|.+.++|++|++ +++..|.++.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            4567899999999999999999999999965 6663    56789999999999999999995 7999999999999988


Q ss_pred             CCCC
Q 003400          265 IPKD  268 (823)
Q Consensus       265 ~pk~  268 (823)
                      .+..
T Consensus        90 ~~~~   93 (102)
T 1wez_A           90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6544

>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=2e-12  Score=119.89  Aligned_cols=72  Identities=14%  Similarity=0.209  Sum_probs=63.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ...++|||+|||.++++++|+++|++||+|..|.+...  |||||+|.+.++|++||+.|++..|.|++|+|.|
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~   85 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   85 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEE
Confidence            45689999999999999999999999999999987544  9999999999999999999999999999955444

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.33  E-value=9e-13  Score=122.82  Aligned_cols=76  Identities=18%  Similarity=0.172  Sum_probs=68.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCc---eEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~---I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ...+|||+|||+++|+++|+++|+.||.   |..|++    .++++|||||+|.+.++|++||+ |||..|.|+.|+|.+
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            4578999999999999999999999998   777765    35678999999999999999999 999999999999999


Q ss_pred             cCCC
Q 003400          349 SRPG  352 (823)
Q Consensus       349 s~~~  352 (823)
                      +.++
T Consensus        95 a~~~   98 (118)
T 2db1_A           95 SHRT   98 (118)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8643

>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=6.1e-13  Score=112.89  Aligned_cols=70  Identities=23%  Similarity=0.463  Sum_probs=64.6

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      +|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++. ++..+.|+.|+|+++
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            6999999999999999999999999999976     356789999999999999999994 899999999999875

>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=99.33  E-value=6.9e-13  Score=122.58  Aligned_cols=78  Identities=14%  Similarity=0.169  Sum_probs=70.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCE-EEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I-~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++|+++|+++|++||.| ..|++    +++++|||||+|.+.++|++|++. ++..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            4567999999999999999999999999999 66664    467899999999999999999996 99999999999999


Q ss_pred             cCCC
Q 003400          264 SIPK  267 (823)
Q Consensus       264 a~pk  267 (823)
                      +.++
T Consensus        91 a~~~   94 (114)
T 2cpy_A           91 VTLE   94 (114)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8654

>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=6.4e-13  Score=127.81  Aligned_cols=120  Identities=13%  Similarity=0.068  Sum_probs=69.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe
Q 003400          230 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE  309 (823)
Q Consensus       230 G~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri  309 (823)
                      |+||.+|.-++.+..++..+... ..+....-......  .........+|||+|||+++|+++|+++|++|| |.+|++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~~--~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i   77 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDSE--FTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHI   77 (139)
T ss_dssp             ----------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEEC
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCCcc--cCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEE
Confidence            56778888777777776654332 23322211111111  111223456999999999999999999999999 668876


Q ss_pred             ----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          310 ----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       310 ----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                          .++++|||||+|.+.++|++|| .+|+..|.|+.|+|..+.+...
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                3567899999999999999999 7999999999999999887653

>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=99.32  E-value=5.5e-13  Score=125.03  Aligned_cols=77  Identities=17%  Similarity=0.200  Sum_probs=68.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEE-E----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-R----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~i-r----i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...+|||+|||+++|+++|+++|+.||.|..+ .    .++.++|||||+|.+.++|++||+ |||..|.|+.|+|.++.
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            45799999999999999999999999998652 1    256779999999999999999999 99999999999999997


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      ++.
T Consensus       103 ~~~  105 (124)
T 1wel_A          103 KKG  105 (124)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.00  E-value=1.3e-13  Score=127.49  Aligned_cols=79  Identities=23%  Similarity=0.319  Sum_probs=71.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEE--------EEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--------IRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  342 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~--------iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr  342 (823)
                      ..++|||+|||.++++++|+++|++||.|..        |++     ++.++|||||+|.+.++|++|++.|||..+.|+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   85 (116)
Confidence            4579999999999999999999999999988        654     356789999999999999999999999999999


Q ss_pred             eEEEEecCCCcc
Q 003400          343 RIKLEPSRPGGA  354 (823)
Q Consensus       343 ~I~V~~s~~~~~  354 (823)
                      +|+|++++++..
T Consensus        86 ~l~V~~a~~~~~   97 (116)
T 2lcw_A           86 PIKVSFATRRAD   97 (116)
Confidence            999999987653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.00  E-value=1.3e-13  Score=127.48  Aligned_cols=82  Identities=22%  Similarity=0.370  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEE--------EEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT--------LYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~--------v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~  255 (823)
                      ..+.++|||+|||.++++++|+++|++||.|..        |++     +++++|||||+|.+.++|++|++.|++..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            457799999999999999999999999999988        553     3567899999999999999999999999999


Q ss_pred             cccccccccCCCCCC
Q 003400          256 RRKLDIHFSIPKDNP  270 (823)
Q Consensus       256 gr~L~V~~a~pk~~~  270 (823)
                      |++|.|.++.++...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999876543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.32  E-value=5.7e-13  Score=120.17  Aligned_cols=80  Identities=23%  Similarity=0.503  Sum_probs=71.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      .+.+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++  ++..+.|+.|.|.+
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            3456799999999999999999999999999999884    45688999999999999999999  88999999999999


Q ss_pred             cCCCCC
Q 003400          264 SIPKDN  269 (823)
Q Consensus       264 a~pk~~  269 (823)
                      +.++..
T Consensus        83 a~~~~~   88 (102)
T 2xs2_A           83 AIRKQN   88 (102)
T ss_dssp             EEECC-
T ss_pred             CCcCcc
Confidence            876543

>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=1.3e-12  Score=135.97  Aligned_cols=78  Identities=15%  Similarity=0.218  Sum_probs=71.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccC--ceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYG--EVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG--~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ...+|||+||++++|+++|+++|++||  .|++|++     +++++|||||+|.+.++|++||+.|||..|.|+.|+|++
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            356899999999999999999999999  9999976     567899999999999999999999999999999999999


Q ss_pred             cCCCc
Q 003400          349 SRPGG  353 (823)
Q Consensus       349 s~~~~  353 (823)
                      +++..
T Consensus       147 a~~~~  151 (229)
T 3q2s_C          147 VNKQF  151 (229)
T ss_dssp             CCHHH
T ss_pred             CCCCc
Confidence            98654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.31  E-value=3.3e-12  Score=117.79  Aligned_cols=74  Identities=16%  Similarity=0.260  Sum_probs=67.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ...+|||+|||+++|+++|+++|+.| .|..|++.    ++++|||||+|.+.++|++|| .||+..|.|+.|+|..+.+
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 88888763    567999999999999999999 6999999999999988754

>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=99.31  E-value=8.3e-13  Score=112.09  Aligned_cols=70  Identities=19%  Similarity=0.477  Sum_probs=64.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       194 tLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +|||+|||.++++++|+++|++||+|..|.+     +++++|||||+|.+.++|++|++. ++..+.|++|.|+++
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            6999999999999999999999999999874     367899999999999999999994 899999999999874

>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=1.1e-12  Score=119.91  Aligned_cols=78  Identities=15%  Similarity=0.102  Sum_probs=70.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCc---eEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGE---VKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~---I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~  347 (823)
                      ....+|||+|||+++|+++|+++|+.||.   |..|++.    +.++|||||+|.+.++|++||+ |||..++|+.|+|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVY   87 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEE
Confidence            35678999999999999999999999998   8888763    5678999999999999999999 99999999999999


Q ss_pred             ecCCCc
Q 003400          348 PSRPGG  353 (823)
Q Consensus       348 ~s~~~~  353 (823)
                      ++.++.
T Consensus        88 ~a~~~~   93 (107)
T 2lmi_A           88 EINNED   93 (107)
T ss_dssp             ECCHHH
T ss_pred             ECCHHH
Confidence            987643

>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=99.31  E-value=2.7e-12  Score=111.90  Aligned_cols=72  Identities=18%  Similarity=0.387  Sum_probs=66.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcC----C-------CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQY----G-------DIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  258 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~f----G-------~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~  258 (823)
                      ++.++|||+|||.++++++|+++|++|    |       .|.++++. +.+|||||+|.+.++|++|+ .|++..+.|++
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 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   81 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEC-SSSSEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEec-CCCcEEEEEcCCHHHHHHHH-hcCCCEECCeE
Confidence            467999999999999999999999999    8       99999764 45899999999999999999 99999999999


Q ss_pred             ccccc
Q 003400          259 LDIHF  263 (823)
Q Consensus       259 L~V~~  263 (823)
                      |+|+.
T Consensus        82 l~V~r   86 (87)
T 2hzc_A           82 LKIRR   86 (87)
T ss_dssp             CEEEC
T ss_pred             EEEeC
Confidence            99874

>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=99.30  E-value=6.1e-13  Score=124.70  Aligned_cols=77  Identities=9%  Similarity=0.176  Sum_probs=68.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEE---E--eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL---Y--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v---~--~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++|+++|+++|++||.|..+   .  .+++++|||||+|.+.++|++|++ |++..|.|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456899999999999999999999999998552   2  357789999999999999999999 999999999999999


Q ss_pred             cCC
Q 003400          264 SIP  266 (823)
Q Consensus       264 a~p  266 (823)
                      +.+
T Consensus       101 a~~  103 (124)
T 1wel_A          101 ITK  103 (124)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            854

>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=99.30  E-value=1.3e-12  Score=114.69  Aligned_cols=77  Identities=19%  Similarity=0.330  Sum_probs=66.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      ..++|||+|||.++++++|+++|++||.|.+|++...++|||||+|.+.++|++|+..  ...+.|++|+|.+++++..
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            3579999999999999999999999999999999777899999999999999764321  3355899999999988754

>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=99.30  E-value=1.9e-12  Score=134.62  Aligned_cols=76  Identities=16%  Similarity=0.237  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCC--CEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYG--DIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG--~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..++|||+|||.++|+++|+++|++||  +|.+|++     +++++|||||+|.+.++|++||+.|++..|.|++|+|.+
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            568999999999999999999999999  9999884     677899999999999999999999999999999999999


Q ss_pred             cCC
Q 003400          264 SIP  266 (823)
Q Consensus       264 a~p  266 (823)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            853

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.30  E-value=1.6e-12  Score=121.16  Aligned_cols=76  Identities=7%  Similarity=0.115  Sum_probs=68.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCC---EEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~---I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...++|||+|||.++|+++|+++|+.||.   |..|++    .++++|||||+|.+.++|++|++ +++..|.|+.|+|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEE
Confidence            45789999999999999999999999998   777663    46789999999999999999999 99999999999999


Q ss_pred             ccCC
Q 003400          263 FSIP  266 (823)
Q Consensus       263 ~a~p  266 (823)
                      ++.+
T Consensus        94 ~a~~   97 (118)
T 2db1_A           94 KSHR   97 (118)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8753

>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=99.29  E-value=5e-12  Score=110.19  Aligned_cols=71  Identities=21%  Similarity=0.383  Sum_probs=65.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhccc----C-------ceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAY----G-------EVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~f----G-------~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I  344 (823)
                      ..++|||+|||.++++++|+++|++|    |       .|.++++. ..+|||||+|.+.++|++|+ .|||..+.|+.|
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 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   82 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEC-SSSSEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEec-CCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEE
Confidence            45799999999999999999999999    8       89999885 45899999999999999999 999999999999


Q ss_pred             EEEe
Q 003400          345 KLEP  348 (823)
Q Consensus       345 ~V~~  348 (823)
                      +|+.
T Consensus        83 ~V~r   86 (87)
T 2hzc_A           83 KIRR   86 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9873

>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=99.29  E-value=6.3e-12  Score=127.31  Aligned_cols=114  Identities=13%  Similarity=0.160  Sum_probs=87.2

Q ss_pred             CHHHHHHHHHHh--cCCccccccccccccCCCCCCCC-----CCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC
Q 003400          238 DIRAARTAMRAL--QNKPLRRRKLDIHFSIPKDNPSD-----KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET  310 (823)
Q Consensus       238 ~~e~A~~Ai~~L--ng~~l~gr~L~V~~a~pk~~~~~-----~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~  310 (823)
                      +.+.+..|++..  ....+.+....|........+..     .....++|||+|||.++|+++|+++|++||.|..|++.
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            667888888866  34445555555554422221111     12345799999999999999999999999999999763


Q ss_pred             ----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          311 ----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       311 ----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                          +.++|||||+|.+.++|++|+..+ +..+.|+.|+|.+++.-
T Consensus       143 ~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          143 RTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             ECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             ECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence                567899999999999999999866 45999999999997653

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.29  E-value=4.1e-12  Score=126.96  Aligned_cols=80  Identities=23%  Similarity=0.439  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ...+.++|||+|||.++++++|+++|++||+|..|.+    +++++|||||+|.+.++|++|++.|++..|.|++|.|+|
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            3456789999999999999999999999999999985    356889999999999999999999999999999999999


Q ss_pred             cCCC
Q 003400          264 SIPK  267 (823)
Q Consensus       264 a~pk  267 (823)
                      +.+.
T Consensus       164 a~~~  167 (177)
T 2f3j_A          164 VASQ  167 (177)
T ss_dssp             ESSG
T ss_pred             ecCC
Confidence            8653

>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=99.29  E-value=1.9e-12  Score=118.34  Aligned_cols=77  Identities=9%  Similarity=0.036  Sum_probs=69.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCC---EEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~---I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....++|||+|||+++|+++|+++|+.||.   |..|++    .++++|||||+|.+.++|++|++ +++..+.|+.|+|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            346789999999999999999999999998   777763    36789999999999999999999 9999999999999


Q ss_pred             cccCC
Q 003400          262 HFSIP  266 (823)
Q Consensus       262 ~~a~p  266 (823)
                      .++.+
T Consensus        87 ~~a~~   91 (107)
T 2lmi_A           87 YEINN   91 (107)
T ss_dssp             EECCH
T ss_pred             EECCH
Confidence            98864

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.28  E-value=1.9e-12  Score=116.75  Aligned_cols=77  Identities=25%  Similarity=0.473  Sum_probs=70.0

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...++|||+|||.++++++|+++|++||.|..|++    ++.++|||||+|.+.++|++|++  +|..+.|+.|.|.++.
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            34579999999999999999999999999999976    45578999999999999999999  9999999999999987


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      ++.
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            654

>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=99.28  E-value=1.7e-12  Score=124.37  Aligned_cols=77  Identities=6%  Similarity=0.088  Sum_probs=69.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCC---EEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGD---IRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~---I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ....++|||+|||+++|+++|+++|++||.   |..|++    .++++|||||+|.+.++|++|++ +++..|.|+.|.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            346789999999999999999999999998   666653    46789999999999999999999 9999999999999


Q ss_pred             cccCC
Q 003400          262 HFSIP  266 (823)
Q Consensus       262 ~~a~p  266 (823)
                      .++.+
T Consensus       120 ~~a~~  124 (136)
T 2hgl_A          120 FKSHR  124 (136)
T ss_dssp             EECCH
T ss_pred             EECCh
Confidence            98753

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.28  E-value=6.8e-12  Score=125.36  Aligned_cols=78  Identities=21%  Similarity=0.297  Sum_probs=72.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ..++|||+|||..+++++|+++|++||.|..|++.    +.++|||||+|.+.++|++|++.|||..|.|+.|+|+++..
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            45799999999999999999999999999999873    55789999999999999999999999999999999999976


Q ss_pred             Cc
Q 003400          352 GG  353 (823)
Q Consensus       352 ~~  353 (823)
                      ..
T Consensus       167 ~~  168 (177)
T 2f3j_A          167 QI  168 (177)
T ss_dssp             GG
T ss_pred             CC
Confidence            53

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.27  E-value=9.6e-12  Score=129.93  Aligned_cols=101  Identities=16%  Similarity=0.206  Sum_probs=76.0

Q ss_pred             ccccccccccccCCCCCCCCCCCCccceeeecCCCCC---------CHHHHHHHhcccCceEEEEeCCCcccEEEEEEcC
Q 003400          253 PLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSV---------SNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYD  323 (823)
Q Consensus       253 ~l~gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~~v---------teedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d  323 (823)
                      .+.|+.....+..............++|||+||+..+         ++++|+++|++||.|.+|++. .++|||||+|.+
T Consensus       110 D~fGr~k~~~~~d~~~g~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~-~~kG~AFV~F~~  188 (240)
T 3u1l_A          110 DCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-ESKNCGFVKFKY  188 (240)
T ss_dssp             CTTSSBCGGGTC---------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESS
T ss_pred             ccccchhcccchhcccCcCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEE-CCCCEEEEEeCC
Confidence            3445554444433222112223456799999999998         799999999999999999986 468999999999


Q ss_pred             HHHHHHHHHHhCCCcc------------CCceEEEEecCCCcc
Q 003400          324 VRAAEAALKSLNRSDI------------AGKRIKLEPSRPGGA  354 (823)
Q Consensus       324 ~e~A~kAl~~LnG~~i------------~Gr~I~V~~s~~~~~  354 (823)
                      .++|+.|+++|+|..|            .|+.|.|+|++....
T Consensus       189 ~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          189 QANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             HHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             HHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCCC
Confidence            9999999999999999            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=8.7e-12  Score=130.24  Aligned_cols=81  Identities=21%  Similarity=0.374  Sum_probs=71.1

Q ss_pred             CCCCcEEEEcCCCCCC---------CHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcc-----
Q 003400          189 EHPSRTLFVRNINSNV---------EDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL-----  254 (823)
Q Consensus       189 e~~srtLfV~NLP~~v---------teeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l-----  254 (823)
                      ....++|||+||+..+         ++++|+++|++||+|.+|++. .++|||||+|.+.++|+.|+++|+|..|     
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            4578999999999998         799999999999999999864 5799999999999999999999999999     


Q ss_pred             -------ccccccccccCCCCCC
Q 003400          255 -------RRRKLDIHFSIPKDNP  270 (823)
Q Consensus       255 -------~gr~L~V~~a~pk~~~  270 (823)
                             .|+.|.|.|+.+..++
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                   8999999999876544

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.24  E-value=5e-12  Score=116.53  Aligned_cols=73  Identities=8%  Similarity=0.174  Sum_probs=66.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..++|||+|||.++|+++|+++|+.| .|..|++    .++++|||||+|.+.++|++|+ .+++..|.|+.|.|..+.
T Consensus        15 ~~~~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           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            45799999999999999999999999 8888874    3678999999999999999999 599999999999998764

>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=99.24  E-value=3.6e-12  Score=122.56  Aligned_cols=79  Identities=9%  Similarity=0.193  Sum_probs=68.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      .....++|||+|||.++|+++|+++|++|| |..|++    .++++|||||+|.+.++|++|+ .+++..|.++.|.|.+
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            345678999999999999999999999999 657774    3678999999999999999999 6899999999999998


Q ss_pred             cCCCC
Q 003400          264 SIPKD  268 (823)
Q Consensus       264 a~pk~  268 (823)
                      +.++.
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            87644

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.23  E-value=3.3e-12  Score=120.28  Aligned_cols=76  Identities=20%  Similarity=0.204  Sum_probs=66.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCce----EEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV----KEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I----~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~  347 (823)
                      ...+|||+|||+++|+++|+++|++||.|    ..|++    +++++|||||+|.+.++|++||+. |+..|.|+.|+|.
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            34689999999999999999999999975    45544    567899999999999999999996 9999999999999


Q ss_pred             ecCCC
Q 003400          348 PSRPG  352 (823)
Q Consensus       348 ~s~~~  352 (823)
                      .+.++
T Consensus       101 ~a~~~  105 (123)
T 2dha_A          101 RSTAA  105 (123)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            88654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.22  E-value=1.4e-11  Score=113.75  Aligned_cols=72  Identities=15%  Similarity=0.302  Sum_probs=60.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----C---CCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----A---CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~---~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ..+++|||+|||.++++++|+++|++||+|. +.+     +   ++++|||||+|.+.++|++|++.|++  +.|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCCcEEEe
Confidence            4679999999999999999999999999999 553     1   57899999999999999999998832  55665555


Q ss_pred             ccc
Q 003400          262 HFS  264 (823)
Q Consensus       262 ~~a  264 (823)
                      ..+
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            543

>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=99.22  E-value=1.2e-11  Score=116.92  Aligned_cols=76  Identities=13%  Similarity=0.193  Sum_probs=66.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEE--EEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIR--TLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~--~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ..+.++|||+|||+++|+++|+++|++| .|.  .|++    .++++|||||+|.+.++|++|++. ++..|.|+.|.|.
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~  116 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVF  116 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEE
Confidence            3457899999999999999999999999 566  7773    367899999999999999999994 7799999999998


Q ss_pred             ccCC
Q 003400          263 FSIP  266 (823)
Q Consensus       263 ~a~p  266 (823)
                      ++.+
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8754

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.21  E-value=3.4e-11  Score=110.18  Aligned_cols=76  Identities=18%  Similarity=0.165  Sum_probs=66.7

Q ss_pred             CccceeeecCCC-----CCCHHHHHHHhcccCceEEEEeC------CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 003400          276 NQGTLVVFNLDP-----SVSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (823)
Q Consensus       276 ~~~tLfV~NLp~-----~vteedL~~~Fs~fG~I~~iri~------~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I  344 (823)
                      ..++|+|.||..     +-++++|+++|++||.|.+|++.      +.++|+|||+|.+.++|.+|++.|||+.+.|+.|
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            456899999963     23789999999999999999762      3578999999999999999999999999999999


Q ss_pred             EEEecCC
Q 003400          345 KLEPSRP  351 (823)
Q Consensus       345 ~V~~s~~  351 (823)
                      +|.++..
T Consensus        87 ~v~~a~~   93 (105)
T 2pe8_A           87 KACFYNL   93 (105)
T ss_dssp             EEEECCH
T ss_pred             EEEEcCH
Confidence            9999865

>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=4.1e-11  Score=110.33  Aligned_cols=82  Identities=17%  Similarity=0.295  Sum_probs=71.1

Q ss_pred             CCCCCcEEEEcCCCCCCC-----------HHHHHHHhhcCCCEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHhcCCccc
Q 003400          188 GEHPSRTLFVRNINSNVE-----------DSELRALFEQYGDIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vt-----------eeeLr~lFs~fG~I~~v~~-~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~  255 (823)
                      ...++++|+|+||....+           +++|+++|++||+|..|.+ ...++|||||+|.+.++|++|++.|+|..+.
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            446789999999954432           6899999999999999875 3457999999999999999999999999999


Q ss_pred             cccccccccCCCCC
Q 003400          256 RRKLDIHFSIPKDN  269 (823)
Q Consensus       256 gr~L~V~~a~pk~~  269 (823)
                      |++|.|.|+.++..
T Consensus        91 gr~l~v~~a~~~~~  104 (112)
T 2dit_A           91 GRQITAQAWDGTTD  104 (112)
T ss_dssp             TEECEEEECCSCCC
T ss_pred             CcEEEEEEeCCCCC
Confidence            99999999977543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.21  E-value=5.5e-12  Score=118.79  Aligned_cols=75  Identities=17%  Similarity=0.215  Sum_probs=65.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCE----EEEE----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDI----RTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I----~~v~----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      .+.++|||+|||+++|+++|+++|++||.|    ..|+    .+++++|||||+|.+.++|++|++. ++..+.++.|.|
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    3444    2577899999999999999999996 999999999998


Q ss_pred             cccC
Q 003400          262 HFSI  265 (823)
Q Consensus       262 ~~a~  265 (823)
                      ..+.
T Consensus       100 ~~a~  103 (123)
T 2dha_A          100 FRST  103 (123)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            8764

>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=99.21  E-value=9.8e-12  Score=117.59  Aligned_cols=75  Identities=23%  Similarity=0.296  Sum_probs=66.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceE--EEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVK--EIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~--~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...+|||+|||+++|+++|+++|++| .|.  +|++    .++++|||||+|.+.++|++||+. ++..|.|+.|+|..+
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-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKS  118 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEEC
Confidence            45789999999999999999999999 566  7765    356799999999999999999984 789999999999988


Q ss_pred             CCC
Q 003400          350 RPG  352 (823)
Q Consensus       350 ~~~  352 (823)
                      .++
T Consensus       119 ~~~  121 (126)
T 2hgm_A          119 SQE  121 (126)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            643

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.20  E-value=2.9e-11  Score=111.65  Aligned_cols=78  Identities=14%  Similarity=0.200  Sum_probs=65.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeC--------CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET--------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~--------~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~  347 (823)
                      ..++|||+|||.++++++|+++|++||.|. +++.        +.++|||||+|.+.++|++|++.|+  .++|+.|.+.
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 6542        4679999999999999999999984  4788888887


Q ss_pred             ecCCCcccc
Q 003400          348 PSRPGGARR  356 (823)
Q Consensus       348 ~s~~~~~r~  356 (823)
                      .+.+...+.
T Consensus        84 ~~~~~~~~~   92 (114)
T 2dnl_A           84 SSPTIKDKP   92 (114)
T ss_dssp             CCSSSCSEE
T ss_pred             cCCCcCCCe
Confidence            666544433

>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=99.20  E-value=4.7e-11  Score=109.96  Aligned_cols=79  Identities=16%  Similarity=0.283  Sum_probs=68.8

Q ss_pred             CCccceeeecCCCCCC-----------HHHHHHHhcccCceEEEEe-CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCc
Q 003400          275 LNQGTLVVFNLDPSVS-----------NEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGK  342 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vt-----------eedL~~~Fs~fG~I~~iri-~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr  342 (823)
                      ...++|+|.||....+           +++|+++|++||.|.+|.+ ...++|||||+|.+.++|++|++.|||..+.|+
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            3567999999954332           5899999999999999976 345789999999999999999999999999999


Q ss_pred             eEEEEecCCCc
Q 003400          343 RIKLEPSRPGG  353 (823)
Q Consensus       343 ~I~V~~s~~~~  353 (823)
                      +|+|.++.++.
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=3.3e-11  Score=110.28  Aligned_cols=77  Identities=16%  Similarity=0.240  Sum_probs=67.9

Q ss_pred             CCCcEEEEcCCCC-----CCCHHHHHHHhhcCCCEEEEEeC------CCcccEEEEEeCCHHHHHHHHHHhcCCcccccc
Q 003400          190 HPSRTLFVRNINS-----NVEDSELRALFEQYGDIRTLYTA------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRK  258 (823)
Q Consensus       190 ~~srtLfV~NLP~-----~vteeeLr~lFs~fG~I~~v~~~------~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~  258 (823)
                      .++++|+|+|+..     +-++++|+++|++||+|.+|++.      ++++|||||+|.+.++|++|++.|+|+.+.|++
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4789999999963     23789999999999999999842      467999999999999999999999999999999


Q ss_pred             ccccccCC
Q 003400          259 LDIHFSIP  266 (823)
Q Consensus       259 L~V~~a~p  266 (823)
                      |.|.|+.+
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999854

>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=99.18  E-value=2.5e-11  Score=137.77  Aligned_cols=80  Identities=28%  Similarity=0.469  Sum_probs=73.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||..+|+++|+++|++||.|..|.+     +++++|||||+|.+.++|++||..|+|..|.|+.|.|.|
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            346789999999999999999999999999999985     566899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 003400          264 SIPKD  268 (823)
Q Consensus       264 a~pk~  268 (823)
                      +.++.
T Consensus       179 a~~~~  183 (437)
T 3pgw_S          179 ERGRT  183 (437)
T ss_pred             eCCCC
Confidence            97643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.15  E-value=2.9e-11  Score=113.84  Aligned_cols=77  Identities=16%  Similarity=0.292  Sum_probs=68.2

Q ss_pred             cceeeecC----CCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcC----HHH----HHHHHH--HhCCCc
Q 003400          278 GTLVVFNL----DPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYD----VRA----AEAALK--SLNRSD  338 (823)
Q Consensus       278 ~tLfV~NL----p~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d----~e~----A~kAl~--~LnG~~  338 (823)
                      ..|||+||    |+.+++++|+++|+.||+|.+|++     ++.++|||||+|.|    +++    |.+|++  .|||..
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            47999999    999999999999999999999964     77889999999996    333    899998  899999


Q ss_pred             cCCceEEEEecCCCcc
Q 003400          339 IAGKRIKLEPSRPGGA  354 (823)
Q Consensus       339 i~Gr~I~V~~s~~~~~  354 (823)
                      |.|++|+|.+-+.+..
T Consensus        83 I~Gr~irV~ln~~g~~   98 (136)
T 2j8a_A           83 IMGFKFEVILNKHSIL   98 (136)
T ss_dssp             ETTEEEEEEECCTTHH
T ss_pred             ecCcEEEEEECcccHH
Confidence            9999999999888765

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.09  E-value=1.6e-10  Score=104.87  Aligned_cols=67  Identities=22%  Similarity=0.275  Sum_probs=60.4

Q ss_pred             CCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          286 DPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       286 p~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      +..+++++|+++|++||.|.+|++.+.++|||||+|.+.++|++|++.+++  +.|++|+|+|++++..
T Consensus        26 ~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           26 KGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            357899999999999999999999888999999999999999999998554  6799999999987653

>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=99.09  E-value=1.3e-10  Score=117.71  Aligned_cols=75  Identities=12%  Similarity=0.318  Sum_probs=67.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ..++|||+|||.++|+++|+++|++||.|..|++    .++++|||||+|.+.++|++|++.+ +..+.|++|.|.++..
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            3589999999999999999999999999999974    3678999999999999999999865 5689999999998753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=6.3e-10  Score=100.93  Aligned_cols=75  Identities=19%  Similarity=0.282  Sum_probs=64.0

Q ss_pred             CcEEEEcCCC-------CCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          192 SRTLFVRNIN-------SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       192 srtLfV~NLP-------~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .++|.|+-..       .++++++|+++|++||+|..|.+.++++|||||+|.+.++|++|++.+++  +.+++|.|.|+
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            4566665443       46899999999999999999998888999999999999999999997544  67999999999


Q ss_pred             CCCC
Q 003400          265 IPKD  268 (823)
Q Consensus       265 ~pk~  268 (823)
                      .++.
T Consensus        88 ~~~~   91 (100)
T 2d9o_A           88 EGQP   91 (100)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            7654

>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=99.08  E-value=2.4e-10  Score=104.52  Aligned_cols=77  Identities=23%  Similarity=0.327  Sum_probs=65.6

Q ss_pred             CccceeeecC--CCCCC--------HHHHHHHhcccCceEEEEeCC-------CcccEEEEEEcCHHHHHHHHHHhCCCc
Q 003400          276 NQGTLVVFNL--DPSVS--------NEDLRQIFGAYGEVKEIRETP-------HKRHHKFIEFYDVRAAEAALKSLNRSD  338 (823)
Q Consensus       276 ~~~tLfV~NL--p~~vt--------eedL~~~Fs~fG~I~~iri~~-------~srG~aFVeF~d~e~A~kAl~~LnG~~  338 (823)
                      +.+.|.|.|+  +.++.        +++|++.|++||.|.+|++..       .++|+|||+|.+.++|.+|++.|||+.
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            4568899998  33443        378999999999999998742       468999999999999999999999999


Q ss_pred             cCCceEEEEecCCC
Q 003400          339 IAGKRIKLEPSRPG  352 (823)
Q Consensus       339 i~Gr~I~V~~s~~~  352 (823)
                      ++||+|+|.++...
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999999998643

>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=99.06  E-value=2.2e-10  Score=104.74  Aligned_cols=76  Identities=16%  Similarity=0.347  Sum_probs=66.7

Q ss_pred             CCCcEEEEcCC--CCCCC--------HHHHHHHhhcCCCEEEEEeC-------CCcccEEEEEeCCHHHHHHHHHHhcCC
Q 003400          190 HPSRTLFVRNI--NSNVE--------DSELRALFEQYGDIRTLYTA-------CKHRGFVMISYYDIRAARTAMRALQNK  252 (823)
Q Consensus       190 ~~srtLfV~NL--P~~vt--------eeeLr~lFs~fG~I~~v~~~-------~ksrG~AFV~F~~~e~A~~Ai~~Lng~  252 (823)
                      .|+++|.|+|+  |.++.        +++|++.|++||+|.+|++.       .+++|+|||+|.+.++|++|++.|+|+
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            57899999998  44443        36899999999999999853       246899999999999999999999999


Q ss_pred             ccccccccccccC
Q 003400          253 PLRRRKLDIHFSI  265 (823)
Q Consensus       253 ~l~gr~L~V~~a~  265 (823)
                      .+.|++|.|.|+.
T Consensus        83 ~f~GR~i~v~~~~   95 (105)
T 3v4m_A           83 KFANRVVVTKYCD   95 (105)
T ss_dssp             EETTEECEEEEEC
T ss_pred             EeCCCEEEEEEeC
Confidence            9999999999874

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.06  E-value=5.9e-11  Score=111.75  Aligned_cols=72  Identities=19%  Similarity=0.326  Sum_probs=64.3

Q ss_pred             cEEEEcCC----CCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCC----HHH----HHHHHH--HhcCCc
Q 003400          193 RTLFVRNI----NSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYD----IRA----ARTAMR--ALQNKP  253 (823)
Q Consensus       193 rtLfV~NL----P~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~----~e~----A~~Ai~--~Lng~~  253 (823)
                      +.|||+||    |+.+++++|+++|+.||+|.+|.     .+++++|||||+|.+    +++    |.+|+.  .|+|..
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    99999999999999999999997     378899999999996    433    889988  789999


Q ss_pred             ccccccccccc
Q 003400          254 LRRRKLDIHFS  264 (823)
Q Consensus       254 l~gr~L~V~~a  264 (823)
                      |.|++|+|.+-
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            99999999975

>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=99.02  E-value=3.3e-10  Score=124.27  Aligned_cols=76  Identities=18%  Similarity=0.338  Sum_probs=66.1

Q ss_pred             CCCCCcEEEEcC--CCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccc---cc--ccc
Q 003400          188 GEHPSRTLFVRN--INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR---RR--KLD  260 (823)
Q Consensus       188 ~e~~srtLfV~N--LP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~---gr--~L~  260 (823)
                      ...++++|||+|  |+..+||++|+++|++||+|.+|.+. .+||||||+|.+.++|++|++.|||..+.   |+  .|+
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            356899999999  57899999999999999999999764 47999999999999999999999999873   33  567


Q ss_pred             cccc
Q 003400          261 IHFS  264 (823)
Q Consensus       261 V~~a  264 (823)
                      |.|+
T Consensus        93 ~~~~   96 (345)
T 3tht_A           93 LNFV   96 (345)
T ss_dssp             EEEC
T ss_pred             EEEe
Confidence            7765

>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=98.99  E-value=1.6e-10  Score=105.40  Aligned_cols=68  Identities=28%  Similarity=0.401  Sum_probs=58.4

Q ss_pred             eecCCCCCCHHHHHHHh------------cccCceEEEEeC----CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 003400          282 VFNLDPSVSNEDLRQIF------------GAYGEVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       282 V~NLp~~vteedL~~~F------------s~fG~I~~iri~----~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      +.||+..+++++|+++|            ++||.|.+|++.    ++++|||||+|.+.++|++|++.|||+.+.|++|+
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            45666677777776666            999999999874    34689999999999999999999999999999999


Q ss_pred             EEec
Q 003400          346 LEPS  349 (823)
Q Consensus       346 V~~s  349 (823)
                      |+++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=98.98  E-value=7.3e-10  Score=121.55  Aligned_cols=74  Identities=23%  Similarity=0.358  Sum_probs=65.5

Q ss_pred             Cccceeeec--CCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccC---Cc--eEEEEe
Q 003400          276 NQGTLVVFN--LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA---GK--RIKLEP  348 (823)
Q Consensus       276 ~~~tLfV~N--Lp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~---Gr--~I~V~~  348 (823)
                      ...+|||+|  |+..+|+++|+++|++||+|++|++.. +||||||+|.+.++|++|++.|||+++.   |+  .|.|.|
T Consensus        17 ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~   95 (345)
T 3tht_A           17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF   95 (345)
T ss_dssp             CCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEE
Confidence            456999999  578999999999999999999998854 7899999999999999999999999873   44  678888


Q ss_pred             cC
Q 003400          349 SR  350 (823)
Q Consensus       349 s~  350 (823)
                      +.
T Consensus        96 ~~   97 (345)
T 3tht_A           96 VE   97 (345)
T ss_dssp             CS
T ss_pred             ee
Confidence            75

>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=1.7e-09  Score=100.34  Aligned_cols=76  Identities=18%  Similarity=0.143  Sum_probs=64.3

Q ss_pred             CccceeeecCCCCC----------CHHHHHHHhcccCceEEEEeCCC-cccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 003400          276 NQGTLVVFNLDPSV----------SNEDLRQIFGAYGEVKEIRETPH-KRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (823)
Q Consensus       276 ~~~tLfV~NLp~~v----------teedL~~~Fs~fG~I~~iri~~~-srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I  344 (823)
                      ..++|.|.|+-..-          -++||++.|++||.|.+|++... .+|++||+|.+.++|.+|++.|||+.++|+.|
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            45678888884322          13688999999999999988543 48999999999999999999999999999999


Q ss_pred             EEEecCC
Q 003400          345 KLEPSRP  351 (823)
Q Consensus       345 ~V~~s~~  351 (823)
                      +|+++..
T Consensus        86 ~v~~~~~   92 (114)
T 3s6e_A           86 TAAYVPL   92 (114)
T ss_dssp             EEEEECH
T ss_pred             EEEEEcH
Confidence            9999854

>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=98.93  E-value=1.3e-09  Score=101.83  Aligned_cols=76  Identities=18%  Similarity=0.277  Sum_probs=64.2

Q ss_pred             CccceeeecCCC--CC---CHHHHHHHhcccCceEEEEeC---------CCcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 003400          276 NQGTLVVFNLDP--SV---SNEDLRQIFGAYGEVKEIRET---------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (823)
Q Consensus       276 ~~~tLfV~NLp~--~v---teedL~~~Fs~fG~I~~iri~---------~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G  341 (823)
                      ..++|+|.|+-.  ++   -++||++.|++||.|.+|++.         +.++|++||+|.+.++|.+|++.|||+.++|
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            346899999832  22   368999999999999999752         2346999999999999999999999999999


Q ss_pred             ceEEEEecCC
Q 003400          342 KRIKLEPSRP  351 (823)
Q Consensus       342 r~I~V~~s~~  351 (823)
                      |.|+|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999854

>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=98.90  E-value=5e-10  Score=102.14  Aligned_cols=68  Identities=21%  Similarity=0.366  Sum_probs=59.4

Q ss_pred             EcCCCCCCCHHHHHHHh------------hcCCCEEEEEeC----CCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          197 VRNINSNVEDSELRALF------------EQYGDIRTLYTA----CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       197 V~NLP~~vteeeLr~lF------------s~fG~I~~v~~~----~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      +.+||..+++++|++.|            ++||+|.+|++.    ++++|||||+|.+.++|++|++.|+|+.+.|++|+
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            45677778888777666            999999999863    45799999999999999999999999999999999


Q ss_pred             cccc
Q 003400          261 IHFS  264 (823)
Q Consensus       261 V~~a  264 (823)
                      |.|+
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=98.90  E-value=1.9e-09  Score=100.68  Aligned_cols=75  Identities=13%  Similarity=0.212  Sum_probs=65.2

Q ss_pred             CCcEEEEcCCCC--CC---CHHHHHHHhhcCCCEEEEEeC---------CCcccEEEEEeCCHHHHHHHHHHhcCCcccc
Q 003400          191 PSRTLFVRNINS--NV---EDSELRALFEQYGDIRTLYTA---------CKHRGFVMISYYDIRAARTAMRALQNKPLRR  256 (823)
Q Consensus       191 ~srtLfV~NLP~--~v---teeeLr~lFs~fG~I~~v~~~---------~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g  256 (823)
                      ++++|+|+|+-.  ++   .++||++.|++||+|.+|++.         ++++|+|||+|.+.++|.+|++.|+|+.+.|
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            789999999842  22   368999999999999998742         2456999999999999999999999999999


Q ss_pred             ccccccccC
Q 003400          257 RKLDIHFSI  265 (823)
Q Consensus       257 r~L~V~~a~  265 (823)
                      +.|.|.|+.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999874

>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=4.9e-09  Score=97.30  Aligned_cols=76  Identities=14%  Similarity=0.208  Sum_probs=65.0

Q ss_pred             CCCcEEEEcCCCCCCC----------HHHHHHHhhcCCCEEEEEeCCC-cccEEEEEeCCHHHHHHHHHHhcCCcccccc
Q 003400          190 HPSRTLFVRNINSNVE----------DSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNKPLRRRK  258 (823)
Q Consensus       190 ~~srtLfV~NLP~~vt----------eeeLr~lFs~fG~I~~v~~~~k-srG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~  258 (823)
                      .++++|.++|+=..-.          ++||++.|++||.|.+|.+... .+|+|||+|.+.++|++|++.|+|+.+.|+.
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~   84 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKM   84 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            4788999999843221          4588999999999999986433 5899999999999999999999999999999


Q ss_pred             ccccccC
Q 003400          259 LDIHFSI  265 (823)
Q Consensus       259 L~V~~a~  265 (823)
                      |.|.|+.
T Consensus        85 i~v~~~~   91 (114)
T 3s6e_A           85 ITAAYVP   91 (114)
T ss_dssp             CEEEEEC
T ss_pred             EEEEEEc
Confidence            9999974

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.71  E-value=3.2e-08  Score=87.53  Aligned_cols=75  Identities=25%  Similarity=0.406  Sum_probs=63.6

Q ss_pred             CCccceeeecCC----CCCCH----HHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEE
Q 003400          275 LNQGTLVVFNLD----PSVSN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL  346 (823)
Q Consensus       275 ~~~~tLfV~NLp----~~vte----edL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V  346 (823)
                      ....||+|.-.+    .+.-+    .+|.+.|.+||+|..+|+..   +.+||+|.+.++|.+||. |||..+.||.|+|
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            356789998876    23333    67999999999999999864   339999999999999998 9999999999999


Q ss_pred             EecCCCc
Q 003400          347 EPSRPGG  353 (823)
Q Consensus       347 ~~s~~~~  353 (823)
                      +++++.-
T Consensus        81 ~lkt~dW   87 (91)
T 2dnr_A           81 ALKSPSG   87 (91)
T ss_dssp             EECCCSS
T ss_pred             EeCCCCc
Confidence            9998753

>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=98.61  E-value=9e-08  Score=85.03  Aligned_cols=84  Identities=21%  Similarity=0.294  Sum_probs=71.6

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcceEEE-eeeccccc-ceeEEEEEecCCcccHHHHHHHhcCCcccCCC-CccE
Q 003400          695 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLY-LPIDFKNK-CNVGYAFINMLSPLHIIPFYEAFNGKKWEKFN-SEKV  771 (823)
Q Consensus       695 Tt~MirNIPnk~~~~~l~~~id~~~~~~ydf~Y-lp~d~~~~-~n~gyafin~~~~~~~~~f~~~f~g~~w~~~~-s~k~  771 (823)
                      |.|.||++|..+|++.++++|+...  ++||+| .|-+...+ +--+.|||||.+++++..|.+.|+|+.|...+ .+-.
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 SKVVIRRLPPTLTKEQLQEHLQPMP--EHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYP   79 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCC--CEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcc--cceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEee
Confidence            7899999999999999999999764  688885 67776654 44578999999999999999999999998653 4577


Q ss_pred             EEEEeeecc
Q 003400          772 ASLAYARIQ  780 (823)
Q Consensus       772 ~~~~~A~iQ  780 (823)
                      +.|.||--|
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            899999877

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.59  E-value=1.8e-07  Score=87.57  Aligned_cols=85  Identities=19%  Similarity=0.159  Sum_probs=70.5

Q ss_pred             CccceeeecCCCC-CCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcC-HHHHHHHHHHhC--CCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYD-VRAAEAALKSLN--RSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~-vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d-~e~A~kAl~~Ln--G~~i~Gr~I~V~~s~~  351 (823)
                      ....|+|+||+.+ ++.++|+++|++||+|..|.+.... ..|||+|.+ .++|.+|++.||  +..|.|..++++...-
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 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEG   95 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCH
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECCC
Confidence            4568999999999 9999999999999999999986443 379999999 899999999995  7799999999988764


Q ss_pred             Ccccchhhhcc
Q 003400          352 GGARRNLMLQL  362 (823)
Q Consensus       352 ~~~r~~~~~ql  362 (823)
                      ..+ +.|...+
T Consensus        96 eeE-~~yw~Ki  105 (121)
T 1owx_A           96 EVE-KEALKKI  105 (121)
T ss_dssp             HHH-HHHHHHH
T ss_pred             HHH-HHHHHHH
Confidence            433 3344433

>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=1.4e-07  Score=83.87  Aligned_cols=73  Identities=22%  Similarity=0.364  Sum_probs=61.6

Q ss_pred             CCccceeeecCCCC-----CCH----HHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 003400          275 LNQGTLVVFNLDPS-----VSN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       275 ~~~~tLfV~NLp~~-----vte----edL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      .+..||+|.-++.+     +-+    .+|.+.|..||+|..+|+....   +||+|.+.++|.+||+ |||.++.||.|+
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            45679999988643     222    5689999999999999986433   9999999999999998 999999999999


Q ss_pred             EEecCC
Q 003400          346 LEPSRP  351 (823)
Q Consensus       346 V~~s~~  351 (823)
                      |++..+
T Consensus        89 V~~k~~   94 (95)
T 1ufw_A           89 ISGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EeccCC
Confidence            988644

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=98.42  E-value=8.8e-08  Score=85.65  Aligned_cols=84  Identities=21%  Similarity=0.343  Sum_probs=70.0

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcceEE-Eeeecccccce-eEEEEEecCCcccHHHHHHHhcCCcccCCC-CccE
Q 003400          695 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFL-YLPIDFKNKCN-VGYAFINMLSPLHIIPFYEAFNGKKWEKFN-SEKV  771 (823)
Q Consensus       695 Tt~MirNIPnk~~~~~l~~~id~~~~~~ydf~-Ylp~d~~~~~n-~gyafin~~~~~~~~~f~~~f~g~~w~~~~-s~k~  771 (823)
                      -.|.||++|..+|++.+++.|+....  .||+ |.|-|...+-+ -..|||||++++++..|.+.|+|+.|...+ .+-.
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~--~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPA--HDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSS--EEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCc--cceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            47999999999999999999997654  4666 57777766433 367999999999999999999999998653 4577


Q ss_pred             EEEEeeecc
Q 003400          772 ASLAYARIQ  780 (823)
Q Consensus       772 ~~~~~A~iQ  780 (823)
                      +.|.||-.|
T Consensus        88 a~VE~APyq   96 (97)
T 2l08_A           88 AVVEFAPFQ   96 (97)
T ss_dssp             EEEEECCCC
T ss_pred             eEEEecCCC
Confidence            889999877

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.41  E-value=6.6e-07  Score=83.66  Aligned_cols=73  Identities=15%  Similarity=0.137  Sum_probs=62.0

Q ss_pred             CCCcEEEEcCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCC-HHHHHHHHHHhc--CCccccccccccc
Q 003400          190 HPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYD-IRAARTAMRALQ--NKPLRRRKLDIHF  263 (823)
Q Consensus       190 ~~srtLfV~NLP~~-vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~-~e~A~~Ai~~Ln--g~~l~gr~L~V~~  263 (823)
                      .+.+.|||+||+.+ +++++|+++|++||+|..|.+.. ....|||.|.+ .++|..|+++|+  +..|.+..+.++.
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~-g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT-TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEec-CCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            46789999999999 99999999999999999998533 34479999999 899999999984  6777787666654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.31  E-value=8.1e-07  Score=78.58  Aligned_cols=74  Identities=20%  Similarity=0.319  Sum_probs=61.4

Q ss_pred             CCCcEEEEcCCC----CCCCH----HHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          190 HPSRTLFVRNIN----SNVED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       190 ~~srtLfV~NLP----~~vte----eeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      .|..||+|.-.+    .++-+    .+|.+.|.+||+|..+++...   .+||+|.+.++|.+|++ |+|..+.|+.|+|
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 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED---KMWVTFLEGSSALNVLS-LNGKELLNRTITI   80 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS---SEEEEESSHHHHHHGGG-GTTCEETTEEEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC---CEEEEECChHHHHHHHh-cCCeEeCCeEEEE
Confidence            356788888776    23434    679999999999999986442   38999999999999999 9999999999999


Q ss_pred             cccCCC
Q 003400          262 HFSIPK  267 (823)
Q Consensus       262 ~~a~pk  267 (823)
                      +++.|.
T Consensus        81 ~lkt~d   86 (91)
T 2dnr_A           81 ALKSPS   86 (91)
T ss_dssp             EECCCS
T ss_pred             EeCCCC
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=98.29  E-value=9.3e-07  Score=90.53  Aligned_cols=63  Identities=19%  Similarity=0.259  Sum_probs=56.8

Q ss_pred             CCHHHHHHHhcccCceEEEEeC---------CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          289 VSNEDLRQIFGAYGEVKEIRET---------PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       289 vteedL~~~Fs~fG~I~~iri~---------~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      -.+++|++.|++||.|.++++.         +.++|++||+|.+.++|.+|++.|||+.++||.|+|.++..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            4568999999999999999762         26789999999999999999999999999999999999753

>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=98.10  E-value=3.5e-06  Score=86.20  Aligned_cols=62  Identities=11%  Similarity=0.129  Sum_probs=56.1

Q ss_pred             CCHHHHHHHhhcCCCEEEEEeC---------CCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          204 VEDSELRALFEQYGDIRTLYTA---------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       204 vteeeLr~lFs~fG~I~~v~~~---------~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      -.+++|++.|++||+|.++.+.         ++++|++||+|.+.++|++|++.|+|+.+.||.|.+.|..
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            4578999999999999999852         2688999999999999999999999999999999999874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.10  E-value=5.3e-06  Score=75.34  Aligned_cols=72  Identities=24%  Similarity=0.252  Sum_probs=65.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhccc-----CceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAY-----GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~f-----G~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ..++|-|-|||.++++..|+.+.+++     |.|+.|.+.+...| |+|+|.|...|.+|.-+|+|.+|.|++|++.-
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~G-Aivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNG-AIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTE-EEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCc-eEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            35689999999999999999999999     99999988766544 99999999999999999999999999999864

>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=97.98  E-value=5.4e-06  Score=73.75  Aligned_cols=72  Identities=15%  Similarity=0.203  Sum_probs=59.6

Q ss_pred             CCCcEEEEcCCCCC-----CCH----HHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          190 HPSRTLFVRNINSN-----VED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       190 ~~srtLfV~NLP~~-----vte----eeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      .|..||+|.-++.+     +-+    .+|.+.|.+||+|..+++....   +||+|.+.++|.+|++ |+|..+.|+.|+
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            46789999988743     222    5689999999999998853322   9999999999999999 999999999999


Q ss_pred             ccccC
Q 003400          261 IHFSI  265 (823)
Q Consensus       261 V~~a~  265 (823)
                      |++..
T Consensus        89 V~~k~   93 (95)
T 1ufw_A           89 ISGPS   93 (95)
T ss_dssp             EECCC
T ss_pred             EeccC
Confidence            98753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.73  E-value=4e-05  Score=69.61  Aligned_cols=72  Identities=14%  Similarity=0.238  Sum_probs=65.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcC-----CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQY-----GDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~f-----G~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ...++|-+-|||..++++.|+.+.+.+     |+|..|.+...+.| |+|+|.|...|-+|.-+|+|..|.|++|++.
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~G-Aivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNG-AIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTE-EEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCc-eEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            346899999999999999999999999     99999987665554 9999999999999999999999999999875

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.54  E-value=0.00065  Score=61.19  Aligned_cols=88  Identities=18%  Similarity=0.244  Sum_probs=72.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhc-----CCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQ-----YGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~-----fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..++|.|.|||++++++.|.-+|+.     =|+|..+....   +-|+|+|.+.+.|++.++. ....|.+.+|.|....
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            4689999999999999999999997     25899987544   7899999999999999983 4677888888887654


Q ss_pred             CCCCCCCCCCCccceeeecCCCCCC
Q 003400          266 PKDNPSDKDLNQGTLVVFNLDPSVS  290 (823)
Q Consensus       266 pk~~~~~~~~~~~tLfV~NLp~~vt  290 (823)
                      +.        ...+|++.+|++.++
T Consensus        83 ~~--------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           83 PR--------APARLLLQGLPPGTS   99 (104)
T ss_dssp             CC--------CCCCCCCCSCCCCCC
T ss_pred             CC--------CcceEeeecCCCCCC
Confidence            32        345899999999875

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.49  E-value=0.00062  Score=61.33  Aligned_cols=83  Identities=24%  Similarity=0.317  Sum_probs=71.5

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcc-----cCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGA-----YGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~-----fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ..+|.|.|||.+++++.|.-.|+.     =|.|..++..+   +-|+|+|.+.+.|++.|+. ..+.+.|..|.|....+
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---CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECCC
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCCC
Confidence            468999999999999999999986     26899998765   6799999999999999983 36799999999999888


Q ss_pred             Ccccchhhhccc
Q 003400          352 GGARRNLMLQLN  363 (823)
Q Consensus       352 ~~~r~~~~~ql~  363 (823)
                      ...+|.+++.+.
T Consensus        84 ~~~~r~ll~gl~   95 (104)
T 2dhx_A           84 RAPARLLLQGLP   95 (104)
T ss_dssp             CCCCCCCCCSCC
T ss_pred             CCcceEeeecCC
Confidence            888887777663

>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=96.81  E-value=0.0011  Score=59.80  Aligned_cols=75  Identities=19%  Similarity=0.237  Sum_probs=62.3

Q ss_pred             cceeeecCCCCC-CH----HHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          278 GTLVVFNLDPSV-SN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       278 ~tLfV~NLp~~v-te----edL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ++|+|.||+.++ ..    +.++++|..|+++......+.-+ -..|.|.+.++|.+|...|++..+.|++|+|-|+++.
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK-RVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT-EEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce-EEEEEeCChHHHHHHHHHhccceecCceeEEEecCCC
Confidence            589999998866 32    56789999999887776543323 4789999999999999999999999999999999854


Q ss_pred             c
Q 003400          353 G  353 (823)
Q Consensus       353 ~  353 (823)
                      .
T Consensus        85 ~   85 (104)
T 1wey_A           85 H   85 (104)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=96.46  E-value=0.0038  Score=56.41  Aligned_cols=75  Identities=20%  Similarity=0.227  Sum_probs=62.5

Q ss_pred             CcEEEEcCCCCCC-C----HHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          192 SRTLFVRNINSNV-E----DSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       192 srtLfV~NLP~~v-t----eeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      .++|+|.||+.++ +    .+.++++|..|+++.+.... ++=.-..|.|.++++|.+|...|++..+.|+.|+|-|+.+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~l-kSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeec-CcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            4789999999876 3    25778999999998876532 3334579999999999999999999999999999999875


Q ss_pred             C
Q 003400          267 K  267 (823)
Q Consensus       267 k  267 (823)
                      .
T Consensus        84 ~   84 (104)
T 1wey_A           84 L   84 (104)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=96.13  E-value=0.013  Score=54.22  Aligned_cols=74  Identities=16%  Similarity=0.206  Sum_probs=60.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCC-ceEEEEecCC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG-KRIKLEPSRP  351 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G-r~I~V~~s~~  351 (823)
                      ....-|.|.+.|... ...|.+.|++||+|.+.... ....+-.|+|.++.+|++||. .||..|.| -.|-|.+...
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~-~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~d   96 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS-NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   96 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC-SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC-CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECCC
Confidence            345689999999885 56788899999999998873 456799999999999999998 59999985 6677777543

>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=96.03  E-value=0.014  Score=51.61  Aligned_cols=64  Identities=5%  Similarity=0.051  Sum_probs=53.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-eCC------CcccEEEEEeCCHHHHHHHHHHhcCCcccc
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-TAC------KHRGFVMISYYDIRAARTAMRALQNKPLRR  256 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-~~~------ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g  256 (823)
                      ++|.||+||+.+||+++.+.+..+.++...+ +.+      ..-.-|+|.|.+.+++....+.++|..+.+
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            5799999999999999999999998776544 222      123469999999999999999999988754

>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=94.72  E-value=0.058  Score=48.09  Aligned_cols=55  Identities=18%  Similarity=0.311  Sum_probs=45.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhc
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ  250 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Ln  250 (823)
                      ...++| +.|+++...||.++|+.||.|.--++.   -..|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wid---DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEE---TTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEEEEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            356677 999999999999999999965533343   4579999999999999999764

>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=94.31  E-value=0.084  Score=47.05  Aligned_cols=54  Identities=19%  Similarity=0.303  Sum_probs=43.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  335 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~Ln  335 (823)
                      ..++| +.|+++...||.++|+.||.|.--.+.   ...|||.|.+++.|..|++.+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wid---DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEE---TTEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCEEEEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            35666 999999999999999999855333332   3469999999999999999764

>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=94.11  E-value=0.12  Score=47.81  Aligned_cols=70  Identities=17%  Similarity=0.186  Sum_probs=56.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccc-ccccccc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR-RKLDIHF  263 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g-r~L~V~~  263 (823)
                      ..+-|.|-+.|+.. ...|...|++||+|.+... .....+..|.|.+..+|++|+. .||..+.+ ..|-|..
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            45789999999885 6777889999999998865 3456799999999999999999 58888864 4444544

>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=93.76  E-value=0.054  Score=48.41  Aligned_cols=53  Identities=19%  Similarity=0.315  Sum_probs=43.3

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhC
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  335 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~Ln  335 (823)
                      .++| +.|+++...||.++|+.||.|.--.+.   ...|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv~I~Wid---DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEEEEEEEE---TTEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCEEEEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            4566 999999999999999999954333333   3469999999999999999875

>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=93.63  E-value=0.076  Score=47.46  Aligned_cols=54  Identities=19%  Similarity=0.321  Sum_probs=44.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhc
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ  250 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Ln  250 (823)
                      ..++| +.|+++...||..+|+.||.|.--++.   -..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~I~Wid---DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEEE---TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEEEEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            45666 999999999999999999955543343   4579999999999999999775

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=93.12  E-value=0.087  Score=47.00  Aligned_cols=67  Identities=7%  Similarity=0.034  Sum_probs=51.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-eCCC------cccEEEEEeCCHHHHHHHHHHhcCCccccc
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACK------HRGFVMISYYDIRAARTAMRALQNKPLRRR  257 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-~~~k------srG~AFV~F~~~e~A~~Ai~~Lng~~l~gr  257 (823)
                      -+-+|.||.||+.+||+++.+.+..+-++...+ +.++      .-.-|+|.|.+.++.....+.++|..+.+.
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~   81 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDS   81 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECT
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeC
Confidence            456899999999999999998888765553322 1111      223599999999999999999999887543

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.67  E-value=0.046  Score=61.95  Aligned_cols=56  Identities=9%  Similarity=0.273  Sum_probs=43.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHH
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR  247 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~  247 (823)
                      ..|.|+|. .|..+++++|.++|++||+|.++.......-||.|+|.+.+++..++.
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            45899997 799999999999999999999997655555699999999999997765

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=92.14  E-value=0.11  Score=48.82  Aligned_cols=72  Identities=18%  Similarity=0.252  Sum_probs=55.5

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEE-EeC----------------C--CcccEEEEEEcCHHHHHHHHHHhCCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-RET----------------P--HKRHHKFIEFYDVRAAEAALKSLNRS  337 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~i-ri~----------------~--~srG~aFVeF~d~e~A~kAl~~LnG~  337 (823)
                      ..-|.|.+.|++.+ ..+-+.|++||.|.+- ...                +  ...++..|+|++..+|.+||. -||.
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            34688888876665 4577889999999772 111                1  135678999999999999998 5999


Q ss_pred             ccCCceEEEEecC
Q 003400          338 DIAGKRIKLEPSR  350 (823)
Q Consensus       338 ~i~Gr~I~V~~s~  350 (823)
                      .|.|..|=|.+..
T Consensus        85 ii~G~mIGV~Py~   97 (132)
T 3p3d_A           85 VFNGVLLGVIPYT   97 (132)
T ss_dssp             EETTEECEEEECC
T ss_pred             EeCcEEEEEEECC
Confidence            9999988888875

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=91.41  E-value=0.074  Score=60.28  Aligned_cols=56  Identities=11%  Similarity=0.156  Sum_probs=43.6

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHH
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS  333 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~  333 (823)
                      .++|+|. .+..+++.+|.+.|++||.|.++........||.|||.+.+++.+++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHhc
Confidence            4689998 7999999999999999999999988766677999999999998877653

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=86.92  E-value=0.43  Score=44.77  Aligned_cols=72  Identities=14%  Similarity=0.173  Sum_probs=52.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-eCC------------------CcccEEEEEeCCHHHHHHHHHHhcC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TAC------------------KHRGFVMISYYDIRAARTAMRALQN  251 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-~~~------------------ksrG~AFV~F~~~e~A~~Ai~~Lng  251 (823)
                      ...-|.|-+.|++. ...+.+.|++||.|.+-. ...                  ....+..|+|.+..+|++|+. .+|
T Consensus         6 ~e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENG   83 (132)
T ss_dssp             --CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTT
T ss_pred             CceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCC
Confidence            34567777887654 456677899999987622 110                  135688999999999999999 599


Q ss_pred             Ccccccccccccc
Q 003400          252 KPLRRRKLDIHFS  264 (823)
Q Consensus       252 ~~l~gr~L~V~~a  264 (823)
                      ..|.|.-|-|.+.
T Consensus        84 ~ii~G~mIGV~Py   96 (132)
T 3p3d_A           84 AVFNGVLLGVIPY   96 (132)
T ss_dssp             CEETTEECEEEEC
T ss_pred             eEeCcEEEEEEEC
Confidence            9998886666654

---

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	823
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-20
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	8e-17
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-15
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	9e-15
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-14
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	7e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-14
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	6e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-14
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	9e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	9e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-09
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	9e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	8e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	8e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	8e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	9e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	9e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	7e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	7e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-10
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	3e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	8e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	9e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-08
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	4e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	6e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	8e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	7e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	9e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-07
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	9e-08
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:) 1e-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-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	8e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.001
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.001
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	3e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	3e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	7e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	6e-04
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	0.001
d1uw4a_	91	d.58.7.4 (A:) RNA processing protein UPF3x, RRM do	0.003

>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 = 85.4 bits (210), Expect = 9e-20
 Identities = 34/171 (19%), Positives = 59/171 (34%), Gaps = 12/171 (7%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAM 246
            R LF+  ++    D  LR+ FEQ+G +            + RGF  ++Y  +     AM
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 247 RALQNKPLRRRKLDIHFSI-PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
            A  +K   R                   L    + V  +        LR  F  YG+++
Sbjct: 66  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125

Query: 306 EI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
            I     R +  KR   F+ F D  + +  +       + G   ++  +  
Sbjct: 126 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS 175

>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 = 74.7 bits (183), Expect = 8e-17
 Identities = 23/111 (20%), Positives = 55/111 (49%), Gaps = 8/111 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALKSLNR 336
            L + NL   ++ E++  IFG YG +++I    TP  R   ++ + D+  A+ A   L+ 
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSG 68

Query: 337 SDIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSPITNSPP 387
            ++  + + +       A +    +++ + ++++ ++L+ + G  I   PP
Sbjct: 69  FNVCNRYLVVLYYNANRAFQ----KMDTKKKEEQLKLLKEKYG--INTDPP 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 = 71.6 bits (175), Expect = 1e-15
 Identities = 21/89 (23%), Positives = 36/89 (40%), Gaps = 2/89 (2%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK--HRGFVMISYYDIRAARTAMRA 248
            +R L++RN+   +   E+  +F +YG IR +        RG   + Y DI  A+ A   
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQ 277
           L    +  R L + +          D  +
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKK 94

>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 = 69.6 bits (170), Expect = 2e-15
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
           +L V +L P V+   L + F   G +  IR      T     + ++ F     AE AL +
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 334 LNRSDIAGKRIKLEPSR 350
           +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 = 59.9 bits (145), Expect = 5e-12
 Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMRA 248
           +L+V +++ +V ++ L   F   G I            +  G+  +++     A  A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 249 LQNKPLRRRKLDIHFS 264
           +    ++ + + I +S
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>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 = 70.0 bits (171), Expect = 2e-15
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
           TL V NL    + E + ++F   G++K+I     K         F+E+Y    AE A++ 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           +N + +  + I+ +        R
Sbjct: 69  INGTRLDDRIIRTDWDAGFKEGR 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 = 63.8 bits (155), Expect = 4e-13
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTA 245
            S TL+V N++    + ++  LF + GDI+ +            GF  + YY    A  A
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
           MR +    L  R +   +    
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGF 87

>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 = 68.9 bits (168), Expect = 4e-15
 Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
            L+V  L   +++ +L  +F A G +   R     +T +   + F++F     ++ A+K 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 334 LNRSDIAGKRIKLEPSRPG 352
           LN   +  KR+K+  +RPG
Sbjct: 64  LNGITVRNKRLKVSYARPG 82

>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 = 57.3 bits (138), Expect = 4e-11
 Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-----FVMISYYDIRAARTAM 246
           +  L V  +  ++ D EL ALF   G I T      ++      +  + +     ++ A+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 247 RALQNKPLRRRKLDIHFSIP 266
           + L    +R ++L + ++ P
Sbjct: 62  KVLNGITVRNKRLKVSYARP 81

>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 = 68.0 bits (166), Expect = 7e-15
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKS 333
           G L+V NLD  VS+ D++++F  +G +K+       +        + F     A  A+K 
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 334 LNRSDIAGKRIKLE 347
            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 = 53.8 bits (129), Expect = 7e-10
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRT----LYTACKHRGFVMISYYDIRAARTAMRALQ 250
           L V N++  V D++++ LF ++G ++        + +  G   + +     A  AM+   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 251 NKPLRRRKLDIHFS 264
             PL  R ++I   
Sbjct: 63  GVPLDGRPMNIQLV 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 = 68.5 bits (167), Expect = 9e-15
 Identities = 20/87 (22%), Positives = 41/87 (47%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEA 329
            S K     TL+  NL  +++ ++L+++F    E++ + +    +   +IEF     AE 
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 330 ALKSLNRSDIAGKRIKLEPSRPGGARR 356
            L+    ++I G+ + L  +   G  R
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 64.3 bits (156), Expect = 2e-13
 Identities = 18/81 (22%), Positives = 37/81 (45%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            +RTL  +N++ N+ + EL+ +FE   +IR +    K +G   I +     A   +   Q
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 74

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
              +  R + ++++  K    
Sbjct: 75  GAEIDGRSVSLYYTGEKGGTR 95

>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 = 67.4 bits (164), Expect = 2e-14
 Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 7/94 (7%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDV 324
           P  +     T+ V  LD  VS   L ++F   G V          T   + + F+EF   
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
             A+ A+K ++   + GK I++  +      +NL
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAH--NKNL 93

>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 = 58.9 bits (142), Expect = 2e-11
 Identities = 13/84 (15%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD-----IRTLYTACKHRGFVMISYYDIRAARTA 245
              T++V  ++  V +  L  LF Q G      +       +H+G+  + +     A  A
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           ++ +    L  + + ++ +   + 
Sbjct: 68  IKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 67.0 bits (163), Expect = 2e-14
 Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG---EVKEIRETPHKRHHKFIEFYDVRA 326
           PS +    G + + NLD S+ N+ L   F A+G     K + +    + + F+ F    A
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 60

Query: 327 AEAALKSLNRSDIAGKRIKLEPSRP 351
           AE A++ +N   +  +++ +   + 
Sbjct: 61  AERAIEKMNGMLLNDRKVFVGRFKS 85

>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 = 56.6 bits (136), Expect = 1e-10
 Identities = 12/79 (15%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRA 248
              +F++N++ ++++  L   F  +G     + +      +G+  + +    AA  A+  
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 249 LQNKPLRRRKLDIHFSIPK 267
           +    L  RK+ +     +
Sbjct: 68  MNGMLLNDRKVFVGRFKSR 86

>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 = 67.4 bits (164), Expect = 3e-14
 Identities = 21/97 (21%), Positives = 44/97 (45%), Gaps = 9/97 (9%)

Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIE 320
           P DN S ++ +  T+    L   +   DL   F A G+V+++R      +   +   ++E
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
           F ++++   A+  L    + G  I ++ S+     +N
Sbjct: 67  FCEIQSVPLAIG-LTGQRLLGVPIIVQASQA---EKN 99

>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 = 54.7 bits (131), Expect = 7e-10
 Identities = 14/86 (16%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAAR 243
           E  +RT+F   + + +   +L   F   G +R +         + +G   + + +I++  
Sbjct: 15  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDN 269
                L  + L    + +  S  + N
Sbjct: 75  -LAIGLTGQRLLGVPIIVQASQAEKN 99

>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 = 66.6 bits (162), Expect = 3e-14
 Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-----IRETPHKRHHKFIEFYDV 324
           P+ +  +  T+ V NL       DL+++F  +G +        + T   +   FI F+  
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 325 RAAEAALKSLNRSDIAGKRIKLEPSRP 351
             A  A+  ++        + +E ++P
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWAKP 87

>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 = 58.5 bits (141), Expect = 2e-11
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTA 245
            + T+ V N++ +  +++L+ LF  +G I  +Y A      + +GF  IS++    A  A
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           +  +         L++ ++ P  N
Sbjct: 67  IAGVSGFGYDHLILNVEWAKPSTN 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 = 65.8 bits (160), Expect = 6e-14
 Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 272 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK---RHHKFIEFYDVRAAE 328
           + D    TL V NL   V+   + Q+F   G  K  +          + F+EFY+ R A 
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 329 AALKSLNRSDIAGKRIKLEPSRPGGARR 356
           AAL ++N   I GK +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 = 59.3 bits (143), Expect = 1e-11
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYY---DIRAARTA 245
           +   RTL+V N++ +V +  +  LF Q G  ++     +H       +    + R A  A
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAA 64

Query: 246 MRALQNKPLRRRKLDIHFSIPKDN 269
           + A+  + +  +++ ++++    +
Sbjct: 65  LAAMNGRKILGKEVKVNWATTPSS 88

>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 = 66.1 bits (161), Expect = 6e-14
 Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAA 327
           D  +       T+    +   ++++ +RQ F  +G++ EIR    ++ + F+ F    +A
Sbjct: 9   DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR-VFPEKGYSFVRFSTHESA 67

Query: 328 EAALKSLNRSDIAGKRIKLEPSRP 351
             A+ S+N + I G  +K    + 
Sbjct: 68  AHAIVSVNGTTIEGHVVKCYWGKE 91

>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 = 59.2 bits (143), Expect = 2e-11
 Identities = 11/81 (13%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
            + T++   I S + D  +R  F  +G I  +      +G+  + +    +A  A+ ++ 
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVN 75

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
              +    +  ++     + +
Sbjct: 76  GTTIEGHVVKCYWGKESPDMT 96

>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 = 65.5 bits (159), Expect = 9e-14
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L V  L   V ++ L   F  +G++ +I      ET   R   F+EF     A AA+ +
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 334 LNRSDIAGKRIKLEPSRP 351
           +N S++ G+ I++  ++P
Sbjct: 67  MNESELFGRTIRVNLAKP 84

>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 = 61.6 bits (149), Expect = 2e-12
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTA 245
             R L+V  +   V+D  L A F  +GDI  +         KHRGF  + +     A  A
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
           +  +    L  R + ++ + P 
Sbjct: 64  IDNMNESELFGRTIRVNLAKPM 85

>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 = 65.1 bits (158), Expect = 9e-14
 Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI--------RTLYTACKHRGFVMISYYDIRAARTAM 246
           LF++N+N +  +  L+ +F + G I        +         GF  + Y     A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 247 RALQNKPLRRRKLDIHFSIPKDNPS 271
           + LQ   +   KL++  S     P+
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKPA 85

>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 = 63.9 bits (155), Expect = 2e-13
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 8/81 (9%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV--------KEIRETPHKRHHKFIEFYDVRAAEAAL 331
           L + NL+ S + E L+ +F   G +        K            F+E+     A+ AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 332 KSLNRSDIAGKRIKLEPSRPG 352
           K L    + G ++++  S   
Sbjct: 61  KQLQGHTVDGHKLEVRISERA 81

>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 = 64.9 bits (158), Expect = 2e-13
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 4/90 (4%)

Query: 269 NPSDKDLNQGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAA 327
             +D       + + NL+   V   D+  IF  YG++         +   F+++ + R A
Sbjct: 7   GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS---VHKGFAFVQYVNERNA 63

Query: 328 EAALKSLNRSDIAGKRIKLEPSRPGGARRN 357
            AA+   +   IAG+ + +  +      R+
Sbjct: 64  RAAVAGEDGRMIAGQVLDINLAAEPKVNRS 93

>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 = 59.1 bits (143), Expect = 2e-11
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 191 PSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
            +  +F+ N+N+  V+ S++ A+F +YG I        H+GF  + Y + R AR A+   
Sbjct: 14  MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVG---CSVHKGFAFVQYVNERNARAAVAGE 70

Query: 250 QNKPLRRRKLDIHFSIPKDNP 270
             + +  + LDI+ +      
Sbjct: 71  DGRMIAGQVLDINLAAEPKVN 91

>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 = 64.7 bits (157), Expect = 2e-13
 Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 9/93 (9%)

Query: 194 TLFVRNINSNVEDSELRALFEQYG-------DIRTLYTACKHRGFVMISYYDIRAARTAM 246
            LF+  I    +  E+     +            +     K+RGF  + Y   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 247 RALQNKPLRR--RKLDIHFSIPKDNPSDKDLNQ 277
           R L    ++    ++ + ++ P+ +  +  +  
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 = 55.5 bits (133), Expect = 4e-10
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 9/82 (10%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE-------IRETPHKRHHKFIEFYDVRAAEAAL 331
            L +  +      E++ +      E            +    R   F+E+   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 332 KSLNRSDI--AGKRIKLEPSRP 351
           + L    I   G +I ++ + P
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEP 84

>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 = 63.5 bits (154), Expect = 3e-13
 Identities = 13/79 (16%), Positives = 37/79 (46%), Gaps = 5/79 (6%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSL 334
           L +  L   ++++ ++++  ++G +K         T   + + F E+ D+   + A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 335 NRSDIAGKRIKLEPSRPGG 353
           N   +  K++ ++ +  G 
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 = 55.0 bits (132), Expect = 3e-10
 Identities = 14/85 (16%), Positives = 32/85 (37%), Gaps = 5/85 (5%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAM 246
           +  LF+  + + + D +++ L   +G ++             +G+    Y DI     A+
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 247 RALQNKPLRRRKLDIHFSIPKDNPS 271
             L    L  +KL +  +      +
Sbjct: 61  AGLNGMQLGDKKLLVQRASVGAKNA 85

>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 = 63.2 bits (153), Expect = 4e-13
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
            L+V  L  +++ E+ R +FG+ GE++  +      T     + F+ + D + AE A+ +
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 334 LNRSDIAGKRIKLEPSRP 351
           LN   +  K IK+  +RP
Sbjct: 64  LNGLRLQTKTIKVSYARP 81

>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 = 53.6 bits (128), Expect = 1e-09
 Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 192 SRT-LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTA 245
           S+T L V  +  N+   E R+LF   G+I +             G+  ++Y D + A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 246 MRALQNKPLRRRKLDIHFSIP 266
           +  L    L+ + + + ++ P
Sbjct: 61  INTLNGLRLQTKTIKVSYARP 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 = 63.4 bits (154), Expect = 4e-13
 Identities = 21/94 (22%), Positives = 45/94 (47%), Gaps = 13/94 (13%)

Query: 265 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE------VKEIRETPHKRHHKF 318
           +PK   + K      ++V N+    +  ++R++F  +GE       K++  T   R   F
Sbjct: 2   VPKKQTTSK------ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 55

Query: 319 IEFYDVRAAEAALKSL-NRSDIAGKRIKLEPSRP 351
           ++F   + A+ A  +L + + + G+R+ LE +  
Sbjct: 56  VDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 89

>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 = 60.3 bits (146), Expect = 6e-12
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 7/87 (8%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC------KHRGFVMISYYDIRAA 242
           +  +  + VRNI       E+R LF  +G+++T+           HRGF  + +   + A
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 243 RTAMRALQN-KPLRRRKLDIHFSIPKD 268
           + A  AL +   L  R+L + ++  + 
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEV 91

>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 = 62.0 bits (150), Expect = 1e-12
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L VF L    +  DLR++F  YG + ++     +++   R   F+ F +V  A+ A + 
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 334 LNRSDIAGKRIK 345
            N  ++ G+RI+
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 = 55.5 bits (133), Expect = 2e-10
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-----FVMISYYDIRAARTA 245
           P+  L V  ++    + +LR +F +YG I  +      +      F  + + ++  A+ A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 246 MRALQNKPLRRRKLDI 261
                   L  R++ +
Sbjct: 68  KERANGMELDGRRIRV 83

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

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]

 Score = 62.0 bits (150), Expect = 1e-12
 Identities = 20/89 (22%), Positives = 46/89 (51%), Gaps = 6/89 (6%)

Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIR--TLYTACKHRGFVMISYYDIRAART 244
           P+ T+++ N+N  ++  EL+    A+F ++G I    +  + K RG   + + ++ +A  
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDK 273
           A+R++Q  P   + + I ++    +   K
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 90

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

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]

 Score = 57.8 bits (139), Expect = 4e-11
 Identities = 16/79 (20%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQ----IFGAYGEVKE--IRETPHKRHHKFIEFYDVRAAEAALK 332
           T+ + NL+  +  ++L++    IF  +G++ +  +  +   R   F+ F +V +A  AL+
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 333 SLNRSDIAGKRIKLEPSRP 351
           S+       K ++++ ++ 
Sbjct: 65  SMQGFPFYDKPMRIQYAKT 83

>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 = 61.6 bits (149), Expect = 1e-12
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 1/80 (1%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
            + L+VRN+  +  +  +   F             K R +  + + +   A  AM+AL  
Sbjct: 8   VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 252 KPLRRRKLDIHFSIPKDNPS 271
           K L    +++  + P D  S
Sbjct: 67  KVLDGSPIEVTLAKPVDKDS 86

>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 = 58.9 bits (142), Expect = 1e-11
 Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V NL  S S E + + F         R     R + F+ F +   A  A+K+LN   
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER-VKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 339 IAGKRIKLEPSRP 351
           + G  I++  ++P
Sbjct: 69  LDGSPIEVTLAKP 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 = 61.5 bits (149), Expect = 1e-12
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVK-----EIRETPHKRHHKFIEFYDVRAAEAALKS 333
            L V NL  +++++ L  IFG YG +        + T   R   F+ +     A+ A+ +
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 334 LNRSDIAGKRIKLE 347
           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 = 56.5 bits (136), Expect = 1e-10
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAM 246
              L+V N+   + D +L  +F +YG I            + RG   + Y     A+ A+
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 247 RALQNKPL--RRRKLDIHF 263
            AL N       + L +  
Sbjct: 66  SALNNVIPEGGSQPLSVRL 84

>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 = 61.5 bits (149), Expect = 2e-12
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V NL P ++ E++R++F  YG+  E+      +   FI       AE A   L+   
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEIAKVELDNMP 68

Query: 339 IAGKRIKLEPSRPGGA 354
           + GK++++  +    +
Sbjct: 69  LRGKQLRVRFACHSAS 84

>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 = 59.6 bits (144), Expect = 9e-12
 Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           GE  + +     LFV N+  ++ + E+R LFE+YG    ++   K +GF  I       A
Sbjct: 1   GEKTFTQR--SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLA 57

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
             A   L N PLR ++L + F+    + +
Sbjct: 58  EIAKVELDNMPLRGKQLRVRFACHSASLT 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 = 61.6 bits (149), Expect = 2e-12
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 3/84 (3%)

Query: 271 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRETPHKRHHKFIEFYDVRAA 327
           S+       L V N+     + DLRQ+FG +G++ +   I      +   F+ F +   A
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 64

Query: 328 EAALKSLNRSDIAGKRIKLEPSRP 351
           + A + L+ + + G++I++  +  
Sbjct: 65  DRAREKLHGTVVEGRKIEVNNATA 88

>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 = 57.0 bits (137), Expect = 8e-11
 Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK---HRGFVMISYYDIRAARTAMR 247
             + L V NI     D +LR +F Q+G I  +         +GF  +++ +   A  A  
Sbjct: 10  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 69

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPS 271
            L    +  RK++++ +  +   +
Sbjct: 70  KLHGTVVEGRKIEVNNATARVMTN 93

>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 = 60.8 bits (147), Expect = 3e-12
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            + V      ++ ++LR+ F  YG+V ++      R   F+ F D + A++         
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLI 64

Query: 339 IAGKRIKLEPSRPGGARRN 357
           I G  + +  + P     +
Sbjct: 65  IKGISVHISNAEPKHNSNS 83

>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 = 58.1 bits (140), Expect = 3e-11
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G   S  +FV     ++ + ELR  F QYGD+  ++     R F  +++ D + A++   
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 248 ALQNKPLRRRKLDIHFSIPKDNPS 271
             ++  ++   + I  + PK N +
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSN 82

>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 = 60.8 bits (147), Expect = 4e-12
 Identities = 14/93 (15%), Positives = 34/93 (36%), Gaps = 6/93 (6%)

Query: 264 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV-----KEIRETPHKRHHKF 318
           ++P +    +      L +  L    + E LR  +  +G++          +   R   F
Sbjct: 7   TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 66

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           + F  +   +AA+       I G+ ++ + +  
Sbjct: 67  VTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA 98

>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 = 56.2 bits (135), Expect = 2e-10
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTA 245
             R LF+  ++    +  LR  +EQ+G +              RGF  +++  +     A
Sbjct: 19  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 78

Query: 246 MRALQNKPLRRRKLDIHFSIPKD 268
           M A +   +  R ++   ++ ++
Sbjct: 79  M-AARPHSIDGRVVEPKRAVARE 100

>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 = 60.2 bits (145), Expect = 5e-12
 Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
           TL + N  PS +  ++R +      V      P  R +      +I+      A   ++ 
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 334 LNRSDIAGKRIKLEPSRP 351
           LN   I G  +  + S P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 80

>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 = 54.8 bits (131), Expect = 3e-10
 Identities = 14/79 (17%), Positives = 22/79 (27%), Gaps = 5/79 (6%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMR 247
            TL++ N   +     +R L +    +              R F  I       AR  + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 248 ALQNKPLRRRKLDIHFSIP 266
            L    +    L    S P
Sbjct: 62  KLNGLKIEGYTLVTKVSNP 80

>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 = 60.1 bits (145), Expect = 6e-12
 Identities = 15/81 (18%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMRA 248
           +F+ N++  +++  L   F  +G I               +G+  I++    A+  A+ A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 249 LQNKPLRRRKLDIHFSIPKDN 269
           +  + L  R + + ++  KD+
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>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 = 59.4 bits (143), Expect = 8e-12
 Identities = 17/82 (20%), Positives = 40/82 (48%), Gaps = 6/82 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR------ETPHKRHHKFIEFYDVRAAEAALKS 333
           + + NLDP +  + L   F A+G + +        +T + + + FI F    A++AA+++
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 334 LNRSDIAGKRIKLEPSRPGGAR 355
           +N   +  + I +  +    ++
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 60.2 bits (145), Expect = 8e-12
 Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 13/93 (13%)

Query: 272 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------------RETPHKRHHKF 318
           D+D +   + V  L+ SV+ +DL   F   G VK               +ET   +    
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 319 IEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           + + D   A+AA++  +  D  G ++K+  +R 
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 52.5 bits (125), Expect = 4e-09
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 13/95 (13%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-------------CKHRGFV 232
           P  +  +  ++V+ +N +V   +L   F+Q G ++                   K +G  
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
            +SY D   A+ A+     K  +  KL +  +  K
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 59.7 bits (144), Expect = 8e-12
 Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVK-----EIRETPHKRHHKFIEFYDVRAAEAALKS 333
            L V ++      +++++ F  YGE+K       R T   + +  +E+   + A AA ++
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 334 LNRSDIAGKRIKLEPSRPGG 353
           LN ++I G+ I+++     G
Sbjct: 69  LNGAEIMGQTIQVDWCFVKG 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 = 56.3 bits (135), Expect = 1e-10
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTA 245
               LFV +I+   ++ E++  F  YG+I+ ++          +G+ ++ Y   + A  A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
             AL    +  + + + +   K
Sbjct: 66  KEALNGAEIMGQTIQVDWCFVK 87

>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 = 60.0 bits (145), Expect = 9e-12
 Identities = 20/102 (19%), Positives = 42/102 (41%), Gaps = 9/102 (8%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYTACKHRGFVMISYYDIRAARTAM 246
           G+ P   + V N+   V    L  +F ++G + + +     ++   ++ Y D  +A+ A 
Sbjct: 3   GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAK 62

Query: 247 RALQNKPL--RRRKLDIHFS------IPKDNPSDKDLNQGTL 280
            +L  + +      L I FS      +  +N   +D  +  L
Sbjct: 63  LSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDL 104

>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 = 58.1 bits (140), Expect = 5e-11
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 11/96 (11%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-RHHKFIEFYDVRAAEAALKSLNRSD 338
           ++V NL   V+ + L QIF  +G V +I       +    +++ D  +A+ A  SL+  +
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 69

Query: 339 I--AGKRIKLEPSRPGGARRNLMLQLNQELEQDESR 372
           I  A   ++++ S+           LN +   D+SR
Sbjct: 70  IYNACCTLRIDFSKLT--------SLNVKYNNDKSR 97

>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 = 59.7 bits (144), Expect = 9e-12
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEFYDVRAAEAALKS 333
           N   + V NL P +  +D+  +F  YG +++I  +         F+EF D R AE A+  
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 72

Query: 334 LNRSDIAGKRIKLEPSRPGGAR 355
            +  D  G R+++E  R G   
Sbjct: 73  RDGYDYDGYRLRVEFPRSGRGT 94

>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 = 55.8 bits (134), Expect = 2e-10
 Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 5/94 (5%)

Query: 176 NGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA--CKHRGFVM 233
           +G G + G  P G      ++V N+  ++   ++  +F +YG IR +          F  
Sbjct: 1   SGGGVIRG--PAGN-NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAF 57

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK 267
           + + D R A  A+           +L + F    
Sbjct: 58  VEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 58.1 bits (140), Expect = 2e-11
 Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH-----HKFIEFYDVRAAEAALKSL 334
           + +  L    + E LR+ FG +GEVKE                F+ F D    +  L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 335 NRSDIAGKRIK 345
           +R ++  K I 
Sbjct: 62  SRHELDSKTID 72

>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 = 49.2 bits (117), Expect = 3e-08
 Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 6/72 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMRAL 249
           +F+  ++       LR  F Q+G+++             RGF  +++ D       + A 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 250 QNKPLRRRKLDI 261
               L  + +D 
Sbjct: 62  SRHELDSKTIDP 73

>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 = 58.2 bits (140), Expect = 3e-11
 Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 5/85 (5%)

Query: 278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYDVRAAEAALK 332
           G L V NL  + S EDL ++F AYG + E+               F+ F     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 333 SLNRSDIAGKRIKLEPSRPGGARRN 357
            ++     G+ + + PS        
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 52.8 bits (126), Expect = 3e-09
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAA 242
           G   S  LFVRN++    + +L  LF  YG +  L+          +GF  +++     A
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
             A   +  +  + R L +  S  K   S
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>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 = 58.1 bits (140), Expect = 3e-11
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            L+V  L    + +DL++ F  +GEV  +      +T H +   F+ F +       +  
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 334 LNRSDIAGKRIKLEPSRPGGAR 355
            +   I G+    +      ++
Sbjct: 70  RH--MIDGRWCDCKLPNSKQSQ 89

>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 = 53.8 bits (129), Expect = 1e-09
 Identities = 11/88 (12%), Positives = 26/88 (29%), Gaps = 7/88 (7%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAA 242
               +  L V  +     + +L+  F  +G++  +           +GF  + + +    
Sbjct: 4   AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNP 270
              M       +  R  D      K + 
Sbjct: 64  VKVMSQRHM--IDGRWCDCKLPNSKQSQ 89

>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 = 57.4 bits (138), Expect = 5e-11
 Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYDVRAAEAALKS 333
            L V  L  +++ ++L Q+F  YG +   R    +         FI F     AE A+K 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 334 LNRSDIAGKRIKLE 347
           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 = 54.3 bits (130), Expect = 7e-10
 Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 7/79 (8%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMR 247
             L+V  +   +   EL  LF QYG I T            RG   I +     A  A++
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 248 ALQNKPL--RRRKLDIHFS 264
            L  +        + + F+
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>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 = 56.7 bits (136), Expect = 7e-11
 Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 6/71 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
           + V  L  + + ED++  F  +G+V +        T   R   F+ F      E   + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 335 NRSDIAGKRIK 345
           +  +I  K ++
Sbjct: 61  HFHEINNKMVE 71

>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 = 42.8 bits (100), Expect = 5e-06
 Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIR-----TLYTACKHRGFVMISYYDIRAARTAMRAL 249
           +FV  ++ N    +++  FEQ+G +         T  +HRGF  +++            +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 250 QNKPLRRRKLDI 261
               +  + ++ 
Sbjct: 61  HFHEINNKMVEC 72

>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 = 56.2 bits (135), Expect = 1e-10
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK- 252
            L++ N++  V   +LR LF                G+  + Y D   A  A+  L  K 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 253 PLRRRKLDIHFSIPKDNPS 271
            L  + +++ +S+ K   S
Sbjct: 62  ELHGKIMEVDYSVSKKLRS 80

>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 = 53.2 bits (127), Expect = 2e-09
 Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN-RS 337
            L + NL P+V+ +DLRQ+FG        +    K  + F+++ D   A  A+++L+ + 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQ-VLLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 338 DIAGKRIKLEPSRPGGAR 355
           ++ GK ++++ S     R
Sbjct: 62  ELHGKIMEVDYSVSKKLR 79

>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 = 56.6 bits (136), Expect = 2e-10
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
            L +++L     ++DL Q+F  +G V   +    K+ +      F+ + +  +A+AA++S
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           +N   I  KR+K++  R     +
Sbjct: 80  MNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 52.0 bits (124), Expect = 7e-09
 Identities = 16/93 (17%), Positives = 40/93 (43%), Gaps = 6/93 (6%)

Query: 182 AGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISY 236
           AG    G      LF+ ++     D +L  +F  +G++ +            + F  +SY
Sbjct: 9   AGSQKEGP-EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 67

Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
            +  +A+ A++++    +  ++L +     K++
Sbjct: 68  DNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 100

>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 = 55.9 bits (134), Expect = 3e-10
 Identities = 25/103 (24%), Positives = 43/103 (41%), Gaps = 6/103 (5%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI-----RTLYTACKHRGFVMISYYDIR 240
           P  +   R++FV NI     + +L+ +F + G +            K +G+    Y D  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSD-KDLNQGTLVV 282
            A +AMR L  +    R L +  +  + N  + K L  G  V+
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAPVI 104

>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 = 53.6 bits (128), Expect = 2e-09
 Identities = 20/95 (21%), Positives = 43/95 (45%), Gaps = 6/95 (6%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYD 323
           +P+  D +  ++ V N+    + E L+ IF   G V   R    +         F E+ D
Sbjct: 1   DPA-VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
              A +A+++LN  + +G+ ++++ +     +  L
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKEEL 94

>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 = 56.5 bits (135), Expect = 4e-10
 Identities = 28/128 (21%), Positives = 54/128 (42%), Gaps = 13/128 (10%)

Query: 233 MISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNE 292
           ++S YD       ++ LQ +  +         IP    + +      L+V  +  +V   
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQH--------IPPTQMNPEPDVLRNLMVNYIPTTVDEV 57

Query: 293 DLRQIFGAYGEVKEIRETPHKRHH-----KFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
            LRQ+F  YG ++ ++    +         F++F    +A+ A+  LN  +I  KR+K+ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 348 PSRPGGAR 355
            +  G  R
Sbjct: 118 LAASGHQR 125

>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 = 49.1 bits (116), Expect = 2e-07
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG-----FVMISYYDIRAARTA 245
             R L V  I + V++ +LR LFE+YG I ++   C         +  + +    +A+ A
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 246 MRALQNKPLRRRKLDIHFSIPKD 268
           +  L    +  ++L +  +    
Sbjct: 101 IAGLNGFNILNKRLKVALAASGH 123

>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 = 55.2 bits (132), Expect = 5e-10
 Identities = 28/104 (26%), Positives = 52/104 (50%), Gaps = 1/104 (0%)

Query: 279 TLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
            L+V NL+P  V+ + L  +FG YG+V+ ++   +K+ +  ++  D   A+ A+  LN  
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 63

Query: 338 DIAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGSP 381
            + GK I++  S+    +     Q +Q L +D      H+   P
Sbjct: 64  KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKP 107

>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 = 47.4 bits (112), Expect = 3e-07
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 1/89 (1%)

Query: 192 SRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           +  L V N+N   V    L  LF  YGD++ +      +   ++   D   A+ AM  L 
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 251 NKPLRRRKLDIHFSIPKDNPSDKDLNQGT 279
              L  + + I  S  ++    ++  +  
Sbjct: 62  GHKLHGKPIRITLSKHQNVQLPREGQEDQ 90

>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 = 54.3 bits (130), Expect = 7e-10
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           P+  L+V  +  N   + L   F+++G IRT+    K   F  I Y  + AA+ A   ++
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMR 74

Query: 251 NKPLRRRKLDIHFSIPKDNPS 271
             PL      +     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 = 46.2 bits (109), Expect = 5e-07
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            L V  L P+ S   L + F  +G ++ I          +I++  + AA+AA   +    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTID-HVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 339 IAG--KRIKLEPSRPG 352
           + G  +R++++ ++ G
Sbjct: 78  LGGPDRRLRVDFAKSG 93

>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 = 53.4 bits (128), Expect = 9e-10
 Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 6/71 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
           + +  L    + +DL+  F  +GEV +        T   R   F+ F +  + +  +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 335 NRSDIAGKRIK 345
               + GK I 
Sbjct: 61  KEHKLNGKVID 71

>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 = 41.5 bits (97), Expect = 2e-05
 Identities = 10/72 (13%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRAL 249
           +F+  ++ +    +L+  F ++G++            + RGF  + + +  +    M   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 250 QNKPLRRRKLDI 261
           +   L  + +D 
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 53.6 bits (128), Expect = 1e-09
 Identities = 20/87 (22%), Positives = 43/87 (49%), Gaps = 5/87 (5%)

Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAA 330
           ++G L V  L    + + L Q+F  YG++ E+       T   R   F+ F ++  A+ A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 331 LKSLNRSDIAGKRIKLEPSRPGGARRN 357
           + ++N   + G++I+++ +      R+
Sbjct: 64  MMAMNGKSVDGRQIRVDQAGKSSDNRS 90

>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 = 48.6 bits (115), Expect = 8e-08
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDI-----RTLYTACKHRGFVMISYYDIRAARTAM 246
              LFV  ++ +  +  L  +F +YG I            + RGF  +++ +I  A+ AM
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 247 RALQNKPLRRRKLDIHFSIPKDN 269
            A+  K +  R++ +  +    +
Sbjct: 65  MAMNGKSVDGRQIRVDQAGKSSD 87

>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 = 53.2 bits (127), Expect = 1e-09
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKE-----IRETPHKRHHKFIEFYDVRAAEAALKSL 334
           L +  L P  +++DL ++   YG++        + T   + + F++F    AA+ A+ +L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 335 NRSDIAGKRIK 345
             S +  +  K
Sbjct: 61  KASGVQAQMAK 71

>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 = 43.2 bits (101), Expect = 4e-06
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDI-----RTLYTACKHRGFVMISYYDIRAARTAMRAL 249
           L++R +     D +L  L + YG I         T  K +G+  + +    AA+ A+ AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 250 QNKPLRRRKL 259
           +   ++ +  
Sbjct: 61  KASGVQAQMA 70

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 6/71 (8%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKSL 334
           + V  L P    E +R+ FG +GEV+ I      + +K     FI F +    +  ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 335 NRSDIAGKRIK 345
              ++   + +
Sbjct: 61  KYHNVGLSKCE 71

>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 = 44.6 bits (105), Expect = 1e-06
 Identities = 12/72 (16%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMRAL 249
           +FV  ++ +  + ++R  F  +G++ ++           RGF  I++ +    +  M   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 250 QNKPLRRRKLDI 261
           +   +   K +I
Sbjct: 61  KYHNVGLSKCEI 72

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {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: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 3e-09
 Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 6/95 (6%)

Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYD 323
           + S KD     + V  L    ++  LR+ F  +G+++E      ++  K     F+   D
Sbjct: 2   HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 324 VRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
             AAE A K  N   I G++  +  +  G   R+L
Sbjct: 62  RAAAERACKDPN-PIIDGRKANVNLAYLGAKPRSL 95

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {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: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 9e-07
 Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 185 HPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDI 239
               +     +FV  +  +  D+ LR  FE +GDI            K RG+  ++  D 
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNP 270
            AA  A +   N  +  RK +++ +     P
Sbjct: 63  AAAERACKDP-NPIIDGRKANVNLAYLGAKP 92

>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 = 52.5 bits (125), Expect = 3e-09
 Identities = 19/93 (20%), Positives = 40/93 (43%), Gaps = 12/93 (12%)

Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDV 324
           PSD      T+ + NL      E L ++   +G++K +      +T H +   F +F   
Sbjct: 2   PSDVT-EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

Query: 325 RAAEAALKSLNRS------DIAGKRIKLEPSRP 351
            AA+  L + +         + G+++K++ +  
Sbjct: 61  EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 93

>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 = 50.6 bits (120), Expect = 2e-08
 Identities = 18/97 (18%), Positives = 41/97 (42%), Gaps = 11/97 (11%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIR 240
           P      +T+F+RN++ + E+  L  + +Q+GD++ +           +G     +    
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 241 AARTAMRALQ------NKPLRRRKLDIHFSIPKDNPS 271
           AA+  + A           L  R+L +  ++ +D  +
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {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: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.9 bits (126), Expect = 3e-09
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 6/90 (6%)

Query: 188 GEHPSRTLFVRNINSNVEDS-----ELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
           G   S  L     N +V        +  +LF  Y    T +   K    V I++ +  +A
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTT-FQYFKSFKRVRINFSNPLSA 59

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPSD 272
             A   L       +++ ++F+      S 
Sbjct: 60  ADARLRLHKTEFLGKEMKLYFAQTLHIGSS 89

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {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: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.2 bits (114), Expect = 1e-07
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 279 TLVVFNLDPSVSNE-----DLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKS 333
            L+    +  V +E         +F  Y +    +     +    I F +  +A  A   
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRV-RINFSNPLSAADARLR 65

Query: 334 LNRSDIAGKRIKLEPSRP 351
           L++++  GK +KL  ++ 
Sbjct: 66  LHKTEFLGKEMKLYFAQT 83

>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 = 52.1 bits (124), Expect = 5e-09
 Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAAR-----TA 245
           P++ L+++N++  V + +L +LF ++ + +      +     M     I          A
Sbjct: 17  PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 76

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPS 271
           +  +    L  + L I F   K   S
Sbjct: 77  LHLVNGYKLYGKILVIEFGKNKKQRS 102

>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 = 51.3 bits (122), Expect = 1e-08
 Identities = 25/94 (26%), Positives = 36/94 (38%), Gaps = 9/94 (9%)

Query: 267 KDNPSDKDLNQG----TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHK 317
           +  P     N G     L + NL P V+  DL  +F  + E K         T   R   
Sbjct: 4   RKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 63

Query: 318 FIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
           FI F +   A  AL  +N   + GK + +E  + 
Sbjct: 64  FITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 97

>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 = 51.2 bits (122), Expect = 7e-09
 Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 6/72 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKE-----IRETPHKRHHKFIEFYDVRAAEAALKS 333
            L +  L    ++E LR  F  +G + +        T   R   F+ +  V   +AA+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66

Query: 334 LNRSDIAGKRIK 345
                + 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 = 45.8 bits (108), Expect = 6e-07
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMR 247
           R LF+  ++    D  LR+ FEQ+G +              RGF  ++Y  +     AM 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 248 ALQNKPLRRRKLDI 261
           A +   +  R ++ 
Sbjct: 67  A-RPHKVDGRVVEP 79

>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 = 51.7 bits (123), Expect = 8e-09
 Identities = 16/100 (16%), Positives = 42/100 (42%), Gaps = 4/100 (4%)

Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISY 236
           G+   +G H      S  + VR +  +V +++L    E++G I  +      +   ++ +
Sbjct: 1   GSSGSSGSHHKVS-VSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEF 58

Query: 237 YDIRAARTAMRALQNKP--LRRRKLDIHFSIPKDNPSDKD 274
            +I +A+  +    + P  +  ++   ++S  K      +
Sbjct: 59  ENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGN 98

>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 = 44.0 bits (103), Expect = 4e-06
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 3/80 (3%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            + V  L  SV   DL +    +G +  +      +    +EF ++ +A+  +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVM-MMPFKRQALVEFENIDSAKECVTFAADVP 75

Query: 339 --IAGKRIKLEPSRPGGARR 356
             IAG++     S      R
Sbjct: 76  VYIAGQQAFFNYSTSKRITR 95

>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 = 50.5 bits (120), Expect = 1e-08
 Identities = 11/80 (13%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           G   S  + V+N+  +    E+  L + Y          +++    ++  +   A+ A++
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYV--DRNKRTAFVTLLNGEQAQNAIQ 58

Query: 248 ALQNKPLRRRKLDIHFSIPK 267
                  R + L +      
Sbjct: 59  MFHQYSFRGKDLIVQLQPTD 78

>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 = 44.7 bits (105), Expect = 1e-06
 Identities = 9/73 (12%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            ++V NL    + +++  +   Y            +   F+   +   A+ A++  ++  
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLK--YCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64

Query: 339 IAGKRIKLEPSRP 351
             GK + ++    
Sbjct: 65  FRGKDLIVQLQPT 77

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {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: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 2e-08
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRS 337
           TL + N+ PSVS EDL+ +F + G V +  +     R    I+   V  A  AL  L+  
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 71

Query: 338 DIA-GKRIKLEPSRP 351
           D+     +++  S+ 
Sbjct: 72  DLGENHHLRVSFSKS 86

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {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: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDI-RTLYTACKHRGFVMISYYDIRAARTAMRAL 249
           PS TL + NI  +V + +L+ LF   G + +      K R   +I    +  A  A+  L
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDL 68

Query: 250 QNKPLRR-RKLDIHFS 264
            N  L     L + FS
Sbjct: 69  HNHDLGENHHLRVSFS 84

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 8/80 (10%)

Query: 279 TLVVFNLDPSVSNED-LRQIFGAYGEVKEI------RETPHKRHHKFIEFYDVRAAEAAL 331
            +++ NL   + +E+ LR+ F  +G +++I      +E        F+ F +  +AE AL
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 332 KSLNRSDIAGKRIKLEPSRP 351
           + +NRS +  + I +  +  
Sbjct: 66  Q-MNRSLLGNREISVSLADK 84

>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 = 47.8 bits (113), Expect = 1e-07
 Identities = 14/83 (16%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 192 SRTLFVRNINSNV-EDSELRALFEQYGDIRTLYTA------CKHRGFVMISYYDIRAART 244
            R + +RN+++ + +++ LR  FE +G I  +           +     + + +  +A  
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 245 AMRALQNKPLRRRKLDIHFSIPK 267
           A+  +    L  R++ +  +  K
Sbjct: 64  AL-QMNRSLLGNREISVSLADKK 85

>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 = 49.3 bits (117), Expect = 4e-08
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 3/73 (4%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
           TL V+  D  ++   LR  F  +G + ++      R+  F+ +  + +A+ A+  LN + 
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLS-MDPPRNCAFVTYEKMESADQAVAELNGTQ 63

Query: 339 IAGKRIKLEPSRP 351
           +   ++K+  +R 
Sbjct: 64  VESVQLKVNIARK 76

>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 = 48.1 bits (114), Expect = 8e-08
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
              TL+V   +  +  + LR  F  +G+I  L           ++Y  + +A  A+  L 
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESADQAVAELN 60

Query: 251 NKPLRRRKLDIHFSIPK 267
              +   +L ++ +  +
Sbjct: 61  GTQVESVQLKVNIARKQ 77

>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 = 49.4 bits (117), Expect = 6e-08
 Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 4/83 (4%)

Query: 273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE----VKEIRETPHKRHHKFIEFYDVRAAE 328
           ++ +   L + NL  S+  ++L  +   +G+          +   R   F         E
Sbjct: 14  QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCE 73

Query: 329 AALKSLNRSDIAGKRIKLEPSRP 351
           A +   N   I        P+ P
Sbjct: 74  AVIGHFNGKFIKTPPGVSAPTEP 96

>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 = 45.9 bits (108), Expect = 8e-07
 Identities = 10/82 (12%), Positives = 26/82 (31%), Gaps = 4/82 (4%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGD----IRTLYTACKHRGFVMISYYDIRAART 244
           E     L++ N+  ++++ EL  + + +G          ++   RG              
Sbjct: 15  EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 245 AMRALQNKPLRRRKLDIHFSIP 266
            +     K ++        + P
Sbjct: 75  VIGHFNGKFIKTPPGVSAPTEP 96

>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 = 48.5 bits (115), Expect = 7e-08
 Identities = 12/77 (15%), Positives = 23/77 (29%), Gaps = 4/77 (5%)

Query: 191 PSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
             R + + +         +L  L E +G I              I       A+ A+   
Sbjct: 7   TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYY 65

Query: 250 QNKP--LRRRKLDIHFS 264
              P  +  + + +H S
Sbjct: 66  TTTPALVFGKPVRVHLS 82

>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 = 41.6 bits (97), Expect = 2e-05
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 4/76 (5%)

Query: 279 TLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLN 335
            + + +          L Q+   +G +       +K +  FIE      A+AA+   +  
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHL-ILNKINEAFIEMATTEDAQAAVDYYTTT 68

Query: 336 RSDIAGKRIKLEPSRP 351
            + + GK +++  S+ 
Sbjct: 69  PALVFGKPVRVHLSQK 84

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {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: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 9e-08
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGE-----VKEIRETPHKRHHKFIEFYDVRAAEAALKS 333
           T  + NL   V+ E +++ F           +E       +   + EF D+ +  +AL  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 75

Query: 334 LNRSDIAGKRIKLEPSRPGGARR 356
           LN   +  KRI+++ +     + 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 98

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {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: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 13/86 (15%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGD-----IRTLYTACKHRGFVMISYYDIRAARTA 245
           P  T F+ N+  +V +  ++  F           R      + +GF    + D+ +  +A
Sbjct: 14  PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPS 271
           + +L  + L  +++ +  +    +  
Sbjct: 74  L-SLNEESLGNKRIRVDVADQAQDKD 98

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

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]

 Score = 47.9 bits (113), Expect = 9e-08
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 1/75 (1%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           P++ LF+ N+     +  L  LF Q+   + +           + +     +  A  ALQ
Sbjct: 7   PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQ 66

Query: 251 NKPL-RRRKLDIHFS 264
              +     + I F+
Sbjct: 67  GFKITPTHAMKITFA 81

>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 = 48.5 bits (115), Expect = 1e-07
 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
                   E   ++   YGEV+E+        H   + +++F     AE A+  LN    
Sbjct: 34  EHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWF 93

Query: 340 AGKRIKLEPS 349
            G+ I  E S
Sbjct: 94  NGQPIHAELS 103

>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 = 40.4 bits (94), Expect = 8e-05
 Identities = 9/74 (12%), Positives = 24/74 (32%), Gaps = 4/74 (5%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAMRALQ 250
           + ++       +     + E+YG++  +             V + +     A  A+  L 
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 251 NKPLRRRKLDIHFS 264
           N+    + +    S
Sbjct: 90  NRWFNGQPIHAELS 103

>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 = 48.4 bits (115), Expect = 1e-07
 Identities = 12/61 (19%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 292 EDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
           EDLR     +G+++++     H      + F D   A+  +++L+     G++I  +   
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWD 93

Query: 351 P 351
            
Sbjct: 94  G 94

>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 = 43.0 bits (101), Expect = 8e-06
 Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 12/91 (13%)

Query: 191 PSRTLFVRNI--NSNVEDS---------ELRALFEQYGDIRTLYTACKH-RGFVMISYYD 238
             R + ++N+    + ED          +LR    ++G IR L    +H  G   +S+ D
Sbjct: 7   HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRD 66

Query: 239 IRAARTAMRALQNKPLRRRKLDIHFSIPKDN 269
              A   ++ L  +    R++         +
Sbjct: 67  PEEADYCIQTLDGRWFGGRQITAQAWDGTTD 97

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {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: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 6/72 (8%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            + V  +        LR  F  YG+++ I     R +  KR   F+ F D  + +  +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 334 LNRSDIAGKRIK 345
                + G   +
Sbjct: 63  QKYHTVNGHNCE 74

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {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: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK-----HRGFVMISYYDIRAARTAMR 247
           + +FV  I  + E+  LR  FEQYG I  +           RGF  +++ D  +    + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV- 61

Query: 248 ALQNKPLRRRKLDIHFSI 265
             +   +     ++  ++
Sbjct: 62  IQKYHTVNGHNCEVRKAL 79

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {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: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.5 bits (112), Expect = 2e-07
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
           PSR L +R +   V ++E+ AL   +G +       K +    +      AA T +    
Sbjct: 7   PSRVLHIRKLPGEVTETEVIALGLPFGKVTN-ILMLKGKNQAFLELATEEAAITMVNYYS 65

Query: 251 NKP--LRRRKLDIHFSIPK 267
                LR + + I +S  K
Sbjct: 66  AVTPHLRNQPIYIQYSNHK 84

>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 = 47.0 bits (111), Expect = 3e-07
 Identities = 12/80 (15%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 190 HPSRTLFVR--NINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
           + +++L V    + + V  ++L  + E+ G +  L     ++ +    Y     ++ A  
Sbjct: 16  YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYV 74

Query: 248 ALQNKPL---RRRKLDIHFS 264
            L  K +     +K+ ++ +
Sbjct: 75  TLNGKEVVDDLGQKITLYLN 94

>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 = 46.6 bits (110), Expect = 4e-07
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 279 TLVVF--NLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           +LVV    L   VS   L  +    G V  +   P  + + F  +     ++ A  +LN 
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALL-MPPNKPYSFARYRTTEESKRAYVTLNG 78

Query: 337 SDI---AGKRIKLEPS 349
            ++    G++I L  +
Sbjct: 79  KEVVDDLGQKITLYLN 94

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {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: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 8e-07
 Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 13/87 (14%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----------ETPHKRHHKFIEFYDVRAAE 328
            L V N+   ++ E +   F A   +  +           +    ++  F+EF  V    
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 329 AALKSLNRSDIAGKRIKLEPSRPGGAR 355
            A+   +     G+ +K+   RP   +
Sbjct: 63  QAMA-FDGIIFQGQSLKI--RRPHDYQ 86

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {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: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 8e-06
 Identities = 14/86 (16%), Positives = 26/86 (30%), Gaps = 13/86 (15%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTL----------YTACKHRGFVMISYYDIRAA 242
           R L+V NI   + +  +   F     +  L              + + F  + +  +   
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKD 268
             AM        + + L I    P D
Sbjct: 62  TQAMA-FDGIIFQGQSLKI--RRPHD 84

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

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]

 Score = 45.6 bits (107), Expect = 1e-06
 Identities = 16/102 (15%), Positives = 34/102 (33%), Gaps = 3/102 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
                +LD     EDL  +F  +GE+K I      +    +     + A    K  N  +
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGN 72

Query: 339 IAGKRIKLEPSRPGGARRNLMLQLNQELEQDESRILQHQVGS 380
           +  +  ++      G       +  +++ +D+   L      
Sbjct: 73  LQLRNKEVTWEVLEGEVEK---EALKKIIEDQQESLNKWKSK 111

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

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]

 Score = 44.8 bits (105), Expect = 3e-06
 Identities = 11/77 (14%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYD-IRAARTAMRALQN 251
              F  +++      +L  LF  +G+I+ +          +I + +  + A    +   N
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANN 70

Query: 252 KPLRRRKLDIHFSIPKD 268
             L+ R  ++ + + + 
Sbjct: 71  GNLQLRNKEVTWEVLEG 87

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {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: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 8/81 (9%), Positives = 27/81 (33%), Gaps = 5/81 (6%)

Query: 273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK----FIEFYDVRAAE 328
            D+   ++ +       + +D+++     G+V  I+             F+ F  + +A+
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 61

Query: 329 AALKSLNRSDIAGKRIKLEPS 349
             ++           + +   
Sbjct: 62  KFVE-TPGQKYKETDLLILFK 81

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {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: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 5e-06
 Identities = 8/80 (10%), Positives = 30/80 (37%), Gaps = 5/80 (6%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAART 244
           +  +R+++++   ++    +++   E  G +  +             + + +  I +A+ 
Sbjct: 3   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 62

Query: 245 AMRALQNKPLRRRKLDIHFS 264
            +     +  +   L I F 
Sbjct: 63  FV-ETPGQKYKETDLLILFK 81

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {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: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 4e-06
 Identities = 11/82 (13%), Positives = 23/82 (28%), Gaps = 2/82 (2%)

Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTA 245
           P        + V  +  +    +L+    + GD+          G V            A
Sbjct: 9   PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYL--RKEDMEYA 66

Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
           +R L +   R  + +  +    
Sbjct: 67  LRKLDDTKFRSHEGETSYIRVY 88

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {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: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.3 bits (96), Expect = 3e-05
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 2/79 (2%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
            ++V  L PS S +DL+      G+V        K     +E+      E AL+ L+ + 
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREAGDVCYAD--VQKDGMGMVEYLRKEDMEYALRKLDDTK 74

Query: 339 IAGKRIKLEPSRPGGARRN 357
                 +    R    R +
Sbjct: 75  FRSHEGETSYIRVYPERSS 93

>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 = 42.4 bits (99), Expect = 1e-05
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 5/74 (6%)

Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
            + V N+  +VS +++   F  Y  +         E         + F     A AA+  
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 334 LNRSDIAGKRIKLE 347
           LN   I  +++KL 
Sbjct: 71  LNDRPIGSRKVKLV 84

>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 = 38.5 bits (89), Expect = 3e-04
 Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH-----RGFVMISYYDIRAA 242
           G+     + V+N+   V   E+   F  Y  I        +      G  M+++     A
Sbjct: 5   GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 64

Query: 243 RTAMRALQNKPLRRRKLDI 261
             A+  L ++P+  RK+ +
Sbjct: 65  TAAVIDLNDRPIGSRKVKL 83

>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 = 0.001
 Identities = 10/75 (13%), Positives = 20/75 (26%), Gaps = 2/75 (2%)

Query: 689 SGEDTRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNVGYAFINMLSP 748
           SG+   T + ++N+P   +   +L                    +     G A +   S 
Sbjct: 4   SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSV--CLKYNEKGMPTGEAMVAFESR 61

Query: 749 LHIIPFYEAFNGKKW 763
                     N +  
Sbjct: 62  DEATAAVIDLNDRPI 76

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

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 = 42.2 bits (98), Expect = 1e-05
 Identities = 12/81 (14%), Positives = 25/81 (30%), Gaps = 5/81 (6%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG----FVMISYYDIRAARTAM 246
               LF+ N+N N   +EL+    +      L       G    F  + +        A+
Sbjct: 12  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71

Query: 247 RALQNKPLRRRKLDIHFSIPK 267
             L    +   ++ +     +
Sbjct: 72  E-LTGLKVFGNEIKLEKPKGR 91

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {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: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.7 bits (97), Expect = 2e-05
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 12/81 (14%)

Query: 277 QGTLV-VFNLDPSVSNEDLRQI------FGAYGEVKEIRETPHKRHHKF-----IEFYDV 324
           Q  LV V  L   +++ ++ +       FG   +V     T +           + +   
Sbjct: 7   QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 325 RAAEAALKSLNRSDIAGKRIK 345
             A  A++ +N   + G+ +K
Sbjct: 67  EDALRAIQCVNNVVVDGRTLK 87

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {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: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 0.001
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 11/78 (14%)

Query: 193 RTLFVRNINSNVEDSELRALFE---QYGDI--------RTLYTACKHRGFVMISYYDIRA 241
             +FV  ++  + D E+    E   ++G I         +   +        ++Y     
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 242 ARTAMRALQNKPLRRRKL 259
           A  A++ + N  +  R L
Sbjct: 69  ALRAIQCVNNVVVDGRTL 86

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

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 = 41.0 bits (95), Expect = 3e-05
 Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 2/78 (2%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           +VV  L PS S +DL+                ++     +EF        A++ L+ +  
Sbjct: 3   VVVSGLPPSGSWQDLKDHM--REAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF 60

Query: 340 AGKRIKLEPSRPGGARRN 357
                +    R       
Sbjct: 61  RSHEGETAYIRVKVDGPR 78

>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 = 40.7 bits (95), Expect = 5e-05
 Identities = 12/95 (12%), Positives = 31/95 (32%), Gaps = 17/95 (17%)

Query: 191 PSRTLFVRNI------NSNVEDSELR-ALFEQYGDIRTLYTACKHR----------GFVM 233
           P+  L + N+        + E  E+   + ++      + +    R          G + 
Sbjct: 3   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62

Query: 234 ISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 268
           + +  +   + AM+ L  +    R +   +  P  
Sbjct: 63  VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS 97

>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 = 39.6 bits (92), Expect = 1e-04
 Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 7/75 (9%)

Query: 284 NLDPSVSNEDLRQIFGAYGEVKEIR-------ETPHKRHHKFIEFYDVRAAEAALKSLNR 336
           + +     ED+R     YG VK I                 F+EF  V   + A++ L  
Sbjct: 21  DEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80

Query: 337 SDIAGKRIKLEPSRP 351
              A + +  +   P
Sbjct: 81  RKFANRVVVTKYCDP 95

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-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: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.6 bits (86), Expect = 3e-04
 Identities = 10/68 (14%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
           +++  L   V+N+++  +   Y    +       +   F+   +   AEAA+ + ++S +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY--ELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRL 58

Query: 340 AGKRIKLE 347
             + + ++
Sbjct: 59  RERELSVQ 66

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-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: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.8 bits (84), Expect = 7e-04
 Identities = 16/74 (21%), Positives = 26/74 (35%), Gaps = 3/74 (4%)

Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
           + +R +  +V + E+  L   Y          K   FV     +   A  A+       L
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVT--LLNGEQAEAAINTFHQSRL 58

Query: 255 RRRKLDIHFSIPKD 268
           R R+L +    P D
Sbjct: 59  RERELSVQLQ-PTD 71

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

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 = 38.4 bits (88), Expect = 4e-04
 Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 4/87 (4%)

Query: 191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ 250
               +  +N+ +    +E++  F ++G +  +          ++ + +   AR A R L 
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAFRHLA 67

Query: 251 NKPLRRRKLDIHFS---IPKDNPSDKD 274
                   L + ++   +    P  KD
Sbjct: 68  YSKFHHVPLYLEWAPIGVFGAAPQKKD 94

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

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]

 Score = 37.9 bits (87), Expect = 6e-04
 Identities = 14/97 (14%), Positives = 33/97 (34%), Gaps = 6/97 (6%)

Query: 267 KDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEF 321
           +            + +  L     N+ +   F     V++     +  + K     F+EF
Sbjct: 8   RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEF 67

Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
            +    +AAL   ++  +  + I++ P    G    +
Sbjct: 68  RNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKI 103

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {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: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.3 bits (85), Expect = 0.001
 Identities = 8/83 (9%), Positives = 20/83 (24%), Gaps = 2/83 (2%)

Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRA 248
           +   R + + N+  +           +       Y   + +    I       A   +  
Sbjct: 15  QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDH 74

Query: 249 LQNKP--LRRRKLDIHFSIPKDN 269
              K    + R + +  S     
Sbjct: 75  CLKKALWFQGRCVKVDLSEKYKK 97

>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 = 35.5 bits (82), Expect = 0.003
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 3/85 (3%)

Query: 695 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFLYLPIDFKNKCNV-GYAFINMLSPLHIIP 753
           + ++I+ +P   T + L   +    +  Y F +   D     ++   A+IN  +   II 
Sbjct: 2   SKVVIRRLPPTLTKEQLQEHLQPMPEHDY-FEFFSNDTSLYPHMYARAYINFKNQEDIIL 60

Query: 754 FYEAFNGKKWE-KFNSEKVASLAYA 777
           F + F+G  +      E  A + +A
Sbjct: 61  FRDRFDGYVFLDNKGQEYPAIVEFA 85

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	823
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.93
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.64
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.63
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.62
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.62
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.62
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.61
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.61
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.61
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.6
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.6
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.6
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.6
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.6
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.59
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.59
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.59
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.59
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.58
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.58
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.58
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.58
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.58
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.58
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.57
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.57
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.57
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.57
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.57
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.57
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.56
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.56
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.56
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.56
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.56
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.55
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.55
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.55
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.55
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.55
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.55
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.55
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.55
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.55
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.55
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.55
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.55
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.55
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.55
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.54
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.54
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.54
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.54
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.54
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.54
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.54
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.54
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.54
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.53
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.53
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.53
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.53
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.53
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.53
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.53
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.53
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.53
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.53
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.53
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.53
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.52
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.52
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.52
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.52
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.52
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.51
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.51
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.51
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	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
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.51
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.51
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.51
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.5
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.5
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.5
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.5
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.49
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.49
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.49
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.49
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.49
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.49
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.49
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.49
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.49
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.49
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.49
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.48
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.48
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.48
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.48
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.48
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.47
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.47
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.47
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.47
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.47
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.47
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.47
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.47
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.46
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.46
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.46
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.46
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.45
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.45
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.45
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.45
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.44
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.44
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.43
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.43
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.43
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.43
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.43
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.43
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.43
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.42
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.42
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.42
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.41
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.4
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.39
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.38
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	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
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.36
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.36
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.36
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.36
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.35
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.35
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.34
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.32
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.27
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.25
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.25
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	99.2
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.19
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.18
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.18
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.16
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.16
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.14
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.11
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.1
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.08
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	99.08
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.07
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.93
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.88
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.87
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.73
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.84
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.37
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	95.99
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.73
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	94.12
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	84.1
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	84.03

>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=99.93  E-value=2.2e-25  Score=220.23  Aligned_cols=162  Identities=20%  Similarity=0.383  Sum_probs=138.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      .|+|||+|||+++|+++|+++|++||+|.++.+     ++.++|||||+|.+.++|++|+.. .+..+..+.+.+....+
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            389999999999999999999999999999873     567899999999999999999984 56667777777766544


Q ss_pred             CCCC--CCCCCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCcc
Q 003400          267 KDNP--SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI  339 (823)
Q Consensus       267 k~~~--~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i  339 (823)
                      ....  .......++|||+|||..+|+++|+++|+.||.|..+.+     ++.++|||||+|.+.++|.+|++ +++..+
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            3321  122345579999999999999999999999999999865     35678999999999999999997 789999


Q ss_pred             CCceEEEEecCCCccc
Q 003400          340 AGKRIKLEPSRPGGAR  355 (823)
Q Consensus       340 ~Gr~I~V~~s~~~~~r  355 (823)
                      .|++|+|.+|.++.++
T Consensus       164 ~G~~i~V~~A~~k~e~  179 (183)
T d1u1qa_         164 NGHNCEVRKALSKQEM  179 (183)
T ss_dssp             TTEEEEEEECCCHHHH
T ss_pred             CCEEEEEEecCCcccc
Confidence            9999999999876543

>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=99.73  E-value=4.4e-18  Score=167.25  Aligned_cols=153  Identities=18%  Similarity=0.284  Sum_probs=121.9

Q ss_pred             ccccccccCCCCCChHHHHHhhcCCCcE---EEeccCccCcccceeEeeecCccccccc---cccccCCCCc-------c
Q 003400          114 MDDFDLRGLPSSLEDLEDYDIFGSGGGM---ELEGEPQESLSMSMSKISISDSASGNGL---LHYSVPNGAG-------T  180 (823)
Q Consensus       114 ~~el~V~~Lp~~~~E~el~dlFs~~G~v---~V~~d~~es~~~g~~~v~~~e~~~a~~~---~~~~l~n~~~-------~  180 (823)
                      .+++||++||..+++.+++++|+++|.|   .+..+...+..++++++.|.+...+...   ....+.....       .
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhc
Confidence            3689999999999999999999999987   5666777788889999999987665411   1111111110       1


Q ss_pred             ccCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccc
Q 003400          181 VAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (823)
Q Consensus       181 ~~~~~~~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~  255 (823)
                      ............++|||+|||.++|+++|+++|+.||.|..+.+     +++++|||||+|.+.++|++|++ +++..+.
T Consensus        86 ~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~  164 (183)
T d1u1qa_          86 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVN  164 (183)
T ss_dssp             TGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEET
T ss_pred             ccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeEC
Confidence            11112234556789999999999999999999999999999873     46788999999999999999997 7888999


Q ss_pred             cccccccccCCC
Q 003400          256 RRKLDIHFSIPK  267 (823)
Q Consensus       256 gr~L~V~~a~pk  267 (823)
                      |++|.|.+|.++
T Consensus       165 G~~i~V~~A~~k  176 (183)
T d1u1qa_         165 GHNCEVRKALSK  176 (183)
T ss_dssp             TEEEEEEECCCH
T ss_pred             CEEEEEEecCCc
Confidence            999999998764

>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=99.64  E-value=2.1e-16  Score=135.86  Aligned_cols=76  Identities=28%  Similarity=0.436  Sum_probs=70.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      .++|||+|||.++|+++|+++|++||.|.++++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+||+|
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            357999999999999999999999999999975     456789999999999999999999999999999999999987


Q ss_pred             C
Q 003400          352 G  352 (823)
Q Consensus       352 ~  352 (823)
                      +
T Consensus        82 g   82 (82)
T d1b7fa1          82 G   82 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.63  E-value=3.9e-16  Score=136.79  Aligned_cols=78  Identities=22%  Similarity=0.357  Sum_probs=72.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+|++
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            5579999999999999999999999999999975     45679999999999999999999999999999999999999


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      |+.
T Consensus        87 p~~   89 (90)
T d2cq0a1          87 PST   89 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>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=99.62  E-value=3.4e-16  Score=134.52  Aligned_cols=75  Identities=23%  Similarity=0.450  Sum_probs=70.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      +++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|+|++|
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            578999999999999999999999999999983     467899999999999999999999999999999999999976

>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=5.3e-16  Score=133.18  Aligned_cols=74  Identities=30%  Similarity=0.515  Sum_probs=69.7

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ++|||+|||.++++++|+++|++||.|.+|++     .+.++|||||+|.+.++|++|++.|||..+.|++|+|+||+|
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            57999999999999999999999999999976     356789999999999999999999999999999999999986

>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=5.4e-16  Score=133.10  Aligned_cols=75  Identities=23%  Similarity=0.478  Sum_probs=70.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      .++|||+|||.++++++|+++|++||+|.+|++     .++++|||||+|.+.++|++|++.|+|..+.|++|+|.|++|
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            468999999999999999999999999999874     467889999999999999999999999999999999999976

>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=99.61  E-value=5.9e-16  Score=135.10  Aligned_cols=79  Identities=24%  Similarity=0.388  Sum_probs=71.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ....+|||+|||.++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34579999999999999999999999999999975     3567899999999999999999999999999999999999


Q ss_pred             CCCc
Q 003400          350 RPGG  353 (823)
Q Consensus       350 ~~~~  353 (823)
                      .+++
T Consensus        85 ~~kG   88 (88)
T d1rk8a_          85 FVKG   88 (88)
T ss_dssp             EECC
T ss_pred             cCCC
Confidence            8753

>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=99.61  E-value=9.3e-16  Score=135.28  Aligned_cols=78  Identities=26%  Similarity=0.330  Sum_probs=72.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|++|+
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            3569999999999999999999999999999975     46789999999999999999999999999999999999998


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            865

>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=99.61  E-value=6.4e-16  Score=134.89  Aligned_cols=79  Identities=20%  Similarity=0.429  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..+.++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|+|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            446789999999999999999999999999999873     467899999999999999999999999999999999999


Q ss_pred             cCCC
Q 003400          264 SIPK  267 (823)
Q Consensus       264 a~pk  267 (823)
                      +.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9764

>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=99.60  E-value=5.8e-16  Score=135.65  Aligned_cols=79  Identities=22%  Similarity=0.459  Sum_probs=73.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .+.++|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|+|+
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            46789999999999999999999999999999974     4678999999999999999999999999999999999999


Q ss_pred             CCCC
Q 003400          265 IPKD  268 (823)
Q Consensus       265 ~pk~  268 (823)
                      +|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8764

>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=1e-15  Score=134.96  Aligned_cols=81  Identities=23%  Similarity=0.313  Sum_probs=73.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+|+.
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            4569999999999999999999999999999976     45678999999999999999999999999999999999997


Q ss_pred             CCcccc
Q 003400          351 PGGARR  356 (823)
Q Consensus       351 ~~~~r~  356 (823)
                      .....+
T Consensus        86 ~~~~gr   91 (93)
T d1h2vz_          86 GFKEGR   91 (93)
T ss_dssp             CCCTTC
T ss_pred             CCCCCC
Confidence            665443

>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=99.60  E-value=1.1e-15  Score=134.71  Aligned_cols=79  Identities=16%  Similarity=0.324  Sum_probs=73.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|+||
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            35689999999999999999999999999999974     4678999999999999999999999999999999999999


Q ss_pred             CCCC
Q 003400          265 IPKD  268 (823)
Q Consensus       265 ~pk~  268 (823)
                      .++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8754

>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=99.60  E-value=5.4e-16  Score=135.59  Aligned_cols=78  Identities=27%  Similarity=0.452  Sum_probs=72.6

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      .++|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..|.|+.|+|+++++
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            469999999999999999999999999999976     467899999999999999999999999999999999999987


Q ss_pred             Ccc
Q 003400          352 GGA  354 (823)
Q Consensus       352 ~~~  354 (823)
                      +..
T Consensus        85 ~~~   87 (89)
T d2cqba1          85 MRI   87 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=1.1e-15  Score=137.12  Aligned_cols=80  Identities=25%  Similarity=0.432  Sum_probs=73.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||+++++++|+++|+.||.|.++++     ++.++|||||+|.+.++|++||+.|||..|.|++|+|++++
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            4568999999999999999999999999998864     45678999999999999999999999999999999999999


Q ss_pred             CCccc
Q 003400          351 PGGAR  355 (823)
Q Consensus       351 ~~~~r  355 (823)
                      ++..+
T Consensus        97 ~k~~~  101 (102)
T d2cpza1          97 SKNDS  101 (102)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            98754

>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=99.59  E-value=2e-15  Score=133.34  Aligned_cols=80  Identities=26%  Similarity=0.518  Sum_probs=73.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHh-cCCccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRAL-QNKPLRRRKLDI  261 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~------~~ksrG~AFV~F~~~e~A~~Ai~~L-ng~~l~gr~L~V  261 (823)
                      ..++++|||+|||.++++++|+++|++||.|..|++      +++++|||||+|.+.++|++|++.| ++..+.|++|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            356789999999999999999999999999999984      4578999999999999999999998 899999999999


Q ss_pred             cccCCCC
Q 003400          262 HFSIPKD  268 (823)
Q Consensus       262 ~~a~pk~  268 (823)
                      .||.++.
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9997654

>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=99.59  E-value=2.2e-15  Score=133.06  Aligned_cols=78  Identities=24%  Similarity=0.477  Sum_probs=72.0

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe------CCCcccEEEEEEcCHHHHHHHHHHh-CCCccCCceEEEEe
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSL-NRSDIAGKRIKLEP  348 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri------~~~srG~aFVeF~d~e~A~kAl~~L-nG~~i~Gr~I~V~~  348 (823)
                      ...+|||+|||.++++++|+++|++||.|.+|++      ++.++|||||+|.+.++|.+|++.| ||..+.|++|+|+|
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            4568999999999999999999999999999986      3567899999999999999999998 89999999999999


Q ss_pred             cCCCc
Q 003400          349 SRPGG  353 (823)
Q Consensus       349 s~~~~  353 (823)
                      |++..
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98764

>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=99.59  E-value=5.5e-16  Score=135.56  Aligned_cols=78  Identities=27%  Similarity=0.500  Sum_probs=73.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      .+++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.|+.
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            5689999999999999999999999999999984     46889999999999999999999999999999999999998


Q ss_pred             CCC
Q 003400          266 PKD  268 (823)
Q Consensus       266 pk~  268 (823)
                      |+.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.59  E-value=2e-15  Score=132.24  Aligned_cols=80  Identities=30%  Similarity=0.406  Sum_probs=72.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~---~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++.   ...++||||+|.+.++|.+|++.|||..+.|+.|+|.|++++
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~   86 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP   86 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            45699999999999999999999999999999762   345789999999999999999999999999999999999877


Q ss_pred             ccc
Q 003400          353 GAR  355 (823)
Q Consensus       353 ~~r  355 (823)
                      ..+
T Consensus        87 ~~~   89 (90)
T d2cqia1          87 SSQ   89 (90)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            644

>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=99.59  E-value=9.5e-16  Score=135.91  Aligned_cols=82  Identities=22%  Similarity=0.366  Sum_probs=76.7

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      ...++|||+|||.++|+++|+++|++||.|..++.++.+++||||+|.+.++|++|++.|||..|.|++|+|+|+.++..
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            34679999999999999999999999999999999889999999999999999999999999999999999999998875


Q ss_pred             cc
Q 003400          355 RR  356 (823)
Q Consensus       355 r~  356 (823)
                      ++
T Consensus        94 ~r   95 (96)
T d1fjca_          94 TR   95 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.59  E-value=2.5e-15  Score=129.61  Aligned_cols=75  Identities=23%  Similarity=0.346  Sum_probs=70.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccC-CceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~-Gr~I~V~~s~  350 (823)
                      +.++|||+|||.++++++|+++|++||.|++|++...++|||||+|.+.++|.+|++.|||..|. |++|+|+||+
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            45799999999999999999999999999999998888899999999999999999999999885 6899999997

>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=99.58  E-value=2.4e-15  Score=137.15  Aligned_cols=99  Identities=21%  Similarity=0.421  Sum_probs=82.0

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri--~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      .++|||+|||.++++++|+++|++||.|++|++  ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|.++.+...
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~   86 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRA   86 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCch
Confidence            468999999999999999999999999999987  456789999999999999999999999999999999999875432


Q ss_pred             cchhhhccccccCHHHHHHHHhhcC
Q 003400          355 RRNLMLQLNQELEQDESRILQHQVG  379 (823)
Q Consensus       355 r~~~~~ql~~~~~~~~l~~~f~~~G  379 (823)
                      .    ........+..+.....++|
T Consensus        87 ~----~~~~~~~~~~~~~~~~~~~g  107 (114)
T d2f9da1          87 F----QKMDTKKKEEQLKLLKEKYG  107 (114)
T ss_dssp             T----TTSCHHHHHHHHHHHHHHHC
T ss_pred             h----hhhHHHHHHHHHHHHHHHhC
Confidence            2    22222334455666666776

>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=1.5e-15  Score=130.07  Aligned_cols=73  Identities=29%  Similarity=0.375  Sum_probs=68.7

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      +|||+|||+++|+++|+++|++||.|.+|++     ++.++|||||+|.++++|.+|++.|||..+.|++|+|.|++.
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            6999999999999999999999999999986     356789999999999999999999999999999999999864

>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=99.58  E-value=1.8e-15  Score=133.45  Aligned_cols=78  Identities=26%  Similarity=0.431  Sum_probs=72.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ..+++|||+|||.++|+++|+++|++||+|.+|.+     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.|+
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            46789999999999999999999999999999984     5678899999999999999999999999999999999998


Q ss_pred             CCC
Q 003400          265 IPK  267 (823)
Q Consensus       265 ~pk  267 (823)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.58  E-value=9.4e-16  Score=134.04  Aligned_cols=78  Identities=22%  Similarity=0.371  Sum_probs=71.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~---~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      .++|||+|||.++++++|+++|++||.|.++++.   ..++|||||+|.+.++|++|++.|||..|.|++|+|++++++.
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            4589999999999999999999999999999873   3357999999999999999999999999999999999999875


Q ss_pred             c
Q 003400          354 A  354 (823)
Q Consensus       354 ~  354 (823)
                      +
T Consensus        88 ~   88 (89)
T d1cvja2          88 E   88 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=2.2e-15  Score=129.86  Aligned_cols=77  Identities=18%  Similarity=0.352  Sum_probs=71.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccc-cccccccccC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR-RRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~-gr~L~V~~a~  265 (823)
                      ..|+++|||+|||.++|+++|+++|++||+|..|++....+|||||+|.+.++|++|++.|+|..+. |++|+|.||+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            4578999999999999999999999999999999987778899999999999999999999999884 6899999985

>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=99.58  E-value=2.1e-15  Score=128.54  Aligned_cols=73  Identities=25%  Similarity=0.395  Sum_probs=68.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ++|||+|||+++++++|+++|++||.|.++++    +++++|||||+|.+.++|++|++.|||..+.|++|+|+++.
T Consensus         1 grl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           1 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            36999999999999999999999999999986    45678899999999999999999999999999999999975

>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=99.58  E-value=3.1e-15  Score=133.21  Aligned_cols=82  Identities=26%  Similarity=0.395  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ...+++|||+|||+++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345788999999999999999999999999999984     467899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 003400          264 SIPKDNP  270 (823)
Q Consensus       264 a~pk~~~  270 (823)
                      +.++...
T Consensus        85 a~~~~~~   91 (99)
T d1whwa_          85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             CCCCCcc
Confidence            9876543

>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=1.2e-15  Score=130.71  Aligned_cols=74  Identities=22%  Similarity=0.287  Sum_probs=66.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      +||||+|||+++|+++|+++|++||.|..+.+     .+.++|||||+|.+.++|++|++.|||..+.|++|+|++++|
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            58999999999999999999999999977654     466799999999999999999999999999999999999987

>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=99.57  E-value=1.1e-15  Score=139.54  Aligned_cols=102  Identities=25%  Similarity=0.399  Sum_probs=84.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      ..+++|||+|||.++|+++|+++|++||+|.+|++  +++++|||||+|.+.++|..|++.|+|..|.|+.|.|.|+.+.
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            35789999999999999999999999999999984  5678999999999999999999999999999999999998643


Q ss_pred             CCCCCCCCCccceeeecCCCCCCHHHHHHHhcccCc
Q 003400          268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE  303 (823)
Q Consensus       268 ~~~~~~~~~~~tLfV~NLp~~vteedL~~~Fs~fG~  303 (823)
                      ....            .......+++++.+.++||.
T Consensus        85 ~~~~------------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          85 RAFQ------------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             HHTT------------TSCHHHHHHHHHHHHHHHCC
T ss_pred             chhh------------hhHHHHHHHHHHHHHHHhCC
Confidence            2111            11222346778888888873

>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=99.57  E-value=5e-15  Score=130.44  Aligned_cols=79  Identities=22%  Similarity=0.390  Sum_probs=72.2

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~---~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ....+|||+|||+++++++|+++|++||.|.+|++.   ..++|||||+|.+.++|++|++.|||..+.|++|+|+++++
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            345689999999999999999999999999999763   34689999999999999999999999999999999999988


Q ss_pred             Cc
Q 003400          352 GG  353 (823)
Q Consensus       352 ~~  353 (823)
                      +.
T Consensus        89 r~   90 (93)
T d2cq3a1          89 RV   90 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.57  E-value=2.7e-15  Score=131.35  Aligned_cols=80  Identities=19%  Similarity=0.442  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      +.+.++|||+|||.++|+++|+++|++||+|.+|++   ....+|||||+|.+.++|++|++.|+|..+.|+.|+|.|+.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            456789999999999999999999999999999984   23468999999999999999999999999999999999997


Q ss_pred             CCC
Q 003400          266 PKD  268 (823)
Q Consensus       266 pk~  268 (823)
                      ++.
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            644

>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=99.57  E-value=5.4e-15  Score=130.25  Aligned_cols=80  Identities=23%  Similarity=0.405  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ....++|||+|||.++++++|+++|++||+|..|++   ...++|||||+|.+.++|++|++.|++..+.|++|+|+|+.
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            345678999999999999999999999999999984   34468999999999999999999999999999999999998


Q ss_pred             CCC
Q 003400          266 PKD  268 (823)
Q Consensus       266 pk~  268 (823)
                      ++.
T Consensus        88 ~r~   90 (93)
T d2cq3a1          88 ARV   90 (93)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            764

>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=1.7e-15  Score=132.43  Aligned_cols=80  Identities=24%  Similarity=0.506  Sum_probs=72.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||+++++++|+++|++||.|..+.+     ++.++|||||+|.++++|++|++.|||..|.|++|+|+++.
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            3467999999999999999999999999999864     45679999999999999999999999999999999999998


Q ss_pred             CCccc
Q 003400          351 PGGAR  355 (823)
Q Consensus       351 ~~~~r  355 (823)
                      ++...
T Consensus        84 ~~~~~   88 (90)
T d1x5sa1          84 KSSDN   88 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77654

>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=99.57  E-value=2.4e-15  Score=134.86  Aligned_cols=79  Identities=16%  Similarity=0.387  Sum_probs=73.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      +.++|||+|||.++++++|+++|++||.|.++++     +++++|||||+|.+.++|++|++.|+|..|.|++|+|+|+.
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            5678999999999999999999999999988873     46789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 003400          266 PKDN  269 (823)
Q Consensus       266 pk~~  269 (823)
                      ++..
T Consensus        97 ~k~~  100 (102)
T d2cpza1          97 SKND  100 (102)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7654

>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=99.56  E-value=4.6e-15  Score=132.10  Aligned_cols=78  Identities=28%  Similarity=0.420  Sum_probs=72.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||+++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..|.|+.|+|++++
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            3568999999999999999999999999999976     45678999999999999999999999999999999999998


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      ++.
T Consensus        87 ~~~   89 (99)
T d1whwa_          87 IKK   89 (99)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            764

>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=99.56  E-value=2.8e-15  Score=129.97  Aligned_cols=75  Identities=17%  Similarity=0.402  Sum_probs=70.6

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      +|||+|||.++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+++.++.
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            6999999999999999999999999999976     46779999999999999999999999999999999999998754

>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=99.56  E-value=2.5e-15  Score=131.35  Aligned_cols=79  Identities=23%  Similarity=0.476  Sum_probs=72.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..++|||+|||+++++++|+++|++||.|..+.+     .++++|||||+|.+.++|++|++.|+|..|.|++|+|+++.
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            4688999999999999999999999999999862     56789999999999999999999999999999999999997


Q ss_pred             CCCC
Q 003400          266 PKDN  269 (823)
Q Consensus       266 pk~~  269 (823)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=1.5e-15  Score=130.09  Aligned_cols=74  Identities=19%  Similarity=0.229  Sum_probs=66.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      +||||+|||+++|+++|+++|++||.|..+.+     .++++|||||+|.+.++|++|++.|+|..+.|++|.|+++.|
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            69999999999999999999999999977652     567899999999999999999999999999999999999976

>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=99.56  E-value=1e-15  Score=137.59  Aligned_cols=81  Identities=23%  Similarity=0.421  Sum_probs=73.5

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      ..+++.++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|
T Consensus         3 ~~~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V   82 (104)
T d1p1ta_           3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRV   82 (104)
T ss_dssp             CSHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEE
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34455689999999999999999999999999999874     4678999999999999999999999999999999999


Q ss_pred             cccCCC
Q 003400          262 HFSIPK  267 (823)
Q Consensus       262 ~~a~pk  267 (823)
                      +|+.++
T Consensus        83 ~~a~~~   88 (104)
T d1p1ta_          83 DNAASE   88 (104)
T ss_dssp             EETTCT
T ss_pred             EECCCC
Confidence            998754

>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=5.1e-15  Score=139.78  Aligned_cols=81  Identities=23%  Similarity=0.455  Sum_probs=73.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ....++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..|.|++|+|+|
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            345689999999999999999999999999999874     467899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 003400          264 SIPKDN  269 (823)
Q Consensus       264 a~pk~~  269 (823)
                      +.++..
T Consensus       119 a~~~~~  124 (139)
T d1u6fa1         119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             cCCCCC
Confidence            976554

>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=99.55  E-value=4.6e-15  Score=140.11  Aligned_cols=78  Identities=28%  Similarity=0.457  Sum_probs=72.1

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      .++|||+|||.++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++||+.|||..|.|++|+|+++++
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            358999999999999999999999999999876     456789999999999999999999999999999999999987


Q ss_pred             Ccc
Q 003400          352 GGA  354 (823)
Q Consensus       352 ~~~  354 (823)
                      +..
T Consensus       122 ~~~  124 (139)
T d1u6fa1         122 GHQ  124 (139)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=5.3e-15  Score=128.01  Aligned_cols=75  Identities=24%  Similarity=0.434  Sum_probs=68.5

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC--ceEEEE
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLE  347 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G--r~I~V~  347 (823)
                      ...++|||+|||.++++++|+++|++||.|.++++     ++.++|||||+|.+.++|.+|++.|||..+.|  ++|+|+
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            34568999999999999999999999999999975     45678999999999999999999999999987  889999


Q ss_pred             ec
Q 003400          348 PS  349 (823)
Q Consensus       348 ~s  349 (823)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.55  E-value=3.8e-15  Score=128.74  Aligned_cols=74  Identities=24%  Similarity=0.465  Sum_probs=67.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCEEEEEeC--------CCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          195 LFVRNINSNVEDSELRALFEQYGDIRTLYTA--------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       195 LfV~NLP~~vteeeLr~lFs~fG~I~~v~~~--------~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      |||+|||.++|+++|+++|++||+|.+|++.        .+++|||||+|.+.++|++|++.|+|..+.|++|.|+|+.+
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            8999999999999999999999999998741        24689999999999999999999999999999999999865


Q ss_pred             CC
Q 003400          267 KD  268 (823)
Q Consensus       267 k~  268 (823)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.55  E-value=4.8e-15  Score=128.39  Aligned_cols=74  Identities=30%  Similarity=0.425  Sum_probs=67.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCC--ceEEEEe
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEP  348 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G--r~I~V~~  348 (823)
                      ..++|||+|||.++|+++|+++|++||.|.++++     ++.++|||||+|.+.++|++|++.|||..+.|  ++|+|+|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            4568999999999999999999999999999976     35678999999999999999999999999998  5699988


Q ss_pred             c
Q 003400          349 S  349 (823)
Q Consensus       349 s  349 (823)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=2.6e-15  Score=136.03  Aligned_cols=78  Identities=13%  Similarity=0.261  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      .+.+++|||+|||.++++++|+++|++||+|..|.+ .+.+|||||+|.+.++|++|++.|+|..|.|++|+|+|+...
T Consensus         7 ~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_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEe-eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            346689999999999999999999999999999976 567899999999999999999999999999999999998543

>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=99.55  E-value=1.8e-15  Score=134.01  Aligned_cols=81  Identities=22%  Similarity=0.385  Sum_probs=76.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      .++.++|||+|||.++|+++|+++|++||.|..++..++++|||||+|.+.++|++|++.|++..|.|++|+|.|+.++.
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            34678999999999999999999999999999988888999999999999999999999999999999999999998765


Q ss_pred             C
Q 003400          269 N  269 (823)
Q Consensus       269 ~  269 (823)
                      .
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=99.55  E-value=4.9e-15  Score=129.00  Aligned_cols=77  Identities=29%  Similarity=0.432  Sum_probs=70.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-eCCCcccEEEEEeCCHHHHHHHHHHhcCCcc-ccccccccccCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-TACKHRGFVMISYYDIRAARTAMRALQNKPL-RRRKLDIHFSIP  266 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l-~gr~L~V~~a~p  266 (823)
                      .|+++|||+|||.++++++|+++|++||.|..+. ...+.+|||||+|.+.++|.+|+..|+|..+ .|++|+|.|+++
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            4689999999999999999999999999998765 5677899999999999999999999999988 589999999864

>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=5.9e-15  Score=127.70  Aligned_cols=75  Identities=24%  Similarity=0.442  Sum_probs=68.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccc--cccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIH  262 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g--r~L~V~  262 (823)
                      ...++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+.|  ++|+|+
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            35678999999999999999999999999999873     46789999999999999999999999999976  889998


Q ss_pred             cc
Q 003400          263 FS  264 (823)
Q Consensus       263 ~a  264 (823)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.55  E-value=3.2e-15  Score=129.57  Aligned_cols=78  Identities=21%  Similarity=0.328  Sum_probs=71.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~  269 (823)
                      ..++|||+|||.++++++|+++|++||.|..+.+ .+++|||||+|.+.++|.+|+..|+|..|.|++|+|+|++|+..
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            3589999999999999999999999999887754 56899999999999999999999999999999999999988654

>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=5e-15  Score=131.35  Aligned_cols=76  Identities=24%  Similarity=0.389  Sum_probs=71.2

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ..+|||+|||.++++++|+++|++||.|.+|++.. .+|||||+|.+.++|++|+..|||..|.|+.|+|.|++++.
T Consensus        18 ~~~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          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe-cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            46899999999999999999999999999999864 48999999999999999999999999999999999998753

>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=99.55  E-value=3.7e-15  Score=128.84  Aligned_cols=74  Identities=24%  Similarity=0.397  Sum_probs=67.5

Q ss_pred             eeeecCCCCCCHHHHHHHhcccCceEEEEeC-----C---CcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-----P---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       280 LfV~NLp~~vteedL~~~Fs~fG~I~~iri~-----~---~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      |||+|||.++|+++|+++|++||.|.++++.     +   .++|||||+|.+.++|++|++.|||..+.|+.|+|+++++
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            7999999999999999999999999998752     1   2579999999999999999999999999999999999976


Q ss_pred             Cc
Q 003400          352 GG  353 (823)
Q Consensus       352 ~~  353 (823)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.55  E-value=6.5e-15  Score=131.14  Aligned_cols=75  Identities=21%  Similarity=0.363  Sum_probs=68.8

Q ss_pred             CccceeeecCC-CCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLD-PSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp-~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ...+|||+||+ ..+++++|+++|++||.|.+|++   ++|||||+|.+.++|++||+.|||+.|.|++|+|++++++.
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            34689999997 56888999999999999999998   58999999999999999999999999999999999997653

>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=7.4e-15  Score=129.80  Aligned_cols=79  Identities=18%  Similarity=0.341  Sum_probs=72.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~--~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ..+.++|||+|||.++|+++|+++|++||.|..+.+  ...+++||||+|.+.++|++|++.|++..|.|++|+|+|+++
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            356689999999999999999999999999999885  456789999999999999999999999999999999999875


Q ss_pred             C
Q 003400          267 K  267 (823)
Q Consensus       267 k  267 (823)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=8.5e-15  Score=129.41  Aligned_cols=77  Identities=31%  Similarity=0.508  Sum_probs=71.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe--CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri--~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ..++|||+|||+++|+++|+++|+.||.|..+++  ....++||||+|.+.++|++||+.|||..|.|++|+|+|+++.
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            4568999999999999999999999999999876  3456899999999999999999999999999999999999865

>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=99.54  E-value=7.6e-15  Score=132.52  Aligned_cols=77  Identities=25%  Similarity=0.380  Sum_probs=71.3

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          192 SRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       192 srtLfV~NLP~-~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      +++|||+|||+ .+|+++|+++|++||+|..|++....+|||||+|.+.++|++|++.|+|..|.|+.|+|+|+....
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            58999999965 599999999999999999999877789999999999999999999999999999999999986543

>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=99.54  E-value=3.9e-15  Score=127.42  Aligned_cols=72  Identities=17%  Similarity=0.367  Sum_probs=68.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       194 tLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      .|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.
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            6999999999999999999999999999984     46788999999999999999999999999999999999984

>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=1e-14  Score=130.40  Aligned_cols=78  Identities=13%  Similarity=0.254  Sum_probs=71.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +.+.++|||+|||.++++++|+++|++||+|..+.+    .++++|||||+|.+.++|++|++.|||..|.|+++.|.++
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            345689999999999999999999999999988763    5678899999999999999999999999999999999887


Q ss_pred             CC
Q 003400          265 IP  266 (823)
Q Consensus       265 ~p  266 (823)
                      .|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.54  E-value=4.3e-15  Score=128.75  Aligned_cols=76  Identities=18%  Similarity=0.413  Sum_probs=70.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      .+|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.++++|++|++.|++..+.|++|.|.|+.+.
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            47999999999999999999999999999974     4788999999999999999999999999999999999999754


Q ss_pred             C
Q 003400          268 D  268 (823)
Q Consensus       268 ~  268 (823)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=3.6e-15  Score=128.34  Aligned_cols=75  Identities=23%  Similarity=0.401  Sum_probs=68.2

Q ss_pred             eeeecCCCCCCHHHHHHHhcccCceEEE-Ee-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-RE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       280 LfV~NLp~~vteedL~~~Fs~fG~I~~i-ri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      |||+|||+++|+++|+++|++||.|.++ ++     +++++|||||+|.+.++|++|++.|||..+.|++|+|+++.++.
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            7999999999999999999999998654 33     45678999999999999999999999999999999999998875


Q ss_pred             c
Q 003400          354 A  354 (823)
Q Consensus       354 ~  354 (823)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.54  E-value=5.8e-15  Score=125.79  Aligned_cols=72  Identities=22%  Similarity=0.443  Sum_probs=68.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       194 tLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      +|||+|||+++++++|+++|++||.|.+|++    +++++|||||+|.+.++|++|++.|+|..+.|++|+|+++.
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            6999999999999999999999999999984    56788999999999999999999999999999999999874

>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=99.54  E-value=9.8e-15  Score=129.15  Aligned_cols=81  Identities=21%  Similarity=0.466  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhc------CCcccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQ------NKPLRR  256 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Ln------g~~l~g  256 (823)
                      .....++|||+|||.++|+++|+++|++||+|.++.+     .++++|||||+|.+.++|++|++.|+      |..+.|
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            3446789999999999999999999999999999873     45689999999999999999999886      566889


Q ss_pred             ccccccccCCCC
Q 003400          257 RKLDIHFSIPKD  268 (823)
Q Consensus       257 r~L~V~~a~pk~  268 (823)
                      ++|+|.|+.++.
T Consensus        84 r~l~v~~a~~k~   95 (98)
T d1x4ha1          84 RQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCC
Confidence            999999998764

>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=99.54  E-value=6.5e-15  Score=133.00  Aligned_cols=76  Identities=29%  Similarity=0.522  Sum_probs=70.8

Q ss_pred             ccceeeecCCC-CCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          277 QGTLVVFNLDP-SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       277 ~~tLfV~NLp~-~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ..+|||+||++ .+|+++|+++|++||.|+.|++...++|||||+|.++++|.+|++.|||..|.|+.|+|+|++..
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~~~   78 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            35899999965 59999999999999999999998888999999999999999999999999999999999998754

>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=1.8e-15  Score=129.63  Aligned_cols=77  Identities=27%  Similarity=0.364  Sum_probs=69.7

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCC-ccCCceEEEEecCCCccc
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS-DIAGKRIKLEPSRPGGAR  355 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~-~i~Gr~I~V~~s~~~~~r  355 (823)
                      .+|||+|||.++|+++|+++|++||.|.++++. .++|||||+|.+.++|++|++.|||. .+.|++|+|+++.++..|
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEe-cccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            379999999999999999999999998876653 46899999999999999999999996 699999999999987654

>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=8.7e-15  Score=126.72  Aligned_cols=73  Identities=25%  Similarity=0.409  Sum_probs=66.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccc--cccccccc
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFS  264 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g--r~L~V~~a  264 (823)
                      .++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|  ++|.|.||
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            578999999999999999999999999999874     46789999999999999999999999999987  45888775

>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=99.53  E-value=3.6e-15  Score=130.22  Aligned_cols=77  Identities=17%  Similarity=0.361  Sum_probs=70.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      ..+|||+|||.++++++|+++|++||.|..|++   ...++|||||+|.+.++|++|++.|+|..+.|++|.|.++.++.
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            468999999999999999999999999999884   34468999999999999999999999999999999999998654

>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=6.3e-15  Score=127.90  Aligned_cols=76  Identities=22%  Similarity=0.390  Sum_probs=67.2

Q ss_pred             CccceeeecCCCCCCH-HHHHHHhcccCceEEEEe------CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          276 NQGTLVVFNLDPSVSN-EDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       276 ~~~tLfV~NLp~~vte-edL~~~Fs~fG~I~~iri------~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      ..++|||+|||.++++ ++|+++|++||.|.+|++      ++.++|||||+|.+.++|++|++ |||..+.|+.|+|++
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            4569999999999865 569999999999999976      34578999999999999999995 999999999999999


Q ss_pred             cCCC
Q 003400          349 SRPG  352 (823)
Q Consensus       349 s~~~  352 (823)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>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=99.53  E-value=9.8e-15  Score=131.02  Aligned_cols=80  Identities=26%  Similarity=0.343  Sum_probs=71.2

Q ss_pred             CCCccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEe
Q 003400          274 DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP  348 (823)
Q Consensus       274 ~~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~  348 (823)
                      +...++|||+|||.++++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++||+.+|+ .|.|++|+|++
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            334567999999999999999999999999999976     356899999999999999999998876 79999999999


Q ss_pred             cCCCcc
Q 003400          349 SRPGGA  354 (823)
Q Consensus       349 s~~~~~  354 (823)
                      +..+..
T Consensus        86 a~~~~~   91 (103)
T d2cqda1          86 AYLGAK   91 (103)
T ss_dssp             STTTCC
T ss_pred             cCCCCC
Confidence            976543

>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=99.53  E-value=9.9e-15  Score=125.61  Aligned_cols=71  Identities=28%  Similarity=0.518  Sum_probs=66.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL  346 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V  346 (823)
                      ..++|||+|||.++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|
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            4579999999999999999999999999999875     3567899999999999999999999999999999987

>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=99.53  E-value=1e-14  Score=126.87  Aligned_cols=77  Identities=29%  Similarity=0.371  Sum_probs=69.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEE-eCCCcccEEEEEEcCHHHHHHHHHHhCCCcc-CCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-ETPHKRHHKFIEFYDVRAAEAALKSLNRSDI-AGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir-i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i-~Gr~I~V~~s~~~  352 (823)
                      +.++|||+|||.++++++|+++|++||.|..++ ..++.++||||+|.+.++|.+|+..|||..+ +|+.|+|+|+++.
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            356899999999999999999999999998765 4667789999999999999999999999988 5899999999863

>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=99.53  E-value=8.4e-15  Score=126.92  Aligned_cols=77  Identities=26%  Similarity=0.264  Sum_probs=71.0

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      .++|||+|||.++++++|+++|++||.|..+++ +.++|||||+|.+.++|.+|+..|||..|.|+.|+|+|++|+..
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~-~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE-EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE-ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            368999999999999999999999999887776 45789999999999999999999999999999999999998753

>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=99.53  E-value=9.2e-15  Score=129.63  Aligned_cols=76  Identities=14%  Similarity=0.326  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      +.++|||+|||.++++++|+++|++||+|.+|++. +.+|||||+|.+.++|++|+..|+|..|.|++|+|.|++++
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            45799999999999999999999999999999864 46999999999999999999999999999999999999764

>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=99.53  E-value=6.7e-15  Score=126.69  Aligned_cols=72  Identities=22%  Similarity=0.444  Sum_probs=67.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDI  261 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V  261 (823)
                      .++++|||+|||.++|+++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            46789999999999999999999999999999874     4678999999999999999999999999999999876

>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=99.53  E-value=2.6e-15  Score=130.97  Aligned_cols=79  Identities=24%  Similarity=0.459  Sum_probs=73.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~  269 (823)
                      ..+++|||+|||.++|+++|+++|++||+|.+|++...++|||||+|.+.++|++|+.  ++..|.|++|.|.++.++..
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            4679999999999999999999999999999999888899999999999999999996  78889999999999987654


Q ss_pred             C
Q 003400          270 P  270 (823)
Q Consensus       270 ~  270 (823)
                      .
T Consensus        81 ~   81 (88)
T d1wf0a_          81 S   81 (88)
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=99.53  E-value=4.8e-15  Score=133.08  Aligned_cols=78  Identities=23%  Similarity=0.391  Sum_probs=71.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      .++|||+|||.++++++|+++|++||+|.+|++     ++.++|||||+|.+.++|++|++.|||..|.|+.|+|+++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            468999999999999999999999999999875     456789999999999999999999999999999999999987


Q ss_pred             Ccc
Q 003400          352 GGA  354 (823)
Q Consensus       352 ~~~  354 (823)
                      ...
T Consensus        88 ~~~   90 (104)
T d1p1ta_          88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             CCC
Confidence            643

>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=99.53  E-value=2.9e-15  Score=134.17  Aligned_cols=76  Identities=21%  Similarity=0.450  Sum_probs=69.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++++++|+++|+.||.|.+|++     ++.++|||||+|.+.++|.+|+. |||..|.|+.|+|++++
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            3468999999999999999999999999999976     46789999999999999999995 99999999999999986


Q ss_pred             CC
Q 003400          351 PG  352 (823)
Q Consensus       351 ~~  352 (823)
                      ++
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=8e-15  Score=127.35  Aligned_cols=76  Identities=25%  Similarity=0.425  Sum_probs=71.0

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      .++|||+|||.++++++|+++|++||+|.+|++. +.++||||+|.+.++|++|++.|||..|.|++|+|+||.++.
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            4579999999999999999999999999999986 457999999999999999999999999999999999998764

>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=1.4e-14  Score=129.91  Aligned_cols=81  Identities=25%  Similarity=0.418  Sum_probs=71.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      +...++|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.+++ .|.|++|.|++
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            345578999999999999999999999999999984     467899999999999999999998875 79999999999


Q ss_pred             cCCCCCC
Q 003400          264 SIPKDNP  270 (823)
Q Consensus       264 a~pk~~~  270 (823)
                      +.++..+
T Consensus        86 a~~~~~p   92 (103)
T d2cqda1          86 AYLGAKP   92 (103)
T ss_dssp             STTTCCC
T ss_pred             cCCCCCC
Confidence            8765443

>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=99.52  E-value=8.4e-15  Score=132.58  Aligned_cols=76  Identities=17%  Similarity=0.267  Sum_probs=70.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ..++|||+|||+++++++|+++|++||.|..|++. ..++||||+|.+.++|++|++.|||..|.|++|.|+|+...
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            34689999999999999999999999999999984 57899999999999999999999999999999999998654

>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=99.52  E-value=5.9e-15  Score=129.40  Aligned_cols=79  Identities=23%  Similarity=0.593  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHH----HhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRA----LFEQYGDIRTLYT--ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~----lFs~fG~I~~v~~--~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      +|+++|||+|||.+++++||++    +|++||+|.+|++  +++++|||||+|.+.++|.+|++.++|..+.|+.|.|.|
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    6899999999985  356789999999999999999999999999999999999


Q ss_pred             cCCCC
Q 003400          264 SIPKD  268 (823)
Q Consensus       264 a~pk~  268 (823)
                      +.++.
T Consensus        81 ak~~~   85 (91)
T d1nu4a_          81 AKTDS   85 (91)
T ss_dssp             CSSCC
T ss_pred             eCCCc
Confidence            97654

>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=99.52  E-value=1.3e-14  Score=127.28  Aligned_cols=78  Identities=14%  Similarity=0.324  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...++|||+|||+++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.  ...|.|+.|.|+++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            45689999999999999999999999999999973     578999999999999999999985  44789999999999


Q ss_pred             CCCCC
Q 003400          265 IPKDN  269 (823)
Q Consensus       265 ~pk~~  269 (823)
                      .++..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87653

>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=1e-14  Score=126.66  Aligned_cols=76  Identities=32%  Similarity=0.566  Sum_probs=70.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      .++|||+|||.++++++|+++|++||+|.+|++. +.+|||||+|.+.++|++|++.|+|..+.|++|+|+||.++.
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            4689999999999999999999999999999864 568999999999999999999999999999999999997653

>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=9.4e-15  Score=124.75  Aligned_cols=74  Identities=22%  Similarity=0.434  Sum_probs=68.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ..++|||+|++  +|+++|+++|++||.|.+|++. +.++||||+|.+.++|.+|++.|||..+.|++|+|+|++++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~-~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeec-cCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            34699999986  9999999999999999999985 46789999999999999999999999999999999999875

>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=99.51  E-value=3.1e-15  Score=128.16  Aligned_cols=76  Identities=22%  Similarity=0.367  Sum_probs=68.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCC-ccccccccccccCCCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK-PLRRRKLDIHFSIPKDN  269 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~-~l~gr~L~V~~a~pk~~  269 (823)
                      .+|||+|||.++|+++|+++|++||.|.++++ .+.+|||||+|.+.++|++|++.|+|. .+.|++|+|+|+.|+..
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~-~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCE-EEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEE-ecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            47999999999999999999999999877643 357899999999999999999999996 59999999999988654

>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=126.19  Aligned_cols=78  Identities=22%  Similarity=0.395  Sum_probs=70.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhC------CCccCCceE
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLN------RSDIAGKRI  344 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~Ln------G~~i~Gr~I  344 (823)
                      ..++|||+|||+++|+++|+++|++||.|.++++     .+.++|||||+|.+.++|.+|++.||      |..+.|++|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            3568999999999999999999999999999875     34578999999999999999999987      567899999


Q ss_pred             EEEecCCCc
Q 003400          345 KLEPSRPGG  353 (823)
Q Consensus       345 ~V~~s~~~~  353 (823)
                      +|++++++.
T Consensus        87 ~v~~a~~k~   95 (98)
T d1x4ha1          87 KVDLAVTRD   95 (98)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999998865

>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=1.1e-14  Score=129.59  Aligned_cols=80  Identities=25%  Similarity=0.368  Sum_probs=70.9

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEE-------------eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-------------ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG  341 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir-------------i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G  341 (823)
                      ....+|||+|||..+|+++|+++|+.||.|..+.             .+++++|||||+|.++++|.+|++.|||..|.|
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            3567999999999999999999999999886432             135678999999999999999999999999999


Q ss_pred             ceEEEEecCCCcc
Q 003400          342 KRIKLEPSRPGGA  354 (823)
Q Consensus       342 r~I~V~~s~~~~~  354 (823)
                      ++|+|++++++..
T Consensus        86 r~i~V~~a~~~~p   98 (101)
T d2cpea1          86 SKLKVSLARKKPP   98 (101)
T ss_dssp             EECEEECSSCCCC
T ss_pred             EEEEEEEcCCCCC
Confidence            9999999987653

>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=1.2e-14  Score=124.14  Aligned_cols=75  Identities=20%  Similarity=0.366  Sum_probs=69.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPK  267 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk  267 (823)
                      +..++|||+||+  +|+++|+++|++||+|.+|++ .+.+|||||+|.+.++|.+|++.|+|..+.|++|+|.|++++
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            457899999996  999999999999999999976 457899999999999999999999999999999999999764

>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=99.51  E-value=4.9e-15  Score=129.14  Aligned_cols=76  Identities=20%  Similarity=0.336  Sum_probs=71.2

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      .++|||+|||.++|+++|+++|++||.|.+|++...+++||||+|.+.++|++|+.  ++..|.|++|+|++++++..
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            56999999999999999999999999999999988889999999999999999986  78899999999999987653

>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=129.80  Aligned_cols=82  Identities=22%  Similarity=0.357  Sum_probs=72.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-------------eCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------------TACKHRGFVMISYYDIRAARTAMRALQNKP  253 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-------------~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~  253 (823)
                      ..+...++|||+|||.++|+++|+++|++||.|..+.             .+++++|||||+|.+.++|++|++.|+|..
T Consensus         3 ~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~   82 (101)
T d2cpea1           3 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   82 (101)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCE
Confidence            3455678999999999999999999999999985432             136788999999999999999999999999


Q ss_pred             cccccccccccCCCC
Q 003400          254 LRRRKLDIHFSIPKD  268 (823)
Q Consensus       254 l~gr~L~V~~a~pk~  268 (823)
                      |.|++|+|+++.++.
T Consensus        83 ~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          83 FQGSKLKVSLARKKP   97 (101)
T ss_dssp             ETTEECEEECSSCCC
T ss_pred             ECCEEEEEEEcCCCC
Confidence            999999999997654

>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=99.51  E-value=4.3e-15  Score=132.68  Aligned_cols=80  Identities=21%  Similarity=0.406  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .|+++|||+|||.++++++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++.|+|..|.|++|+|.|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            4789999999999999999999999999887654     36789999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 003400          265 IPKDN  269 (823)
Q Consensus       265 ~pk~~  269 (823)
                      .++..
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87654

>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=99.50  E-value=2.2e-14  Score=125.67  Aligned_cols=77  Identities=21%  Similarity=0.391  Sum_probs=69.4

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...+|||+|||+++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++||+.  +..|+|+.|.|+++.
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            4568999999999999999999999999999975     577899999999999999999984  458999999999998


Q ss_pred             CCcc
Q 003400          351 PGGA  354 (823)
Q Consensus       351 ~~~~  354 (823)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            8653

>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=99.50  E-value=5.3e-15  Score=127.26  Aligned_cols=74  Identities=20%  Similarity=0.483  Sum_probs=67.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCEEEE-E-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          195 LFVRNINSNVEDSELRALFEQYGDIRTL-Y-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       195 LfV~NLP~~vteeeLr~lFs~fG~I~~v-~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      |||+|||.++|+++|+++|++||.|..+ +     .+++++|||||+|.+.++|++|++.|+|..+.|++|+|+|+.++.
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 3     246789999999999999999999999999999999999998754

>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=1.1e-14  Score=130.82  Aligned_cols=77  Identities=17%  Similarity=0.306  Sum_probs=70.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      .++|||+|||+++++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++ ++|..|.|+.|.|+++.+
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            368999999999999999999999999999976     35679999999999999999996 799999999999999988


Q ss_pred             Ccc
Q 003400          352 GGA  354 (823)
Q Consensus       352 ~~~  354 (823)
                      +.+
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>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=1.9e-14  Score=128.13  Aligned_cols=76  Identities=28%  Similarity=0.520  Sum_probs=69.2

Q ss_pred             CCCcEEEEcCCC-CCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          190 HPSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       190 ~~srtLfV~NLP-~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      ...++|||+||| ..+++++|+++|++||.|.+|++   ++|||||+|.+.++|++|++.|+|..|.|++|+|.|+.++.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            445789999997 56889999999999999999987   68999999999999999999999999999999999997643

>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=99.49  E-value=9.2e-15  Score=126.87  Aligned_cols=76  Identities=18%  Similarity=0.394  Sum_probs=67.5

Q ss_pred             CCcEEEEcCCCCCCC-HHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          191 PSRTLFVRNINSNVE-DSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       191 ~srtLfV~NLP~~vt-eeeLr~lFs~fG~I~~v~~------~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      ..++|||+|||.+++ +++|+++|++||+|.+|++      +++++|||||+|.+.++|++|++ |++..+.|++|+|++
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            468999999999986 5669999999999999984      45688999999999999999996 999999999999999


Q ss_pred             cCCC
Q 003400          264 SIPK  267 (823)
Q Consensus       264 a~pk  267 (823)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9764

>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=99.49  E-value=1.6e-14  Score=129.13  Aligned_cols=77  Identities=21%  Similarity=0.278  Sum_probs=69.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ..++|||+|||.++++++|+++|++||.|..+++    ++.++|||||+|.+.++|++|++.|||..|.|+++.|.+++|
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            3468999999999999999999999999988864    456789999999999999999999999999999999988876


Q ss_pred             C
Q 003400          352 G  352 (823)
Q Consensus       352 ~  352 (823)
                      -
T Consensus        97 l   97 (101)
T d1x5oa1          97 L   97 (101)
T ss_dssp             B
T ss_pred             c
Confidence            3

>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=3.7e-14  Score=122.54  Aligned_cols=74  Identities=19%  Similarity=0.338  Sum_probs=67.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++|+++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++ +++..|.|+.|+|+.|.
T Consensus         5 ~~~~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           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            3468999999999999999999999999999875     46789999999999999999997 69999999999998874

>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=99.49  E-value=3.4e-14  Score=120.11  Aligned_cols=71  Identities=15%  Similarity=0.338  Sum_probs=65.3

Q ss_pred             eeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCC
Q 003400          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       280 LfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      |||+|||+++++++|+++|++|| +..+++ ++++|||||+|.+.++|++|++.|||..+.|++|+|++++..
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 555555 467899999999999999999999999999999999999764

>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=99.49  E-value=1e-14  Score=130.22  Aligned_cols=80  Identities=29%  Similarity=0.343  Sum_probs=72.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      +.++|||+|||.++++++|+++|+.||.|..+++     ++.++|||||+|.+.++|.+|++.|||..|.|++|+|+|++
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            4578999999999999999999999998877643     57789999999999999999999999999999999999999


Q ss_pred             CCccc
Q 003400          351 PGGAR  355 (823)
Q Consensus       351 ~~~~r  355 (823)
                      ++..|
T Consensus        97 ~k~~r  101 (102)
T d2cpxa1          97 NKKQR  101 (102)
T ss_dssp             CCSCC
T ss_pred             CcccC
Confidence            87654

>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=99.49  E-value=2.4e-14  Score=129.47  Aligned_cols=81  Identities=21%  Similarity=0.286  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHhcCCcc--ccccccccccC
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKPL--RRRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l--~gr~L~V~~a~  265 (823)
                      ..+..+|||+|||.++|+++|+++|++||.|.+|.+ ..+++|||||+|.+.++|++|++.|+|..|  .+++|+|.|+.
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            346688999999999999999999999999999874 345789999999999999999999999998  47889999987


Q ss_pred             CCCC
Q 003400          266 PKDN  269 (823)
Q Consensus       266 pk~~  269 (823)
                      ++..
T Consensus        84 ~~~~   87 (108)
T d2adba1          84 LTSL   87 (108)
T ss_dssp             SCSC
T ss_pred             Cccc
Confidence            6543

>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=99.49  E-value=2.8e-14  Score=126.17  Aligned_cols=81  Identities=21%  Similarity=0.338  Sum_probs=70.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCC-EEEEEe------CCCcccEEEEEeCCHHHHHHHHHHhcC--Ccccccccccc
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGD-IRTLYT------ACKHRGFVMISYYDIRAARTAMRALQN--KPLRRRKLDIH  262 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~-I~~v~~------~~ksrG~AFV~F~~~e~A~~Ai~~Lng--~~l~gr~L~V~  262 (823)
                      +++|||+|||.++++++|+++|++||+ |..+.+      .++++|||||+|.+.++|.+|++.|++  ..+.|++|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 888874      356889999999999999999999965  44579999999


Q ss_pred             ccCCCCCCCC
Q 003400          263 FSIPKDNPSD  272 (823)
Q Consensus       263 ~a~pk~~~~~  272 (823)
                      ||.|+..+..
T Consensus        81 ~A~p~~~~~~   90 (96)
T d2disa1          81 WAEPEIDVDE   90 (96)
T ss_dssp             ESCSSCSTTT
T ss_pred             EcCCCCCCCh
Confidence            9998776644

>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=99.49  E-value=1.4e-14  Score=126.36  Aligned_cols=75  Identities=13%  Similarity=0.290  Sum_probs=66.2

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ..+|||+|||.+++++||+++|++|| ++.+.+ +..++||||+|.+.++|++|++.|||..+.|++|+|++++++.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~-~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            45899999999999999999999999 333333 3568999999999999999999999999999999999997653

>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=99.49  E-value=1.7e-14  Score=126.37  Aligned_cols=78  Identities=22%  Similarity=0.448  Sum_probs=70.3

Q ss_pred             ccceeeecCCCCCCHHHHHH----HhcccCceEEEEeC--CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQ----IFGAYGEVKEIRET--PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~----~Fs~fG~I~~iri~--~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      .++|||+|||.+++++||++    +|++||+|.+|++.  +.++|||||+|.+.++|.+|++.|||..+.|+.|+|.|++
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak   82 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK   82 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            46899999999999999864    68999999999873  3468999999999999999999999999999999999998


Q ss_pred             CCcc
Q 003400          351 PGGA  354 (823)
Q Consensus       351 ~~~~  354 (823)
                      ++.+
T Consensus        83 ~~~~   86 (91)
T d1nu4a_          83 TDSD   86 (91)
T ss_dssp             SCCT
T ss_pred             CCch
Confidence            8654

>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=99.49  E-value=2.8e-14  Score=120.59  Aligned_cols=70  Identities=20%  Similarity=0.371  Sum_probs=64.4

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      +|||+|||+++|+++|+++|++||.|..+++     +++++|||||+|.+.++|++|++ +++..|.|+.|+|+.|
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            4899999999999999999999999999975     46679999999999999999997 7999999999998654

>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=99.49  E-value=3.7e-14  Score=126.14  Aligned_cols=80  Identities=14%  Similarity=0.193  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          187 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       187 ~~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ...+..++|||+|||.++++++|+++|++||+|..|.+.  .+|||||+|.+.++|++|++.|++..|.|+.|+|.++.+
T Consensus        10 ~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~   87 (98)
T d1wg4a_          10 PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ--KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             CCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE--TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhhccccccccc--ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEec
Confidence            344567899999999999999999999999999999863  569999999999999999999999999999999999876


Q ss_pred             CC
Q 003400          267 KD  268 (823)
Q Consensus       267 k~  268 (823)
                      +.
T Consensus        88 ~~   89 (98)
T d1wg4a_          88 YP   89 (98)
T ss_dssp             EC
T ss_pred             CC
Confidence            54

>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=99.48  E-value=4.9e-14  Score=122.59  Aligned_cols=80  Identities=24%  Similarity=0.342  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHh--cCCccccccccccccC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL--QNKPLRRRKLDIHFSI  265 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~L--ng~~l~gr~L~V~~a~  265 (823)
                      ...|+++|||+|||.++++++|+++|++||.|.++++ .+.++||||+|.+.++|++|++.+  ++..+.|++|+|.|+.
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~-~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk   82 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   82 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccc-cccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECC
Confidence            3468999999999999999999999999999999975 456899999999999999999876  4678999999999997


Q ss_pred             CCC
Q 003400          266 PKD  268 (823)
Q Consensus       266 pk~  268 (823)
                      .+.
T Consensus        83 ~~~   85 (88)
T d2cq1a1          83 HKE   85 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            554

>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=99.48  E-value=2e-14  Score=125.36  Aligned_cols=76  Identities=14%  Similarity=0.339  Sum_probs=67.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      .+++|||+|||.+++++||+++|++|| +..+. ..+.+|||||+|.+.++|++|++.|++..+.|++|+|+|+.++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~-~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCY-VDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEE-EEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeee-eeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            468999999999999999999999999 22232 35689999999999999999999999999999999999986543

>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=99.48  E-value=4e-14  Score=125.55  Aligned_cols=77  Identities=29%  Similarity=0.515  Sum_probs=70.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccc--ccccccccCCC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRR--RKLDIHFSIPK  267 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g--r~L~V~~a~pk  267 (823)
                      .|+++|||+|||.++++++|+++|++||+|..|++. +.++||||+|.+.++|++|++.|++..|.|  ++|+|.|+++.
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            578999999999999999999999999999999864 468999999999999999999999999976  58999998754

>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=99.48  E-value=1.2e-14  Score=123.67  Aligned_cols=71  Identities=28%  Similarity=0.443  Sum_probs=65.9

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ++|||+|||.++|+++|+++|++||.|.++++     +++++|||||+|.+.++|++|++ +|++.++|+.|+|+.|
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            47999999999999999999999999998865     46789999999999999999997 7999999999999876

>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=99.48  E-value=3.3e-14  Score=122.84  Aligned_cols=74  Identities=23%  Similarity=0.447  Sum_probs=68.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++ +++..|.|+.|+|+.|.
T Consensus         5 ~~~~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           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            3479999999999999999999999999999874     57899999999999999999998 69999999999998774

>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=99.47  E-value=1.5e-14  Score=125.73  Aligned_cols=73  Identities=21%  Similarity=0.187  Sum_probs=67.7

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      +|||+|||+++++++|+++|++||.|.++++.  .+|||||+|.+.++|++||+.|||..|.|+.|+|.+++++.
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            69999999999999999999999999999985  45899999999999999999999999999999998876543

>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=99.47  E-value=2.2e-14  Score=128.82  Aligned_cols=77  Identities=18%  Similarity=0.436  Sum_probs=70.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      .++|||+|||+++++++|+++|++||+|..+.+     +++++|||||+|.+.++|++|++ +++..|.|+.|.|.++.+
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            479999999999999999999999999999984     46789999999999999999997 799999999999999987


Q ss_pred             CCC
Q 003400          267 KDN  269 (823)
Q Consensus       267 k~~  269 (823)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            653

>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=4e-14  Score=119.62  Aligned_cols=70  Identities=14%  Similarity=0.386  Sum_probs=64.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       194 tLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +|||+|||+++|+++|+++|++||+|..|.+     +++++|||||+|.+.++|++|++ +++..|.|+.|.|+.|
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            5899999999999999999999999999983     57789999999999999999998 7999999999998754

>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=99.47  E-value=2.6e-14  Score=124.22  Aligned_cols=74  Identities=15%  Similarity=0.181  Sum_probs=67.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCCCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD  268 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~  268 (823)
                      .+|||+|||+++++++|+++|++||+|..+++.  ..|||||+|.+.++|++|++.|+|..|.|+.|+|.++.++.
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            369999999999999999999999999999864  35999999999999999999999999999999999976543

>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=6.3e-14  Score=124.25  Aligned_cols=77  Identities=22%  Similarity=0.404  Sum_probs=70.7

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCC--ceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG--KRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~G--r~I~V~~s~~~~  353 (823)
                      +.++|||+|||.++++++|+++|++||.|..+++.. .++||||+|.+.++|++|++.|||..|.|  ++|+|+|+++..
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~-~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec-cccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCC
Confidence            457999999999999999999999999999999864 57899999999999999999999999987  589999998754

>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=99.47  E-value=7.2e-15  Score=131.59  Aligned_cols=76  Identities=17%  Similarity=0.382  Sum_probs=70.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .+.++|||+|||.++++++|+++|+.||+|.+|++     +++++|||||+|.+.++|++|++ |+|..|.|++|.|+++
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            34689999999999999999999999999999984     57899999999999999999996 9999999999999987


Q ss_pred             CC
Q 003400          265 IP  266 (823)
Q Consensus       265 ~p  266 (823)
                      .+
T Consensus        95 ~~   96 (101)
T d2cq4a1          95 QA   96 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=127.85  Aligned_cols=76  Identities=24%  Similarity=0.335  Sum_probs=69.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ...+|||+|||+++|+++|+++|+.||.|..+++    +++++|||||+|.+.++|++||+ |||..+.|++|+|++++.
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            4568999999999999999999999998877654    57789999999999999999996 999999999999999976


Q ss_pred             C
Q 003400          352 G  352 (823)
Q Consensus       352 ~  352 (823)
                      +
T Consensus        91 k   91 (91)
T d1fjeb1          91 R   91 (91)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.47  E-value=3.2e-14  Score=119.62  Aligned_cols=70  Identities=20%  Similarity=0.340  Sum_probs=64.9

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      +|||+|||+++|+++|+++|+.||.|..+.+     ++.+++||||+|.+.++|++|++ |||+.|+|++|+|++|
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            4899999999999999999999999999864     45678999999999999999997 9999999999999875

>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=99.46  E-value=6.1e-14  Score=119.27  Aligned_cols=71  Identities=18%  Similarity=0.359  Sum_probs=65.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ++|||+|||+++|+++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++ |||+.|.|+.|+|+.|
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            58999999999999999999999999999865     45678999999999999999986 8999999999999876

>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=99.46  E-value=4.3e-14  Score=120.24  Aligned_cols=72  Identities=24%  Similarity=0.484  Sum_probs=66.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      .++|||+|||+++|+++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++ ++|..|.|++|.|+.|
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            489999999999999999999999999999873     56789999999999999999996 8999999999999876

>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=99.46  E-value=2.6e-14  Score=129.20  Aligned_cols=77  Identities=25%  Similarity=0.305  Sum_probs=69.2

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeC-CCcccEEEEEEcCHHHHHHHHHHhCCCcc--CCceEEEEecCCCc
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET-PHKRHHKFIEFYDVRAAEAALKSLNRSDI--AGKRIKLEPSRPGG  353 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~-~~srG~aFVeF~d~e~A~kAl~~LnG~~i--~Gr~I~V~~s~~~~  353 (823)
                      ..+|||+|||+++|+++|+++|++||.|.+|++. .+++|+|||+|.+.++|++|++.|||..|  .|++|+|.+++++.
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~   86 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS   86 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCcc
Confidence            4579999999999999999999999999998763 34689999999999999999999999988  47899999998754

>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=99.46  E-value=1.8e-13  Score=122.75  Aligned_cols=81  Identities=15%  Similarity=0.231  Sum_probs=71.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhc--CCccccccccccccC
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ--NKPLRRRKLDIHFSI  265 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Ln--g~~l~gr~L~V~~a~  265 (823)
                      ...++++|||+|||.++||++|+++|++||.|..|++ .+.+++|||+|.+.++|++|++.|+  +..+.|++|+|.|+.
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            3457899999999999999999999999999999976 4678999999999999999999884  456789999999997


Q ss_pred             CCCC
Q 003400          266 PKDN  269 (823)
Q Consensus       266 pk~~  269 (823)
                      .+..
T Consensus        90 ~~~~   93 (104)
T d1wexa_          90 SKRI   93 (104)
T ss_dssp             SSSC
T ss_pred             CCcc
Confidence            6543

>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=99.45  E-value=1.8e-14  Score=122.61  Aligned_cols=71  Identities=17%  Similarity=0.428  Sum_probs=65.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ++|||+|||+++|+++|+++|++||+|.++++     +++++|||||+|.+.++|++|++ +++..+.|++|.|+.|
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            57999999999999999999999999988873     57899999999999999999998 7999999999999875

>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=99.45  E-value=9.3e-15  Score=128.32  Aligned_cols=76  Identities=16%  Similarity=0.207  Sum_probs=69.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ...++|||+|||.++|+++|+++|++||.|..++    .+++++|||||+|.+.++|++|++ |++..+.|++|+|.++.
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            4567999999999999999999999999877654    367899999999999999999996 99999999999999986


Q ss_pred             C
Q 003400          266 P  266 (823)
Q Consensus       266 p  266 (823)
                      .
T Consensus        90 ~   90 (91)
T d1fjeb1          90 G   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.45  E-value=6.8e-14  Score=118.27  Aligned_cols=70  Identities=19%  Similarity=0.454  Sum_probs=64.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccCC
Q 003400          195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       195 LfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      |||+|||.++++++|+++|++|| +..++ ..+.+|||||+|.+.++|++|++.|+|..+.|++|+|+|+..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~-~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCF-VDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEE-EETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-cccee-ecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999999 55554 467899999999999999999999999999999999999954

>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=99.45  E-value=1e-13  Score=124.19  Aligned_cols=80  Identities=16%  Similarity=0.382  Sum_probs=69.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT------ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~------~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      ..+.++|||+|||.++|+++|+++|++|| |..+.+      .++++|||||+|.+.++|++|++ |++..|.|++|+|.
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-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            34679999999999999999999999999 656552      45678999999999999987775 99999999999999


Q ss_pred             ccCCCCCC
Q 003400          263 FSIPKDNP  270 (823)
Q Consensus       263 ~a~pk~~~  270 (823)
                      ++.++...
T Consensus        90 ~a~~~~~~   97 (104)
T d1wi8a_          90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>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=99.44  E-value=5.8e-14  Score=124.86  Aligned_cols=76  Identities=21%  Similarity=0.186  Sum_probs=70.3

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCCCc
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGG  353 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~  353 (823)
                      ...+|||+|||+++++++|+++|++||+|+.+++.  ++|||||+|.+.++|++||+.|||..+.|+.|+|.+.+...
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            34689999999999999999999999999999985  56999999999999999999999999999999999987654

>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=8.8e-14  Score=120.38  Aligned_cols=74  Identities=12%  Similarity=0.327  Sum_probs=68.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      ..++|||+|||.++|+++|+++|+.||.|..|++    +++++|||||+|.+.++|++|++ +++..+.|+.|.|.|..
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            4689999999999999999999999999999984    46788999999999999999997 79999999999999863

>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=1e-13  Score=122.51  Aligned_cols=78  Identities=19%  Similarity=0.229  Sum_probs=68.6

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCc-eEEEEe------CCCcccEEEEEEcCHHHHHHHHHHhCCC--ccCCceEEEEe
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGE-VKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRS--DIAGKRIKLEP  348 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~-I~~iri------~~~srG~aFVeF~d~e~A~kAl~~LnG~--~i~Gr~I~V~~  348 (823)
                      ++|||+|||.++++++|+++|++||. |..+++      .+.++|||||+|.+.++|.+|++.|++.  .+.|+.|+|+|
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            57999999999999999999999996 888876      2457899999999999999999999754  56799999999


Q ss_pred             cCCCccc
Q 003400          349 SRPGGAR  355 (823)
Q Consensus       349 s~~~~~r  355 (823)
                      |+++...
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9886543

>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=99.43  E-value=5e-14  Score=119.21  Aligned_cols=70  Identities=23%  Similarity=0.453  Sum_probs=64.2

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      +|||+|||+++|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++||+ +++..|.|+.|.|+.|
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            4899999999999999999999999999975     46689999999999999999997 5788999999999865

>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=99.43  E-value=9.2e-14  Score=121.31  Aligned_cols=72  Identities=14%  Similarity=0.385  Sum_probs=64.2

Q ss_pred             CccceeeecCCCCCCHHHH---HHHhcccCceEEEEeC-----C---CcccEEEEEEcCHHHHHHHHHHhCCCccCCceE
Q 003400          276 NQGTLVVFNLDPSVSNEDL---RQIFGAYGEVKEIRET-----P---HKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI  344 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL---~~~Fs~fG~I~~iri~-----~---~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I  344 (823)
                      ..++|||+|||+++++++|   +++|++||.|..|++.     +   ..+|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3468999999999999999   7789999999999762     1   234899999999999999999999999999999


Q ss_pred             EEE
Q 003400          345 KLE  347 (823)
Q Consensus       345 ~V~  347 (823)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.43  E-value=2.4e-13  Score=118.16  Aligned_cols=78  Identities=15%  Similarity=0.180  Sum_probs=70.4

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHh--CCCccCCceEEEEecCCC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~L--nG~~i~Gr~I~V~~s~~~  352 (823)
                      .+.++|||+|||.++++++|+++|++||.|.++++. ..+++|||+|.+.++|++|++.+  ++..+.|++|+|.|++.+
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~-~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~   84 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML-KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   84 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccc-ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCC
Confidence            356799999999999999999999999999999886 45789999999999999999865  567999999999999875


Q ss_pred             c
Q 003400          353 G  353 (823)
Q Consensus       353 ~  353 (823)
                      .
T Consensus        85 ~   85 (88)
T d2cq1a1          85 E   85 (88)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.43  E-value=5.5e-14  Score=118.16  Aligned_cols=70  Identities=16%  Similarity=0.401  Sum_probs=64.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       194 tLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +|||+|||.++|+++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++ +++..|.|++|.|++|
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            5999999999999999999999999998873     46788999999999999999997 9999999999999875

>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=1.4e-13  Score=116.20  Aligned_cols=71  Identities=20%  Similarity=0.207  Sum_probs=64.3

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEeC---CCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRET---PHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~---~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      .+|||+|||+++++++|+++|+.||.|+.+++.   ...++||||+|.+.++|++|+. +|++.|+|++|.|+.+
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            379999999999999999999999999999762   3456799999999999999995 8999999999999864

>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=1.5e-13  Score=118.89  Aligned_cols=74  Identities=9%  Similarity=0.166  Sum_probs=67.6

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ..++|||+|||.++|+++|+++|+.||.|..|++    ++.++|||||+|.+.++|++||+ ++|..+.|+.|+|.+++
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            4569999999999999999999999999999976    35678999999999999999996 79999999999999853

>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=99.42  E-value=2.2e-13  Score=121.89  Aligned_cols=77  Identities=23%  Similarity=0.364  Sum_probs=66.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe------CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri------~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...+|||+|||.++|+++|+++|+.|| |.++++      ++.++|||||+|.+.++|++|+ .||+..|.|+.|+|+++
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            347999999999999999999999999 666653      3457899999999999998766 59999999999999999


Q ss_pred             CCCcc
Q 003400          350 RPGGA  354 (823)
Q Consensus       350 ~~~~~  354 (823)
                      .++..
T Consensus        92 ~~~~~   96 (104)
T d1wi8a_          92 DQAQD   96 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.42  E-value=8e-14  Score=116.45  Aligned_cols=66  Identities=23%  Similarity=0.437  Sum_probs=62.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          195 LFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       195 LfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      |||+|||.++|+++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+
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            799999999999999999999999999873     567899999999999999999999999999999875

>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=6.6e-14  Score=118.45  Aligned_cols=70  Identities=19%  Similarity=0.469  Sum_probs=64.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       194 tLfV~NLP~~vteeeLr~lFs~fG~I~~v~~-----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +|||+|||+++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++ .++..+.|+.|.|+.|
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            5999999999999999999999999999983     57799999999999999999997 5778899999988764

>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=99.41  E-value=5.3e-13  Score=119.64  Aligned_cols=78  Identities=18%  Similarity=0.185  Sum_probs=70.3

Q ss_pred             CCccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHh--CCCccCCceEEEEecCCC
Q 003400          275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~L--nG~~i~Gr~I~V~~s~~~  352 (823)
                      ....+|||+|||.++|+++|+++|++||.|+.+++. +.+++|||+|.+.++|++|++.|  ++..+.|++|+|.|++.+
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 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEE-ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCC
Confidence            356799999999999999999999999999999986 46799999999999999999988  566789999999999765


Q ss_pred             c
Q 003400          353 G  353 (823)
Q Consensus       353 ~  353 (823)
                      .
T Consensus        92 ~   92 (104)
T d1wexa_          92 R   92 (104)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=99.40  E-value=6.8e-14  Score=116.92  Aligned_cols=66  Identities=24%  Similarity=0.439  Sum_probs=61.4

Q ss_pred             eeeecCCCCCCHHHHHHHhcccCceEEEEe-----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 003400          280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       280 LfV~NLp~~vteedL~~~Fs~fG~I~~iri-----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      |||+|||.++|+++|+++|++||.|..+++     ++.++|+|||+|.+.++|++|++.|||..|.|+.|+
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            799999999999999999999999999865     456789999999999999999999999999998764

>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=2.9e-13  Score=120.48  Aligned_cols=76  Identities=20%  Similarity=0.200  Sum_probs=68.6

Q ss_pred             CccceeeecCCCC-CCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHH--HhCCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALK--SLNRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~-vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~--~LnG~~i~Gr~I~V~~s~~~  352 (823)
                      ..++|||+|||.+ +|+++|.++|++||.|.++++. ..+++|||+|.+.++|.+|++  .+++..+.|+.|+|.+|+.+
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~-~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEe-ecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCc
Confidence            4568999999985 8999999999999999999986 457999999999999999998  57888999999999999765

>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=99.38  E-value=2.1e-13  Score=117.78  Aligned_cols=74  Identities=22%  Similarity=0.260  Sum_probs=65.9

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEE-E----eCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-R----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~i-r----i~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ...+|||+|||++++++||+++|+.||.|... .    .++.++|+|||+|.+.++|++|++.|||..|.|++|+|+++
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            34579999999999999999999999987542 2    25678999999999999999999999999999999999875

>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=99.38  E-value=3.3e-13  Score=120.07  Aligned_cols=78  Identities=17%  Similarity=0.213  Sum_probs=69.4

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHH--HhcCCccccccccccccC
Q 003400          189 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR--ALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~~-vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~--~Lng~~l~gr~L~V~~a~  265 (823)
                      ..++++|||+|||.+ +|+++|+++|++||.|.+|.+ .+.+|||||+|.+.++|.+|++  .+++..+.|++|+|.|+.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~-~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~   93 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE   93 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEE-eecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcC
Confidence            456799999999985 899999999999999999976 3568999999999999999998  467888999999999996


Q ss_pred             CC
Q 003400          266 PK  267 (823)
Q Consensus       266 pk  267 (823)
                      .+
T Consensus        94 ~~   95 (99)
T d1x4fa1          94 KY   95 (99)
T ss_dssp             SC
T ss_pred             Cc
Confidence            44

>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=3.2e-13  Score=114.05  Aligned_cols=71  Identities=17%  Similarity=0.254  Sum_probs=64.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~---~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ++|||+|||.++++++|+++|+.||+|..|++   ....++||||+|.+.++|++|+. +++..|.|++|.|..+
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            58999999999999999999999999999884   34456799999999999999996 8999999999998754

>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=4.7e-13  Score=116.80  Aligned_cols=77  Identities=14%  Similarity=0.159  Sum_probs=69.0

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHh--cCCccccccccccccC
Q 003400          189 EHPSRTLFVRNINSN-VEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRAL--QNKPLRRRKLDIHFSI  265 (823)
Q Consensus       189 e~~srtLfV~NLP~~-vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~L--ng~~l~gr~L~V~~a~  265 (823)
                      ..++++|||+|||.. +|++||+++|++||+|..|.+. +.+++|||+|.+.++|..|++.|  ++..+.|++|+|.|+.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~-~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~   83 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   83 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEee-ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECC
Confidence            457899999999986 8999999999999999999864 46789999999999999999976  5667999999999986


Q ss_pred             C
Q 003400          266 P  266 (823)
Q Consensus       266 p  266 (823)
                      .
T Consensus        84 ~   84 (89)
T d1x4da1          84 K   84 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=1.1e-12  Score=117.44  Aligned_cols=77  Identities=23%  Similarity=0.255  Sum_probs=68.5

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEE-e----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-E----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~ir-i----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      +..+|||+|||+++|++||+++|..||.|..+. +    ++.++|||||+|.++++|++|++ +|+..|.||.|+|.++.
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            456899999999999999999999999887743 2    45678999999999999999996 89999999999999998


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      +..
T Consensus        93 ~~~   95 (104)
T d1wg5a_          93 RAE   95 (104)
T ss_dssp             TTT
T ss_pred             HHH
Confidence            764

>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=99.36  E-value=1.7e-13  Score=118.44  Aligned_cols=75  Identities=20%  Similarity=0.285  Sum_probs=66.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEE-EE----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRT-LY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~-v~----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ....+|||+|||.+++++||+++|+.||.|.. +.    .+++++|+|||+|.+.++|++|++.|++..+.|++|+|.++
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            34567999999999999999999999998754 22    35778999999999999999999999999999999999764

>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=99.36  E-value=1e-12  Score=117.77  Aligned_cols=79  Identities=11%  Similarity=0.162  Sum_probs=69.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHhcCCccccccccccc
Q 003400          189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF  263 (823)
Q Consensus       189 e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~  263 (823)
                      .....+|||+|||+++|++||+++|..||.|..+.     .+++++|||||+|.+.++|++|++ +++..|.|+.|+|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            34566899999999999999999999999987754     256788999999999999999996 899999999999999


Q ss_pred             cCCCC
Q 003400          264 SIPKD  268 (823)
Q Consensus       264 a~pk~  268 (823)
                      +.+++
T Consensus        91 ~~~~~   95 (104)
T d1wg5a_          91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            87654

>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=119.16  Aligned_cols=72  Identities=18%  Similarity=0.328  Sum_probs=63.7

Q ss_pred             CCcEEEEcCCCCCCCHHHH---HHHhhcCCCEEEEEeC--------CCcccEEEEEeCCHHHHHHHHHHhcCCccccccc
Q 003400          191 PSRTLFVRNINSNVEDSEL---RALFEQYGDIRTLYTA--------CKHRGFVMISYYDIRAARTAMRALQNKPLRRRKL  259 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeL---r~lFs~fG~I~~v~~~--------~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L  259 (823)
                      ..++|||+|||+++++++|   +++|++||+|..|.+.        ...+|||||+|.+.++|++|++.|+|..+.|++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3578999999999999999   6789999999999841        2245899999999999999999999999999999


Q ss_pred             ccc
Q 003400          260 DIH  262 (823)
Q Consensus       260 ~V~  262 (823)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            873

>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=99.36  E-value=2.6e-13  Score=121.98  Aligned_cols=78  Identities=18%  Similarity=0.225  Sum_probs=69.5

Q ss_pred             CccceeeecCCCCC-CH----HHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSV-SN----EDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~v-te----edL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...+|||+||+.++ ++    ++|+++|++||.|+++++. ++++||||+|.+.++|.+|++.|||..|.|++|+|.|++
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~-k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe-cCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            34689999999986 33    5699999999999999886 568899999999999999999999999999999999998


Q ss_pred             CCcc
Q 003400          351 PGGA  354 (823)
Q Consensus       351 ~~~~  354 (823)
                      +...
T Consensus        83 ~~~~   86 (104)
T d1weya_          83 TLHI   86 (104)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            7653

>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=99.35  E-value=8.7e-13  Score=115.05  Aligned_cols=76  Identities=17%  Similarity=0.232  Sum_probs=68.4

Q ss_pred             CccceeeecCCCC-CCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHh--CCCccCCceEEEEecCCC
Q 003400          276 NQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSL--NRSDIAGKRIKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~-vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~L--nG~~i~Gr~I~V~~s~~~  352 (823)
                      ..++|||+|||.. +|++||.++|++||.|.+|++.. .+++|||+|++.++|.+|++.|  ++..+.|++|+|.||++.
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 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN-KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   85 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS-SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeec-cceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCc
Confidence            4568999999986 88999999999999999999864 5689999999999999999966  677899999999999764

>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=99.35  E-value=7e-13  Score=118.46  Aligned_cols=80  Identities=10%  Similarity=0.217  Sum_probs=68.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE---eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY---TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       188 ~e~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~---~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ......+|||+|||+++|++||+++|+.||.+....   ..++.+|||||+|.+.++|++|++ +++..|.||.|+|.++
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            344567999999999999999999999999553222   356789999999999999999986 8999999999999998


Q ss_pred             CCCC
Q 003400          265 IPKD  268 (823)
Q Consensus       265 ~pk~  268 (823)
                      .++.
T Consensus        90 ~~~~   93 (102)
T d1weza_          90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=7.8e-13  Score=118.13  Aligned_cols=77  Identities=13%  Similarity=0.195  Sum_probs=67.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP  351 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~~  351 (823)
                      ...+|||+|||+++|++||+++|+.||.+ .|++    .+..+|||||+|.+.++|++|++ ||+..|.||.|+|.++.+
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            45689999999999999999999999854 4432    45678999999999999999986 899999999999999887


Q ss_pred             Ccc
Q 003400          352 GGA  354 (823)
Q Consensus       352 ~~~  354 (823)
                      ...
T Consensus        92 ~~~   94 (102)
T d1weza_          92 AGT   94 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.32  E-value=4.2e-13  Score=120.60  Aligned_cols=79  Identities=19%  Similarity=0.217  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCC-CH----HHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNV-ED----SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~v-te----eeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ..+++|||+||+.++ ++    ++|+++|++||+|.++++ .++++||||+|.+.++|.+|++.|+|..|.|++|+|.|+
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            457899999999986 33    569999999999999975 468999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 003400          265 IPKDN  269 (823)
Q Consensus       265 ~pk~~  269 (823)
                      .++..
T Consensus        82 ~~~~~   86 (104)
T d1weya_          82 QTLHI   86 (104)
T ss_dssp             CCSSC
T ss_pred             ccCCC
Confidence            76543

>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=99.27  E-value=1.5e-12  Score=116.23  Aligned_cols=75  Identities=12%  Similarity=0.161  Sum_probs=66.2

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEE-EEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE-IRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~-iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...+|||+|||+++|+++|+++|+.||.|.. +.+    ++.++|+|||+|.+.++|++||+ |||..|.|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            3468999999999999999999999998764 332    56789999999999999999996 99999999999999875


Q ss_pred             C
Q 003400          351 P  351 (823)
Q Consensus       351 ~  351 (823)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=2.1e-13  Score=118.88  Aligned_cols=72  Identities=17%  Similarity=0.317  Sum_probs=63.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE----------eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccc
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY----------TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH  262 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~----------~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~  262 (823)
                      |+|||+|||.++|+++|+++|++||.|..+.          .+.+++|||||+|.+.++|++|++ |+|..+.|++|+|+
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            7899999999999999999999999876543          235689999999999999999995 99999999999998


Q ss_pred             ccC
Q 003400          263 FSI  265 (823)
Q Consensus       263 ~a~  265 (823)
                      .+.
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.25  E-value=1.3e-12  Score=116.61  Aligned_cols=75  Identities=16%  Similarity=0.202  Sum_probs=66.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEE-EE----eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRT-LY----TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~-v~----~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ...++|||+|||.++|+++|+++|+.||.|.. +.    ..++++|||||+|.+.++|++|++ |++..|.|+.|.|.++
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            34578999999999999999999999998764 22    356789999999999999999996 8999999999999886


Q ss_pred             C
Q 003400          265 I  265 (823)
Q Consensus       265 ~  265 (823)
                      .
T Consensus        85 ~   85 (103)
T d2cpya1          85 T   85 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.20  E-value=1.8e-12  Score=116.39  Aligned_cols=72  Identities=24%  Similarity=0.272  Sum_probs=67.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe----CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEec
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPS  349 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s  349 (823)
                      ..++|.++..++++++|+++|++||.|.+|++    +++++|+|||+|.+.++|.+|++.|||+.++|++|+|+|+
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            46999999999999999999999999999987    4567899999999999999999999999999999999986

>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=99.19  E-value=3.6e-13  Score=117.44  Aligned_cols=70  Identities=19%  Similarity=0.329  Sum_probs=61.9

Q ss_pred             cceeeecCCCCCCHHHHHHHhcccCceEEEEe----------CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEE
Q 003400          278 GTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE----------TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE  347 (823)
Q Consensus       278 ~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri----------~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~  347 (823)
                      ++|||+|||.++|+++|+++|+.||.|..+.+          ++.++|||||+|.+.++|++|++ |||..+.|+.|+|+
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            47999999999999999999999998765532          34578999999999999999985 99999999999996


Q ss_pred             e
Q 003400          348 P  348 (823)
Q Consensus       348 ~  348 (823)
                      .
T Consensus        81 r   81 (90)
T d1u2fa_          81 R   81 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.18  E-value=1.4e-11  Score=109.84  Aligned_cols=66  Identities=18%  Similarity=0.329  Sum_probs=59.8

Q ss_pred             CCCCcEEEEcC--CCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCccc
Q 003400          189 EHPSRTLFVRN--INSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLR  255 (823)
Q Consensus       189 e~~srtLfV~N--LP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~  255 (823)
                      ..|+++|+|.|  ||.++|+++|+++|++||.|..|++ .+.++||||+|.+.++|++|++.|+|..+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~-~~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEEC-CTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEee-ccCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            45789999965  9999999999999999999999975 456899999999999999999999998873

>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=99.18  E-value=6.3e-12  Score=114.08  Aligned_cols=77  Identities=17%  Similarity=0.203  Sum_probs=67.1

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEE-----EeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~i-----ri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      ...+|||+|||+++|+++|+++|+.||.|..+     ...+.++|+|||+|.+.++|++|++ |||..|+|+.|.|..+.
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            34589999999999999999999999987542     2357789999999999999999996 99999999999999886


Q ss_pred             CCc
Q 003400          351 PGG  353 (823)
Q Consensus       351 ~~~  353 (823)
                      +..
T Consensus        96 ~~~   98 (112)
T d1wela1          96 KKG   98 (112)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            544

>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=99.16  E-value=5.4e-12  Score=114.52  Aligned_cols=75  Identities=9%  Similarity=0.182  Sum_probs=66.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEE---E--eCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTL---Y--TACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       190 ~~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v---~--~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      ....+|||+|||.++|+++|+++|+.||.|..+   .  ..++++|||||+|.+.++|++|++ |++..|.|+.|.|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            356799999999999999999999999987532   1  367889999999999999999996 8999999999999876


Q ss_pred             C
Q 003400          265 I  265 (823)
Q Consensus       265 ~  265 (823)
                      .
T Consensus        95 ~   95 (112)
T d1wela1          95 T   95 (112)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=2.4e-11  Score=108.34  Aligned_cols=63  Identities=24%  Similarity=0.372  Sum_probs=57.4

Q ss_pred             Cccceeeec--CCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCcc
Q 003400          276 NQGTLVVFN--LDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI  339 (823)
Q Consensus       276 ~~~tLfV~N--Lp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i  339 (823)
                      +..+|+|.|  ||.++|+++|+++|++||.|+.|++.. .++||||+|.+.++|.+|++.|||+.|
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 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-TCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeecc-CccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            346888866  999999999999999999999999864 578999999999999999999999977

>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=99.14  E-value=2.9e-11  Score=107.34  Aligned_cols=83  Identities=19%  Similarity=0.320  Sum_probs=71.3

Q ss_pred             CCCCCCCcEEEEcCC--CCCCC---------HHHHHHHhhcCCCEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 003400          186 PYGEHPSRTLFVRNI--NSNVE---------DSELRALFEQYGDIRTLYT-ACKHRGFVMISYYDIRAARTAMRALQNKP  253 (823)
Q Consensus       186 ~~~e~~srtLfV~NL--P~~vt---------eeeLr~lFs~fG~I~~v~~-~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~  253 (823)
                      |.....+++|+|+||  |.++.         +++|++.|++||.|..|++ ....+|+|||+|.+.++|.+|+..|+|..
T Consensus         2 p~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           2 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            344567899999999  65432         3689999999999999984 56678999999999999999999999999


Q ss_pred             cccccccccccCCCC
Q 003400          254 LRRRKLDIHFSIPKD  268 (823)
Q Consensus       254 l~gr~L~V~~a~pk~  268 (823)
                      +.|++|.|+|..++.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999987654

>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=99.11  E-value=3.5e-11  Score=109.32  Aligned_cols=75  Identities=21%  Similarity=0.215  Sum_probs=65.9

Q ss_pred             ceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCH-HHHHHHHHHhCCCccCCceEEEEecCCCcc
Q 003400          279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDV-RAAEAALKSLNRSDIAGKRIKLEPSRPGGA  354 (823)
Q Consensus       279 tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~-e~A~kAl~~LnG~~i~Gr~I~V~~s~~~~~  354 (823)
                      .+||+|||+++|+++|+++|++||.|.+|++. ..++||||+|.+. ++|.+|+..||+..+.++.+.|.++...+.
T Consensus        13 ~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~-~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~~~   88 (113)
T d1owxa_          13 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGE   88 (113)
T ss_dssp             EEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCHH
T ss_pred             EEEECCCCCCCCHHHHHHHHHhcCChheEEEe-cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeeccch
Confidence            56999999999999999999999999999996 4689999999985 789999999999998887777777665543

>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=99.10  E-value=5.7e-11  Score=105.40  Aligned_cols=78  Identities=17%  Similarity=0.299  Sum_probs=67.4

Q ss_pred             CccceeeecC--CCCCC---------HHHHHHHhcccCceEEEEe-CCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce
Q 003400          276 NQGTLVVFNL--DPSVS---------NEDLRQIFGAYGEVKEIRE-TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR  343 (823)
Q Consensus       276 ~~~tLfV~NL--p~~vt---------eedL~~~Fs~fG~I~~iri-~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~  343 (823)
                      ..++|+|.||  |.++.         ++||++.|++||.|..|++ .+..+|+|||+|.+.++|.+|++.|||..++|++
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~   86 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQ   86 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCEE
Confidence            4579999999  54331         3689999999999999986 4566899999999999999999999999999999


Q ss_pred             EEEEecCCCc
Q 003400          344 IKLEPSRPGG  353 (823)
Q Consensus       344 I~V~~s~~~~  353 (823)
                      |+|++..++.
T Consensus        87 i~v~~~~g~~   96 (99)
T d2dita1          87 ITAQAWDGTT   96 (99)
T ss_dssp             CEEEECCSCC
T ss_pred             EEEEEeCCcC
Confidence            9999987653

>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=8.2e-11  Score=106.79  Aligned_cols=73  Identities=15%  Similarity=0.243  Sum_probs=65.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCH-HHHHHHHHHhcCCccccccccccccCC
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDI-RAARTAMRALQNKPLRRRKLDIHFSIP  266 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~-e~A~~Ai~~Lng~~l~gr~L~V~~a~p  266 (823)
                      ..+||+|||.++|+++|+++|++||+|..|.+. +.+|||||.|.+. ++|..|+..+++..+.++.+.|.+...
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~-~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEe-cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            466999999999999999999999999999864 5789999999995 789999999999999988888887643

>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=99.08  E-value=8.1e-12  Score=112.03  Aligned_cols=72  Identities=14%  Similarity=0.225  Sum_probs=67.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccccccc
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS  264 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~----~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a  264 (823)
                      +.++|++++.+++|++|+++|++||+|.+|++    +++++|||||+|.+.++|.+|++.|+|+.+.|++|.|+|+
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            46888999999999999999999999999985    4678999999999999999999999999999999999986

>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=99.07  E-value=9e-11  Score=100.33  Aligned_cols=74  Identities=16%  Similarity=0.198  Sum_probs=63.8

Q ss_pred             CccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCce-EEEEecCCC
Q 003400          276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKR-IKLEPSRPG  352 (823)
Q Consensus       276 ~~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~-I~V~~s~~~  352 (823)
                      +++.|+|.++|++.+++.| ++|++||+|.++++. ..++||||+|.++++|++||+ +||..|+|+. |.|..+..+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~-~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS-NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC-SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec-CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            4567999999999987655 579999999999974 568999999999999999996 9999999975 678887654

>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=98.93  E-value=4.9e-10  Score=95.64  Aligned_cols=72  Identities=18%  Similarity=0.207  Sum_probs=61.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccc-ccccccC
Q 003400          191 PSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRK-LDIHFSI  265 (823)
Q Consensus       191 ~srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~-L~V~~a~  265 (823)
                      +.+.|+|.++|++++++.| +.|++||+|.++++ .+.++||||+|.+.++|++|++ ++|..|.|+. |.|..+.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~-~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEe-cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            3578999999999987655 57999999999975 5678999999999999999996 8999999984 5577654

>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=8.6e-10  Score=98.42  Aligned_cols=76  Identities=24%  Similarity=0.330  Sum_probs=64.4

Q ss_pred             CccceeeecC--CCCCC--------HHHHHHHhcccCceEEEEeCC-------CcccEEEEEEcCHHHHHHHHHHhCCCc
Q 003400          276 NQGTLVVFNL--DPSVS--------NEDLRQIFGAYGEVKEIRETP-------HKRHHKFIEFYDVRAAEAALKSLNRSD  338 (823)
Q Consensus       276 ~~~tLfV~NL--p~~vt--------eedL~~~Fs~fG~I~~iri~~-------~srG~aFVeF~d~e~A~kAl~~LnG~~  338 (823)
                      +.++|.|.||  +.++.        .+||++.|++||.|++|.+..       ...|++||+|.+.++|.+|++.|||+.
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            3568999999  54443        367999999999999998732       245899999999999999999999999


Q ss_pred             cCCceEEEEecCC
Q 003400          339 IAGKRIKLEPSRP  351 (823)
Q Consensus       339 i~Gr~I~V~~s~~  351 (823)
                      ++||.|+|.|...
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999864

>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=98.87  E-value=9.2e-10  Score=98.24  Aligned_cols=76  Identities=16%  Similarity=0.347  Sum_probs=65.5

Q ss_pred             CCCcEEEEcCC--CCCCC--------HHHHHHHhhcCCCEEEEEeC-------CCcccEEEEEeCCHHHHHHHHHHhcCC
Q 003400          190 HPSRTLFVRNI--NSNVE--------DSELRALFEQYGDIRTLYTA-------CKHRGFVMISYYDIRAARTAMRALQNK  252 (823)
Q Consensus       190 ~~srtLfV~NL--P~~vt--------eeeLr~lFs~fG~I~~v~~~-------~ksrG~AFV~F~~~e~A~~Ai~~Lng~  252 (823)
                      .|+++|.|+|+  |.++.        .+||++.|++||.|.+|.+.       ....|++||+|.+.++|.+|+..|+|+
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            47899999999  55543        35799999999999999852       234589999999999999999999999


Q ss_pred             ccccccccccccC
Q 003400          253 PLRRRKLDIHFSI  265 (823)
Q Consensus       253 ~l~gr~L~V~~a~  265 (823)
                      .+.||+|.+.|..
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCeEEEEEEcC
Confidence            9999999999974

>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=98.73  E-value=1.4e-08  Score=87.93  Aligned_cols=84  Identities=21%  Similarity=0.330  Sum_probs=71.9

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcceEE-Eeeecccccce-eEEEEEecCCcccHHHHHHHhcCCcccCCCC-ccE
Q 003400          695 TTLMIKNIPNKYTSKMLLAAIDENHKGTYDFL-YLPIDFKNKCN-VGYAFINMLSPLHIIPFYEAFNGKKWEKFNS-EKV  771 (823)
Q Consensus       695 Tt~MirNIPnk~~~~~l~~~id~~~~~~ydf~-Ylp~d~~~~~n-~gyafin~~~~~~~~~f~~~f~g~~w~~~~s-~k~  771 (823)
                      |.|.||++|..+|++.+++.|+  ..+++||+ |.|-|...+-+ -..|||||.+++++..|.+.|+|+.+..-+. +-.
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            8999999999999999999998  47889998 57777776544 3789999999999999999999999986543 457


Q ss_pred             EEEEeeecc
Q 003400          772 ASLAYARIQ  780 (823)
Q Consensus       772 ~~~~~A~iQ  780 (823)
                      +.|.||--|
T Consensus        80 a~VE~AP~q   88 (91)
T d1uw4a_          80 AIVEFAPFQ   88 (91)
T ss_dssp             CEEEECSSC
T ss_pred             eEEEEcCcc
Confidence            889998776

>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=96.84  E-value=0.0015  Score=52.56  Aligned_cols=59  Identities=25%  Similarity=0.426  Sum_probs=52.6

Q ss_pred             HHHHHHhcccCceEEEEeCCCccc--EEEEEEcCHHHHHHHHHHhCCCccCCceEEEEecC
Q 003400          292 EDLRQIFGAYGEVKEIRETPHKRH--HKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSR  350 (823)
Q Consensus       292 edL~~~Fs~fG~I~~iri~~~srG--~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~V~~s~  350 (823)
                      +.|..+|.++|.|.++.+.+.+.+  .|-|...+.++|.-|+..|+.++|++|+|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            446678999999999999776655  69999999999999999999999999999999875

>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=96.37  E-value=0.002  Score=54.35  Aligned_cols=72  Identities=22%  Similarity=0.403  Sum_probs=56.9

Q ss_pred             CCccceeeecCCCCCC---------HHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhCCCccCCceEE
Q 003400          275 LNQGTLVVFNLDPSVS---------NEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIK  345 (823)
Q Consensus       275 ~~~~tLfV~NLp~~vt---------eedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~LnG~~i~Gr~I~  345 (823)
                      ..+.||.|.=...+..         -.+|.+.|..||+|.-||+..   +...|+|.+-+.|.+|++ |+|.++.|+.|+
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 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ---GQMLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET---TEEEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeC---CeEEEEECCcHHHHHHhc-cCCeEEcceEEE
Confidence            3456777754432222         256889999999999999864   568999999999999998 899999999999


Q ss_pred             EEecC
Q 003400          346 LEPSR  350 (823)
Q Consensus       346 V~~s~  350 (823)
                      |..-.
T Consensus        89 It~~~   93 (95)
T d1ufwa_          89 ISGPS   93 (95)
T ss_dssp             EECCC
T ss_pred             EecCC
Confidence            87543

>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=95.99  E-value=0.0072  Score=51.32  Aligned_cols=64  Identities=5%  Similarity=0.051  Sum_probs=53.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhhcCCCEEEEE-eCC------CcccEEEEEeCCHHHHHHHHHHhcCCcccc
Q 003400          193 RTLFVRNINSNVEDSELRALFEQYGDIRTLY-TAC------KHRGFVMISYYDIRAARTAMRALQNKPLRR  256 (823)
Q Consensus       193 rtLfV~NLP~~vteeeLr~lFs~fG~I~~v~-~~~------ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~g  256 (823)
                      ++|.||.||+++||+++.+.+...|++...+ ..+      ..-.-|+|.|.+.++.....+.++|..+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            5899999999999999999999999887765 111      122469999999999999999999988854

>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=95.73  E-value=0.0071  Score=48.56  Aligned_cols=59  Identities=12%  Similarity=0.216  Sum_probs=51.8

Q ss_pred             HHHHHHhhcCCCEEEEEeCCCccc--EEEEEeCCHHHHHHHHHHhcCCccccccccccccC
Q 003400          207 SELRALFEQYGDIRTLYTACKHRG--FVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSI  265 (823)
Q Consensus       207 eeLr~lFs~fG~I~~v~~~~ksrG--~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~V~~a~  265 (823)
                      +.|.+.|.++|.|.++.+...+.|  .|-|...+..+|..|+..|+..+|++++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            345678899999999998666665  79999999999999999999999999999998864

>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=94.12  E-value=0.026  Score=47.40  Aligned_cols=70  Identities=19%  Similarity=0.329  Sum_probs=55.6

Q ss_pred             CCCcEEEEcCCCCCCCH---------HHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhcCCcccccccc
Q 003400          190 HPSRTLFVRNINSNVED---------SELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLD  260 (823)
Q Consensus       190 ~~srtLfV~NLP~~vte---------eeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Lng~~l~gr~L~  260 (823)
                      .+.-||.|.=..++.++         .+|.+.|..||+|.-|+.   -.+...|+|.+-+.|-+|+. ++|.++.|+.|+
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRF---v~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~   88 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRI---NQGQMLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEE---ETTEEEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEE---eCCeEEEEECCcHHHHHHhc-cCCeEEcceEEE
Confidence            46678888655444433         468889999999988864   23568999999999999999 899999999998


Q ss_pred             ccc
Q 003400          261 IHF  263 (823)
Q Consensus       261 V~~  263 (823)
                      |.-
T Consensus        89 It~   91 (95)
T d1ufwa_          89 ISG   91 (95)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            864

>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=84.10  E-value=1.2  Score=37.45  Aligned_cols=56  Identities=14%  Similarity=0.250  Sum_probs=46.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHhc
Q 003400          192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQ  250 (823)
Q Consensus       192 srtLfV~NLP~~vteeeLr~lFs~fG~I~~v~~~~ksrG~AFV~F~~~e~A~~Ai~~Ln  250 (823)
                      ...||.-..|..+...||.++|+.||.|.--.+.   ---|||...+.++|+.++..+.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswId---dTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEE---TTEEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEec---CceEEEEecCHHHHHHHHHHhc
Confidence            3568888899999999999999999988755553   3379999999999999887654

>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=84.03  E-value=0.98  Score=38.11  Aligned_cols=56  Identities=14%  Similarity=0.284  Sum_probs=46.1

Q ss_pred             ccceeeecCCCCCCHHHHHHHhcccCceEEEEeCCCcccEEEEEEcCHHHHHHHHHHhC
Q 003400          277 QGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN  335 (823)
Q Consensus       277 ~~tLfV~NLp~~vteedL~~~Fs~fG~I~~iri~~~srG~aFVeF~d~e~A~kAl~~Ln  335 (823)
                      ..-+|.-..|..+...||.++|++||.|.-.-+..   --|||.-.+.++|+.+++.++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIdd---TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDD---TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEET---TEEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEecC---ceEEEEecCHHHHHHHHHHhc
Confidence            34688888999999999999999999876555532   259999999999999888654